Python SparqlQueryBuilder.SparqlQueryBuilder类代码示例

    def positionable_attr(self):
        """
        Return the positionable attributes in common between two positionable entity
        """
        #FIXEME: Rewrite this ugly method

        body = self.request.json_body
        data = {}

        sqb = SparqlQueryBuilder(self.settings, self.request.session)
        ql = QueryLauncher(self.settings, self.request.session)

        # Check if the two entity are positionable
        positionable1 = ql.process_query(sqb.get_if_positionable(body['node']).query)
        positionable2 = ql.process_query(sqb.get_if_positionable(body['node']).query)

        if positionable1 == 0 or positionable2 == 0:
            data['error'] = 'not positionable nodes'
            return data

        results = ql.process_query(sqb.get_common_positionable_attributes(body['node'], body['second_node']).query)
        self.log.debug(results)

        data['results'] = {}

        list_pos_attr = []

        for elem in results:
            if elem['pos_attr'] not in list_pos_attr:
                list_pos_attr.append(elem['pos_attr'].replace("http://www.semanticweb.org/irisa/ontologies/2016/1/igepp-ontology#", ""))

        for elem in list_pos_attr:
            data['results'][elem] = False not in [bool(int(p['status'])) for p in results if p['pos_attr'] == "http://www.semanticweb.org/irisa/ontologies/2016/1/igepp-ontology#"+elem]

        return data

 def empty(self):
     #empty database
     sqb = SparqlQueryBuilder(self.settings, self.request.session)
     ql = QueryLauncher(self.settings, self.request.session)
     namedGraphs = self.list_named_graphs()
     for graph in namedGraphs:
         ql.execute_query(sqb.get_delete_query_string(graph).query)

    def insert_metadatas(self,accessL):
        """
        Insert the metadatas into the parent graph
        """

        self.log.debug('--- insert_metadatas ---')

        sqb = SparqlQueryBuilder(self.settings, self.session)
        query_laucher = QueryLauncher(self.settings, self.session)

        valAcces = 'public' if accessL else 'private'

        ttl = '<' + self.graph + '> prov:generatedAtTime "' + self.timestamp + '"^^xsd:dateTime .\n'
        ttl += '<' + self.graph + '> dc:creator "' + self.session['username'] + '" .\n'
        ttl += '<' + self.graph + '> :accessLevel "' +  valAcces + '" .\n'
        ttl += '<' + self.graph + '> foaf:Group "' +  self.session['group']  + '" .\n'
        ttl += '<' + self.graph + '> prov:wasDerivedFrom "' + self.name + '" .\n'
        ttl += '<' + self.graph + '> dc:hasVersion "' + get_distribution('Askomics').version + '" .\n'
        ttl += '<' + self.graph + '> prov:describesService "' + os.uname()[1] + '" .\n'

        if self.is_defined("askomics.endpoint"):
            ttl += '<' + self.graph + '> prov:atLocation "' + self.get_param("askomics.endpoint") + '" .\n'
        else:
            raise ValueError("askomics.endpoint does not exit.")

        sparql_header = sqb.header_sparql_config('')

        query_laucher.insert_data(ttl, self.graph, sparql_header)

    def compare_file_to_database(self, headers):
        """ Ask the database to compare the headers of a file to convert to the corresponding class in the database """
        curr_entity = headers[0]
        sqb = SparqlQueryBuilder(self.settings, self.session)
        ql = QueryLauncher(self.settings, self.session)
        sparql_template = self.get_template_sparql(self.ASKOMICS_get_class_info_from_abstraction_queryFile)
        query = sqb.load_from_file(sparql_template, {"#nodeClass#": curr_entity}).query

        results = ql.process_query(query)
        if results == []:
            return [], headers, []
        bdd_relations, new_headers, missing_headers, present_headers = [], [], [], []
        for result in results:
            bdd_relation = result["relation"].replace(self.get_param("askomics.prefix"), "").replace("has_", "")
            bdd_relations.append(bdd_relation)
            if bdd_relation not in headers:
                self.log.warning('Relation "%s" not found in tables columns: %s.', bdd_relation, repr(headers))
                missing_headers.append(bdd_relation)
        for header in headers:
            if header != curr_entity:
                if header not in bdd_relations:
                    self.log.info('Adding column "%s".', header)
                    new_headers.append(header)
                elif header not in missing_headers:
                    present_headers.append(header)
        return missing_headers, new_headers, present_headers

    def deleteMoState(self,urimo):
        self.log.debug(' ***** Delete module '+urimo+' on TPS ***** ')
        sqb = SparqlQueryBuilder(self.settings, self.session)
        ql = QueryLauncher(self.settings, self.session)

        ql.execute_query(sqb.prepare_query(
        """
        DELETE WHERE { GRAPH <"""+self.graph_modules+"""> { <"""+urimo+"""> ?p ?o } }
        """
        ).query)

