def resource(request, ref=None):
saved = False # set saved to false until post is successful
uri = Namespace("http://data.library.oregonstate.edu/person/")[ref]
data = ''
# deal with updates if this is a form submit
if request.method == 'POST':
# get data to delete
resource = queryManager.describe(uri)
try:
resource = resource
except:
resource = {}
# get form data and put it in a dict
resForm = ResourceForm(request.POST)
VariantFormSet = formset_factory(VariantForm)
varForm = VariantFormSet(request.POST)
if resForm.is_valid() and varForm.is_valid():
data = {
'res': resForm.cleaned_data,
'var': varForm.cleaned_data
}
saved = processForm(uri, data, resource)
# if the uri exists, try to describe it and build an edit form
# retrieving data again if we just processed a form
resource = queryManager.describe(uri)
if resource:
forms = buildForm(resource)
else:
#TODO: return a useful error
return HttpResponse("resource not found", status=404)
return render_to_response("resource.tpl", {'uri': str(uri), 'short': uri.split('/')[-1], 'res': resource, 'form': forms['form'], 'variants': forms['variants'], 'saved': saved, 'data': resource})
def create_ontology(self,tr,predicate,subClass,address,booktitle):
LDT= Namespace("http://www.JceFinalProjectOntology.com/")
ut=Namespace("http://www.JceFinalProjectOntology.com/subject/#")
usubClass=URIRef("http://www.JceFinalProjectOntology.com/subject/"+subClass.strip()+'#')
#LDT.subClass=LDT[subClass]
print(ut)
print(usubClass)
store=IOMemory()
sty=LDT[predicate]
g = rdflib.Graph(store=store,identifier=LDT)
t = ConjunctiveGraph(store=store,identifier=ut)
print ('Triples in graph before add: ', len(t))
#g.add((LDT,RDF.type,RDFS.Class))
g.add((URIRef(LDT),RDF.type,RDFS.Class))
g.add((URIRef(LDT),RDFS.label,Literal("JFPO")))
g.add((URIRef(LDT),RDFS.comment,Literal('class of all properties')))
for v in self.symbols.values():
if self.if_compoTerm(v)==True:
vs=self.splitTerms(v)[0]
else:
vs =v
g.add((LDT[vs],RDF.type,RDF.Property))
g.add((LDT[vs],RDFS.label,Literal('has'+vs)))
g.add((LDT[vs],RDFS.comment,Literal(v)))
g.add((LDT[vs],RDFS.range,OWL.Class))
g.add((LDT[vs],RDFS.domain,Literal(vs)))
g.bind('JFPO',LDT)
#g.commit()
g.serialize('trtst.rdf',format='turtle')
t.add( (ut[tr], RDF.type,OWL.Class) )
t.add((ut[tr],RDFS.subClassOf,OWL.Thing))
t.add((ut[tr],RDFS.label,Literal(tr)))
t.add((ut[tr],DC.title,Literal(booktitle)))
t.add((ut[tr],DC.source,Literal(address)))
t.add((ut[tr],DC[predicate],URIRef(usubClass)))
t.add((ut[tr],LDT[predicate],RDF.Property))
t.add((ut[tr],DC[predicate],URIRef(usubClass)))
t.add((ut[tr],DC[predicate],URIRef(usubClass)))
relation='has'+predicate
t.add((ut[tr],LDT.term(predicate),URIRef(usubClass)))
t.add( (usubClass,RDF.type,OWL.Class))
t.add((usubClass,RDFS.subClassOf,OWL.Thing))
t.add((usubClass,RDFS.subClassOf,URIRef(sty)))
t.add((usubClass,RDFS.label,Literal(subClass)))
#tc=Graph(store=store,identifier=usubClass)
t.bind("dc", "http://http://purl.org/dc/elements/1.1/")
t.bind('JFPO',LDT)
t.commit()
#print(t.serialize(format='pretty-xml'))
t.serialize('test2.owl',format='turtle')
def new(request, ref=None):
uriNeeded = True
while uriNeeded == True:
# assign an identifier
identifier = pynoid.mint('zeek', random.randint(0, 100000))
uri = Namespace("http://data.library.oregonstate.edu/person/")[identifier]
uriNeeded = queryManager.ask(uri) # if this identifier is already in use, let's get another one
forms = buildForm()
return render_to_response("resource.tpl", {'uri': str(uri), 'short': uri.split('/')[-1], 'res': {}, 'form': forms['form'], 'variants': forms['variants']})
def serialize(self, add, delete):
diff = Namespace("http://topbraid.org/diff#")
g = ConjunctiveGraph()
namespace_manager = NamespaceManager(g)
namespace_manager.bind('diff', diff, override=False)
namespace_manager.bind('owl', OWL, override=False)
graphUris = set(delete.keys()) | set(add.keys())
for graphUri in graphUris:
if (graphUri in delete.keys() and len(delete[graphUri]) > 0) or (graphUri in add.keys() and len(add[graphUri]) > 0):
changeset = Namespace("urn:diff:" + str(uuid.uuid1()))
graphTerm = changeset.term("")
if str(graphUri) != 'http://quitdiff.default/':
g.add((graphTerm, OWL.imports, graphUri, graphTerm))
g.add((graphTerm, RDF.type, OWL.Ontology, graphTerm))
g.add((graphTerm, OWL.imports, diff.term(""), graphTerm))
if graphUri in delete.keys() and len(delete[graphUri]) > 0:
i = 0
for triple in delete[graphUri]:
deleteStatementName = BNode()
