diff options
Diffstat (limited to 'notes')
56 files changed, 10943 insertions, 0 deletions
diff --git a/notes/backfill_scalding_rewrite.txt b/notes/backfill_scalding_rewrite.txt new file mode 100644 index 0000000..f5fb1d1 --- /dev/null +++ b/notes/backfill_scalding_rewrite.txt @@ -0,0 +1,22 @@ + +Background context needed: +- CDX text file format +- rough arch outline (what runs where) +- basic hadoop+hbase overview +- hbase schema +- quick look at hadoop and hbase web interfaces +- maybe quick re-profile? + +Plan/Steps: +x together: get *any* JVM map/reduce thing to build and run on cluster +x together: get something to build that talks to hbase +x basic JVM test infra; HBase mockup. "shopping" + => scalding and/or cascading +x simple hbase scan report generation (counts/stats) +x CDX parsing +- complete backfill script + +Spec for CDX backfill script: +- input is CDX, output to HBase table +- filter input before anything ("defensive"; only PDF, HTTP 200, size limit) +- reads HBase before insert; don't overwrite diff --git a/notes/crawl_cdx_merge.md b/notes/crawl_cdx_merge.md new file mode 100644 index 0000000..d330e9b --- /dev/null +++ b/notes/crawl_cdx_merge.md @@ -0,0 +1,29 @@ + +## New Way + +Run script from scratch repo: + + ~/scratch/bin/cdx_collection.py CRAWL-2000 + + zcat CRAWL-2000.cdx.gz | wc -l + + # update crawl README/ANALYSIS/whatever + +Assuming we're just looking at PDFs: + + zcat CRAWL-2000.cdx.gz | rg -i pdf | sort -S 4G -u > CRAWL-2000.sorted.cdx + +## Old Way + +Use metamgr to export an items list. + +Get all the CDX files and merge/sort: + + mkdir CRAWL-2000 && cd CRAWL-2000 + cat ../CRAWL-2000.items | shuf | parallel --bar -j6 ia download {} {}.cdx.gz + ls */*.cdx.gz | parallel --bar -j1 zcat {} > CRAWL-2000.unsorted.cdx + sort -S 4G -u CRAWL-2000.unsorted.cdx > CRAWL-2000.cdx + wc -l CRAWL-2000.cdx + rm CRAWL-2000.unsorted.cdx + + # gzip and upload to petabox, or send to HDFS, or whatever diff --git a/notes/fuzzy_match_notes.md b/notes/fuzzy_match_notes.md new file mode 100644 index 0000000..a87364c --- /dev/null +++ b/notes/fuzzy_match_notes.md @@ -0,0 +1,148 @@ + +These are notes on how bibliographic metadata matches (of records) and +slugification (to create lookup keys on title strings) worked in the past in +the sandcrawler repository. Eg, circa 2018. + +## Scala Slug-ification + +Original title strings longer than 1023 characters were rejected (before +slug-ifying). + +There was a "slug-denylist". Additionally, scorable strings needed to be +between 8 and 1023 characters (not bytes) long (inclusive) + +Slugification transform was: + +- lower-case +- remove whitespace ("\s") +- strip specific accent characters: + '\u0141' -> 'L', + '\u0142' -> 'l', // Letter ell + '\u00d8' -> 'O', + '\u00f8' -> 'o' +- remove all '\p{InCombiningDiacriticalMarks}' +- remove punctuation: + \p{Punct} + ’·“”‘’“”«»「」¿–±§ + +Partially adapted from apache commons: <https://git-wip-us.apache.org/repos/asf?p=commons-lang.git;a=blob;f=src/main/java/org/apache/commons/lang3/StringUtils.java;h=1d7b9b99335865a88c509339f700ce71ce2c71f2;hb=HEAD#l934> + +My original notes/proposal: + +1. keep only \p{Ideographic}, \p{Alphabetic}, and \p{Digit} +2. strip accents +3. "lower-case" (unicode-aware) +4. do any final custom/manual mappings + +Resulting slugs less than 8 characters long were rejected, and slugs were +checked against a denylist. + +Only 554 entries in the denylist; could just ship that in the library. + + +## Python Tokenization + +- "'" -> "'" +- remove non "isalnum()" characters +- encode as ASCII; this removes diacritics etc, but also all non-latin character sets +- optionally remove all whitespace + + +## Python GROBID Cleanups + +These are likely pretty GROBID-specific. Article title was required, but any of +the other filtered-out fields just resulted in partial metadata. These filters +are the result of lots of manual verification of results, and doing things like +taking truncating titles and looking at the most popular prefixes for a large +random sample. + +Same denylist for title slugs as Scala, plus: + + editorial + advertisement + bookreviews + reviews + nr + abstractoriginalarticle + originalarticle + impactfactor + articlenumber + +Other filters on title strings (any of these bad): + +- 500 or more characters long +- tokenized string less than 10 characters +- tokenized starts with 'nr' or 'issn' +- lowercase starts with 'int j' or '.int j' +- contains both "volume" and "issue" +- contains "downloadedfrom" +- fewer than 2 or more than 50 tokens (words) +- more than 12 tokens only a single character long +- more than three ":"; more than one "|"; more than one "." + +Remove title prefixes (but allow): + + "Title: " + "Original Article: " + "Original Article " + "Article: " + +Denylist for authors: + + phd + phdstudent + +Journal name processing: + +- apply title denylist +- remove prefixes + characters: /~&© + Original Research Article + Original Article + Research Article + Available online www.jocpr.com +- remove suffixes + Available online at www.sciarena.com + Original Article + Available online at + ISSN + ISSUE +- remove anywhere + e-ISSN + p-ISSN + +## Python Grouping Comparison + +Would consume joined groups, row-by-row. At most 10 matches per group; any more +and skip (this was for file-to-release). + +Overall matching requirements: + +- string similarity threshold from scala code + https://oldfashionedsoftware.com/2009/11/19/string-distance-and-refactoring-in-scala/ + https://stackoverflow.com/questions/955110/similarity-string-comparison-in-java/16018452#16018452 +- authors should be consistent + - convert one author list into space-separated tokens + - remove "jr." from all author token lists + - the last word for each author full name in the other list (eg, the lastname), + tokenized, must be in the token set +- if both years defined, then must match exactly (integers) + +In the code, there is a note: + + Note: the actual importer/merger should filter the following patterns out: + - container title has "letter" and "diar" + - contribs (authors) contain "&NA;" + - dates differ (not just year) + + +## Scala Metadata Keys + +Only the titles were ever actually used (in scala), but the keys allowed were: + +- title +- authors (list of strings) +- year (int) +- contentType +- doi + diff --git a/notes/grobid_munging.txt b/notes/grobid_munging.txt new file mode 100644 index 0000000..013e458 --- /dev/null +++ b/notes/grobid_munging.txt @@ -0,0 +1,70 @@ + +In docker: + + kafkacat -C -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.grobid-output-pg | pv -l | rg 'OA-JOURNAL-CRAWL-2019-08' > OA-JOURNAL-CRAWL-2019-08.grobid.json + # 5.01M 0:31:04 [2.69k/s] + # 277 GByte grobid-output.prod.json + +Then: + + cat grobid-output.prod.json | rg 'OA-JOURNAL-CRAWL-2019-08' | pv -l > OA-JOURNAL-CRAWL-2019-08.grobid.json + # 265k 0:32:12 [ 137 /s] + + pigz grobid-output.prod.json + # 63 GByte grobid-output.prod.json.gz + + cat OA-JOURNAL-CRAWL-2019-08.grobid.json | pv -l | jq "[.key, .status, .status_code, .error_msg] | @tsv" -r | sort -u -S 4G | uniq --check-chars 40 > OA-JOURNAL-CRAWL-2019-08.grobid.tsv + # 265k + + wc -l OA-JOURNAL-CRAWL-2019-08.grobid.tsv + # 212879 OA-JOURNAL-CRAWL-2019-08.grobid.tsv + + cut -f2 OA-JOURNAL-CRAWL-2019-08.grobid.tsv | sort | uniq -c + # 14087 error + # 198792 success + +In sandcrawler pipenv: + + head -n100 /grande/oa-crawl-grobid/OA-JOURNAL-CRAWL-2019-08.grobid.json | ./grobid_tool.py transform --metadata-only - > /grande/oa-crawl-grobid/OA-JOURNAL-CRAWL-2019-08.metadata.json.sample + + cat /grande/oa-crawl-grobid/OA-JOURNAL-CRAWL-2019-08.grobid.json | parallel --linebuffer --round-robin --pipe -j8 ./grobid_tool.py transform --metadata-only - > /grande/oa-crawl-grobid/OA-JOURNAL-CRAWL-2019-08.metadata.json + + cat OA-JOURNAL-CRAWL-2019-08.metadata.json | rg -v '"fatcat_release": null' > OA-JOURNAL-CRAWL-2019-08.metadata.matched.json + + wc -l OA-JOURNAL-CRAWL-2019-08.metadata.matched.json OA-JOURNAL-CRAWL-2019-08.grobid.tsv + # 28162 OA-JOURNAL-CRAWL-2019-08.metadata.matched.json + # 212879 OA-JOURNAL-CRAWL-2019-08.grobid.tsv + +Next steps: +- import the matched files (while verifying match) +- some web interface to make sandcrawler easier? + input: sha1 or url + view: grobid status and metadata, ML results, fatcat metadata (via API lookup) + links/actions: view PDF, re-run GROBID, add to a release (via API) + +## BAD/BROKEN + +All these following didn't work because old versions of kafkacat only read +partial results. Ended up using docker to run more recent ubuntu, sigh. + + kafkacat -C -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.grobid-output-pg -e | pv -l > grobid-output.prod.json + + cat grobid-output.prod.json | rg '"status": "success"' > grobid-output.prod.success.json + + kafkacat -C -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.grobid-output-pg -e | pv -l | rg '"status": "success"' > grobid-output.prod.success.json + + kafkacat -C -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.grobid-output-pg -e | pv -l | rg 'OA-JOURNAL-CRAWL-2019-08' > OA-JOURNAL-CRAWL-2019-08.grobid.json + + head -n200 /grande/oa-crawl-grobid/grobid-output.prod.success.json | ./grobid_tool.py transform --metadata-only - | jq "[.fatcat_release, .biblio.title]" -c | less + + + cat OA-JOURNAL-CRAWL-2019-08.grobid.json | parallel --pipe -j8 jq .status -r | sort | uniq -c + 1879 error + 26698 success + + +For full grobid-output was looking like: + + 318561 error + 199607 success + diff --git a/notes/hadoop_job_log.md b/notes/hadoop_job_log.md new file mode 100644 index 0000000..f812c0a --- /dev/null +++ b/notes/hadoop_job_log.md @@ -0,0 +1,210 @@ + +### QA matchcrossref + +[D8C7F2CA7620450991838D540489948D/8B17786779BE44579C98D8A325AC5959] sandcrawler.ScoreJob/(1/1) ...-24-2102.32-matchcrossref + +Submitted: Fri Aug 24 21:03:09 UTC 2018 +Started: Fri Aug 24 21:03:20 UTC 2018 +Finished: Sat Aug 25 09:46:55 UTC 2018 +Elapsed: 12hrs, 43mins, 34sec +Diagnostics: +Average Map Time 24mins, 31sec +Average Shuffle Time 15sec +Average Merge Time 21sec +Average Reduce Time 7mins, 17sec + +Map 2312 2312 +Reduce 100 100 + +crossref-rows-filtered 73901964 0 73901964 +grobid-rows-filtered 1092992 0 1092992 +joined-rows 0 623837 623837 + +cascading.flow.StepCounters +Tuples_Read 94831255 0 94831255 +Tuples_Written 0 623837 623837 + +Read_Duration 7108430 352241 7460671 +Tuples_Read 94831255 74994956 169826211 +Tuples_Written 74994956 623837 75618793 +Write_Duration 7650302 21468 7671770 + +## QA UnGrobided + +Submitted: Sat Aug 25 01:23:22 UTC 2018 +Started: Sat Aug 25 05:06:36 UTC 2018 +Finished: Sat Aug 25 05:13:45 UTC 2018 +Elapsed: 7mins, 8sec +Diagnostics: +Average Map Time 1mins, 20sec +Average Shuffle Time 12sec +Average Merge Time 15sec +Average Reduce Time 29sec + +Map 48 48 +Reduce 1 1 + +bnewbold@bnewbold-dev$ gohdfs du -sh sandcrawler/output-qa/2018-08-25-0122.54-dumpungrobided/part* +56.8M /user/bnewbold/sandcrawler/output-qa/2018-08-25-0122.54-dumpungrobided/part-00000 + +## Prod UnGrobided + +[D76F6BF91D894E879E747C868B0DEDE7/394A1AFC44694992B71E6920AF8BA3FB] sandcrawler.DumpUnGrobidedJob/(1/1) ...26-0910.25-dumpungrobided + +Map 278 278 +Reduce 1 1 + +Submitted: Sun Aug 26 09:10:51 UTC 2018 +Started: Sun Aug 26 09:18:21 UTC 2018 +Finished: Sun Aug 26 10:29:28 UTC 2018 +Elapsed: 1hrs, 11mins, 7sec +Diagnostics: +Average Map Time 4mins, 48sec +Average Shuffle Time 24mins, 17sec +Average Merge Time 14sec +Average Reduce Time 13mins, 54sec + + +cading.flow.StepCounters +Name +Map +Reduce +Total +Tuples_Read 64510564 0 64510564 +Tuples_Written 0 21618164 21618164 + +## Prod Crossref Match + +[6C063C0809244446BA8602C3BE99CEC2/5FE5D87899154F38991A1ED58BEB34D4] sandcrawler.ScoreJob/(1/1) ...-25-1753.01-matchcrossref + +Map 2427 2427 +Reduce 50 50 + +Submitted: Sat Aug 25 17:53:50 UTC 2018 +Started: Sat Aug 25 17:53:59 UTC 2018 +Finished: Sun Aug 26 11:22:52 UTC 2018 +Elapsed: 17hrs, 28mins, 52sec +Diagnostics: +Average Map Time 31mins, 20sec +Average Shuffle Time 1mins, 21sec +Average Merge Time 41sec +Average Reduce Time 3hrs, 14mins, 39sec + +crossref-rows-filtered 73901964 0 73901964 +grobid-rows-filtered 14222226 0 14222226 +joined-rows 0 14115453 14115453 + +## "Prod" Fatcat Group Works (run 2019-08-10) + + ./please --prod groupworks-fatcat hdfs:///user/bnewbold/release_export.2019-07-07.json + + job_1559844455575_118299 + http://ia802401.us.archive.org:6988/proxy/application_1559844455575_118299 + +## Re-GROBID batch (2019-11-12) + +Want to re-process "old" GROBID output with newer (0.5.5+fatcat) GROBID version +(vanilla training) plus biblio-glutton identification. Hoping to make a couple +million new fatcat matches; will probably do a later round of ML matching over +this batch as well. + + # in /grande/regrobid + + # as postgres + psql sandcrawler < dump_regrobid_pdf.sql > dump_regrobid_pdf.txt + + # as bnewbold + cat dump_regrobid_pdf.txt | sort -S 4G | uniq -w 40 | cut -f2 | pv -l > dump_regrobid_pdf.2019-11-12.json + # 41.5M lines, uniq by SHA1 + # NOTE: not the full 56m+ from GROBID table... some in archive.org, others + # not application/pdf type. Will need to follow-up on those later + + # intend to have 3 worker machines, but splitting 6 ways in case we need to + # re-balance load or get extra machines or something + split -n l/6 -a1 -d --additional-suffix=.json dump_regrobid_pdf.2019-11-12.json regrobid_cdx.split_ + + # distribute to tmp001, tmp002, tmp003: + tmp001: 0,1 + tmp002: 2,3 + tmp003: 4,5 + + # test local grobid config: + head /srv/sandcrawler/tasks/regrobid_cdx.split_0.json | pv -l | ./grobid_tool.py --grobid-host http://localhost:8070 -j0 extract-json - > example_out.json + # expect at least a couple fatcat matches + cat example_out.json | jq .tei_xml -r | rg fatcat + + # test GROBID+kafka config: + cat /srv/sandcrawler/tasks/regrobid_cdx.split_*.json | pv -l | head | parallel -j40 --linebuffer --round-robin --pipe ./grobid_tool.py --kafka-env prod --kafka-hosts wbgrp-svc263.us.archive.org:9092,wbgrp-svc284.us.archive.org:9092,wbgrp-svc285.us.archive.org:9092 --kafka-mode --grobid-host http://localhost:8070 -j0 extract-json - + + # full run, in a screen session + cat /srv/sandcrawler/tasks/regrobid_cdx.split_*.json | pv -l | parallel -j40 --linebuffer --round-robin --pipe ./grobid_tool.py --kafka-env prod --kafka-hosts wbgrp-svc263.us.archive.org:9092,wbgrp-svc284.us.archive.org:9092,wbgrp-svc285.us.archive.org:9092 --kafka-mode --grobid-host http://localhost:8070 -j0 extract-json - + +NOTE: really should get parallel kafka worker going soon. if there is a reboot +or something in the middle of this process, will need to re-run from the start. + +Was getting a bunch of weird kafka INVALID_MSG errors on produce. Would be nice to be able to retry, so doing: + + cat /srv/sandcrawler/tasks/regrobid_cdx.split_*.json | pv -l | parallel --joblog regrobid_job.log --retries 5 -j40 --linebuffer --pipe ./grobid_tool.py --kafka-env prod --kafka-hosts wbgrp-svc263.us.archive.org:9092,wbgrp-svc284.us.archive.org:9092,wbgrp-svc285.us.archive.org:9092 --kafka-mode --grobid-host http://localhost:8070 -j0 extract-json - + +Never mind, going to split into chunks which can be retried. + + cd /srv/sandcrawler/tasks + sudo chown sandcrawler:staff . + cat regrobid_cdx.split_* | split -l 20000 -a4 -d --additional-suffix=.json - chunk_ + ls /srv/sandcrawler/tasks/chunk_*.json | parallel -j4 ./extract_chunk.sh {} + +extract_chunk.sh: + + + #!/bin/bash + + set -x -e -u -o pipefail + + if [ -f $1.SUCCESS ]; then + echo "Skipping: $1..." + exit + fi + + echo "Extracting $1..." + + date + cat $1 | parallel -j10 --linebuffer --round-robin --pipe ./grobid_tool.py --kafka-env prod --kafka-hosts wbgrp-svc263.us.archive.org:9092,wbgrp-svc284.us.archive.org:9092,wbgrp-svc285.us.archive.org:9092 --kafka-mode --grobid-host http://localhost:8070 -j0 extract-json - + + touch $1.SUCCESS + +seems to be working better! tested and if there is a problem with one chunk the others continue + +## Pig Joins (around 2019-12-24) + +Partial (as a start): + + pig -param INPUT_CDX="/user/bnewbold/pdfs/gwb-pdf-20191005172329" -param INPUT_DIGEST="/user/bnewbold/scihash/shadow.20191222.sha1b32.sorted" -param OUTPUT="/user/bnewbold/scihash/gwb-pdf-20191005172329.shadow.20191222.join.cdx" join-cdx-sha1.pig + + HadoopVersion PigVersion UserId StartedAt FinishedAt Features +2.6.0-cdh5.11.2 0.12.0-cdh5.0.1 bnewbold 2019-12-27 00:39:38 2019-12-27 15:32:44 HASH_JOIN,ORDER_BY,DISTINCT,FILTER + + Success! + + Job Stats (time in seconds): + JobId Maps Reduces MaxMapTime MinMapTIme AvgMapTime MedianMapTime MaxReduceTime MinReduceTime AvgReduceTime MedianReducetime Alias Feature Outputs + job_1574819148370_46540 4880 0 143 10 27 21 n/a n/a n/a n/a cdx MAP_ONLY + job_1574819148370_46541 19 0 59 9 25 18 n/a n/a n/a n/a digests MAP_ONLY + job_1574819148370_46773 24 1 17 7 10 9 6 6 6 6 digests SAMPLER + job_1574819148370_46774 7306 1 55 4 7 7 25 25 25 25 cdx SAMPLER + job_1574819148370_46778 7306 40 127 8 18 15 4970 1936 2768 2377 cdx ORDER_BY + job_1574819148370_46779 24 20 80 24 60 66 90 26 38 37 digests ORDER_BY + job_1574819148370_46822 22 3 101 27 53 48 1501 166 735 539 DISTINCT + job_1574819148370_46828 7146 959 122 7 16 14 91 21 35 32 full_join,result HASH_JOIN /user/bnewbold/scihash/gwb-pdf-20191005172329.shadow.20191222.join.cdx, + + Input(s): + Successfully read 1968654006 records (654323590996 bytes) from: "/user/bnewbold/pdfs/gwb-pdf-20191005172329" + Successfully read 74254196 records (2451575849 bytes) from: "/user/bnewbold/scihash/shadow.20191222.sha1b32.sorted" + + Output(s): + Successfully stored 0 records in: "/user/bnewbold/scihash/gwb-pdf-20191005172329.shadow.20191222.join.cdx" + +Oops! Didn't upper-case the sha1b32 output. + +Full GWB: + + pig -param INPUT_CDX="/user/bnewbold/pdfs/gwb-pdf-20191005172329" -param INPUT_DIGEST="/user/bnewbold/scihash/shadow.20191222.sha1b32.sorted" -param OUTPUT="/user/bnewbold/scihash/gwb-pdf-20191005172329.shadow.20191222.join.cdx" join-cdx-sha1.pig diff --git a/notes/hbase_table_sizes.txt b/notes/hbase_table_sizes.txt new file mode 100644 index 0000000..97bbb16 --- /dev/null +++ b/notes/hbase_table_sizes.txt @@ -0,0 +1,12 @@ + +As of 2018-05-29: +- qa rows: 1,246,013 +- prod rows: 8,974,188 + +As of 2018-06-16: +- qa: 1,246,013 +- prod: 18,308,086 + +As of 2018-08-01: +- qa: 1,246,013 +- prod: 18,308,141 diff --git a/notes/html_ingest_notes.md b/notes/html_ingest_notes.md new file mode 100644 index 0000000..a1a91f3 --- /dev/null +++ b/notes/html_ingest_notes.md @@ -0,0 +1,318 @@ + +## Current Plan + +- selectolax to extract metadata and quickly filter (speed) + => eg, differentiate landing pages from fulltext + => also embed URLs? +- trafilatura for fulltext body extract +- no solution yet for reference parsing + => maybe trafilatura XML-TEI parsing, then GROBID? + => especially if DOI/identifier/URL is in the reference + + + +TODO: +x print/wrap error condition better +x serialize dates (pydantic) +x CDX lookup "closest" to capture datetime (or by month) +x firstmonday no extracted fulltext/XML +x apply URL base fixup to fulltext URLs +x XML alternative detection +x basic ingest worker, kafka topics, persist workers, sql table, etc +- ingest worker: landing page to actual fulltext (eg, OJS) +- broken? https://betterexplained.com/articles/colorized-math-equations/ + +Ponder: +- CDX lookup older successful captures + http://www.altdevblogaday.com/2011/05/17/understanding-the-fourier-transform/ + => optional filter by status? "reduce" by month/year? +- detect scope heuristically + bepress_is_article_cover_page 1 + citation_fulltext_world_readable "" (eg, distill) +- non-success subresource fetches + https://www.europenowjournal.org/2020/10/11/a-social-history-of-early-rock-n-roll-in-germany-hamburg-from-burlesque-to-the-beatles-1956-1969/ +- redirects: keep start URL? + +Later: +- XML URL extraction + https://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-19652002000200001&lng=en&nrm=iso&tlng=pt + <a href="http://www.scielo.br/scieloOrg/php/articleXML.php?pid=S0100-19652002000200001&lang=en" rel="nofollow" target="xml"> +- selectolax bug? hangs: `css_first("meta['thing']")` +- youtube embed + => download/include actual video file? +- parse references in citation headers +- try parsing references in HTML fulltext + +## Testing URLs + +- PLOS + https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0093949 + TODO: "May 9, 2014" + TODO: appendix +- peerj + https://peerj.com/articles/4375/ +- scielo + http://scielo.iics.una.py/scielo.php?script=sci_arttext&pid=S1683-98032020000200081&lng=en&nrm=iso&tlng=es + bunch of little icon .png, but ok + redirect of an image not saved in webcapture +- wordpress + https://www.europenowjournal.org/2020/10/11/a-social-history-of-early-rock-n-roll-in-germany-hamburg-from-burlesque-to-the-beatles-1956-1969/ + no HTML meta? hrm +- old OJS + (pdf only) http://rjh.folium.ru/index.php/rjh/article/view/1511 +- new OJS + https://firstmonday.org/ojs/index.php/fm/article/view/10274/9729 +- plain HTML + http://journal.sjdm.org/12/12627/jdm12627.html +- blogs/essays + http://symbolflux.com/lodessay/ + https://betterexplained.com/articles/colorized-math-equations/ + https://web.archive.org/web/20120418231513/http://www.altdevblogaday.com/2011/05/17/understanding-the-fourier-transform/ + https://research.google.com/bigpicture/attacking-discrimination-in-ml/ + http://www.econgraphs.org/ +- journal homepage (not fulltext) +- OJS new landing page (not fulltext) +- OJS old (not fulltext) + http://rjh.folium.ru/index.php/rjh/index + http://rjh.folium.ru/index.php/rjh/issue/view/106 + http://rjh.folium.ru/index.php/rjh/article/view/382 +- distill + https://distill.pub/2020/bayesian-optimization/ + https://distill.pub/2018/feature-wise-transformations/ +- youtube video embed + http://www.cond.org/persalog.html +- youtube video direct? +- github: project README? +- wikipedia + +## Background Research + +- scrapy (?) +- requests-html: can run javascript + => good for metadata extraction? +- selectolax +- scrapely: give HTML and extracted text, it builds the parser + => good for difficult one-off cases? +- https://rushter.com/blog/python-fast-html-parser/ +- WET generation from WARC, a la common crawl +- https://towardsdatascience.com/categorizing-world-wide-web-c130abd9b717 + +Other random stuff: +- distilBERT: most BERT accuracy, 0.4 factor latency (faster)? + https://medium.com/huggingface/distilbert-8cf3380435b5 +- htmldate: finds "date of publication" for a document +- adblockparser + => good as a filter in HTML ingest +- w3lib: utility library. unicode conversion; cleanups; etc +- courlan: clean/normalize/sample large URL lists + => https://github.com/adbar/courlan + +### Main Text Extraction + +Things to try: + +- newspaper3k + => basic article extraction. lxml +- trafilatura + => TEI-XML output! + => looks very promising + => falls back to readability and justext +- python-readability + => improved vs newspaper? +- dragnet +- eatiht +- jusText +- inscriptis + => emphasis on shape/readability of text output? compare with lynx +- Goose3 + => metadata and article text +- news-please + => very full-featured. build on scrapy, newspaper, readability + => can iterate over common crawl? +- html2text + => actually HTML-to-markdown; no or little "boilerplate removal" +- boilerpipe (Java) + boilerpipe3 (wrapper) + boilerpy3 (port) + +Comparisons and articles: + +- https://www.diffbot.com/benefits/comparison/ +- https://github.com/scrapinghub/article-extraction-benchmark + - https://github.com/scrapinghub/article-extraction-benchmark/releases/download/v1.0.0/paper-v1.0.0.pdf +- https://github.com/rundimeco/waddle + +- https://moz.com/devblog/benchmarking-python-content-extraction-algorithms-dragnet-readability-goose-and-eatiht +- https://hal.archives-ouvertes.fr/hal-02768510v3/document (fr; June 2020) + https://translate.google.com/translate?sl=auto&tl=en&u=https%3A%2F%2Fhal.archives-ouvertes.fr%2Fhal-02768510v3%2Fdocument +- http://eprints.fri.uni-lj.si/1718/1/Kovacic-1.pdf (2012) +- "Generic Web Content Extraction with Open-Source Software" (2020; trafilatura) +- "Out-of-the-Box and Into the Ditch? Multilingual Evaluation of Generic Text Extraction Tools" + https://hal.archives-ouvertes.fr/hal-02732851/document + very on-topic +- https://cloud.google.com/blog/products/gcp/problem-solving-with-ml-automatic-document-classification + +### Reference/Citation Extraction + +"Locating and parsing bibliographic references in HTML medical articles" +https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2903768/ + +cb2bib (in debian/ubuntu) + + +### Metadata Extraction + +OJS 3.x seems to have `citation_fulltext_html_url`. Annoyingly, has an iframe. + +http://documents.clockss.org/index.php/LOCKSS:_Extracting_Bibliographic_Metadata + +https://blog.dshr.org/2013/04/talk-on-lockss-metadata-extraction-at.html + +"OXPath": declaritive XPath extension for scraping metadata +https://journal.code4lib.org/articles/13007 + + +## newspaper3k experimentation + + import newspaper + + import nltk + nltk.download('punkt') + + # first mondays (OJS) fulltext + monday = newspaper.Article("https://firstmonday.org/ojs/index.php/fm/article/download/10274/9729?inline=1") + # => ugh, iframe + monday.download() + monday.parse() # several seconds + + monday.title + # Surveillance, stigma and sociotechnical design for HIV + monday.text + # reasonable; similar to pdftotext? + monday.authors + # empty + monday.images + # reasonable? + + nih = newspaper.Article('https://www.nlm.nih.gov/pubs/techbull/ja02/ja02_locatorplus_merge.html') + nih.download() + nih.parse() + nih.nlp() + + nih.title + # Migration of Monographic Citations to LocatorPlus: Merge Project. NLM Technical Bulletin. Jul-Aug 2002 + # duplicate journal name in title + nih.authors + # none + nih.text + # Ok. missing first character, weirdly + + genders = newspaper.Article('https://web.archive.org/web/20141230080932id_/http://www.genders.org/g58/g58_fairlie.html') + genders.download() + genders.parse() + + genders.title + # Presenting innovative theories in art, literature, history, music, TV and film. + # nope: this is title of the journal + + genders.text + # Ok. includes title and author in the body. + + dlib = newspaper.Article('http://www.dlib.org/dlib/may17/vanhyning/05vanhyning.html') + dlib.download() + dlib.parse() + + dlib.title + # Transforming Libraries and Archives through Crowdsourcing + dlib.authors() + # none + dlib.text + # some other junk, but main body there + +## trafilatura experimentation + + trafilatura --json -u 'http://www.dlib.org/dlib/may17/vanhyning/05vanhyning.html' | jq . + + trafilatura --xmltei -u 'http://www.dlib.org/dlib/may17/vanhyning/05vanhyning.html' + +Does not work with `first_monday_ojs_inline`? + +May need to test/compare more. + +Examples/bugs: + + http://web.archive.org/web/20081120141035id_/http://www.mundanebehavior.org/issues/v5n1/jones.htm + poor title detection + + generally, author detection not great. + not, apparently, using detection of dc.authors etc + + +## Prod Deployment Notes (2020-12-14) + +Created `html_meta` table in `sandcrawler-db`. + +Updated ansible roles to deploy persist and import workers. Then ran the roles +and enabled: + +- sandcrawler database (aitio) + - sandcrawler-persist-ingest-file-worker@1: restarted +- blobs (wbgrp-svc169) + - sandcrawler-persist-html-teixml-worker@1: started and enabled + - sandcrawler-persist-xml-doc-worker@1: started and enabled +- fatcat prod worker (wbgrp-svc502) + - fatcat-import-ingest-web-worker: started and enabled + +Test some d-lib and first monday ingests: + + # dlib + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --ingest-type html --limit 50 container --container-id ugbiirfvufgcjkx33r3cmemcuu + => Counter({'estimate': 803, 'ingest_request': 50, 'elasticsearch_release': 50, 'kafka': 50}) + + # first monday + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --ingest-type html --limit 50 container --container-id svz5ul6qozdjhjhk7d627avuja + +Starting: + + d-lib: 253 / 1056 preserved (https://fatcat.wiki/container/ugbiirfvufgcjkx33r3cmemcuu/coverage) + +Initially, `fatcat-import-ingest-web-worker` is seeing these but doesn't seem +to be importing. + + # postgresql shell + select sha1hex, updated, status, scope, has_teixml, has_thumbnail, word_count from html_meta; + => initially has_teixml is false for all + => fixed in an update + + # weed shell + > fs.ls /buckets/sandcrawler/html_body + [...] + > fs.cat /buckets/sandcrawler/html_body/77/75/7775adf8c7e19151bbe887bfa08a575483291d7c.tei.xml + [looks like fine TEI-XML] + +Going to debug ingest issue by dumping results to disk and importing manually +(best way to see counts): + + kafkacat -C -b wbgrp-svc284.us.archive.org:9092 -t sandcrawler-prod.ingest-file-results -o -10 | rg html | head -n10 | jq . -c > web_ingest_results.json + + export FATCAT_AUTH_WORKER_CRAWL=[...] + ./fatcat_import.py ingest-web-results web_ingest_results.json + => Counter({'total': 10, 'skip-update-disabled': 9, 'skip': 1, 'skip-hit': 1, 'insert': 0, 'update': 0, 'exists': 0}) + + # did some patching (f7a75a01), then re-ran twice and got: + => Counter({'total': 10, 'insert': 9, 'skip': 1, 'skip-hit': 1, 'update': 0, 'exists': 0}) + => Counter({'total': 10, 'exists': 9, 'skip': 1, 'skip-hit': 1, 'insert': 0, 'update': 0}) + + # looks good! + +Re-ingesting all of d-lib: + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --ingest-type html container --container-id ugbiirfvufgcjkx33r3cmemcuu + => Expecting 803 release objects in search queries + => Counter({'ingest_request': 803, 'elasticsearch_release': 803, 'estimate': 803, 'kafka': 803}) + +TODO: + +- release ES transform isn't counting these as `in_ia` or preserved (code-only change) +- no indication in search results (ES schema change) +- ingest tool should probably look at `in_ia_html` or `in_ia_pdf` for PDF/XML queries (or a `types_in_ia` list?) diff --git a/notes/ingest/.gitignore b/notes/ingest/.gitignore new file mode 100644 index 0000000..343a25c --- /dev/null +++ b/notes/ingest/.gitignore @@ -0,0 +1,2 @@ +*.csv +*.json diff --git a/notes/ingest/2019-10-23_testing.md b/notes/ingest/2019-10-23_testing.md new file mode 100644 index 0000000..481c4e2 --- /dev/null +++ b/notes/ingest/2019-10-23_testing.md @@ -0,0 +1,8 @@ + +exported not-archived DOIs for elife, as well as general list. + + wc -l recent\ missing\ oa\ releases.csv + 161828 recent missing oa releases.csv + + wc -l missing\ elife\ DOIs.csv + 1779 missing elife DOIs.csv diff --git a/notes/ingest/2020-01-14_bulk.md b/notes/ingest/2020-01-14_bulk.md new file mode 100644 index 0000000..9d05cda --- /dev/null +++ b/notes/ingest/2020-01-14_bulk.md @@ -0,0 +1,26 @@ + +Generate ingest requests from arabesque: + + zcat /data/arabesque/ARXIV-CRAWL-2019-10.arabesque.json.gz | ./arabesque2ingestrequest.py --link-source arxiv --extid-type arxiv --release-stage submitted - | shuf > /data/arabesque/ARXIV-CRAWL-2019-10.arabesque.ingest_request.json + + zcat /data/arabesque/PUBMEDCENTRAL-CRAWL-2019-10.arabesque.json.gz | ./arabesque2ingestrequest.py --link-source pmc --extid-type pmcid - | shuf > /data/arabesque/PUBMEDCENTRAL-CRAWL-2019-10.arabesque.ingest_request.json + + +Quick tests locally: + + time head -n100 /data/arabesque/ARXIV-CRAWL-2019-10.arabesque.ingest_request.json |./ingest_file.py requests - > sample_arxiv.json + time head -n100 /data/arabesque/PUBMEDCENTRAL-CRAWL-2019-10.arabesque.ingest_request.json |./ingest_file.py requests - > sample_pubmed.json + +These are all wayback success; looking good! Single threaded, from home laptop +(over tunnel), took about 9 minutes, or 5.5sec/pdf. That's pretty slow even +with 30x parallelism. Should re-test on actual server. GROBID pre-check should +help? + +With new bulk topic: + + head PUBMEDCENTRAL-CRAWL-2019-10.arabesque.ingest_request.json -n1000 | kafkacat -P -b localhost -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + +Ok, let them rip: + + cat PUBMEDCENTRAL-CRAWL-2019-10.arabesque.ingest_request.json -n1000 | kafkacat -P -b localhost -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + cat ARXIV-CRAWL-2019-10.arabesque.ingest_request.json | kafkacat -P -b localhost -t sandcrawler-prod.ingest-file-requests-bulk -p -1 diff --git a/notes/ingest/2020-02-04_ingest_backfills.md b/notes/ingest/2020-02-04_ingest_backfills.md new file mode 100644 index 0000000..73a42ef --- /dev/null +++ b/notes/ingest/2020-02-04_ingest_backfills.md @@ -0,0 +1,148 @@ + + +## Using Fatcat Tool + +Want to enqueue some backfill URLs to crawl, now that SPNv2 is on the mend. + +Example dry-run: + + ./fatcat_ingest.py --dry-run --limit 50 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --after-year 2020 container --name elife + +Big OA from 2020 (past month): + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --after-year 2020 container --name elife + Will send ingest requests to kafka topic: sandcrawler-prod.ingest-file-requests + Expecting 158 release objects in search queries + Counter({'ingest_request': 158, 'estimate': 158, 'kafka': 158, 'elasticsearch_release': 158}) + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --name elife + Will send ingest requests to kafka topic: sandcrawler-prod.ingest-file-requests + Expecting 2312 release objects in search queries + Counter({'kafka': 2312, 'ingest_request': 2312, 'elasticsearch_release': 2312, 'estimate': 2312}) + + # note: did 100 first to test + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --after-year 2020 container --name plos + Will send ingest requests to kafka topic: sandcrawler-prod.ingest-file-requests + Expecting 1185 release objects in search queries + Counter({'estimate': 1185, 'ingest_request': 1185, 'elasticsearch_release': 1185, 'kafka': 1185}) + + ./fatcat_ingest.py --limit 500 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --after-year 2020 container --publisher elsevier + Will send ingest requests to kafka topic: sandcrawler-prod.ingest-file-requests + Expecting 89 release objects in search queries + Counter({'elasticsearch_release': 89, 'estimate': 89, 'ingest_request': 89, 'kafka': 89}) + + ./fatcat_ingest.py --limit 500 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --after-year 2020 container --publisher ieee + Will send ingest requests to kafka topic: sandcrawler-prod.ingest-file-requests + Expecting 499 release objects in search queries + Counter({'kafka': 499, 'ingest_request': 499, 'estimate': 499, 'elasticsearch_release': 499}) + + ./fatcat_ingest.py --limit 500 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --after-year 2020 container --name bmj + Will send ingest requests to kafka topic: sandcrawler-prod.ingest-file-requests + Expecting 28 release objects in search queries + Counter({'elasticsearch_release': 28, 'ingest_request': 28, 'kafka': 28, 'estimate': 28}) + + ./fatcat_ingest.py --dry-run --limit 500 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --after-year 2020 container --publisher springer + Will send ingest requests to kafka topic: sandcrawler-prod.ingest-file-requests + Expecting 6225 release objects in search queries + Counter({'estimate': 6225, 'kafka': 500, 'elasticsearch_release': 500, 'ingest_request': 500}) + + ./fatcat_ingest.py --limit 1000 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa container --container-id zpobyv4vbranllc7oob56tgci4 + Will send ingest requests to kafka topic: sandcrawler-prod.ingest-file-requests + Expecting 2920 release objects in search queries + Counter({'estimate': 2920, 'elasticsearch_release': 1001, 'ingest_request': 1000, 'kafka': 1000}) + +Hip corona virus papers: + + ./fatcat_ingest.py --limit 2000 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa query coronavirus + Will send ingest requests to kafka topic: sandcrawler-prod.ingest-file-requests + Expecting 5332 release objects in search queries + Counter({'estimate': 5332, 'elasticsearch_release': 2159, 'ingest_request': 2000, 'kafka': 2000}) + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa query 2019-nCoV + Will send ingest requests to kafka topic: sandcrawler-prod.ingest-file-requests + Expecting 110 release objects in search queries + Counter({'ingest_request': 110, 'kafka': 110, 'elasticsearch_release': 110, 'estimate': 110}) + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa query MERS-CoV + Will send ingest requests to kafka topic: sandcrawler-prod.ingest-file-requests + Expecting 589 release objects in search queries + Counter({'estimate': 589, 'elasticsearch_release': 589, 'ingest_request': 552, 'kafka': 552}) + + +Mixed eLife results: + + ["wrong-mimetype",null,"https://elifesciences.org/articles/54551"] + ["success",null,"https://elifesciences.org/download/aHR0cHM6Ly9jZG4uZWxpZmVzY2llbmNlcy5vcmcvYXJ0aWNsZXMvNTE2OTEvZWxpZmUtNTE2OTEtdjEucGRm/elife-51691-v1.pdf?_hash=Jp1cLog1NzIlU%2BvjgLdbM%2BuphOwe5QWUn%2F97tbQBNG4%3D"] + +## Re-Request Failed + +Select some failed injest request rows to re-enqueue: + + COPY ( + SELECT row_to_json(ingest_request.*) FROM ingest_request + LEFT JOIN ingest_file_result ON ingest_file_result.base_url = ingest_request.base_url + WHERE ingest_request.ingest_type = 'pdf' + AND ingest_file_result.ingest_type = 'pdf' + AND ingest_file_result.updated < NOW() - '2 day'::INTERVAL + AND ingest_file_result.hit = false + AND ingest_file_result.status = 'spn2-cdx-lookup-failure' + ) TO '/grande/snapshots/reingest_spn2cdx_20200205.rows.json'; + -- 1536 rows + +Transform back to full requests: + + ./scripts/ingestrequest_row2json.py reingest_spn2cdx_20200205.rows.json > reingest_spn2cdx_20200205.json + +Push into kafka (on a kafka broker node): + + cat ~/reingest_spn2cdx_20200205.json | jq . -c | kafkacat -P -b localhost -t sandcrawler-prod.ingest-file-requests -p -1 + +More: + + COPY ( + SELECT row_to_json(ingest_request.*) FROM ingest_request + LEFT JOIN ingest_file_result ON ingest_file_result.base_url = ingest_request.base_url + WHERE ingest_request.ingest_type = 'pdf' + AND ingest_file_result.ingest_type = 'pdf' + AND ingest_file_result.updated < NOW() - '2 day'::INTERVAL + AND ingest_file_result.hit = false + AND ingest_file_result.status like 'error:%' + ) TO '/grande/snapshots/reingest_spn2err1_20200205.rows.json'; + -- COPY 1516 + + COPY ( + SELECT row_to_json(ingest_request.*) FROM ingest_request + LEFT JOIN ingest_file_result ON ingest_file_result.base_url = ingest_request.base_url + WHERE ingest_request.ingest_type = 'pdf' + AND ingest_file_result.ingest_type = 'pdf' + AND ingest_file_result.updated < NOW() - '2 day'::INTERVAL + AND ingest_file_result.hit = false + AND ingest_file_result.status like 'spn2-error%' + ) TO '/grande/snapshots/reingest_spn2err2_20200205.rows.json'; + -- COPY 16678 + +The next large ones to try would be `wayback-error` and `cdx-error`, though +these are pretty generic. Could go kafka output to try and understand those +error classes better. + +Oof, as a mistake enqueued to partition 1 instead of -1 (random), so these will +take a week or more to actually process. Re-enqueued as -1; ingesting from +wayback is pretty fast, this should result mostly wayback ingests. Caught up by +end of weekend? + +## Check Coverages + +As follow-ups: + + elife: https://fatcat.wiki/container/en4qj5ijrbf5djxx7p5zzpjyoq/coverage + => 2020-02-24: 7187 / 8101 = 88% preserved + archivist: https://fatcat.wiki/container/zpobyv4vbranllc7oob56tgci4/coverage + => 85 preserved + => 2020-02-24: 85 / 3005 preserved (TODO) + jcancer: https://fatcat.wiki/container/nkkzpwht7jd3zdftc6gq4eoeey/coverage + => 2020 preserved + => 2520 preserved + => 2020-02-24: 2700 / 2766 preserved + plos: https://fatcat.wiki/container/23nqq3odsjhmbi5tqavvcn7cfm/coverage + => 2020-02-24: 7580 / 7730 = 98% preserved + diff --git a/notes/ingest/2020-02-18_ingest_backfills.md b/notes/ingest/2020-02-18_ingest_backfills.md new file mode 100644 index 0000000..1ab18f4 --- /dev/null +++ b/notes/ingest/2020-02-18_ingest_backfills.md @@ -0,0 +1,42 @@ + +Select: + + COPY ( + SELECT row_to_json(ingest_request.*) FROM ingest_request + LEFT JOIN ingest_file_result ON ingest_file_result.base_url = ingest_request.base_url + WHERE ingest_request.ingest_type = 'pdf' + AND ingest_file_result.ingest_type = 'pdf' + AND ingest_file_result.updated < NOW() - '2 day'::INTERVAL + AND ingest_file_result.hit = false + AND ingest_file_result.status like 'spn2-error%' + ) TO '/grande/snapshots/reingest_spn2err_20200218.rows.json'; + => COPY 6537 + + COPY ( + SELECT row_to_json(ingest_request.*) FROM ingest_request + LEFT JOIN ingest_file_result ON ingest_file_result.base_url = ingest_request.base_url + WHERE ingest_request.ingest_type = 'pdf' + AND ingest_file_result.ingest_type = 'pdf' + AND ingest_file_result.hit = false + AND ingest_file_result.status like 'wayback-error' + ) TO '/grande/snapshots/reingest_waybackerr_20200218.rows.json'; + => COPY 33022 + +Transform: + + ./scripts/ingestrequest_row2json.py reingest_spn2err_20200218.rows.json > reingest_spn2err_20200218.json + ./scripts/ingestrequest_row2json.py reingest_waybackerr_20200218.rows.json > reingest_waybackerr_20200218.json + +Push to kafka: + + cat reingest_spn2err_20200218.json | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests -p -1 + cat reingest_waybackerr_20200218.json | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests -p -1 + +Many had null `ingest_request_source`, so won't actually import into fatcat: + + bnewbold@ia601101$ cat reingest_waybackerr_20200218.json | jq .ingest_request_source | sort | uniq -c | sort -n + 1 "savepapernow-web" + 112 "fatcat-ingest-container" + 11750 "fatcat-changelog" + 21159 null + diff --git a/notes/ingest/2020-02-21_ingest_backfills.md b/notes/ingest/2020-02-21_ingest_backfills.md new file mode 100644 index 0000000..48df910 --- /dev/null +++ b/notes/ingest/2020-02-21_ingest_backfills.md @@ -0,0 +1,104 @@ + +Follow-ups to last ingest backfill. Only run these when ingest request topic is +empty, and full persist chain has run successfully. + +## Corona virus stuff + + ./fatcat_ingest.py --limit 2000 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa query coronavirus + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa query 2019-nCoV + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa query MERS-CoV + +## Large OA Publishers + +Should probably check domain stats/success for all of these first. + +Would also be good to have a "randomize" option. Could fake that by dumping to +disk first. + + ./fatcat_ingest.py --limit 2000 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --after-year 2020 container --publisher elsevier + + ./fatcat_ingest.py --dry-run --limit 500 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --after-year 2020 container --publisher springer + + # ??? + ./fatcat_ingest.py --limit 1000 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa container --container-id zpobyv4vbranllc7oob56tgci4 + +## Fixed OA Publishers (small tests) + + # american archivist + ./fatcat_ingest.py --limit 25 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa container --container-id zpobyv4vbranllc7oob56tgci4 + => Expecting 2920 release objects in search queries + => Counter({'estimate': 2920, 'elasticsearch_release': 26, 'ingest_request': 25, 'kafka': 25}) + => good + + ./fatcat_ingest.py --limit 25 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --publisher Gruyter + => Expecting 42897 release objects in search queries + => Counter({'estimate': 42897, 'ingest_request': 25, 'kafka': 25, 'elasticsearch_release': 25}) + + ./fatcat_ingest.py --limit 25 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --publisher frontiers + => Expecting 35427 release objects in search queries + => Counter({'estimate': 35427, 'kafka': 25, 'elasticsearch_release': 25, 'ingest_request': 25}) + => mixed results? + + ./fatcat_ingest.py --limit 25 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --publisher mdpi + => Expecting 43111 release objects in search queries + => Counter({'estimate': 43111, 'elasticsearch_release': 25, 'ingest_request': 25, 'kafka': 25}) + => success, fast + + ./fatcat_ingest.py --limit 25 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --publisher "American Heart Association" + => Expecting 185240 release objects in search queries + => Counter({'estimate': 185240, 'kafka': 25, 'ingest_request': 25, 'elasticsearch_release': 25}) + => no success? or mixed? skip for now + + # Environmental Health Perspectives (NIH) + ./fatcat_ingest.py --limit 25 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --container-id 3w6amv3ecja7fa3ext35ndpiky + => ["no-pdf-link",null,"https://ehp.niehs.nih.gov/doi/10.1289/ehp.113-a51"] + => ["no-pdf-link",null,"https://ehp.niehs.nih.gov/doi/10.1289/ehp.113-a51"] + => FIXED + => good (but slow?) + + ./fatcat_ingest.py --limit 50 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --publisher "Tomsk State University" + => Expecting 578057 release objects in search queries + => Counter({'estimate': 578057, 'elasticsearch_release': 50, 'kafka': 50, 'ingest_request': 50}) + => nothing from tsu.ru? skip for now + + ./fatcat_ingest.py --limit 25 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --name "cogent" + => Expecting 4602 release objects in search queries + => Counter({'estimate': 4602, 'kafka': 25, 'elasticsearch_release': 25, 'ingest_request': 25}) + => good + + ./fatcat_ingest.py --limit 25 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org query "doi:10.26434\/chemrxiv*" + => Expecting 5690 release objects in search queries + => Counter({'estimate': 5690, 'ingest_request': 25, 'kafka': 25, 'elasticsearch_release': 25}) + => good + + +## Fixed OA Publishers (full runs) + + # american archivist + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa container --container-id zpobyv4vbranllc7oob56tgci4 + Expecting 2920 release objects in search queries + Counter({'estimate': 2920, 'elasticsearch_release': 2920, 'kafka': 2911, 'ingest_request': 2911}) + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --publisher Gruyter + Expecting 42986 release objects in search queries + Counter({'estimate': 42986, 'elasticsearch_release': 42986, 'kafka': 42935, 'ingest_request': 42935}) + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --publisher mdpi + Expecting 43108 release objects in search queries + Counter({'estimate': 43108, 'elasticsearch_release': 43108, 'ingest_request': 41262, 'kafka': 41262}) + + # Environmental Health Perspectives (NIH) + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --container-id 3w6amv3ecja7fa3ext35ndpiky + Expecting 12699 release objects in search queries + Counter({'elasticsearch_release': 12699, 'estimate': 12699, 'kafka': 12615, 'ingest_request': 12615}) + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --name "cogent" + Expecting 4602 release objects in search queries + Counter({'estimate': 4602, 'ingest_request': 4602, 'kafka': 4602, 'elasticsearch_release': 4602}) + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org query "doi:10.26434\/chemrxiv*" + Expecting 5690 release objects in search queries + Counter({'ingest_request': 5690, 'kafka': 5690, 'estimate': 5690, 'elasticsearch_release': 5690}) + diff --git a/notes/ingest/2020-02-22_fixed_domain.txt b/notes/ingest/2020-02-22_fixed_domain.txt new file mode 100644 index 0000000..a60de42 --- /dev/null +++ b/notes/ingest/2020-02-22_fixed_domain.txt @@ -0,0 +1,246 @@ + +www.degruyter.com + + "/view/books/" didn't have citation_pdf_url, so added custom URL rule. + + Not sure why redirect-loop happening, but isn't with current live ingest + tool? + + domain | status | count + -------------------+-------------------------+------- + www.degruyter.com | redirect-loop | 22023 + www.degruyter.com | no-pdf-link | 8773 + www.degruyter.com | no-capture | 8617 + www.degruyter.com | success | 840 + www.degruyter.com | link-loop | 59 + www.degruyter.com | terminal-bad-status | 23 + www.degruyter.com | wrong-mimetype | 12 + www.degruyter.com | spn-error | 4 + www.degruyter.com | spn2-cdx-lookup-failure | 4 + www.degruyter.com | spn2-error:proxy-error | 1 + www.degruyter.com | spn-remote-error | 1 + www.degruyter.com | gateway-timeout | 1 + www.degruyter.com | petabox-error | 1 + (13 rows) + +www.frontiersin.org + + no pdf link + + seems to live ingest fine? files served from "*.blob.core.windows.net" + no fix, just re-ingest. + + domain | status | count + ---------------------+-------------------------+------- + www.frontiersin.org | no-pdf-link | 17503 + www.frontiersin.org | terminal-bad-status | 6696 + www.frontiersin.org | wayback-error | 203 + www.frontiersin.org | no-capture | 20 + www.frontiersin.org | spn-error | 6 + www.frontiersin.org | gateway-timeout | 3 + www.frontiersin.org | wrong-mimetype | 3 + www.frontiersin.org | spn2-cdx-lookup-failure | 2 + www.frontiersin.org | spn2-error:job-failed | 2 + www.frontiersin.org | spn-remote-error | 1 + www.frontiersin.org | cdx-error | 1 + (11 rows) + +www.mdpi.com + + terminal-bad-status + + Seems to ingest fine live? No fix, just re-ingest. + + domain | status | count + --------------+-------------------------+------- + www.mdpi.com | terminal-bad-status | 13866 + www.mdpi.com | wrong-mimetype | 2693 + www.mdpi.com | wayback-error | 513 + www.mdpi.com | redirect-loop | 505 + www.mdpi.com | success | 436 + www.mdpi.com | no-capture | 214 + www.mdpi.com | no-pdf-link | 43 + www.mdpi.com | spn2-cdx-lookup-failure | 34 + www.mdpi.com | gateway-timeout | 3 + www.mdpi.com | petabox-error | 2 + (10 rows) + +www.ahajournals.org | no-pdf-link | 5727 + + SELECT domain, status, COUNT((domain, status)) + FROM (SELECT status, substring(terminal_url FROM '[^/]+://([^/]*)') AS domain FROM ingest_file_result) t1 + WHERE t1.domain = 'www.ahajournals.org' + GROUP BY domain, status + ORDER BY COUNT DESC; + + SELECT * FROM ingest_file_result + WHERE terminal_url LIKE '%www.ahajournals.org%' + AND status = 'no-pdf-link' + ORDER BY updated DESC + LIMIT 10; + + domain | status | count + ---------------------+----------------+------- + www.ahajournals.org | no-pdf-link | 5738 + www.ahajournals.org | wrong-mimetype | 84 + (2 rows) + + + pdf | https://doi.org/10.1161/circ.110.19.2977 | 2020-02-23 00:28:55.256296+00 | f | no-pdf-link | https://www.ahajournals.org/action/cookieAbsent | 20200217122952 | 200 | + pdf | https://doi.org/10.1161/str.49.suppl_1.tp403 | 2020-02-23 00:27:34.950059+00 | f | no-pdf-link | https://www.ahajournals.org/action/cookieAbsent | 20200217122952 | 200 | + pdf | https://doi.org/10.1161/str.49.suppl_1.tp168 | 2020-02-23 00:25:54.611271+00 | f | no-pdf-link | https://www.ahajournals.org/action/cookieAbsent | 20200217122952 | 200 | + pdf | https://doi.org/10.1161/jaha.119.012131 | 2020-02-23 00:24:44.244511+00 | f | no-pdf-link | https://www.ahajournals.org/action/cookieAbsent | 20200217122952 | 200 | + + Ah, the ol' annoying 'cookieAbsent'. Works with live SPNv2 via soft-404 + detection, but that status wasn't coming through, and needed custom + pdf-link detection. + + FIXED: added pdf-link detection + +ehp.niehs.nih.gov | no-pdf-link | 5772 + + simple custom URL format. but are they also blocking? + + SELECT domain, status, COUNT((domain, status)) + FROM (SELECT status, substring(terminal_url FROM '[^/]+://([^/]*)') AS domain FROM ingest_file_result) t1 + WHERE t1.domain = 'ehp.niehs.nih.gov' + GROUP BY domain, status + ORDER BY COUNT DESC; + + domain | status | count + -------------------+----------------+------- + ehp.niehs.nih.gov | no-pdf-link | 5791 + ehp.niehs.nih.gov | wrong-mimetype | 11 + (2 rows) + + FIXED: mostly just slow, custom URL seems to work + +journals.tsu.ru | no-pdf-link | 4404 + + SELECT domain, status, COUNT((domain, status)) + FROM (SELECT status, substring(terminal_url FROM '[^/]+://([^/]*)') AS domain FROM ingest_file_result) t1 + WHERE t1.domain = 'journals.tsu.ru' + GROUP BY domain, status + ORDER BY COUNT DESC; + + SELECT * FROM ingest_file_result + WHERE terminal_url LIKE '%journals.tsu.ru%' + AND status = 'no-pdf-link' + ORDER BY updated DESC + LIMIT 10; + + domain | status | count + -----------------+----------------+------- + journals.tsu.ru | no-pdf-link | 4409 + journals.tsu.ru | success | 1 + journals.tsu.ru | wrong-mimetype | 1 + (3 rows) + + + pdf | https://doi.org/10.17223/18572685/57/3 | 2020-02-23 00:45:49.003593+00 | f | no-pdf-link | http://journals.tsu.ru/rusin/&journal_page=archive&id=1907&article_id=42847 | 20200213132322 | 200 | + pdf | https://doi.org/10.17223/17267080/71/4 | 2020-02-23 00:31:25.715416+00 | f | no-pdf-link | http://journals.tsu.ru/psychology/&journal_page=archive&id=1815&article_id=40405 | 20200211151825 | 200 | + pdf | https://doi.org/10.17223/15617793/399/33 | 2020-02-23 00:29:45.414865+00 | f | no-pdf-link | http://journals.tsu.ru/vestnik/&journal_page=archive&id=1322&article_id=24619 | 20200208152715 | 200 | + pdf | https://doi.org/10.17223/19988613/58/15 | 2020-02-23 00:25:24.402838+00 | f | no-pdf-link | http://journals.tsu.ru//history/&journal_page=archive&id=1827&article_id=40501 | 20200212200320 | 200 | + + FIXED: simple new custom PDF link pattern + +www.cogentoa.com | no-pdf-link | 4282 + + SELECT domain, status, COUNT((domain, status)) + FROM (SELECT status, substring(terminal_url FROM '[^/]+://([^/]*)') AS domain FROM ingest_file_result) t1 + WHERE t1.domain = 'www.cogentoa.com' + GROUP BY domain, status + ORDER BY COUNT DESC; + + SELECT * FROM ingest_file_result + WHERE terminal_url LIKE '%www.cogentoa.com%' + AND status = 'no-pdf-link' + ORDER BY updated DESC + LIMIT 10; + + domain | status | count + ------------------+-------------+------- + www.cogentoa.com | no-pdf-link | 4296 + (1 row) + + pdf | https://doi.org/10.1080/23311932.2015.1022632 | 2020-02-23 01:06:14.040013+00 | f | no-pdf-link | https://www.cogentoa.com/article/10.1080/23311932.2015.1022632 | 20200208054228 | 200 | + pdf | https://doi.org/10.1080/23322039.2020.1730079 | 2020-02-23 01:04:53.754117+00 | f | no-pdf-link | https://www.cogentoa.com/article/10.1080/23322039.2020.1730079 | 20200223010431 | 200 | + pdf | https://doi.org/10.1080/2331186x.2018.1460901 | 2020-02-23 01:04:03.47563+00 | f | no-pdf-link | https://www.cogentoa.com/article/10.1080/2331186X.2018.1460901 | 20200207200958 | 200 | + pdf | https://doi.org/10.1080/23311975.2017.1412873 | 2020-02-23 01:03:08.063545+00 | f | no-pdf-link | https://www.cogentoa.com/article/10.1080/23311975.2017.1412873 | 20200209034602 | 200 | + pdf | https://doi.org/10.1080/23311916.2017.1293481 | 2020-02-23 01:02:42.868424+00 | f | no-pdf-link | https://www.cogentoa.com/article/10.1080/23311916.2017.1293481 | 20200208101623 | 200 | + + FIXED: simple custom URL-based pattern + +chemrxiv.org | no-pdf-link | 4186 + + SELECT domain, status, COUNT((domain, status)) + FROM (SELECT status, substring(terminal_url FROM '[^/]+://([^/]*)') AS domain FROM ingest_file_result) t1 + WHERE t1.domain = 'chemrxiv.org' + GROUP BY domain, status + ORDER BY COUNT DESC; + + SELECT * FROM ingest_file_result + WHERE terminal_url LIKE '%chemrxiv.org%' + AND status = 'no-pdf-link' + ORDER BY updated DESC + LIMIT 10; + + domain | status | count + --------------+-------------------------+------- + chemrxiv.org | no-pdf-link | 4202 + chemrxiv.org | wrong-mimetype | 64 + chemrxiv.org | wayback-error | 14 + chemrxiv.org | success | 12 + chemrxiv.org | terminal-bad-status | 4 + chemrxiv.org | spn2-cdx-lookup-failure | 1 + + pdf | https://doi.org/10.26434/chemrxiv.9912812.v1 | 2020-02-23 01:08:34.585084+00 | f | no-pdf-link | https://chemrxiv.org/articles/Proximity_Effect_in_Crystalline_Framework_Materials_Stacking-Induced_Functionality_in_MOFs_and_COFs/9912812/1 | 20200215072929 | 200 | + pdf | https://doi.org/10.26434/chemrxiv.7150097 | 2020-02-23 01:05:48.957624+00 | f | no-pdf-link | https://chemrxiv.org/articles/Systematic_Engineering_of_a_Protein_Nanocage_for_High-Yield_Site-Specific_Modification/7150097 | 20200213002430 | 200 | + pdf | https://doi.org/10.26434/chemrxiv.7833500.v1 | 2020-02-23 00:55:41.013109+00 | f | no-pdf-link | https://chemrxiv.org/articles/Formation_of_Neutral_Peptide_Aggregates_Studied_by_Mass_Selective_IR_Action_Spectroscopy/7833500/1 | 20200210131343 | 200 | + pdf | https://doi.org/10.26434/chemrxiv.8146103 | 2020-02-23 00:52:00.193328+00 | f | no-pdf-link | https://chemrxiv.org/articles/On-Demand_Guest_Release_from_MOF-5_Sealed_with_Nitrophenylacetic_Acid_Photocapping_Groups/8146103 | 20200207215449 | 200 | + pdf | https://doi.org/10.26434/chemrxiv.10101419 | 2020-02-23 00:46:14.086913+00 | f | no-pdf-link | https://chemrxiv.org/articles/Biradical_Formation_by_Deprotonation_in_Thiazole-Derivatives_The_Hidden_Nature_of_Dasatinib/10101419 | 20200214044153 | 200 | + + FIXED: complex JSON PDF url extraction; maybe for all figshare? + +TODO: +x many datacite prefixes go to IRs, but have is_oa:false. we should probably crawl by default based on release_type + => fatcat branch bnewbold-more-ingest +- re-ingest all degruyter (doi_prefix:10.1515) + 1456169 doi:10.1515\/* + 89942 doi:10.1515\/* is_oa:true + 36350 doi:10.1515\/* in_ia:false is_oa:true + 1290830 publisher:Gruyter + 88944 publisher:Gruyter is_oa:true + 40034 publisher:Gruyter is_oa:true in_ia:false +- re-ingest all frontiersin + 248165 publisher:frontiers + 161996 publisher:frontiers is_oa:true + 36093 publisher:frontiers is_oa:true in_ia:false + 121001 publisher:frontiers in_ia:false +- re-ingest all mdpi + 43114 publisher:mdpi is_oa:true in_ia:false +- re-ingest all ahajournals.org + 132000 doi:10.1161\/* + 6606 doi:10.1161\/* in_ia:false is_oa:true + 81349 publisher:"American Heart Association" + 5986 publisher:"American Heart Association" is_oa:true in_ia:false +- re-ingest all ehp.niehs.nih.gov + 25522 doi:10.1289\/* + 15315 publisher:"Environmental Health Perspectives" + 8779 publisher:"Environmental Health Perspectives" in_ia:false + 12707 container_id:3w6amv3ecja7fa3ext35ndpiky in_ia:false is_oa:true +- re-ingest all journals.tsu.ru + 12232 publisher:"Tomsk State University" + 11668 doi:10.17223\/* + 4861 publisher:"Tomsk State University" in_ia:false is_oa:true +- re-ingest all www.cogentoa.com + 3421898 doi:10.1080\/* + 4602 journal:cogent is_oa:true in_ia:false + 5631 journal:cogent is_oa:true (let's recrawl all from publisher domain) +- re-ingest chemrxiv + 8281 doi:10.26434\/chemrxiv* + 6918 doi:10.26434\/chemrxiv* in_ia:false + +Submit all the above with limits of 1000, then follow up later to check that +there was success? + diff --git a/notes/ingest/2020-02_unpaywall.md b/notes/ingest/2020-02_unpaywall.md new file mode 100644 index 0000000..e18a2ff --- /dev/null +++ b/notes/ingest/2020-02_unpaywall.md @@ -0,0 +1,624 @@ + +## Stats and Things + + zcat unpaywall_snapshot_2019-11-22T074546.jsonl.gz | jq .oa_locations[].url_for_pdf -r | rg -v ^null | cut -f3 -d/ | sort | uniq -c | sort -nr > top_domains.txt + +## Transform + + zcat unpaywall_snapshot_2019-11-22T074546.jsonl.gz | ./unpaywall2ingestrequest.py - | pv -l > /dev/null + => 22M 1:31:25 [ 4k/s] + +Shard it into batches of roughly 1 million (all are 1098096 +/- 1): + + zcat unpaywall_snapshot_2019-11-22.ingest_request.shuf.json.gz | split -n r/20 -d - unpaywall_snapshot_2019-11-22.ingest_request.split_ --additional-suffix=.json + +Test ingest: + + head -n200 unpaywall_snapshot_2019-11-22.ingest_request.split_00.json | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + +Add a single batch like: + + cat unpaywall_snapshot_2019-11-22.ingest_request.split_00.json | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + +## Progress/Status + +There are 21,961,928 lines total, in batches of 1,098,097. + + unpaywall_snapshot_2019-11-22.ingest_request.split_00.json + => 2020-02-24 21:05 local: 1,097,523 ~22 results/sec (combined) + => 2020-02-25 10:35 local: 0 + unpaywall_snapshot_2019-11-22.ingest_request.split_01.json + unpaywall_snapshot_2019-11-22.ingest_request.split_02.json + unpaywall_snapshot_2019-11-22.ingest_request.split_03.json + unpaywall_snapshot_2019-11-22.ingest_request.split_04.json + => 2020-02-25 11:26 local: 4,388,997 + => 2020-02-25 10:14 local: 1,115,821 + => 2020-02-26 16:00 local: 265,116 + unpaywall_snapshot_2019-11-22.ingest_request.split_05.json + unpaywall_snapshot_2019-11-22.ingest_request.split_06.json + unpaywall_snapshot_2019-11-22.ingest_request.split_07.json + unpaywall_snapshot_2019-11-22.ingest_request.split_08.json + unpaywall_snapshot_2019-11-22.ingest_request.split_09.json + => 2020-02-26 16:01 local: 6,843,708 + => 2020-02-26 16:31 local: 4,839,618 + => 2020-02-28 10:30 local: 2,619,319 + unpaywall_snapshot_2019-11-22.ingest_request.split_10.json + unpaywall_snapshot_2019-11-22.ingest_request.split_11.json + unpaywall_snapshot_2019-11-22.ingest_request.split_12.json + unpaywall_snapshot_2019-11-22.ingest_request.split_13.json + unpaywall_snapshot_2019-11-22.ingest_request.split_14.json + unpaywall_snapshot_2019-11-22.ingest_request.split_15.json + unpaywall_snapshot_2019-11-22.ingest_request.split_16.json + unpaywall_snapshot_2019-11-22.ingest_request.split_17.json + unpaywall_snapshot_2019-11-22.ingest_request.split_18.json + unpaywall_snapshot_2019-11-22.ingest_request.split_19.json + => 2020-02-28 10:50 local: 13,551,887 + => 2020-03-01 23:38 local: 4,521,076 + => 2020-03-02 10:45 local: 2,827,071 + => 2020-03-02 21:06 local: 1,257,176 + added about 500k bulk re-ingest to try and work around cdx errors + => 2020-03-02 21:30 local: 1,733,654 + +## Investigate Failures + +Guessing than some domains are ultimately going to need direct "recrawl" via +SPNv2. + + -- top domain failures for unpaywall GWB history ingest + SELECT domain, status, COUNT((domain, status)) + FROM ( + SELECT + ingest_file_result.ingest_type, + ingest_file_result.status, + substring(ingest_file_result.terminal_url FROM '[^/]+://([^/]*)') AS domain + FROM ingest_file_result + LEFT JOIN ingest_request + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_file_result.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + ) t1 + WHERE t1.domain != '' + AND t1.status != 'success' + AND t1.status != 'no-capture' + GROUP BY domain, status + ORDER BY COUNT DESC + LIMIT 30; + + domain | status | count + -----------------------------------+---------------------+-------- + watermark.silverchair.com | terminal-bad-status | 258432 + www.tandfonline.com | no-pdf-link | 203873 + journals.sagepub.com | no-pdf-link | 126317 + iopscience.iop.org | terminal-bad-status | 112526 + files-journal-api.frontiersin.org | terminal-bad-status | 112499 + pubs.acs.org | no-pdf-link | 94772 + www.degruyter.com | redirect-loop | 89801 + www.ahajournals.org | no-pdf-link | 84025 + society.kisti.re.kr | no-pdf-link | 72849 + www.nature.com | redirect-loop | 53575 + babel.hathitrust.org | terminal-bad-status | 41063 + www.ncbi.nlm.nih.gov | redirect-loop | 40363 + scialert.net | no-pdf-link | 38340 + www.degruyter.com | terminal-bad-status | 34913 + www.journal.csj.jp | no-pdf-link | 30881 + espace.library.uq.edu.au | redirect-loop | 24570 + www.jci.org | redirect-loop | 24409 + aip.scitation.org | wrong-mimetype | 22144 + www.vr-elibrary.de | no-pdf-link | 17436 + www.biorxiv.org | wrong-mimetype | 15524 + ajph.aphapublications.org | no-pdf-link | 15083 + zookeys.pensoft.net | redirect-loop | 14867 + dialnet.unirioja.es | redirect-loop | 14486 + asa.scitation.org | wrong-mimetype | 14261 + www.nrcresearchpress.com | no-pdf-link | 14254 + dl.acm.org | redirect-loop | 14223 + osf.io | redirect-loop | 14103 + www.oecd-ilibrary.org | redirect-loop | 12835 + journals.sagepub.com | redirect-loop | 12229 + iopscience.iop.org | redirect-loop | 11825 + (30 rows) + + -- top no-capture terminal domains + SELECT domain, status, COUNT((domain, status)) + FROM ( + SELECT + ingest_file_result.ingest_type, + ingest_file_result.status, + substring(ingest_file_result.terminal_url FROM '[^/]+://([^/]*)') AS domain + FROM ingest_file_result + LEFT JOIN ingest_request + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_file_result.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + ) t1 + WHERE t1.domain != '' + AND t1.status = 'no-capture' + GROUP BY domain, status + ORDER BY COUNT DESC + LIMIT 30; + + => very few from any domain, interesting. Guess many of these are URLs that have truely never been crawled + + -- top no-capture base domains + SELECT domain, status, COUNT((domain, status)) + FROM ( + SELECT + ingest_file_result.ingest_type, + ingest_file_result.status, + substring(ingest_file_result.base_url FROM '[^/]+://([^/]*)') AS domain + FROM ingest_file_result + LEFT JOIN ingest_request + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_file_result.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + ) t1 + WHERE t1.domain != '' + AND t1.status = 'no-capture' + GROUP BY domain, status + ORDER BY COUNT DESC + LIMIT 30; + + domain | status | count + ------------------------------+------------+-------- + academic.oup.com | no-capture | 429888 + www.nature.com | no-capture | 273825 + dergipark.org.tr | no-capture | 119847 + www.biodiversitylibrary.org | no-capture | 110220 + escholarship.org | no-capture | 106307 + onlinelibrary.wiley.com | no-capture | 89771 + journals.sagepub.com | no-capture | 79297 + www.cell.com | no-capture | 64242 + deepblue.lib.umich.edu | no-capture | 58080 + babel.hathitrust.org | no-capture | 52286 + hal.archives-ouvertes.fr | no-capture | 48549 + iopscience.iop.org | no-capture | 42591 + dash.harvard.edu | no-capture | 40767 + www.tandfonline.com | no-capture | 40638 + discovery.ucl.ac.uk | no-capture | 40633 + www.jstage.jst.go.jp | no-capture | 39780 + www.doiserbia.nb.rs | no-capture | 39261 + dspace.mit.edu | no-capture | 37703 + zookeys.pensoft.net | no-capture | 34562 + repositorio.unesp.br | no-capture | 34437 + ashpublications.org | no-capture | 34112 + www.cambridge.org | no-capture | 33959 + kclpure.kcl.ac.uk | no-capture | 31455 + society.kisti.re.kr | no-capture | 30427 + pure.mpg.de | no-capture | 27650 + download.atlantis-press.com | no-capture | 27253 + dialnet.unirioja.es | no-capture | 26886 + link.springer.com | no-capture | 26257 + www.valueinhealthjournal.com | no-capture | 24798 + dspace.library.uu.nl | no-capture | 23234 + (30 rows) + + -- top no-capture base domains + SELECT domain, status, COUNT((domain, status)) + FROM ( + SELECT + ingest_file_result.ingest_type, + ingest_file_result.status, + substring(ingest_file_result.base_url FROM '[^/]+://([^/]*)') AS domain + FROM ingest_file_result + LEFT JOIN ingest_request + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_file_result.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + ) t1 + WHERE t1.domain != '' + AND t1.status = 'no-capture' + GROUP BY domain, status + ORDER BY COUNT DESC + LIMIT 30; + + domain | status | count + ------------------------------+------------+-------- + academic.oup.com | no-capture | 429888 + www.nature.com | no-capture | 273825 + dergipark.org.tr | no-capture | 119847 + www.biodiversitylibrary.org | no-capture | 110220 + escholarship.org | no-capture | 106307 + onlinelibrary.wiley.com | no-capture | 89771 + journals.sagepub.com | no-capture | 79297 + www.cell.com | no-capture | 64242 + deepblue.lib.umich.edu | no-capture | 58080 + babel.hathitrust.org | no-capture | 52286 + hal.archives-ouvertes.fr | no-capture | 48549 + iopscience.iop.org | no-capture | 42591 + dash.harvard.edu | no-capture | 40767 + www.tandfonline.com | no-capture | 40638 + discovery.ucl.ac.uk | no-capture | 40633 + www.jstage.jst.go.jp | no-capture | 39780 + www.doiserbia.nb.rs | no-capture | 39261 + dspace.mit.edu | no-capture | 37703 + zookeys.pensoft.net | no-capture | 34562 + repositorio.unesp.br | no-capture | 34437 + ashpublications.org | no-capture | 34112 + www.cambridge.org | no-capture | 33959 + kclpure.kcl.ac.uk | no-capture | 31455 + society.kisti.re.kr | no-capture | 30427 + pure.mpg.de | no-capture | 27650 + download.atlantis-press.com | no-capture | 27253 + dialnet.unirioja.es | no-capture | 26886 + link.springer.com | no-capture | 26257 + www.valueinhealthjournal.com | no-capture | 24798 + dspace.library.uu.nl | no-capture | 23234 + (30 rows) + + -- how many ingest requests not crawled at all? + SELECT count(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + AND ingest_file_result.status IS NULL; + => 0 + + -- "cookie absent" terminal pages, by domain + SELECT domain, status, COUNT((domain, status)) + FROM ( + SELECT + ingest_file_result.ingest_type, + ingest_file_result.status, + substring(ingest_file_result.terminal_url FROM '[^/]+://([^/]*)') AS domain + FROM ingest_file_result + LEFT JOIN ingest_request + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_file_result.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + AND ingest_file_result.terminal_url LIKE '%/cookieAbsent' + ) t1 + WHERE t1.domain != '' + AND t1.status != 'success' + AND t1.status != 'no-capture' + GROUP BY domain, status + ORDER BY COUNT DESC + LIMIT 30; + + domain | status | count + --------------------------------+----------------+-------- + journals.sagepub.com | no-pdf-link | 126295 + www.tandfonline.com | no-pdf-link | 116690 + pubs.acs.org | no-pdf-link | 94619 + www.ahajournals.org | no-pdf-link | 84016 + www.journal.csj.jp | no-pdf-link | 30881 + aip.scitation.org | wrong-mimetype | 22143 + www.vr-elibrary.de | no-pdf-link | 17436 + ajph.aphapublications.org | no-pdf-link | 15080 + asa.scitation.org | wrong-mimetype | 14261 + www.nrcresearchpress.com | no-pdf-link | 14253 + journals.ametsoc.org | no-pdf-link | 10500 + www.journals.uchicago.edu | no-pdf-link | 6917 + www.icevirtuallibrary.com | no-pdf-link | 6484 + www.journals.uchicago.edu | wrong-mimetype | 6191 + www.healthaffairs.org | no-pdf-link | 5732 + pubsonline.informs.org | no-pdf-link | 5672 + pinnacle-secure.allenpress.com | no-pdf-link | 5013 + www.worldscientific.com | no-pdf-link | 4560 + www.ajronline.org | wrong-mimetype | 4523 + ehp.niehs.nih.gov | no-pdf-link | 4514 + www.future-science.com | no-pdf-link | 4091 + pubs.acs.org | wrong-mimetype | 4015 + aip.scitation.org | no-pdf-link | 3916 + www.futuremedicine.com | no-pdf-link | 3821 + asa.scitation.org | no-pdf-link | 3644 + www.liebertpub.com | no-pdf-link | 3345 + physicstoday.scitation.org | no-pdf-link | 3005 + pubs.cif-ifc.org | no-pdf-link | 2761 + epubs.siam.org | wrong-mimetype | 2583 + www.ajronline.org | no-pdf-link | 2563 + (30 rows) + + -- "cookie absent" terminal pages, by domain + SELECT count(*) + FROM ingest_file_result + LEFT JOIN ingest_request + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_file_result.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + AND ingest_file_result.status != 'success' + AND ingest_file_result.terminal_url LIKE '%/cookieAbsent'; + + => 654885 + + -- NOT "cookie absent" terminal page failures, total count + SELECT count(*) + FROM ingest_file_result + LEFT JOIN ingest_request + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_file_result.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + AND ingest_file_result.status != 'success' + AND ingest_file_result.terminal_url NOT LIKE '%/cookieAbsent'; + + => 1403837 + +Looks like these domains are almost all "cookieAbsent" blocking: +- journals.sagepub.com +- pubs.acs.org +- ahajournals.org +- www.journal.csj.jp +- aip.scitation.org + +Grab some individual URLs to test: + + SELECT ingest_file_result.status, ingest_file_result.base_url, ingest_file_result.terminal_url + FROM ingest_file_result + LEFT JOIN ingest_request + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_file_result.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + AND ingest_file_result.status != 'success' + AND ingest_file_result.terminal_url NOT LIKE '%/cookieAbsent' + ORDER BY updated DESC + LIMIT 25; + +NOT cookieAbsent testing with regular ingest tool: +- iopscience.iop.org, terminal-bad-status, SPNv2 fetch, success +- academic.oup.com => silverchair, terminal-bad-status, SPNv2 fetch, succes +- osf.io success + + SELECT ingest_file_result.status, ingest_file_result.base_url, ingest_file_result.terminal_url + FROM ingest_file_result + LEFT JOIN ingest_request + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_file_result.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + AND ingest_file_result.status != 'success' + AND ingest_file_result.terminal_url LIKE '%/cookieAbsent' + ORDER BY updated DESC + LIMIT 25; + +cookieAbsent testing with regular ingest tool: +- www.tandfonline.com failure (no-pdf-link via wayback), but force-recrawl works + +The main distinguisher is status. terminal-bad-status can be ingested (live) +successfully, while no-pdf-link, redirect-loop, etc need to be re-crawled. + +## Heritrix Plan + +Generate following ingest request batches: + +- no-capture status from unpaywall +- all other failures except /cookieAbsent +- /cookieAbsent failures + +Plan will be to crawl no-capture first (to completion), then try the other +non-/cookieAbsent failures. /cookieAbsent means we'll need to use SPNv2. + +Because there are so few "no-capture on second hop" cases, will not enqueue +both terminal urls and base urls, only base urls. + +Should definitely skip/filter: + +- www.ncbi.nlm.nih.gov + +## Ingest Request Export + + COPY ( + SELECT row_to_json(ingest_request.*) FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + AND ingest_file_result.status = 'no-capture' + ) TO '/grande/snapshots/unpaywall_nocapture_20200304.rows.json'; + => 4,855,142 + + COPY ( + SELECT row_to_json(ingest_request.*) FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + AND ingest_file_result.status != 'success' + AND ingest_file_result.terminal_url NOT LIKE '%/cookieAbsent' + ) TO '/grande/snapshots/unpaywall_fail_nocookie_20200304.rows.json'; + => 1,403,837 + + ./scripts/ingestrequest_row2json.py /grande/snapshots/unpaywall_nocapture_20200304.rows.json > unpaywall_nocapture_20200304.json + ./scripts/ingestrequest_row2json.py /grande/snapshots/unpaywall_fail_nocookie_20200304.rows.json > unpaywall_fail_nocookie_20200304.json + +Note: will probably end up re-running the below after crawling+ingesting the above: + + COPY ( + SELECT row_to_json(ingest_request.*) FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + AND ingest_file_result.status != 'success' + AND ingest_file_result.status = 'terminal-bad-status' + AND ingest_file_result.terminal_url LIKE '%/cookieAbsent' + ) TO '/grande/snapshots/unpaywall_fail_cookie_badstatus_20200304.rows.json'; + => 0 + + COPY ( + SELECT row_to_json(ingest_request.*) FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + AND ingest_file_result.status != 'success' + AND ingest_file_result.status != 'terminal-bad-status' + AND ingest_file_result.terminal_url LIKE '%/cookieAbsent' + ) TO '/grande/snapshots/unpaywall_fail_cookie_other_20200304.rows.json'; + => 654,885 + +## Batch Ingest + +Test small batch: + + head -n200 /grande/snapshots/unpaywall_nocapture_20200304.rows.json | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + +Full batch: + + cat /grande/snapshots/unpaywall_nocapture_20200304.rows.json | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + + # there was a broken line in there, so... + # parse error: Expected separator between values at line 1367873, column 175 + # tail -n+1367875 /grande/snapshots/unpaywall_nocapture_20200304.rows.json | rg -v "\\\\" | jq . -c > /dev/null + tail -n+1367875 /grande/snapshots/unpaywall_nocapture_20200304.rows.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + +Note that the crawl is not entirely complete and not all CDX seem to have been +loaded, so may need to iterate. About 10% are still "no capture". May want or +need to additionally crawl the terminal URLs, not the base URLs. + +## Post-ingest stats + +Overall status: + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + status | count + -------------------------+---------- + success | 17354494 + no-pdf-link | 1471076 + no-capture | 1135992 + redirect-loop | 837842 + terminal-bad-status | 803081 + cdx-error | 219746 + wrong-mimetype | 100723 + link-loop | 16013 + wayback-error | 12448 + null-body | 9444 + redirects-exceeded | 600 + petabox-error | 411 + bad-redirect | 17 + bad-gzip-encoding | 4 + spn2-cdx-lookup-failure | 3 + gateway-timeout | 1 + spn2-error:job-failed | 1 + spn2-error | 1 + (18 rows) + +Failures by domain: + + SELECT domain, status, COUNT((domain, status)) + FROM ( + SELECT + ingest_file_result.ingest_type, + ingest_file_result.status, + substring(ingest_file_result.terminal_url FROM '[^/]+://([^/]*)') AS domain + FROM ingest_file_result + LEFT JOIN ingest_request + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_file_result.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + ) t1 + WHERE t1.domain != '' + AND t1.status != 'success' + AND t1.status != 'no-capture' + GROUP BY domain, status + ORDER BY COUNT DESC + LIMIT 30; + + domain | status | count + -----------------------------------+---------------------+-------- + academic.oup.com | no-pdf-link | 330211 + watermark.silverchair.com | terminal-bad-status | 324599 + www.tandfonline.com | no-pdf-link | 242724 + journals.sagepub.com | no-pdf-link | 202050 + iopscience.iop.org | terminal-bad-status | 144063 + files-journal-api.frontiersin.org | terminal-bad-status | 121719 + pubs.acs.org | no-pdf-link | 104535 + www.ahajournals.org | no-pdf-link | 102653 + society.kisti.re.kr | no-pdf-link | 101787 + www.degruyter.com | redirect-loop | 95130 + www.nature.com | redirect-loop | 87534 + onlinelibrary.wiley.com | no-pdf-link | 84432 + www.cell.com | redirect-loop | 61496 + www.degruyter.com | terminal-bad-status | 42919 + babel.hathitrust.org | terminal-bad-status | 41813 + www.ncbi.nlm.nih.gov | redirect-loop | 40488 + scialert.net | no-pdf-link | 38341 + ashpublications.org | no-pdf-link | 34889 + dialnet.unirioja.es | terminal-bad-status | 32076 + www.journal.csj.jp | no-pdf-link | 30881 + pure.mpg.de | redirect-loop | 26163 + www.jci.org | redirect-loop | 24701 + espace.library.uq.edu.au | redirect-loop | 24591 + www.valueinhealthjournal.com | redirect-loop | 23740 + www.vr-elibrary.de | no-pdf-link | 23332 + aip.scitation.org | wrong-mimetype | 22144 + osf.io | redirect-loop | 18513 + www.journals.elsevier.com | no-pdf-link | 16710 + www.spandidos-publications.com | redirect-loop | 15711 + www.biorxiv.org | wrong-mimetype | 15513 + (30 rows) + +Dump lists for another iteration of bulk ingest: + + COPY ( + SELECT row_to_json(ingest_request.*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + AND ingest_file_result.status = 'no-capture' + ) TO '/grande/snapshots/unpaywall_nocapture_20200323.rows.json'; + => 278,876 + + COPY ( + SELECT row_to_json(ingest_request.*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + AND ingest_file_result.status != 'success' + AND ingest_file_result.terminal_url NOT LIKE '%/cookieAbsent' + ) TO '/grande/snapshots/unpaywall_fail_nocookie_20200323.rows.json'; + => + + + ./scripts/ingestrequest_row2json.py /grande/snapshots/unpaywall_nocapture_20200323.rows.json > unpaywall_nocapture_20200323.json + + cat unpaywall_nocapture_20200323.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + diff --git a/notes/ingest/2020-03-02_ingests.txt b/notes/ingest/2020-03-02_ingests.txt new file mode 100644 index 0000000..e98ef33 --- /dev/null +++ b/notes/ingest/2020-03-02_ingests.txt @@ -0,0 +1,174 @@ + +## protocols.io + +Tested that single ingest is working, and they fixed PDF format on their end +recently. + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa container --name protocols.io + => Expecting 8448 release objects in search queries + => Counter({'estimate': 8448, 'kafka': 8448, 'ingest_request': 8448, 'elasticsearch_release': 8448}) + +## backfill follow-ups + +- re-ingest all degruyter (doi_prefix:10.1515) + 89942 doi:10.1515\/* is_oa:true + 36350 doi:10.1515\/* in_ia:false is_oa:true + 40034 publisher:Gruyter is_oa:true in_ia:false + => update: + 135926 doi:10.1515\/* is_oa:true + 50544 doi:10.1515\/* in_ia:false is_oa:true + 54880 publisher:Gruyter is_oa:true in_ia:false +- re-ingest all frontiersin + 36093 publisher:frontiers is_oa:true in_ia:false + => update + 22444 publisher:frontiers is_oa:true in_ia:false + 22029 doi_prefix:10.3389 is_oa:true in_ia:false + + select status, count(*) from ingest_file_result where base_url like 'https://doi.org/10.3389/%' group by status order by count(*) desc; + + status | count + -------------------------------------+------- + success | 34721 + no-pdf-link | 18157 + terminal-bad-status | 6799 + cdx-error | 1805 + wayback-error | 333 + no-capture | 301 + [...] + + select * from ingest_file_result where base_url like 'https://doi.org/10.17723/aarc%' and status = 'no-pdf-link' order by updated desc limit 100; + +- re-ingest all mdpi + 43114 publisher:mdpi is_oa:true in_ia:false + => update + 8548 publisher:mdpi is_oa:true in_ia:false + + select status, count(*) from ingest_file_result where base_url like 'https://doi.org/10.3390/%' group by status order by count(*) desc; + status | count + -------------------------------------+-------- + success | 108971 + cdx-error | 6655 + wrong-mimetype | 3359 + terminal-bad-status | 1299 + wayback-error | 151 + spn2-cdx-lookup-failure | 87 + + => added hack for gzip content-encoding coming through pdf fetch + => will re-ingest all after pushing fix + +- re-ingest all ahajournals.org + 132000 doi:10.1161\/* + 6606 doi:10.1161\/* in_ia:false is_oa:true + 81349 publisher:"American Heart Association" + 5986 publisher:"American Heart Association" is_oa:true in_ia:false + => update + 1337 publisher:"American Heart Association" is_oa:true in_ia:false + + status | count + -------------------------------------+------- + success | 1480 + cdx-error | 1176 + spn2-cdx-lookup-failure | 514 + no-pdf-link | 85 + wayback-error | 25 + spn2-error:job-failed | 18 + + => will re-run errors +- re-ingest all ehp.niehs.nih.gov + 25522 doi:10.1289\/* + 15315 publisher:"Environmental Health Perspectives" + 8779 publisher:"Environmental Health Perspectives" in_ia:false + 12707 container_id:3w6amv3ecja7fa3ext35ndpiky in_ia:false is_oa:true + => update + 7547 container_id:3w6amv3ecja7fa3ext35ndpiky in_ia:false is_oa:true +- re-ingest all journals.tsu.ru + 12232 publisher:"Tomsk State University" + 11668 doi:10.17223\/* + 4861 publisher:"Tomsk State University" in_ia:false is_oa:true + => update + 2605 publisher:"Tomsk State University" in_ia:false is_oa:true + => just need to retry these? seem fine +- re-ingest all www.cogentoa.com + 3421898 doi:10.1080\/* + 4602 journal:cogent is_oa:true in_ia:false + 5631 journal:cogent is_oa:true (let's recrawl all from publisher domain) + => update + 254 journal:cogent is_oa:true in_ia:false +- re-ingest chemrxiv + 8281 doi:10.26434\/chemrxiv* + 6918 doi:10.26434\/chemrxiv* in_ia:false + => update + 4890 doi:10.26434\/chemrxiv* in_ia:false + => re-ingest + => allow non-OA + + # american archivist + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa container --container-id zpobyv4vbranllc7oob56tgci4 + Counter({'estimate': 2920, 'elasticsearch_release': 2920, 'kafka': 2911, 'ingest_request': 2911}) + => 2020-02-04: 85 / 3,005 + => 2020-03-02: 2,182 / 3,005 preserved. some no-pdf-link, otherwise just a bunch of spn2-error + => looks like the no-pdf-url due to pinnacle-secure.allenpress.com soft-blocking loop + + +## backfill re-ingests + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa --force-recrawl container --container-id zpobyv4vbranllc7oob56tgci4 + => Counter({'elasticsearch_release': 823, 'estimate': 823, 'ingest_request': 814, 'kafka': 814}) + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --publisher Gruyter + => Counter({'elasticsearch_release': 54880, 'estimate': 54880, 'kafka': 51497, 'ingest_request': 51497}) + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org query 'publisher:"Tomsk State University"' + => Counter({'ingest_request': 2605, 'kafka': 2605, 'elasticsearch_release': 2605, 'estimate': 2605}) + + ./fatcat_ingest.py --limit 25 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org query "doi:10.26434\/chemrxiv*" + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --publisher mdpi + => Counter({'estimate': 8548, 'elasticsearch_release': 8548, 'ingest_request': 6693, 'kafka': 6693}) + => NOTE: about 2k not enqueued + +## re-ingest all broken + + COPY ( + SELECT row_to_json(ingest_request.*) FROM ingest_request + LEFT JOIN ingest_file_result ON ingest_file_result.base_url = ingest_request.base_url + WHERE ingest_request.ingest_type = 'pdf' + AND ingest_file_result.ingest_type = 'pdf' + AND ingest_file_result.updated < NOW() - '1 day'::INTERVAL + AND ingest_file_result.hit = false + AND ingest_file_result.status like 'spn2-%' + ) TO '/grande/snapshots/reingest_spn2_20200302.rows.json'; + => COPY 14849 + + COPY ( + SELECT row_to_json(ingest_request.*) FROM ingest_request + LEFT JOIN ingest_file_result ON ingest_file_result.base_url = ingest_request.base_url + WHERE ingest_request.ingest_type = 'pdf' + AND ingest_file_result.ingest_type = 'pdf' + AND ingest_file_result.hit = false + AND ingest_file_result.status like 'cdx-error' + ) TO '/grande/snapshots/reingest_cdxerr_20200302.rows.json'; + => COPY 507610 + + This is a huge number! Re-ingest via bulk? + +Transform: + + ./scripts/ingestrequest_row2json.py /grande/snapshots/reingest_spn2_20200302.rows.json > reingest_spn2_20200302.json + ./scripts/ingestrequest_row2json.py /grande/snapshots/reingest_cdxerr_20200302.rows.json > reingest_cdxerr_20200302.json + +Push to kafka: + + cat reingest_spn2err_20200218.json | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests -p -1 + # accidentially also piped the above through ingest-file-requests-bulk... + # which could actually be bad + cat reingest_cdxerr_20200302.json | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + +## biorxiv/medrxiv + + 8026 doi:10.1101\/20* + 2159 doi:10.1101\/20* in_ia:false + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa query 'doi:10.1101\/20* in_ia:false' + => Counter({'estimate': 2159, 'ingest_request': 2159, 'elasticsearch_release': 2159, 'kafka': 2159}) + diff --git a/notes/ingest/2020-03-oa_but_not_marked.md b/notes/ingest/2020-03-oa_but_not_marked.md new file mode 100644 index 0000000..73396bd --- /dev/null +++ b/notes/ingest/2020-03-oa_but_not_marked.md @@ -0,0 +1,25 @@ + +These are large journals with a high fraction of "in IA", but not marked as OA +so not crawling regularly. + +TODO: add things like list of unpaywall ISSN / OA status to try and find more +"practical" / bronze OA + +## First Run + +https://fatcat.wiki/container/vmv647omwrhzzgeclyrnpc4him +https://fatcat.wiki/container/waxwzq3cnbet3cmwccpuk4bel4 +https://fatcat.wiki/container/hjoli2j6qffdpaalkszryuidk4 +https://fatcat.wiki/container/fci57bxfsffvzllbssocnfsr3e +https://fatcat.wiki/container/hd23c57sunhcnar5fbgxsn36lm +https://fatcat.wiki/container/bliguyxhonfb7ghuykxgtg3oqe + +## TODO + +https://fatcat.wiki/container/kn6dhptylrb77b5atyiom5ysjm no-pdf-link (but accessible) +https://fatcat.wiki/container/s7bticdwizdmhll4taefg57jde no-pdf-link (easy?) + +https://fatcat.wiki/container/zm56axre7rgihh5sznxp65np5i large; no-pdf-link? +https://fatcat.wiki/container/eb2lcnpf2zeezkmfckcvxw2pgi huge (20k+), not all OA? +https://fatcat.wiki/container/adgy773dtra3xmrsynghcednqm broken? +https://fatcat.wiki/container/w3gj5mynrnbtndalcc5jnhymym not OA? link-loop diff --git a/notes/ingest/2020-03_mag.md b/notes/ingest/2020-03_mag.md new file mode 100644 index 0000000..428ce05 --- /dev/null +++ b/notes/ingest/2020-03_mag.md @@ -0,0 +1,576 @@ + +Rough plan: + +- run bulk and/or regular ingest requests for just those of AIT partners (200k?) +- persist ingest requests (22 million or so) +- run bulk ingest over 'no status' / 'no match' requests (aka, those not in unpaywall) +- crawl those which are no-capture + + +## Generate Requests + +Newer version of `mag_ingest_request.sh` script requires venv with urlcanon +installed. + +Starting with the 2020-01-23 MAG dump, will generate a full ingest request set +(including DOI `ext_id` when available), with any dominant domains removed (eg, +arxiv.org): + + export LC_ALL=C + cat PaperUrls_mag_url_doi.all.txt | rg -a -v arxiv.org | rg -a "://" | ./mag_ingest_request.py - --created-date 2020-01-23 | pv -l > ingest_requests_mag-2020-01-23.doi.json + => previously 25.6M + => 25.6M 2:29:43 [2.85k/s] + + export LC_ALL=C + zcat PaperUrls_mag_url_pmid.txt.gz | rg -a -v arxiv.org | rg -a "://" | ./mag_ingest_request.py - --created-date 2020-01-23 --pmid | pv -l > ingest_requests_mag-2020-01-23.pmid.json + => 4.3M 0:25:45 [2.78k/s] + + export LC_ALL=C + cat ingest_requests_mag-2020-01-23.json | jq -r "[.base_url, .ext_ids.doi] | @tsv" | sort -u -S 4G > ingest_requests_mag-2020-01-23.full.seed_id + + zcat PaperUrls_PaperExtendedAttributes_pdf.txt.gz | wc -l + => 6,504,907 + + zcat PaperUrls_mag_url_pmid.txt.gz | wc -l + => 4,369,832 + + cat ingest_requests_mag-2020-01-23.json | jq .ext_ids.doi -r | rg -a -v '^null$' | wc -l + => previously 15,707,405 + => 15,702,581 + + cat ingest_requests_mag-2020-01-23.pmid.json | jq .base_url -r | rg ' ' | wc -l + => 0 + URL encoding seems to be working + +## Persist Ingest Requests + +First pmid ingest requests, then the all/doi file. The reason to do this order +is that the all/doi file will have some rows with no DOI (and thus no +`ext_id`), while the PMID file will not. + + # small sample + head /schnell/mag/20200123/ingest_requests_mag-2020-01-23.pmid.json | ./persist_tool.py ingest-request - + Worker: Counter({'total': 10, 'skip-result-fields': 10}) + JSON lines pushed: Counter({'total': 10, 'pushed': 10}) + + cat /schnell/mag/20200123/ingest_requests_mag-2020-01-23.pmid.json | ./persist_tool.py ingest-request - + => 4.3M 0:16:46 [4.27k/s] + Worker: Counter({'total': 4295026, 'insert-requests': 4241862, 'update-requests': 0}) + JSON lines pushed: Counter({'total': 4295026, 'pushed': 4295026}) + => hit a bug on first attempt, which is why total/insert results don't match + + cat /schnell/mag/20200123/ingest_requests_mag-2020-01-23.doi.json | ./persist_tool.py ingest-request - + => 25.6M 2:21:54 [3.01k/s] + Worker: Counter({'total': 25596559, 'insert-requests': 21348393, 'update-requests': 0}) + JSON lines pushed: Counter({'pushed': 25596559, 'total': 25596559}) + + +## Crawl/Dupe Status + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'mag' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + +After just PMID links: + + status | count + ---------------------+--------- + | 3000115 + success | 1126881 + no-capture | 69459 + terminal-bad-status | 30259 + redirect-loop | 11656 + no-pdf-link | 2836 + wrong-mimetype | 1456 + link-loop | 1259 + wayback-error | 1232 + cdx-error | 932 + null-body | 85 + petabox-error | 50 + bad-redirect | 1 + (13 rows) + +After all links: + + SELECT COUNT(*) + FROM ingest_request + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'mag'; + => 25596563 + + + status | count + ---------------------+---------- + | 21130841 + success | 3915682 + no-capture | 391813 + terminal-bad-status | 76488 + redirect-loop | 44202 + wrong-mimetype | 16418 + no-pdf-link | 10995 + wayback-error | 3679 + cdx-error | 3414 + link-loop | 2098 + null-body | 709 + petabox-error | 221 + bad-gzip-encoding | 2 + bad-redirect | 1 + (14 rows) + +Somewhat more un-ingested than expected. + +Dump requests: + + COPY ( + SELECT row_to_json(ingest_request.*) FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'mag' + AND ingest_file_result.status IS NULL + ) TO '/grande/snapshots/mag_noingest_20200305.rows.json'; + => COPY 21,130,841 + +Transform and shuf: + + ./scripts/ingestrequest_row2json.py /grande/snapshots/mag_noingest_20200305.rows.json | pv -l | shuf | gzip > /grande/snapshots/mag_noingest_20200305.shuf.json.gz + => 21.1M 0:18:57 [18.6k/s] + +## Bulk Ingest Partner Output + +These are subsets of the full list from potential AIT-S partners; want to run +these through the pipeline before the full batch. Duplication against the full +batch should be minimal. + +Size: + + bnewbold@ia601101$ cat ingest_requests_mag-2020-01-23.cornell.json | jq .ext_ids.doi | rg -v '^null$' | wc -l + 29007 + bnewbold@ia601101$ wc -l ingest_requests_mag-2020-01-23.cornell.json + 34265 ingest_requests_mag-2020-01-23.cornell.json + +Test ingest: + + head -n200 ingest_requests_mag-2020-01-23.cornell.json | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + +Full ingests: + + cat ingest_requests_mag-2020-01-23.cornell.json | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + cat ingest_requests_mag-2020-01-23.alberta.json | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + cat ingest_requests_mag-2020-01-23.columbia.json | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + cat ingest_requests_mag-2020-01-23.emory.json | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + cat ingest_requests_mag-2020-01-23.stanford.json | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + +## Bulk Ingest + +Shard it into batches of roughly 1 million: + + cd /grande/snapshots/ + zcat /grande/snapshots/mag_noingest_20200305.shuf.json.gz | split -n r/20 -d - mag_noingest_20200305.ingest_request.split_ --additional-suffix=.json + +Add a single batch like: + + cat mag_noingest_20200305.ingest_request.split_00.json | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + + partner ingests (see above) + => 2020-03-05 12:49: 118,396 + 1056543 mag_noingest_20200305.ingest_request.split_00.json + => 2020-03-05 14:34: 1,055,224 + => check on stats/ratios; filter by ingest update time? + 1056542 mag_noingest_20200305.ingest_request.split_01.json + 1056542 mag_noingest_20200305.ingest_request.split_02.json + 1056542 mag_noingest_20200305.ingest_request.split_03.json + 1056542 mag_noingest_20200305.ingest_request.split_04.json + 1056542 mag_noingest_20200305.ingest_request.split_05.json + 1056542 mag_noingest_20200305.ingest_request.split_06.json + 1056542 mag_noingest_20200305.ingest_request.split_07.json + 1056542 mag_noingest_20200305.ingest_request.split_08.json + 1056542 mag_noingest_20200305.ingest_request.split_09.json + => 2020-03-05 18:04: 10,009,297 + => 2020-03-06 16:53: 6,553,946 + 1056542 mag_noingest_20200305.ingest_request.split_10.json + 1056542 mag_noingest_20200305.ingest_request.split_11.json + 1056542 mag_noingest_20200305.ingest_request.split_12.json + 1056542 mag_noingest_20200305.ingest_request.split_13.json + 1056542 mag_noingest_20200305.ingest_request.split_14.json + 1056542 mag_noingest_20200305.ingest_request.split_15.json + 1056542 mag_noingest_20200305.ingest_request.split_16.json + 1056542 mag_noingest_20200305.ingest_request.split_17.json + 1056542 mag_noingest_20200305.ingest_request.split_18.json + 1056542 mag_noingest_20200305.ingest_request.split_19.json + => 2020-03-06 16:59: 17,001,032 + +Stats from bulk ingest: + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'mag' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + status | count + ---------------------+---------- + no-capture | 12237193 + success | 11991293 + no-pdf-link | 521691 + redirect-loop | 437192 + terminal-bad-status | 231181 + link-loop | 92633 + cdx-error | 33631 + wrong-mimetype | 28638 + wayback-error | 19651 + null-body | 2682 + petabox-error | 727 + | 47 + bad-redirect | 44 + bad-gzip-encoding | 7 + (14 rows) + +Failures by domain: + + SELECT domain, status, COUNT((domain, status)) + FROM ( + SELECT + ingest_file_result.ingest_type, + ingest_file_result.status, + substring(ingest_file_result.terminal_url FROM '[^/]+://([^/]*)') AS domain + FROM ingest_file_result + LEFT JOIN ingest_request + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_file_result.ingest_type = 'pdf' + AND ingest_request.link_source = 'mag' + ) t1 + WHERE t1.domain != '' + AND t1.status != 'success' + AND t1.status != 'no-capture' + GROUP BY domain, status + ORDER BY COUNT DESC + LIMIT 30; + + domain | status | count + --------------------------------------+---------------------+-------- + dialnet.unirioja.es | redirect-loop | 240967 + onlinelibrary.wiley.com | no-pdf-link | 147696 + agupubs.onlinelibrary.wiley.com | no-pdf-link | 72639 + iopscience.iop.org | terminal-bad-status | 69591 + febs.onlinelibrary.wiley.com | no-pdf-link | 49874 + www.researchgate.net | redirect-loop | 42859 + journals.sagepub.com | no-pdf-link | 27448 + papers.ssrn.com | redirect-loop | 27328 + dialnet.unirioja.es | terminal-bad-status | 20320 + physoc.onlinelibrary.wiley.com | no-pdf-link | 20232 + science.sciencemag.org | link-loop | 17811 + espace.library.uq.edu.au | redirect-loop | 17185 + bpspubs.onlinelibrary.wiley.com | no-pdf-link | 15785 + obgyn.onlinelibrary.wiley.com | no-pdf-link | 15301 + anthrosource.onlinelibrary.wiley.com | no-pdf-link | 13746 + www.tandfonline.com | no-pdf-link | 13303 + aasldpubs.onlinelibrary.wiley.com | no-pdf-link | 11070 + link.springer.com | redirect-loop | 10594 + www.redalyc.org:9081 | no-pdf-link | 10515 + watermark.silverchair.com | terminal-bad-status | 9739 + www.bmj.com | link-loop | 9389 + www.repository.naturalis.nl | redirect-loop | 8213 + bjp.rcpsych.org | link-loop | 8045 + aslopubs.onlinelibrary.wiley.com | no-pdf-link | 7814 + nph.onlinelibrary.wiley.com | no-pdf-link | 7801 + iopscience.iop.org | redirect-loop | 7697 + journals.tubitak.gov.tr | wrong-mimetype | 7159 + www.biorxiv.org | wrong-mimetype | 7067 + www.erudit.org | redirect-loop | 6819 + besjournals.onlinelibrary.wiley.com | no-pdf-link | 6254 + (30 rows) + +Domains to follow-up (eg, sandcrawler ingest tests/tweaks): +- dialnet.unirioja.es | redirect-loop | 240967 +- www.researchgate.net | redirect-loop | 42859 +- www.redalyc.org:9081 | no-pdf-link | 10515 +- www.repository.naturalis.nl | redirect-loop | 8213 +- bjp.rcpsych.org | link-loop | 8045 +- journals.tubitak.gov.tr | wrong-mimetype | 7159 +- www.erudit.org | redirect-loop | 6819 + +The dialnet.unirioja.es ones may be worth re-crawling via heritrix? + +Top uncrawled domains: + + SELECT domain, status, COUNT((domain, status)) + FROM ( + SELECT + ingest_file_result.ingest_type, + ingest_file_result.status, + substring(ingest_file_result.base_url FROM '[^/]+://([^/]*)') AS domain + FROM ingest_file_result + LEFT JOIN ingest_request + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_file_result.ingest_type = 'pdf' + AND ingest_request.link_source = 'mag' + ) t1 + WHERE t1.domain != '' + AND t1.status = 'no-capture' + GROUP BY domain, status + ORDER BY COUNT DESC + LIMIT 30; + + domain | status | count + ---------------------------------+------------+-------- + ieeexplore.ieee.org | no-capture | 957835 + link.springer.com | no-capture | 394121 + www.researchgate.net | no-capture | 376974 + cyberleninka.ru | no-capture | 376012 + iopscience.iop.org | no-capture | 348791 + papers.ssrn.com | no-capture | 286860 + dergipark.org.tr | no-capture | 217556 + dialnet.unirioja.es | no-capture | 214398 + academic.oup.com | no-capture | 212364 + www.tandfonline.com | no-capture | 148940 + journals.sagepub.com | no-capture | 144695 + www.papersearch.net | no-capture | 138986 + absimage.aps.org | no-capture | 111976 + apps.dtic.mil | no-capture | 106984 + www.cambridge.org | no-capture | 97533 + www.bmj.com | no-capture | 92437 + bioone.org | no-capture | 87573 + science.sciencemag.org | no-capture | 75723 + shodhganga.inflibnet.ac.in:8080 | no-capture | 75395 + www.jstor.org | no-capture | 73230 + works.bepress.com | no-capture | 68747 + www.scielo.org.co | no-capture | 59650 + hrcak.srce.hr | no-capture | 59332 + muse.jhu.edu | no-capture | 57828 + onlinelibrary.wiley.com | no-capture | 55621 + www.jbc.org | no-capture | 54608 + www.jstage.jst.go.jp | no-capture | 53631 + www.redalyc.org | no-capture | 50406 + lup.lub.lu.se | no-capture | 47469 + www.dtic.mil | no-capture | 41820 + (30 rows) + +## Heritrix Seedlist Generation + +Dump ingest requests (filtered for some domains that don't expect to crawl via +heritrix): + + COPY ( + SELECT row_to_json(ingest_request.*) FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'mag' + AND ingest_file_result.status = 'no-capture' + AND ingest_request.base_url NOT LIKE '%journals.sagepub.com%' + AND ingest_request.base_url NOT LIKE '%pubs.acs.org%' + AND ingest_request.base_url NOT LIKE '%ahajournals.org%' + AND ingest_request.base_url NOT LIKE '%www.journal.csj.jp%' + AND ingest_request.base_url NOT LIKE '%aip.scitation.org%' + AND ingest_request.base_url NOT LIKE '%academic.oup.com%' + AND ingest_request.base_url NOT LIKE '%tandfonline.com%' + ) TO '/grande/snapshots/mag_nocapture_20200313.rows.json'; + => COPY 11714199 + + # in sandcrawler pipenv + ./scripts/ingestrequest_row2json.py /grande/snapshots/mag_nocapture_20200313.rows.json > /grande/snapshots/mag_nocapture_20200313.json + +## Bulk Ingest of Heritrix Content + +Small sample: + + head -n 1000 mag_nocapture_20200313.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + +Full run: + + cat mag_nocapture_20200313.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + + 2020-04-07 12:19 (pacific): 11,703,871 + +## Post-bulk-ingest + +Around 2020-04-28, seems like main wave of bulk ingest is complete. Will need +to re-try things like cdx-error. + +Current status: + + status | count + -------------------------------+---------- + success | 18491799 + redirect-loop | 1968530 + no-capture | 1373657 + no-pdf-link | 1311842 + link-loop | 1296439 + terminal-bad-status | 627577 + cdx-error | 418278 + wrong-mimetype | 50141 + wayback-error | 37159 + petabox-error | 11249 + null-body | 6295 + gateway-timeout | 3051 + spn2-cdx-lookup-failure | 328 + spn2-error:invalid-url-syntax | 93 + bad-redirect | 75 + | 47 + invalid-host-resolution | 28 + spn2-error | 10 + bad-gzip-encoding | 7 + redirects-exceeded | 2 + (20 rows) + +Lots of cdx-error to retry. + +The no-capture links are probably a mix of domain-blocklist and things that +failed in bulk mode. Will dump and re-attempt them: + + + COPY ( + SELECT row_to_json(ingest_request.*) FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'mag' + AND ingest_file_result.status = 'no-capture' + AND ingest_request.base_url NOT LIKE '%journals.sagepub.com%' + AND ingest_request.base_url NOT LIKE '%pubs.acs.org%' + AND ingest_request.base_url NOT LIKE '%ahajournals.org%' + AND ingest_request.base_url NOT LIKE '%www.journal.csj.jp%' + AND ingest_request.base_url NOT LIKE '%aip.scitation.org%' + AND ingest_request.base_url NOT LIKE '%academic.oup.com%' + AND ingest_request.base_url NOT LIKE '%tandfonline.com%' + ) TO '/grande/snapshots/mag_nocapture_20200420.rows.json'; + => 859849 + +What domains are these? + + cat mag_nocapture_20200420.rows.json | jq .base_url -r | cut -f3 -d/ | sort | uniq -c | sort -nr | head -n30 + +Let's filter down more: + + cat mag_nocapture_20200420.rows.json | rg -v 'www.researchgate.net' | rg -v 'muse.jhu.edu' | rg -v 'www.omicsonline.org' | rg -v 'link.springer.com' | rg -v 'iopscience.iop.org' | rg -v 'ieeexplore.ieee.org' | shuf > mag_nocapture_20200420.rows.filtered.json + + wc -l mag_nocapture_20200420.rows.filtered.json + 423085 mag_nocapture_20200420.rows.filtered.json + +Ok, enqueue! + + cat mag_nocapture_20200420.rows.filtered.json | shuf | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests -p -1 + +## Final Stats + +... for this round of ingest: + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'mag' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + + status | count + -------------------------------------+---------- + success | 18712849 + redirect-loop | 2008110 + no-pdf-link | 1337012 + link-loop | 1326761 + no-capture | 1030693 + terminal-bad-status | 637143 + gateway-timeout | 193194 + cdx-error | 125907 + spn2-cdx-lookup-failure | 77842 + wrong-mimetype | 50882 + wayback-error | 40278 + invalid-host-resolution | 35201 + petabox-error | 11254 + null-body | 6485 + spn2-error | 1643 + spn2-error:job-failed | 747 + spn2-error:invalid-url-syntax | 325 + spn2-error:soft-time-limit-exceeded | 190 + bad-redirect | 77 + | 47 + (20 rows) + +Failures by domain: + + SELECT domain, status, COUNT((domain, status)) + FROM ( + SELECT + ingest_file_result.ingest_type, + ingest_file_result.status, + substring(ingest_file_result.terminal_url FROM '[^/]+://([^/]*)') AS domain + FROM ingest_file_result + LEFT JOIN ingest_request + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_file_result.ingest_type = 'pdf' + AND ingest_request.link_source = 'mag' + ) t1 + WHERE t1.domain != '' + AND t1.status != 'success' + GROUP BY domain, status + ORDER BY COUNT DESC + LIMIT 30; + + + domain | status | count + ---------------------------------+---------------------+-------- + ieeexplore.ieee.org | redirect-loop | 677712 + cyberleninka.ru | link-loop | 308390 + papers.ssrn.com | link-loop | 281804 + ieeexplore.ieee.org | link-loop | 273559 + dialnet.unirioja.es | redirect-loop | 240504 + dialnet.unirioja.es | terminal-bad-status | 232481 + onlinelibrary.wiley.com | no-pdf-link | 220932 + iopscience.iop.org | terminal-bad-status | 172480 + validate.perfdrive.com | no-pdf-link | 172312 + link.springer.com | redirect-loop | 130398 + agupubs.onlinelibrary.wiley.com | no-pdf-link | 113382 + iopscience.iop.org | redirect-loop | 105234 + www.bmj.com | link-loop | 100354 + www.researchgate.net | redirect-loop | 84366 + www.cambridge.org | link-loop | 83171 + jamanetwork.com | no-pdf-link | 75053 + febs.onlinelibrary.wiley.com | no-pdf-link | 74872 + www.jstor.org | redirect-loop | 72059 + journals.sagepub.com | no-pdf-link | 63028 + science.sciencemag.org | redirect-loop | 62927 + profile.thieme.de | no-pdf-link | 62406 + cyberleninka.ru | redirect-loop | 56733 + link.springer.com | link-loop | 47608 + physoc.onlinelibrary.wiley.com | no-pdf-link | 30180 + science.sciencemag.org | link-loop | 29908 + papers.ssrn.com | redirect-loop | 27255 + obgyn.onlinelibrary.wiley.com | no-pdf-link | 26789 + www.computer.org | no-pdf-link | 26444 + watermark.silverchair.com | terminal-bad-status | 25934 + www.nature.com | redirect-loop | 25306 + (30 rows) diff --git a/notes/ingest/2020-03_s2.md b/notes/ingest/2020-03_s2.md new file mode 100644 index 0000000..fedaba0 --- /dev/null +++ b/notes/ingest/2020-03_s2.md @@ -0,0 +1,35 @@ + +Crawled some 6 million new PDFs from pdfs.semanticscholar.org. Should get these +ingested, as well as any previous existing content. + +Also, there are a bunch of PDF outlinks to the web; should do S2-specific +matching and ingest of those. + +There are a few categories of paper from pdfs.s.o: + +1. we had previous GWB crawl, didn't re-crawl +2. we had PDF from elsewhere on the web, didn't re-crawl +3. crawled successfully +4. crawl failed + +In this ingest, want to get all of categories 1 and 3. Could try to do this by +dumping sandcrawler CDX table matching pdfs.s.o (which includes recent crawl), +and join that against the ingest request list. + +For other random web URLs, can do the usual persist/backfill/recrawl pipeline. + +## Create Seedlist + + zcat s2-corpus-pdfUrls.json.gz | parallel -j5 --linebuffer --round-robin --pipe ./s2_ingestrequest.py - | pv -l | gzip > s2-corpus-pdfUrls.2019.ingest_request.json.gz + zcat s2-corpus-s2PdfUrl.json.gz | parallel -j5 --linebuffer --round-robin --pipe ./s2_ingestrequest.py - | pv -l | gzip > s2-corpus-s2PdfUrl.2019.ingest_request.json.gz + + zcat s2-corpus-s2PdfUrl.json.gz | jq .id -r | sort -u -S 2G > s2-corpus-s2PdfUrl.id_list + zcat s2-corpus-pdfUrls.json.gz | jq .id -r | sort -u -S 2G > s2-corpus-pdfUrls.id_list + + zcat s2-corpus-pdfUrls.2019.ingest_request.json.gz s2-corpus-s2PdfUrl.2019.ingest_request.json.gz | rg pdfs.semanticscholar.org | sort -u -S 3G | gzip > s2_hosted_ingestrequest.json.gz + zcat s2-corpus-pdfUrls.2019.ingest_request.json.gz s2-corpus-s2PdfUrl.2019.ingest_request.json.gz | rg -v pdfs.semanticscholar.org | sort -u -S 3G | gzip > s2_external_ingestrequest.json.gz + + zcat s2_external_ingestrequest.json.gz | wc -l + 41201427 + zcat s2_hosted_ingestrequest.json.gz | wc -l + 23345761 diff --git a/notes/ingest/2020-04-13_covid19.md b/notes/ingest/2020-04-13_covid19.md new file mode 100644 index 0000000..b442d69 --- /dev/null +++ b/notes/ingest/2020-04-13_covid19.md @@ -0,0 +1,73 @@ + +Want to ensure seedlists from Wanfang and CNKI are captured in wayback. + +Wanfang URLs seem normal. Let's just submit them in a single queue via SPNv2. +They are heterogenous after redirect. + +CNKI are trickier. The PDF URLs definitely can't be crawled directly... but the +info ones probably can, then crawl on to PDF? At least some seem to capture Ok. + +Need scope and identifiers for ingest requests. Let's do: + + cnki_covid19 / <ident> + wanfang_covid19 / <ident> + +Source: scrape-covid19 + +## Commands + + # in sandcrawler pipenv + cat ~/code/covid19.fatcat.wiki/extra/scrape/cnki_metadata.2020-04-14.json | ./scripts/covid2ingestrequest.py - > ~/code/covid19.fatcat.wiki/extra/scrape/cnki_ingest_request.2020-04-14.json + cat ~/code/covid19.fatcat.wiki/extra/scrape/wanfang*.2020-04-14.json | ./scripts/covid2ingestrequest.py - > ~/code/covid19.fatcat.wiki/extra/scrape/wanfang_ingest_request.2020-04-14.json + + + cat /tmp/wanfang_ingest_request.2020-04-14.json | shuf | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests -p 4 + cat /tmp/cnki_ingest_request.2020-04-14.json | shuf | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests -p 8 + +## Status + + SELECT ingest_request.ingest_type, + ingest_file_result.status, + COUNT(*) + FROM ingest_file_result + LEFT JOIN ingest_request + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.ingest_request_source = 'scrape-covid19' + GROUP BY ingest_request.ingest_type, ingest_file_result.status + ORDER BY COUNT(*) DESC; + +2020-04-15: + + ingest_type | status | count + -------------+-------------------------------------+------- + pdf | spn2-cdx-lookup-failure | 1588 + pdf | success | 671 + pdf | gateway-timeout | 507 + pdf | no-pdf-link | 181 + pdf | wayback-error | 30 + pdf | spn2-error:job-failed | 20 + pdf | spn2-error | 7 + pdf | spn2-error:soft-time-limit-exceeded | 3 + pdf | spn2-error:pending | 2 + (9 rows) + +## Re-Try + + COPY ( + SELECT row_to_json(ingest_request.*) FROM ingest_request + LEFT JOIN ingest_file_result ON ingest_file_result.base_url = ingest_request.base_url + WHERE ingest_request.ingest_type = 'pdf' + AND ingest_request.ingest_request_source = 'scrape-covid19' + AND ingest_file_result.ingest_type = 'pdf' + AND ingest_file_result.hit = false + AND ingest_file_result.status != 'no-pdf-link' + AND ingest_file_result.status != 'link-loop' + ) TO '/grande/snapshots/reingest_covid19.rows.json'; + + ./scripts/ingestrequest_row2json.py /grande/snapshots/reingest_covid19.rows.json | shuf > reingest_covid19.json + + cat reingest_covid19.json | shuf | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests -p 9 + diff --git a/notes/ingest/2020-04_datacite.md b/notes/ingest/2020-04_datacite.md new file mode 100644 index 0000000..0fc7e67 --- /dev/null +++ b/notes/ingest/2020-04_datacite.md @@ -0,0 +1,121 @@ + +After the broad datacite crawl, want to ingest paper PDFs into fatcat. But many +of the DOIs are for, eg, datasets, and don't want to waste time on those. + +Instead of using full ingest request file from the crawl, will generate a new +ingest request file using `fatcat_ingest.py` and set that up for bulk crawling. + +## Generate Requests + + ./fatcat_ingest.py --allow-non-oa --release-types article-journal,paper-conference,article,report,thesis,book,chapter query "doi_registrar:datacite" | pv -l > /srv/fatcat/snapshots/datacite_papers_20200407.ingest_request.json + => Expecting 8905453 release objects in search queries + => 8.91M 11:49:50 [ 209 /s] + => Counter({'elasticsearch_release': 8905453, 'ingest_request': 8905453, 'estimate': 8905453}) + +## Bulk Ingest + + cat /srv/fatcat/snapshots/datacite_papers_20200407.ingest_request.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + +## Ingest Stats + +Note that this will have a small fraction of non-datacite results mixed in (eg, +from COVID-19 targeted crawls): + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'doi' + AND ingest_request.ingest_type = 'pdf' + AND ingest_request.ingest_request_source = 'fatcat-ingest' + AND created >= '2020-04-07' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + status | count + -------------------------------------+--------- + no-pdf-link | 4646767 + redirect-loop | 1447229 + no-capture | 860235 + success | 849501 + terminal-bad-status | 174869 + cdx-error | 159805 + wayback-error | 18076 + wrong-mimetype | 11169 + link-loop | 8410 + gateway-timeout | 4034 + spn2-cdx-lookup-failure | 510 + petabox-error | 339 + null-body | 251 + spn2-error | 19 + spn2-error:job-failed | 14 + bad-gzip-encoding | 13 + timeout | 5 + spn2-error:soft-time-limit-exceeded | 4 + invalid-host-resolution | 2 + spn2-error:pending | 1 + (20 rows) + +Top domains/statuses (including success): + + SELECT domain, status, COUNT((domain, status)) + FROM ( + SELECT + ingest_file_result.ingest_type, + ingest_file_result.status, + substring(ingest_file_result.terminal_url FROM '[^/]+://([^/]*)') AS domain + FROM ingest_file_result + LEFT JOIN ingest_request + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'doi' + AND ingest_request.ingest_type = 'pdf' + AND ingest_request.ingest_request_source = 'fatcat-ingest' + AND created >= '2020-04-07' + ) t1 + WHERE t1.domain != '' + AND t1.status != 'success' + GROUP BY domain, status + ORDER BY COUNT DESC + LIMIT 30; + + domain | status | count + ---------------------------------------+---------------------+-------- + ssl.fao.org | no-pdf-link | 862277 + www.e-periodica.ch | no-pdf-link | 746781 + www.researchgate.net | redirect-loop | 664524 + dlc.library.columbia.edu | no-pdf-link | 493111 + www.die-bonn.de | redirect-loop | 352903 + figshare.com | no-pdf-link | 319709 + statisticaldatasets.data-planet.com | no-pdf-link | 309584 + catalog.paradisec.org.au | redirect-loop | 225396 + zenodo.org | no-capture | 193201 + digi.ub.uni-heidelberg.de | no-pdf-link | 184974 + open.library.ubc.ca | no-pdf-link | 167841 + zenodo.org | no-pdf-link | 130617 + www.google.com | no-pdf-link | 111312 + www.e-manuscripta.ch | no-pdf-link | 79192 + ds.iris.edu | no-pdf-link | 77649 + data.inra.fr | no-pdf-link | 69440 + www.tib.eu | no-pdf-link | 63872 + www.egms.de | redirect-loop | 53877 + archaeologydataservice.ac.uk | redirect-loop | 52838 + d.lib.msu.edu | no-pdf-link | 45297 + www.e-rara.ch | no-pdf-link | 45163 + springernature.figshare.com | no-pdf-link | 42527 + boris.unibe.ch | no-pdf-link | 40816 + www.research-collection.ethz.ch | no-capture | 40350 + spectradspace.lib.imperial.ac.uk:8443 | no-pdf-link | 33059 + repository.dri.ie | terminal-bad-status | 32760 + othes.univie.ac.at | no-pdf-link | 32558 + repositories.lib.utexas.edu | no-capture | 31526 + posterng.netkey.at | no-pdf-link | 30315 + zenodo.org | terminal-bad-status | 29614 + (30 rows) + diff --git a/notes/ingest/2020-04_unpaywall.md b/notes/ingest/2020-04_unpaywall.md new file mode 100644 index 0000000..a5e3bb1 --- /dev/null +++ b/notes/ingest/2020-04_unpaywall.md @@ -0,0 +1,312 @@ + +A new snapshot was released in April 2020 (the snapshot is from 2020-02-25, but +not released for more than a month). + +Primary goal is: + +- generate ingest requests for only *new* URLs +- bulk ingest these new URLs +- crawl any no-capture URLs from that batch +- re-bulk-ingest the no-capture batch +- analytics on failed ingests. eg, any particular domains that are failing to crawl + +This ingest pipeline was started on 2020-04-07 by bnewbold. + +Ran through the first two steps again on 2020-05-03 after unpaywall had +released another dump (dated 2020-04-27). + +## Transform and Load + + # in sandcrawler pipenv on aitio + zcat /schnell/UNPAYWALL-PDF-CRAWL-2020-04/unpaywall_snapshot_2020-02-25T115244.jsonl.gz | ./scripts/unpaywall2ingestrequest.py - | pv -l > /grande/snapshots/unpaywall_snapshot_2020-02-25.ingest_request.json + => 24.7M 5:17:03 [ 1.3k/s] + + cat /grande/snapshots/unpaywall_snapshot_2020-02-25.ingest_request.json | pv -l | ./persist_tool.py ingest-request - + => 24.7M + => Worker: Counter({'total': 24712947, 'insert-requests': 4282167, 'update-requests': 0}) + +Second time: + + # in sandcrawler pipenv on aitio + zcat /schnell/UNPAYWALL-PDF-CRAWL-2020-04/unpaywall_snapshot_2020-04-27T153236.jsonl.gz | ./scripts/unpaywall2ingestrequest.py - | pv -l > /grande/snapshots/unpaywall_snapshot_2020-04-27.ingest_request.json + => 25.2M 3:16:28 [2.14k/s] + + cat /grande/snapshots/unpaywall_snapshot_2020-04-27.ingest_request.json | pv -l | ./persist_tool.py ingest-request - + => Worker: Counter({'total': 25189390, 'insert-requests': 1408915, 'update-requests': 0}) + => JSON lines pushed: Counter({'pushed': 25189390, 'total': 25189390}) + + +## Dump new URLs and Bulk Ingest + + COPY ( + SELECT row_to_json(ingest_request.*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + AND date(ingest_request.created) > '2020-04-01' + AND ingest_file_result.status IS NULL + ) TO '/grande/snapshots/unpaywall_noingest_2020-04-08.rows.json'; + => 3696189 + + WARNING: forgot to transform from rows to ingest requests. + + cat /grande/snapshots/unpaywall_noingest_2020-04-08.rows.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + +Second time: + + COPY ( + SELECT row_to_json(ingest_request.*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + AND date(ingest_request.created) > '2020-05-01' + AND ingest_file_result.status IS NULL + ) TO '/grande/snapshots/unpaywall_noingest_2020-05-03.rows.json'; + => 1799760 + + WARNING: forgot to transform from rows to ingest requests. + + cat /grande/snapshots/unpaywall_noingest_2020-05-03.rows.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + +## Dump no-capture, Run Crawl + +Make two ingest request dumps: one with "all" URLs, which we will have heritrix +attempt to crawl, and then one with certain domains filtered out, which we may +or may not bother trying to ingest (due to expectation of failure). + + COPY ( + SELECT row_to_json(ingest_request.*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + AND date(ingest_request.created) > '2020-04-01' + AND ingest_file_result.status = 'no-capture' + ) TO '/grande/snapshots/unpaywall_nocapture_all_2020-05-04.rows.json'; + => 2734145 + + COPY ( + SELECT row_to_json(ingest_request.*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + AND date(ingest_request.created) > '2020-04-01' + AND ingest_file_result.status = 'no-capture' + AND ingest_request.base_url NOT LIKE '%journals.sagepub.com%' + AND ingest_request.base_url NOT LIKE '%pubs.acs.org%' + AND ingest_request.base_url NOT LIKE '%ahajournals.org%' + AND ingest_request.base_url NOT LIKE '%www.journal.csj.jp%' + AND ingest_request.base_url NOT LIKE '%aip.scitation.org%' + AND ingest_request.base_url NOT LIKE '%academic.oup.com%' + AND ingest_request.base_url NOT LIKE '%tandfonline.com%' + ) TO '/grande/snapshots/unpaywall_nocapture_2020-05-04.rows.json'; + => 2602408 + +NOTE: forgot here to transform from "rows" to ingest requests. + +Not actually a very significant size difference after all. + +See `journal-crawls` repo for details on seedlist generation and crawling. + +## Re-Ingest Post-Crawl + +NOTE: if we *do* want to do cleanup eventually, could look for fatcat edits +between 2020-04-01 and 2020-05-25 which have limited "extra" metadata (eg, no +evidence or `oa_status`). + +The earlier bulk ingests were done wrong (forgot to transform from rows to full +ingest request docs), so going to re-do those, which should be a superset of +the nocapture crawl URLs.: + + ./scripts/ingestrequest_row2json.py /grande/snapshots/unpaywall_noingest_2020-04-08.rows.json | pv -l > /grande/snapshots/unpaywall_noingest_2020-04-08.json + => 1.26M 0:00:58 [21.5k/s] + => previously: 3,696,189 + + ./scripts/ingestrequest_row2json.py /grande/snapshots/unpaywall_noingest_2020-05-03.rows.json | pv -l > /grande/snapshots/unpaywall_noingest_2020-05-03.json + => 1.26M 0:00:56 [22.3k/s] + +Crap, looks like the 2020-04-08 segment got overwriten with 2020-05 data by +accident. Hrm... need to re-ingest *all* recent unpaywall URLs: + + COPY ( + SELECT row_to_json(ingest_request.*) + FROM ingest_request + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + AND date(ingest_request.created) > '2020-04-01' + ) TO '/grande/snapshots/unpaywall_all_recent_requests_2020-05-26.rows.json'; + => COPY 5691106 + + ./scripts/ingestrequest_row2json.py /grande/snapshots/unpaywall_all_recent_requests_2020-05-26.rows.json | pv -l | shuf > /grande/snapshots/unpaywall_all_recent_requests_2020-05-26.requests.json + => 5.69M 0:04:26 [21.3k/s] + +Start small: + + cat /grande/snapshots/unpaywall_all_recent_requests_2020-05-26.requests.json | head -n200 | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + +Looks good (whew), run the full thing: + + cat /grande/snapshots/unpaywall_all_recent_requests_2020-05-26.requests.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + +## Post-ingest stats (2020-08-28) + +Overall status: + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + status | count + -------------------------------------+---------- + success | 22063013 + no-pdf-link | 2192606 + redirect-loop | 1471135 + terminal-bad-status | 995106 + no-capture | 359440 + cdx-error | 358909 + wrong-mimetype | 111685 + wayback-error | 50705 + link-loop | 29359 + null-body | 13667 + gateway-timeout | 3689 + spn2-cdx-lookup-failure | 1229 + petabox-error | 1007 + redirects-exceeded | 747 + invalid-host-resolution | 464 + spn2-error | 107 + spn2-error:job-failed | 91 + bad-redirect | 26 + spn2-error:soft-time-limit-exceeded | 9 + bad-gzip-encoding | 5 + (20 rows) + +Failures by domain: + + SELECT domain, status, COUNT((domain, status)) + FROM ( + SELECT + ingest_file_result.ingest_type, + ingest_file_result.status, + substring(ingest_file_result.terminal_url FROM '[^/]+://([^/]*)') AS domain + FROM ingest_file_result + LEFT JOIN ingest_request + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_file_result.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + ) t1 + WHERE t1.domain != '' + AND t1.status != 'success' + AND t1.status != 'no-capture' + GROUP BY domain, status + ORDER BY COUNT DESC + LIMIT 30; + + domain | status | count + -----------------------------------+---------------------+-------- + academic.oup.com | no-pdf-link | 415441 + watermark.silverchair.com | terminal-bad-status | 345937 + www.tandfonline.com | no-pdf-link | 262488 + journals.sagepub.com | no-pdf-link | 235707 + onlinelibrary.wiley.com | no-pdf-link | 225876 + iopscience.iop.org | terminal-bad-status | 170783 + www.nature.com | redirect-loop | 145522 + www.degruyter.com | redirect-loop | 131898 + files-journal-api.frontiersin.org | terminal-bad-status | 126091 + pubs.acs.org | no-pdf-link | 119223 + society.kisti.re.kr | no-pdf-link | 112401 + www.ahajournals.org | no-pdf-link | 105953 + dialnet.unirioja.es | terminal-bad-status | 96505 + www.cell.com | redirect-loop | 87560 + www.ncbi.nlm.nih.gov | redirect-loop | 49890 + ageconsearch.umn.edu | redirect-loop | 45989 + ashpublications.org | no-pdf-link | 45833 + pure.mpg.de | redirect-loop | 45278 + www.degruyter.com | terminal-bad-status | 43642 + babel.hathitrust.org | terminal-bad-status | 42057 + osf.io | redirect-loop | 41119 + scialert.net | no-pdf-link | 39009 + dialnet.unirioja.es | redirect-loop | 38839 + www.jci.org | redirect-loop | 34209 + www.spandidos-publications.com | redirect-loop | 33167 + www.journal.csj.jp | no-pdf-link | 30915 + journals.openedition.org | redirect-loop | 30409 + www.valueinhealthjournal.com | redirect-loop | 30090 + dergipark.org.tr | no-pdf-link | 29146 + journals.ametsoc.org | no-pdf-link | 29133 + (30 rows) + +Enqueue internal failures for re-ingest: + + COPY ( + SELECT row_to_json(ingest_request.*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + AND ( + ingest_file_result.status = 'cdx-error' OR + ingest_file_result.status = 'wayback-error' + ) + ) TO '/grande/snapshots/unpaywall_errors_2020-08-28.rows.json'; + => 409606 + + ./scripts/ingestrequest_row2json.py /grande/snapshots/unpaywall_errors_2020-08-28.rows.json | pv -l | shuf > /grande/snapshots/unpaywall_errors_2020-08-28.requests.json + + cat /grande/snapshots/unpaywall_errors_2020-08-28.requests.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + +And after *that* (which ran quickly): + + status | count + -------------------------------------+---------- + success | 22281874 + no-pdf-link | 2258352 + redirect-loop | 1499251 + terminal-bad-status | 1004781 + no-capture | 401333 + wrong-mimetype | 112068 + cdx-error | 32259 + link-loop | 30137 + null-body | 13886 + wayback-error | 11653 + gateway-timeout | 3689 + spn2-cdx-lookup-failure | 1229 + petabox-error | 1036 + redirects-exceeded | 749 + invalid-host-resolution | 464 + spn2-error | 107 + spn2-error:job-failed | 91 + bad-redirect | 26 + spn2-error:soft-time-limit-exceeded | 9 + bad-gzip-encoding | 5 + (20 rows) + +22063013 -> 22281874 = + 218,861 success, not bad! diff --git a/notes/ingest/2020-05_oai_pmh.md b/notes/ingest/2020-05_oai_pmh.md new file mode 100644 index 0000000..fe22c75 --- /dev/null +++ b/notes/ingest/2020-05_oai_pmh.md @@ -0,0 +1,428 @@ + +Primary Goal: start large crawl of OAI landing pages that we haven't seen + +Fields of interest for ingest: +- oai identifer +- doi +- formats +- urls (maybe also "relations") +- types (type+stage) + +## Other Tasks + +About 150 million total lines. + +Types coverage + + zstdcat oai.ndjson.zst | pv -l | jq "select(.types != null) | .types[]" -r | sort -S 5G | uniq -c | sort -nr -S 1G > types_counts.txt + +Dump all ISSNs, with counts, quick check how many are in chocula/fatcat + + zstdcat oai.ndjson.zst | pv -l | jq "select(.issn != null) | .issn[]" -r | sort -S 5G | uniq -c | sort -nr -S 1G > issn_counts.txt + +Language coverage + + zstdcat oai.ndjson.zst | pv -l | jq "select(.languages != null) | .languages[]" -r | sort -S 5G | uniq -c | sort -nr -S 1G > languages_counts.txt + +Format coverage + + zstdcat oai.ndjson.zst | pv -l | jq "select(.formats != null) | .formats[]" -r | sort -S 5G | uniq -c | sort -nr -S 1G > formats_counts.txt + => 150M 0:56:14 [44.7k/s] + +Have a DOI? + + zstdcat oai.ndjson.zst | pv -l | rg '"doi":' | rg '"10.' | wc -l + => 16,013,503 + + zstdcat oai.ndjson.zst | pv -l | jq "select(.doi != null) | .doi[]" -r | sort -u -S 5G > doi_raw.txt + => 11,940,950 + +## Transform, Load, Bulk Ingest + + zstdcat oai.ndjson.zst | ./oai2ingestrequest.py - | pv -l | gzip > oai.202002.requests.json.gz + => 80M 6:36:55 [3.36k/s] + + time zcat /schnell/oai-pmh/oai.202002.requests.json.gz | pv -l | ./persist_tool.py ingest-request - + => 80M 4:00:21 [5.55k/s] + => Worker: Counter({'total': 80013963, 'insert-requests': 51169081, 'update-requests': 0}) + => JSON lines pushed: Counter({'pushed': 80013963, 'total': 80013963}) + + => real 240m21.207s + => user 85m12.576s + => sys 3m29.580s + + select count(*) from ingest_request where ingest_type = 'pdf' and link_source = 'oai'; + => 51,185,088 + +Why so many (30 million) skipped? Not unique? + + zcat oai.202002.requests.json.gz | jq '[.link_source_id, .base_url]' -c | sort -u -S 4G | wc -l + => 51,185,088 + + zcat oai.202002.requests.json.gz | jq .base_url -r | pv -l | sort -u -S 4G > request_url.txt + wc -l request_url.txt + => 50,002,674 request_url.txt + + zcat oai.202002.requests.json.gz | jq .link_source_id -r | pv -l | sort -u -S 4G > requires_oai.txt + wc -l requires_oai.txt + => 34,622,083 requires_oai.txt + +Yup, tons of duplication. And remember this is exact URL, not SURT or similar. + +How many of these are URLs we have seen and ingested already? + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'oai' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + status | count + -------------------------+---------- + | 49491452 + success | 1469113 + no-capture | 134611 + redirect-loop | 59666 + no-pdf-link | 8947 + cdx-error | 7561 + terminal-bad-status | 6704 + null-body | 5042 + wrong-mimetype | 879 + wayback-error | 722 + petabox-error | 198 + gateway-timeout | 86 + link-loop | 51 + invalid-host-resolution | 24 + spn2-cdx-lookup-failure | 22 + spn2-error | 4 + bad-gzip-encoding | 4 + spn2-error:job-failed | 2 + (18 rows) + +Dump ingest requests: + + COPY ( + SELECT row_to_json(ingest_request.*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'oai' + AND date(ingest_request.created) > '2020-05-01' + AND ingest_file_result.status IS NULL + ) TO '/grande/snapshots/oai_noingest_20200506.rows.json'; + => COPY 49491452 + + WARNING: should have transformed from rows to requests here + + cat /grande/snapshots/oai_noingest_20200506.rows.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + +## Crawl and re-ingest + +Updated stats after ingest (NOTE: ingest requests not really formed correctly, +but doesn't matter because fatcat wasn't importing these anyways): + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'oai' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + status | count + -------------------------+---------- + no-capture | 42565875 + success | 5227609 + no-pdf-link | 2156341 + redirect-loop | 559721 + cdx-error | 260446 + wrong-mimetype | 148871 + terminal-bad-status | 109725 + link-loop | 92792 + null-body | 30688 + | 15287 + petabox-error | 11109 + wayback-error | 6261 + skip-url-blocklist | 184 + gateway-timeout | 86 + bad-gzip-encoding | 25 + invalid-host-resolution | 24 + spn2-cdx-lookup-failure | 22 + bad-redirect | 15 + spn2-error | 4 + spn2-error:job-failed | 2 + (20 rows) + +Dump again for crawling: + + COPY ( + SELECT row_to_json(ingest_request.*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'oai' + AND date(ingest_request.created) > '2020-05-01' + AND (ingest_file_result.status = 'no-capture' or ingest_file_result.status = 'cdx-error') + ) TO '/grande/snapshots/oai_tocrawl_20200526.rows.json'; + +Notes about crawl setup are in `journal-crawls` repo. Excluded the following domains: + + 4876135 www.kb.dk REMOVE: too large and generic + 3110009 kb-images.kb.dk REMOVE: dead? + 1274638 mdz-nbn-resolving.de REMOVE: maybe broken + 982312 aggr.ukm.um.si REMOVE: maybe broken + +And went from about 42,826,313 rows to 31,773,874 unique URLs to crawl, so +expecting at least 11,052,439 `no-capture` ingest results (and should probably +filter for these or even delete from the ingest request table). + +Ingest progress: + + 2020-08-05 14:02: 32,571,018 + 2020-08-06 13:49: 31,195,169 + 2020-08-07 10:11: 29,986,169 + 2020-08-10 10:43: 26,497,196 + 2020-08-12 11:02: 23,811,845 + 2020-08-17 13:34: 19,460,502 + 2020-08-20 09:49: 15,069,507 + 2020-08-25 09:56: 9,397,035 + 2020-09-02 15:02: 305,889 (72k longest queue) + 2020-09-03 14:30: done + +## Post-ingest stats + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'oai' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + status | count + -------------------------+---------- + no-capture | 16804277 + no-pdf-link | 14895249 + success | 13898603 + redirect-loop | 2709730 + cdx-error | 827024 + terminal-bad-status | 740037 + wrong-mimetype | 604242 + link-loop | 532553 + null-body | 95721 + wayback-error | 41864 + petabox-error | 19204 + | 15287 + gateway-timeout | 510 + bad-redirect | 318 + skip-url-blocklist | 184 + bad-gzip-encoding | 114 + timeout | 78 + spn2-cdx-lookup-failure | 59 + invalid-host-resolution | 19 + blocked-cookie | 6 + (20 rows) + +Hrm, +8 million or so 'success', but that is a lot of no-capture. May be worth +dumping the full kafka result topic, filter to OAI requests, and extracting the +missing URLs. + +Top counts by OAI prefix: + + SELECT + oai_prefix, + COUNT(CASE WHEN status = 'success' THEN 1 END) as success, + COUNT(*) as total + FROM ( + SELECT + ingest_file_result.status as status, + -- eg "oai:cwi.nl:4881" + substring(ingest_request.link_source_id FROM 'oai:([^:]+):.*') AS oai_prefix + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'oai' + ) t1 + GROUP BY oai_prefix + ORDER BY total DESC + LIMIT 25; + + oai_prefix | success | total + --------------------------+---------+--------- + kb.dk | 0 | 7989412 (excluded) + repec | 1118591 | 2783448 + bnf.fr | 0 | 2187277 + hispana.mcu.es | 19404 | 1492639 + bdr.oai.bsb-muenchen.de | 73 | 1319882 (excluded?) + hal | 564700 | 1049607 + ukm.si | 0 | 982468 (excluded) + hsp.org | 0 | 810281 + www.irgrid.ac.cn | 17578 | 748828 + cds.cern.ch | 72811 | 688091 + americanae.aecid.es | 69678 | 572792 + biodiversitylibrary.org | 2121 | 566154 + juser.fz-juelich.de | 22777 | 518551 + espace.library.uq.edu.au | 6494 | 508960 + igi.indrastra.com | 58689 | 478577 + archive.ugent.be | 63654 | 424014 + hrcak.srce.hr | 395031 | 414897 + zir.nsk.hr | 153889 | 397200 + renati.sunedu.gob.pe | 78399 | 388355 + hypotheses.org | 3 | 374296 + rour.neicon.ru | 7963 | 354529 + generic.eprints.org | 261221 | 340470 + invenio.nusl.cz | 6184 | 325867 + evastar-karlsruhe.de | 62044 | 317952 + quod.lib.umich.edu | 5 | 309135 + (25 rows) + +Top counts by OAI prefix and status: + + SELECT + oai_prefix, + status, + COUNT((oai_prefix,status)) + FROM ( + SELECT + ingest_file_result.status as status, + -- eg "oai:cwi.nl:4881" + substring(ingest_request.link_source_id FROM 'oai:([^:]+):.*') AS oai_prefix + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'oai' + ) t1 + GROUP BY oai_prefix, status + ORDER BY COUNT DESC + LIMIT 30; + + + oai_prefix | status | count + --------------------------+---------------+--------- + kb.dk | no-capture | 7955231 (excluded) + bdr.oai.bsb-muenchen.de | no-capture | 1270209 (excluded?) + repec | success | 1118591 + hispana.mcu.es | no-pdf-link | 1118092 + bnf.fr | no-capture | 1100591 + ukm.si | no-capture | 976004 (excluded) + hsp.org | no-pdf-link | 773496 + repec | no-pdf-link | 625629 + bnf.fr | no-pdf-link | 607813 + hal | success | 564700 + biodiversitylibrary.org | no-pdf-link | 531409 + cds.cern.ch | no-capture | 529842 + repec | redirect-loop | 504393 + juser.fz-juelich.de | no-pdf-link | 468813 + bnf.fr | redirect-loop | 436087 + americanae.aecid.es | no-pdf-link | 409954 + hrcak.srce.hr | success | 395031 + www.irgrid.ac.cn | no-pdf-link | 362087 + hal | no-pdf-link | 352111 + www.irgrid.ac.cn | no-capture | 346963 + espace.library.uq.edu.au | no-pdf-link | 315302 + igi.indrastra.com | no-pdf-link | 312087 + repec | no-capture | 309882 + invenio.nusl.cz | no-pdf-link | 302657 + hypotheses.org | no-pdf-link | 298750 + rour.neicon.ru | redirect-loop | 291922 + renati.sunedu.gob.pe | no-capture | 276388 + t2r2.star.titech.ac.jp | no-pdf-link | 264109 + generic.eprints.org | success | 261221 + quod.lib.umich.edu | no-pdf-link | 253937 + (30 rows) + +If we remove excluded prefixes, and some large/generic prefixes (bnf.fr, +hispana.mcu.es, hsp.org), then the aggregate counts are: + + no-capture | 16,804,277 -> 5,502,242 + no-pdf-link | 14,895,249 -> 12,395,848 + +Top status by terminal domain: + + SELECT domain, status, COUNT((domain, status)) + FROM ( + SELECT + ingest_file_result.ingest_type, + ingest_file_result.status, + substring(ingest_file_result.terminal_url FROM '[^/]+://([^/]*)') AS domain + FROM ingest_file_result + LEFT JOIN ingest_request + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_file_result.ingest_type = 'pdf' + AND ingest_request.link_source = 'oai' + ) t1 + WHERE t1.domain != '' + GROUP BY domain, status + ORDER BY COUNT DESC + LIMIT 30; + + domain | status | count + ----------------------------------+---------------+-------- + hispana.mcu.es | no-pdf-link | 709701 (national scope) + gallica.bnf.fr | no-pdf-link | 601193 (national scope) + discover.hsp.org | no-pdf-link | 524212 (historical) + www.biodiversitylibrary.org | no-pdf-link | 479288 + gallica.bnf.fr | redirect-loop | 435981 (national scope) + hrcak.srce.hr | success | 389673 + hemerotecadigital.bne.es | no-pdf-link | 359243 + juser.fz-juelich.de | no-pdf-link | 345112 + espace.library.uq.edu.au | no-pdf-link | 304299 + invenio.nusl.cz | no-pdf-link | 302586 + igi.indrastra.com | no-pdf-link | 292006 + openrepository.ru | redirect-loop | 291555 + hal.archives-ouvertes.fr | success | 278134 + t2r2.star.titech.ac.jp | no-pdf-link | 263971 + bib-pubdb1.desy.de | no-pdf-link | 254879 + quod.lib.umich.edu | no-pdf-link | 250382 + encounters.hsp.org | no-pdf-link | 248132 + americanae.aecid.es | no-pdf-link | 245295 + www.irgrid.ac.cn | no-pdf-link | 242496 + publikationen.bibliothek.kit.edu | no-pdf-link | 222041 + www.sciencedirect.com | no-pdf-link | 211756 + dialnet.unirioja.es | redirect-loop | 203615 + edoc.mpg.de | no-pdf-link | 195526 + bibliotecadigital.jcyl.es | no-pdf-link | 184671 + hal.archives-ouvertes.fr | no-pdf-link | 183809 + www.sciencedirect.com | redirect-loop | 173439 + lup.lub.lu.se | no-pdf-link | 165788 + orbi.uliege.be | no-pdf-link | 158313 + www.erudit.org | success | 155986 + lib.dr.iastate.edu | success | 153384 + (30 rows) + +Follow-ups are TBD but could include: +- crawling the ~5m no-capture links directly (eg, not `base_url`) from the + ingest result JSON, while retaining the ingest request for later re-ingest +- investigating and iterating on PDF link extraction, both for large platforms + and randomly sampled from long tail +- classifying OAI prefixes by type (subject repository, institutional + repository, journal, national-library, historical docs, greylit, law, etc) +- running pdftrio over some/all of this corpus diff --git a/notes/ingest/2020-05_pubmed.md b/notes/ingest/2020-05_pubmed.md new file mode 100644 index 0000000..36d00a1 --- /dev/null +++ b/notes/ingest/2020-05_pubmed.md @@ -0,0 +1,10 @@ + +From ARXIV-PUBMEDCENTRAL-CRAWL-2020-04, on fatcat-prod1. + +Test small batch: + + zcat ingest_file_pmcid_20200424.json.gz | head -n200 | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + +Run the whole batch: + + zcat ingest_file_pmcid_20200424.json.gz | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 diff --git a/notes/ingest/2020-07_mag.md b/notes/ingest/2020-07_mag.md new file mode 100644 index 0000000..1d33162 --- /dev/null +++ b/notes/ingest/2020-07_mag.md @@ -0,0 +1,353 @@ + +Using 2020-06-25 upstream MAG corpus snapshot. + +Ran munging from `scratch:ingest/mag` notes first. + +Expecting a couple million new ingest request URLs; this is the first "patch" +MAG ingest on top of existing already-run requests. + +Planning to skip the initial bulk ingest step, on the assumption that new URLs +have either been ingested already (eg, via continuous ingest pipeline) or need +crawling. + +## Generate Requests + + export LC_ALL=C + cat PaperUrls_mag_url_doi.all.txt | rg -a -v arxiv.org | rg -a "://" | ./mag_ingest_request.py - --created-date 2020-06-25 | pv -l > ingest_requests_mag-2020-06-25.json + => 28.7M 2:36:48 [3.06k/s] + + export LC_ALL=C + zcat PaperUrls_mag_url_pmid.txt.gz | rg -a -v arxiv.org | rg -a "://" | ./mag_ingest_request.py - --created-date 2020-06-25 --pmid | pv -l > ingest_requests_mag-2020-06-25.pmid.json + => 5.66M 0:29:28 [ 3.2k/s] + +## Persist Ingest Requests + + # small sample + head -n1000 /schnell/mag/20200625/ingest_requests_mag-2020-06-25.pmid.json | ./persist_tool.py ingest-request - + => Worker: Counter({'total': 1000, 'insert-requests': 319, 'update-requests': 0}) + + head -n1000 /schnell/mag/20200625/ingest_requests_mag-2020-06-25.json | ./persist_tool.py ingest-request - + Worker: Counter({'total': 1000, 'insert-requests': 304, 'update-requests': 0}) + + cat /schnell/mag/20200625/ingest_requests_mag-2020-06-25.pmid.json | ./persist_tool.py ingest-request - + => Worker: Counter({'total': 5662486, 'insert-requests': 1984605, 'update-requests': 0}) + + cat /schnell/mag/20200625/ingest_requests_mag-2020-06-25.json | ./persist_tool.py ingest-request - + => Worker: Counter({'total': 28743819, 'insert-requests': 7433465, 'update-requests': 0}) + +## Crawl/Dupe Status + +Overall status for old and new seeds, filtering out large (blocking) +publishers: + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'mag' + AND ingest_request.base_url NOT LIKE '%journals.sagepub.com%' + AND ingest_request.base_url NOT LIKE '%pubs.acs.org%' + AND ingest_request.base_url NOT LIKE '%ahajournals.org%' + AND ingest_request.base_url NOT LIKE '%www.journal.csj.jp%' + AND ingest_request.base_url NOT LIKE '%aip.scitation.org%' + AND ingest_request.base_url NOT LIKE '%academic.oup.com%' + AND ingest_request.base_url NOT LIKE '%tandfonline.com%' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + status | count + -------------------------------------+---------- + success | 19477651 + | 8238898 + redirect-loop | 2036494 + link-loop | 1330036 + no-pdf-link | 1304820 + terminal-bad-status | 648150 + no-capture | 545785 + gateway-timeout | 200143 + cdx-error | 149995 + spn2-cdx-lookup-failure | 80010 + wrong-mimetype | 57052 + wayback-error | 41032 + invalid-host-resolution | 37203 + petabox-error | 11167 + null-body | 6662 + spn2-error | 1698 + spn2-error:job-failed | 775 + spn2-error:invalid-url-syntax | 335 + spn2-error:soft-time-limit-exceeded | 191 + bad-redirect | 77 + (20 rows) + +Just the new seeds: + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'mag' + AND ingest_request.base_url NOT LIKE '%journals.sagepub.com%' + AND ingest_request.base_url NOT LIKE '%pubs.acs.org%' + AND ingest_request.base_url NOT LIKE '%ahajournals.org%' + AND ingest_request.base_url NOT LIKE '%www.journal.csj.jp%' + AND ingest_request.base_url NOT LIKE '%aip.scitation.org%' + AND ingest_request.base_url NOT LIKE '%academic.oup.com%' + AND ingest_request.base_url NOT LIKE '%tandfonline.com%' + AND ingest_request.created > '2020-06-20' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + status | count + -------------------------------------+--------- + | 8238851 + success | 787174 + no-capture | 42864 + redirect-loop | 31718 + terminal-bad-status | 31493 + no-pdf-link | 13025 + cdx-error | 11275 + wrong-mimetype | 6238 + link-loop | 3365 + wayback-error | 748 + gateway-timeout | 506 + null-body | 191 + spn2-cdx-lookup-failure | 99 + petabox-error | 89 + invalid-host-resolution | 70 + spn2-error | 7 + spn2-error:job-failed | 2 + spn2-error:soft-time-limit-exceeded | 1 + bad-gzip-encoding | 1 + (19 rows) + +Where are no-capture results terminating? May need to add or update heritrix +crawl config so that we get better yield without needing to do SPNv2 crawling. + + SELECT initial_domain, terminal_domain, COUNT(*) + FROM ( + SELECT + ingest_file_result.status as status, + substring(ingest_file_result.base_url FROM '[^/]+://([^/]*)') AS initial_domain, + substring(ingest_file_result.terminal_url FROM '[^/]+://([^/]*)') AS terminal_domain + FROM ingest_file_result + LEFT JOIN ingest_request + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'mag' + AND ingest_file_result.status = 'no-capture' + ) t1 + GROUP BY initial_domain, terminal_domain + ORDER BY COUNT DESC + LIMIT 25; + + initial_domain | terminal_domain | count + ---------------------------------+---------------------+-------- + www.researchgate.net | | 334145 + academic.oup.com | | 205820 + www.tandfonline.com | | 148638 + journals.sagepub.com | | 144196 + muse.jhu.edu | | 55957 + hrcak.srce.hr | | 25317 + www.omicsonline.org | | 22426 + link.springer.com | | 21044 + iopscience.iop.org | | 12385 + bioone.org | | 9097 + tandfonline.com | | 8512 + or.nsfc.gov.cn | | 4823 + ieeexplore.ieee.org | ieeexplore.ieee.org | 4398 + pubs.acs.org | | 3708 + archive-ouverte.unige.ch | | 2743 + dergipark.ulakbim.gov.tr | | 2677 + hal.archives-ouvertes.fr | | 1258 + dergipark.org.tr | | 1207 + apo.org.au | | 1186 + spire.sciencespo.fr | | 989 + cyberleninka.ru | | 895 + lirias.kuleuven.be | | 855 + tel.archives-ouvertes.fr | | 786 + pub.uni-bielefeld.de | | 728 + www.research-collection.ethz.ch | | 670 + (25 rows) + +## Heritrix Seedlist Generation + +Dump ingest requests (filtered for some domains that don't expect to crawl via +heritrix): + + COPY ( + SELECT row_to_json(ingest_request.*) FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'mag' + AND (ingest_file_result.status = 'no-capture' + OR ingest_file_result.status IS NULL) + AND ingest_request.base_url NOT LIKE '%journals.sagepub.com%' + AND ingest_request.base_url NOT LIKE '%pubs.acs.org%' + AND ingest_request.base_url NOT LIKE '%ahajournals.org%' + AND ingest_request.base_url NOT LIKE '%www.journal.csj.jp%' + AND ingest_request.base_url NOT LIKE '%aip.scitation.org%' + AND ingest_request.base_url NOT LIKE '%academic.oup.com%' + AND ingest_request.base_url NOT LIKE '%tandfonline.com%' + ) TO '/grande/snapshots/mag_nocapture_20200708.rows.json'; + => 8784683 + + # in sandcrawler pipenv + ./scripts/ingestrequest_row2json.py /grande/snapshots/mag_nocapture_20200708.rows.json > /grande/snapshots/mag_nocapture_20200708.json + +Seedlist transform from here on covered in MAG crawl notes. + +## Bulk Ingest + +Run ingest requests on everything we crawled: + + cat /grande/snapshots/mag_nocapture_20200708.json | | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + +Small sample: + + head -n1000 /grande/snapshots/mag_nocapture_20200708.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + +Full run: + + cat /grande/snapshots/mag_nocapture_20200708.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + +## Updated Overall Stats + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'mag' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + status | count + -------------------------------------+---------- + success | 24574294 + redirect-loop | 2633731 + no-capture | 2458694 + no-pdf-link | 1896871 + link-loop | 1510899 + terminal-bad-status | 878821 + cdx-error | 387574 + gateway-timeout | 200246 + | 170304 + wayback-error | 97572 + spn2-cdx-lookup-failure | 80284 + wrong-mimetype | 65097 + invalid-host-resolution | 37204 + petabox-error | 12097 + null-body | 8549 + spn2-error | 1706 + spn2-error:job-failed | 775 + spn2-error:invalid-url-syntax | 335 + spn2-error:soft-time-limit-exceeded | 191 + bad-redirect | 90 + (20 rows) + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'mag' + AND ingest_request.base_url NOT LIKE '%journals.sagepub.com%' + AND ingest_request.base_url NOT LIKE '%pubs.acs.org%' + AND ingest_request.base_url NOT LIKE '%ahajournals.org%' + AND ingest_request.base_url NOT LIKE '%www.journal.csj.jp%' + AND ingest_request.base_url NOT LIKE '%aip.scitation.org%' + AND ingest_request.base_url NOT LIKE '%academic.oup.com%' + AND ingest_request.base_url NOT LIKE '%tandfonline.com%' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + status | count + -------------------------------------+---------- + success | 24557382 + redirect-loop | 2630582 + no-capture | 1947066 + no-pdf-link | 1778206 + link-loop | 1510790 + terminal-bad-status | 857173 + cdx-error | 384525 + gateway-timeout | 200143 + wayback-error | 96390 + spn2-cdx-lookup-failure | 80010 + wrong-mimetype | 64908 + invalid-host-resolution | 37203 + petabox-error | 12087 + null-body | 8548 + spn2-error | 1698 + spn2-error:job-failed | 775 + spn2-error:invalid-url-syntax | 335 + spn2-error:soft-time-limit-exceeded | 191 + bad-redirect | 90 + | 69 + (20 rows) + +Just the new seeds: + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'mag' + AND ingest_request.base_url NOT LIKE '%journals.sagepub.com%' + AND ingest_request.base_url NOT LIKE '%pubs.acs.org%' + AND ingest_request.base_url NOT LIKE '%ahajournals.org%' + AND ingest_request.base_url NOT LIKE '%www.journal.csj.jp%' + AND ingest_request.base_url NOT LIKE '%aip.scitation.org%' + AND ingest_request.base_url NOT LIKE '%academic.oup.com%' + AND ingest_request.base_url NOT LIKE '%tandfonline.com%' + AND ingest_request.created > '2020-06-20' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + + status | count + -------------------------------------+--------- + success | 5860601 + no-capture | 1489959 + redirect-loop | 619121 + no-pdf-link | 473703 + terminal-bad-status | 234753 + cdx-error | 231575 + link-loop | 184093 + wayback-error | 56068 + wrong-mimetype | 14046 + null-body | 2068 + petabox-error | 1006 + gateway-timeout | 506 + spn2-cdx-lookup-failure | 99 + invalid-host-resolution | 70 + | 22 + bad-redirect | 13 + spn2-error | 7 + timeout | 3 + spn2-error:job-failed | 2 + spn2-error:soft-time-limit-exceeded | 1 + (20 rows) + diff --git a/notes/ingest/2020-08_daily_improvements.md b/notes/ingest/2020-08_daily_improvements.md new file mode 100644 index 0000000..da57065 --- /dev/null +++ b/notes/ingest/2020-08_daily_improvements.md @@ -0,0 +1,202 @@ + +Goal is to increase rate of successful daily changelog crawling, but reduce +wasted attempts. + +Status by domain, past 30 days: + + domain | status | count + --------------------------------------+-----------------+------- + arxiv.org | success | 21792 + zenodo.org | success | 10646 + res.mdpi.com | success | 10449 + springernature.figshare.com | no-pdf-link | 10430 + s3-eu-west-1.amazonaws.com | success | 8966 + zenodo.org | no-pdf-link | 8137 + hkvalidate.perfdrive.com | no-pdf-link | 5943 + www.ams.org:80 | no-pdf-link | 5799 + assets.researchsquare.com | success | 4651 + pdf.sciencedirectassets.com | success | 4145 + fjfsdata01prod.blob.core.windows.net | success | 3500 + sage.figshare.com | no-pdf-link | 3174 + onlinelibrary.wiley.com | no-pdf-link | 2869 + www.e-periodica.ch | no-pdf-link | 2709 + revistas.uned.es | success | 2631 + figshare.com | no-pdf-link | 2500 + www.sciencedirect.com | link-loop | 2477 + linkinghub.elsevier.com | gateway-timeout | 1878 + downloads.hindawi.com | success | 1819 + www.scielo.br | success | 1691 + jps.library.utoronto.ca | success | 1590 + www.ams.org | no-pdf-link | 1568 + digi.ub.uni-heidelberg.de | no-pdf-link | 1496 + research-repository.griffith.edu.au | success | 1412 + journals.plos.org | success | 1330 + (25 rows) + +Status by DOI prefix, past 30 days: + + doi_prefix | status | count + ------------+-------------------------+------- + 10.6084 | no-pdf-link | 14410 <- figshare; small fraction success + 10.6084 | success | 4007 + 10.6084 | cdx-error | 1746 + + 10.13140 | gateway-timeout | 9689 <- researchgate + 10.13140 | cdx-error | 4154 + + 10.5281 | success | 9408 <- zenodo + 10.5281 | no-pdf-link | 6079 + 10.5281 | cdx-error | 3200 + 10.5281 | wayback-error | 2098 + + 10.1090 | no-pdf-link | 7420 <- AMS (ams.org) + + 10.3390 | success | 6599 <- MDPI + 10.3390 | cdx-error | 3032 + 10.3390 | wayback-error | 1636 + + 10.1088 | no-pdf-link | 3227 <- IOP science + + 10.1101 | gateway-timeout | 3168 <- coldspring harbor: press, biorxiv, medrxiv, etc + 10.1101 | cdx-error | 1147 + + 10.21203 | success | 3124 <- researchsquare + 10.21203 | cdx-error | 1181 + + 10.1016 | success | 3083 <- elsevier + 10.1016 | cdx-error | 2465 + 10.1016 | gateway-timeout | 1682 + 10.1016 | wayback-error | 1567 + + 10.25384 | no-pdf-link | 3058 <- sage figshare + 10.25384 | success | 2456 + + 10.1007 | gateway-timeout | 2913 <- springer + 10.1007 | cdx-error | 1164 + + 10.5944 | success | 2831 + 10.1186 | success | 2650 + 10.5169 | no-pdf-link | 2644 <- www.e-periodica.ch + 10.3389 | success | 2279 + 10.24411 | gateway-timeout | 2184 <- cyberleninka.ru + 10.1038 | gateway-timeout | 2143 <- nature group + 10.1177 | gateway-timeout | 2038 <- SAGE + 10.11588 | no-pdf-link | 1574 <- journals.ub.uni-heidelberg.de (OJS?) + 10.25904 | success | 1416 + 10.1155 | success | 1304 + 10.21994 | no-pdf-link | 1268 <- loar.kb.dk + 10.18720 | spn2-cdx-lookup-failure | 1232 <- elib.spbstu.ru + 10.24411 | cdx-error | 1202 + 10.1055 | no-pdf-link | 1170 <- thieme-connect.de + (40 rows) + +code changes for ingest: +x hkvalidate.perfdrive.com: just bail when we see this +x skip large publishers which gateway-timeout (for now) + - springerlink (10.1007) + - nature group (10.1038) + - SAGE (10.1177) + - IOP (10.1088) + +fatcat: +x figshare (by `doi_prefix`): if not versioned (suffix), skip crawl +x zenodo: also try to not crawl if unversioned (group) +x figshare import metadata + +sandcrawler: +x ends with `cookieAbsent` or `cookieSet=1` -> status as cookie-blocked +x https://profile.thieme.de/HTML/sso/ejournals/login.htm[...] => blocklist +x verify that we do quick-get for arxiv.org + europmc.org (+ figshare/zenodo?) + => we were not! +x shorten post-SPNv2 CDX pause? for throughput, given that we are re-trying anyways +x ensure that we store uncrawled URL somewhere on no-capture status + => in HTML or last of hops + => not in DB, but that is a bigger change + +- try to get un-blocked: + - coldspring harbor has been blocking since 2020-06-22? yikes! + - cyberleninka.ru + - arxiv.org + +- no-pdf-link + x www.ams.org (10.1090) + => these seem to be stale captures, eg from 2008. newer captures have citation_pdf_url + => should consider recrawling all of ams.org? + => not sure why these crawl requests are happening only now + => on the order of 15k OA articles not in ia; 43k total not preserved + => force recrawl OA subset (DONE) + x www.e-periodica.ch (10.5169) + => TODO: dump un-preserved URLs, transform to PDF urls, heritrix crawl, re-ingest + x digi.ub.uni-heidelberg.de (10.11588) + => TODO: bulk re-enqueue? then heritrix crawl? + - https://loar.kb.dk/handle/1902/6988 (10.21994) + => TODO: bulk re-enqueue + => site was updated recently (august 2020); now it crawls fine. need to re-ingest all? + => 7433 hits + - thieme-connect.de (10.1055) + => 600k+ missing + => TODO: bulk re-enqueue? then heritrix crawl? + => https://profile.thieme.de/HTML/sso/ejournals/login.htm[...] => blocklist + => generally just need to re-crawl all? + +Unresolved: +- why so many spn2-errors on https://elib.spbstu.ru/ (10.18720)? + +## figshare + +10.6084 regular figshare +10.25384 SAGE figshare + +For sage, "collections" are bogus? can we detect these in datacite metadata? + +If figshare types like: + + ris: "GEN", + bibtex: "misc", + citeproc: "article", + schemaOrg: "Collection", + resourceType: "Collection", + resourceTypeGeneral: "Collection" + +then mark as 'stub'. + +"Additional file" items don't seem like "stub"; -> "component". + +title:"Figure {} from " -> component + +current types are mostly: article, stub, dataset, graphic, article-journal + +If DOI starts with "sage.", then publisher is "Sage" (not figshare). Container +name should be... sage.figshare.com? + +set version to the version from DOI + +## zenodo + +doi_prefix: 10.5281 + +if on zenodo, and has a "Identical to" relation, then this is a pre-print. in +that case, drop container_id and set container_name to zenodo.org. *But*, there +are some journals now publishing exclusively to zenodo.org, so retain that +metadata. examples: + + "Detection of keyboard vibrations and effects on perceived piano quality" + https://fatcat.wiki/release/mufzkdgt2nbzfha44o7p7gkrpy + + "Editing LAF: Educate, don't defend!" + https://zenodo.org/record/2583025 + +version number not available in zenodo metadata + +## Gitlab MR Notes + +The main goal of this group of changes is to do a better job at daily ingest. + +Currently we have on the order of 20k new releases added to the index every day, and about half of them get are marked as OA (either CC license or via container being in DOAJ or ROAD), and pass some filters (eg, release_type), and are selected for ingest. Of those, about half fail to crawl to fulltext, either due to blocking (gateway-timeout, cookie tests, anti-bot detection, loginwall, etc). On the other hand, we don't attempt to crawl lots of "bronze" OA, which is content that is available from the publisher website, but isn't marked explicitly OA. + +Based on investigating daily crawling from the past month (will commit these notes to sandcrawler soon), I have identified some DOI prefixes that almost always fail ingest via SPNv2. I also have some patches to sandcrawler ingest to improve ability to crawl some large repositories etc. + +Some of the biggest "OA but failed to crawl" are from figshare and zenodo, which register a relatively large fraction of daily OA DOIs. We want to crawl most of that content, but both of these platforms register at least DOIs for each piece of content (a "group" DOI and a "versioned" DOI), and we only need to crawl one. There were also some changes needed to release-type filtering and assignment specific to these platforms, or based on the title of entities. + +This MR mixes changes to the datacite metadata import routing (including some refactors out of the main parse_record method) and behavior changes to the entity updater (which is where the code to decide about whether to send an ingest request on release creation lives). I will have a separate MR for importer metadata changes that don't impact ingest behavior. + diff --git a/notes/ingest/2020-09_oa_doi.md b/notes/ingest/2020-09_oa_doi.md new file mode 100644 index 0000000..f5c853d --- /dev/null +++ b/notes/ingest/2020-09_oa_doi.md @@ -0,0 +1,352 @@ + +It seems that many gold OA DOIs on were not ingesting simply because the HTML +url extraction was not working for a particular version of OJS. + +Let's re-try all ~2.5 million of these in bulk mode and see how many are +'no-capture' vs. other errors, then possibly re-crawl a large number. + +## Bulk Ingest + +Dump ingest requests + + ./fatcat_ingest.py query 'is_oa:true preservation:none !arxiv_id:* !pmcid:* !publisher_type:big5 type:article-journal' | pv -l > /srv/fatcat/snapshots/oa_doi_20200915.ingest_request.json + Expecting 2569876 release objects in search queries + Counter({'elasticsearch_release': 2569880, 'estimate': 2569880, 'ingest_request': 2063034}) + +Enqueue + + cat /srv/fatcat/snapshots/oa_doi_20200915.ingest_request.