def main():
"""
Generate the enums for positions
"""
print datetime.now(), "Start"
parms = get_parms()
# person via Orcid
query = """
SELECT (MIN (?xshort) AS ?short) ?vivo
WHERE
{
?vivo vivo:orcidId ?xshort .
}
GROUP BY ?vivo
ORDER BY ?short
"""
create_enum("orcid_enum.txt", query, parms)
# department via label
query = """
SELECT (MIN (?xlabel) AS ?short) ?vivo
WHERE
{
{?vivo a vivo:Department . } UNION {?vivo a vivo:Institute . } UNION {?vivo a vivo:School . }
UNION {?vivo a vivo:Center .} UNION {?vivo a vivo:College . }
?vivo rdfs:label ?xlabel .
}
GROUP BY ?vivo
ORDER BY ?short
"""
create_enum("dept_enum.txt", query, parms)
# dates via datetime
query = """
SELECT ?short ?vivo
WHERE
{
?vivo a vivo:DateTimeValue .
# ?vivo vivo:dateTimePrecision vivo:yearMonthDayPrecision .
?vivo vivo:dateTime ?short .
}
ORDER BY ?short
"""
create_enum("date_enum.txt", query, parms, trim=10)
print datetime.now(), "End"
def main():
"""
Generate the enums for positions
"""
print datetime.now(), "Start"
parms = get_parms()
# person via Orcid
query = """
SELECT (MIN (?xshort) AS ?short) ?vivo
WHERE
{
?vivo vivo:orcidId ?xshort .
}
GROUP BY ?vivo
ORDER BY ?short
"""
create_enum("orcid_enum.txt", query, parms)
# department via label
query = """
SELECT (MIN (?xlabel) AS ?short) ?vivo
WHERE
{
{?vivo a vivo:Department . } UNION {?vivo a vivo:Institute . } UNION {?vivo a vivo:School . }
UNION {?vivo a vivo:Center .} UNION {?vivo a vivo:College . }
?vivo rdfs:label ?xlabel .
}
GROUP BY ?vivo
ORDER BY ?short
"""
create_enum("dept_enum.txt", query, parms)
# dates via datetime
query = """
SELECT ?short ?vivo
WHERE
{
?vivo a vivo:DateTimeValue .
# ?vivo vivo:dateTimePrecision vivo:yearMonthDayPrecision .
?vivo vivo:dateTime ?short .
}
ORDER BY ?short
"""
create_enum("date_enum.txt", query, parms, trim=10)
print datetime.now(), "End"
def main():
"""
Generate the enums for positions
"""
print datetime.now(), "Start"
parms = get_parms()
# person via Orcid
query = """
SELECT (MIN (?xshort) AS ?short) ?vivo
WHERE
{
?vivo vivo:orcidId ?xshort .
}
GROUP BY ?vivo
ORDER BY ?short
"""
create_enum("orcid_enum.txt", query, parms)
# journals via issn
query = """
SELECT (MIN (?xlabel) AS ?short) ?vivo
WHERE
{
?vivo a bibo:Journal .
?vivo rdfs:label ?xlabel .
}
GROUP BY ?vivo
ORDER BY ?short
"""
create_enum("journal_enum.txt", query, parms)
# dates via datetime
query = """
SELECT ?short ?vivo
WHERE
{
?vivo a vivo:DateTimeValue .
# ?vivo vivo:dateTimePrecision vivo:yearMonthDayPrecision .
?vivo vivo:dateTime ?short .
}
ORDER BY ?short
"""
create_enum("date_enum.txt", query, parms, trim=10)
print datetime.now(), "End"
def main():
"""
Generate the enums for positions
"""
print datetime.now(), "Start"
parms = get_parms()
# person via Orcid
query = """
SELECT (MIN (?xshort) AS ?short) ?vivo
WHERE
{
?vivo vivo:orcidId ?xshort .
}
GROUP BY ?vivo
ORDER BY ?short
"""
create_enum("orcid_enum.txt", query, parms)
# journals via issn
query = """
SELECT (MIN (?xlabel) AS ?short) ?vivo
WHERE
{
?vivo a bibo:Journal .
?vivo rdfs:label ?xlabel .
}
GROUP BY ?vivo
ORDER BY ?short
"""
create_enum("journal_enum.txt", query, parms)
# dates via datetime
query = """
SELECT ?short ?vivo
WHERE
{
?vivo a vivo:DateTimeValue .
# ?vivo vivo:dateTimePrecision vivo:yearMonthDayPrecision .
?vivo vivo:dateTime ?short .
