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import sys
import json
import sqlite3
import itertools
import fatcat_client
from .common import FatcatImporter
#row = row.split('\t')
#assert len(row) == 2
#sha1 = row[0].replace('sha1:')
#sha1 = base64.b16encode(base64.b32decode(sha1)).lower()
#print(sha1)
#dois = [d.lower() for d in json.loads(row[1])]
class MatchedImporter(FatcatImporter):
"""
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)
self.skip_file_updates = kwargs.get("skip_file_updates", False)
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 fatcat_client.FileEntityUrls(url=raw, rel=rel)
def parse_matched_dict(self, obj):
sha1 = obj['sha1']
dois = [d.lower() for d in obj.get('dois', [])]
# lookup sha1, or create new entity
fe = None
if not self.skip_file_updates:
try:
fe = self.api.lookup_file(sha1=sha1)
except fatcat_client.rest.ApiException as err:
if err.status != 404:
raise err
if fe is None:
fe = fatcat_client.FileEntity(
sha1=sha1,
release_ids=[],
urls=[],
)
# 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)
if len(re_list) == 0:
return None
if fe.release_ids == set(re_list):
return None
re_list.update(fe.release_ids)
fe.release_ids = list(re_list)
# parse URLs and CDX
existing_urls = [feu.url for feu in fe.urls]
for url in obj.get('url', []):
if url not in existing_urls:
url = self.make_url(url)
if url != None:
fe.urls.append(url)
for cdx in obj.get('cdx', []):
original = cdx['url']
wayback = "https://web.archive.org/web/{}/{}".format(
cdx['dt'],
original)
if wayback not in existing_urls:
fe.urls.append(
fatcat_client.FileEntityUrls(url=wayback, rel="webarchive"))
if original not in existing_urls:
url = self.make_url(original)
if url != None:
fe.urls.append(url)
if obj.get('size') != None:
fe.size = int(obj['size'])
fe.sha256 = obj.get('sha256', fe.sha256)
fe.md5 = obj.get('md5', fe.sha256)
if obj.get('mimetype') is None:
if fe.mimetype is None:
fe.mimetype = self.default_mime
else:
fe.mimetype = obj.get('mimetype')
return fe
def create_row(self, row, editgroup_id=None):
obj = json.loads(row)
fe = self.parse_matched_dict(obj)
if fe is not None:
if fe.ident is None:
self.api.create_file(fe, editgroup_id=editgroup_id)
self.counts['insert'] += 1
else:
self.api.update_file(fe.ident, fe, editgroup_id=editgroup_id)
self.counts['update'] += 1
def create_batch(self, batch):
"""Reads and processes in batches (not API-call-per-line)"""
objects = [self.parse_matched_dict(json.loads(l))
for l in batch if l != None]
new_objects = [o for o in objects if o != None and o.ident == None]
update_objects = [o for o in objects if o != None and o.ident != None]
if len(update_objects):
update_eg = self._editgroup().editgroup_id
for obj in update_objects:
self.api.update_file(obj.ident, obj, editgroup_id=update_eg)
self.api.accept_editgroup(update_eg)
if len(new_objects) > 0:
self.api.create_file_batch(new_objects, autoaccept="true")
self.counts['update'] += len(update_objects)
self.counts['insert'] += len(new_objects)
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