semtk3 package

semtk3.build_constraint(sparql_id, operator, operand_list)

Build a contraint to be used as a query parameter :param _sphinx_paramlinks_semtk3.build_constraint.sparql_id: the variable name :param _sphinx_paramlinks_semtk3.build_constraint.operator: operator {MATCHES,REGEX,GREATERTHAN,GREATERTHANOREQUALS,LESSTHAN,LESSTHANOREQUALS,VALUEBETWEEN,VALUEBETWEENUNINCLUSIVE} :param _sphinx_paramlinks_semtk3.build_constraint.operand_list: list of values :return: the constraint :rettype: RuntimeConstraint

semtk3.check_services()

logs success or failure of each service :return: did all pings succeed :rtype: boolean

semtk3.clear_graph(conn_json_str, model_or_data, index)

Clear a graph :param _sphinx_paramlinks_semtk3.clear_graph.conn_json_str: connection json as a string :param _sphinx_paramlinks_semtk3.clear_graph.model_or_data: string “model” or “data” :param _sphinx_paramlinks_semtk3.clear_graph.index: integer specifying which model or data graph to use :return: message :rtype: string

semtk3.create_nodegroup(conn_json_str, class_uri, sparql_id=None)

Create a nodegroup containing a single uri :param _sphinx_paramlinks_semtk3.create_nodegroup.conn_json_str: connection json string :param _sphinx_paramlinks_semtk3.create_nodegroup.class_uri: class to add :param _sphinx_paramlinks_semtk3.create_nodegroup.sparql_id: optional sparqlID if different from ?ClassName :return: nodegroup :rettype: nodegroup json string

semtk3.delete_nodegroup_from_store(nodegroup_id)

Delete nodegroup_id from the store :param _sphinx_paramlinks_semtk3.delete_nodegroup_from_store.nodegroup_id: the id

semtk3.delete_nodegroups_from_store(regex_str)

Delete matching nodegroups from store :param _sphinx_paramlinks_semtk3.delete_nodegroups_from_store.regex_str: pattern to match on nodegroup id’s

semtk3.fdc_cache_bootstrap_table(conn_json_str, spec_id, bootstrap_table, recache_after_sec)

Run an fdc cache spec :param _sphinx_paramlinks_semtk3.fdc_cache_bootstrap_table.conn_json_str: connection containing model and data graphs :param _sphinx_paramlinks_semtk3.fdc_cache_bootstrap_table.spec_id: the fdc cache spec identifier :param _sphinx_paramlinks_semtk3.fdc_cache_bootstrap_table.bootstrap_table: semtktable to kick off the cache :param _sphinx_paramlinks_semtk3.fdc_cache_bootstrap_table.recache_after_sec: maximum age of cache

semtk3.get_constraints_by_id(nodegroup_id)

Get runtime constraints for a stored nodegroup :param _sphinx_paramlinks_semtk3.get_constraints_by_id.nodegroup_id: the id :return: columns valueId, itemType and valueType :rtype: semtktable

semtk3.get_filter_values_by_id(nodegroup_id, target_obj_sparql_id, override_conn_json_str=None, limit_override=None, offset_override=None, runtime_constraints=None, edc_constraints=None, flags=None)

Run a filter values query, which returns all the existing values for a given variable in the nodegroup :param _sphinx_paramlinks_semtk3.get_filter_values_by_id.nodegroup_id: the id :param _sphinx_paramlinks_semtk3.get_filter_values_by_id.target_obj_sparql_id: the variable to be interrogated :param _sphinx_paramlinks_semtk3.get_filter_values_by_id.override_conn_json_str: optional override connection json string :param _sphinx_paramlinks_semtk3.get_filter_values_by_id.limit_override: optional override of LIMIT clause :param _sphinx_paramlinks_semtk3.get_filter_values_by_id.offset_override: optional override of OFFSET clause :param _sphinx_paramlinks_semtk3.get_filter_values_by_id.runtime_constraints: optional runtime constraints built by build_constraint() :param _sphinx_paramlinks_semtk3.get_filter_values_by_id.edc_constraints: optional edc constraints :param _sphinx_paramlinks_semtk3.get_filter_values_by_id.flags: optional query flags :return: results :rtype semtktable

semtk3.get_logger()
semtk3.get_nodegroup_by_id(nodegroup_id)

Retrieve a nodegroup from the store :param _sphinx_paramlinks_semtk3.get_nodegroup_by_id.nodegroup_id: the id :return: a nodegroup :rettype: json string

semtk3.get_nodegroup_store_data()

Get list of everything in the nodegroup store :return: SemtkTable with columns ‘ID’, ‘comments’, ‘creationDate’, ‘creator’ :rettype: semtktable

semtk3.get_oinfo_uri_label_table(conn_json_str)

Get a table describing the ontology model :param _sphinx_paramlinks_semtk3.get_oinfo_uri_label_table.conn_json_str: connection string of graph(s) holding the model :rettype: semtktable

semtk3.get_table(jobid)

Get a table from an async job :param _sphinx_paramlinks_semtk3.get_table.jobid: the job id :rettype: semtktable

semtk3.ingest_by_id(nodegroup_id, csv_str, override_conn_json_str=None)

