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-rw-r--r--extra/sitemap/README.md2
-rwxr-xr-xextra/sitemap/container_url_lists.sh1
-rw-r--r--notes/cleanups/case_sensitive_dois.md71
-rw-r--r--notes/cleanups/file_release_ingest_bug.md192
-rw-r--r--notes/cleanups/scripts/fetch_full_cdx_ts.py201
-rw-r--r--notes/cleanups/wayback_timestamps.md291
-rw-r--r--proposals/2021-04-02_crawlability.md76
-rw-r--r--python/fatcat_tools/cleanups/file_release_bugfix.py241
-rw-r--r--python/fatcat_tools/cleanups/file_short_wayback_ts.py344
-rw-r--r--python/fatcat_tools/cleanups/release_lowercase_doi.py154
-rw-r--r--python/fatcat_tools/importers/common.py9
-rw-r--r--python/fatcat_tools/importers/pubmed.py7
-rw-r--r--python/fatcat_web/types.py2
13 files changed, 1588 insertions, 3 deletions
diff --git a/extra/sitemap/README.md b/extra/sitemap/README.md
index f72893cd..581ee9f3 100644
--- a/extra/sitemap/README.md
+++ b/extra/sitemap/README.md
@@ -8,7 +8,7 @@ After a container dump, as `fatcat` user on prod server:
/srv/fatcat/src/extra/sitemap/container_url_lists.sh $DATE /srv/fatcat/snapshots/container_export.json.gz
/srv/fatcat/src/extra/sitemap/release_url_lists.sh $DATE /srv/fatcat/snapshots/release_export_expanded.json.gz
# delete old sitemap url lists
- /srv/fatcat/src/extra/sitemap/generate_sitemap_indices.py
+ python3.8 /srv/fatcat/src/extra/sitemap/generate_sitemap_indices.py
## Background
diff --git a/extra/sitemap/container_url_lists.sh b/extra/sitemap/container_url_lists.sh
index fcc0f4b6..1a37c220 100755
--- a/extra/sitemap/container_url_lists.sh
+++ b/extra/sitemap/container_url_lists.sh
@@ -15,6 +15,7 @@ DATE="$1"
# eg, container_export.json.gz
EXPORT_FILE_GZ="$2"
+# TODO: remove stubs? only if we have releases?
zcat $EXPORT_FILE_GZ \
| jq .ident -r \
| awk '{print "https://fatcat.wiki/container/" $1 }' \
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/notes/cleanups/file_release_ingest_bug.md b/notes/cleanups/file_release_ingest_bug.md
new file mode 100644
index 00000000..d818905b
--- /dev/null
+++ b/notes/cleanups/file_release_ingest_bug.md
@@ -0,0 +1,192 @@
+
+We want to find cases where the `file_edit` metadata for a file entity does not match the DOI of the release it is linked to.
+
+## Background
+
+
+Seems to mostly happen when the `link_source_id` DOI is not found during a
+fatcat 'lookup', eg due to upstream DOI metadata not including a 'title' field
+(required by fatcat schema). Many of these seem to be 'journal-issue' or
+something like that. Presumably upstream (unpaywall) crawled and found some PDF
+for the DOI and indexes that.
+
+TODO: what was the specific code bug that caused this? time window of edits?
+https://github.com/internetarchive/fatcat/commit/d8cf02dbdc6848be4de2710e54f4463d702b6e7c
+
+TODO: how many empty-title Crossref DOIs are there? perhaps we should import these after all, in some situations? eg, pull `html_biblio`?
+TODO: examples of other mismatches? edits from the same timespan with mismatching identifiers
+
+## Queries
+
+ file_edit
+ ident_id
+ rev_id
+ extra_json->>'link_source_id'::text
+ file_rev_release
+ file_rev
+ target_release_ident_id
+ release_ident
+ id
+ rev_id
+ release_rev
+ id
+ doi
+
+Query some samples:
+
+ SELECT file_edit.ident_id as file_ident, release_ident.id as release_ident, file_edit.extra_json->>'link_source_id' as file_edit_doi, release_rev.doi as release_doi
+ FROM file_edit
+ LEFT JOIN file_rev_release ON file_edit.rev_id = file_rev_release.file_rev
+ LEFT JOIN release_ident ON file_rev_release.target_release_ident_id = release_ident.id
+ LEFT JOIN release_rev ON release_rev.id = release_ident.rev_id
+ WHERE
+ file_edit.extra_json->>'ingest_request_source' = 'unpaywall'
+ AND release_rev.doi != file_edit.extra_json->>'link_source_id'
+ LIMIT 20;
+
+ file_ident | release_ident | file_edit_doi | release_doi
+ --------------------------------------+--------------------------------------+---------------------------------------+-------------------------------------
+ 8fe6eb2a-da3a-4e1c-b281-85fad3cae601 | 0a0cbabd-3f04-4296-94d5-b61c27fddee4 | 10.7167/2013/520930/dataset/3 | 10.7167/2013/520930
+ cbb2d4e7-a9a7-41df-be1d-faf9dd552ee1 | d7b356c7-de6b-4885-b37d-ea603849a30a | 10.1525/elementa.124.t1 | 10.1525/elementa.124
+ 26242648-2a7b-42ea-b2ca-e4fba8f0a2c7 | d2647e07-fbb3-47f5-b06a-de2872bf84ec | 10.1023/a:1000301702170 | 10.1007/bfb0085374
+ f774854a-3939-4aa9-bf73-7e0573908b88 | e19ce792-422d-4feb-92ba-dd8536a60618 | 10.32835/2223-5752.2018.17.14-21 | 10.31652/2412-1142-2018-50-151-156
+ 615ddf8c-2d91-4c1c-b04a-76b69f07b300 | e7af8377-9542-4711-9444-872f45521dc1 | 10.5644/sjm.10.1.00 | 10.5644/sjm.10.1.01
+ 43fa1b53-eddb-4f31-96af-bc9bd3bb31b6 | e1ec5d8a-ff88-49f4-8540-73ee4906e119 | 10.1136/bjo.81.11.934 | 10.1038/sj.bjc.6690790
+ 64b04cbc-ab3d-4cef-aff5-9d6b2532c47a | 43c387d1-e4c9-49f3-9995-552451a9a246 | 10.1023/a:1002015330987 | 10.1006/jnth.1998.2271
+ 31e6e1a8-8457-4c93-82d3-12a51c0dc1bb | a2ec4305-63d2-4164-8470-02bf5c4ba74c | 10.1186/1742-4690-2-s1-s84 | 10.1038/nm0703-847
+ 3461024a-1800-44a0-a7be-73f14bac99dd | 6849d39f-6bae-460b-8a9d-d6b86fbac2d3 | 10.17265/2328-2150/2014.11 | 10.1590/s0074-02762002000900009
+ c2707e43-6a4b-4f5d-8fb4-babe16b42b4d | 82127faf-d125-4cd4-88b9-9a8618392019 | 10.1055/s-005-28993 | 10.1055/s-0034-1380711
+ 0fe72304-1884-4dde-98c6-7cf3aec5bf31 | e3fe46cd-0205-42e4-8255-490e0eba38ea | 10.1787/5k4c1s0z2gs1-en | 10.1787/9789282105931-2-en
+ 686a1508-b6c5-4060-9035-1dd8a4b85be1 | dcecd03d-e0f6-40ce-a376-7e64bd90bdca | 10.15406/jlprr.2.3 | 10.15406/jlprr.2015.02.00039
+ 9403bc0e-2a50-4c8a-ab79-943bce20e583 | 3073dee2-c8f7-42ed-a727-12306d86fa35 | 10.1787/5jrtgzfl6g9w-en | 10.1111/1468-2443.00004
+ 9a080a6f-aaaf-4f4b-acab-3eda2bfacc22 | af28a167-2ddc-43db-98ca-1cc29b863f9f | 10.13040/ijpsr.0975-8232.4(6).2094-05 | 10.1002/chin.201418290
+ 810f1a00-623f-4a5c-88e2-7240232ae8f9 | 639d4ddd-ef24-49dc-8d4e-ea626b0b85f8 | 10.13040/ijpsr.0975-8232.5(6).2216-24 | 10.1006/phrs.1997.0184
+ 10.13040/IJPSR.0975-8232.5(6).2216-24
+ 72752c59-9532-467d-8b4f-fe4d994bcff5 | cc3db36c-27e9-45bf-96b0-56d1119b93d6 | 10.22201/facmed.2007865xe.2018.26 | 10.22201/facmed.2007865x.2018.26.01
+ a0740fc2-a1db-4bc8-ac98-177ccebde24f | 0a7136ac-86ad-4636-9c2a-b56a6d5a3a27 | 10.24966/cmph-1978/vol6iss1 | 10.1093/milmed/146.4.283
+ 5b05df6a-7a0e-411b-a4e1-0081d7522673 | dc0cb585-c709-4990-a82e-c7c9b254fc74 | 10.15406/jig.3.1 | 10.15406/jig.2016.03.00039
+ 011964dd-24a6-4d25-b9dd-921077f1947e | deabab6d-7381-4567-bf56-5294ab081e20 | 10.17265/1537-1506/2013.01 | 10.1109/icsssm.2016.7538527
+ 4d7efa59-30c7-4015-bea9-d7df171a97ed | a05449a0-34d7-4f45-9b92-bcf71db4918d | 10.14413/herj.2017.01.09 | 10.14413/herj.2017.01.09.
