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-rw-r--r--python/fatcat_tools/importers/__init__.py1
-rw-r--r--python/fatcat_tools/importers/datacite.py458
2 files changed, 459 insertions, 0 deletions
diff --git a/python/fatcat_tools/importers/__init__.py b/python/fatcat_tools/importers/__init__.py
index bb9c5b17..d936605f 100644
--- a/python/fatcat_tools/importers/__init__.py
+++ b/python/fatcat_tools/importers/__init__.py
@@ -14,6 +14,7 @@ To run an import you combine two classes; one each of:
from .common import EntityImporter, JsonLinePusher, LinePusher, CsvPusher, SqlitePusher, Bs4XmlFilePusher, Bs4XmlLargeFilePusher, Bs4XmlLinesPusher, Bs4XmlFileListPusher, KafkaJsonPusher, make_kafka_consumer, clean, is_cjk, LANG_MAP_MARC
from .crossref import CrossrefImporter, CROSSREF_TYPE_MAP, lookup_license_slug
+from .datacite import DataciteImporter
from .jalc import JalcImporter
from .jstor import JstorImporter
from .arxiv import ArxivRawImporter
diff --git a/python/fatcat_tools/importers/datacite.py b/python/fatcat_tools/importers/datacite.py
new file mode 100644
index 00000000..faa8e2be
--- /dev/null
+++ b/python/fatcat_tools/importers/datacite.py
@@ -0,0 +1,458 @@
+"""
+WIP: Importer for datacite.org data.
+
+Example doc at: https://gist.github.com/miku/5610a2d64e3fee82d16f5d3f3a295fc8
+"""
+
+from .common import EntityImporter
+import dateparser
+import datetime
+import fatcat_openapi_client
+import json
+import sys
+
+# https://guide.fatcat.wiki/entity_container.html#container_type-vocabulary
+CONTAINER_TYPE_MAP = {
+ 'Journal': 'journal',
+ 'Series': 'journal',
+ 'Book Series': 'book-series',
+}
+
+# TODO(martin): merge this with other maps, maybe.
+LICENSE_SLUG_MAP = {
+ "//creativecommons.org/licenses/by/2.0": "CC-BY",
+ "//creativecommons.org/licenses/by/2.0/uk/legalcode": "CC-BY",
+ "//creativecommons.org/licenses/by/3.0": "CC-BY",
+ "//creativecommons.org/licenses/by/3.0/us": "CC-BY",
+ "//creativecommons.org/licenses/by/4.0": "CC-BY",
+ "//creativecommons.org/licenses/by/4.0/deed.de": "CC-BY",
+ "//creativecommons.org/licenses/by/4.0/deed.en_US": "CC-BY",
+ "//creativecommons.org/licenses/by/4.0/legalcode": "CC-BY",
+ "//creativecommons.org/licenses/by-nc/2.0": "CC-BY-NC",
+ "//creativecommons.org/licenses/by-nc/3.0": "CC-BY-NC",
+ "//creativecommons.org/licenses/by-nc/4.0": "CC-BY-NC",
+ "//creativecommons.org/licenses/by-nc/4.0/legalcode": "CC-BY-NC",
+ "//creativecommons.org/licenses/by-nc-nd/3.0": "CC-BY-NC-ND",
+ "//creativecommons.org/licenses/by-nc-nd/3.0/gr": "CC-BY-NC-ND",
+ "//creativecommons.org/licenses/by-nc-nd/4.0": "CC-BY-NC-ND",
+ "//creativecommons.org/licenses/by-nc-nd/4.0": "CC-BY-ND",
+ "//creativecommons.org/licenses/by-nc-nd/4.0/legalcode": "CC-BY-ND",
+ "//creativecommons.org/licenses/by-nc-sa/4.0": "CC-BY-NC-SA",
+ "//creativecommons.org/licenses/by-nc-sa/4.0": "CC-BY-SA",
+ "//creativecommons.org/licenses/by-nd/4.0": "CC-BY-ND",
+ "//creativecommons.org/licenses/by-sa/3.0/de": "CC-BY-SA",
+ "//creativecommons.org/licenses/by-sa/3.0/gr": "CC-BY-SA",
+ "//creativecommons.org/licenses/by-sa/4.0": "CC-BY-SA",
+ "//creativecommons.org/licenses/by-sa/4.0/legalcode": "CC-BY-SA",
+ "//creativecommons.org/licenses/CC-BY/4.0": "CC-BY",
+ "//creativecommons.org/licenses/publicdomain/zero/1.0": "CC-0",
+ "//creativecommons.org/publicdomain/zero/1.0": "CC-0",
+ "//creativecommons.org/publicdomain/zero/1.0": "CC-0",
+ "//creativecommons.org/publicdomain/zero/1.0/legalcode": "CC-0",
+ "//opensource.org/licenses/MIT": "MIT",
+ "//www.elsevier.com/open-access/userlicense/1.0": "ELSEVIER-USER-1.0",
+ "//www.gnu.org/licenses/gpl-3.0.en.html": "GPLv3",
+ "//www.gnu.org/licenses/old-licenses/gpl-2.0.en.html": "GPLv2",
+ "//www.karger.com/Services/SiteLicenses": "KARGER",
+ "//www.opensource.org/licenses/Apache-2.0": "Apache-2.0",
+ "//www.opensource.org/licenses/BSD-3-Clause": "BSD-3-Clause",
+ "//www.opensource.org/licenses/EUPL-1.1": "EUPL-1.1", # redirects to EUPL-1.2
+ "//www.opensource.org/licenses/MIT": "MIT",
+ # "http://royalsocietypublishing.org/licence": "", # OA and "normal", https://royalsociety.org/journals/authors/licence-to-publish/
+ # "http://rsc.li/journals-terms-of-use": "RSC",
+ # "http://www.fu-berlin.de/sites/refubium/rechtliches/Nutzungsbedingungen": "", # 53 UrhG.
