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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, clean, make_rel_url, SANE_MAX_RELEASES, SANE_MAX_URLS
class MatchedImporter(EntityImporter):
"""
Importer for "file to crossref DOI" matches.
These matches are currently generated by Internet Archive hadoop jobs
written in scala (part of the 'sandcrawler' repo/project), but could be
generated by other parties as well.
Input format is JSON with keys:
- dois (list)
- sha1 (hex)
- md5 (hex)
- sha256 (hex)
- size (int)
- cdx (list of objects)
- dt (optional; if included creates wayback link)
- url
- mimetype
- urls (list of strings... or objects?)
Future handlings/extensions:
- core_id, wikidata_id, pmcid, pmid: not as lists
"""
def __init__(self, api, **kwargs):
eg_desc = kwargs.pop('editgroup_description',
"Import of large-scale file-to-release match results. Source of metadata varies.")
eg_extra = kwargs.pop('editgroup_extra', dict())
eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.MatchedImporter')
super().__init__(api,
editgroup_description=eg_desc,
editgroup_extra=eg_extra,
**kwargs)
self.default_link_rel = kwargs.get("default_link_rel", "web")
self.default_mimetype = kwargs.get("default_mimetype", None)
def want(self, raw_record):
return True
def parse_record(self, obj):
dois = [d.lower() for d in obj.get('dois', [])]
# lookup dois
re_list = set()
for doi in dois:
doi = clean_doi(doi)
if not doi:
self.counts['skip-bad-doi'] += 1
return None
try:
re = self.api.lookup_release(doi=doi)
except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
re = None
if re is None:
#print("DOI not found: {}".format(doi))
pass
else:
re_list.add(re.ident)
# look up other external ids
for extid_type in ('arxiv', 'pmid', 'pmcid', 'jstor', 'wikidata_qid', 'core', 'isbn13', 'ark'):
extid = obj.get(extid_type)
if extid:
try:
re = self.api.lookup_release(**{extid_type: extid})
except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
re = None
if re is None:
pass
else:
re_list.add(re.ident)
release_ids = list(re_list)
if len(release_ids) == 0:
self.counts['skip-no-releases'] += 1
return None
if len(release_ids) > SANE_MAX_RELEASES:
self.counts['skip-too-many-releases'] += 1
return None
# parse URLs and CDX
urls = set()
for url in obj.get('urls', []):
url = make_rel_url(url, default_link_rel=self.default_link_rel)
if url != None:
urls.add(url)
for cdx in obj.get('cdx', []):
original = cdx['url']
if cdx.get('dt'):
wayback = "https://web.archive.org/web/{}/{}".format(
cdx['dt'],
original)
urls.add(("webarchive", wayback))
url = make_rel_url(original, default_link_rel=self.default_link_rel)
if url != None:
urls.add(url)
urls = [fatcat_openapi_client.FileUrl(rel=rel, url=url) for (rel, url) in urls]
if len(urls) == 0:
self.counts['skip-no-urls'] += 1
return None
if len(urls) > SANE_MAX_URLS:
self.counts['skip-too-many-urls'] += 1
return None
size = obj.get('size')
if size:
size = int(size)
mimetype = obj.get('mimetype', self.default_mimetype)
if not mimetype and urls:
if urls[0].url.endswith('.pdf'):
mimetype = 'application/pdf'
fe = fatcat_openapi_client.FileEntity(
md5=obj.get('md5'),
sha1=obj['sha1'],
sha256=obj.get('sha256'),
size=size,
mimetype=mimetype,
release_ids=release_ids,
urls=urls,
)
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
combined_release_ids = list(set(fe.release_ids + existing.release_ids))
if set(combined_release_ids) == set(existing.release_ids) and len(existing.urls) > 0:
# no new release matches *and* there are already existing URLs
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
# 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'
# special case: if importing *new* from archive.org arxiv collections,
# blow away any existing release_id mappings; this is a direct arxiv_id
# map. This *should* be safe to run in all matched imports.
is_arxiv = False
for u in fe.urls:
if 'archive.org/download/arxiv' in u.url.lower():
is_arxiv = True
break
if is_arxiv and fe.release_ids:
existing.release_ids = fe.release_ids
# merge the existing into this one and update
existing.urls = list(set([(u.rel, u.url) for u in fe.urls + existing.urls]))
existing.urls = [fatcat_openapi_client.FileUrl(rel=rel, url=url) for (rel, url) in existing.urls]
if len(existing.urls) > SANE_MAX_URLS:
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:
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)
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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