diff options
Diffstat (limited to 'python/fatcat_tools')
| -rw-r--r-- | python/fatcat_tools/biblio_lookup_tables.py | 623 | ||||
| -rw-r--r-- | python/fatcat_tools/importers/__init__.py | 3 | ||||
| -rw-r--r-- | python/fatcat_tools/importers/common.py | 61 | ||||
| -rw-r--r-- | python/fatcat_tools/importers/crossref.py | 94 | ||||
| -rw-r--r-- | python/fatcat_tools/importers/datacite.py | 155 | ||||
| -rw-r--r-- | python/fatcat_tools/importers/doaj_article.py | 5 | ||||
| -rw-r--r-- | python/fatcat_tools/importers/grobid_metadata.py | 6 | ||||
| -rw-r--r-- | python/fatcat_tools/importers/jstor.py | 3 | ||||
| -rw-r--r-- | python/fatcat_tools/importers/pubmed.py | 319 | ||||
| -rw-r--r-- | python/fatcat_tools/normal.py | 115 |
10 files changed, 682 insertions, 702 deletions
diff --git a/python/fatcat_tools/biblio_lookup_tables.py b/python/fatcat_tools/biblio_lookup_tables.py new file mode 100644 index 00000000..a9a097ae --- /dev/null +++ b/python/fatcat_tools/biblio_lookup_tables.py @@ -0,0 +1,623 @@ +""" +This file contains lookup tables and other static data structures used in +bibliographic metadata munging. +""" + +from typing import Dict, Optional + +# These are very close, but maybe not exactly 1-to-1 with 639-2? Some mix of +# 2/T and 2/B? +# PubMed/MEDLINE and JSTOR use these MARC codes +# https://www.loc.gov/marc/languages/language_name.html +LANG_MAP_MARC: Dict[str, Optional[str]] = { + "afr": "af", + "alb": "sq", + "amh": "am", + "ara": "ar", + "arm": "hy", + "aze": "az", + "ben": "bn", + "bos": "bs", + "bul": "bg", + "cat": "ca", + "chi": "zh", + "cze": "cs", + "dan": "da", + "dut": "nl", + "eng": "en", + "epo": "eo", + "est": "et", + "fin": "fi", + "fre": "fr", + "geo": "ka", + "ger": "de", + "gla": "gd", + "gre": "el", + "heb": "he", + "hin": "hi", + "hrv": "hr", + "hun": "hu", + "ice": "is", + "ind": "id", + "ita": "it", + "jpn": "ja", + "kin": "rw", + "kor": "ko", + "lat": "la", + "lav": "lv", + "lit": "lt", + "mac": "mk", + "mal": "ml", + "mao": "mi", + "may": "ms", + "nor": "no", + "per": "fa", + "per": "fa", + "pol": "pl", + "por": "pt", + "pus": "ps", + "rum": "ro", + "rus": "ru", + "san": "sa", + "slo": "sk", + "slv": "sl", + "spa": "es", + "srp": "sr", + "swe": "sv", + "tha": "th", + "tur": "tr", + "ukr": "uk", + "urd": "ur", + "vie": "vi", + "wel": "cy", + # additions + "gle": "ga", # "Irish" (Gaelic) + "jav": "jv", # Javanese + "welsh": "cy", # Welsh + "oci": "oc", # Occitan + # Don't have ISO 639-1 codes + "grc": "el", # Ancient Greek; map to modern greek + "map": None, # Austronesian (collection) + "syr": None, # Syriac, Modern + "gem": None, # Old Saxon + "non": None, # Old Norse + "emg": None, # Eastern Meohang + "neg": None, # Negidal + "mul": None, # Multiple languages + "und": None, # Undetermined +} + +# these are mappings from web domains to URL 'rel' for things like file entity +# URL notation +DOMAIN_REL_MAP: Dict[str, str] = { + "archive.org": "archive", + # LOCKSS, Portico, DuraSpace, etc would also be "archive" + "arxiv.org": "repository", + "babel.hathitrust.org": "repository", + "cds.cern.ch": "repository", + "deepblue.lib.umich.edu": "repository", + "europepmc.org": "repository", + "hal.inria.fr": "repository", + "scielo.isciii.es": "repository", + "www.dtic.mil": "repository", + "www.jstage.jst.go.jp": "repository", + "www.jstor.org": "repository", + "www.ncbi.nlm.nih.gov": "repository", + "ftp.ncbi.nlm.nih.gov": "repository", + "www.scielo.br": "repository", + "www.scielo.cl": "repository", + "www.scielo.org.mx": "repository", + "zenodo.org": "repository", + "www.biorxiv.org": "repository", + "www.medrxiv.org": "repository", + "citeseerx.ist.psu.edu": "aggregator", + "publisher-connector.core.ac.uk": "aggregator", + "core.ac.uk": "aggregator", + "static.aminer.org": "aggregator", + "aminer.org": "aggregator", + "pdfs.semanticscholar.org": "aggregator", + "semanticscholar.org": "aggregator", + "www.semanticscholar.org": "aggregator", + "academic.oup.com": "publisher", + "cdn.elifesciences.org": "publisher", + "cell.com": "publisher", + "dl.acm.org": "publisher", + "downloads.hindawi.com": "publisher", + "elifesciences.org": "publisher", + "iopscience.iop.org": "publisher", + "journals.plos.org": "publisher", + "link.springer.com": "publisher", + "onlinelibrary.wiley.com": "publisher", + "works.bepress.com": "publisher", + "www.biomedcentral.com": "publisher", + "www.cell.com": "publisher", + "www.nature.com": "publisher", + "www.pnas.org": "publisher", + "www.tandfonline.com": "publisher", + "www.frontiersin.org": "publisher", + "www.degruyter.com": "publisher", + "www.mdpi.com": "publisher", + "www.ahajournals.org": "publisher", + "ehp.niehs.nih.gov": "publisher", + "journals.tsu.ru": "publisher", + "www.cogentoa.com": "publisher", + "www.researchgate.net": "academicsocial", + "academia.edu": "academicsocial", + "wayback.archive-it.org": "webarchive", + "web.archive.org": "webarchive", + "archive.is": "webarchive", +} + +# from: