def save_publications_list(publications_list, orcid):
"""
Method to save the list of publications if the publication is not already in the database
"""
client = MongoClient(mongo_constants['server_name'],
mongo_constants['port_number'])
db = client[mongo_constants['database']]
coll = db[mongo_constants['publication_list']]
for publication in publications_list:
if coll.find({'doi': publication['doi']}).count() != 0:
pub = coll.find_one({'doi': publication['doi']})
if orcid not in pub['authorIDs']:
pub['authorIDs'].append(orcid)
coll.update({'doi': pub['doi']},
{"$unset": {
'authorIDs': pub['authorIDs']
}},
upsert=False,
multi=False)
coll.update({'doi': pub['doi']},
{"$set": {
'authorIDs': pub['authorIDs']
}},
upsert=False,
multi=False)
elif coll.find({'title': publication['title']}).count() != 0:
pub = coll.find_one({'title': publication['title']})
if orcid not in pub['authorIDs']:
pub['authorIDs'].append(orcid)
coll.update({'title': pub['title']},
{"$unset": {
'authorIDs': pub['authorIDs']
}},
upsert=False,
multi=False)
coll.update({'title': pub['title']},
{"$set": {
'authorIDs': pub['authorIDs']
}},
upsert=False,
multi=False)
else:
if orcid not in publication['authorIDs']:
publication['authorIDs'].append(orcid)
if 'doi' in publication:
ieee_doi_get_result = IEEE_Parser.ieee_doi_get_parser(
publication['doi'])
if ieee_doi_get_result is not None:
for key in ieee_doi_get_result:
if key not in publication:
publication[key] = ieee_doi_get_result[key]
if 'authors' in ieee_doi_get_result:
publication['authorsIeee'] = ieee_doi_get_result[
'authors']
publication['authorsSearched'] = 0
coll.insert(publication)
print 'Inserted Publication: ' + publication['doi']
def save_publications_list(publications_list, orcid):
"""
Method to save the list of publications if the publication is not already in the database
"""
client = MongoClient(mongo_constants['server_name'], mongo_constants['port_number'])
db = client[mongo_constants['database']]
coll = db[mongo_constants['publication_list']]
for publication in publications_list:
if coll.find({'doi': publication['doi']}).count() != 0:
pub = coll.find_one({'doi': publication['doi']})
if orcid not in pub['authorIDs']:
pub['authorIDs'].append(orcid)
coll.update({'doi': pub['doi']}, {"$unset": {'authorIDs': pub['authorIDs']}}, upsert=False, multi=False)
coll.update({'doi': pub['doi']}, {"$set": {'authorIDs': pub['authorIDs']}}, upsert=False, multi=False)
elif coll.find({'title': publication['title']}).count() != 0:
pub = coll.find_one({'title': publication['title']})
if orcid not in pub['authorIDs']:
pub['authorIDs'].append(orcid)
coll.update({'title': pub['title']}, {"$unset": {'authorIDs': pub['authorIDs']}}, upsert=False, multi=False)
coll.update({'title': pub['title']}, {"$set": {'authorIDs': pub['authorIDs']}}, upsert=False, multi=False)
else:
if orcid not in publication['authorIDs']:
publication['authorIDs'].append(orcid)
if 'doi' in publication:
ieee_doi_get_result = IEEE_Parser.ieee_doi_get_parser(publication['doi'])
if ieee_doi_get_result is not None:
for key in ieee_doi_get_result:
if key not in publication:
publication[key] = ieee_doi_get_result[key]
if 'authors' in ieee_doi_get_result:
publication['authorsIeee'] = ieee_doi_get_result['authors']
publication['authorsSearched'] = 0
coll.insert(publication)
print 'Inserted Publication: ' + publication['doi']
def orcid_author_works_get_parser(orcid):
"""
Method to parse the author works from ORCID website into a dictionary object, given the orcid of the author
"""
out_file = "data/orcid_author_works_get.xml"
fout = open(out_file, "w")
print >> fout, ORCID.orcid_author_works_get(orcid,
kind="xml").encode('utf-8')
fout.close()
tree = ET.parse(out_file)
root_element = tree.getroot()
ns = '{http://www.orcid.org/ns/orcid}'
author = {'works': []}
for child1 in root_element:
if (child1.tag == ns + 'orcid-profile'):
for child2 in child1:
if (child2.tag == ns + 'orcid-identifier'):
for child3 in child2:
if (child3.tag == ns + 'path'):
author['orcid'] = child3.text
elif (child2.tag == ns + 'orcid-activities'):
for child3 in child2:
if (child3.tag == ns + 'orcid-works'):
for child4 in child3:
if (child4.tag == ns + 'orcid-work'):