Perform data ingestion :param _sphinx_paramlinks_semtk3.ingest_by_id.nodegroup_id: nodegroup with ingestion template :param _sphinx_paramlinks_semtk3.ingest_by_id.csv_str: string csv data :param _sphinx_paramlinks_semtk3.ingest_by_id.override_conn_json_str: optional override connection :return: table of errors :rettype: semtktable

semtk3.override_ports(query_port=None, status_port=None, results_port=None, hive_port=None, oinfo_port=None, nodegroup_exec_port=None, nodegroup_port=None, fdcache_port=None)

Override the default port(s) for Semtk service(s) :param _sphinx_paramlinks_semtk3.override_ports.query_port: optional :param _sphinx_paramlinks_semtk3.override_ports.status_port: optional :param _sphinx_paramlinks_semtk3.override_ports.results_port: optional :param _sphinx_paramlinks_semtk3.override_ports.hive_port: optional :param _sphinx_paramlinks_semtk3.override_ports.oinfo_port: optional :param _sphinx_paramlinks_semtk3.override_ports.nodegroup_exec_port: optional :param _sphinx_paramlinks_semtk3.override_ports.nodegroup_port: optional :param _sphinx_paramlinks_semtk3.override_ports.fdcache_port: optional

semtk3.query(query, conn_json_str, model_or_data='data', conn_index=0)

Run a raw SPARQL query :param _sphinx_paramlinks_semtk3.query.query: SPARQL :param _sphinx_paramlinks_semtk3.query.conn_json_str: connection json string :param _sphinx_paramlinks_semtk3.query.model_or_data: optional “model” or “data” specifying which endpoint in the sparql connection, defaults to “model” :param _sphinx_paramlinks_semtk3.query.conn_index: index specifying which of the model or data endpoints in the sparql connection, defaults to 0 :return: results :rettype: semtktable

semtk3.query_hive(hiveserver_host, hiveserver_port, hiveserver_database, query)

Execute a hive quiery :param _sphinx_paramlinks_semtk3.query_hive.hiveserver_host: hive host :param _sphinx_paramlinks_semtk3.query_hive.hiveserver_port: hive port :param _sphinx_paramlinks_semtk3.query_hive.hiveserver_database: hive database :param _sphinx_paramlinks_semtk3.query_hive.query: sql :return: SemtkTable with columns ‘ID’, ‘comments’, ‘creationDate’, ‘creator’ :rettype: semtktable

semtk3.retrieve_from_store(regex_str, folder_path)

Retrieve all nodegroups matching a pattern, create store_data.csv :param _sphinx_paramlinks_semtk3.retrieve_from_store.regex_str: pattern to match on nodegroup id’s :param _sphinx_paramlinks_semtk3.retrieve_from_store.folder_path: target folder

semtk3.select_by_id(nodegroup_id, limit_override=0, offset_override=0, runtime_constraints=None, edc_constraints=None, flags=None)

Execute a select query for a given nodegroup id :param _sphinx_paramlinks_semtk3.select_by_id.nodegroup_id: id of nodegroup in the store :param _sphinx_paramlinks_semtk3.select_by_id.limit_override: optional override of LIMIT clause :param _sphinx_paramlinks_semtk3.select_by_id.offset_override: optional override of OFFSET clause :param _sphinx_paramlinks_semtk3.select_by_id.runtime_constraints: optional runtime constraints built by build_constraint() :param _sphinx_paramlinks_semtk3.select_by_id.edc_constraints: optional edc constraints :param _sphinx_paramlinks_semtk3.select_by_id.flags: optional query flags :return: results :rtype: semtktable

semtk3.set_headers(headers)
semtk3.set_host(hostUrl)
semtk3.store_nodegroup(nodegroup_id, comments, creator, nodegroup_json_str)

Saves a single nodegroup to the store, fails if nodegroup_id already exists :param _sphinx_paramlinks_semtk3.store_nodegroup.nodegroup_id: the id :param _sphinx_paramlinks_semtk3.store_nodegroup.comments: comment string :param _sphinx_paramlinks_semtk3.store_nodegroup.creator: creator string :param _sphinx_paramlinks_semtk3.store_nodegroup.nodegroup_json_str: nodegroup in json string form :return: status :rettype: string

semtk3.store_nodegroups(folder_path)
Reads a file of the standard “store_data.csv” format

ID,comments,creator,jsonfile id27,Test comments,200001111,file.json

…and saves the specified nodegroups to the store.

Parameters

folder_path – target folder

semtk3.upload_owl(owl_file_path, conn_json_str, user_name, password, model_or_data='model', conn_index=0)

Upload an owl file :param _sphinx_paramlinks_semtk3.upload_owl.owl_file_path: path to the file :param _sphinx_paramlinks_semtk3.upload_owl.conn_json_str: connection json string :param _sphinx_paramlinks_semtk3.upload_owl.user_name: optional user name :param _sphinx_paramlinks_semtk3.upload_owl.password: optional password :param _sphinx_paramlinks_semtk3.upload_owl.model_or_data: optional “model” or “data” specifying which endpoint in the sparql connection, defaults to “model” :param _sphinx_paramlinks_semtk3.upload_owl.conn_index: index specifying which of the model or data endpoints in the sparql connection, defaults to 0 :return: message :rettype: string