https://www.ncbi.nlm.nih.gov/books/NBK3827/table/pubmedhelp.T.publication_types/?report=objectonly +PUBMED_RELEASE_TYPE_MAP = { + # Adaptive Clinical Trial + "Address": "speech", + "Autobiography": "book", + # Bibliography + "Biography": "book", + # Case Reports + "Classical Article": "article-journal", + # Clinical Conference + # Clinical Study + # Clinical Trial + # Clinical Trial, Phase I + # Clinical Trial, Phase II + # Clinical Trial, Phase III + # Clinical Trial, Phase IV + # Clinical Trial Protocol + # Clinical Trial, Veterinary + # Collected Works + # Comparative Study + # Congress + # Consensus Development Conference + # Consensus Development Conference, NIH + # Controlled Clinical Trial + "Dataset": "dataset", + # Dictionary + # Directory + # Duplicate Publication + "Editorial": "editorial", + # English Abstract # doesn't indicate that this is abstract-only + # Equivalence Trial + # Evaluation Studies + # Expression of Concern + # Festschrift + # Government Document + # Guideline + "Historical Article": "article-journal", + # Interactive Tutorial + "Interview": "interview", + "Introductory Journal Article": "article-journal", + "Journal Article": "article-journal", + "Lecture": "speech", + "Legal Case": "legal_case", + "Legislation": "legislation", + "Letter": "letter", + # Meta-Analysis + # Multicenter Study + # News + "Newspaper Article": "article-newspaper", + # Observational Study + # Observational Study, Veterinary + # Overall + # Patient Education Handout + # Periodical Index + # Personal Narrative + # Portrait + # Practice Guideline + # Pragmatic Clinical Trial + # Publication Components + # Publication Formats + # Publication Type Category + # Randomized Controlled Trial + # Research Support, American Recovery and Reinvestment Act + # Research Support, N.I.H., Extramural + # Research Support, N.I.H., Intramural + # Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. + # Research Support, U.S. Gov't, P.H.S. + # Review # in the "literature review" sense, not "product review" + # Scientific Integrity Review + # Study Characteristics + # Support of Research + # Systematic Review + "Technical Report": "report", + # Twin Study + # Validation Studies + # Video-Audio Media + # Webcasts +} + +MONTH_ABBR_MAP: Dict[str, int] = { + "Jan": 1, + "01": 1, + "Feb": 2, + "02": 2, + "Mar": 3, + "03": 3, + "Apr": 4, + "04": 4, + "May": 5, + "05": 5, + "Jun": 6, + "06": 6, + "Jul": 7, + "07": 7, + "Aug": 8, + "08": 8, + "Sep": 9, + "09": 9, + "Oct": 10, + "10": 10, + "Nov": 11, + "11": 11, + "Dec": 12, + "12": 12, +} + +# From: https://www.ncbi.nlm.nih.gov/books/NBK7249/ +COUNTRY_NAME_MAP: Dict[str, str] = { + "Afghanistan": "af", + "Albania": "al", + "Algeria": "dz", + "Andorra": "ad", + "Angola": "ao", + "Antigua and Barbuda": "ag", + "Argentina": "ar", + "Armenia": "am", + "Australia": "au", + "Austria": "at", + "Azerbaijan": "az", + "Bahamas": "bs", + "Bahrain": "bh", + "Bangladesh": "bd", + "Barbados": "bb", + "Belarus": "by", + "Belgium": "be", + "Belize": "bz", + "Benin": "bj", + "Bhutan": "bt", + "Bolivia": "bo", + "Bosnia and Herzegowina": "ba", + "Botswana": "bw", + "Brazil": "br", + "Brunei Darussalam": "bn", + "Bulgaria": "bg", + "Burkina Faso": "bf", + "Burundi": "bi", + "Cambodia": "kh", + "Cameroon": "cm", + "Canada": "ca", + "Cape Verde": "cv", + "Central African Republic": "cf", + "Chad": "td", + "Chile": "cl", + "China": "cn", + "Colombia": "co", + "Comoros": "km", + "Congo, Democratic Republic": "cd", + "Congo, People’s Republic": "cg", + "Costa Rica": "cr", + "Cote d'Ivoire": "ci", + "Croatia (Local Name: Hrvatska)": "hr", + "Cuba": "cu", + "Cyprus": "cy", + "Czech Republic": "cz", + "Denmark": "dk", + "Djibouti": "dj", + "Dominica": "dm", + "Dominican Republic": "do", + "East Timor": "tl", + "Ecuador": "ec", + "El Salvador": "sv", + "Equatorial Guinea": "gq", + "Eritrea": "er", + "Estonia": "ee", + "Ethiopia": "et", + "Fiji": "fj", + "Finland": "fi", + "France": "fr", + "Gabon": "ga", + "Gambia": "gm", + "Georgia": "ge", + "Germany": "de", + "Ghana": "gh", + "Greece": "gr", + "Greenland": "gl", + "Grenada": "gd", + "Guatemala": "gt", + "Guinea": "gn", + "Guinea-Bissau": "gw", + "Guyana": "gy", + "Haiti": "ht", + "Honduras": "hn", + "Hong Kong": "hk", + "Hungary": "hu", + "Iceland": "is", + "India": "in", + "Indonesia": "id", + "Iran": "ir", + "Iraq": "iq", + "Ireland": "ie", + "Israel": "il", + "Italy": "it", + "Jamaica": "jm", + "Japan": "jp", + "Jordan": "jo", + "Kazakhstan": "kz", + "Kenya": "ke", + "Kiribati": "ki", + "Korea, Democratic People's Republic": "kp", + "Korea, Republic": "kr", + "Kuwait": "kw", + "Kyrgyzstan": "kg", + "Laos": "la", + "Latvia": "lv", + "Lebanon": "lb", + "Lesotho": "ls", + "Liberia": "lr", + "Libya": "ly", + "Liechtenstein": "li", + "Lithuania": "lt", + "Luxembourg": "lu", + "Macedonia": "mk", + "Madagascar": "mg", + "Malawi": "mw", + "Malaysia": "my", + "Maldives": "mv", + "Mali": "ml", + "Malta": "mt", + "Marshall