Merge pull request #18 from stanfordnmbl/treadmill_gait_analysis

Add treadmill gait analysis

.github/workflows/treadmill_gait_analysis-dev.yml

@@ -0,0 +1,74 @@
+# This workflow will build and push a new container image to Amazon ECR,
+# and then will deploy a new task definition to Amazon ECS, on every push
+# to the master branch.
+#
+# To use this workflow, you will need to complete the following set-up steps:
+#
+# 1. Create an ECR repository to store your images.
+#    For example: `aws ecr create-repository --repository-name my-ecr-repo --region us-east-2`.
+#    Replace the value of `ECR_REPOSITORY` in the workflow below with your repository's name.
+#    Replace the value of `aws-region` in the workflow below with your repository's region.
+#
+# 2. Create an ECS task definition, an ECS cluster, and an ECS service.
+#    For example, follow the Getting Started guide on the ECS console:
+#      https://us-east-2.console.aws.amazon.com/ecs/home?region=us-east-2#/firstRun
+#    Replace the values for `service` and `cluster` in the workflow below with your service and cluster names.
+#
+# 3. Store your ECS task definition as a JSON file in your repository.
+#    The format should follow the output of `aws ecs register-task-definition --generate-cli-skeleton`.
+#    Replace the value of `task-definition` in the workflow below with your JSON file's name.
+#    Replace the value of `container-name` in the workflow below with the name of the container
+#    in the `containerDefinitions` section of the task definition.
+#
+# 4. Store an IAM user access key in GitHub Actions secrets named `AWS_ACCESS_KEY_ID` and `AWS_SECRET_ACCESS_KEY`.
+#    See the documentation for each action used below for the recommended IAM policies for this IAM user,
+#    and best practices on handling the access key credentials.
+
+on:
+  push:
+    branches:
+      - dev
+    paths:
+      - 'treadmill_gait_analysis/**'
+  workflow_dispatch:
+
+name: DEV Analysis "treadmill gait analysis" build & deployment
+
+jobs:
+  deploy:
+    name: Deploy
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v1
+
+    - name: Configure AWS credentials
+      uses: aws-actions/configure-aws-credentials@v1
+      with:
+        aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
+        aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+        aws-region: us-west-2
+
+    - name: Login to Amazon ECR
+      id: login-ecr
+      uses: aws-actions/amazon-ecr-login@v1
+
+    - name: Build, tag, and push image to Amazon ECR
+      id: build-image
+      env:
+        IMAGE_TAG: latest # ${{ github.sha }}
+      run: |
+        # Build a docker container and
+        # push it to ECR so that it can
+        # be deployed to ECS.
+        cd treadmill_gait_analysis
+        docker build -f Dockerfile -t 660440363484.dkr.ecr.us-west-2.amazonaws.com/opencap-analysis/treadmill_gait_analysis-dev:$IMAGE_TAG .
+        docker push 660440363484.dkr.ecr.us-west-2.amazonaws.com/opencap-analysis/treadmill_gait_analysis-dev:$IMAGE_TAG
+        echo "::set-output name=image::660440363484.dkr.ecr.us-west-2.amazonaws.com/opencap-analysis/treadmill_gait_analysis-dev:$IMAGE_TAG"
+
+    - name: Force deployment
+      env:
+        IMAGE_TAG: latest # ${{ github.sha }}
+      run: |
+        aws lambda update-function-code --function-name treadmill-gait-analysis-dev --image-uri 660440363484.dkr.ecr.us-west-2.amazonaws.com/opencap-analysis/treadmill_gait_analysis-dev:$IMAGE_TAG | jq 'if .Environment.Variables.API_TOKEN? then .Environment.Variables.API_TOKEN = "REDACTED" else . end'

