def t32_faculty(faculty):
"""
Given faculty participating in a T32, augment with VIVO data for
attributes of interest to the NIH
"""
new_faculty = {}
for row, f in faculty.items():
uri = find_person(f['UFID'])
person = vt.get_person(uri, get_positions=True, get_degrees=True)
f['rank'] = person['preferred_title']
f['degrees'] = person['degrees']
f['positions'] = person['positions']
new_faculty[row] = f
return new_faculty
print "\nOrganization"
print vt.get_organization("http://vivo.ufl.edu/individual/n182882417")
print vt.remove_uri("http://vivo.ufl.edu/individual/n182882417")
print "\nAuthorship"
print vt.get_authorship("http://vivo.ufl.edu/individual/n148010391")
print vt.remove_uri("http://vivo.ufl.edu/individual/n148010391")
print "\nRole"
print vt.get_role("http://vivo.ufl.edu/individual/n1864549239")
print vt.remove_uri("http://vivo.ufl.edu/individual/n1864549239")
print "\nPerson"
print vt.get_person("http://vivo.ufl.edu/individual/n39051")
print vt.remove_uri("http://vivo.ufl.edu/individual/n39051")
print "\nNot Found"
print vt.remove_uri("http://vivo.ufl.edu/notfound")
print "\nPublication Venue"
print vt.get_publication("http://vivo.ufl.edu/individual/n378789540")
print vt.remove_uri("http://vivo.ufl.edu/individual/n378789540")
print "\nGrant"
print vt.get_grant("http://vivo.ufl.edu/individual/n614029206")
print vt.remove_uri("http://vivo.ufl.edu/individual/n614029206")
print "\nWebpage"
print vt.get_webpage("http://vivo.ufl.edu/individual/n104143")
print vt.remove_uri("http://vivo.ufl.edu/individual/n182882417")
print "\nOrganization"
print vt.get_organization("http://vivo.ufl.edu/individual/n182882417")
print vt.remove_uri("http://vivo.ufl.edu/individual/n182882417")
print "\nAuthorship"
print vt.get_authorship("http://vivo.ufl.edu/individual/n148010391")
print vt.remove_uri("http://vivo.ufl.edu/individual/n148010391")
print "\nRole"
print vt.get_role("http://vivo.ufl.edu/individual/n1864549239")
print vt.remove_uri("http://vivo.ufl.edu/individual/n1864549239")
print "\nPerson"
print vt.get_person("http://vivo.ufl.edu/individual/n39051")
print vt.remove_uri("http://vivo.ufl.edu/individual/n39051")
print "\nNot Found"
print vt.remove_uri("http://vivo.ufl.edu/notfound")
print "\nPublication Venue"
print vt.get_publication("http://vivo.ufl.edu/individual/n378789540")
print vt.remove_uri("http://vivo.ufl.edu/individual/n378789540")
print "\nGrant"
print vt.get_grant("http://vivo.ufl.edu/individual/n614029206")
print vt.remove_uri("http://vivo.ufl.edu/individual/n614029206")
print "\nWebpage"
print vt.get_webpage("http://vivo.ufl.edu/individual/n104143")
Disambiguation Report
For each publication with one or more authors to disambiguate, list the paper, and
then the authors in question with each of the possible URIs to be disambiguated, show the URI
of the paper, and then for each author that needs to be disambiguated on the paper, show
the last name, first name and middle initial and the all the URIs in VIVO for UF persons
with the same names.
