add parameters for owl:imports and entity output. PLugin doc imported…

… from md files

CHANGELOG.md

@@ -9,6 +9,8 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/) and this p
 ### Added
 
  - defined input and output schema
+ - Reason: parameters to import the result graph in the ontology graph and to import the ontology graph in the result graph
+ - Validate: parameter to enable/disable entity output
 
 ### Fixed
 

cmem_plugin_reason/plugin_reason.py

@@ -9,6 +9,7 @@
 
 import validators.url
 from cmem.cmempy.dp.proxy.graph import get
+from cmem.cmempy.dp.proxy.update import post
 from cmem_plugin_base.dataintegration.context import ExecutionContext, ExecutionReport
 from cmem_plugin_base.dataintegration.description import Icon, Plugin, PluginParameter
 from cmem_plugin_base.dataintegration.parameter.choice import ChoiceParameterType
@@ -25,6 +26,7 @@
     MAX_RAM_PERCENTAGE_PARAMETER,
     ONTOLOGY_GRAPH_IRI_PARAMETER,
     OUTPUT_GRAPH_IRI_PARAMETER,
+    REASON_DOC,
     REASONERS,
     VALIDATE_PROFILES_PARAMETER,
     create_xml_catalog_file,
@@ -45,9 +47,7 @@
     label="Reason",
     icon=Icon(file_name="fluent--brain-circuit-24-regular.svg", package=__package__),
     description="Performs OWL reasoning.",
-    documentation="""A task performing OWL reasoning. With an OWL ontology and a data graph as input
-    the reasoning result is written to a specified graph. The following reasoners are supported:
-    ELK, Expression Materializing Reasoner, HermiT, JFact, Structural Reasoner and Whelk.""",
+    documentation=REASON_DOC,
     parameters=[
         ONTOLOGY_GRAPH_IRI_PARAMETER,
         OUTPUT_GRAPH_IRI_PARAMETER,
@@ -181,6 +181,22 @@
             default_value=False,
             advanced=True,
         ),
+        PluginParameter(
+            param_type=BoolParameterType(),
+            name="import_ontology",
+            label="Add ontology graph import to result graph.",
+            description="""Add the triple <output_graph_iri> owl:imports <ontology_graph_iri> to the
+            output graph.""",
+            default_value=True,
+        ),
+        PluginParameter(
+            param_type=BoolParameterType(),
+            name="import_result",
+            label="Add result graph import to ontology graph.",
+            description="""Add the triple <ontology_graph_iri> owl:imports <output_graph_iri> to the
+            ontology graph.""",
+            default_value=False,
+        ),
         PluginParameter(
             param_type=StringParameterType(),
             name="valid_profiles",
@@ -215,6 +231,8 @@ def __init__(  # noqa: PLR0913, C901
         sub_data_property: bool = False,
         sub_object_property: bool = False,
         validate_profile: bool = False,
+        import_ontology: bool = True,
+        import_result: bool = False,
         input_profiles: bool = False,
         max_ram_percentage: int = MAX_RAM_PERCENTAGE_DEFAULT,
         valid_profiles: str = "",
@@ -250,6 +268,11 @@ def __init__(  # noqa: PLR0913, C901
             errors += 'Invalid value for parameter "Reasoner". '
         if True not in self.axioms.values():
             errors += "No axiom generator selected. "
+        if import_result and import_ontology:
+            errors += (
+                'Enable only one of "Add result graph import to ontology graph" and "Add '
+                'ontology graph import to result graph". '
+            )
         if (
             input_profiles
             and valid_profiles
@@ -268,6 +291,8 @@ def __init__(  # noqa: PLR0913, C901
         self.output_graph_iri = output_graph_iri
         self.reasoner = reasoner
         self.validate_profile = validate_profile
+        self.import_ontology = import_ontology
+        self.import_result = import_result
         self.input_profiles = input_profiles
         self.max_ram_percentage = max_ram_percentage
         self.valid_profiles = valid_profiles
@@ -285,25 +310,20 @@ def get_graphs(self, graphs: dict, context: ExecutionContext) -> None:
             with (Path(self.temp) / filename).open("w", encoding="utf-8") as file:
                 setup_cmempy_user_access(context.user)
                 for line in get(iri).text.splitlines():
-                    if line != (
-                        f"<{iri}> <http://www.w3.org/2002/07/owl#imports> "
-                        f"<{self.output_graph_iri}> ."
+                    if not line.endswith(
+                        f"<http://www.w3.org/2002/07/owl#imports> <{self.output_graph_iri}> ."
                     ):
                         file.write(line + "\n")
-                if iri == self.data_graph_iri:
-                    file.write(
-                        f"<{iri}> <http://www.w3.org/2002/07/owl#imports> "
-                        f"<{self.ontology_graph_iri}> ."
-                    )
 
