diff options
Diffstat (limited to 'python/fatcat_tools/importers/crossref.py')
| -rw-r--r-- | python/fatcat_tools/importers/crossref.py | 209 |
1 files changed, 36 insertions, 173 deletions
diff --git a/python/fatcat_tools/importers/crossref.py b/python/fatcat_tools/importers/crossref.py index a41e2bf5..52bd7465 100644 --- a/python/fatcat_tools/importers/crossref.py +++ b/python/fatcat_tools/importers/crossref.py @@ -1,11 +1,13 @@ import datetime -import sqlite3 from typing import Any, Dict, List, Optional, Sequence import fatcat_openapi_client from fatcat_openapi_client import ApiClient, ReleaseContrib, ReleaseEntity -from .common import EntityImporter, clean +from fatcat_tools.biblio_lookup_tables import CONTAINER_TYPE_MAP +from fatcat_tools.normal import clean_doi, clean_str, lookup_license_slug + +from .common import EntityImporter # The docs/guide should be the canonical home for these mappings; update there # first @@ -32,104 +34,11 @@ CROSSREF_TYPE_MAP: Dict[str, Optional[str]] = { "standard": "standard", } -CONTAINER_TYPE_MAP: Dict[str, str] = { - "article-journal": "journal", - "paper-conference": "conference", - "book": "book-series", -} - -# These are based, informally, on sorting the most popular licenses found in -# Crossref metadata. There were over 500 unique strings and only a few most -# popular are here; many were variants of the CC URLs. Would be useful to -# normalize CC licenses better. -# The current norm is to only add license slugs that are at least partially OA. -LICENSE_SLUG_MAP: Dict[str, str] = { - "//creativecommons.org/publicdomain/mark/1.0": "CC-0", - "//creativecommons.org/publicdomain/mark/1.0/": "CC-0", - "//creativecommons.org/publicdomain/mark/1.0/deed.de": "CC-0", - "//creativecommons.org/publicdomain/mark/1.0/deed.de": "CC-0", - "//creativecommons.org/publicdomain/zero/1.0/": "CC-0", - "//creativecommons.org/publicdomain/zero/1.0/legalcode": "CC-0", - "//creativecommons.org/share-your-work/public-domain/cc0/": "CC-0", - "//creativecommons.org/licenses/by/2.0/": "CC-BY", - "//creativecommons.org/licenses/by/3.0/": "CC-BY", - "//creativecommons.org/licenses/by/4.0/": "CC-BY", - "//creativecommons.org/licenses/by-sa/3.0/": "CC-BY-SA", - "//creativecommons.org/licenses/by-sa/4.0/": "CC-BY-SA", - "//creativecommons.org/licenses/by-nd/3.0/": "CC-BY-ND", - "//creativecommons.org/licenses/by-nd/4.0/": "CC-BY-ND", - "//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-sa/3.0/": "CC-BY-NC-SA", - "//creativecommons.org/licenses/by-nc-sa/4.0/": "CC-BY-NC-SA", - "//creativecommons.org/licenses/by-nc-nd/3.0/": "CC-BY-NC-ND", - "//creativecommons.org/licenses/by-nc-nd/4.0/": "CC-BY-NC-ND", - "//spdx.org/licenses/CC0-1.0.json": "CC-0", - "//spdx.org/licenses/CC-BY-1.0.json": "CC-BY", - "//spdx.org/licenses/CC-BY-4.0.json": "CC-BY", - "//spdx.org/licenses/CC-BY-NC-4.0.json": "CC-BY-NC", - "//spdx.org/licenses/CC-BY-SA-3.0.json": "CC-BY-SA", - "//spdx.org/licenses/CC-BY-SA-4.0.json": "CC-BY-SA", - "//spdx.org/licenses/MIT.json": "MIT", - "//spdx.org/licenses/OGL-Canada-2.0.json": "OGL-Canada", - "//www.elsevier.com/open-access/userlicense/1.0/": "ELSEVIER-USER-1.0", - "//www.karger.com/Services/SiteLicenses": "KARGER", - "//pubs.acs.org/page/policy/authorchoice_termsofuse.html": "ACS-CHOICE", - "//pubs.acs.org/page/policy/authorchoice_ccby_termsofuse.html": "CC-BY", - "//www.biologists.com/user-licence-1-1/": "BIOLOGISTS-USER", - "//www.biologists.com/user-licence-1-1": "BIOLOGISTS-USER", - "//www.apa.org/pubs/journals/resources/open-access.aspx": "APA", - "//www.ametsoc.org/PUBSReuseLicenses": "AMETSOC", - # //onlinelibrary.wiley.com/termsAndConditions doesn't seem like a license - # //www.springer.com/tdm doesn't seem like a license - # //iopscience.iop.org/page/copyright is closed - # //www.acm.org/publications/policies/copyright_policy#Background is closed - # //rsc.li/journals-terms-of-use is closed for vor (am