def post(self):
json = request.json
abort_if_invalid_request_params(json, ['code', 'name'])
organization = Organization()
organization.code = json['code']
organization.name = json['name']
if 'description' in json:
organization.description = json['description']
organization.save()
return me_obj_to_serializable(organization)
def get_orgs(self):
url = 'http://registry.usa.gov/accounts.json?service_id=github'
r = requests.get(url)
if r.status_code == 200:
for acct in r.json['accounts']:
org = Organization.query.filter_by(username=acct['account']).first()
if org is None:
org = Organization()
org.name = acct['organization']
org.username = acct['account']
db.session.add(org)
db.session.commit()
else:
print 'Error importing organizations'
def get(self):
self.response.headers['Content-Type'] = 'application/json'
user = User.get_by_username(self.request.get('username'))
new = False
if len(self.request.get('organization')) > 0:
organization = Organization.get_by_key(self.request.get('organization'))
else:
new = True
organization = Organization()
organization.owner = user.key
if new or len(self.request.get('name')) > 0:
organization.name = self.request.get('name')
if new or len(self.request.get('owner')) > 0:
organization.owner = self.request.get('owner')
if new or len(self.request.get('address1')) > 0:
organization.address1 = self.request.get('address1')
if new or len(self.request.get('address2')) > 0:
organization.address2 = self.request.get('address2')
if new or len(self.request.get('city')) > 0:
organization.city = self.request.get('city')
if new or len(self.request.get('zipcode')) > 0:
organization.zipcode = self.request.get('zipcode')
if new or len(self.request.get('state')) > 0:
organization.state = self.request.get('state')
if new or len(self.request.get('country')) > 0:
organization.country = self.request.get('country')
if new or len(self.request.get('phone')) > 0:
organization.phone = self.request.get('phone')
if new or len(self.request.get('notes')) > 0:
organization.notes = self.request.get('notes')
organization.put()
if OrganizationUser.get_combo(user.key, organization.key) is None:
organizationUser = OrganizationUser()
organizationUser.user = user.key
organizationUser.organization = organization.key
organizationUser.put()
self.response.write(json.dumps({'status': 0, 'message': 'La escuela fue agregada/modificada.', 'organization': {'key': organization.key.urlsafe(), 'name': organization.name, 'address1': organization.address1, 'address2': organization.address2, 'zipcode': organization.zipcode, 'state': organization.state, 'country': organization.country, 'notes': organization.notes}}))
def org_edit(id=0):
setExits()
id = cleanRecordID(id)
if id < 0:
flash("That is not a valid ID")
return redirect(g.listURL)
timeZones = getTimeZones()
if not request.form:
""" if no form object, send the form page """
# get the Org record if you can
rec = None
if int(id) > 0:
rec = Organization.query.get(id)
return render_template('org/org_edit.html', rec=rec, timeZones=timeZones)
#have the request form
if validForm():
if id > 0:
rec = Organization.query.get(id)
else:
## create a new record stub
rec = Organization(request.form['name'],request.form['email'],request.form["defaultTimeZone"])
db.session.add(rec)
#update the record
rec.name = request.form['name']
rec.email = request.form['email']
rec.defaultTimeZone = request.form["defaultTimeZone"]
try:
db.session.commit()
except Exception as e:
flash(printException('Error attempting to create '+g.title+' record.',"error",e))
db.session.rollback()
return redirect(url_for('.org_list'))
# form not valid - redisplay
return render_template('org/org_edit.html', rec=request.form, timeZones=timeZones)
def extract_paper_info(self):
# DOI
doi = self.soup.teiheader.find("idno", type="DOI")
if doi:
self.paper.doi = elem_to_text(doi)
elif self.document:
self.paper.doi = self.document['doi']
# Title
title = self.soup.teiheader.find("title")
if title:
self.paper.title = elem_to_text(title)
# Authors
authors = self.get_authors(self.soup.analytic.find_all('author'))
if authors:
self.paper.authors = authors
if self.soup.abstract:
self.paper.abstract = elem_to_text(self.soup.abstract)
# Year
published = self.soup.analytic.find("publicationstmt")
if published:
self.paper.year = elem_to_text(published.find("date", type="when"))
# Organization / Affiliations
affiliations = self.soup.analytic.find_all('affiliation')
for affiliation in affiliations:
org = Organization()
org.type = "institution"
org.name = elem_to_text(affiliation.find("orgname", type="institution"))
address = Address()
addr = affiliation.find("address")
if addr:
address.place = elem_to_text(addr.find("settlement"))
address.region = elem_to_text(addr.find("region"))
