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import argparse
import os
import sys
from fatcat_openapi_client import ApiClient, 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().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 existing.status != "active":
self.counts["skip-existing-entity-status"] += 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()
|