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + +Started at about: + + Thu Sep 17 00:15:00 UTC 2020 + 2020-09-17T00:15:00Z + +## Stats + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.ingest_request_source = 'fatcat-ingest' + AND ingest_file_result.updated >= '2020-09-16' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 30; + + status | count + -------------------------------------+-------- + no-capture | 513462 + success | 206042 + no-pdf-link | 186779 + terminal-bad-status | 40372 + redirect-loop | 33103 + cdx-error | 24078 + link-loop | 13494 + spn2-cdx-lookup-failure | 10247 + gateway-timeout | 4407 + wrong-mimetype | 3213 + petabox-error | 866 + null-body | 449 + spn2-error | 217 + wayback-error | 129 + spn2-error:job-failed | 64 + bad-redirect | 6 + spn2-error:soft-time-limit-exceeded | 1 + (17 rows) + +This was only about half the requests. Try... broader? + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'doi' + AND (ingest_request.ingest_request_source = 'fatcat-ingest' + OR ingest_request.ingest_request_source = 'fatcat-changelog') + AND ingest_file_result.updated >= '2020-09-15' + AND ingest_file_result.updated <= '2020-09-20' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 30; + + status | count + -------------------------------------+-------- + no-capture | 579952 + success | 387325 + no-pdf-link | 380406 + terminal-bad-status | 63743 + redirect-loop | 53893 + cdx-error | 46024 + spn2-cdx-lookup-failure | 28347 + link-loop | 22573 + gateway-timeout | 11686 + wrong-mimetype | 6294 + null-body | 3509 + petabox-error | 2388 + spn2-error | 1023 + spn2-error:job-failed | 462 + wayback-error | 347 + spn2-error:soft-time-limit-exceeded | 20 + bad-redirect | 11 + (17 rows) + +What top domains for those `no-pdf-link` (or similar)? + + SELECT domain, status, COUNT((domain, status)) + FROM ( + SELECT + ingest_file_result.ingest_type, + ingest_file_result.status, + substring(ingest_file_result.terminal_url FROM '[^/]+://([^/]*)') AS domain + FROM ingest_file_result + LEFT JOIN ingest_request + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'doi' + AND (ingest_request.ingest_request_source = 'fatcat-ingest' + OR ingest_request.ingest_request_source = 'fatcat-changelog') + AND ingest_file_result.updated >= '2020-09-15' + AND ingest_file_result.updated <= '2020-09-20' + ) t1 + WHERE t1.domain != '' + AND t1.status != 'success' + AND t1.status != 'no-capture' + GROUP BY domain, status + ORDER BY COUNT DESC + LIMIT 30; + + domain | status | count + ------------------------------+-------------------------+------- + zenodo.org | no-pdf-link | 56488 + figshare.com | no-pdf-link | 55337 + www.egms.de | redirect-loop | 22686 + zenodo.org | terminal-bad-status | 22128 + tandf.figshare.com | no-pdf-link | 20027 + springernature.figshare.com | no-pdf-link | 17181 + cairn.info | terminal-bad-status | 13836 + www.persee.fr | terminal-bad-status | 7565 + projecteuclid.org | link-loop | 7449 + www.cairn.info | no-pdf-link | 6992 + scialert.net | no-pdf-link | 6621 + www.cairn.info | link-loop | 5870 + utpjournals.press | no-pdf-link | 5772 + journals.openedition.org | redirect-loop | 5464 + www.egms.de | no-pdf-link | 5223 + archaeologydataservice.ac.uk | no-pdf-link | 4881 + rs.figshare.com | no-pdf-link | 4773 + www.degruyter.com | spn2-cdx-lookup-failure | 4763 + koreascience.or.kr | no-pdf-link | 4487 + cancerres.aacrjournals.org | no-pdf-link | 4124 + cms.math.ca | no-pdf-link | 3441 + volcano.si.edu | no-pdf-link | 3424 + www.mathnet.ru | no-pdf-link | 3229 + tidsskriftet.no | no-pdf-link | 3012 + journals.plos.org | no-pdf-link | 3005 + tudigit.ulb.tu-darmstadt.de | no-pdf-link | 2796 + www.cairn.info:80 | link-loop | 2647 + hammer.figshare.com | no-pdf-link | 2627 + www.psychosocial.com | no-pdf-link | 2457 + osf.io | terminal-bad-status | 2388 + (30 rows) + +Should look at link extraction for: + +- scialert.net +- utpjournals.press +- koreascience.or.kr +- cancerres.aacrjournals.org +- cms.math.ca +- volcano.si.edu +- www.mathnet.ru +- www.psychosocial.com + +## Re-Ingest + +Re-run ingest to handle `no-capture` cases, to extract the missing terminal URLs: + + COPY ( + SELECT row_to_json(ingest_request.*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'doi' + AND (ingest_request.ingest_request_source = 'fatcat-ingest' + OR ingest_request.ingest_request_source = 'fatcat-changelog') + AND ingest_file_result.updated >= '2020-09-15' + AND ingest_file_result.updated <= '2020-09-20' + AND ingest_file_result.status = 'no-capture' + -- AND ingest_request.base_url NOT LIKE '%journals.sagepub.com%' + ) TO '/grande/snapshots/oa_doi_reingest_nocapture_20201012.rows.json'; + => COPY 579952 + + ./scripts/ingestrequest_row2json.py /grande/snapshots/oa_doi_reingest_nocapture_20201012.rows.json | pv -l | shuf > /grande/snapshots/oa_doi_reingest_nocapture_20201012.ingest_request.json + => 579k 0:00:22 [25.9k/s] + + cat /grande/snapshots/oa_doi_reingest_nocapture_20201012.ingest_request.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + +Resuming progress on this in early December 2020. + +Filtered requests to re-crawl: + + COPY ( + SELECT row_to_json(t1.*) + FROM ( + SELECT ingest_request.*, ingest_file_result as result + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.base_url = ingest_request.base_url + AND ingest_file_result.ingest_type = ingest_request.ingest_type + WHERE + ingest_request.link_source = 'doi' + AND (ingest_request.ingest_request_source = 'fatcat-ingest' + OR ingest_request.ingest_request_source = 'fatcat-changelog') + AND ((ingest_file_result.updated >= '2020-09-15' AND ingest_file_result.updated <= '2020-09-20') + OR (ingest_file_result.updated >= '2020-10-11')) + AND ingest_file_result.status != 'success' + AND ingest_request.base_url NOT LIKE '%journals.sagepub.com%' + AND ingest_request.base_url NOT LIKE '%pubs.acs.org%' + AND ingest_request.base_url NOT LIKE '%ahajournals.org%' + AND ingest_request.base_url NOT LIKE '%www.journal.csj.jp%' + AND ingest_request.base_url NOT LIKE '%aip.scitation.org%' + AND ingest_request.base_url NOT LIKE '%academic.oup.com%' + AND ingest_request.base_url NOT LIKE '%tandfonline.com%' + AND ingest_request.base_url NOT LIKE '%://archive.org/%' + AND ingest_request.base_url NOT LIKE '%://web.archive.org/%' + AND ingest_request.base_url NOT LIKE '%://www.archive.org/%' + AND ingest_file_result.terminal_url NOT LIKE '%journals.sagepub.com%' + AND ingest_file_result.terminal_url NOT LIKE '%pubs.acs.org%' + AND ingest_file_result.terminal_url NOT LIKE '%ahajournals.org%' + AND ingest_file_result.terminal_url NOT LIKE '%www.journal.csj.jp%' + AND ingest_file_result.terminal_url NOT LIKE '%aip.scitation.org%' + AND ingest_file_result.terminal_url NOT LIKE '%academic.oup.com%' + AND ingest_file_result.terminal_url NOT LIKE '%tandfonline.com%' + AND ingest_file_result.terminal_url NOT LIKE '%://archive.org/%' + AND ingest_file_result.terminal_url NOT LIKE '%://web.archive.org/%' + AND ingest_file_result.terminal_url NOT LIKE '%://www.archive.org/%' + ) t1 + ) TO '/grande/snapshots/oa_doi_seedlist_2020-12-08.rows.json'; + => COPY 2352614 + +Prep ingest requests (for post-crawl use): + + ./scripts/ingestrequest_row2json.py /grande/snapshots/oa_doi_seedlist_2020-12-08.rows.json | pv -l > /grande/snapshots/oa_doi_seedlist_2020-12-08.ingest_request.json + +And actually dump seedlist(s): + + cat /grande/snapshots/oa_doi_seedlist_2020-12-08.rows.json | jq -r .base_url | rg '://' | sort -u -S 4G > /grande/snapshots/oa_doi_seedlist_2020-12-08.base_url.txt + cat /grande/snapshots/oa_doi_seedlist_2020-12-08.rows.json | rg '"no-capture"' | jq -r .result.terminal_url | rg -v ^null$ | rg '://' | sort -u -S 4G > /grande/snapshots/oa_doi_seedlist_2020-12-08.no_capture_terminal_url.txt + + wc -l /grande/snapshots/oa_doi_seedlist_2020-12-08.*.txt + 2352614 /grande/snapshots/oa_doi_seedlist_2020-12-08.base_url.txt + 481910 /grande/snapshots/oa_doi_seedlist_2020-12-08.no_capture_terminal_url.txt + +Top DOI prefixes (same old usual suspects): + + cat /grande/snapshots/oa_doi_seedlist_2020-12-08.*url.txt | rg ^http | rg "://doi.org/" | cut -f4 -d/ | sort | uniq -c | sort -nr | head -n20 + 353695 10.5281 zenodo.org + 121888 10.6084 figshare.org + 115093 10.3917 cairn.info + 113252 10.3406 persee.fr + 95414 10.1515 degruyter.com + 90448 10.4324 taylorfrancis.com + 83927 10.1016 elsevier + 60303 10.1109 IEEE + 48490 10.4000 openedition.org + 28498 10.3205 egms.de + 23433 10.1163 brill.com + 23276 10.17615 cdr.lib.unc.edu + 21386 10.1093 oup.com + 20783 10.3138 utpjournals.press + 19987 10.1201 tandfonline.com + 17916 10.34847 cocoon.huma-num.fr + 16970 10.1002 wiley.com + 15958 10.1097 lww.com (and others?) + 15835 10.1017 cambridge.org + 15466 10.24355 publikationsserver.tu-braunschweig.de (IR) + +Top domains (not doi.org): + + cat /grande/snapshots/oa_doi_seedlist_2020-12-08.*url.txt | rg ^http | rg -v "://doi.org/" | cut -f3 -d/ | sort | uniq -c | sort -nr | head -n20 + 104148 zenodo.org + 85245 www.persee.fr + 52931 www.cairn.info + 4791 www.jstage.jst.go.jp + 4411 archive.monthlyreview.org + 4129 osf.io + 2841 www.indianjournals.com + 2746 www.impan.pl + 2620 platform.almanhal.com + 2019 www.nomos-elibrary.de + 1209 dergipark.org.tr + 1027 pubs.geoscienceworld.org + 973 www.pdcnet.org + 923 www.hanspub.org + 914 www.repository.cam.ac.uk + 863 mediarep.org + 812 www.cartographicperspectives.org + 687 www.degruyter.com + 578 192.168.7.24 + 566 journals.eco-vector.com + +TODO: infer `publisher_type` and platform from DOI prefix in more cases + +## Re-Ingest + +Crawl has completed. Starting this bulk ingest on 2020-12-31; roughly 2.3 +million requests. Note these are all `pdf` requests, but crawl was done in an +HTML-friendly way, so should be able to do domain/journal-specific HTML ingests +in the future. + + cat /grande/snapshots/oa_doi_seedlist_2020-12-08.ingest_request.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + +Stats, for this ingest period (fuzzy; will have some daily ingest stuff): + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'doi' + AND (ingest_request.ingest_request_source = 'fatcat-ingest' + OR ingest_request.ingest_request_source = 'fatcat-changelog') + AND ingest_file_result.updated >= '2020-12-28' + AND ingest_request.created <= '2020-12-09' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 30; + + status | count + -----------------------+-------- + no-pdf-link | 962714 + success | 539305 + no-capture | 306590 + redirect-loop | 192149 + link-loop | 184797 + terminal-bad-status | 141721 + wrong-mimetype | 10362 + null-body | 10277 + skip-url-blocklist | 1985 + wayback-content-error | 1300 + cdx-error | 869 + petabox-error | 160 + bad-redirect | 72 + wayback-error | 46 + bad-gzip-encoding | 7 + timeout | 1 + max-hops-exceeded | 1 + (17 rows) + diff --git a/notes/ingest/2020-09_reingest.md b/notes/ingest/2020-09_reingest.md new file mode 100644 index 0000000..ec4e536 --- /dev/null +++ b/notes/ingest/2020-09_reingest.md @@ -0,0 +1,197 @@ + +Goal: re-bulk-ingest some older existing crawls which hung on errors like +`cdx-error` or `wayback-error`, indicating that ingest might actually succeed +on retry. + +Sources: +- unpaywall (again) +- doi (ingest, changelog, etc) +- mag +- oai + +## DOI + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'doi' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 25; + + status | count + -------------------------------------+--------- + no-pdf-link | 8304582 + success | 3461708 + no-capture | 1881269 + redirect-loop | 1851541 + gateway-timeout | 355820 + cdx-error | 341848 + terminal-bad-status | 328650 + skip-url-blocklist | 220474 + spn2-cdx-lookup-failure | 125521 + link-loop | 109352 + wayback-error | 101525 + null-body | 73539 + wrong-mimetype | 53151 + spn-error | 13579 + spn2-error | 6848 + spn2-error:job-failed | 4381 + spn-remote-error | 4180 + other-mimetype | 2305 + petabox-error | 904 + timeout | 710 + spn2-error:soft-time-limit-exceeded | 557 + spn2-error:proxy-error | 437 + spn2-error:browser-running-error | 273 + invalid-host-resolution | 233 + pending | 116 + (25 rows) + +Bulk: + + COPY ( + SELECT row_to_json(ingest_request.*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'doi' + AND ( + ingest_file_result.status = 'cdx-error' OR + ingest_file_result.status = 'wayback-error' + ) + ) TO '/grande/snapshots/ingest_doi_errors_2020-09-03.rows.json'; + => 443421 + + ./scripts/ingestrequest_row2json.py /grande/snapshots/ingest_doi_errors_2020-09-03.rows.json | pv -l | shuf > /grande/snapshots/ingest_doi_errors_2020-09-03.requests.json + + cat /grande/snapshots/ingest_doi_errors_2020-09-03.requests.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + => done + +Additional 27,779 success status? Hard to tell because lots of other ingest +running in parallel. + +Live: + + COPY ( + SELECT row_to_json(ingest_request.*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'doi' + AND ( + ingest_file_result.status = 'spn-error' OR + ingest_file_result.status = 'spn2-cdx-lookup-failure' OR + ingest_file_result.status = 'spn2-error:job-failed' OR + ingest_file_result.status = 'spn2-error:proxy-error' + ) + ) TO '/grande/snapshots/ingest_doi_spn_errors_2020-09-03.rows.json'; + => 143984 + + ./scripts/ingestrequest_row2json.py /grande/snapshots/ingest_doi_spn_errors_2020-09-03.rows.json | pv -l | shuf > /grande/snapshots/ingest_doi_errors_2020-09-03.requests.json + + cat /grande/snapshots/ingest_doi_spn_errors_2020-09-03.requests.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests -p -1 + +## Unpaywall (again) + +Bulk: + + COPY ( + SELECT row_to_json(ingest_request.*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + AND ( + ingest_file_result.status = 'cdx-error' OR + ingest_file_result.status = 'wayback-error' + ) + ) TO '/grande/snapshots/ingest_unpaywall_errors_2020-09-03.rows.json'; + => 43912 + + ./scripts/ingestrequest_row2json.py /grande/snapshots/ingest_unpaywall_errors_2020-09-03.rows.json | pv -l | shuf > /grande/snapshots/ingest_unpaywall_errors_2020-09-03.requests.json + + cat /grande/snapshots/ingest_unpaywall_errors_2020-09-03.requests.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + => done + +## MAG + + COPY ( + SELECT row_to_json(ingest_request.*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'mag' + AND ( + ingest_file_result.status = 'cdx-error' OR + ingest_file_result.status = 'wayback-error' + ) + ) TO '/grande/snapshots/ingest_mag_errors_2020-09-03.rows.json'; + => 188175 + + ./scripts/ingestrequest_row2json.py /grande/snapshots/ingest_mag_errors_2020-09-03.rows.json | pv -l | shuf > /grande/snapshots/ingest_mag_errors_2020-09-03.requests.json + + cat /grande/snapshots/ingest_mag_errors_2020-09-03.requests.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + => done + +## OAI-PMH + + COPY ( + SELECT row_to_json(ingest_request.*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'oai' + AND ( + ingest_file_result.status = 'cdx-error' OR + ingest_file_result.status = 'wayback-error' + ) + ) TO '/grande/snapshots/ingest_oai_errors_2020-09-03.rows.json'; + => 851056 + + ./scripts/ingestrequest_row2json.py /grande/snapshots/ingest_oai_errors_2020-09-03.rows.json | pv -l | shuf > /grande/snapshots/ingest_oai_errors_2020-09-03.requests.json + + cat /grande/snapshots/ingest_oai_errors_2020-09-03.requests.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + => done + +--------- + + COPY ( + SELECT row_to_json(ingest_request.*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + AND date(ingest_request.created) > '2020-04-01' + AND ingest_file_result.status = 'no-capture' + AND ingest_request.base_url NOT LIKE '%journals.sagepub.com%' + AND ingest_request.base_url NOT LIKE '%pubs.acs.org%' + AND ingest_request.base_url NOT LIKE '%ahajournals.org%' + AND ingest_request.base_url NOT LIKE '%www.journal.csj.jp%' + AND ingest_request.base_url NOT LIKE '%aip.scitation.org%' + AND ingest_request.base_url NOT LIKE '%academic.oup.com%' + AND ingest_request.base_url NOT LIKE '%tandfonline.com%' + ) TO '/grande/snapshots/unpaywall_nocapture_2020-05-04.rows.json'; + diff --git a/notes/ingest/2020-09_scielo.md b/notes/ingest/2020-09_scielo.md new file mode 100644 index 0000000..4ec6fbd --- /dev/null +++ b/notes/ingest/2020-09_scielo.md @@ -0,0 +1,21 @@ + +As a follow-up to `SCIELO-CRAWL-2020-07`, going to bulk ingest all existing +fatcat releases with no IA copy and with `publisher_type:scielo`. There are +200k+ such releases. + +It seems like some of these are HTML or XML, eg: https://doi.org/10.4321/s1132-12962011000300008 + +Could try XML ingest of these! + +## Bulk Ingest + +Dump ingest requests + + ./fatcat_ingest.py --allow-non-oa query "publisher_type:scielo" | pv -l > /srv/fatcat/snapshots/scielo_papers_20200914.ingest_request.json + Expecting 212529 release objects in search queries + +Enqueue + + cat /srv/fatcat/snapshots/scielo_papers_20200914.ingest_request.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + => done 2020-09-14 + diff --git a/notes/ingest/2020-10_daily.md b/notes/ingest/2020-10_daily.md new file mode 100644 index 0000000..d2bb50b --- /dev/null +++ b/notes/ingest/2020-10_daily.md @@ -0,0 +1,193 @@ + +Quick notes on how daily ingest is going, circa September/October 2020. + + + SELECT ingest_request.ingest_type, + date(ingest_request.created), + COUNT(*) as total, + COUNT(CASE ingest_file_result.status WHEN 'success' THEN 1 ELSE null END) as success + FROM ingest_file_result + LEFT JOIN ingest_request + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE ingest_request.created >= NOW() - '1 month'::INTERVAL + AND ingest_request.ingest_type = 'pdf' + AND ingest_request.ingest_request_source = 'fatcat-changelog' + GROUP BY ingest_request.ingest_type, ingest_file_result.ingest_type, date(ingest_request.created) + ORDER BY date(ingest_request.created) DESC; + + ingest_type | date | total | success + -------------+------------+-------+--------- + pdf | 2020-10-10 | 6145 | 1368 + pdf | 2020-10-09 | 28453 | 6461 + pdf | 2020-10-08 | 15105 | 3803 + pdf | 2020-10-07 | 34213 | 10813 + pdf | 2020-10-06 | 22263 | 8565 + pdf | 2020-10-05 | 7910 | 3200 + pdf | 2020-10-04 | 10865 | 4579 + pdf | 2020-10-03 | 27745 | 10818 + pdf | 2020-10-02 | 34320 | 13523 + pdf | 2020-10-01 | 32548 | 13252 + pdf | 2020-09-30 | 34798 | 14113 + pdf | 2020-09-29 | 22463 | 8328 + pdf | 2020-09-28 | 4117 | 1278 + pdf | 2020-09-27 | 5894 | 1732 + pdf | 2020-09-26 | 34949 | 13901 + pdf | 2020-09-25 | 33680 | 10605 + pdf | 2020-09-24 | 15125 | 5785 + pdf | 2020-09-23 | 20866 | 6584 + pdf | 2020-09-22 | 20949 | 7167 + pdf | 2020-09-21 | 22483 | 7308 + pdf | 2020-09-20 | 45644 | 16981 + pdf | 2020-09-19 | 95571 | 31991 + pdf | 2020-09-18 | 50849 | 15875 + pdf | 2020-09-17 | 20121 | 3158 + pdf | 2020-09-16 | 39184 | 12150 + pdf | 2020-09-15 | 16986 | 7705 + (26 rows) + + + SELECT ingest_file_result.ingest_type, ingest_file_result.status, COUNT(*) + FROM ingest_file_result + LEFT JOIN ingest_request + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE ingest_request.created >= NOW() - '30 day'::INTERVAL + AND ingest_request.ingest_type = 'pdf' + AND ingest_request.ingest_request_source = 'fatcat-changelog' + GROUP BY ingest_file_result.ingest_type, ingest_file_result.status + ORDER BY COUNT DESC + LIMIT 20; + + ingest_type | status | count + -------------+-------------------------------------+-------- + pdf | success | 241047 + pdf | no-pdf-link | 143084 + pdf | spn2-cdx-lookup-failure | 108311 + pdf | gateway-timeout | 97250 + pdf | cdx-error | 61820 + pdf | link-loop | 31350 + pdf | wayback-error | 9139 + pdf | spn2-error:job-failed | 4240 + pdf | spn2-error | 3893 + pdf | wrong-mimetype | 1010 + pdf | no-capture | 851 + pdf | null-body | 605 + pdf | redirect-loop | 261 + pdf | spn2-error:soft-time-limit-exceeded | 126 + pdf | terminal-bad-status | 120 + pdf | petabox-error | 105 + pdf | timeout | 29 + pdf | spn2-error:no-status | 2 + pdf | spn2-error:invalid-server-response | 2 + pdf | bad-gzip-encoding | 1 + (20 rows) + + SELECT domain, status, COUNT((domain, status)) + FROM ( + SELECT + ingest_file_result.ingest_type, + ingest_file_result.status, + substring(ingest_file_result.terminal_url FROM '[^/]+://([^/]*)') AS domain + FROM ingest_file_result + LEFT JOIN ingest_request + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + -- ingest_request.created >= NOW() - '3 day'::INTERVAL + ingest_file_result.updated >= NOW() - '30 day'::INTERVAL + AND ingest_request.ingest_type = 'pdf' + AND ingest_request.ingest_request_source = 'fatcat-changelog' + ) t1 + WHERE t1.domain != '' + AND t1.status != 'success' + GROUP BY domain, status + ORDER BY COUNT DESC + LIMIT 25; + + + domain | status | count + ------------------------------+-------------------------+------- + zenodo.org | no-pdf-link | 52767 + www.degruyter.com | link-loop | 17666 + www.degruyter.com | spn2-cdx-lookup-failure | 17597 + ieeexplore.ieee.org | gateway-timeout | 15290 + www.sciencedirect.com | no-pdf-link | 14043 + apps.crossref.org | no-pdf-link | 11531 + figshare.com | no-pdf-link | 8966 + tandf.figshare.com | no-pdf-link | 7276 + zenodo.org | no-capture | 7191 + springernature.figshare.com | no-pdf-link | 6485 + www.taylorfrancis.com | link-loop | 6266 + www.persee.fr | terminal-bad-status | 6031 + journals.openedition.org | gateway-timeout | 5639 + www.cairn.info | link-loop | 5618 + archaeologydataservice.ac.uk | no-pdf-link | 5359 + www.taylorfrancis.com | spn2-cdx-lookup-failure | 4748 + www.e-periodica.ch | no-pdf-link | 4722 + osf.io | no-capture | 4247 + cancerres.aacrjournals.org | no-pdf-link | 4136 + dlc.library.columbia.edu | no-pdf-link | 4085 + www.egms.de | no-pdf-link | 3304 + journals.lww.com | no-pdf-link | 3218 + journals.plos.org | no-pdf-link | 3005 + linkinghub.elsevier.com | gateway-timeout | 2833 + www.egms.de | redirect-loop | 2606 + (25 rows) + + SELECT domain, status, COUNT((domain, status)) + FROM ( + SELECT + ingest_file_result.ingest_type, + ingest_file_result.status, + substring(ingest_file_result.terminal_url FROM '[^/]+://([^/]*)') AS domain + FROM ingest_file_result + LEFT JOIN ingest_request + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + -- ingest_request.created >= NOW() - '3 day'::INTERVAL + ingest_file_result.updated >= NOW() - '30 day'::INTERVAL + AND ingest_request.ingest_type = 'pdf' + AND ingest_request.ingest_request_source = 'fatcat-changelog' + ) t1 + WHERE t1.domain != '' + AND t1.status = 'success' + GROUP BY domain, status + ORDER BY COUNT DESC + LIMIT 25; + + domain | status | count + --------------------------------------+---------+------- + zenodo.org | success | 55549 + arxiv.org | success | 24450 + s3-eu-west-1.amazonaws.com | success | 18156 + res.mdpi.com | success | 13493 + www.degruyter.com | success | 12009 + journals.openedition.org | success | 11235 + www.jstage.jst.go.jp | success | 9460 + peer.asee.org | success | 9416 + www.e-periodica.ch | success | 8105 + ir.canterbury.ac.nz | success | 6381 + europepmc.org | success | 5670 + www.repository.cam.ac.uk | success | 4858 + assets.researchsquare.com | success | 4765 + fjfsdata01prod.blob.core.windows.net | success | 4130 + tidsskrift.dk | success | 3964 + research-journal.org | success | 3127 + ieeexplore.ieee.org | success | 2947 + dergipark.org.tr | success | 2892 + watermark.silverchair.com | success | 2315 + journals.plos.org | success | 2304 + journal.fi | success | 1996 + publications.rwth-aachen.de | success | 1954 + www.brazilianjournals.com | success | 1637 + article.sciencepublishinggroup.com | success | 1589 + revistas.upr.edu | success | 1467 + (25 rows) + +Casual take-aways: +- wonder what `apps.crossref.org` is +- sciencedirect crawling broken? +- figshare might be broken? or just very little success +- seems like a lot of journals.plos.org failures diff --git a/notes/ingest/2020-10_unpaywall.md b/notes/ingest/2020-10_unpaywall.md new file mode 100644 index 0000000..a991025 --- /dev/null +++ b/notes/ingest/2020-10_unpaywall.md @@ -0,0 +1,286 @@ + +New snapshot released 2020-10-09. Want to do a mostly straight-forward +load/ingest/crawl. + +Proposed changes this time around: + +- have bulk ingest store missing URLs in a new sandcrawler-db for `no-capture` + status, and to include those URLs in heritrix3 crawl +- tweak heritrix3 config for additional PDF URL extraction patterns, + particularly to improve OJS yield + + +## Transform and Load + + # in sandcrawler pipenv on aitio + zcat /schnell/unpaywall/unpaywall_snapshot_2020-10-09T153852.jsonl.gz | ./scripts/unpaywall2ingestrequest.py - | pv -l > /grande/snapshots/unpaywall_snapshot_2020-10-09.ingest_request.json + => 28.3M 3:19:03 [2.37k/s] + + cat /grande/snapshots/unpaywall_snapshot_2020-04-27.ingest_request.json | pv -l | ./persist_tool.py ingest-request - + => 28.3M 1:11:29 [ 6.6k/s] + => Worker: Counter({'total': 28298500, 'insert-requests': 4119939, 'update-requests': 0}) + => JSON lines pushed: Counter({'total': 28298500, 'pushed': 28298500}) + +## Dump new URLs, Transform, Bulk Ingest + + COPY ( + SELECT row_to_json(ingest_request.*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + -- AND date(ingest_request.created) > '2020-10-09' + AND (ingest_file_result.status IS NULL + OR ingest_file_result.status = 'no-capture') + ) TO '/grande/snapshots/unpaywall_noingest_2020-10-09.rows.json'; + => COPY 4216339 + + ./scripts/ingestrequest_row2json.py /grande/snapshots/unpaywall_noingest_2020-10-09.rows.json | pv -l | shuf > /grande/snapshots/unpaywall_noingest_2020-10-09.ingest_request.json + => 4.22M 0:02:48 [ 25k/s] + +Start small, to test no-capture behavior: + + cat /grande/snapshots/unpaywall_noingest_2020-10-09.ingest_request.json | head -n1000 | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + +`no-capture` change looks good. Enqueue the whole batch: + + cat /grande/snapshots/unpaywall_noingest_2020-10-09.ingest_request.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + + +## Check Pre-Crawl Status + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + + status | count + -------------------------+---------- + success | 23661282 + no-capture | 3015447 + no-pdf-link | 2302102 + redirect-loop | 1542566 + terminal-bad-status | 1044676 + wrong-mimetype | 114315 + link-loop | 36358 + cdx-error | 20150 + null-body | 14513 + wayback-error | 13644 + gateway-timeout | 3776 + spn2-cdx-lookup-failure | 1260 + petabox-error | 1171 + redirects-exceeded | 752 + invalid-host-resolution | 464 + spn2-error | 147 + bad-redirect | 131 + spn2-error:job-failed | 91 + wayback-content-error | 45 + timeout | 19 + (20 rows) + +## Dump Seedlist + +Dump rows: + + COPY ( + SELECT row_to_json(t1.*) + FROM ( + SELECT ingest_request.*, ingest_file_result as result + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + AND (ingest_file_result.status = 'no-capture' + OR ingest_file_result.status = 'cdx-error' + OR ingest_file_result.status = 'wayback-error' + OR ingest_file_result.status = 'gateway-timeout' + OR ingest_file_result.status = 'spn2-cdx-lookup-failure' + ) + AND ingest_request.base_url NOT LIKE '%journals.sagepub.com%' + AND ingest_request.base_url NOT LIKE '%pubs.acs.org%' + AND ingest_request.base_url NOT LIKE '%ahajournals.org%' + AND ingest_request.base_url NOT LIKE '%www.journal.csj.jp%' + AND ingest_request.base_url NOT LIKE '%aip.scitation.org%' + AND ingest_request.base_url NOT LIKE '%academic.oup.com%' + AND ingest_request.base_url NOT LIKE '%tandfonline.com%' + AND ingest_file_result.terminal_url NOT LIKE '%journals.sagepub.com%' + AND ingest_file_result.terminal_url NOT LIKE '%pubs.acs.org%' + AND ingest_file_result.terminal_url NOT LIKE '%ahajournals.org%' + AND ingest_file_result.terminal_url NOT LIKE '%www.journal.csj.jp%' + AND ingest_file_result.terminal_url NOT LIKE '%aip.scitation.org%' + AND ingest_file_result.terminal_url NOT LIKE '%academic.oup.com%' + AND ingest_file_result.terminal_url NOT LIKE '%tandfonline.com%' + ) t1 + ) TO '/grande/snapshots/unpaywall_seedlist_2020-11-02.rows.json'; + => 2,936,404 + + # TODO: in the future also exclude "www.archive.org" + +Prep ingest requests (for post-crawl use): + + ./scripts/ingestrequest_row2json.py /grande/snapshots/unpaywall_seedlist_2020-11-02.rows.json | pv -l > /grande/snapshots/unpaywall_crawl_ingest_2020-11-02.json + +And actually dump seedlist(s): + + cat /grande/snapshots/unpaywall_seedlist_2020-11-02.rows.json | jq -r .base_url | sort -u -S 4G > /grande/snapshots/unpaywall_seedlist_2020-11-02.url.txt + cat /grande/snapshots/unpaywall_seedlist_2020-11-02.rows.json | rg '"no-capture"' | jq -r .result.terminal_url | rg -v ^null$ | sort -u -S 4G > /grande/snapshots/unpaywall_seedlist_2020-11-02.terminal_url.txt + cat /grande/snapshots/unpaywall_seedlist_2020-11-02.rows.json | rg -v '"no-capture"' | jq -r .base_url | sort -u -S 4G > /grande/snapshots/unpaywall_seedlist_2020-11-02.no_terminal_url.txt + + wc -l unpaywall_seedlist_2020-11-02.*.txt + 2701178 unpaywall_seedlist_2020-11-02.terminal_url.txt + 2713866 unpaywall_seedlist_2020-11-02.url.txt + +With things like jsessionid, suspect that crawling just the terminal URLs is +going to work better than both full and terminal. + +Finding a fraction of `no-capture` which have partial/stub URLs as terminal. + +TODO: investigate scale of partial/stub `terminal_url` (eg, not HTTP/S or FTP). + + +## Bulk Ingest and Status + +Note, removing archive.org links: + + cat /grande/snapshots/unpaywall_crawl_ingest_2020-11-02.json | rg -v www.archive.org | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + +Overall status (checked 2020-12-08): + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + status | count + -------------------------+---------- + success | 25004559 + no-pdf-link | 2531841 + redirect-loop | 1671375 + terminal-bad-status | 1389463 + no-capture | 893880 + wrong-mimetype | 119332 + link-loop | 66508 + wayback-content-error | 30339 + cdx-error | 21790 + null-body | 20710 + wayback-error | 13976 + gateway-timeout | 3775 + petabox-error | 2420 + spn2-cdx-lookup-failure | 1218 + redirects-exceeded | 889 + invalid-host-resolution | 464 + bad-redirect | 147 + spn2-error | 112 + spn2-error:job-failed | 91 + timeout | 21 + (20 rows) + +Ingest stats broken down by publication stage: + + SELECT ingest_request.release_stage, ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + GROUP BY release_stage, status + ORDER BY release_stage, COUNT DESC + LIMIT 100; + + + release_stage | status | count + ---------------+-------------------------------------+---------- + accepted | success | 1101090 + accepted | no-pdf-link | 28590 + accepted | redirect-loop | 10923 + accepted | no-capture | 9540 + accepted | terminal-bad-status | 6339 + accepted | cdx-error | 952 + accepted | wrong-mimetype | 447 + accepted | link-loop | 275 + accepted | wayback-error | 202 + accepted | petabox-error | 177 + accepted | redirects-exceeded | 122 + accepted | null-body | 27 + accepted | wayback-content-error | 14 + accepted | spn2-cdx-lookup-failure | 5 + accepted | gateway-timeout | 4 + accepted | bad-redirect | 1 + published | success | 18595278 + published | no-pdf-link | 2434935 + published | redirect-loop | 1364110 + published | terminal-bad-status | 1185328 + published | no-capture | 718792 + published | wrong-mimetype | 112923 + published | link-loop | 63874 + published | wayback-content-error | 30268 + published | cdx-error | 17302 + published | null-body | 15209 + published | wayback-error | 10782 + published | gateway-timeout | 1966 + published | petabox-error | 1611 + published | spn2-cdx-lookup-failure | 879 + published | redirects-exceeded | 760 + published | invalid-host-resolution | 453 + published | bad-redirect | 115 + published | spn2-error:job-failed | 77 + published | spn2-error | 75 + published | timeout | 21 + published | bad-gzip-encoding | 5 + published | spn2-error:soft-time-limit-exceeded | 4 + published | spn2-error:pending | 1 + published | blocked-cookie | 1 + published | | 1 + published | pending | 1 + submitted | success | 5308166 + submitted | redirect-loop | 296322 + submitted | terminal-bad-status | 197785 + submitted | no-capture | 165545 + submitted | no-pdf-link | 68274 + submitted | wrong-mimetype | 5962 + submitted | null-body | 5474 + submitted | cdx-error | 3536 + submitted | wayback-error | 2992 + submitted | link-loop | 2359 + submitted | gateway-timeout | 1805 + submitted | petabox-error | 632 + submitted | spn2-cdx-lookup-failure | 334 + submitted | wayback-content-error | 57 + submitted | spn2-error | 37 + submitted | bad-redirect | 31 + submitted | spn2-error:job-failed | 14 + submitted | | 12 + submitted | invalid-host-resolution | 11 + submitted | redirects-exceeded | 7 + submitted | spn2-error:soft-time-limit-exceeded | 5 + submitted | bad-gzip-encoding | 1 + submitted | skip-url-blocklist | 1 + | no-pdf-link | 42 + | success | 25 + | redirect-loop | 20 + | terminal-bad-status | 11 + | no-capture | 3 + (70 rows) diff --git a/notes/ingest/2020-11-04_arxiv.md b/notes/ingest/2020-11-04_arxiv.md new file mode 100644 index 0000000..f9abe09 --- /dev/null +++ b/notes/ingest/2020-11-04_arxiv.md @@ -0,0 +1,12 @@ + +Ran a bulk dump using fatcat ingest tool several months ago, and had Martin run +a crawl. + +Crawl is now done, so going to ingest, hoping to get the majority of the +millions of remaining arxiv.org PDFs. + + zcat /grande/snapshots/fatcat_missing_arxiv_ingest_request.2020-08-21.json.gz | wc -l + => 1,288,559 + + zcat /grande/snapshots/fatcat_missing_arxiv_ingest_request.2020-08-21.json.gz | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + diff --git a/notes/ingest/2020-11_doaj.md b/notes/ingest/2020-11_doaj.md new file mode 100644 index 0000000..473dd0d --- /dev/null +++ b/notes/ingest/2020-11_doaj.md @@ -0,0 +1,295 @@ + +This is the first ingest (and crawl) of URLs from DOAJ article-level metadata. +It will include at least 'pdf' and 'html' ingest requests, not just 'pdf' as in +the past. + +Working off a 2020-11-13 snapshot. + +## Transform and Load + + # in sandcrawler pipenv on aitio + zcat /schnell/DOAJ-CRAWL-2020-11/doaj_article_data_2020-11-13_all.json.gz | ./scripts/doaj2ingestrequest.py - | pv -l > /schnell/DOAJ-CRAWL-2020-11/doaj_20201113.ingest_request.json + => 6.7M 0:24:28 [4.57k/s] + + cat /schnell/DOAJ-CRAWL-2020-11/doaj_20201113.ingest_request.json | pv -l | ./persist_tool.py ingest-request - + => ran in to error with blank `base_url` + +Second try after patches: + + zcat /schnell/DOAJ-CRAWL-2020-11/doaj_article_data_2020-11-13_all.json.gz | ./scripts/doaj2ingestrequest.py - | pv -l > /schnell/DOAJ-CRAWL-2020-11/doaj_20201113.ingest_request.json + => 6.7M 0:24:29 [4.56k/s] + + cat /schnell/DOAJ-CRAWL-2020-11/doaj_20201113.ingest_request.json | pv -l | ./persist_tool.py ingest-request - + => Worker: Counter({'total': 6703036, 'insert-requests': 163854, 'update-requests': 0}) + => JSON lines pushed: Counter({'total': 6703036, 'pushed': 6703036}) + +## Check Pre-Crawl Status + + SELECT ingest_request.ingest_type, ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.link_source = 'doaj' + GROUP BY ingest_request.ingest_type, status + -- next time include ingest_type in sort + ORDER BY COUNT DESC + LIMIT 30; + + + ingest_type | status | count + -------------+-------------------------+--------- + pdf | | 3711532 + html | | 2429003 + pdf | success | 454403 + pdf | redirect-loop | 48587 + pdf | no-pdf-link | 24901 + pdf | no-capture | 11569 + xml | | 9442 + pdf | link-loop | 8466 + pdf | terminal-bad-status | 2015 + pdf | wrong-mimetype | 1441 + pdf | null-body | 1057 + pdf | petabox-error | 299 + pdf | cdx-error | 124 + pdf | gateway-timeout | 114 + pdf | wayback-error | 77 + pdf | spn2-cdx-lookup-failure | 20 + pdf | invalid-host-resolution | 4 + pdf | spn2-error | 1 + (18 rows) + +## Dump new URLs, Transform, Bulk Ingest (PDF and XML only) + +Dump: + + COPY ( + SELECT row_to_json(ingest_request.*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.base_url = ingest_request.base_url + AND ingest_file_result.ingest_type = ingest_request.ingest_type + WHERE + (ingest_request.ingest_type = 'pdf' + OR ingest_request.ingest_type = 'xml') + AND ingest_request.link_source = 'doaj' + -- AND date(ingest_request.created) > '2020-12-01' + AND (ingest_file_result.status IS NULL + OR ingest_file_result.status = 'no-capture') + ) TO '/grande/snapshots/doaj_noingest_2020-11-19.rows.json'; + => COPY 3732543 + +Transform: + + ./scripts/ingestrequest_row2json.py /grande/snapshots/doaj_noingest_2020-11-19.rows.json | pv -l | shuf > /grande/snapshots/doaj_noingest_2020-11-19.ingest_request.json + => 3.73M 0:02:18 [26.9k/s] + +Definitely some non-URL strings in there; should try to filter those out +earlier in the transform process. And/or have a constraint on the URL column in +the database. + +Enqueue the whole batch: + + cat /grande/snapshots/doaj_noingest_2020-11-19.ingest_request.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + +Started this batch off at 2020-11-19 18:10 (Pacific time) + +Stats after run: + + SELECT ingest_request.ingest_type, ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.link_source = 'doaj' + GROUP BY ingest_request.ingest_type, status + ORDER BY ingest_request.ingest_type, COUNT DESC + LIMIT 30; + +## Dump Seedlist + +After preliminary bulk ingest attempts, dump rows: + + COPY ( + SELECT row_to_json(t1.*) + FROM ( + SELECT ingest_request.*, ingest_file_result as result + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.base_url = ingest_request.base_url + AND ingest_file_result.ingest_type = ingest_request.ingest_type + WHERE + ingest_request.link_source = 'doaj' + AND (ingest_request.ingest_type = 'pdf' + OR ingest_request.ingest_type = 'xml') + AND ingest_file_result.status != 'success' + AND ingest_request.base_url NOT LIKE '%journals.sagepub.com%' + AND ingest_request.base_url NOT LIKE '%pubs.acs.org%' + AND ingest_request.base_url NOT LIKE '%ahajournals.org%' + AND ingest_request.base_url NOT LIKE '%www.journal.csj.jp%' + AND ingest_request.base_url NOT LIKE '%aip.scitation.org%' + AND ingest_request.base_url NOT LIKE '%academic.oup.com%' + AND ingest_request.base_url NOT LIKE '%tandfonline.com%' + AND ingest_request.base_url NOT LIKE '%://archive.org/%' + AND ingest_request.base_url NOT LIKE '%://web.archive.org/%' + AND ingest_request.base_url NOT LIKE '%://www.archive.org/%' + AND ingest_file_result.terminal_url NOT LIKE '%journals.sagepub.com%' + AND ingest_file_result.terminal_url NOT LIKE '%pubs.acs.org%' + AND ingest_file_result.terminal_url NOT LIKE '%ahajournals.org%' + AND ingest_file_result.terminal_url NOT LIKE '%www.journal.csj.jp%' + AND ingest_file_result.terminal_url NOT LIKE '%aip.scitation.org%' + AND ingest_file_result.terminal_url NOT LIKE '%academic.oup.com%' + AND ingest_file_result.terminal_url NOT LIKE '%tandfonline.com%' + AND ingest_file_result.terminal_url NOT LIKE '%://archive.org/%' + AND ingest_file_result.terminal_url NOT LIKE '%://web.archive.org/%' + AND ingest_file_result.terminal_url NOT LIKE '%://www.archive.org/%' + ) t1 + ) TO '/grande/snapshots/doaj_seedlist_2020-11-19.rows.json'; + => 1,899,555 + +TODO: filter for valid URLs + +Prep ingest requests (for post-crawl use): + + ./scripts/ingestrequest_row2json.py /grande/snapshots/doaj_seedlist_2020-11-19.rows.json | pv -l > /grande/snapshots/doaj_crawl_ingest_2020-11-19.json + +And actually dump seedlist(s): + + cat /grande/snapshots/doaj_seedlist_2020-11-19.rows.json | jq -r .base_url | sort -u -S 4G > /grande/snapshots/doaj_seedlist_2020-11-19.url.txt + cat /grande/snapshots/doaj_seedlist_2020-11-19.rows.json | rg '"no-capture"' | jq -r .result.terminal_url | rg -v ^null$ | sort -u -S 4G > /grande/snapshots/doaj_seedlist_2020-11-19.terminal_url.txt + cat /grande/snapshots/doaj_seedlist_2020-11-19.rows.json | rg -v '"no-capture"' | jq -r .base_url | sort -u -S 4G > /grande/snapshots/doaj_seedlist_2020-11-19.no_terminal_url.txt + + wc -l doaj_seedlist_2020-11-19.*.txt + +## Post-Crawl Ingest + +Re-run all ingests, from original batch (pdf, xml, and html), now that DOAJ +identifiers are all in fatcat: + + cat /schnell/DOAJ-CRAWL-2020-11/doaj_20201113.ingest_request.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + + # started 2020-12-23 15:05 (Pacific) + # finished around 2020-12-31, after one long/slow partition + +Stats again after everything: + + SELECT ingest_request.ingest_type, ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.link_source = 'doaj' + GROUP BY ingest_request.ingest_type, status + ORDER BY ingest_request.ingest_type, COUNT DESC + LIMIT 50; + + ingest_type | status | count + -------------+--------------------------+--------- + html | wrong-scope | 1089423 + html | no-capture | 423917 + html | redirect-loop | 212910 + html | unknown-scope | 204069 + html | html-resource-no-capture | 165587 + html | success | 122937 + html | null-body | 100296 + html | wayback-content-error | 53918 + html | wrong-mimetype | 18908 + html | terminal-bad-status | 14059 + html | petabox-error | 13520 + html | cdx-error | 6823 + html | wayback-error | 890 + html | | 620 + html | blocked-cookie | 543 + html | blocked-captcha | 250 + html | redirects-exceeded | 135 + html | too-many-resources | 111 + html | max-hops-exceeded | 84 + html | bad-redirect | 3 + pdf | success | 2851324 + pdf | no-pdf-link | 529914 + pdf | redirect-loop | 349494 + pdf | no-capture | 272202 + pdf | null-body | 129027 + pdf | terminal-bad-status | 91796 + pdf | link-loop | 25267 + pdf | wrong-mimetype | 6504 + pdf | wayback-error | 2968 + pdf | | 2068 + pdf | wayback-content-error | 1548 + pdf | cdx-error | 1095 + pdf | petabox-error | 1024 + pdf | bad-redirect | 203 + pdf | redirects-exceeded | 135 + pdf | timeout | 20 + pdf | max-hops-exceeded | 19 + pdf | bad-gzip-encoding | 2 + xml | success | 6897 + xml | null-body | 2353 + xml | wrong-mimetype | 184 + xml | no-capture | 5 + xml | cdx-error | 3 + (43 rows) + + +And on filtered subset that we actually crawled: + + SELECT ingest_request.ingest_type, ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.link_source = 'doaj' + AND (ingest_request.ingest_type = 'pdf' + OR ingest_request.ingest_type = 'xml') + AND ingest_request.base_url NOT LIKE '%journals.sagepub.com%' + AND ingest_request.base_url NOT LIKE '%pubs.acs.org%' + AND ingest_request.base_url NOT LIKE '%ahajournals.org%' + AND ingest_request.base_url NOT LIKE '%www.journal.csj.jp%' + AND ingest_request.base_url NOT LIKE '%aip.scitation.org%' + AND ingest_request.base_url NOT LIKE '%academic.oup.com%' + AND ingest_request.base_url NOT LIKE '%tandfonline.com%' + AND ingest_request.base_url NOT LIKE '%://archive.org/%' + AND ingest_request.base_url NOT LIKE '%://web.archive.org/%' + AND ingest_request.base_url NOT LIKE '%://www.archive.org/%' + AND ingest_file_result.terminal_url NOT LIKE '%journals.sagepub.com%' + AND ingest_file_result.terminal_url NOT LIKE '%pubs.acs.org%' + AND ingest_file_result.terminal_url NOT LIKE '%ahajournals.org%' + AND ingest_file_result.terminal_url NOT LIKE '%www.journal.csj.jp%' + AND ingest_file_result.terminal_url NOT LIKE '%aip.scitation.org%' + AND ingest_file_result.terminal_url NOT LIKE '%academic.oup.com%' + AND ingest_file_result.terminal_url NOT LIKE '%tandfonline.com%' + AND ingest_file_result.terminal_url NOT LIKE '%://archive.org/%' + AND ingest_file_result.terminal_url NOT LIKE '%://web.archive.org/%' + AND ingest_file_result.terminal_url NOT LIKE '%://www.archive.org/%' + GROUP BY ingest_request.ingest_type, status + ORDER BY ingest_request.ingest_type, COUNT DESC + LIMIT 50; + + ingest_type | status | count + -------------+-----------------------+--------- + pdf | success | 2851286 + pdf | no-pdf-link | 527495 + pdf | redirect-loop | 345138 + pdf | no-capture | 268140 + pdf | null-body | 129027 + pdf | terminal-bad-status | 91125 + pdf | link-loop | 25267 + pdf | wrong-mimetype | 6504 + pdf | wayback-error | 2907 + pdf | petabox-error | 363 + pdf | wayback-content-error | 242 + pdf | bad-redirect | 203 + pdf | redirects-exceeded | 135 + pdf | max-hops-exceeded | 19 + pdf | cdx-error | 15 + pdf | bad-gzip-encoding | 2 + xml | success | 6897 + xml | null-body | 2353 + xml | wrong-mimetype | 184 + xml | no-capture | 5 + (20 rows) + diff --git a/notes/ingest/2020-12-08_patch_crawl_notes.md b/notes/ingest/2020-12-08_patch_crawl_notes.md new file mode 100644 index 0000000..5979753 --- /dev/null +++ b/notes/ingest/2020-12-08_patch_crawl_notes.md @@ -0,0 +1,111 @@ + +Notes here about re-ingesting or re-crawling large batches. Goal around end of +2020 is to generate a broad patch crawl of terminal no-capture attempts for all +major sources crawled thus far. Have already tried run this process for unpaywall. + +For each, want filtered ingest request JSON objects (filtering out platforms +that don't crawl well, and possibly things like figshare+zenodo), and a broader +seedlist (including terminal URLs). Will de-dupe all the seedlist URLs and do a +heritrix crawl with new config, then re-ingest all the requests individually. + +Summary of what to do here: + + OA DOI: expecting some 2.4 million seeds + OAI-PMH: expecting some 5 million no-capture URLs, plus more from missing PDF URL not found + Unpaywall: another ~900k no-capture URLs (maybe filtered?) + +For all, re-attempt for these status codes: + + no-capture + cdx-error + wayback-error + petabox-error + gateway-timeout (?) + +And at least do bulk re-ingest for these, if updated before 2020-11-20 or so: + + no-pdf-link + +## OAI-PMH + +Need to re-ingest all of the (many!) no-capture and no-pdf-link + +TODO: repec-specific URL extraction? + +Skip these OAI prefixes: + + kb.dk + bnf.fr + hispana.mcu.es + bdr.oai.bsb-muenchen.de + ukm.si + hsp.org + +Skip these domains: + + www.kb.dk (kb.dk) + kb-images.kb.dk (kb.dk) + mdz-nbn-resolving.de (TODO: what prefix?) + aggr.ukm.um.si (ukm.si) + +Check PDF link extraction for these prefixes, or skip them (TODO): + + repec (mixed success) + biodiversitylibrary.org + juser.fz-juelich.de + americanae.aecid.es + www.irgrid.ac.cn + hal + espace.library.uq.edu.au + igi.indrastra.com + invenio.nusl.cz + hypotheses.org + t2r2.star.titech.ac.jp + quod.lib.umich.edu + + domain: hemerotecadigital.bne.es + domain: bib-pubdb1.desy.de + domain: publikationen.bibliothek.kit.edu + domain: edoc.mpg.de + domain: bibliotecadigital.jcyl.es + domain: lup.lub.lu.se + domain: orbi.uliege.be + +TODO: +- consider deleting ingest requests from skipped prefixes (large database use) + + +## Unpaywall + +About 900k `no-pdf-link`, and up to 2.5 million more `no-pdf-link`. + +Re-bulk-ingest filtered requests which hit `no-pdf-link` before 2020-11-20: + + COPY ( + SELECT row_to_json(ingest_request.*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + AND date(ingest_request.created) < '2020-11-20' + AND ingest_file_result.status = 'no-pdf-link' + AND ingest_request.base_url NOT LIKE '%journals.sagepub.com%' + AND ingest_request.base_url NOT LIKE '%pubs.acs.org%' + AND ingest_request.base_url NOT LIKE '%ahajournals.org%' + AND ingest_request.base_url NOT LIKE '%www.journal.csj.jp%' + AND ingest_request.base_url NOT LIKE '%aip.scitation.org%' + AND ingest_request.base_url NOT LIKE '%academic.oup.com%' + AND ingest_request.base_url NOT LIKE '%tandfonline.com%' + AND ingest_request.base_url NOT LIKE '%://archive.org/%' + AND ingest_request.base_url NOT LIKE '%://web.archive.org/%' + AND ingest_request.base_url NOT LIKE '%://www.archive.org/%' + ) TO '/grande/snapshots/unpaywall_nopdflink_2020-12-08.rows.json'; + => COPY 1309990 + + ./scripts/ingestrequest_row2json.py /grande/snapshots/unpaywall_nopdflink_2020-12-08.rows.json | pv -l | shuf > /grande/snapshots/unpaywall_nopdflink_2020-12-08.ingest_request.json + => 1.31M 0:00:51 [25.6k/s] + + cat /grande/snapshots/unpaywall_nopdflink_2020-12-08.rows.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 diff --git a/notes/ingest/2021-04_unpaywall.md b/notes/ingest/2021-04_unpaywall.md new file mode 100644 index 0000000..d7643f4 --- /dev/null +++ b/notes/ingest/2021-04_unpaywall.md @@ -0,0 +1,368 @@ + +New snapshot released 2021-02-18, finally getting around to a crawl two months +later. + +Intend to do same style of crawl as in the past. One change is that +sandcrawler-db has moved to a focal VM. + + +## Transform and Load + + # in sandcrawler pipenv on sandcrawler1-vm (svc506) + zcat /srv/sandcrawler/tasks/unpaywall_snapshot_2021-02-18T160139.jsonl.gz | ./scripts/unpaywall2ingestrequest.py - | pv -l > /srv/sandcrawler/tasks/unpaywall_snapshot_2021-02-18.ingest_request.json + => 30.0M 3:14:59 [2.57k/s] + + cat /srv/sandcrawler/tasks/unpaywall_snapshot_2021-02-18.ingest_request.json | pv -l | ./persist_tool.py ingest-request - + => Worker: Counter({'total': 30027007, 'insert-requests': 2703999, 'update-requests': 0}) + => JSON lines pushed: Counter({'total': 30027007, 'pushed': 30027007}) + +## Dump new URLs, Transform, Bulk Ingest + + COPY ( + SELECT row_to_json(ingest_request.*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + -- AND date(ingest_request.created) > '2021-01-01' + AND (ingest_file_result.status IS NULL + OR ingest_file_result.status = 'no-capture') + ) TO '/srv/sandcrawler/tasks/unpaywall_noingest_2021-02-18.rows.json'; + => COPY 3277484 + + # previous, 2020-10 run: COPY 4216339 + + ./scripts/ingestrequest_row2json.py /srv/sandcrawler/tasks/unpaywall_noingest_2021-02-18.rows.json | pv -l | shuf > /srv/sandcrawler/tasks/unpaywall_noingest_2021-02-18.ingest_request.json + => 3.28M 0:01:42 [32.1k/s] + +Enqueue the whole batch: + + cat /srv/sandcrawler/tasks/unpaywall_noingest_2021-02-18.ingest_request.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + + +## Check Pre-Crawl Status + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + + status | count + -------------------------+---------- + success | 26385866 + no-pdf-link | 2132565 + no-capture | 2092111 + redirect-loop | 1732543 + terminal-bad-status | 1504555 + wayback-content-error | 357345 + wrong-mimetype | 126070 + link-loop | 76808 + cdx-error | 22756 + null-body | 22066 + wayback-error | 13768 + gateway-timeout | 3804 + petabox-error | 3608 + spn2-cdx-lookup-failure | 1225 + redirects-exceeded | 892 + invalid-host-resolution | 505 + bad-redirect | 151 + spn2-error | 108 + spn2-error:job-failed | 91 + bad-gzip-encoding | 27 + (20 rows) + +Only the recent bulk ingest: + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + AND date(ingest_request.created) > '2021-01-01' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + status | count + -------------------------+--------- + success | 1348623 + no-capture | 1231582 + redirect-loop | 45622 + no-pdf-link | 37312 + terminal-bad-status | 24162 + wrong-mimetype | 6684 + link-loop | 5757 + null-body | 1288 + wayback-content-error | 1123 + cdx-error | 831 + petabox-error | 697 + wayback-error | 185 + invalid-host-resolution | 41 + gateway-timeout | 29 + blocked-cookie | 22 + bad-gzip-encoding | 20 + spn2-cdx-lookup-failure | 7 + bad-redirect | 4 + timeout | 3 + redirects-exceeded | 3 + (20 rows) + +## Dump Seedlist + +Dump rows: + + COPY ( + SELECT row_to_json(t1.*) + FROM ( + SELECT ingest_request.*, ingest_file_result as result + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + AND (ingest_file_result.status = 'no-capture' + OR ingest_file_result.status = 'cdx-error' + OR ingest_file_result.status = 'wayback-error' + OR ingest_file_result.status = 'gateway-timeout' + OR ingest_file_result.status = 'spn2-cdx-lookup-failure' + ) + AND ingest_request.base_url NOT LIKE '%journals.sagepub.com%' + AND ingest_request.base_url NOT LIKE '%pubs.acs.org%' + AND ingest_request.base_url NOT LIKE '%ahajournals.org%' + AND ingest_request.base_url NOT LIKE '%www.journal.csj.jp%' + AND ingest_request.base_url NOT LIKE '%aip.scitation.org%' + AND ingest_request.base_url NOT LIKE '%academic.oup.com%' + AND ingest_request.base_url NOT LIKE '%tandfonline.com%' + AND ingest_request.base_url NOT LIKE '%.archive.org%' + AND ingest_request.base_url NOT LIKE '%://archive.org%' + AND ingest_file_result.terminal_url NOT LIKE '%journals.sagepub.com%' + AND ingest_file_result.terminal_url NOT LIKE '%pubs.acs.org%' + AND ingest_file_result.terminal_url NOT LIKE '%ahajournals.org%' + AND ingest_file_result.terminal_url NOT LIKE '%www.journal.csj.jp%' + AND ingest_file_result.terminal_url NOT LIKE '%aip.scitation.org%' + AND ingest_file_result.terminal_url NOT LIKE '%academic.oup.com%' + AND ingest_file_result.terminal_url NOT LIKE '%tandfonline.com%' + AND ingest_file_result.terminal_url NOT LIKE '%.archive.org%' + AND ingest_file_result.terminal_url NOT LIKE '%://archive.org%' + ) t1 + ) TO '/srv/sandcrawler/tasks/unpaywall_seedlist_2021-02-18.rows.json'; + => 2020-10: 2,936,404 + => 2021-04: 1,805,192 + +Prep ingest requests (for post-crawl use): + + ./scripts/ingestrequest_row2json.py /srv/sandcrawler/tasks/unpaywall_seedlist_2021-02-18.rows.json | pv -l > /srv/sandcrawler/tasks/unpaywall_crawl_ingest_2021-02-18.json + => 1.81M 0:01:27 [20.6k/s] + +And actually dump seedlist(s): + + cat /srv/sandcrawler/tasks/unpaywall_seedlist_2021-02-18.rows.json | jq -r .base_url | sort -u -S 4G > /srv/sandcrawler/tasks/unpaywall_seedlist_2021-02-18.url.txt + cat /srv/sandcrawler/tasks/unpaywall_seedlist_2021-02-18.rows.json | rg '"no-capture"' | jq -r .result.terminal_url | rg -v ^null$ | sort -u -S 4G > /srv/sandcrawler/tasks/unpaywall_seedlist_2021-02-18.terminal_url.txt + cat /srv/sandcrawler/tasks/unpaywall_seedlist_2021-02-18.rows.json | rg -v '"no-capture"' | jq -r .base_url | sort -u -S 4G > /srv/sandcrawler/tasks/unpaywall_seedlist_2021-02-18.no_terminal_url.txt + + wc -l /srv/sandcrawler/tasks/unpaywall_seedlist_2021-02-18.