+ (20 rows)
+
+Total counts, broken DOIs, by source:
+
+ SELECT file_edit.extra_json->>'ingest_request_source' as source, COUNT(*) as broken_files
+ FROM file_edit
+ LEFT JOIN file_rev_release ON file_edit.rev_id = file_rev_release.file_rev
+ LEFT JOIN release_ident ON file_rev_release.target_release_ident_id = release_ident.id
+ LEFT JOIN release_rev ON release_rev.id = release_ident.rev_id
+ WHERE
+ file_edit.extra_json->>'link_source_id' IS NOT NULL
+ AND file_edit.extra_json->>'link_source_id' LIKE '10.%'
+ AND release_rev.doi != file_edit.extra_json->>'link_source_id'
+ GROUP BY file_edit.extra_json->>'ingest_request_source';
+
+
+ source | broken_files
+ ------------------+--------------
+ fatcat-changelog | 872
+ unpaywall | 227954
+ (2 rows)
+
+## Cleanup Pseudocode
+
+Dump file idents from above SQL queries. Transform from UUID to fatcat ident.
+
+For each file ident, fetch file entity, with releases expanded. Also fetch edit
+history. Filter by:
+
+- single release for file
+- single edit in history, matching broken agent
+- edit metadata indicates a DOI, which doesn't match release DOI (or release doesn't have DOI?)
+
+If all that is the case, do a lookup by the correct DOI. If there is a match,
+update the file entity to point to that release (and only that release).
+Operate in batches.
+
+Write cleanup bot, run in QA to test. Run SQL query again and iterate if some
+files were not updated. Merge to master, run full dump and update in prod.
+
+## Export Matches Needing Fix
+
+ COPY (
+ SELECT row_to_json(row.*) FROM (
+ SELECT file_edit.ident_id as file_ident, release_ident.id as wrong_release_ident, file_edit.extra_json as edit_extra
+ FROM file_edit
+ LEFT JOIN file_rev_release ON file_edit.rev_id = file_rev_release.file_rev
+ LEFT JOIN release_ident ON file_rev_release.target_release_ident_id = release_ident.id
+ LEFT JOIN release_rev ON release_rev.id = release_ident.rev_id
+ WHERE
+ file_edit.extra_json->>'link_source_id' IS NOT NULL
+ AND file_edit.extra_json->>'link_source_id' LIKE '10.%'
+ AND release_rev.doi != file_edit.extra_json->>'link_source_id'
+ -- LIMIT 20;
+ ) as row
+ ) TO '/srv/fatcat/snapshots/file_release_bugfix_20211105.unfiltered.json';
+ # COPY 228,827
+
+Then need to do a `sed` pass, and a `rg` pass, to filter out bad escapes:
+
+ cat /srv/fatcat/snapshots/file_release_bugfix_20211105.unfiltered.json \
+ | sed 's/\\"/\"/g' \
+ | rg -v "\\\\" \
+ | rg '^\{' \
+ | pv -l \
+ > /srv/fatcat/snapshots/file_release_bugfix_20211105.json
+ # 228k 0:00:00 [ 667k/s]
+
+ wc -l /srv/fatcat/snapshots/file_release_bugfix_20211105.json
+ # 228,826
+
+And create a sample file:
+
+ shuf -n10000 /srv/fatcat/snapshots/file_release_bugfix_20211105.json > /srv/fatcat/snapshots/file_release_bugfix_20211105.10k_sample.json
+
+
+## Testing in QA
+
+ export FATCAT_AUTH_WORKER_CLEANUP=[...]
+
+ head -n10 /srv/fatcat/snapshots/file_release_bugfix_20211105.10k_sample.json \
+ | python -m fatcat_tools.cleanups.file_release_bugfix -
+ # Counter({'total': 10, 'update': 10, 'skip': 0, 'insert': 0, 'exists': 0})
+
+ file_wmjzuybuorfrjdgnr2d32vg5va: was wrong, now correct, no other files
+ file_wgszcwehlffnzmoypr4l2yhvza: was correct, now correct, no other files. multiple articles in single PDF
+ file_p4r5sbminzgrhn4yaiqyr7ahwi: was correct, now wrong (!!!)
+ doi:10.1055/s-0036-1579844
+ PDF says: 10.4103/0028-3886.158210
+ unpaywall still has this incorrect linkage
+ file_n5jtvrnodbfdbccl5d6hshhvw4: now stub, was wrong
+ doi:10.19080/bboaj.2018.04.555640 release_suvtcm7hdbbr3fczcxxt4thgoi seems correct?
+ doi:10.19080/bboaj.4.4 is the bad DOI, not in fatcat. is registered, as an entire issue
+ file_kt5fv4d5lrbk7j3dxxgcm7hph4: was wrong, now correct
+ file_jq4juugnynhsdkh3whkcjod46q: was wrong, now correct
+ file_ef7w6y7k4jhjhgwmfai37yjjmm: was wrong, now correct
+ file_ca2svhd6knfnff4dktuonp45du: was correct, now correct. complicated, multiple DOIs/copies/files of same work
+ file_borst2aewvcwzhucnyth2vf3lm: was correct, now correct. complicated, multiple DOIs, single file of same work
+
+Overall, seems like this might not be as much of an obvious improvement as
+hoped! But still progress and more correct.
+
+ head -n1000 /srv/fatcat/snapshots/file_release_bugfix_20211105.10k_sample.json \
+ | python -m fatcat_tools.cleanups.file_release_bugfix -
+ # Counter({'total': 1000, 'update': 929, 'skip-existing-history-updated': 58, 'skip-existing-fixed': 10, 'skip': 3, 'skip-link-source': 3, 'insert': 0, 'exists': 0})
+
+Looking at `skip-link-source`, it is cases where `link_source` is 'doi' not
+'fatcat-changelog'. Will update filter behavior, 'fatcat-changelog' is a
+`ingest_request_source`.
+
+Checking another 10 examples. They all seem to end up as correct matches.
