Adresses #3215 NTRs ureter #2891
Workflow file for this run
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# Basic ODK workflow | |
name: CI | |
# Controls when the action will run. | |
on: | |
# Triggers the workflow on push or pull request events but only for the master branch | |
push: | |
branches: [ master ] | |
paths: | |
- 'src/**' | |
pull_request: | |
branches: [ master ] | |
paths: | |
- 'src/**' | |
# 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@v3 | |
- name: Run ontology QC checks | |
id: check | |
continue-on-error: true | |
env: | |
DEFAULT_BRANCH: master | |
ROBOT_JAVA_ARGS: -Xmx6G | |
run: cd src/ontology && mkdir -p tmp reports mirror && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' GH_ACTION=true BRI=true MIR=false IMP=false test > TESTLOG.log | |
- name: Reason over taxon constraints | |
id: explaintc | |
continue-on-error: true | |
if: steps.check.outcome == 'failure' | |
run: | | |
if [ -s src/ontology/reports/taxon-constraint-check.txt ]; then | |
robot explain -i src/ontology/tmp/uberon-edit-plus-tax-equivs.owl -M unsatisfiability -u all -r ELK -e taxon-unsats.md | |
echo "<details>\n<summary>This PR violates some taxon constraints. Here is what the reasoner has to say:</summary>\n" > comment.md | |
cat taxon-unsats.md >> comment.md | |
echo "</details>" >> comment.md | |
exit 1 | |
fi | |
- name: Post explanation for taxon constraint violations | |
if: steps.explaintc.outcome == 'failure' | |
uses: NejcZdovc/comment-pr@v2 | |
with: | |
github_token: ${{secrets.GITHUB_TOKEN}} | |
file: "../../comment.md" | |
identifier: "TAXON_CONSTRAINTS_REASONING" | |
- name: Last rows of QC report | |
if: steps.check.outcome == 'failure' | |
run: | | |
tail -20 src/ontology/TESTLOG.log | |
exit 1 |