*.txt + 6 /srv/sandcrawler/tasks/unpaywall_seedlist_2021-02-18.no_terminal_url.txt + 1668524 /srv/sandcrawler/tasks/unpaywall_seedlist_2021-02-18.terminal_url.txt + 1685717 /srv/sandcrawler/tasks/unpaywall_seedlist_2021-02-18.url.txt + +## Post-Crawl Bulk Ingest + + cat /srv/sandcrawler/tasks/unpaywall_crawl_ingest_2021-02-18.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + => 1,804,211 consumer group lag + +## Post-Ingest Stats + +Overall status (unpaywall, all time): + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + status | count + -------------------------+---------- + success | 27242251 + no-pdf-link | 2746237 + redirect-loop | 1821132 + terminal-bad-status | 1553441 + no-capture | 478559 + wayback-content-error | 357390 + wrong-mimetype | 127365 + link-loop | 79389 + cdx-error | 23170 + null-body | 23169 + wayback-error | 13704 + gateway-timeout | 3803 + petabox-error | 3642 + redirects-exceeded | 1427 + spn2-cdx-lookup-failure | 1214 + invalid-host-resolution | 505 + bad-redirect | 153 + spn2-error | 107 + spn2-error:job-failed | 91 + body-too-large | 84 + (20 rows) + +Ingest stats broken down by publication stage: + + SELECT ingest_request.release_stage, ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + GROUP BY release_stage, status + ORDER BY release_stage, COUNT DESC + LIMIT 100; + + release_stage | status | count + ---------------+-------------------------------------+---------- + accepted | success | 1213335 + accepted | no-pdf-link | 29292 + accepted | redirect-loop | 12769 + accepted | terminal-bad-status | 11264 + accepted | no-capture | 10187 + accepted | cdx-error | 1015 + accepted | wayback-content-error | 757 + accepted | wrong-mimetype | 501 + accepted | link-loop | 407 + accepted | wayback-error | 207 + accepted | petabox-error | 189 + accepted | redirects-exceeded | 125 + accepted | null-body | 34 + accepted | spn2-cdx-lookup-failure | 5 + accepted | gateway-timeout | 4 + accepted | blocked-cookie | 2 + accepted | bad-redirect | 1 + accepted | body-too-large | 1 + published | success | 20196774 + published | no-pdf-link | 2647969 + published | redirect-loop | 1477558 + published | terminal-bad-status | 1320013 + published | wayback-content-error | 351931 + published | no-capture | 297603 + published | wrong-mimetype | 115440 + published | link-loop | 76431 + published | cdx-error | 18125 + published | null-body | 17559 + published | wayback-error | 10466 + published | petabox-error | 2684 + published | gateway-timeout | 1979 + published | redirects-exceeded | 947 + published | spn2-cdx-lookup-failure | 877 + published | invalid-host-resolution | 457 + published | bad-redirect | 120 + published | spn2-error:job-failed | 77 + published | spn2-error | 70 + published | body-too-large | 39 + published | bad-gzip-encoding | 24 + published | timeout | 24 + published | blocked-cookie | 23 + published | spn2-error:soft-time-limit-exceeded | 4 + published | | 2 + published | pending | 1 + published | spn2-error:pending | 1 + published | too-many-redirects | 1 + submitted | success | 5832117 + submitted | redirect-loop | 330785 + submitted | terminal-bad-status | 222152 + submitted | no-capture | 170766 + submitted | no-pdf-link | 68934 + submitted | wrong-mimetype | 11424 + submitted | null-body | 5576 + submitted | wayback-content-error | 4702 + submitted | cdx-error | 4030 + submitted | wayback-error | 3031 + submitted | link-loop | 2551 + submitted | gateway-timeout | 1820 + submitted | petabox-error | 769 + submitted | redirects-exceeded | 355 + submitted | spn2-cdx-lookup-failure | 332 + submitted | invalid-host-resolution | 48 + submitted | body-too-large | 44 + submitted | spn2-error | 37 + submitted | bad-redirect | 32 + submitted | spn2-error:job-failed | 14 + submitted | | 13 + submitted | spn2-error:soft-time-limit-exceeded | 5 + submitted | timeout | 4 + submitted | bad-gzip-encoding | 3 + submitted | skip-url-blocklist | 1 + | no-pdf-link | 42 + | success | 25 + | redirect-loop | 20 + | terminal-bad-status | 12 + | no-capture | 3 + (76 rows) + + +Only the recent updates: + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + AND date(ingest_request.created) > '2021-04-01' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + status | count + -------------------------+--------- + success | 2192376 + no-capture | 152183 + no-pdf-link | 144174 + redirect-loop | 125988 + terminal-bad-status | 67307 + link-loop | 8292 + wrong-mimetype | 7942 + null-body | 2270 + cdx-error | 1223 + wayback-content-error | 1147 + petabox-error | 728 + wayback-error | 155 + body-too-large | 82 + invalid-host-resolution | 41 + gateway-timeout | 28 + blocked-cookie | 22 + bad-gzip-encoding | 20 + timeout | 7 + bad-redirect | 6 + redirects-exceeded | 4 + (20 rows) + +In total, this iteration of unpaywall ingest resulted in: + +- 2,703,999 raw ingest requests (new URLs total) +- 1,231,582 (45.5%) of these had not been seen/crawled from any source yet +- 843,753 (31.2%) success from new heritrix crawling +- 2,192,376 (81.1%) total success (including crawled initially for other reasons; out of all new URLs including those not expected to be success) diff --git a/notes/ingest/2021-05_daily_improvements.md b/notes/ingest/2021-05_daily_improvements.md new file mode 100644 index 0000000..e8748fa --- /dev/null +++ b/notes/ingest/2021-05_daily_improvements.md @@ -0,0 +1,480 @@ + +Summary of top large broken domains (2021-04-21 "30 day" snapshot): + +## acervus.unicamp.br + + domain | status | count +---------------------------------------+-------------------------+-------- + acervus.unicamp.br | | 1967 + acervus.unicamp.br | no-pdf-link | 1853 + +select * from ingest_file_result where updated >= '2021-03-01' and terminal_url like '%acervus.unicamp.br%' and status = 'no-pdf-link' limit 5; + +http://acervus.unicamp.br/index.asp?codigo_sophia=963332 + +seems like many of these were captures with a blank page? or a redirect to +the homepage? + +http://web.archive.org/web/20200129110523/http://acervus.unicamp.br/index.html + +messy, going to move on. + + +## apex.ipk-gatersleben.de + +apex.ipk-gatersleben.de | | 1253 +apex.ipk-gatersleben.de | no-pdf-link | 1132 + +select * from ingest_file_result where updated >= '2021-03-01' and terminal_url like '%apex.ipk-gatersleben.de%' and status = 'no-pdf-link' limit 5; + +https://doi.org/10.25642/ipk/rescoll/4886 +https://apex.ipk-gatersleben.de/apex/f?p=PGRDOI:RESOLVE:::NO:RP:DOI:10.25642/IPK/RESCOLL/7331 + +seem to be datasets/species, not articles. + +prefix: 10.25642/ipk + +## crossref.org + + apps.crossref.org | | 4693 + apps.crossref.org | no-pdf-link | 4075 + +https://doi.org/10.1515/9781501747045-013 +https://apps.crossref.org/coaccess/coaccess.html?doi=10.1515%2F9781501747045-013 + +Derp, they are doing a dynamic/AJAX thing, so access links are not in the HTML. + +## openeditiong + + books.openedition.org | | 1784 + books.openedition.org | no-pdf-link | 1466 + +https://doi.org/10.4000/books.pul.34492 +https://books.openedition.org/pul/34492 + +these are not actually OA books (or at least, not all are) + +## chemrxiv.org (figshare) + + chemrxiv.org | | 857 + chemrxiv.org | no-pdf-link | 519 + +https://doi.org/10.26434/chemrxiv.14411081 +https://chemrxiv.org/articles/preprint/Prediction_and_Optimization_of_Ion_Transport_Characteristics_in_Nanoparticle-Based_Electrolytes_Using_Convolutional_Neural_Networks/14411081 + +these all seem to be *multi-file* entities, thus not good for single file ingest pipeline. + +## direct.mit.edu + + direct.mit.edu | | 996 + direct.mit.edu | no-pdf-link | 869 + +https://doi.org/10.7551/mitpress/14056.003.0004 +https://direct.mit.edu/books/monograph/5111/chapter-abstract/3060134/Adding-Technology-to-Contact-Tracing?redirectedFrom=fulltext + +"not available" + +https://doi.org/10.7551/mitpress/12444.003.0004 + +"not available" + + +## dlc.library.columbia.edu + + dlc.library.columbia.edu | | 4225 + dlc.library.columbia.edu | no-pdf-link | 2395 + dlc.library.columbia.edu | spn2-wayback-error | 1568 + +https://doi.org/10.7916/d8-506w-kk49 +https://dlc.library.columbia.edu/durst/cul:18931zcrk9 + +document repository. +this one goes to IA! actually many seem to. +added extractor, should re-ingest with: + + publisher:"Columbia University" doi_prefix:10.7916 !journal:* + +actually, that is like 600k+ results and many are not digitized, so perhaps not. + +## doi.ala.org.au + + doi.ala.org.au | | 2570 + doi.ala.org.au | no-pdf-link | 2153 + +https://doi.org/10.26197/ala.811d55e3-2ff4-4501-b3e7-e19249507052 +https://doi.ala.org.au/doi/811d55e3-2ff4-4501-b3e7-e19249507052 + +this is a data repository, with filesets, not papers. datacite metadata is +incorrect. + +## fldeploc.dep.state.fl.us + + fldeploc.dep.state.fl.us | | 774 + fldeploc.dep.state.fl.us | no-pdf-link | 718 + + +https://doi.org/10.35256/ic29 +http://fldeploc.dep.state.fl.us/geodb_query/fgs_doi.asp?searchCode=IC29 + +re-ingest with: + + # only ~800 works + doi_prefix:10.35256 publisher:Florida + +## geoscan.nrcan.gc.ca + + geoscan.nrcan.gc.ca | | 2056 + geoscan.nrcan.gc.ca | no-pdf-link | 2019 + +https://doi.org/10.4095/295366 +https://geoscan.nrcan.gc.ca/starweb/geoscan/servlet.starweb?path=geoscan/fulle.web&search1=R=295366 + +this is a geographic repository, not papers. + +## kiss.kstudy.com + + kiss.kstudy.com | | 747 + kiss.kstudy.com | no-pdf-link | 686 + +https://doi.org/10.22143/hss21.12.1.121 +http://kiss.kstudy.com/thesis/thesis-view.asp?key=3862523 + +Korean. seems to not actually be theses? can't download. + +## linkinghub.elsevier.com + + linkinghub.elsevier.com | | 5079 + linkinghub.elsevier.com | forbidden | 2226 + linkinghub.elsevier.com | spn2-wayback-error | 1625 + linkinghub.elsevier.com | spn2-cdx-lookup-failure | 758 + +skipping for now, looks like mostly 'forbidden'? + +## osf.io + +These are important! + + osf.io | | 3139 + osf.io | not-found | 2288 + osf.io | spn2-wayback-error | 582 + +https://doi.org/10.31219/osf.io/jux3w +https://accounts.osf.io/login?service=https://osf.io/jux3w/download + +many of these are 404s by browser as well. what does that mean? + +## peerj.com + + peerj.com | | 785 + peerj.com | no-pdf-link | 552 + +https://doi.org/10.7287/peerj.11155v0.1/reviews/2 +https://peerj.com/articles/11155/reviews/ + +these are HTML reviews, not papers + +## preprints.jmir.org + + preprints.jmir.org | | 763 + preprints.jmir.org | no-pdf-link | 611 + +https://doi.org/10.2196/preprints.22556 +https://preprints.jmir.org/preprint/22556 + +UGH, looks simple, but javascript. + +could try to re-write URL into S3 format? meh. + +## psyarxiv.com (OSF?) + + psyarxiv.com | | 641 + psyarxiv.com | no-pdf-link | 546 + +https://doi.org/10.31234/osf.io/5jaqg +https://psyarxiv.com/5jaqg/ + +Also infuriatingly Javascript, but can do URL hack. + +Should reingest, and potentially force-recrawl: + + # about 67k + publisher:"Center for Open Science" in_ia:false + +## publons.com + + publons.com | | 6998 + publons.com | no-pdf-link | 6982 + +https://doi.org/10.1002/jmor.21338/v2/review1 +https://publons.com/publon/40260824/ + +These are just HTML reviews, not papers. + +## saemobilus.sae.org + + saemobilus.sae.org | | 795 + saemobilus.sae.org | no-pdf-link | 669 + +https://doi.org/10.4271/as1426c +https://saemobilus.sae.org/content/as1426c + +These seem to be standards, and are not open access (paywall) + +## scholar.dkyobobook.co.kr + + scholar.dkyobobook.co.kr | | 1043 + scholar.dkyobobook.co.kr | no-pdf-link | 915 + +https://doi.org/10.22471/crisis.2021.6.1.18 +http://scholar.dkyobobook.co.kr/searchDetail.laf?barcode=4010028199536 + +Korean. complex javascript, skipping. + +## unreserved.rba.gov.au + + unreserved.rba.gov.au | | 823 + unreserved.rba.gov.au | no-pdf-link | 821 + +https://doi.org/10.47688/rba_archives_2006/04129 +https://unreserved.rba.gov.au/users/login + +Don't need to login when I tried in browser? document repo, not papers. + +## wayf.switch.ch + + wayf.switch.ch | | 1169 + wayf.switch.ch | no-pdf-link | 809 + +https://doi.org/10.24451/arbor.11128 +https://wayf.switch.ch/SWITCHaai/WAYF?entityID=https%3A%2F%2Farbor.bfh.ch%2Fshibboleth&return=https%3A%2F%2Farbor.bfh.ch%2FShibboleth.sso%2FLogin%3FSAMLDS%3D1%26target%3Dss%253Amem%253A5056fc0a97aeab16e5007ca63bede254cb5669d94173064d6c74c62a0f88b022 + +Loginwall + +## + + www.bloomsburycollections.com | | 1745 + www.bloomsburycollections.com | no-pdf-link | 1571 + +https://doi.org/10.5040/9781849664264.0008 +https://www.bloomsburycollections.com/book/the-political-economies-of-media-the-transformation-of-the-global-media-industries/the-political-economies-of-media-and-the-transformation-of-the-global-media-industries + +These are primarily not OA/available. + +## + + www.emc2020.eu | | 791 + www.emc2020.eu | no-pdf-link | 748 + +https://doi.org/10.22443/rms.emc2020.146 +https://www.emc2020.eu/abstract/evaluation-of-different-rectangular-scan-strategies-for-hrstem-imaging.html + +These are just abstracts, not papers. + +## Emerald + + www.emerald.com | | 2420 + www.emerald.com | no-pdf-link | 1986 + +https://doi.org/10.1108/ramj-11-2020-0065 +https://www.emerald.com/insight/content/doi/10.1108/RAMJ-11-2020-0065/full/html + +Note that these URLs are already HTML fulltext. but the PDF is also available and easy. + +re-ingest: + + # only ~3k or so missing + doi_prefix:10.1108 publisher:emerald in_ia:false is_oa:true + +## + + www.humankineticslibrary.com | | 1122 + www.humankineticslibrary.com | no-pdf-link | 985 + +https://doi.org/10.5040/9781718206625.ch-002 +https://www.humankineticslibrary.com/encyclopedia-chapter?docid=b-9781718206625&tocid=b-9781718206625-chapter2 + +paywall + +## + + www.inderscience.com | | 1532 + www.inderscience.com | no-pdf-link | 1217 + +https://doi.org/10.1504/ijdmb.2020.10036342 +https://www.inderscience.com/info/ingeneral/forthcoming.php?jcode=ijdmb + +paywall + +## + + www.ingentaconnect.com | | 885 + www.ingentaconnect.com | no-pdf-link | 783 + +https://doi.org/10.15258/sst.2021.49.1.07 +https://www.ingentaconnect.com/content/ista/sst/pre-prints/content-7_sst.2021.49.1_63-71;jsessionid=1joc5mmi1juht.x-ic-live-02 + +Annoying javascript, but easy to work around. + +re-ingest: + + # only a couple hundred; also re-ingest + doi_prefix:10.15258 in_ia:false year:>2018 + +## + + www.nomos-elibrary.de | | 2235 + www.nomos-elibrary.de | no-pdf-link | 1128 + www.nomos-elibrary.de | spn2-wayback-error | 559 + +https://doi.org/10.5771/9783748907084-439 +https://www.nomos-elibrary.de/10.5771/9783748907084-439/verzeichnis-der-autorinnen-und-autoren + +Javascript obfuscated download button? + +## + + www.oecd-ilibrary.org | | 3046 + www.oecd-ilibrary.org | no-pdf-link | 2869 + +https://doi.org/10.1787/543e84ed-en +https://www.oecd-ilibrary.org/development/applying-evaluation-criteria-thoughtfully_543e84ed-en + +Paywall. + +## + + www.osapublishing.org | | 821 + www.osapublishing.org | no-pdf-link | 615 + +https://doi.org/10.1364/boe.422199 +https://www.osapublishing.org/boe/abstract.cfm?doi=10.1364/BOE.422199 + +Some of these are "pre-registered" DOIs, not published yet. Many of the +remaining are actually HTML articles, and/or have some stuff in the +`citation_pdf_url`. A core problem is captchas. + +Have started adding support to fatcat for HTML crawl type based on container. + +re-ingest: + + container_twtpsm6ytje3nhuqfu3pa7ca7u (optica) + container_cg4vcsfty5dfvgmat5wm62wgie (optics express) + +## + + www.oxfordscholarlyeditions.com | | 759 + www.oxfordscholarlyeditions.com | no-pdf-link | 719 + +https://doi.org/10.1093/oseo/instance.00266789 +https://www.oxfordscholarlyeditions.com/view/10.1093/actrade/9780199593668.book.1/actrade-9780199593668-div1-27 + +loginwall/paywall + +## + + www.schweizerbart.de | | 730 + www.schweizerbart.de | no-pdf-link | 653 + +https://doi.org/10.1127/zfg/40/1996/461 +https://www.schweizerbart.de/papers/zfg/detail/40/97757/Theoretical_model_of_surface_karstic_processes?af=crossref + +paywall + +## + + www.sciencedirect.com | | 14757 + www.sciencedirect.com | no-pdf-link | 12733 + www.sciencedirect.com | spn2-wayback-error | 1503 + +https://doi.org/10.1016/j.landurbplan.2021.104104 +https://www.sciencedirect.com/science/article/pii/S0169204621000670 + +Bunch of crazy new hacks, but seems to be working! + +re-ingest: + + # to start! about 50k + doi_prefix:10.1016 is_oa:true year:2021 + +## + + www.sciendo.com | | 1955 + www.sciendo.com | no-pdf-link | 1176 + +https://doi.org/10.2478/awutm-2019-0012 +https://www.sciendo.com/article/10.2478/awutm-2019-0012 + +uses lots of javascript, hard to scrape. + + +## Others (for reference) + + | | 725990 + | no-pdf-link | 209933 + | success | 206134 + | spn2-wayback-error | 127015 + | spn2-cdx-lookup-failure | 53384 + | blocked-cookie | 35867 + | link-loop | 25834 + | too-many-redirects | 16430 + | redirect-loop | 14648 + | forbidden | 13794 + | terminal-bad-status | 8055 + | not-found | 6399 + | remote-server-error | 2402 + | wrong-mimetype | 2011 + | spn2-error:unauthorized | 912 + | bad-redirect | 555 + | read-timeout | 530 + +## Re-ingests + +All the above combined: + + container_twtpsm6ytje3nhuqfu3pa7ca7u (optica) + container_cg4vcsfty5dfvgmat5wm62wgie (optics express) + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --ingest-type html container --container-id twtpsm6ytje3nhuqfu3pa7ca7u + => Counter({'ingest_request': 1142, 'elasticsearch_release': 1142, 'estimate': 1142, 'kafka': 1142}) + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --ingest-type html container --container-id cg4vcsfty5dfvgmat5wm62wgie + => Counter({'elasticsearch_release': 33482, 'estimate': 33482, 'ingest_request': 32864, 'kafka': 32864}) + + # only ~800 works + doi_prefix:10.35256 publisher:Florida + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa query "doi_prefix:10.35256 publisher:Florida" + => Counter({'ingest_request': 843, 'elasticsearch_release': 843, 'estimate': 843, 'kafka': 843}) + + # only ~3k or so missing + doi_prefix:10.1108 publisher:emerald in_ia:false is_oa:true + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org query "doi_prefix:10.1108 publisher:emerald" + => Counter({'ingest_request': 3812, 'elasticsearch_release': 3812, 'estimate': 3812, 'kafka': 3812}) + + + # only a couple hundred; also re-ingest + doi_prefix:10.15258 in_ia:false year:>2018 + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa --force-recrawl query "doi_prefix:10.15258 year:>2018" + => Counter({'ingest_request': 140, 'elasticsearch_release': 140, 'estimate': 140, 'kafka': 140}) + + # to start! about 50k + doi_prefix:10.1016 is_oa:true year:2020 + doi_prefix:10.1016 is_oa:true year:2021 + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org query "doi_prefix:10.1016 year:2020" + => Counter({'ingest_request': 75936, 'elasticsearch_release': 75936, 'estimate': 75936, 'kafka': 75936}) + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org query "doi_prefix:10.1016 year:2021" + => Counter({'ingest_request': 54824, 'elasticsearch_release': 54824, 'estimate': 54824, 'kafka': 54824}) + + pmcid:* year:2018 + pmcid:* year:2019 + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --force-recrawl query "pmcid:* year:2018" + => Counter({'ingest_request': 25366, 'elasticsearch_release': 25366, 'estimate': 25366, 'kafka': 25366}) + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --force-recrawl query "pmcid:* year:2019" + => Counter({'ingest_request': 55658, 'elasticsearch_release': 55658, 'estimate': 55658, 'kafka': 55658}) + diff --git a/notes/ingest/2021-07_unpaywall.md b/notes/ingest/2021-07_unpaywall.md new file mode 100644 index 0000000..8b6ac09 --- /dev/null +++ b/notes/ingest/2021-07_unpaywall.md @@ -0,0 +1,320 @@ + +New snapshot released 2021-07-02. Should be "boring" ingest and crawl. + + +## Transform and Load + + # in sandcrawler pipenv on sandcrawler1-vm (svc506) + zcat /srv/sandcrawler/tasks/unpaywall_snapshot_2021-07-02T151134.jsonl.gz | ./scripts/unpaywall2ingestrequest.py - | pv -l > /srv/sandcrawler/tasks/unpaywall_snapshot_2021-07-02.ingest_request.json + => 32.2M 3:01:52 [2.95k/s] + + cat /srv/sandcrawler/tasks/unpaywall_snapshot_2021-07-02.ingest_request.json | pv -l | ./persist_tool.py ingest-request - + => Worker: Counter({'total': 32196260, 'insert-requests': 3325954, 'update-requests': 0}) + => JSON lines pushed: Counter({'total': 32196260, 'pushed': 32196260}) + + +## Dump new URLs, Transform, Bulk Ingest + + COPY ( + SELECT row_to_json(ingest_request.*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + -- AND date(ingest_request.created) > '2021-01-01' + AND (ingest_file_result.status IS NULL + OR ingest_file_result.status = 'no-capture') + ) TO '/srv/sandcrawler/tasks/unpaywall_noingest_2021-07-02.rows.json'; + => COPY 3556146 + + # previous, 2020-10 run: COPY 4216339 + # previous, 2021-07 run: COPY 3277484 + +Oops, should have run instead, with the date filter: + + COPY ( + SELECT row_to_json(ingest_request.*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + AND date(ingest_request.created) > '2021-07-01' + AND (ingest_file_result.status IS NULL + OR ingest_file_result.status = 'no-capture') + ) TO '/srv/sandcrawler/tasks/unpaywall_noingest_2021-07-02.rows.json'; + +But didn't, so processed all instead. + + ./scripts/ingestrequest_row2json.py /srv/sandcrawler/tasks/unpaywall_noingest_2021-07-02.rows.json | pv -l | shuf > /srv/sandcrawler/tasks/unpaywall_noingest_2021-07-02.ingest_request.json + => 3.56M 0:01:59 [29.8k/s] + +Enqueue the whole batch: + + cat /srv/sandcrawler/tasks/unpaywall_noingest_2021-07-02.ingest_request.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + => done, on 2021-07-13 + + +## Check Pre-Crawl Status + +Only the recent bulk ingest: + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + AND date(ingest_request.created) > '2021-07-01' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + status | count + -------------------------+--------- + no-capture | 1831827 + success | 1343604 + redirect-loop | 103999 + terminal-bad-status | 19845 + no-pdf-link | 17448 + link-loop | 5027 + wrong-mimetype | 2270 + cdx-error | 523 + body-too-large | 321 + null-body | 298 + wayback-content-error | 242 + petabox-error | 155 + gateway-timeout | 138 + invalid-host-resolution | 120 + wayback-error | 109 + blocked-cookie | 9 + timeout | 7 + | 3 + bad-redirect | 3 + spn2-cdx-lookup-failure | 3 + (20 rows) + + +## Dump Seedlist + +Dump rows: + + COPY ( + SELECT row_to_json(t1.*) + FROM ( + SELECT ingest_request.*, ingest_file_result as result + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND date(ingest_request.created) > '2021-07-01' + AND ingest_request.link_source = 'unpaywall' + AND (ingest_file_result.status = 'no-capture' + OR ingest_file_result.status = 'cdx-error' + OR ingest_file_result.status = 'wayback-error' + OR ingest_file_result.status = 'gateway-timeout' + OR ingest_file_result.status = 'spn2-cdx-lookup-failure' + ) + AND ingest_request.base_url NOT LIKE '%journals.sagepub.com%' + AND ingest_request.base_url NOT LIKE '%pubs.acs.org%' + AND ingest_request.base_url NOT LIKE '%ahajournals.org%' + AND ingest_request.base_url NOT LIKE '%www.journal.csj.jp%' + AND ingest_request.base_url NOT LIKE '%aip.scitation.org%' + AND ingest_request.base_url NOT LIKE '%academic.oup.com%' + AND ingest_request.base_url NOT LIKE '%tandfonline.com%' + AND ingest_request.base_url NOT LIKE '%.archive.org%' + AND ingest_request.base_url NOT LIKE '%://archive.org%' + AND ingest_file_result.terminal_url NOT LIKE '%journals.sagepub.com%' + AND ingest_file_result.terminal_url NOT LIKE '%pubs.acs.org%' + AND ingest_file_result.terminal_url NOT LIKE '%ahajournals.org%' + AND ingest_file_result.terminal_url NOT LIKE '%www.journal.csj.jp%' + AND ingest_file_result.terminal_url NOT LIKE '%aip.scitation.org%' + AND ingest_file_result.terminal_url NOT LIKE '%academic.oup.com%' + AND ingest_file_result.terminal_url NOT LIKE '%tandfonline.com%' + AND ingest_file_result.terminal_url NOT LIKE '%.archive.org%' + AND ingest_file_result.terminal_url NOT LIKE '%://archive.org%' + ) t1 + ) TO '/srv/sandcrawler/tasks/unpaywall_seedlist_2021-07-02.rows.json'; + => COPY 1743186 + +Prep ingest requests (for post-crawl use): + + ./scripts/ingestrequest_row2json.py /srv/sandcrawler/tasks/unpaywall_seedlist_2021-07-02.rows.json | pv -l > /srv/sandcrawler/tasks/unpaywall_crawl_ingest_2021-07-02.json + => 1.74M 0:01:33 [18.6k/s] + +And actually dump seedlist(s): + + cat /srv/sandcrawler/tasks/unpaywall_seedlist_2021-07-02.rows.json | jq -r .base_url | sort -u -S 4G > /srv/sandcrawler/tasks/unpaywall_seedlist_2021-07-02.url.txt + cat /srv/sandcrawler/tasks/unpaywall_seedlist_2021-07-02.rows.json | rg '"no-capture"' | jq -r .result.terminal_url | rg -v ^null$ | sort -u -S 4G > /srv/sandcrawler/tasks/unpaywall_seedlist_2021-07-02.terminal_url.txt + cat /srv/sandcrawler/tasks/unpaywall_seedlist_2021-07-02.rows.json | rg -v '"no-capture"' | jq -r .base_url | sort -u -S 4G > /srv/sandcrawler/tasks/unpaywall_seedlist_2021-07-02.no_terminal_url.txt + + wc -l /srv/sandcrawler/tasks/unpaywall_seedlist_2021-07-02.*.txt + 1 /srv/sandcrawler/tasks/unpaywall_seedlist_2021-07-02.no_terminal_url.txt + 1643963 /srv/sandcrawler/tasks/unpaywall_seedlist_2021-07-02.terminal_url.txt + 1644028 /srv/sandcrawler/tasks/unpaywall_seedlist_2021-07-02.url.txt + 3287992 total + +Then run crawl (see `journal-crawls` git repo). + +## Post-Crawl Bulk Ingest + + cat /srv/sandcrawler/tasks/unpaywall_crawl_ingest_2021-07-02.json | rg -v "\\\\" | jq . -c | pv -l | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + => 1.74M 0:01:59 [14.6k/s] + +## Post-Ingest Stats + +Only the recent updates: + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + AND date(ingest_request.created) > '2021-07-01' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + status | count + -------------------------+--------- + success | 2690258 + redirect-loop | 227328 + no-capture | 157368 + terminal-bad-status | 118943 + no-pdf-link | 92698 + blocked-cookie | 19478 + link-loop | 9249 + wrong-mimetype | 4918 + cdx-error | 1786 + wayback-error | 1497 + null-body | 1302 + body-too-large | 433 + wayback-content-error | 245 + petabox-error | 171 + gateway-timeout | 138 + invalid-host-resolution | 120 + timeout | 12 + bad-redirect | 4 + | 3 + spn2-cdx-lookup-failure | 1 + (20 rows) + +Only the recent updates, by publication stage: + + SELECT ingest_request.release_stage, ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + AND date(ingest_request.created) > '2021-07-01' + GROUP BY release_stage, status + ORDER BY release_stage, COUNT DESC + LIMIT 100; + + release_stage | status | count + ---------------+-------------------------+--------- + accepted | success | 103144 + accepted | no-pdf-link | 53981 + accepted | terminal-bad-status | 4102 + accepted | link-loop | 2799 + accepted | no-capture | 2315 + accepted | redirect-loop | 2171 + accepted | blocked-cookie | 234 + accepted | cdx-error | 140 + accepted | wayback-error | 101 + accepted | wrong-mimetype | 38 + accepted | null-body | 10 + accepted | petabox-error | 5 + accepted | wayback-content-error | 4 + accepted | gateway-timeout | 2 + accepted | body-too-large | 2 + published | success | 1919100 + published | no-capture | 130104 + published | redirect-loop | 127482 + published | terminal-bad-status | 43118 + published | no-pdf-link | 33505 + published | blocked-cookie | 19034 + published | link-loop | 6241 + published | wrong-mimetype | 4163 + published | null-body | 1195 + published | cdx-error | 1151 + published | wayback-error | 1105 + published | wayback-content-error | 197 + published | body-too-large | 195 + published | petabox-error | 118 + published | gateway-timeout | 35 + published | invalid-host-resolution | 13 + published | timeout | 8 + published | bad-redirect | 2 + published | spn2-cdx-lookup-failure | 1 + published | bad-gzip-encoding | 1 + submitted | success | 668014 + submitted | redirect-loop | 97675 + submitted | terminal-bad-status | 71723 + submitted | no-capture | 24949 + submitted | no-pdf-link | 5212 + submitted | wrong-mimetype | 717 + submitted | cdx-error | 495 + submitted | wayback-error | 291 + submitted | body-too-large | 236 + submitted | blocked-cookie | 210 + submitted | link-loop | 209 + submitted | invalid-host-resolution | 107 + submitted | gateway-timeout | 101 + submitted | null-body | 97 + submitted | petabox-error | 48 + submitted | wayback-content-error | 44 + submitted | timeout | 4 + submitted | | 3 + submitted | bad-redirect | 2 + submitted | remote-server-error | 1 + (55 rows) + +In total, this iteration of unpaywall ingest resulted in: + +- 3,325,954 raw ingest requests (new URLs total) +- 1,743,186 (52% of all) of these had not been seen/crawled from any source yet (?), and attempted to crawl +- 1,346,654 (77% of crawled) success from new heritrix crawling +- 2,690,258 (80%) total success (including crawled initially for other reasons; out of all new URLs including those not expected to be success) + +## Live Ingest Follow-Up + +Will run SPN requests on the ~160k `no-capture` URLs: + + COPY ( + SELECT row_to_json(ingest_request.*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'unpaywall' + AND date(ingest_request.created) > '2021-07-01' + AND (ingest_file_result.status IS NULL + OR ingest_file_result.status = 'no-capture') + ) TO '/srv/sandcrawler/tasks/unpaywall_noingest_2021-07-30.rows.json'; + => COPY 157371 + + ./scripts/ingestrequest_row2json.py /srv/sandcrawler/tasks/unpaywall_noingest_2021-07-30.rows.json | pv -l | shuf > /srv/sandcrawler/tasks/unpaywall_noingest_2021-07-30.ingest_request.json + => 157k 0:00:04 [31.6k/s] + +Enqueue the whole batch: + + cat /srv/sandcrawler/tasks/unpaywall_noingest_2021-07-30.ingest_request.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests -p -1 + => DONE diff --git a/notes/ingest/2021-08_mag.md b/notes/ingest/2021-08_mag.md new file mode 100644 index 0000000..5f92196 --- /dev/null +++ b/notes/ingest/2021-08_mag.md @@ -0,0 +1,400 @@ + +Using 2021-06-07 upstream MAG snapshot to run a crawl and do some re-ingest. +Also want to re-ingest some old/failed ingests, now that pipeline/code has +improved. + +Ran munging from `scratch:ingest/mag` notes first. Yielded 22.5M PDF URLs. + + +## Persist Ingest Requests + + zcat /srv/sandcrawler/tasks/ingest_requests_mag-2021-06-07.json.gz | head -n1000 | pv -l | ./persist_tool.py ingest-request - + => Worker: Counter({'total': 1000, 'insert-requests': 276, 'update-requests': 0}) + => JSON lines pushed: Counter({'total': 1000, 'pushed': 1000}) + + zcat /srv/sandcrawler/tasks/ingest_requests_mag-2021-06-07.json.gz | pv -l | ./persist_tool.py ingest-request - + => 22.5M 0:46:00 [8.16k/s] + => Worker: Counter({'total': 22527585, 'insert-requests': 8686315, 'update-requests': 0}) + => JSON lines pushed: Counter({'total': 22527585, 'pushed': 22527585}) + +Roughly 8.6 million new URLs + +## Pre-Crawl Status Counts + +Status of combined old and new requests, with some large domains removed: + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'mag' + AND ingest_request.base_url NOT LIKE '%journals.sagepub.com%' + AND ingest_request.base_url NOT LIKE '%pubs.acs.org%' + AND ingest_request.base_url NOT LIKE '%ahajournals.org%' + AND ingest_request.base_url NOT LIKE '%www.journal.csj.jp%' + AND ingest_request.base_url NOT LIKE '%aip.scitation.org%' + AND ingest_request.base_url NOT LIKE '%academic.oup.com%' + AND ingest_request.base_url NOT LIKE '%tandfonline.com%' + AND ingest_request.base_url NOT LIKE '%researchgate.net%' + AND ingest_request.base_url NOT LIKE '%muse.jhu.edu%' + AND ingest_request.base_url NOT LIKE '%omicsonline.org%' + AND ingest_request.base_url NOT LIKE '%link.springer.com%' + AND ingest_request.base_url NOT LIKE '%ieeexplore.ieee.org%' + -- AND ingest_request.created > '2021-06-01' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + status | count + -------------------------------+---------- + success | 26123975 + | 6664846 + no-pdf-link | 1859908 + redirect-loop | 1532405 + no-capture | 1199126 + link-loop | 1157010 + terminal-bad-status | 832362 + gateway-timeout | 202158 + spn2-cdx-lookup-failure | 81406 + wrong-mimetype | 69087 + invalid-host-resolution | 37262 + wayback-error | 21340 + petabox-error | 11237 + null-body | 9414 + wayback-content-error | 2199 + cdx-error | 1893 + spn2-error | 1741 + spn2-error:job-failed | 971 + blocked-cookie | 902 + spn2-error:invalid-url-syntax | 336 + (20 rows) + +And just the new URLs (note that domain filter shouldn't be required, but +keeping for consistency): + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'mag' + AND ingest_request.base_url NOT LIKE '%journals.sagepub.com%' + AND ingest_request.base_url NOT LIKE '%pubs.acs.org%' + AND ingest_request.base_url NOT LIKE '%ahajournals.org%' + AND ingest_request.base_url NOT LIKE '%www.journal.csj.jp%' + AND ingest_request.base_url NOT LIKE '%aip.scitation.org%' + AND ingest_request.base_url NOT LIKE '%academic.oup.com%' + AND ingest_request.base_url NOT LIKE '%tandfonline.com%' + AND ingest_request.base_url NOT LIKE '%researchgate.net%' + AND ingest_request.base_url NOT LIKE '%muse.jhu.edu%' + AND ingest_request.base_url NOT LIKE '%omicsonline.org%' + AND ingest_request.base_url NOT LIKE '%link.springer.com%' + AND ingest_request.base_url NOT LIKE '%ieeexplore.ieee.org%' + AND ingest_request.created > '2021-06-01' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + status | count + -------------------------+--------- + | 6664780 + success | 1957844 + redirect-loop | 23357 + terminal-bad-status | 9385 + no-pdf-link | 8315 + no-capture | 6892 + link-loop | 4517 + wrong-mimetype | 3864 + cdx-error | 1749 + blocked-cookie | 842 + null-body | 747 + wayback-error | 688 + wayback-content-error | 570 + gateway-timeout | 367 + petabox-error | 340 + spn2-cdx-lookup-failure | 150 + read-timeout | 122 + not-found | 119 + invalid-host-resolution | 63 + spn2-error | 23 + (20 rows) + +## Dump Initial Bulk Ingest Requests + +Note that this is all-time, not just recent, and will re-process a lot of +"no-pdf-link": + + COPY ( + SELECT row_to_json(ingest_request.*) FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'mag' + AND ( + ingest_file_result.status IS NULL + OR ingest_file_result.status = 'no-pdf-link' + OR ingest_file_result.status = 'cdx-error' + ) + AND ingest_request.base_url NOT LIKE '%journals.sagepub.com%' + AND ingest_request.base_url NOT LIKE '%pubs.acs.org%' + AND ingest_request.base_url NOT LIKE '%ahajournals.org%' + AND ingest_request.base_url NOT LIKE '%www.journal.csj.jp%' + AND ingest_request.base_url NOT LIKE '%aip.scitation.org%' + AND ingest_request.base_url NOT LIKE '%academic.oup.com%' + AND ingest_request.base_url NOT LIKE '%tandfonline.com%' + AND ingest_request.base_url NOT LIKE '%researchgate.net%' + AND ingest_request.base_url NOT LIKE '%muse.jhu.edu%' + AND ingest_request.base_url NOT LIKE '%omicsonline.org%' + AND ingest_request.base_url NOT LIKE '%link.springer.com%' + AND ingest_request.base_url NOT LIKE '%ieeexplore.ieee.org%' + ) TO '/srv/sandcrawler/tasks/mag_ingest_request_2021-08-03.rows.json'; + => COPY 8526647 + +Transform to ingest requests: + + ./scripts/ingestrequest_row2json.py /srv/sandcrawler/tasks/mag_ingest_request_2021-08-03.rows.json | pv -l | shuf > /srv/sandcrawler/tasks/mag_ingest_request_2021-08-03.ingest_request.json + => 8.53M 0:03:40 + +Enqueue the whole batch: + + cat /srv/sandcrawler/tasks/mag_ingest_request_2021-08-03.ingest_request.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + => DONE + +Updated stats after running initial bulk ingest: + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'mag' + AND ingest_request.base_url NOT LIKE '%journals.sagepub.com%' + AND ingest_request.base_url NOT LIKE '%pubs.acs.org%' + AND ingest_request.base_url NOT LIKE '%ahajournals.org%' + AND ingest_request.base_url NOT LIKE '%www.journal.csj.jp%' + AND ingest_request.base_url NOT LIKE '%aip.scitation.org%' + AND ingest_request.base_url NOT LIKE '%academic.oup.com%' + AND ingest_request.base_url NOT LIKE '%tandfonline.com%' + AND ingest_request.base_url NOT LIKE '%researchgate.net%' + AND ingest_request.base_url NOT LIKE '%muse.jhu.edu%' + AND ingest_request.base_url NOT LIKE '%omicsonline.org%' + AND ingest_request.base_url NOT LIKE '%link.springer.com%' + AND ingest_request.base_url NOT LIKE '%ieeexplore.ieee.org%' + AND ingest_request.created > '2021-06-01' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + status | count + -------------------------+--------- + success | 5184994 + no-capture | 3284416 + redirect-loop | 98685 + terminal-bad-status | 28733 + link-loop | 28518 + blocked-cookie | 22338 + no-pdf-link | 19073 + wrong-mimetype | 9122 + null-body | 2793 + wayback-error | 2128 + wayback-content-error | 1233 + cdx-error | 1198 + petabox-error | 617 + gateway-timeout | 395 + not-found | 130 + read-timeout | 128 + | 111 + invalid-host-resolution | 63 + spn2-cdx-lookup-failure | 24 + spn2-error | 20 + (20 rows) + +## Generate Seedlist + +For crawling, do a similar (but not identical) dump: + + COPY ( + SELECT row_to_json(t1.*) + FROM ( + SELECT ingest_request.*, ingest_file_result as result + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'mag' + AND ( + ingest_file_result.status IS NULL + OR ingest_file_result.status = 'no-capture' + OR ingest_file_result.status = 'cdx-error' + OR ingest_file_result.status = 'wayback-error' + OR ingest_file_result.status = 'wayback-content-error' + OR ingest_file_result.status = 'petabox-error' + OR ingest_file_result.status = 'spn2-cdx-lookup-failure' + ) + AND ingest_request.base_url NOT LIKE '%journals.sagepub.com%' + AND ingest_request.base_url NOT LIKE '%pubs.acs.org%' + AND ingest_request.base_url NOT LIKE '%ahajournals.org%' + AND ingest_request.base_url NOT LIKE '%www.journal.csj.jp%' + AND ingest_request.base_url NOT LIKE '%aip.scitation.org%' + AND ingest_request.base_url NOT LIKE '%academic.oup.com%' + AND ingest_request.base_url NOT LIKE '%tandfonline.com%' + AND ingest_request.base_url NOT LIKE '%researchgate.net%' + AND ingest_request.base_url NOT LIKE '%muse.jhu.edu%' + AND ingest_request.base_url NOT LIKE '%omicsonline.org%' + AND ingest_request.base_url NOT LIKE '%link.springer.com%' + AND ingest_request.base_url NOT LIKE '%ieeexplore.ieee.org%' + ) t1 + ) TO '/srv/sandcrawler/tasks/mag_ingest_request_2021-08-11.rows.json'; + => COPY 4599519 + +Prep ingest requests (for post-crawl use): + + ./scripts/ingestrequest_row2json.py /srv/sandcrawler/tasks/mag_ingest_request_2021-08-11.rows.json | pv -l > /srv/sandcrawler/tasks/mag_ingest_request_2021-08-11.ingest_request.json + => 4.60M 0:02:55 [26.2k/s] + +And actually dump seedlist(s): + + cat /srv/sandcrawler/tasks/mag_ingest_request_2021-08-11.rows.json | jq -r .base_url | sort -u -S 4G > /srv/sandcrawler/tasks/mag_seedlist_2021-08-11.base_url.txt + cat /srv/sandcrawler/tasks/mag_ingest_request_2021-08-11.rows.json | rg '"no-capture"' | jq -r .result.terminal_url | rg -v ^null$ | sort -u -S 4G > /srv/sandcrawler/tasks/mag_seedlist_2021-08-11.terminal_url.txt + cat /srv/sandcrawler/tasks/mag_seedlist_2021-08-11.terminal_url.txt /srv/sandcrawler/tasks/mag_seedlist_2021-08-11.base_url.txt | sort -u -S 4G > /srv/sandcrawler/tasks/mag_seedlist_2021-08-11.combined.txt + => DONE + + wc -l /srv/sandcrawler/tasks/mag_seedlist_2021-08-11.*.txt + 4593238 /srv/sandcrawler/tasks/mag_seedlist_2021-08-11.base_url.txt + 4632911 /srv/sandcrawler/tasks/mag_seedlist_2021-08-11.combined.txt + 3294710 /srv/sandcrawler/tasks/mag_seedlist_2021-08-11.terminal_url.txt + +## Post-Crawl Bulk Re-Ingest + +Got about 1.8 million new PDFs from crawl, and a sizable fraction of dupes (by +hash, URL agnostic). + +Enqueue for buik re-ingest: + + cat /srv/sandcrawler/tasks/mag_ingest_request_2021-08-11.ingest_request.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests-bulk -p -1 + => Thu 19 Aug 2021 09:10:59 PM UTC + + +## Post-Ingest Stats + +Just the new stuff (compare against above for delta): + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'mag' + AND ingest_request.base_url NOT LIKE '%journals.sagepub.com%' + AND ingest_request.base_url NOT LIKE '%pubs.acs.org%' + AND ingest_request.base_url NOT LIKE '%ahajournals.org%' + AND ingest_request.base_url NOT LIKE '%www.journal.csj.jp%' + AND ingest_request.base_url NOT LIKE '%aip.scitation.org%' + AND ingest_request.base_url NOT LIKE '%academic.oup.com%' + AND ingest_request.base_url NOT LIKE '%tandfonline.com%' + AND ingest_request.base_url NOT LIKE '%researchgate.net%' + AND ingest_request.base_url NOT LIKE '%muse.jhu.edu%' + AND ingest_request.base_url NOT LIKE '%omicsonline.org%' + AND ingest_request.base_url NOT LIKE '%link.springer.com%' + AND ingest_request.base_url NOT LIKE '%ieeexplore.ieee.org%' + AND ingest_request.created > '2021-06-01' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + status | count + -------------------------+--------- + success | 7748241 89.2% + no-capture | 429688 4.9% + redirect-loop | 172831 2.0% + terminal-bad-status | 94029 1.1% + no-pdf-link | 86437 1.0% + blocked-cookie | 67903 0.8% + link-loop | 50622 + wrong-mimetype | 21064 + null-body | 6650 + cdx-error | 3313 + wayback-error | 2630 + gateway-timeout | 399 + petabox-error | 268 + wayback-content-error | 170 + not-found | 130 + read-timeout | 128 + | 109 + invalid-host-resolution | 63 + bad-redirect | 39 + spn2-error | 20 + (20 rows) + +New success due to crawl (new batch only): 7748241 - 1957844 = 5,790,397 + +Overall success of new batch: 7748241. / 8686315 = 89.2% + +And combined (old and new) status again: + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'mag' + AND ingest_request.base_url NOT LIKE '%journals.sagepub.com%' + AND ingest_request.base_url NOT LIKE '%pubs.acs.org%' + AND ingest_request.base_url NOT LIKE '%ahajournals.org%' + AND ingest_request.base_url NOT LIKE '%www.journal.csj.jp%' + AND ingest_request.base_url NOT LIKE '%aip.scitation.org%' + AND ingest_request.base_url NOT LIKE '%academic.oup.com%' + AND ingest_request.base_url NOT LIKE '%tandfonline.com%' + AND ingest_request.base_url NOT LIKE '%researchgate.net%' + AND ingest_request.base_url NOT LIKE '%muse.jhu.edu%' + AND ingest_request.base_url NOT LIKE '%omicsonline.org%' + AND ingest_request.base_url NOT LIKE '%link.springer.com%' + AND ingest_request.base_url NOT LIKE '%ieeexplore.ieee.org%' + -- AND ingest_request.created > '2021-06-01' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + status | count + -------------------------------------+---------- + success | 31990062 + redirect-loop | 1704717 + no-capture | 1263462 + link-loop | 1218280 + blocked-cookie | 1213838 + no-pdf-link | 1096664 + terminal-bad-status | 960070 + gateway-timeout | 202190 + wrong-mimetype | 86557 + invalid-host-resolution | 37262 + null-body | 15443 + wayback-error | 12839 + cdx-error | 4047 + spn2-error | 1731 + spn2-error:job-failed | 962 + petabox-error | 463 + wayback-content-error | 379 + spn2-error:invalid-url-syntax | 336 + spn2-error:soft-time-limit-exceeded | 203 + | 175 + (20 rows) + +New success total: 31990062 - 26123975 = 5,866,087 + +A full 1,263,462 no-capture that could be attempted... though many of those may +be excluded for a specific reason. diff --git a/notes/ingest/2021-09-02_oai_pmh_patch.md b/notes/ingest/2021-09-02_oai_pmh_patch.md new file mode 100644 index 0000000..fded7b3 --- /dev/null +++ b/notes/ingest/2021-09-02_oai_pmh_patch.md @@ -0,0 +1,1578 @@ + +Just a "patch" of previous OAI-PMH crawl/ingest: re-ingesting and potentially +re-crawling content which failed to ingest the first time. + +May fold this in with more general patch crawling. + +## Basic Counts + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'oai' + AND ingest_request.link_source_id NOT LIKE 'oai:kb.dk:%' + AND ingest_request.link_source_id NOT LIKE 'oai:bdr.oai.bsb-muenchen.de:%' + AND ingest_request.link_source_id NOT LIKE 'oai:hispana.mcu.es:%' + AND ingest_request.link_source_id NOT LIKE 'oai:bnf.fr:%' + AND ingest_request.link_source_id NOT LIKE 'oai:ukm.si:%' + AND ingest_request.link_source_id NOT LIKE 'oai:biodiversitylibrary.org:%' + AND ingest_request.link_source_id NOT LIKE 'oai:hsp.org:%' + AND ingest_request.base_url NOT LIKE '%www.kb.dk%' + AND ingest_request.base_url NOT LIKE '%kb-images.kb.dk%' + AND ingest_request.base_url NOT LIKE '%mdz-nbn-resolving.de%' + AND ingest_request.base_url NOT LIKE '%aggr.ukm.um.si%' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + status | count + -----------------------+---------- + success | 14145387 + no-pdf-link | 12063022 + no-capture | 5485640 + redirect-loop | 2092705 + terminal-bad-status | 747372 + wrong-mimetype | 597219 + link-loop | 542144 + null-body | 93566 + cdx-error | 19798 + petabox-error | 17943 + | 15283 + wayback-error | 13897 + gateway-timeout | 511 + skip-url-blocklist | 184 + wayback-content-error | 146 + bad-redirect | 137 + redirects-exceeded | 120 + bad-gzip-encoding | 116 + timeout | 80 + blocked-cookie | 64 + (20 rows) + + SELECT + oai_prefix, + COUNT(CASE WHEN status = 'success' THEN 1 END) as success, + COUNT(*) as total + FROM ( + SELECT + ingest_file_result.status as status, + -- eg "oai:cwi.nl:4881" + substring(ingest_request.link_source_id FROM 'oai:([^:]+):.*') AS oai_prefix + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'oai' + AND ingest_request.link_source_id NOT LIKE 'oai:kb.dk:%' + AND ingest_request.link_source_id NOT LIKE 'oai:bdr.oai.bsb-muenchen.de:%' + AND ingest_request.link_source_id NOT LIKE 'oai:hispana.mcu.es:%' + AND ingest_request.link_source_id NOT LIKE 'oai:bnf.fr:%' + AND ingest_request.link_source_id NOT LIKE 'oai:ukm.si:%' + AND ingest_request.link_source_id NOT LIKE 'oai:biodiversitylibrary.org:%' + AND ingest_request.link_source_id NOT LIKE 'oai:hsp.org:%' + AND ingest_request.base_url NOT LIKE '%www.kb.dk%' + AND ingest_request.base_url NOT LIKE '%kb-images.kb.dk%' + AND ingest_request.base_url NOT LIKE '%mdz-nbn-resolving.de%' + AND ingest_request.base_url NOT LIKE '%aggr.ukm.um.si%' + ) t1 + GROUP BY oai_prefix + ORDER BY total DESC + LIMIT 40; + + + oai_prefix | success | total + ---------------------------+---------+--------- + repec | 1133175 | 2783448 + hal | 573218 | 1049607 + www.irgrid.ac.cn | 18007 | 748828 + cds.cern.ch | 74078 | 688091 + americanae.aecid.es | 71310 | 572792 + juser.fz-juelich.de | 23026 | 518551 + espace.library.uq.edu.au | 6649 | 508960 + igi.indrastra.com | 59629 | 478577 + archive.ugent.be | 65306 | 424014 + hrcak.srce.hr | 404085 | 414897 + zir.nsk.hr | 156753 | 397200 + renati.sunedu.gob.pe | 79362 | 388355 + hypotheses.org | 3 | 374296 + rour.neicon.ru | 7997 | 354529 + generic.eprints.org | 263566 | 340470 + invenio.nusl.cz | 6340 | 325867 + evastar-karlsruhe.de | 62282 | 317952 + quod.lib.umich.edu | 5 | 309135 + diva.org | 67917 | 298348 + t2r2.star.titech.ac.jp | 1085 | 289388 + edpsciences.org | 139495 | 284972 + repository.ust.hk | 10245 | 283417 + revues.org | 151156 | 277497 + pure.atira.dk | 13492 | 260754 + bibliotecadigital.jcyl.es | 50606 | 254134 + escholarship.org/ark | 140835 | 245203 + ojs.pkp.sfu.ca | 168029 | 229387 + lup.lub.lu.se | 49358 | 226602 + library.wur.nl | 15051 | 216738 + digitalrepository.unm.edu | 111704 | 211749 + infoscience.tind.io | 60166 | 207299 + edoc.mpg.de | 0 | 205252 + erudit.org | 168490 | 197803 + delibra.bg.polsl.pl | 38666 | 196652 + n/a | 0 | 193814 + aleph.bib-bvb.de | 4349 | 186666 + serval.unil.ch | 41643 | 186372 + orbi.ulg.ac.be | 2400 | 184551 + digitalcommons.unl.edu | 144025 | 184372 + bib-pubdb1.desy.de | 33525 | 182717 + (40 rows) + +Top counts by OAI prefix and status: + + SELECT + oai_prefix, + status, + COUNT((oai_prefix,status)) + FROM ( + SELECT + ingest_file_result.status as status, + -- eg "oai:cwi.nl:4881" + substring(ingest_request.link_source_id FROM 'oai:([^:]+):.