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Merge branch 'master' into 1466-add-periphytic-biofilm-subclass-of-bi…
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…ofilm-with-subclasses-of-its-own
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@cmungall
cmungall authored Dec 8, 2023
2 parents edc5660 + 110c73c commit 1914f4c
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37 changes: 31 additions & 6 deletions .github/workflows/ontobot.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,9 +6,32 @@ on:
types: [ opened, edited ]

jobs:
check:
runs-on: ubuntu-latest
outputs:
phraseExists: ${{ steps.check-body.outputs.result }}
steps:
- name: Check if issue body contains 'Hey ontobot'
id: check-body
uses: actions/github-script@v6
with:
script: |
const issue = await github.rest.issues.get({
owner: context.repo.owner,
repo: context.repo.repo,
issue_number: context.issue.number
});
if (!issue.data.body) {
console.log('Issue body is empty or null');
return false;
}
return issue.data.body.toLowerCase().includes('hey ontobot');
build:
needs: check
if: needs.check.outputs.phraseExists == 'true'
runs-on: ${{ matrix.os }}
container: obolibrary/odkfull:v1.4.1
container: obolibrary/odkfull:v1.4.3
strategy:
matrix:
python-version: ["3.9"]
Expand Down Expand Up @@ -43,8 +66,11 @@ jobs:
echo "resource=src/envo/envo-edit.owl" >> $GITHUB_ENV
echo "branch-name=kgcl_automation_"${{ steps.gh-script-issue.outputs.result }} >> $GITHUB_ENV
- name: Get jar & create alias command.
run: wget https://github.com/gouttegd/kgcl-java/releases/download/kgcl-0.2.0/kgcl-robot-standalone-0.2.0.jar -O kgcl-robot.jar
- name: Get jar & enable plugin.
run: |
mkdir -p robot-plugins
wget https://github.com/gouttegd/kgcl-java/releases/download/kgcl-0.2.0/kgcl-robot-plugin-0.2.0.jar -O robot-plugins/kgcl.jar
echo "ROBOT_PLUGINS_DIRECTORY=$(pwd)/robot-plugins/" >> "$GITHUB_ENV"
- name: Install dependencies
run: |
Expand All @@ -56,11 +82,10 @@ jobs:
ochange process-issue ${{ env.resource }} \
-r ${{ steps.gh-script-repo.outputs.result }} \
-n ${{ steps.gh-script-issue.outputs.result }} \
-g ${{ secrets.GH_TOKEN }} \
-j kgcl-robot.jar
-g ${{ secrets.GH_TOKEN }}
- name: Clean-up
run: rm -f kgcl-robot.jar
run: rm -rf robot-plugins

- name: Create Pull Request
uses: peter-evans/create-pull-request@v5
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16 changes: 8 additions & 8 deletions src/envo/envo-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -4328,8 +4328,8 @@ Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000116>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000232>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000425>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0100001>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/OMO_0003004>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/envo#EnvO-Lite-GSC>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/envo#PLURAL>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/envo#disconnected_from>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/envo#disposition_slim>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/envo#environmental_hazards>))
Expand Down Expand Up @@ -4434,16 +4434,16 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000425> "exp

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0100001> "term replaced by")

# Annotation Property: <http://purl.obolibrary.org/obo/OMO_0003004> (plural form)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OMO_0003004> "plural form")
SubAnnotationPropertyOf(<http://purl.obolibrary.org/obo/OMO_0003004> <http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty>)

# Annotation Property: <http://purl.obolibrary.org/obo/envo#EnvO-Lite-GSC> (<http://purl.obolibrary.org/obo/envo#EnvO-Lite-GSC>)

AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/envo#EnvO-Lite-GSC> "EnvO-Lite-GSC")
SubAnnotationPropertyOf(<http://purl.obolibrary.org/obo/envo#EnvO-Lite-GSC> <http://www.geneontology.org/formats/oboInOwl#SubsetProperty>)

# Annotation Property: <http://purl.obolibrary.org/obo/envo#PLURAL> (plurals)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/envo#PLURAL> "plurals")
SubAnnotationPropertyOf(<http://purl.obolibrary.org/obo/envo#PLURAL> <http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty>)

# Annotation Property: <http://purl.obolibrary.org/obo/envo#disconnected_from> (disconnected_from)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <https://orcid.org/0000-0002-6601-2165>) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/envo#disconnected_from> "A is disconnected_from B if they have no parts in common.")
Expand Down Expand Up @@ -10869,7 +10869,7 @@ AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#has
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "USGS:SDTS") <http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym> <http://purl.obolibrary.org/obo/ENVO_00000413> "mount")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ENVO_00000413> "https://en.wikipedia.org/wiki/Pingo")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Pingo") <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_00000413> "hydrolaccolith")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasSynonymType> <http://purl.obolibrary.org/obo/envo#PLURAL>) <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_00000413> "pingos")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasSynonymType> <http://purl.obolibrary.org/obo/OMO_0003004>) <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_00000413> "pingos")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/ENVO_00000413> "bugor")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/ENVO_00000413> "bulginniakh")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/ENVO_00000413> "envoPolar")
Expand Down Expand Up @@ -21751,7 +21751,7 @@ SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01000278> ObjectSomeValuesFrom(<
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Ice_Lens") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_01000279> "An ice mass which is formed when moisture, diffused within soil or rock, accumulates and freezes in a localized zone, wedging soil or rock apart.")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#created_by> <http://purl.obolibrary.org/obo/ENVO_01000279> "ORCID:0000-0002-4366-3088")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#creation_date> <http://purl.obolibrary.org/obo/ENVO_01000279> "2013-10-13T12:20:34Z")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasSynonymType> <http://purl.obolibrary.org/obo/envo#PLURAL>) <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_01000279> "ice lenses")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasSynonymType> <http://purl.obolibrary.org/obo/OMO_0003004>) <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_01000279> "ice lenses")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/ENVO_01000279> "envoPolar")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_01000279> "ice lens")
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01000279> <http://purl.obolibrary.org/obo/ENVO_01001547>)
Expand Down

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