mustrd 0.2.0__py3-none-any.whl → 0.2.1__py3-none-any.whl

mustrd/mustrdAnzo.py

@@ -1,220 +1,236 @@
-"""
-MIT License
-
-Copyright (c) 2023 Semantic Partners Ltd
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
-"""
-
-import requests
-from pyanzo import AnzoClient
-from rdflib import Graph, ConjunctiveGraph, Literal, URIRef
-from requests import ConnectTimeout, Response, HTTPError, RequestException, ConnectionError
-from bs4 import BeautifulSoup
-import logging
-
-
-# https://github.com/Semantic-partners/mustrd/issues/73
-def manage_anzo_response(response: Response) -> str:
-    content_string = response.content.decode("utf-8")
-    if response.status_code == 200:
-        return content_string
-    elif response.status_code == 403:
-        html = BeautifulSoup(content_string, 'html.parser')
-        title_tag = html.title.string
-        raise HTTPError(f"Anzo authentication error, status code: {response.status_code}, content: {title_tag}")
-    else:
-        raise RequestException(f"Anzo error, status code: {response.status_code}, content: {content_string}")
-
-def query_with_bindings(bindings: dict, when: str) -> str:
-    values = ""
-    for key, value in bindings.items():
-        values += f"VALUES ?{key} {{{value.n3()}}} "
-    split_query = when.lower().split("where {", 1)
-    return f"{split_query[0].strip()} WHERE {{ {values} {split_query[1].strip()}"
-
-def execute_select (triple_store: dict,  when: str, bindings: dict = None) -> str:
-    if bindings:
-        when = query_with_bindings(bindings, when)
-    # Just remove ${fromSources} if we are executing a query step; the sources are defined using http parameters 
-    when = when.replace("${fromSources}", "")
-    return execute_sparql(triple_store, False, when, triple_store['input_graph'])
-
-PARAMS = {
-    # Update parameters for INSERT / DELETE
-    True: {
-        "default-graph-param": "using-graph-uri",
-        "named-graph-param":"using-named-graph-uri",
-        "Content-Type": "application/sparql-update"
-    },
-    # Query parameters for SELECT / CONSTRUCT  
-    False: {
-        "default-graph-param": "default-graph-uri",
-        "named-graph-param":"named-graph-uri",
-        "Content-Type": "application/sparql-query"
-    }
-}
-def execute_sparql(triple_store: dict, is_update: bool, sparql, graph: str, format: str = "application/sparql-results+json"):
-    params = {
-        "format" : format,
-        "datasourceURI" : triple_store['gqe_uri'],
-        "skipCache": "true",
-        # Default and named datasets have different query param for query and update
-        PARAMS[is_update]["default-graph-param"] : graph,
-        PARAMS[is_update]["named-graph-param"] : graph
-    }
-    headers={"Content-Type": PARAMS[is_update]["Content-Type"]}
-    try:
-        response = manage_anzo_response(requests.post(url=f"https://{triple_store['url']}:{triple_store['port']}/sparql",
-                                                    params=params,
-                                                    auth=(triple_store['username'], triple_store['password']),
-                                                    headers=headers,
-                                                    data=sparql,
-                                                    verify=False))
-        logging.debug(f'response {response}')
-        return response
-    except (ConnectionError, TimeoutError, HTTPError, ConnectTimeout) as e:
-        logging.error(f'response {e}')
-        raise
-
-def execute_update(triple_store: dict, when: str, bindings: dict = None) -> Graph:
-    logging.debug(f"updating in anzo! {triple_store=} {when=}")
-
-    # FIXME If query doesn't contain ${targetGraph}, then graph should be defined explicitly in the query
-    substituted_query = when.replace("${usingSources}", "").replace(
-        "${targetGraph}", f"<{triple_store['output_graph']}>")
-    
-    execute_sparql(triple_store, True, substituted_query, triple_store['input_graph'], "ttl")
-    
-    new_graph = execute_construct(triple_store, "construct {?s ?p ?o} { ?s ?p ?o }")
-    
-    logging.debug(f"new_graph={new_graph.serialize(format='ttl')}")
-    
-    return new_graph
-
-
