build chem-dis v11

removed unused label from bluebert 10 epochs simplified sentences
UCDenver-ccp · Apr 28, 2024 · 675934c · 675934c
1 parent 692a33e
commit 675934c
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diff --git a/.github/workflows/bert-models-cicd.yaml b/.github/workflows/bert-models-cicd.yaml
@@ -47,44 +47,44 @@ 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.
+# # 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"
 
 # # ----------------------------------------------------------------------------------- #
 #   # ----------------------------------------------------------------------------------- #
@@ -335,156 +335,156 @@ jobs:
 #         docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$MODEL_VERSION"
 
 
-  # # # # # ----------------------------------------------------------------------------------- #
-  # # # # # ----------------------------------------------------------------------------------- #
-  # # # # # ----------------------------------------------------------------------------------- #
-  # # # # #              TRAIN BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE MODEL               #
-  # # # # # ----------------------------------------------------------------------------------- #
-  # # # # # ----------------------------------------------------------------------------------- #
-  # # # # # ----------------------------------------------------------------------------------- #
-
-  # 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
+  # # # # ----------------------------------------------------------------------------------- #
+  # # # # ----------------------------------------------------------------------------------- #
+  # # # # ----------------------------------------------------------------------------------- #
+  # # # #              TRAIN BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE MODEL               #
+  # # # # ----------------------------------------------------------------------------------- #
+  # # # # ----------------------------------------------------------------------------------- #
+  # # # # ----------------------------------------------------------------------------------- #
 
-  #   - name: Set MODEL_VERSION env
-  #     run: |
-  #       echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV
+  build_push_train-bl_chemical_to_disease_or_phenotypic_feature-train:
+    name: "build/push/train bl_chemical_to_disease_or_phenotypic_feature model"
+    # needs: "build_push-bert-base"
+    runs-on: ubuntu-latest
+    env:
+      TASK_NAME: bl_chemical_to_disease_or_phenotypic_feature
+      DOCKERFILE: train.Dockerfile
+      ENTRYPOINT_FILE: scripts/train.entrypoint.sh
+      BASE_DOCKERFILE: base.Dockerfile
+      DATA_FILE: data/bl_chemical_to_disease_or_phenotypic_feature/data.tsv
+      MODEL_VERSION_KEY: BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE
+      AI_PLATFORM_JOB_NAME: "bl_chemical_to_disease_or_phenotypic_feature_train_${{ 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: Set BASE_VERSION env
-  #     run: |
-  #       echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV
+    - name: Configure Docker Authentication
+      run: |
+        gcloud --quiet auth configure-docker
 
-  #   - name: Set NUM_EPOCHS env
-  #     run: |
-  #       echo "NUM_EPOCHS=5.0" >> $GITHUB_ENV
+    - name: Set MODEL_VERSION env
+      run: |
+        echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV
 
-  #   - name: 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 ${{ env.DOCKERFILE }} .
+    - name: Set BASE_VERSION env
+      run: |
+        echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV
 
-  #   - name: Publish Docker Image to Google Container Registry
-  #     run: |
-  #       docker push "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION"
+    - name: Set NUM_EPOCHS env
+      run: |
+        echo "NUM_EPOCHS=10.0" >> $GITHUB_ENV
 
-  #   - 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: 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: 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"
+
+    - 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 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 decreases_risk_for exacerbates exposure_is_origin_of has_excessive_amount_in increases_risk_for is_biomarker_for is_contraindicated_for is_deficient_in prevents results_in_side_effect treats 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
+  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 decreases_risk_for exacerbates exposure_is_origin_of has_excessive_amount_in increases_risk_for is_biomarker_for is_contraindicated_for is_deficient_in prevents results_in_side_effect treats 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 '=')" >> $GITHUB_ENV
+    - name: Set MODEL_VERSION env
+      run: |
+        echo "MODEL_VERSION=$(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/IMAGE_VERSIONS_PREDICT b/IMAGE_VERSIONS_PREDICT
@@ -1 +1 @@
-BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE=0.10
+BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE=0.11
diff --git a/MODEL_VERSIONS b/MODEL_VERSIONS
@@ -1,5 +1,5 @@
 BASE=0.6.1
-BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE=0.10
+BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE=0.11
 BL_CHEMICAL_TO_GENE=0.1
 BL_DISEASE_TO_PHENOTYPIC_FEATURE=0.1
 BL_GENE_REGULATORY_RELATIONSHIP=0.1
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE=0.10
		BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE=0.11