Update bert-models-cicd.yaml

UCDenver-ccp · Feb 7, 2024 · 6956c1d · 6956c1d
1 parent 09cb503
commit 6956c1d
Showing 1 changed file with 92 additions and 92 deletions.
diff --git a/.github/workflows/bert-models-cicd.yaml b/.github/workflows/bert-models-cicd.yaml
@@ -343,95 +343,18 @@ jobs:
   # # # ----------------------------------------------------------------------------------- #
   # # # ----------------------------------------------------------------------------------- #
 
-  build_push_train-bl_chemical_to_disease_or_phenotypic_feature-train:
-    name: "build/push/train bl_chemical_to_disease_or_phenotypic_feature model"
-    # needs: "build_push-bert-base"
-    runs-on: ubuntu-latest
-    env:
-      TASK_NAME: bl_chemical_to_disease_or_phenotypic_feature
-      DOCKERFILE: train.Dockerfile
-      ENTRYPOINT_FILE: scripts/train.entrypoint.sh
-      BASE_DOCKERFILE: base.Dockerfile
-      DATA_FILE: data/bl_chemical_to_disease_or_phenotypic_feature/data.tsv
-      MODEL_VERSION_KEY: BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE
-      AI_PLATFORM_JOB_NAME: "bl_chemical_to_disease_or_phenotypic_feature_train_${{ github.run_number }}"
-    steps:
-    - uses: actions/checkout@v4
-      with:
-        fetch-depth: 0
-    - id: 'auth'
-      uses: 'google-github-actions/auth@v2'
-      with:
-        project_id: ${{ secrets.GCE_PROJECT }}
-        service_account: ${{ secrets.SERVICE_ACCOUNT }}
-        credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }}
-    - name: 'Set up Cloud SDK'
-      uses: 'google-github-actions/setup-gcloud@v2'
-      with:
-        version: '>= 363.0.0'
-    - name: Setup Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.7
-
-    - name: Configure Docker Authentication
-      run: |
-        gcloud --quiet auth configure-docker
-
-    - name: Set MODEL_VERSION env
-      run: |
-        echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV
-
-    - name: Set BASE_VERSION env
-      run: |
-        echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV
-
-    - name: Build Docker Image
-      run: |
-        docker build --build-arg "PROJECT_ID=$PROJECT_ID" \
-                     --build-arg "TASK_NAME=$TASK_NAME" \
-                     --build-arg "BASE_VERSION=$BASE_VERSION" \
-                     --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \
-                     --tag "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \
-                     -f ${{ env.DOCKERFILE }} .
-
-    - name: Publish Docker Image to Google Container Registry
-      run: |
-        docker push "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION"
-
-    - name: Submit a training job to AI Plaform to train and cache the model
-      run: |
-        gcloud ai-platform jobs submit training ${{ env.AI_PLATFORM_JOB_NAME }} \
-        --scale-tier basic_gpu --region "$GCE_REGION" \
-        --master-image-uri "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \
-        -- \
-        NO_ARG \
-        "gs://$MODEL_STORAGE_BUCKET"
-
-    - name: Monitor the training job
-      run: |
-        sh -c ".github/workflows/monitor-ai-platform-job.sh ${{ env.AI_PLATFORM_JOB_NAME }}"
-      timeout-minutes: 500
-
-  # # # -------------------------------------------------------------------------------------- #
-  # # # BUILD/PUSH BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE CLASSIFICATION CONTAINER IMAGE #
-  # # # -------------------------------------------------------------------------------------- #
-
-  # build_push-bl_chemical_to_disease_or_phenotypic_feature-predict:
-  #   name: "build/push bl_chemical_to_disease_or_phenotypic_feature predict container"
-  #   # needs: "build_push_train-bl_chemical_to_disease_or_phenotypic_feature-train"
+  # build_push_train-bl_chemical_to_disease_or_phenotypic_feature-train:
+  #   name: "build/push/train bl_chemical_to_disease_or_phenotypic_feature model"
+  #   # needs: "build_push-bert-base"
   #   runs-on: ubuntu-latest
   #   env:
   #     TASK_NAME: bl_chemical_to_disease_or_phenotypic_feature
-  #     DOCKERFILE: predict.Dockerfile
-  #     TRAIN_DOCKERFILE: train.Dockerfile
-  #     TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh
-  #     ENTRYPOINT_FILE: scripts/predict.entrypoint.sh
+  #     DOCKERFILE: train.Dockerfile
+  #     ENTRYPOINT_FILE: scripts/train.entrypoint.sh
   #     BASE_DOCKERFILE: base.Dockerfile
-  #     MODEL_VERSION_KEY: BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE
-  #     #CLASSIFICATION_LABELS: "treats causes_or_contributes_to false"
-  #     CLASSIFICATION_LABELS: "associated_with_resistance_to associated_with_sensitivity_to decreases_risk_for exacerbates exposure_is_origin_of has_excessive_amount_in has_no_effect_on increases_risk_for is_biomarker_for is_contraindicated_for is_deficient_in prevents results_in_side_effect treats used_in_diagnosis_of other"
   #     DATA_FILE: data/bl_chemical_to_disease_or_phenotypic_feature/data.tsv
+  #     MODEL_VERSION_KEY: BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE
+  #     AI_PLATFORM_JOB_NAME: "bl_chemical_to_disease_or_phenotypic_feature_train_${{ github.run_number }}"
   #   steps:
   #   - uses: actions/checkout@v4
   #     with:
@@ -450,6 +373,7 @@ jobs:
   #     uses: actions/setup-python@v2
   #     with:
   #       python-version: 3.7
+
   #   - name: Configure Docker Authentication
   #     run: |
   #       gcloud --quiet auth configure-docker
@@ -458,10 +382,6 @@ jobs:
   #     run: |
   #       echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV
 
