def __init__(
self,
json_def_filename="data/pump_def.json",
out_filename="data/pump_data.txt",
verbose=False,
nofilters=False,
inter='\t',
intra=';',
query_parms={
'query_uri': 'http://localhost:8080/vivo/api/sparqlQuery',
'username': '******',
'password': '******'
},
uri_prefix='http://vivo.school.edu/individual/'):
"""
Initialize the pump
:param json_def_filename: File name of file containing JSON pump definition
"""
from vivopump import read_update_def
self.update_def = read_update_def(json_def_filename)
self.update_data = None
self.original_graph = None
self.update_graph = None
self.filter = not nofilters
self.enum = load_enum(self.update_def)
self.json_def_filename = json_def_filename
self.verbose = verbose
self.intra = intra
self.inter = inter
self.out_filename = out_filename
self.query_parms = query_parms
self.uri_prefix = uri_prefix
def __init__(self, json_def_filename="pump_def.json", out_filename="pump_data.txt", verbose=False,
nofilters=False, inter='\t', intra=';', rdfprefix="pump",
query_parms={'queryuri': 'http://localhost:8080/vivo/api/sparqlQuery',
'username': '******',
'password': '******',
'uriprefix': 'http://vivo.school.edu/individual/n',
'prefix':
'''
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX swrl: <http://www.w3.org/2003/11/swrl#>
PREFIX swrlb: <http://www.w3.org/2003/11/swrlb#>
PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#>
PREFIX wgs84: <http://www.w3.org/2003/01/geo/wgs84_pos#>
PREFIX bibo: <http://purl.org/ontology/bibo/>
PREFIX c4o: <http://purl.org/spar/c4o/>
PREFIX cito: <http://purl.org/spar/cito/>
PREFIX event: <http://purl.org/NET/c4dm/event.owl#>
PREFIX fabio: <http://purl.org/spar/fabio/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX geo: <http://aims.fao.org/aos/geopolitical.owl#>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX ocrer: <http://purl.org/net/OCRe/research.owl#>
PREFIX ocresd: <http://purl.org/net/OCRe/study_design.owl#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX uf: <http://vivo.school.edu/ontology/uf-extension#>
PREFIX vcard: <http://www.w3.org/2006/vcard/ns#>
PREFIX vitro-public: <http://vitro.mannlib.cornell.edu/ns/vitro/public#>
PREFIX vivo: <http://vivoweb.org/ontology/core#>
PREFIX scires: <http://vivoweb.org/ontology/scientific-research#>
'''
}):
"""
Initialize the pump
:param json_def_filename: File name of file containing JSON pump definition
"""
from vivopump import read_update_def, load_enum
self.update_def = read_update_def(json_def_filename, query_parms['prefix'])
self.update_data = None
self.original_graph = None
self.update_graph = None
self.filter = not nofilters
self.enum = load_enum(self.update_def)
self.json_def_filename = json_def_filename
self.verbose = verbose
self.intra = intra
self.inter = inter
self.rdfprefix = rdfprefix
self.out_filename = out_filename
self.query_parms = query_parms
def __init__(self, json_def_filename="data/pump_def.json", out_filename="data/pump_data.txt", verbose=False,
nofilters=False, inter='\t', intra=';',
query_parms={'query_uri': 'http://localhost:8080/vivo/api/sparqlQuery',
'username': '******', 'password': '******'},
uri_prefix='http://vivo.school.edu/individual/'):
"""
Initialize the pump
:param json_def_filename: File name of file containing JSON pump definition
"""
from vivopump import read_update_def
self.update_def = read_update_def(json_def_filename)
self.update_data = None
self.original_graph = None
self.update_graph = None
self.filter = not nofilters
self.enum = load_enum(self.update_def)
self.json_def_filename = json_def_filename
self.verbose = verbose
self.intra = intra
self.inter = inter
self.out_filename = out_filename
self.query_parms = query_parms
self.uri_prefix = uri_prefix
def __init__(self, defn="pump_def.json", src="pump_data.txt"):
"""
Initialize the pump
:param defn: File name of file containing JSON pump definition
:param src: file name of the csv file to contain VIVO data (get), or csv containing data to update VIVO (update)
"""
from vivopump import read_update_def, load_enum, DefNotFoundException
self.update_data = None
self.original_graph = None
self.update_graph = None
self.entity_uri = None # the entity_uri of the current row being processed in the update_data
self.out_filename = src
self.json_def_filename = defn
# Simple public instance variables
self.filter = True
self.intra = ';'
self.inter = '\t'
self.rdfprefix = 'pump'
self.uriprefix="http://vivo.school.edu/individual/n"
# Query parms should be properties of the query, not the Pump. Refactor this
self.queryuri="http://localhost:8080/vivo/api/sparqlQuery"
self.username="******"
self.password="******"
self.prefix=('PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n'
'PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\n'
'PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>\n'
'PREFIX owl: <http://www.w3.org/2002/07/owl#>\n'
'PREFIX swrl: <http://www.w3.org/2003/11/swrl#>\n'