g.add((deleteStatementName, RDF.type, diff.DeletedTripleDiff, graphTerm))
g.add((deleteStatementName, RDF.subject, triple[0], graphTerm))
g.add((deleteStatementName, RDF.predicate, triple[1], graphTerm))
g.add((deleteStatementName, RDF.object, triple[2], graphTerm))
i += 1
if graphUri in add.keys() and len(add[graphUri]) > 0:
i = 0
for triple in add[graphUri]:
insertGraphName = BNode()
g.add((insertGraphName, RDF.type, diff.AddedTripleDiff, graphTerm))
g.add((insertGraphName, RDF.subject, triple[0], graphTerm))
g.add((insertGraphName, RDF.predicate, triple[1], graphTerm))
g.add((insertGraphName, RDF.object, triple[2], graphTerm))
i += 1
return g.serialize(format="trig").decode("utf-8")
def merge(request, uriMerge=None, uriTarget=None):
uriMerge = Namespace("http://data.library.oregonstate.edu/person/")[uriMerge]
uriTarget = Namespace("http://data.library.oregonstate.edu/person/")[uriTarget]
merge = queryManager.describe(uriMerge)
target = queryManager.describe(uriTarget)
if request.method == 'POST':
sameAs = "INSERT DATA {<" + uriMerge + "> owl:sameAs <" + uriTarget + "> .}"
queryManager.update(sameAs)
# get form data and put it in a dict
resForm = ResourceForm(request.POST)
VariantFormSet = formset_factory(VariantForm)
varForm = VariantFormSet(request.POST)
if resForm.is_valid() and varForm.is_valid():
data = {
'res': resForm.cleaned_data,
'var': varForm.cleaned_data
}
saved = processForm(uriTarget, data, resource)
# these labels will be merged into the target as skos:hiddenLabel
#TODO: exclude duplicate names
mergeLabels = [str(ns['skos']['prefLabel']), str(ns['skos']['altLabel']), str(ns['skos']['hiddenLabel']), str(ns['foaf']['name'])]
for field in merge:
if field in mergeLabels:
for value in merge[field]:
if str(ns['skos']['hiddenLabel']) in target:
target[str(ns['skos']['hiddenLabel'])].append(value)
else:
target[str(ns['skos']['hiddenLabel'])] = merge[field]
#TODO: mark old record for deletion
# do this with a hidden form?
forms = buildForm(target)
data = target
return render_to_response("merge.tpl", {'uriMerge': str(uriMerge), 'uri': str(uriTarget), 'mergeShort': uriMerge.split('/')[-1], 'short': uriTarget.split('/')[-1], 'res': target, 'form': forms['form'], 'variants': forms['variants']})
def make_component_hierarchy(component_map, component_part_map):
g = rdflib.Graph()
indra_ns = 'http://sorger.med.harvard.edu/indra/'
ln = Namespace(indra_ns + 'locations/')
rn = Namespace(indra_ns + 'relations/')
part_of = rn.term('partof')
has_name = rn.term('hasName')
for comp_id, comp_name in component_map.items():
g.add((ln.term(comp_id), has_name, Literal(comp_name)))
sups = component_part_map.get(comp_id)
if sups is not None:
for sup_id in sups:
g.add((ln.term(comp_id), part_of, ln.term(sup_id)))
return g
import sys
import json
from os.path import join, dirname, abspath
from rdflib import Graph, Namespace, Literal
from indra.sources import sofia
# Note that this is just a placeholder, it doesn't resolve as a URL
sofia_ns = Namespace('http://cs.cmu.edu/sofia/')
indra_ns = 'http://sorger.med.harvard.edu/indra/'
indra_rel_ns = Namespace(indra_ns + 'relations/')
isa = indra_rel_ns.term('isa')
def save_ontology(g, path):
with open(path, 'wb') as out_file:
g_bytes = g.serialize(format='nt')
# Replace extra new lines in string and get rid of empty line at end
g_bytes = g_bytes.replace(b'\n\n', b'\n').strip()
# Split into rows and sort
rows = g_bytes.split(b'\n')
rows.sort()
g_bytes = b'\n'.join(rows)
out_file.write(g_bytes)
def build_ontology(ont_json, rdf_path):
G = Graph()
for top_key, entries in ont_json.items():
for entry_key, examples in entries.items():
if '/' in entry_key:
turtle_folder_fao = "/home/iati/mappings/FAO/"
dbpedia_file = "/home/iati/mappings/DBPedia/dbpedia-countries-via-factbook.ttl"
if not os.path.isdir(turtle_folder_oecd):
os.makedirs(turtle_folder_oecd)
if not os.path.isdir(turtle_folder_bfs):
os.makedirs(turtle_folder_bfs)
if not os.path.isdir(turtle_folder_ecb):
os.makedirs(turtle_folder_ecb)
if not os.path.isdir(turtle_folder_fao):
os.makedirs(turtle_folder_fao)
start_time = datetime.datetime.now()
# Namespaces
Iati = Namespace("http://purl.org/collections/iati/")
countries_oecd = Graph()
countries_oecd.bind('iati-country', "http://purl.org/collections/iati/codelist/Country/")
countries_oecd.bind('owl', "http://www.w3.org/2002/07/owl#")
countries_bfs = Graph()
countries_bfs.bind('iati-country', "http://purl.org/collections/iati/codelist/Country/")
