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diff --git a/README.md b/README.md new file mode 100644 index 0000000..2ae80e8 --- /dev/null +++ b/README.md @@ -0,0 +1,327 @@ + +Going to look something like: + + zcat DOI-LANDING-CRAWL-2018-06-full_crawl_logs/DOI-LANDING-CRAWL-2018-06.$SHARD.us.archive.org.crawl.log.gz | tr -cd '[[:print:]]\n\r\t' | rg '//doi.org/' | /fast/scratch/unpaywall/make_doi_list.py > doi_list.$SHARD.txt + + zcat /fast/unpaywall-munging/DOI-LANDING-CRAWL-2018-06/DOI-LANDING-CRAWL-2018-06-full_crawl_logs/DOI-LANDING-CRAWL-2018-06.$SHARD.us.archive.org.crawl.log.gz | pv | /fast/scratch/unpaywall/make_map.py redirectmap.$SHARD.db + + cat /fast/unpaywall-munging/DOI-LANDING-CRAWL-2018-06/doi_list.$SHARD.txt | pv | /fast/scratch/unpaywall/make_output.py redirectmap.$SHARD.db > doi_index.$SHARD.tsv + +Let's start with: + + mkdir UNPAYWALL-PDF-CRAWL-2018-07 + ia download UNPAYWALL-PDF-CRAWL-2018-07-full_crawl_logs + +export SHARD=wbgrp-svc279 # running +export SHARD=wbgrp-svc280 # running +export SHARD=wbgrp-svc281 # running +export SHARD=wbgrp-svc282 # running +zcat UNPAYWALL-PDF-CRAWL-2018-07-full_crawl_logs/UNPAYWALL-PDF-CRAWL-2018-07.$SHARD.us.archive.org.crawl.log.gz | pv | /fast/scratch/unpaywall/make_map.py redirectmap.$SHARD.db +zcat UNPAYWALL-PDF-CRAWL-2018-07-full_crawl_logs/UNPAYWALL-PDF-CRAWL-2018-07-PATCH.$SHARD.us.archive.org.crawl.log.gz | pv | /fast/scratch/unpaywall/make_map.py redirectmap.$SHARD-PATCH.db + +### Design + +If possible, we'd like something that will work with as many crawls as +possible. Want to work with shards, then merge outputs. + +Output: JSON and/or sqlite rows with: + +- identifier (optional?) +- initial-uri (indexed) +- breadcrumbs +- final-uri +- final-http-status +- final-sha1 +- final-mimetype-normalized +- final-was-dedupe (boolean) +- final-cdx (string, if would be extracted) + +This will allow filtering on various fields, checking success stats, etc. + +Components: + +- {identifier, initial-uri} input (basically, seedlist) +- full crawl logs +- raw CDX, indexed by final-uri +- referer map + +Process: + +- use full crawl logs to generate a referer map; this is a dict with keys as + URI, and value as {referer URI, status, breadcrumb, was-dedupe, mimetype}; + the referer may be null. database can be whatever. +- iterate through CDX, filtering by HTTP status and mimetype (including + revists). for each potential, lookup in referer map. if mimetype is + confirmed, then iterate through full referer chain, and print a final line + which is all-but-identifier +- iterate through identifier/URI list, inserting identifier columns + +Complications: + +- non-PDF terminals: error codes, or HTML only (failed to find PDF) +- multiple terminals per seed; eg, multiple PDFs, or PDF+postscript+HTML or + whatever + +Process #2: + +- use full crawl logs to generate a bi-directional referer map: sqlite3 table + with uri, referer-uri both indexed. also {status, breadcrumb, was-dedupe, + mimetype} rows +- iterate through CDX, selecting successful "terminal" lines (mime, status). + use referer map to iterate back to an initial URI, and generate a row. lookup + output table by initial-uri; if an entry already exists, behavior is + flag-dependent: overwrite if "better", or add a second line +- in a second pass, update rows with identifier based on URI. if rows not + found/updated, then do a "forwards" lookup to a terminal condition, and write + that status. note that these rows