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import sys
import json
import base64
import itertools
import fatcat_openapi_client
from .common import EntityImporter, clean, make_rel_url, SANE_MAX_RELEASES, SANE_MAX_URLS, b32_hex
class IngestFileResultImporter(EntityImporter):
def __init__(self, api, require_grobid=True, **kwargs):
eg_desc = kwargs.pop('editgroup_description', None) or "Files crawled from web using sandcrawler ingest tool"
eg_extra = kwargs.pop('editgroup_extra', dict())
eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.IngestFileResultImporter')
kwargs['do_updates'] = kwargs.get("do_updates", False)
super().__init__(api,
editgroup_description=eg_desc,
editgroup_extra=eg_extra,
**kwargs)
self.use_glutton_match = False
self.default_link_rel = kwargs.get("default_link_rel", "web")
assert self.default_link_rel
self.require_grobid = require_grobid
if self.require_grobid:
print("Requiring GROBID status == 200")
else:
print("NOT checking GROBID success")
self.ingest_request_source_whitelist = [
'fatcat-changelog',
'fatcat-ingest-container',
'fatcat-ingest',
'arabesque',
'mag-corpus',
'mag',
'unpaywall-corpus',
'unpaywall',
's2-corpus',
's2',
]
if kwargs.get('skip_source_whitelist', False):
self.ingest_request_source_whitelist = []
def want(self, row):
"""
Logic here probably needs work (TODO):
- Direct ingests via DOI from fatcat-changelog should probably go
through regardless of GROBID status
- We should filter/block things like single-page PDFs here
- public/anonymous submissions could require successful biblio-glutton
match, or some other sanity check on the fatcat side (eg, fuzzy title
match)
- handle the case of release_stage not being 'published'; if pre-print,
potentially create a new release.
The current logic is intentionally conservative as a first step.
"""
if row.get('hit') != True:
self.counts['skip-hit'] += 1
return False
source = row['request'].get('ingest_request_source')
if not source:
self.counts['skip-ingest_request_source'] += 1
return False
if self.ingest_request_source_whitelist and source not in self.ingest_request_source_whitelist:
self.counts['skip-ingest_request_source'] += 1
return False
if source.startswith('arabesque'):
if row['request'].get('link_source') not in ('arxiv', 'pmc', 'unpaywall', 'doi', 'mag', 's2'):
self.counts['skip-arabesque-source'] += 1
return False
if source.startswith('savepapernow'):
# never process async savepapernow requests
self.counts['skip-savepapernow'] += 1
return False
if not row.get('file_meta'):
self.counts['skip-file-meta'] += 1
return False
if self.require_grobid and row.get('grobid', {}).get('status_code') != 200:
self.counts['skip-grobid'] += 1
return False
return True
def parse_record(self, row):
request = row['request']
fatcat = request.get('fatcat')
file_meta = row['file_meta']
# identify release by fatcat ident, or extid lookup, or biblio-glutton match
release_ident = None
if fatcat and fatcat.get('release_ident'):
release_ident = fatcat.get('release_ident')
elif request.get('ext_ids'):
# if no fatcat ident, try extids
for extid_type in ('doi', 'pmid', 'pmcid', 'arxiv'):
extid = request['ext_ids'].get(extid_type)
if not extid:
continue
try:
release = self.api.lookup_release(**{extid_type: extid})
except fatcat_openapi_client.rest.ApiException as err:
if err.status == 404:
continue
elif err.status == 400:
self.counts['warn-extid-invalid'] += 1
continue
raise err
release_ident = release.ident
break
if self.use_glutton_match and not release_ident and row.get('grobid'):
# try biblio-glutton extracted hit
if row['grobid'].get('fatcat_release'):
release_ident = row['grobid']['fatcat_release'].split('_')[-1]
self.counts['glutton-match'] += 1
if not release_ident:
self.counts['skip-release-not-found'] += 1
return None
terminal = row.get('terminal')
if not terminal:
# support old cdx-only ingest results
cdx = row.get('cdx')
if not cdx:
