SHACL testing (#13)

* Basic setup for testing SHACL. * Basic SHACL test. * Explicitly typed every Node as obo:CDAO_0000140. * Command line options to check for version number and help. * Python script that invokes Java program for testing. * Install Java 8 and use Maven in Travis for CI testing * For now, need to compile uber-JAR locally, then upload it for testing. See #14.
phyloref · Nov 22, 2016 · 5349dc7 · 5349dc7
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diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,9 @@
+# Mac files
+.DS_Store
+
+# IDE files
+.project
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

diff --git a/.travis.yml b/.travis.yml
@@ -1,13 +1,19 @@
+# Our primary language is Python.
 language: python
 python:
   - "2.7"
-# command to install dependencies
-#
-# unfortunately needs to be custom because updating setuptools from within
-# requirements.txt fails to be seen by the html5lib installation, and the
-# version pre-installed on Travis is too low.
+
+# We need Java 8 for SHACL testing.
+addons:
+  apt:
+    packages:
+      - oracle-java8-set-default
+
+# Install pip requirements.
 install: 
-  - "pip install -U setuptools"
-  - "pip install -r requirements.txt"
-# command to run tests
+  - pip install --upgrade pip
+  - pip install -r requirements.txt
+  - pip install pytest
+
+# Run the py.test suite.
 script: py.test tests
diff --git a/examples/trees/pg_2357.owl b/examples/trees/pg_2357.owl
@@ -62,6 +62,7 @@
 
     <owl:Thing rdf:about="&pg_2357;Node_1">
         <rdf:type rdf:resource="&owl;NamedIndividual"/>
+        <rdf:type rdf:resource="&obo;CDAO_0000140" />
         <obo:CDAO_0000149 rdf:resource="&pg_2357;Node_2"/>
         <obo:CDAO_0000149 rdf:resource="&pg_2357;Alobevania_gattiae"/>
         <obo:CDAO_0000149 rdf:resource="&pg_2357;Decevania_reticulata"/>
@@ -71,6 +72,7 @@
 
     <owl:Thing rdf:about="&pg_2357;Node_2">
         <rdf:type rdf:resource="&owl;NamedIndividual"/>
+        <rdf:type rdf:resource="&obo;CDAO_0000140" />
         <obo:CDAO_0000149 rdf:resource="&pg_2357;Node_3"/>
         <obo:CDAO_0000149 rdf:resource="&pg_2357;Rothevania_valdivianus"/>
         <obo:CDAO_0000149 rdf:resource="&pg_2357;Hyptia_thoracica"/>
@@ -82,6 +84,7 @@
 
     <owl:Thing rdf:about="&pg_2357;Node_3">
         <rdf:type rdf:resource="&owl;NamedIndividual"/>
+        <rdf:type rdf:resource="&obo;CDAO_0000140" />
         <obo:CDAO_0000149 rdf:resource="&pg_2357;Node_4"/>
         <obo:CDAO_0000149 rdf:resource="&pg_2357;Node_7"/>
         <phyloref:has_Sibling rdf:resource="&pg_2357;Rothevania_valdivianus"/>
@@ -92,6 +95,7 @@
 
     <owl:Thing rdf:about="&pg_2357;Node_4">
         <rdf:type rdf:resource="&owl;NamedIndividual"/>
+        <rdf:type rdf:resource="&obo;CDAO_0000140" />
         <obo:CDAO_0000149 rdf:resource="&pg_2357;Node_5"/>
         <obo:CDAO_0000149 rdf:resource="&pg_2357;Evaniscus_lansdownei"/>
         <phyloref:has_Sibling rdf:resource="&pg_2357;Node_7"/>
@@ -101,6 +105,7 @@
 
     <owl:Thing rdf:about="&pg_2357;Node_5">
         <rdf:type rdf:resource="&owl;NamedIndividual"/>
+        <rdf:type rdf:resource="&obo;CDAO_0000140" />
         <obo:CDAO_0000149 rdf:resource="&pg_2357;Node_6"/>
         <obo:CDAO_0000149 rdf:resource="&pg_2357;Evaniscus_marginatus"/>
         <phyloref:has_Sibling rdf:resource="&pg_2357;Evaniscus_lansdownei"/>
@@ -110,6 +115,7 @@
 