+ # "http://www.nrcresearchpress.com/page/about/CorporateTextAndDataMining": "",
+ # "http://www.springer.com/tdm": "",
+ # "https://cds.unistra.fr/vizier-org/licences_vizier.html": "", # Maybe try to "SPN" those: https://web.archive.org/web/*/https://cds.unistra.fr/vizier-org/licences_vizier.html
+ # "https://link.aps.org/licenses/aps-default-accepted-manuscript-license": "",
+ # "https://oparu.uni-ulm.de/xmlui/license_opod_v1": "",
+ # "https://publikationen.bibliothek.kit.edu/kitopen-lizenz": "",
+ # "https://rightsstatements.org/page/InC/1.0?language=en": "",
+ # "https://services.ceda.ac.uk/cedasite/register/info": "",
+ # "https://wdc.dlr.de/ndmc/userfiles/file/NDMC-Data_Sharing_Principles.pdf": "", # 404
+ # "https://www.cambridge.org/core/terms": "",
+ # "https://www.elsevier.com/tdm/userlicense/1.0",
+ # "info:eu-repo/semantics/closedAccess": "", # https://wiki.surfnet.nl/display/standards/info-eu-repo/#info-eu-repo-AccessRights
+ # "info:eu-repo/semantics/embargoedAccess": "",
+ # "info:eu-repo/semantics/openAccess": "",
+}
+
+class DataciteImporter(EntityImporter):
+ """
+ Importer for datacite records. TODO(martin): Do we need issn_map_file?
+ """
+
+ def __init__(self, api, issn_map_file, **kwargs):
+
+ eg_desc = kwargs.get('editgroup_description',
+ "Automated import of Datacite DOI metadata, harvested from REST API")
+ eg_extra = kwargs.get('editgroup_extra', dict())
+ eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.DataciteImporter')
+ super().__init__(api,
+ issn_map_file=issn_map_file,
+ editgroup_description=eg_desc,
+ editgroup_extra=eg_extra,
+ **kwargs)
+
+ self.create_containers = kwargs.get('create_containers', True)
+ self.read_issn_map_file(issn_map_file)
+
+ def parse_record(self, obj):
+ """
+ TODO(martin): Map datacite to RE.
+
+ WIP, notes:
+
+ * Many subjects, should they end up in extra?
+ * attributes.creators and attributes.contributors
+
+ $ jq '.attributes.creators[]?.nameType?' datacite.500k | sort | uniq -c | sort -nr
+ 3963663 "Personal"
+ 289795 null
+ 8892 "Organizational"
+
+ Shall we use issued, available?
+
+ {
+ "date": "2011-11-18",
+ "dateType": "Accepted"
+ },
+ {
+ "date": "2011-11-18",
+ "dateType": "Available"
+ },
+ {
+ "date": "2011-11-07",
+ "dateType": "Copyrighted"
+ },
+ {
+ "date": "2011-11-18",
+ "dateType": "Issued"
+ },
+ {
+ "date": "2011-11-07",
+ "dateType": "Issued"
+ }
+
+ TODO(martin): Quick analysis of dates and stages.
