fix validate_profiles, test import tree

eccenca · Aug 28, 2024 · e3517c7 · e3517c7
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,12 +10,16 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/) and this p
 
  - Validate: added "mode" parameter
 
+### Fixed
+
+- respect owl:imports in OWL2 profile validation
+
 ### Changed
 
  - Validate: the entity output includes the reasoner option on path "reason"
  - Detailed axiom generator documentation
- - The axiom generator ObjectPropertyCharacteristic does not yield results possibly due to a bug in the OWL API. Currently,
-this axiom generator and its (working) counterpart DataPropertyCharacteristic are removed from the Reason plugin.
+ - The axiom generator ObjectPropertyCharacteristic does not yield results. Currently, this axiom generator and its
+ - (working) counterpart DataPropertyCharacteristic are removed from the Reason plugin.
 
 ## [1.0.0beta5] 2024-08-15
 

diff --git a/cmem_plugin_reason/plugin_reason.py b/cmem_plugin_reason/plugin_reason.py
@@ -37,121 +37,6 @@
 
 REASONER_PARAMETER.description += " Select axiom generators below [Click (?) for documentation]."
 
-#
-# SUBCLASS_DESC = """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`.
-# """
-#
-# EQUIVALENCE_DESC = """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`.
-# """
-#
-# DISJOINT_DESC = """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_PROP_CHAR_DESC = """The reasoner will infer characteristics of data properties, i.e.
-# # `Characteristics:` statements. For data properties, this only pertains to functionality.
-# #
-# # If there are data properties `identifier` and `enrollmentNumber`, such that `enrollmentNumber
-# # SubPropertyOf: identifier` and `identifier Characteristics: Functional` holds, the reasoner will
-# # infer `enrollmentNumber Characteristics: Functional`.
-# # """
-#
-# DATA_PROP_EQUIV_DESC = """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_PROP_SUB_DESC = """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`.
-# """
-#
-# CLASS_ASSERT_DESC = """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`.
-# """
-#
-# PROPERTY_ASSERT_DESC = """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_PROP_CHAR_DESC = """The reasoner will infer characteristics of object properties, i.e.
-# # `Characteristics:` statements.
-# #
-# # If there are object properties `enrolledIn` and `studentOf`, such that `enrolledIn
-# # SubPropertyOf: studentOf` and `enrolledIn Characteristics: Functional` holds, the reasoner will
-# # infer `studentOf Characteristics: Functional`. **Note: this inference does neither work in JFact
-# # nor in HermiT!**
-# # """
-#
-# OBJECT_PROP_EQUIV_DESC = """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_PROP_SUB_DESC = """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_PROP_INV_DESC = """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_PROP_RANGE_DESC = """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_PROP_DOMAIN_DESC = """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`.
-# """
-
 
 @Plugin(
     label="Reason",

diff --git a/cmem_plugin_reason/utils.py b/cmem_plugin_reason/utils.py
@@ -209,7 +209,7 @@ def validate_profiles(plugin: WorkflowPlugin, graphs: dict) -> list:
     valid_profiles = []
     for profile in ("Full", "DL", "EL", "QL", "RL"):
         plugin.log.info(f"Validating {profile} profile.")
-        cmd = f"validate-profile --profile {profile} --input {ontology_location}"
+        cmd = f"merge --input {ontology_location} validate-profile --profile {profile}"
         response = robot(cmd, plugin.max_ram_percentage)
         if response.stdout.endswith(b"[Ontology and imports closure in profile]\n\n"):
             valid_profiles.append(profile)

diff --git a/poetry.lock b/poetry.lock
diff --git a/tests/test_reason.py b/tests/test_reason.py
@@ -20,9 +20,13 @@
 