# TODO: support archive.org hits?
self.counts['skip-no-terminal'] += 1
return None
else:
terminal = {
'terminal_url': cdx['url'],
'terminal_dt': cdx['datetime'],
'terminal_status_code': cdx.get('status_code') or cdx.get('http_status'),
}
# work around old schema
if not 'terminal_url' in terminal:
terminal['terminal_url'] = terminal['url']
if not 'terminal_dt' in terminal:
terminal['terminal_dt'] = terminal['dt']
assert len(terminal['terminal_dt']) == 14
default_rel = self.default_link_rel
if request.get('link_source') == 'doi':
default_rel = 'publisher'
default_rel = request.get('rel', default_rel)
url = make_rel_url(terminal['terminal_url'], default_rel)
if not url:
self.counts['skip-url'] += 1
return None
wayback = "https://web.archive.org/web/{}/{}".format(
terminal['terminal_dt'],
terminal['terminal_url'])
urls = [url, ("webarchive", wayback)]
urls = [fatcat_openapi_client.FileUrl(rel=rel, url=url) for (rel, url) in urls]
fe = fatcat_openapi_client.FileEntity(
md5=file_meta['md5hex'],
sha1=file_meta['sha1hex'],
sha256=file_meta['sha256hex'],
size=file_meta['size_bytes'],
mimetype=file_meta['mimetype'],
release_ids=[release_ident],
urls=urls,
)
if request.get('edit_extra'):
fe.edit_extra = request['edit_extra']
else:
fe.edit_extra = dict()
if request.get('ingest_request_source'):
fe.edit_extra['ingest_request_source'] = request['ingest_request_source']
if request.get('link_source') and request.get('link_source_id'):
fe.edit_extra['link_source'] = request['link_source']
fe.edit_extra['link_source_id'] = request['link_source_id']
if not fe.edit_extra:
fe.edit_extra = None
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
# check for existing edits-in-progress with same file hash
for other in self._entity_queue:
if other.sha1 == fe.sha1:
self.counts['skip-in-queue'] += 1
return False
if not existing:
return True
# NOTE: the following checks all assume there is an existing item
if (fe.release_ids[0] in existing.release_ids) and existing.urls:
# TODO: could still, in theory update with the new URL?
self.counts['exists'] += 1
return False
if not self.do_updates:
self.counts['skip-update-disabled'] += 1
return False
# TODO: for now, never update
self.counts['skip-update-disabled'] += 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))
class SavePaperNowFileImporter(IngestFileResultImporter):
"""
This worker ingests from the same feed as IngestFileResultImporter, but
only imports files from anonymous save-paper-now requests, and "submits"
them for further human review (as opposed to accepting by default).
"""
def __init__(self, api, submit_mode=True, **kwargs):
eg_desc = kwargs.pop('editgroup_description', None) or "Files crawled after a public 'Save Paper Now' request"
eg_extra = kwargs.pop('editgroup_extra', dict())
eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.IngestFileSavePaperNow')
kwargs['submit_mode'] = submit_mode
kwargs['require_grobid'] = True
kwargs['do_updates'] = False
super().__init__(api,
editgroup_description=eg_desc,
editgroup_extra=eg_extra,
**kwargs)
def want(self, row):
source = row['request'].get('ingest_request_source')
if not source:
self.counts['skip-ingest_request_source'] += 1
return False
if not source.startswith('savepapernow'):
self.counts['skip-not-savepapernow'] += 1
return False
if row.get('hit') != True:
self.counts['skip-hit'] += 1
return False
if not row.get('file_meta'):
self.counts['skip-file-meta'] += 1
return False
if self.require_grobid and row.get('grobid', {}).get('status_code') != 200:
self.counts['skip-grobid'] += 1
return False
return True
def insert_batch(self, batch):
"""
Usually running in submit_mode, so we can't use auto_batch method
"""
if self.submit_mode:
eg = self.api.create_editgroup(fatcat_openapi_client.Editgroup(
description=self.editgroup_description,
extra=self.editgroup_extra))
for fe in batch:
self.api.create_file(eg.editgroup_id, fe)
self.api.update_editgroup(eg.editgroup_id, eg, submit=True)
else:
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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