won't have CDX. + +More Complications: + +- handling revisits correctly... raw CDX probably not actually helpful for PDF + case, only landing/HTML case +- given above, should probably just (or as a mode) iterate over only crawl logs + in "backwards" stage +- fan-out of "forward" redirect map, in the case of embeds and PDF link + extraction +- could pull out first and final URI domains for easier SQL stats/reporting +- should include final datetime (for wayback lookups) + +NOTE/TODO: journal-level dumps of fatcat metadata would be cool... could +roll-up release dumps as an alternative to hitting elasticsearch? or just hit +elasticsearch and both dump to sqlite and enrich elastic doc? should probably +have an indexed "last updated" timestamp in all elastic docs + +### Crawl Log Notes + +Fields: + + 0 timestamp (ISO8601) of log line + 1 status code (HTTP or negative) + 2 size in bytes (content only) + 3 URI of this download + 4 discovery breadcrumbs + 5 "referer" URI + 6 mimetype (as reported?) + 7 worker thread + 8 full timestamp (start of network fetch; this is dt?) + 9 SHA1 + 10 source tag + 11 annotations + 12 partial CDX JSON + +### External Prep for, Eg, Unpaywall Crawl + + export LC_ALL=C + sort -S 8G -u seedlist.shard > seedlist.shard.sorted + + zcat unpaywall_20180621.pdf_meta.tsv.gz | awk '{print $2 "\t" $1}' | sort -S 8G -u > unpaywall_20180621.seed_id.tsv + + join -t $'\t' unpaywall_20180621.seed_id.tsv unpaywall_crawl_patch_seedlist.split_3.schedule.sorted > seed_id.shard.tsv + +TODO: why don't these sum/match correctly? + + bnewbold@orithena$ wc -l seed_id.shard.tsv unpaywall_crawl_patch_seedlist.split_3.schedule.sorted + 880737 seed_id.shard.tsv + 929459 unpaywall_crawl_patch_seedlist.split_3.schedule.sorted + + why is: + http://00ec89c.netsolhost.com/brochures/200605_JAWMA_Hg_Paper_Lee_Hastings.pdf + in unpaywall_crawl_patch_seedlist, but not unpaywall_20180621.pdf_meta? + + # Can't even filter on HTTP 200, because revisits are '-' + #zcat UNPAYWALL-PDF-CRAWL-2018-07.cdx.gz | rg 'wbgrp-svc282' | rg ' 200 ' | rg '(pdf)|(revisit)' > UNPAYWALL-PDF-CRAWL-2018-07.svc282.filtered.cdx + + zcat UNPAYWALL-PDF-CRAWL-2018-07.cdx.gz | rg 'UNPAYWALL-PDF-CRAWL-2018-07-PATCH' | rg 'wbgrp-svc282' | rg '(pdf)|( warc/revisit )|(postscript)|( unk )' > UNPAYWALL-PDF-CRAWL-2018-07-PATCH.svc282.filtered.cdx + +TODO: spaces in URLs, like 'https://www.termedia.pl/Journal/-7/pdf-27330-10?filename=A case.pdf' + +### Revisit Notes + +Neither CDX nor crawl logs seem to have revisits actually point to final +content, they just point to the revisit record in the (crawl-local) WARC. + +### sqlite3 stats + + select count(*) from crawl_result; + + select count(*) from crawl_result where identifier is null; + + select breadcrumbs, count(*) from crawl_result group by breadcrumbs; + + select final_was_dedupe, count(*) from crawl_result group by final_was_dedupe; + + select final_http_status, count(*) from crawl_result group by final_http_status; + + select final_mimetype, count(*) from crawl_result group by final_mimetype; + + select * from crawl_result where final_mimetype = 'text/html' and final_http_status = '200' order by random() limit 5; + + select count(*) from crawl_result where final_uri like 'https://academic.oup.com/Govern%'; + + select count(distinct identifier) from crawl_result where final_sha1 is not null; + +### testing shard notes + +880737 `seed_id` lines +21776 breadcrumbs are null (no crawl logs line); mostly normalized