/
publication.py
511 lines (450 loc) · 20.4 KB
/
publication.py
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from time import gmtime, strftime, sleep
import datetime
import difflib
import argparse
import sys
import os
import requests
from dateutil import parser as du
from wikidataintegrator import wdi_core, wdi_login
from wikidataintegrator.wdi_config import config
from wikidataintegrator.wdi_helpers import prop2qid, PROPS, try_write
class PubmedItem:
def __init__(self):
raise ValueError("PubmedItem is deprecated. Please use PublicationHelper")
class Publication:
# https://github.com/shexSpec/schemas/blob/master/Wikidata/wikicite/wikicite_scholarly_article.shex
ID_TYPES = {
"doi": "P356",
"pmid": "P698",
"pmcid": "P932"
}
INSTANCE_OF = {
"scientific_article": "Q13442814",
"publication": "Q732577"
}
SOURCES = {
'crossref': 'Q5188229',
'europepmc': 'Q5412157'
}
def __init__(self, title=None, instance_of=None, subtitle=None, authors=list(),
publication_date=None, original_language_of_work=None,
published_in_issn=None, published_in_isbn=None,
volume=None, issue=None, pages=None, number_of_pages=None, cites=None,
editor=None, license=None, full_work_available_at=None, language_of_work_or_name=None,
main_subject=None, commons_category=None, sponsor=None, data_available_at=None,
ids=None, ref_url=None, source=None):
"""
:param title:
:type title: str
:param instance_of: one of `INSTANCE_OF`
:type instance_of: str
:param authors: authors is a list of dicts, containing the following keys: full_name, orcid (optional)
example: {'full_name': "Andrew I. Su", 'orcid': "0000-0002-9859-4104"}
If author name can't be parsed, use value None. i.e. {'full_name': None}
:type authors: list
:param publication_date:
:type publication_date: datetime.datetime
:param published_in_issn: The issn# for the journal
:type published_in_issn: str or list
:param published_in_isbn: The isbn#
:type published_in_isbn: str or list
:param volume:
:type volume: str
:param issue:
:type issue: str
:param pages:
:type pages: str
:param ids: may contain the following keys: doi, pmid, pmcid, article_id, arxiv_id, bibcode, zoobank_pub_id,
jstor_article_id, ssrn_id, nioshtic2_id, dialnet_article, opencitations_id, acmdl_id, publons_id
example: {'doi': 'xxx', 'pmid': '1234'}
:type ids: dict
:param ref_url: Ref url (for the api call)
:type ref_url: str
:param source: One of {'crossref', 'europepmc'}
:type source: str
:param subtitle: Not implemented
:param original_language_of_work: Not implemented
:param number_of_pages: Not implemented
:param cites: Not implemented
:param editor: Not implemented
:param license: Not implemented
:param full_work_available_at: Not implemented
:param language_of_work_or_name: Not implemented
:param main_subject: Not implemented
:param commons_category: Not implemented
:param sponsor: Not implemented
:param data_available_at: Not implemented
"""
# Input is an API agnostic representation of a publication
self.warnings = []
self._instance_of = instance_of
self.instance_of_qid = None
self._published_in_isbn = published_in_isbn
self._published_in_issn = published_in_issn
self.published_in_qid = None
self._authors = authors
self.title = title
self.publication_date = publication_date
self.volume = volume
self.issue = issue
self.pages = pages
self.ids = ids
self.source = source
self.ref_url = ref_url
### not implemented ###
self.subtitle = subtitle
self.original_language_of_work = original_language_of_work
self.cites = cites
self.editor = editor
self.license = license
self.full_work_available_at = full_work_available_at
self.language_of_work_or_name = language_of_work_or_name
self.main_subject = main_subject
self.commons_category = commons_category
self.sponsor = sponsor
self.data_available_at = data_available_at
self.number_of_pages = number_of_pages
### wikidata related things ###
self.reference = None
self.statements = []
@property
def instance_of(self):
return self._instance_of
@instance_of.setter
def instance_of(self, value):
self._instance_of = value
self.instance_of_qid = self.INSTANCE_OF.get(value) if value in self.INSTANCE_OF else self.INSTANCE_OF[
'publication']
if value not in self.INSTANCE_OF:
self.warnings.append("instance of {} not found".format(value))
@property
def published_in_issn(self):
return self._published_in_issn
@published_in_issn.setter
def published_in_issn(self, value):
assert self.published_in_isbn is None, "Can't give both ISSN and ISBN"
if not isinstance(value, list):
value = [value]
self._published_in_issn = value
qids = set(prop2qid(PROPS['ISSN'], v) for v in value)
