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import sys
import json
import base64
import sqlite3
import itertools
import fatcat_client
from .common import EntityImporter, clean, make_rel_url
def b32_hex(s):
s = s.strip().split()[0].lower()
if s.startswith("sha1:"):
s = s[5:]
if len(s) != 32:
return s
return base64.b16encode(base64.b32decode(s.upper())).lower().decode('utf-8')
ARABESQUE_MATCH_WHERE_CLAUSE='WHERE hit = 1 AND identifier IS NOT NULL'
class ArabesqueMatchImporter(EntityImporter):
"""
Importer for arabesque crawl report .sqlite files, which contain
file/identifier matches based on URL/identifier seedlists.
Uses a SQL query to iterate through table looking for rows with:
- GROBID status 200
- known SHA-1 (base32 format)
- known timestamp
Looks up release (by identifier) and file (by SHA-1). If no release exists,
bail.
If no file exists, create one from metadata (using both direct and wayback
URLs), link to release, and insert.
If file exists, optionally update it:
- if no release match, match to the release
- if new URL not included, add it (and wayback)
Config options:
- default URL rel
- crawl id (for editgroup metadata)
- identifier type
TODO:
- a mode to insert bare files even if identifier not known?
"""
def __init__(self, api, extid_type, require_grobid=True, **kwargs):
eg_desc = kwargs.get('editgroup_description',
"Match web crawl files to releases based on identifier/URL seedlist")
eg_extra = kwargs.get('editgroup_extra', dict())
eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.ArabesqueMatchImporter')
if kwargs.get('crawl_id'):
eg_extra['crawl_id'] = eg_extra.get('crawl_id')
super().__init__(api,
editgroup_description=eg_desc,
editgroup_extra=eg_extra,
**kwargs)
assert extid_type in ('doi', 'pmcid', 'pmid')
self.extid_type = extid_type
self.default_link_rel = kwargs.get("default_link_rel", "web")
self.default_mime = kwargs.get("default_mime", None)
self.do_updates = kwargs.get("do_updates", False)
self.require_grobid = require_grobid
if self.require_grobid:
print("Requiring GROBID status == 200")
else:
print("NOT checking GROBID status column")
def want(self, row):
if self.require_grobid and not row['postproc_status'] == "200":
return False
if (row['hit'] == True
and row['final_sha1']
and row['final_timestamp'] and row['final_timestamp'] != "-"
and row['final_mimetype']
and row['hit'] == True
and row['identifier']):
return True
else:
return False
def parse_record(self, row):
extid = row['identifier'].strip()
# check/cleanup DOI
if self.extid_type == 'doi':
self.extid_type.replace('http://doi.org/', '')
self.extid_type.replace('https://doi.org/', '')
if not extid.startswith('10.'):
self.counts['skip-bad-doi']
return None
# lookup extid
try:
re = self.api.lookup_release(**{self.extid_type: extid})
except fatcat_client.rest.ApiException as err:
if err.status != 404:
raise err
# bail on 404 (release not in DB)
self.counts['skip-extid-not-found'] += 1
return None
url = make_rel_url(row['final_url'], self.default_link_rel)
if not url:
self.counts['skip-url'] += 1
return None
wayback = "https://web.archive.org/web/{}/{}".format(
row['final_timestamp'],
row['final_url'])
urls = [url, ("webarchive", wayback)]
urls = [fatcat_client.FileEntityUrls(rel=rel, url=url) for (rel, url) in urls]
fe = fatcat_client.FileEntity(
sha1=b32_hex(row['final_sha1']),
mimetype=row['final_mimetype'],
release_ids=[re.ident],
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
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['update-disabled'] += 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
self.api.update_file(existing.ident, existing, editgroup_id=self.get_editgroup_id())
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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