add '[processed ontology] a owl:Ontology' to output graph, use config…

… port input for valid OWL2 profiles in Reasin plugin

CHANGELOG.md

@@ -23,6 +23,8 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/) and this p
 The ontology IRI on the input overrides the plugin setting.
 - update execution report
 - Output graph IRI selectable from existing graphs
+- When "input_profiles" is enabled the ontology IRI and list of valid OWL2 profiles is now taken from the config port.
+The list of valid profiles is a comma-separated string (e.g. "Full,DL")
 
 ## [1.0.0beta4] 2024-07-12
 

README.md

@@ -88,10 +88,8 @@ Validate the input ontology against OWL profiles (DL, EL, QL, RL, and Full). The
 
 ### Process valid OWL profiles from input
 
-If enabled along with the "Validate OWL2 profiles" parameter, the list of valid profiles is taken from the plugin input, 
-without validating the ontology against the profiles in the plugin. The inputs need to include the entity paths "profile"
-for the valid profiles, and "ontology" for the ontology IRI, the latter overriding the setting in the "Reason" plugin.
-If the "Validate OWL2 profiles" parameter is enabled in the "Validate" plugin, it can be directly connected to the input
+If enabled along with the "Validate OWL2 profiles" parameter, the ontology IRI and list of valid profiles is taken from the config port input, 
+without validating the ontology against the profiles in the plugin. If the "Validate OWL2 profiles" parameter is enabled in the "Validate" plugin, it can be directly connected to the input
 of the "Reason" plugin.
 
 

cmem_plugin_reason/plugin_reason.py

@@ -1,6 +1,5 @@
 """Reasoning workflow plugin module"""
 
-from collections.abc import Sequence
 from datetime import UTC, datetime
 from os import environ
 from pathlib import Path
@@ -12,12 +11,12 @@
 from cmem.cmempy.dp.proxy.graph import get
 from cmem_plugin_base.dataintegration.context import ExecutionContext, ExecutionReport
 from cmem_plugin_base.dataintegration.description import Icon, Plugin, PluginParameter
-from cmem_plugin_base.dataintegration.entity import Entities, EntityPath, EntitySchema
+from cmem_plugin_base.dataintegration.entity import EntityPath, EntitySchema
 from cmem_plugin_base.dataintegration.parameter.choice import ChoiceParameterType
 from cmem_plugin_base.dataintegration.parameter.graph import GraphParameterType
 from cmem_plugin_base.dataintegration.plugins import WorkflowPlugin
-from cmem_plugin_base.dataintegration.ports import FixedNumberOfInputs, FixedSchemaPort
-from cmem_plugin_base.dataintegration.types import BoolParameterType
+from cmem_plugin_base.dataintegration.ports import FixedNumberOfInputs
+from cmem_plugin_base.dataintegration.types import BoolParameterType, StringParameterType
 from cmem_plugin_base.dataintegration.utils import setup_cmempy_user_access
 from inflection import underscore
 from urllib3.exceptions import InsecureRequestWarning
@@ -177,11 +176,20 @@
             name="input_profiles",
             label="Process valid OWL profiles from input",
             description="""If the "validate OWL profiles" parameter is enabled, the valid profiles
-            and ontology IRI is taken from the input (paths "profile" and "ontology") instead of
-            running the validation in the plugin.""",
+            and ontology IRI is taken from the config port input (parameters "valid_profiles" and
+            "ontology_graph_iri") instead of from running the validation in the plugin. The valid
+            profiles input is a comma-separated string (e.g. "Full,DL").""",
             default_value=False,
             advanced=True,
         ),
+        PluginParameter(
+            param_type=StringParameterType(),
+            name="valid_profiles",
+            label="Valid OWL2 profiles",
+            description="Valid OWL2 profiles for the processed ontology.",
+            default_value="",
+            visible=False,
+        ),
     ],
 )
 class ReasonPlugin(WorkflowPlugin):
@@ -210,6 +218,7 @@ def __init__(  # noqa: PLR0913, C901
         validate_profile: bool = False,
         input_profiles: bool = False,
         max_ram_percentage: int = MAX_RAM_PERCENTAGE_DEFAULT,
+        valid_profiles: str = "",
     ) -> None:
         self.axioms = {
             "SubClass": sub_class,
@@ -254,14 +263,12 @@ def __init__(  # noqa: PLR0913, C901
         self.validate_profile = validate_profile
         self.input_profiles = input_profiles
         self.max_ram_percentage = max_ram_percentage
+        self.valid_profiles = valid_profiles
 
         for k, v in self.axioms.items():
             self.__dict__[underscore(k)] = v
 
-        if validate_profile and input_profiles:
-            self.input_ports = FixedNumberOfInputs([FixedSchemaPort(self.generate_input_schema())])
-        else:
-            self.input_ports = FixedNumberOfInputs([])
+        self.input_ports = FixedNumberOfInputs([])
         self.output_port = None
 
     def generate_input_schema(self) -> EntitySchema:
@@ -324,17 +331,7 @@ def reason(self, graphs: dict) -> None:
                 raise OSError(response.stderr.decode())
             raise OSError("ROBOT error")
 
