build base 0.22

UCDenver-ccp · Aug 28, 2024 · 1ed7d9a · 1ed7d9a
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diff --git a/.github/workflows/bert-models-cicd.yaml b/.github/workflows/bert-models-cicd.yaml
@@ -50,41 +50,41 @@ 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
-  #   env:
-  #     IMAGE_NAME: bluebert-base
-  #     DOCKERFILE: base.Dockerfile
-  #   permissions:
-  #     contents: 'read'
-  #     id-token: 'write'
-  #   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 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV
-  #   - name: Build Docker Image
-  #     run: docker build --tag "gcr.io/$PROJECT_ID/$IMAGE_NAME:$MODEL_VERSION" -f ${{ env.DOCKERFILE }} .
-  #   - name: Publish Docker Image to Google Container Registry
-  #     run: docker push "gcr.io/$PROJECT_ID/$IMAGE_NAME:$MODEL_VERSION"
+  build_push-bert-base:
+    name: "build/push bluebert-base container image"
+    runs-on: ubuntu-latest
+    env:
+      IMAGE_NAME: bluebert-base
+      DOCKERFILE: base.Dockerfile
+    permissions:
+      contents: 'read'
+      id-token: 'write'
+    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 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV
+    - name: Build Docker Image
+      run: docker build --tag "gcr.io/$PROJECT_ID/$IMAGE_NAME:$MODEL_VERSION" -f ${{ env.DOCKERFILE }} .
+    - name: Publish Docker Image to Google Container Registry
+      run: docker push "gcr.io/$PROJECT_ID/$IMAGE_NAME:$MODEL_VERSION"
 
 
 # # # # # # # ----------------------------------------------------------------------------------- #
@@ -2248,159 +2248,159 @@ jobs:
 #         docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION"
 
 
-# # # # # ----------------------------------------------------------------------------------- #
-#   # # # # ----------------------------------------------------------------------------------- #
-#   # # # # ----------------------------------------------------------------------------------- #
-#   # # # #              TRAIN BL_GENE_TO_GENE MODEL               #
-#   # # # # ----------------------------------------------------------------------------------- #
-#   # # # # ----------------------------------------------------------------------------------- #
-#   # # # # ----------------------------------------------------------------------------------- #
+# # # # # # ----------------------------------------------------------------------------------- #
+# #   # # # # ----------------------------------------------------------------------------------- #
+# #   # # # # ----------------------------------------------------------------------------------- #
+# #   # # # #              TRAIN BL_GENE_TO_GENE MODEL               #
+# #   # # # # ----------------------------------------------------------------------------------- #
+# #   # # # # ----------------------------------------------------------------------------------- #
+# #   # # # # ----------------------------------------------------------------------------------- #
 
-  build_push_train-bl_gene_to_gene-train:
-    name: "build/push/train bl_gene_to_gene model"
-    # needs: "build_push-bert-base"
-    runs-on: ubuntu-latest
-    env:
-      TASK_NAME: bl_gene_to_gene
-      DOCKERFILE: train.Dockerfile
-      ENTRYPOINT_FILE: scripts/train.entrypoint.sh
-      BASE_DOCKERFILE: base.Dockerfile
-      DATA_FILE: data/bl_gene_to_gene/data.tsv
-      MODEL_VERSION_KEY: BL_GENE_TO_GENE
-      AI_PLATFORM_JOB_NAME: "bl_gene_to_gene_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: ${{ secrets.SERVICE_ACCOUNT_KEY }}
-    - name: 'Set up Cloud SDK'
-      uses: 'google-github-actions/setup-gcloud@v2'
-      with:
-        version: '>= 363.0.0'
-    - name: Setup Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.7
+#   build_push_train-bl_gene_to_gene-train:
+#     name: "build/push/train bl_gene_to_gene model"
+#     # needs: "build_push-bert-base"
+#     runs-on: ubuntu-latest
+#     env:
+#       TASK_NAME: bl_gene_to_gene
+#       DOCKERFILE: train.Dockerfile
+#       ENTRYPOINT_FILE: scripts/train.entrypoint.sh
+#       BASE_DOCKERFILE: base.Dockerfile
+#       DATA_FILE: data/bl_gene_to_gene/data.tsv
+#       MODEL_VERSION_KEY: BL_GENE_TO_GENE
+#       AI_PLATFORM_JOB_NAME: "bl_gene_to_gene_train_${{ 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: 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: Set NUM_EPOCHS env
-      run: |
-        echo "NUM_EPOCHS=5.0" >> $GITHUB_ENV
+#     - name: Set NUM_EPOCHS env
+#       run: |
+#         echo "NUM_EPOCHS=5.0" >> $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 "EPOCHS=$NUM_EPOCHS" \
-                     --tag "gcr.io/$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=$MODEL_VERSION" \
+#                      --build-arg "EPOCHS=$NUM_EPOCHS" \
+#                      --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 ${{ env.AI_PLATFORM_JOB_NAME }} \
-        --scale-tier=CUSTOM \
-        --master-machine-type=n1-standard-8 \
-        --master-accelerator=count=1,type=nvidia-tesla-v100 \
-        --region "$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 ${{ env.AI_PLATFORM_JOB_NAME }}"
-      timeout-minutes: 500
+#     - name: Publish Docker Image to Google Container Registry
+#       run: |
+#         docker push "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION"
 