address.country = elem_to_text(addr.find("country"))
org.address = address
self.paper.affiliations.append(org)
# University Ranking
if self.paper.affiliations:
if self.paper.affiliations[0] != '':
self.paper.uni_rank = self.uni_rank.get_rank(self.paper.affiliations[0].name)
elif len(self.paper.affiliations) > 1:
self.paper.uni_rank = self.uni_rank.get_rank(self.paper.affiliations[1].name)
else:
self.paper.uni_rank = self.uni_rank.get_rank('Random')
# Citations
bibliography = self.soup.listbibl.find_all('biblstruct')
for bibl in bibliography:
citation = Citation()
cited_paper = bibl.analytic
if cited_paper:
citation.title = elem_to_text(cited_paper.find("title", type="main"))
citation_authors = self.get_authors(cited_paper.find_all("author"))
citation.doi = elem_to_text(cited_paper.find("idno", type="DOI"))
if citation_authors:
citation.authors = citation_authors
cited_journal = bibl.monogr
if cited_journal:
citation.source = elem_to_text(cited_journal.find("title"))
try:
citation.publish_year = cited_journal.imprint.date['when']
except TypeError:
pass
self.paper.citations.append(citation)
# NER - Ack pairs - Funding status
self.paper.ack_pairs = self.get_funding_status()
er_list = [org for (entity, org) in self.paper.ack_pairs]
if 'ORG' in er_list:
self.paper.funded = 1
else:
self.paper.funded = 0
# SJR
api_resp = self.get_sjr(self.paper.doi, self.paper.title,self.db)
# Adding the paragraphs from the paper to the corpus
extractor = ClaimEvidenceExtractor(self.xml, self.soup,self.test_csv)
os.chdir("/scifact/")
extractor.make_corpus()
# Get response for claim evidence using request to API
response = requests.get('http://0.0.0.0:8000/getclaimevidence')
print(response)
self.support, self.refute, self.ratio = extractor.get_results()
print('support:',self.support,'refute:',self.refute,'ratio:',self.ratio)
os.chdir("../")
if api_resp:
self.paper.cited_by_count = api_resp["num_citations"]
self.paper.sjr = api_resp["sjr"]
self.paper.subject = api_resp["subject"]
self.paper.subject_code = api_resp["subject_code"]
self.paper.normalized = api_resp["normalized_citations"]
self.paper.velocity = api_resp["citationVelocity"]
self.paper.influentialcitations = api_resp["influentialCitationCount"]
self.paper.references = api_resp["references_count"]
self.paper.flag = api_resp["openaccessflag"]
self.paper.influentialref = api_resp["influentialReferencesCount"]
self.paper.ref_background = api_resp["reference_background"]
self.paper.ref_result = api_resp["reference_result"]
self.paper.ref_method = api_resp["reference_methodology"]
self.paper.cite_background = api_resp["citations_background"]
self.paper.cite_result = api_resp["citations_result"]
self.paper.cite_method = api_resp["citations_methodology"]
self.paper.cite_next = api_resp["citations_next"]
self.paper.influential_references_methodology = api_resp["upstream_influential_methodology_count"]
self.paper.issn = api_resp["ISSN"]
self.paper.auth = api_resp["authors"]
self.paper.age = api_resp["age"]
if api_resp["abstract"]:
self.paper.abstract = api_resp["abstract"]
# Set self-citations
self.paper.self_citations = self.paper.set_self_citations()
# return paper
#calculate coCitations
t2,t3 = coCite(self.paper.doi, self.db)
#calculate NLP features
reading_score = self.get_reading_score(self.paper.abstract)
subjectivity = self.get_subjectivity(self.paper.abstract)
sentiment = self.get_sentiment(self.paper.abstract)
return {"doi": self.paper.doi, "title": self.paper.title, "num_citations": self.paper.cited_by_count,
"author_count": len(self.paper.authors),"sjr": self.paper.sjr, "u_rank": self.paper.uni_rank,
"funded": self.paper.funded,"self_citations": self.paper.self_citations, "subject": self.paper.subject,
"subject_code": self.paper.subject_code, "citationVelocity": self.paper.velocity,
"influentialCitationCount": self.paper.influentialcitations, "references_count": self.paper.references,
"openaccessflag": self.paper.flag, "influentialReferencesCount": self.paper.influentialref,
"normalized_citations": self.paper.normalized, "reference_background": self.paper.ref_background,
"reference_result": self.paper.ref_result, "reference_methodology": self.paper.ref_method,
"citations_background": self.paper.cite_background, "citations_result": self.paper.cite_result,
"citations_methodology": self.paper.cite_method, "citations_next": self.paper.cite_next,
"upstream_influential_methodology_count": self.paper.influential_references_methodology,
"coCite2":t2, "coCite3":t3, "ISSN":self.paper.issn, "authors":self.paper.auth,"citations":api_resp["citations"],"age":self.paper.age,
"reading_score":reading_score, "subjectivity":subjectivity, "sentiment":sentiment, "supporting_sentences":self.support, "refuting_sentences":self.refute, "ratio_support":self.ratio}
