diff options
Diffstat (limited to 'postgresql/backfill.md')
| -rw-r--r-- | postgresql/backfill.md | 117 |
1 files changed, 117 insertions, 0 deletions
diff --git a/postgresql/backfill.md b/postgresql/backfill.md new file mode 100644 index 0000000..f97c901 --- /dev/null +++ b/postgresql/backfill.md @@ -0,0 +1,117 @@ + +SQL Backfill Notes +----------------------- + +GROBID is going to be somewhat complex. + +TODO: +x CDX backfill script (CDX to postgresql direct, bulk inserts, python) +x `file_meta` bulk insert (TSV to postgresql direct, bulk upserts, python) +x GROBID insert (python, dump TSV to minio then postgresql) + +## `cdx` + + #cat example.cdx | rg ' 200 ' | cut -d' ' -f2,3,4,6,9,10,11 + #cat example.cdx | rg ' 200 ' | awk '{print $6 "\t" $3 "\t" $2 "\t" $4 "\t\t" $6 "\t" $11 "\t" $9 "\t" $10}' | b32_hex.py | awk '{print $2 "\t" $3 "\t" $4 "\t" $1 "\t" $6 "\t" $7 "\t" $8}' > cdx.example.tsv + cat example.cdx | ./filter_transform_cdx.py > cdx.example.tsv + + COPY cdx (url, datetime, sha1hex, mimetype, warc_path, warc_csize, warc_offset) FROM '/sandcrawler-db/backfill/cdx/cdx.example.tsv' WITH (FORMAT TEXT, DELIMITER E'\t', NULL ''); + +Big HDFS import: + + # but actually didn't import those; don't want to need to re-import + hdfs dfs -get journal_crawl_cdx/* + + cat citeseerx_crawl_2017.cdx | rg ' 200 ' | ./filter_transform_cdx.py > cdx.citeseerx_crawl_2017.tsv + cat gwb-pdf-20171227034923-surt-filter/* | rg ' 200 ' | ./filter_transform_cdx.py > gwb-pdf-20171227034923-surt-filter.tsv + cat UNPAYWALL-PDF-CRAWL-2018-07.filtered.cdx | rg ' 200 ' | ./filter_transform_cdx.py > cdx.UNPAYWALL-PDF-CRAWL-2018-07.filtered.tsv + cat MSAG-PDF-CRAWL-2017.cdx | rg ' 200 ' | ./filter_transform_cdx.py > cdx.MSAG-PDF-CRAWL-2017.tsv + + cat CORE-UPSTREAM-CRAWL-2018-11.sorted.cdx | rg ' 200 ' | ./filter_transform_cdx.py > cdx.CORE-UPSTREAM-CRAWL-2018-11.sorted.tsv + cat DIRECT-OA-CRAWL-2019.pdfs.cdx | rg ' 200 ' | ./filter_transform_cdx.py > cdx.DIRECT-OA-CRAWL-2019.pdfs.tsv + cat DOI-LANDING-CRAWL-2018-06.200_pdf.cdx | rg ' 200 ' | ./filter_transform_cdx.py > cdx.DOI-LANDING-CRAWL-2018-06.200_pdf.tsv + cat OA-JOURNAL-TESTCRAWL-TWO-2018.pdf.cdx | rg ' 200 ' | ./filter_transform_cdx.py > cdx.OA-JOURNAL-TESTCRAWL-TWO-2018.pdf.tsv + cat SEMSCHOLAR-PDF-CRAWL-2017.cdx | rg ' 200 ' | ./filter_transform_cdx.py > cdx.SEMSCHOLAR-PDF-CRAWL-2017.tsv + cat TARGETED-PDF-CRAWL-2017.cdx | rg ' 200 ' | ./filter_transform_cdx.py > cdx.TARGETED-PDF-CRAWL-2017.tsv + cat UNPAYWALL-PDF-CRAWL-2019-04.pdfs_sorted.cdx | rg ' 200 ' | ./filter_transform_cdx.py > cdx.UNPAYWALL-PDF-CRAWL-2019-04.pdfs_sorted.tsv + +TODO: nasty escaping? + +In psql: + + COPY cdx (url, datetime, sha1hex, mimetype, warc_path, warc_csize, warc_offset) FROM '/sandcrawler-db/backfill/cdx/cdx.UNPAYWALL-PDF-CRAWL-2018-07.filtered.tsv' WITH (FORMAT TEXT, DELIMITER E'\t', NULL ''); + # ERROR + COPY cdx (url, datetime, sha1hex, mimetype, warc_path, warc_csize, warc_offset) FROM '/sandcrawler-db/backfill/cdx/cdx.MSAG-PDF-CRAWL-2017.tsv' WITH (FORMAT TEXT, DELIMITER E'\t', NULL ''); + # ERROR + COPY cdx (url, datetime, sha1hex, mimetype, warc_path, warc_csize, warc_offset) FROM '/sandcrawler-db/backfill/cdx/cdx.citeseerx_crawl_2017.tsv' WITH (FORMAT TEXT, DELIMITER E'\t', NULL ''); + # COPY 1653840 + COPY cdx (url, datetime, sha1hex, mimetype, warc_path, warc_csize, warc_offset) FROM '/sandcrawler-db/backfill/cdx/cdx.CORE-UPSTREAM-CRAWL-2018-11.sorted.tsv' WITH (FORMAT TEXT, DELIMITER E'\t', NULL ''); + # COPY 2827563 + COPY cdx (url, datetime, sha1hex, mimetype, warc_path, warc_csize, warc_offset) FROM '/sandcrawler-db/backfill/cdx/cdx.DIRECT-OA-CRAWL-2019.pdfs.tsv' WITH (FORMAT TEXT, DELIMITER E'\t', NULL ''); + # COPY 10651736 + COPY cdx (url, datetime, sha1hex, mimetype, warc_path, warc_csize, warc_offset) FROM '/sandcrawler-db/backfill/cdx/cdx.DOI-LANDING-CRAWL-2018-06.200_pdf.tsv' WITH (FORMAT TEXT, DELIMITER E'\t', NULL ''); + # COPY 768565 + COPY cdx (url, datetime, sha1hex, mimetype, warc_path, warc_csize, warc_offset) FROM '/sandcrawler-db/backfill/cdx/cdx.OA-JOURNAL-TESTCRAWL-TWO-2018.pdf.tsv' WITH (FORMAT TEXT, DELIMITER E'\t', NULL ''); + # COPY 5310017 + COPY cdx (url, datetime, sha1hex, mimetype, warc_path, warc_csize, warc_offset) FROM '/sandcrawler-db/backfill/cdx/cdx.SEMSCHOLAR-PDF-CRAWL-2017.tsv' WITH (FORMAT TEXT, DELIMITER E'\t', NULL ''); + # COPY 2219839 + COPY cdx (url, datetime, sha1hex, mimetype, warc_path, warc_csize, warc_offset) FROM '/sandcrawler-db/backfill/cdx/cdx.TARGETED-PDF-CRAWL-2017.tsv' WITH (FORMAT TEXT, DELIMITER E'\t', NULL ''); + # ERROR + COPY cdx (url, datetime, sha1hex, mimetype, warc_path, warc_csize, warc_offset) FROM '/sandcrawler-db/backfill/cdx/cdx.UNPAYWALL-PDF-CRAWL-2019-04.pdfs_sorted.tsv' WITH (FORMAT TEXT, DELIMITER E'\t', NULL ''); + # ERROR + +NOTE: these largely didn't work; will need to write a batch importer. + +Batch import process: + + cat UNPAYWALL-PDF-CRAWL-2018-07.filtered.cdx MSAG-PDF-CRAWL-2017.cdx TARGETED-PDF-CRAWL-2017.cdx UNPAYWALL-PDF-CRAWL-2019-04.pdfs_sorted.cdx | ./backfill_cdx.py + +## `fatcat_file` + + zcat file_export.2019-07-07.json.gz | pv -l | jq -r 'select(.sha1 != null) | [.sha1, .ident, .release_ids[0]] | @tsv' | sort -S 8G | uniq -w 40 > /sandcrawler-db/backfill/fatcat_file.2019-07-07.tsv + +In psql: + + COPY fatcat_file FROM '/sandcrawler-db/backfill/fatcat_file.2019-07-07.tsv' WITH (FORMAT TEXT, DELIMITER E'\t', NULL ''); + # => COPY 24727350 + +## `file_meta` + + zcat /fast/download/file_export.2019-07-07.json.gz | pv -l | jq -r 'select(.md5 != null) | [.sha1, .sha256, .md5, .size, .mimetype] | @tsv' | sort -S 8G | uniq -w 40 > /sandcrawler-db/backfill/file_meta.2019-07-07.tsv + +In psql: + + COPY file_meta FROM '/sandcrawler-db/backfill/file_meta.2019-07-07.tsv' WITH (FORMAT TEXT, DELIMITER E'\t', NULL ''); + # -> COPY 5860092 + +## `petabox` + + zcat /fast/download/file_export.2019-07-07.json.gz | rg '//archive.org/' | pigz > /fast/download/file_export.2019-07-07.petabox.json.gz + zcat /fast/download/file_export.2019-07-07.petabox.json.gz | ./petabox_transform.py | sort -u -S 8G | awk '{print $3 "\t" $1 "\t" $2}' | uniq -s40 | awk '{print $2 "\t" $3 "\t" $1}' > petabox.fatcat_2019-07-07.tsv + +In psql: + + COPY petabox FROM '/sandcrawler-db/backfill/petabox.fatcat_2019-07-07.tsv' WITH (FORMAT TEXT, DELIMITER E'\t', NULL ''); + # -> COPY 2887834 + +## `grobid` + +Quick test: + + zcat /bigger/unpaywall-transfer/2019-07-17-1741.30-dumpgrobidxml/part-00000.gz | cut -f2 | head | ./backfill_grobid.py + +Run big batch: + + ls /bigger/unpaywall-transfer/2019-07-17-1741.30-dumpgrobidxml/part*gz |arallel --progress -j8 'zcat {} | cut -f2 | ./backfill_grobid.py' + +## rough table sizes + + table_name | table_size | indexes_size | total_size + --------------------------------------------------------------+------------+--------------+------------ + "public"."cdx" | 11 GB | 8940 MB | 20 GB + "public"."shadow" | 8303 MB | 7205 MB | 15 GB + "public"."fatcat_file" | 5206 MB | 2094 MB | 7300 MB + "public"."file_meta" | 814 MB | 382 MB | 1196 MB + "public"."petabox" | 403 MB | 594 MB | 997 MB + [...] + |