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authorBryan Newbold <bnewbold@robocracy.org>2021-11-05 16:31:36 -0700
committerBryan Newbold <bnewbold@robocracy.org>2021-11-09 14:17:35 -0800
commitad050445ac4f3e218ec101790bbf187731646361 (patch)
tree61c84095262fd1b199a69a0e7107b62f306f97b9 /python/fatcat_tools
parent2712b56580c7d5e2e07fdccd990e1918c43880f9 (diff)
downloadfatcat-ad050445ac4f3e218ec101790bbf187731646361.tar.gz
fatcat-ad050445ac4f3e218ec101790bbf187731646361.zip
cleanups: initial lowercase DOI cleanup script
Diffstat (limited to 'python/fatcat_tools')
-rw-r--r--python/fatcat_tools/cleanups/release_lowercase_doi.py145
1 files changed, 145 insertions, 0 deletions
diff --git a/python/fatcat_tools/cleanups/release_lowercase_doi.py b/python/fatcat_tools/cleanups/release_lowercase_doi.py
new file mode 100644
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+++ b/python/fatcat_tools/cleanups/release_lowercase_doi.py
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+import argparse
+import copy
+import os
+import sys
+from typing import Any, Dict
+
+import fatcat_openapi_client
+from fatcat_openapi_client import ApiClient, ReleaseEntity, ReleaseExtIds
+
+from fatcat_tools import authenticated_api, entity_from_dict, 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().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
+ existing = self.api.get_release(re.ident)
+
+ if not existing:
+ self.counts["skip-existing-not-found"] += 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(), re.ident, re)
+ 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()