base 0.7

UCDenver-ccp · May 1, 2024 · 9ed5e28 · 9ed5e28
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diff --git a/.github/workflows/bert-models-cicd.yaml b/.github/workflows/bert-models-cicd.yaml
@@ -50,40 +50,40 @@ jobs:
 # Note: when trying to run build_push-bert-base with other jobs below, an error is reported on line 90. 
 #       However, when run on its own it works fine.
 
-  # build_push-bert-base:
-  #   name: "build/push bluebert-base container image"
-  #   runs-on: ubuntu-latest
-  #   # Add "id-token" with the intended permissions.
-  #   permissions:
-  #     contents: "read"
-  #     id-token: "write"
-  #   env:
-  #     IMAGE_NAME: bluebert-base
-  #     DOCKERFILE: base.Dockerfile
-  #   steps:
-  #   - name: Checkout repository
-  #     uses: actions/checkout@v2
-  #   - name: Authenticate to Google Cloud
-  #     uses: google-github-actions/auth@v0
-  #     with:
-  #       workload_identity_provider: ${{ secrets.WORKLOAD_IDENTITY_PROVIDER_LOCATION }}
-  #       service_account: "${{ secrets.SERVICE_ACCOUNT }}@${{ secrets.GCE_PROJECT }}.iam.gserviceaccount.com"
-  #   - name: 'Set up Cloud SDK'
-  #     uses: 'google-github-actions/setup-gcloud@v1'
-  #     with:
-  #       version: '>= 363.0.0'
-  #   - name: Configure Docker Authentication
-  #     # if: contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE)
-  #     run: gcloud --quiet auth configure-docker
-  #   - name: Set MODEL_VERSION env
-  #     # if: contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE)
-  #     run: echo "MODEL_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV
-  #   - name: Build Docker Image
-  #     # if: contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE)
-  #     run: docker build --tag "gcr.io/$PROJECT_ID/$IMAGE_NAME:$MODEL_VERSION" -f ${{ env.DOCKERFILE }} .
-  #   - name: Publish Docker Image to Google Container Registry
-  #     # if: contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE)
-  #     run: docker push "gcr.io/$PROJECT_ID/$IMAGE_NAME:$MODEL_VERSION"
+  build_push-bert-base:
+    name: "build/push bluebert-base container image"
+    runs-on: ubuntu-latest
+    # Add "id-token" with the intended permissions.
+    permissions:
+      contents: "read"
+      id-token: "write"
+    env:
+      IMAGE_NAME: bluebert-base
+      DOCKERFILE: base.Dockerfile
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+    - name: Authenticate to Google Cloud
+      uses: google-github-actions/auth@v0
+      with:
+        workload_identity_provider: ${{ secrets.WORKLOAD_IDENTITY_PROVIDER_LOCATION }}
+        service_account: "${{ secrets.SERVICE_ACCOUNT }}@${{ secrets.GCE_PROJECT }}.iam.gserviceaccount.com"
+    - name: 'Set up Cloud SDK'
+      uses: 'google-github-actions/setup-gcloud@v1'
+      with:
+        version: '>= 363.0.0'
+    - name: Configure Docker Authentication
+      # if: contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE)
+      run: gcloud --quiet auth configure-docker
+    - name: Set MODEL_VERSION env
+      # if: contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE)
+      run: echo "MODEL_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV
+    - name: Build Docker Image
+      # if: contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE)
+      run: docker build --tag "gcr.io/$PROJECT_ID/$IMAGE_NAME:$MODEL_VERSION" -f ${{ env.DOCKERFILE }} .
+    - name: Publish Docker Image to Google Container Registry
+      # if: contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE)
+      run: docker push "gcr.io/$PROJECT_ID/$IMAGE_NAME:$MODEL_VERSION"
 
 # # ----------------------------------------------------------------------------------- #
 #   # ----------------------------------------------------------------------------------- #
@@ -2388,132 +2388,132 @@ jobs:
 
 
 
