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Merge pull request #276 from OBOFoundry/run-qc-weekly
Set Integration Testing to Run Monthly
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Diff for: ‎.github/workflows/qc-compliance.yml

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# Basic ODK workflow
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name: QC COB Compliance suite
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on:
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# Runs once per month
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schedule:
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- cron: "0 0 1 * *"
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# Allows you to run this workflow manually from the Actions tab
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workflow_dispatch:
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# A workflow run is made up of one or more jobs that can run sequentially or in parallel
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jobs:
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# This workflow contains a single job called "ontology_qc"
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ontology_qc:
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# The type of runner that the job will run on
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runs-on: ubuntu-latest
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container: obolibrary/odkfull:v1.5.2
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# Steps represent a sequence of tasks that will be executed as part of the job
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steps:
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# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
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- uses: actions/checkout@v2
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- name: Run COB Integration test suite
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env:
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DEFAULT_BRANCH: master
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run: cd src/ontology && mkdir -p reports tmp && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' cob_test IMP=false PAT=false -B
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- name: Read and crop the contents of SUMMARY.txt
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id: read_summary
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run: |
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summary_content=$(cat products/SUMMARY.txt)
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max_length=65500 # Slightly less than the max limit to account for metadata or other content
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if [ ${#summary_content} -gt $max_length ]; then
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summary_content="${summary_content:0:$max_length}"
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summary_content="${summary_content}\n\n...Content cropped due to length limits."
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fi
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# Wrap the content in a collapsible details block
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wrapped_content="<details><summary>Latest integration report</summary>\n\n${summary_content}\n\n</details>"
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echo "::set-output name=summary::${wrapped_content}"
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shell: bash
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- name: Post summary to the issue
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run: gh issue comment 278 --body "$SUMMARY_CONTENT"
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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SUMMARY_CONTENT: ${{ steps.read_summary.outputs.summary }}
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Diff for: ‎.gitignore

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

Diff for: ‎src/ontology/components/cob-annotations.owl

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

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xmlns:skos="http://www.w3.org/2004/02/skos/core#"
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xmlns:terms="http://purl.org/dc/terms/">
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<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/cob/cob-examples.owl">
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<owl:imports rdf:resource="http://purl.obolibrary.org/obo/cob/cob-edit.owl"/>
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</owl:Ontology>
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Diff for: ‎src/ontology/components/cob-to-external.owl

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