move cleanup to utils.py, annotate inferred axioms not advanced param…

…eter

CHANGELOG.md

@@ -10,9 +10,10 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/) and this p
 
 - valid range of "Maximum RAM Percentage" parameter in Validate plugin (1-100)
 
-### Change
+### Changed
 
 - completed validation for IRI parameters
+- "Annnotate inferred subclass axioms" is now not an advanced parameter
 
 ## [1.0.0alpha3] 2024-06-28
 

cmem_plugin_reason/plugin_reason.py

@@ -25,6 +25,7 @@
     ROBOT,
     create_xml_catalog_file,
     get_graphs_tree,
+    remove_temp,
     send_result,
 )
 
@@ -57,7 +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(
@@ -162,10 +163,9 @@
             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.",
+            description="⚠️ This parameter can only be enabled if the only enabled axiom generator "
+            "is SubClass.",
             default_value=False,
-            advanced=True,
         ),
     ],
 )
@@ -211,7 +211,6 @@ def __init__(  # noqa: PLR0913, C901
             "ObjectPropertyRange": object_property_range,
             "ObjectPropertyDomain": object_property_domain,
         }
-
         errors = ""
         if not validators.url(data_graph_iri):
             errors += 'Invalid IRI for parameter "Data graph IRI". '
@@ -299,20 +298,6 @@ 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: tuple, context: ExecutionContext) -> None:  # noqa: ARG002
         """Execute plugin"""
         setup_cmempy_user_access(context.user)
@@ -322,4 +307,4 @@ def execute(self, inputs: tuple, context: ExecutionContext) -> None:  # noqa: AR
         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

@@ -32,6 +32,7 @@
     ROBOT,
     create_xml_catalog_file,
     get_graphs_tree,
+    remove_temp,
     send_result,
 )
 
@@ -112,7 +113,6 @@ def __init__(  # noqa: PLR0913
             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
@@ -174,31 +174,20 @@ 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: 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:
@@ -209,7 +198,7 @@ def execute(self, inputs: tuple, context: ExecutionContext) -> Entities | None:
             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.")

cmem_plugin_reason/utils.py

@@ -1,4 +1,4 @@
-"""Common functions"""
+"""Common constants and functions"""
 
 import re
 import unicodedata
@@ -10,6 +10,7 @@
 from cmem_plugin_base.dataintegration.description import PluginParameter
 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.types import IntParameterType
 from defusedxml import minidom
 
@@ -105,3 +106,16 @@ def send_result(iri: str, filepath: Path) -> None:
         replace=True,
         content_type="text/turtle",
     )
+
+
+def remove_temp(plugin: WorkflowPlugin, files: list) -> None:
+    """Remove temproray files"""
+    for file in files:
+        try:
+            (Path(plugin.temp) / file).unlink()
+        except (OSError, FileNotFoundError) as err:
+            plugin.log.warning(f"Cannot remove file {file} ({err})")
+    try:
+        Path(plugin.temp).rmdir()
+    except (OSError, FileNotFoundError) as err:
+        plugin.log.warning(f"Cannot remove directory {plugin.temp} ({err})")