countries_bfs.bind('bfs-country', "http://bfs.270a.info/code/1.0/CL_STATES_AND_TERRITORIES/")
countries_bfs.bind('owl', "http://www.w3.org/2002/07/owl#")
countries_ecb = Graph()
countries_ecb.bind('iati-country', "http://purl.org/collections/iati/codelist/Country/")
countries_ecb.bind('ecb-country', "http://ecb.270a.info/code/1.0/CL_AREA_EE/")
countries_ecb.bind('owl', "http://www.w3.org/2002/07/owl#")
all_store = None
# print(len(all_store['problem_domain']))
stop_words = set(stopwords.words('english'))
pos_list = [
'CC', 'CD', 'DT', 'EX', 'JJR', 'JJS', 'PRP', 'PRP$', '$', 'RB', 'RBR',
'RBS', 'RP', 'WDT', 'WP$', 'WP', 'WRB', 'MD'
]
word_list = [
'definition', 'definitions', 'update', 'updates', 'sequence', 'sequences',
'associated', 'involved', 'accessed', 'invokes', 'invoke', 'are', 'list'
]
#Defining the prefixes
symbol = Namespace("http://smartKT/ns/symbol#")
comment = Namespace("http://smartKT/ns/comment#")
prop = Namespace("http://smartKT/ns/properties#")
g.bind("symbol", symbol)
g.bind("comment", comment)
g.bind("prop", prop)
def get_id(nodeId):
while nodeId and nodeId != mapping_extra_id[nodeId]:
nodeId = mapping_extra_id[nodeId]
return nodeId
"""
#%% md
## Constructing an ontology from Scratch
#%%
from rdflib import Namespace, Literal, Graph
from funowl import SubObjectPropertyOf, InverseObjectProperties, FunctionalObjectProperty, \
InverseFunctionalObjectProperty, ObjectPropertyDomain, ObjectPropertyRange, SubClassOf
from funowl.annotations import AnnotationValue
from funowl.ontology_document import OntologyDocument, Ontology
DC = Namespace("http://purl.org/dc/elements/1.1/")
TERMS = Namespace("http://purl.org/dc/terms/")
PIZZA = Namespace("http://www.co-ode.org/ontologies/pizza#")
pizza_doc = OntologyDocument()
pizza_doc.prefixes(PIZZA, dc=DC, terms=TERMS)
pizza = Ontology("http://www.co-ode.org/ontologies/pizza",
"http://www.co-ode.org/ontologies/pizza/2.0.0")
pizza_doc.ontology = pizza
pizza.annotation(DC.title, "pizza")
pizza.annotation(TERMS.contributor, "Alan Rector")
pizza.annotation(TERMS.contributor, "Matthew Horridge")
pizza.annotation(TERMS.contributor, "Chris Wroe")
pizza.annotation(TERMS.contributor, "Robert Stevens")
pizza.annotation(
DC.description,
from lxml import etree
tree = etree.parse('input.xml')
root = tree.getroot()
base_uri = root.get('{http://www.w3.org/XML/1998/namespace}base')
edition_id = root.get('{http://www.w3.org/XML/1998/namespace}id')
tei = {'tei': 'http://www.tei-c.org/ns/1.0'}
from rdflib import Graph, Literal, BNode, Namespace, URIRef
from rdflib.namespace import RDF, RDFS, XSD, DCTERMS, OWL
agrelon = Namespace("https://d-nb.info/standards/elementset/agrelon#")
crm = Namespace("http://www.cidoc-crm.org/cidoc-crm/")
frbroo = Namespace("http://iflastandards.info/ns/fr/frbr/frbroo/")
pro = Namespace("http://purl.org/spar/pro/")
proles = Namespace("http://www.essepuntato.it/2013/10/politicalroles/")
prov = Namespace("http://www.w3.org/ns/prov#")
ti = Namespace("http://www.essepuntato.it/2012/04/tvc/")
g = Graph()
g.bind("agrelon", agrelon)
g.bind("crm", crm)
g.bind("frbroo", frbroo)
g.bind("dcterms", DCTERMS)
g.bind("owl", OWL)
g.bind("pro", pro)
class Differential_Pressure_Proportional_Band_Setpoint(
Proportional_Band_Setpoint):
rdf_type = Namespace('https://brickschema.org/schema/1.0.2/Brick#'
).Differential_Pressure_Proportional_Band_Setpoint
import csv, os, time, shutil
from progress import Progress
def is_specified(val):
unspecified_indicators = ['\\N']
return val not in unspecified_indicators
identifier = 'yearsGraph'
uri_base = 'http://www.ourmoviedb.org/'
output = 'outs/' + identifier + '.ttl.n3'
# Create graph
g = Graph(identifier=identifier)
n = Namespace(uri_base)
years = range(1870, 2050)
progress = Progress(len(years))
start = time.time()
for year in range(1870, 2050):
year_node = n['Year/' + str(year)]
class_node = n['Year']
g.add((year_node, RDF.type, class_node))
g.add((year_node, n.YearValue, Literal(year, datatype=XSD.gYear)))
# Let's name the decades
# I want to isolate the
if year < 2010 and year >= 1950:
decade_prefix = str(year)[2]
# -*- coding: utf-8 -*-
"""
Created on Thu Apr 29 08:28:28 2021
@author: ChrisLe
"""
from rdflib import Graph # Importamos la clase Graph de rdflib
from rdflib import Namespace # Namespace nos servira para almacernar nuestros espacios de nombre
from rdflib import Literal # Nos permitira almacenar una variable como un literal (Valor Constante)
FOAF = Namespace(
"http://xmlns.com/foaf/0.1/"
