cleanups: initial lowercase DOI cleanup script

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
index 00000000..812262d4
--- /dev/null
+++ b/python/fatcat_tools/cleanups/release_lowercase_doi.py
@@ -0,0 +1,145 @@
+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()