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import sys
import json
import sqlite3
import itertools
import fatcat_openapi_client
from fatcat_tools.normal import *
from .common import EntityImporter, make_rel_url, SANE_MAX_RELEASES, SANE_MAX_URLS
class ShadowLibraryImporter(EntityImporter):
"""
Importer for shadow library files (matched to releases)
Input format is JSON with keys:
- shadow
- shadow_corpus (string slug)
- shadow_id (string)
- doi
- pmid
- isbn13
- file_meta
- sha1hex
- sha256hex
- md5hex
- size_bytes
- mimetype
- cdx (may be null)
- url
- datetime
"""
def __init__(self, api, **kwargs):
eg_desc = kwargs.pop('editgroup_description', None) or "Import of 'Shadow Library' file/release matches"
eg_extra = kwargs.pop('editgroup_extra', dict())
eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.ShadowLibraryImporter')
super().__init__(api,
editgroup_description=eg_desc,
editgroup_extra=eg_extra,
**kwargs)
self.default_link_rel = kwargs.get("default_link_rel", "web")
def want(self, raw_record):
"""
Only want to import records with complete file-level metadata
"""
fm = raw_record['file_meta']
if not (fm['mimetype'] and fm['md5hex'] and fm['sha256hex'] and fm['size_bytes']):
self.counts['skip-file-meta-incomplete'] += 1
return False
if fm['mimetype'] != 'application/pdf':
self.counts['skip-not-pdf'] += 1
return False
return True
def parse_record(self, obj):
"""
We do the release lookup in this method. Try DOI, then PMID, last ISBN13.
"""
shadow_corpus = obj['shadow']['shadow_corpus']
assert shadow_corpus == shadow_corpus.strip().lower()
doi = clean_doi(obj['shadow'].get('doi'))
pmid = clean_pmid(obj['shadow'].get('pmid'))
isbn13 = clean_isbn13(obj['shadow'].get('isbn13'))
shadow_id = obj['shadow'].get('shadow_id').strip()
assert shadow_id
extra = { '{}_id'.format(shadow_corpus): shadow_id }
for (ext_type, ext_id) in [('doi', doi), ('pmid', pmid), ('isbn13', isbn13)]:
if not ext_id:
continue
extra['{}_{}'.format(shadow_corpus, ext_type)] = ext_id
# lookup release via several idents
re = None
for (ext_type, ext_id) in [('doi', doi), ('pmid', pmid), ('isbn13', isbn13)]:
if not ext_id:
continue
try:
re = self.api.lookup_release(**{ext_type: ext_id})
except fatcat_openapi_client.rest.ApiException as err:
if err.status not in (404, 400):
raise err
re = None
if re:
break
if not re:
self.counts['skip-release-not-found'] += 1
return None
release_ids = [re.ident,]
# parse single CDX into URLs (if exists)
urls = []
if obj.get('cdx'):
url = make_rel_url(obj['cdx']['url'], default_link_rel=self.default_link_rel)
if url != None:
urls.append(url)
wayback = "https://web.archive.org/web/{}/{}".format(
obj['cdx']['datetime'],
obj['cdx']['url'])
urls.append(("webarchive", wayback))
urls = [fatcat_openapi_client.FileUrl(rel=rel, url=url) for (rel, url) in urls]
fe = fatcat_openapi_client.FileEntity(
md5=obj['file_meta']['md5hex'],
sha1=obj['file_meta']['sha1hex'],
sha256=obj['file_meta']['sha256hex'],
size=int(obj['file_meta']['size_bytes']),
mimetype=obj['file_meta']['mimetype'] or None,
release_ids=release_ids,
urls=urls,
extra=dict(shadows=extra),
)
return fe
def try_update(self, fe):
# lookup sha1, or create new entity
existing = None
try:
existing = self.api.lookup_file(sha1=fe.sha1)
except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
if not existing:
return True
if not existing.extra:
existing.extra = {}
if existing.extra.get('shadows') and list(fe.extra['shadows'].keys())[0] in existing.extra['shadows']:
# already imported from this shadow library; skip
self.counts['exists'] += 1
return False
# check for edit conflicts
if existing.ident in [e.ident for e in self._edits_inflight]:
self.counts['skip-update-inflight'] += 1
return False
if fe.sha1 in [e.sha1 for e in self._edits_inflight]:
raise Exception("Inflight insert; shouldn't happen")
# minimum viable "existing" URL cleanup to fix dupes and broken links:
# remove 'None' wayback URLs, and set archive.org rel 'archive'
existing.urls = [u for u in existing.urls if not ('://web.archive.org/web/None/' in u.url)]
for i in range(len(existing.urls)):
u = existing.urls[i]
if u.rel == 'repository' and '://archive.org/download/' in u.url:
existing.urls[i].rel = 'archive'
if u.rel == 'social':
u.rel = 'academicsocial'
# new wayback URLs, could replace bad old short wayback URLs (from arabesque bug)
new_wb_urls = [u.url for u in fe.urls]
new_short_wb_urls = ['https://web.archive.org/web/{}/{}'.format(
u.split('/')[4][:12], '/'.join(u.split('/')[5:])) for u in new_wb_urls]
existing.urls = [u for u in existing.urls if not u.url in new_short_wb_urls]
# merge the existing into this one and update
merged_urls = {}
for u in fe.urls + existing.urls:
merged_urls[u.url] = u
existing.urls = list(merged_urls.values())
if not existing.extra.get('shadows'):
existing.extra['shadows'] = fe.extra['shadows']
else:
existing.extra['shadows'].update(fe.extra['shadows'])
# do these "plus ones" because we really want to do these updates when possible
if len(existing.urls) > SANE_MAX_URLS + 1:
self.counts['skip-update-too-many-url'] += 1
return None
existing.release_ids = list(set(fe.release_ids + existing.release_ids))
if len(existing.release_ids) > SANE_MAX_RELEASES + 1:
self.counts['skip-update-too-many-releases'] += 1
return None
existing.mimetype = existing.mimetype or fe.mimetype
existing.size = existing.size or fe.size
existing.md5 = existing.md5 or fe.md5
existing.sha1 = existing.sha1 or fe.sha1
existing.sha256 = existing.sha256 or fe.sha256
edit = self.api.update_file(self.get_editgroup_id(), existing.ident, existing)
# add sha1 to non-entity edit row, so we can do more aggressive
# group-level de-dupe
edit.sha1 = existing.sha1
self._edits_inflight.append(edit)
self.counts['update'] += 1
return False
def insert_batch(self, batch):
self.api.create_file_auto_batch(fatcat_openapi_client.FileAutoBatch(
editgroup=fatcat_openapi_client.Editgroup(
description=self.editgroup_description,
extra=self.editgroup_extra),
entity_list=batch))
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