"""
for uri in disambiguation_report.keys():
print >> rpt_file, "The publication at", uri, "has one or more authors in question"
for key, value in disambiguation_report[uri].items():
uris = value[9].split(";")
print >> rpt_file, " ", value[4], value[5], value[6], ":"
for u in uris:
person = vivotools.get_person(u)
if 'last_name' not in person:
person['last_name'] = "No last name"
if 'middle_name' not in person:
person['middle_name'] = "No middle name"
if 'first_name' not in person:
person['first_name'] = "No first name"
if 'home_department_name' not in person:
person['home_department_name'] = "No home department"
npubs = len(person['authorship_uris'])
print >>rpt_file," ",u,person['last_name'], \
person['first_name'],person['middle_name'], \
person['home_department_name'],"Number of pubs = ",npubs
print >> rpt_file
print >> rpt_file
#
from rtfng.Renderer import Renderer
from rtfng.Elements import Document, PAGE_NUMBER
from rtfng.Styles import TextStyle, ParagraphStyle
from rtfng.document.section import Section
from rtfng.document.paragraph import Paragraph, Table, Cell
from rtfng.document.character import B, I
from rtfng.PropertySets import MarginsPropertySet, BorderPropertySet, \
FramePropertySet, TabPropertySet, TextPropertySet, ParagraphPropertySet
from rtfng.document.base import TAB
# Start here. Get person data. Setup the document
print str(datetime.datetime.now())
person = vt.get_person("http://vivo.ufl.edu/individual/n25562",
get_positions=True, get_publications=True, get_degrees=True,
get_grants=True)
##person = vt.get_person("http://vivo.ufl.edu/individual/n31445",
## get_positions=True, get_publications=True, get_degrees=True,
## get_grants=True)
##person = vt.get_person("http://vivo.ufl.edu/individual/n11937",
## get_positions=True, get_publications=True, get_degrees=True,
## get_grants=True)
if 'overview' not in person:
person['overview'] = ''
if 'era_commons' not in person:
person['era_commons'] = ''
if 'first_name' not in person:
person['first_name'] = ''
if 'last_name' not in person:
person['last_name'] = ''
#
print datetime.now(),"Start"
data = vt.read_csv("name-parts.csv")
print datetime.now(),"Source data has",len(data),"elements"
ardf = vt.rdf_header()
srdf = vt.rdf_header()
i = 0
for row in sorted(data.keys()):
i = i + 1
[last,first,middle,suffix] = name_parts(data[row]['display_name'])
print i,data[row]['display_name'],":",last,first,middle,suffix
uri = data[row]['uri']
person = vt.get_person(uri)
if not 'last_name' in person:
person['last_name'] = None
if not 'first_name' in person:
person['first_name'] = None
if not 'middle_name' in person:
person['middle_name'] = None
if not 'name_suffix' in person:
person['name_suffix'] = None
[add,sub] = vt.update_data_property(uri,'foaf:lastName',person['last_name'],last)
ardf = ardf + add
srdf = srdf + sub
[add,sub] = vt.update_data_property(uri,'foaf:firstName',person['first_name'],first)
ardf = ardf + add
srdf = srdf + sub
[add,sub] = vt.update_data_property(uri,'vivo:middleName',person['middle_name'],middle)
Disambiguation Report
For each publication with one or more authors to disambiguate, list the paper, and
then the authors in question with each of the possible URIs to be disambiguated, show the URI
of the paper, and then for each author that needs to be disambiguated on the paper, show
the last name, first name and middle initial and the all the URIs in VIVO for UF persons
with the same names.