 UID = "e02aaed014c94e0c91bf960fed127750"
 REASON_DATA_GRAPH_IRI = f"https://ns.eccenca.com/reasoning/{UID}/data/"
-REASON_ONTOLOGY_GRAPH_IRI = f"https://ns.eccenca.com/reasoning/{UID}/vocab/"
+REASON_ONTOLOGY_GRAPH_IRI_1 = f"https://ns.eccenca.com/reasoning/{UID}/vocab/"
+REASON_ONTOLOGY_GRAPH_IRI_2 = f"https://ns.eccenca.com/reasoning/{UID}/vocab2/"
+REASON_ONTOLOGY_GRAPH_IRI_3 = f"https://ns.eccenca.com/reasoning/{UID}/vocab3/"
 REASON_RESULT_GRAPH_IRI = f"https://ns.eccenca.com/reasoning/{UID}/result/"
-VALIDATE_ONTOLOGY_GRAPH_IRI = f"https://ns.eccenca.com/validateontology/{UID}/vocab/"
+VALIDATE_ONTOLOGY_GRAPH_IRI_1 = f"https://ns.eccenca.com/validateontology/{UID}/vocab/"
+VALIDATE_ONTOLOGY_GRAPH_IRI_2 = f"https://ns.eccenca.com/validateontology/{UID}/vocab2/"
+VALIDATE_ONTOLOGY_GRAPH_IRI_3 = f"https://ns.eccenca.com/validateontology/{UID}/vocab3/"
 OUTPUT_GRAPH_IRI = f"https://ns.eccenca.com/validateontology/{UID}/output/"
 MD_FILENAME = f"{UID}.md"
 PROJECT_ID = f"validate_plugin_test_project_{UID}"
@@ -37,31 +41,39 @@ def get_value_dict(entities: Entities) -> dict:
     return value_dict
 
 
+def import_graph(iri: str, filename: str) -> None:
+    """Import graph to CMEM"""
+    res = post(iri, Path(__path__[0]) / filename, replace=True)
+    if res.status_code != 204:  # noqa: PLR2004
+        raise ValueError(f"Response {res.status_code}: {res.url}")
+
+
 @pytest.fixture()
 def _setup(request: pytest.FixtureRequest) -> None:
     """Set up"""
-    res = post(REASON_DATA_GRAPH_IRI, Path(__path__[0]) / "dataset_owl.ttl", replace=True)
-    if res.status_code != 204:  # noqa: PLR2004
-        raise ValueError(f"Response {res.status_code}: {res.url}")
-    res = post(REASON_ONTOLOGY_GRAPH_IRI, Path(__path__[0]) / "vocab.ttl", replace=True)
-    if res.status_code != 204:  # noqa: PLR2004
-        raise ValueError(f"Response {res.status_code}: {res.url}")
+    import_graph(REASON_DATA_GRAPH_IRI, "dataset_owl.ttl")
+    import_graph(REASON_ONTOLOGY_GRAPH_IRI_1, "test_reason_ontology_1.ttl")
+    import_graph(REASON_ONTOLOGY_GRAPH_IRI_2, "test_reason_ontology_2.ttl")
+    import_graph(REASON_ONTOLOGY_GRAPH_IRI_3, "test_reason_ontology_3.ttl")
 
     with suppress(Exception):
         delete_project(PROJECT_ID)
     make_new_project(PROJECT_ID)
-    res = post(
-        VALIDATE_ONTOLOGY_GRAPH_IRI, Path(__path__[0]) / "test_validate_ontology.ttl", replace=True
-    )
-    if res.status_code != 204:  # noqa: PLR2004
-        raise ValueError(f"Response {res.status_code}: {res.url}")
+
+    import_graph(VALIDATE_ONTOLOGY_GRAPH_IRI_1, "test_validate_ontology_1.ttl")
+    import_graph(VALIDATE_ONTOLOGY_GRAPH_IRI_2, "test_validate_ontology_2.ttl")
+    import_graph(VALIDATE_ONTOLOGY_GRAPH_IRI_3, "test_validate_ontology_3.ttl")
 
     request.addfinalizer(lambda: delete(REASON_DATA_GRAPH_IRI))
-    request.addfinalizer(lambda: delete(REASON_ONTOLOGY_GRAPH_IRI))
+    request.addfinalizer(lambda: delete(REASON_ONTOLOGY_GRAPH_IRI_1))
+    request.addfinalizer(lambda: delete(REASON_ONTOLOGY_GRAPH_IRI_2))
+    request.addfinalizer(lambda: delete(REASON_ONTOLOGY_GRAPH_IRI_3))
     request.addfinalizer(lambda: delete(REASON_RESULT_GRAPH_IRI))
     request.addfinalizer(lambda: delete_project(PROJECT_ID))
     request.addfinalizer(lambda: delete(OUTPUT_GRAPH_IRI))
-    request.addfinalizer(lambda: delete(VALIDATE_ONTOLOGY_GRAPH_IRI))  # noqa: PT021
+    request.addfinalizer(lambda: delete(VALIDATE_ONTOLOGY_GRAPH_IRI_1))
+    request.addfinalizer(lambda: delete(VALIDATE_ONTOLOGY_GRAPH_IRI_2))
+    request.addfinalizer(lambda: delete(VALIDATE_ONTOLOGY_GRAPH_IRI_3))  # noqa: PT021
 