+
+Did a small update and running the whole batch:
+
+ cat /srv/fatcat/snapshots/file_release_bugfix_20211105.10k_sample.json \
+ | python -m fatcat_tools.cleanups.file_release_bugfix -
+ # Counter({'total': 10000, 'update': 8499, 'skip-existing-fixed': 939, 'skip-existing-history-updated': 560, 'skip': 2, 'skip-wrong-release-is-ok': 2, 'insert': 0, 'exists': 0})
+
+I think this is ready to go! Example with parallel:
+
+ cat /srv/fatcat/snapshots/file_release_bugfix_20211105.10k_sample.json \
+ | parallel -j8 --linebuffer --round-robin --pipe python -m fatcat_tools.cleanups.file_release_bugfix -
+
diff --git a/notes/cleanups/scripts/fetch_full_cdx_ts.py b/notes/cleanups/scripts/fetch_full_cdx_ts.py
new file mode 100644
index 00000000..ebcf0d62
--- /dev/null
+++ b/notes/cleanups/scripts/fetch_full_cdx_ts.py
@@ -0,0 +1,201 @@
+#!/usr/bin/env python3
+
+import sys
+import json
+import base64
+from typing import Optional, List
+
+import requests
+from requests.adapters import HTTPAdapter
+from requests.packages.urllib3.util.retry import Retry # pylint: disable=import-error
+
+def requests_retry_session(
+ retries: int = 10,
+ backoff_factor: int = 3,
+ status_forcelist: List[int] = [500, 502, 504],
+ session: requests.Session = None,
+) -> requests.Session:
+ """
+ From: https://www.peterbe.com/plog/best-practice-with-retries-with-requests
+ """
+ session = session or requests.Session()
+ retry = Retry(
+ total=retries,
+ read=retries,
+ connect=retries,
+ backoff_factor=backoff_factor,
+ status_forcelist=status_forcelist,
+ )
+ adapter = HTTPAdapter(max_retries=retry)
+ session.mount("http://", adapter)
+ session.mount("https://", adapter)
+ return session
+
+def b32_hex(s: str) -> str:
+ """
+ Converts a base32-encoded SHA-1 checksum into hex-encoded
+
+ base32 checksums are used by, eg, heritrix and in wayback CDX files
+ """
+ s = s.strip().split()[0].lower()
+ if s.startswith("sha1:"):
+ s = s[5:]
+ if len(s) != 32:
+ if len(s) == 40:
+ return s
+ raise ValueError("not a base-32 encoded SHA-1 hash: {}".format(s))
+ return base64.b16encode(base64.b32decode(s.upper())).lower().decode("utf-8")
+
+
+SANDCRAWLER_POSTGREST_URL = "http://wbgrp-svc506.us.archive.org:3030"
+
+def get_db_cdx(url: str, http_session) -> List[dict]:
+ resp = http_session.get(SANDCRAWLER_POSTGREST_URL + "/cdx", params=dict(url="eq." + url))
+ resp.raise_for_status()
+ rows = resp.json()
+ return rows or []
+
+CDX_API_URL = "https://web.archive.org/cdx/search/cdx"
+
+def get_api_cdx(url: str, partial_dt: str, http_session) -> Optional[dict]:
+
+ params = {
+ "url": url,
+ "from": partial_dt,
+ "to": partial_dt,
+ "matchType": "exact",
+ "output": "json",
+ "limit": 20,
+ # can't filter status because might be warc/revisit
+ #"filter": "statuscode:200",
+ }
+ resp = http_session.get(CDX_API_URL, params=params)
+ resp.raise_for_status()
+ rows = resp.json()
+
+ if not rows:
+ return None
+ #print(rows, file=sys.stderr)
+ if len(rows) < 2:
+ return None
+
+ for raw in rows[1:]:
+ record = dict(
+ surt=raw[0],
+ datetime=raw[1],
+ url=raw[2],
+ mimetype=raw[3],
+ status_code=raw[4],
+ sha1b32=raw[5],
+ sha1hex=b32_hex(raw[5]),
+ )
+ if record['url'] != url:
+ # TODO: could allow HTTP/HTTPS fuzzy match
+ print("CDX API near match: URL", file=sys.stderr)
+ continue
+ if not record['datetime'].startswith(partial_dt):
+ print(f"CDX API near match: datetime {partial_dt} {record['datetime']}", file=sys.stderr)
+ continue
+ if record['status_code'] == "200" or (record['status_code'] == '-' and record['mimetype'] == 'warc/revisit'):
+ return record
+ else:
+ print(f"CDX API near match: status {record['status_code']}", file=sys.stderr)
+ return None
+
+def process_file(fe, session) -> dict:
+ short_urls = []
+ self_urls = dict()
+ full_urls = dict()
+ status = "unknown"
+
+ for pair in fe['urls']:
+ u = pair['url']
+ if not '://web.archive.org/web/' in u:
+ continue
+ seg = u.split('/')
+ assert seg[2] == "web.archive.org"
+ assert seg[3] == "web"
+ if not seg[4].isdigit():
+ continue
+ original_url = "/".join(seg[5:])
+ if len(seg[4]) == 12 or len(seg[4]) == 4:
+ short_urls.append(u)
+ elif len(seg[4]) == 14:
+ self_urls[original_url] = u
+ else:
+ print(f"other bogus ts: {seg[4]}", file=sys.stderr)
+ return dict(file_entity=fe, full_urls=full_urls, status="fail-bogus-ts")
+
+ if len(short_urls) == 0:
+ return dict(file_entity=fe, full_urls=[], status="skip-no-shorts")
+
+ for short in list(set(short_urls)):
+ seg = short.split('/')
+ ts = seg[4]
+ assert len(ts) in [12,4] and ts.isdigit()
+ original_url = '/'.join(seg[5:])
+
+ if short in full_urls:
+ continue
+
+ if original_url in self_urls and ts in self_urls[original_url]:
+ full_urls[short] = self_urls[original_url]
+ status = "success-self"
+ continue
+
+ cdx_row_list = get_db_cdx(original_url, http_session=session)
+ for cdx_row in cdx_row_list:
+ if cdx_row['sha1hex'] == fe['sha1'] and cdx_row['url'] == original_url and cdx_row['datetime'].startswith(ts):
+ assert len(cdx_row['datetime']) == 14 and cdx_row['datetime'].isdigit()
+ full_urls[short] = f"https://web.archive.org/web/{cdx_row['datetime']}/{original_url}"
+ status = "success-db"
+ break
+ else:
+ #print(f"cdx DB found, but no match", file=sys.stderr)
+ pass
+ cdx_row = None
+
+ if short in full_urls:
+ continue
+
+ cdx_record = None
+ try:
+ cdx_record = get_api_cdx(original_url, partial_dt=ts, http_session=session)
+ except requests.exceptions.HTTPError as e:
+ if e.response.status_code == 403:
+ return dict(file_entity=fe, full_urls=full_urls, status="fail-cdx-403")
+ else:
+ raise
+ if cdx_record:
+ if cdx_record['sha1hex'] == fe['sha1'] and cdx_record['url'] == original_url and cdx_record['datetime'].startswith(ts):
+ assert len(cdx_record['datetime']) == 14 and cdx_record['datetime'].isdigit()
+ full_urls[short] = f"https://web.archive.org/web/{cdx_record['datetime']}/{original_url}"
+ status = "success-api"
+ break
+ else:
+ print(f"cdx API found, but no match", file=sys.stderr)
+ else:
+ print(f"no CDX API record found: {original_url}", file=sys.stderr)
+
+ if short not in full_urls:
+ return dict(file_entity=fe, full_urls=full_urls, status="fail-not-found")
+
+ return dict(
+ file_entity=fe,
+ full_urls=full_urls,
+ status=status,
+ )
+
+def main():
+ session = requests_retry_session()
+ session.headers.update({
+ "User-Agent": "Mozilla/5.0 fatcat.CdxFixupBot",
+ })
+ for line in sys.stdin:
+ if not line.strip():
+ continue
+ fe = json.loads(line)
+ print(json.dumps(process_file(fe, session=session)))
+
+if __name__=="__main__":
+ main()
diff --git a/notes/cleanups/wayback_timestamps.md b/notes/cleanups/wayback_timestamps.md
new file mode 100644
index 00000000..38bc3f7d
--- /dev/null
+++ b/notes/cleanups/wayback_timestamps.md
@@ -0,0 +1,291 @@
+
+At some point, using the arabesque importer (from targetted crawling), we
+accidentially imported a bunch of files with wayback URLs that have 12-digit
+timestamps, instead of the full canonical 14-digit timestamps.
