Merge pull request #2 from eipm/develop

Develop

.gitignore

@@ -1 +1,2 @@
-data
+data
+.vscode

README.md

@@ -1,48 +1,52 @@
-flask swagger
-flask uploader
-flask and nginx
+# Stork
 
-# Export Requirements
+Classify IVF images in real time.
 
-```bash
-pip freeze > requirements.txt
-```
+[![Python 3.6](https://img.shields.io/badge/python-3.6-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)
 
-## Production Consideration
-Use a production WSGI server instead
+![Stork Logo](docs/images/logo.jpg)
 
-## Run Manually
+## Stork Requirements
 
-```bash
-$ python convert.py ../Images/train process/ 0
-$ cd run
-$ chmod 777 load_inception_v1.sh
-$ cd ..
-$ ./run/load_inception_v1.sh
-$ python predict.py v1 ../result/ ../../Images/test output.txt 2
-```
+- Docker. Get it from [here](https://www.docker.com/).
+- `process` and `result` folders from ML training (Not included in this repository).
 
-### Run with Docker
+## Running Stork using Docker
 
-#### Environment Variables
+### Load Environment Variables
 
 ```bash
-OUTPUT_DIR=~/Documents/2.GitHub/eipm/stork-ui/data/output/
-UPLOAD_DIR=~/Documents/2.GitHub/eipm/stork-ui/data/uploads/
-PROCESS_DIR=~/Documents/2.GitHub/eipm/stork-ui/data/process/
-RESULT_DIR=~/Documents/2.GitHub/eipm/stork-ui/data/result/
+DOCKER_CONTAINER_NAME=stork \
+STORK_PORT=3000 \
+OUTPUT_DIR=/stork/data/output/
+UPLOAD_DIR=/stork/data/uploads/
+PROCESS_DIR=/stork/data/process/
+RESULT_DIR=/stork/data/result/
+STORK_TAG=latest
 ```
 
--v ${INPUT_DIR}:/input:ro \
+### Run Docker Container
 
 ```bash
-docker run -it --rm --name stork \
--p 3000:80 \
+docker run -d --name ${DOCKER_CONTAINER_NAME} \
+--restart on-failure:5 \
+-p ${STORK_PORT}:80 \
 -v ${OUTPUT_DIR}:/output \
 -v ${UPLOAD_DIR}:/uploads \
 -v ${PROCESS_DIR}:/stork/src/stork_src/process:ro \
 -v ${RESULT_DIR}:/stork/src/stork_src/result:ro \
-stork:latest /bin/bash
+--env USERS_DICT="{ 'eipm': 'stork', 'embryology': 'RyJv3n', 'reviewer': 'e9wR8S' }" \
+eipm/stork:${STORK_TAG}
 ```
 
-python3 ${PREDICT_DIR}/predict.py v1 ${RESULT_DIR} /uploads /output/output_results.txt 2
+Where:
+
+- **${DOCKER_CONTAINER_NAME}**: The Stork docker container name.
+- **${STORK_PORT}**: The Stork host port.
+- **${OUTPUT_DIR}**: Where Stork image classification logs will be written.
+- **${UPLOAD_DIR}**: Where Stork image will be saved.
+- **${PROCESS_DIR}**: Required directory from ML training.
+- **${RESULT_DIR}**: Required directory from ML training.
+- **${USERS_DICT}**: The users credentials dictionary to authenticate.
+- **${STORK_TAG}**: The stork version to deploy.

src/api/app.py

@@ -1,11 +1,13 @@
 import os
 import random
-from flask import Flask, jsonify, flash, request, redirect, url_for,send_from_directory
+from flask import Flask, jsonify, flash, request, redirect, url_for,send_from_directory,make_response
 from werkzeug.utils import secure_filename
 from flask_cors import CORS
+import uuid as myuuid
 import csv
 import ntpath
 import datetime
+from ast import literal_eval
 
 # Relative Imports
 from api.version import api_version
@@ -25,6 +27,8 @@
 app.config['CORS_HEADERS'] = 'Content-Type'
 CORS(app)
 
+users_dict = literal_eval(os.environ['USERS_DICT'])
+
 def allowed_file(filename):
     return '.' in filename and \
            filename.rsplit('.', 1)[1].lower() in ALLOWED_EXTENSIONS
@@ -45,55 +49,76 @@ def api_swagger():
 def healthcheck():
     return jsonify({'status':'Healthy', 'version':api_version()})
 