 
 @needs_cmem
@@ -81,7 +93,7 @@ def get_remote_graph(iri: str) -> Graph:
     def test_reasoner(reasoner: str, err_list: list) -> list:
         ReasonPlugin(
             data_graph_iri=REASON_DATA_GRAPH_IRI,
-            ontology_graph_iri=REASON_ONTOLOGY_GRAPH_IRI,
+            ontology_graph_iri=REASON_ONTOLOGY_GRAPH_IRI_1,
             output_graph_iri=REASON_RESULT_GRAPH_IRI,
             reasoner=reasoner,
             sub_class=False,
@@ -99,7 +111,7 @@ def test_reasoner(reasoner: str, err_list: list) -> list:
 
     def test_validate(errors: str) -> str:
         result = ValidatePlugin(
-            ontology_graph_iri=VALIDATE_ONTOLOGY_GRAPH_IRI,
+            ontology_graph_iri=VALIDATE_ONTOLOGY_GRAPH_IRI_1,
             output_graph_iri=OUTPUT_GRAPH_IRI,
             reasoner="elk",
             validate_profile=True,
@@ -116,7 +128,7 @@ def test_validate(errors: str) -> str:
 
         if value_dict["markdown"] != md_test:
             val_errors += 'EntityPath "markdown" output error. '
-        if value_dict["ontology_graph_iri"] != VALIDATE_ONTOLOGY_GRAPH_IRI:
+        if value_dict["ontology_graph_iri"] != VALIDATE_ONTOLOGY_GRAPH_IRI_1:
             val_errors += 'EntityPath "ontology_graph_iri" output error. '
         if value_dict["reasoner"] != "elk":
             val_errors += 'EntityPath "reasoner" output error. '

diff --git a/tests/vocab.ttl → tests/test_reason_ontology_1.ttl b/tests/vocab.ttl → tests/test_reason_ontology_1.ttl
@@ -9,7 +9,8 @@
 <https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/vocab/> rdf:type owl:Ontology ;
                                                    rdfs:comment "Vocabulary for a reasoning use case"@en ;
                                                    rdfs:label "Eccenca Reasoning Vocabulary"@en ;
-                                                   rdfs:seeAlso <http://owl.man.ac.uk/2006/07/sssw/people> .
+                                                   rdfs:seeAlso <http://owl.man.ac.uk/2006/07/sssw/people> ;
+                                                   owl:imports <https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/vocab2/> .
 
 #################################################################
 #    Object Properties
@@ -141,16 +142,6 @@ owl:Thing rdf:type owl:Class .
        rdfs:label "adult"^^xsd:string .
 
 
-###  https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/vocab/animal
-:animal rdf:type owl:Class ;
-        rdfs:subClassOf [ rdf:type owl:Restriction ;
-                          owl:onProperty :eats ;
-                          owl:someValuesFrom owl:Thing
-                        ] ;
-        rdfs:comment ""^^xsd:string ;
-        rdfs:isDefinedBy <https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/vocab/> ;
-        rdfs:label "animal"^^xsd:string .
-
 
 ###  https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/vocab/animal_lover
 :animal_lover rdf:type owl:Class ;
@@ -261,19 +252,6 @@ owl:Thing rdf:type owl:Class .
            rdfs:label "cat liker"^^xsd:string .
 
 
-###  https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/vocab/cat_owner
-:cat_owner rdf:type owl:Class ;
-           owl:equivalentClass [ owl:intersectionOf ( :person
-                                                      [ rdf:type owl:Restriction ;
-                                                        owl:onProperty :has_pet ;
-                                                        owl:someValuesFrom :cat
-                                                      ]
-                                                    ) ;
-                                 rdf:type owl:Class
-                               ] ;
-           rdfs:comment ""^^xsd:string ;
-           rdfs:isDefinedBy <https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/vocab/> ;
-           rdfs:label "cat owner"^^xsd:string .
 
 
 ###  https://ns.eccenca.com/reasoning/e02aaed014c94e0c91bf960fed127750/vocab/company