-def execute_construct(triple_store: dict, when: str, bindings: dict = None) -> Graph:
-    if bindings:
-        when = query_with_bindings(bindings, when)
-    response = execute_sparql(triple_store, False, when, triple_store['input_graph'], "ttl")
-    return Graph().parse(data=response)
-
-
-# Get Given or then from the content of a graphmart
-def get_spec_component_from_graphmart(triple_store: dict, graphmart: URIRef, layer: URIRef = None) -> ConjunctiveGraph:
-    try:
-        anzo_client = AnzoClient(triple_store['url'], triple_store['port'], 
-                                 username=triple_store['username'],
-                                 password=triple_store['password'])
-        return anzo_client.query_graphmart(graphmart=graphmart,
-                                           data_layers=layer,
-                                           query_string="CONSTRUCT {?s ?p ?o} WHERE {?s ?p ?o}",
-                                           skip_cache=True).as_quad_store().as_rdflib_graph()
-    except RuntimeError as e:
-        raise ConnectionError(f"Anzo connection error, {e}")
-
-
-def get_query_from_querybuilder(triple_store: dict, folder_name: Literal, query_name: Literal) -> str:
-    query = f"""SELECT ?query WHERE {{
-        graph ?queryFolder {{
-            ?bookmark a <http://www.cambridgesemantics.com/ontologies/QueryPlayground#QueryBookmark>;
-                        <http://openanzo.org/ontologies/2008/07/System#query> ?query;
-                        <http://purl.org/dc/elements/1.1/title> "{query_name}"
-            }}
-            ?queryFolder a <http://www.cambridgesemantics.com/ontologies/QueryPlayground#QueryFolder>;
-                        <http://purl.org/dc/elements/1.1/title> "{folder_name}"
-    }}"""
-    anzo_client = AnzoClient(triple_store['url'], triple_store['port'], 
-                             username=triple_store['username'],
-                             password=triple_store['password'])
-    
-    result = anzo_client.query_journal(query_string=query).as_table_results().as_record_dictionaries()
-    if len(result) == 0:
-        raise FileNotFoundError(f"Query {query_name} not found in folder {folder_name}")
-    return result[0].get("query")
-
-
-# https://github.com/Semantic-partners/mustrd/issues/102
-def get_query_from_step(triple_store: dict, query_step_uri: URIRef) -> str:
-    query = f"""SELECT ?stepUri ?query WHERE {{
-        BIND(<{query_step_uri}> as ?stepUri)
-            ?stepUri a <http://cambridgesemantics.com/ontologies/Graphmarts#Step>;
-                     <http://cambridgesemantics.com/ontologies/Graphmarts#transformQuery> ?query
-    }}
-    # """
-    anzo_client = AnzoClient(triple_store['url'], triple_store['port'], 
-                             username=triple_store['username'],
-                             password=triple_store['password'])
-    record_dictionaries = anzo_client.query_journal(query_string=query).as_table_results().as_record_dictionaries()
-
-    return record_dictionaries[0].get(
-        "query")
-
-def get_queries_from_templated_step(triple_store: dict, query_step_uri: URIRef) -> dict:
-
-    query = f"""SELECT ?stepUri ?param_query ?query_template WHERE {{
-        BIND(<{query_step_uri}> as ?stepUri)
-            ?stepUri    a <http://cambridgesemantics.com/ontologies/Graphmarts#Step> ;
-   					    <http://cambridgesemantics.com/ontologies/Graphmarts#parametersTemplate> ?param_query ;
-					    <http://cambridgesemantics.com/ontologies/Graphmarts#template> ?query_template .
-    }}
-    """
-    anzo_client = AnzoClient(triple_store['url'], triple_store['port'], 
-                             username=triple_store['username'],
-                             password=triple_store['password'])
-    record_dictionaries = anzo_client.query_journal(query_string=query).as_table_results().as_record_dictionaries()
-    return record_dictionaries[0]
-
-
-def get_queries_for_layer(triple_store: dict, graphmart_layer_uri: URIRef):
-    query = f"""PREFIX graphmarts: <http://cambridgesemantics.com/ontologies/Graphmarts#>
-    PREFIX anzo: <http://openanzo.org/ontologies/2008/07/Anzo#>
-SELECT ?query ?param_query ?query_template
-  {{ <{graphmart_layer_uri}> graphmarts:step ?step .