     <owl:Thing rdf:about="&pg_2357;Node_6">
         <rdf:type rdf:resource="&owl;NamedIndividual"/>
+        <rdf:type rdf:resource="&obo;CDAO_0000140" />
         <obo:CDAO_0000149 rdf:resource="&pg_2357;Evaniscus_rufithorax"/>
         <obo:CDAO_0000149 rdf:resource="&pg_2357;Evaniscus_sulcigenis"/>
         <phyloref:has_Sibling rdf:resource="&pg_2357;Evaniscus_marginatus"/>
@@ -119,34 +125,39 @@
 
     <owl:Thing rdf:about="&pg_2357;Evaniscus_rufithorax">
         <rdf:type rdf:resource="&owl;NamedIndividual"/>
+        <rdf:type rdf:resource="&obo;CDAO_0000140" />
         <phyloref:has_Sibling rdf:resource="&pg_2357;Evaniscus_sulcigenis"/>
     </owl:Thing>
 
     <!-- http://phyloinformatics.net/phylo/pg_2357#Evaniscus_sulcigenis -->
 
     <owl:Thing rdf:about="&pg_2357;Evaniscus_sulcigenis">
         <rdf:type rdf:resource="&owl;NamedIndividual"/>
+        <rdf:type rdf:resource="&obo;CDAO_0000140" />
         <phyloref:has_Sibling rdf:resource="&pg_2357;Evaniscus_rufithorax"/>
     </owl:Thing>
 
     <!-- http://phyloinformatics.net/phylo/pg_2357#Evaniscus_marginatus -->
 
     <owl:Thing rdf:about="&pg_2357;Evaniscus_marginatus">
         <rdf:type rdf:resource="&owl;NamedIndividual"/>
+        <rdf:type rdf:resource="&obo;CDAO_0000140" />
         <phyloref:has_Sibling rdf:resource="&pg_2357;Node_6"/>
     </owl:Thing>
 
     <!-- http://phyloinformatics.net/phylo/pg_2357#Evaniscus_lansdownei -->
 
     <owl:Thing rdf:about="&pg_2357;Evaniscus_lansdownei">
         <rdf:type rdf:resource="&owl;NamedIndividual"/>
+        <rdf:type rdf:resource="&obo;CDAO_0000140" />
         <phyloref:has_Sibling rdf:resource="&pg_2357;Node_5"/>
     </owl:Thing>
 
     <!-- http://phyloinformatics.net/phylo/pg_2357#Node_7 -->
 
     <owl:Thing rdf:about="&pg_2357;Node_7">
         <rdf:type rdf:resource="&owl;NamedIndividual"/>
+        <rdf:type rdf:resource="&obo;CDAO_0000140" />
         <obo:CDAO_0000149 rdf:resource="&pg_2357;Evaniscus_tibialis"/>
         <obo:CDAO_0000149 rdf:resource="&pg_2357;Evaniscus_rafaeli"/>
         <phyloref:has_Sibling rdf:resource="&pg_2357;Node_4"/>
@@ -156,20 +167,23 @@
 
     <owl:Thing rdf:about="&pg_2357;Evaniscus_tibialis">
         <rdf:type rdf:resource="&owl;NamedIndividual"/>
+        <rdf:type rdf:resource="&obo;CDAO_0000140" />
         <phyloref:has_Sibling rdf:resource="&pg_2357;Evaniscus_rafaeli"/>
     </owl:Thing>
 
     <!-- http://phyloinformatics.net/phylo/pg_2357#Evaniscus_rafaeli -->
 
     <owl:Thing rdf:about="&pg_2357;Evaniscus_rafaeli">
         <rdf:type rdf:resource="&owl;NamedIndividual"/>
+        <rdf:type rdf:resource="&obo;CDAO_0000140" />
         <phyloref:has_Sibling rdf:resource="&pg_2357;Evaniscus_tibialis"/>
     </owl:Thing>
 
