def parse_ontology_file(terminology):
print "Parsing " + terminology
#get the URI of the terminology and create a new instance of ontology
re= requests.get(terminology)
jo = json.loads(re.text)
onto = ontology.ontology(terminology)
#get all terms of the termonology
re1= requests.get("http://terminologies.gfbio.org/api/terminologies/" + jo["results"][0]["acronym"] + "/allterms")
jo1 = json.loads(re1.text)
tempElems = []
#get all terms and create them as instances of onto_elem
for term in jo1["results"]:
elem = onto_element.onto_elem(term["uri"], "", "")
elem.add_child(onto_element.onto_elem("{http://www.w3.org/2000/01/rdf-schema#}label", "{http://www.w3.org/2000/01/rdf-schema#}label", term["label"]))
#get the synonyms
re2= requests.get("http://terminologies.gfbio.org/api/terminologies/" + jo["results"][0]["acronym"] + "/synonyms?uri=" + term["uri"])
jo2 = json.loads(re2.text)
if "synonyms" in jo2["results"]:
elem.add_attribute("synonyms", jo2["results"]["synonyms"])
#save the term
tempElems.append(elem)
#print elem.tostring()
if onto != "" and len(tempElems) > 0:
onto.add_elements(tempElems)
if onto != "":
#util.write2File("onto.txt", str(onto) + os.linesep, "a")
#util.write2File("onto.txt", str(onto.get_elements()) + os.linesep, "a")
return onto
else:
return ""
def parse_ontology_file(ontology_file):
print "Parsing " + ontology_file
tree = defusedxml.ElementTree.parse(ontology_file)
root = tree.getroot()
#check if the file could even be an OWL file in RDF XML syntax
if root.tag == "{http://www.w3.org/1999/02/22-rdf-syntax-ns#}RDF":
onto_info = root.findall("{http://www.w3.org/2002/07/owl#}Ontology")
#look if there is exactly one 'Ontology' element from namespace 'owl'
if onto_info[0].tag.replace("{http://www.w3.org/2002/07/owl#}", "") == "Ontology":
#get the name of the ontology
onto = ontology.ontology(onto_info[0].attrib["{http://www.w3.org/1999/02/22-rdf-syntax-ns#}about"])
tempProps = []
tempElems = []
#go through all elements
for item in root.getchildren():
#get the properties of the ontology
if re.match("{http://www.w3.org/2002/07/owl#}.*Property", item.tag):
new_prop = onto_element.onto_elem(item.attrib["{http://www.w3.org/1999/02/22-rdf-syntax-ns#}about"], item.tag.replace("{http://www.w3.org/2002/07/owl#}", ""), item.text)
add_children(new_prop, item.getchildren())
tempProps.append(new_prop)
#get all class elements
elif item.tag == "{http://www.w3.org/2002/07/owl#}Class":
#create a new ontology element
elem = onto_element.onto_elem(item.attrib["{http://www.w3.org/1999/02/22-rdf-syntax-ns#}about"], item.tag.replace("{http://www.w3.org/2002/07/owl#}", ""), item.text)
#util.write2File("test1.txt", "Created " + item.attrib["{http://www.w3.org/1999/02/22-rdf-syntax-ns#}about"] + ": " + str(elem) + "\n", "a")
for attr in item.attrib:
elem.add_attribute(attr, item.attrib[attr])
#get the children
add_children(elem, item.getchildren())
tempElems.append(elem)
#if the ontology is populated with individuals, get them, too
elif item.tag == "{http://www.w3.org/2002/07/owl#}NamedIndividual":
#create a new ontology element
elem = onto_element.onto_elem(item.attrib["{http://www.w3.org/1999/02/22-rdf-syntax-ns#}about"], item.tag.replace("{http://www.w3.org/2002/07/owl#}", ""), item.text)
#util.write2File("test1.txt", "Created " + item.attrib["{http://www.w3.org/1999/02/22-rdf-syntax-ns#}about"] + ": " + str(elem) + "\n", "a")
for attr in item.attrib:
elem.add_attribute(attr, item.attrib[attr])
#get the children
add_children(elem, item.getchildren())
tempElems.append(elem)
if onto != "" and len(tempProps) > 0:
onto.add_properties(tempProps)
if onto != "" and len(tempElems) > 0:
onto.add_elements(tempElems)
#get the namespaces from the RDF element (the root) and put them into the ontology
for attr in root.attrib:
onto.add_namespace(attr, root.attrib[attr])
if onto != "":
#util.write2File("onto.txt", str(onto) + os.linesep, "a")
#util.write2File("onto.txt", str(onto.get_elements()) + os.linesep, "a")
return onto
else:
return ""
def add_children(node, children):
for child in children:
new_elem = onto_element.onto_elem(child.tag, child.tag.split("}")[-1], child.text)
for attr in child.attrib:
new_elem.add_attribute(attr, child.attrib[attr])
if len(child.getchildren()) > 0:
add_children(new_elem, child)
node.add_child(new_elem)
def parse_ontology_file(terminology_file):
print "Parsing " + terminology_file
#get the URI of the terminology and create a new instance of ontology
json_content = util.readFileContentAsString(terminology_file)
jo = json.loads(json_content)
onto = ontology.ontology(os.path.basename(terminology_file))
#get all terms of the termonology
tempElems = []
#get all terms and create them as instances of onto_elem
for term in jo["results"]:
elem = onto_element.onto_elem(term["uri"], "", "")
elem.add_child(onto_element.onto_elem("{http://www.w3.org/2000/01/rdf-schema#}label", "{http://www.w3.org/2000/01/rdf-schema#}label", term["label"]))
#save the term
tempElems.append(elem)
#print elem.tostring()
if onto != "" and len(tempElems) > 0:
onto.add_elements(tempElems)
if onto != "":
#util.write2File("onto.txt", str(onto) + os.linesep, "a")
#util.write2File("onto.txt", str(onto.get_elements()) + os.linesep, "a")
return onto
else:
return ""