) # De esta forma almacenamos el nombre de dominio para hacermos más facil su uso
EX = Namespace("http://example.org/foovocab#")
def main():
# Creamos el grafo
s = Graph()
#Ahora asignaremos un prefijo a cada uno de los espacios de nombre en el grafo
s.bind('dc', EX) #Mediante bind podemos hacerlo
#bind (prefijo, espacioNombre)
s.bind('foaf', FOAF)
#Ahora leeremos del archivo rdf, para ello usaremos parse
import json
from rdflib import URIRef, BNode, Literal, Graph, Namespace
from rdflib.namespace import RDF, FOAF, OWL, RDFS, NamespaceManager
from rdflib.extras.infixowl import Restriction, Individual
import pandas as pd
import numpy as np
from urllib.request import urlopen, quote
import SemanticProcessor.mappings as mappings
import SemanticProcessor.concepts as concepts
#from SemanticProcessor.snomed import getDescriptionsByString
chronicals = Namespace(concepts.BASE_URL)
namespace_manager = NamespaceManager(Graph())
def add_sample(g, id, symptoms, diagnose, prev_attacks, characterisation,
severity, location, duration):
# Creates an URI with its ID and says it's from type chron:Headache
headache = URIRef(concepts.BASE_URL + 'headache#' + str(id))
g.add((headache, RDF.type, concepts.headache_type))
# For each symptom, we create another triple
for symptom in symptoms:
g.add((headache, concepts.symptom_predicate,
mappings.symptom_to_URI[symptom]))
# Triple for our diagnose
g.add((headache, concepts.diagnose_predicate,
mappings.diagnoses_to_URI[diagnose]))
# Add triple with previous attacks
def __init__(self):
self.g = Graph()
self.n = Namespace('http://home.eps.hw.ac.uk/~qz1/')
self.file_abs = '/Users/silvia/Documents/code/reverseProxy/db/knowledgeBase.ttl'
self.clearGraph()
self.getGraph()
class VAV_Box_Operating_Mode_Status(Mode_Status):
rdf_type = Namespace('https://brickschema.org/schema/1.0.2/Brick#'
).VAV_Box_Operating_Mode_Status
# @author Yuan Jin # @contact [email protected] # @created Sept. 24, 2012 # @updated Sept. 25, 2012 # import sys reload(sys) sys.setdefaultencoding('UTF-8') from nltk import load_parser from rdflib import Namespace, URIRef # PATTERN = raw_input('enter pattern config file: ') PATTERN = 'searchet.fcfg' searchet = Namespace("http://searchet.baidu.com/ontology#") class PatternLoader: def __init__(self, pattern): self.pattern = pattern self.c = load_parser(PATTERN) def pattern_converter(self): '''docs''' def load(self): '''docs''' # print str(self.c.nbest_parse(self.pattern)) return '_'.join(self.c.nbest_parse(self.pattern)[0].node['SEM'])
class Heat_Exchanger_Outside_Air_Temperature_Low_Reset_Setpoint(
Outside_Air_Temperature_Low_Reset_Setpoint):
rdf_type = Namespace(
'https://brickschema.org/schema/1.0.2/Brick#'
).Heat_Exchanger_Outside_Air_Temperature_Low_Reset_Setpoint
if args.open:
hostname = '0.0.0.0'
else:
hostname = socket.gethostname()
# Directory Service Graph
dsgraph = Graph()
# Vinculamos todos los espacios de nombre a utilizar
dsgraph.bind('acl', ACL)
dsgraph.bind('rdf', RDF)
dsgraph.bind('rdfs', RDFS)
dsgraph.bind('foaf', FOAF)
dsgraph.bind('dso', DSO)
agn = Namespace("http://www.agentes.org#")
DirectoryAgent = Agent('DirectoryAgent', agn.Directory,
'http://%s:%d/Register' % (hostname, port),
'http://%s:%d/Stop' % (hostname, port))
app = Flask(__name__)
mss_cnt = 0
cola1 = Queue() # Cola de comunicacion entre procesos
@app.route("/Register")
def register():
"""
Entry point del agente que recibe los mensajes de registro
La respuesta es enviada al retornar la funcion,
no hay necesidad de enviar el mensaje explicitamente
import os
import re
from typing import Optional, Callable
from rdflib import Graph, Namespace, OWL
from biolinkml import METAMODEL_NAMESPACE
from biolinkml.utils.generator import Generator
from tests import DEFAULT_LOG_LEVEL
from tests.utils.test_environment import TestEnvironment, TestEnvironmentTestCase
BIOLINK_NS = Namespace("https://w3id.org/biolink/vocab/")
class GeneratorTestCase(TestEnvironmentTestCase):
model_name: str = None # yaml name (sans '.yaml')
@staticmethod
def _print_triples(g: Graph):
""" Pretty print the contents of g, removing the prefix declarations """
g.bind('BIOLINK', BIOLINK_NS)
g.bind('meta', METAMODEL_NAMESPACE)
g.bind('owl', OWL)
g_text = re.sub(r'@prefix.*\n', '',
g.serialize(format="turtle").decode())
print(g_text)
def single_file_generator(self,
suffix: str,
gen: type(Generator),
*,
from rdflib import RDF, RDFS, OWL, Namespace, Graph
import brickschema
from .util import make_readable
import sys
sys.path.append("..")