-    def post_valid_profiles(self, inputs: Sequence[Entities], graphs: dict) -> None:
-        """Post valid profiles. Optionally get valid profiles from input."""
-        if self.input_profiles:
-            values = next(inputs[0].entities).values
-            paths = [p.path for p in inputs[0].schema.paths]
-            valid_profiles = values[paths.index("profile")]
-        else:
-            valid_profiles = validate_profiles(self, graphs)
-        post_profiles(self, valid_profiles)
-
-    def _execute(self, inputs: Sequence[Entities], context: ExecutionContext) -> None:
+    def _execute(self, context: ExecutionContext) -> None:
         """`Execute plugin"""
         setup_cmempy_user_access(context.user)
         graphs = get_graphs_tree(
@@ -346,7 +343,11 @@ def _execute(self, inputs: Sequence[Entities], context: ExecutionContext) -> Non
         setup_cmempy_user_access(context.user)
         send_result(self.output_graph_iri, Path(self.temp) / "result.ttl")
         if self.validate_profile:
-            self.post_valid_profiles(inputs, graphs)
+            if self.input_profiles:
+                valid_profiles = self.valid_profiles.split(",")
+            else:
+                valid_profiles = validate_profiles(self, graphs)
+            post_profiles(self, valid_profiles)
         post_provenance(self, get_provenance(self, context))
 
         context.report.update(
@@ -357,35 +358,13 @@ def _execute(self, inputs: Sequence[Entities], context: ExecutionContext) -> Non
             )
         )
 
-    def execute(self, inputs: Sequence[Entities], context: ExecutionContext) -> None:
+    def execute(self, inputs: None, context: ExecutionContext) -> None:  # noqa: ARG002
         """Validate input, execute plugin with temporary directory"""
         context.report.update(
             ExecutionReport(
                 operation="reason",
                 operation_desc="ontologies and data graphs processed.",
             )
         )
-        if self.input_profiles:
-            errors = ""
-            values = next(inputs[0].entities).values
-            paths = [p.path for p in inputs[0].schema.paths]
-            if not inputs:
-                raise OSError(
-                    'Input entities needed if "Process valid OWL profiles from input" is enabled'
-                )
-            if "profile" not in paths:
-                errors += 'No value for "profile" given on input. '
-            if "ontology" not in paths:
-                errors += 'No value for "ontology" given on input. '
-            self.ontology_graph_iri = values[paths.index("ontology")][0]
-            if not validators.url(self.ontology_graph_iri):
-                errors += 'Invalid IRI for parameter "Ontology graph IRI". '
-            if self.ontology_graph_iri == self.data_graph_iri:
-                errors += "Ontology graph IRI cannot be the same as the data graph IRI. "
-            if self.ontology_graph_iri == self.output_graph_iri:
-                errors += "Ontology graph IRI cannot be the same as the output graph IRI. "
-            if errors:
-                raise ValueError(errors[:-1])
-
         with TemporaryDirectory() as self.temp:
-            self._execute(inputs, context)
+            self._execute(context)

cmem_plugin_reason/plugin_validate.py

@@ -127,9 +127,9 @@ def __init__(  # noqa: PLR0913
 
     def generate_output_schema(self) -> EntitySchema:
         """Generate the output schema."""
-        paths = [EntityPath("markdown"), EntityPath("ontology")]
+        paths = [EntityPath("markdown"), EntityPath("ontology_graph_iri")]
         if self.validate_profile:
-            paths.append(EntityPath("profile"))
+            paths.append(EntityPath("valid_profiles"))
         return EntitySchema(type_uri="validate", paths=paths)
 
     def get_graphs(self, graphs: dict, context: ExecutionContext) -> None:
@@ -191,7 +191,7 @@ def make_entities(self, text: str, valid_profiles: list) -> Entities:
         """Make entities"""
         values = [[text], [self.ontology_graph_iri]]
         if self.validate_profile:
-            values.append(valid_profiles)
+            values.append([",".join(valid_profiles)])
         entities = [
             Entity(
                 uri="https://eccenca.com/plugin_validateontology/result",
@@ -246,7 +246,7 @@ def _execute(self, context: ExecutionContext) -> Entities:
 
         return self.make_entities(text, valid_profiles)
 
-    def execute(self, inputs: tuple, context: ExecutionContext) -> Entities:  # noqa: ARG002
+    def execute(self, inputs: None, context: ExecutionContext) -> Entities:  # noqa: ARG002
         """Remove temp files on error"""
         context.report.update(
             ExecutionReport(

cmem_plugin_reason/utils.py

@@ -230,7 +230,7 @@ def post_profiles(plugin: WorkflowPlugin, valid_profiles: list) -> None:
         query = f"""
             INSERT DATA {{
                 GRAPH <{plugin.output_graph_iri}> {{
-                    <{plugin.ontology_graph_iri}>
+                    <{plugin.ontology_graph_iri}> a <http://www.w3.org/2002/07/owl#Ontology> ;
                         <https://vocab.eccenca.com/plugin/reason/profile> "{profiles}" .
                 }}
             }}

tests/test_elk.ttl

@@ -126,5 +126,6 @@
                                                               vocab:pet_owner .
 
