initial file/release bugfix cleanup worker and notes

2 files changed, 375 insertions, 0 deletions

diff --git a/notes/cleanups/file_release_ingest_bug.md b/notes/cleanups/file_release_ingest_bug.md
new file mode 100644
index 00000000..8690157a
--- /dev/null
+++ b/notes/cleanups/file_release_ingest_bug.md
@@ -0,0 +1,144 @@
+
+We want to find cases where the `file_edit` metadata for a file entity does not match the DOI of the release it is linked to.
+
+## Background
+
+
+Seems to mostly happen when the `link_source_id` DOI is not found during a
+fatcat 'lookup', eg due to upstream DOI metadata not including a 'title' field
+(required by fatcat schema). Many of these seem to be 'journal-issue' or
+something like that. Presumably upstream (unpaywall) crawled and found some PDF
+for the DOI and indexes that.
+
+TODO: what was the specific code bug that caused this? time window of edits?
+https://github.com/internetarchive/fatcat/commit/d8cf02dbdc6848be4de2710e54f4463d702b6e7c
+
+TODO: how many empty-title Crossref DOIs are there? perhaps we should import these after all, in some situations? eg, pull `html_biblio`?
+TODO: examples of other mismatches? edits from the same timespan with mismatching identifiers
+
+## Queries
+
+    file_edit
+        ident_id
+        rev_id
+        extra_json->>'link_source_id'::text
+    file_rev_release
+        file_rev
+        target_release_ident_id
+    release_ident
+        id
+        rev_id
+    release_rev
+        id
+        doi
+
+Query some samples:
+
+    SELECT file_edit.ident_id as file_ident, release_ident.id as release_ident, file_edit.extra_json->>'link_source_id' as file_edit_doi, release_rev.doi as release_doi
+    FROM file_edit
+        LEFT JOIN file_rev_release ON file_edit.rev_id = file_rev_release.file_rev
+        LEFT JOIN release_ident ON file_rev_release.target_release_ident_id = release_ident.id
+        LEFT JOIN release_rev ON release_rev.id = release_ident.rev_id
+    WHERE
+        file_edit.extra_json->>'ingest_request_source' = 'unpaywall'
+        AND release_rev.doi != file_edit.extra_json->>'link_source_id'
+    LIMIT 20;
+
+                  file_ident              |            release_ident             |             file_edit_doi             |             release_doi             
+    --------------------------------------+--------------------------------------+---------------------------------------+-------------------------------------
+     8fe6eb2a-da3a-4e1c-b281-85fad3cae601 | 0a0cbabd-3f04-4296-94d5-b61c27fddee4 | 10.7167/2013/520930/dataset/3         | 10.7167/2013/520930
+     cbb2d4e7-a9a7-41df-be1d-faf9dd552ee1 | d7b356c7-de6b-4885-b37d-ea603849a30a | 10.1525/elementa.124.t1               | 10.1525/elementa.124
+     26242648-2a7b-42ea-b2ca-e4fba8f0a2c7 | d2647e07-fbb3-47f5-b06a-de2872bf84ec | 10.1023/a:1000301702170               | 10.1007/bfb0085374
+     f774854a-3939-4aa9-bf73-7e0573908b88 | e19ce792-422d-4feb-92ba-dd8536a60618 | 10.32835/2223-5752.2018.17.14-21      | 10.31652/2412-1142-2018-50-151-156
+     615ddf8c-2d91-4c1c-b04a-76b69f07b300 | e7af8377-9542-4711-9444-872f45521dc1 | 10.5644/sjm.10.1.00                   | 10.5644/sjm.10.1.01
+     43fa1b53-eddb-4f31-96af-bc9bd3bb31b6 | e1ec5d8a-ff88-49f4-8540-73ee4906e119 | 10.1136/bjo.81.11.934                 | 10.1038/sj.bjc.6690790
+     64b04cbc-ab3d-4cef-aff5-9d6b2532c47a | 43c387d1-e4c9-49f3-9995-552451a9a246 | 10.1023/a:1002015330987               | 10.1006/jnth.1998.2271
+     31e6e1a8-8457-4c93-82d3-12a51c0dc1bb | a2ec4305-63d2-4164-8470-02bf5c4ba74c | 10.1186/1742-4690-2-s1-s84            | 10.1038/nm0703-847