-  #   - name: Set IMAGE_VERSION env
-  #     run: |
-  #       echo "IMAGE_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} IMAGE_VERSIONS_PREDICT | cut -f 2 -d '=')" >> $GITHUB_ENV
-
   #   - name: Set BASE_VERSION env
   #     run: |
   #       echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV
@@ -472,14 +392,94 @@ jobs:
   #                    --build-arg "TASK_NAME=$TASK_NAME" \
   #                    --build-arg "BASE_VERSION=$BASE_VERSION" \
   #                    --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \
-  #                    --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \
-  #                    --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \
-  #                    --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" \
+  #                    --tag "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \
   #                    -f ${{ env.DOCKERFILE }} .
 
   #   - name: Publish Docker Image to Google Container Registry
   #     run: |
-  #       docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION"
+  #       docker push "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION"
+
+  #   - name: Submit a training job to AI Plaform to train and cache the model
+  #     run: |
+  #       gcloud ai-platform jobs submit training ${{ env.AI_PLATFORM_JOB_NAME }} \
+  #       --scale-tier basic_gpu --region "$GCE_REGION" \
+  #       --master-image-uri "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \
+  #       -- \
+  #       NO_ARG \
+  #       "gs://$MODEL_STORAGE_BUCKET"
+
+  #   - name: Monitor the training job
+  #     run: |
+  #       sh -c ".github/workflows/monitor-ai-platform-job.sh ${{ env.AI_PLATFORM_JOB_NAME }}"
+  #     timeout-minutes: 500
+
+  # # -------------------------------------------------------------------------------------- #
+  # # BUILD/PUSH BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE CLASSIFICATION CONTAINER IMAGE #
+  # # -------------------------------------------------------------------------------------- #
+
+  build_push-bl_chemical_to_disease_or_phenotypic_feature-predict:
+    name: "build/push bl_chemical_to_disease_or_phenotypic_feature predict container"
+    # needs: "build_push_train-bl_chemical_to_disease_or_phenotypic_feature-train"
+    runs-on: ubuntu-latest
+    env:
+      TASK_NAME: bl_chemical_to_disease_or_phenotypic_feature
+      DOCKERFILE: predict.Dockerfile
+      TRAIN_DOCKERFILE: train.Dockerfile
+      TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh
+      ENTRYPOINT_FILE: scripts/predict.entrypoint.sh
+      BASE_DOCKERFILE: base.Dockerfile
+      MODEL_VERSION_KEY: BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE
+      #CLASSIFICATION_LABELS: "treats causes_or_contributes_to false"
+      CLASSIFICATION_LABELS: "associated_with_resistance_to associated_with_sensitivity_to decreases_risk_for exacerbates exposure_is_origin_of has_excessive_amount_in has_no_effect_on increases_risk_for is_biomarker_for is_contraindicated_for is_deficient_in prevents results_in_side_effect treats used_in_diagnosis_of other"
+      DATA_FILE: data/bl_chemical_to_disease_or_phenotypic_feature/data.tsv
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    - id: 'auth'
+      uses: 'google-github-actions/auth@v2'
+      with:
+        project_id: ${{ secrets.GCE_PROJECT }}
+        service_account: ${{ secrets.SERVICE_ACCOUNT }}
+        credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }}
+    - name: 'Set up Cloud SDK'
+      uses: 'google-github-actions/setup-gcloud@v2'
+      with:
+        version: '>= 363.0.0'
+    - name: Setup Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.7
+    - name: Configure Docker Authentication
+      run: |
+        gcloud --quiet auth configure-docker
+
+    - name: Set MODEL_VERSION env
+      run: |
+        echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV
+
+    - name: Set IMAGE_VERSION env
+      run: |
+        echo "IMAGE_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} IMAGE_VERSIONS_PREDICT | cut -f 2 -d '=')" >> $GITHUB_ENV
+
+    - name: Set BASE_VERSION env
+      run: |
+        echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV
+
+    - name: Build Docker Image
+      run: |
+        docker build --build-arg "PROJECT_ID=$PROJECT_ID" \
+                     --build-arg "TASK_NAME=$TASK_NAME" \
+                     --build-arg "BASE_VERSION=$BASE_VERSION" \
+                     --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \
+                     --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \
+                     --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \
+                     --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" \
+                     -f ${{ env.DOCKERFILE }} .
+
+    - name: Publish Docker Image to Google Container Registry
+      run: |
+        docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION"