move corpus changes to 'notes/bulk_edits'

3 files changed, 285 insertions, 0 deletions

diff --git a/notes/bulk_edits/2019-06-24_unpaywall_archiveorg.md b/notes/bulk_edits/2019-06-24_unpaywall_archiveorg.md
new file mode 100644
index 00000000..2f3bbb98
--- /dev/null
+++ b/notes/bulk_edits/2019-06-24_unpaywall_archiveorg.md
@@ -0,0 +1,262 @@
+
+Goal is to import:
+
+- UNPAYWALL-PDF-CRAWL-2019-04.published dataset; about 6 million lines, expect
+  about half (3 million) new release fulltext matches
+- archive.org fulltext, about 1.8 million files
+
+## QA UNPAYWALL-PDF-CRAWL-2019-04
+
+    export FATCAT_AUTH_WORKER_CRAWL=...
+
+    # this wasn't a random sample
+    zcat /srv/fatcat/datasets/UNPAYWALL-PDF-CRAWL-2019-04.published.json.gz | head -n200 | ./fatcat_import.py arabesque --json-file - --extid-type doi --crawl-id UNPAYWALL-PDF-CRAWL-2019-04
+
+    # this was!
+    zcat /srv/fatcat/datasets/UNPAYWALL-PDF-CRAWL-2019-04.published.json.gz | shuf -n200 | ./fatcat_import.py arabesque --json-file - --extid-type doi --crawl-id UNPAYWALL-PDF-CRAWL-2019-04
+    [...]
+    Counter({'total': 199, 'insert': 106, 'exists': 62, 'skip': 31, 'skip-extid-not-found': 20, 'skip-update-disabled': 1, 'update': 0})
+
+    # ok, big import
+    zcat /srv/fatcat/datasets/UNPAYWALL-PDF-CRAWL-2019-04.published.json.gz | pv -l | time parallel -j12 --round-robin --pipe ./fatcat_import.py arabesque --json-file - --extid-type doi --crawl-id UNPAYWALL-PDF-CRAWL-2019-04
+    # ran a few hundred thousand and looked good
+
+## prod UNPAYWALL-PDF-CRAWL-2019-04
+
+    export FATCAT_AUTH_WORKER_CRAWL=...
+
+    zcat /srv/fatcat/datasets/UNPAYWALL-PDF-CRAWL-2019-04.published.json.gz | shuf -n200 | ./fatcat_import.py arabesque --json-file - --extid-type doi --crawl-id UNPAYWALL-PDF-CRAWL-2019-04
+    Counter({'total': 198, 'insert': 115, 'exists': 56, 'skip': 27, 'skip-extid-not-found': 13, 'skip-update-disabled': 2, 'update': 0})
+
+    zcat /srv/fatcat/datasets/UNPAYWALL-PDF-CRAWL-2019-04.published.json.gz | pv -l | time parallel -j12 --round-robin --pipe ./fatcat_import.py arabesque --json-file - --extid-type doi --crawl-id UNPAYWALL-PDF-CRAWL-2019-04
+    [...]
+    Requiring GROBID status == 200
+    Counter({'total': 520139, 'insert': 282524, 'exists': 155371, 'skip': 82244, 'skip-extid-not-found': 40000, 'skip-update-disabled': 6319, 'update': 0})
+    19008.63user 729.06system 3:01:57elapsed 180%CPU (0avgtext+0avgdata 51440maxresident)k
+    8552inputs+4335032outputs (54major+370893minor)pagefaults 0swaps
+
+    (loosely repeated 12x times, of course)
+
+    oh no, lots of duplicate inserts... ugh. needed a uniq in there, but really
+    only "one hit per file" export. or a shuf? blech.
+
+    (python)fatcat@wbgrp-svc502:/srv/fatcat/datasets$ zcat UNPAYWALL-PDF-CRAWL-2019-04.published.json.gz | jq .final_sha1 -r | sort -S 4G -u | wc -l
+    5621882
+    (python)fatcat@wbgrp-svc502:/srv/fatcat/datasets$ zcat UNPAYWALL-PDF-CRAWL-2019-04.published.json.gz | wc -l
+    6181191
+
+    ugh. how did this get missed in QA? sloppy.