-  # # -------------------------------------------------------------------------------------- #
-  # # BUILD/PUSH BL_GENE_TO_GENE CLASSIFICATION CONTAINER IMAGE #
-  # # -------------------------------------------------------------------------------------- #
+#     - name: Submit a training job to AI Plaform to train and cache the model
+#       run: |
+#         gcloud ai-platform jobs submit training ${{ env.AI_PLATFORM_JOB_NAME }} \
+#         --scale-tier=CUSTOM \
+#         --master-machine-type=n1-standard-8 \
+#         --master-accelerator=count=1,type=nvidia-tesla-v100 \
+#         --region "$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_GENE_TO_GENE CLASSIFICATION CONTAINER IMAGE #
+#   # # -------------------------------------------------------------------------------------- #
 
-  build_push-bl_gene_to_gene-predict:
-    name: "build/push bl_gene_to_gene predict container"
-    needs: "build_push_train-bl_gene_to_gene-train"
-    runs-on: ubuntu-latest
-    env:
-      TASK_NAME: bl_gene_to_gene
-      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_GENE_TO_GENE
-      # Don't forget to change labels
-      CLASSIFICATION_LABELS: "interacts_with activates deactivates other"
-      DATA_FILE: data/bl_gene_to_gene/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
+#   build_push-bl_gene_to_gene-predict:
+#     name: "build/push bl_gene_to_gene predict container"
+#     needs: "build_push_train-bl_gene_to_gene-train"
+#     runs-on: ubuntu-latest
+#     env:
+#       TASK_NAME: bl_gene_to_gene
+#       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_GENE_TO_GENE
+#       # Don't forget to change labels
+#       CLASSIFICATION_LABELS: "interacts_with activates deactivates other"
+#       DATA_FILE: data/bl_gene_to_gene/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 '=')" >> $GITHUB_ENV
+#     - name: Set MODEL_VERSION env
+#       run: |
+#         echo "MODEL_VERSION=$(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 '=')" >> $GITHUB_ENV
+#     - name: Set IMAGE_VERSION env
+#       run: |
+#         echo "IMAGE_VERSION=$(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 '=')" >> $GITHUB_ENV
+#     - name: Set BASE_VERSION env
+#       run: |
+#         echo "BASE_VERSION=$(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 ${{ env.DOCKERFILE }} .
+#     - name: Build Docker Image
+#       run: |
+#         docker build --build-arg "PROJECT_ID=$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:$IMAGE_VERSION"
+#     - name: Publish Docker Image to Google Container Registry
+#       run: |
+#         docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION"
 
 
   # # # # # ----------------------------------------------------------------------------------- #

diff --git a/MODEL_VERSIONS b/MODEL_VERSIONS
@@ -1,4 +1,4 @@
-BASE=0.21
+BASE=0.22
 BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE=0.16
 BL_CHEMICAL_TO_GENE=0.3
 BL_CHEMICAL_TO_PROCESS=0.2