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authorBryan Newbold <bnewbold@robocracy.org>2019-04-18 15:27:41 -0700
committerBryan Newbold <bnewbold@robocracy.org>2019-04-18 15:27:41 -0700
commitfb53198956843954a981dbbe83b4727b25ae6427 (patch)
treeab16fda4e3738b72b54596ecfd37ed52fb601cbf /python/fatcat_tools/importers/arabesque.py
parent873a167634167838568ad9303ff29673339a4641 (diff)
downloadfatcat-fb53198956843954a981dbbe83b4727b25ae6427.tar.gz
fatcat-fb53198956843954a981dbbe83b4727b25ae6427.zip
arabesque importer
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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))
+