summaryrefslogtreecommitdiffstats
path: root/python
diff options
context:
space:
mode:
Diffstat (limited to 'python')
-rw-r--r--python/fatcat_tools/cleanups/file_release_bugfix.py241
-rw-r--r--python/fatcat_tools/cleanups/file_short_wayback_ts.py344
-rw-r--r--python/fatcat_tools/cleanups/release_lowercase_doi.py154
-rw-r--r--python/fatcat_tools/importers/common.py9
-rw-r--r--python/fatcat_tools/importers/pubmed.py7
-rw-r--r--python/fatcat_web/types.py2
6 files changed, 755 insertions, 2 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..dc27f9b5
--- /dev/null
+++ b/python/fatcat_tools/cleanups/file_release_bugfix.py
@@ -0,0 +1,241 @@
+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", "doi"]:
+ self.counts["skip-link-source"] += 1
+ return False
+ if row["edit_extra"].get("ingest_request_source") not in [
+ "unpaywall",
+ "fatcat-changelog",
+ ]:
+ self.counts["skip-ingest-request-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", "doi"]
+ 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 existing.state != "active":
+ self.counts["skip-existing-entity-state"] += 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)
+
+ for entry in history:
+ if entry.editgroup.editor.is_bot is not True:
+ self.counts["skip-existing-edit-history-human"] += 1
+ return False
+
+ bad_edit = history[-1].edit
+ if bad_edit.extra != fe.edit_extra:
+ self.counts["skip-existing-edit-history-extra-mismatch"] += 1
+ return False
+
+ bad_editgroup = history[-1].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()
diff --git a/python/fatcat_tools/cleanups/file_short_wayback_ts.py b/python/fatcat_tools/cleanups/file_short_wayback_ts.py
new file mode 100644
index 00000000..bdd49f9b
--- /dev/null
+++ b/python/fatcat_tools/cleanups/file_short_wayback_ts.py
@@ -0,0 +1,344 @@
+import argparse
+import copy
+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, entity_from_dict, public_api
+from fatcat_tools.importers.common import EntityImporter, JsonLinePusher
+
+
+class FileShortWaybackTimestampCleanup(EntityImporter):
+ """
+ This is a one-off / one-time cleanup script for file entities, fix short
+ timestamps in wayback URLs. These timestamps are supposed to have 14 digits
+ (datetime with year, hour, seconds, etc). Some legacy file imports ended up
+ with only 4 or 12 digits.
+
+ 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_short_wayback_ts - < blah.json
+ """
+
+ def __init__(self, api: ApiClient, **kwargs):
+
+ eg_desc = (
+ kwargs.pop("editgroup_description", None)
+ or "Expand trunacted timestamps in wayback URLs"
+ )
+ eg_extra = kwargs.pop("editgroup_extra", dict())
+ eg_extra["agent"] = eg_extra.get(
+ "agent", "fatcat_tools.FileShortWaybackTimestampCleanup"
+ )
+ 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 row["status"].startswith("success"):
+ return True
+ else:
+ self.counts["skip-status"] += 1
+ return False
+
+ def parse_record(self, row: Dict[str, Any]) -> FileEntity:
+
+ # bezerk mode doesn't make sense for this importer
+ assert self.bezerk_mode is False
+
+ fe: FileEntity = entity_from_dict(row["file_entity"], FileEntity)
+ status: str = row["status"]
+ assert status.startswith("success")
+ url_expansions: Dict[str, str] = row["full_urls"]
+ assert len(url_expansions) >= 1
+
+ # actual cleanup happens here
+ any_fixed = False
+ for fe_url in fe.urls:
+ if "://web.archive.org/web/" not in fe_url.url:
+ continue
+ seq = fe_url.url.split("/")