}
ORDER BY ?short
"""
create_enum("date_enum.txt", query, parms, trim=10)
print datetime.now(), "End"
def main():
"""
Generate the enums for degrees
"""
print datetime.now(), "Start"
parms = get_parms()
# person
query = """
SELECT (MIN (?xlabel) AS ?short) ?vivo
WHERE
{
?vivo rdf:type vivo:GeographicLocation .
?vivo rdfs:label ?xlabel .
}
GROUP BY ?vivo
ORDER BY ?short
"""
create_enum("location_enum.txt", query, parms)
print datetime.now(), "End"
def main():
"""
Generate the enums for concepts
"""
print datetime.now(), "Start"
parms = get_parms()
# Concept
query = """
SELECT (MIN (?xlabel) AS ?short) ?vivo
WHERE
{
?vivo rdf:type skos:Concept .
?vivo rdfs:label ?xlabel .
}
GROUP BY ?vivo
ORDER BY ?short
"""
create_enum("concept_enum.txt", query, parms)
print datetime.now(), "End"
from vivopump import read_csv_fp, write_csv_fp, get_vivo_authors, get_parms
import sys
def disambiguate_author(author, vivo_authors):
"""
Given an author dictionary with name parts, find matches in the data structure returned by get_vivo_authors
:param author: dictionary of name parts
:param vivo_authors: authors in VIVO, seven dictionaries with seven keys based on various types of name parts
:return: list of uri in vivo matching the author
"""
author_uri_list = []
return author_uri_list
parms = get_parms()
data_in = read_csv_fp(sys.stdin)
print >> sys.stderr, len(data_in)
vivo_authors = get_vivo_authors(
parms) # get dictionaries of authors keyed by name parts
print >> sys.stderr, 'VIVO authors', len(vivo_authors)
print >> sys.stderr, vivo_authors
data_out = {}
row_out = 0
for row, data in data_in.items():
if data['uf'] == 'false': # Always put in the non-UF author as new
row_out += 1
data_out[row_out] = data
data_out[row_out]['uri'] = ''
else:
1. Course in VIVO and in Source => Update VIVO from source
1. Course in VIVO, not in source => nothing to do
1. Course not in VIVO, is in source => Add to VIVO
See CHANGELOG.md for history
"""
__author__ = "Michael Conlon"
__copyright__ = "Copyright 2015 (c) Michael Conlon"
__license__ = "New BSD License"
__version__ = "0.02"
from vivopump import read_csv_fp, write_csv_fp, get_vivo_ccn, get_parms
import sys
parms = get_parms()
data_in = read_csv_fp(sys.stdin)
print >>sys.stderr, len(data_in)
data_out = {}
vivo_courses = get_vivo_ccn(parms) # get dictionary of course uri keyed by ccn
print >>sys.stderr, 'VIVO courses', len(vivo_courses)
for row, data in data_in.items():
new_data = dict(data)
if data['ccn'] in vivo_courses: # ccn is in vivo and source
new_data['uri'] = vivo_courses[data['ccn']]
else: # key is in source, not in vivo
new_data['uri'] = ''
data_out[row] = new_data
print >>sys.stderr, 'data out', len(data_out)
def main():
"""
Generate the enums for teaching
"""
print datetime.now(), "Start"
parms = get_parms()
# person via Orcid
query = """
SELECT (MIN (?xshort) AS ?short) ?vivo
WHERE
{
?vivo vivo:orcidId ?xshort .
}
GROUP BY ?vivo
ORDER BY ?short
"""
create_enum("orcid_enum.txt", query, parms)
# Course via label
query = """
SELECT (MIN (?xlabel) AS ?short) ?vivo
WHERE
{
?vivo a vivo:Course .
?vivo rdfs:label ?xlabel .
}
GROUP BY ?vivo
ORDER BY ?short
"""
create_enum("course_enum.txt", query, parms)
# Concept via label
query = """
SELECT (MIN (?xlabel) AS ?short) ?vivo
WHERE
{
?vivo a skos:Concept .
?vivo rdfs:label ?xlabel .
}
GROUP BY ?vivo
ORDER BY ?short
"""
create_enum("concept_enum.txt", query, parms)
# dates via datetime
query = """
SELECT ?short ?vivo
WHERE
{
?vivo a vivo:DateTimeValue .
# ?vivo vivo:dateTimePrecision vivo:yearMonthDayPrecision .
?vivo vivo:dateTime ?short .