work = {
'identifiers': [],
'authorIDs': []
}
for child5 in child4:
if (child5.tag == ns +
'work-title'):
for child6 in child5:
if (child6.tag == ns +
'title'):
work[
'title'] = child6.text
elif (child5.tag == ns +
'journal-title'):
work[
'journalTitle'] = child5.text
elif (child5.tag == ns +
'work-citation'):
for child6 in child5:
if (child6.tag == ns +
'work-citation-type'
):
work[
'work-citation-type'] = child6.text
elif (child6.tag == ns +
'citation'):
citation = child6.text
if (work['work-citation-type']
== 'bibtex'):
work[
'authors'] = ORCID_Parser.get_authors_list_from_bibtex(
citation)
elif (work[
'work-citation-type']
==
'formatted-unspecified'):
work[
'authors'] = ORCID_Parser.get_authors_list_from_unformattedtext(
citation)
elif (child5.tag == ns +
'publication-date'):
for child6 in child5:
if (child6.tag == ns +
'year'):
work[
'year'] = child6.text
elif (child5.tag == ns +
'work-external-identifiers'):
for child6 in child5:
if (child6.tag == ns +
'work-external-identifier'
):
identifier = {}
for child7 in child6:
if (child7.tag ==
ns +
'work-external-identifier-type'
):
key = None
if (child7.text
==
'doi'):
key = 'doi'
elif (child7.tag ==
ns +
'work-external-identifier-id'
):
value = child7.text
if key is not None:
identifier[
key] = value
work[key] = value
work[
'identifiers'].append(
identifier)
if 'title' not in work:
work['title'] = ''
if 'doi' not in work:
publications = IEEE_Parser.ieee_publication_search_parser(
work['title'])
if (len(publications) == 1):
for publication in publications:
work['doi'] = publication[
'doi']
else:
work['doi'] = ''
if 'authors' not in work:
work['authors'] = []
author['works'].append(work)
return author
def orcid_author_works_get_parser(orcid):
"""
Method to parse the author works from ORCID website into a dictionary object, given the orcid of the author
"""
out_file = "data/orcid_author_works_get.xml"
fout = open(out_file, "w")
print >> fout, ORCID.orcid_author_works_get(orcid, kind="xml").encode('utf-8')
fout.close()
tree = ET.parse(out_file)
root_element = tree.getroot()
ns = '{http://www.orcid.org/ns/orcid}'
author = {'works': []}
for child1 in root_element:
if(child1.tag == ns + 'orcid-profile'):
for child2 in child1:
if(child2.tag == ns + 'orcid-identifier'):
for child3 in child2:
if(child3.tag == ns + 'path'):
author['orcid'] = child3.text
elif(child2.tag == ns + 'orcid-activities'):
for child3 in child2:
if(child3.tag == ns + 'orcid-works'):
for child4 in child3:
if(child4.tag == ns + 'orcid-work'):
work = {'identifiers': [], 'authorIDs': []}
for child5 in child4:
if(child5.tag == ns + 'work-title'):
for child6 in child5:
if(child6.tag == ns + 'title'):
work['title'] = child6.text
elif(child5.tag == ns + 'journal-title'):
work['journalTitle'] = child5.text
elif(child5.tag == ns + 'work-citation'):
for child6 in child5:
if(child6.tag == ns + 'work-citation-type'):
work['work-citation-type'] = child6.text
elif(child6.tag == ns + 'citation'):
citation = child6.text
if(work['work-citation-type'] == 'bibtex'):
work['authors'] = ORCID_Parser.get_authors_list_from_bibtex(citation)
elif(work['work-citation-type'] == 'formatted-unspecified'):
work['authors'] = ORCID_Parser.get_authors_list_from_unformattedtext(citation)
elif(child5.tag == ns + 'publication-date'):
for child6 in child5:
if(child6.tag == ns + 'year'):
work['year'] = child6.text
elif(child5.tag == ns + 'work-external-identifiers'):
for child6 in child5:
if(child6.tag == ns + 'work-external-identifier'):
identifier = {}
for child7 in child6:
if(child7.tag == ns + 'work-external-identifier-type'):
key = None
if(child7.text == 'doi'):
key = 'doi'
elif(child7.tag == ns + 'work-external-identifier-id'):
value = child7.text
if key is not None:
identifier[key] = value
work[key] = value
work['identifiers'].append(identifier)
if 'title' not in work:
work['title'] = ''
if 'doi' not in work:
publications = IEEE_Parser.ieee_publication_search_parser(work['title'])
if(len(publications) == 1):
for publication in publications:
work['doi'] = publication['doi']
else:
work['doi'] = ''
if 'authors' not in work:
work['authors'] = []
author['works'].append(work)
return author