+ partial_ts = seq[4]
+ original_url = "/".join(seq[5:])
+ if seq[2] != "web.archive.org":
+ continue
+ if len(partial_ts) not in [4, 12]:
+ continue
+ if fe_url.url in url_expansions:
+ fix_url = url_expansions[fe_url.url]
+ # defensive checks
+ if not (
+ f"/web/{partial_ts}" in fix_url
+ and fe_url.url.endswith(original_url)
+ and fix_url.endswith(original_url)
+ ):
+ print(
+ f"bad replacement URL: partial_ts={partial_ts} original={original_url} fix_url={fix_url}",
+ file=sys.stderr,
+ )
+ self.counts["skip-bad-replacement"] += 1
+ return None
+ assert "://" in fix_url
+ fe_url.url = fix_url
+ any_fixed = True
+
+ if not any_fixed:
+ self.counts["skip-no-fixes"] += 1
+ return None
+
+ # do any other generic file entity cleanups
+ # this includes removing duplicates
+ fe = self.generic_file_cleanups(fe)
+
+ # verify that there are no exact duplicates
+ final_urls = [u.url for u in fe.urls]
+ assert len(final_urls) == len(list(set(final_urls)))
+
+ return fe
+
+ def try_update(self, fe: FileEntity) -> bool:
+
+ # should always be existing
+ 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 existing.state != "active":
+ self.counts["skip-existing-entity-state"] += 1
+ return False
+
+ if existing.sha1 != fe.sha1:
+ self.counts["skip-existing-mismatch"] += 1
+ return False
+
+ assert fe.revision and existing.revision
+ if existing.revision != fe.revision:
+ self.counts["skip-revision-changed"] += 1
+ return False
+
+ # verify that at least one URL remains
+ if not fe.urls or len(fe.urls) < 1:
+ self.counts["skip-no-urls"] += 1
+ return False
+
+ # verify that all wayback urls have 14-digit timestamps, and are generally well-formed
+ for u in fe.urls:
+ if "://web.archive.org/web/" not in u.url:
+ continue
+ if u.rel != "webarchive":
+ self.counts["skip-bad-wayback-rel"] += 1
+ return False
+ seg = u.url.split("/")
+ if (
+ len(seg) < 6
+ or seg[0] != "https:"
+ or seg[2] != "web.archive.org"
+ or seg[3] != "web"
+ ):
+ self.counts["skip-bad-wayback"] += 1
+ return False
+ if len(seg[4]) != 14 or not seg[4].isdigit():
+ self.counts["skip-bad-wayback-timestamp"] += 1
+ return False
+
+ if existing == fe or existing.urls == fe.urls:
+ self.counts["skip-no-change"] += 1
+ return False
+
+ # not doing a check for "in current editgroup", because the source of
+ # these corrections (entity dump) contains no dupes
+
+ if not self.testing_mode:
+ # note: passing 'fe' instead of 'existing' here, which is not
+ # usually how it goes!
+ self.api.update_file(self.get_editgroup_id(), fe.ident, fe)
+ self.counts["update"] += 1
+ return False
+
+
+def test_short_wayback_ts() -> None:
+ api = public_api("http://localhost:9411/v0")
+ fswtc = FileShortWaybackTimestampCleanup(api=api)
+ fswtc.testing_mode = True
+
+ assert fswtc.want({"status": "fail"}) is False
+ assert fswtc.want({"status": "success-self"}) is True
+
+ example_line: Dict[str, Any] = {
+ "status": "success-db",
+ "file_entity": {
+ # note: doesn't match actual entity
+ "release_ids": ["waldfsctnbcpdbmasgduhaaaaa"],
+ "mimetype": "application/pdf",
+ "urls": [
+ {
+ "url": "https://papiro.unizar.es/ojs/index.php/ais/article/download/2187/1971",
+ "rel": "web",
+ },
+ {
+ "url": "https://web.archive.org/web/201904301022/https://papiro.unizar.es/ojs/index.php/ais/article/download/2187/1971",
+ "rel": "webarchive",
+ },
+ ],
+ "sha256": "0b9e09480ed2e1f08f3c6c72f57ce12b52ea265f580f8810e606b49d64234b29",
