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)