remove "annotate inferred axioms" parameter, edit README

CHANGELOG.md

@@ -12,8 +12,8 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/) and this p
 
 ### Changed
 
-- completed validation for IRI parameters
-- "Annnotate inferred subclass axioms" is now not an advanced parameter
+- complete validation for IRI parameters
+- Remove "Annnotate inferred subclass axioms" parameter
 
 ## [1.0.0alpha3] 2024-06-28
 

README-public.md

@@ -1,6 +1,6 @@
 # cmem-plugin-reason
 
-This [eccenca](https://eccenca.com) [Corporate Memory](https://documentation.eccenca.com) workflow plugin performs reasoning using [ROBOT](http://robot.obolibrary.org/). It takes an OWL ontology and a data graph as inputs and writes the reasoning result to a specified graph.
+This [eccenca](https://eccenca.com) [Corporate Memory](https://documentation.eccenca.com) workflow plugin performs reasoning using [ROBOT](http://robot.obolibrary.org/).
 
 ROBOT is published under the [BSD 3-Clause "New" or "Revised" License](https://choosealicense.com/licenses/bsd-3-clause/).
 Copyright © 2015, the Authors

README.md

@@ -2,9 +2,7 @@
 
 # cmem-plugin-reason
 
-Reasoning with ROBOT
-
-This eccenca Corporate Memory workflow plugin performs reasoning using [ROBOT](http://robot.obolibrary.org/). It takes an OWL ontology and a data graph as inputs and writes the reasoning result to a specified graph.
+This [eccenca](https://eccenca.com) [Corporate Memory](https://documentation.eccenca.com) workflow plugin bundle contains plugins performing reasoning (Reason) and ontology consistency checking (Validate) using [ROBOT](http://robot.obolibrary.org/).
 
 [![eccenca Corporate Memory](https://img.shields.io/badge/eccenca-Corporate%20Memory-orange)](https://documentation.eccenca.com) [![workflow](https://github.com/eccenca/cmem-plugin-pyshacl/actions/workflows/check.yml/badge.svg)](https://github.com/eccenca/cmem-plugin-pyshacl/actions) [![pypi version](https://img.shields.io/pypi/v/cmem-plugin-reason)](https://pypi.org/project/cmem-plugin-reason/) [![license](https://img.shields.io/pypi/l/cmem-plugin-reason)](https://pypi.org/project/cmem-plugin-reasom)
 
