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-rwxr-xr-xpython/fatcat_cleanup.py59
-rw-r--r--python/fatcat_tools/cleanups/NOTES.txt24
-rw-r--r--python/fatcat_tools/cleanups/__init__.py3
-rw-r--r--python/fatcat_tools/cleanups/common.py140
-rw-r--r--python/fatcat_tools/cleanups/files.py74
5 files changed, 300 insertions, 0 deletions
diff --git a/python/fatcat_cleanup.py b/python/fatcat_cleanup.py
new file mode 100755
index 00000000..42887299
--- /dev/null
+++ b/python/fatcat_cleanup.py
@@ -0,0 +1,59 @@
+#!/usr/bin/env python3
+
+import os, sys, argparse
+from fatcat_tools import authenticated_api
+from fatcat_tools.importers import JsonLinePusher
+from fatcat_tools.cleanups import *
+
+
+def run_files(args):
+ fmi = FileCleaner(args.api,
+ dry_run_mode=args.dry_run,
+ edit_batch_size=args.batch_size,
+ editgroup_description=args.editgroup_description_override)
+ JsonLinePusher(fmi, args.json_file).run()
+
+def main():
+ parser = argparse.ArgumentParser()
+ 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.add_argument('--editgroup-description-override',
+ help="editgroup description override",
+ default=None, type=str)
+ parser.add_argument('--dry-run',
+ help="dry-run mode (don't actually update)",
+ default=False, type=bool)
+ subparsers = parser.add_subparsers()
+
+ sub_files = subparsers.add_parser('files')
+ sub_files.set_defaults(
+ func=run_files,
+ auth_var="FATCAT_AUTH_WORKER_CLEANUP",
+ )
+ sub_files.add_argument('json_file',
+ help="files JSON file to import from",
+ default=sys.stdin, type=argparse.FileType('r'))
+
+ args = parser.parse_args()
+ if not args.__dict__.get("func"):
+ print("tell me what to do!")
+ sys.exit(-1)
+
+ # allow editgroup description override via env variable (but CLI arg takes
+ # precedence)
+ if not args.editgroup_description_override \
+ and os.environ.get('FATCAT_EDITGROUP_DESCRIPTION'):
+ args.editgroup_description_override = os.environ.get('FATCAT_EDITGROUP_DESCRIPTION')
+
+ 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))
+ args.func(args)
+
+if __name__ == '__main__':
+ main()
diff --git a/python/fatcat_tools/cleanups/NOTES.txt b/python/fatcat_tools/cleanups/NOTES.txt
new file mode 100644
index 00000000..cdaed6b1
--- /dev/null
+++ b/python/fatcat_tools/cleanups/NOTES.txt
@@ -0,0 +1,24 @@
+
+design is to iterate over JSON list of full entities. perform transforms/fixes.
+if no changes, bail early. if changes, do a request to check that current rev
+of entity is same as processed, to prevent race conditions; if a match, do
+update (in import/merge batch style).
+
+should pre-filter entities piped in. also have a CLI mode to do a single
+entity; check+update code should be distinct from fix code.
+
+releases
+- extra.subtitle => subtitle
+- has pmid, type is journal-article, title like "Retraction:" => type is retraction
+- similar to above, title like "Retracted:" => status is retracted
+- longtail release year is bogus (like > 2030?) => remove release year
+
+files
+- URL has ://archive.org/ link with rel=repository => rel=archive
+- URL has ://web.archive.org/web/None/ link => delete URL
+- URL has short wayback date ("2017") and another url with that as prefix => delete URL
+- mimetype is bogus like (???) => clean mimetype
+
+container
+- extra.issnp = "NA" => delete key
+ => in general, issne or issnp not valid ISSNs -> delete key
diff --git a/python/fatcat_tools/cleanups/__init__.py b/python/fatcat_tools/cleanups/__init__.py
new file mode 100644
index 00000000..587c7b9b
--- /dev/null
+++ b/python/fatcat_tools/cleanups/__init__.py
@@ -0,0 +1,3 @@
+
+from .common import EntityCleaner
+from .files import FileCleaner
diff --git a/python/fatcat_tools/cleanups/common.py b/python/fatcat_tools/cleanups/common.py
new file mode 100644
index 00000000..ad2ff858
--- /dev/null
+++ b/python/fatcat_tools/cleanups/common.py
@@ -0,0 +1,140 @@
+
+import json
+import copy
+import subprocess
+from collections import Counter
+
+from fatcat_openapi_client import ApiClient, Editgroup
+from fatcat_openapi_client.rest import ApiException
+from fatcat_tools.transforms import entity_from_dict, entity_to_dict
+
+
+class EntityCleaner:
+ """
+ API for individual jobs:
+
+ # record iterators sees
+ push_record(record)
+ finish()
+
+ # provided helpers
+ self.api
+ self.get_editgroup_id()
+ counts({'lines', 'skip', 'merged', 'updated'})
+
+ # implemented per-task
+ try_merge(idents, primary=None) -> int (entities updated)
+
+ This class is pretty similar to EntityImporter, but isn't subclassed.
+ """
+
+ def __init__(self, api, entity_type, **kwargs):
+
+ eg_extra = kwargs.get('editgroup_extra', dict())
+ eg_extra['git_rev'] = eg_extra.get('git_rev',
+ subprocess.check_output(["git", "describe", "--always"]).strip()).decode('utf-8')
+ eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.EntityCleaner')
+
+ self.api = api
+ self.entity_type = entity_type
+ self.dry_run_mode = kwargs.get('dry_run_mode', True)
+ self.edit_batch_size = kwargs.get('edit_batch_size', 50)
+ self.editgroup_description = kwargs.get('editgroup_description')
+ self.editgroup_extra = eg_extra
+ self.reset()
+ self.ac = ApiClient()
+
+ if self.dry_run_mode:
+ print("Running in dry-run mode!")