+ "sha1": "be714299b9be21b5afdaa7affd7d710c58269433",
+ "md5": "9edb542be5b3446a1905e61a8a3abebd",
+ "size": 666242,
+ "revision": "fe949be8-7bf9-4c17-be28-8e3e90fb85bd",
+ "ident": "4ghpvs2t2rdtrdum2mkreh62me",
+ "state": "active",
+ },
+ "full_urls": {
+ "https://web.archive.org/web/201904301022/https://papiro.unizar.es/ojs/index.php/ais/article/download/2187/1971": "https://web.archive.org/web/20190430102239/https://papiro.unizar.es/ojs/index.php/ais/article/download/2187/1971"
+ },
+ }
+ example_fe = entity_from_dict(example_line["file_entity"], FileEntity)
+
+ fe1 = copy.copy(example_fe)
+ fe1.urls[
+ 1
+ ].url = "https://web.archive.org/web/20190430102239/https://papiro.unizar.es/ojs/index.php/ais/article/download/2187/1971"
+ assert fswtc.parse_record(example_line) == fe1
+
+ # update code path; requires a known file ident and API running locally
+ assert fswtc.counts["update"] == 0
+ dummy_fe = api.get_file("aaaaaaaaaaaaamztaaaaaaaaai")
+ fe1.ident = dummy_fe.ident
+
+ assert fswtc.try_update(fe1) is False
+ assert fswtc.counts["skip-existing-mismatch"] == 1
+
+ fe1.sha1 = dummy_fe.sha1
+ assert fswtc.try_update(fe1) is False
+ assert fswtc.counts["skip-revision-changed"] == 1
+
+ fe1.revision = dummy_fe.revision
+ assert fswtc.try_update(fe1) is False
+ print(fswtc.counts)
+ assert fswtc.counts["update"] == 1
+
+ # another example, which failed with an assertion in prod due to duplicated URLs
+ example_line2: Dict[str, Any] = {
+ "file_entity": {
+ "release_ids": ["22jt7euq4fafhblzullmnesso4"],
+ "mimetype": "application/pdf",
+ "urls": [
+ {
+ "url": "https://www.jstage.jst.go.jp/article/ibk/59/1/59_KJ00007115297/_pdf",
+ "rel": "repository",
+ },
+ {
+ "url": "https://web.archive.org/web/201811010021/https://www.jstage.jst.go.jp/article/ibk/59/1/59_KJ00007115297/_pdf",
+ "rel": "webarchive",
+ },
+ {
+ "url": "https://web.archive.org/web/20181101002154/https://www.jstage.jst.go.jp/article/ibk/59/1/59_KJ00007115297/_pdf",
+ "rel": "webarchive",
+ },
+ ],
+ "sha256": "51ec58e7a2325d28d1deb0a4bc6422c0e4ae7b12ffb0b6298981a7b8b7730b19",
+ "sha1": "ad96a584fc6073b9a23736bc61ae0ec4a5661433",
+ "md5": "3d509743359649e34a27ae70c5cd3018",
+ "size": 430665,
+ "extra": {
+ "shadows": {"scimag_doi": "10.4259/ibk.59.1_194", "scimag_id": "69089904"}
+ },
+ "revision": "f1fa11ff-d521-45cf-9db1-cb3c8bd3ea48",
+ "ident": "duymhmxk3fgtzk37yp2pvthtxq",
+ "state": "active",
+ },
+ "full_urls": {
+ "https://web.archive.org/web/201811010021/https://www.jstage.jst.go.jp/article/ibk/59/1/59_KJ00007115297/_pdf": "https://web.archive.org/web/20181101002154/https://www.jstage.jst.go.jp/article/ibk/59/1/59_KJ00007115297/_pdf"
+ },
+ "status": "success-self",
+ }
+
+ fe2 = fswtc.parse_record(example_line2)
+ assert len(fe2.urls) == 2
+ assert fe2.urls[0].rel == "repository"
+ assert (
+ fe2.urls[1].url
+ == "https://web.archive.org/web/20181101002154/https://www.jstage.jst.go.jp/article/ibk/59/1/59_KJ00007115297/_pdf"
+ )
+
+ # ensure URL order is stable
+ example_line3: Dict[str, Any] = {
+ "file_entity": {
+ "release_ids": ["5rin7f2cdvc5hjkqqw53z7sr3i"],
+ "mimetype": "application/pdf",
+ "urls": [
+ {"url": "https://pubs.usgs.gov/bul/1108/report.pdf", "rel": "web"},
+ {
+ "url": "https://web.archive.org/web/201904291643/https://pubs.usgs.gov/bul/1108/report.pdf",
+ "rel": "webarchive",
+ },
+ ],
+ "sha256": "714cd48c2577e9b058b8f16b4574765da685f67582cc53898a9d6933e45d6cc0",