-        # #  # # ----------------------------------------------------------------------------------- #
-        # # # # ----------------------------------------------------------------------------------- #
-        # # # # ----------------------------------------------------------------------------------- #
-        # # # #                        TRAIN CRAFT_RELATIONS MODEL  - PR_TAXON                   #
-        # # # # ----------------------------------------------------------------------------------- #
-        # # # # ----------------------------------------------------------------------------------- #
-        # # # # ----------------------------------------------------------------------------------- #
+        # # #  # # ----------------------------------------------------------------------------------- #
+        # # # # # ----------------------------------------------------------------------------------- #
+        # # # # # ----------------------------------------------------------------------------------- #
+        # # # # #                        TRAIN CRAFT_RELATIONS MODEL  - PR_TAXON                   #
+        # # # # # ----------------------------------------------------------------------------------- #
+        # # # # # ----------------------------------------------------------------------------------- #
+        # # # # # ----------------------------------------------------------------------------------- #
 
-        build_push_train-craft_100-train:
-          name: "build/push/train craft_100 model"
-          # needs: "build_push-bert-base"
-          runs-on: ubuntu-latest
-          permissions:
-            contents: "read"
-            id-token: "write"
-          env:
-            TASK_NAME: craft_100
-            DOCKERFILE: train.Dockerfile
-            ENTRYPOINT_FILE: scripts/train.entrypoint.sh
-            BASE_DOCKERFILE: base.Dockerfile
-            DATA_FILE: data/craft_100/data.tsv
-            MODEL_VERSION_KEY: CRAFT_100
-            AI_PLATFORM_JOB_NAME: "craft_100_train_${{ github.run_number }}"
-          steps:
-          - name: Checkout repository
-            uses: actions/checkout@v2
-
-          - name: Authenticate to Google Cloud
-            uses: google-github-actions/auth@v0
-            with:
-              workload_identity_provider: ${{ secrets.WORKLOAD_IDENTITY_PROVIDER_LOCATION }}
-              service_account: "${{ secrets.SERVICE_ACCOUNT }}@${{ secrets.GCE_PROJECT }}.iam.gserviceaccount.com"
-
-          - name: Configure Docker Authentication
-            run: |
-              gcloud --quiet auth configure-docker
+        # build_push_train-craft_100-train:
+        #   name: "build/push/train craft_100 model"
+        #   # needs: "build_push-bert-base"
+        #   runs-on: ubuntu-latest
+        #   permissions:
+        #     contents: "read"
+        #     id-token: "write"
+        #   env:
+        #     TASK_NAME: craft_100
+        #     DOCKERFILE: train.Dockerfile
+        #     ENTRYPOINT_FILE: scripts/train.entrypoint.sh
+        #     BASE_DOCKERFILE: base.Dockerfile
+        #     DATA_FILE: data/craft_100/data.tsv
+        #     MODEL_VERSION_KEY: CRAFT_100
+        #     AI_PLATFORM_JOB_NAME: "craft_100_train_${{ github.run_number }}"
+        #   steps:
+        #   - name: Checkout repository
+        #     uses: actions/checkout@v2
+
+        #   - name: Authenticate to Google Cloud
+        #     uses: google-github-actions/auth@v0
+        #     with:
+        #       workload_identity_provider: ${{ secrets.WORKLOAD_IDENTITY_PROVIDER_LOCATION }}
+        #       service_account: "${{ secrets.SERVICE_ACCOUNT }}@${{ secrets.GCE_PROJECT }}.iam.gserviceaccount.com"
+
+        #   - 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 '=')" >> $GITHUB_ENV
+        #   - name: Set MODEL_VERSION env
+        #     run: |
+        #       echo "MODEL_VERSION=$(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 '=')" >> $GITHUB_ENV
+        #   - name: Set BASE_VERSION env
+        #     run: |
+        #       echo "BASE_VERSION=$(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 ${{ env.DOCKERFILE }} .
+        #   - name: Build Docker Image
+        #     run: |
+        #       docker build --build-arg "PROJECT_ID=$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:$MODEL_VERSION"
+        #   - name: Publish Docker Image to Google Container Registry
+        #     run: |
+        #       docker push "gcr.io/$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: 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: 180
+        #   - name: Monitor the training job
+        #     run: |
+        #       sh -c ".github/workflows/monitor-ai-platform-job.sh ${{ env.AI_PLATFORM_JOB_NAME }}"
+        #     timeout-minutes: 180
 
