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diff --git a/postgrest/backfill/backfill.md b/postgrest/backfill/backfill.md deleted file mode 100644 index f1a5f86..0000000 --- a/postgrest/backfill/backfill.md +++ /dev/null @@ -1,135 +0,0 @@ - -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 - # Done: Counter({'raw_lines': 123254127, 'total': 51365599, 'batches': 51365}) - -## `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 | parallel --progress -j8 'zcat {} | cut -f2 | ./backfill_grobid.py' - # [...] - # Done: Counter({'minio-success': 161605, 'total': 161605, 'raw_lines': 161605, 'batches': 161}) - # [...] - -Was running slow with lots of iowait and 99% jdb2. This seems to be disk I/O. Going to try: - - sudo mount /dev/sdc1 /sandcrawler-minio/ -o data=writeback,noatime,nobarrier - - # -j8: 20+ M/s write, little jdb2 - # -j16: 30+ M/s write, little jdb2 - # -j12: 30+ M/s write, going with this - -For general use should go back to: - - sudo mount /dev/sdc1 /sandcrawler-minio/ -o data=noatime - - # -j4: Still pretty slow, only ~3-5 M/s disk write. jbd2 consistently at 99%, 360 K/s write - -## 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 - [...] - |