fixing import bug

CHANGELOG.md

@@ -6,15 +6,20 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/) and this p
 
 ## [Unreleased]
 
-
 ### Added
 
  - defined input and output schema
 
+### Fixed
+
+ - incorrect stopping of workflow if "validate_profiles" and "stop_at_inconsistencies" is enabled in Validate plugin
+
 ### Changed
 
 - raise OSError on post result graph error
 - removed write_md and produce_graph bool parameters
+- if "input_profiles" is enabled the Reason plugin expects ontology_iri and "profile" non the input.
+The ontologi iri on the input overrides the plugin setting.
 
 ## [1.0.0beta4] 2024-07-12
 

cmem_plugin_reason/plugin_reason.py

@@ -294,12 +294,25 @@ def get_graphs(self, graphs: dict, context: ExecutionContext) -> None:
 
     def reason(self, graphs: dict) -> None:
         """Reason"""
+        # remove_query = f"""
+        # SELECT ?s ?p ?o
+        # WHERE {{
+        #   ?s <http://www.w3.org/2002/07/owl#imports> <{self.output_graph_iri}> .
+        # }}
+        # """
+        # filtered_file = Path(self.temp) / "filtered_triples.owl"
+        # query_file = Path(self.temp) / "remove.rq"
+        # with query_file.open("w") as rqfile:
+        #     rqfile.write(remove_query)
+
         axioms = " ".join(k for k, v in self.axioms.items() if v)
         data_location = f"{self.temp}/{graphs[self.data_graph_iri]}"
         utctime = str(datetime.fromtimestamp(int(time()), tz=UTC))[:-6].replace(" ", "T") + "Z"
         cmd = (
             f'merge --input "{data_location}" '
             "--collapse-import-closure false "
+            # f'--query query.sparql {filtered_file} '
+            # f'remove --input "{data_location}" --input {filtered_file} --select "triples" '
             f"reason --reasoner {self.reasoner} "
             f'--axiom-generators "{axioms}" '
             f"--include-indirect true "
@@ -341,7 +354,9 @@ def post_valid_profiles(self, inputs: Sequence[Entities], graphs: dict) -> None:
     def _execute(self, inputs: Sequence[Entities], context: ExecutionContext) -> None:
         """`Execute plugin"""
         setup_cmempy_user_access(context.user)
-        graphs = get_graphs_tree((self.data_graph_iri, self.ontology_graph_iri))
+        graphs = get_graphs_tree(
+            (self.data_graph_iri, self.ontology_graph_iri, self.output_graph_iri)
+        )
         self.get_graphs(graphs, context)
         create_xml_catalog_file(self.temp, graphs)
         self.reason(graphs)

cmem_plugin_reason/plugin_validate.py

@@ -208,7 +208,7 @@ def make_entities(self, text: str, valid_profiles: list) -> Entities:
     def _execute(self, context: ExecutionContext) -> Entities:
         """Run the workflow operator."""
         setup_cmempy_user_access(context.user)
-        graphs = get_graphs_tree((self.ontology_graph_iri,))
+        graphs = get_graphs_tree((self.ontology_graph_iri, self.output_graph_iri))
         self.get_graphs(graphs, context)
         create_xml_catalog_file(self.temp, graphs)
         self.explain(graphs)

cmem_plugin_reason/utils.py

@@ -86,15 +86,15 @@ def create_xml_catalog_file(dir_: str, graphs: dict) -> None:
 
 
 def get_graphs_tree(graph_iris: tuple) -> dict:
-    """Get graph import tree"""
+    """Get graph import tree. Last item in tuple is output_graph_iri which is excluded"""
     graphs = {}
-    for graph_iri in graph_iris:
+    for graph_iri in graph_iris[:-1]:
         if graph_iri not in graphs:
             graphs[graph_iri] = f"{token_hex(8)}.nt"
             tree = get_graph_import_tree(graph_iri)
             for value in tree["tree"].values():
                 for iri in value:
-                    if iri not in graphs:
+                    if iri not in graphs and iri != graph_iri[-1]:
                         graphs[iri] = f"{token_hex(8)}.nt"
     return graphs