+
+fixup is going to be
+- filter input list for duplicated sha1hex
+- for each duplicated sha1hex:
+    - fetch file entity. if not single release_id, bail
+    - fetch release expanded with files
+    - find all files with same sha1 that *aren't* the fetched file
+    - print file entity id
+- iterate over file entity ids, batches of 100x
+    - create editgroup
+    - delete files
+    - accept editgroup
+
+fetch_dupes.py:
+
+    
+    #!/usr/bin/env python3
+
+    import sys
+    import fatcat_client
+    from fatcat_tools import public_api
+
+    def do_sha1(api, sha1hex):
+        try:
+            fe = api.lookup_file(sha1=sha1hex)
+        except:
+            return
+        if len(fe.release_ids) != 1:
+            return
+        try:
+            re = api.get_release(fe.release_ids[0], expand='files', hide='refs,contribs,abstracts')
+        except:
+            return
+        for f in re.files:
+            if f.sha1 == fe.sha1 and f.ident != fe.ident and f.release_ids == [re.ident]:
+                print(f.ident)
+
+    def run():
+        api = public_api('https://api.qa.fatcat.wiki/v0')
+        for l in sys.stdin:
+            if l:
+                do_sha1(api, l.strip())
+
+    if __name__ == '__main__':
+        run()
+
+delete_dupes.py:
+
+
+    #!/usr/bin/env python3
+
+    import sys
+    import fatcat_client
+    from fatcat_tools import authenticated_api
+
+    #API_ENDPOINT = 'https://api.qa.fatcat.wiki/v0'
+    API_ENDPOINT = 'https://api.fatcat.wiki/v0'
+
+    def do_batch(api, batch):
+        eg = api.create_editgroup(
+            fatcat_client.Editgroup(description="Cleaning up duplicated file insertions from UNPAYWALL-CRAWL-2019-04 insert"))
+        for ident in batch:
+            api.delete_file(eg.editgroup_id, ident)
+        api.accept_editgroup(eg.editgroup_id)
+        print("deleted {} - {}...".format(eg.editgroup_id, len(batch)))
+
+    def run():
+        api = authenticated_api(API_ENDPOINT)
+        batch = []
+        for l in sys.stdin:
+            l = l.strip()
+            if not l:
+                continue
+            try:
+                fe = api.get_file(l)
+            except:
+                continue
+            if fe.state == 'active' and fe.release_ids:
+                batch.append(l)
+                if len(batch) >= 100:
+                    do_batch(api, batch)
+                    batch = []
+        if batch:
+            do_batch(api, batch)
+
+    if __name__ == '__main__':
+        run()
+
+commands:
+
+    zcat UNPAYWALL-PDF-CRAWL-2019-04.published.json.gz | jq .final_sha1 -r | b32_hex.py | sort -S 4G | uniq -d > repeated_sha1.tsv
+
+    cat repeated_sha1.tsv | pv -l | ./fetch_dupes.py > repeated_file_idents.tsv
+
+    export FATCAT_API_AUTH_TOKEN=... (crawl bot)
+    cat repeated_file_idents.tsv | ./delete_dupes.py
+
+## QA archive.org files
+
+Start with arxiv:
+
+    # FATCAT_AUTH_WORKER_ARCHIVE_ORG
+    export FATCAT_API_AUTH_TOKEN=...
+
+    # had a 500 "unexpected internal error: invalid length at 196", which was
+    due to syntax error in API token. should have a better error response
+
+    # try sample of arxiv_id
+    zcat /srv/fatcat/datasets/arxiv.match.json.gz | head -n100 | ./fatcat_import.py --editgroup-description-override "Import fulltext from archive.org journals collection" matched --default-mimetype application/pdf --default-link-rel archive -
+    Counter({'skip': 100, 'total': 100, 'skip-no-releases': 72, 'skip-no-urls': 28, 'update': 0, 'insert': 0, 'exists': 0})
+
+    # TODO: shouldn't re-insert if URL already in there under a different reltyp
+
+    # Ok, made a bunch of code changes to "clean up" at least arxiv URLs. All
+    # arxiv.org files should be 1-to-1 with releases that have full arxiv_ids
+
+Ok, try JSTOR:
+
+    zcat /srv/fatcat/datasets/jstor.match.json.gz | shuf -n1000 | ./fatcat_import.py --editgroup-description-override "Import fulltext from archive.org journals collection" matched --default-mimetype application/pdf --default-link-rel archive -
+    [...]
+    Counter({'total': 1000, 'skip': 763, 'skip-no-releases': 763, 'insert': 162, 'exists': 74, 'update': 1})
+
+larger import got:
+
+    HTTP response body: {"success":false,"error":"ConstraintViolation","message":"unexpected database error: duplicate key value violates unique constraint \"file_edit_editgroup_id_ident_id_key\""}
+
+could try getting around this with shuf?