if len(qids) == 1:
self.published_in_qid = list(qids)[0]
else:
self.warnings.append("conflictings ISSN qids: {}".format(qids))
if not self.published_in_qid:
self.warnings.append("ISSN:{} not found".format(value))
@property
def published_in_isbn(self):
return self._published_in_isbn
@published_in_isbn.setter
def published_in_isbn(self, value):
assert self.published_in_issn is None, "Can't give both ISSN and ISBN"
if not isinstance(value, list):
value = [value]
self._published_in_isbn = value
qids = set(prop2qid(PROPS['ISBN-13'], v) for v in value)
if len(qids) == 1:
self.published_in_qid = list(qids)[0]
else:
self.warnings.append("conflictings ISBN qids: {}".format(qids))
if not self.published_in_qid:
self.warnings.append("ISBN:{} not found".format(value))
@property
def authors(self):
return self._authors
@authors.setter
def authors(self, value):
self._authors = value
for author in self._authors:
author['qid'] = Publication.lookup_author(author['orcid']) if 'orcid' in author else None
@staticmethod
def lookup_author(orcid_id):
return prop2qid(PROPS['orcid id'], orcid_id)
def validate(self):
assert self.title is not None and len(self.title) > 1
assert self.publication_date is None or isinstance(self.publication_date, datetime.datetime)
assert self.source in self.SOURCES
assert self.ref_url is not None and len(self.ref_url) > 1
def make_reference(self):
if self.source == "crossref":
assert 'doi' in self.ids
extid = wdi_core.WDString(self.ids['doi'], PROPS['DOI'], is_reference=True)
ref_url = wdi_core.WDUrl(self.ref_url, PROPS['reference URL'], is_reference=True)
stated_in = wdi_core.WDItemID(self.SOURCES[self.source], PROPS['stated in'], is_reference=True)
retrieved = wdi_core.WDTime(strftime("+%Y-%m-%dT00:00:00Z", gmtime()), PROPS['retrieved'],
is_reference=True)
self.reference = [stated_in, extid, ref_url, retrieved]
elif self.source == "europepmc":
assert 'pmcid' in self.ids
extid = wdi_core.WDString(self.ids['pmcid'], PROPS['PMCID'], is_reference=True)
ref_url = wdi_core.WDUrl(self.ref_url, PROPS['reference URL'], is_reference=True)
stated_in = wdi_core.WDItemID(self.SOURCES[self.source], PROPS['stated in'], is_reference=True)
retrieved = wdi_core.WDTime(strftime("+%Y-%m-%dT00:00:00Z", gmtime()), PROPS['retrieved'],
is_reference=True)
self.reference = [stated_in, extid, ref_url, retrieved]
def set_label(self, item):
# item is a WDItemEngine
# check if lenght is > 250, warn if so and truncate
# self.title
if item.get_label() == "":
if len(self.title) > 249:
self.warnings.append("title cropped to 250 chars")
item.set_label(self.title[:249])
def set_description(self, item):
# item is a WDItemEngine
if item.get_description() == "" and self.publication_date:
item.set_description("{} published on {}".format(self.instance_of.replace("_", " "),
self.publication_date.strftime("%d %B %Y")))
elif item.get_description() == "":
item.set_description("{}".format(self.instance_of.replace("_", " ")))
def make_statements(self):
self.statements.append(
wdi_core.WDItemID(self.instance_of_qid, PROPS['instance of'], references=[self.reference]))
self.statements.append(wdi_core.WDMonolingualText(self.title, PROPS['title'], references=[self.reference]))
if self.publication_date:
date = self.publication_date.strftime("+%Y-%m-%dT00:00:00Z")
self.statements.append(
wdi_core.WDTime(date, PROPS['publication date'], references=[self.reference]))
if self.published_in_qid:
self.statements.append(
wdi_core.WDItemID(self.published_in_qid, PROPS['published in'], references=[self.reference]))
if self.volume:
self.statements.append(wdi_core.WDString(self.volume, PROPS['volume'], references=[self.reference]))
if self.pages:
self.statements.append(wdi_core.WDString(self.pages, PROPS['page(s)'], references=[self.reference]))
if self.issue:
self.statements.append(wdi_core.WDString(self.issue, PROPS['issue'], references=[self.reference]))
def make_author_statements(self):
# this function exists separately because if the item already exists, we don't want to touch the authors
s = []
for n, author in enumerate(self.authors, 1):
series_ordinal = wdi_core.WDString(str(n), PROPS['series ordinal'], is_qualifier=True)
if author.get("qid"):
s.append(wdi_core.WDItemID(author['qid'], PROPS['author'],
references=[self.reference], qualifiers=[series_ordinal]))
elif author['full_name']:
s.append(wdi_core.WDString(author['full_name'], PROPS['author name string'],
references=[self.reference], qualifiers=[series_ordinal]))
self.statements.extend(s)
def make_ext_id_statements(self):