}
ORDER BY ?short
"""
create_enum("date_enum.txt", query, parms, trim=10)
print datetime.now(), "End"
def main():
"""
Generate the enums for awards
"""
print datetime.now(), "Start"
parms = get_parms()
# person
query = """
SELECT ?short ?vivo
WHERE {
?vivo a foaf:Person .
?vivo rdfs:label ?short .
}
ORDER BY ?short
"""
create_enum("person_enum.txt", query, parms)
# school
query = """
SELECT ?short ?vivo
WHERE {
?vivo a foaf:Organization .
?vivo rdfs:label ?short .
}
ORDER BY ?short
"""
create_enum("org_enum.txt", query, parms)
# date
query = """
SELECT ?short ?vivo
WHERE {
?vivo a vivo:DateTimeValue .
?vivo vivo:dateTimePrecision vivo:yearPrecision .
?vivo vivo:dateTime ?short .
}
ORDER BY ?short
"""
create_enum("date_enum.txt", query, parms, trim=4)
# academic degree
query = """
SELECT ?short ?vivo
WHERE {
?vivo a vivo:Award .
?vivo rdfs:label ?short .
}
ORDER BY ?short
"""
create_enum("award_enum.txt", query, parms)
print datetime.now(), "End"
return None
def main():
"""
Generate the enums for awards
"""
print datetime.now(), "Start"
parms = get_parms()
# person
query = """
SELECT ?short ?vivo
WHERE {
?vivo a foaf:Person .
?vivo rdfs:label ?short .
}
ORDER BY ?short
"""
create_enum("person_enum.txt", query, parms)
# school
query = """
SELECT ?short ?vivo
WHERE {
?vivo a foaf:Organization .
?vivo rdfs:label ?short .
}
ORDER BY ?short
"""
create_enum("org_enum.txt", query, parms)
# date
query = """
SELECT ?short ?vivo
WHERE {
?vivo a vivo:DateTimeValue .
?vivo vivo:dateTimePrecision vivo:yearPrecision .
?vivo vivo:dateTime ?short .
}
ORDER BY ?short
"""
create_enum("date_enum.txt", query, parms, trim=4)
# academic degree
query = """
SELECT ?short ?vivo
WHERE {
?vivo a vivo:Award .
?vivo rdfs:label ?short .
}
ORDER BY ?short
"""
create_enum("award_enum.txt", query, parms)
print datetime.now(), "End"
return None
def main():
"""
Generate the enums for degrees
"""
print datetime.now(), "Start"
parms = get_parms()
# person
query = """
SELECT (MIN (?xlabel) AS ?short) ?vivo
WHERE
{
?vivo a foaf:Person .
?vivo rdfs:label ?xlabel .
}
GROUP BY ?vivo
ORDER BY ?short
"""
create_enum("person_enum.txt", query, parms)
# degree
query = """
SELECT (MIN (?xlabel) AS ?short) ?vivo
WHERE
{
?vivo a vivo:AcademicDegree .
?vivo rdfs:label ?xlabel .
}
GROUP BY ?vivo
ORDER BY ?short
"""
create_enum("degree_enum.txt", query, parms)
# school
query = """
SELECT (MIN (?xlabel) AS ?short) ?vivo
WHERE
{
?vivo a vivo:University .
?vivo rdfs:label ?xlabel .
}
GROUP BY ?vivo
ORDER BY ?short
"""
create_enum("school_enum.txt", query, parms)
# dates
query = """
SELECT ?short ?vivo
WHERE
{
?vivo a vivo:DateTimeValue .
# ?vivo vivo:dateTimePrecision vivo:yearMonthPrecision .
?vivo vivo:dateTime ?short .
}
ORDER BY ?short
"""
create_enum("date_enum.txt", query, parms, trim=7)
print datetime.now(), "End"
def main():
"""
Generate the enums for teaching
"""
print datetime.now(), "Start"
parms = get_parms()
# person via Orcid
query = """
SELECT (MIN (?xshort) AS ?short) ?vivo
WHERE
{
?vivo vivo:orcidId ?xshort .
}
GROUP BY ?vivo
ORDER BY ?short
"""
create_enum("orcid_enum.txt", query, parms)
# Course via label
query = """
SELECT (MIN (?xlabel) AS ?short) ?vivo
WHERE
{
?vivo a vivo:Course .
?vivo rdfs:label ?xlabel .
}
GROUP BY ?vivo
ORDER BY ?short
"""
create_enum("course_enum.txt", query, parms)
# Concept via label
query = """
SELECT (MIN (?xlabel) AS ?short) ?vivo
WHERE
{
?vivo a skos:Concept .
?vivo rdfs:label ?xlabel .