-  ?step         anzo:index ?index ;
-                anzo:orderedValue ?query_step .
-  ?query_step graphmarts:enabled true ; 
-  OPTIONAL {{  ?query_step
-   				graphmarts:parametersTemplate ?param_query ;
-           		graphmarts:template ?query_template ;
-      . }}
-  OPTIONAL {{  ?query_step
-   				graphmarts:transformQuery ?query ;
-      . }}
-  }}
-  ORDER BY ?index"""
-    anzo_client = AnzoClient(triple_store['url'], triple_store['port'], 
-                             username=triple_store['username'],
-                             password=triple_store['password'])
-    return anzo_client.query_journal(query_string=query).as_table_results().as_record_dictionaries()
-
-
-def upload_given(triple_store: dict, given: Graph):
-    logging.debug(f"upload_given {triple_store} {given}")
-    clear_graph(triple_store, triple_store['input_graph'])
-    clear_graph(triple_store, triple_store['output_graph'])
-    serialized_given = given.serialize(format="nt")
-    
-    insert_query = f"INSERT DATA {{graph <{triple_store['input_graph']}>{{{serialized_given}}}}}"
-    execute_sparql(triple_store, True, insert_query, None, None)
-
-
-def clear_graph(triple_store: dict, graph_uri: str):
-    execute_sparql(triple_store, True, f"CLEAR GRAPH <{graph_uri}>", None, None)
-
+"""
+MIT License
+
+Copyright (c) 2023 Semantic Partners Ltd
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+"""
+
+import requests
+from pyanzo import AnzoClient
+from rdflib import Graph, ConjunctiveGraph, Literal, URIRef
+from requests import ConnectTimeout, Response, HTTPError, RequestException, ConnectionError
+from bs4 import BeautifulSoup
+import logging
+from .namespace import MUST
+
+
+# https://github.com/Semantic-partners/mustrd/issues/73
+def manage_anzo_response(response: Response) -> str:
+    content_string = response.content.decode("utf-8")
+    if response.status_code == 200:
+        return content_string
+    elif response.status_code == 403:
+        html = BeautifulSoup(content_string, 'html.parser')
+        title_tag = html.title.string
+        raise HTTPError(f"Anzo authentication error, status code: {response.status_code}, content: {title_tag}")
+    else:
+        raise RequestException(f"Anzo error, status code: {response.status_code}, content: {content_string}")
+
+
+def query_with_bindings(bindings: dict, when: str) -> str:
+    values = ""
+    for key, value in bindings.items():
+        values += f"VALUES ?{key} {{{value.n3()}}} "
+    split_query = when.lower().split("where {", 1)
+    return f"{split_query[0].strip()} WHERE {{ {values} {split_query[1].strip()}"
+
+def execute_select (triple_store: dict,  when: str, bindings: dict = None) -> str:
+    try:
+        if bindings:
+            when = query_with_bindings(bindings, when)
+        when = when.replace("${fromSources}", f"FROM <{triple_store['input_graph']}>\nFROM <{triple_store['output_graph']}>").replace(
+        "${targetGraph}", f"<{triple_store['output_graph']}>")
+        data = {'datasourceURI': triple_store['gqe_uri'], 'query': when,
+                 'skipCache': 'true'}
+        url = f"https://{triple_store['url']}:{triple_store['port']}/sparql?format=application/sparql-results+json"
+        return manage_anzo_response(requests.post(url=url,
+                                                  auth=(triple_store['username'], triple_store['password']),
+                                                  data=data,
+                                                  verify=False))
+    except (ConnectionError, TimeoutError, HTTPError, ConnectTimeout):
+        raise
+
+def execute_update(triple_store: dict, when: str, bindings: dict = None) -> Graph:
+    logging.debug(f"updating in anzo! {triple_store=} {when=}")
+    input_graph = triple_store['input_graph']
+    output_graph = triple_store['output_graph']
+
+    substituted_query = when.replace("${usingSources}", f"USING <{triple_store['input_graph']}> \nUSING <{triple_store['output_graph']}>").replace(
+        "${targetGraph}", f"<{output_graph}>")
+   
+    data = {'datasourceURI': triple_store['gqe_uri'], 'update': substituted_query,
+                'default-graph-uri': input_graph, 'skipCache': 'true'}
+    url = f"https://{triple_store['url']}:{triple_store['port']}/sparql?format=ttl"
+    response = manage_anzo_response(requests.post(url=url,
+            auth=(triple_store['username'],
+                triple_store['password']),
+            data=data,
+            verify=False))
+    logging.debug(f'response {response}')
+    check_data = {'datasourceURI': triple_store['gqe_uri'], 'query': "construct {?s ?p ?o} { ?s ?p ?o }",
