Set Integration Testing to Run Monthly

.github/workflows/qc-compliance.yml

@@ -0,0 +1,52 @@
+# Basic ODK workflow
+
+name: QC COB Compliance suite
+
+on:
+  # Runs once per month
+  schedule:
+    - cron: "0 0 1 * *"
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "ontology_qc"
+  ontology_qc:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+    container: obolibrary/odkfull:v1.5.2
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v2
+
+      - name: Run COB Integration test suite
+        env:
+          DEFAULT_BRANCH: master
+        run: cd src/ontology && mkdir -p reports tmp && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' cob_test IMP=false PAT=false -B
+
+      - name: Read and crop the contents of SUMMARY.txt
+        id: read_summary
+        run: |
+          summary_content=$(cat products/SUMMARY.txt)
+          max_length=65500  # Slightly less than the max limit to account for metadata or other content
+          if [ ${#summary_content} -gt $max_length ]; then
+            summary_content="${summary_content:0:$max_length}"
+            summary_content="${summary_content}\n\n...Content cropped due to length limits."
+          fi
+
+          # Wrap the content in a collapsible details block
+          wrapped_content="<details><summary>Latest integration report</summary>\n\n${summary_content}\n\n</details>"
+
+          echo "::set-output name=summary::${wrapped_content}"
+        shell: bash
+
+      - name: Post summary to the issue
+        run: gh issue comment <issue_number> --body "$SUMMARY_CONTENT"
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          SUMMARY_CONTENT: ${{ steps.read_summary.outputs.summary }}
+

.github/workflows/qc.yml

@@ -19,7 +19,7 @@ jobs:
   ontology_qc:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.4
+    container: obolibrary/odkfull:v1.5.2
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:

.gitignore

@@ -50,3 +50,5 @@ src/ontology/README-editors.md
 src/ontology/products/
 src/ontology/cob-native.owl
 src/ontology/cob.ttl
+src/ontology/cob-base-reasoned.owl
+src/ontology/cob-examples-reasoned.owl

src/ontology/components/cob-annotations.owl

@@ -9,7 +9,7 @@
      xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/cob/components/cob-annotations.owl">
-        <owl:versionInfo>2023-11-16</owl:versionInfo>
+        <owl:versionInfo>2024-08-20</owl:versionInfo>
     </owl:Ontology>
 
 
@@ -82,7 +82,6 @@
         <obo:COB_based_on>http://purl.obolibrary.org/obo/CARO_0001008</obo:COB_based_on>
     </rdf:Description>
     <rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000022">
-        <obo:COB_based_on>http://purl.obolibrary.org/obo/CARO_0001010</obo:COB_based_on>
         <obo:COB_based_on>http://purl.obolibrary.org/obo/OBI_0100026</obo:COB_based_on>
     </rdf:Description>
     <rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000025">
@@ -214,5 +213,5 @@
 
 
 
-<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->
+<!-- Generated by the OWL API (version 4.5.29) https://github.com/owlcs/owlapi -->
 

src/ontology/components/cob-examples.owl

@@ -11,7 +11,6 @@
      xmlns:skos="http://www.w3.org/2004/02/skos/core#"
      xmlns:terms="http://purl.org/dc/terms/">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/cob/cob-examples.owl">
-        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/cob/cob-edit.owl"/>
     </owl:Ontology>
 
 

src/ontology/components/cob-to-external.owl

@@ -36,9 +36,9 @@
      xmlns:semapv="https://w3id.org/semapv/vocab/"
      xmlns:NCBITaxon="http://purl.obolibrary.org/obo/NCBITaxon_">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/cob/components/cob-to-external.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2024-03-22/components/cob-to-external.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2024-08-20/components/cob-to-external.owl"/>
         <dc1:license rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://creativecommons.org/publicdomain/zero/1.0/</dc1:license>
-        <owl:versionInfo>2024-03-22</owl:versionInfo>
+        <owl:versionInfo>2024-08-20</owl:versionInfo>
         <sssom:mapping_set_id rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://purl.obolibrary.org/obo/cob/components/cob-to-external.tsv</sssom:mapping_set_id>
     </owl:Ontology>
 
@@ -388,6 +388,22 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/COB_0000078 -->
+
+    <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/COB_0000078">
+        <owl:equivalentProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000059"/>
+    </owl:ObjectProperty>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/COB_0000078"/>
+        <owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#equivalentProperty"/>
+        <owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/RO_0000059"/>
+        <sssom:mapping_justification rdf:resource="https://w3id.org/semapv/vocab/ManualMappingCuration"/>
+        <sssom:object_label>concretizes</sssom:object_label>
+        <sssom:subject_label>concretizes</sssom:subject_label>
+    </owl:Axiom>
+
+
+
     <!-- http://purl.obolibrary.org/obo/COB_0000086 -->
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/COB_0000086">
@@ -502,6 +518,12 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/RO_0000059 -->
+
+    <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000059"/>
+
+
+
     <!-- http://purl.obolibrary.org/obo/RO_0002333 -->
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002333"/>
@@ -712,22 +734,6 @@
 
 
 
-    <!-- http://purl.obolibrary.org/obo/CARO_0001010 -->
-
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/CARO_0001010">
-        <owl:equivalentClass rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
-    </owl:Class>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/CARO_0001010"/>
-        <owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#equivalentClass"/>
-        <owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
-        <sssom:mapping_justification rdf:resource="https://w3id.org/semapv/vocab/ManualMappingCuration"/>
-        <sssom:object_label>organism or virus or viroid</sssom:object_label>
-        <sssom:subject_label>organism</sssom:subject_label>
-    </owl:Axiom>
-
-
-
     <!-- http://purl.obolibrary.org/obo/CARO_0010004 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/CARO_0010004">
@@ -2262,5 +2268,5 @@
 
 
 
-<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->
+<!-- Generated by the OWL API (version 4.5.29) https://github.com/owlcs/owlapi -->