def extract_paper_info(self):
# DOI
doi = self.soup.teiheader.find("idno", type="DOI")
if doi:
self.paper.doi = elem_to_text(doi)
elif self.document:
self.paper.doi = self.document['doi']
# Title
title = self.soup.teiheader.find("title")
if title:
self.paper.title = elem_to_text(title)
# Authors
authors = self.get_authors(self.soup.analytic.find_all('author'))
if authors:
self.paper.authors = authors
# Year
published = self.soup.analytic.find("publicationstmt")
if published:
self.paper.year = elem_to_text(published.find("date", type="when"))
# Organization / Affiliations
affiliations = self.soup.analytic.find_all('affiliation')
for affiliation in affiliations:
org = Organization()
org.type = "institution"
org.name = elem_to_text(
affiliation.find("orgname", type="institution"))
address = Address()
addr = affiliation.find("address")
if addr:
address.place = elem_to_text(addr.find("settlement"))
address.region = elem_to_text(addr.find("region"))
address.country = elem_to_text(addr.find("country"))
org.address = address
self.paper.affiliations.append(org)
# University Ranking
if self.paper.affiliations:
if self.paper.affiliations[0] != '':
self.paper.uni_rank = self.uni_rank.get_rank(
self.paper.affiliations[0].name)
elif len(self.paper.affiliations) > 1:
self.paper.uni_rank = self.uni_rank.get_rank(
self.paper.affiliations[1].name)
else:
self.paper.uni_rank = self.uni_rank.get_rank('Random')
# Citations
bibliography = self.soup.listbibl.find_all('biblstruct')
for bibl in bibliography:
citation = Citation()
cited_paper = bibl.analytic
if cited_paper:
citation.title = elem_to_text(
cited_paper.find("title", type="main"))
citation_authors = self.get_authors(
cited_paper.find_all("author"))
citation.doi = elem_to_text(
cited_paper.find("idno", type="DOI"))
if citation_authors:
citation.authors = citation_authors
cited_journal = bibl.monogr
if cited_journal:
citation.source = elem_to_text(cited_journal.find("title"))
try:
citation.publish_year = cited_journal.imprint.date['when']
except TypeError:
pass
self.paper.citations.append(citation)
# NER - Ack pairs - Funding status
self.paper.ack_pairs = self.get_funding_status()
er_list = [org for (entity, org) in self.paper.ack_pairs]
if 'ORG' in er_list:
self.paper.funded = 1
else:
self.paper.funded = 0
# SJR
api_resp = self.get_sjr(self.paper.doi, self.paper.title)
if api_resp:
self.paper.cited_by_count = api_resp["num_citations"]
self.paper.sjr = api_resp["sjr"]
self.paper.subject = api_resp["subject"]
self.paper.subject_code = api_resp["subject_code"]
self.paper.normalized = api_resp["normalized_citations"]
self.paper.velocity = api_resp["citationVelocity"]
self.paper.influentialcitations = api_resp[
"influentialCitationCount"]
self.paper.references = api_resp["references_count"]
self.paper.flag = api_resp["openaccessflag"]
self.paper.influentialref = api_resp["influentialReferencesCount"]
self.paper.ref_background = api_resp["reference_background"]
self.paper.ref_result = api_resp["reference_result"]
self.paper.ref_method = api_resp["reference_methodology"]
self.paper.cite_background = api_resp["citations_background"]
self.paper.cite_result = api_resp["citations_result"]
self.paper.cite_method = api_resp["citations_methodology"]
self.paper.cite_next = api_resp["citations_next"]
# Set self-citations
self.paper.self_citations = self.paper.set_self_citations()
# Set influential_methodology_references
self.paper.influential_references_methodology = self.set_influential_references_methodology(
)
# return paper
t2, t3 = coCite(self.paper.doi)
return {
"doi": self.paper.doi,
"title": self.paper.title,
"num_citations": self.paper.cited_by_count,
"author_count": len(self.paper.authors),
"sjr": self.paper.sjr,
"u_rank": self.paper.uni_rank,
"funded": self.paper.funded,
"self_citations": self.paper.self_citations,
"subject": self.paper.subject,
"subject_code": self.paper.subject_code,
"citationVelocity": self.paper.velocity,
"influentialCitationCount": self.paper.influentialcitations,
"references_count": self.paper.references,
"openaccessflag": self.paper.flag,
"influentialReferencesCount": self.paper.influentialref,
"normalized_citations": self.paper.normalized,
"reference_background": self.paper.ref_background,
"reference_result": self.paper.ref_result,
"reference_methodology": self.paper.ref_method,
"citations_background": self.paper.cite_background,
"citations_result": self.paper.cite_result,
"citations_methodology": self.paper.cite_method,
"citations_next": self.paper.cite_next,
"upstream_influential_methodology_count":
self.paper.influential_references_methodology,
"coCite2": t2,
"coCite3": t3
}