.github/workflows/treadmill_gait_analysis.yml

@@ -0,0 +1,74 @@
+# This workflow will build and push a new container image to Amazon ECR,
+# and then will deploy a new task definition to Amazon ECS, on every push
+# to the master branch.
+#
+# To use this workflow, you will need to complete the following set-up steps:
+#
+# 1. Create an ECR repository to store your images.
+#    For example: `aws ecr create-repository --repository-name my-ecr-repo --region us-east-2`.
+#    Replace the value of `ECR_REPOSITORY` in the workflow below with your repository's name.
+#    Replace the value of `aws-region` in the workflow below with your repository's region.
+#
+# 2. Create an ECS task definition, an ECS cluster, and an ECS service.
+#    For example, follow the Getting Started guide on the ECS console:
+#      https://us-east-2.console.aws.amazon.com/ecs/home?region=us-east-2#/firstRun
+#    Replace the values for `service` and `cluster` in the workflow below with your service and cluster names.
+#
+# 3. Store your ECS task definition as a JSON file in your repository.
+#    The format should follow the output of `aws ecs register-task-definition --generate-cli-skeleton`.
+#    Replace the value of `task-definition` in the workflow below with your JSON file's name.
+#    Replace the value of `container-name` in the workflow below with the name of the container
+#    in the `containerDefinitions` section of the task definition.
+#
+# 4. Store an IAM user access key in GitHub Actions secrets named `AWS_ACCESS_KEY_ID` and `AWS_SECRET_ACCESS_KEY`.
+#    See the documentation for each action used below for the recommended IAM policies for this IAM user,
+#    and best practices on handling the access key credentials.
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - 'treadmill_gait_analysis/**'
+  workflow_dispatch:
+
+name: PROD Analysis "treadmill gait analysis" build & deployment
+
+jobs:
+  deploy:
+    name: Deploy
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v1
+
+    - name: Configure AWS credentials
+      uses: aws-actions/configure-aws-credentials@v1
+      with:
+        aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
+        aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+        aws-region: us-west-2
+
+    - name: Login to Amazon ECR
+      id: login-ecr
+      uses: aws-actions/amazon-ecr-login@v1
+
+    - name: Build, tag, and push image to Amazon ECR
+      id: build-image
+      env:
+        IMAGE_TAG: latest # ${{ github.sha }}
+      run: |
+        # Build a docker container and
+        # push it to ECR so that it can
+        # be deployed to ECS.
+        cd treadmill_gait_analysis
+        docker build -f Dockerfile -t 660440363484.dkr.ecr.us-west-2.amazonaws.com/opencap-analysis/treadmill_gait_analysis:$IMAGE_TAG .
+        docker push 660440363484.dkr.ecr.us-west-2.amazonaws.com/opencap-analysis/treadmill_gait_analysis:$IMAGE_TAG
+        echo "::set-output name=image::660440363484.dkr.ecr.us-west-2.amazonaws.com/opencap-analysis/treadmill_gait_analysis:$IMAGE_TAG"
+
+    - name: Force deployment
+      env:
+        IMAGE_TAG: latest # ${{ github.sha }}
+      run: |
+        aws lambda update-function-code --function-name treadmill-gait-analysis --image-uri 660440363484.dkr.ecr.us-west-2.amazonaws.com/opencap-analysis/treadmill_gait_analysis:$IMAGE_TAG | jq 'if .Environment.Variables.API_TOKEN? then .Environment.Variables.API_TOKEN = "REDACTED" else . end'

treadmill_gait_analysis/.dockerignore

@@ -0,0 +1,4 @@
+.git
+Data/
+.env
+docker

treadmill_gait_analysis/.gitignore

@@ -0,0 +1,7 @@
+__pycache__
+.env
+*.log
+*.ipynb_checkpoints
+Data/*
+
+*DS_Store

treadmill_gait_analysis/Dockerfile

@@ -0,0 +1,30 @@
+FROM stanfordnmbl/opensim-python:4.3
+
+ARG FUNCTION_DIR="/function"
+
+RUN apt-get update && \
+    apt-get install -y \
+    build-essential \
+    python3-dev \
+    g++ \
+    make \
+    cmake \
+    unzip \
+    libcurl4-openssl-dev
+
+# Copy function code
+RUN mkdir -p ${FUNCTION_DIR}
+COPY ./requirements.txt /requirements.txt
+# Install the requirements.txt
+RUN python3.8 -m pip install --no-cache-dir -r  /requirements.txt
+RUN python3.8 -m pip install --target ${FUNCTION_DIR} awslambdaric
+
+ADD https://github.com/aws/aws-lambda-runtime-interface-emulator/releases/latest/download/aws-lambda-rie /usr/bin/aws-lambda-rie
+RUN chmod +x /usr/bin/aws-lambda-rie
+
+COPY ./function ${FUNCTION_DIR}
+RUN chmod +x ${FUNCTION_DIR}/entrypoint
+WORKDIR ${FUNCTION_DIR}
+
+ENTRYPOINT ["./entrypoint"]
+CMD ["handler.handler"]

treadmill_gait_analysis/docker-compose.yml

@@ -0,0 +1,12 @@
+version: '3.8'
+
+services:
+  gait_analysis:
+#    platform: linux/amd64
+    build:
+      context: .
+      dockerfile: ./Dockerfile
+    ports:
+      - 9005:8080
+    env_file:
+      - ./.env

treadmill_gait_analysis/function/entrypoint

@@ -0,0 +1,6 @@
+#!/bin/bash
+if [ -z "${AWS_LAMBDA_RUNTIME_API}" ]; then
+  exec /usr/bin/aws-lambda-rie /usr/bin/python3.8 -m awslambdaric $@
+else
+  exec /usr/bin/python3.8 -m awslambdaric $@
+fi