*') AS oai_prefix + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'oai' + AND ingest_request.link_source_id NOT LIKE 'oai:kb.dk:%' + AND ingest_request.link_source_id NOT LIKE 'oai:bdr.oai.bsb-muenchen.de:%' + AND ingest_request.link_source_id NOT LIKE 'oai:hispana.mcu.es:%' + AND ingest_request.link_source_id NOT LIKE 'oai:bnf.fr:%' + AND ingest_request.link_source_id NOT LIKE 'oai:ukm.si:%' + AND ingest_request.link_source_id NOT LIKE 'oai:biodiversitylibrary.org:%' + AND ingest_request.link_source_id NOT LIKE 'oai:hsp.org:%' + AND ingest_request.base_url NOT LIKE '%www.kb.dk%' + AND ingest_request.base_url NOT LIKE '%kb-images.kb.dk%' + AND ingest_request.base_url NOT LIKE '%mdz-nbn-resolving.de%' + AND ingest_request.base_url NOT LIKE '%aggr.ukm.um.si%' + ) t1 + GROUP BY oai_prefix, status + ORDER BY COUNT DESC + LIMIT 50; + + oai_prefix | status | count + ---------------------------+---------------+--------- + repec | success | 1133175 + repec | no-pdf-link | 638105 + hal | success | 573218 + cds.cern.ch | no-capture | 540380 + repec | redirect-loop | 516451 + juser.fz-juelich.de | no-pdf-link | 477881 + americanae.aecid.es | no-pdf-link | 417766 + hrcak.srce.hr | success | 404085 + www.irgrid.ac.cn | no-pdf-link | 370908 + hal | no-pdf-link | 359252 + www.irgrid.ac.cn | no-capture | 355532 + espace.library.uq.edu.au | no-pdf-link | 320479 + igi.indrastra.com | no-pdf-link | 318242 + repec | no-capture | 316981 + invenio.nusl.cz | no-pdf-link | 309802 + rour.neicon.ru | redirect-loop | 300911 + hypotheses.org | no-pdf-link | 300251 + renati.sunedu.gob.pe | no-capture | 282800 + t2r2.star.titech.ac.jp | no-pdf-link | 272045 + generic.eprints.org | success | 263566 + quod.lib.umich.edu | no-pdf-link | 259661 + archive.ugent.be | no-capture | 256127 + evastar-karlsruhe.de | no-pdf-link | 248939 + zir.nsk.hr | link-loop | 226919 + repository.ust.hk | no-pdf-link | 208569 + edoc.mpg.de | no-pdf-link | 199758 + bibliotecadigital.jcyl.es | no-pdf-link | 188433 + orbi.ulg.ac.be | no-pdf-link | 172373 + diva.org | no-capture | 171115 + lup.lub.lu.se | no-pdf-link | 168652 + erudit.org | success | 168490 + ojs.pkp.sfu.ca | success | 168029 + lib.dr.iastate.edu | success | 158494 + zir.nsk.hr | success | 156753 + digital.kenyon.edu | success | 154900 + revues.org | success | 151156 + books.openedition.org | no-pdf-link | 149607 + freidok.uni-freiburg.de | no-pdf-link | 146837 + digitalcommons.unl.edu | success | 144025 + escholarship.org/ark | success | 140835 + culeuclid | link-loop | 140291 + edpsciences.org | success | 139495 + serval.unil.ch | no-pdf-link | 138644 + bib-pubdb1.desy.de | no-pdf-link | 133815 + krm.or.kr | no-pdf-link | 132461 + pure.atira.dk | no-pdf-link | 132179 + oai-gms.dimdi.de | redirect-loop | 131409 + aleph.bib-bvb.de | no-capture | 128261 + library.wur.nl | no-pdf-link | 124718 + lirias2repo.kuleuven.be | no-capture | 123106 + (50 rows) + +Note: could just delete the "excluded" rows? and not harvest them in the +future, and filter them at ingest time (in transform script). + + + +## Investigate no-pdf-link sandcrawler improvements + +Do some spot-sampling of 'no-pdf-link' domains, see if newer sandcrawler works: + + SELECT + ingest_request.link_source_id AS oai_id, + ingest_request.base_url as base_url , + ingest_file_result.terminal_url as terminal_url + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'oai' + AND ingest_request.link_source_id NOT LIKE 'oai:kb.dk:%' + AND ingest_request.link_source_id NOT LIKE 'oai:bdr.oai.bsb-muenchen.de:%' + AND ingest_request.link_source_id NOT LIKE 'oai:hispana.mcu.es:%' + AND ingest_request.link_source_id NOT LIKE 'oai:bnf.fr:%' + AND ingest_request.link_source_id NOT LIKE 'oai:ukm.si:%' + AND ingest_request.link_source_id NOT LIKE 'oai:biodiversitylibrary.org:%' + AND ingest_request.link_source_id NOT LIKE 'oai:hsp.org:%' + AND ingest_request.base_url NOT LIKE '%www.kb.dk%' + AND ingest_request.base_url NOT LIKE '%kb-images.kb.dk%' + AND ingest_request.base_url NOT LIKE '%mdz-nbn-resolving.de%' + AND ingest_request.base_url NOT LIKE '%aggr.ukm.um.si%' + AND ingest_file_result.status = 'no-pdf-link' + AND ingest_request.link_source_id LIKE 'oai:library.wur.nl:%' + ORDER BY random() + LIMIT 10; + +Random sampling of *all* 'no-pdf-link' URLs (see if newer sandcrawler works): + + \x auto + + SELECT + ingest_request.link_source_id AS oai_id, + ingest_request.base_url as base_url , + ingest_file_result.terminal_url as terminal_url + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'oai' + AND ingest_request.link_source_id NOT LIKE 'oai:kb.dk:%' + AND ingest_request.link_source_id NOT LIKE 'oai:bdr.oai.bsb-muenchen.de:%' + AND ingest_request.link_source_id NOT LIKE 'oai:hispana.mcu.es:%' + AND ingest_request.link_source_id NOT LIKE 'oai:bnf.fr:%' + AND ingest_request.link_source_id NOT LIKE 'oai:ukm.si:%' + AND ingest_request.link_source_id NOT LIKE 'oai:biodiversitylibrary.org:%' + AND ingest_request.link_source_id NOT LIKE 'oai:hsp.org:%' + AND ingest_request.base_url NOT LIKE '%www.kb.dk%' + AND ingest_request.base_url NOT LIKE '%kb-images.kb.dk%' + AND ingest_request.base_url NOT LIKE '%mdz-nbn-resolving.de%' + AND ingest_request.base_url NOT LIKE '%aggr.ukm.um.si%' + AND ingest_file_result.status = 'no-pdf-link' + ORDER BY random() + LIMIT 30; + +### repec (SKIP-PREFIX) + +-[ RECORD 1 ]+---------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:repec:eee:jmacro:v:54:y:2017:i:pb:p:332-351 +base_url | http://www.sciencedirect.com/science/article/pii/S0164070417301593 +terminal_url | http://www.sciencedirect.com/science/article/pii/S0164070417301593 +-[ RECORD 2 ]+---------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:repec:eee:jomega:v:16:y:1988:i:2:p:107-115 +base_url | http://www.sciencedirect.com/science/article/pii/0305-0483(88)90041-2 +terminal_url | https://www.sciencedirect.com/science/article/abs/pii/0305048388900412 +-[ RECORD 3 ]+---------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:repec:sgm:pzwzuw:v:14:i:59:y:2016:p:73-92 +base_url | http://pz.wz.uw.edu.pl/en +terminal_url | http://pz.wz.uw.edu.pl:80/en +-[ RECORD 1 ]+-------------------------------------------------------------------------------------------------------- +-------------------------------------- +oai_id | oai:repec:eee:jmacro:v:54:y:2017:i:pb:p:332-351 +base_url | http://www.sciencedirect.com/science/article/pii/S0164070417301593 +terminal_url | http://www.sciencedirect.com/science/article/pii/S0164070417301593 +-[ RECORD 2 ]+-------------------------------------------------------------------------------------------------------- +-------------------------------------- +oai_id | oai:repec:eee:jomega:v:16:y:1988:i:2:p:107-115 +base_url | http://www.sciencedirect.com/science/article/pii/0305-0483(88)90041-2 +terminal_url | https://www.sciencedirect.com/science/article/abs/pii/0305048388900412 +-[ RECORD 3 ]+-------------------------------------------------------------------------------------------------------- +-------------------------------------- +oai_id | oai:repec:sgm:pzwzuw:v:14:i:59:y:2016:p:73-92 +base_url | http://pz.wz.uw.edu.pl/en +terminal_url | http://pz.wz.uw.edu.pl:80/en +-[ RECORD 4 ]+---------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:repec:erv:rccsrc:y:2016:i:2016_11:35 +base_url | http://www.eumed.net/rev/caribe/2016/11/estructura.html +terminal_url | http://www.eumed.net:80/rev/caribe/2016/11/estructura.html +-[ RECORD 5 ]+---------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:repec:pio:envira:v:33:y:2001:i:4:p:629-647 +base_url | http://www.envplan.com/epa/fulltext/a33/a3319.pdf +terminal_url | http://uk.sagepub.com:80/en-gb/eur/pion-journals-published +-[ RECORD 6 ]+---------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:repec:tpr:qjecon:v:100:y:1985:i:3:p:651-75 +base_url | http://links.jstor.org/sici?sici=0033-5533%28198508%29100%3A3%3C651%3ATCOCEA%3E2.0.CO%3B2-2&origin=repec +terminal_url | https://www.jstor.org/stable/1884373 + +Huh! This is just a catalog of other domains. Should probably skip + +DONE: skip/filter repec + +### juser.fz-juelich.de (SCOPE) + +-[ RECORD 1 ]+------------------------------------------------------------ +oai_id | oai:juser.fz-juelich.de:132217 +base_url | http://juser.fz-juelich.de/record/132217 +terminal_url | http://juser.fz-juelich.de/record/132217 + +Poster; no files. + +-[ RECORD 2 ]+------------------------------------------------------------ +oai_id | oai:juser.fz-juelich.de:268598 +base_url | http://juser.fz-juelich.de/record/268598 +terminal_url | http://juser.fz-juelich.de/record/268598 + +Journal. + +-[ RECORD 3 ]+------------------------------------------------------------ +oai_id | oai:juser.fz-juelich.de:126613 +base_url | http://juser.fz-juelich.de/record/126613 +terminal_url | http://juser.fz-juelich.de/record/126613 + +-[ RECORD 4 ]+------------------------------------------------------------ +oai_id | oai:juser.fz-juelich.de:67362 +base_url | http://juser.fz-juelich.de/record/67362 +terminal_url | http://juser.fz-juelich.de/record/67362 +-[ RECORD 5 ]+------------------------------------------------------------ +oai_id | oai:juser.fz-juelich.de:869189 +base_url | http://juser.fz-juelich.de/record/869189 +terminal_url | http://juser.fz-juelich.de/record/869189 +-[ RECORD 6 ]+------------------------------------------------------------ +oai_id | oai:juser.fz-juelich.de:810746 +base_url | http://juser.fz-juelich.de/record/810746 +terminal_url | http://juser.fz-juelich.de/record/810746 +-[ RECORD 7 ]+------------------------------------------------------------ +oai_id | oai:juser.fz-juelich.de:52897 +base_url | http://juser.fz-juelich.de/search?p=id:%22PreJuSER-52897%22 +terminal_url | http://juser.fz-juelich.de/search?p=id:%22PreJuSER-52897%22 +-[ RECORD 8 ]+------------------------------------------------------------ +oai_id | oai:juser.fz-juelich.de:114755 +base_url | http://juser.fz-juelich.de/record/114755 +terminal_url | http://juser.fz-juelich.de/record/114755 +-[ RECORD 9 ]+------------------------------------------------------------ +oai_id | oai:juser.fz-juelich.de:58025 +base_url | http://juser.fz-juelich.de/search?p=id:%22PreJuSER-58025%22 +terminal_url | http://juser.fz-juelich.de/search?p=id:%22PreJuSER-58025%22 + +The search URLs seem redundant? Not going to try to handle those. + +"Powered by Invenio v1.1.7" + +All of these examples seem to be not papers. Maybe we can filter these better +at the harvest or transform stage? + +### americanae.aecid.es (MIXED) + +-[ RECORD 1 ]+--------------------------------------------------------------------------------------------- +oai_id | oai:americanae.aecid.es:502896 +base_url | http://biblioteca.clacso.edu.ar/gsdl/cgi-bin/library.cgi?a=d&c=mx/mx-010&d=60327292007oai +terminal_url | http://biblioteca.clacso.edu.ar/gsdl/cgi-bin/library.cgi?a=d&c=mx/mx-010&d=60327292007oai + +just a metadata record? links to redalyc + +METADATA-ONLY + +-[ RECORD 2 ]+--------------------------------------------------------------------------------------------- +oai_id | oai:americanae.aecid.es:534600 +base_url | http://bdh-rd.bne.es/viewer.vm?id=0000077778&page=1 +terminal_url | http://bdh-rd.bne.es/viewer.vm?id=0000077778&page=1 +-[ RECORD 3 ]+--------------------------------------------------------------------------------------------- +oai_id | oai:americanae.aecid.es:524567 +base_url | http://americanae.aecid.es/americanae/es/registros/registro.do?tipoRegistro=MTD&idBib=524567 +terminal_url | http://americanae.aecid.es/americanae/es/registros/registro.do?tipoRegistro=MTD&idBib=524567 + +NOT-FOUND (404) + +-[ RECORD 4 ]+--------------------------------------------------------------------------------------------- +oai_id | oai:americanae.aecid.es:378914 +base_url | http://americanae.aecid.es/americanae/es/registros/registro.do?tipoRegistro=MTD&idBib=378914 +terminal_url | http://americanae.aecid.es/americanae/es/registros/registro.do?tipoRegistro=MTD&idBib=378914 + +Some single-page image archival thing? bespoke, skipping. + +SKIP-BESPOKE + +-[ RECORD 5 ]+--------------------------------------------------------------------------------------------- +oai_id | oai:americanae.aecid.es:526142 +base_url | http://americanae.aecid.es/americanae/es/registros/registro.do?tipoRegistro=MTD&idBib=526142 +terminal_url | http://americanae.aecid.es/americanae/es/registros/registro.do?tipoRegistro=MTD&idBib=526142 + +NOT-FOUND (404) + +-[ RECORD 6 ]+--------------------------------------------------------------------------------------------- +oai_id | oai:americanae.aecid.es:373408 +base_url | http://americanae.aecid.es/americanae/es/registros/registro.do?tipoRegistro=MTD&idBib=373408 +terminal_url | http://americanae.aecid.es/americanae/es/registros/registro.do?tipoRegistro=MTD&idBib=373408 + +NOT-FOUND (404) + +### www.irgrid.ac.cn (SKIP-PREFIX) + +Chinese Academy of Sciences Institutional Repositories Grid + +-[ RECORD 1 ]+--------------------------------------------- +oai_id | oai:www.irgrid.ac.cn:1471x/1749980 +base_url | http://www.irgrid.ac.cn/handle/1471x/1749980 +terminal_url | http://www.irgrid.ac.cn/handle/1471x/1749980 + +Can't access + +FORBIDDEN + +-[ RECORD 2 ]+--------------------------------------------- +oai_id | oai:www.irgrid.ac.cn:1471x/857397 +base_url | http://www.irgrid.ac.cn/handle/1471x/857397 +terminal_url | http://www.irgrid.ac.cn/handle/1471x/857397 + +Just linking to another IR; skip it. + +http://ir.ipe.ac.cn/handle/122111/10608 + +requires login + +DONE: '/password-login;jsessionid' as a loginwall URL pattern + http://ir.ipe.ac.cn/handle/122111/10608 + http://ir.ipe.ac.cn/bitstream/122111/10608/2/%e9%92%9d%e9%a1%b6%e8%9e%ba%e6%97%8b%e8%97%bb%e5%9c%a8%e4%b8%8d%e5%90%8c%e5%85%89%e7%85%a7%e6%9d%a1%e4%bb%b6%e4%b8%8b%e7%9a%84%e6%94%be%e6%b0%a7%e7%89%b9%e6%80%a7_%e8%96%9b%e5%8d%87%e9%95%bf.pdf + +-[ RECORD 3 ]+--------------------------------------------- +oai_id | oai:www.irgrid.ac.cn:1471x/1060447 +base_url | http://www.irgrid.ac.cn/handle/1471x/1060447 +terminal_url | http://www.irgrid.ac.cn/handle/1471x/1060447 +-[ RECORD 4 ]+--------------------------------------------- +oai_id | oai:www.irgrid.ac.cn:1471x/1671377 +base_url | http://ir.iggcas.ac.cn/handle/132A11/68622 +terminal_url | http://ir.iggcas.ac.cn/handle/132A11/68622 +-[ RECORD 5 ]+--------------------------------------------- +oai_id | oai:www.irgrid.ac.cn:1471x/1178430 +base_url | http://www.irgrid.ac.cn/handle/1471x/1178430 +terminal_url | http://www.irgrid.ac.cn/handle/1471x/1178430 +-[ RECORD 6 ]+--------------------------------------------- +oai_id | oai:www.irgrid.ac.cn:1471x/2488017 +base_url | http://www.irgrid.ac.cn/handle/1471x/2488017 +terminal_url | http://www.irgrid.ac.cn/handle/1471x/2488017 +-[ RECORD 7 ]+--------------------------------------------- +oai_id | oai:www.irgrid.ac.cn:1471x/977147 +base_url | http://www.irgrid.ac.cn/handle/1471x/977147 +terminal_url | http://www.irgrid.ac.cn/handle/1471x/977147 +-[ RECORD 8 ]+--------------------------------------------- +oai_id | oai:www.irgrid.ac.cn:1471x/2454503 +base_url | http://ir.nwipb.ac.cn/handle/363003/9957 +terminal_url | http://ir.nwipb.ac.cn/handle/363003/9957 + +this domain is a disapointment :( + +should continue crawling, as the metadata is open and good. but won't get fulltext? + +### hal (FIXED-PARTIAL) + +-[ RECORD 1 ]+------------------------------------------------------------------------------ +oai_id | oai:hal:hal-00744951v1 +base_url | https://hal.archives-ouvertes.fr/hal-00744951 +terminal_url | https://hal.archives-ouvertes.fr/hal-00744951 + +Off-site OA link. + +FIXED-HAL + +-[ RECORD 2 ]+------------------------------------------------------------------------------ +oai_id | oai:hal:hal-01065398v1 +base_url | https://hal.archives-ouvertes.fr/hal-01065398/file/AbstractSGE14_B_assaad.pdf +terminal_url | https://hal.archives-ouvertes.fr/index/index +-[ RECORD 3 ]+------------------------------------------------------------------------------ +oai_id | oai:hal:lirmm-00371599v1 +base_url | https://hal-lirmm.ccsd.cnrs.fr/lirmm-00371599 +terminal_url | https://hal-lirmm.ccsd.cnrs.fr/lirmm-00371599 + +To elsevier :( + +-[ RECORD 4 ]+------------------------------------------------------------------------------ +oai_id | oai:hal:hal-00284780v1 +base_url | https://hal.archives-ouvertes.fr/hal-00284780 +terminal_url | https://hal.archives-ouvertes.fr/hal-00284780 + +METADATA-ONLY + +-[ RECORD 5 ]+------------------------------------------------------------------------------ +oai_id | oai:hal:hal-00186151v1 +base_url | https://hal.archives-ouvertes.fr/hal-00186151 +terminal_url | https://hal.archives-ouvertes.fr/hal-00186151 + +METADATA-ONLY + +-[ RECORD 6 ]+------------------------------------------------------------------------------ +oai_id | oai:hal:hal-00399754v1 +base_url | https://hal.archives-ouvertes.fr/hal-00399754 +terminal_url | https://hal.archives-ouvertes.fr/hal-00399754 + +METADATA-ONLY + + +### espace.library.uq.edu.au (SKIP) + +-[ RECORD 1 ]+------------------------------------------------ +oai_id | oai:espace.library.uq.edu.au:uq:136497 +base_url | https://espace.library.uq.edu.au/view/UQ:136497 +terminal_url | https://espace.library.uq.edu.au/view/UQ:136497 +-[ RECORD 2 ]+------------------------------------------------ +oai_id | oai:espace.library.uq.edu.au:uq:411389 +base_url | https://espace.library.uq.edu.au/view/UQ:411389 +terminal_url | https://espace.library.uq.edu.au/view/UQ:411389 +-[ RECORD 3 ]+------------------------------------------------ +oai_id | oai:espace.library.uq.edu.au:uq:401773 +base_url | https://espace.library.uq.edu.au/view/UQ:401773 +terminal_url | https://espace.library.uq.edu.au/view/UQ:401773 +-[ RECORD 4 ]+------------------------------------------------ +oai_id | oai:espace.library.uq.edu.au:uq:675334 +base_url | https://espace.library.uq.edu.au/view/UQ:675334 +terminal_url | https://espace.library.uq.edu.au/view/UQ:675334 +-[ RECORD 5 ]+------------------------------------------------ +oai_id | oai:espace.library.uq.edu.au:uq:312311 +base_url | https://espace.library.uq.edu.au/view/UQ:312311 +terminal_url | https://espace.library.uq.edu.au/view/UQ:312311 +-[ RECORD 6 ]+------------------------------------------------ +oai_id | oai:espace.library.uq.edu.au:uq:209401 +base_url | https://espace.library.uq.edu.au/view/UQ:209401 +terminal_url | https://espace.library.uq.edu.au/view/UQ:209401 +-[ RECORD 7 ]+------------------------------------------------ +oai_id | oai:espace.library.uq.edu.au:uq:327188 +base_url | https://espace.library.uq.edu.au/view/UQ:327188 +terminal_url | https://espace.library.uq.edu.au/view/UQ:327188 + +Very javascript heavy (skeletal HTML). And just links to fulltext on publisher +sites. + +### igi.indrastra.com (METADATA-ONLY) + +-[ RECORD 1 ]+--------------------------------------------------------- +oai_id | oai:igi.indrastra.com:267221 +base_url | http://igi.indrastra.com/items/show/267221 +terminal_url | http://igi.indrastra.com/items/show/267221 +-[ RECORD 2 ]+--------------------------------------------------------- +oai_id | oai:igi.indrastra.com:181799 +base_url | http://igi.indrastra.com/items/show/181799 +terminal_url | http://igi.indrastra.com/items/show/181799 +-[ RECORD 3 ]+--------------------------------------------------------- +oai_id | oai:igi.indrastra.com:125382 +base_url | http://igi.indrastra.com/items/show/125382 +terminal_url | http://igi.indrastra.com/items/show/125382 +-[ RECORD 4 ]+--------------------------------------------------------- +oai_id | oai:igi.indrastra.com:47266 +base_url | http://igi.indrastra.com/items/show/47266 +terminal_url | http://igi.indrastra.com/items/show/47266 +-[ RECORD 5 ]+--------------------------------------------------------- +oai_id | oai:igi.indrastra.com:12872 +base_url | http://igi.indrastra.com/items/show/12872 +terminal_url | http://igi.indrastra.com/items/show/12872 +-[ RECORD 6 ]+--------------------------------------------------------- +oai_id | oai:igi.indrastra.com:231620 +base_url | http://igi.indrastra.com/items/show/231620 +terminal_url | http://igi.indrastra.com/items/show/231620 + +"Proudly powered by Omeka" + +### invenio.nusl.cz (METADATA-ONLY) + + oai_id | base_url | terminal_url +----------------------------+------------------------------------+-------------------------------------- + oai:invenio.nusl.cz:237409 | http://www.nusl.cz/ntk/nusl-237409 | http://invenio.nusl.cz/record/237409 + oai:invenio.nusl.cz:180783 | http://www.nusl.cz/ntk/nusl-180783 | http://invenio.nusl.cz/record/180783 + oai:invenio.nusl.cz:231961 | http://www.nusl.cz/ntk/nusl-231961 | http://invenio.nusl.cz/record/231961 + oai:invenio.nusl.cz:318800 | http://www.nusl.cz/ntk/nusl-318800 | http://invenio.nusl.cz/record/318800 + oai:invenio.nusl.cz:259695 | http://www.nusl.cz/ntk/nusl-259695 | http://invenio.nusl.cz/record/259695 + oai:invenio.nusl.cz:167393 | http://www.nusl.cz/ntk/nusl-167393 | http://invenio.nusl.cz/record/167393 + oai:invenio.nusl.cz:292987 | http://www.nusl.cz/ntk/nusl-292987 | http://invenio.nusl.cz/record/292987 + oai:invenio.nusl.cz:283396 | http://www.nusl.cz/ntk/nusl-283396 | http://invenio.nusl.cz/record/283396 + oai:invenio.nusl.cz:241512 | http://www.nusl.cz/ntk/nusl-241512 | http://invenio.nusl.cz/record/241512 + oai:invenio.nusl.cz:178631 | http://www.nusl.cz/ntk/nusl-178631 | http://invenio.nusl.cz/record/178631 + +Metadata only (at least this set) + +### hypotheses.org + +-[ RECORD 1 ]+--------------------------------------------- +oai_id | oai:hypotheses.org:mittelalter/9529 +base_url | http://mittelalter.hypotheses.org/9529 +terminal_url | https://mittelalter.hypotheses.org/9529 +-[ RECORD 2 ]+--------------------------------------------- +oai_id | oai:hypotheses.org:archivalia/18638 +base_url | http://archivalia.hypotheses.org/18638 +terminal_url | https://archivalia.hypotheses.org/18638 +-[ RECORD 3 ]+--------------------------------------------- +oai_id | oai:hypotheses.org:archivalia/13614 +base_url | http://archivalia.hypotheses.org/13614 +terminal_url | https://archivalia.hypotheses.org/13614 +-[ RECORD 4 ]+--------------------------------------------- +oai_id | oai:hypotheses.org:teteschercheuses/2785 +base_url | http://teteschercheuses.hypotheses.org/2785 +terminal_url | https://teteschercheuses.hypotheses.org/2785 +-[ RECORD 5 ]+--------------------------------------------- +oai_id | oai:hypotheses.org:altervsego/608 +base_url | http://altervsego.hypotheses.org/608 +terminal_url | http://altervsego.hypotheses.org/608 +-[ RECORD 6 ]+--------------------------------------------- +oai_id | oai:hypotheses.org:archivewk1/21905 +base_url | http://archivewk1.hypotheses.org/21905 +terminal_url | https://archivewk1.hypotheses.org/21905 +-[ RECORD 7 ]+--------------------------------------------- +oai_id | oai:hypotheses.org:slkdiaspo/3321 +base_url | http://slkdiaspo.hypotheses.org/3321 +terminal_url | https://slkdiaspo.hypotheses.org/3321 +-[ RECORD 8 ]+--------------------------------------------- +oai_id | oai:hypotheses.org:diga/280 +base_url | http://diga.hypotheses.org/280 +terminal_url | https://diga.hypotheses.org/280 + +These are all a big mix... basically blogs. Should continue crawling, but expect no yield. + +### t2r2.star.titech.ac.jp (METADATA-ONLY) + +-[ RECORD 1 ]+---------------------------------------------------------------------------------------------------- +oai_id | oai:t2r2.star.titech.ac.jp:00105099 +base_url | http://t2r2.star.titech.ac.jp/cgi-bin/publicationinfo.cgi?q_publication_content_number=CTT100499795 +terminal_url | http://t2r2.star.titech.ac.jp/cgi-bin/publicationinfo.cgi?q_publication_content_number=CTT100499795 +-[ RECORD 2 ]+---------------------------------------------------------------------------------------------------- +oai_id | oai:t2r2.star.titech.ac.jp:00101346 +base_url | http://t2r2.star.titech.ac.jp/cgi-bin/publicationinfo.cgi?q_publication_content_number=CTT100495549 +terminal_url | http://t2r2.star.titech.ac.jp/cgi-bin/publicationinfo.cgi?q_publication_content_number=CTT100495549 +-[ RECORD 3 ]+---------------------------------------------------------------------------------------------------- +oai_id | oai:t2r2.star.titech.ac.jp:50161100 +base_url | http://t2r2.star.titech.ac.jp/cgi-bin/publicationinfo.cgi?q_publication_content_number=CTT100632554 +terminal_url | http://t2r2.star.titech.ac.jp/cgi-bin/publicationinfo.cgi?q_publication_content_number=CTT100632554 +-[ RECORD 4 ]+---------------------------------------------------------------------------------------------------- +oai_id | oai:t2r2.star.titech.ac.jp:00232407 +base_url | http://t2r2.star.titech.ac.jp/cgi-bin/publicationinfo.cgi?q_publication_content_number=CTT100527528 +terminal_url | http://t2r2.star.titech.ac.jp/cgi-bin/publicationinfo.cgi?q_publication_content_number=CTT100527528 +-[ RECORD 5 ]+---------------------------------------------------------------------------------------------------- +oai_id | oai:t2r2.star.titech.ac.jp:50120040 +base_url | http://t2r2.star.titech.ac.jp/cgi-bin/publicationinfo.cgi?q_publication_content_number=CTT100612598 +terminal_url | http://t2r2.star.titech.ac.jp/cgi-bin/publicationinfo.cgi?q_publication_content_number=CTT100612598 +-[ RECORD 6 ]+---------------------------------------------------------------------------------------------------- +oai_id | oai:t2r2.star.titech.ac.jp:50321440 +base_url | http://t2r2.star.titech.ac.jp/cgi-bin/publicationinfo.cgi?q_publication_content_number=CTT100713492 +terminal_url | http://t2r2.star.titech.ac.jp/cgi-bin/publicationinfo.cgi?q_publication_content_number=CTT100713492 +-[ RECORD 7 ]+---------------------------------------------------------------------------------------------------- +oai_id | oai:t2r2.star.titech.ac.jp:50235666 +base_url | http://t2r2.star.titech.ac.jp/cgi-bin/publicationinfo.cgi?q_publication_content_number=CTT100668778 +terminal_url | http://t2r2.star.titech.ac.jp/cgi-bin/publicationinfo.cgi?q_publication_content_number=CTT100668778 + + +### quod.lib.umich.edu + +-[ RECORD 1 ]+------------------------------------------------------------------------------------------------------- +oai_id | oai:quod.lib.umich.edu:acf2679.0015.003-2 +base_url | http://name.umdl.umich.edu/acf2679.0015.003 +terminal_url | https://quod.lib.umich.edu/cgi/t/text/text-idx?c=moajrnl;idno=acf2679.0015.003 +-[ RECORD 2 ]+------------------------------------------------------------------------------------------------------- +oai_id | oai:quod.lib.umich.edu:b14970.0001.001 +base_url | http://name.umdl.umich.edu/B14970.0001.001 +terminal_url | https://quod.lib.umich.edu/cgi/t/text/text-idx?c=eebo2;idno=B14970.0001.001 +-[ RECORD 3 ]+------------------------------------------------------------------------------------------------------- +oai_id | oai:quod.lib.umich.edu:acf2679.0009.010-3 +base_url | http://name.umdl.umich.edu/ACF2679-1623SOUT-209 +terminal_url | https://quod.lib.umich.edu/cgi/t/text/text-idx?c=moajrnl;idno=acf2679.0009.010;node=acf2679.0009.010:3 +-[ RECORD 4 ]+------------------------------------------------------------------------------------------------------- +oai_id | oai:quod.lib.umich.edu:acg2248.1-16.006-43 +base_url | http://name.umdl.umich.edu/acg2248.1-16.006 +terminal_url | https://quod.lib.umich.edu/cgi/t/text/text-idx?c=moajrnl;idno=acg2248.1-16.006 +-[ RECORD 5 ]+------------------------------------------------------------------------------------------------------- +oai_id | oai:quod.lib.umich.edu:acg2248.1-14.011-9 +base_url | http://name.umdl.umich.edu/ACG2248-1489LADI-364 +terminal_url | https://quod.lib.umich.edu/cgi/t/text/text-idx?c=moajrnl;idno=acg2248.1-14.011;node=acg2248.1-14.011:9 +-[ RECORD 6 ]+------------------------------------------------------------------------------------------------------- +oai_id | oai:quod.lib.umich.edu:acg1336.1-24.006-9 +base_url | http://name.umdl.umich.edu/acg1336.1-24.006 +terminal_url | https://quod.lib.umich.edu/cgi/t/text/text-idx?c=moajrnl;idno=acg1336.1-24.006 +-[ RECORD 7 ]+------------------------------------------------------------------------------------------------------- +oai_id | oai:quod.lib.umich.edu:africanamer.0002.32a +base_url | http://name.umdl.umich.edu/africanamer.0002.32a +terminal_url | https://quod.lib.umich.edu/cgi/t/text/text-idx?c=africanamer;idno=africanamer.0002.32a + +These are... issues of journals? Should continue to crawl, but not expect much. + +### evastar-karlsruhe.de (METADATA-ONLY) + +-[ RECORD 1 ]+---------------------------------------------------- +oai_id | oai:evastar-karlsruhe.de:270011444 +base_url | https://publikationen.bibliothek.kit.edu/270011444 +terminal_url | https://publikationen.bibliothek.kit.edu/270011444 +-[ RECORD 2 ]+---------------------------------------------------- +oai_id | oai:evastar-karlsruhe.de:1000050117 +base_url | https://publikationen.bibliothek.kit.edu/1000050117 +terminal_url | https://publikationen.bibliothek.kit.edu/1000050117 +-[ RECORD 3 ]+---------------------------------------------------- +oai_id | oai:evastar-karlsruhe.de:362296 +base_url | https://publikationen.bibliothek.kit.edu/362296 +terminal_url | https://publikationen.bibliothek.kit.edu/362296 +-[ RECORD 4 ]+---------------------------------------------------- +oai_id | oai:evastar-karlsruhe.de:23042000 +base_url | https://publikationen.bibliothek.kit.edu/23042000 +terminal_url | https://publikationen.bibliothek.kit.edu/23042000 +-[ RECORD 5 ]+---------------------------------------------------- +oai_id | oai:evastar-karlsruhe.de:1000069945 +base_url | https://publikationen.bibliothek.kit.edu/1000069945 +terminal_url | https://publikationen.bibliothek.kit.edu/1000069945 + + +### repository.ust.hk + +-[ RECORD 1 ]+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:repository.ust.hk:1783.1-67233 +base_url | http://repository.ust.hk/ir/Record/1783.1-67233 +terminal_url | http://repository.ust.hk/ir/Record/1783.1-67233 +-[ RECORD 2 ]+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:repository.ust.hk:1783.1-63232 +base_url | http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=LinksAMR&SrcApp=PARTNER_APP&DestLinkType=FullRecord&DestApp=WOS&KeyUT=A1981KV47900017 +terminal_url | http://login.webofknowledge.com/error/Error?Src=IP&Alias=WOK5&Error=IPError&Params=DestParams%3D%253FUT%253DWOS%253AA1981KV47900017%2526customersID%253DLinksAMR%2526product%253DWOS%2526action%253Dretrieve%2526mode%253DFullRecord%26DestApp%3DWOS%26SrcApp%3DPARTNER_APP%26SrcAuth%3DLinksAMR&PathInfo=%2F&RouterURL=http%3A%2F%2Fwww.webofknowledge.com%2F&Domain=.webofknowledge.com +-[ RECORD 3 ]+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:repository.ust.hk:1783.1-2891 +base_url | http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=LinksAMR&SrcApp=PARTNER_APP&DestLinkType=FullRecord&DestApp=WOS&KeyUT=000240035400103 +terminal_url | https://login.webofknowledge.com/error/Error?Src=IP&Alias=WOK5&Error=IPError&Params=DestParams%3D%253FUT%253DWOS%253A000240035400103%2526customersID%253DLinksAMR%2526product%253DWOS%2526action%253Dretrieve%2526mode%253DFullRecord%26DestApp%3DWOS%26SrcApp%3DPARTNER_APP%26SrcAuth%3DLinksAMR&PathInfo=%2F&RouterURL=https%3A%2F%2Fwww.webofknowledge.com%2F&Domain=.webofknowledge.com +-[ RECORD 4 ]+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:repository.ust.hk:1783.1-56231 +base_url | http://repository.ust.hk/ir/Record/1783.1-56231 +terminal_url | http://repository.ust.hk/ir/Record/1783.1-56231 + +[...] + +-[ RECORD 6 ]+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:repository.ust.hk:1783.1-24872 +base_url | http://repository.ust.hk/ir/Record/1783.1-24872 +terminal_url | http://repository.ust.hk/ir/Record/1783.1-24872 +-[ RECORD 7 ]+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:repository.ust.hk:1783.1-3457 +base_url | http://lbdiscover.ust.hk/uresolver?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rfr_id=info:sid/HKUST:SPI&rft.genre=article&rft.issn=0003-6870&rft.volume=40&rft.issue=2&rft.date=2009&rft.spage=267&rft.epage=279&rft.aulast=Witana&rft.aufirst=Channa+R.&rft.atitle=Effects+of+surface+characteristics+on+the+plantar+shape+of+feet+and+subjects'+perceived+sensations +terminal_url | http://lbdiscover.ust.hk/uresolver/?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rfr_id=info:sid/HKUST:SPI&rft.genre=article&rft.issn=0003-6870&rft.volume=40&rft.issue=2&rft.date=2009&rft.spage=267&rft.epage=279&rft.aulast=Witana&rft.aufirst=Channa+R.&rft.atitle=Effects+of+surface+characteristics+on+the+plantar+shape+of+feet+and+subjects'+perceived+sensations +-[ RECORD 8 ]+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:repository.ust.hk:1783.1-73215 +base_url | http://repository.ust.hk/ir/Record/1783.1-73215 +terminal_url | http://repository.ust.hk/ir/Record/1783.1-73215 + +DONE: gateway.isiknowledge.com is bogus/blocking? + + +### edoc.mpg.de (SKIP-DEPRECATED) + + oai_id | base_url | terminal_url +------------------------+---------------------------+--------------------------- + oai:edoc.mpg.de:416650 | http://edoc.mpg.de/416650 | http://edoc.mpg.de/416650 + oai:edoc.mpg.de:8195 | http://edoc.mpg.de/8195 | http://edoc.mpg.de/8195 + oai:edoc.mpg.de:379655 | http://edoc.mpg.de/379655 | http://edoc.mpg.de/379655 + oai:edoc.mpg.de:641179 | http://edoc.mpg.de/641179 | http://edoc.mpg.de/641179 + oai:edoc.mpg.de:607141 | http://edoc.mpg.de/607141 | http://edoc.mpg.de/607141 + oai:edoc.mpg.de:544412 | http://edoc.mpg.de/544412 | http://edoc.mpg.de/544412 + oai:edoc.mpg.de:314531 | http://edoc.mpg.de/314531 | http://edoc.mpg.de/314531 + oai:edoc.mpg.de:405047 | http://edoc.mpg.de/405047 | http://edoc.mpg.de/405047 + oai:edoc.mpg.de:239650 | http://edoc.mpg.de/239650 | http://edoc.mpg.de/239650 + oai:edoc.mpg.de:614852 | http://edoc.mpg.de/614852 | http://edoc.mpg.de/614852 + +This whole instance seems to have been replaced + +### bibliotecadigital.jcyl.es (SKIP-DIGITIZED) + +-[ RECORD 1 ]+-------------------------------------------------------------------------------- +oai_id | oai:bibliotecadigital.jcyl.es:10000039962 +base_url | http://bibliotecadigital.jcyl.es/i18n/catalogo_imagenes/grupo.cmd?path=10044664 +terminal_url | http://bibliotecadigital.jcyl.es/i18n/catalogo_imagenes/grupo.cmd?path=10044664 +-[ RECORD 2 ]+-------------------------------------------------------------------------------- +oai_id | oai:bibliotecadigital.jcyl.es:14075 +base_url | http://bibliotecadigital.jcyl.es/i18n/consulta/registro.cmd?id=14075 +terminal_url | http://bibliotecadigital.jcyl.es/i18n/consulta/registro.cmd?id=14075 +-[ RECORD 3 ]+-------------------------------------------------------------------------------- +oai_id | oai:bibliotecadigital.jcyl.es:4842 +base_url | http://bibliotecadigital.jcyl.es/i18n/consulta/registro.cmd?id=4842 +terminal_url | http://bibliotecadigital.jcyl.es/i18n/consulta/registro.cmd?id=4842 +-[ RECORD 4 ]+-------------------------------------------------------------------------------- +oai_id | oai:bibliotecadigital.jcyl.es:14799 +base_url | http://bibliotecadigital.jcyl.es/i18n/consulta/registro.cmd?id=14799 +terminal_url | http://bibliotecadigital.jcyl.es/i18n/consulta/registro.cmd?id=14799 +-[ RECORD 5 ]+-------------------------------------------------------------------------------- +oai_id | oai:bibliotecadigital.jcyl.es:821 +base_url | http://bibliotecadigital.jcyl.es/i18n/catalogo_imagenes/grupo.cmd?path=1003474 +terminal_url | http://bibliotecadigital.jcyl.es/i18n/catalogo_imagenes/grupo.cmd?path=1003474 + +Digitized images as pages; too much to deal with for now. + +### orbi.ulg.ac.be + +-[ RECORD 1 ]+---------------------------------------------------------------- +oai_id | oai:orbi.ulg.ac.be:2268/128079 +base_url | https://orbi.uliege.be/handle/2268/128079 +terminal_url | https://orbi.uliege.be/handle/2268/128079 +-[ RECORD 2 ]+---------------------------------------------------------------- +oai_id | oai:orbi.ulg.ac.be:2268/67659 +base_url | https://orbi.uliege.be/handle/2268/67659 +terminal_url | https://orbi.uliege.be/handle/2268/67659 +-[ RECORD 3 ]+---------------------------------------------------------------- +oai_id | oai:orbi.ulg.ac.be:2268/35521 +base_url | https://orbi.uliege.be/handle/2268/35521 +terminal_url | https://orbi.uliege.be/handle/2268/35521 +-[ RECORD 4 ]+---------------------------------------------------------------- +oai_id | oai:orbi.ulg.ac.be:2268/107922 +base_url | https://orbi.uliege.be/handle/2268/107922 +terminal_url | https://orbi.uliege.be/handle/2268/107922 +-[ RECORD 5 ]+---------------------------------------------------------------- +oai_id | oai:orbi.ulg.ac.be:2268/215694 +base_url | https://orbi.uliege.be/handle/2268/215694 +terminal_url | https://orbi.uliege.be/handle/2268/215694 + +Described below. + +### library.wur.nl (FIXED-BESPOKE) + + oai_id | base_url | terminal_url + -----------------------------------+------------------------------------------------+------------------------------------------------ + oai:library.wur.nl:wurpubs/440939 | https://library.wur.nl/WebQuery/wurpubs/440939 | https://library.wur.nl/WebQuery/wurpubs/440939 + oai:library.wur.nl:wurpubs/427707 | https://library.wur.nl/WebQuery/wurpubs/427707 | https://library.wur.nl/WebQuery/wurpubs/427707 + oai:library.wur.nl:wurpubs/359208 | https://library.wur.nl/WebQuery/wurpubs/359208 | https://library.wur.nl/WebQuery/wurpubs/359208 + oai:library.wur.nl:wurpubs/433378 | https://library.wur.nl/WebQuery/wurpubs/433378 | https://library.wur.nl/WebQuery/wurpubs/433378 + oai:library.wur.nl:wurpubs/36416 | https://library.wur.nl/WebQuery/wurpubs/36416 | https://library.wur.nl/WebQuery/wurpubs/36416 + oai:library.wur.nl:wurpubs/469930 | https://library.wur.nl/WebQuery/wurpubs/469930 | https://library.wur.nl/WebQuery/wurpubs/469930 + oai:library.wur.nl:wurpubs/350076 | https://library.wur.nl/WebQuery/wurpubs/350076 | https://library.wur.nl/WebQuery/wurpubs/350076 + oai:library.wur.nl:wurpubs/19109 | https://library.wur.nl/WebQuery/wurpubs/19109 | https://library.wur.nl/WebQuery/wurpubs/19109 + oai:library.wur.nl:wurpubs/26146 | https://library.wur.nl/WebQuery/wurpubs/26146 | https://library.wur.nl/WebQuery/wurpubs/26146 + oai:library.wur.nl:wurpubs/529922 | https://library.wur.nl/WebQuery/wurpubs/529922 | https://library.wur.nl/WebQuery/wurpubs/529922 + (10 rows) + +Seems like a one-off site? But added a pattern. + +### pure.atira.dk + +-[ RECORD 1 ]+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +oai_id | oai:pure.atira.dk:publications/a27762fd-0919-4753-af55-00b9b26d02e0 +base_url | https://www.research.manchester.ac.uk/portal/en/publications/hightech-cities-and-the-primitive-jungle-visionary-urbanism-in-europe-and-japan-of-the-1960s(a27762fd-0919-4753-af55-00b9b26d02e0).html +terminal_url | https://www.research.manchester.ac.uk/portal/en/publications/hightech-cities-and-the-primitive-jungle-visionary-urbanism-in-europe-and-japan-of-the-1960s(a27762fd-0919-4753-af55-00b9b26d02e0).html +-[ RECORD 2 ]+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +oai_id | oai:pure.atira.dk:publications/215c8b96-a821-4947-bee4-c7470e9fbaf8 +base_url | https://www.research.manchester.ac.uk/portal/en/publications/service-recovery-in-health-services--understanding-the-desired-qualities-and-behaviours-of-general-practitioners-during-service-recovery-encounters(215c8b96-a821-4947-bee4-c7470e9fbaf8).html +terminal_url | https://www.research.manchester.ac.uk/portal/en/publications/service-recovery-in-health-services--understanding-the-desired-qualities-and-behaviours-of-general-practitioners-during-service-recovery-encounters(215c8b96-a821-4947-bee4-c7470e9fbaf8).html +-[ RECORD 3 ]+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +oai_id | oai:pure.atira.dk:publications/95d4920a-12c7-4e25-b86c-5f075ea23a38 +base_url | https://www.tandfonline.com/doi/full/10.1080/03057070.2016.1197694 +terminal_url | https://www.tandfonline.com/action/cookieAbsent +-[ RECORD 4 ]+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +oai_id | oai:pure.atira.dk:publications/8a2508ee-14c9-4c6a-851a-6db442090f41 +base_url | https://www.research.manchester.ac.uk/portal/en/publications/microstructure-and-grain-size-dependence-of-ferroelectric-properties-of-batio3-thin-films-on-lanio3-buffered-si(8a2508ee-14c9-4c6a-851a-6db442090f41).html +terminal_url | https://www.research.manchester.ac.uk/portal/en/publications/microstructure-and-grain-size-dependence-of-ferroelectric-properties-of-batio3-thin-films-on-lanio3-buffered-si(8a2508ee-14c9-4c6a-851a-6db442090f41).html + +Metadata only + +DONE: /cookieAbsent is cookie block + https://www.tandfonline.com/action/cookieAbsent + +### bib-pubdb1.desy.de (FIXED-INVENIO) + +-[ RECORD 2 ]+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:bib-pubdb1.desy.de:96756 +base_url | http://bib-pubdb1.desy.de/record/96756 +terminal_url | http://bib-pubdb1.desy.de/record/96756 + +Metadata only. + +-[ RECORD 3 ]+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:bib-pubdb1.desy.de:416556 +base_url | http://bib-pubdb1.desy.de/record/416556 +terminal_url | http://bib-pubdb1.desy.de/record/416556 + +Fixed! + +-[ RECORD 4 ]+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:bib-pubdb1.desy.de:414545 +base_url | http://bib-pubdb1.desy.de/search?p=id:%22PUBDB-2018-04027%22 +terminal_url | http://bib-pubdb1.desy.de/search?p=id:%22PUBDB-2018-04027%22 +-[ RECORD 5 ]+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:bib-pubdb1.desy.de:170169 +base_url | http://bib-pubdb1.desy.de/record/170169 +terminal_url | http://bib-pubdb1.desy.de/record/170169 +-[ RECORD 6 ]+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:bib-pubdb1.desy.de:191154 +base_url | http://bib-pubdb1.desy.de/record/191154 +terminal_url | http://bib-pubdb1.desy.de/record/191154 + +Metadata only + +-[ RECORD 7 ]+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:bib-pubdb1.desy.de:155092 +base_url | http://bib-pubdb1.desy.de/record/155092 +terminal_url | http://bib-pubdb1.desy.de/record/155092 + +Fixed! + +-[ RECORD 8 ]+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:bib-pubdb1.desy.de:97158 +base_url | http://bib-pubdb1.desy.de/record/97158 +terminal_url | http://bib-pubdb1.desy.de/record/97158 + +Metadata only + +"Powered by Invenio v1.1.7" + +Can/should skip the "search" URLs + +### serval.unil.ch + +-[ RECORD 1 ]+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:serval.unil.ch:bib_60346fc75171 +base_url | https://serval.unil.ch/notice/serval:BIB_60346FC75171 +terminal_url | https://serval.unil.ch/en/notice/serval:BIB_60346FC75171 +-[ RECORD 2 ]+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:serval.unil.ch:bib_4db47fc4b593 +base_url | https://serval.unil.ch/notice/serval:BIB_4DB47FC4B593 +terminal_url | https://serval.unil.ch/en/notice/serval:BIB_4DB47FC4B593 +-[ RECORD 3 ]+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:serval.unil.ch:bib_57aac24fe115 +base_url | http://nbn-resolving.org/urn/resolver.pl?urn=urn:nbn:ch:serval-BIB_57AAC24FE1154 +terminal_url | https://nbn-resolving.org/urn/resolver.pl?urn=urn:nbn:ch:serval-BIB_57AAC24FE1154 +-[ RECORD 4 ]+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:serval.unil.ch:bib_deabae6baf6c +base_url | https://serval.unil.ch/notice/serval:BIB_DEABAE6BAF6C +terminal_url | https://serval.unil.ch/en/notice/serval:BIB_DEABAE6BAF6C +-[ RECORD 5 ]+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:serval.unil.ch:bib_a5ec0df1370f +base_url | https://serval.unil.ch/notice/serval:BIB_A5EC0DF1370F +terminal_url | https://wayf.switch.ch/SWITCHaai/WAYF?entityID=https%3A%2F%2Fmy.unil.ch%2Fshibboleth&return=https%3A%2F%2Fserval.unil.ch%2FShibboleth.sso%2FLogin%3FSAMLDS%3D1%26target%3Dss%253Amem%253Aed270c26d4a36cefd1bf6a840472abe0ee5556cb5f3b42de708f3ea984775dfd +-[ RECORD 6 ]+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:serval.unil.ch:bib_080300c2e23c +base_url | https://serval.unil.ch/resource/serval:BIB_080300C2E23C.P001/REF.pdf +terminal_url | https://wayf.switch.ch/SWITCHaai/WAYF?entityID=https%3A%2F%2Fmy.unil.ch%2Fshibboleth&return=https%3A%2F%2Fserval.unil.ch%2FShibboleth.sso%2FLogin%3FSAMLDS%3D1%26target%3Dss%253Amem%253A154453d78a0fb75ffa220f7b6fe73b29447fa6ed048addf31897b41001f44679 +-[ RECORD 7 ]+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:serval.unil.ch:bib_de777dd2b07f +base_url | https://serval.unil.ch/notice/serval:BIB_DE777DD2B07F +terminal_url | https://serval.unil.ch/en/notice/serval:BIB_DE777DD2B07F +-[ RECORD 8 ]+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:serval.unil.ch:bib_5e824e244c27 +base_url | https://serval.unil.ch/notice/serval:BIB_5E824E244C27 +terminal_url | https://serval.unil.ch/en/notice/serval:BIB_5E824E244C27 + +Metadata only? See elsewhere. + +### Random Links + +-[ RECORD 1 ]+--------------------------------------------------------------------------------------------------------------------- +oai_id | oai:dbc.wroc.pl:41031 +base_url | https://dbc.wroc.pl/dlibra/docmetadata?showContent=true&id=41031 +terminal_url | https://dbc.wroc.pl/dlibra/docmetadata?showContent=true&id=41031 + +This is some platform/package thing. PDF is in an iframe. Platform is "DLibra". +FIXED-DLIBRA + +-[ RECORD 2 ]+--------------------------------------------------------------------------------------------------------------------- +oai_id | oai:orbi.ulg.ac.be:2268/174291 +base_url | https://orbi.uliege.be/handle/2268/174291 +terminal_url | https://orbi.uliege.be/handle/2268/174291 + +DSpace platform. There are multiple files, and little to "select" on. + +https://orbi.uliege.be/handle/2268/174200 has only single PDF and easier to work with + +PARTIAL-DSPACE + +-[ RECORD 3 ]+--------------------------------------------------------------------------------------------------------------------- +oai_id | oai:library.tue.nl:664163 +base_url | http://repository.tue.nl/664163 +terminal_url | http://repository.tue.nl/664163 + +Ah, this is the Pure platform from Elsevier. +Redirects to: https://research.tue.nl/en/publications/lowering-the-threshold-for-computers-in-early-design-some-advance + +FIXED-PURE + + +-[ RECORD 4 ]+--------------------------------------------------------------------------------------------------------------------- +oai_id | oai:juser.fz-juelich.de:49579 +base_url | http://juser.fz-juelich.de/search?p=id:%22PreJuSER-49579%22 +terminal_url | http://juser.fz-juelich.de/search?p=id:%22PreJuSER-49579%22 + +(handled above) + +-[ RECORD 5 ]+--------------------------------------------------------------------------------------------------------------------- +oai_id | oai:dspace.mit.edu:1721.1/97937 +base_url | https://orcid.org/0000-0002-2066-2082 +terminal_url | https://orcid.org/0000-0002-2066-2082 + +ORCID! Skip it. + +DONE: skip orcid.org in `terminal_url`, and/or at harvest/transform time. + +-[ RECORD 6 ]+--------------------------------------------------------------------------------------------------------------------- +oai_id | oai:edoc.mpg.de:360269 +base_url | http://edoc.mpg.de/360269 +terminal_url | http://edoc.mpg.de/360269 + +Seems like this whole repo has disapeared, or been replaced by... pure? maybe a different pure? + +DONE: edoc.mpg.de -> pure.mpg.de + +-[ RECORD 7 ]+--------------------------------------------------------------------------------------------------------------------- +oai_id | oai:books.openedition.org:msha/17716 +base_url | http://books.openedition.org/msha/17716 +terminal_url | https://books.openedition.org/msha/17716 + +Open edition is free to read HTML, but not PDF (or epub, etc). + +TODO: for some? all? openedition books records, try HTML ingest (not PDF ingest) + +HTML-WORKED + +-[ RECORD 8 ]+--------------------------------------------------------------------------------------------------------------------- +oai_id | oai:epub.oeaw.ac.at:0x003aba48 +base_url | http://epub.oeaw.ac.at/?arp=8609-0inhalt/B02_2146_FP_Flores%20Castillo.pdf +terminal_url | http://epub.oeaw.ac.at/?arp=8609-0inhalt/B02_2146_FP_Flores%20Castillo.pdf + +requires login + +FORBIDDEN + +-[ RECORD 9 ]+--------------------------------------------------------------------------------------------------------------------- +oai_id | oai:dspace.mit.edu:1721.1/88986 +base_url | https://orcid.org/0000-0002-4147-2560 +terminal_url | https://orcid.org/0000-0002-4147-2560 + +DONE: skip orcids + +-[ RECORD 10 ]--------------------------------------------------------------------------------------------------------------------- +oai_id | oai:repository.ust.hk:1783.1-28786 +base_url | http://repository.ust.hk/ir/Record/1783.1-28786 +terminal_url | http://repository.ust.hk/ir/Record/1783.1-28786 + +Generator: VuFind 5.1.1 +just a metadata record + +METADATA-ONLY + +-[ RECORD 11 ]--------------------------------------------------------------------------------------------------------------------- +oai_id | oai:rcin.org.pl:50797 +base_url | http://195.187.71.10/ipac20/ipac.jsp?profile=iblpan&index=BOCLC&term=cc95215472 +terminal_url | http://195.187.71.10/ipac20/ipac.jsp?profile=iblpan&index=BOCLC&term=cc95215472 + +Seems like a software platform? not sure. + +METADATA-ONLY + +-[ RECORD 12 ]--------------------------------------------------------------------------------------------------------------------- +oai_id | oai:dea.lib.unideb.hu:2437/69641 +base_url | http://webpac.lib.unideb.hu:8082/WebPac/CorvinaWeb?action=cclfind&resultview=long&ccltext=idno+bibFSZ1008709 +terminal_url | https://webpac.lib.unideb.hu/WebPac/CorvinaWeb?action=cclfind&resultview=long&ccltext=idno+bibFSZ1008709 + +-[ RECORD 13 ]--------------------------------------------------------------------------------------------------------------------- +oai_id | oai:unsworks.library.unsw.edu.au:1959.4/64871 +base_url | http://handle.unsw.edu.au/1959.4/64871 +terminal_url | https://www.unsworks.unsw.edu.au/primo-explore/fulldisplay?vid=UNSWORKS&docid=unsworks_62832&context=L + +-[ RECORD 14 ]--------------------------------------------------------------------------------------------------------------------- +oai_id | oai:www.wbc.poznan.pl:225930 +base_url | https://www.wbc.poznan.pl/dlibra/docmetadata?showContent=true&id=225930 +terminal_url | https://www.wbc.poznan.pl/dlibra/docmetadata?showContent=true&id=225930 + +SOFT-404 + +-[ RECORD 15 ]--------------------------------------------------------------------------------------------------------------------- +oai_id | oai:repository.erciyes.edu.tr:105 +base_url | http://repository.erciyes.edu.tr/bilimname/items/show/105 +terminal_url | http://repository.erciyes.edu.tr:80/bilimname/items/show/105 + +GONE (domain not registered) + +-[ RECORD 16 ]--------------------------------------------------------------------------------------------------------------------- +oai_id | oai:digi.ub.uni-heidelberg.de:37500 +base_url | https://archivum-laureshamense-digital.de/view/sad_a1_nr_20_13 +terminal_url | https://archivum-laureshamense-digital.de/view/sad_a1_nr_20_13 + +Seems like a bespoke site + +SKIP-BESPOKE + +-[ RECORD 17 ]--------------------------------------------------------------------------------------------------------------------- +oai_id | oai:t2r2.star.titech.ac.jp:50401364 +base_url | http://t2r2.star.titech.ac.jp/cgi-bin/publicationinfo.cgi?q_publication_content_number=CTT100758313 +terminal_url | http://t2r2.star.titech.ac.jp/cgi-bin/publicationinfo.cgi?q_publication_content_number=CTT100758313 + +METADATA-ONLY + +-[ RECORD 18 ]--------------------------------------------------------------------------------------------------------------------- +oai_id | oai:epubs.cclrc.ac.uk:work/4714 +base_url | http://purl.org/net/epubs/work/4714 +terminal_url | https://epubs.stfc.ac.uk/work/4714 + +It's got a purl! haha. + +METADATA-ONLY + +------ + +Another batch! With some repeat domains removed. + +-[ RECORD 1 ]+----------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:cris.vtt.fi:persons/142c030f-ba7b-491a-8669-a361088355cc +base_url | https://cris.vtt.fi/en/persons/142c030f-ba7b-491a-8669-a361088355cc +terminal_url | https://cris.vtt.fi/en/persons/oleg-antropov + +SKIP + +-[ RECORD 2 ]+----------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:etd.adm.unipi.it:etd-05302014-183910 +base_url | http://etd.adm.unipi.it/theses/available/etd-05302014-183910/ +terminal_url | https://etd.adm.unipi.it/theses/available/etd-05302014-183910/ + +Some software platform? Pretty basic/bespoke + +FIXED-PARTIAL + +-[ RECORD 3 ]+----------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:bibliotecadigital.jcyl.es:10000098246 +base_url | http://bibliotecadigital.jcyl.es/i18n/catalogo_imagenes/grupo.cmd?path=10316451 +terminal_url | http://bibliotecadigital.jcyl.es/i18n/catalogo_imagenes/grupo.cmd?path=10316451 + +SKIP (see elsewhere) + +-[ RECORD 7 ]+----------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:elektra.cdaea.es:documento.29259 +base_url | https://www.juntadeandalucia.es/cultura/cdaea/elektra/catalogo_execute.html?tipoObjeto=1&id=29259 +terminal_url | https://www.juntadeandalucia.es/cultura/cdaea/elektra/catalogo_execute.html?tipoObjeto=1&id=29259 + +Photo. + +SKIP-SCOPE + +-[ RECORD 9 ]+----------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:unsworks.library.unsw.edu.au:1959.4/unsworks_60829 +base_url | http://handle.unsw.edu.au/1959.4/unsworks_60829 +terminal_url | https://www.unsworks.unsw.edu.au/primo-explore/fulldisplay?vid=UNSWORKS&docid=unsworks_modsunsworks_60829&context=L + +METADATA-ONLY + +-[ RECORD 12 ]----------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:pure.leuphana.de:publications/7d040cf2-b3b5-4671-8906-76b5bc8d870a +base_url | http://fox.leuphana.de/portal/de/publications/studies-in-childrens-literature-1500--2000-editors-celia-keenan-(7d040cf2-b3b5-4671-8906-76b5bc8d870a).html +terminal_url | http://fox.leuphana.de/portal/de/publications/studies-in-childrens-literature-1500--2000-editors-celia-keenan-(7d040cf2-b3b5-4671-8906-76b5bc8d870a).html + +unsure + +-[ RECORD 16 ]----------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:library.wur.nl:wurpubs/369344 +base_url | https://library.wur.nl/WebQuery/wurpubs/369344 +terminal_url | https://library.wur.nl/WebQuery/wurpubs/369344 + +this specific record not OA (but site is fine/fixed) + +-[ RECORD 17 ]----------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:escholarship.umassmed.edu:oapubs-2146 +base_url | https://escholarship.umassmed.edu/oapubs/1147 +terminal_url | http://escholarship.umassmed.edu/oapubs/1147/ + +just links to publisher (no content in repo) + +-[ RECORD 18 ]----------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:digitalcommons.usu.edu:wild_facpub-1010 +base_url | https://digitalcommons.usu.edu/wild_facpub/11 +terminal_url | http://digitalcommons.usu.edu/wild_facpub/11/ + +also just links to publisher (no content in repo) + +-[ RECORD 25 ]----------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:igi.indrastra.com:306768 +base_url | http://igi.indrastra.com/items/show/306768 +terminal_url | http://igi.indrastra.com/items/show/306768 + +(see elsewhere) + +-[ RECORD 26 ]----------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:fau.digital.flvc.org:fau_9804 +base_url | http://purl.flvc.org/fcla/dt/12932 +terminal_url | http://fau.digital.flvc.org/islandora/object/fau%3A9804 + +Islandora. + +-[ RECORD 27 ]----------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:dspace.lu.lv:7/16019 +base_url | https://dspace.lu.lv/dspace/handle/7/16019 +terminal_url | https://dspace.lu.lv/dspace/handle/7/16019 + +LOGINWALL + +-[ RECORD 28 ]----------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:zir.nsk.hr:umas_218 +base_url | https://repozitorij.svkst.unist.hr/islandora/object/umas:218 +terminal_url | https://repozitorij.svkst.unist.hr/islandora/object/umas:218 + +REMOVED + + +-[ RECORD 29 ]----------------------------------------------------------------------------------------------------------------------------------------------------------------- +oai_id | oai:digi.ub.uni-heidelberg.de:36390 +base_url | https://digi.hadw-bw.de/view/sbhadwmnkl_a_1917_5 +terminal_url | https://digi.hadw-bw.de/view/sbhadwmnkl_a_1917_5 + +Book, with chapters, not an individual work. + +-[ RECORD 2 ]+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +oai_id | oai:krm.or.kr:10056135m201r +base_url | https://www.krm.or.kr/krmts/link.html?dbGubun=SD&m201_id=10056135&res=y +terminal_url | https://www.krm.or.kr/krmts/search/detailview/research.html?dbGubun=SD&category=Research&m201_id=10056135 + +research results repository; keep crawling + +SKIP-SCOPE + +-[ RECORD 3 ]+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +oai_id | oai:www.db-thueringen.de:dbt_mods_00005191 +base_url | https://www.db-thueringen.de/receive/dbt_mods_00005191 +terminal_url | https://www.db-thueringen.de/receive/dbt_mods_00005191 + +powered by "MyCoRe" + +FIXED-MYCORE + +-[ RECORD 6 ]+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +oai_id | oai:bibliotecavirtualandalucia.juntadeandalucia.es:1017405 +base_url | http://www.bibliotecavirtualdeandalucia.es/catalogo/es/consulta/registro.cmd?id=1017405 +terminal_url | http://www.bibliotecavirtualdeandalucia.es/catalogo/es/consulta/registro.cmd?id=1017405 + +seems to be a general purpose regional library? not research-specific + +SKIP-UNSURE + +-[ RECORD 7 ]+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +oai_id | oai:etd.adm.unipi.it:etd-02272019-123644 +base_url | http://etd.adm.unipi.it/theses/available/etd-02272019-123644/ +terminal_url | https://etd.adm.unipi.it/theses/available/etd-02272019-123644/ + +This specific URL is not available (FORBIDDEN) + +others have multiple files, not just a single PDF: +https://etd.adm.unipi.it/t/etd-09102013-124430/ + +SKIP-UNSURE + +-[ RECORD 9 ]+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +oai_id | oai:commons.ln.edu.hk:sw_master-5408 +base_url | https://commons.ln.edu.hk/sw_master/4408 +terminal_url | https://commons.ln.edu.hk/sw_master/4408/ + +worth crawling I guess + +METADATA-ONLY + +-[ RECORD 10 ]------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +oai_id | oai:mouseion.jax.org:ssbb1976-1224 +base_url | https://mouseion.jax.org/ssbb1976/225 +terminal_url | https://mouseion.jax.org/ssbb1976/225/ + +METADATA-ONLY + +-[ RECORD 13 ]------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +oai_id | oai:aleph.bib-bvb.de:bvb01-016604343 +base_url | http://bvbm1.bib-bvb.de/webclient/DeliveryManager?pid=176332&custom_att_2=simple_viewer +terminal_url | http://digital.bib-bvb.de/view/action/singleViewer.do?dvs=1593269021002~476&locale=en_US&VIEWER_URL=/view/action/singleViewer.do?