Develop (#2)

* valid range of "Maximum RAM Percentage" parameter in Validate plugin

* edit CHANGELOG

* edit parameter validation

* edits

* move cleanup to utils.py, annotate inferred axioms not advanced parameter

* remove "annotate inferred axioms" parameter, edit README

CHANGELOG.md

@@ -4,6 +4,16 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](http://keepachangelog.com/) and this project adheres to [Semantic Versioning](https://semver.org/)
 
+## [Unreleased]
+
+### Fixed
+
+- valid range of "Maximum RAM Percentage" parameter in Validate plugin (1-100)
+
+### Changed
+
+- 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

@@ -1,7 +1,6 @@
 """Reasoning workflow plugin module"""
 
 import shlex
-from collections.abc import Sequence
 from datetime import UTC, datetime
 from pathlib import Path
 from subprocess import run
@@ -12,7 +11,6 @@
 from cmem.cmempy.dp.proxy.graph import get
 from cmem_plugin_base.dataintegration.context import ExecutionContext
 from cmem_plugin_base.dataintegration.description import Icon, Plugin, PluginParameter
-from cmem_plugin_base.dataintegration.entity import Entities
 from cmem_plugin_base.dataintegration.parameter.graph import GraphParameterType
 from cmem_plugin_base.dataintegration.plugins import WorkflowPlugin
 from cmem_plugin_base.dataintegration.types import BoolParameterType, StringParameterType
@@ -27,6 +25,7 @@
     ROBOT,
     create_xml_catalog_file,
     get_graphs_tree,
+    remove_temp,
     send_result,
 )
 
@@ -59,7 +58,7 @@
             param_type=StringParameterType(),
             name="result_graph_iri",
             label="Result graph IRI",
-            description="The IRI of the output graph for the reasoning result. ⚠️ Existing graph "
+            description="The IRI of the output graph for the reasoning result. ⚠️ Existing graphs "
             "will be overwritten.",
         ),
         PluginParameter(
@@ -160,19 +159,10 @@
             description="",
             default_value=False,
         ),
-        PluginParameter(
-            param_type=BoolParameterType(),
-            name="annotate_inferred_axioms",
-            label="Annnotate inferred subclass axioms",
-            description="Annotate inferred subclass axioms. ⚠️ This parameter can only be enabled "
-            "if the only enabled axiom generator is SubClass.",
-            default_value=False,
-            advanced=True,
-        ),
     ],
 )
 class ReasonPlugin(WorkflowPlugin):
-    """Robot reasoning plugin"""
+    """Reason plugin"""
 
     def __init__(  # noqa: PLR0913
         self,
@@ -194,10 +184,8 @@ def __init__(  # noqa: PLR0913
         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:
-        """Init"""
         self.axioms = {
             "SubClass": sub_class,
             "EquivalentClass": equivalent_class,
@@ -214,16 +202,13 @@ def __init__(  # noqa: PLR0913
             "ObjectPropertyRange": object_property_range,
             "ObjectPropertyDomain": object_property_domain,
         }
-
         errors = ""
-        iris = {
-            "Data graph IRI": data_graph_iri,
-            "Ontology graph IRI": ontology_graph_iri,
-            "Result graph IRI": result_graph_iri,
-        }
-        not_iri = sorted([k for k, v in iris.items() if not validators.url(v)])
-        if not_iri:
-            errors += f"Invalid IRI for parameters: {', '.join(not_iri)}. "
+        if not validators.url(data_graph_iri):
+            errors += 'Invalid IRI for parameter "Data graph IRI". '
+        if not validators.url(ontology_graph_iri):
+            errors += 'Invalid IRI for parameter "Ontology graph IRI". '
+        if not validators.url(result_graph_iri):
+            errors += 'Invalid IRI for parameter "Result graph IRI". '
         if result_graph_iri and result_graph_iri == data_graph_iri:
             errors += "Result graph IRI cannot be the same as the data graph IRI. "
         if result_graph_iri and result_graph_iri == ontology_graph_iri:
@@ -232,21 +217,14 @@ def __init__(  # noqa: PLR0913
             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:
             raise ValueError(errors[:-1])
-
         self.data_graph_iri = data_graph_iri
         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}"
 
@@ -275,7 +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 "
@@ -305,21 +282,7 @@ def reason(self, graphs: dict) -> None:
                 raise OSError(response.stderr.decode())
             raise OSError("ROBOT error")
 
-    def clean_up(self, graphs: dict) -> None:
-        """Remove temporary files"""
-        files = ["catalog-v001.xml", "result.ttl"]
-        files += list(graphs.values())
-        for file in files:
-            try:
-                (Path(self.temp) / file).unlink()
-            except (OSError, FileNotFoundError) as err:
-                self.log.warning(f"Cannot remove file {file} ({err})")
-        try:
-            Path(self.temp).rmdir()
-        except (OSError, FileNotFoundError) as err:
-            self.log.warning(f"Cannot remove directory {self.temp} ({err})")
-
-    def execute(self, inputs: Sequence[Entities], context: ExecutionContext) -> None:  # noqa: ARG002
+    def execute(self, inputs: tuple, context: ExecutionContext) -> None:  # noqa: ARG002
         """Execute plugin"""
         setup_cmempy_user_access(context.user)
         graphs = get_graphs_tree((self.data_graph_iri, self.ontology_graph_iri))
@@ -328,4 +291,4 @@ def execute(self, inputs: Sequence[Entities], context: ExecutionContext) -> None
         self.reason(graphs)
         setup_cmempy_user_access(context.user)
         send_result(self.result_graph_iri, Path(self.temp) / "result.ttl")
-        self.clean_up(graphs)
+        remove_temp(self, ["catalog-v001.xml", "result.ttl", *graphs.values()])

