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jmillanacostajmillanacosta
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Refactor into matrix for concurrent run
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‎.github/workflows/build.yml‎

Lines changed: 57 additions & 141 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
name: Build slims
1+
name: Build slims (Matrix)
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on:
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workflow_dispatch:
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pull_request:
@@ -18,17 +18,21 @@ on:
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schedule:
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- cron: 1 0 1 1-12 *
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jobs:
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build:
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setup:
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runs-on: ubuntu-latest
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outputs:
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slimmer: ${{ steps.config.outputs.slimmer }}
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robot: ${{ steps.config.outputs.robot }}
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robot_jar: ${{ steps.config.outputs.robot_jar }}
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steps:
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- name: Check out repository
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uses: actions/checkout@v3
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with:
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token: ${{ secrets.PAT }}
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token: ${{ secrets.PAT }}
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- name: Convert slimmer config to ROBOT term files
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run: bash scripts/build-workflow/slimmer2robot.sh
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# Get slimmer and robot
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- name: add slimmer and robot URLs to environment
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- name: Extract config values
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id: config
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run: |
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echo $(java --version)
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config_file="config.yaml"
@@ -54,142 +58,55 @@ jobs:
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echo SLIMMER: $slimmer
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echo ROBOT JAR: $robot_jar
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echo ROBOT WRAPPER: $robot
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echo 'slimmer='${slimmer}'' >> $GITHUB_ENV
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echo 'robot='${robot}'' >> $GITHUB_ENV
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echo 'robot_jar='${robot_jar}'' >> $GITHUB_ENV
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echo "slimmer=${slimmer}" >> $GITHUB_OUTPUT
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echo "robot=${robot}" >> $GITHUB_OUTPUT
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echo "robot_jar=${robot_jar}" >> $GITHUB_OUTPUT
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- name: Authorize running build scripts
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run: chmod 755 scripts/build-workflow/*.sh
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build:
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needs: setup
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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ontology: [aopo, bao, bfo, bto, ccont, cheminf, chebi, chmo, clo, efo, envo, fabio, go, iao, ncit, npo, oae, obcs, obi, pato, sio, uberon, uo, msio]
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steps:
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- name: Check out repository
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uses: actions/checkout@v3
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with:
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token: ${{ secrets.PAT }}
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- name: get slimmer
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run: wget ${{ env.slimmer }}
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run: wget ${{ needs.setup.outputs.slimmer }}
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- name: get robot
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run: |
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wget ${{ env.robot }}
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wget ${{ env.robot_jar}}
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# build all ontologies
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# Authorize running build script
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- name: authorize running build scripts
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run: chmod 755 scripts/build-workflow/*.sh
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# build aopo
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- name: build-aopo
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if: always()
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run: bash scripts/build-workflow/build.sh aopo
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# build bao
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- name: build-bao
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if: always()
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run: bash scripts/build-workflow/build.sh bao
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# build bfo
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- name: build-bfo
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if: always()
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run: bash scripts/build-workflow/build.sh bfo
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# build bto
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- name: build-bto
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if: always()
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run: bash scripts/build-workflow/build.sh bto
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# build ccont
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- name: build-ccont
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if: always()
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run: bash scripts/build-workflow/build.sh ccont
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# build cheminf
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- name: build-cheminf
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if: always()
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run: bash scripts/build-workflow/build.sh cheminf
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# build chebi
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- name: build-chebi
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if: always()
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run: bash scripts/build-workflow/build.sh chebi
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# build chmo
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- name: build-chmo
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if: always()
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run: bash scripts/build-workflow/build.sh chmo
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# build clo
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- name: build-clo
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if: always()
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run: bash scripts/build-workflow/build.sh clo
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# build efo
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- name: build-efo
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if: always()
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run: bash scripts/build-workflow/build.sh efo
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# build envo
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- name: build-envo
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if: always()
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run: bash scripts/build-workflow/build.sh envo
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# build fabio
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- name: build-fabio
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if: always()
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run: bash scripts/build-workflow/build.sh fabio
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# build go
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- name: build-go
134-
if: always()
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run: bash scripts/build-workflow/build.sh go
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# build iao
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- name: build-iao
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if: always()
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run: bash scripts/build-workflow/build.sh iao
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# build ncit
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- name: build-ncit
144-
if: always()
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run: bash scripts/build-workflow/build.sh ncit
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# build npo
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- name: build-npo
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if: always()
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run: bash scripts/build-workflow/build.sh npo
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# build oae
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- name: build-oae
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if: always()
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run: bash scripts/build-workflow/build.sh oae
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# build obcs
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- name: build-obcs
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if: always()
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run: bash scripts/build-workflow/build.sh obcs
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# build obi
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- name: build-obi
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if: always()
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run: bash scripts/build-workflow/build.sh obi
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# build pato
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- name: build-pato
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if: always()
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run: bash scripts/build-workflow/build.sh pato
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# build sio
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- name: build-sio
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if: always()
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run: bash scripts/build-workflow/build.sh sio
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# build uberon
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- name: build-uberon
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if: always()
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run: bash scripts/build-workflow/build.sh uberon
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# build uo
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- name: build-uo
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if: always()
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run: bash scripts/build-workflow/build.sh uo
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# build msio
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- name: build-msio
189-
if: always()
190-
run: bash scripts/build-workflow/build.sh msio
83+
wget ${{ needs.setup.outputs.robot }}
84+
wget ${{ needs.setup.outputs.robot_jar }}
85+
- name: build-${{ matrix.ontology }}
86+
run: bash scripts/build-workflow/build.sh ${{ matrix.ontology }}
87+
- name: Upload built ontology
88+
uses: actions/upload-artifact@v3
89+
with:
90+
name: ${{ matrix.ontology }}-owl
91+
path: external-dev/${{ matrix.ontology }}.owl
92+
retention-days: 1
19193

192-
# Commit and push
94+
commit:
95+
needs: [setup, build]
96+
runs-on: ubuntu-latest
97+
steps:
98+
- name: Check out repository
99+
uses: actions/checkout@v3
100+
with:
101+
token: ${{ secrets.PAT }}
102+
- name: Download all built ontologies
103+
uses: actions/download-artifact@v3
104+
with:
105+
path: artifacts
106+
- name: Move artifacts to external-dev
107+
run: |
108+
mkdir -p external-dev
109+
find artifacts -name "*.owl" -exec cp {} external-dev/ \;
193110
- name: Commit OWL files
194111
run: |
195112
if [[ "${{ github.ref_name }}" == *"merge"* ]]; then
@@ -204,14 +121,13 @@ jobs:
204121
if git diff-index --quiet HEAD --; then
205122
echo "No changes to commit."
206123
else
207-
git commit -m "Actions - build updated" ./external-dev/*.owl || true
208-
fi
124+
git commit -m "Actions - build updated" ./external-dev/*.owl || true
125+
fi
209126
# Check if there are changes to push
210127
if [[ $(git rev-parse --abbrev-ref HEAD) == "${{ github.ref_name }}" ]]; then
211128
if [ -n "$(git cherry -v)" ]; then
212129
git push || echo "Push failed."
213130
else
214131
echo "No changes to push."
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fi
216-
fi
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133+
fi

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