"""
for uri in disambiguation_report.keys():
print >>rpt_file,"The publication at",uri,"has one or more authors in question"
for key,value in disambiguation_report[uri].items():
uris = value[9].split(";")
print >>rpt_file," ",value[4],value[5],value[6],":"
for u in uris:
person = vivotools.get_person(u)
if 'last_name' not in person:
person['last_name'] = "No last name"
if 'middle_name' not in person:
person['middle_name'] = "No middle name"
if 'first_name' not in person:
person['first_name'] = "No first name"
if 'home_department_name' not in person:
person['home_department_name'] = "No home department"
npubs = len(person['authorship_uris'])
print >>rpt_file," ",u,person['last_name'], \
person['first_name'],person['middle_name'], \
person['home_department_name'],"Number of pubs = ",npubs
print >>rpt_file
print >>rpt_file
#
previousYear = year
p = Paragraph(ss.ParagraphStyles.Heading2)
p. append(rfa)
section.append(p)
previousRFA = rfa
elif previousRFA != rfa:
p = Paragraph(ss.ParagraphStyles.Heading2)
p. append(rfa)
section.append(p)
previousRFA = rfa
[found_person, person_uri] = vt.find_person(ufid, ufid_dictionary)
if not found_person:
print '\n', n, name, "not Found", "ufid", ufid
continue
person = vt.get_person(person_uri, get_publications=True, get_grants=True)
p = Paragraph(ss.ParagraphStyles.Heading3)
p. append(title)
section.append(p)
p = Paragraph(ss.ParagraphStyles.Heading4)
p. append(name)
section.append(p)
if len(person['grants']) > 0:
for grant in person['grants']:
try:
print 'grant',\
int(grant['start_date']['date']['year']), int(year)
except:
continue
"""
test_get_person.py -- Given a URIof a person entity in VIVO, return a
python sturcture containing attrbutes of the person
Version 0.1 MC 2013-12-27
-- Initial version.
"""
__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
print datetime.now(),"Start"
print "\n",vt.get_person("http://vivo.ufl.edu/individual/n13049",get_grants=True,
get_publications=True,get_positions=True) # Richard Macmaster
print "\n",vt.get_person("http://vivo.ufl.edu/individual/n3698",
get_positions=True) # Chelsea Dinsmore
print "\n",vt.get_person("http://vivo.ufl.edu/individual/n25562",
get_degrees=True) # Mike Conlon
print "\n",vt.get_person("http://vivo.ufl.edu/individual/n1770144435",
get_positions=True) # Colleen Abad
print datetime.now(),"Finish"
from rtfng.Renderer import Renderer
from rtfng.Elements import Document, PAGE_NUMBER
from rtfng.Styles import TextStyle, ParagraphStyle
from rtfng.document.section import Section
from rtfng.document.paragraph import Paragraph, Table, Cell
from rtfng.document.character import B, I
from rtfng.PropertySets import MarginsPropertySet, BorderPropertySet, \
FramePropertySet, TabPropertySet, TextPropertySet, ParagraphPropertySet
from rtfng.document.base import TAB
# Start here. Get person data. Setup the document
print str(datetime.datetime.now())
person = vt.get_person("http://vivo.ufl.edu/individual/n25562",
get_positions=True,
get_publications=True,
get_degrees=True,
get_grants=True)
##person = vt.get_person("http://vivo.ufl.edu/individual/n31445",
## get_positions=True, get_publications=True, get_degrees=True,
## get_grants=True)
##person = vt.get_person("http://vivo.ufl.edu/individual/n11937",
## get_positions=True, get_publications=True, get_degrees=True,
## get_grants=True)
if 'overview' not in person:
person['overview'] = ''
if 'era_commons' not in person:
person['era_commons'] = ''
if 'first_name' not in person:
person['first_name'] = ''
if 'last_name' not in person:
ufid = row['ufid']
if ufid.startswith('http'):
uri = ufid
ufid = None
else:
uri = find_vivo_uri("ufVivo:ufid", ufid)
if uri is None:
print ufid,' not found'
person = {}
person['display_name'] = 'UFID '+ ufid + ' not found'
p = Paragraph(ss.ParagraphStyles.Heading1)
p. append(person['display_name'])
section.append(p)
previousPerson = person
continue
person = get_person(uri, get_publications=True)
print uri
print person
print person['display_name'], len(person['publications']), "publications"
if previousPerson != person:
p = Paragraph(ss.ParagraphStyles.Heading1)
p. append(person['display_name'])
section.append(p)
previousPerson = person
if len(person['publications']) > 0:
for pub in person['publications']:
if 'date' not in pub:
pub['date'] = {'year': None}
for publication in sorted(person['publications'],