+ """
+
+ if 'attributes' not in obj:
+ return None
+
+ attributes = obj['attributes']
+
+ # > Contributors
+ #
+ # "attributes.creators[].contributorType": [
+ # "author"
+ # ],
+ # "attributes.creators[].nameIdentifiers[].nameIdentifierScheme": [
+ # "LCNA",
+ # "GND",
+ # "email",
+ # "NAF",
+ # "OSF",
+ # "RRID",
+ # "ORCID",
+ # "SCOPUS",
+ # "NRCPID",
+ # "schema.org",
+ # "GRID",
+ # "MGDS",
+ # "VIAF",
+ # "JACoW-ID"
+ # ],
+ #
+ # "https://orcid.org/0000-0002-9902-738X",
+ # "http://jacow.org/JACoW-00001280",
+ # "Wiebe_Peter",
+ # "https://osf.io/https://osf.io/kjfuy/",
+ # "http://www.viaf.org176549220",
+ # "2239",
+ # "Jeffries_Martin",
+ # "https://orcid.org/0000-0002-1493-6630",
+ # "0000-0002-6233-612X",
+ #
+ # "creators": [
+ # {
+ # "name": "Bögli, Hans",
+ # "nameType": "Personal",
+ # "givenName": "Hans",
+ # "familyName": "Bögli",
+ # "affiliation": []
+ # }
+ # ],
+
+ contribs = []
+
+ for i, c in enumerate(attributes['creators']):
+ if not c.get('nameType') == 'Personal':
+ continue
+ creator_id = None
+ for nid in c.get('nameIdentifiers', []):
+ if not nid.get('nameIdentifierScheme').lower() == "orcid":
+ continue
+ orcid = nid.get('nameIdentifier', '').replace('https://orcid.org/', '')
+ if not orcid:
+ continue
+ creator_id = self.lookup_orcid(orcid)
+ # If creator_id is None, should we create creators?
+ contribs.append(fatcat_openapi_client.ReleaseContrib(
+ creator_id=creator_id,
+ index=i,
+ raw_name=c.get('name'),
+ given_name=c.get('givenName'),
+ surname=c.get('familyName'),
+ ))
+
+ # > Title
+ #
+ # "attributes.titles[].titleType": [
+ # "AlternativeTitle",
+ # "Other",
+ # "Subtitle",
+ # null,
+ # "TranslatedTitle"
+ # ],
+ title, subtitle = None, None
+
+ for entry in attributes.get('titles', []):
+ if not title and 'titleType' not in entry:
+ title = entry.get('title').strip()
+ if entry.get('titleType') == 'Subtitle':
+ subtitle = entry.get('title').strip()
+
+ # > Dates
+ #
+ # "attributes.dates[].dateType": [
+ # "Accepted",
+ # "Available"
+ # "Collected",
+ # "Copyrighted",
+ # "Created",
+ # "Issued",
+ # "Submitted",
+ # "Updated",
+ # "Valid",
+ # ],
+ #
+ # Different documents have different dates defined. Choose the topmost
+ # available from prio list.
+ date_type_prio = (
+ 'Valid',
+ 'Issued',
+ 'Available',
+ 'Accepted',
+ 'Submitted',
+ 'Copyrighted',
+ 'Collected',
+ 'Created',
+ 'Updated',
+ )
+
+ release_year, release_date = None, None
+ for prio in date_type_prio:
+ dates = attributes.get('dates', []) or [] # Never be None.
+ for item in dates:
+ if not item.get('dateType') == prio:
+ continue
+ result = dateparser.parse(item.get('date'))
+ if result is None:
+ # Unparsable date.
+ continue
+ release_date = result
+ release_year = result.year
+ if 1000 < release_year < datetime.date.today().year + 5:
+ # Skip possibly bogus dates.
+ continue
+ break
+ else:
+ continue
+ break
+
+ # > Publisher
+ #
+ # A few NA values. A few bogus values.
+ #
+ publisher = attributes.get('publisher')
+
+ if publisher in ('(:unav)', 'Unknown', 'n.a.', '[s.n.]', '(:unap)'):
+ publisher = None
+ if publisher is not None and len(publisher) > 80:
+ # Arbitrary magic value, TODO(martin): better heuristic.
+ # Example: "ETH-Bibliothek Zürich, Bildarchiv / Fotograf: Feller,
+ # Elisabeth, Empfänger, Unbekannt, Fotograf / Fel_041033-RE / Unbekannt,
+ # Nutzungsrechte müssen durch den Nutzer abgeklärt werden",
+ # TODO(martin): log misses.
+ publisher = None
+
+ # > Container
+ #
+ # For the moment, only ISSN as container.
