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Add distinct action that runs integration tests once per month.
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Fixing an important issue in compliance suite (removing weird import in "examples" file)
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matentzn committed Aug 20, 2024
1 parent 966b957 commit 45bf899
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52 changes: 52 additions & 0 deletions .github/workflows/qc-compliance.yml
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# 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 }}

2 changes: 0 additions & 2 deletions .github/workflows/qc.yml
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Expand Up @@ -9,8 +9,6 @@ on:
branches: [ master ]
pull_request:
branches: [ master ]
schedule:
- cron: "0 0 1 * *"

# Allows you to run this workflow manually from the Actions tab
workflow_dispatch:
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2 changes: 2 additions & 0 deletions .gitignore
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Expand Up @@ -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
5 changes: 2 additions & 3 deletions src/ontology/components/cob-annotations.owl
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Expand Up @@ -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>


Expand Down Expand Up @@ -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">
Expand Down Expand Up @@ -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 -->

1 change: 0 additions & 1 deletion src/ontology/components/cob-examples.owl
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Expand Up @@ -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>


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44 changes: 25 additions & 19 deletions src/ontology/components/cob-to-external.owl
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Expand Up @@ -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>

Expand Down Expand Up @@ -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">
Expand Down Expand Up @@ -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"/>
Expand Down Expand Up @@ -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">
Expand Down Expand Up @@ -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 -->

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