+
+
+## Prep (2021-11-04)
+
+Download most recent file export:
+
+ wget https://archive.org/download/fatcat_bulk_exports_2021-10-07/file_export.json.gz
+
+Filter to files with problem of interest:
+
+ zcat file_export.json.gz \
+ | pv -l \
+ | rg 'web.archive.org/web/\d{12}/' \
+ | gzip \
+ > files_20211007_shortts.json.gz
+ # 111M 0:12:35
+
+ zcat files_20211007_shortts.json.gz | wc -l
+ # 7,935,009
+
+ zcat files_20211007_shortts.json.gz | shuf -n10000 > files_20211007_shortts.10k_sample.json
+
+Wow, this is a lot more than I thought!
+
+There might also be some other short URL patterns, check for those:
+
+ zcat file_export.json.gz \
+ | pv -l \
+ | rg 'web.archive.org/web/\d{1,11}/' \
+ | gzip \
+ > files_20211007_veryshortts.json.gz
+ # skipped, mergine with below
+
+ zcat file_export.json.gz \
+ | rg 'web.archive.org/web/None/' \
+ | pv -l \
+ > /dev/null
+ # 0.00 0:10:06 [0.00 /s]
+ # whew, that pattern has been fixed it seems
+
+ zcat file_export.json.gz | rg '/None/' | pv -l > /dev/null
+ # 2.00 0:10:01 [3.33m/s]
+
+ zcat file_export.json.gz \
+ | rg 'web.archive.org/web/\d{13}/' \
+ | pv -l \
+ > /dev/null
+ # 0.00 0:10:09 [0.00 /s]
+
+Yes, 4-digit is a popular pattern as well, need to handle those:
+
+ zcat file_export.json.gz \
+ | pv -l \
+ | rg 'web.archive.org/web/\d{4,12}/' \
+ | gzip \
+ > files_20211007_moreshortts.json.gz
+ # 111M 0:13:22 [ 139k/s]
+
+ zcat files_20211007_moreshortts.json.gz | wc -l
+ # 9,958,854
+
+ zcat files_20211007_moreshortts.json.gz | shuf -n10000 > files_20211007_moreshortts.10k_sample.json
+
+
+## Fetch Complete URL
+
+Want to export JSON like:
+
+ file_entity
+ [existing file entity]
+ full_urls[]: list of Dicts[str,str]
+ <short_url>: <full_url>
+ status: str
+
+Status one of:
+
+- 'success-self': the file already has a fixed URL internally
+- 'success-db': lookup URL against sandcrawler-db succeeded, and SHA1 matched
+- 'success-cdx': CDX API lookup succeeded, and SHA1 matched
+- 'fail-not-found': no matching CDX record found
+
+Ran over a sample:
+
+ cat files_20211007_shortts.10k_sample.json | ./fetch_full_cdx_ts.py > sample_out.json
+
+ cat sample_out.json | jq .status | sort | uniq -c
+ 5 "fail-not-found"
+ 576 "success-api"
+ 7212 "success-db"
+ 2207 "success-self"
+
+ head -n1000 | ./fetch_full_cdx_ts.py > sample_out.json
+
+ zcat files_20211007_veryshortts.json.gz | head -n1000 | ./fetch_full_cdx_ts.py | jq .status | sort | uniq -c
+ 2 "fail-not-found"
+ 168 "success-api"
+ 208 "success-db"
+ 622 "success-self"
+
+Investigating the "fail-not-found", they look like http/https URL
+not-exact-matches. Going to put off handling these for now because it is a
+small fraction and more delicate.
+
+Again with the broader set:
+
+ cat files_20211007_moreshortts.10k_sample.json | ./fetch_full_cdx_ts.py > sample_out.json
+
+ cat sample_out.json | jq .status | sort | uniq -c
+ 9 "fail-not-found"
+ 781 "success-api"
+ 6175 "success-db"
+ 3035 "success-self"
+
+While running a larger batch, got a CDX API error:
+
+ requests.exceptions.HTTPError: 403 Client Error: Forbidden for url: https://web.archive.org/cdx/search/cdx?url=https%3A%2F%2Fwww.psychologytoday.com%2Ffiles%2Fu47%2FHenry_et_al.pdf&from=2017&to=2017&matchType=exact&output=json&limit=20
+
+ org.archive.util.io.RuntimeIOException: org.archive.wayback.exception.AdministrativeAccessControlException: Blocked Site Error
+
+So maybe need to use credentials after all.
+
+
+## Cleanup Process
+
+Other possible cleanups to run at the same time, which would not require
+external requests or other context:
+
+- URL has ://archive.org/ link with rel=repository => rel=archive
+- mimetype is bogus => clean mimetype
+- bogus file => set some new extra field, like scope=stub or scope=partial (?)
+
+It looks like the rel swap is already implemented in `generic_file_cleanups()`.
+From sampling it seems like the mimetype issue is pretty small, so not going to
+bite that off now. The "bogus file" issue requires thought, so also skipping.
+
+
+## Commands (old)
+
+Running with 8x parallelism to not break things; expecting some errors along
+the way, may need to add handlers for connection errors etc:
+
+ # OLD SNAPSHOT
+ zcat files_20211007_moreshortts.json.gz \
+ | parallel -j8 --linebuffer --round-robin --pipe ./fetch_full_cdx_ts.py \
+ | pv -l \
+ | gzip \
+ > files_20211007_moreshortts.fetched.json.gz
+
+At 300 records/sec, this should take around 9-10 hours to process.
+
+
+
+## Prep Again (2021-11-09)
+
+After fixing "sort" issue and re-dumping file entities (2021-11-05 snapshot).
+
+Filter again:
+
+ # note: in the future use pigz instead of gzip here
+ zcat file_export.json.gz \
+ | pv -l \
+ | rg 'web.archive.org/web/\d{4,12}/' \
+ | gzip \
+ > files_20211105_moreshortts.json.gz
+ # 112M 0:13:27 [ 138k/s]
+
+ zcat files_20211105_moreshortts.json.gz | wc -l
+ # 9,958,854
+ # good, exact same number as previous snapshot
+
+ zcat files_20211105_moreshortts.json.gz | shuf -n10000 > files_20211105_moreshortts.10k_sample.json
+ # done
+
+ cat files_20211105_moreshortts.10k_sample.json \
+ | ./fetch_full_cdx_ts.py \
+ | pv -l \
+ > files_20211105_moreshortts.10k_sample.fetched.json
+ # 10.0k 0:03:36 [46.3 /s]
+
+ cat files_20211105_moreshortts.10k_sample.fetched.json | jq .status | sort | uniq -c
+ 13 "fail-not-found"
+ 774 "success-api"
+ 6193 "success-db"
+ 3020 "success-self"
+
+After tweaking `success-self` logic:
+
+ 13 "fail-not-found"
+ 859 "success-api"
+ 6229 "success-db"
+ 2899 "success-self"
+
+
+## Testing in QA
+
+Copied `sample_out.json` to fatcat QA instance and renamed as `files_20211007_moreshortts.10k_sample.fetched.json`
+
+ # OLD ATTEMPT
+ export FATCAT_API_AUTH_TOKEN=[...]
+ head -n10 /srv/fatcat/datasets/files_20211007_moreshortts.10k_sample.fetched.json \
+ | python -m fatcat_tools.cleanups.file_short_wayback_ts -
+
+Ran in to issues, iterated above.