    def empty_database(self):
        """
        Delete all triples in the triplestore
        """

        self.log.debug("=== DELETE ALL TRIPLES ===")

        sqb = SparqlQueryBuilder(self.settings, self.request.session)
        ql = QueryLauncher(self.settings, self.request.session)

        ql.execute_query(sqb.get_delete_query_string().query)

    def test_print_ids(self):
        from askomics.libaskomics.rdfdb.SparqlQueryBuilder import SparqlQueryBuilder

        request = testing.DummyRequest()

        sqb = SparqlQueryBuilder(self.settings, request.session)

        graph = {'limit': 30, 'return_only_query': False, 'filter_cat': [], 'constraint': [{'type': 'node', 'id': 'entity1', 'uri': 'http://www.semanticweb.org/irisa/ontologies/2016/1/igepp-ontology#entity'}], 'filter_str': [{'id': 'entity1', 'value': 'xxxx'}], 'display': [{'id': 'entity1'}, {}], 'export': 0, 'filter_num': [], 'uploaded': ''}

        query = sqb.load_from_query_json(graph).query

        self.assertIn('?entity1 a :entity .\n\tFILTER (regex(str(?entity1), "xxxx", "i")) .', query)

    def list_named_graphs(self):
        sqb = SparqlQueryBuilder(self.settings, self.request.session)
        ql = QueryLauncher(self.settings, self.request.session)

        res = ql.execute_query(sqb.get_list_named_graphs().query)

        namedGraphs = []

        for indexResult in range(len(res['results']['bindings'])):
            namedGraphs.append(res['results']['bindings'][indexResult]['g']['value'])

        return namedGraphs

    def launch_query(self):
        """ Converts the constraints table created by the graph to a sparql query, send it to the database and compile the results"""
        data = {}
        body = self.request.json_body

        export = bool(int(body['export']))
        sqb = SparqlQueryBuilder(self.settings, self.request.session)
        return_only_query = bool(int(body['return_only_query']))

        if body['uploaded'] != '':
            if export:
                query = body['uploaded'].replace('LIMIT 30', 'LIMIT 10000')
            else:
                query = body['uploaded']
        else:
            query = sqb.load_from_query_json(body).query

        if return_only_query:
            data['query'] = query
            return data

        ql = QueryLauncher(self.settings, self.request.session)
        rb = ResultsBuilder(self.settings, self.request.session)


        results = ql.process_query(query)

        if export:
            data['file'] = ql.format_results_csv(rb.build_csv_table(results))
        else:
            entity_name_list, entity_list_attributes = rb.organize_attribute_and_entity(results, body['constraint'])

            data['results_entity_name'] = entity_name_list
            data['results_entity_attributes'] = entity_list_attributes

            data['results'] = [
                {
                    k: res[k].replace(self.settings["askomics.prefix"], '')
                    for k in res.keys()
                }
                for res in results
            ]

        self.log.debug("== results ==")
        for elt in results:
            self.log.debug(elt)

    #    data['query'] = query

        return data

    def get_attributes_of(self, uri):
        """
        Get all attributes of a node class (identified by his uri). These
        attributes are known thanks to the domain knowledge of your RDF database.

        :param uri: Uri of the node class
        :type uri: str
        :return: All attributes of a node class
        :rtype: Attribute list
        """
        self.log.debug(" =========== TripleStoreExplorer:get_attributes_of ===========")
        attributes = []
        results = []

        sqb = SparqlQueryBuilder(self.settings, self.session)
        ql = QueryLauncher(self.settings, self.session)

        fragment = uri.rsplit('#', 1)[-1]
        parent = fragment + str(self.get_new_id(fragment))

        # Send a request to know all the neighbors of a node (from uri).
        sparql_template = self.get_template_sparql(self.ASKOMICS_neighbor_query_file)

        query = sqb.load_from_file(sparql_template, {
            "nodeClass": '<%s>' % uri,
            "neighborClass": "?nodeUri"
            }).query

        results = (ql.process_query(query))
        for result in results:
            neighbor_uri = result["relationUri"]
            if 'nodeLabel' in result:
                neighbor_label = result["nodeLabel"]
            else:
                neighbor_label = result["relationLabel"]

            neighbor_id = neighbor_label + str(self.get_new_id(neighbor_label))

            if self.has_setting(result["nodeUri"], 'attribute') or self.has_setting(neighbor_uri, 'attribute'):
                attributes.append(
                    Attribute(neighbor_id,
                        neighbor_uri,
                        result["nodeUri"],
                        neighbor_label,
                        parent)
                    )

        return attributes

    def delete_graph(self):
        """
        Delete triples from a list of graph
        """
        self.log.debug("=== DELETE SELECTED GRAPHS ===")