+@app.route('/login', methods = ['GET'])
+def serve_login_page():
+    return send_from_directory(static_file_dir, 'login.html')
+
+@app.route('/api/login', methods = ['POST'])
+def login():
+    username = request.form['username']
+    password = request.form['password']
+    if username and users_dict[username] == password:
+        redirect_to_index = redirect('/')
+        response = make_response(redirect_to_index)
+        uuid = str(myuuid.uuid4())
+        response.set_cookie('stork-auth', uuid, max_age=3600)
+        return response
+    return jsonify({}), 401
+
 @app.route('/api/upload', methods = ['POST'])
 def upload_image():
-
-    if request.method == 'POST':
-        # check if the post request has the file part
-        if 'image' not in request.files:
-            flash('No file part')
-            return redirect(request.url)
-
-        # 1. Create request directory
-        request_id = datetime.datetime.now().strftime("%Y_%m_%d_%H_%M_%S_%f")
-        request_dir = (os.path.join(app.config['UPLOAD_DIR'], request_id))
-        if not os.path.exists(request_dir):
-            os.makedirs(request_dir)
-
-        response_dict = {}
-        images_dict = {}
-        # For each uploaded image
-        for image in request.files.getlist("image"):
-
-            # 2. Save Image
-            filename = secure_filename(image.filename)
-            image.save(os.path.join(request_dir, filename))
-
-            images_dict[filename] = image.filename
-
-            # =============#
-            # Analyze Data #
-            # =============#
-
-        # 3. Specify Output log            
-        output_filename = 'output_' + request_id + '.txt'
-        output_file = os.path.join(OUTPUT_DIR, output_filename)
-
-        # 4. Run Stork
-        python_command='python3 ' + os.environ['PREDICT_DIR'] + '/predict.py v1 ' + os.environ['RESULT_DIR'] + ' ' + request_dir + ' ' + output_file + ' 2'
-        os.system(python_command)
-
-        # 5. Parse Stork Results            
-        image_results = list(csv.reader(open(output_file, 'r', encoding='utf8'), delimiter='\t'))
-
-        # ==================#
-        # Send JSON Results #
-        # ==================#
-
-        for image_result in image_results:
-            response_dict[images_dict[ntpath.basename(image_result[0])]] = { 'Good': image_result[1], 'Poor': image_result[2]}
-
-        return jsonify(response_dict), 200
+    auth_token = None
+    auth_header = request.headers.get('Authorization')
+    print(auth_header)
+    if auth_header is None or auth_header.split(" ")[1] is None:
+        flash('No Authorization header')
+        return jsonify({}), 401
+
+    # check if the post request has the file part
+    if 'image' not in request.files:
+        flash('No file part')
+        return redirect(request.url)
+
+    # 1. Create request directory
+    request_id = datetime.datetime.now().strftime("%Y_%m_%d_%H_%M_%S_%f")
+    request_dir = (os.path.join(app.config['UPLOAD_DIR'], request_id))
+    if not os.path.exists(request_dir):
+        os.makedirs(request_dir)
+
+    response_dict = {}
+    images_dict = {}
+    # For each uploaded image
+    for image in request.files.getlist("image"):
+
+        # 2. Save Image
+        filename = secure_filename(image.filename)
+        image.save(os.path.join(request_dir, filename))
+
+        images_dict[filename] = image.filename
+
+        # =============#
+        # Analyze Data #
+        # =============#
+
+    # 3. Specify Output log            
+    output_filename = 'output_' + request_id + '.txt'
+    output_file = os.path.join(OUTPUT_DIR, output_filename)
+
+    # 4. Run Stork
+    python_command='python3 ' + os.environ['PREDICT_DIR'] + '/predict.py v1 ' + os.environ['RESULT_DIR'] + ' ' + request_dir + ' ' + output_file + ' 2'
+    os.system(python_command)
+
+    # 5. Parse Stork Results            
+    image_results = list(csv.reader(open(output_file, 'r', encoding='utf8'), delimiter='\t'))
+
+    # ==================#
+    # Send JSON Results #
+    # ==================#
+
+    for image_result in image_results:
+        response_dict[images_dict[ntpath.basename(image_result[0])]] = { 'Good': image_result[1], 'Poor': image_result[2]}
+
+    return jsonify(response_dict), 200
 
 if __name__ == '__main__':
     app.run(host='0.0.0.0', port=80)

src/static/assets/stork.css

@@ -7,6 +7,27 @@ body {
     margin:20px;
 }
 
+footer {
+    position: absolute;
+    right: 0;
+    left: 0;
+    bottom: 0;
+    text-align: center;
+    background-color: whitesmoke;
+    background-origin: padding-box;
+    display: block;
+    font-size: 12px;
+    min-height: 125px;
+    margin-top: 40px;
+    padding: 12px;
+    align-items: center;
+}
+
+.footer-logo {
+    margin: 10px;
+    height: 40px;
+}
+
 .btn {
     background-color: #3498db;
 }
@@ -25,6 +46,7 @@ body {
 
 .center {
     text-align: center;
+    margin: auto;
 }
 
 .loader {
@@ -53,6 +75,17 @@ body {
     100% { transform: rotate(360deg); }
 }
 
+.login-container {
+    background-color: whitesmoke;
+    padding: 40px;
+    margin-top: 100px;
+    max-width: 300px
+}
+
+.login-title {
+    margin-bottom: 30px;
+}
+
 #imageCards-placeholder {
     background-color: whitesmoke;
     padding: 5px;