     def reason(self, graphs: dict) -> None:
         """Reason"""
         axioms = " ".join(k for k, v in self.axioms.items() if v)
         data_location = f"{self.temp}/{graphs[self.data_graph_iri]}"
+        ontology_location = f"{self.temp}/{graphs[self.ontology_graph_iri]}"
         utctime = str(datetime.fromtimestamp(int(time()), tz=UTC))[:-6].replace(" ", "T") + "Z"
         cmd = (
-            f'reason --input "{data_location}" '
-            f"--reasoner {self.reasoner} "
+            f'merge --input "{data_location}" --input "{ontology_location}" '
+            f"reason --reasoner {self.reasoner} "
             f'--axiom-generators "{axioms}" '
             f"--include-indirect true "
             f"--exclude-duplicate-axioms true "
@@ -321,8 +341,10 @@ def reason(self, graphs: dict) -> None:
             f'--link-annotation dc:source "{self.data_graph_iri}" '
             f'--link-annotation dc:source "{self.ontology_graph_iri}" '
             f'--typed-annotation dc:created "{utctime}" xsd:dateTime '
-            f'--output "{self.temp}/result.ttl"'
         )
+        if self.import_ontology:
+            cmd += f'--link-annotation owl:imports "{self.ontology_graph_iri}" '
+        cmd += f'--output "{self.temp}/result.ttl"'
         response = robot(cmd, self.max_ram_percentage)
         if response.returncode != 0:
             if response.stdout:
@@ -331,6 +353,18 @@ def reason(self, graphs: dict) -> None:
                 raise OSError(response.stderr.decode())
             raise OSError("ROBOT error")
 
+    def add_result_import(self) -> None:
+        """Add result graph import to ontology graph"""
+        query = f"""
+            INSERT DATA {{
+                GRAPH <{self.ontology_graph_iri}> {{
+                    <{self.ontology_graph_iri}> <http://www.w3.org/2002/07/owl#imports>
+                        <{self.output_graph_iri}>
+                }}
+            }}
+        """
+        post(query=query)
+
     def _execute(self, context: ExecutionContext) -> None:
         """`Execute plugin"""
         setup_cmempy_user_access(context.user)
@@ -349,6 +383,9 @@ def _execute(self, context: ExecutionContext) -> None:
                 valid_profiles = validate_profiles(self, graphs)
             post_profiles(self, valid_profiles)
         post_provenance(self, get_provenance(self, context))
+        if self.import_result:
+            setup_cmempy_user_access(context.user)
+            self.add_result_import()
 