+
+    zcat /srv/fatcat/datasets/jstor.match.json.gz | shuf | pv -l | ./fatcat_import.py --editgroup-description-override "Import fulltext from archive.org journals collection" matched --default-mimetype application/pdf --default-link-rel archive -
+
+got the same errors so added "inflight" edit protection and rolled back to earlier command:
+
+    zcat /srv/fatcat/datasets/jstor.match.json.gz | shuf -n1000 | ./fatcat_import.py --editgroup-description-override "Import fulltext from archive.org journals collection" matched --default-mimetype application/pdf --default-link-rel archive -
+    [...]
+    451k 0:25:32 [ 294 /s]
+    Counter({'total': 451178, 'skip-no-releases': 351287, 'skip': 351287, 'insert': 59644, 'exists': 39198, 'update': 1049, 'skip-update-inflight': 26})
+
+many/most of these files were already in fatcat due to earlier "paper-manifest"
+work... keep forgetting that!
+
+ok, next pmc:
+
+    zcat /srv/fatcat/datasets/pmc.match.json.gz | shuf -n1000 | ./fatcat_import.py --editgroup-description-override "Import fulltext from archive.org journals collection" matched --default-mimetype application/pdf --default-link-rel archive -
+    [...]
+    Counter({'total': 1000, 'exists': 895, 'insert': 77, 'skip-no-releases': 22, 'skip': 22, 'update': 6})
+
+    that's a surprisingly large fraction (2.2%) with `skip-no-releases`. some
+    because pubmed import failed, some because multiple PMCID identifiers? hrm.
+
+ok, an finally paper-doi:
+
+    zcat /srv/fatcat/datasets/paper-doi.match.json.gz | shuf -n1000 | ./fatcat_import.py --editgroup-description-override "Import fulltext from archive.org journals collection" matched --default-mimetype application/pdf --default-link-rel archive -
+    [...]
+    Counter({'total': 1000, 'exists': 720, 'insert': 280, 'update': 0, 'skip': 0})
+
+    lots exist! probably from the pre-1923 stuff? yup.
+
+## prod archive.org files
+
+    # try sample of arxiv_id
+    zcat /srv/fatcat/datasets/arxiv.match.json.gz | shuf -n100 | ./fatcat_import.py --editgroup-description-override "Import fulltext from archive.org journals collection" matched --default-mimetype application/pdf --default-link-rel archive -
+    Counter({'total': 100, 'insert': 80, 'update': 20, 'exists': 0, 'skip': 0})
+
+    # all arxiv_id
+    zcat /srv/fatcat/datasets/arxiv.match.json.gz | pv -l | time parallel -j12 --round-robin --pipe ./fatcat_import.py --editgroup-description-override '"Import fulltext from archive.org journals collection"' matched --default-mimetype application/pdf --default-link-rel archive -
+    [...]
+    Counter({'total': 62296, 'insert': 49503, 'update': 12413, 'exists': 269, 'skip': 111, 'skip-no-releases': 111, 'skip-update-inflight': 10})
+    2497.78user 98.87system 27:31.22elapsed 157%CPU (0avgtext+0avgdata 47604maxresident)k
+    360inputs+266104outputs (3major+265297minor)pagefaults 0swaps
+
+    # derp, some of those were crawl-bot but should have been archive-org-bot. ctrl-c and re-ran
+
+    # sample jstor
+    zcat /srv/fatcat/datasets/jstor.match.json.gz | shuf -n100 | ./fatcat_import.py --editgroup-description-override "Import fulltext from archive.org journals collection" matched --default-mimetype application/pdf --default-link-rel archive -
+    Counter({'total': 100, 'insert': 69, 'exists': 29, 'update': 1, 'skip': 1, 'skip-no-releases': 1})
+
+    # all jstor
+    zcat /srv/fatcat/datasets/jstor.match.json.gz | pv -l | time parallel -j12 --round-robin --pipe ./fatcat_import.py --editgroup-description-override '"Import fulltext from archive.org journals collection"' matched --default-mimetype application/pdf --default-link-rel archive -
+    [...]
+    Counter({'total': 41072, 'insert': 27783, 'exists': 11926, 'update': 1307, 'skip-update-inflight': 117, 'skip': 56, 'skip-no-releases': 56})
+    1257.93user 54.42system 12:45.96elapsed 171%CPU (0avgtext+0avgdata 45248maxresident)k
+    5384inputs+157016outputs (38major+259749minor)pagefaults 0swaps
+
+    good, pretty low `skip-no-releases` for JSTOR imports
+
+    # sample pmc
+    zcat /srv/fatcat/datasets/pmc.match.json.gz | shuf -n100 | ./fatcat_import.py --editgroup-description-override "Import fulltext from archive.org journals collection" matched --default-mimetype application/pdf --default-link-rel archive -
+    Counter({'total': 100, 'exists': 92, 'insert': 5, 'skip-no-releases': 2, 'skip': 2, 'update': 1})
+
+    interesting, at least one longtail file which is actually known: https://fatcat.wiki/file/xnc3sarc3jfsnceeagn34zi5la
+    almost all known!