for id_type, id_value in self.ids.items():
if id_value:
id_value = id_value.upper()
self.statements.append(wdi_core.WDExternalID(id_value, self.ID_TYPES[id_type], references=[self.reference]))
def get_or_create(self, login):
self.validate()
self.make_reference()
self.make_statements()
self.make_ext_id_statements()
self.make_author_statements()
item = wdi_core.WDItemEngine(
item_name=self.title, data=self.statements,
domain="scientific_article",
append_value=[PROPS['DOI'], PROPS['PMCID'], PROPS['PubMed ID']],
# ref_handler=update_retrieved_if_new_multiple_refs()
)
if item.wd_item_id:
return item.wd_item_id, self.warnings, True
self.set_label(item)
self.set_description(item)
success = try_write(item, self.ids['doi'], PROPS["DOI"], login)
return item.wd_item_id, self.warnings, success
def crossref_api_to_publication(ext_id, id_type="doi"):
assert id_type == "doi", "Unsupported id type in crossref: {}".format(id_type)
url = "https://api.crossref.org/v1/works/http://dx.doi.org/{}"
url = url.format(ext_id)
response = requests.get(url)
response.raise_for_status()
r = response.json()
assert r['status'] == 'ok'
r = r['message']
p = Publication(source="crossref", ref_url=url)
if r['type'] == "journal-article":
p.instance_of = "scientific_article"
else:
p.warnings.append("unknown type: {}".format(r['type']))
p.title = r['title'][0]
p.published_in_issn = r.get('ISSN', [None])[0]
p.publication_date = datetime.datetime.fromtimestamp(int(r['created']['timestamp']) / 1000)
p.issue = r.get('issue')
p.volume = r.get('volume')
p.pages = r.get('page')
if 'author' in r:
p.authors = [{'full_name': x['given'] + " " + x['family'],
'orcid': x.get("ORCID", "").replace("http://orcid.org/", "")} for x in r['author']]
p.ids = {'doi': ext_id}
return p
def europepmc_api_to_publication(ext_id, id_type):
# https://europepmc.org/docs/EBI_Europe_PMC_Web_Service_Reference.pdf
assert id_type in Publication.ID_TYPES, "id_type must be in {}".format(Publication.ID_TYPES.keys())
# Request the data
if id_type == "pmcid":
url = 'https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC{}&resulttype=core&format=json'
url = url.format(ext_id)
elif id_type == "doi":
url = "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DOI:%22{}%22&resulttype=core&format=json"
url = url.format(ext_id)
elif id_type == "pmid":
url = 'https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:{}%20AND%20SRC:MED&resulttype=core&format=json'
url = url.format(ext_id, id_type)
else:
raise ValueError("id_type must be in {}".format(Publication.ID_TYPES.keys()))
headers = {
'User-Agent': config['USER_AGENT_DEFAULT']
}
response = requests.get(url, headers=headers)
response.raise_for_status()
d = response.json()
if d['hitCount'] != 1:
raise ValueError("No results")
article = d['resultList']['result'][0]
p = Publication()
p.ref_url = url
p.source = "europepmc"
original_title = article['title']
# to remove trailing dot
# to exclude '...' and abbreviations such as U.S.A.
p.title = original_title
if original_title[-1] == '.' and original_title[-3] != '.':
p.title = original_title[:-1] # drop the trailing dot
authors = []
authorlist = article["authorList"]["author"]
for author in authorlist:
full_name = None
if 'firstName' in author and 'lastName' in author:
full_name = author['firstName'] + ' ' + author['lastName']
elif 'fullName' in author:
full_name = author['fullName']
elif 'collectiveName' in author:
full_name = author['collectiveName']
else:
msg = "unknown author: {}".format(author)
p.warnings.append(msg)
# orcids
orcid = None
if 'authorId' in author:
if author['authorId']['type'] == "ORCID":
orcid = author['authorId']['value']
authors.append({'full_name': full_name, 'orcid': orcid})
p.authors = authors
p.publication_date = du.parse(article['firstPublicationDate'])
p.volume = article['journalInfo'].get('volume')
p.issue = article['journalInfo'].get('issue')
p.pages = article.get('pageInfo')
p.ids = dict()
p.ids['doi'] = article.get('doi')
p.ids['pmid'] = article.get('pmid')
p.ids['pmcid'] = article.get('pmcid', '').replace("PMC", "")
if 'pageInfo' in article:
# according to documentation, they should be in the form : 145-178, but also "D36-42" has been in the responses
try:
pageString = article['pageInfo']
pageStringParts = pageString.split('-')
pageStartString = pageStringParts[0]
if pageStartString.startswith('D'):
pageStartString = pageStartString[1:]
pageStart = int(pageStartString)
pageEndString = pageStringParts[1]
pageEnd = int(pageEndString)
pages = pageEnd - pageStart + 1
p.number_of_pages = pages
except Exception:
pass
"""