         context.report.update(
             ExecutionReport(

cmem_plugin_reason/plugin_validate.py

@@ -27,6 +27,7 @@
     ONTOLOGY_GRAPH_IRI_PARAMETER,
     OUTPUT_GRAPH_IRI_PARAMETER,
     REASONERS,
+    VALIDATE_DOC,
     VALIDATE_PROFILES_PARAMETER,
     create_xml_catalog_file,
     get_graphs_tree,
@@ -45,11 +46,7 @@
 @Plugin(
     label="Validate OWL consistency",
     description="Validates the consistency of an OWL ontology.",
-    documentation="""A task validating the consistency of an OWL ontology and generating an
-    explanation if inconsistencies are found. The explanation can be written to the project as a
-    Markdown file and/or to a specified graph. The Markdown string is also provided as an output
-    entity using the path "text". The following reasoners are supported: ELK, Expression
-    Materializing Reasoner, HermiT, JFact, Structural Reasoner and Whelk.""",
+    documentation=VALIDATE_DOC,
     icon=Icon(file_name="file-icons--owl.svg", package=__package__),
     parameters=[
         ONTOLOGY_GRAPH_IRI_PARAMETER,
@@ -78,6 +75,15 @@
             "not output entities.",
             default_value=False,
         ),
+        PluginParameter(
+            param_type=BoolParameterType(),
+            name="output_entities",
+            label="Output entities",
+            description="""Output entities. The plugin outputs the explanation as text in Markdown
+            format on the path "markdown", the ontology IRI on the path "ontology_graph_iri", and,
+            if enabled, the valid OWL2 profiles on the path "valid_profiles".""",
+            default_value=False,
+        ),
     ],
 )
 class ValidatePlugin(WorkflowPlugin):
@@ -90,6 +96,7 @@ def __init__(  # noqa: PLR0913
         output_graph_iri: str = "",
         md_filename: str = "",
         validate_profile: bool = False,
+        output_entities: bool = False,
         stop_at_inconsistencies: bool = False,
         max_ram_percentage: int = MAX_RAM_PERCENTAGE_DEFAULT,
     ) -> None:
@@ -104,6 +111,8 @@ def __init__(  # noqa: PLR0913
             errors += 'Invalid value for parameter "Reasoner". '
         if md_filename and not is_valid_filename(md_filename):
             errors += 'Invalid filename for parameter "Output filename". '
+        if not output_graph_iri and not md_filename and not output_entities:
+            errors += "No output selected. "
         if max_ram_percentage not in range(1, 101):
             errors += 'Invalid value for parameter "Maximum RAM Percentage". '
         if errors:
@@ -119,14 +128,18 @@ def __init__(  # noqa: PLR0913
             self.md_filename = "mdfile.md"
             self.write_md = False
         self.validate_profile = validate_profile
+        self.output_entities = output_entities
         self.max_ram_percentage = max_ram_percentage
 
         self.input_ports = FixedNumberOfInputs([])
-        self.schema = self.generate_output_schema()
-        self.output_port = FixedSchemaPort(self.schema)
+        if self.output_entities:
+            self.schema = self.generate_output_schema()
+            self.output_port = FixedSchemaPort(self.schema)
+        else:
+            self.output_port = None
 
-    def generate_output_schema(self) -> EntitySchema:
-        """Generate the output schema."""
+    def generate_output_schema(self) -> EntitySchema | None:
+        """Generate output entity schema."""
         paths = [EntityPath("markdown"), EntityPath("ontology_graph_iri")]
         if self.validate_profile:
             paths.append(EntityPath("valid_profiles"))
@@ -243,8 +256,8 @@ def _execute(self, context: ExecutionContext) -> Entities:
                     entity_count=1,
                 )
             )
-
-        return self.make_entities(text, valid_profiles)
+        if self.output_entities:
+            return self.make_entities(text, valid_profiles)
 
     def execute(self, inputs: None, context: ExecutionContext) -> Entities:  # noqa: ARG002
         """Remove temp files on error"""