Islands": "mh", + "Mauritania": "mr", + "Mauritius": "mu", + "Mexico": "mx", + "Micronesia": "fm", + "Moldova": "md", + "Monaco": "mc", + "Mongolia": "mn", + "Morocco": "ma", + "Mozambique": "mz", + "Myanmar": "mm", + "Namibia": "na", + "Nauru": "nr", + "Nepal": "np", + "Netherlands": "nl", + "New Zealand": "nz", + "Nicaragua": "ni", + "Niger": "ne", + "Nigeria": "ng", + "Norway": "no", + "Oman": "om", + "Pakistan": "pk", + "Palau": "pw", + "Panama": "pa", + "Papua New Guinea": "pg", + "Paraguay": "py", + "Peru": "pe", + "Philippines": "ph", + "Poland": "pl", + "Portugal": "pt", + "Puerto Rico": "pr", + "Qatar": "qa", + "Romania": "ro", + "Russian Federation": "ru", + "Rwanda": "rw", + "Saint Kitts and Nevis": "kn", + "Saint Lucia": "lc", + "Saint Vincent and the Grenadines": "vc", + "Samoa": "ws", + "San Marino": "sm", + "Sao Tome and Príncipe": "st", + "Saudi Arabia": "sa", + "Senegal": "sn", + "Serbia and Montenegro": "cs", + "Seychelles": "sc", + "Sierra Leone": "sl", + "Singapore": "sg", + "Slovakia (Slovak Republic)": "sk", + "Slovenia": "si", + "Solomon Islands": "sb", + "Somalia": "so", + "South Africa": "za", + "Spain": "es", + "Sri Lanka": "lk", + "Sudan": "sd", + "Suriname": "sr", + "Swaziland": "sz", + "Sweden": "se", + "Switzerland": "ch", + "Syrian Arab Republic": "sy", + "Taiwan": "tw", + "Tajikistan": "tj", + "Tanzania": "tz", + "Tanzania": "tz", + "Thailand": "th", + "Togo": "tg", + "Tonga": "to", + "Trinidad and Tobago": "tt", + "Tunisia": "tn", + "Turkey": "tr", + "Turkmenistan": "tm", + "Tuvalu": "tv", + "Uganda": "ug", + "Ukraine": "ua", + "United Arab Emirates": "ae", + "United Kingdom": "gb", + "United States": "us", + "Uruguay": "uy", + # Additions from running over large files + "Bosnia and Herzegovina": "ba", + # "International" + "China (Republic : 1949- )": "tw", # pretty sure this is tw not cn + "Russia (Federation)": "ru", + "Scotland": "gb", + "England": "gb", + "Korea (South)": "kr", + "Georgia (Republic)": "ge", + "Egypt": "eg", +} + +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/publicdomain/mark/1.0/deed.de": "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", + "//creativecommons.org/share-your-work/public-domain/cc0/": "CC-0", + "//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.elsevier.com/tdm/userlicense/1.0/": "ELSEVIER-USER-1.0", + "//www.karger.com/Services/SiteLicenses": "KARGER", + "//www.karger.com/Services/SiteLicenses/": "KARGER", + "//archaeologydataservice.ac.uk/advice/termsofuseandaccess.xhtml/": "ADS-UK", + "//archaeologydataservice.ac.uk/advice/termsofuseandaccess/": "ADS-UK", + "//homepage.data-planet.com/terms-use/": "SAGE-DATA-PLANET", + "//publikationen.bibliothek.kit.edu/kitopen-lizenz/": "KIT-OPEN", + "//pubs.acs.org/page/policy/authorchoice_ccby_termsofuse.html": "CC-BY", + "//pubs.acs.org/page/policy/authorchoice_ccby_termsofuse.html/": "CC-BY", + "//pubs.acs.org/page/policy/authorchoice_termsofuse.html": "ACS-CHOICE", + "//pubs.acs.org/page/policy/authorchoice_termsofuse.html/": "ACS-CHOICE", + "//www.ametsoc.org/PUBSReuseLicenses": "AMETSOC", + "//www.ametsoc.org/PUBSReuseLicenses/": "AMETSOC", + "//www.apa.org/pubs/journals/resources/open-access.aspx": "APA", + "//www.apa.org/pubs/journals/resources/open-access.aspx/": "APA", + "//www.biologists.com/user-licence-1-1": "BIOLOGISTS-USER", + "//www.biologists.com/user-licence-1-1/": "BIOLOGISTS-USER", + "//www.biologists.com/user-licence-1-1/": "BIOLOGISTS-USER", + "//www.gnu.org/licenses/gpl-3.0.en.html/": "GPLv3", + "//www.gnu.org/licenses/old-licenses/gpl-2.0.en.html/": "GPLv2", + # //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", + # skip these TDM licenses; they don't apply to content + # "//www.springer.com/tdm/": "SPRINGER-TDM", + # "//journals.sagepub.com/page/policies/text-and-data-mining-license/": "SAGE-TDM", + # "//doi.wiley.com/10.1002/tdm_license_1.1/": "WILEY-TDM-1.1", +} + +# Map various datacite type types to CSL-ish types. None means TODO or remove. +DATACITE_TYPE_MAP: Dict[str, Dict[str, Optional[str]]] = { + "ris": { + "THES": "thesis", + "SOUND": "song", # 99.9% maps to citeproc song, so use that (exception: report) + "CHAP": "chapter", + "FIGURE": "figure", + "RPRT": "report", + "JOUR": "article-journal", + "MPCT": "motion_picture", + "GEN": "article-journal", # GEN consist of 99% article and report, post-weblog, misc - and one dataset + "BOOK": "book", + "DATA": "dataset", + "COMP": "software", + }, + "schemaOrg": { + "Dataset": "dataset", + "Book": "book", + "ScholarlyArticle": "article-journal", + "ImageObject": "graphic", + "Collection": None, + "MediaObject": None, + "Event": None, + "SoftwareSourceCode": "software", + "Chapter": "chapter", + "CreativeWork": None, # Seems to be a catch-all resourceType, from PGRFA Material, Pamphlet, to music