open) - # //www.ieee.org/publications_standards/publications/rights/ieeecopyrightform.pdf is 404 (!) - "//arxiv.org/licenses/nonexclusive-distrib/1.0/": "ARXIV-1.0", -} - - -def lookup_license_slug(raw: Optional[str]) -> Optional[str]: - 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) - - -def test_lookup_license_slug() -> None: - - assert lookup_license_slug("https://creativecommons.org/licenses/by-nc/3.0/") == "CC-BY-NC" - assert ( - lookup_license_slug("http://creativecommons.org/licenses/by/2.0/uk/legalcode") - == "CC-BY" - ) - assert ( - lookup_license_slug("https://creativecommons.org/publicdomain/zero/1.0/legalcode") - == "CC-0" - ) - assert lookup_license_slug("http://creativecommons.org/licenses/by/4.0") == "CC-BY" - assert ( - lookup_license_slug("https://creativecommons.org/licenses/by-nc-sa/4.0/") - == "CC-BY-NC-SA" - ) - assert lookup_license_slug("https://www.ametsoc.org/PUBSReuseLicenses") == "AMETSOC" - assert lookup_license_slug("https://www.amec.org/PUBSReuseLicenses") is None - assert lookup_license_slug("") is None - assert lookup_license_slug(None) is None - class CrossrefImporter(EntityImporter): """ Importer for Crossref metadata. - Can use a local sqlite3 file for faster "external identifier" lookups - See https://github.com/CrossRef/rest-api-doc for JSON schema notes """ @@ -150,50 +59,8 @@ class CrossrefImporter(EntityImporter): ) self.create_containers: bool = kwargs.get("create_containers", True) - extid_map_file = kwargs.get("extid_map_file") - self.extid_map_db: Optional[Any] = None - if extid_map_file: - db_uri = "file:{}?mode=ro".format(extid_map_file) - print("Using external ID map: {}".format(db_uri)) - self.extid_map_db = sqlite3.connect(db_uri, uri=True) - else: - print("Not using external ID map") - self.read_issn_map_file(issn_map_file) - def lookup_ext_ids(self, doi: str) -> Optional[Any]: - if self.extid_map_db is None: - return dict( - core_id=None, - pmid=None, - pmcid=None, - wikidata_qid=None, - arxiv_id=None, - jstor_id=None, - ) - row = self.extid_map_db.execute( - "SELECT core, pmid, pmcid, wikidata FROM ids WHERE doi=? LIMIT 1", [doi.lower()] - ).fetchone() - if row is None: - return dict( - core_id=None, - pmid=None, - pmcid=None, - wikidata_qid=None, - arxiv_id=None, - jstor_id=None, - ) - row = [str(cell or "") or None for cell in row] - return dict( - core_id=row[0], - pmid=row[1], - pmcid=row[2], - wikidata_qid=row[3], - # TODO: - arxiv_id=None, - jstor_id=None, - ) - def map_release_type(self, crossref_type: str) -> Optional[str]: return CROSSREF_TYPE_MAP.get(crossref_type) @@ -275,21 +142,21 @@ class CrossrefImporter(EntityImporter): if len(affiliation_list) > 1: # note: affiliation => more_affiliations extra["more_affiliations"] = [ - clean(a["name"]) for a in affiliation_list[1:] + clean_str(a["name"]) for a in affiliation_list[1:] ] if am.get("sequence") and am.get("sequence") != "additional": - extra["seq"] = clean(am.get("sequence")) + extra["seq"] = clean_str(am.get("sequence")) assert ctype in ("author", "editor", "translator") - raw_name = clean(raw_name) + raw_name = clean_str(raw_name) # TODO: what if 'raw_name' is None? contribs.append( ReleaseContrib( creator_id=creator_id, index=index, raw_name=raw_name, - given_name=clean(am.get("given")), - surname=clean(am.get("family")), - raw_affiliation=clean(raw_affiliation), + given_name=clean_str(am.get("given")), + surname=clean_str(am.get("family")), + raw_affiliation=clean_str(raw_affiliation), role=ctype, extra=extra or None, ) @@ -306,11 +173,11 @@ class CrossrefImporter(EntityImporter): container_id = None if issnl: container_id = self.lookup_issnl(issnl) - publisher = clean(obj.get("publisher")) + publisher = clean_str(obj.get("publisher")) container_name = obj.get("container-title") if container_name: - container_name = clean(container_name[0], force_xml=True) + container_name = clean_str(container_name[0], force_xml=True) if not container_name: container_name = None