+
+    # all pmc
+    zcat /srv/fatcat/datasets/pmc.match.json.gz | pv -l | time parallel -j12 --round-robin --pipe ./fatcat_import.py --editgroup-description-override '"Import fulltext from archive.org journals collection"' matched --default-mimetype application/pdf --default-link-rel archive -
+    [...]
+    Counter({'total': 18720, 'exists': 16701, 'insert': 1461, 'skip': 357, 'skip-no-releases': 357, 'update': 201, 'skip-update-inflight': 1})
+
+    # sample paper-doi
+    zcat /srv/fatcat/datasets/paper-doi.match.json.gz | shuf -n100 | ./fatcat_import.py --editgroup-description-override "Import fulltext from archive.org journals collection" matched --default-mimetype application/pdf --default-link-rel archive -
+    Counter({'total': 100, 'exists': 73, 'insert': 27, 'skip': 0, 'update': 0})
+
+    # all paper-doi
+    zcat /srv/fatcat/datasets/paper-doi.match.json.gz | pv -l | time parallel -j12 --round-robin --pipe ./fatcat_import.py --editgroup-description-override '"Import fulltext from archive.org journals collection"' matched --default-mimetype application/pdf --default-link-rel archive -
+    Counter({'total': 3014, 'exists': 2280, 'insert': 734, 'update': 0, 'skip': 0})
+    Counter({'total': 3464, 'exists': 2483, 'insert': 981, 'update': 0, 'skip': 0})
+    Counter({'total': 3437, 'exists': 2303, 'insert': 1134, 'update': 0, 'skip': 0})
+    Counter({'total': 3450, 'exists': 2379, 'insert': 1071, 'update': 0, 'skip': 0})
+    Counter({'total': 3467, 'exists': 2486, 'insert': 981, 'skip': 0, 'update': 0})
+    Counter({'total': 3481, 'exists': 2583, 'insert': 898, 'skip': 0, 'update': 0})
+    Counter({'total': 3423, 'exists': 2178, 'insert': 1245, 'update': 0, 'skip': 0})
+    62.41user 3.17system 0:31.18elapsed 210%CPU (0avgtext+0avgdata 49852maxresident)k
+    96inputs+13184outputs (7major+159215minor)pagefaults 0swaps
+
+All done!
diff --git a/notes/bulk_edits/2019-09-03_chocula.md b/notes/bulk_edits/2019-09-03_chocula.md
new file mode 100644
index 00000000..03311c8c
--- /dev/null
+++ b/notes/bulk_edits/2019-09-03_chocula.md
@@ -0,0 +1,23 @@
+
+Ran on my laptop, from master branch (`00e4ec6865782e4453d4dcec24ee205bf7c13ecf`).
+
+In QA:
+
+    time ./fatcat_import.py --host-url https://api.qa.fatcat.wiki/v0 chocula ~/code/chocula/export_fatcat.json
+    [...]
+    Counter({'total': 139032, 'exists': 76952, 'exists-skip-update': 65528, 'update': 46157, 'insert': 13605, 'exists-by-issnl': 8879, 'exists-not-found': 2538, 'skip': 2318, 'skip-unknown-new-issnl': 2318, 'exists-inactive': 7})
+    real    32m30.009s
+    user    4m44.176s
+    sys     0m12.544s
+
+In prod:
+
+    time ./fatcat_import.py --host-url https://api.fatcat.wiki/v0 chocula ~/code/chocula/export_fatcat.2019-09-03.json
+
+    Counter({'total': 139032, 'update': 66802, 'exists': 47586, 'exists-skip-update': 47428, 'insert': 22326, 'skip-unknown-new-issnl': 2318, 'skip': 2318, 'exists-by-issnl': 158})
+
+    real    34m16.930s
+    user    5m5.116s
+    sys     0m13.560s
+
+The container auto-updater is currently broken, so needed to manually dump/load into elastic.
diff --git a/notes/CHANGELOG_corpus_prod.md b/notes/bulk_edits/CHANGELOG.md
index 97b8f8a2..97b8f8a2 100644
--- a/notes/CHANGELOG_corpus_prod.md
+++ b/notes/bulk_edits/CHANGELOG.md