__license__ = "BSD 3-Clause license"
__version__ = "0.1"
import vivotools as vt
from datetime import datetime
from Bio import Entrez
print datetime.now(),"Start"
pmids = [
"18068940",
"18089571",
"19206997",
"21822356",
"19247798",
"21493414",
"12099768",
"11410031",
"20143936",
"16934145"
]
for pmid in pmids:
handle = Entrez.efetch(db="pubmed", id=pmid, retmode="xml")
records = Entrez.parse(handle)
for record in records:
print "\n",pmid,"\n", \
vt.string_from_document(vt.document_from_pubmed(record))
print datetime.now(),"Finish"
#
# to get PubMed publications from the Harvard service, we need a person's email address and name. Middle can be empty ("")
#
first = "Michael"
middle = ""
last = "Conlon"
email = "*****@*****.**"
#
# call the Harvard Catalyst service to get a list of PMIDs for this author
#
print "Results for ",first,middle,last,email
result = vivotools.catalyst_pmid_request(first,middle,last,email)
dom = parseString(result) # create a document Object Model (DOM) from the Harvard Catalyst result
#
# For each PMID in the DOM, grab the ID from the DOM, call Pubmed, display the results
#
for node in dom.getElementsByTagName('PMID'):
pmid = node.toxml()
pmid = pmid.replace('<PMID>','')
pmid = pmid.replace('</PMID>','')
handle = Entrez.efetch(db="pubmed", id=pmid, retmode="xml")
records = Entrez.parse(handle)
for record in records:
doc = vivotools.document_from_pubmed(record)
[found,uri] = vivotools.find_title(doc['title'],title_dictionary)
print
print found,uri
print vivotools.string_from_document(doc)
[pubmed_rdf, sub] = vivotools.update_pubmed(publication_uri,\
value.fields['doi'])
if sub != "":
raise Exception("Non empty subtraction RDF"+\
"for Update PubMed")
# Publication
publication_rdf = make_publication_rdf(value,\
title,publication_uri,datetime_uri,authorship_uris)
print >>rdf_file, datetime_rdf, publisher_rdf, journal_rdf,\
publisher_journal_rdf, author_rdf, authorship_rdf,\
author_in_authorship_rdf, journal_publication_rdf,\
publication_rdf, pubmed_rdf
print >> rdf_file, "<!-- End RDF for " + title + " -->"
print >>lst_file, vivotools.string_from_document(document),\
'VIVO uri', publication_uri, '\n'
update_disambiguation_report(authors, publication_uri)
else:
title_report[title][0] = "Found"
title_report[title][1] = uri
print >> rdf_file, "<!-- Found: " + title + " No RDF necessary -->"
print >> rdf_file, vivotools.rdf_footer()
#
# Reports
#
print >> rpt_file, """
Publisher Report
[pubmed_rdf, sub] = vivotools.update_pubmed(publication_uri,\
value.fields['doi'])
if sub != "":
raise Exception("Non empty subtraction RDF"+\
"for Update PubMed")
# Publication
publication_rdf = make_publication_rdf(value,\
title,publication_uri,datetime_uri,authorship_uris)
print >>rdf_file, datetime_rdf, publisher_rdf, journal_rdf,\
publisher_journal_rdf, author_rdf, authorship_rdf,\
author_in_authorship_rdf, journal_publication_rdf,\
publication_rdf, pubmed_rdf
print >>rdf_file, "<!-- End RDF for " + title + " -->"
print >>lst_file, vivotools.string_from_document(document),\
'VIVO uri', publication_uri, '\n'
update_disambiguation_report(authors, publication_uri)
else:
title_report[title][0] = "Found"
title_report[title][1] = uri
print >>rdf_file, "<!-- Found: " + title + " No RDF necessary -->"
print >>rdf_file, vivotools.rdf_footer()
#
# Reports
#
print >>rpt_file,"""
Publisher Report
if 'date' in pub and 'publication_type' in pub and \
pub['publication_type'] == 'academic-article':
key = pub['date']['year']+pub['title']
publications[key] = pub
last_pub = min(25, len(publications))
npub = 0
for key in sorted(publications.keys(), reverse=True):
npub = npub + 1
if npub > last_pub:
break
pub = publications[key]
para_props = ParagraphPropertySet()
para_props.SetFirstLineIndent(-720)
para_props.SetLeftIndent(720)
p = Paragraph(ss.ParagraphStyles.Normal, para_props)
p.append(str(npub), ". ", vt.string_from_document(pub))
section.append(p)
# Section D -- Research Support
p = Paragraph(ss.ParagraphStyles.Heading3)
p.append("D.", TAB, "Research Support")
section.append(p)
grants = {}
print person['grants']
for grant in person['grants']:
if 'end_date' in grant and 'title' in grant and \
datetime.datetime(int(grant['end_date']['date']['year']),
int(grant['end_date']['date']['month']),
int(grant['end_date']['date']['day'])) + \
for grant in person['grants']:
try:
print 'grant',\
int(grant['start_date']['date']['year']), int(year)
except:
continue
if int(grant['start_date']['date']['year']) >= int(year):
para_props = ParagraphPropertySet()