from bricksrc.namespaces import BRICK, TAG, A, SKOS # noqa: E402
BLDG = Namespace(f"https://brickschema.org/schema/ExampleBuilding#")
g = Graph()
g.parse("Brick.ttl", format="turtle")
# Instances
g.add((BLDG.Coil_1, A, BRICK.Heating_Coil))
g.add((BLDG.Coil_2, BRICK.hasTag, TAG.Equipment))
g.add((BLDG.Coil_2, BRICK.hasTag, TAG.Coil))
g.add((BLDG.Coil_2, BRICK.hasTag, TAG.Heat))
g.add((BLDG.AHU1, A, BRICK.AHU))
g.add((BLDG.VAV1, A, BRICK.VAV))
g.add((BLDG.AHU1, BRICK.feedsAir, BLDG.VAV1))
g.add((BLDG.CH1, A, BRICK.Chiller))
# This gets inferred as an air temperature sensor
g.add((BLDG.TS1, A, BRICK.Temperature_Sensor))
g.add((BLDG.TS1, BRICK.measures, BRICK.Air))
g.add((BLDG.TS2, A, BRICK.Air_Temperature_Sensor))
# add air flow sensor
class Heat_Exchanger_Valve_Command(Valve_Command):
rdf_type = Namespace('https://brickschema.org/schema/1.0.2/Brick#').Heat_Exchanger_Valve_Command
class TestSupport(unittest.TestCase):
resp_agent = 'http://resp_agent.test/'
pro = Namespace("http://purl.org/spar/pro/")
def setUp(self):
self.graph_set = GraphSet("http://test/", "./info_dir/", "", False)
self.prov_set = ProvSet(self.graph_set, "http://test/", "./info_dir/",
False)
self.br = self.graph_set.add_br(self.resp_agent)
def _prepare_ordered_authors_list(self, list_len):
# First of all, we must cleanup the GraphSet:
self.br.remove_contributor()
for ar in self.graph_set.get_ar():
del self.graph_set.res_to_entity[ar.res]
for ra in self.graph_set.get_ra():
del self.graph_set.res_to_entity[ra.res]
# Then, we initialize a new well-formed linked list of authors:
ar_ordered_list = []
for i in range(list_len):
ra = self.graph_set.add_ra(self.resp_agent)
ar = self.graph_set.add_ar(self.resp_agent)
ar.create_author()
ar.is_held_by(ra)
self.br.has_contributor(ar)
ar_ordered_list.append(ar)
# Here each node of the list gets linked to the next one:
for i in range(list_len - 1):
ar_ordered_list[i].has_next(ar_ordered_list[i + 1])
return ar_ordered_list
@staticmethod
def _extract_ra_list(ar_list):
# Here the RA list is built and returned:
ra_list = []
for i in range(len(ar_list)):
ra = ar_list[i].get_is_held_by()
if ra is not None:
ra_list.append(ra)
return ra_list
def test_get_ordered_contributors_from_br(self):
list_len = 100
with self.subTest("Empty linked list"):
result = get_ordered_contributors_from_br(self.br, self.pro.author)
self.assertIsNotNone(result)
self.assertListEqual([], result)
with self.subTest("Well-formed linked list"):
correct_list = self._prepare_ordered_authors_list(list_len)
result = get_ordered_contributors_from_br(self.br, self.pro.author)
self.assertIsNotNone(result)
ar_list = self._extract_ra_list(correct_list)
self.assertListEqual(ar_list, result)
with self.subTest("Linked list with a loop"):
correct_list = self._prepare_ordered_authors_list(list_len)
# Here we corrupt the well-formed linked list introducing a loop:
correct_list[80].has_next(correct_list[50])
self.assertRaises(ValueError, get_ordered_contributors_from_br,
self.br, self.pro.author)
with self.subTest("Linked list split in two sub-lists"):
correct_list = self._prepare_ordered_authors_list(list_len)
# Here we corrupt the well-formed linked list introducing a loop:
correct_list[64].remove_next()
self.assertRaises(ValueError, get_ordered_contributors_from_br,
self.br, self.pro.author)
class AHU_Supply_Air_Temperature_Sensor(Discharge_Air_Temperature_Sensor,
Supply_Air_Temperature_Sensor):
rdf_type = Namespace('https://brickschema.org/schema/1.0.2/Brick#'
).AHU_Supply_Air_Temperature_Sensor
def __init__(self,
graph: Graph = None,
thesaurus_path="data/agrovoc.rdf",
skos_xl_labels=True,
lang="fr"):
if graph is None:
self.graph = Graph()
else:
self.graph = graph
logger.info("Loading thesaurus... [{}]".format(thesaurus_path))
self.graph.load(thesaurus_path)
string_entries = []
if skos_xl_labels:
query = f"""SELECT ?x ?lf WHERE {{
?x a skos:Concept;
skosxl:prefLabel ?l.
?l skosxl:literalForm ?lf.
FILTER(lang(?lf)='{lang}')
}}
"""
pref_labels = self.graph.query(
query,
initNs={
'skos': Namespace("http://www.w3.org/2004/02/skos/core#"),
'skosxl': Namespace("http://www.w3.org/2008/05/skos-xl#")
})
else:
query = f"""SELECT ?x ?lf WHERE {{
?x a skos:Concept;
skos:prefLabel ?lf.