+
+Trying again with updated script and sample file:
+
+ export FATCAT_AUTH_WORKER_CLEANUP=[...]
+
+ head -n10 /srv/fatcat/datasets/files_20211105_moreshortts.10k_sample.fetched.json \
+ | python -m fatcat_tools.cleanups.file_short_wayback_ts -
+ # Counter({'total': 10, 'update': 10, 'skip': 0, 'insert': 0, 'exists': 0})
+
+Manually inspected and these look good. Trying some repeats and larger batched:
+
+ head -n10 /srv/fatcat/datasets/files_20211105_moreshortts.10k_sample.fetched.json \
+ | python -m fatcat_tools.cleanups.file_short_wayback_ts -
+ # Counter({'total': 10, 'skip-revision-changed': 10, 'skip': 0, 'insert': 0, 'update': 0, 'exists': 0})
+
+ head -n1000 /srv/fatcat/datasets/files_20211105_moreshortts.10k_sample.fetched.json \
+ | python -m fatcat_tools.cleanups.file_short_wayback_ts -
+
+ [...]
+ bad replacement URL: partial_ts=201807271139 original=http://www.scielo.br/pdf/qn/v20n1/4918.pdf fix_url=https://web.archive.org/web/20170819080342/http://www.scielo.br/pdf/qn/v20n1/4918.pdf
+ bad replacement URL: partial_ts=201904270207 original=https://www.matec-conferences.org/articles/matecconf/pdf/2018/62/matecconf_iccoee2018_03008.pdf fix_url=https://web.archive.org/web/20190501060839/https://www.matec-conferences.org/articles/matecconf/pdf/2018/62/matecconf_iccoee2018_03008.pdf
+ bad replacement URL: partial_ts=201905011445 original=https://cdn.intechopen.com/pdfs/5886.pdf fix_url=https://web.archive.org/web/20190502203832/https://cdn.intechopen.com/pdfs/5886.pdf
+ [...]
+
+ # Counter({'total': 1000, 'update': 969, 'skip': 19, 'skip-bad-replacement': 18, 'skip-revision-changed': 10, 'skip-bad-wayback-timestamp': 2, 'skip-status': 1, 'insert': 0, 'exists': 0})
+
+
+It looks like these "bad replacement URLs" are due to timestamp mismatches. Eg, the partial timestamp is not part of the final timestamp.
+
+Tweaked fetch script and re-ran:
+
+ # Counter({'total': 1000, 'skip-revision-changed': 979, 'update': 18, 'skip-bad-wayback-timestamp': 2, 'skip': 1, 'skip-status': 1, 'insert': 0, 'exists': 0})
+
+Cool. Sort of curious what the deal is with those `skip-bad-wayback-timestamp`.
+
+Run the rest through:
+
+ cat /srv/fatcat/datasets/files_20211105_moreshortts.10k_sample.fetched.json \
+ | python -m fatcat_tools.cleanups.file_short_wayback_ts -
+ # Counter({'total': 10000, 'update': 8976, 'skip-revision-changed': 997, 'skip-bad-wayback-timestamp': 14, 'skip': 13, 'skip-status': 13, 'insert': 0, 'exists': 0})
+
+Should tweak batch size to 100 (vs. 50).
+
+How to parallelize import:
+
+ # from within pipenv
+ cat /srv/fatcat/datasets/files_20211105_moreshortts.10k_sample.fetched.json \
+ | parallel -j8 --linebuffer --round-robin --pipe python -m fatcat_tools.cleanups.file_short_wayback_ts -
+
+
+## Full Batch Commands
+
+Running in bulk again:
+
+ zcat files_20211105_moreshortts.json.gz \
+ | parallel -j8 --linebuffer --round-robin --pipe ./fetch_full_cdx_ts.py \
+ | pv -l \
+ | gzip \
+ > files_20211105_moreshortts.fetched.json.gz
+
+Ran in to one: `requests.exceptions.HTTPError: 503 Server Error: Service
+Temporarily Unavailable for url: [...]`. Will try again, if there are more
+failures may need to split up in smaller chunks.
+
+Unexpected:
+
+ Traceback (most recent call last):
+ File "./fetch_full_cdx_ts.py", line 200, in <module>
+ main()
+ File "./fetch_full_cdx_ts.py", line 197, in main
+ print(json.dumps(process_file(fe, session=session)))
+ File "./fetch_full_cdx_ts.py", line 118, in process_file
+ assert seg[4].isdigit()
+ AssertionError
+ 3.96M 3:04:46 [ 357 /s]
+
+Ugh.
+
+ zcat files_20211105_moreshortts.json.gz \
+ | tac \
+ | parallel -j8 --linebuffer --round-robin --pipe ./fetch_full_cdx_ts.py \
+ | pv -l \
+ | gzip \
+ > files_20211105_moreshortts.fetched.json.gz
diff --git a/proposals/2021-04-02_crawlability.md b/proposals/2021-04-02_crawlability.md
new file mode 100644
index 00000000..ee9f3c5b
--- /dev/null
+++ b/proposals/2021-04-02_crawlability.md
@@ -0,0 +1,76 @@
+
+status: not-implemented
+
+Crawlability Improvements
+--------------------------
+
+NOTE: After some back and forth on this topic, we have decided for now to focus
+on having scholar.archive.org indexed, not fatcat.wiki. This proposal document
+document is being kept as documentation of that decision.
+
+
+## Original Intro
+
+We are interested in making the fatcat corpus more crawlable/indexable by
+aggregators and academic search enginges. For example, CiteseerX, Google
+Scholar, or Microsoft Academic (when themselves get used by other projects).
+
+Some open questions:
+
+- is the web.archive.org iframe for PDFs ok, or should we redirect to PDFs with `id_` in the datetime?
+
+
+
+## Redirect URLs and `citation_pdf_url`
+
+We suspect that some crawlers do not like that fatcat.wiki landing pages have
+`citation_pdf_url` fields that point to a different registered domain.
+`www.semanticscholar.org -> pdfs.semanticscholar.org` is presumably ok, but
+maybe `fatcat.wiki -> web.archive.org` and `fatcat.wiki -> archive.org` are
+not.
+
+Google Scholar docs also request the PDF link be "in the same subdirectory"
+(though this obviously isn't true on, eg, semanticscholar.org):
+
+> If this page shows only the abstract of the paper and you have the full text
+> in a separate file, e.g., in the PDF format, please specify the locations of
+> all full text versions using citation_pdf_url or DC.identifier tags. The
+> content of the tag is the absolute URL of the PDF file; for security reasons,
+> it must refer to a file in the same subdirectory as the HTML abstract.
+
+Also suspect that a redirect is probably find. If a journal links from a
+landing page to a `.pdf` URL on the same domain, often there is an HTTP
+redirect to, eg, amazon AWS. These seem to get indexed fine.
+
+So, potentially have `citation_pdf_url` point to something on `fatcat.wiki`,
+which then redirects to `web.archive.org` or `archive.org`, would be
+sufficient. This would also be a reasonable URL for external services to point
+to, in that which specific access mechanism is redirected would vary as the
+catalog is improved.
+
+So, proposing two new web fatcat.wiki endpoints:
+
+ /release/<ident>/access-redirect
+ /file/<ident>/access-redirect
+
+Both of these would use an HTTP 302 "temporary" redirect to the "best" archival
+fulltext copy.
+
+If somebody wants to link to a specific file (by hash), they should use the
+file link. If they want to link to any fulltext access copy, then should use
+the release link.
+
+Open questions:
+
+- should the redirect only ever go to archive.org properties?
+- for releases, should the file type and access type be filtered? maybe with a
+ query parameter, or a `.pdf` suffix?