}
GROUP BY ?vivo
ORDER BY ?short
"""
create_enum("concept_enum.txt", query, parms)
# dates via datetime
query = """
SELECT ?short ?vivo
WHERE
{
?vivo a vivo:DateTimeValue .
# ?vivo vivo:dateTimePrecision vivo:yearMonthDayPrecision .
?vivo vivo:dateTime ?short .
}
ORDER BY ?short
"""
create_enum("date_enum.txt", query, parms, trim=10)
print datetime.now(), "End"
def main():
"""
Generate the enums for degrees
"""
print datetime.now(), "Start"
parms = get_parms()
# person via Orcid
query = """
SELECT (MIN (?xshort) AS ?short) ?vivo
WHERE
{
?vivo vivo:orcidId ?xshort .
}
GROUP BY ?vivo
ORDER BY ?short
"""
create_enum("orcid_enum.txt", query, parms)
# degree
query = """
SELECT (MIN (?xlabel) AS ?short) ?vivo
WHERE
{
?vivo a vivo:AcademicDegree .
?vivo rdfs:label ?xlabel .
}
GROUP BY ?vivo
ORDER BY ?short
"""
create_enum("degree_enum.txt", query, parms)
# dates
query = """
SELECT ?short ?vivo
WHERE
{
?vivo a vivo:DateTimeValue .
?vivo vivo:dateTimePrecision vivo:yearPrecision .
?vivo vivo:dateTime ?short .
}
ORDER BY ?short
"""
create_enum("date_enum.txt", query, parms, trim=4)
# Concept via label
query = """
SELECT (MIN (?xlabel) AS ?short) ?vivo
WHERE
{
?vivo a skos:Concept .
?vivo rdfs:label ?xlabel .
}
GROUP BY ?vivo
ORDER BY ?short
"""
create_enum("concept_enum.txt", query, parms)
print datetime.now(), "End"
def main():
"""
Generate the enums for degrees
"""
print datetime.now(), "Start"
parms = get_parms()
# person
query = """
SELECT (MIN (?xlabel) AS ?short) ?vivo
WHERE
{
?vivo a foaf:Person .
?vivo rdfs:label ?xlabel .
}
GROUP BY ?vivo
ORDER BY ?short
"""
create_enum("person_enum.txt", query, parms)
# degree
query = """
SELECT (MIN (?xlabel) AS ?short) ?vivo
WHERE
{
?vivo a vivo:AcademicDegree .
?vivo rdfs:label ?xlabel .
}
GROUP BY ?vivo
ORDER BY ?short
"""
create_enum("degree_enum.txt", query, parms)
# school
query = """
SELECT (MIN (?xlabel) AS ?short) ?vivo
WHERE
{
?vivo a vivo:University .
?vivo rdfs:label ?xlabel .
}
GROUP BY ?vivo
ORDER BY ?short
"""
create_enum("school_enum.txt", query, parms)
# dates
query = """
SELECT ?short ?vivo
WHERE
{
?vivo a vivo:DateTimeValue .
# ?vivo vivo:dateTimePrecision vivo:yearMonthPrecision .
?vivo vivo:dateTime ?short .
}
ORDER BY ?short
"""
create_enum("date_enum.txt", query, parms, trim=7)
print datetime.now(), "End"
def main():
"""
Generate the enums for degrees
"""
print datetime.now(), "Start"
parms = get_parms()
# person via Orcid
query = """
SELECT (MIN (?xshort) AS ?short) ?vivo
WHERE
{
?vivo vivo:orcidId ?xshort .
}
GROUP BY ?vivo
ORDER BY ?short
"""
create_enum("orcid_enum.txt", query, parms)
# degree
query = """
SELECT (MIN (?xlabel) AS ?short) ?vivo
WHERE
{
?vivo a vivo:AcademicDegree .
?vivo rdfs:label ?xlabel .
}
GROUP BY ?vivo
ORDER BY ?short
"""
create_enum("degree_enum.txt", query, parms)
# dates
query = """
SELECT ?short ?vivo
WHERE
{
?vivo a vivo:DateTimeValue .
?vivo vivo:dateTimePrecision vivo:yearPrecision .
?vivo vivo:dateTime ?short .
}
ORDER BY ?short
"""
create_enum("date_enum.txt", query, parms, trim=4)
# Concept via label
query = """
SELECT (MIN (?xlabel) AS ?short) ?vivo
WHERE
{
?vivo a skos:Concept .
?vivo rdfs:label ?xlabel .
}
GROUP BY ?vivo
ORDER BY ?short
"""
create_enum("concept_enum.txt", query, parms)
print datetime.now(), "End"