# this is probably a list, and we need to be able to look up a qid from "NCI NIH HHS" for example...
if "grantsList" in article and "grant" in article['grantsList'] and "agency" in article['grantsList']["grant"]:
p.sponsor = article['grantsList']["grant"]["agency"]
"""
# get the type of publication
# if not told that it is a research-article, we will make it a general publication
isScientificArticle = False
if 'pubTypeList' in article:
pubtypes = article['pubTypeList']['pubType']
if isinstance(pubtypes, str):
if pubtypes == 'research-article':
isScientificArticle = True
elif isinstance(pubtypes, list):
if 'research-article' in pubtypes:
isScientificArticle = True
if isScientificArticle:
p.instance_of = "scientific_article"
else:
p.instance_of = "publication"
p.warnings.append("unknown publication type, assuming publication")
issns = []
if 'issn' in article['journalInfo']['journal']:
issns.append(article['journalInfo']['journal']['issn'])
elif 'essn' in article['journalInfo']['journal']:
issns.append(article['journalInfo']['journal']['essn'])
else:
msg = "unknown journal: {}".format(article['journalInfo']['journal'])
p.warnings.append(msg)
p.published_in_issn = issns
return p
class PublicationHelper:
SOURCE_FUNCT = {
'crossref': crossref_api_to_publication,
'europepmc': europepmc_api_to_publication,
}
def __init__(self, ext_id, id_type, source):
"""
PublicationHelper: Helper to create wikidata items about literature
Supported data sources and (ID types): crossref (doi), europepmc (pmid, pmcid, doi)
:param ext_id: the external ID to use
:type ext_id: str
:param id_type: one of {'pmid', 'pmcid', 'doi'}
:type id_type: str
:param source: one of {'crossref', 'europepmc'}
:type source: str
"""
assert source in self.SOURCE_FUNCT
self.f = self.SOURCE_FUNCT[source]
self.e = None
try:
self.p = self.f(ext_id, id_type=id_type)
except Exception as e:
self.p = None
self.e = e
def get_or_create(self, login):
"""
Get the qid of the item by its external id or create if doesn't exist
:param login: WDLogin item
:return: tuple of (qid, list of warnings (strings), success (True if success, returns the Exception otherwise))
"""
if self.p:
try:
return self.p.get_or_create(login)
except Exception as e:
return None, self.p.warnings, e
else:
return None, [], self.e
if __name__ == "__main__":
try:
from local import WDUSER, WDPASS
except ImportError:
if "WDUSER" in os.environ and "WDPASS" in os.environ:
WDUSER = os.environ['WDUSER']
WDPASS = os.environ['WDPASS']
else:
raise ValueError("WDUSER and WDPASS must be specified in local.py or as environment variables")
parser = argparse.ArgumentParser(description='run publication creator')
parser.add_argument("ext_id", help="comma-separated list of IDs")
parser.add_argument("--source", help="API to use (crossref or europepmc)", default="crossref")
parser.add_argument("--idtype", help="external id type (doi, pmcid, pmid, etc...)", default="doi")
args = parser.parse_args()
login = wdi_login.WDLogin(WDUSER, WDPASS)
ext_ids = sorted(list(set(map(str.strip, args.ext_id.split(",")))))
id_type = args.idtype
source = args.source
with open("log.txt", "a") as f:
for ext_id in ext_ids:
try:
p = PublicationHelper(ext_id, id_type=id_type, source=source)
qid, warnings, success = p.get_or_create(login)
print("{},{},{},{}".format(ext_id, qid, "|".join(warnings), success))
print("{},{},{},{}".format(ext_id, qid, "|".join(warnings), success), file=f)
sleep(3)
except Exception as e:
print("{},{},{},{}".format(ext_id, None, e, False))
print("{},{},{},{}".format(ext_id, None, e, False), file=f)