keep output if no inconsistencies found with validate plugin, fix pro…

…venance info in output graphs
eccenca · Jul 1, 2024 · 6fd6f1a · 6fd6f1a
1 parent 68d2447
commit 6fd6f1a
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,17 @@ 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
+
+- `prov:generatedBy` in output graphs now refers to a plugin IRI instead of a literal
+
+### Changed
+
+- Keep original output ("No explanations found.") if no inconsistencies found with Validate plugin
+
+
 ## [1.0.0beta1] 2024-07-01
 
 ### Fixed
@@ -13,14 +24,14 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/) and this p
 ### Changed
 
 - complete validation for IRI parameters
-- Remove "Annnotate inferred subclass axioms" parameter
+- remove "Annnotate inferred subclass axioms" parameter in Reason plugin
 
 ## [1.0.0alpha3] 2024-06-28
 
 ### Added
 
 - "Annotate inferred axioms" parameter in Reason plugin
-- "Maximum RAM percentage" parameter in Reason and Validate plugins
+- "Maximum RAM percentage" parameter
 
 ### Changed
 

diff --git a/README.md b/README.md
@@ -90,7 +90,7 @@ Maximum heap size for the Java virtual machine in the DI container running the r
 
 # Validate
 
-In case ontology inconsistencies are found, the plugin outputs the explanation as text in Markdown format using the path "text".
+The plugin outputs the explanation as text in Markdown format using the path "text".
 
 ## Options
 
@@ -122,6 +122,10 @@ The IRI of the output graph for the reasoning result.
 
 If enabled, an explanation markdown file is written to the project.
 
+### Output filename
+
+The filename of the Markdown file with the explanation of inconsistencies.
+
 :warning: Existing files will be overwritten.
 
 ### Stop at inconsistencies

diff --git a/cmem_plugin_reason/plugin_reason.py b/cmem_plugin_reason/plugin_reason.py
@@ -29,6 +29,8 @@
     send_result,
 )
 
+PLUGIN_IRI = "https://plugin.eccenca.com/cmem-plugin-reason/reason"
+
 
 @Plugin(
     label="Reason",
@@ -266,8 +268,7 @@ def reason(self, graphs: dict) -> None:
             f"--language-annotation rdfs:comment "
             f'"Reasoning result set of <{self.data_graph_iri}> and '
             f'<{self.ontology_graph_iri}>" en '
-            f"--language-annotation prov:wasGeneratedBy "
-            f'"cmem-plugin-reason ({self.reasoner})" en '
+            f'--link-annotation prov:wasGeneratedBy "{PLUGIN_IRI}/{self.reasoner}" '
             f'--link-annotation prov:wasDerivedFrom "{self.data_graph_iri}" '
             f"--link-annotation prov:wasDerivedFrom "
             f'"{self.ontology_graph_iri}" '
@@ -291,4 +292,4 @@ 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")
-        remove_temp(self, ["catalog-v001.xml", "result.ttl", *graphs.values()])
+        remove_temp(self)
diff --git a/cmem_plugin_reason/plugin_validate.py b/cmem_plugin_reason/plugin_validate.py
@@ -36,9 +36,11 @@
     send_result,
 )
 
+PLUGIN_IRI = "https://plugin.eccenca.com/cmem-plugin-reason/validate"
+
 
 @Plugin(
-    label="Validate ontology consistency",
+    label="Validate",
     description="",
     documentation="""""",
     icon=Icon(package=__package__, file_name="obofoundry.png"),
@@ -50,8 +52,7 @@
             param_type=BoolParameterType(),
             name="write_md",
             label="Write Markdown explanation file",
-            description="Write Markdown file with explanation to project. ⚠️ Existing files will "
-            "be overwritten.",
+            description="Write Markdown file with explanation to project.",
             default_value=False,
         ),
         PluginParameter(
@@ -73,7 +74,7 @@
             name="md_filename",
             label="Output filename",
             description="The filename of the Markdown file with the explanation of "
-            "inconsistencies.",
+            "inconsistencies.⚠️ Existing files will be overwritten.",
         ),
         PluginParameter(
             param_type=BoolParameterType(),
@@ -151,8 +152,7 @@ def validate(self, graphs: dict) -> None:
                 f'--language-annotation rdfs:label "Ontology Validation Result {utctime}" en '
                 f"--language-annotation rdfs:comment "
                 f'"Ontology validation of <{self.ontology_graph_iri}>" en '
-                f"--language-annotation prov:wasGeneratedBy "
-                f'"cmem-plugin-validate ({self.reasoner})" en '
+                f'--link-annotation prov:wasGeneratedBy "{PLUGIN_IRI}/{self.reasoner}" '
                 f'--link-annotation prov:wasDerivedFrom "{self.ontology_graph_iri}" '
                 f'--typed-annotation dc:created "{utctime}" xsd:dateTime '
                 f'--output "{self.temp}/output.ttl"'
@@ -182,26 +182,18 @@ def execute(self, inputs: tuple, context: ExecutionContext) -> Entities | None:
         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.":
-            remove_temp(self, files)
-            return None
 
         if self.produce_graph:
             setup_cmempy_user_access(context.user)
             send_result(self.output_graph_iri, Path(self.temp) / "output.ttl")
-
         if self.write_md:
             setup_cmempy_user_access(context.user)
             self.make_resource(context)
+        text = (Path(self.temp) / self.md_filename).read_text()
 
-        remove_temp(self, files)
+        remove_temp(self)
 
-        if self.stop_at_inconsistencies:
+        if self.stop_at_inconsistencies and text != "No explanations found.":
             raise RuntimeError("Inconsistencies found in Ontology.")
 