score. + "PublicationIssue": "article", + "AudioObject": None, + "Thesis": "thesis", + }, + "citeproc": { + "article": "article", + "article-journal": "article-journal", + "article-magazine": "article-magazine", + "article-newspaper": "article-newspaper", + "bill": "bill", + "book": "book", + "broadcast": "broadcast", + "chapter": "chapter", + "dataset": "dataset", + "entry-dictionary": "entry-dictionary", + "entry-encyclopedia": "entry-encyclopedia", + "entry": "entry", + "figure": "figure", + "graphic": "graphic", + "interview": "interview", + "legal_case": "legal_case", + "legislation": "legislation", + "manuscript": "manuscript", + "map": "map", + "motion_picture": "motion_picture", + "musical_score": "musical_score", + "pamphlet": "pamphlet", + "paper-conference": "paper-conference", + "patent": "patent", + "personal_communication": "personal_communication", + "post": "post", + "post-weblog": "post-weblog", + "report": "report", + "review-book": "review-book", + "review": "review", + "song": "song", + "speech": "speech", + "thesis": "thesis", + "treaty": "treaty", + "webpage": "webpage", + }, # https://docs.citationstyles.org/en/master/specification.html#appendix-iii-types + "bibtex": { + "phdthesis": "thesis", + "inbook": "chapter", + "misc": None, + "article": "article-journal", + "book": "book", + }, + "resourceTypeGeneral": { + "Image": "graphic", + "Dataset": "dataset", + "PhysicalObject": None, + "Collection": None, + "Text": None, # "Greyliterature, labnotes, accompanyingmaterials" + "Sound": None, + "InteractiveResource": None, + "Event": None, + "Software": "software", + "Other": None, + "Workflow": None, + "Audiovisual": None, + }, # https://schema.datacite.org/meta/kernel-4.0/doc/DataCite-MetadataKernel_v4.0.pdf#page=32 +} diff --git a/python/fatcat_tools/importers/__init__.py b/python/fatcat_tools/importers/__init__.py index 4d4d696b..654be2e9 100644 --- a/python/fatcat_tools/importers/__init__.py +++ b/python/fatcat_tools/importers/__init__.py @@ -26,9 +26,8 @@ from .common import ( KafkaJsonPusher, LinePusher, SqlitePusher, - make_kafka_consumer, ) -from .crossref import CROSSREF_TYPE_MAP, CrossrefImporter, lookup_license_slug +from .crossref import CrossrefImporter from .datacite import DataciteImporter from .dblp_container import DblpContainerImporter from .dblp_release import DblpReleaseImporter diff --git a/python/fatcat_tools/importers/common.py b/python/fatcat_tools/importers/common.py index 56c3d32e..7c587395 100644 --- a/python/fatcat_tools/importers/common.py +++ b/python/fatcat_tools/importers/common.py @@ -27,71 +27,14 @@ from fatcat_openapi_client import ( from fatcat_openapi_client.rest import ApiException from fuzzycat.matching import match_release_fuzzy +from fatcat_tools.biblio_lookup_tables import DOMAIN_REL_MAP from fatcat_tools.normal import clean_doi from fatcat_tools.transforms import entity_to_dict DATE_FMT: str = "%Y-%m-%d" SANE_MAX_RELEASES: int = 200 SANE_MAX_URLS: int = 100 - -DOMAIN_REL_MAP: Dict[str, str] = { - "archive.org": "archive", - # LOCKSS, Portico, DuraSpace, etc would also be "archive" - "arxiv.org": "repository", - "babel.hathitrust.org": "repository", - "cds.cern.ch": "repository", - "deepblue.lib.umich.edu": "repository", - "europepmc.org": "repository", - "hal.inria.fr": "repository", - "scielo.isciii.es": "repository", - "www.dtic.mil": "repository", - "www.jstage.jst.go.jp": "repository", - "www.jstor.org": "repository", - "www.ncbi.nlm.nih.gov": "repository", - "ftp.ncbi.nlm.nih.gov": "repository", - "www.scielo.br": "repository", - "www.scielo.cl": "repository", - "www.scielo.org.mx": "repository", - "zenodo.org": "repository", - "www.biorxiv.org": "repository", - "www.medrxiv.org": "repository", - "citeseerx.ist.psu.edu": "aggregator", - "publisher-connector.core.ac.uk": "aggregator", - "core.ac.uk": "aggregator", - "static.aminer.org": "aggregator", - "aminer.org": "aggregator", - "pdfs.semanticscholar.org": "aggregator", - "semanticscholar.org": "aggregator", - "www.semanticscholar.org": "aggregator", - "academic.oup.com": "publisher", - "cdn.elifesciences.org": "publisher", - "cell.com": "publisher", - "dl.acm.org": "publisher", - "downloads.hindawi.com": "publisher", - "elifesciences.org": "publisher", - "iopscience.iop.org": "publisher", - "journals.plos.org": "publisher", - "link.springer.com": "publisher", - "onlinelibrary.wiley.com": "publisher", - "works.bepress.com": "publisher", - "www.biomedcentral.com": "publisher", - "www.cell.com": "publisher", - "www.nature.com": "publisher", - "www.pnas.org": "publisher", - "www.tandfonline.com": "publisher", - "www.frontiersin.org": "publisher", - "www.degruyter.com": "publisher", - "www.mdpi.com": "publisher", - "www.ahajournals.org": "publisher", - "ehp.niehs.nih.gov": "publisher", - "journals.tsu.ru": "publisher", - "www.cogentoa.com": "publisher", - "www.researchgate.net": "academicsocial", - "academia.edu": "academicsocial", - "wayback.archive-it.org": "webarchive", - "web.archive.org": "webarchive", - "archive.is": "webarchive", -} +MAX_ABSTRACT_LENGTH: int = 2048 def make_rel_url(raw_url: str, default_link_rel: str = "web") -> Tuple[str, str]: diff --git a/python/fatcat_tools/importers/crossref.py b/python/fatcat_tools/importers/crossref.py index 8f5a4265..52bd7465 100644 --- a/python/fatcat_tools/importers/crossref.py +++ b/python/fatcat_tools/importers/crossref.py @@ -4,7 +4,8 @@ from typing import Any, Dict, List, Optional, Sequence import fatcat_openapi_client from fatcat_openapi_client import ApiClient, ReleaseContrib, ReleaseEntity -from fatcat_tools.normal import clean_doi, clean_str +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 @@ -33,97 +34,6 @@ 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): """ diff --git a/python/fatcat_tools/importers/datacite.py b/python/fatcat_tools/importers/datacite.py index 441514b8..b310f8bc 100644 --- a/python/fatcat_tools/importers/datacite.py +++ b/python/fatcat_tools/importers/datacite.py @@ -21,113 +21,19 @@ import langdetect import pycountry from fatcat_openapi_client import ApiClient, ReleaseContrib, ReleaseEntity -from fatcat_tools.normal import clean_doi, clean_str +from fatcat_tools.biblio_lookup_tables import DATACITE_TYPE_MAP +from fatcat_tools.normal import clean_doi, clean_str, lookup_license_slug from fatcat_tools.transforms import entity_to_dict -from .common import EntityImporter - -# Cutoff length for abstracts. -MAX_ABSTRACT_LENGTH = 2048 +from .common import MAX_ABSTRACT_LENGTH, EntityImporter # https://guide.fatcat.wiki/entity_container.html#container_type-vocabulary -CONTAINER_TYPE_MAP: Dict[str, str] = { +DATACITE_CONTAINER_TYPE_MAP: Dict[str, str] = { "Journal": "journal", "Series": "journal", "Book Series": "book-series", } -# The docs/guide should be the canonical home for these mappings; update there -# first. Map various datacite type types to CSL-ish types. None means TODO or -# remove. -DATACITE_TYPE_MAP: Dict[str, Dict[str, Optional[str]]] = { - "ris": { - "THES": "thesis", - "SOUND": "song", # 99.9% maps to citeproc song, so use that (exception: report) - "CHAP": "chapter", - "FIGURE": "figure", - "RPRT": "report", - "JOUR": "article-journal", - "MPCT": "motion_picture", - "GEN": "article-journal", # GEN consist of 99% article and report, post-weblog, misc - and one dataset - "BOOK": "book", - "DATA": "dataset", - "COMP": "software", - }, - "schemaOrg": { - "Dataset": "dataset", - "Book": "book", - "ScholarlyArticle": "article-journal", - "ImageObject": "graphic", - "Collection": None, - "MediaObject": None, - "Event": None, - "SoftwareSourceCode": "software", - "Chapter": "chapter", - "CreativeWork": None, # Seems to be a catch-all resourceType, from PGRFA Material, Pamphlet, to music score. - "PublicationIssue": "article", - "AudioObject": None, - "Thesis": "thesis", - }, - "citeproc": { - "article": "article", - "article-journal": "article-journal", - "article-magazine": "article-magazine", - "article-newspaper": "article-newspaper", - "bill": "bill", - "book": "book", - "broadcast": "broadcast", - "chapter": "chapter", - "dataset": "dataset", - "entry-dictionary": "entry-dictionary", - "entry-encyclopedia": "entry-encyclopedia", - "entry": "entry", - "figure": "figure", - "graphic": "graphic", - "interview": "interview", - "legal_case": "legal_case", - "legislation": "legislation", - "manuscript": "manuscript", - "map": "map", - "motion_picture": "motion_picture", - "musical_score": "musical_score", - "pamphlet": "pamphlet", - "paper-conference": "paper-conference", - "patent": "patent", - "personal_communication": "personal_communication", - "post": "post", - "post-weblog": "post-weblog", - "report": "report", - "review-book": "review-book", - "review": "review", - "song": "song", - "speech": "speech", - "thesis": "thesis", - "treaty": "treaty", - "webpage": "webpage", - }, # https://docs.citationstyles.org/en/master/specification.html#appendix-iii-types - "bibtex": { - "phdthesis": "thesis", - "inbook": "chapter", - "misc": None, - "article": "article-journal", - "book": "book", - }, - "resourceTypeGeneral": { - "Image": "graphic", - "Dataset": "dataset", - "PhysicalObject": None, - "Collection": None, - "Text": None, # "Greyliterature, labnotes, accompanyingmaterials" - "Sound": None, - "InteractiveResource": None, - "Event": None, - "Software": "software", - "Other": None, - "Workflow": None, - "Audiovisual": None, - }, # https://schema.datacite.org/meta/kernel-4.0/doc/DataCite-MetadataKernel_v4.0.pdf#page=32 -} - # DATACITE_UNKNOWN_MARKERS via https://support.datacite.org/docs/schema-values-unknown-information-v43. DATACITE_UNKNOWN_MARKERS: List[str] = [ "(:unac)", # temporarily inaccessible @@ -180,43 +86,6 @@ DATACITE_TITLE_SPAM_WORDGROUPS: List[Dict[str, Any]] = [ } ] -# TODO(martin): merge this with other maps and lookup functions, eventually. -LICENSE_SLUG_MAP: Dict[str, str] = { - "//archaeologydataservice.ac.uk/advice/termsofuseandaccess.xhtml/": "ADS-UK", - "//archaeologydataservice.ac.uk/advice/termsofuseandaccess/": "ADS-UK", - "//arxiv.org/licenses/nonexclusive-distrib/1.0/": "ARXIV-1.0", - "//doi.wiley.com/10.1002/tdm_license_1.1/": "WILEY-TDM-1.1", - "//homepage.data-planet.com/terms-use/": "SAGE-DATA-PLANET", - "//onlinelibrary.wiley.com/termsandconditions/": "WILEY", - "//publikationen.bibliothek.kit.edu/kitopen-lizenz/": "KIT-OPEN", - "//pubs.acs.org/page/policy/authorchoice_ccby_termsofuse.html/": "CC-BY", - "//pubs.acs.org/page/policy/authorchoice_termsofuse.html/": "ACS-CHOICE", - "//www.ametsoc.org/PUBSReuseLicenses/": "AMETSOC", - "//www.apa.org/pubs/journals/resources/open-access.aspx/": "APA", - "//www.biologists.com/user-licence-1-1/": "BIOLOGISTS-USER", - "//www.elsevier.com/open-access/userlicense/1.0/": "ELSEVIER-USER-1.0", - "//www.elsevier.com/tdm/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.springer.com/tdm/": "SPRINGER-TDM", - "//journals.sagepub.com/page/policies/text-and-data-mining-license/": "SAGE-TDM", - "//creativecommons.org/publicdomain/mark/1.0/deed.de": "CC-0", - "//creativecommons.org/publicdomain/mark/1.0": "CC-0", - "//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/share-your-work/public-domain/cc0/": "CC-0", - "//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", -} - class DataciteImporter(EntityImporter): """ @@ -406,8 +275,8 @@ class DataciteImporter(EntityImporter): container_name = 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("type") in DATACITE_CONTAINER_TYPE_MAP.keys(): + container_type = DATACITE_CONTAINER_TYPE_MAP.get(container["type"]) if container.get("identifier") and container.get("identifierType") == "ISSN": issn = container.get("identifier") if issn and len(issn) == 8: @@ -488,7 +357,7 @@ class DataciteImporter(EntityImporter): license_extra = [] for lic in attributes.get("rightsList", []): - slug = lookup_license_slug(lic.get("rightsUri")) + slug = datacite_lookup_license_slug(lic.get("rightsUri")) if slug: license_slug = slug license_extra.append(lic) @@ -968,7 +837,7 @@ def contributor_list_contains_contributor( return False -def lookup_license_slug(raw: Optional[str]) -> Optional[str]: +def datacite_lookup_license_slug(raw: Optional[str]) -> Optional[str]: """ Resolve a variety of strings into a some pseudo-canonical form, e.g. CC-BY-ND, CC-0, MIT and so on. @@ -1063,12 +932,8 @@ def lookup_license_slug(raw: Optional[str]) -> Optional[str]: return None return "RS-{}".format(name.upper()) - # Fallback to mapped values. - raw = raw.lower() - raw = raw.strip().replace("http://", "//").replace("https://", "//") - if not raw.endswith("/"): - raw = raw + "/" - return LICENSE_SLUG_MAP.get(raw) + # Fallback to generic license lookup + return lookup_license_slug(raw) def find_original_language_title( diff --git a/python/fatcat_tools/importers/doaj_article.py b/python/fatcat_tools/importers/doaj_article.py index f5c886a2..92dbe574 100644 --- a/python/fatcat_tools/importers/doaj_article.py +++ b/python/fatcat_tools/importers/doaj_article.py @@ -11,7 +11,7 @@ from typing import Any, Dict, List, Optional, Sequence import fatcat_openapi_client from fatcat_openapi_client import ApiClient, ReleaseEntity -from fatcat_tools.importers.common import EntityImporter +from fatcat_tools.importers.common import MAX_ABSTRACT_LENGTH, EntityImporter from fatcat_tools.normal import ( clean_doi, clean_orcid, @@ -24,9 +24,6 @@ from fatcat_tools.normal import ( parse_month, ) -# Cutoff length for abstracts. -MAX_ABSTRACT_LENGTH = 2048 - class DoajArticleImporter(EntityImporter): def __init__(self, api: ApiClient, issn_map_file: Sequence, **kwargs) -> None: diff --git a/python/fatcat_tools/importers/grobid_metadata.py b/python/fatcat_tools/importers/grobid_metadata.py index 9db499a0..3c85132c 100644 --- a/python/fatcat_tools/importers/grobid_metadata.py +++ b/python/fatcat_tools/importers/grobid_metadata.py @@ -9,9 +9,7 @@ from fatcat_openapi_client import ApiClient, FileEntity, ReleaseEntity from fatcat_tools.normal import clean_doi, clean_str -from .common import EntityImporter, make_rel_url - -MAX_ABSTRACT_BYTES = 4096 +from .common import MAX_ABSTRACT_LENGTH, EntityImporter, make_rel_url class GrobidMetadataImporter(EntityImporter): @@ -84,7 +82,7 @@ class GrobidMetadataImporter(EntityImporter): extra_grobid: Dict[str, Any] = dict() abstract = obj.get("abstract") - if abstract and len(abstract) < MAX_ABSTRACT_BYTES and len(abstract) > 10: + if abstract and len(abstract) < MAX_ABSTRACT_LENGTH and len(abstract) > 10: abobj = fatcat_openapi_client.ReleaseAbstract( mimetype="text/plain", content=clean_str(obj.get("abstract")) ) diff --git a/python/fatcat_tools/importers/jstor.py b/python/fatcat_tools/importers/jstor.py index c2f650b0..79691c9a 100644 --- a/python/fatcat_tools/importers/jstor.py +++ b/python/fatcat_tools/importers/jstor.py @@ -8,7 +8,8 @@ import fatcat_openapi_client from bs4 import BeautifulSoup from fatcat_openapi_client import ApiClient, ReleaseEntity -from fatcat_tools.normal import LANG_MAP_MARC, clean_doi, clean_str +from fatcat_tools.biblio_lookup_tables import