-        # # # ----------------------------------------------------------------------------------- #
-        # # #          BUILD/PUSH CRAFT_RELATIONS INFLUENCE CLASSIFICATION CONTAINER IMAGE       #
-        # # # ----------------------------------------------------------------------------------- #
+        # # # # ----------------------------------------------------------------------------------- #
+        # # # #          BUILD/PUSH CRAFT_RELATIONS INFLUENCE CLASSIFICATION CONTAINER IMAGE       #
+        # # # # ----------------------------------------------------------------------------------- #
 
-        build_push-craft_100-predict:
-          name: "build/push craft_100 predict container"
-          needs: "build_push_train-craft_100-train"
-          runs-on: ubuntu-latest
-          permissions:
-            contents: "read"
-            id-token: "write"
-          env:
-            TASK_NAME: craft_100
-            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: CRAFT_100
-            CLASSIFICATION_LABELS: "label1 label2 false"
-            DATA_FILE: data/craft_100/data.tsv
-          steps:
-          - name: Checkout repository
-            uses: actions/checkout@v2
-
-          - name: Authenticate to Google Cloud
-            uses: google-github-actions/auth@v0
-            with:
-              workload_identity_provider: ${{ secrets.WORKLOAD_IDENTITY_PROVIDER_LOCATION }}
-              service_account: "${{ secrets.SERVICE_ACCOUNT }}@${{ secrets.GCE_PROJECT }}.iam.gserviceaccount.com"
+        # build_push-craft_100-predict:
+        #   name: "build/push craft_100 predict container"
+        #   needs: "build_push_train-craft_100-train"
+        #   runs-on: ubuntu-latest
+        #   permissions:
+        #     contents: "read"
+        #     id-token: "write"
+        #   env:
+        #     TASK_NAME: craft_100
+        #     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: CRAFT_100
+        #     CLASSIFICATION_LABELS: "label1 label2 false"
+        #     DATA_FILE: data/craft_100/data.tsv
+        #   steps:
+        #   - name: Checkout repository
+        #     uses: actions/checkout@v2
+
+        #   - name: Authenticate to Google Cloud
+        #     uses: google-github-actions/auth@v0
+        #     with:
+        #       workload_identity_provider: ${{ secrets.WORKLOAD_IDENTITY_PROVIDER_LOCATION }}
+        #       service_account: "${{ secrets.SERVICE_ACCOUNT }}@${{ secrets.GCE_PROJECT }}.iam.gserviceaccount.com"
 
-          - name: Configure Docker Authentication
-            run: |
-              gcloud --quiet auth configure-docker
+        #   - 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 '=')" >> $GITHUB_ENV
+        #   - name: Set MODEL_VERSION env
+        #     run: |
+        #       echo "MODEL_VERSION=$(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 '=')" >> $GITHUB_ENV
+        #   - name: Set BASE_VERSION env
+        #     run: |
+        #       echo "BASE_VERSION=$(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:$MODEL_VERSION" \
-                           -f ${{ env.DOCKERFILE }} .
+        #   - name: Build Docker Image
+        #     run: |
+        #       docker build --build-arg "PROJECT_ID=$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/$TASK_NAME-predict:$MODEL_VERSION" \
+        #                    -f ${{ env.DOCKERFILE }} .
 
-          - name: Publish Docker Image to Google Container Registry
-            run: |
-              docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$MODEL_VERSION" 
+        #   - name: Publish Docker Image to Google Container Registry
+        #     run: |
+        #       docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$MODEL_VERSION" 
diff --git a/MODEL_VERSIONS b/MODEL_VERSIONS
@@ -1,4 +1,4 @@
-BASE=0.3.3
+BASE=0.7
 BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE=0.1
 BL_CHEMICAL_TO_GENE=0.1
 BL_DISEASE_TO_PHENOTYPIC_FEATURE=0.1