+                'default-graph-uri': output_graph, 'skipCache': 'true'}
+    everything_response = manage_anzo_response(requests.post(url=url,
+            auth=(triple_store['username'],
+                triple_store['password']),
+            data=check_data,
+            verify=False))
+    # todo deal with error responses
+    new_graph = Graph().parse(data=everything_response)
+    logging.debug(f"new_graph={new_graph.serialize(format='ttl')}")
+    return new_graph
+
+
+def execute_construct(triple_store: dict, when: str, bindings: dict = None) -> Graph:
+    try:
+        if bindings:
+            when = query_with_bindings(bindings, when)
+        data = {'datasourceURI': triple_store['gqe_uri'], 'query': when,
+                'default-graph-uri': triple_store['input_graph'], 'skipCache': 'true'}
+        url = f"https://{triple_store['url']}:{triple_store['port']}/sparql?format=ttl"
+        response = requests.post(url=url,
+            auth=(triple_store['username'],
+                triple_store['password']),
+            data=data,
+            verify=False)
+        logging.debug(f'response {response}')
+        return Graph().parse(data=manage_anzo_response(response))
+    except (ConnectionError, TimeoutError, HTTPError, ConnectTimeout) as e:
+        logging.error(f'response {e}')
+        raise
+
+
+# Get Given or then from the content of a graphmart
+def get_spec_component_from_graphmart(triple_store: dict, graphmart: URIRef, layer: URIRef = None) -> ConjunctiveGraph:
+    try:
+        anzo_client = AnzoClient(triple_store['url'], triple_store['port'], 
+                                 username=triple_store['username'],
+                                 password=triple_store['password'])
+        return anzo_client.query_graphmart(graphmart=graphmart,
+                                           data_layers=layer,
+                                           query_string="CONSTRUCT {?s ?p ?o} WHERE {?s ?p ?o}",
+                                           skip_cache=True).as_quad_store().as_rdflib_graph()
+    except RuntimeError as e:
+        raise ConnectionError(f"Anzo connection error, {e}")
+
+
+def get_query_from_querybuilder(triple_store: dict, folder_name: Literal, query_name: Literal) -> str:
+    query = f"""SELECT ?query WHERE {{
+        graph ?queryFolder {{
+            ?bookmark a <http://www.cambridgesemantics.com/ontologies/QueryPlayground#QueryBookmark>;
+                        <http://openanzo.org/ontologies/2008/07/System#query> ?query;
+                        <http://purl.org/dc/elements/1.1/title> "{query_name}"
+            }}
+            ?queryFolder a <http://www.cambridgesemantics.com/ontologies/QueryPlayground#QueryFolder>;
+                        <http://purl.org/dc/elements/1.1/title> "{folder_name}"
+    }}"""
+    anzo_client = AnzoClient(triple_store['url'], triple_store['port'], 
+                             username=triple_store['username'],
+                             password=triple_store['password'])
+    
+    result = anzo_client.query_journal(query_string=query).as_table_results().as_record_dictionaries()
+    if len(result) == 0:
+        raise FileNotFoundError(f"Query {query_name} not found in folder {folder_name}")
+    return result[0].get("query")
+
+
+# https://github.com/Semantic-partners/mustrd/issues/102
+def get_query_from_step(triple_store: dict, query_step_uri: URIRef) -> str:
+    query = f"""SELECT ?stepUri ?query WHERE {{
+        BIND(<{query_step_uri}> as ?stepUri)
+            ?stepUri a <http://cambridgesemantics.com/ontologies/Graphmarts#Step>;
+                     <http://cambridgesemantics.com/ontologies/Graphmarts#transformQuery> ?query
+    }}
+    # """
+    anzo_client = AnzoClient(triple_store['url'], triple_store['port'], 
+                             username=triple_store['username'],
+                             password=triple_store['password'])
+    record_dictionaries = anzo_client.query_journal(query_string=query).as_table_results().as_record_dictionaries()
+
+    return record_dictionaries[0].get(
+        "query")
+
+def get_queries_from_templated_step(triple_store: dict, query_step_uri: URIRef) -> dict:
+
+    query = f"""SELECT ?stepUri ?param_query ?query_template WHERE {{
+        BIND(<{query_step_uri}> as ?stepUri)
+            ?stepUri    a <http://cambridgesemantics.com/ontologies/Graphmarts#Step> ;
+   					    <http://cambridgesemantics.com/ontologies/Graphmarts#parametersTemplate> ?param_query ;
+					    <http://cambridgesemantics.com/ontologies/Graphmarts#template> ?query_template .