+     3461024a-1800-44a0-a7be-73f14bac99dd | 6849d39f-6bae-460b-8a9d-d6b86fbac2d3 | 10.17265/2328-2150/2014.11            | 10.1590/s0074-02762002000900009
+     c2707e43-6a4b-4f5d-8fb4-babe16b42b4d | 82127faf-d125-4cd4-88b9-9a8618392019 | 10.1055/s-005-28993                   | 10.1055/s-0034-1380711
+     0fe72304-1884-4dde-98c6-7cf3aec5bf31 | e3fe46cd-0205-42e4-8255-490e0eba38ea | 10.1787/5k4c1s0z2gs1-en               | 10.1787/9789282105931-2-en
+     686a1508-b6c5-4060-9035-1dd8a4b85be1 | dcecd03d-e0f6-40ce-a376-7e64bd90bdca | 10.15406/jlprr.2.3                    | 10.15406/jlprr.2015.02.00039
+     9403bc0e-2a50-4c8a-ab79-943bce20e583 | 3073dee2-c8f7-42ed-a727-12306d86fa35 | 10.1787/5jrtgzfl6g9w-en               | 10.1111/1468-2443.00004
+     9a080a6f-aaaf-4f4b-acab-3eda2bfacc22 | af28a167-2ddc-43db-98ca-1cc29b863f9f | 10.13040/ijpsr.0975-8232.4(6).2094-05 | 10.1002/chin.201418290
+     810f1a00-623f-4a5c-88e2-7240232ae8f9 | 639d4ddd-ef24-49dc-8d4e-ea626b0b85f8 | 10.13040/ijpsr.0975-8232.5(6).2216-24 | 10.1006/phrs.1997.0184
+                                                                                   10.13040/IJPSR.0975-8232.5(6).2216-24
+     72752c59-9532-467d-8b4f-fe4d994bcff5 | cc3db36c-27e9-45bf-96b0-56d1119b93d6 | 10.22201/facmed.2007865xe.2018.26     | 10.22201/facmed.2007865x.2018.26.01
+     a0740fc2-a1db-4bc8-ac98-177ccebde24f | 0a7136ac-86ad-4636-9c2a-b56a6d5a3a27 | 10.24966/cmph-1978/vol6iss1           | 10.1093/milmed/146.4.283
+     5b05df6a-7a0e-411b-a4e1-0081d7522673 | dc0cb585-c709-4990-a82e-c7c9b254fc74 | 10.15406/jig.3.1                      | 10.15406/jig.2016.03.00039
+     011964dd-24a6-4d25-b9dd-921077f1947e | deabab6d-7381-4567-bf56-5294ab081e20 | 10.17265/1537-1506/2013.01            | 10.1109/icsssm.2016.7538527
+     4d7efa59-30c7-4015-bea9-d7df171a97ed | a05449a0-34d7-4f45-9b92-bcf71db4918d | 10.14413/herj.2017.01.09              | 10.14413/herj.2017.01.09.
+    (20 rows)
+
+Total counts, broken DOIs, by source:
+
+    SELECT file_edit.extra_json->>'ingest_request_source' as source, COUNT(*) as broken_files
+    FROM file_edit
+        LEFT JOIN file_rev_release ON file_edit.rev_id = file_rev_release.file_rev
+        LEFT JOIN release_ident ON file_rev_release.target_release_ident_id = release_ident.id
+        LEFT JOIN release_rev ON release_rev.id = release_ident.rev_id
+    WHERE
+        file_edit.extra_json->>'link_source_id' IS NOT NULL
+        AND file_edit.extra_json->>'link_source_id' LIKE '10.%'
+        AND release_rev.doi != file_edit.extra_json->>'link_source_id'
+    GROUP BY file_edit.extra_json->>'ingest_request_source';
+
+
+          source      | broken_files
+    ------------------+--------------
+     fatcat-changelog |          872
+     unpaywall        |       227954
+    (2 rows)
+
+## Cleanup Pseudocode
+
+Dump file idents from above SQL queries. Transform from UUID to fatcat ident.
+
+For each file ident, fetch file entity, with releases expanded. Also fetch edit
+history. Filter by:
+
+- single release for file
+- single edit in history, matching broken agent
+- edit metadata indicates a DOI, which doesn't match release DOI (or release doesn't have DOI?)
+
+If all that is the case, do a lookup by the correct DOI. If there is a match,
+update the file entity to point to that release (and only that release).
+Operate in batches.
+
+Write cleanup bot, run in QA to test. Run SQL query again and iterate if some
+files were not updated. Merge to master, run full dump and update in prod.
