fix validation issues (#9)

* define schemas, remove write_md and produc_graph bool parameters

* fix condition to write MD file to project

* validate inputs (Reason)

* use ontology IRI from input if input_profiles=True

* fix incorrect stopping of workflow if 'validate_profiles' is enabled in Validate

* remove iter cast from output entities

* fixing import bug

* fix error when result graph is imported in input graph

* edit readme

* fixes (CMEM-5913), use custom paramter type for output graph IRI

* edit parameter description

* init ExecutionReport

* edit parameter label

* use GraphParameterType(allow_only_autocompleted_values=False) instead of custom parameter for output graph IRI

* set allowed classes for output graph list to Dataset and Ontology

* fix indentation

* removee reason merge in reason

* remove robot merge in Validate

* refactor parameter variable generation

* add '[processed ontology] a owl:Ontology' to output graph, use config port input for valid OWL2 profiles in Reasin plugin

* edit readme

* fix test

* remove unused method

* verify valid_profiles input

* add parameters for owl:imports and entity output. PLugin doc imported from md files

* fix tests

* edit docs

* edit doc

* edit doc

* edit parameters

* remove SSL_VERIFY env variable setting

* specify output entity paths in Validate tests

---------

Co-authored-by: muddymudskipper <thomas.wilmering@gmail.com>

CHANGELOG.md

@@ -6,9 +6,27 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/) and this p
 
 ## [Unreleased]
 
+### 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
+
+ - incorrect stopping of workflow if "validate_profiles" and "stop_at_inconsistencies" is enabled in Validate plugin
+ - fixed error when output graph is imported by input graph; the import is removed in-memory before reasoning
+
 ### Changed
 
 - raise OSError on post result graph error
+- removed write_md and produce_graph bool parameters
+- if "input_profiles" is enabled the Reason plugin expects "ontology_iri" and "profile" on the input.
+The ontology IRI on the input overrides the plugin setting.
+- update execution report
+- Output graph IRI selectable from existing graphs
+- When "input_profiles" is enabled the ontology IRI and list of valid OWL2 profiles is now taken from the config port.
+The list of valid profiles is a comma-separated string (e.g. "Full,DL")
 
 ## [1.0.0beta4] 2024-07-12
 

README.md

@@ -84,15 +84,21 @@ parameters to include inferred axiom generators:
 
 ### Validate OWL2 profiles
 
-Validate the input ontology against OWL profiles (DL, EL, QL, RL, and Full). The ontology is annotated in the output graph. 
+Validate the input ontology against OWL profiles (DL, EL, QL, RL, and Full) and annotate the result graph. 
 
 ### Process valid OWL profiles from input
 
-If enabled along with the "Validate OWL2 profiles" parameter, the list of valid profiles is taken from the plugin input, 
-without validating the ontology against the profiles in the plugin. The inputs need to include the entity paths "profile"
-for the valid profiles, and "ontology" for the ontology IRI. If the "Validate OWL2 profiles" parameter is enabled in the
-"Validate" plugin, it can be directly connected to the input of the "Reason" plugin.
+If enabled along with the "Validate OWL2 profiles" parameter, the valid profiles and ontology IRI is taken from the
+config port input (parameters "valid_profiles" and "ontology_graph_iri") instead of from running the validation in the 
+plugin. The valid profiles input is a comma-separated string (e.g. "Full,DL").
 
+### Add ontology graph import to result graph
+
+Add the triple `<output_graph_iri> owl:imports <ontology_graph_iri>` to the output graph.
+
+### Add result graph import to ontology graph
+
+Add the triple `<ontology_graph_iri> owl:imports <output_graph_iri>` to the ontology graph
 
 ### Maximum RAM Percentage
 
@@ -102,7 +108,9 @@ Maximum heap size for the Java virtual machine in the DI container running the r
 
 # Validate
 
-The plugin outputs the explanation as text in Markdown format using the path "markdown".
+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
 
@@ -145,9 +153,12 @@ Raise an error if inconsistencies are found. If enabled, the plugin does not out
 
 ### 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 "profile",
-and the ontology IRI with path "ontology".
+Validate the input ontology against OWL profiles (DL, EL, QL, RL, and Full) and annotate the result graph.
+
+### Output entities
+
+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
 
 ### Maximum RAM Percentage