cmem_plugin_reason/plugin_validate.py

@@ -1,7 +1,6 @@
 """Ontology consistency validation workflow plugin module"""
 
 import shlex
-from collections.abc import Sequence
 from datetime import UTC, datetime
 from pathlib import Path
 from subprocess import run
@@ -22,7 +21,7 @@
 from cmem_plugin_base.dataintegration.plugins import WorkflowPlugin
 from cmem_plugin_base.dataintegration.types import BoolParameterType, StringParameterType
 from cmem_plugin_base.dataintegration.utils import setup_cmempy_user_access
-from pathvalidate import validate_filename
+from pathvalidate import is_valid_filename
 
 from cmem_plugin_reason.utils import (
     MAX_RAM_PERCENTAGE_DEFAULT,
@@ -33,6 +32,7 @@
     ROBOT,
     create_xml_catalog_file,
     get_graphs_tree,
+    remove_temp,
     send_result,
 )
 
@@ -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(),
@@ -85,7 +86,7 @@
     ],
 )
 class ValidatePlugin(WorkflowPlugin):
-    """Example Workflow Plugin: Random Values"""
+    """Validate plugin"""
 
     def __init__(  # noqa: PLR0913
         self,
@@ -100,28 +101,26 @@ def __init__(  # noqa: PLR0913
     ) -> None:
         errors = ""
         if not validators.url(ontology_graph_iri):
-            errors += "Invalid IRI for parameter Ontology graph IRI. "
-        if reasoner not in REASONERS:
-            errors += "Invalid value for parameter Reasoner. "
+            errors += 'Invalid IRI for parameter "Ontology graph IRI." '
         if produce_graph and not validators.url(output_graph_iri):
-            errors += "Invalid IRI for parameter Output graph IRI. "
-        if write_md:
-            try:
-                validate_filename(md_filename)
-            except:  # noqa: E722
-                errors += "Invalid filename for parameter Output filename. "
-        if max_ram_percentage not in range(1, 100):
-            errors += "Invalid value for parameter Maximum RAM Percentage. "
+            errors += 'Invalid IRI for parameter "Output graph IRI". '
+        if produce_graph and output_graph_iri == ontology_graph_iri:
+            errors += "Output graph IRI cannot be the same as the Ontology graph IRI. "
+        if reasoner not in REASONERS:
+            errors += 'Invalid value for parameter "Reasoner". '
+        if write_md and not is_valid_filename(md_filename):
+            errors += 'Invalid filename for parameter "Output filename". '
+        if max_ram_percentage not in range(1, 101):
+            errors += 'Invalid value for parameter "Maximum RAM Percentage". '
         if errors:
             raise ValueError(errors[:-1])
-
         self.ontology_graph_iri = ontology_graph_iri
         self.reasoner = reasoner
         self.produce_graph = produce_graph
         self.output_graph_iri = output_graph_iri
         self.write_md = write_md
         self.stop_at_inconsistencies = stop_at_inconsistencies
-        self.md_filename = md_filename if md_filename and write_md else "mdfile.md"
+        self.md_filename = md_filename if write_md else "mdfile.md"
         self.max_ram_percentage = max_ram_percentage
         self.temp = f"reason_{uuid4().hex}"
 
@@ -176,35 +175,20 @@ def make_resource(self, context: ExecutionContext) -> None:
             replace=True,
         )
 
-    def clean_up(self, graphs: dict) -> None:
-        """Remove temporary files"""
-        files = ["catalog-v001.xml", "output.ttl", self.md_filename]
-        files += list(graphs.values())
-        for file in files:
-            try:
-                (Path(self.temp) / file).unlink()
-            except (OSError, FileNotFoundError) as err:
-                self.log.warning(f"Cannot remove file {file} ({err})")
-        try:
-            Path(self.temp).rmdir()
-        except (OSError, FileNotFoundError) as err:
-            self.log.warning(f"Cannot remove directory {self.temp} ({err})")
-
-    def execute(
-        self,
-        inputs: Sequence[Entities],  # noqa: ARG002
-        context: ExecutionContext,
-    ) -> Entities | None:
+    def execute(self, inputs: tuple, context: ExecutionContext) -> Entities | None:  # noqa: ARG002
         """Run the workflow operator."""
         setup_cmempy_user_access(context.user)
         graphs = get_graphs_tree((self.ontology_graph_iri,))
         self.get_graphs(graphs, context)
         create_xml_catalog_file(self.temp, graphs)
         self.validate(graphs)
+        files = ["catalog-v001.xml", self.md_filename, *graphs.values()]
+        if self.produce_graph:
+            files.append("output.ttl")
 
         text = (Path(self.temp) / self.md_filename).read_text()
         if text == "No explanations found.":
-            self.clean_up(graphs)
+            remove_temp(self, files)
             return None
 
         if self.produce_graph:
@@ -215,7 +199,7 @@ def execute(
             setup_cmempy_user_access(context.user)
             self.make_resource(context)
 
-        self.clean_up(graphs)
+        remove_temp(self, files)
 
         if self.stop_at_inconsistencies:
             raise RuntimeError("Inconsistencies found in Ontology.")