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Add ChemRxiv publications #170

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merged 5 commits into from Jan 24, 2021
Merged

Add ChemRxiv publications #170

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cd954f7
Add chemrxiv stub
cthoyt Jan 20, 2021
5a9f10b
Add chemrxiv uploader
cthoyt Jan 20, 2021
31bfdca
Update publication.py
cthoyt Jan 20, 2021
50f1d84
Reorganize author processing
cthoyt Jan 20, 2021
804782c
Update publication.py
cthoyt Jan 20, 2021
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35 changes: 35 additions & 0 deletions wikidataintegrator/wdi_helpers/publication.py
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Expand Up @@ -39,6 +39,7 @@ class Publication:
'europepmc': 'Q5412157',
'arxiv': 'Q118398',
'biorxiv': 'Q19835482',
'chemrxiv': 'Q50012382',
}

def __init__(self, title=None, instance_of=None, subtitle=None, authors=None,
Expand Down Expand Up @@ -209,6 +210,8 @@ def make_reference(self):
edt_id_id, ext_id_prop = self.ids['arxiv'], PROPS['arxiv id']
elif self.source == 'biorxiv':
edt_id_id, ext_id_prop = self.ids['biorxiv'], self.ID_TYPES['biorxiv']
elif self.source == 'chemrxiv':
edt_id_id, ext_id_prop = self.ids['doi'], self.ID_TYPES['doi']
else:
raise ValueError(f'Unhandled source: {self.source}')

Expand Down Expand Up @@ -548,12 +551,44 @@ def biorxiv_api_to_publication(biorxiv_id: str, id_type='biorxiv') -> Publicatio
return publication


def chemrxiv_api_to_publication(chemrxiv_id: str, id_type='chemrxiv') -> Publication:
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In theory, this could be used for other figshare *Rxiv servers as well, but the JSON response doesn't give any hints as to which database the result is actually part of

"""Make a :class:`Publication` from a ChemRxiv identifier."""
url = f'https://api.figshare.com/v2/articles/{chemrxiv_id}'
headers = {
'User-Agent': config['USER_AGENT_DEFAULT']
}
res = requests.get(url, headers=headers)
res.raise_for_status()
res_json = res.json()

publication = Publication(
title=res_json['title'],
ref_url=res_json['figshare_url'],
authors=[
{
'full_name': author['full_name'],
'orcid': author.get('orcid_id'),
}
for author in res_json['authors']
],
publication_date=datetime.datetime.strptime(res_json['published_date'], '%Y-%m-%dT%H:%M:%SZ'),
ids={
'doi': res_json['doi'],
},
source='chemrxiv',
)
publication.instance_of = 'preprint'
publication.published_in_qid = Publication.SOURCES['chemrxiv']
return publication


class PublicationHelper:
SOURCE_FUNCT = {
'crossref': crossref_api_to_publication,
'europepmc': europepmc_api_to_publication,
'arxiv': arxiv_api_to_publication,
'biorxiv': biorxiv_api_to_publication,
'chemrxiv': chemrxiv_api_to_publication,
}

def __init__(self, ext_id, id_type, source):
Expand Down