para_props.SetFirstLineIndent(TabPropertySet.DEFAULT_WIDTH*-1)
para_props.SetLeftIndent(TabPropertySet.DEFAULT_WIDTH*2)
p = Paragraph(ss.ParagraphStyles.Normal, para_props)
p.append(vt.string_from_grant(grant))
section.append(p)
if len(person['publications']) > 0:
for publication in person['publications']:
try:
print 'pub', int(publication['date']['year']), int(year)
except:
continue
if int(publication['date']['year']) >= int(year):
para_props = ParagraphPropertySet()
para_props.SetFirstLineIndent(TabPropertySet.DEFAULT_WIDTH*-1)
para_props.SetLeftIndent(TabPropertySet.DEFAULT_WIDTH*2)
p = Paragraph(ss.ParagraphStyles.Normal, para_props)
p.append(vt.string_from_document(publication))
section.append(p)
print str(datetime.datetime.now())
Renderer().Write(doc, file("report.rtf", "w"))
# to get PubMed publications from the Harvard service, we need a person's email address and name. Middle can be empty ("")
#
first = "Michael"
middle = ""
last = "Conlon"
email = "*****@*****.**"
#
# call the Harvard Catalyst service to get a list of PMIDs for this author
#
print "Results for ",first,middle,last,email
result = vivotools.catalyst_pmid_request(first,middle,last,email)
dom = parseString(result) # create a document Object Model (DOM) from the Harvard Catalyst result
#
# For each PMID in the DOM, grab the ID from the DOM, call Pubmed, display the results
#
for node in dom.getElementsByTagName('PMID'):
pmid = node.toxml()
pmid = pmid.replace('<PMID>','')
pmid = pmid.replace('</PMID>','')
handle = Entrez.efetch(db="pubmed", id=pmid, retmode="xml")
records = Entrez.parse(handle)
for record in records:
doc = vivotools.document_from_pubmed(record)
[found,uri] = vivotools.find_title(doc['title'],title_dictionary)
print
print found,uri
print vivotools.string_from_document(doc)
if 'date' in pub and 'publication_type' in pub and \
pub['publication_type'] == 'academic-article':
key = pub['date']['year'] + pub['title']
publications[key] = pub
last_pub = min(25, len(publications))
npub = 0
for key in sorted(publications.keys(), reverse=True):
npub = npub + 1
if npub > last_pub:
break
pub = publications[key]
para_props = ParagraphPropertySet()
para_props.SetFirstLineIndent(-720)
para_props.SetLeftIndent(720)
p = Paragraph(ss.ParagraphStyles.Normal, para_props)
p.append(str(npub), ". ", vt.string_from_document(pub))
section.append(p)
# Section D -- Research Support
p = Paragraph(ss.ParagraphStyles.Heading3)
p.append("D.", TAB, "Research Support")
section.append(p)
grants = {}
print person['grants']
for grant in person['grants']:
if 'end_date' in grant and 'title' in grant and \
datetime.datetime(int(grant['end_date']['date']['year']),
int(grant['end_date']['date']['month']),
int(grant['end_date']['date']['day'])) + \
"""
__author__ = "Michael Conlon"
__copyright__ = "Copyright 2013, University of Florida"
__license__ = "BSD 3-Clause license"
__version__ = "0.1"
import vivotools as vt
from datetime import datetime
import json
print datetime.now(), "Start"
publications = [
"http://vivo.ufl.edu/individual/n2592711416",
"http://vivo.ufl.edu/individual/n49408",
"http://vivo.ufl.edu/individual/n5988333327",
"http://vivo.ufl.edu/individual/n697590874",
"http://vivo.ufl.edu/individual/n7170943995",
"http://vivo.ufl.edu/individual/no-such-pub",
"http://vivo.ufl.edu/individual/n536643140",
"http://vivo.ufl.edu/individual/n5202165124",
"http://vivo.ufl.edu/individual/n898775618",
"http://vivo.ufl.edu/individual/n5755807043"
]
for publication in publications:
pub = vt.get_publication(publication, get_authors=True)
print "\n", json.dumps(pub, indent=4)
print vt.string_from_document(pub)
print datetime.now(), "Finish"
"""
__author__ = "Michael Conlon"
__copyright__ = "Copyright 2013, University of Florida"
__license__ = "BSD 3-Clause license"
__version__ = "0.1"
import vivotools as vt
from datetime import datetime
import json
print datetime.now(),"Start"
publications = [
"http://vivo.ufl.edu/individual/n2592711416",
"http://vivo.ufl.edu/individual/n49408",
"http://vivo.ufl.edu/individual/n5988333327",
"http://vivo.ufl.edu/individual/n697590874",
"http://vivo.ufl.edu/individual/n7170943995",
"http://vivo.ufl.edu/individual/no-such-pub",
"http://vivo.ufl.edu/individual/n536643140",
"http://vivo.ufl.edu/individual/n5202165124",
"http://vivo.ufl.edu/individual/n898775618",
"http://vivo.ufl.edu/individual/n5755807043"
]
for publication in publications:
pub = vt.get_publication(publication, get_authors=True)
print "\n",json.dumps(pub, indent=4)
print vt.string_from_document(pub)
print datetime.now(),"Finish"