updates to lowercase DOI cleanup

2 files changed, 86 insertions, 7 deletions

diff --git a/notes/cleanups/case_sensitive_dois.md b/notes/cleanups/case_sensitive_dois.md
new file mode 100644
index 00000000..1bf1901e
--- /dev/null
+++ b/notes/cleanups/case_sensitive_dois.md
@@ -0,0 +1,71 @@
+
+Relevant github issue: https://github.com/internetarchive/fatcat/issues/83
+
+How many existing fatcat releases have a non-lowercase DOI? As of June 2021:
+
+    zcat release_extid.tsv.gz | cut -f3 | rg '[A-Z]' | pv -l | wc -l
+    139964
+
+## Prep
+
+    wget https://archive.org/download/fatcat_bulk_exports_2021-11-05/release_extid.tsv.gz
+
+    # scratch:bin/fcid.py is roughly the same as `fatcat_util.py uuid2fcid`
+
+    zcat release_extid.tsv.gz \
+        | cut -f1,3 \
+        | rg '[A-Z]' \
+        | /fast/scratch/bin/fcid.py \
+        | pv -l \
+        > nonlowercase_doi_releases.tsv
+    # 140k 0:03:54 [ 599 /s]
+
+    wc -l nonlowercase_doi_releases.tsv
+    140530 nonlowercase_doi_releases.tsv
+
+Uhoh, there are ~500 more than previously? Guess those are from after the fix?
+
+Create a sample for testing:
+
+    shuf -n10000 nonlowercase_doi_releases.tsv \
+        > nonlowercase_doi_releases.10k_sample.tsv
+
+## Test in QA
+
+In pipenv:
+
+    export FATCAT_AUTH_WORKER_CLEANUP=[...]
+
+    head -n100 /srv/fatcat/datasets/nonlowercase_doi_releases.10k_sample.tsv \
+        | python -m fatcat_tools.cleanups.release_lowercase_doi -
+    # Counter({'total': 100, 'update': 100, 'skip': 0, 'insert': 0, 'exists': 0})
+
+    head -n100 /srv/fatcat/datasets/nonlowercase_doi_releases.10k_sample.tsv \
+        | python -m fatcat_tools.cleanups.release_lowercase_doi -
+    # Counter({'total': 100, 'skip-existing-doi-fine': 100, 'skip': 0, 'insert': 0, 'update': 0, 'exists': 0})
+
+    head -n2000 /srv/fatcat/datasets/nonlowercase_doi_releases.10k_sample.tsv \
+        | python -m fatcat_tools.cleanups.release_lowercase_doi -
+    # no such release_ident found: dcjsybvqanffhmu4dhzdnptave
+
+Presumably because this is being run in QA, and there are some newer prod releases in the snapshot.
+
+Did a quick update, and then:
+
+    head -n2000 /srv/fatcat/datasets/nonlowercase_doi_releases.10k_sample.tsv \
+        | python -m fatcat_tools.cleanups.release_lowercase_doi -
+    # Counter({'total': 2000, 'skip-existing-doi-fine': 1100, 'update': 898, 'skip-existing-not-found': 2, 'skip': 0, 'insert': 0, 'exists': 0})
+
+Did some spot checking in QA. Out of 20 DOIs checked, 15 were valid, 5 were not
+valid (doi.org 404). It seems like roughly 1/3 have a dupe DOI (the lower-case
+DOI exists); didn't count exact numbers.
+
+This cleanup is simple and looks good to go. Batch size of 50 is good for full
+releases.
+
+Example of parallelization:
+
+    cat /srv/fatcat/datasets/nonlowercase_doi_releases.10k_sample.tsv \
+        | parallel -j8 --linebuffer --round-robin --pipe python -m fatcat_tools.cleanups.release_lowercase_doi -
+
+Ready to go!
diff --git a/python/fatcat_tools/cleanups/release_lowercase_doi.py b/python/fatcat_tools/cleanups/release_lowercase_doi.py
index 4e5a6f43..5e3275db 100644
--- a/python/fatcat_tools/cleanups/release_lowercase_doi.py
+++ b/python/fatcat_tools/cleanups/release_lowercase_doi.py
@@ -2,7 +2,7 @@ import argparse
 import os
 import sys
 
-from fatcat_openapi_client import ApiClient, ReleaseEntity, ReleaseExtIds
+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
@@ -45,7 +45,10 @@ class ReleaseLowercaseDoiCleanup(EntityImporter):
         self.testing_mode = False
 
     def want(self, row: str) -> bool:
-        row = row.strip().split()[0]
+        row = row.strip()
+        if not row:
+            return False
+        row = row.split()[0]
         if len(row) == 26:
             return True
         else:
@@ -66,15 +69,20 @@ class ReleaseLowercaseDoiCleanup(EntityImporter):
 
     def try_update(self, re: ReleaseEntity) -> bool:
 
-        # should always be existing
-        existing = self.api.get_release(re.ident)
+        # 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.status != "active":
-            self.counts["skip-existing-entity-status"] += 1
+        if existing.state != "active":
+            self.counts["skip-existing-entity-state"] += 1
             return False
 
         if not existing.ext_ids.doi:
@@ -91,7 +99,7 @@ class ReleaseLowercaseDoiCleanup(EntityImporter):
         # these corrections (entity dump) contains no dupes
 
         if not self.testing_mode:
-            self.api.update_release(self.get_editgroup_id(), re.ident, re)
+            self.api.update_release(self.get_editgroup_id(), existing.ident, existing)
         self.counts["update"] += 1
         return False