 
-vocab: <https://vocab.eccenca.com/plugin/reason/profile>  "DL" , "Full" .
+vocab: a owl:Ontology ;
+       <https://vocab.eccenca.com/plugin/reason/profile>  "DL" , "Full" .
 

tests/test_emr.ttl

@@ -126,4 +126,5 @@
                                                               vocab:pet_owner .
 
 
-vocab: <https://vocab.eccenca.com/plugin/reason/profile>  "DL" , "Full" .
+vocab: a owl:Ontology ;
+       <https://vocab.eccenca.com/plugin/reason/profile>  "DL" , "Full" .

tests/test_hermit.ttl

@@ -194,4 +194,5 @@
                                                                  <https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/data/Louie> .
 
 
-vocab: <https://vocab.eccenca.com/plugin/reason/profile>  "DL" , "Full" .
+vocab: a owl:Ontology ;
+       <https://vocab.eccenca.com/plugin/reason/profile>  "DL" , "Full" .

tests/test_jfact.ttl

@@ -194,4 +194,5 @@
                                                                  <https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/data/Louie> .
 
 
-vocab: <https://vocab.eccenca.com/plugin/reason/profile>  "DL" , "Full" .
+vocab: a owl:Ontology ;
+       <https://vocab.eccenca.com/plugin/reason/profile>  "DL" , "Full" .

tests/test_reason.py

@@ -77,9 +77,10 @@ def test_reasoner(reasoner: str, err_list: list) -> list:
             class_assertion=True,
             property_assertion=True,
             validate_profile=True,
-        ).execute((), context=TestExecutionContext())
+        ).execute(None, context=TestExecutionContext())
 
         result = get_remote_graph(REASON_RESULT_GRAPH_IRI)
+        result.serialize(f"temp/{reasoner}.ttl", format="turtle")
         test = Graph().parse(Path(__path__[0]) / f"test_{reasoner}.ttl", format="turtle")
         if to_isomorphic(result) != to_isomorphic(test):
             err_list.append(reasoner)
@@ -91,16 +92,16 @@ def test_validate(errors: str) -> str:
             output_graph_iri=OUTPUT_GRAPH_IRI,
             validate_profile=True,
             md_filename=MD_FILENAME,
-        ).execute((), context=TestExecutionContext(PROJECT_ID))
+        ).execute(None, context=TestExecutionContext(PROJECT_ID))
 
         val_errors = ""
         md_test = (Path(__path__[0]) / "test_validate.md").read_text()
 
         if next(iter(result.entities)).values[0][0] != md_test:  # type: ignore[union-attr]
             val_errors += 'EntityPath "markdown" output error. '
 
-        if next(iter(result.entities)).values[2] != ["Full", "DL", "EL", "QL", "RL"]:  # type: ignore[union-attr]
-            val_errors += 'EntityPath "profile" output error. '
+        if next(iter(result.entities)).values[2][0] != "Full,DL,EL,QL,RL":  # type: ignore[union-attr]
+            val_errors += 'EntityPath "valid_profile" output error. '
 
         if md_test != get_resource(PROJECT_ID, MD_FILENAME).decode():
             val_errors += "Markdown file error. "

tests/test_structural.ttl

@@ -97,4 +97,5 @@
                                                               vocab:animal .
 
 
-vocab: <https://vocab.eccenca.com/plugin/reason/profile>  "DL" , "Full" .
+vocab: a owl:Ontology ;
+       <https://vocab.eccenca.com/plugin/reason/profile>  "DL" , "Full" .

tests/test_validate_output.ttl

@@ -18,5 +18,6 @@
 
 <https://ns.eccenca.com/validateontology/e02aaed014c94e0c91bf960fed127750/vocab/B> a owl:Class .
 
-<https://ns.eccenca.com/validateontology/e02aaed014c94e0c91bf960fed127750/vocab/> <https://vocab.eccenca.com/plugin/reason/profile> "Full", "DL", "EL", "QL", "RL" .
+<https://ns.eccenca.com/validateontology/e02aaed014c94e0c91bf960fed127750/vocab/> a owl:Ontology ;
+    <https://vocab.eccenca.com/plugin/reason/profile> "Full", "DL", "EL", "QL", "RL" .
 

tests/test_whelk.ttl

@@ -188,4 +188,5 @@
                                                                  <https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/data/Louie> .
 
 
-vocab: <https://vocab.eccenca.com/plugin/reason/profile>  "DL" , "Full" .
+vocab: a owl:Ontology ;
+       <https://vocab.eccenca.com/plugin/reason/profile>  "DL" , "Full" .