cmem-plugin-reason 1.0.0__tar.gz

cmem_plugin_reason-1.0.0/LICENSE

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cmem_plugin_reason-1.0.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: cmem-plugin-reason
+Version: 1.0.0
+Summary: Perform reasoning tasks and validate OWL consistency.
+Home-page: https://github.com/eccenca/cmem-plugin-reason
+License: Apache-2.0
+Keywords: eccenca Corporate Memory,plugin
+Author: eccenca GmbH
+Author-email: cmempy-developer@eccenca.com
+Requires-Python: >=3.11,<4.0
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Plugins
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Dist: cmem-plugin-base (>=4.7.0,<5.0.0)
+Requires-Dist: defusedxml (>=0.7.1,<0.8.0)
+Requires-Dist: inflection (>=0.5.1,<0.6.0)
+Requires-Dist: pathvalidate (>=3.2.0,<4.0.0)
+Requires-Dist: validators (>=0.33.0,<0.34.0)
+Description-Content-Type: text/markdown
+
+# cmem-plugin-reason
+
+Perform reasoning tasks and validate OWL consistency.
+
+ROBOT is published under the [BSD 3-Clause "New" or "Revised" License](https://choosealicense.com/licenses/bsd-3-clause/).
+Copyright © 2015, the authors. All rights reserved.
+
+### Installation
+
+```
+➜ cmemc admin workspace python install cmem-plugin-reason
+```
+
+

cmem_plugin_reason-1.0.0/README-public.md

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+# cmem-plugin-reason
+
+Perform reasoning tasks and validate OWL consistency.
+
+ROBOT is published under the [BSD 3-Clause "New" or "Revised" License](https://choosealicense.com/licenses/bsd-3-clause/).
+Copyright © 2015, the authors. All rights reserved.
+
+### Installation
+
+```
+➜ cmemc admin workspace python install cmem-plugin-reason
+```
+

cmem_plugin_reason-1.0.0/cmem_plugin_reason/__init__.py

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+"""reason - main package"""

cmem_plugin_reason-1.0.0/cmem_plugin_reason/doc/__init__.py

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+"""doc"""
+
+from pathlib import Path
+
+with (Path(__path__[0]) / "reason_doc.md").open("r") as f:
+    REASON_DOC = f.read()
+
+with (Path(__path__[0]) / "validate_doc.md").open("r") as f:
+    VALIDATE_DOC = f.read()