         entities = [

diff --git a/cmem_plugin_reason/utils.py b/cmem_plugin_reason/utils.py
@@ -4,6 +4,7 @@
 import unicodedata
 from collections import OrderedDict
 from pathlib import Path
+from shutil import rmtree
 from xml.etree.ElementTree import Element, SubElement, tostring
 
 from cmem.cmempy.dp.proxy.graph import get_graph_import_tree, post_streamed
@@ -108,14 +109,9 @@ def send_result(iri: str, filepath: Path) -> None:
     )
 
 
-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})")
+def remove_temp(plugin: WorkflowPlugin) -> None:
+    """Remove temporary files"""
     try:
-        Path(plugin.temp).rmdir()
+        rmtree(plugin.temp)
     except (OSError, FileNotFoundError) as err:
         plugin.log.warning(f"Cannot remove directory {plugin.temp} ({err})")
diff --git a/tests/test_elk.ttl b/tests/test_elk.ttl
@@ -13,7 +13,7 @@
                                                     rdfs:comment "Reasoning result set of <https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/data/> and <https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/vocab/>"@en ;
                                                     prov:wasDerivedFrom
                 <https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/data/> , <https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/vocab/> ;
-                                                                            prov:wasGeneratedBy "cmem-plugin-reason (elk)"@en .
+                                                                            prov:wasGeneratedBy <https://plugin.eccenca.com/cmem-plugin-reason/reason/elk> .
 
 #################################################################
 #    Individuals

diff --git a/tests/test_emr.ttl b/tests/test_emr.ttl
@@ -13,7 +13,7 @@
                                                     rdfs:comment "Reasoning result set of <https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/data/> and <https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/vocab/>"@en ;
                                                     prov:wasDerivedFrom
                 <https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/data/> , <https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/vocab/> ;
-                                                                            prov:wasGeneratedBy "cmem-plugin-reason (emr)"@en .
+                                                                            prov:wasGeneratedBy <https://plugin.eccenca.com/cmem-plugin-reason/reason/emr> .
 
 #################################################################
 #    Individuals

diff --git a/tests/test_hermit.ttl b/tests/test_hermit.ttl
@@ -13,7 +13,7 @@
                                                     rdfs:comment "Reasoning result set of <https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/data/> and <https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/vocab/>"@en ;
                                                     prov:wasDerivedFrom
                 <https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/data/> , <https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/vocab/> ;
-                                                                            prov:wasGeneratedBy "cmem-plugin-reason (hermit)"@en .
+                                                                            prov:wasGeneratedBy <https://plugin.eccenca.com/cmem-plugin-reason/reason/hermit> .
 
 #################################################################
 #    Individuals

diff --git a/tests/test_jfact.ttl b/tests/test_jfact.ttl
@@ -13,7 +13,7 @@
                                                     rdfs:comment "Reasoning result set of <https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/data/> and <https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/vocab/>"@en ;
                                                     prov:wasDerivedFrom
                 <https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/data/> , <https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/vocab/> ;
-                                                                            prov:wasGeneratedBy "cmem-plugin-reason (jfact)"@en .
+                                                                            prov:wasGeneratedBy <https://plugin.eccenca.com/cmem-plugin-reason/reason/jfact> .
 
 #################################################################
 #    Individuals

diff --git a/tests/test_structural.ttl b/tests/test_structural.ttl
@@ -13,7 +13,7 @@
                                                     rdfs:comment "Reasoning result set of <https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/data/> and <https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/vocab/>"@en ;
                                                     prov:wasDerivedFrom
                 <https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/data/> , <https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/vocab/> ;
-                                                                            prov:wasGeneratedBy "cmem-plugin-reason (structural)"@en .
+                                                                            prov:wasGeneratedBy <https://plugin.eccenca.com/cmem-plugin-reason/reason/structural> .
 
 #################################################################
 #    Individuals

diff --git a/tests/test_validate_output.ttl b/tests/test_validate_output.ttl
@@ -8,7 +8,7 @@
 <https://ns.eccenca.com/validateontology/e02aaed014c94e0c91bf960fed127750/output/> a owl:Ontology ;
     rdfs:comment "Ontology validation of <https://ns.eccenca.com/validateontology/e02aaed014c94e0c91bf960fed127750/vocab/>"@en ;
     prov:wasDerivedFrom <https://ns.eccenca.com/validateontology/e02aaed014c94e0c91bf960fed127750/vocab/> ;
-    prov:wasGeneratedBy "cmem-plugin-validate (elk)"@en .
+    prov:wasGeneratedBy <https://plugin.eccenca.com/cmem-plugin-reason/validate/elk> .
 
 <https://ns.eccenca.com/validateontology/e02aaed014c94e0c91bf960fed127750/vocab/D_6> a owl:NamedIndividual,
         <https://ns.eccenca.com/validateontology/e02aaed014c94e0c91bf960fed127750/vocab/A> .

diff --git a/tests/test_whelk.ttl b/tests/test_whelk.ttl
@@ -13,7 +13,7 @@
                                                     rdfs:comment "Reasoning result set of <https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/data/> and <https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/vocab/>"@en ;
                                                     prov:wasDerivedFrom
                 <https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/data/> , <https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/vocab/> ;
-                                                                            prov:wasGeneratedBy "cmem-plugin-reason (whelk)"@en .
+                                                                            prov:wasGeneratedBy <https://plugin.eccenca.com/cmem-plugin-reason/reason/whelk> .
 
 #################################################################
 #    Individuals