+ #
+ # "container": {
+ # "type": "Journal",
+ # "issue": "8",
+ # "title": "Angewandte Chemie International Edition",
+ # "volume": "57",
+ # "lastPage": "2080",
+ # "firstPage": "2077",
+ # "identifier": "14337851",
+ # "identifierType": "ISSN"
+ # },
+ #
+ # "attributes.container.type": [
+ # "DataRepository",
+ # "Journal",
+ # "Series",
+ # "Book Series"
+ # ],
+ #
+ # "attributes.container.identifierType": [
+ # "Handle",
+ # "ISBN",
+ # "LISSN",
+ # "DOI",
+ # "EISSN",
+ # "URL",
+ # "ISSN"
+ # ],
+
+ container_id = None
+ container = attributes.get('container', {}) or {}
+ if container.get('type') in CONTAINER_TYPE_MAP.keys():
+ container_type = CONTAINER_TYPE_MAP.get(container['type'])
+ if container.get('identifier') and container.get('identifierType') == 'ISSN':
+ issn = container.get('identifier')
+ if len(issn) == 8:
+ issn = issn[:4] + "-" + issn[4:]
+ issnl = self.issn2issnl(issn)
+ container_id = self.lookup_issnl(issnl)
+
+ if container_id is None and container.get('title'):
+ ce = fatcat_openapi_client.ContainerEntity(
+ issnl=issnl,
+ container_type=container_type,
+ name=container.get('title'),
+ )
+ ce_edit = self.create_container(ce)
+ container_id = ce_edit.ident
+ self._issnl_id_map[issnl] = container_id
+
+ # > License
+ #
+ # attributes.rightsList[].rightsUri
+ # attributes.rightsList[].rights
+ # attributes.rightsList[].lang
+ #
+
+ license_slug = None
+ license_extra = []
+ for l in attributes.get('rightsList', []):
+ slug = lookup_license_slug(l.get('rightsUri'))
+ if slug:
+ license_slug = slug
+ license_extra.append(l)
+
+ # > Release type.
+ #
+ # Datacite has some fine granular typing (e.g. "Supplementary
+ # Collection of Datasets", "Taxonomic treatment", "blog_entry", ...
+ #
+ # Additional, coarse: resourceTypeGeneral
+ #
+ # "attributes.types.resourceTypeGeneral": [
+ # "Image",
+ # "Dataset",
+ # "PhysicalObject",
+ # "Collection",
+ # "Text",
+ # "Sound",
+ # "InteractiveResource",
+ # "Event",
+ # "Software",
+ # "Other",
+ # "Workflow",
+ # "Audiovisual"
+ # ],
+
+ # > Extra information.
+ extra, extra_datacite = dict(), dict()
+ if license_extra:
+ extra_datacite['license'] = license_extra
+
+ if extra_datacite:
+ extra['datacite'] = extra_datacite
+
+ # https://guide.fatcat.wiki/entity_release.html
+ re = fatcat_openapi_client.ReleaseEntity(
+ work_id=None,
+ container_id=container_id,
+ release_type=None,
+ release_stage=None,
+ title=title, # attributes.titles, various titleType
+ subtitle=subtitle,
+ original_title=title, # AlternativeTitle?
+ release_year=release_year, # publicationYear
+ release_date=release_date, # date issues/available?
+ publisher=publisher, # attributes.publisher
+ ext_ids=fatcat_openapi_client.ReleaseExtIds(
+ doi=attributes.get('doi'), # attributes.doi,
+ # Can we add handle.net link?
+ ),
+ contribs=contribs,
+ volume=None,
+ issue=None,
+ pages=None,
+ language=None,
+ abstracts=None,
+ refs=None,
+ extra=extra,
+ license_slug=license_slug,
+ )
+ return re
+
+ def try_update(self, re, debug=True):
+ if debug is True:
+ # print(type(re))
+ print(json.dumps(re.to_dict(), default=extended_encoder))
+ return
+ return False
+
+ def insert_batch(self, batch):
+ # Debugging.
+ for item in batch:
+ print(item)
+ return
+
+ # Orig.
+ self.api.create_release_auto_batch(fatcat_openapi_client.ReleaseAutoBatch(
+ editgroup=fatcat_openapi_client.Editgroup(
+ description=self.editgroup_description,
+ extra=self.editgroup_extra),
+ entity_list=batch))
+
+def extended_encoder(value):
+ """
+ Can be used with json.dumps(value, default=extended_encoder) to serialize
+ value not serializable by default. https://docs.python.org/3/library/json.html#basic-usage
+ """
+ if isinstance(value, (datetime.datetime, datetime.date)):
+ return value.isoformat()
+ if isinstance(value, set):
+ return list(value)
+
+def lookup_license_slug(raw):
+ """
+ TODO(martin): reuse from crossref, maybe.
+ """
+ if not raw:
+ return None
+ raw = raw.strip().replace('http://', '//').replace('https://', '//')
+ if 'creativecommons.org' in raw.lower():
+ raw = raw.lower()
+ raw = raw.replace('/legalcode', '/').replace('/uk', '')
+ if not raw.endswith('/'):
+ raw = raw + '/'
+ return LICENSE_SLUG_MAP.get(raw)
generated by cgit v1.2.3 (git 2.39.1) at 2024-11-23 10:28:43 +0000