From f98e71922b8b88f84e9eb075b38812f94de22219 Mon Sep 17 00:00:00 2001
From: Bill Baumgartner <bill.baumgartner@gmail.com>
Date: Wed, 28 Aug 2024 17:08:49 -0600
Subject: [PATCH] train disease-anatomy v0.2

---
 .github/workflows/bert-models-cicd.yaml | 314 ++++++++++++------------
 1 file changed, 157 insertions(+), 157 deletions(-)

diff --git a/.github/workflows/bert-models-cicd.yaml b/.github/workflows/bert-models-cicd.yaml
index 3366c2bf..36b8bf20 100644
--- a/.github/workflows/bert-models-cicd.yaml
+++ b/.github/workflows/bert-models-cicd.yaml
@@ -50,15 +50,63 @@ 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"
+  # 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"
+
+
+# # # # # # ----------------------------------------------------------------------------------- #
+# #   # # # # ----------------------------------------------------------------------------------- #
+# #   # # # # ----------------------------------------------------------------------------------- #
+# #   # # # #              TRAIN BL_DISEASE_TO_ANATOMY MODEL               #
+# #   # # # # ----------------------------------------------------------------------------------- #
+# #   # # # # ----------------------------------------------------------------------------------- #
+# #   # # # # ----------------------------------------------------------------------------------- #
+
+  build_push_train-bl_disease_to_anatomy-train:
+    name: "build/push/train bl_disease_to_anatomy model"
+    # needs: "build_push-bert-base"
     runs-on: ubuntu-latest
     env:
-      IMAGE_NAME: bluebert-base
-      DOCKERFILE: base.Dockerfile
-    permissions:
-      contents: 'read'
-      id-token: 'write'
+      TASK_NAME: bl_disease_to_anatomy
+      DOCKERFILE: train.Dockerfile
+      ENTRYPOINT_FILE: scripts/train.entrypoint.sh
+      BASE_DOCKERFILE: base.Dockerfile
+      DATA_FILE: data/bl_disease_to_anatomy/data.tsv
+      MODEL_VERSION_KEY: BL_DISEASE_TO_ANATOMY
+      AI_PLATFORM_JOB_NAME: "bl_disease_to_anatomy_train_${{ github.run_number }}"
     steps:
     - uses: actions/checkout@v4
       with:
@@ -77,169 +125,121 @@ jobs:
       uses: actions/setup-python@v2
       with:
         python-version: 3.7
-    - name: Configure Docker Authentication
-      run: gcloud --quiet auth configure-docker
-    - name: Set MODEL_VERSION env
-      run: echo "MODEL_VERSION=$(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"
-
-
-# # # # # # # ----------------------------------------------------------------------------------- #
-# # #   # # # # ----------------------------------------------------------------------------------- #
-# # #   # # # # ----------------------------------------------------------------------------------- #
-# # #   # # # #              TRAIN BL_DISEASE_TO_ANATOMY MODEL               #
-# # #   # # # # ----------------------------------------------------------------------------------- #
-# # #   # # # # ----------------------------------------------------------------------------------- #
-# # #   # # # # ----------------------------------------------------------------------------------- #
 
-#   build_push_train-bl_disease_to_anatomy-train:
-#     name: "build/push/train bl_disease_to_anatomy model"
-#     # needs: "build_push-bert-base"
-#     runs-on: ubuntu-latest
-#     env:
-#       TASK_NAME: bl_disease_to_anatomy
-#       DOCKERFILE: train.Dockerfile
-#       ENTRYPOINT_FILE: scripts/train.entrypoint.sh
-#       BASE_DOCKERFILE: base.Dockerfile
-#       DATA_FILE: data/bl_disease_to_anatomy/data.tsv
-#       MODEL_VERSION_KEY: BL_DISEASE_TO_ANATOMY
-#       AI_PLATFORM_JOB_NAME: "bl_disease_to_anatomy_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: 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=5.0" >> $GITHUB_ENV
 
-#     - name: Submit a training job to AI Plaform to train and cache the model
-#       run: |
-#         gcloud ai-platform jobs submit training ${{ env.AI_PLATFORM_JOB_NAME }} \
-#         --scale-tier=CUSTOM \
-#         --master-machine-type=n1-standard-8 \
-#         --master-accelerator=count=1,type=nvidia-tesla-v100 \
-#         --region "$GCE_REGION" \
-#         --master-image-uri "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \
-#         -- \
-#         NO_ARG \
-#         "gs://$MODEL_STORAGE_BUCKET"
+    - name: 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 ${{ env.AI_PLATFORM_JOB_NAME }} \
+        --scale-tier=CUSTOM \
+        --master-machine-type=n1-standard-8 \
+        --master-accelerator=count=1,type=nvidia-tesla-v100 \
+        --region "$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_DISEASE_TO_ANATOMY CLASSIFICATION CONTAINER IMAGE #
-#   # # -------------------------------------------------------------------------------------- #
+  # # -------------------------------------------------------------------------------------- #
+  # # BUILD/PUSH BL_DISEASE_TO_ANATOMY CLASSIFICATION CONTAINER IMAGE #
+  # # -------------------------------------------------------------------------------------- #
     
-#   build_push-bl_disease_to_anatomy-predict:
-#     name: "build/push bl_disease_to_anatomy predict container"
-#     needs: "build_push_train-bl_disease_to_anatomy-train"
-#     runs-on: ubuntu-latest
-#     env:
-#       TASK_NAME: bl_disease_to_anatomy
-#       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_DISEASE_TO_ANATOMY
-#       # Don't forget to change labels
-#       CLASSIFICATION_LABELS: "has_basis_in other"
-#       DATA_FILE: data/bl_disease_to_anatomy/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_disease_to_anatomy-predict:
+    name: "build/push bl_disease_to_anatomy predict container"
+    needs: "build_push_train-bl_disease_to_anatomy-train"
+    runs-on: ubuntu-latest
+    env:
+      TASK_NAME: bl_disease_to_anatomy
+      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_DISEASE_TO_ANATOMY
+      # Don't forget to change labels
+      CLASSIFICATION_LABELS: "has_basis_in other"
+      DATA_FILE: data/bl_disease_to_anatomy/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"
 
 # # # # # # # ----------------------------------------------------------------------------------- #
 # # #   # # # # ----------------------------------------------------------------------------------- #