+ "sha1": "4efbdb517c0ff3f58136e4efbbec2bd9315400d3",
+ "md5": "89b6e6cc4e0259317e26ddf1a9a336a0",
+ "size": 41265,
+ "revision": "926fcf73-e644-4446-a24b-4d0940a2cf65",
+ "ident": "lvnz23nzijaapf5iti45zez6zu",
+ "state": "active",
+ },
+ "full_urls": {
+ "https://web.archive.org/web/201904291643/https://pubs.usgs.gov/bul/1108/report.pdf": "https://web.archive.org/web/20190429164342/https://pubs.usgs.gov/bul/1108/report.pdf"
+ },
+ "status": "success-db",
+ }
+
+ fe3 = fswtc.parse_record(example_line3)
+ assert len(fe3.urls) == 2
+ assert fe3.urls[0].rel == "web"
+ assert fe3.urls[0].url == "https://pubs.usgs.gov/bul/1108/report.pdf"
+ assert fe3.urls[1].rel == "webarchive"
+
+
+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=100, type=int)
+ parser.set_defaults(
+ auth_var="FATCAT_AUTH_WORKER_CLEANUP",
+ )
+ parser.add_argument(
+ "json_file",
+ help="File with jsonlines from file_meta schema to import from",
+ 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),
+ )
+
+ fswtc = FileShortWaybackTimestampCleanup(
+ api,
+ edit_batch_size=args.batch_size,
+ )
+ JsonLinePusher(fswtc, args.json_file).run()
+
+
+if __name__ == "__main__":
+ main()
diff --git a/python/fatcat_tools/cleanups/release_lowercase_doi.py b/python/fatcat_tools/cleanups/release_lowercase_doi.py
new file mode 100644
index 00000000..5e3275db
--- /dev/null
+++ b/python/fatcat_tools/cleanups/release_lowercase_doi.py
@@ -0,0 +1,154 @@
+import argparse
+import os
+import sys
+
+from fatcat_openapi_client import ApiClient, ApiException, ReleaseEntity, ReleaseExtIds
+
+from fatcat_tools import authenticated_api, public_api
+from fatcat_tools.importers.common import EntityImporter, LinePusher
+
+
+class ReleaseLowercaseDoiCleanup(EntityImporter):
+ """
+ This is a one-off / one-time cleanup script for release entities, to fix
+ upper-case DOIs. In fatcat, all DOIs should be normalized to lowercase.
+
+ 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.release_lowercase_doi - < blah.tsv
+
+ It expects to get a simple text line on stdin, which is a release entity.
+ The correction is implemented by fetching the current version of the
+ entity, verifying the issue, and updating if it is still a problem.
+
+ This does not try to do any merging, just corrects the case in a single
+ update.
+ """
+
+ def __init__(self, api: ApiClient, **kwargs):
+
+ eg_desc = (
+ kwargs.pop("editgroup_description", None)
+ or "Normalize release DOIs (extid) to lower-case"
+ )
+ eg_extra = kwargs.pop("editgroup_extra", dict())
+ eg_extra["agent"] = eg_extra.get("agent", "fatcat_tools.ReleaseLowercaseDoiCleanup")
+ super().__init__(
+ api,
+ do_updates=True,
+ editgroup_description=eg_desc,
+ editgroup_extra=eg_extra,
+ **kwargs,
+ )
+ self.testing_mode = False
+
+ def want(self, row: str) -> bool:
+ row = row.strip()
+ if not row:
+ return False
+ row = row.split()[0]
+ if len(row) == 26:
+ return True
+ else:
+ return False
+
+ def parse_record(self, row: str) -> ReleaseEntity:
+
+ # bezerk mode doesn't make sense for this importer
+ assert self.bezerk_mode is False
+
+ ident = row.strip().split()[0]
+ assert len(ident) == 26
+
+ return ReleaseEntity(
+ ident=ident,
+ ext_ids=ReleaseExtIds(),
+ )
+
+ def try_update(self, re: ReleaseEntity) -> bool:
+
+ # should always be existing, but sometimes not because of prod/QA flip
+ existing = None
+ try:
+ existing = self.api.get_release(re.ident)