+
+
+## "Browsable" Site
+
+Another improvement would be to make the site more "browsable". To start, an
+index of journals (by first letter, publisher, country, or similar), then
+organize papers under the journal by volume, year, etc. This would give
+crawlers a way to spider all papers in the index.
+
diff --git a/python/fatcat_tools/cleanups/file_release_bugfix.py b/python/fatcat_tools/cleanups/file_release_bugfix.py
new file mode 100644
index 00000000..dc27f9b5
--- /dev/null
+++ b/python/fatcat_tools/cleanups/file_release_bugfix.py
@@ -0,0 +1,241 @@
+import argparse
+import os
+import sys
+from typing import Any, Dict
+
+import fatcat_openapi_client
+from fatcat_openapi_client import ApiClient, FileEntity
+
+from fatcat_tools import authenticated_api, public_api, uuid2fcid
+from fatcat_tools.importers.common import EntityImporter, JsonLinePusher
+from fatcat_tools.normal import clean_doi
+
+
+class FileReleaseBugfix(EntityImporter):
+ """
+ This is a one-off / one-time cleanup script for file entities which got
+ imported with incorrect release ident mappings, due to a bug in the file
+ ingest importer.
+
+ 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.file_release_bugfix - < blah.json
+ """
+
+ def __init__(self, api: ApiClient, **kwargs):
+
+ eg_desc = (
+ kwargs.pop("editgroup_description", None)
+ or "Correct bad file/release import mappings"
+ )
+ eg_extra = kwargs.pop("editgroup_extra", dict())
+ eg_extra["agent"] = eg_extra.get("agent", "fatcat_tools.FileReleaseBugfix")
+ super().__init__(
+ api,
+ do_updates=True,
+ editgroup_description=eg_desc,
+ editgroup_extra=eg_extra,
+ **kwargs,
+ )
+ self.testing_mode = False
+
+ def want(self, row: Dict[str, Any]) -> bool:
+ if not (
+ row.get("edit_extra")
+ and row["edit_extra"].get("link_source")
+ and row["edit_extra"].get("link_source_id")
+ ):
+ self.counts["skip-partial"] += 1
+ return False
+ if row["edit_extra"]["link_source"] not in ["unpaywall", "doi"]:
+ self.counts["skip-link-source"] += 1
+ return False
+ if row["edit_extra"].get("ingest_request_source") not in [
+ "unpaywall",
+ "fatcat-changelog",
+ ]:
+ self.counts["skip-ingest-request-source"] += 1
+ return False
+ if not row["edit_extra"]["link_source_id"].startswith("10."):
+ self.counts["skip-source-id-not-doi"] += 1
+ return False
+ return True
+
+ def parse_record(self, row: Dict[str, Any]) -> FileEntity:
+
+ # bezerk mode doesn't make sense for this importer
+ assert self.bezerk_mode is False
+
+ file_ident = uuid2fcid(row["file_ident"])
+ wrong_release_ident = uuid2fcid(row["wrong_release_ident"])
+ edit_extra = row["edit_extra"]
+ assert edit_extra["link_source"] in ["unpaywall", "doi"]
+ file_edit_doi = clean_doi(edit_extra["link_source_id"])
+
+ if not file_edit_doi:
+ self.counts["skip-bad-doi"] += 1
+ return False
+
+ # check that the "wrong" release exists and doesn't have the DOI
+ wrong_release = None
+ try:
+ wrong_release = self.api.get_release(wrong_release_ident)
+ except fatcat_openapi_client.rest.ApiException as err:
+ if err.status != 404:
+ raise err
+
+ if not wrong_release:
+ self.counts["skip-wrong-release-missing"] += 1
+ return None
+
+ if clean_doi(wrong_release.ext_ids.doi) == file_edit_doi:
+ self.counts["skip-wrong-release-is-ok"] += 1
+ return None
+
+ # fetch the "correct" release, if any
+ fixed_release_ids = []
+ correct_release = None
+ try:
+ correct_release = self.api.lookup_release(doi=file_edit_doi)
+ except fatcat_openapi_client.rest.ApiException as err:
+ if err.status != 404:
+ raise err
+
+ if correct_release:
+ fixed_release_ids.append(correct_release.ident)
+
+ fe = FileEntity(
+ ident=file_ident,
+ release_ids=fixed_release_ids,
+ edit_extra=edit_extra,
+ )
+ fe._wrong_release_ident = wrong_release_ident
+ return fe
+
+ def try_update(self, fe: FileEntity) -> bool:
+
+ wrong_release_ident = fe._wrong_release_ident
+ assert len(wrong_release_ident) == 26
+
+ # should always be existing... but in QA it might not be
+ existing = None
+ try:
+ existing = self.api.get_file(fe.ident)
+ except fatcat_openapi_client.rest.ApiException as err:
+ if err.status != 404:
+ raise err
+
+ if not existing:
+ self.counts["skip-existing-not-found"] += 1
+ return False
+
+ if existing.state != "active":
+ self.counts["skip-existing-entity-state"] += 1
+ return False
+
+ if wrong_release_ident not in existing.release_ids:
+ self.counts["skip-existing-fixed"] += 1
+ return False
+
+ # fetch existing history to verify mismatch
+ history = self.api.get_file_history(existing.ident)
+
+ for entry in history:
+ if entry.editgroup.editor.is_bot is not True:
+ self.counts["skip-existing-edit-history-human"] += 1
+ return False
+
+ bad_edit = history[-1].edit
+ if bad_edit.extra != fe.edit_extra:
+ self.counts["skip-existing-edit-history-extra-mismatch"] += 1
+ return False
+
+ bad_editgroup = history[-1].editgroup
+ if not bad_editgroup.extra:
+ self.counts["skip-existing-editgroup-missing-extra"] += 1
+ return False
+
+ if (
+ bad_editgroup.editor_id != "scmbogxw25evtcesfcab5qaboa"
+ or bad_editgroup.extra.get("agent") != "fatcat_tools.IngestFileResultImporter"
+ or not bad_editgroup.extra.get("git_rev", "").startswith("v0.3")
+ or bad_editgroup.created.year != 2020
+ ):
+ self.counts["skip-existing-edit-history-mismatch"] += 1
+ return False
+
+ existing.release_ids = [ri for ri in existing.release_ids if ri != wrong_release_ident]
+
+ if len(fe.release_ids) == 1:
+ if fe.release_ids[0] not in existing.release_ids:
+ existing.release_ids.append(fe.release_ids[0])
+
+ existing.edit_extra = fe.edit_extra
+
+ # 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_file(self.get_editgroup_id(), existing.ident, existing)
+ self.counts["update"] += 1
+ return False
+
+
+def test_file_release_bugfix() -> None:
+ api = public_api("http://localhost:9411/v0")
+ frbc = FileReleaseBugfix(api=api)
+ frbc.testing_mode = True
+
+ assert frbc.want({"this": "asdf"}) is False
+
+ example_line: Dict[str, Any] = {
+ "file_ident": "00000000-0000-0000-3333-000000000002",
+ "wrong_release_ident": "00000000-0000-0000-4444-000000000002",
+ "edit_extra": {
+ "link_source": "unpaywall",
+ "link_source_id": "10.1371/journal.pmed.0020124",
+ "ingest_request_source": "unpaywall",
+ },
+ }
+
+ fe1 = frbc.parse_record(example_line)
+ print(frbc.counts)
+ frbc.try_update(fe1)
+
+ # NOTE: this test is pretty incompleted
+
+
+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(
+ "json_file",
+ help="File with jsonlines with cleanup context",
+ 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),
+ )
+
+ frbc = FileReleaseBugfix(
+ api,
+ edit_batch_size=args.batch_size,
+ )
+ JsonLinePusher(frbc, args.json_file).run()
+
+
+if __name__ == "__main__":
+ main()
diff --git a/python/fatcat_tools/cleanups/file_short_wayback_ts.py b/python/fatcat_tools/cleanups/file_short_wayback_ts.py
new file mode 100644
index 00000000..bdd49f9b
--- /dev/null
+++ b/python/fatcat_tools/cleanups/file_short_wayback_ts.py
@@ -0,0 +1,344 @@
+import argparse
+import copy
+import os
+import sys
+from typing import Any, Dict
+
+import fatcat_openapi_client
+from fatcat_openapi_client import ApiClient, FileEntity
+
+from fatcat_tools import authenticated_api, entity_from_dict, public_api
+from fatcat_tools.importers.common import EntityImporter, JsonLinePusher
+
+
+class FileShortWaybackTimestampCleanup(EntityImporter):
+ """
+ This is a one-off / one-time cleanup script for file entities, fix short
+ timestamps in wayback URLs. These timestamps are supposed to have 14 digits
+ (datetime with year, hour, seconds, etc). Some legacy file imports ended up
+ with only 4 or 12 digits.