'PREFIX swrlb: <http://www.w3.org/2003/11/swrlb#>\n'
'PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#>\n'
'PREFIX wgs84: <http://www.w3.org/2003/01/geo/wgs84_pos#>\n'
'PREFIX bibo: <http://purl.org/ontology/bibo/>\n'
'PREFIX c4o: <http://purl.org/spar/c4o/>\n'
'PREFIX cito: <http://purl.org/spar/cito/>\n'
'PREFIX event: <http://purl.org/NET/c4dm/event.owl#>\n'
'PREFIX fabio: <http://purl.org/spar/fabio/>\n'
'PREFIX foaf: <http://xmlns.com/foaf/0.1/>\n'
'PREFIX geo: <http://aims.fao.org/aos/geopolitical.owl#>\n'
'PREFIX obo: <http://purl.obolibrary.org/obo/>\n'
'PREFIX ocrer: <http://purl.org/net/OCRe/research.owl#>\n'
'PREFIX ocresd: <http://purl.org/net/OCRe/study_design.owl#>\n'
'PREFIX skos: <http://www.w3.org/2004/02/skos/core#>\n'
'PREFIX uf: <http://vivo.school.edu/ontology/uf-extension#>\n'
'PREFIX vcard: <http://www.w3.org/2006/vcard/ns#>\n'
'PREFIX vitro-public: <http://vitro.mannlib.cornell.edu/ns/vitro/public#>\n'
'PREFIX vivo: <http://vivoweb.org/ontology/core#>\n'
'PREFIX scires: <http://vivoweb.org/ontology/scientific-research#>\n')
# Ugly mutable param. Refactor this
self.query_parms = {'queryuri': self.queryuri, 'username': self.username, 'password': self.password,
'uriprefix': self.uriprefix, 'prefix': self.prefix}
# Create the update_def and enumerations
try:
self.update_def = read_update_def(defn, self.prefix)
except IOError:
raise DefNotFoundException(defn)
else:
self.enum = load_enum(self.update_def) # When the def changes, the enum must be updated
def __init__(self, defn="pump_def.json", src="pump_data.txt"):
"""
Initialize the pump
:param defn: File name of file containing JSON pump definition
:param src: file name of the csv file to contain VIVO data (get), or csv containing data to update VIVO (update)
"""
from vivopump import read_update_def, load_enum, DefNotFoundException
self.update_data = None
self.original_graph = None
self.update_graph = None
self.out_filename = src
self.json_def_filename = defn
# Simple public instance variables
self.filter = True
self.intra = ';'
self.inter = '\t'
self.rdfprefix = 'pump'
self.uriprefix="http://vivo.school.edu/individual/n"
# Query parms should be properties of the query, not the Pump. Refactor this
self.queryuri="http://localhost:8080/vivo/api/sparqlQuery"
self.username="******"
self.password="******"
self.prefix=('PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n'
'PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\n'
'PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>\n'
'PREFIX owl: <http://www.w3.org/2002/07/owl#>\n'
'PREFIX swrl: <http://www.w3.org/2003/11/swrl#>\n'
'PREFIX swrlb: <http://www.w3.org/2003/11/swrlb#>\n'
'PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#>\n'
'PREFIX wgs84: <http://www.w3.org/2003/01/geo/wgs84_pos#>\n'
'PREFIX bibo: <http://purl.org/ontology/bibo/>\n'
'PREFIX c4o: <http://purl.org/spar/c4o/>\n'
'PREFIX cito: <http://purl.org/spar/cito/>\n'
'PREFIX event: <http://purl.org/NET/c4dm/event.owl#>\n'
'PREFIX fabio: <http://purl.org/spar/fabio/>\n'
'PREFIX foaf: <http://xmlns.com/foaf/0.1/>\n'
'PREFIX geo: <http://aims.fao.org/aos/geopolitical.owl#>\n'
'PREFIX obo: <http://purl.obolibrary.org/obo/>\n'
'PREFIX ocrer: <http://purl.org/net/OCRe/research.owl#>\n'
'PREFIX ocresd: <http://purl.org/net/OCRe/study_design.owl#>\n'
'PREFIX skos: <http://www.w3.org/2004/02/skos/core#>\n'
'PREFIX uf: <http://vivo.school.edu/ontology/uf-extension#>\n'
'PREFIX vcard: <http://www.w3.org/2006/vcard/ns#>\n'
'PREFIX vitro-public: <http://vitro.mannlib.cornell.edu/ns/vitro/public#>\n'
'PREFIX vivo: <http://vivoweb.org/ontology/core#>\n'
'PREFIX scires: <http://vivoweb.org/ontology/scientific-research#>\n')
# Ugly mutable param. Refactor this
self.query_parms = {'queryuri': self.queryuri, 'username': self.username, 'password': self.password,
'uriprefix': self.uriprefix, 'prefix': self.prefix}
# Create the update_def and enumerations
try:
self.update_def = read_update_def(defn, self.prefix)
except IOError:
raise DefNotFoundException(defn)
else:
self.enum = load_enum(self.update_def) # When the def changes, the enum must be updated
def test_make_query(self):
update_def = read_update_def('data/grant_def.json')
for path in update_def['column_defs'].values():
update_query = make_update_query(update_def['entity_def']['entity_sparql'], path)
print update_query
self.assertTrue(len(update_query) > 0)
def test_update_def_order(self):
update_def = read_update_def('data/grant_def.json')
self.assertEqual(update_def['entity_def']['order'][0:4], [u'deptid', u'direct_costs', u'cois', u'end_date'])
def test_read_normal_def(self):
update_def = read_update_def('data/grant_def.json')
self.assertTrue(update_def.keys() == ['entity_def', 'column_defs'])
def test_normal_case(self):
update_def = read_update_def('data/grant_def.json')
a = get_graph(update_def)
print len(a)
self.assertTrue(len(a) == 241611)