Merge pull request #8 from eipm/develop

v.1.0.0

Author: alexsigaras

.dockerignore

@@ -0,0 +1,6 @@
+README.md
+
+.git
+.github
+**/stork_v/models
+**/data

.github/workflows/docker-publish.yml

@@ -0,0 +1,86 @@
+name: Docker
+
+on:
+  push:
+    # Publish `main` as Docker `latest` image and `develop` as `develop` image.
+    branches:
+      - main
+      - develop
+
+    # Publish `v1.2.3` tags as releases.
+    tags:
+      - v*
+
+  # Run tests for any PRs.
+  pull_request:
+
+env:
+  # TODO: Change variable to your image's name.
+  IMAGE_NAME: stork-v
+
+jobs:
+  # Push image to GitHub Packages.
+  # See also https://docs.docker.com/docker-hub/builds/
+  push:
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push'
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Build image
+        run: docker build . --file Dockerfile --tag $IMAGE_NAME
+
+      - name: Log into GitHub Container Registry
+        run: echo "${{ secrets.GHCR_TOKEN }}" | docker login https://ghcr.io -u ${{ secrets.GHCR_SVC_ACCOUNT }} --password-stdin
+
+      - name: Push image to GitHub Container Registry
+        run: |
+          IMAGE_ID=ghcr.io/${{ github.repository_owner }}/$IMAGE_NAME
+
+          # Change all uppercase to lowercase
+          IMAGE_ID=$(echo $IMAGE_ID | tr '[A-Z]' '[a-z]')
+
+          # Strip git ref prefix from version
+          VERSION=$(echo "${{ github.ref }}" | sed -e 's,.*/\(.*\),\1,')
+
+          # Strip "v" prefix from tag name
+          [[ "${{ github.ref }}" == "refs/tags/"* ]] && VERSION=$(echo $VERSION | sed -e 's/^v//')
+
+          # Use Docker `latest` tag convention for main and `develop` for develop
+          [ "$VERSION" == "main" ] && VERSION=latest
+          [ "$VERSION" == "develop" ] && VERSION=develop
+
+          echo IMAGE_ID=$IMAGE_ID
+          echo VERSION=$VERSION
+
+          docker tag $IMAGE_NAME $IMAGE_ID:$VERSION
+          docker push $IMAGE_ID:$VERSION
+      - name: Login to EIPM DockerHub
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.EIPM_DOCKER_HUB_USERNAME }}
+          password: ${{ secrets.EIPM_DOCKER_HUB_TOKEN }}
+
+      - name: Push image to EIPM Docker Hub
+        run: |
+          IMAGE_ID=eipm/$IMAGE_NAME
+
+          # Change all uppercase to lowercase
+          IMAGE_ID=$(echo $IMAGE_ID | tr '[A-Z]' '[a-z]')
+
+          # Strip git ref prefix from version
+          VERSION=$(echo "${{ github.ref }}" | sed -e 's,.*/\(.*\),\1,')
+
+          # Strip "v" prefix from tag name
+          [[ "${{ github.ref }}" == "refs/tags/"* ]] && VERSION=$(echo $VERSION | sed -e 's/^v//')
+
+          # Use Docker `latest` tag convention for main and `develop` for develop
+          [ "$VERSION" == "main" ] && VERSION=latest
+          [ "$VERSION" == "develop" ] && VERSION=develop
+
+          echo IMAGE_ID=$IMAGE_ID
+          echo VERSION=$VERSION
+
+          docker tag $IMAGE_NAME $IMAGE_ID:$VERSION
+          docker push $IMAGE_ID:$VERSION

.gitignore

@@ -127,3 +127,12 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# Model files
+*Model
+
+# zip and avi files
+*.zip
+!src/static/assets/images/test-images.zip
+*.avi
+**/data/**

.vscode/launch.json

@@ -0,0 +1,24 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python: Flask",
+            "type": "python",
+            "request": "launch",
+            "program": "${workspaceFolder}/src/main.py",
+            "env": {
+              "USERS_DICT": "{'user1': 'stork'}",
+            },
+            "args": [
+                "run",
+                "--no-debugger",
+                "--no-reload"
+            ],
+            "jinja": true,
+            "justMyCode": true
+        }
+    ]
+}

Dockerfile

@@ -0,0 +1,39 @@
+FROM python:3.8.16-slim
+#===============================#
+# Docker Image Configuration	#
+#===============================#
+LABEL org.opencontainers.image.source='https://github.com/eipm/stork-v' \
+    vendor='Englander Institute for Precision Medicine' \
+    description='STORK-V' \
+    maintainer='paz2010@med.cornell.edu' \
+    base_image='python' \
+    base_image_version='3.8.16-slim'
+
+ENV APP_NAME='stork-v' \
+    TZ='US/Eastern'
+
+#===================================#
+# Install Prerequisites             #
+#===================================#
+COPY requirements.txt /${APP_NAME}/requirements.txt
+RUN apt-get update && apt-get install ffmpeg libsm6 libxext6  -y
+RUN pip install --upgrade pip && pip install -r /${APP_NAME}/requirements.txt
+#===================================#
+# Copy Files and set work directory	#
+#===================================#
+COPY src /${APP_NAME}
+WORKDIR /${APP_NAME}
+#===================================#
+# Startup                           #
+#===================================#
+EXPOSE 80
+ENV PATH=$PATH:/${APP_NAME}
+ENV PYTHONPATH /${APP_NAME}
+VOLUME /${APP_NAME}/data
+VOLUME /${APP_NAME}/temp
+VOLUME /${APP_NAME}/stork_v/models
+
+HEALTHCHECK --interval=30s --timeout=30s --retries=3 \
+    CMD curl -f -k http://0.0.0.0/api/healthcheck || exit 1
+
+CMD python3 /${APP_NAME}/main.py