+    }}
+    """
+    anzo_client = AnzoClient(triple_store['url'], triple_store['port'], 
+                             username=triple_store['username'],
+                             password=triple_store['password'])
+    record_dictionaries = anzo_client.query_journal(query_string=query).as_table_results().as_record_dictionaries()
+    return record_dictionaries[0]
+
+
+def get_queries_for_layer(triple_store: dict, graphmart_layer_uri: URIRef):
+    query = f"""PREFIX graphmarts: <http://cambridgesemantics.com/ontologies/Graphmarts#>
+    PREFIX anzo: <http://openanzo.org/ontologies/2008/07/Anzo#>
+SELECT ?query ?param_query ?query_template
+  {{ <{graphmart_layer_uri}> graphmarts:step ?step .
+  ?step         anzo:index ?index ;
+                anzo:orderedValue ?query_step .
+  ?query_step graphmarts:enabled true ; 
+  OPTIONAL {{  ?query_step
+   				graphmarts:parametersTemplate ?param_query ;
+           		graphmarts:template ?query_template ;
+      . }}
+  OPTIONAL {{  ?query_step
+   				graphmarts:transformQuery ?query ;
+      . }}
+  }}
+  ORDER BY ?index"""
+    anzo_client = AnzoClient(triple_store['url'], triple_store['port'], 
+                             username=triple_store['username'],
+                             password=triple_store['password'])
+    return anzo_client.query_journal(query_string=query).as_table_results().as_record_dictionaries()
+
+
+def upload_given(triple_store: dict, given: Graph):
+    logging.debug(f"upload_given {triple_store} {given}")
+
+    try:
+        input_graph = triple_store['input_graph']
+        output_graph = triple_store['output_graph']
+        clear_graph(triple_store, input_graph)
+        clear_graph(triple_store, output_graph)
+        serialized_given = given.serialize(format="nt")
+        insert_query = f"INSERT DATA {{graph <{triple_store['input_graph']}>{{{serialized_given}}}}}"
+        data = {'datasourceURI': triple_store['gqe_uri'], 'update': insert_query}
+        response = requests.post(url=f"https://{triple_store['url']}:{triple_store['port']}/sparql",
+                                    auth=(triple_store['username'], triple_store['password']), data=data, verify=False)
+        manage_anzo_response(response)
+    except (ConnectionError, TimeoutError, HTTPError, ConnectTimeout):
+        raise
+
+
+def clear_graph(triple_store: dict, graph_uri: str):
+    try:
+        clear_query = f"CLEAR GRAPH <{graph_uri}>"
+        data = {'datasourceURI': triple_store['gqe_uri'], 'update': clear_query}
+        url = f"https://{triple_store['url']}:{triple_store['port']}/sparql"
+        response = requests.post(url=url,
+                                 auth=(triple_store['username'], triple_store['password']), data=data, verify=False)
+        manage_anzo_response(response)
+    except (ConnectionError, TimeoutError, HTTPError, ConnectTimeout):
+        raise
+