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-rw-r--r--notes/cleanups/file_sha1_dedupe.md64
-rwxr-xr-xnotes/cleanups/scripts/file_dupe_to_json.py72
2 files changed, 136 insertions, 0 deletions
diff --git a/notes/cleanups/file_sha1_dedupe.md b/notes/cleanups/file_sha1_dedupe.md
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+++ b/notes/cleanups/file_sha1_dedupe.md
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+
+
+## Prep
+
+Using `check_hashes.sh`:
+
+ zcat $HASH_FILE \
+ | awk '{print $3 "\t" $1}' \
+ | rg -v '^\t' \
+ | sort -S 4G \
+ | uniq -D -w 40 \
+ > sha1_ident.dupes.tsv
+
+ wc -l sha1_ident.dupes.tsv
+ # 6,350
+
+ cut -f1 sha1_ident.dupes.tsv | uniq | wc -l
+ # 2,039
+
+Want to create JSON for each group, like:
+
+ entity_type: "file"
+ primary_id: str or None
+ duplicate_ids: [str]
+ evidence:
+ extid: str
+ extid_type: "sha1"
+
+Run transform script:
+
+ cat sha1_ident.dupes.tsv | ./file_dupe_to_json.py | pv -l > file_sha1_dupes.json
+ # 2.04k 0:00:00 [9.16k/s]
+
+
+## QA Testing
+
+ export FATCAT_AUTH_API_TOKEN=[...]
+
+ head -n25 /srv/fatcat/datasets/file_sha1_dupes.json \
+ | python -m fatcat_tools.mergers.files --editgroup-description-override "Automated merging of file entities with duplicate SHA-1 hashes" --dry-run merge-files -
+
+Hit some small bugs running in QA; test coverage isn't great, but I think hits
+the important parts.
+
+ head -n25 /srv/fatcat/datasets/file_sha1_dupes.json \
+ | python -m fatcat_tools.mergers.files --editgroup-description-override "Automated merging of file entities with duplicate SHA-1 hashes" --dry-run merge-files -
+ # Running in dry-run mode!
+ # Counter({'updated-entities': 60, 'lines': 25, 'merged': 25, 'skip': 0, 'updated-total': 0})
+
+Dry-run mode didn't actually work, and edits actually happened (!).
+
+Edits do look good.
+
+Try again, not dry-run, to ensure that case is handled:
+
+ head -n25 /srv/fatcat/datasets/file_sha1_dupes.json | python -m fatcat_tools.mergers.files --editgroup-description-override "Automated merging of file entities with duplicate SHA-1 hashes" merge-files -
+ # Counter({'lines': 25, 'skip': 25, 'skip-not-active-entity': 25, 'merged': 0, 'updated-total': 0})
+
+And then run 500 through for more testing:
+
+ head -n500 /srv/fatcat/datasets/file_sha1_dupes.json | python -m fatcat_tools.mergers.files --editgroup-description-override "Automated merging of file entities with duplicate SHA-1 hashes" merge-files -
+ # Counter({'updated-entities': 1341, 'lines': 500, 'merged': 474, 'skip': 26, 'skip-not-active-entity': 25, 'skip-entity-not-found': 1, 'updated-total': 0})
+
+The majority of merges seem to be cases where there are multiple articles in the same PDF.
diff --git a/notes/cleanups/scripts/file_dupe_to_json.py b/notes/cleanups/scripts/file_dupe_to_json.py
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index 00000000..2064dc1c
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+++ b/notes/cleanups/scripts/file_dupe_to_json.py
@@ -0,0 +1,72 @@
+#!/usr/bin/env python3
+
+"""
+This script can be used to transform duplicate file entity hash export rows
+into JSON objects which can be passed to the file entity merger.
+
+The input is expected to be a TSV with two columns: a hash value in the first
+column, and a fatcat file entity ident (in UUID format, not "fatcat ident"
+encoded) in the second column. The rows are assumed to be sorted by hash value
+(the first column), and duplicate values (same hash, differing UUID) are
+contiguous.
+
+File hashes aren't really "external identifiers" (ext_id), but we treat them as
+such here.
+
+Script is pretty simple, should be possible to copy and reuse for release,
+container, creator entity duplicates.
+"""
+
+import json, sys
+from typing import Optional
+import base64, uuid
+
+EXTID_TYPE = "sha1"
+
+def uuid2fcid(s: str) -> str:
+ """
+ Converts a uuid.UUID object to a fatcat identifier (base32 encoded string)
+ """
+ raw = uuid.UUID(s).bytes
+ return base64.b32encode(raw)[:26].lower().decode("utf-8")
+
+def print_group(extid, dupe_ids):
+ if len(dupe_ids) < 2:
+ return
+ group = dict(
+ entity_type="file",
+ primary_id=None,
+ duplicate_ids=dupe_ids,
+ evidence=dict(
+ extid=extid,
+ extid_type=EXTID_TYPE,
+ ),
+ )
+ print(json.dumps(group, sort_keys=True))
+
+def run():
+ last_extid = None
+ dupe_ids = []
+ for l in sys.stdin:
+ l = l.strip()
+ if not l:
+ continue
+ (row_extid, row_uuid) = l.split("\t")[0:2]
+ if EXTID_TYPE == "sha1":
+ assert len(row_extid) == 40
+ else:
+ raise Exception(f"extid type not supported yet: {EXTID_TYPE}")
+ row_id = uuid2fcid(row_uuid)
+ if row_extid == last_extid:
+ dupe_ids.append(row_id)
+ continue
+ elif dupe_ids:
+ print_group(last_extid, dupe_ids)
+ last_extid = row_extid
+ dupe_ids = [row_id]
+ if last_extid and dupe_ids:
+ print_group(last_extid, dupe_ids)
+
+
+if __name__=="__main__":
+ run()