SQL backfill notes and python scripts

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+
+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
+    [...]
+