        sqb = SparqlQueryBuilder(self.settings, self.request.session)
        ql = QueryLauncher(self.settings, self.request.session)

        graphs = self.request.json_body['namedGraphs']

        for graph in graphs:
            self.log.debug("--- DELETE GRAPH : %s", graph)
            ql.execute_query(sqb.get_drop_named_graph(graph).query)
            #delete metadatas
            ql.execute_query(sqb.get_delete_metadatas_of_graph(graph).query)

    def moStateOnTPS(self):
        '''
            check if module files state is saved on the TPS.
            if not all modules files are saved with the unchecked status !
        '''
        sqb = SparqlQueryBuilder(self.settings, self.session)
        ql = QueryLauncher(self.settings, self.session)
        results = ql.process_query(sqb.build_query_on_the_fly({
            'select': '?uri ?module ?comment ?version ?graph ?state',
            'from'  : [self.graph_modules],
            'query': '{\n'+
                     '?uri rdfs:label ?module .\n'+
                     '?uri rdfs:comment ?comment .\n'+
                     '?uri :module_version ?version .\n'+
                     '?uri :module_state ?state .\n'+
                     'OPTIONAL { ?uri :module_graph ?graph . } \n'+
                     '}\n'
        }, True).query)

        self.log.debug(' ***** module on TPS ***** ')
        listMoOnTps = {}
        for result in results:
            result['checked'] = (result['state'] == "ok")
            result['wait'] = (result['state'] == "wait")
            listMoOnTps[result['module']] = 0
            self.log.debug('module : '+result['module'])
            #=======================*************** A ENLEVER *********=======================================
            #pour debugger
            #if result['wait'] :
            #    result['wait'] = False
            #==============================================================

        self.log.debug(' ***** check Available Modules ***** ')

        requestAgain = False

        for mo in self.moduleFiles:
            self.log.debug(" --> module "+mo);
            if mo not in listMoOnTps:
                self.log.debug(" --====== > new module < =======");
                self.importMoSate(self.moduleFiles[mo],'off')
                requestAgain = True

        if requestAgain :
            return False

        return results

    def get_metadatas(self):
        """
        Create metadatas and insert them into AskOmics main graph.
        """
        self.log.debug("====== INSERT METADATAS ======")
        sqb = SparqlQueryBuilder(self.settings, self.session)
        ql = QueryLauncher(self.settings, self.session)

        ttlMetadatas = "<" + self.metadatas['graphName'] + "> " + "prov:generatedAtTime " + '"' + self.metadatas['loadDate'] + '"^^xsd:dateTime .\n'
        ttlMetadatas += "<" + self.metadatas['graphName'] + "> " + "dc:creator " + '"' + self.metadatas['username'] + '"^^xsd:string  .\n'
        ttlMetadatas += "<" + self.metadatas['graphName'] + "> " + "prov:wasDerivedFrom " + '"' + self.metadatas['fileName'] + '"^^xsd:string .\n'
        ttlMetadatas += "<" + self.metadatas['graphName'] + "> " + "dc:hasVersion " + '"' + self.metadatas['version'] + '"^^xsd:string .\n'
        ttlMetadatas += "<" + self.metadatas['graphName'] + "> " + "prov:describesService " + '"' + self.metadatas['server'] + '"^^xsd:string .'

        sparqlHeader = sqb.header_sparql_config("")

        ql.insert_data(ttlMetadatas, self.get_param("askomics.graph"), sparqlHeader)

    def get_list_named_graphs(self):
        """
        Return a list with all the named graphs.
        """

        self.log.debug("=== LIST OF NAMED GRAPHS ===")

        sqb = SparqlQueryBuilder(self.settings, self.request.session)
        ql = QueryLauncher(self.settings, self.request.session)

        res = ql.execute_query(sqb.get_list_named_graphs().query)

        namedGraphs = []

        for indexResult in range(len(res['results']['bindings'])):
            namedGraphs.append(res['results']['bindings'][indexResult]['g']['value'])

        return namedGraphs

    def has_category(self, entity, category, uri_category):
        """
        Get different categories for a node class.

        :param entity : Name of the entity associated with the node
        :param uri: Name of the node
        :type uri: str
        :return: List of categories
        :rtype: list

        """
        self.log.debug(" =========== TripleStoreExplorer:has_category ===========[ entity:"+ entity + ", category:"+ category+"]")
        sqb = SparqlQueryBuilder(self.settings, self.session)
        ql = QueryLauncher(self.settings, self.session)
        sparql_template = self.get_template_sparql(self.ASKOMICS_has_category_query_file)
        query = sqb.load_from_file(sparql_template, {"#nodeClass#": uri_category, "#category#" : category, "#entity#" : entity}).query
        results = ql.process_query(query)

        return [res["label"] for res in results]