FILTER(lang(?lf)='{lang}')
}}
"""
pref_labels = self.graph.query(
query,
initNs=dict(
skos=Namespace("http://www.w3.org/2004/02/skos/core#")))
for result in pref_labels:
string_entries.append((str(result[0]), str(result[1])))
if skos_xl_labels:
query = f"""SELECT ?x ?lf WHERE {{
?x a skos:Concept;
skosxl:prefLabel ?l.
?l skosxl:literalForm ?lf.
FILTER(lang(?lf)='{lang}')
}}
"""
alt_labels = self.graph.query(
query,
initNs=dict(
skos=Namespace("http://www.w3.org/2004/02/skos/core#"),
skosxl=Namespace("http://www.w3.org/2008/05/skos-xl#")))
else:
query = f"""SELECT ?x ?lf WHERE {{
?x a skos:Concept;
skos:altLabel ?lf.
FILTER(lang(?lf)='{lang}')
}}
"""
alt_labels = self.graph.query(
query,
initNs=dict(
skos=Namespace("http://www.w3.org/2004/02/skos/core#")))
for result in alt_labels:
string_entries.append((str(result[0]), str(result[1])))
dictionary_loader = StringDictionaryLoader(string_entries)
dictionary_loader.load()
if lang == 'fr':
self.concept_recognizer = IntersStemConceptRecognizer(
dictionary_loader, "data/stopwordsfr.txt",
"data/termination_termsfr.txt")
else:
self.concept_recognizer = IntersStemConceptRecognizer(
dictionary_loader, "data/stopwordsen.txt",
"data/termination_termsen.txt")
self.concept_recognizer.initialize()
from rdflib.serializer import Serializer
from rdflib.namespace import RDF, RDFS, XSD
import requests
import csv
import re
import hashlib
import docker
import time
client = docker.from_env()
container_it = client.containers.get("c9e896401036")
container_en = client.containers.get("233d97c53c0a")
g = graph.Graph()
cro = Namespace("http://www.cityrank.org/ontology/")
geo = Namespace("https://schema.org/GeoCoordinates")
plc = Namespace("https://schema.org/Place")
schema = Namespace("https://schema.org")
owl = Namespace("http://www.w3.org/2002/07/owl")
addr = Namespace("https://schema.org/PostalAddress")
rdfs = Namespace("http://www.w3.org/2000/01/rdf-schema#")
base = "http://www.cityrank.org/resource/"
dbpediaurl = "http://dbpedia.org/resource/"
not_found = {}
g.bind("cro", cro)
g.bind("geo", geo)
g.bind("schema", schema)
g.bind("addr", addr)
g.bind("owl", owl)
g.bind("rdfs", rdfs)
class Water_System_Water_Meter(Water_Meter):
rdf_type = Namespace(
'https://brickschema.org/schema/1.0.2/Brick#').Water_System_Water_Meter
import rdflib
from rdflib import URIRef
from rdflib import Literal
from rdflib import BNode
from rdflib import Namespace
if rdflib.__version__ >= "3.0.0" :
from rdflib import RDF as ns_rdf
from rdflib import RDFS as ns_rdfs
from rdflib import Graph
else :
from rdflib.RDFS import RDFSNS as ns_rdfs
from rdflib.RDF import RDFNS as ns_rdf
from rdflib.Graph import Graph
# Namespace, in the RDFLib sense, for the rdfa vocabulary
ns_rdfa = Namespace("http://www.w3.org/ns/rdfa#")
from .extras.httpheader import acceptable_content_type, content_type
from .transform.prototype import handle_prototypes
# Vocabulary terms for vocab reporting
RDFA_VOCAB = ns_rdfa["usesVocabulary"]
# Namespace, in the RDFLib sense, for the XSD Datatypes
ns_xsd = Namespace('http://www.w3.org/2001/XMLSchema#')
# Namespace, in the RDFLib sense, for the distiller vocabulary, used as part of the processor graph
ns_distill = Namespace("http://www.w3.org/2007/08/pyRdfa/vocab#")
debug = False
def main():
indra_ns = 'http://sorger.med.harvard.edu/indra/'
rn = Namespace(indra_ns + 'relations/')
en = Namespace(indra_ns + 'entities/')
g = Graph()
isa = rn.term('isa')
g.add((en.term('phosphorylation'), isa, en.term('modification')))
g.add((en.term('ubiquitination'), isa, en.term('modification')))
g.add((en.term('sumoylation'), isa, en.term('modification')))
g.add((en.term('acetylation'), isa, en.term('modification')))
g.add((en.term('hydroxylation'), isa, en.term('modification')))
save_hierarchy(g, hierarchy_path)
try:
import rdflib
except:
show_install_message("rdflib not found")
else:
version = tuple([int(x) for x in rdflib.__version__.split(".", 2)])
REQUIRED = (2, 1, 0)
if version < REQUIRED:
show_install_message("rdflib %s or greater required. Found rdflib version %s" % ("%s.%s.%s" % REQUIRED, rdflib.__version__))
logging.info("rdflib version: %s" % rdflib.__version__)
from rdflib import RDF, RDFS, Graph, URIRef, BNode, Namespace
REDFOOT = Namespace("http://redfoot.net/2005/redfoot#")
REDFOOT.Globals = REDFOOT["Globals"]
REDFOOT.program = REDFOOT["program"]
REDFOOT.code = REDFOOT["code"]
REDFOOT.Defaults = REDFOOT["Defaults"]
class BootLoader(Graph):
def __init__(self, backend):
backend = backend or "Sleepycat"
super(BootLoader, self).__init__(backend)
self.__log = None
self.__config = None
def __get_log(self):
class VFD_Fault_Status(VFD_Status,Fault_Status):
rdf_type = Namespace('https://brickschema.org/schema/1.0.2/Brick#').VFD_Fault_Status
class CRAC_Low_Humidity_Alarm(Low_Humidity_Alarm):