&DELIVERY_RULE_ID=31&frameId=1&usePid1=true&usePid2=true + +SOFT-404 / FORBIDDEN (cookie timeout) + +-[ RECORD 14 ]------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +oai_id | oai:bivaldi.gva.es:11740 +base_url | https://bivaldi.gva.es/es/consulta/registro.do?id=11740 +terminal_url | https://bivaldi.gva.es/es/consulta/registro.do?id=11740 + + +-[ RECORD 16 ]------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +oai_id | oai:library.wur.nl:wurpubs/443282 +base_url | https://library.wur.nl/WebQuery/wurpubs/443282 +terminal_url | https://library.wur.nl/WebQuery/wurpubs/443282 + +DIGIBIS platform (like some others) + +FIXED-PARTIAL + +-[ RECORD 18 ]------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +oai_id | oai:hal:in2p3-00414135v1 +base_url | http://hal.in2p3.fr/in2p3-00414135 +terminal_url | http://hal.in2p3.fr:80/in2p3-00414135 + +METADATA-ONLY + +-[ RECORD 19 ]------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +oai_id | oai:aaltodoc.aalto.fi:123456789/13201 +base_url | https://aaltodoc.aalto.fi/handle/123456789/13201 +terminal_url | https://aaltodoc.aalto.fi/handle/123456789/13201 + +This specific record is not accessible. +Another: https://aaltodoc.aalto.fi/handle/123456789/38002 + +DSpace 5.4 + +Worked (from recent changes) + + +-[ RECORD 20 ]------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +oai_id | oai:sedici.unlp.edu.ar:10915/40144 +base_url | http://xjornadaslc.fahce.unlp.edu.ar/actas/Ramon_Esteban_Chaparro.pdf/view +terminal_url | http://xjornadaslc.fahce.unlp.edu.ar/actas/Ramon_Esteban_Chaparro.pdf/view + +This is a journal! Cool. Plone software platform. + +FIXED + +## Top no-capture Domains + +Top terminal no-capture domains: + + SELECT domain, COUNT(domain) + FROM ( + SELECT + ingest_file_result.ingest_type, + ingest_file_result.status, + substring(ingest_file_result.terminal_url FROM '[^/]+://([^/]*)') AS domain + FROM ingest_file_result + LEFT JOIN ingest_request + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'oai' + AND ingest_file_result.status = 'no-capture' + ) t1 + WHERE t1.domain != '' + AND t1.status != 'success' + GROUP BY domain + ORDER BY COUNT DESC + LIMIT 30; + + domain | count + -----------------------------------+------- + digitalrepository.unm.edu | 94087 + escholarship.org | 80632 + ir.opt.ac.cn | 70504 + idus.us.es | 67908 + www.cambridge.org | 56376 + www.ssoar.info | 52534 + rep.bntu.by | 52127 + scholarworks.umt.edu | 48546 + publikationen.ub.uni-frankfurt.de | 46987 + dk.um.si | 45753 + repositorio.uladech.edu.pe | 37028 + uu.diva-portal.org | 34929 + digitalcommons.law.byu.edu | 31732 + sedici.unlp.edu.ar | 31233 + elib.sfu-kras.ru | 29131 + jyx.jyu.fi | 28144 + www.repository.cam.ac.uk | 27728 + nagoya.repo.nii.ac.jp | 26673 + www.duo.uio.no | 25258 + www.persee.fr | 24968 + www2.senado.leg.br | 24426 + tesis.ucsm.edu.pe | 24049 + digitalcommons.unl.edu | 21974 + www.degruyter.com | 21940 + www.igi-global.com | 20736 + thekeep.eiu.edu | 20712 + docs.lib.purdue.edu | 20538 + repositorio.cepal.org | 20280 + elib.bsu.by | 19620 + minds.wisconsin.edu | 19473 + (30 rows) + +These all seem worth crawling. A couple publishers (cambridge.org), and +persee.fr will probably fail, but not too many URLs. + +## Summary of Filtered Prefixes and Domains (OAI-PMH) + +oai:kb.dk: + too large and generic +oai:bdr.oai.bsb-muenchen.de: + too large and generic +oai:hispana.mcu.es: + too large and generic +oai:bnf.fr: + too large and generic +oai:ukm.si: + too large and generic +oai:biodiversitylibrary.org: + redundant with other ingest and archive.org content +oai:hsp.org: + large; historical content only +oai:repec: + large; mostly (entirely?) links to publisher sites +oai:n/a: + meta? +oai:quod.lib.umich.edu: + entire issues? hard to crawl so skip for now +oai:hypotheses.org: + HTML, not PDF +oai:americanae.aecid.es: + large, complex. skip for now +oai:www.irgrid.ac.cn: + aggregator of other IRs +oai:espace.library.uq.edu.au: + large; metadata only; javascript heavy (poor heritrix crawling) +oai:edoc.mpg.de: + deprecated domain, with no redirects +oai:bibliotecadigital.jcyl.es: + digitized historical docs; hard to crawl, skip for now +oai:repository.erciyes.edu.tr: + gone (domain lapsed) +oai:krm.or.kr: + "research results repository" (metadata only) + +www.kb.dk + large, general purpose, scope +kb-images.kb.dk + deprecated +mdz-nbn-resolving.de + multiple prefixes end up here. historical docs, scope +aggr.ukm.um.si + large, out of scope +edoc.mpg.de + deprecated domain +doaj.org + index (metadata only) +orcid.org + out of scope +gateway.isiknowledge.com + clarivate login/payall (skipping in ingest) + +Needs filtering to a subset of records (by 'set' or other filtering?): + +oai:igi.indrastra.com: +oai:invenio.nusl.cz: +oai:t2r2.star.titech.ac.jp: +oai:evastar-karlsruhe.de: +oai:repository.ust.hk: +oai:serval.unil.ch: +oai:pure.atira.dk: + +FIlters in SQL syntax: + + AND ingest_request.link_source_id NOT LIKE 'oai:kb.dk:%' + AND ingest_request.link_source_id NOT LIKE 'oai:bdr.oai.bsb-muenchen.de:%' + AND ingest_request.link_source_id NOT LIKE 'oai:hispana.mcu.es:%' + AND ingest_request.link_source_id NOT LIKE 'oai:bnf.fr:%' + AND ingest_request.link_source_id NOT LIKE 'oai:ukm.si:%' + AND ingest_request.link_source_id NOT LIKE 'oai:biodiversitylibrary.org:%' + AND ingest_request.link_source_id NOT LIKE 'oai:hsp.org:%' + AND ingest_request.link_source_id NOT LIKE 'oai:repec:%' + AND ingest_request.link_source_id NOT LIKE 'oai:n/a:%' + AND ingest_request.link_source_id NOT LIKE 'oai:quod.lib.umich.edu:%' + AND ingest_request.link_source_id NOT LIKE 'oai:americanae.aecid.es:%' + AND ingest_request.link_source_id NOT LIKE 'oai:www.irgrid.ac.cn:%' + AND ingest_request.link_source_id NOT LIKE 'oai:espace.library.uq.edu:%' + AND ingest_request.link_source_id NOT LIKE 'oai:edoc.mpg.de:%' + AND ingest_request.link_source_id NOT LIKE 'oai:bibliotecadigital.jcyl.es:%' + AND ingest_request.link_source_id NOT LIKE 'oai:repository.erciyes.edu.tr:%' + AND ingest_request.link_source_id NOT LIKE 'oai:krm.or.kr:%' + AND ingest_request.base_url NOT LIKE '%www.kb.dk%' + AND ingest_request.base_url NOT LIKE '%kb-images.kb.dk%' + AND ingest_request.base_url NOT LIKE '%mdz-nbn-resolving.de%' + AND ingest_request.base_url NOT LIKE '%aggr.ukm.um.si%' + AND ingest_request.base_url NOT LIKE '%edoc.mpg.de%' + AND ingest_request.base_url NOT LIKE '%doaj.org%' + AND ingest_request.base_url NOT LIKE '%orcid.org%' + AND ingest_request.base_url NOT LIKE '%gateway.isiknowledge.com%' + +and in some contexts (PDFs; switch to HTML): + + AND ingest_request.link_source_id NOT LIKE 'oai:hypotheses.org:%' + +## Overall Summary of OAI-PMH Stuff + +Big picture is that the majority of `no-pdf-link` crawl status are because of +repository scope, record scope, or content format issues. That being said, +there was a sizable fraction of sites which were platforms (like DSpace) which +were not ingesting well. + +A significant fraction of records are "metadata only" (of papers), or non-paper +entity types (like persons, grants, or journal titles), and a growing fraction +(?) are metadata plus link to OA publisher fulltext (offsite). Might be +possible to detect these at ingest time, or earlier at OAI-PMH +harvest/transform time and filter them out. + +It may be worthwhile to attempt ingest of multiple existing captures +(timestamps) in the ingest pipeline. Eg, isntead of chosing a single "best" +capture, if therea are multiple HTTP 200 status captures, try ingest with each +(or at least a couple). This is because repository software gets upgraded, so +old "no-capture" or "not found" or "link loop" type captures may work when +recrawled. + +New summary with additional filters: + + SELECT ingest_file_result.status, COUNT(*) + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.ingest_type = 'pdf' + AND ingest_request.link_source = 'oai' + AND ingest_request.link_source_id NOT LIKE 'oai:kb.dk:%' + AND ingest_request.link_source_id NOT LIKE 'oai:bdr.oai.bsb-muenchen.de:%' + AND ingest_request.link_source_id NOT LIKE 'oai:hispana.mcu.es:%' + AND ingest_request.link_source_id NOT LIKE 'oai:bnf.fr:%' + AND ingest_request.link_source_id NOT LIKE 'oai:ukm.si:%' + AND ingest_request.link_source_id NOT LIKE 'oai:biodiversitylibrary.org:%' + AND ingest_request.link_source_id NOT LIKE 'oai:hsp.org:%' + AND ingest_request.link_source_id NOT LIKE 'oai:repec:%' + AND ingest_request.link_source_id NOT LIKE 'oai:n/a:%' + AND ingest_request.link_source_id NOT LIKE 'oai:quod.lib.umich.edu:%' + AND ingest_request.link_source_id NOT LIKE 'oai:americanae.aecid.es:%' + AND ingest_request.link_source_id NOT LIKE 'oai:www.irgrid.ac.cn:%' + AND ingest_request.link_source_id NOT LIKE 'oai:espace.library.uq.edu:%' + AND ingest_request.link_source_id NOT LIKE 'oai:edoc.mpg.de:%' + AND ingest_request.link_source_id NOT LIKE 'oai:bibliotecadigital.jcyl.es:%' + AND ingest_request.link_source_id NOT LIKE 'oai:repository.erciyes.edu.tr:%' + AND ingest_request.link_source_id NOT LIKE 'oai:krm.or.kr:%' + AND ingest_request.base_url NOT LIKE '%www.kb.dk%' + AND ingest_request.base_url NOT LIKE '%kb-images.kb.dk%' + AND ingest_request.base_url NOT LIKE '%mdz-nbn-resolving.de%' + AND ingest_request.base_url NOT LIKE '%aggr.ukm.um.si%' + AND ingest_request.base_url NOT LIKE '%edoc.mpg.de%' + AND ingest_request.base_url NOT LIKE '%doaj.org%' + AND ingest_request.base_url NOT LIKE '%orcid.org%' + AND ingest_request.base_url NOT LIKE '%gateway.isiknowledge.com%' + AND ingest_request.link_source_id NOT LIKE 'oai:hypotheses.org:%' + GROUP BY status + ORDER BY COUNT DESC + LIMIT 20; + + status | count + -----------------------+---------- + success | 12872279 + no-pdf-link | 9329602 + no-capture | 4696362 + redirect-loop | 1541458 + terminal-bad-status | 660418 + link-loop | 452831 + wrong-mimetype | 434868 + null-body | 71065 + cdx-error | 17005 + | 15275 + petabox-error | 12743 + wayback-error | 11759 + skip-url-blocklist | 182 + gateway-timeout | 122 + redirects-exceeded | 120 + bad-redirect | 117 + bad-gzip-encoding | 111 + wayback-content-error | 102 + timeout | 72 + blocked-cookie | 62 + (20 rows) + diff --git a/notes/ingest/2021-09-03_daily_improvements.md b/notes/ingest/2021-09-03_daily_improvements.md new file mode 100644 index 0000000..a0bb0c5 --- /dev/null +++ b/notes/ingest/2021-09-03_daily_improvements.md @@ -0,0 +1,1021 @@ + +Periodic check-in of daily crawling/ingest. + +Overall ingest status, past 30 days: + + SELECT ingest_file_result.ingest_type, ingest_file_result.status, COUNT(*) + FROM ingest_file_result + LEFT JOIN ingest_request + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE ingest_request.created >= NOW() - '30 day'::INTERVAL + AND ingest_request.ingest_type = 'pdf' + AND ingest_request.ingest_request_source = 'fatcat-changelog' + GROUP BY ingest_file_result.ingest_type, ingest_file_result.status + ORDER BY COUNT DESC + LIMIT 20; + + ingest_type | status | count + -------------+-------------------------+-------- + pdf | no-pdf-link | 158474 + pdf | spn2-cdx-lookup-failure | 135344 + pdf | success | 127938 + pdf | spn2-error | 65411 + pdf | gateway-timeout | 63112 + pdf | blocked-cookie | 26338 + pdf | terminal-bad-status | 24853 + pdf | link-loop | 15699 + pdf | spn2-error:job-failed | 13862 + pdf | redirect-loop | 11432 + pdf | cdx-error | 2376 + pdf | too-many-redirects | 2186 + pdf | wrong-mimetype | 2142 + pdf | forbidden | 1758 + pdf | spn2-error:no-status | 972 + pdf | not-found | 820 + pdf | bad-redirect | 536 + pdf | read-timeout | 392 + pdf | wayback-error | 251 + pdf | remote-server-error | 220 + (20 rows) + +Hrm, that is a healthy fraction of `no-pdf-link`. + +Broken domains, past 30 days: + + SELECT domain, status, COUNT((domain, status)) + FROM ( + SELECT + ingest_file_result.ingest_type, + ingest_file_result.status, + substring(ingest_file_result.terminal_url FROM '[^/]+://([^/]*)') AS domain + FROM ingest_file_result + LEFT JOIN ingest_request + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + -- ingest_request.created >= NOW() - '3 day'::INTERVAL + ingest_file_result.updated >= NOW() - '30 day'::INTERVAL + AND ingest_request.ingest_type = 'pdf' + AND ingest_request.ingest_request_source = 'fatcat-changelog' + ) t1 + WHERE t1.domain != '' + AND t1.status != 'success' + GROUP BY domain, status + ORDER BY COUNT DESC + LIMIT 25; + + domain | status | count + -------------------------+-------------------------+------- + zenodo.org | no-pdf-link | 39678 + osf.io | gateway-timeout | 29809 + acervus.unicamp.br | no-pdf-link | 21978 + osf.io | terminal-bad-status | 18727 + zenodo.org | spn2-cdx-lookup-failure | 17008 + doi.org | spn2-cdx-lookup-failure | 15503 + www.degruyter.com | no-pdf-link | 15122 + ieeexplore.ieee.org | spn2-error:job-failed | 12921 + osf.io | spn2-cdx-lookup-failure | 11123 + www.tandfonline.com | blocked-cookie | 8096 + www.morressier.com | no-pdf-link | 4655 + ieeexplore.ieee.org | spn2-cdx-lookup-failure | 4580 + pubs.acs.org | blocked-cookie | 4415 + www.frontiersin.org | no-pdf-link | 4163 + www.degruyter.com | spn2-cdx-lookup-failure | 3788 + www.taylorfrancis.com | no-pdf-link | 3568 + www.sciencedirect.com | no-pdf-link | 3128 + www.taylorfrancis.com | spn2-cdx-lookup-failure | 3116 + acervus.unicamp.br | spn2-cdx-lookup-failure | 2797 + www.mdpi.com | spn2-cdx-lookup-failure | 2719 + brill.com | link-loop | 2681 + linkinghub.elsevier.com | spn2-cdx-lookup-failure | 2657 + www.sciencedirect.com | spn2-cdx-lookup-failure | 2546 + apps.crossref.org | no-pdf-link | 2537 + onlinelibrary.wiley.com | blocked-cookie | 2528 + (25 rows) + +Summary of significant domains and status, past 30 days, minus spn2-cdx-lookup-failure: + + SELECT domain, status, count + FROM ( + SELECT domain, status, COUNT((domain, status)) as count + FROM ( + SELECT + ingest_file_result.ingest_type, + ingest_file_result.status, + substring(ingest_file_result.terminal_url FROM '[^/]+://([^/]*)') AS domain + FROM ingest_file_result + LEFT JOIN ingest_request + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_file_result.updated >= NOW() - '30 day'::INTERVAL + AND ingest_request.ingest_type = 'pdf' + AND ingest_request.ingest_request_source = 'fatcat-changelog' + AND ingest_file_result.status != 'spn2-cdx-lookup-failure' + ) t1 + WHERE t1.domain != '' + GROUP BY CUBE (domain, status) + ) t2 + WHERE count > 200 + ORDER BY domain ASC , count DESC; + + + domain | status | count + -----------------------------------------------------------------+-----------------------+-------- + academic.oup.com | | 2405 + academic.oup.com | no-pdf-link | 1240 + academic.oup.com | link-loop | 1010 + acervus.unicamp.br | | 21980 + acervus.unicamp.br | no-pdf-link | 21978 ** + aclanthology.org | | 208 + acp.copernicus.org | | 365 + acp.copernicus.org | success | 356 + aip.scitation.org | | 1071 + aip.scitation.org | blocked-cookie | 843 + aip.scitation.org | redirect-loop | 227 + apps.crossref.org | | 2537 + apps.crossref.org | no-pdf-link | 2537 + arxiv.org | | 17817 + arxiv.org | success | 17370 + arxiv.org | terminal-bad-status | 320 + asmedigitalcollection.asme.org | | 401 + asmedigitalcollection.asme.org | link-loop | 364 + assets.researchsquare.com | | 3706 + assets.researchsquare.com | success | 3706 + avmj.journals.ekb.eg | | 605 + avmj.journals.ekb.eg | success | 595 + bfa.journals.ekb.eg | | 224 + bfa.journals.ekb.eg | success | 214 + biorxiv.org | redirect-loop | 895 + biorxiv.org | | 895 + birdsoftheworld.org | | 286 + birdsoftheworld.org | no-pdf-link | 285 + bmjopen.bmj.com | success | 232 + bmjopen.bmj.com | | 232 + books.openedition.org | | 396 + books.openedition.org | no-pdf-link | 396 + brill.com | | 4272 + brill.com | link-loop | 2681 + brill.com | no-pdf-link | 1410 + cas.columbia.edu | | 1038 + cas.columbia.edu | no-pdf-link | 1038 ** + cdr.lib.unc.edu | | 513 + cdr.lib.unc.edu | success | 469 + chemrxiv.org | | 278 + chemrxiv.org | success | 275 + classiques-garnier.com | | 531 + classiques-garnier.com | no-pdf-link | 487 * + content.iospress.com | | 275 + content.iospress.com | link-loop | 230 + cris.maastrichtuniversity.nl | | 318 + cris.maastrichtuniversity.nl | success | 284 + cyberleninka.ru | | 1165 + cyberleninka.ru | success | 1134 + deepblue.lib.umich.edu | | 289 + dergipark.org.tr | | 1185 + dergipark.org.tr | success | 774 + dergipark.org.tr | no-pdf-link | 320 + didaktorika.gr | | 688 + didaktorika.gr | redirect-loop | 688 + digi.ub.uni-heidelberg.de | | 292 + digi.ub.uni-heidelberg.de | no-pdf-link | 292 + direct.mit.edu | | 236 + direct.mit.edu | no-pdf-link | 207 * + dl.acm.org | | 2319 + dl.acm.org | blocked-cookie | 2230 + dmtcs.episciences.org | | 733 + dmtcs.episciences.org | success | 730 + doi.ala.org.au | no-pdf-link | 2373 ** + doi.ala.org.au | | 2373 + doi.org | | 732 + doi.org | terminal-bad-status | 673 + downloads.hindawi.com | success | 1452 + downloads.hindawi.com | | 1452 + drive.google.com | | 216 + drive.google.com | no-pdf-link | 211 + dtb.bmj.com | | 674 + dtb.bmj.com | link-loop | 669 + easy.dans.knaw.nl | no-pdf-link | 261 * + easy.dans.knaw.nl | | 261 + ebooks.marilia.unesp.br | | 688 + ebooks.marilia.unesp.br | no-pdf-link | 688 * + ehp.niehs.nih.gov | | 766 + ehp.niehs.nih.gov | blocked-cookie | 765 + ejournal.mandalanursa.org | | 307 + ejournal.mandalanursa.org | success | 305 + elib.spbstu.ru | | 264 + elib.spbstu.ru | redirect-loop | 257 + elibrary.ru | | 1367 + elibrary.ru | redirect-loop | 1169 + elibrary.vdi-verlag.de | | 1251 + elibrary.vdi-verlag.de | no-pdf-link | 646 + elibrary.vdi-verlag.de | link-loop | 537 + elifesciences.org | | 328 + elifesciences.org | success | 323 + figshare.com | | 803 + figshare.com | no-pdf-link | 714 * + files.osf.io | | 745 + files.osf.io | success | 614 + hammer.purdue.edu | | 244 + hammer.purdue.edu | no-pdf-link | 243 + heiup.uni-heidelberg.de | | 277 + heiup.uni-heidelberg.de | no-pdf-link | 268 + hkvalidate.perfdrive.com | no-pdf-link | 370 * + hkvalidate.perfdrive.com | | 370 + ieeexplore.ieee.org | | 16675 + ieeexplore.ieee.org | spn2-error:job-failed | 12927 + ieeexplore.ieee.org | success | 1952 + ieeexplore.ieee.org | too-many-redirects | 1193 + ieeexplore.ieee.org | no-pdf-link | 419 + jamanetwork.com | | 339 + jamanetwork.com | success | 216 + jmstt.ntou.edu.tw | | 244 + jmstt.ntou.edu.tw | success | 241 + journal.ipb.ac.id | | 229 + journal.ipb.ac.id | success | 206 + journal.nafe.org | | 221 + journals.aps.org | | 614 + journals.aps.org | gateway-timeout | 495 + journals.asm.org | | 463 + journals.asm.org | blocked-cookie | 435 + journals.flvc.org | | 230 + journals.lww.com | | 1300 + journals.lww.com | link-loop | 1284 + journals.openedition.org | | 543 + journals.openedition.org | success | 311 + journals.ub.uni-heidelberg.de | | 357 + journals.ub.uni-heidelberg.de | success | 311 + jov.arvojournals.org | | 431 + jov.arvojournals.org | no-pdf-link | 422 * + kiss.kstudy.com | | 303 + kiss.kstudy.com | no-pdf-link | 303 * + library.iated.org | | 364 + library.iated.org | redirect-loop | 264 + library.seg.org | blocked-cookie | 301 + library.seg.org | | 301 + link.aps.org | redirect-loop | 442 + link.aps.org | | 442 + linkinghub.elsevier.com | | 515 + linkinghub.elsevier.com | gateway-timeout | 392 + mc.sbm.org.br | | 224 + mc.sbm.org.br | success | 224 + mdpi-res.com | | 742 + mdpi-res.com | success | 742 + mdsoar.org | | 220 + mediarep.org | | 269 + mediarep.org | success | 264 + medrxiv.org | redirect-loop | 290 + medrxiv.org | | 290 + muse.jhu.edu | | 429 + muse.jhu.edu | terminal-bad-status | 391 + mvmj.journals.ekb.eg | | 306 + oapub.org | | 292 + oapub.org | success | 289 + onepetro.org | | 426 + onepetro.org | link-loop | 406 + onlinelibrary.wiley.com | | 2835 + onlinelibrary.wiley.com | blocked-cookie | 2531 + onlinelibrary.wiley.com | redirect-loop | 264 + open.library.ubc.ca | | 569 + open.library.ubc.ca | no-pdf-link | 425 * + opendata.uni-halle.de | | 407 + opendata.uni-halle.de | success | 263 + osf.io | | 49022 + osf.io | gateway-timeout | 29810 + osf.io | terminal-bad-status | 18731 + osf.io | spn2-error | 247 + osf.io | not-found | 205 + oxford.universitypressscholarship.com | | 392 + oxford.universitypressscholarship.com | link-loop | 233 + panor.ru | no-pdf-link | 433 * + panor.ru | | 433 + papers.ssrn.com | | 1630 + papers.ssrn.com | link-loop | 1598 + pdf.sciencedirectassets.com | | 3063 + pdf.sciencedirectassets.com | success | 3063 + peerj.com | | 464 + peerj.com | no-pdf-link | 303 * + periodicos.ufpe.br | | 245 + periodicos.ufpe.br | success | 232 + periodicos.unb.br | | 230 + periodicos.unb.br | success | 221 + preprints.jmir.org | | 548 + preprints.jmir.org | cdx-error | 499 + publications.rwth-aachen.de | | 213 + publikationen.bibliothek.kit.edu | | 346 + publikationen.bibliothek.kit.edu | success | 314 + publikationen.uni-tuebingen.de | | 623 + publikationen.uni-tuebingen.de | no-pdf-link | 522 * + publons.com | no-pdf-link | 934 * + publons.com | | 934 + pubs.acs.org | | 4507 + pubs.acs.org | blocked-cookie | 4406 + pubs.rsc.org | | 1638 + pubs.rsc.org | link-loop | 1054 + pubs.rsc.org | redirect-loop | 343 + pubs.rsc.org | success | 201 + repositorio.ufu.br | | 637 + repositorio.ufu.br | success | 607 + repository.dri.ie | | 1852 + repository.dri.ie | no-pdf-link | 1852 ** + repository.library.brown.edu | | 293 + repository.library.brown.edu | no-pdf-link | 291 * + res.mdpi.com | | 10367 + res.mdpi.com | success | 10360 + retrovirology.biomedcentral.com | | 230 + revistas.ufrj.br | | 284 + revistas.ufrj.br | success | 283 + revistas.uptc.edu.co | | 385 + revistas.uptc.edu.co | success | 344 + royalsocietypublishing.org | | 231 + rsdjournal.org | | 347 + rsdjournal.org | success | 343 + s3-ap-southeast-2.amazonaws.com | | 400 + s3-ap-southeast-2.amazonaws.com | success | 392 + s3-eu-west-1.amazonaws.com | | 2096 + s3-eu-west-1.amazonaws.com | success | 2091 + s3-euw1-ap-pe-df-pch-content-store-p.s3.eu-west-1.amazonaws.com | | 289 + s3-euw1-ap-pe-df-pch-content-store-p.s3.eu-west-1.amazonaws.com | success | 286 + s3.ca-central-1.amazonaws.com | | 202 + sage.figshare.com | | 242 + sage.figshare.com | no-pdf-link | 241 + sajeb.org | | 246 + sajeb.org | no-pdf-link | 243 + scholar.dkyobobook.co.kr | | 332 + scholar.dkyobobook.co.kr | no-pdf-link | 328 * + search.mandumah.com | | 735 + search.mandumah.com | redirect-loop | 726 + secure.jbs.elsevierhealth.com | | 1112 + secure.jbs.elsevierhealth.com | blocked-cookie | 1108 + stm.bookpi.org | no-pdf-link | 468 * + stm.bookpi.org | | 468 + storage.googleapis.com | | 1012 + storage.googleapis.com | success | 1012 + tandf.figshare.com | | 469 + tandf.figshare.com | no-pdf-link | 466 + teses.usp.br | | 739 + teses.usp.br | success | 730 + tidsskrift.dk | | 360 + tidsskrift.dk | success | 346 + tiedejaedistys.journal.fi | | 224 + tind-customer-agecon.s3.amazonaws.com | success | 332 + tind-customer-agecon.s3.amazonaws.com | | 332 + valep.vc.univie.ac.at | no-pdf-link | 280 + valep.vc.univie.ac.at | | 280 + watermark.silverchair.com | | 1729 + watermark.silverchair.com | success | 1719 + www.academia.edu | | 387 + www.academia.edu | no-pdf-link | 386 + www.ahajournals.org | | 430 + www.ahajournals.org | blocked-cookie | 413 + www.atenaeditora.com.br | | 572 + www.atenaeditora.com.br | terminal-bad-status | 513 + www.atlantis-press.com | success | 722 + www.atlantis-press.com | | 722 + www.aup-online.com | | 419 + www.aup-online.com | no-pdf-link | 419 * + www.beck-elibrary.de | | 269 + www.beck-elibrary.de | no-pdf-link | 268 * + www.biodiversitylibrary.org | no-pdf-link | 528 * + www.biodiversitylibrary.org | | 528 + www.bloomsburycollections.com | | 623 + www.bloomsburycollections.com | no-pdf-link | 605 * + www.cabi.org | | 2191 + www.cabi.org | no-pdf-link | 2186 * + www.cairn.info | | 1283 + www.cairn.info | no-pdf-link | 713 + www.cairn.info | link-loop | 345 + www.cambridge.org | | 4128 + www.cambridge.org | no-pdf-link | 1531 + www.cambridge.org | success | 1441 + www.cambridge.org | link-loop | 971 + www.cureus.com | no-pdf-link | 526 * + www.cureus.com | | 526 + www.dbpia.co.kr | | 637 + www.dbpia.co.kr | redirect-loop | 631 + www.deboni.he.com.br | | 382 + www.deboni.he.com.br | success | 381 + www.degruyter.com | | 17783 + www.degruyter.com | no-pdf-link | 15102 + www.degruyter.com | success | 2584 + www.dovepress.com | | 480 + www.dovepress.com | success | 472 + www.e-manuscripta.ch | | 1350 + www.e-manuscripta.ch | no-pdf-link | 1350 * + www.e-periodica.ch | | 1276 + www.e-periodica.ch | no-pdf-link | 1275 + www.e-rara.ch | | 202 + www.e-rara.ch | no-pdf-link | 202 + www.elgaronline.com | | 495 + www.elgaronline.com | link-loop | 290 + www.elibrary.ru | | 922 + www.elibrary.ru | no-pdf-link | 904 + www.emerald.com | | 2155 + www.emerald.com | no-pdf-link | 1936 * + www.emerald.com | success | 219 + www.eurekaselect.com | | 518 + www.eurekaselect.com | no-pdf-link | 516 * + www.frontiersin.org | | 4163 + www.frontiersin.org | no-pdf-link | 4162 ** + www.hanser-elibrary.com | | 444 + www.hanser-elibrary.com | blocked-cookie | 444 + www.hanspub.org | | 334 + www.hanspub.org | no-pdf-link | 314 + www.idunn.no | | 1736 + www.idunn.no | link-loop | 596 + www.idunn.no | success | 577 + www.idunn.no | no-pdf-link | 539 + www.igi-global.com | terminal-bad-status | 458 + www.igi-global.com | | 458 + www.ijcai.org | | 533 + www.ijcai.org | success | 532 + www.ijraset.com | success | 385 + www.ijraset.com | | 385 + www.inderscience.com | | 712 + www.inderscience.com | no-pdf-link | 605 * + www.ingentaconnect.com | | 456 + www.ingentaconnect.com | no-pdf-link | 413 * + www.internationaljournalssrg.org | | 305 + www.internationaljournalssrg.org | no-pdf-link | 305 * + www.isca-speech.org | | 2392 + www.isca-speech.org | no-pdf-link | 2391 ** + www.journals.uchicago.edu | | 228 + www.journals.uchicago.edu | blocked-cookie | 227 + www.jstage.jst.go.jp | | 1492 + www.jstage.jst.go.jp | success | 1185 + www.jstage.jst.go.jp | no-pdf-link | 289 + www.jstor.org | | 301 + www.jurology.com | | 887 + www.jurology.com | redirect-loop | 887 + www.karger.com | | 318 + www.liebertpub.com | | 507 + www.liebertpub.com | blocked-cookie | 496 + www.morressier.com | | 4781 + www.morressier.com | no-pdf-link | 4655 ** + www.ncl.ecu.edu | | 413 + www.ncl.ecu.edu | success | 413 + www.nomos-elibrary.de | | 526 + www.nomos-elibrary.de | no-pdf-link | 391 + www.oecd-ilibrary.org | no-pdf-link | 1170 ** + www.oecd-ilibrary.org | | 1170 + www.openagrar.de | no-pdf-link | 221 + www.openagrar.de | | 221 + www.osapublishing.org | | 900 + www.osapublishing.org | link-loop | 615 + www.osapublishing.org | no-pdf-link | 269 + www.osti.gov | | 630 + www.osti.gov | link-loop | 573 + www.oxfordlawtrove.com | no-pdf-link | 476 * + www.oxfordlawtrove.com | | 476 + www.pdcnet.org | | 298 + www.pdcnet.org | terminal-bad-status | 262 + www.pedocs.de | | 203 + www.pnas.org | | 222 + www.preprints.org | | 372 + www.preprints.org | success | 366 + www.repository.cam.ac.uk | | 801 + www.repository.cam.ac.uk | success | 359 + www.repository.cam.ac.uk | no-pdf-link | 239 + www.research-collection.ethz.ch | | 276 + www.research-collection.ethz.ch | terminal-bad-status | 274 + www.revistas.usp.br | | 207 + www.revistas.usp.br | success | 204 + www.rina.org.uk | no-pdf-link | 1009 ** + www.rina.org.uk | | 1009 + www.schweizerbart.de | no-pdf-link | 202 + www.schweizerbart.de | | 202 + www.scielo.br | | 544 + www.scielo.br | redirect-loop | 526 + www.sciencedirect.com | | 3901 + www.sciencedirect.com | no-pdf-link | 3127 ** + www.sciencedirect.com | link-loop | 701 + www.sciendo.com | | 384 + www.sciendo.com | success | 363 + www.sciengine.com | | 225 + www.scirp.org | | 209 + www.spandidos-publications.com | | 205 + www.tandfonline.com | | 8925 + www.tandfonline.com | blocked-cookie | 8099 + www.tandfonline.com | terminal-bad-status | 477 + www.tandfonline.com | redirect-loop | 322 + www.taylorfrancis.com | | 6119 + www.taylorfrancis.com | no-pdf-link | 3567 + www.taylorfrancis.com | link-loop | 2169 + www.taylorfrancis.com | terminal-bad-status | 353 + www.thieme-connect.de | | 1047 + www.thieme-connect.de | redirect-loop | 472 + www.thieme-connect.de | spn2-error:job-failed | 343 + www.tib.eu | | 206 + www.trp.org.in | | 311 + www.trp.org.in | success | 311 + www.un-ilibrary.org | no-pdf-link | 597 * + www.un-ilibrary.org | | 597 + www.vr-elibrary.de | | 775 + www.vr-elibrary.de | blocked-cookie | 774 + www.wjgnet.com | | 204 + www.wjgnet.com | no-pdf-link | 204 + www.worldscientific.com | | 974 + www.worldscientific.com | blocked-cookie | 971 + www.worldwidejournals.com | | 242 + www.worldwidejournals.com | no-pdf-link | 203 + www.wto-ilibrary.org | no-pdf-link | 295 + www.wto-ilibrary.org | | 295 + www.zora.uzh.ch | | 222 + zenodo.org | | 49460 + zenodo.org | no-pdf-link | 39721 + zenodo.org | success | 8954 + zenodo.org | wrong-mimetype | 562 + | | 445919 + | no-pdf-link | 168035 + | success | 140875 + | gateway-timeout | 31809 + | blocked-cookie | 26431 + | terminal-bad-status | 25625 + | link-loop | 19006 + | spn2-error:job-failed | 13962 + | redirect-loop | 12512 + | wrong-mimetype | 2302 + | spn2-error | 1689 + | too-many-redirects | 1203 + | bad-redirect | 732 + | cdx-error | 539 + | not-found | 420 + | spn2-error:no-status | 256 + (419 rows) + +Get random subsets by terminal domain: + + \x auto + SELECT + ingest_request.link_source_id AS link_source_id, + ingest_request.base_url as base_url , + ingest_file_result.terminal_url as terminal_url + FROM ingest_request + LEFT JOIN ingest_file_result + ON ingest_file_result.ingest_type = ingest_request.ingest_type + AND ingest_file_result.base_url = ingest_request.base_url + WHERE + ingest_request.created >= NOW() - '30 day'::INTERVAL + AND ingest_request.ingest_type = 'pdf' + AND ingest_request.ingest_request_source = 'fatcat-changelog' + AND ingest_file_result.status = 'no-pdf-link' + AND ingest_file_result.terminal_url LIKE '%//DOMAIN/%' + ORDER BY random() + LIMIT 5; + +## acervus.unicamp.br + +Previously flagged as messy (2021-05_daily_improvements.md) + +## cas.columbia.edu + +-[ RECORD 1 ]--+------------------------------------------------------------------------------------------------------------------ +link_source_id | 10.7916/d8-2ety-qm51 +base_url | https://doi.org/10.7916/d8-2ety-qm51 +terminal_url | https://cas.columbia.edu/cas/login?TARGET=https%3A%2F%2Fdlc.library.columbia.edu%2Fusers%2Fauth%2Fsaml%2Fcallback +-[ RECORD 2 ]--+------------------------------------------------------------------------------------------------------------------ +link_source_id | 10.7916/d8-0zf6-d167 +base_url | https://doi.org/10.7916/d8-0zf6-d167 +terminal_url | https://cas.columbia.edu/cas/login?TARGET=https%3A%2F%2Fdlc.library.columbia.edu%2Fusers%2Fauth%2Fsaml%2Fcallback +-[ RECORD 3 ]--+------------------------------------------------------------------------------------------------------------------ +link_source_id | 10.7916/d8-k6ha-sn43 +base_url | https://doi.org/10.7916/d8-k6ha-sn43 +terminal_url | https://cas.columbia.edu/cas/login?TARGET=https%3A%2F%2Fdlc.library.columbia.edu%2Fusers%2Fauth%2Fsaml%2Fcallback +-[ RECORD 4 ]--+------------------------------------------------------------------------------------------------------------------ +link_source_id | 10.7916/d8-bj6t-eb07 +base_url | https://doi.org/10.7916/d8-bj6t-eb07 +terminal_url | https://cas.columbia.edu/cas/login?TARGET=https%3A%2F%2Fdlc.library.columbia.edu%2Fusers%2Fauth%2Fsaml%2Fcallback +-[ RECORD 5 ]--+------------------------------------------------------------------------------------------------------------------ +link_source_id | 10.7916/d8-xjac-j502 +base_url | https://doi.org/10.7916/d8-xjac-j502 +terminal_url | https://cas.columbia.edu/cas/login?TARGET=https%3A%2F%2Fdlc.library.columbia.edu%2Fusers%2Fauth%2Fsaml%2Fcallback + +these are not public (loginwalls) + +DONE: '/login?TARGET=' as a login wall pattern + +## doi.ala.org.au + +Previously flagged as dataset repository; datacite metadata is wrong. (2021-05_daily_improvements.md) + +NOTE: look at ingesting datasets + +## www.isca-speech.org + +-[ RECORD 1 ]--+---------------------------------------------------------------------------------- +link_source_id | 10.21437/interspeech.2014-84 +base_url | https://doi.org/10.21437/interspeech.2014-84 +terminal_url | https://www.isca-speech.org/archive/interspeech_2014/li14b_interspeech.html +-[ RECORD 2 ]--+---------------------------------------------------------------------------------- +link_source_id | 10.21437/interspeech.2004-319 +base_url | https://doi.org/10.21437/interspeech.2004-319 +terminal_url | https://www.isca-speech.org/archive/interspeech_2004/delcroix04_interspeech.html +-[ RECORD 3 ]--+---------------------------------------------------------------------------------- +link_source_id | 10.21437/interspeech.2006-372 +base_url | https://doi.org/10.21437/interspeech.2006-372 +terminal_url | https://www.isca-speech.org/archive/interspeech_2006/lei06c_interspeech.html +-[ RECORD 4 ]--+---------------------------------------------------------------------------------- +link_source_id | 10.21437/interspeech.2015-588 +base_url | https://doi.org/10.21437/interspeech.2015-588 +terminal_url | https://www.isca-speech.org/archive/interspeech_2015/polzehl15b_interspeech.html +-[ RECORD 5 ]--+---------------------------------------------------------------------------------- +link_source_id | 10.21437/interspeech.2006-468 +base_url | https://doi.org/10.21437/interspeech.2006-468 +terminal_url | https://www.isca-speech.org/archive/interspeech_2006/chitturi06b_interspeech.html + +Bespoke site. Added rule to sandcrawler. + +NOTE: re-ingest/recrawl all isca-speech.org no-pdf-link terminal URLs (fatcat-ingest?) + +## www.morressier.com + + +-[ RECORD 1 ]--+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +link_source_id | 10.1115/1.0002858v +base_url | https://doi.org/10.1115/1.0002858v +terminal_url | https://www.morressier.com/article/development-new-single-highdensity-heatflux-gauges-unsteady-heat-transfer-measurements-rotating-transonic-turbine/60f162805d86378f03b49af5 +-[ RECORD 2 ]--+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +link_source_id | 10.1115/1.0003896v +base_url | https://doi.org/10.1115/1.0003896v +terminal_url | https://www.morressier.com/article/experimental-investigation-proton-exchange-membrane-fuel-cell-platinum-nafion-along-inplane-direction/60f16d555d86378f03b50038 +-[ RECORD 3 ]--+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +link_source_id | 10.1115/1.0004476v +base_url | https://doi.org/10.1115/1.0004476v +terminal_url | https://www.morressier.com/article/effect-air-release-agents-performance-results-fabric-lined-bushings/60f16d585d86378f03b502d5 +-[ RECORD 4 ]--+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +link_source_id | 10.1115/1.0001286v +base_url | https://doi.org/10.1115/1.0001286v +terminal_url | https://www.morressier.com/article/development-verification-modelling-practice-cfd-calculations-obtain-current-loads-fpso/60f15d3fe537565438d70ece +-[ RECORD 5 ]--+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +link_source_id | 10.1115/1.0000315v +base_url | https://doi.org/10.1115/1.0000315v +terminal_url | https://www.morressier.com/article/fire-event-analysis-fire-frequency-estimation-japanese-nuclear-power-plant/60f15a6f5d86378f03b43874 + +Many of these seem to be presentations, as both video and slides. PDFs seem broken though. + +NOTE: add to list of interesting rich media to crawl/preserve (video+slides+data) + +## www.oecd-ilibrary.org + +Paywall (2021-05_daily_improvements.md) + +## www.rina.org.uk + +-[ RECORD 1 ]--+------------------------------------------------------- +link_source_id | 10.3940/rina.ws.2002.10 +base_url | https://doi.org/10.3940/rina.ws.2002.10 +terminal_url | https://www.rina.org.uk/showproducts.html?product=4116 +-[ RECORD 2 ]--+------------------------------------------------------- +link_source_id | 10.3940/rina.pass.2003.16 +base_url | https://doi.org/10.3940/rina.pass.2003.16 +terminal_url | https://www.rina.org.uk/showproducts.html?product=3566 +-[ RECORD 3 ]--+------------------------------------------------------- +link_source_id | 10.3940/rina.icsotin.2013.15 +base_url | https://doi.org/10.3940/rina.icsotin.2013.15 +terminal_url | https://www.rina.org.uk/showproducts.html?product=8017 +-[ RECORD 4 ]--+------------------------------------------------------- +link_source_id | 10.3940/rina.wfa.2010.23 +base_url | https://doi.org/10.3940/rina.wfa.2010.23 +terminal_url | https://www.rina.org.uk/showproducts.html?product=8177 +-[ RECORD 5 ]--+------------------------------------------------------- +link_source_id | 10.3940/rina.icsotin15.2015.01 +base_url | https://doi.org/10.3940/rina.icsotin15.2015.01 +terminal_url | https://www.rina.org.uk/showproducts.html?product=7883 + +Site is broken in some way + +## www.sciencedirect.com + +-[ RECORD 1 ]--+----------------------------------------------------------------------------------------------------------------------------------------------------- +link_source_id | 10.1016/j.jhlste.2021.100332 +base_url | https://doi.org/10.1016/j.jhlste.2021.100332 +terminal_url | https://www.sciencedirect.com/science/article/abs/pii/S1473837621000332 +-[ RECORD 2 ]--+----------------------------------------------------------------------------------------------------------------------------------------------------- +link_source_id | 10.1016/j.hazadv.2021.100006 +base_url | https://doi.org/10.1016/j.hazadv.2021.100006 +terminal_url | https://www.sciencedirect.com/science/article/pii/S2772416621000061/pdfft?md5=e51bfd495bb53073c7a379d25cb11a32&pid=1-s2.0-S2772416621000061-main.pdf +-[ RECORD 3 ]--+----------------------------------------------------------------------------------------------------------------------------------------------------- +link_source_id | 10.1016/b978-0-12-822844-9.00009-8 +base_url | https://doi.org/10.1016/b978-0-12-822844-9.00009-8 +terminal_url | https://www.sciencedirect.com/science/article/pii/B9780128228449000098 +-[ RECORD 4 ]--+----------------------------------------------------------------------------------------------------------------------------------------------------- +link_source_id | 10.1016/j.colcom.2021.100490 +base_url | https://doi.org/10.1016/j.colcom.2021.100490 +terminal_url | https://www.sciencedirect.com/science/article/abs/pii/S2215038221001308 +-[ RECORD 5 ]--+----------------------------------------------------------------------------------------------------------------------------------------------------- +link_source_id | 10.1016/b978-0-323-85245-6.00012-6 +base_url | https://doi.org/10.1016/b978-0-323-85245-6.00012-6 +terminal_url | https://www.sciencedirect.com/science/article/pii/B9780323852456000126 + +These no-pdf-url ones seem to just be not OA, which is expected for much of the +domain. + +## repository.dri.ie + + link_source_id | base_url | terminal_url +-----------------------+---------------------------------------+--------------------------------------------- + 10.7486/dri.t148v5941 | https://doi.org/10.7486/dri.t148v5941 | https://repository.dri.ie/catalog/t148v5941 + 10.7486/dri.2z119c98f | https://doi.org/10.7486/dri.2z119c98f | https://repository.dri.ie/catalog/2z119c98f + 10.7486/dri.qf8621102 | https://doi.org/10.7486/dri.qf8621102 | https://repository.dri.ie/catalog/qf8621102 + 10.7486/dri.js95m457t | https://doi.org/10.7486/dri.js95m457t | https://repository.dri.ie/catalog/js95m457t + 10.7486/dri.c534vb726 | https://doi.org/10.7486/dri.c534vb726 | https://repository.dri.ie/catalog/c534vb726 + +"Digital repository of Ireland" + +Historical scanned content. Bespoke site. Fixed. + +NOTE: recrawl/retry this domain + +## www.frontiersin.org + +-[ RECORD 1 ]--+------------------------------------------------------------------------------------------------------------------ +link_source_id | 10.3389/978-2-88971-147-5 +base_url | https://doi.org/10.3389/978-2-88971-147-5 +terminal_url | https://www.frontiersin.org/research-topics/9081/neuroimaging-approaches-to-the-study-of-tinnitus-and-hyperacusis +-[ RECORD 2 ]--+------------------------------------------------------------------------------------------------------------------ +link_source_id | 10.3389/fnins.2021.722592 +base_url | https://doi.org/10.3389/fnins.2021.722592 +terminal_url | https://www.frontiersin.org/articles/10.3389/fnins.2021.722592/full +-[ RECORD 3 ]--+------------------------------------------------------------------------------------------------------------------ +link_source_id | 10.3389/fcell.2021.683209 +base_url | https://doi.org/10.3389/fcell.2021.683209 +terminal_url | https://www.frontiersin.org/articles/10.3389/fcell.2021.683209/full +-[ RECORD 4 ]--+------------------------------------------------------------------------------------------------------------------ +link_source_id | 10.3389/fmicb.2021.692474 +base_url | https://doi.org/10.3389/fmicb.2021.692474 +terminal_url | https://www.frontiersin.org/articles/10.3389/fmicb.2021.692474/full +-[ RECORD 5 ]--+------------------------------------------------------------------------------------------------------------------ +link_source_id | 10.3389/fneur.2021.676527 +base_url | https://doi.org/10.3389/fneur.2021.676527 +terminal_url | https://www.frontiersin.org/articles/10.3389/fneur.2021.676527/full + +All the `/research-topics/` URLs are out of scope. + +NOTE: recrawl missing frontiersin.org articles for PDFs +NOTE: recrawl missing frontiersin.org articles for XML (?) + +------- + +## direct.mit.edu + +Previously "not available" (2021-05_daily_improvements.md) + +## figshare.com + +-[ RECORD 1 ]--+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +link_source_id | 10.6084/m9.figshare.15052236.v6 +base_url | https://doi.org/10.6084/m9.figshare.15052236.v6 +terminal_url | https://figshare.com/articles/software/RCL-tree_rar/15052236/6 +-[ RECORD 2 ]--+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +link_source_id | 10.6084/m9.figshare.14907846.v5 +base_url | https://doi.org/10.6084/m9.figshare.14907846.v5 +terminal_url | https://figshare.com/articles/book/Conservation_of_Limestone_Ecosystems_of_Malaysia_Part_I_Acknowledgements_Methodology_Overview_of_limestone_outcrops_in_Malaysia_References_Detailed_information_on_limestone_outcrops_of_the_states_Johor_Negeri_Sembilan_Terengganu_Selangor_Pe/14907846/5 +-[ RECORD 3 ]--+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +link_source_id | 10.6084/m9.figshare.15157614.v1 +base_url | https://doi.org/10.6084/m9.figshare.15157614.v1 +terminal_url | https://figshare.com/articles/software/code_for_NN-A72265C/15157614/1 +-[ RECORD 4 ]--+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +link_source_id | 10.6084/m9.figshare.15172926.v1 +base_url | https://doi.org/10.6084/m9.figshare.15172926.v1 +terminal_url | https://figshare.com/articles/preprint/History_of_the_internet/15172926/1 +-[ RECORD 5 ]--+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +link_source_id | 10.6084/m9.figshare.16532574.v1 +base_url | https://doi.org/10.6084/m9.figshare.16532574.v1 +terminal_url | https://figshare.com/articles/media/Helen_McConnell_How_many_trees_do_you_think_you_have_planted_/16532574/1 + +NOTE: can determine from the redirect URL, I guess. This is helpful for ingest! +Could also potentially correct fatcat release_type using this info. + +We seem to be getting the ones we can (eg, papers) just fine + +## hkvalidate.perfdrive.com + +Should be skipping/bailing on this domain, but not for some reason. + +-[ RECORD 1 ]--+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +link_source_id | 10.3847/1538-4357/ac05cc +base_url | https://doi.org/10.3847/1538-4357/ac05cc +terminal_url | https://hkvalidate.perfdrive.com/?ssa=1716a049-aeaa-4a89-8f82-bd733adaa2e7&ssb=43981203877&ssc=https%3A%2F%2Fiopscience.iop.org%2Farticle%2F10.3847%2F1538-4357%2Fac05cc&ssi=0774dd12-8427-4e27-a2ac-759c8cc2ec0e&ssk=support@shieldsquare.com&ssm=07370915269044035109047683305266&ssn=e69c743cc3d66619f960f924b562160d637e8d7f1b0f-d3bb-44d4-b075ed&sso=75a8bd85-4a097fb40f99bfb9c97b0a4ca0a38fd6d79513a466e82cc7&ssp=92054607321628531005162856888275586&ssq=33809984098158010864140981653938424553916&ssr=MjA3LjI0MS4yMjUuMTM5&sst=Mozilla/5.0%20(Windows%20NT%2010.0;%20Win64;%20x64)%20AppleWebKit/537.36%20(KHTML,%20like%20Gecko)%20Chrome/74.0.3729.169%20Safari/537.36&ssv=&ssw= +-[ RECORD 2 ]--+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +link_source_id | 10.3847/1538-4357/ac0429 +base_url | https://doi.org/10.3847/1538-4357/ac0429 +terminal_url | https://hkvalidate.perfdrive.com/?ssa=12bca70d-0af4-4241-9c9b-384befd96a88&ssb=92559232428&ssc=https%3A%2F%2Fiopscience.iop.org%2Farticle%2F10.3847%2F1538-4357%2Fac0429&ssi=cff72ab0-8427-4acd-a0e7-db1b04cf7ce7&ssk=support@shieldsquare.com&ssm=27895673282814430105287068829605&ssn=9af36a8e10efd239c9367a2f31dde500f7455c4d5f45-bf11-4b99-ad29ea&sso=26bd22d2-b23e1bd9558f2fd9ed0768ef1acecb24715d1d463328a229&ssp=16502500621628222613162823304820671&ssq=11469693950387070477339503456478590533604&ssr=MjA3LjI0MS4yMjUuMTYw&sst=Mozilla/5.0%20(Windows%20NT%2010.0;%20Win64;%20x64)%20AppleWebKit/537.36%20(KHTML,%20like%20Gecko)%20Chrome/74.0.3729.169%20Safari/537.36&ssv=&ssw= +-[ RECORD 3 ]--+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +link_source_id | 10.1149/1945-7111/ac1a85 +base_url | https://doi.org/10.1149/1945-7111/ac1a85 +terminal_url | https://hkvalidate.perfdrive.com/?ssa=b0fef51a-0f44-476e-b951-3341bde6aa67&ssb=84929220393&ssc=https%3A%2F%2Fiopscience.iop.org%2Farticle%2F10.1149%2F1945-7111%2Fac1a85&ssi=48c05577-8427-4421-acd3-735ca29a46e6&ssk=support@shieldsquare.com&ssm=81129482524077974103852241068134&ssn=cf6c261d2b20d518b2ebe57e40ffaec9ab4cd1955dcb-7877-4f5b-bc3b1e&sso=1d196cae-6850f1ed8143e460f2bfbb61a8ae15cfe6b53d3bcdc528ca&ssp=99289867941628195224162819241830491&ssq=16897595632212421273956322948987630170313&ssr=MjA3LjI0MS4yMjUuMjM2&sst=Mozilla/5.0%20(Windows%20NT%2010.0;%20Win64;%20x64)%20AppleWebKit/537.36%20(KHTML,%20like%20Gecko)%20Chrome/74.0.3729.169%20Safari/537.36&ssv=&ssw= +-[ RECORD 4 ]--+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +link_source_id | 10.35848/1882-0786/ac1b0d +base_url | https://doi.org/10.35848/1882-0786/ac1b0d +terminal_url | https://hkvalidate.perfdrive.com/?ssa=6debdd23-c46b-4b40-b73c-d5540f04454e&ssb=95627212532&ssc=https%3A%2F%2Fiopscience.iop.org%2Farticle%2F10.35848%2F1882-0786%2Fac1b0d&ssi=78b34ff9-8427-4d07-a0db-78a3aa2c7332&ssk=support@shieldsquare.com&ssm=54055111549093989106852695053789&ssn=cb51949e15a02cb99a8d0b57c4d06327b72e8d5c87a8-d006-4ffa-939ffb&sso=1b7fd62d-8107746fe28fca252fd45ffa403937e272bf75b452b68d4a&ssp=77377533171628212164162820021422494&ssq=02679025218797637682252187852000657274192&ssr=MjA3LjI0MS4yMzMuMTIx&sst=Mozilla/5.0%20(Windows%20NT%2010.0;%20Win64;%20x64)%20AppleWebKit/537.36%20(KHTML,%20like%20Gecko)%20Chrome/74.0.3729.169%20Safari/537.36&ssv=&ssw= +-[ RECORD 5 ]--+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +link_source_id | 10.3847/1538-4357/ac05ba +base_url | https://doi.org/10.3847/1538-4357/ac05ba +terminal_url | https://hkvalidate.perfdrive.com/?ssa=f127eb3d-6a05-459d-97f2-499715c04b13&ssb=06802230353&ssc=https%3A%2F%2Fiopscience.iop.org%2Farticle%2F10.3847%2F1538-4357%2Fac05ba&ssi=8d087719-8427-4046-91fb-5e96af401560&ssk=support@shieldsquare.com&ssm=21056861072205974105064006574997&ssn=d05a73cff6d9af57acd6e2c366e716176752e1164d39-b9a7-408c-837d11&sso=d3f38d1e-a562a19195042d7e471a5e4fab03b6ca16ff1711c7c61804&ssp=68781137401628744693162877909483738&ssq=79454859841502433261398415426689546750534&ssr=MjA3LjI0MS4yMzIuMTg5&sst=Mozilla/5.0%20(Windows%20NT%2010.0;%20Win64;%20x64)%20AppleWebKit/537.36%20(KHTML,%20like%20Gecko)%20Chrome/74.0.3729.169%20Safari/537.36&ssv=&ssw= + +Was failing to check against blocklist again at the end of attempts. + +Could retry all these to update status, but probably not worth it. + +## jov.arvojournals.org + + link_source_id | base_url | terminal_url +-----------------------+---------------------------------------+------------------------------------------------------------- + 10.1167/jov.21.9.1933 | https://doi.org/10.1167/jov.21.9.1933 | https://jov.arvojournals.org/article.aspx?articleid=2777021 + 10.1167/jov.21.9.2910 | https://doi.org/10.1167/jov.21.9.2910 | https://jov.arvojournals.org/article.aspx?articleid=2777561 + 10.1167/jov.21.9.1895 | https://doi.org/10.1167/jov.21.9.1895 | https://jov.arvojournals.org/article.aspx?articleid=2777057 + 10.1167/jov.21.9.2662 | https://doi.org/10.1167/jov.21.9.2662 | https://jov.arvojournals.org/article.aspx?articleid=2777793 + 10.1167/jov.21.9.2246 | https://doi.org/10.1167/jov.21.9.2246 | https://jov.arvojournals.org/article.aspx?articleid=2777441 + +These seem to just not be published/available yet. + +But they also use watermark.silverchair.com + +NOTE: re-crawl (force-retry?) all non-recent papers with fatcat-ingest +NOTE: for watermark.silverchair.com terminal bad-status, re-crawl from initial URL (base_url) using heritrix + +## kiss.kstudy.com + +Previously unable to download (2021-05_daily_improvements.md) + +## open.library.ubc.ca + + link_source_id | base_url | terminal_url +--------------------+------------------------------------+---------------------------------------------------------------------------------- + 10.14288/1.0400664 | https://doi.org/10.14288/1.0400664 | https://open.library.ubc.ca/collections/bcnewspapers/nelsondaily/items/1.0400664 + 10.14288/1.0401189 | https://doi.org/10.14288/1.0401189 | https://open.library.ubc.ca/collections/bcnewspapers/nelsondaily/items/1.0401189 + 10.14288/1.0401487 | https://doi.org/10.14288/1.0401487 | https://open.library.ubc.ca/cIRcle/collections/48630/items/1.0401487 + 10.14288/1.0400994 | https://doi.org/10.14288/1.0400994 | https://open.library.ubc.ca/collections/bcnewspapers/nelsondaily/items/1.0400994 + 10.14288/1.0401312 | https://doi.org/10.14288/1.0401312 | https://open.library.ubc.ca/collections/bcnewspapers/nelsondaily/items/1.0401312 + +Historical newspapers, out of scope? + +Video content: +https://open.library.ubc.ca/cIRcle/collections/48630/items/1.0401487 + +Another video: https://open.library.ubc.ca/cIRcle/collections/48630/items/1.0400764 + +NOTE: add video link to alternative content demo ingest: https://open.library.ubc.ca/cIRcle/collections/48630/items/1.0400764 +NOTE: handle this related withdrawn notice? https://open.library.ubc.ca/cIRcle/collections/48630/items/1.0401512 + + +## panor.ru + + link_source_id | base_url | terminal_url +-------------------------+-----------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------- + 10.33920/med-14-2108-06 | https://doi.org/10.33920/med-14-2108-06 | https://panor.ru/articles/otsenka-dinamiki-pokazateley-morfofunktsionalnykh-kharakteristik-kozhi-upatsientov-s-spr-pod-vliyaniem-kompleksnoy-fototerapii/66351.html + 10.33920/nik-02-2105-01 | https://doi.org/10.33920/nik-02-2105-01 | https://panor.ru/articles/innovatsionnost-obrazovatelnykh-tekhnologiy-kak-istoricheski-oposredovannyy-fenomen/65995.html + 10.33920/pro-1-2101-10 | https://doi.org/10.33920/pro-1-2101-10 | https://panor.ru/articles/obespechenie-bezopasnosti-na-promyshlennykh-predpriyatiyakh-s-pomoshchyu-sredstv-individualnoy-zashchity/66299.html + 10.33920/sel-4-2008-04 | https://doi.org/10.33920/sel-4-2008-04 | https://panor.ru/articles/osobennosti-regulirovaniya-zemelnykh-otnosheniy-na-prigranichnykh-territoriyakh-rossiyskoy-federatsii/66541.html + 10.33920/pro-2-2104-03 | https://doi.org/10.33920/pro-2-2104-03 | https://panor.ru/articles/organizatsiya-samorazvivayushchegosya-proizvodstva-v-realnykh-usloviyakh/65054.html + +"The full version of the article is available only to subscribers of the journal" + +Paywall + +## peerj.com + +Previously: this is HTML of reviews (2021-05_daily_improvements.md) + +NOTE: Should be HTML ingest, possibly special case scope + +## publons.com + +Previously: this is HTML (2021-05_daily_improvements.md) + +NOTE: Should be HTML ingest, possibly special case scope (length of works) + +## stm.bookpi.org + + link_source_id | base_url | terminal_url +-----------------------------+---------------------------------------------+---------------------------------------------------- + 10.9734/bpi/nfmmr/v7/11547d | https://doi.org/10.9734/bpi/nfmmr/v7/11547d | https://stm.bookpi.org/NFMMR-V7/article/view/3231 + 10.9734/bpi/ecafs/v1/9773d | https://doi.org/10.9734/bpi/ecafs/v1/9773d | https://stm.bookpi.org/ECAFS-V1/article/view/3096 + 10.9734/bpi/mpebm/v5/3391f | https://doi.org/10.9734/bpi/mpebm/v5/3391f | https://stm.bookpi.org/MPEBM-V5/article/view/3330 + 10.9734/bpi/castr/v13/3282f | https://doi.org/10.9734/bpi/castr/v13/3282f | https://stm.bookpi.org/CASTR-V13/article/view/2810 + 10.9734/bpi/hmms/v13 | https://doi.org/10.9734/bpi/hmms/v13 | https://stm.bookpi.org/HMMS-V13/issue/view/274 + +These are... just abstracts of articles within a book? Weird. Maybe sketchy? DOIs via Crossref + +## www.cabi.org + + link_source_id | base_url | terminal_url +--------------------------+------------------------------------------+---------------------------------------------------- + 10.1079/dfb/20133414742 | https://doi.org/10.1079/dfb/20133414742 | https://www.cabi.org/cabreviews/review/20133414742 + 10.1079/dmpd/20056500471 | https://doi.org/10.1079/dmpd/20056500471 | https://www.cabi.org/cabreviews/review/20056500471 + 10.1079/dmpp/20056600544 | https://doi.org/10.1079/dmpp/20056600544 | https://www.cabi.org/cabreviews/review/20056600544 + 10.1079/dmpd/20056500117 | https://doi.org/10.1079/dmpd/20056500117 | https://www.cabi.org/cabreviews/review/20056500117 + 10.1079/dmpp20056600337 | https://doi.org/10.1079/dmpp20056600337 | https://www.cabi.org/cabreviews/review/20056600337 + +Reviews? but just abstracts? + +## www.cureus.com + +-[ RECORD 1 ]--+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +link_source_id | 10.7759/cureus.17547 +base_url | https://doi.org/10.7759/cureus.17547 +terminal_url | https://www.cureus.com/articles/69542-tramadol-induced-jerks +-[ RECORD 2 ]--+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +link_source_id | 10.7759/cureus.16867 +base_url | https://doi.org/10.7759/cureus.16867 +terminal_url | https://www.cureus.com/articles/66793-advanced-squamous-cell-carcinoma-of-gall-bladder-masquerading-as-liver-abscess-with-review-of-literature-review-on-advanced-biliary-tract-cancer +-[ RECORD 3 ]--+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +link_source_id | 10.7759/cureus.17425 +base_url | https://doi.org/10.7759/cureus.17425 +terminal_url | https://www.cureus.com/articles/67438-attitudes-and-knowledge-of-medical-students-towards-healthcare-for-lesbian-gay-bisexual-and-transgender-seniors-impact-of-a-case-based-discussion-with-facilitators-from-the-community +-[ RECORD 4 ]--+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +link_source_id | 10.7759/cureus.17313 +base_url | https://doi.org/10.7759/cureus.17313 +terminal_url | https://www.cureus.com/articles/67258-utilizing-google-trends-to-track-online-interest-in-elective-hand-surgery-during-the-covid-19-pandemic +-[ RECORD 5 ]--+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +link_source_id | 10.7759/cureus.16943 +base_url | https://doi.org/10.7759/cureus.16943 +terminal_url | https://www.cureus.com/articles/19364-small-bowel-obstruction-a-rare-presentation-of-the-inferior-pancreaticoduodenal-artery-pseudoaneurysm-bleed + +Ugh, stupid "email to get PDF". but ingest seems to work anyways? + +NOTE: re-crawl/re-ingest all (eg, fatcat-ingest or similar) + +## www.e-manuscripta.ch + + link_source_id | base_url | terminal_url +------------------------------+----------------------------------------------+------------------------------------------------------------------- + 10.7891/e-manuscripta-114031 | https://doi.org/10.7891/e-manuscripta-114031 | https://www.e-manuscripta.ch/swa/doi/10.7891/e-manuscripta-114031 + 10.7891/e-manuscripta-112064 | https://doi.org/10.7891/e-manuscripta-112064 | https://www.e-manuscripta.ch/zut/doi/10.7891/e-manuscripta-112064 + 10.7891/e-manuscripta-112176 | https://doi.org/10.7891/e-manuscripta-112176 | https://www.e-manuscripta.ch/zut/doi/10.7891/e-manuscripta-112176 + 10.7891/e-manuscripta-115200 | https://doi.org/10.7891/e-manuscripta-115200 | https://www.e-manuscripta.ch/swa/doi/10.7891/e-manuscripta-115200 + 10.7891/e-manuscripta-114008 | https://doi.org/10.7891/e-manuscripta-114008 | https://www.e-manuscripta.ch/swa/doi/10.7891/e-manuscripta-114008 + +Historical docs, single pages, but do have full PDF downloads. + +NOTE: re-ingest + +## www.inderscience.com + +Previously: paywall (2021-05_daily_improvements.md) + +## www.un-ilibrary.org + + link_source_id | base_url | terminal_url +----------------------------+--------------------------------------------+------------------------------------------------------------- + 10.18356/9789210550307 | https://doi.org/10.18356/9789210550307 | https://www.un-ilibrary.org/content/books/9789210550307 + 10.18356/9789210586719c011 | https://doi.org/10.18356/9789210586719c011 | https://www.un-ilibrary.org/content/books/9789210586719c011 + 10.18356/9789210058575c014 | https://doi.org/10.18356/9789210058575c014 | https://www.un-ilibrary.org/content/books/9789210058575c014 + 10.18356/9789210550307c020 | https://doi.org/10.18356/9789210550307c020 | https://www.un-ilibrary.org/content/books/9789210550307c020 + 10.18356/9789213631423c005 | https://doi.org/10.18356/9789213631423c005 | https://www.un-ilibrary.org/content/books/9789213631423c005 + +Books and chapters. Doesn't seem to have actual download ability? + +# Re-Ingest / Re-Crawl + +Using fatcat-ingest helper tool. + +- www.isca-speech.org doi_prefix:10.21437 + doi:* doi_prefix:10.21437 in_ia:false + 9,233 + ./fatcat_ingest.py --allow-non-oa query 'doi:* doi_prefix:10.21437' > /srv/fatcat/tasks/2021-09-03_ingest_isca.json + => Counter({'ingest_request': 9221, 'elasticsearch_release': 9221, 'estimate': 9221}) +- repository.dri.ie doi_prefix:10.7486 + doi:* in_ia:false doi_prefix:10.7486 + 56,532 + ./fatcat_ingest.py --allow-non-oa query 'doi:* doi_prefix:10.7486' > /srv/fatcat/tasks/2021-09-03_ingest_dri.json + => Counter({'ingest_request': 56532, 'elasticsearch_release': 56532, 'estimate': 56532}) +- *.arvojournals.org doi_prefix:10.1167 (force recrawl if no-pdf-link) + 25,598 + many are meeting abstracts + ./fatcat_ingest.py --allow-non-oa query doi_prefix:10.1167 > /srv/fatcat/tasks/2021-09-03_ingest_arvo.json + => Counter({'ingest_request': 25598, 'elasticsearch_release': 25598, 'estimate': 25598}) +- www.cureus.com doi_prefix:10.7759 + 1,537 + ./fatcat_ingest.py --allow-non-oa query doi_prefix:10.7759 > /srv/fatcat/tasks/2021-09-03_ingest_cureus.json + => Counter({'ingest_request': 1535, 'elasticsearch_release': 1535, 'estimate': 1535}) +- www.e-manuscripta.ch doi_prefix:10.7891 10.7891/e-manuscripta + 110,945 + TODO: all are marked 'unpublished', but that is actually probably right? +- www.frontiersin.org doi_prefix:10.3389 (both PDF and XML!) + doi:* in_ia:false doi_prefix:10.3389 + 212,370 + doi:10.3389/conf.