cmem_plugin_reason/reason_doc.md

@@ -0,0 +1,72 @@
+A task performing OWL reasoning. With an OWL ontology and a data graph as input the reasoning result is written to a specified graph.
+
+## Options
+
+### Data graph IRI
+
+The IRI of the input data graph. The graph IRI is selected from a list of graphs of types `di:Dataset`, `void:Dataset`
+and `owl:Ontology`.
+
+### Ontology graph IRI
+
+The IRI of the input ontology graph. The graph IRI is selected from a list of graphs of type`owl:Ontology`.
+
+### Result graph IRI
+
+The IRI of the output graph for the reasoning result.
+
+⚠️ Existing graphs will be overwritten.
+
+### Reasoner
+
+The following reasoner options are supported: 
+- [ELK](https://code.google.com/p/elk-reasoner/) (elk)
+- [Expression Materializing Reasoner](http://static.javadoc.io/org.geneontology/expression-materializing-reasoner/0.1.3/org/geneontology/reasoner/ExpressionMaterializingReasoner.html) (emr)
+- [HermiT](http://www.hermit-reasoner.com/) (hermit)
+- [JFact](http://jfact.sourceforge.net/) (jfact)
+- [Structural Reasoner](http://owlcs.github.io/owlapi/apidocs_4/org/semanticweb/owlapi/reasoner/structural/StructuralReasoner.html) (structural)
+- [Whelk](https://github.com/balhoff/whelk) (whelk)
+
+### Generated Axioms
+
+By default, the reason operation will only assert inferred subclass axioms. The plugin provides the following 
+parameters to include inferred axiom generators:
+
+#### Class axiom generators
+-  SubClass
+- EquivalentClass
+- DisjointClasses
+
+#### Data property axiom generators
+- DataPropertyCharacteristic
+- EquivalentDataProperties
+- SubDataProperty
+
+#### Individual axiom generators
+- ClassAssertion
+- PropertyAssertion
+
+#### Object property axiom generators
+- EquivalentObjectProperty
+- InverseObjectProperties
+- ObjectPropertyCharacteristic
+- SubObjectProperty
+- ObjectPropertyRange
+- ObjectPropertyDomain
+
+### Validate OWL2 profiles
+
+Validate the input ontology against OWL profiles (DL, EL, QL, RL, and Full). The ontology is annotated in the output graph. 
+
+### Process valid OWL profiles from 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.
+
+
+### Maximum RAM Percentage
+
+Maximum heap size for the Java virtual machine in the DI container running the reasoning process.
+
+⚠️ Setting the percentage too high may result in an out of memory error.

cmem_plugin_reason/utils.py

@@ -20,6 +20,12 @@
 
 from . import __path__
 
+with (Path(__path__[0]) / "reason_doc.md").open("r") as f:
+    REASON_DOC = f.read()
+
+with (Path(__path__[0]) / "validate_doc.md").open("r") as f:
+    VALIDATE_DOC = f.read()
+
 REASONERS = OrderedDict(
     {
         "elk": "ELK",

cmem_plugin_reason/validate_doc.md

@@ -0,0 +1,54 @@
+A task validating the consistency of an OWL ontology and generating an explanation if inconsistencies are found. 
+The plugin outputs the explanation as text in Markdown format on the path "markdown", the ontology IRI on the path 
+"ontology_graph_iri", and, if enabled, the valid OWL2 profiles on the path "valid_profiles" as a comma-separated string.
+
+## Options
+
+### Ontology graph IRI
+
+The IRI of the input ontology graph. The graph IRI is selected from a list of graphs of type`owl:Ontology`.
+
+### Reasoner
+
+The following reasoner options are supported: 
+- [ELK](https://code.google.com/p/elk-reasoner/) (elk)
+- [Expression Materializing Reasoner](http://static.javadoc.io/org.geneontology/expression-materializing-reasoner/0.1.3/org/geneontology/reasoner/ExpressionMaterializingReasoner.html) (emr)
+- [HermiT](http://www.hermit-reasoner.com/) (hermit)
+- [JFact](http://jfact.sourceforge.net/) (jfact)
+- [Structural Reasoner](http://owlcs.github.io/owlapi/apidocs_4/org/semanticweb/owlapi/reasoner/structural/StructuralReasoner.html) (structural)
+- [Whelk](https://github.com/balhoff/whelk) (whelk)
+
+### Produce output graph
+
+If enabled, an explanation graph is created.
+
+### Output graph IRI
+
+The IRI of the output graph for the reasoning result.
+
+⚠️ Existing graphs will be overwritten.
+
+### Write markdown explanation file
+
+If enabled, an explanation markdown file is written to the project.
+
+### Output filename
+
+The filename of the Markdown file with the explanation of inconsistencies.
+
+⚠️ Existing files will be overwritten.
+
+### Stop at inconsistencies
+Raise an error if inconsistencies are found. If enabled, the plugin does not output entities.
+
+### Validate OWL2 profiles
+
+Validate the input ontology against OWL profiles (DL, EL, QL, RL, and Full). The valid profiles are added to the output 
+Markdown file and the ontology is annotated in the output graph. The plugin outputs the profiles with path "valid_profiles",
+and the ontology IRI with path "ontology_graph_iri".
+
+### Maximum RAM Percentage
+
+Maximum heap size for the Java virtual machine in the DI container running the reasoning process.
+
+⚠️ Setting the percentage too high may result in an out of memory error.