rdf_type = Namespace(
'https://brickschema.org/schema/1.0.2/Brick#').CRAC_Low_Humidity_Alarm
# You should have received a copy of the GNU Lesser General Public License
# along with RDF-REST. If not, see <http://www.gnu.org/licenses/>.
from time import sleep
from nose.tools import assert_raises
from rdflib import BNode, Graph, Literal, Namespace, RDF, RDFS, XSD
import example2 # can not import do_tests directly, nose tries to run it...
from example2 import EXAMPLE, Group2Implementation, Item2Implementation, \
make_example2_service
from rdfrest.exceptions import InvalidDataError
from rdfrest.cores.factory import unregister_service
from rdfrest.util.config import get_service_configuration
OTHER = Namespace("http://example.org/other/")
EXPECTING_LITERAL = (EXAMPLE.label, )
class TestMixins:
#ROOT_URI = URIRef("http://localhost:11235/foo/")
service = None
root = None
item = None
def setUp(self):
service_config = get_service_configuration()
service_config.set('server', 'port', '11235')
service_config.set('server', 'base-path', '/foo')
class UnobservedSignal(Signal):
rdf_type = Namespace(
'https://brickschema.org/schema/1.0.2/BrickFrame#').UnobservedSignal
import sys
from rdflib import Graph, Namespace, Literal
import csv
import urllib2
if __name__ == '__main__':
indra_ns = 'http://sorger.med.harvard.edu/indra/'
if len(sys.argv) > 1:
proteins_file = sys.argv[1]
else:
proteins_file = '../../data/ras_pathway_proteins.csv'
rn = Namespace(indra_ns + 'relations/')
en = Namespace(indra_ns + 'entities/')
g = Graph()
has_name = rn.term('hasName')
has_long_name = rn.term('hasLongName')
has_synonym = rn.term('hasSynonym')
isa = rn.term('isa')
# Read BEL family names
res = urllib2.urlopen('http://resource.belframework.org/belframework/'+\
'latest-release/namespace/selventa-protein-families.belns')
belns_text = res.read()
start = belns_text.find('[Values]')
lines = belns_text[start:].split('\n')
bel_family_names = []
for l in lines:
if l.endswith(' Family|P'):
family_name = l[:-2].replace(' ', '_').replace('/', '_')
bel_family_names.append(family_name)
class Medium_Temperature_Hot_Water_Differential_Pressure_Load_Shed_Status(
Medium_Temperature_Hot_Water, Differential_Pressure_Load_Shed_Status):
rdf_type = Namespace(
'https://brickschema.org/schema/1.0.2/Brick#'
).Medium_Temperature_Hot_Water_Differential_Pressure_Load_Shed_Status
def serialize(self, add, delete):
commit = Namespace("urn:commit:" + str(uuid.uuid1()) + ":")
eccrev = Namespace("https://vocab.eccenca.com/revision/")
g = ConjunctiveGraph()
namespace_manager = NamespaceManager(g)
namespace_manager.bind('eccrev', eccrev, override=False)
g.add((commit.term(""), RDF.type, eccrev.Commit))
graphUris = set(delete.keys()) | set(add.keys())
for graphUri in graphUris:
if (graphUri in delete.keys() and len(delete[graphUri]) > 0) or (graphUri in add.keys() and len(add[graphUri]) > 0):
revision = Namespace("urn:revision:" + str(uuid.uuid1()) + ":")
g.add((commit.term(""), eccrev.hasRevision, revision.term("")))
g.add((revision.term(""), RDF.type, eccrev.Revision))
if str(graphUri) != 'http://quitdiff.default/':
g.add((revision.term(""), eccrev.hasRevisionGraph, graphUri))
if graphUri in delete.keys() and len(delete[graphUri]) > 0:
deleteGraphName = revision.term(":delete")
g.add((revision.term(""), eccrev.deltaDelete, deleteGraphName))
for triple in delete[graphUri]:
g.add(triple + (deleteGraphName,))
if graphUri in add.keys() and len(add[graphUri]) > 0:
insertGraphName = revision.term(":insert")
g.add((revision.term(""), eccrev.deltaInsert, insertGraphName))
for triple in add[graphUri]:
g.add(triple + (insertGraphName,))
return g.serialize(format="trig").decode("utf-8")
def populate_graph(articles, persons, relationships):
"""
Adds triples to an RDF graph with the following structure:
Person triples, we store only the wikidata id and the surface string(s) by which is referred
to in the news articles;
<wiki_URI, SKOS.altLabel, name>
Article triples:
<url, DC.title, title>
<url, DC.data, date)
Relationships as Blank Node:
- <_rel, ns1.type, rel_type>
- <_rel, ns1.score, rel_score>
- <_rel, ns1.url, url>
- g.add((_rel, ns1.ent1, URIRef(f"http://www.wikidata.org/entity/{rel.ent1}")))
- g.add((_rel, ns1.ent2, URIRef(f"http://www.wikidata.org/entity/{rel.ent2}")))
- g.add((_rel, ns1.ent1_str, Literal(rel.ent1_str)))
- g.add((_rel, ns1.ent2_str, Literal(rel.ent2_str)))