URLs? +24985 "first" URIs with no identifier; mostly normalized URLs? + +backward: Counter({'skip-cdx-scope': 807248, 'inserted': 370309, 'skip-map-scope': 2913}) +forward (dirty): Counter({'inserted': 509242, 'existing-id-updated': 347218, 'map-uri-missing': 15556, 'existing-complete': 8721, '_normalized-seed-uri': 5520}) + +874131 identifier is not null +881551 breadcrumbs is not null +376057 final_mimetype is application/pdf +370309 final_sha1 is not null +332931 application/pdf in UNPAYWALL-PDF-CRAWL-2018-07-PATCH.svc282.filtered.cdx + +summary: + 370309/874131 42% got a PDF + 264331/874131 30% some domain dead-end + 196747/874131 23% onlinelibrary.wiley.com + 33879/874131 4% www.nature.com + 11074/874131 1% www.tandfonline.com + 125883/874131 14% blocked, 404, other crawl failures + select count(*) from crawl_result where final_http_status >= '400' or final_http_status < '200'; + 121028/874131 14% HTTP 200, but not pdf + 105317/874131 12% academic.oup.com; all rate-limited or cookie fail + 15596/874131 1.7% didn't even try crawling (null final status) + +TODO: +- add "success" flag (instead of "final_sha1 is null") +- + + http://oriental-world.org.ua/sites/default/files/Archive/2017/3/4.pdf 10.15407/orientw2017.03.021 - http://oriental-world.org.ua/sites/default/files/Archive/2017/3/4.pdf 403 ¤ application/pdf 0 ¤ + +Iterated: + +./arabesque.py backward UNPAYWALL-PDF-CRAWL-2018-07-PATCH.svc282.filtered.cdx map.sqlite out.sqlite +Counter({'skip-cdx-scope': 813760, 'inserted': 370435, 'skip-map-scope': 4620, 'skip-tiny-octetstream-': 30}) + +./arabesque.py forward unpaywall_20180621.seed_id.shard.tsv map.sqlite out.sqlite +Counter({'inserted': 523594, 'existing-id-updated': 350009, '_normalized-seed-uri': 21371, 'existing-complete': 6638, 'map-uri-missing': 496}) + +894029 breadcrumbs is not null +874102 identifier is not null +20423 identifier is null +496 breadcrumbs is null +370435 final_sha1 is not null + +### URL/seed non-match issues! + +Easily fixable: +- capitalization of domains +- empty port number, like `http://genesis.mi.ras.ru:/~razborov/hadamard.ps` + +Encodable: +- URL encoding + http://accounting.rutgers.edu/docs/seminars/Fall11/Clawbacks_9-27-11[1].pdf + http://accounting.rutgers.edu/docs/seminars/Fall11/Clawbacks_9-27-11%5B1%5D.pdf +- whitespace in URL (should be url-encoded) + https://www.termedia.pl/Journal/-7/pdf-27330-10?filename=A case.pdf + https://www.termedia.pl/Journal/-7/pdf-27330-10?filename=A%EF%BF%BD%EF%BF%BDcase.pdf +- tricky hidden unicode + http://goldhorde.ru/wp-content/uploads/2017/03/ЗО-1-2017-206-212.pdf + http://goldhorde.ru/wp-content/uploads/2017/03/%EF%BF%BD%EF%BF%BD%EF%BF%BD%EF%BF%BD-1-2017-206-212.pdf + +Harder/Custom? +- paths including "/../" or "/./" are collapsed +- port number 80, like `http://fermet.misis.ru:80/jour/article/download/724/700` +- aos2.uniba.it:8080papers + +- fragments stripped by crawler: 'https://www.termedia.pl/Journal/-85/pdf-27083-10?filename=BTA#415-06-str307-316.pdf' + +### Debugging "redirect terminal" issue + +Some are redirect loops; fine. + +Some are from 'cookieSet=1' redirects, like 'http://journals.sagepub.com/doi/pdf/10.1177/105971230601400206?cookieSet=1'. This comes through like: + + sqlite> select * from crawl_result where initial_uri = 'http://adb.sagepub.com/cgi/reprint/14/2/147.pdf'; + initial_uri identifier breadcrumbs final_uri final_http_status final_sha1 final_mimetype final_was_dedupe final_cdx + http://adb.sagepub.com/cgi/reprint/14/2/147.pdf 10.1177/105971230601400206 R http://journals.sagepub.com/doi/pdf/10.1177/105971230601400206 302 ¤ text/html 0 ¤ + +Using 'http' (note: this is not an OA article): + + http://adb.sagepub.com/cgi/reprint/14/2/147.pdf + https://journals.sagepub.com/doi/pdf/10.1177/105971230601400206 + https://journals.sagepub.com/doi/pdf/10.1177/105971230601400206?cookieSet=1 + http://journals.sagepub.com/action/cookieAbsent + +Is heritrix refusing to do that second redirect? In some cases it will do at +leat the first, like: + + http://pubs.rsna.org/doi/pdf/10.1148/radiographics.11.1.1996385 + http://pubs.rsna.org/doi/pdf/10.1148/radiographics.11.1.1996385?cookieSet=1 + http://pubs.rsna.org/action/cookieAbsent + +I think the vast majority of redirect terminals are when we redirect to a page +that has already been crawled. This is a bummer because we can't find the +redirect target in the logs. + +Eg, academic.oup.com sometimes redirects to cookieSet, then cookieAbsent; other +times it redirects to Governer. It's important to distinguish between these. + +### Scratch + +What are actual advantages/use-cases of CDX mode? +=> easier CDX-to-WARC output mode +=> sending CDX along with WARCs as an index + +Interested in scale-up behavior: full unpaywall PDF crawls, and/or full DOI landing crawls +=> eatmydata +dentifier is not null + + + zcat UNPAYWALL-PDF-CRAWL-2018-07-PATCH* | time /fast/scratch/unpaywall/arabesque.py referrer - UNPAYWALL-PDF-CRAWL-2018-07-PATCH.map.sqlite + [snip] + ... referrer 5542000 + Referrer map complete. + 317.87user 274.57system 21:20.22elapsed 46%CPU (0avgtext+0avgdata 22992maxresident)k + 24inputs+155168464outputs (0major+802114minor)pagefaults 0swaps + + bnewbold@ia601101$ ls -lathr + -rw-r--r-- 1 bnewbold bnewbold 1.7G Dec 12 12:33 UNPAYWALL-PDF-CRAWL-2018-07-PATCH.map.sqlite + +Scaling! + + 16,736,800 UNPAYWALL-PDF-CRAWL-2018-07.wbgrp-svc282.us.archive.org.crawl.log + 17,215,895 unpaywall_20180621.seed_id.tsv + +Oops; need to shard the seed_id file. + +Ugh, this one is a little derp because I didn't sort correctly. Let's say close enough though... + + 4318674 unpaywall_crawl_seedlist.svc282.tsv + 3901403 UNPAYWALL-PDF-CRAWL-2018-07.wbgrp-svc282.seed_id.tsv + + +/fast/scratch/unpaywall/arabesque.py everything CORE-UPSTREAM-CRAWL-2018-11.combined.log core_2018-03-01_metadata.seed_id.tsv CORE-UPSTREAM-CRAWL-2018-11.out.sqlite + + Counter({'inserted': 3226191, 'skip-log-scope': 2811395, 'skip-log-prereq': 108932, 'skip-tiny-octetstream-': 855, 'skip-map-scope': 2}) + Counter({'existing-id-updated': 3221984, 'inserted': 809994, 'existing-complete': 228909, '_normalized-seed-uri': 17287, 'map-uri-missing': 2511, '_redirect-recursion-limit': 221, 'skip-bad-seed-uri': 17}) + +time /fast/scratch/unpaywall/arabesque.py everything UNPAYWALL-PDF-CRAWL-2018-07.wbgrp-svc282.us.archive.org.crawl.log UNPAYWALL-PDF-CRAWL-2018-07.wbgrp-svc282.seed_id.tsv UNPAYWALL-PDF-CRAWL-2018-07.out.sqlite + + Everything complete! + Counter({'skip-log-scope': 13476816, 'inserted': 2536452, 'skip-log-prereq': 682460, 'skip-tiny-octetstream-': 41067}) + Counter({'existing-id-updated': 1652463, 'map-uri-missing': 1245789, 'inserted': 608802, 'existing-complete': 394349, '_normalized-seed-uri': 22573, '_redirect-recursion-limit': 157}) + + real 63m42.124s + user 53m31.007s + sys 6m50.535s + +### Performance + +Before tweaks: + + real 2m55.975s + user 2m6.772s + sys 0m12.684s + +After: + + real 1m51.500s + user 1m44.600s + sys 0m3.496s + |