     <!-- http://phyloinformatics.net/phylo/pg_2357#Rothevania_valdivianus -->
 
     <owl:Thing rdf:about="&pg_2357;Rothevania_valdivianus">
         <rdf:type rdf:resource="&owl;NamedIndividual"/>
+        <rdf:type rdf:resource="&obo;CDAO_0000140" />
         <phyloref:has_Sibling rdf:resource="&pg_2357;Node_3"/>
         <phyloref:has_Sibling rdf:resource="&pg_2357;Hyptia_thoracica"/>
     </owl:Thing>
@@ -178,6 +192,7 @@
 
     <owl:Thing rdf:about="&pg_2357;Hyptia_thoracica">
         <rdf:type rdf:resource="&owl;NamedIndividual"/>
+        <rdf:type rdf:resource="&obo;CDAO_0000140" />
         <phyloref:has_Sibling rdf:resource="&pg_2357;Node_3"/>
         <phyloref:has_Sibling rdf:resource="&pg_2357;Rothevania_valdivianus"/>
     </owl:Thing>
@@ -186,6 +201,7 @@
 
     <owl:Thing rdf:about="&pg_2357;Alobevania_gattiae">
         <rdf:type rdf:resource="&owl;NamedIndividual"/>
+        <rdf:type rdf:resource="&obo;CDAO_0000140" />
         <phyloref:has_Sibling rdf:resource="&pg_2357;Node_2"/>
         <phyloref:has_Sibling rdf:resource="&pg_2357;Decevania_reticulata"/>
     </owl:Thing>
@@ -194,6 +210,7 @@
 
     <owl:Thing rdf:about="&pg_2357;Decevania_reticulata">
         <rdf:type rdf:resource="&owl;NamedIndividual"/>
+        <rdf:type rdf:resource="&obo;CDAO_0000140" />
         <phyloref:has_Sibling rdf:resource="&pg_2357;Node_2"/>
         <phyloref:has_Sibling rdf:resource="&pg_2357;Alobevania_gattiae"/>
     </owl:Thing>

diff --git a/templates/individual.txt b/templates/individual.txt
@@ -2,6 +2,7 @@
 
     <owl:Thing rdf:about="&{{name}};{{term}}">
         <rdf:type rdf:resource="&owl;NamedIndividual"/>
+        <rdf:type rdf:resource="&obo;CDAO_0000140" />
         {{#children}}
         <obo:CDAO_0000149 rdf:resource="&{{name}};{{child}}"/>
         {{/children}}

diff --git a/tests/ValidationShapes.ttl b/tests/ValidationShapes.ttl
@@ -0,0 +1,37 @@
+@prefix ex: <http://phyloref.org/example/test_shacl.ttl#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix sh: <http://www.w3.org/ns/shacl#> .
+@prefix obo: <http://purl.obolibrary.org/obo/> .
+@prefix phyloref: <http://phyloinformatics.net/phyloref.owl#> .
+@prefix dash: <http://datashapes.org/dash#> .
+@prefix rdf: <http://www.w3.org/2002/07/owl#> .
+
+#
+# ex:Node 
+# A node in a phylogeny.
+#
+
+ex:Node a sh:Shape;
+    # Matches all nodes.
+    sh:targetClass obo:CDAO_0000140;
+
+    # Every node must either have:
+    sh:or (
+        [
+            # 1. A CDAO:hasChild relationship with another node.
+            sh:property [
+                sh:predicate obo:CDAO_0000149;
+                sh:class obo:CDAO_0000140;
+                sh:minCount 1;
+            ];
+        ]
+        [
+            # 2. A phyloref:has_Sibling relationship with another node.
+            sh:property [
+                sh:predicate phyloref:has_Sibling;
+                sh:class obo:CDAO_0000140;
+                sh:minCount 1;
+            ];
+        ]
+    );
+.