+
+## Export Matches Needing Fix
+
+    COPY (
+        SELECT row_to_json(row.*) FROM (
+            SELECT file_edit.ident_id as file_ident, release_ident.id as wrong_release_ident, file_edit.extra_json as edit_extra
+            FROM file_edit
+                LEFT JOIN file_rev_release ON file_edit.rev_id = file_rev_release.file_rev
+                LEFT JOIN release_ident ON file_rev_release.target_release_ident_id = release_ident.id
+                LEFT JOIN release_rev ON release_rev.id = release_ident.rev_id
+            WHERE
+                file_edit.extra_json->>'link_source_id' IS NOT NULL
+                AND file_edit.extra_json->>'link_source_id' LIKE '10.%'
+                AND release_rev.doi != file_edit.extra_json->>'link_source_id'
+            -- LIMIT 20;
+        ) as row
+    ) TO '/srv/fatcat/snapshots/file_release_bugfix_20211105.unfiltered.json';
+    # COPY 228,827
+
+Then need to do a `sed` pass, and a `rg` pass, to filter out bad escapes:
+
+    cat /srv/fatcat/snapshots/file_release_bugfix_20211105.unfiltered.json \
+        | sed 's/\\"/\"/g' \
+        | rg -v "\\\\" \
+        | rg '^\{' \
+        | pv -l \
+        > /srv/fatcat/snapshots/file_release_bugfix_20211105.json
+    # 228k 0:00:00 [ 667k/s]
+
+    wc -l /srv/fatcat/snapshots/file_release_bugfix_20211105.json
+    # 228,826
+
+And create a sample file:
+
+    shuf -n10000 /srv/fatcat/snapshots/file_release_bugfix_20211105.json > /srv/fatcat/snapshots/file_release_bugfix_20211105.10k_sample.json
+
diff --git a/python/fatcat_tools/cleanups/file_release_bugfix.py b/python/fatcat_tools/cleanups/file_release_bugfix.py
new file mode 100644
index 00000000..025c1370
--- /dev/null
+++ b/python/fatcat_tools/cleanups/file_release_bugfix.py
@@ -0,0 +1,231 @@
+import argparse
+import os
+import sys
+from typing import Any, Dict
+
+import fatcat_openapi_client
+from fatcat_openapi_client import ApiClient, FileEntity
+
+from fatcat_tools import authenticated_api, public_api, uuid2fcid
+from fatcat_tools.importers.common import EntityImporter, JsonLinePusher
+from fatcat_tools.normal import clean_doi
+
+
+class FileReleaseBugfix(EntityImporter):
+    """
+    This is a one-off / one-time cleanup script for file entities which got
+    imported with incorrect release ident mappings, due to a bug in the file
+    ingest importer.
+
+    While this calls itself a cleanup, it is based on the import code path. It
+    is not integrated into the `fatcat_import` or `fatcat_cleanup` controller;
+    instead it has a __main__ function and is invoked like:
+
+        python -m fatcat_tools.cleans.file_release_bugfix - < blah.json
+    """
+
+    def __init__(self, api: ApiClient, **kwargs):
+
+        eg_desc = (
+            kwargs.pop("editgroup_description", None)
+            or "Correct bad file/release import mappings"
+        )
+        eg_extra = kwargs.pop("editgroup_extra", dict())
+        eg_extra["agent"] = eg_extra.get("agent", "fatcat_tools.FileReleaseBugfix")
+        super().__init__(
+            api,
+            do_updates=True,
+            editgroup_description=eg_desc,
+            editgroup_extra=eg_extra,
+            **kwargs,
+        )
+        self.testing_mode = False
+
+    def want(self, row: Dict[str, Any]) -> bool:
+        if not (
+            row.get("edit_extra")
+            and row["edit_extra"].get("link_source")
+            and row["edit_extra"].get("link_source_id")
+        ):
+            self.counts["skip-partial"] += 1
+            return False
+        if row["edit_extra"]["link_source"] not in ["unpaywall", "fatcat-changelog"]:
+            self.counts["skip-link-source"] += 1
+            return False
+        if not row["edit_extra"]["link_source_id"].startswith("10."):
+            self.counts["skip-source-id-not-doi"] += 1
+            return False
+        return True
+
+    def parse_record(self, row: Dict[str, Any]) -> FileEntity:
+
+        # bezerk mode doesn't make sense for this importer
+        assert self.bezerk_mode is False
+
+        file_ident = uuid2fcid(row["file_ident"])
+        wrong_release_ident = uuid2fcid(row["wrong_release_ident"])
+        edit_extra = row["edit_extra"]
+        assert edit_extra["link_source"] in ["unpaywall", "fatcat-changelog"]
+        file_edit_doi = clean_doi(edit_extra["link_source_id"])
+
+        if not file_edit_doi:
+            self.counts["skip-bad-doi"] += 1
+            return False
+
+        # check that the "wrong" release exists and doesn't have the DOI
+        wrong_release = None
+        try:
+            wrong_release = self.api.get_release(wrong_release_ident)
+        except fatcat_openapi_client.rest.ApiException as err:
+            if err.status != 404:
+                raise err
+
+        if not wrong_release:
+            self.counts["skip-wrong-release-missing"] += 1
