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import sys
import json
import sqlite3
import itertools
import fatcat_client
from .common import EntityImporter, clean
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
- 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.get('editgroup_description',
"Import of large-scale file-to-release match results. Source of metadata varies.")
eg_extra = kwargs.get('editgroup_extra', dict())
eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.MatchedImporter')
super().__init__(api,
editgroup_description=eg_desc,
editgroup_extra=eg_extra)
self.default_link_rel = kwargs.get("default_link_rel", "web")
self.default_mime = kwargs.get("default_mime", None)
def make_url(self, raw):
rel = self.default_link_rel
# TODO: this is where we could map specific domains to rel types,
# and also filter out bad domains, invalid URLs, etc
if "//archive.org/" in raw or "//arxiv.org/" in raw:
# TODO: special-case the arxiv.org bulk mirror?
rel = "repository"
elif "//web.archive.org/" in raw or "//archive.is/" in raw:
rel = "webarchive"
return (rel, raw)
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:
try:
re = self.api.lookup_release(doi=doi)
except fatcat_client.rest.ApiException as err:
if err.status != 404:
raise err
re = None
if re is None:
print("DOI not found: {}".format(doi))
else:
re_list.add(re.ident)
release_ids = list(re_list)
if len(release_ids) == 0:
return None
# parse URLs and CDX
urls = set()
for url in obj.get('url', []):
url = self.make_url(url)
if url != None:
urls.add(url)
for cdx in obj.get('cdx', []):
original = cdx['url']
wayback = "https://web.archive.org/web/{}/{}".format(
cdx['dt'],
original)
urls.add(("webarchive", wayback))
url = self.make_url(original)
if url != None:
urls.add(url)
urls = [fatcat_client.FileEntityUrls(rel, url) for (rel, url) in urls]
if len(urls) == 0:
return None
size = obj.get('size')
if size:
size = int(size)
fe = fatcat_client.FileEntity(
md5=obj.get('md5'),
sha1=obj['sha1'],
sha256=obj.get('sha256'),
size=size,
mimetype=obj.get('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_client.rest.ApiException as err:
if err.status != 404:
raise err
if not existing:
return True
fe.release_ids = list(set(fe.release_ids + existing.release_ids))
if set(fe.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
# 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_client.FileEntityUrls(rel=rel, url=url) for (rel, url) in existing.urls]
existing.release_ids = list(set(fe.release_ids + existing.release_ids))
existing.mimetype = existing.mimetype or fe.mimetype
existing.size = existing.size or fe.size
existing.md5 = existing.md5 or fe.md5
existing.sha256 = existing.sha256 or fe.sha256
self.api.update_file(existing.ident, existing, editgroup_id=self._get_editgroup())
self.counts['update'] += 1
return False
def insert_batch(self, batch):
self.api.create_file_batch(batch,
autoaccept=True,
description=self.editgroup_description,
extra=json.dumps(self.editgroup_extra))
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