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authorBryan Newbold <bnewbold@robocracy.org>2018-11-12 23:18:56 -0800
committerBryan Newbold <bnewbold@robocracy.org>2018-11-12 23:18:56 -0800
commitb03bfc8f3fd84141738f775b273a99850d78e1ff (patch)
tree64858e474fa38aa015f06f5e15b851dcc85da421 /python/fatcat_tools/grobid_metadata_importer.py
parent055c464deea8cdaccf3ed384995d4409b0f51409 (diff)
downloadfatcat-b03bfc8f3fd84141738f775b273a99850d78e1ff.tar.gz
fatcat-b03bfc8f3fd84141738f775b273a99850d78e1ff.zip
refactor python modules
Diffstat (limited to 'python/fatcat_tools/grobid_metadata_importer.py')
-rwxr-xr-xpython/fatcat_tools/grobid_metadata_importer.py168
1 files changed, 168 insertions, 0 deletions
diff --git a/python/fatcat_tools/grobid_metadata_importer.py b/python/fatcat_tools/grobid_metadata_importer.py
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+++ b/python/fatcat_tools/grobid_metadata_importer.py
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+#!/usr/bin/env python3
+
+import sys
+import json
+import base64
+import datetime
+import fatcat_client
+from fatcat.importer_common import FatcatImporter
+
+MAX_ABSTRACT_BYTES=4096
+
+
+class FatcatGrobidMetadataImporter(FatcatImporter):
+
+ def __init__(self, host_url, default_link_rel="web"):
+ super().__init__(host_url)
+ self.default_link_rel = default_link_rel
+
+ def parse_grobid_json(self, obj):
+
+ if not obj.get('title'):
+ return None
+
+ release = dict()
+ extra = dict()
+
+ if obj.get('abstract') and len(obj.get('abstract')) < MAX_ABSTRACT_BYTES:
+ abobj = dict(
+ mimetype="text/plain",
+ language=None,
+ content=obj.get('abstract').strip())
+ abstracts = [abobj]
+ else:
+ abstracts = None
+
+ contribs = []
+ for i, a in enumerate(obj.get('authors', [])):
+ c = dict(raw_name=a['name'], role="author")
+ contribs.append(fatcat_client.ReleaseContrib(
+ index=i,
+ raw_name=a['name'],
+ role="author",
+ extra=None))
+
+ refs = []
+ for raw in obj.get('citations', []):
+ cite_extra = dict()
+ ref = dict()
+ ref['key'] = raw.get('id')
+ if raw.get('title'):
+ ref['title'] = raw['title'].strip()
+ if raw.get('date'):
+ try:
+ year = int(raw['date'].strip()[:4])
+ ref['year'] = year
+ except:
+ pass
+ for key in ('volume', 'url', 'issue', 'publisher'):
+ if raw.get(key):
+ cite_extra[key] = raw[key].strip()
+ if raw.get('authors'):
+ cite_extra['authors'] = [a['name'] for a in raw['authors']]
+ if cite_extra:
+ cite_extra = dict(grobid=cite_extra)
+ else:
+ cite_extra = None
+ ref['extra'] = cite_extra
+ refs.append(ref)
+
+ release_type = "journal-article"
+ release_date = None
+ if obj.get('date'):
+ # TODO: only returns year, ever? how to handle?
+ release_date = datetime.datetime(year=int(obj['date'][:4]), month=1, day=1)
+
+ if obj.get('doi'):
+ extra['doi'] = obj['doi']
+ if obj['journal'] and obj['journal'].get('name'):
+ extra['container_name'] = obj['journal']['name']
+
+ extra['is_longtail_oa'] = True
+
+ # TODO: ISSN/eISSN handling? or just journal name lookup?
+
+ if extra:
+ extra = dict(grobid=extra)
+ else:
+ extra = None
+
+ re = fatcat_client.ReleaseEntity(
+ title=obj['title'].strip(),
+ contribs=contribs,
+ refs=refs,
+ publisher=obj['journal'].get('publisher'),
+ volume=obj['journal'].get('volume'),
+ issue=obj['journal'].get('issue'),
+ abstracts=abstracts,
+ extra=extra)
+ return re
+
+ # TODO: make this a common function somewhere
+ 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_file_metadata(self, sha1_key, cdx, mimetype, file_size):
+
+ sha1 = base64.b16encode(base64.b32decode(sha1_key.replace('sha1:', ''))).decode('ascii').lower()
+
+ # lookup existing SHA1, or create new entity
+ try:
+ existing_file = self.api.lookup_file(sha1=sha1)
+ except fatcat_client.rest.ApiException as err:
+ if err.status != 404:
+ raise err
+ existing_file = None
+
+ if existing_file:
+ # if file is already in here, presumably not actually long-tail
+ return None
+ fe = fatcat_client.FileEntity(
+ sha1=sha1,
+ size=int(file_size),
+ mimetype=mimetype,
+ releases=[],
+ urls=[],
+ )
+
+ # parse URLs and CDX
+ original = cdx['url']
+ wayback = "https://web.archive.org/web/{}/{}".format(
+ cdx['dt'],
+ original)
+ fe.urls.append(
+ fatcat_client.FileEntityUrls(url=wayback, rel="webarchive"))
+ original_url = self.make_url(original)
+ if original_url != None:
+ fe.urls.append(original_url)
+
+ return fe
+
+ def create_row(self, row, editgroup=None):
+ if not row:
+ return
+ fields = row.split('\t')
+ sha1_key = fields[0]
+ cdx = json.loads(fields[1])
+ mimetype = fields[2]
+ file_size = int(fields[3])
+ grobid_meta = json.loads(fields[4])
+ fe = self.parse_file_metadata(sha1_key, cdx, mimetype, file_size)
+ re = self.parse_grobid_json(grobid_meta)
+ if fe and re:
+ release_entity = self.api.create_release(re, editgroup=editgroup)
+ # release ident can't already be in release list because we just
+ # created it
+ fe.releases.append(release_entity.ident)
+ file_entity = self.api.create_file(fe, editgroup=editgroup)
+ self.insert_count = self.insert_count + 1
+
+ # NB: batch mode not implemented