+            return None
+
+        if clean_doi(wrong_release.ext_ids.doi) == file_edit_doi:
+            self.counts["skip-wrong-release-is-ok"] += 1
+            return None
+
+        # fetch the "correct" release, if any
+        fixed_release_ids = []
+        correct_release = None
+        try:
+            correct_release = self.api.lookup_release(doi=file_edit_doi)
+        except fatcat_openapi_client.rest.ApiException as err:
+            if err.status != 404:
+                raise err
+
+        if correct_release:
+            fixed_release_ids.append(correct_release.ident)
+
+        fe = FileEntity(
+            ident=file_ident,
+            release_ids=fixed_release_ids,
+            edit_extra=edit_extra,
+        )
+        fe._wrong_release_ident = wrong_release_ident
+        return fe
+
+    def try_update(self, fe: FileEntity) -> bool:
+
+        wrong_release_ident = fe._wrong_release_ident
+        assert len(wrong_release_ident) == 26
+
+        # should always be existing... but in QA it might not be
+        existing = None
+        try:
+            existing = self.api.get_file(fe.ident)
+        except fatcat_openapi_client.rest.ApiException as err:
+            if err.status != 404:
+                raise err
+
+        if not existing:
+            self.counts["skip-existing-not-found"] += 1
+            return False
+
+        if wrong_release_ident not in existing.release_ids:
+            self.counts["skip-existing-fixed"] += 1
+            return False
+
+        # fetch existing history to verify mismatch
+        history = self.api.get_file_history(existing.ident)
+
+        if len(history) != 1:
+            self.counts["skip-existing-history-updated"] += 1
+            return False
+
+        bad_edit = history[0].edit
+        if bad_edit.extra != fe.edit_extra:
+            self.counts["skip-existing-edit-history-extra-mismatch"] += 1
+            return False
+
+        bad_editgroup = history[0].editgroup
+
+        if not bad_editgroup.extra:
+            self.counts["skip-existing-editgroup-missing-extra"] += 1
+            return False
+
+        if (
+            bad_editgroup.editor_id != "scmbogxw25evtcesfcab5qaboa"
+            or bad_editgroup.extra.get("agent") != "fatcat_tools.IngestFileResultImporter"
+            or not bad_editgroup.extra.get("git_rev", "").startswith("v0.3")
+            or bad_editgroup.created.year != 2020
+        ):
+            self.counts["skip-existing-edit-history-mismatch"] += 1
+            return False
+
+        existing.release_ids = [ri for ri in existing.release_ids if ri != wrong_release_ident]
+
+        if len(fe.release_ids) == 1:
+            if fe.release_ids[0] not in existing.release_ids:
+                existing.release_ids.append(fe.release_ids[0])
+
+        existing.edit_extra = fe.edit_extra
+
+        # not doing a check for "in current editgroup", because the source of
+        # these corrections (entity dump) contains no dupes
+
+        if not self.testing_mode:
+            self.api.update_file(self.get_editgroup_id(), existing.ident, existing)
+        self.counts["update"] += 1
+        return False
+
+
+def test_file_release_bugfix() -> None:
+    api = public_api("http://localhost:9411/v0")
+    frbc = FileReleaseBugfix(api=api)
+    frbc.testing_mode = True
+
+    assert frbc.want({"this": "asdf"}) is False
+
+    example_line: Dict[str, Any] = {
+        "file_ident": "00000000-0000-0000-3333-000000000002",
+        "wrong_release_ident": "00000000-0000-0000-4444-000000000002",
+        "edit_extra": {
+            "link_source": "unpaywall",
+            "link_source_id": "10.1371/journal.pmed.0020124",
+            "ingest_request_source": "unpaywall",
+        },
+    }
+
+    fe1 = frbc.parse_record(example_line)
+    print(frbc.counts)
+    frbc.try_update(fe1)
+
+    # NOTE: this test is pretty incompleted
+
+
+def main() -> None:
+    parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser.add_argument(
+        "--host-url", default="http://localhost:9411/v0", help="connect to this host/port"
+    )
+    parser.add_argument("--batch-size", help="size of batch to send", default=50, type=int)
+    parser.set_defaults(
+        auth_var="FATCAT_AUTH_WORKER_CLEANUP",
+    )
+    parser.add_argument(
+        "json_file",
+        help="File with jsonlines with cleanup context",
+        default=sys.stdin,
+        type=argparse.FileType("r"),
+    )
+
+    args = parser.parse_args()
+    api = authenticated_api(
+        args.host_url,
+        # token is an optional kwarg (can be empty string, None, etc)
+        token=os.environ.get(args.auth_var),
+    )
+
+    frbc = FileReleaseBugfix(
+        api,
+        edit_batch_size=args.batch_size,
+    )
+    JsonLinePusher(frbc, args.json_file).run()
+
+
+if __name__ == "__main__":
+    main()