LANG_MAP_MARC +from fatcat_tools.normal import clean_doi, clean_str from .common import EntityImporter from .crossref import CONTAINER_TYPE_MAP diff --git a/python/fatcat_tools/importers/pubmed.py b/python/fatcat_tools/importers/pubmed.py index 3274234f..5bc7a9ff 100644 --- a/python/fatcat_tools/importers/pubmed.py +++ b/python/fatcat_tools/importers/pubmed.py @@ -8,325 +8,16 @@ import fatcat_openapi_client from bs4 import BeautifulSoup from fatcat_openapi_client import ApiClient, ReleaseEntity -from fatcat_tools.normal import ( +from fatcat_tools.biblio_lookup_tables import ( + COUNTRY_NAME_MAP, LANG_MAP_MARC, - clean_doi, - clean_issn, - clean_pmcid, - clean_pmid, - clean_str, + MONTH_ABBR_MAP, + PUBMED_RELEASE_TYPE_MAP, ) +from fatcat_tools.normal import clean_doi, clean_issn, clean_pmcid, clean_pmid, clean_str from .common import EntityImporter -# from: https://www.ncbi.nlm.nih.gov/books/NBK3827/table/pubmedhelp.T.publication_types/?report=objectonly -PUBMED_RELEASE_TYPE_MAP = { - # Adaptive Clinical Trial - "Address": "speech", - "Autobiography": "book", - # Bibliography - "Biography": "book", - # Case Reports - "Classical Article": "article-journal", - # Clinical Conference - # Clinical Study - # Clinical Trial - # Clinical Trial, Phase I - # Clinical Trial, Phase II - # Clinical Trial, Phase III - # Clinical Trial, Phase IV - # Clinical Trial Protocol - # Clinical Trial, Veterinary - # Collected Works - # Comparative Study - # Congress - # Consensus Development Conference - # Consensus Development Conference, NIH - # Controlled Clinical Trial - "Dataset": "dataset", - # Dictionary - # Directory - # Duplicate Publication - "Editorial": "editorial", - # English Abstract # doesn't indicate that this is abstract-only - # Equivalence Trial - # Evaluation Studies - # Expression of Concern - # Festschrift - # Government Document - # Guideline - "Historical Article": "article-journal", - # Interactive Tutorial - "Interview": "interview", - "Introductory Journal Article": "article-journal", - "Journal Article": "article-journal", - "Lecture": "speech", - "Legal Case": "legal_case", - "Legislation": "legislation", - "Letter": "letter", - # Meta-Analysis - # Multicenter Study - # News - "Newspaper Article": "article-newspaper", - # Observational Study - # Observational Study, Veterinary - # Overall - # Patient Education Handout - # Periodical Index - # Personal Narrative - # Portrait - # Practice Guideline - # Pragmatic Clinical Trial - # Publication Components - # Publication Formats - # Publication Type Category - # Randomized Controlled Trial - # Research Support, American Recovery and Reinvestment Act - # Research Support, N.I.H., Extramural - # Research Support, N.I.H., Intramural - # Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. - # Research Support, U.S. Gov't, P.H.S. - # Review # in the "literature review" sense, not "product review" - # Scientific Integrity Review - # Study Characteristics - # Support of Research - # Systematic Review - "Technical Report": "report", - # Twin Study - # Validation Studies - # Video-Audio Media - # Webcasts -} - -MONTH_ABBR_MAP = { - "Jan": 1, - "01": 1, - "Feb": 2, - "02": 2, - "Mar": 3, - "03": 3, - "Apr": 4, - "04": 4, - "May": 5, - "05": 5, - "Jun": 6, - "06": 6, - "Jul": 7, - "07": 7, - "Aug": 8, - "08": 8, - "Sep": 9, - "09": 9, - "Oct": 10, - "10": 10, - "Nov": 11, - "11": 11, - "Dec": 12, - "12": 12, -} - -# From: https://www.ncbi.nlm.nih.gov/books/NBK7249/ -COUNTRY_NAME_MAP = { - "Afghanistan": "af", - "Albania": "al", - "Algeria": "dz", - "Andorra": "ad", - "Angola": "ao", - "Antigua and Barbuda": "ag", - "Argentina": "ar", - "Armenia": "am", - "Australia": "au", - "Austria": "at", - "Azerbaijan": "az", - "Bahamas": "bs", - "Bahrain": "bh", - "Bangladesh": "bd", - "Barbados": "bb", - "Belarus": "by", - "Belgium": "be", - "Belize": "bz", - "Benin": "bj", - "Bhutan": "bt", - "Bolivia": "bo", - "Bosnia and Herzegowina": "ba", - "Botswana": "bw", - "Brazil": "br", - "Brunei Darussalam": "bn", - "Bulgaria": "bg", - "Burkina Faso": "bf", - "Burundi": "bi", - "Cambodia": "kh", - "Cameroon": "cm", - "Canada": "ca", - "Cape Verde": "cv", - "Central African Republic": "cf", - "Chad": "td", - "Chile": "cl", - "China": "cn", - "Colombia": "co", - "Comoros": "km", - "Congo, Democratic Republic": "cd", - "Congo, People’s Republic": "cg", - "Costa Rica": "cr", - "Cote d'Ivoire": "ci", - "Croatia (Local Name: Hrvatska)": "hr", - "Cuba": "cu", - "Cyprus": "cy", - "Czech Republic": "cz", - "Denmark": "dk", - "Djibouti": "dj", - "Dominica": "dm", - "Dominican Republic": "do", - "East Timor": "tl", - "Ecuador": "ec", - "El Salvador": "sv", - "Equatorial Guinea": "gq", - "Eritrea": "er", - "Estonia": "ee", - "Ethiopia": "et", - "Fiji": "fj", - "Finland": "fi", - "France": "fr", - "Gabon": "ga", - "Gambia": "gm", - "Georgia": "ge", - "Germany": "de", - "Ghana": "gh", - "Greece": "gr", - "Greenland": "gl", - "Grenada": "gd", - "Guatemala": "gt", - "Guinea": "gn", - "Guinea-Bissau": "gw", - "Guyana": "gy", - "Haiti": "ht", - "Honduras": "hn", - "Hong