+
+ 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.file_short_wayback_ts - < blah.json
+ """
+
+ def __init__(self, api: ApiClient, **kwargs):
+
+ eg_desc = (
+ kwargs.pop("editgroup_description", None)
+ or "Expand trunacted timestamps in wayback URLs"
+ )
+ eg_extra = kwargs.pop("editgroup_extra", dict())
+ eg_extra["agent"] = eg_extra.get(
+ "agent", "fatcat_tools.FileShortWaybackTimestampCleanup"
+ )
+ super().__init__(
+ api,
+ do_updates=True,
+ editgroup_description=eg_desc,
+ editgroup_extra=eg_extra,
+ **kwargs,
+ )
+ self.testing_mode = False
+
+ def want(self, row: Dict[str, Any]) -> bool:
+ if row["status"].startswith("success"):
+ return True
+ else:
+ self.counts["skip-status"] += 1
+ return False
+
+ def parse_record(self, row: Dict[str, Any]) -> FileEntity:
+
+ # bezerk mode doesn't make sense for this importer
+ assert self.bezerk_mode is False
+
+ fe: FileEntity = entity_from_dict(row["file_entity"], FileEntity)
+ status: str = row["status"]
+ assert status.startswith("success")
+ url_expansions: Dict[str, str] = row["full_urls"]
+ assert len(url_expansions) >= 1
+
+ # actual cleanup happens here
+ any_fixed = False
+ for fe_url in fe.urls:
+ if "://web.archive.org/web/" not in fe_url.url:
+ continue
+ seq = fe_url.url.split("/")
+ partial_ts = seq[4]
+ original_url = "/".join(seq[5:])
+ if seq[2] != "web.archive.org":
+ continue
+ if len(partial_ts) not in [4, 12]:
+ continue
+ if fe_url.url in url_expansions:
+ fix_url = url_expansions[fe_url.url]
+ # defensive checks
+ if not (
+ f"/web/{partial_ts}" in fix_url
+ and fe_url.url.endswith(original_url)
+ and fix_url.endswith(original_url)
+ ):
+ print(
+ f"bad replacement URL: partial_ts={partial_ts} original={original_url} fix_url={fix_url}",
+ file=sys.stderr,
+ )
+ self.counts["skip-bad-replacement"] += 1
+ return None
+ assert "://" in fix_url
+ fe_url.url = fix_url
+ any_fixed = True
+
+ if not any_fixed:
+ self.counts["skip-no-fixes"] += 1
+ return None
+
+ # do any other generic file entity cleanups
+ # this includes removing duplicates
+ fe = self.generic_file_cleanups(fe)
+
+ # verify that there are no exact duplicates
+ final_urls = [u.url for u in fe.urls]
+ assert len(final_urls) == len(list(set(final_urls)))
+
+ return fe
+
+ def try_update(self, fe: FileEntity) -> bool:
+
+ # should always be existing
+ try:
+ existing = self.api.get_file(fe.ident)
+ except fatcat_openapi_client.rest.ApiException as err:
+ if err.status != 404:
+ raise err
+
+ if not existing:
+ self.counts["skip-existing-not-found"] += 1
+ return False
+
+ if existing.state != "active":
+ self.counts["skip-existing-entity-state"] += 1
+ return False
+
+ if existing.sha1 != fe.sha1:
+ self.counts["skip-existing-mismatch"] += 1
+ return False
+
+ assert fe.revision and existing.revision
+ if existing.revision != fe.revision:
+ self.counts["skip-revision-changed"] += 1
+ return False
+
+ # verify that at least one URL remains
+ if not fe.urls or len(fe.urls) < 1:
+ self.counts["skip-no-urls"] += 1
+ return False
+
+ # verify that all wayback urls have 14-digit timestamps, and are generally well-formed
+ for u in fe.urls:
+ if "://web.archive.org/web/" not in u.url:
+ continue
+ if u.rel != "webarchive":
+ self.counts["skip-bad-wayback-rel"] += 1
+ return False
+ seg = u.url.split("/")
+ if (
+ len(seg) < 6
+ or seg[0] != "https:"
+ or seg[2] != "web.archive.org"
+ or seg[3] != "web"
+ ):
+ self.counts["skip-bad-wayback"] += 1
+ return False
+ if len(seg[4]) != 14 or not seg[4].isdigit():
+ self.counts["skip-bad-wayback-timestamp"] += 1
+ return False
+
+ if existing == fe or existing.urls == fe.urls:
+ self.counts["skip-no-change"] += 1
+ return False
+
+ # not doing a check for "in current editgroup", because the source of
+ # these corrections (entity dump) contains no dupes
+
+ if not self.testing_mode:
+ # note: passing 'fe' instead of 'existing' here, which is not
+ # usually how it goes!