NOTE: linked-data vocabularies can be seen here: https://lov.linkeddata.es/dataset/lov/
"""
g = Graph()
ns1 = Namespace("http://www.politiquices.pt/")
g.bind("politiquices", ns1)
wiki_prop = Namespace("http://www.wikidata.org/prop/direct/")
wiki_item = Namespace("http://www.wikidata.org/entity/")
g.bind("wd", wiki_item)
g.bind("wdt", wiki_prop)
print("\nadding Persons")
for wikidata_id, person in persons.items():
# state that in 'politiquices' this is a human, following the same as wikidata.org
g.add((URIRef(f"http://www.wikidata.org/entity/{wikidata_id}"),
wiki_prop.P31, wiki_item.Q5))
for name in person.known_as:
g.add((
URIRef(f"http://www.wikidata.org/entity/{wikidata_id}"),
SKOS.altLabel,
Literal(name, lang="pt"),
))
print("adding Articles")
for article in articles:
g.add((URIRef(article.url), DC.title, Literal(article.title,
lang="pt")))
g.add((URIRef(article.url), DC.date,
Literal(article.crawled_date, datatype=XSD.date)))
print("adding Relationships")
for rel in relationships:
_rel = BNode()
g.add((_rel, ns1.type, Literal(rel.rel_type)))
g.add((_rel, ns1.score, Literal(rel.rel_score, datatype=XSD.float)))
g.add((_rel, ns1.url, URIRef(rel.url)))
g.add((_rel, ns1.ent1,
URIRef(f"http://www.wikidata.org/entity/{rel.ent1}")))
g.add((_rel, ns1.ent2,
URIRef(f"http://www.wikidata.org/entity/{rel.ent2}")))
g.add((_rel, ns1.ent1_str, Literal(rel.ent1_str)))
g.add((_rel, ns1.ent2_str, Literal(rel.ent2_str)))
date_time = datetime.now().strftime("%Y-%m-%d_%H%M")
f_name = f"politiquices_{date_time}.ttl"
g.serialize(destination=f_name, format="turtle")
print("graph has {} statements.".format(len(g)))
print()
print("persons : ", len(persons))
print("articles : ", len(articles))
print("relationships: ", len(relationships))
print()
def main():
indra_ns = 'http://sorger.med.harvard.edu/indra/'
rn = Namespace(indra_ns + 'relations/')
act = Namespace(indra_ns + 'activities/')
g = Graph()
isa = rn.term('isa')
g.add((act.term('transcription'), isa, act.term('activity')))
g.add((act.term('catalytic'), isa, act.term('activity')))
g.add((act.term('gtpbound'), isa, act.term('activity')))
g.add((act.term('kinase'), isa, act.term('catalytic')))
g.add((act.term('phosphatase'), isa, act.term('catalytic')))
g.add((act.term('gef'), isa, act.term('catalytic')))
g.add((act.term('gap'), isa, act.term('catalytic')))
save_hierarchy(g, hierarchy_path)
class VFD_Current_Sensor(Current_Sensor):
rdf_type = Namespace(
'https://brickschema.org/schema/1.0.2/Brick#').VFD_Current_Sensor
# -*- coding: utf-8 -*-
from pymongo import MongoClient
from rdflib import Graph, Literal, BNode, Namespace, RDF, URIRef
from rdflib.namespace import DC, FOAF, XSD
from entity_to_rdf import EntityConvert
lobbyFacts = Namespace('https://studi.f4.htw-berlin.de/~s0539710/lobbyradar#')
lobbyOntology = Namespace('https://studi.f4.htw-berlin.de/~s0539710/lobbyradar/ontology#')
org = Namespace('http://www.w3.org/ns/org#')
rdf = Namespace('http://www.w3.org/1999/02/22-rdf-syntax-ns#')
vcard = Namespace('http://www.w3.org/2006/vcard/ns#')
# Connect to database and create variables for the collections
client = MongoClient()
db = client.lobbyradar
entities = db.entities
relations = db.relations
# Print some statistics about our database dump
print("Collections in database: " + ", ".join(db.collection_names(include_system_collections=False)))
print("Entities: %s documents" % entities.count())
print("Relations: %s documents" % relations.count())
# Create a graph and prepare by loading ontology and binding prefixes
g = Graph()
relationGraph = Graph()
converter = EntityConvert(g)
entity = entities.find_one({'name': 'Rudolf Henke'})
all_entities = entities.find()
for i,e in enumerate(all_entities):
if (i % (entities.count() / 20) == 0):
# Check the README file for full details.
#
# This programme takes as sole argument the ontology module name:
#
# python3 generateDoc.py glosis_main
#
# SPDX-License-Identifier: CC-BY-NC-SA-3.0-IGO
import os
import sys
import json
import configparser
from rdflib import Graph, Namespace
from rdflib.namespace import RDF, FOAF, RDFS, OWL
DCT = Namespace("http://purl.org/dc/terms/")
SCHEMA = Namespace("http://schema.org/")
mapPreds = {
"thisVersionURI": OWL.versionIRI,
"ontologyRevisionNumber": OWL.versionInfo,
"ontologyTitle": DCT.title,
"abstract": DCT.abstract
}
widoco_jar = "/opt/widoco/widoco-1.4.15-jar-with-dependencies.jar"
ont_file = "glosis_main"
templ_file = "template.json"
creators = []
contributors = []