cmem_plugin_reason-1.0.0/cmem_plugin_reason/doc/reason_doc.md

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+A task performing OWL reasoning. With an OWL ontology and a data graph as input the reasoning result is written to a specified graph.
+    
+## Options
+
+### Data graph IRI
+
+The IRI of the input data graph. The graph IRI is selected from a list of graphs of types `di:Dataset`, `void:Dataset`
+and `owl:Ontology`.
+
+### Ontology graph IRI
+
+The IRI of the input ontology graph. The graph IRI is selected from a list of graphs of type`owl:Ontology`.
+
+### Output graph IRI
+
+The IRI of the output graph for the reasoning result.
+
+⚠️ Existing graphs will be overwritten.
+
+### 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)
+
+### Generated Axioms
+
+The plugin provides the following parameters to include inferred axiom generators:
+
+#### Class axiom generators
+- **Class inclusion (rdfs:subClassOf)**  
+The reasoner will infer assertions about the hierarchy of classes, i.e.
+`SubClassOf:` statements.  
+If there are classes `Person`, `Student` and `Professor`, such that `Person DisjointUnionOf:
+Student, Professor` holds, the reasoner will infer `Student SubClassOf: Person`.  
+
+
+- **Class equivalence (owl:equivalentClass)**  
+The reasoner will infer assertions about the equivalence of classes, i.e.
+`EquivalentTo:` statements.  
+If there are classes `Person`, `Student` and `Professor`, such that `Person DisjointUnionOf:
+Student, Professor` holds, the reasoner will infer `Person EquivalentTo: Student and Professor`.
+
+
+- **Class disjointness (owl:disjointWith)**  
+The reasoner will infer assertions about the disjointness of classes, i.e.
+`DisjointClasses:` statements.  
+If there are classes `Person`, `Student` and `Professor`, such that `Person DisjointUnionOf:
+Student, Professor` holds, the reasoner will infer `DisjointClasses: Student, Professor`.
+
+  
+- **Data property equivalence (owl:equivalentProperty)**  
+The reasoner will infer axioms about the equivalence of data properties,
+ i.e. `EquivalentProperties` statements.  
+If there are data properties `identifier` and `enrollmentNumber`, such that `enrollmentNumber
+SubPropertyOf: identifier` and `identifier SubPropertyOf: enrollmentNumber` holds, the reasoner
+will infer `Student EquivalentProperties: identifier, enrollmentNumber`.
+
+
+- **Data property inclusion (rdfs:subPropertyOf)**  
+The reasoner will infer axioms about the hierarchy of data properties,
+i.e. `SubPropertyOf:` statements.  
+If there are data properties `identifier`, `studentIdentifier` and `enrollmentNumber`, such that
+`studentIdentifier SubPropertyOf: identifier` and `enrollmentNumber SubPropertyOf:
+studentIdentifier` holds, the reasoner will infer `enrollmentNumber SubPropertyOf: identifier`.
+
+
+#### Individual axiom generators
+- **Individual class assertions (rdf:type)**  
+The reasoner will infer assertions about the classes of individuals, i.e.
+`Types:` statements.  
+Assume, there are classes `Person`, `Student` and `University` as well as the property
+`enrolledIn`, such that `Student EquivalentTo: Person and enrolledIn some University` holds. For
+the individual `John` with the assertions `John Types: Person; Facts: enrolledIn
+LeipzigUniversity`, the reasoner will infer `John Types: Student`.
+
+
+- **Individual property assertions**  
+The reasoner will infer assertions about the properties of individuals,
+i.e. `Facts:` statements.  
+Assume, there are properties `enrolledIn` and `offers`, such that `enrolled SubPropertyChain:
+enrolledIn o inverse (offers)` holds. For the individuals `John`and `LeipzigUniversity` with the
+assertions `John Facts: enrolledIn KnowledgeRepresentation` and `LeipzigUniversity Facts: offers
+KnowledgeRepresentation`,  the reasoner will infer `John Facts: enrolledIn LeipzigUniversity`.
+
+
+#### Object property axiom generators
+- **Object property equivalence (owl:equivalentProperty)**  
+The reasoner will infer assertions about the equivalence of object
+properties, i.e. `EquivalentTo:` statements.  
+If there are object properties `hasAlternativeLecture` and `hasSameTopicAs`, such that
+`hasAlternativeLecture Characteristics: Symmetric` and `hasSameTopicAs InverseOf:
+hasAlternativeLecture` holds, the reasoner will infer `EquivalentProperties: hasAlternativeLecture,
+hasSameTopicAs`.
+
+
+- **Object property inversion (owl:inverseOf)**  
+The reasoner will infer axioms about the inversion about object
+properties, i.e. `InverseOf:` statements.  
+If there is a object property `hasAlternativeLecture`, such that `hasAlternativeLecture
+Characteristics: Symmetric` holds, the reasoner will infer `hasAlternativeLecture InverseOf:
+hasAlternativeLecture`.
+
+
+- **Object property inclusion (rdfs:subPropertyOf)**  
+The reasoner will infer axioms about the inclusion of object properties,
+i.e. `SubPropertyOf:` statements.  
+If there are object properties `enrolledIn`, `studentOf` and `hasStudent`, such that `enrolledIn
+SubPropertyOf: studentOf` and `enrolledIn InverseOf: hasStudent` holds, the reasoner will infer
+`hasStudent SubPropertyOf: inverse (studentOf)`.
+
+
+- **Object property ranges (rdfs:range)**  
+The reasoner will infer axioms about the ranges of object properties,
+i.e. `Range:` statements.  
+If there are classes `Student` and `Lecture` as wells as object properties `hasStudent` and
+`enrolledIn`, such that `hasStudent Range: Student and enrolledIn some Lecture` holds, the
+reasoner will infer `hasStudent Range: Student`.
+
+
+- **Object property domains (rdfs:domain)**  
+The reasoner will infer axioms about the domains of object
+properties, i.e. `Domain:` statements.  
+If there are classes `Person`, `Student` and `Professor` as wells as the object property
+`hasRoleIn`, such that `Professor SubClassOf: Person`, `Student SubClassOf: Person` and
+`hasRoleIn Domain: Professor or Student` holds, the reasoner will infer `hasRoleIn Domain: Person`.
+
+
+### Validate OWL2 profiles
+
+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 valid profiles, ontology IRI and reasoner option is
+taken from the config port input (parameters "valid_profiles", "ontology_graph_iri" and "reasoner") and the OWL2
+profiles validation is not done 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
+
+Maximum heap size for the Java virtual machine in the DI container running the reasoning process.
+
+⚠️ Setting the percentage too high may result in an out of memory error.

cmem_plugin_reason-1.0.0/cmem_plugin_reason/doc/validate_doc.md

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+A task validating the consistency of an OWL ontology and generating an explanation if inconsistencies are found. 
+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
+
+### 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.
+
+⚠️ Existing graphs will be overwritten.
+
+### Write markdown explanation file
+
+If enabled, an explanation markdown file is written to the project.
+
+### Output filename
+
+The filename of the Markdown file with the explanation of inconsistencies.
+
+⚠️ Existing files will be overwritten.
+
+### Stop at inconsistencies
+Raise an error if inconsistencies are found. If enabled, the plugin does not output entities.
+
+### Validate OWL2 profiles
+
+Validate the input ontology against OWL profiles (DL, EL, QL, RL, and Full) and annotate the result graph.
+
+### Mode
+Mode _inconsistency_ generates an explanation for an inconsistent ontology.  
+Mode _unsatisfiability_ generates explanations for many unsatisfiable classes at once.
+
+### 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", the reasoner option on the path "reasoner", and, if enabled, the valid OWL2 profiles
+on the path "valid_profiles".
+
+### Maximum RAM Percentage
+
+Maximum heap size for the Java virtual machine in the DI container running the reasoning process.
+
+⚠️ Setting the percentage too high may result in an out of memory error.

cmem_plugin_reason-1.0.0/cmem_plugin_reason/file-icons--owl.svg

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