* => most seem to be just abstracts? how many like this? + container_id:kecnf6vtpngn7j2avgfpdyw5ym => "topics" (2.2k) + fatcat-cli search release 'doi:* in_ia:false doi_prefix:10.3389 !container_id:kecnf6vtpngn7j2avgfpdyw5ym' --index-json -n0 | jq '[.ident, .container_id, .doi] | @tsv' -r | rg -v 10.3389/conf | pv -l | gzip > frontiers_to_crawl.tsv.gz + => 191k + but many might be components? this is actually kind of a mess + fatcat-cli search release 'doi:* in_ia:false doi_prefix:10.3389 !container_id:kecnf6vtpngn7j2avgfpdyw5ym !type:component stage:published' --index-json -n0 | jq '[.ident, .container_id, .doi] | @tsv' -r | rg -v 10.3389/conf | pv -l | gzip > frontiers_to_crawl.tsv.gz + => 19.2k + ./fatcat_ingest.py --allow-non-oa query 'doi:* in_ia:false doi_prefix:10.3389 !container_id:kecnf6vtpngn7j2avgfpdyw5ym !type:component stage:published' | rg -v 10.3389/conf > /srv/fatcat/tasks/2021-09-03_frontiers.json + +# Remaining Tasks / Domains (TODO) + +more complex crawling/content: +- add video link to alternative content demo ingest: https://open.library.ubc.ca/cIRcle/collections/48630/items/1.0400764 +- watermark.silverchair.com: if terminal-bad-status, then do recrawl via heritrix with base_url +- www.morressier.com: interesting site for rich web crawling/preservation (video+slides+data) +- doi.ala.org.au: possible dataset ingest source +- peerj.com, at least reviews, should be HTML ingest? or are some PDF? +- publons.com should be HTML ingest, possibly special case for scope +- frontiersin.org: any 'component' releases with PDF file are probably a metadata bug + +other tasks: +- handle this related withdrawn notice? https://open.library.ubc.ca/cIRcle/collections/48630/items/1.0401512 +- push/deploy sandcrawler changes diff --git a/notes/ingest/NEXT.md b/notes/ingest/NEXT.md new file mode 100644 index 0000000..8cdd6df --- /dev/null +++ b/notes/ingest/NEXT.md @@ -0,0 +1,52 @@ + +biorxiv +medrxiv + doi:10.1101\/20* + +persee.fr 147k + publisher:persee in_ia:false is_oa:true + https://www.persee.fr/doc/pumus_1164-5385_1992_num_2_1_1013 + +cairn.info: 161k + doi_prefix:10.3917 in_ia:false is_oa:true + https://www.cairn.info/revue-afrique-contemporaine-2011-3-page-161.htm + https://www.cairn.info/revue-cahiers-de-psychologie-clinique-2014-1-page-209.htm + +IOP OA: 169k + doi_prefix:10.1088 is_oa:true in_ia:false + +indian journals platform? 124k + doi_prefix:10.4103 in_ia:false is_oa:true + http://www.urologyannals.com/article.asp?issn=0974-7796;year=2011;volume=3;issue=3;spage=138;epage=140;aulast=Ahmad + http://www.neurologyindia.com/article.asp?issn=0028-3886;year=2011;volume=59;issue=4;spage=612;epage=615;aulast=Utsuki + +openedition? 48k + doi_prefix:10.4000 is_oa:true in_ia:false + +german medical science (GMS) 28k + doi_prefix:10.3205 in_ia:false is_oa:true + https://www.egms.de/static/en/journals/zma/2015-32/zma000965.shtml + +siberian chemistry 28k + doi_prefix:10.2298 in_ia:false is_oa:true + http://www.doiserbia.nb.rs/Article.aspx?ID=0352-51391000105H + +jalc oa doi: 82k + doi_registrar:jalc in_ia:false is_oa:true + +sage OA papers + https://journals.sagepub.com/doi/10.1177/034003529802400510 + +Scientific Reports: 25k + in_ia:false container_id:"tnqhc2x2aneavcd3gx5h7mswhm" + +U Toronto press: 23k + publisher:"Toronto Press" in_ia:false is_oa:true + has an annoying bounce page + +ASHA (speech-language-hearing association): 7k + publisher:Speech-Language-Hearing in_ia:false is_oa:true + +MIT press journals + + diff --git a/notes/ingest/es_csv_to_json.py b/notes/ingest/es_csv_to_json.py new file mode 100755 index 0000000..4cd1811 --- /dev/null +++ b/notes/ingest/es_csv_to_json.py @@ -0,0 +1,37 @@ +#!/usr/bin/env python3 + +""" + input like: + + doi,ident,"release_stage" + "10.7554/elife.38904",mxj534diw5gatc26rkif3io5xm,published + "10.7554/elife.41855",kag74qc6dfex7ftpfkf7iaus44,published + "10.7554/elife.41156",ienee5vxcbbbfhs2q54h4455hu,published + "10.7554/elife.43230",52rpllol2rcndjqs3xfwcldeka,published + "10.7554/elife.42591",fpz642gihrc3jd2vibg6gnjrxm,published + + output like: + + { + "base_url": "https://doi.org/10.7554/elife.38904", + "ext_ids": { + "doi": "10.7554/elife.38904" + }, + "fatcat_release": "mxj534diw5gatc26rkif3io5xm", + "release_stage": "published" + } +""" + +import csv, sys, json + +reader = csv.DictReader(sys.stdin) +for row in reader: + d = { + "base_url": "https://doi.org/{}".format(row['doi']), + "ext_ids": { + "doi": row['doi'], + }, + "fatcat_release": row['ident'], + "release_stage": row['release_stage'], + } + print(json.dumps(d)) diff --git a/notes/library_shopping.txt b/notes/library_shopping.txt new file mode 100644 index 0000000..bf876a5 --- /dev/null +++ b/notes/library_shopping.txt @@ -0,0 +1,10 @@ + +potential helpers: +- https://github.com/martinblech/xmltodict +- https://github.com/trananhkma/fucking-awesome-python#text-processing +- https://github.com/blaze/blaze (for catalog/analytics) +- validation: https://github.com/pyeve/cerberus +- testing (to replace nose): + - https://github.com/CleanCut/green + - pytest + - mamba ("behavior driven") diff --git a/notes/match_filter_enrich.txt b/notes/match_filter_enrich.txt new file mode 100644 index 0000000..0c1f7df --- /dev/null +++ b/notes/match_filter_enrich.txt @@ -0,0 +1,31 @@ + +This could all be a single scalding job eventually. + +First, run matchcrossref and dumpfilemeta, and copy the output down to an SSD +somewhere. + + bnewbold@ia601101$ zcat 2018-09-14-0559.05-dumpfilemeta.tsv.gz | wc -l + 30728100 + +Reduce down the scored matches to just {sha1, dois}, sorted: + + zcat 2018-08-27-2352.17-matchcrossref.tsv.gz | ./filter_scored_matches.py | pv -l | sort -S 8G > 2018-08-27-2352.17-matchcrossref.filtered.tsv + # 5.79M 0:18:54 [5.11k/s] + +Join/merge the output: + + zcat 2018-09-14-0559.05-dumpfilemeta.tsv.gz | LC_ALL=C join -t$'\t' 2018-08-27-2352.17-matchcrossref.filtered.tsv - | pv -l | ./enrich_scored_matches.py | gzip > 2018-08-27-2352.17-matchcrossref.insertable.json.gz + # 5.79M 0:09:09 [10.5k/s] + +## Fatcat Insertable + +I can't remember now what the plan was for the 'insertable' output mode, which +bundles {key, cdx, mime, and size} info along with the {slug, score, json1, +json2} columns from the regular match script. The filter_scored_matches.py +doesn't know what to do with those columns at the moment, and the output isn't +sorted by slug... need to tweak scripts to fix this. + +In the meanwhile, as a work around just take the columns we want and re-sort: + + export LC_ALL=C + zcat 2018-12-18-2237.09-matchcrossref.insertable.tsv.gz | cut -f2-5 | sort -S 8G -u | gzip > 2018-12-18-2237.09-matchcrossref.tsv.gz diff --git a/notes/old_extract_results.txt b/notes/old_extract_results.txt new file mode 100644 index 0000000..0327b8b --- /dev/null +++ b/notes/old_extract_results.txt @@ -0,0 +1,50 @@ + +command: + + ./extraction_cdx_grobid.py --hbase-table wbgrp-journal-extract-0-qa --hbase-host bnewbold-dev.us.archive.org --grobid-uri http://wbgrp-svc096.us.archive.org:8070 -r hadoop -c mrjob.conf --archive $VENVSHORT.tar.gz#venv hdfs:///user/bnewbold/journal_crawl_cdx/citeseerx_crawl_2017.cdx --jobconf mapred.line.input.format.linespermap=8000 --jobconf mapreduce.job.queuename=extraction + +Started: Wed Apr 11 05:54:54 UTC 2018 +Finished: Sun Apr 15 20:42:37 UTC 2018 +(late saturday night PST fixed grobid parallelism) + +Elapsed: 110hrs, 47mins, 42sec + +line counts: + error 3896 + existing 311209 + invalid 2311343 + skip 195641 + success 1143094 + total 3,965,183 + +## Against prod table + +Started: Sun Apr 15 21:38:24 UTC 2018 +Finished: Wed Apr 18 17:36:44 UTC 2018 +Elapsed: 67hrs, 58mins, 20sec + +lines + error 143 + existing 213292 + invalid 2311343 + skip 195641 + success 1,244,764 + total 3,965,183 + +## TARGETED + +Job job_1513499322977_358533 failed with state FAILED due to: Task failed task_1513499322977_358533_m_000323 + +Started: Thu Apr 19 05:21:25 UTC 2018 +Finished: Sat Apr 21 11:01:58 UTC 2018 +Elapsed: 53hrs, 40mins, 33sec + +lines + error=4093 + existing=55448 + invalid=688873 + skip=257533 + success=1,282,053 + total=2,288,000 + + diff --git a/notes/petabox_ia_metadata.txt b/notes/petabox_ia_metadata.txt new file mode 100644 index 0000000..f46ea61 --- /dev/null +++ b/notes/petabox_ia_metadata.txt @@ -0,0 +1,56 @@ + +Ran in aitio:/schnell/iamine-journals in December 2018. + +Output uploaded to https://archive.org/details/ia-petabox-journal-metadata-2018 + +Commands: + + # didn't work! + #ia-mine --search collection:journals --itemlist > journals.20181218.itemlist + + # fetched manually via metamgr, using prefix matches + cat metamgr-* > metamgr-journals-loose.20181218.items + + ia-mine metamgr-journals-loose.20181218.items > journals.20181218.json + + export LC_ALL=C + cat journals-ia.20181218.json | jq 'select(.files) | .files[] | select(.format == "Text PDF") | .sha1' -r | sort -S 4G -u > journals-ia.20181218.pdf-sha1.tsv + +Size/results: + + bnewbold@ia601101$ wc -l journals-ia.20181218.json metamgr-journals-loose.20181218.items + 2043877 journals-ia.20181218.json + 2044362 metamgr-journals-loose.20181218.items + + # missed about 500; meh + + -rw-rw-r-- 1 bnewbold bnewbold 9.5G Dec 19 23:26 journals-ia.20181218.json + + bnewbold@ia601101$ wc -l journals-ia.20181218.pdf-sha1.tsv + 1748645 journals-ia.20181218.pdf-sha1.tsv + +## June 2019 Ingest + + bnewbold@ia601101$ pwd + /schnell/iamine-journals + + zcat journals-ia.20181218.json.gz | rg '"identifier": "arxiv-' > arxiv.json + zcat journals-ia.20181218.json.gz | rg '"identifier": "jstor-' > jstor.json + zcat journals-ia.20181218.json.gz | rg '"identifier": "paper-doi-10_' > paper-doi.json + zcat journals-ia.20181218.json.gz | rg '"identifier": "pubmed-PMC' > pmc.json + + cat arxiv.json | ./ia_pdf_match.py > arxiv.match.json + cat jstor.json | ./ia_pdf_match.py > jstor.match.json + cat paper-doi.json | ./ia_pdf_match.py > paper-doi.match.json + cat pmc.json | ./ia_pdf_match.py > pmc.match.json + + bnewbold@ia601101$ wc -l arxiv.*json jstor.*json paper-doi.*json pmc.*json + 1076012 arxiv.json + 740970 arxiv.match.json + 451204 jstor.json + 451204 jstor.match.json + 77838 paper-doi.json + 23736 paper-doi.match.json + 209787 pmc.json + 189093 pmc.match.json + diff --git a/notes/tasks/2020-01-06_heuristic_cdx.txt b/notes/tasks/2020-01-06_heuristic_cdx.txt new file mode 100644 index 0000000..209fa4f --- /dev/null +++ b/notes/tasks/2020-01-06_heuristic_cdx.txt @@ -0,0 +1,37 @@ + +Wanted to include a large number of additional CDX lines based on regex +pattern. These are primarily .edu domains with things that look like user +accounts *and* .pdf file extensions in the path. + +## Commands + +aitio:/fast/gwb_pdfs + + pdfs/gwb-pdf-20191005172329-url-heuristics-edu + pdfs/gwb-pdf-20191005172329-url-heuristics + + +to filter as url/sha1 uniq: + + cat raw.cdx | sort -u -t' ' -k3,6 -S 4G > uniq.cdx + + cat gwb-pdf-20191005172329-url-heuristics-edu/part-r-000* | sort -u -t' ' -k3,6 -S 4G > gwb-pdf-20191005172329-url-heuristics-edu.uniq_url_sha1.cdx + cat gwb-pdf-20191005172329-url-heuristics/part-r-000* | sort -u -t' ' -k3,6 -S 4G > gwb-pdf-20191005172329-url-heuristics.uniq_url_sha1.cdx + + 7241795 gwb-pdf-20191005172329-url-heuristics-edu.uniq_url_sha1.cdx + 41137888 gwb-pdf-20191005172329-url-heuristics.uniq_url_sha1.cdx + + cut -d' ' -f6 gwb-pdf-20191005172329-url-heuristics-edu.uniq_url_sha1.cdx | sort -u -S 4G | wc -l + 7241795 + + cut -d' ' -f6 gwb-pdf-20191005172329-url-heuristics.uniq_url_sha1.cdx | sort -u -S 4G | wc -l + 41137888 + + ./persist_tool.py cdx /fast/gwb_pdf/gwb-pdf-20191005172329-url-heuristics-edu.uniq_url_sha1.cdx + Worker: Counter({'total': 7239153, 'insert-cdx': 6845283, 'update-cdx': 0}) + CDX lines pushed: Counter({'total': 7241795, 'pushed': 7239153, 'skip-parse': 2603, 'skip-mimetype': 39}) + + ./persist_tool.py cdx /fast/gwb_pdf/gwb-pdf-20191005172329-url-heuristics.uniq_url_sha1.cdx + Worker: Counter({'total': 41030360, 'insert-cdx': 22430064, 'update-cdx': 0}) + CDX lines pushed: Counter({'total': 41137888, 'pushed': 41030360, 'skip-mimetype': 87341, 'skip-parse': 20187}) + diff --git a/notes/tasks/2020-01-27_cleanup_cdx.md b/notes/tasks/2020-01-27_cleanup_cdx.md new file mode 100644 index 0000000..54db92e --- /dev/null +++ b/notes/tasks/2020-01-27_cleanup_cdx.md @@ -0,0 +1,34 @@ + +Accidentally seem to have backfilled many CDX lines with non-PDF content. +Should clear these out! + +Something like: + + mimetype = 'text/html' + not in file_meta + +Or maybe instead: + + mimetype = 'text/html' + not in file_meta + +SQL: + + SELECT * FROM cdx WHERE mimetype = 'text/html' AND row_created < '2019-10-01' LIMIT 5; + SELECT COUNT(1) FROM cdx WHERE mimetype = 'text/html' AND row_created < '2019-10-01'; + => 24841846 + + SELECT * FROM cdx LEFT JOIN file_meta ON file_meta.sha1hex = cdx.sha1hex WHERE cdx.mimetype = 'text/html' AND file_meta.sha256hex IS NULL LIMIT 5; + SELECT COUNT(1) FROM cdx LEFT JOIN file_meta ON cdx.sha1hex = file_meta.sha1hex WHERE cdx.mimetype = 'text/html' AND file_meta.sha256hex IS NULL; + => 24547552 + + DELETE FROM cdx + WHERE sha1hex IN + (SELECT cdx.sha1hex + FROM cdx + LEFT JOIN file_meta ON file_meta.sha1hex = cdx.sha1hex + WHERE cdx.mimetype = 'text/html' AND file_meta.sha256hex IS NULL); + => DELETE 24553428 + +Slightly more... probably should have had a "AND cdx.mimetype = 'text/html'" in +the DELETE WHERE clause. diff --git a/notes/tasks/2020-01-27_grobid_backfill.md b/notes/tasks/2020-01-27_grobid_backfill.md new file mode 100644 index 0000000..d70e203 --- /dev/null +++ b/notes/tasks/2020-01-27_grobid_backfill.md @@ -0,0 +1,40 @@ + +Recently added a bunch of PDFs to sandcrawler-db. Want to GROBID extract the +~15m which haven't been processed yet. Also want to re-GROBID a batch of +PDFs-in-zipfiles from archive.org; will probably also want to re-GROBID other +petabox files soon. + +## pre-1923 zipfile re-extraction + +Exact commands (in parallel): + + fd .zip /srv/sandcrawler/tasks/crossref-pre-1909-scholarly-works/ | \ + parallel -j16 --progress --joblog extract_tasks.log --resume-failed \ + './grobid_tool.py --kafka-mode --kafka-env prod --kafka-hosts wbgrp-svc263.us.archive.org:9092,wbgrp-svc284.us.archive.org:9092,wbgrp-svc285.us.archive.org:9092 --grobid-host http://localhost:8070 extract-zipfile {}' + + fd .zip /srv/sandcrawler/tasks/crossref-pre-1923-scholarly-works/ | \ + parallel -j16 --progress --joblog extract_tasks_1923.log --resume-failed \ + './grobid_tool.py --kafka-mode --kafka-env prod --kafka-hosts wbgrp-svc263.us.archive.org:9092,wbgrp-svc284.us.archive.org:9092,wbgrp-svc285.us.archive.org:9092 --grobid-host http://localhost:8070 extract-zipfile {}' + +## petabox re-extraction + +This was run around 2020-02-03. There are a few million remaining PDFs that +have only partial file metadata (`file_meta`), meaning run with old version of +sandcrawler code. Want to get them all covered, maybe even DELETE the missing +ones, so re-grobiding petabox-only files. + +There are about 2,887,834 files in petabox, only 46,232 need re-processing (!). + + psql sandcrawler < dump_regrobid_pdf_petabox.sql + cat dump_regrobid_pdf_petabox.2020-02-03.json | sort -S 4G | uniq -w 40 | cut -f2 > dump_regrobid_pdf_petabox.2020-02-03.uniq.json + +This is pretty few... maybe even would have been caught by wayback backfill? + +Small start: + + head /srv/sandcrawler/tasks/dump_regrobid_pdf_petabox.2020-02-03.uniq.json | ./grobid_tool.py --kafka-env prod --kafka-hosts wbgrp-svc263.us.archive.org:9092,wbgrp-svc284.us.archive.org:9092,wbgrp-svc285.us.archive.org:9092 --kafka-mode --grobid-host http://localhost:8070 -j0 extract-json - + +Full batch, 25x parallel: + + cat /srv/sandcrawler/tasks/dump_regrobid_pdf_petabox.2020-02-03.uniq.json | pv -l | parallel -j25 --pipe ./grobid_tool.py --kafka-env prod --kafka-hosts wbgrp-svc263.us.archive.org:9092,wbgrp-svc284.us.archive.org:9092,wbgrp-svc285.us.archive.org:9092 --kafka-mode --grobid-host http://localhost:8070 -j0 extract-json - + diff --git a/notes/tasks/2020-02-14_pdftrio.md b/notes/tasks/2020-02-14_pdftrio.md new file mode 100644 index 0000000..e6f8d8e --- /dev/null +++ b/notes/tasks/2020-02-14_pdftrio.md @@ -0,0 +1,162 @@ + +First end-to-end `pdf_trio` results! + +## Source + +Will use AIT partner #1830 (U Alberta) CDX as input. These are unique by +digest, about 100k. + + ArchiveIt-Collection-1830.download.cdx + +## Testing/Prep + +Versions/setup: + + sandcrawler: f613f69a40fcc9a445f21cadd35d7c36c8061db8 + => patched to 'auto' mode + + pdf_trio: 03bd3fdc15418462b2b1582e4f967f26ddcb43e2 + + pdftrio: 'auto' mode + + uwsgi: 16x processes + + sudo docker run --rm -p 8501:8501 -e TF_XLA_FLAGS=--tf_xla_cpu_global_jit -e KMP_AFFINITY=granularity=fine,compact,1,0 -e KMP_BLOCKTIME=0 -e OMP_NUM_THREADS=24 -e TENSORFLOW_INTER_OP_PARALLELISM=1 -e TENSORFLOW_INTRA_OP_PARALLELISM=24 -v /srv/pdftrio//models/bert_models:/models/bert_model -v /srv/pdftrio//models/pdf_image_classifier_model:/models/image_model -v /srv/pdftrio//config/tfserving_models_docker.config:/models/tfserving_models.config -v /srv/pdftrio/config/tfserving_batch.config:/models/tfserving_batch.config --name pdftrio-tfserving tensorflow/serving --model_config_file=/models/tfserving_models.config --enable_batching=true --batching_parameters_file=/models/tfserving_batch.config + +Basic testing:: + + head -n100 /srv/sandcrawler/tasks/ArchiveIt-Collection-1830.download.cdx | parallel -j20 --pipe --linebuffer ./pdftrio_tool.py --pdftrio-host http://localhost:3939 -j0 classify-pdf-cdx - | jq . + + head -n100 /srv/sandcrawler/tasks/ArchiveIt-Collection-1830.download.cdx | parallel -j20 --pipe --linebuffer ./pdftrio_tool.py --kafka-mode --kafka-env qa --kafka-hosts wbgrp-svc263.us.archive.org,wbgrp-svc284.us.archive.org,wbgrp-svc285.us.archive.org --pdftrio-host http://localhost:3939 -j0 classify-pdf-cdx - + => Running in kafka output mode, publishing to sandcrawler-qa.pdftrio-output + + +On the persist side: + + kafkacat -C -b wbgrp-svc263.us.archive.org -t sandcrawler-qa.pdftrio-output | head | jq . + => looks fine + + ./sandcrawler_worker.py --kafka-hosts wbgrp-svc263.us.archive.org --env qa persist-pdftrio + => Consuming from kafka topic sandcrawler-qa.pdftrio-output, group persist-pdftrio + +Ah, don't forget, start persist before writing to topic! Or would need to reset +offsets to start. + +Seems to be only a single pdftext instance running? Very low CPU + + head -n500 /srv/sandcrawler/tasks/ArchiveIt-Collection-1830.download.cdx | parallel -j40 -N1 --pipe --round-robin --linebuffer ./pdftrio_tool.py --kafka-mode --kafka-env qa --kafka-hosts wbgrp-svc263.us.archive.org,wbgrp-svc284.us.archive.org,wbgrp-svc285.us.archive.org --pdftrio-host http://localhost:3939 -j0 classify-pdf-cdx - + +That is much better! CPU still not pegged, so maybe could do 50x processes? Lots of I/O wait. Blech. + +Zero ("0") not getting persisted for any columns (fixed in sandcrawler/db.py) + +`models_date` not getting set. Added `PDFTRIO_MODELS_DATE="2020-01-01"` to env. (TODO: ansible) + +## Prod Run + + ./sandcrawler_worker.py --kafka-hosts wbgrp-svc263.us.archive.org --env prod persist-pdftrio + + time cat /srv/sandcrawler/tasks/ArchiveIt-Collection-1830.download.cdx | parallel -j40 -N1 --pipe --round-robin --linebuffer ./pdftrio_tool.py --kafka-mode --kafka-env prod --kafka-hosts wbgrp-svc263.us.archive.org,wbgrp-svc284.us.archive.org,wbgrp-svc285.us.archive.org --pdftrio-host http://localhost:3939 -j0 classify-pdf-cdx - + +Worker CPU basically blocked on pdftotext, multiple 100% CPU. Presumably I/O +wait? Though not totally sure. + +htop: + + PID USER PRI NI VIRT RES SHR S CPU% MEM% TIME+ Command + 17951 pdftrio 20 0 51756 12868 5856 R 90.1 0.0 0:06.61 pdftotext -nopgbrk -eol unix -enc UTF-8 /tmp/research-p + 17870 pdftrio 20 0 52004 12964 5684 R 87.4 0.0 0:08.61 pdftotext -nopgbrk -eol unix -enc UTF-8 /tmp/research-p + 13735 root 20 0 10.4G 3815M 4144 S 79.6 7.6 48h02:37 tensorflow_model_server --port=8500 --rest_api_port=850 + 14522 pdftrio 20 0 2817M 1331M 16896 R 43.1 2.6 0:57.75 /usr/bin/uwsgi --ini /srv/pdftrio/src/uwsgi.ini + 18027 pdftrio 20 0 49192 10692 6116 R 39.8 0.0 0:00.61 pdftotext -nopgbrk -eol unix -enc UTF-8 /tmp/research-p + 14518 pdftrio 20 0 2818M 1336M 16836 S 33.3 2.7 0:47.46 /usr/bin/uwsgi --ini /srv/pdftrio/src/uwsgi.ini + 14504 pdftrio 20 0 2731M 1310M 13164 D 32.6 2.6 0:34.81 /usr/bin/uwsgi --ini /srv/pdftrio/src/uwsgi.ini + 14526 pdftrio 20 0 2816M 1333M 16832 R 28.7 2.7 0:57.22 /usr/bin/uwsgi --ini /srv/pdftrio/src/uwsgi.ini + 14500 pdftrio 20 0 2729M 1306M 13160 R 20.9 2.6 0:22.57 /usr/bin/uwsgi --ini /srv/pdftrio/src/uwsgi.ini + 14492 pdftrio 20 0 2729M 1307M 13156 S 17.6 2.6 0:17.91 /usr/bin/uwsgi --ini /srv/pdftrio/src/uwsgi.ini + 14508 pdftrio 20 0 2734M 1312M 14380 D 14.4 2.6 0:38.75 /usr/bin/uwsgi --ini /srv/pdftrio/src/uwsgi.ini + 14496 pdftrio 20 0 2728M 1300M 13160 S 13.7 2.6 0:18.00 /usr/bin/uwsgi --ini /srv/pdftrio/src/uwsgi.ini + 17314 sandcrawl 20 0 56668 18228 4304 D 13.7 0.0 0:02.31 perl /usr/bin/parallel -j40 -N1 --pipe --round-robin -- + 14472 pdftrio 20 0 2725M 1283M 13136 S 12.4 2.6 0:05.69 /usr/bin/uwsgi --ini /srv/pdftrio/src/uwsgi.ini + 14513 pdftrio 20 0 2730M 1309M 14300 S 11.1 2.6 0:40.32 /usr/bin/uwsgi --ini /srv/pdftrio/src/uwsgi.ini + 14480 pdftrio 20 0 2725M 1291M 13144 S 10.4 2.6 0:08.77 /usr/bin/uwsgi --ini /srv/pdftrio/src/uwsgi.ini + 14488 pdftrio 20 0 2725M 1294M 13152 S 9.8 2.6 0:08.18 /usr/bin/uwsgi --ini /srv/pdftrio/src/uwsgi.ini + 14468 pdftrio 20 0 2717M 1271M 13088 S 6.5 2.5 0:02.42 /usr/bin/uwsgi --ini /srv/pdftrio/src/uwsgi.ini + 17411 sandcrawl 20 0 556M 53840 14936 S 6.5 0.1 0:01.57 python3 ./pdftrio_tool.py --kafka-mode --kafka-env qa - + 14530 pdftrio 20 0 2524M 1252M 3492 S 4.6 2.5 0:12.72 /usr/bin/uwsgi --ini /srv/pdftrio/src/uwsgi.ini + 7311 bnewbold 20 0 27716 5520 3128 R 3.9 0.0 0:41.59 htop + 17444 sandcrawl 20 0 552M 50456 14892 S 3.9 0.1 0:01.54 python3 ./pdftrio_tool.py --kafka-mode --kafka-env qa - + 18042 pdftrio 20 0 46068 6588 5328 R 3.3 0.0 0:00.05 pdftotext -nopgbrk -eol unix -enc UTF-8 /tmp/research-p + 18043 pdftrio 20 0 4 4 0 R 2.6 0.0 0:00.04 + 2203 grobid 20 0 6334M 126M 4188 S 0.7 0.3 3h27:32 /usr/lib/jvm/java-8-openjdk-amd64/bin/java -XX:MaxMetas + 17419 sandcrawl 20 0 619M 116M 15248 S 0.7 0.2 0:02.68 python3 ./pdftrio_tool.py --kafka-mode --kafka-env qa - + 17440 sandcrawl 20 0 578M 76948 15160 S 0.7 0.1 0:01.54 python3 ./pdftrio_tool.py --kafka-mode --kafka-env qa - + 13848 root 20 0 0 0 0 D 0.7 0.0 0:00.69 kworker/u60:1 + 17443 sandcrawl 20 0 578M 76500 14912 S 0.7 0.1 0:01.74 python3 ./pdftrio_tool.py --kafka-mode --kafka-env qa - + 17414 sandcrawl 20 0 580M 77720 15036 S 0.0 0.2 0:01.77 python3 ./pdftrio_tool.py --kafka-mode --kafka-env qa - + 17432 sandcrawl 20 0 563M 61460 14976 S 0.0 0.1 0:01.59 python3 ./pdftrio_tool.py --kafka-mode --kafka-env qa - + 17442 sandcrawl 20 0 561M 53096 15240 S 0.0 0.1 0:01.47 python3 ./pdftrio_tool.py --kafka-mode --kafka-env qa - + 17433 sandcrawl 20 0 559M 57160 15176 S 0.0 0.1 0:01.52 python3 ./pdftrio_tool.py --kafka-mode --kafka-env qa - + 17431 sandcrawl 20 0 554M 50960 14892 S 0.0 0.1 0:01.37 python3 ./pdftrio_tool.py --kafka-mode --kafka-env qa - + 17413 sandcrawl 20 0 554M 52376 14920 S 0.0 0.1 0:01.57 python3 ./pdftrio_tool.py --kafka-mode --kafka-env qa - + +dstat: + + ----total-cpu-usage---- -dsk/total- -net/total- ---paging-- ---system-- + usr sys idl wai hiq siq| read writ| recv send| in out | int csw + 32 9 22 37 0 0| 0 37M| 20M 12M| 0 0 | 35k 64k + 20 6 24 50 0 0| 0 20M| 30M 5662k| 0 0 | 27k 48k + 27 7 24 43 0 0| 0 26M|8712k 6289k| 0 0 | 21k 114k + 30 8 23 38 0 0|4096B 61M| 17M 20M| 0 0 | 31k 54k + 33 6 17 44 0 0| 0 32M| 14M 6384k| 0 0 | 27k 46k + 25 6 24 44 0 0| 0 19M| 18M 13M| 0 0 | 27k 179k + 40 6 19 35 0 0|8192B 25M|7855k 6661k| 0 0 | 31k 85k + 59 8 12 20 0 0| 0 39M|4177k 33M| 0 0 | 34k 64k + 34 4 17 44 0 0| 0 16M|7527k 11M| 0 0 | 22k 45k + 44 7 17 32 0 0| 0 30M| 20M 291k| 0 0 | 36k 62k + +Create tmpfs: + + sudo mkdir -p /pdftrio-ramdisk + #sudo mount -t tmpfs -o size=2g tmpfs /pdftrio-ramdisk + sudo mount -t tmpfs -o size=6g tmpfs /pdftrio-ramdisk + +add to pdftrio config env and restart: + + TEMP=/run/pdf_trio + +Seems to have worked. Pretty much maxed CPU, may need to back-off parallelism. Doing more than 31/sec. + +Errors were not getting encoded correctly: + + File "/fast/sandcrawler/python/sandcrawler/persist.py", line 331, in push_batch + r['pdf_trio']['key'] = r['key'] + KeyError: 'pdf_trio' + +Fixed in sandcrawler worker, and patched persist to work around this. + + time cat /srv/sandcrawler/tasks/ArchiveIt-Collection-1830.download.cdx | parallel -j30 -N1 --pipe --round-robin --linebuffer ./pdftrio_tool.py --kafka-mode --kafka-env prod --kafka-hosts wbgrp-svc263.us.archive.org,wbgrp-svc284.us.archive.org,wbgrp-svc285.us.archive.org --pdftrio-host http://localhost:3939 -j0 classify-pdf-cdx - + +Wow, 30x parallelism waaaay less? + + time cat /srv/sandcrawler/tasks/ArchiveIt-Collection-1830.download.cdx | parallel -j30 -N1 --pipe --round-robin --linebuffer ./pdftrio_tool.py --kafka-mode --kafka-env prod --kafka-hosts wbgrp-svc263.us.archive.org,wbgrp-svc284.us.archive.org,wbgrp-svc285.us.archive.org --pdftrio-host http://localhost:3939 -j0 classify-pdf-cdx - + +What changed? Confused. Load average was like 40. + +Via kafka, as much as 69.71/sec! Errors? + +Hrm, this whole `auto` thing. I am very skeptical. Should also do a run as `all`, -j20. + + Worker: Counter({'total': 1916, 'pushed': 1916}) + CDX lines pushed: Counter({'total': 1934, 'pushed': 1916, 'skip-parse': 18}) + +Hit some bugs, causing failure, but still seem to have processed a good chunk. + +Switched to `all`, running a different batch: + + time cat /srv/sandcrawler/tasks/ArchiveIt-Collection-1914.download.cdx | parallel -j20 -N1 --pipe --round-robin --linebuffer ./pdftrio_tool.py --kafka-mode --kafka-env prod --kafka-hosts wbgrp-svc263.us.archive.org,wbgrp-svc284.us.archive.org,wbgrp-svc285.us.archive.org --pdftrio-host http://localhost:3939 -j0 classify-pdf-cdx - + +After flag change, another batch in `all`: + + time cat /srv/sandcrawler/tasks/ArchiveIt-Collection-2566.download.cdx | parallel -j20 -N1 --pipe --round-robin --linebuffer ./pdftrio_tool.py --kafka-mode --kafka-env prod --kafka-hosts wbgrp-svc263.us.archive.org,wbgrp-svc284.us.archive.org,wbgrp-svc285.us.archive.org --pdftrio-host http://localhost:3939 -j0 classify-pdf-cdx - + diff --git a/notes/tasks/2020-07-22_processing_holes.md b/notes/tasks/2020-07-22_processing_holes.md new file mode 100644 index 0000000..70e2b59 --- /dev/null +++ b/notes/tasks/2020-07-22_processing_holes.md @@ -0,0 +1,120 @@ + +Want to clean up missing/partial processing (GROBID, `pdf_meta`, `file_meta`) +in sandcrawler database. + + +## `pdf_meta` for petabox rows + +Ran `dump_unextracted_pdf_petabox.sql` SQL, which resulted in a .json file. + + wc -l dump_unextracted_pdf_petabox.2020-07-22.json + 1503086 dump_unextracted_pdf_petabox.2020-07-22.json + +Great, 1.5 million, not too many. Start small: + + head -n1000 dump_unextracted_pdf_petabox.2020-07-22.json | rg -v "\\\\" | jq . -c | pv -l | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.unextracted -p -1 + +Full batch: + + cat dump_unextracted_pdf_petabox.2020-07-22.json | rg -v "\\\\" | jq . -c | pv -l | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.unextracted -p -1 + +Re-ran on 2020-08-19: + + wc -l dump_unextracted_pdf_petabox.2020-08-19.json + 971194 dump_unextracted_pdf_petabox.2020-08-19.json + +## `pdf_meta` missing CDX rows + +First, the GROBID-ized rows but only if has a fatcat file as well. + +10,755,365! That is a lot still to process. + + cat dump_unextracted_pdf.fatcat.2020-07-22.json | rg -v "\\\\" | jq . -c | pv -l | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.unextracted -p -1 + +Re-ran on 2020-08-19: + + wc -l dump_unextracted_pdf.fatcat.2020-08-19.json + 65517 dump_unextracted_pdf.fatcat.2020-08-19.json + +Enqueued! + +## `GROBID` missing petabox rows + + wc -l /grande/snapshots/dump_ungrobided_pdf_petabox.2020-07-22.json + 972221 /grande/snapshots/dump_ungrobided_pdf_petabox.2020-07-22.json + +Start small: + + head -n1000 dump_ungrobided_pdf_petabox.2020-07-22.json | rg -v "\\\\" | jq . -c | pv -l | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ungrobided-pg -p -1 + +Full batch: + + cat dump_ungrobided_pdf_petabox.2020-07-22.json | rg -v "\\\\" | jq . -c | pv -l | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ungrobided-pg -p -1 + +Re-ran on 2020-08-19: + + wc -l dump_ungrobided_pdf_petabox.2020-08-19.json + 933 dump_ungrobided_pdf_petabox.2020-08-19.json + +Enqueued! + +## `GROBID` for missing CDX rows in fatcat + + wc -l dump_ungrobided_pdf.fatcat.2020-07-22.json + 1808580 dump_ungrobided_pdf.fatcat.2020-07-22.json + +Full batch: + + cat dump_ungrobided_pdf.fatcat.2020-07-22.json | rg -v "\\\\" | jq . -c | pv -l | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ungrobided-pg -p -1 + +## `GROBID` for bad status + +Eg, wayback errors. + +TODO + +## `pdf_trio` for OA journal crawls + +TODO + +## `pdf_trio` for "included by heuristic", not in fatcat + +TODO + +## Live-ingest missing arxiv papers + + ./fatcat_ingest.py --allow-non-oa --limit 10000 query arxiv_id:* > /srv/fatcat/snapshots/arxiv_10k_ingest_requests.json + => Expecting 1505184 release objects in search queries + + cat /srv/fatcat/snapshots/arxiv_10k_ingest_requests.json | rg -v "\\\\" | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests -p 22 + +Repeating this every few days should (?) result in all the backlog of arxiv +papers getting indexed. Could focus on recent years to start (with query +filter). + +## re-ingest spn2 errors (all time) + +Eg: + + spn2-cdx-lookup-failure: 143963 + spn-error: 101773 + spn2-error: 16342 + +TODO + +## re-try CDX errors + +Eg, for unpaywall only, bulk ingest all `cdx-error`. + +TODO + +## live ingest unpaywall `no-capture` URLs + +After re-trying the CDX errors for unpaywall URLs (see above), count all the +no-capture URLs, and if reasonable recrawl them all in live more ("reasonable" +meaning fewer than 200k or so URLs). + +Could also force recrawl (not using CDX lookups) for some publisher platforms +if that made sense. + +TODO diff --git a/notes/tasks/2020-08-20_file_meta.md b/notes/tasks/2020-08-20_file_meta.md new file mode 100644 index 0000000..39c84dd --- /dev/null +++ b/notes/tasks/2020-08-20_file_meta.md @@ -0,0 +1,66 @@ + +Want to update fatcat file entities with "full" file metadata for those which are missing it. + +How many `file_meta` rows *still* don't have metadata? + + SELECT COUNT(*) FROM file_meta WHERE sha256hex IS NULL; + => 62962 + +First generate list of sha1hex from most recent bulk export which are missing +at least some metadata (based on missing sha256): + + zcat file_hashes.tsv.gz | rg '\t\t' | cut -f3 | sort -u -S 4G | pv -l > fatcat_file_partial_sha1hex.tsv + => 18.7M 0:05:46 [53.8k/s] + +Then dump the entire sandcrawler `file_meta` table as TSV, with first column +sha1hex and second column JSON with all the file metadata fields: + + COPY ( + SELECT sha1hex, row_to_json(file_meta) + FROM file_meta + WHERE sha256hex IS NOT NULL + ORDER BY sha1hex ASC + ) + TO '/grande/snapshots/file_meta_dump.tsv' + WITH NULL ''; + +Join/cut: + + export LC_ALL=C + join -t$'\t' fatcat_file_partial_sha1hex.tsv /grande/snapshots/file_meta_dump.tsv | uniq -w 40 | cut -f2 | pv -l > fatcat_file_partial.file_meta.json + => 18.1M 0:03:37 [83.2k/s] + +Check counts: + + cat fatcat_file_partial.file_meta.json | jq .sha1hex -r | sort -u -S 4G | wc -l + => 18135313 + + zcat fatcat_file_partial.file_meta.json.gz | jq .mimetype -r | sort -S 4G | uniq -c | sort -nr + 18103860 application/pdf + 29977 application/octet-stream + 876 text/html + 199 application/postscript + 171 application/gzip + 84 text/plain + 48 application/xml + 38 application/vnd.ms-powerpoint + 16 application/msword + 8 application/vnd.openxmlformats-officedocument.wordprocessingml.document + 6 image/jpeg + 4 message/rfc822 + 4 application/zip + 4 application/vnd.openxmlformats-officedocument.presentationml.presentation + 3 text/x-tex + 3 application/x-dosexec + 2 application/x-tar + 2 application/vnd.ms-tnef + 1 video/mpeg + 1 image/tiff + 1 image/svg+xml + 1 image/png + 1 image/gif + 1 audio/x-ape + 1 application/vnd.ms-office + 1 application/CDFV2-unknown + +TODO: fatcat importer diff --git a/notes/tasks/2020-10-21_pdfextract_holes.md b/notes/tasks/2020-10-21_pdfextract_holes.md new file mode 100644 index 0000000..c0bb65e --- /dev/null +++ b/notes/tasks/2020-10-21_pdfextract_holes.md @@ -0,0 +1,74 @@ + +Realized I had not enabled persisting of PDF extraction results (thumbnail, +text) in ingest worker when added over the summer. So now need to run a +catch-up. This applied to both "live" and "bulk" ingest. + +## `cdx` / `ingest` / `grobid` catch-up + +First, re-run extraction for cases where we did an ingest, and grobid ran +successfully, and we have a CDX row, but no `pdf_meta`: + + -- this is a slow query + COPY ( + SELECT DISTINCT ON (cdx.sha1hex) row_to_json(cdx) + FROM grobid + LEFT JOIN cdx ON grobid.sha1hex = cdx.sha1hex + --LEFT JOIN fatcat_file ON grobid.sha1hex = fatcat_file.sha1hex + LEFT JOIN ingest_file_result ON grobid.sha1hex = ingest_file_result.terminal_sha1hex + LEFT JOIN pdf_meta ON grobid.sha1hex = pdf_meta.sha1hex + WHERE cdx.sha1hex IS NOT NULL + --AND fatcat_file.sha1hex IS NOT NULL + AND ingest_file_result.terminal_sha1hex IS NOT NULL + AND pdf_meta.sha1hex IS NULL + ) + TO '/grande/snapshots/dump_unextracted_pdf.ingest.2020-10-21.json' + WITH NULL ''; + => 19,676,116 + +Wow, that is a lot. Many from recent OAI-PMH and OA crawls, presumably. + + cat /grande/snapshots/dump_unextracted_pdf.ingest.2020-10-21.json | rg -v "\\\\" | jq . -c | pv -l | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.unextracted -p -1 + +And again, after a couple partitions got hung up: + + COPY ( + SELECT DISTINCT ON (cdx.sha1hex) row_to_json(cdx) + FROM grobid + LEFT JOIN cdx ON grobid.sha1hex = cdx.sha1hex + --LEFT JOIN fatcat_file ON grobid.sha1hex = fatcat_file.sha1hex + LEFT JOIN ingest_file_result ON grobid.sha1hex = ingest_file_result.terminal_sha1hex + LEFT JOIN pdf_meta ON grobid.sha1hex = pdf_meta.sha1hex + WHERE cdx.sha1hex IS NOT NULL + --AND fatcat_file.sha1hex IS NOT NULL + AND ingest_file_result.terminal_sha1hex IS NOT NULL + AND pdf_meta.sha1hex IS NULL + ) + TO '/grande/snapshots/dump_unextracted_pdf.ingest.2020-11-04.json' + WITH NULL ''; + + + cat /grande/snapshots/dump_unextracted_pdf.ingest.2020-11-04.json | rg -v "\\\\" | jq . -c | pv -l | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.unextracted -p -1 + => 562k 0:00:16 [34.6k/s] + +## `petabox` / `grobid` catch-up + +These didn't all seem to extract correctly before after 1.5m rows, there will +still 900k unprocessed. Trying again. + + COPY ( + SELECT DISTINCT ON (petabox.sha1hex) row_to_json(petabox) + FROM grobid + LEFT JOIN petabox ON grobid.sha1hex = petabox.sha1hex + LEFT JOIN pdf_meta ON grobid.sha1hex = pdf_meta.sha1hex + WHERE petabox.sha1hex IS NOT NULL + AND pdf_meta.sha1hex IS NULL + ) + TO '/grande/snapshots/dump_unextracted_pdf_petabox.2020-11-04.json' + WITH NULL ''; + + cat /grande/snapshots/dump_unextracted_pdf_petabox.ingest.2020-11-04.json | rg -v "\\\\" | jq . -c | pv -l | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.unextracted -p -1 + +## `cdx` / `grobid` catch-up + +Next will be to process PDFs with GROBID and CDX but no ingest. + diff --git a/notes/tasks/2021-09-09_pdf_url_lists.md b/notes/tasks/2021-09-09_pdf_url_lists.md new file mode 100644 index 0000000..52a3264 --- /dev/null +++ b/notes/tasks/2021-09-09_pdf_url_lists.md @@ -0,0 +1,66 @@ + +Want to dump a URL list to share with partners, filtered to content we think is +likely to be scholarly. + +Columns to include: + +- original URL +- capture timestamp +- SHA1 + +## Stats Overview + +file_meta table, mimetype=application/pdf: 173,816,433 + +cdx table, mimetype=application/pdf: 131,346,703 + +ingest_file_result table, pdf, success: 66,487,928 + +## Ingested PDF URLs + +"Ingested" URLs: ingest_file_result table, pdf and hit=true; include base URL also? + + COPY ( + SELECT + base_url as start_url, + terminal_url as pdf_url, + terminal_dt as pdf_url_timestamp, + terminal_sha1hex as pdf_sha1hex + FROM ingest_file_result + WHERE + ingest_type = 'pdf' + AND status = 'success' + ) + TO '/srv/sandcrawler/tasks/wayback_pdf_targeted.2021-09-09.tsv' + WITH NULL ''; + => 77,892,849 + +## CDX PDFs + +"All web PDFs": CDX query; left join file_meta, but don't require + + COPY ( + SELECT + cdx.url as pdf_url, + cdx.datetime as pdf_url_timestamp, + cdx.sha1hex as pdf_sha1hex + FROM cdx + LEFT JOIN file_meta + ON + cdx.sha1hex = file_meta.sha1hex + WHERE + file_meta.mimetype = 'application/pdf' + OR ( + file_meta.mimetype IS NULL + AND cdx.mimetype = 'application/pdf' + ) + ) + TO '/srv/sandcrawler/tasks/wayback_pdf_speculative.2021-09-09.tsv' + WITH NULL ''; + => 147,837,935 + +## Processed web PDFs + +"Parsed web PDFs": `file_meta`, left join CDX + +(didn't do this one) diff --git a/notes/url_pattern_heuristic_backfill.txt b/notes/url_pattern_heuristic_backfill.txt new file mode 100644 index 0000000..8e422f5 --- /dev/null +++ b/notes/url_pattern_heuristic_backfill.txt @@ -0,0 +1,104 @@ + +/user/bnewbold/pdfs/gwb-pdf-20171227034923-surt-filter + 21,434,960 + +/user/bnewbold/pdfs/gwb-pdf-20171227034923-join-msag + 13,637,948 + +/user/bnewbold/pdfs/gwb-pdf-20171227034923-join-unpaywall-20180329 + 3,393,658 + +######### + +Goal: backfill a bunch of existing content into the HBase table. Bonus for +being re-runable in the future. + +Source data: +- GWB PDF CDX list +- archive.org JSTOR files (?) +- arxiv.org bulk files (?) +- large URL lists (MSAG, etc) + +Methods: +- pig filter GWB PDF CDX list based on regexes +- pig join GWB PDF CDX list to known URL lists (then remove join) +x iterate URL lists, hitting CDX API and saving response + + +- (.edu, .ac.uk) domain with a tilde in the URL + +#http://www.stanford.edu:80/~johntayl/Papers/taylor2.pdf +#http://met.nps.edu/~mtmontgo/papers/isabel_part2.pdf +#http://www.pitt.edu:80/~druzdzel/psfiles/ecai06.pdf +#http://www.comp.hkbu.edu.hk/~ymc/papers/conference/ijcnn03_710.pdf + +hk,edu,hkbu,comp)/~ymc/papers/conference/ijcnn03_710.pdf +edu,stanford,www)/~johntayl/Papers/taylor2.pdf +edu,nps,met)/~mtmontgo/papers/isabel_part2.pdf +edu,pitt,www)/~druzdzel/psfiles/ecai06.pdf +jp,ak,pitt,www)/~druzdzel/psfiles/ecai06.pdf +co,edu,pitt,www)/~druzdzel/psfiles/ecai06.pdf + +NOT: com,corp,edu,,www)/~druzdzel/psfiles/ecai06.pdf + +- the words in URL: paper(s), pubs, research, publications, article, proceedings + +#http://personal.ee.surrey.ac.uk/Personal/R.Bowden/publications/2012/Gilbert_ACCV_2012pp.pdf +#http://files.eric.ed.gov/fulltext/EJ798626.pdf +#http://www.hbs.edu/research/pdf/10-108.pdf +#http://www.unifr.ch/biochem/assets/files/albrecht/publications/Abraham06.pdf +#http://www.cnbc.cmu.edu/cns/papers/Kassetal2005.pdf +#http://www.macrothink.org/journal/index.php/ijhrs/article/download/5765/4663 +#http://www.pims.math.ca:80/science/2004/fpsac/Papers/Liskovets.pdf +#http://www.risc.uni-linz.ac.at/publications/download/risc_3287/synasc_revised.pdf +#http://softsys.cs.uoi.gr/dbglobe/publications/wi04.pdf +#http://lexikos.journals.ac.za/pub/article/download/1048/564 +#http://www.siam.org/proceedings/analco/2007/anl07_029ecesaratto.pdf +#http://www.cs.bris.ac.uk/Publications/Papers/2000249.pdf + +uk,ac,surrey,ee,personal)/Personal/R.Bowden/publications/2012/Gilbert_ACCV_2012pp.pdf +gov,ed,eric,files)/fulltext/EJ798626.pdf +edu,hbs,www)/research/pdf/10-108.pdf +ch,unifr,www)/biochem/assets/files/albrecht/publications/Abraham06.pdf +edu,cmu,cnbc,www)/cns/papers/Kassetal2005.pdf +org,macrothink,www)/journal/index.php/ijhrs/article/download/5765/4663 +ca,math,pims,www)/science/2004/fpsac/Papers/Liskovets.pdf +at,ac,uni-linz,risc,www)/publications/download/risc_3287/synasc_revised.pdf +gr,uoi,cs,softsys)/dbglobe/publications/wi04.pdf +za,ac,journals,lexikos)/pub/article/download/1048/564 +org,siam,www)/proceedings/analco/2007/anl07_029ecesaratto.pdf +uk,ac,bris,cs,www)/Publications/Papers/2000249.pdf + + +- words in domains: hal., eprint, research., journal + +#http://research.fit.edu/sealevelriselibrary/documents/doc_mgr/448/Florida_Keys_Low_Island_Biodiversity_&_SLR_-_Ross_et_al_2009.pdf +#http://ijs.sgmjournals.org:80/cgi/reprint/54/6/2217.pdf +#http://eprints.ecs.soton.ac.uk/12020/1/mind-the-semantic-gap.pdf +#http://eprint.uq.edu.au/archive/00004120/01/R103_Forrester_pp.pdf + +edu,fit,research)/sealevelriselibrary/documents/doc_mgr/448/Florida_Keys_Low_Island_Biodiversity_&_SLR_-_Ross_et_al_2009.pdf +org,sgmjournals,ijs)//cgi/reprint/54/6/2217.pdf +uk,ac,soton,ecs,eprints)/12020/1/mind-the-semantic-gap.pdf +au,edu,uq,eprint)/archive/00004120/01/R103_Forrester_pp.pdf + +- doi-like pattern in URL +#http://journals.ametsoc.org/doi/pdf/10.1175/2008BAMS2370.1 +#http://www.nejm.org:80/doi/pdf/10.1056/NEJMoa1013607 + +org,ametsoc,journals)/doi/pdf/10.1175/2008BAMS2370.1 +org,nejm,www)/doi/pdf/10.1056/NEJMoa1013607 + +- short list of hosts/domains? + *.core.ac.uk + *scielo* + *.redalyc.org + +#http://www.scielo.br:80/pdf/cagro/v33n1/v33n1a19.pdf +#https://revistas.unal.edu.co/index.php/dyna/article/viewFile/51385/57892 +#http://rives.revues.org:80/pdf/449 + +br,scielo,www)/pdf/cagro/v33n1/v33n1a19.pdf +co,edu,unal,revistas)/index.php/dyna/article/viewFile/51385/57892 +org,revues,rives)/pdf/449 + diff --git a/notes/url_pattern_heuristic_verification.txt b/notes/url_pattern_heuristic_verification.txt new file mode 100644 index 0000000..7b35b88 --- /dev/null +++ b/notes/url_pattern_heuristic_verification.txt @@ -0,0 +1,52 @@ + +## URL pattern regexing + +/user/bnewbold/pdfs/gwb-pdf-20171227034923-surt-filter/part* + +N https://nsarchive2.gwu.edu//rus/text_files/Volkogonov/1918.10.13%20Speech%20by%20BK,%20to%20Red%20Army%20Soldiers,%20R13977.pdf speech, russian + +edu tilde: + N http://www.d.umn.edu/~kgilbert/ened3342-1/Field%20Interp%202/snow/CloudIDKey.pdf homework? + N http://www.mech.utah.edu/~minor/BIOSKETCH-minor-october%202007.pdf CV + N http://web.archive.org/web/20030724175610/http://www.ssc.wisc.edu:80/~sseverin/lect12f01.pdf slides + N http://web.archive.org/web/20050117195001/http://www.csie.ntu.edu.tw:80/~b90013/DBhw7.pdf + Y http://web.archive.org/web/20040220222413/http://homepages.uc.edu:80/~lukovib/aiaa_02_0857.pdf + Y http://www.kki.yamanashi.ac.jp/~ohbuchi/online_pubs/IEEE_bigMM2015_Matsuda/BigMM_20150224b_web.pdf + +other words: + N https://files.eric.ed.gov/fulltext/ED069848.pdf tech report? + N http://istitutocomprensivopescara2.gov.it/attachments/article/164/griglia_osservativa_bes_terza_fascia.pdf table + M https://jfjustice.net/userfiles/file/Research/Report%20of%20the%20Outreach%20Forums%20on%20the%20PIL%20Cases%20on%20Sexual%20Gender%20Based%20Violence.pdf report + M http://www.iitk.ac.in/nicee/wcee/article/13_9035.pdf filler page? like a paper + Y http://www.dtic.mil/dtic/tr/fulltext/u2/314095.pdf + Y https://www.casact.org/pubs/proceed/proceed25/25400.pdf + Y http://circres.ahajournals.org/content/circresaha/111/8/1002.full.pdf + Y http://web.archive.org/web/20170313034332/http://thixomet.ru/UserFiles/File/Articles/1/2.CHM_2006_02-2.pdf + Y http://www.redalyc.org/pdf/873/87313713019.pdf + Y http://ukacc.group.shef.ac.uk/proceedings/control2004/Papers/213.pdf + Y http://periodicos.uem.br:80/ojs/index.php/RbhrAnpuh/article/download/23988/13095 + Y http://w3.uqo.ca/photonique/papers/measurement.pdf + Y http://web.archive.org/web/20140312150030/http://afms.org.au/proceedings/9/Griffiths.pdf + Y http://www.hal.inserm.fr/file/index/docid/580194/filename/PROSTATE_SEGMENTATION_IN_HIFU_THERAPY.pdf + Y http://journal.ipb.ac.id/index.php/jmht/article/download/6003/4658 + +publications: + N http://web.archive.org/web/20060527120026/http://www.merenkulkulaitos.fi:80/e/services/informationservices/publications/bulletin/avaa.php?id=336 treaty? + N http://orbit.dtu.dk/en/publications/status-for-skarven-i-danmark(8ffaf614-387e-429f-9fd4-4677ee5016ae).pdf?nofollow=true&rendering=standard related to a paper? + N http://community.trinity.nsw.edu.au/navbar/publications/docs/news/2_pn/2016/ps160103.pdf newsletter + N http://web.archive.org/web/20170216001602/https://www.nass.usda.gov/Statistics_by_State/New_Mexico/Publications/Annual_Statistical_Bulletin/2005/03_05.pdf report + N http://web.archive.org/web/20110109080048/http://www.ipria.org/publications/on-line-bulletins/austdev/AusDevsBulletin07.09.pdf + N http://web.archive.org/web/20060930192249/http://www.nmmfa.org/publications/CensusTracts/35031940200.pdf + N http://web.archive.org/web/20100621152841/http://psychologymatters.org/workforce/publications/01-doc-empl/table-11.pdf + N http://www.dtce.org.pk/DTCE/Publications/PN2 final report-dr8-F.pdf + Y https://www.frbatlanta.org/-/media/Documents/research/publications/wp/1995/wp9513.pdf + Y http://irrec.ifas.ufl.edu/IRSWS/publications/Lu_ESPR_2011.pdf + +doi: + M https://page-one.live.cf.public.springer.com/pdf/preview/10.1007/s11229-012-0117-8 paper, but only fragment (!?!?!) + + +TODO: +- drop "publications", "research", "pubs" +- edu tilde is borderline... but keep it for now +- black-list page-one.* |