diff options
Diffstat (limited to 'python/fatcat_tools')
| -rw-r--r-- | python/fatcat_tools/cleanups/file_release_bugfix.py | 231 |
1 files changed, 231 insertions, 0 deletions
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() |