@@ -29,6 +27,7 @@ Alternatively, the _build_ and _installation_ process can be initiated with the
 ➜ task deploy
 ```
 
+# Reason
 ## Options
 
 ### Data graph IRI
@@ -46,7 +45,6 @@ The IRI of the output graph for the reasoning result.
 
 :warning: Existing graphs will be overwritten.
 
-
 ### Reasoner
 
 The following reasoner options are supported: 
@@ -84,3 +82,54 @@ parameters to include inferred axiom generators:
 - ObjectPropertyRange
 - ObjectPropertyDomain
 
+### Maximum RAM Percentage
+
+Maximum heap size for the Java virtual machine in the DI container running the reasoning process.
+
+:warning: Setting the percentage too high may result in an out of memory error.
+
+# Validate
+
+In case ontology inconsistencies are found, the plugin outputs the explanation as text in Markdown format using the path "text".
+
+## 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.
+
+:warning: Existing graphs will be overwritten.
+
+### Write markdown explanation file
+
+If enabled, an explanation markdown file is written to the project.
+
+:warning: Existing files will be overwritten.
+
+### Stop at inconsistencies
+
+Raise an error if inconsistencies are found. If enabled, the plugin does not output entities.
+
+### Maximum RAM Percentage
+
+Maximum heap size for the Java virtual machine in the DI container running the reasoning process.
+
+:warning: Setting the percentage too high may result in an out of memory error.

cmem_plugin_reason/plugin_reason.py

@@ -159,20 +159,12 @@
             description="",
             default_value=False,
         ),
-        PluginParameter(
-            param_type=BoolParameterType(),
-            name="annotate_inferred_axioms",
-            label="Annnotate inferred subclass axioms",
-            description="⚠️ This parameter can only be enabled if the only enabled axiom generator "
-            "is SubClass.",
-            default_value=False,
-        ),
     ],
 )
 class ReasonPlugin(WorkflowPlugin):
     """Reason plugin"""
 
-    def __init__(  # noqa: PLR0913, C901
+    def __init__(  # noqa: PLR0913
         self,
         data_graph_iri: str = "",
         ontology_graph_iri: str = "",
@@ -192,7 +184,6 @@ def __init__(  # noqa: PLR0913, C901
         sub_class: bool = True,
         sub_data_property: bool = False,
         sub_object_property: bool = False,
-        annotate_inferred_axioms: bool = False,
         max_ram_percentage: int = MAX_RAM_PERCENTAGE_DEFAULT,
     ) -> None:
         self.axioms = {
@@ -226,11 +217,6 @@ def __init__(  # noqa: PLR0913, C901
             errors += 'Invalid value for parameter "Reasoner". '
         if True not in self.axioms.values():
             errors += "No axiom generator selected. "
-        if annotate_inferred_axioms and [k for k, v in self.axioms.items() if v] != ["SubClass"]:
-            errors += (
-                'Parameter "Annnotate inferred subclass axioms" can only be enabled if the only '
-                "enabled axiom generator is SubClass. "
-            )
         if max_ram_percentage not in range(1, 101):
             errors += 'Invalid value for parameter "Maximum RAM Percentage". '
         if errors:
@@ -239,7 +225,6 @@ def __init__(  # noqa: PLR0913, C901
         self.ontology_graph_iri = ontology_graph_iri
         self.result_graph_iri = result_graph_iri
         self.reasoner = reasoner
-        self.annotate_inferred_axioms = str(annotate_inferred_axioms).lower()
         self.max_ram_percentage = max_ram_percentage
         self.temp = f"reason_{uuid4().hex}"
 
@@ -268,7 +253,6 @@ def reason(self, graphs: dict) -> None:
             "--collapse-import-closure false "
             f"reason --reasoner {self.reasoner} "
             f'--axiom-generators "{axioms}" '
-            f"--annotate-inferred-axioms {self.annotate_inferred_axioms} "
             f"--include-indirect true "
             f"--exclude-duplicate-axioms true "
             f"--exclude-owl-thing true "

cmem_plugin_reason/plugin_validate.py

@@ -50,7 +50,8 @@
             param_type=BoolParameterType(),
             name="write_md",
             label="Write Markdown explanation file",
-            description="Write Markdownn file with explanation to project.",
+            description="Write Markdown file with explanation to project. ⚠️ Existing files will "
+            "be overwritten.",
             default_value=False,
         ),
         PluginParameter(
@@ -65,7 +66,7 @@
             name="output_graph_iri",
             label="Output graph IRI",
             description="The IRI of the output graph for the inconsistency validation. ⚠️ Existing "
-            "graph will be overwritten.",
+            "graphs will be overwritten.",
         ),
         PluginParameter(
             param_type=StringParameterType(),

cmem_plugin_reason/utils.py

@@ -67,9 +67,9 @@ def convert_iri_to_filename(value: str) -> str:
     return value + ".nt"
 
 
-def create_xml_catalog_file(temp: str, graphs: dict) -> None:
+def create_xml_catalog_file(dir_: str, graphs: dict) -> None:
     """Create XML catalog file"""
-    file_name = Path(temp) / "catalog-v001.xml"
+    file_name = Path(dir_) / "catalog-v001.xml"
     catalog = Element("catalog")
     catalog.set("prefer", "public")
     catalog.set("xmlns", "urn:oasis:names:tc:entity:xmlns:xml:catalog")