+ except ApiException as err:
+ if err.status != 404:
+ raise err
+
+ if not existing:
+ self.counts["skip-existing-not-found"] += 1
+ return False
+
+ if existing.state != "active":
+ self.counts["skip-existing-entity-state"] += 1
+ return False
+
+ if not existing.ext_ids.doi:
+ self.counts["skip-existing-no-doi"] += 1
+ return False
+
+ if existing.ext_ids.doi == existing.ext_ids.doi.lower():
+ self.counts["skip-existing-doi-fine"] += 1
+ return False
+
+ existing.ext_ids.doi = existing.ext_ids.doi.lower()
+
+ # 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_release(self.get_editgroup_id(), existing.ident, existing)
+ self.counts["update"] += 1
+ return False
+
+
+def test_lowercase_doi() -> None:
+ api = public_api("http://localhost:9411/v0")
+ rldc = ReleaseLowercaseDoiCleanup(api=api)
+ rldc.testing_mode = True
+
+ assert rldc.want("") is False
+ assert rldc.want("aaaaaaaaaaaaarceaaaaaaaaai") is True
+ assert rldc.want("aaaaaaaaaaaaarceaaaaaaaaai\t10.1234/ABCD") is True
+ rldc.parse_record("aaaaaaaaaaaaarceaaaaaaaaai")
+
+ dummy_re = api.get_release("aaaaaaaaaaaaarceaaaaaaaaai")
+ assert rldc.try_update(dummy_re) is False
+ assert rldc.counts["skip-existing-doi-fine"] == 1
+ # this isn't a very complete test, doesn't get to update part
+
+
+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(
+ "idents_file",
+ help="File with release identifier to try updating",
+ 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),
+ )
+
+ rldc = ReleaseLowercaseDoiCleanup(
+ api,
+ edit_batch_size=args.batch_size,
+ )
+ LinePusher(rldc, args.idents_file).run()
+
+
+if __name__ == "__main__":
+ main()
diff --git a/python/fatcat_tools/importers/common.py b/python/fatcat_tools/importers/common.py
index 7c587395..e2157ee5 100644
--- a/python/fatcat_tools/importers/common.py
+++ b/python/fatcat_tools/importers/common.py
@@ -375,6 +375,15 @@ class EntityImporter:
if u.rel == "social":
u.rel = "academicsocial"
+ # remove exact URL duplicates, while preserving order, and removing
+ # "later" copies, not "first" copies
+ # this is sensitive to both url.url and url.rel combined!
+ dedupe_urls = []
+ for url_pair in existing.urls:
+ if url_pair not in dedupe_urls:
+ dedupe_urls.append(url_pair)
+ existing.urls = dedupe_urls
+
# remove URLs which are near-duplicates
redundant_urls = []
all_urls = [u.url for u in existing.urls]
diff --git a/python/fatcat_tools/importers/pubmed.py b/python/fatcat_tools/importers/pubmed.py
index 5bc7a9ff..a6c7409d 100644
--- a/python/fatcat_tools/importers/pubmed.py
+++ b/python/fatcat_tools/importers/pubmed.py
@@ -466,7 +466,12 @@ class PubmedImporter(EntityImporter):
self.counts["exists"] += 1
return False
- if existing and existing.ext_ids.pmid and (existing.refs or not re.refs):
+ if (
+ existing
+ and existing.ext_ids.pmid
+ and (existing.ext_ids.pmcid or not re.ext_ids.pmcid)
+ and (existing.refs or not re.refs)
+ ):
# TODO: any other reasons to do an update?
# don't update if it already has PMID
self.counts["exists"] += 1
diff --git a/python/fatcat_web/types.py b/python/fatcat_web/types.py
index f5182d71..f373825f 100644
--- a/python/fatcat_web/types.py
+++ b/python/fatcat_web/types.py
@@ -1,4 +1,4 @@
-from typing import Any, Tuple, Union
+from typing import Tuple, Union
from flask import Response as FlaskResponse
from werkzeug.wrappers import Response as WerkzeugResponse
generated by cgit v1.2.3 (git 2.39.1) at 2024-12-14 19:56:12 +0000