README.md

@@ -1 +1,33 @@
-# stork-v
+# stork-v
+
+[![Actions Status](https://github.com/eipm/stork-v/workflows/Docker/badge.svg)](https://github.com/eipm/stork-v/actions) [![Github](https://img.shields.io/badge/github-1.0.0-green?style=flat&logo=github)](https://github.com/eipm/stork-v) [![EIPM Docker Hub](https://img.shields.io/badge/EIPM%20docker%20hub-1.0.0-blue?style=flat&logo=docker)](https://hub.docker.com/repository/docker/eipm/stork-v) [![GitHub Container Registry](https://img.shields.io/badge/GitHub%20Container%20Registry-1.0.0-blue?style=flat&logo=docker)](https://github.com/orgs/eipm/packages/container/package/stork-v) [![Python 3.8.16](https://img.shields.io/badge/python-3.8.16-blue.svg)](https://www.python.org/downloads/release/python-360/) [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+## Set up local environment and install dependencies
+
+Install requirements from requirements.txt
+`pip install -r requirements.txt`
+
+Add the models in the folder
+`src/stork_v/models`
+
+## Execute a model as script
+
+Add the zip file in the expeted location `src/data/78645636.zip` and run the command
+`python src/test.py`
+
+## Docker run command
+
+
+```
+PATH_TO_MODELS=<set the location of your models directory>
+PATH_TO_DATA=<set the location of you data directory>
+PATH_TO_TEMP=<set the location of the temp directory used for creating the videos>
+
+docker run --name stork-v \
+-v $PATH_TO_MODELS:/stork-v/stork_v/models \
+-v $PATH_TO_DATA:/stork-v/data \
+-v $PATH_TO_TEMP:/stork-v/temp \
+-e USERS_DICT="{'user1': 'stork'}" \
+-p 8080:80 \
+stork-v
+```

requirements.txt

@@ -0,0 +1,56 @@
+absl-py==1.3.0
+astunparse==1.6.3
+cachetools==5.2.0
+certifi==2022.12.7
+charset-normalizer==2.1.1
+click==8.1.3
+Flask==2.2.2
+Flask-Cors==3.0.10
+flatbuffers==2.0.7
+gast==0.4.0
+google-auth==2.15.0
+google-auth-oauthlib==0.4.6
+google-pasta==0.2.0
+grpcio==1.51.1
+h5py==3.7.0
+idna==3.4
+importlib-metadata==5.1.0
+itsdangerous==2.1.2
+Jinja2==3.1.2
+joblib==1.2.0
+keras==2.7.0
+Keras-Preprocessing==1.1.2
+libclang==14.0.6
+Markdown==3.4.1
+MarkupSafe==2.1.1
+marshmallow==3.19.0
+numpy==1.23.5
+oauthlib==3.2.2
+opencv-python==4.6.0.66
+opt-einsum==3.3.0
+packaging==22.0
+pandas==1.5.2
+protobuf==3.20.3
+pyasn1==0.4.8
+pyasn1-modules==0.2.8
+python-dateutil==2.8.2
+pytz==2022.6
+requests==2.28.1
+requests-oauthlib==1.3.1
+rsa==4.9
+scikit-learn==1.2.0
+scipy==1.9.3
+six==1.16.0
+tensorboard==2.11.0
+tensorboard-data-server==0.6.1
+tensorboard-plugin-wit==1.8.1
+tensorflow==2.7.0
+tensorflow-estimator==2.7.0
+tensorflow-io-gcs-filesystem==0.28.0
+termcolor==2.1.1
+threadpoolctl==3.1.0
+typing_extensions==4.4.0
+urllib3==1.26.13
+Werkzeug==2.2.2
+wrapt==1.14.1
+zipp==3.11.0

src/.editorconfig

@@ -0,0 +1,24 @@
+# top-most EditorConfig file
+root = true
+
+# Unix-style newlines with a newline ending every file
+[*]
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+charset = utf-8
+
+# 4 space indentation
+[*.{py,html}]
+indent_style = space
+indent_size = 4
+
+# 2 space indentation
+[*.{js,json,y{a,}ml,cwl}]
+indent_style = space
+indent_size = 2
+
+[*.{md}]
+trim_trailing_whitespace = false
+indent_style = space
+indent_size = 2