Kong": "hk", - "Hungary": "hu", - "Iceland": "is", - "India": "in", - "Indonesia": "id", - "Iran": "ir", - "Iraq": "iq", - "Ireland": "ie", - "Israel": "il", - "Italy": "it", - "Jamaica": "jm", - "Japan": "jp", - "Jordan": "jo", - "Kazakhstan": "kz", - "Kenya": "ke", - "Kiribati": "ki", - "Korea, Democratic People's Republic": "kp", - "Korea, Republic": "kr", - "Kuwait": "kw", - "Kyrgyzstan": "kg", - "Laos": "la", - "Latvia": "lv", - "Lebanon": "lb", - "Lesotho": "ls", - "Liberia": "lr", - "Libya": "ly", - "Liechtenstein": "li", - "Lithuania": "lt", - "Luxembourg": "lu", - "Macedonia": "mk", - "Madagascar": "mg", - "Malawi": "mw", - "Malaysia": "my", - "Maldives": "mv", - "Mali": "ml", - "Malta": "mt", - "Marshall Islands": "mh", - "Mauritania": "mr", - "Mauritius": "mu", - "Mexico": "mx", - "Micronesia": "fm", - "Moldova": "md", - "Monaco": "mc", - "Mongolia": "mn", - "Morocco": "ma", - "Mozambique": "mz", - "Myanmar": "mm", - "Namibia": "na", - "Nauru": "nr", - "Nepal": "np", - "Netherlands": "nl", - "New Zealand": "nz", - "Nicaragua": "ni", - "Niger": "ne", - "Nigeria": "ng", - "Norway": "no", - "Oman": "om", - "Pakistan": "pk", - "Palau": "pw", - "Panama": "pa", - "Papua New Guinea": "pg", - "Paraguay": "py", - "Peru": "pe", - "Philippines": "ph", - "Poland": "pl", - "Portugal": "pt", - "Puerto Rico": "pr", - "Qatar": "qa", - "Romania": "ro", - "Russian Federation": "ru", - "Rwanda": "rw", - "Saint Kitts and Nevis": "kn", - "Saint Lucia": "lc", - "Saint Vincent and the Grenadines": "vc", - "Samoa": "ws", - "San Marino": "sm", - "Sao Tome and Príncipe": "st", - "Saudi Arabia": "sa", - "Senegal": "sn", - "Serbia and Montenegro": "cs", - "Seychelles": "sc", - "Sierra Leone": "sl", - "Singapore": "sg", - "Slovakia (Slovak Republic)": "sk", - "Slovenia": "si", - "Solomon Islands": "sb", - "Somalia": "so", - "South Africa": "za", - "Spain": "es", - "Sri Lanka": "lk", - "Sudan": "sd", - "Suriname": "sr", - "Swaziland": "sz", - "Sweden": "se", - "Switzerland": "ch", - "Syrian Arab Republic": "sy", - "Taiwan": "tw", - "Tajikistan": "tj", - "Tanzania": "tz", - "Tanzania": "tz", - "Thailand": "th", - "Togo": "tg", - "Tonga": "to", - "Trinidad and Tobago": "tt", - "Tunisia": "tn", - "Turkey": "tr", - "Turkmenistan": "tm", - "Tuvalu": "tv", - "Uganda": "ug", - "Ukraine": "ua", - "United Arab Emirates": "ae", - "United Kingdom": "gb", - "United States": "us", - "Uruguay": "uy", - # Additions from running over large files - "Bosnia and Herzegovina": "ba", - # "International" - "China (Republic : 1949- )": "tw", # pretty sure this is tw not cn - "Russia (Federation)": "ru", - "Scotland": "gb", - "England": "gb", - "Korea (South)": "kr", - "Georgia (Republic)": "ge", - "Egypt": "eg", -} - class PubmedImporter(EntityImporter): """ diff --git a/python/fatcat_tools/normal.py b/python/fatcat_tools/normal.py index 0d2c84ce..fc80411c 100644 --- a/python/fatcat_tools/normal.py +++ b/python/fatcat_tools/normal.py @@ -12,6 +12,8 @@ import ftfy import langdetect import pycountry +from .biblio_lookup_tables import LICENSE_SLUG_MAP + DOI_REGEX = re.compile(r"^10.\d{3,6}/\S+$") @@ -606,84 +608,35 @@ def test_parse_country_name() -> None: assert parse_country_name("Japan") == "jp" -# These are very close, but maybe not exactly 1-to-1 with 639-2? Some mix of -# 2/T and 2/B? -# PubMed/MEDLINE and JSTOR use these MARC codes -# https://www.loc.gov/marc/languages/language_name.html -LANG_MAP_MARC = { - "afr": "af", - "alb": "sq", - "amh": "am", - "ara": "ar", - "arm": "hy", - "aze": "az", - "ben": "bn", - "bos": "bs", - "bul": "bg", - "cat": "ca", - "chi": "zh", - "cze": "cs", - "dan": "da", - "dut": "nl", - "eng": "en", - "epo": "eo", - "est": "et", - "fin": "fi", - "fre": "fr", - "geo": "ka", - "ger": "de", - "gla": "gd", - "gre": "el", - "heb": "he", - "hin": "hi", - "hrv": "hr", - "hun": "hu", - "ice": "is", - "ind": "id", - "ita": "it", - "jpn": "ja", - "kin": "rw", - "kor": "ko", - "lat": "la", - "lav": "lv", - "lit": "lt", - "mac": "mk", - "mal": "ml", - "mao": "mi", - "may": "ms", - "nor": "no", - "per": "fa", - "per": "fa", - "pol": "pl", - "por": "pt", - "pus": "ps", - "rum": "ro", - "rus": "ru", - "san": "sa", - "slo": "sk", - "slv": "sl", - "spa": "es", - "srp": "sr", - "swe": "sv", - "tha": "th", - "tur": "tr", - "ukr": "uk", - "urd": "ur", - "vie": "vi", - "wel": "cy", - # additions - "gle": "ga", # "Irish" (Gaelic) - "jav": "jv", # Javanese - "welsh": "cy", # Welsh - "oci": "oc", # Occitan - # Don't have ISO 639-1 codes - "grc": "el", # Ancient Greek; map to modern greek - "map": None, # Austronesian (collection) - "syr": None, # Syriac, Modern - "gem": None, # Old Saxon - "non": None, # Old Norse - "emg": None, # Eastern Meohang - "neg": None, # Negidal - "mul": None, # Multiple languages - "und": None, # Undetermined -} +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 |