if ( @@ -366,7 +233,7 @@ class CrossrefImporter(EntityImporter): ref_extra["journal-title"] = rm["journal-title"] if rm.get("DOI"): ref_extra["doi"] = rm.get("DOI").lower() - author = clean(rm.get("author")) + author = clean_str(rm.get("author")) if author: ref_extra["authors"] = [author] for k in ( @@ -390,8 +257,8 @@ class CrossrefImporter(EntityImporter): "series-title", "volume-title", ): - if clean(rm.get(k)): - ref_extra[k] = clean(rm[k]) + if clean_str(rm.get(k)): + ref_extra[k] = clean_str(rm[k]) refs.append( fatcat_openapi_client.ReleaseRef( index=i, @@ -399,9 +266,9 @@ class CrossrefImporter(EntityImporter): target_release_id=None, key=key, year=year, - container_name=clean(ref_container_name), - title=clean(rm.get("article-title")), - locator=clean(rm.get("first-page")), + container_name=clean_str(ref_container_name), + title=clean_str(rm.get("article-title")), + locator=clean_str(rm.get("first-page")), # TODO: just dump JSON somewhere here? extra=ref_extra or None, ) @@ -409,7 +276,7 @@ class CrossrefImporter(EntityImporter): # abstracts abstracts = [] - abstract = clean(obj.get("abstract")) + abstract = clean_str(obj.get("abstract")) if abstract and len(abstract) > 10: abstracts.append( fatcat_openapi_client.ReleaseAbstract( @@ -430,9 +297,9 @@ class CrossrefImporter(EntityImporter): if type(val) == list: val = val[0] if type(val) == str: - val = clean(val) + val = clean_str(val) if val: - extra[key] = clean(val) + extra[key] = clean_str(val) else: extra[key] = val # crossref-nested extra keys @@ -440,14 +307,14 @@ class CrossrefImporter(EntityImporter): val = obj.get(key) if val: if type(val) == str: - extra_crossref[key] = clean(val) + extra_crossref[key] = clean_str(val) else: extra_crossref[key] = val if license_extra: extra_crossref["license"] = license_extra if len(obj["title"]) > 1: - aliases = [clean(t) for t in obj["title"][1:]] + aliases = [clean_str(t) for t in obj["title"][1:]] aliases = [t for t in aliases if t] if aliases: extra["aliases"] = aliases @@ -473,9 +340,6 @@ class CrossrefImporter(EntityImporter): # unknown release_stage = None - # external identifiers - extids: Dict[str, Any] = self.lookup_ext_ids(doi=obj["DOI"].lower()) or {} - # filter out unreasonably huge releases if len(abstracts) > 100: self.counts["skip-huge-abstracts"] += 1 @@ -505,19 +369,24 @@ class CrossrefImporter(EntityImporter): if obj.get("original-title"): ot = obj.get("original-title") if ot is not None: - original_title = clean(ot[0], force_xml=True) + original_title = clean_str(ot[0], force_xml=True) title: Optional[str] = None if obj.get("title"): - title = clean(obj["title"][0], force_xml=True) + title = clean_str(obj["title"][0], force_xml=True) if not title or len(title) <= 1: # title can't be just a single character self.counts["skip-blank-title"] += 1 return None + doi = clean_doi(obj["DOI"].lower()) + if not doi: + self.counts["skip-bad-doi"] += 1 + return None + subtitle = None if obj.get("subtitle"): - subtitle = clean(obj["subtitle"][0], force_xml=True) + subtitle = clean_str(obj["subtitle"][0], force_xml=True) if not subtitle or len(subtitle) <= 1: # subtitle can't be just a single character subtitle = None @@ -537,19 +406,13 @@ class CrossrefImporter(EntityImporter): release_year=release_year, publisher=publisher, ext_ids=fatcat_openapi_client.ReleaseExtIds( - doi=obj["DOI"].lower(), - pmid=extids["pmid"], - pmcid=extids["pmcid"], - wikidata_qid=extids["wikidata_qid"], + doi=doi, isbn13=isbn13, - core=extids["core_id"], - arxiv=extids["arxiv_id"], - jstor=extids["jstor_id"], ), - volume=clean(obj.get("volume")), - issue=clean(obj.get("issue")), - pages=clean(obj.get("page")), - language=clean(obj.get("language")), + volume=clean_str(obj.get("volume")), + issue=clean_str(obj.get("issue")), + pages=clean_str(obj.get("page")), + language=clean_str(obj.get("language")), license_slug=license_slug, extra=extra or None, abstracts=abstracts or None, |