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Add bl chemical to disease #4

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Add bl chemical to disease #4

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e302d00
Update .gitignore
bill-baumgartner Sep 25, 2021
ebd57be
add bl_chemical_to_disease data from krista
bill-baumgartner Sep 25, 2021
3751e6b
Update bert-models-cicd.yaml
bill-baumgartner Sep 25, 2021
d04ccdb
Update bert-models-cicd.yaml
bill-baumgartner Sep 25, 2021
7a3b8cc
Update data.tsv
bill-baumgartner Sep 25, 2021
0a34241
bl_chemical_to_disease v0.3
bill-baumgartner Sep 25, 2021
432ab91
Update bert-models-cicd.yaml
bill-baumgartner Nov 17, 2021
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38 changes: 19 additions & 19 deletions .github/workflows/bert-models-cicd.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -57,36 +57,36 @@ jobs:
- uses: actions/checkout@v2
with:
fetch-depth: 0
- name: Get changed files
id: changed-files
uses: tj-actions/changed-files@v7
- name: List all modified files
run: |
for file in "${{ steps.changed-files.outputs.all_modified_files }}"; do
echo "$file was modified"
done
- name: Run step when a file changes
if: contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE)
run: |
echo "Your file ${{ env.DOCKERFILE }} has been modified."
# - name: Get changed files
# id: changed-files
# uses: tj-actions/changed-files@v7
# - name: List all modified files
# run: |
# for file in "${{ steps.changed-files.outputs.all_modified_files }}"; do
# echo "$file was modified"
# done
# - name: Run step when a file changes
# if: contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE)
# run: |
# echo "Your file ${{ env.DOCKERFILE }} has been modified."
- name: Set up Cloud SDK
if: contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE)
# if: contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE)
uses: google-github-actions/setup-gcloud@master
with:
project_id: ${{ secrets.GCE_PROJECT }}
service_account_key: ${{ secrets.GCE_SA_KEY }}
version: '290.0.1'
- name: Configure Docker Authentication
if: contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE)
# if: contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE)
run: gcloud --quiet auth configure-docker
- name: Set MODEL_VERSION env
if: contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE)
# if: contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE)
run: echo "MODEL_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV
- name: Build Docker Image
if: contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE)
# if: contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE)
run: docker build --tag "gcr.io/$PROJECT_ID/$IMAGE_NAME:$MODEL_VERSION" -f ${{ env.DOCKERFILE }} .
- name: Publish Docker Image to Google Container Registry
if: contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE)
# if: contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE)
run: docker push "gcr.io/$PROJECT_ID/$IMAGE_NAME:$MODEL_VERSION"

# ----------------------------------------------------------------------------------- #
Expand Down Expand Up @@ -216,7 +216,7 @@ jobs:
contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE)
run: |
sh -c ".github/workflows/monitor-ai-platform-job.sh ${{ env.AI_PLATFORM_JOB_NAME }}"
timeout-minutes: 180
timeout-minutes: 1800

# -------------------------------------------------------------------------------------- #
# BUILD/PUSH BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE CLASSIFICATION CONTAINER IMAGE #
Expand All @@ -234,7 +234,7 @@ jobs:
ENTRYPOINT_FILE: scripts/predict.entrypoint.sh
BASE_DOCKERFILE: base.Dockerfile
MODEL_VERSION_KEY: BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE
CLASSIFICATION_LABELS: "treats false"
CLASSIFICATION_LABELS: "treats contributes_to false"
DATA_FILE: data/bl_chemical_to_disease_or_phenotypic_feature/data.tsv
steps:
- uses: actions/checkout@v2
Expand Down
1 change: 1 addition & 0 deletions .gitignore
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@@ -1,3 +1,4 @@
code/
.DS_Store
cloudbuild*.yaml
test.Dockerfile
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4 changes: 2 additions & 2 deletions MODEL_VERSIONS
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
BASE=0.1
BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE=0.1
BASE=0.3
BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE=0.3
BL_CHEMICAL_TO_GENE=0.1
BL_DISEASE_TO_PHENOTYPIC_FEATURE=0.1
BL_GENE_REGULATORY_RELATIONSHIP=0.1
Expand Down
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