+
+ def reset(self):
+ self.counts = Counter({'lines': 0, 'cleaned': 0, 'updated': 0})
+ self._edit_count = 0
+ self._editgroup_id = None
+ self._entity_queue = []
+ self._idents_inflight = []
+
+ def push_record(self, record):
+ """
+ Intended to be called by "pusher" class (which could be pulling from
+ JSON file, Kafka, whatever).
+
+ Input is expected to be an entity in JSON-like dict form.
+
+ Returns nothing.
+ """
+ self.counts['lines'] += 1
+ if (not record):
+ self.counts['skip-null'] += 1
+ return
+
+ entity = entity_from_dict(record, self.entity_type, api_client=self.ac)
+
+ if entity.state != 'active':
+ self.counts['skip-inactive'] += 1
+ return
+
+ cleaned = self.clean_entity(copy.deepcopy(entity))
+ if entity == cleaned:
+ self.counts['skip-clean'] += 1
+ return
+ else:
+ self.counts['cleaned'] += 1
+
+ if self.dry_run_mode:
+ entity_dict = entity_to_dict(entity, api_client=self.ac)
+ print(json.dumps(entity_dict))
+ return
+
+ if entity.ident in self._idents_inflight:
+ raise ValueError("Entity already part of in-process update: {}".format(entity.ident))
+
+ updated = self.try_update(cleaned)
+ if updated:
+ self.counts['updated'] += updated
+ self._edit_count += updated
+ self._idents.inflight.append(entity.ident)
+
+ if self._edit_count >= self.edit_batch_size:
+ self.api.accept_editgroup(self._editgroup_id)
+ self._editgroup_id = None
+ self._edit_count = 0
+ self._idents_inflight = []
+ return
+
+ def clean_entity(self, entity):
+ """
+ Mutates entity in-place and returns it
+ """
+ # implementations should fill this in
+ raise NotImplementedError
+
+ def try_update(self, entity):
+ """
+ Returns edit count (number of entities updated).
+
+ If >= 1, does not need to update self.counts. If no entities updated,
+ do need to update counts internally.
+ """
+ # implementations should fill this in
+ raise NotImplementedError
+
+ def finish(self):
+ if self._edit_count > 0:
+ self.api.accept_editgroup(self._editgroup_id)
+ self._editgroup_id = None
+ self._edit_count = 0
+ self._idents_inflight = []
+
+ return self.counts
+
+ def get_editgroup_id(self):
+
+ if not self._editgroup_id:
+ eg = self.api.create_editgroup(
+ Editgroup(
+ description=self.editgroup_description,
+ extra=self.editgroup_extra))
+ self._editgroup_id = eg.editgroup_id
+
+ return self._editgroup_id
diff --git a/python/fatcat_tools/cleanups/files.py b/python/fatcat_tools/cleanups/files.py
new file mode 100644
index 00000000..c2733ba0
--- /dev/null
+++ b/python/fatcat_tools/cleanups/files.py
@@ -0,0 +1,74 @@
+
+from fatcat_openapi_client.rest import ApiException
+from fatcat_openapi_client.models import FileEntity
+from fatcat_tools.transforms import entity_to_dict, entity_from_json
+
+from .common import EntityCleaner
+
+
+class FileCleaner(EntityCleaner):
+ """
+ File fixups!
+ """
+
+ def __init__(self, api, **kwargs):
+
+ eg_desc = kwargs.pop('editgroup_description',
+ "Automated cleanup of file entities (eg, remove bad URLs)")
+ eg_extra = kwargs.pop('editgroup_extra', dict())
+ eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.FileCleaner')
+ super().__init__(api,
+ entity_type=FileEntity,
+ editgroup_description=eg_desc,
+ editgroup_extra=eg_extra,
+ **kwargs)
+
+ def clean_entity(self, entity):
+ """
+ TODO: mimetype is bogus like (???) => clean mimetype
+ """
+
+ # URL has ://web.archive.org/web/None/ link => delete URL
+ entity.urls = [u for u in entity.urls if not '://web.archive.org/web/None/' in u.url]
+
+ # URL has ://archive.org/ link with rel=repository => rel=archive
+ for u in entity.urls:
+ if '://archive.org/' in u.url and u.rel == 'repository':
+ u.rel = 'archive'
+
+ # URL has short wayback date ("2017") and another url with that as prefix => delete URL
+ stub_wayback_urls = []
+ full_wayback_urls = []
+ for u in entity.urls:
+ if '://web.archive.org/web/' in u.url:
+ if len(u.url.split('/')[4]) <= 8:
+ stub_wayback_urls.append(u.url)
+ else:
+ full_wayback_urls.append('/'.join(u.url.split('/')[5:]))
+ for stub in stub_wayback_urls:
+ target = '/'.join(stub.split('/')[5:])
+ if target in full_wayback_urls:
+ entity.urls = [u for u in entity.urls if u.url != stub]
+
+ return entity
+
+ def try_update(self, entity):
+
+ try:
+ existing = self.api.get_file(entity.ident)
+ except ApiException as err:
+ if err.status != 404:
+ raise err
+ self.counts['skip-not-found'] += 1
+ return 0
+
+ if existing.state != 'active':
+ self.counts['skip-existing-inactive'] += 1
+ return 0
+ if existing.revision != entity.revision:
+ self.counts['skip-revision'] += 1
+ return 0
+
+ self.update_file(self.get_editgroup_id(), entity.ident, entity)
+ return 1
+