+ self.api.update_file(self.get_editgroup_id(), fe.ident, fe)
+ self.counts["update"] += 1
+ return False
+
+
+def test_short_wayback_ts() -> None:
+ api = public_api("http://localhost:9411/v0")
+ fswtc = FileShortWaybackTimestampCleanup(api=api)
+ fswtc.testing_mode = True
+
+ assert fswtc.want({"status": "fail"}) is False
+ assert fswtc.want({"status": "success-self"}) is True
+
+ example_line: Dict[str, Any] = {
+ "status": "success-db",
+ "file_entity": {
+ # note: doesn't match actual entity
+ "release_ids": ["waldfsctnbcpdbmasgduhaaaaa"],
+ "mimetype": "application/pdf",
+ "urls": [
+ {
+ "url": "https://papiro.unizar.es/ojs/index.php/ais/article/download/2187/1971",
+ "rel": "web",
+ },
+ {
+ "url": "https://web.archive.org/web/201904301022/https://papiro.unizar.es/ojs/index.php/ais/article/download/2187/1971",
+ "rel": "webarchive",
+ },
+ ],
+ "sha256": "0b9e09480ed2e1f08f3c6c72f57ce12b52ea265f580f8810e606b49d64234b29",
+ "sha1": "be714299b9be21b5afdaa7affd7d710c58269433",
+ "md5": "9edb542be5b3446a1905e61a8a3abebd",
+ "size": 666242,
+ "revision": "fe949be8-7bf9-4c17-be28-8e3e90fb85bd",
+ "ident": "4ghpvs2t2rdtrdum2mkreh62me",
+ "state": "active",
+ },
+ "full_urls": {
+ "https://web.archive.org/web/201904301022/https://papiro.unizar.es/ojs/index.php/ais/article/download/2187/1971": "https://web.archive.org/web/20190430102239/https://papiro.unizar.es/ojs/index.php/ais/article/download/2187/1971"
+ },
+ }
+ example_fe = entity_from_dict(example_line["file_entity"], FileEntity)
+
+ fe1 = copy.copy(example_fe)
+ fe1.urls[
+ 1
+ ].url = "https://web.archive.org/web/20190430102239/https://papiro.unizar.es/ojs/index.php/ais/article/download/2187/1971"
+ assert fswtc.parse_record(example_line) == fe1
+
+ # update code path; requires a known file ident and API running locally
+ assert fswtc.counts["update"] == 0
+ dummy_fe = api.get_file("aaaaaaaaaaaaamztaaaaaaaaai")
+ fe1.ident = dummy_fe.ident
+
+ assert fswtc.try_update(fe1) is False
+ assert fswtc.counts["skip-existing-mismatch"] == 1
+
+ fe1.sha1 = dummy_fe.sha1
+ assert fswtc.try_update(fe1) is False
+ assert fswtc.counts["skip-revision-changed"] == 1
+
+ fe1.revision = dummy_fe.revision
+ assert fswtc.try_update(fe1) is False
+ print(fswtc.counts)
+ assert fswtc.counts["update"] == 1
+
+ # another example, which failed with an assertion in prod due to duplicated URLs
+ example_line2: Dict[str, Any] = {
+ "file_entity": {
+ "release_ids": ["22jt7euq4fafhblzullmnesso4"],
+ "mimetype": "application/pdf",
+ "urls": [
+ {
+ "url": "https://www.jstage.jst.go.jp/article/ibk/59/1/59_KJ00007115297/_pdf",
+ "rel": "repository",
+ },
+ {
+ "url": "https://web.archive.org/web/201811010021/https://www.jstage.jst.go.jp/article/ibk/59/1/59_KJ00007115297/_pdf",
+ "rel": "webarchive",
+ },
+ {
+ "url": "https://web.archive.org/web/20181101002154/https://www.jstage.jst.go.jp/article/ibk/59/1/59_KJ00007115297/_pdf",
+ "rel": "webarchive",
+ },
+ ],
+ "sha256": "51ec58e7a2325d28d1deb0a4bc6422c0e4ae7b12ffb0b6298981a7b8b7730b19",
+ "sha1": "ad96a584fc6073b9a23736bc61ae0ec4a5661433",
+ "md5": "3d509743359649e34a27ae70c5cd3018",
+ "size": 430665,
+ "extra": {
+ "shadows": {"scimag_doi": "10.4259/ibk.59.1_194", "scimag_id": "69089904"}
+ },
+ "revision": "f1fa11ff-d521-45cf-9db1-cb3c8bd3ea48",
+ "ident": "duymhmxk3fgtzk37yp2pvthtxq",
+ "state": "active",
+ },
+ "full_urls": {
+ "https://web.archive.org/web/201811010021/https://www.jstage.jst.go.jp/article/ibk/59/1/59_KJ00007115297/_pdf": "https://web.archive.org/web/20181101002154/https://www.jstage.jst.go.jp/article/ibk/59/1/59_KJ00007115297/_pdf"
+ },
+ "status": "success-self",
+ }
+
+ fe2 = fswtc.parse_record(example_line2)
+ assert len(fe2.urls) == 2
+ assert fe2.urls[0].rel == "repository"
+ assert (
+ fe2.urls[1].url
+ == "https://web.archive.org/web/20181101002154/https://www.jstage.jst.go.jp/article/ibk/59/1/59_KJ00007115297/_pdf"
+ )
+
+ # ensure URL order is stable
+ example_line3: Dict[str, Any] = {
+ "file_entity": {
+ "release_ids": ["5rin7f2cdvc5hjkqqw53z7sr3i"],
+ "mimetype": "application/pdf",
+ "urls": [
+ {"url": "https://pubs.usgs.gov/bul/1108/report.pdf", "rel": "web"},
+ {
+ "url": "https://web.archive.org/web/201904291643/https://pubs.usgs.gov/bul/1108/report.pdf",
+ "rel": "webarchive",
+ },
+ ],
+ "sha256": "714cd48c2577e9b058b8f16b4574765da685f67582cc53898a9d6933e45d6cc0",
+ "sha1": "4efbdb517c0ff3f58136e4efbbec2bd9315400d3",
+ "md5": "89b6e6cc4e0259317e26ddf1a9a336a0",
+ "size": 41265,
+ "revision": "926fcf73-e644-4446-a24b-4d0940a2cf65",
+ "ident": "lvnz23nzijaapf5iti45zez6zu",
+ "state": "active",
+ },
+ "full_urls": {
+ "https://web.archive.org/web/201904291643/https://pubs.usgs.gov/bul/1108/report.pdf": "https://web.archive.org/web/20190429164342/https://pubs.usgs.gov/bul/1108/report.pdf"
+ },
+ "status": "success-db",
+ }
+
+ fe3 = fswtc.parse_record(example_line3)
+ assert len(fe3.urls) == 2
+ assert fe3.urls[0].rel == "web"
+ assert fe3.urls[0].url == "https://pubs.usgs.gov/bul/1108/report.pdf"
+ assert fe3.urls[1].rel == "webarchive"
+
+
+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=100, type=int)
+ parser.set_defaults(
+ auth_var="FATCAT_AUTH_WORKER_CLEANUP",
+ )
+ parser.add_argument(
+ "json_file",
+ help="File with jsonlines from file_meta schema to import from",
+ 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),
+ )
+
+ fswtc = FileShortWaybackTimestampCleanup(
+ api,
+ edit_batch_size=args.batch_size,
+ )
+ JsonLinePusher(fswtc, args.json_file).run()
+
+
+if __name__ == "__main__":
+ main()
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..5e3275db
--- /dev/null
+++ b/python/fatcat_tools/cleanups/release_lowercase_doi.py
@@ -0,0 +1,154 @@
+import argparse
+import os
+import sys
+
+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
+
+
+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()
+ if not row:
+ return False
+ row = row.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, 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.state != "active":
+ self.counts["skip-existing-entity-state"] += 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(), existing.ident, existing)
+ 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()
diff --git a/python/fatcat_tools/importers/common.py b/python/fatcat_tools/importers/common.py
index 7c587395..e2157ee5 100644
--- a/python/fatcat_tools/importers/common.py
+++ b/python/fatcat_tools/importers/common.py
@@ -375,6 +375,15 @@ class EntityImporter:
if u.rel == "social":
u.rel = "academicsocial"
+ # remove exact URL duplicates, while preserving order, and removing
+ # "later" copies, not "first" copies
+ # this is sensitive to both url.url and url.rel combined!
+ dedupe_urls = []
+ for url_pair in existing.urls:
+ if url_pair not in dedupe_urls:
+ dedupe_urls.append(url_pair)
+ existing.urls = dedupe_urls
+
# remove URLs which are near-duplicates
redundant_urls = []
all_urls = [u.url for u in existing.urls]
diff --git a/python/fatcat_tools/importers/pubmed.py b/python/fatcat_tools/importers/pubmed.py
index 5bc7a9ff..a6c7409d 100644
--- a/python/fatcat_tools/importers/pubmed.py
+++ b/python/fatcat_tools/importers/pubmed.py
@@ -466,7 +466,12 @@ class PubmedImporter(EntityImporter):
self.counts["exists"] += 1
return False
- if existing and existing.ext_ids.pmid and (existing.refs or not re.refs):
+ if (
+ existing
+ and existing.ext_ids.pmid
+ and (existing.ext_ids.pmcid or not re.ext_ids.pmcid)
+ and (existing.refs or not re.refs)
+ ):
# TODO: any other reasons to do an update?
# don't update if it already has PMID
self.counts["exists"] += 1
diff --git a/python/fatcat_web/types.py b/python/fatcat_web/types.py
index f5182d71..f373825f 100644
--- a/python/fatcat_web/types.py
+++ b/python/fatcat_web/types.py
@@ -1,4 +1,4 @@
-from typing import Any, Tuple, Union
+from typing import Tuple, Union
from flask import Response as FlaskResponse
from werkzeug.wrappers import Response as WerkzeugResponse
generated by cgit v1.2.3 (git 2.39.1) at 2024-12-04 19:21:34 +0000