Merge branch 'development' of github.com:datasci4health/harena-logger…

… into development

README.md

@@ -1 +1,119 @@
-# harena-logger
+[![GitHub license](https://img.shields.io/github/license/Naereen/StrapDown.js.svg)](https://github.com/datasci4health/harena-manager/blob/master/LICENSE)
+[![Docker Automated](https://img.shields.io/docker/cloud/automated/datasci4health/harena-manager.svg?style=flat)](https://cloud.docker.com/u/datasci4health/repository/registry-1.docker.io/datasci4health/harena-manager)
+[![Docker Build](https://img.shields.io/docker/cloud/build/datasci4health/harena-manager.svg?style=flat)](https://cloud.docker.com/u/datasci4health/repository/registry-1.docker.io/datasci4health/harena-manager)
+[![Docker Pulls](https://img.shields.io/docker/pulls/datasci4health/harena-manager.svg?style=flat)](https://cloud.docker.com/u/datasci4health/repository/registry-1.docker.io/datasci4health/harena-manager)
+[![Docker Stars](https://img.shields.io/docker/stars/datasci4health/harena-manager.svg?style=flat)](https://cloud.docker.com/u/datasci4health/repository/registry-1.docker.io/datasci4health/harena-manager)
+
+# herena-logger
+
+[Harena](https://github.com/datasci4health/harena)'s API for managing users and clinical cases.
+
+## Table of Contents 
+
+   * [herena-manager](#herena-manager)
+      * [Table of Contents](#table-of-contents)
+      * [Getting Started](#getting-started)
+         * [Running as Docker containers - Linux](#running-as-docker-containers---linux)
+         * [Running as Docker containers - Windows](#running-as-docker-containers---windows)
+         * [Running locally - Linux](#running-locally---linux)
+         * [Running locally - Windows](#running-locally---windows)
+      * [System Requirements](#system-requirements)
+         * [For running as Docker containers](#for-running-as-linuxwindows-docker-containers)
+         * [For running locally](#for-running-locally)
+      * [Configuration](#configuration)
+         * [Virtualenvs: AdonisJS](#virtualenvs-adonisjs)
+         * [Virtualenvs: Database](#virtualenvs-database)
+      * [Contributing](#contributing)
+         * [Project organization](#project-organization)
+         * [Branch organization (future CI/CD)](#branch-organization-future-cicd)
+
+## Getting Started
+
+### Running as Docker containers - Linux
+
+```bash
+sudo apt-get install -y wget
+wget https://github.com/datasci4health/harena-manager/blob/master/docker-compose.yml
+sudo docker-compose up
+```
+
+<small> Make sure you have **node.js** and **npm** already installed (see [system requirements](#system-requirements) for more details). </small>
+
+
+### Running as Docker containers - Windows
+
+//to do
+
+### Running as Docker containers - Linux´
+```bash
+sudo docker run datasci4health/harena-logger:latest
+```
+
+### Running locally - Linux
+
+First, clone this repository and enter the folder:
+
+```bash
+git clone https://github.com/datasci4health/harena-logger 
+cd harena-logger
+```
+```bash
+cd modules/relayer                     # entering the source folder
+pip3 install -r requirements.txt       # installing requirements packages for python
+export FLASK_APP=server.py             # defining flask application
+flask run                              # running the application
+``` 
+
+### Running locally - Windows
+
+//to do
+
+## System Requirements
+
+### For running as Docker containers
+
+* [docker]()
+* [docker-compose]()
+
+### For running locally
+
+##### System dependencies
+
+* flask
+* flask-restful
+* flask-cors
+* paho-mqtt
+* pymongo
+
+## Configuration
+
+### Virtualenvs
+
+* HARENA_LOGGER_BROKER_HOST = mqtt host
+* HARENA_LOGGER_BROKER_PORT = mqtt host port
+
+* HARENA_LOGGER_FLASK_HOST  = Flask host
+* HARENA_LOGGER_FLASK_PORT  = Flask port
+* HARENA_LOGGER_FLASK_DEBUG = Flask debug
+
+* HARENA_LOGGER_MONGODB_HOST = mongo host
+* HARENA_LOGGER_MONGODB_PORT = mongo port
+* HARENA_LOGGER_MONGODB_DB  = mongo database name
+* HARENA_LOGGER_MONGODB_COLLECTION = mongo current document
+
+## Contributing
+
+### Project organization
+
+//to do
+
+### Branch organization (future CI/CD)
+* **feature/< label >:**
+    * new features.
+* **development:**
+    * Protected. Must use _pull request_ to merge new features.
+* **master:**
+    * Version running at http://cloud.lis.ic.unicamp.br/harena/latest .
+    * Protected. Must use _pull request_ to merge evolutions of the _development_ branch.
+* **tags:**
+    * Are used for creating Dockerhub image versions at https://cloud.docker.com/u/datasci4health/repository/docker/datasci4health/harena-logger .    

modules/relayer/Dockerfile

@@ -4,7 +4,7 @@ WORKDIR /app
 
 COPY requirements.txt .
 
-RUN pip3 install -r requirements.txt
+RUN pip3 install -U -r requirements.txt
 
 ADD . .
 

modules/relayer/requirements.txt

@@ -1,6 +1,7 @@
 #python-dotenv
 flask
 flask_restful
+flask-cors
 #Flask-MongoAlchemy
 #flask-migrate
 paho-mqtt

modules/relayer/src/config.py

@@ -0,0 +1,15 @@
+import os
+
+class Config(object):
+
+    HARENA_LOGGER_BROKER_HOST        = os.environ.get('HARENA_LOGGER_BROKER_HOST',         'localhost')
+    HARENA_LOGGER_BROKER_PORT        = int(os.environ.get('HARENA_LOGGER_BROKER_PORT',           1883))
+
+    HARENA_LOGGER_FLASK_HOST         = os.environ.get('HARENA_LOGGER_FLASK_HOST',            '0.0.0.0')
+    HARENA_LOGGER_FLASK_PORT         = int(os.environ.get('HARENA_LOGGER_FLASK_PORT',            5000))
+    HARENA_LOGGER_FLASK_DEBUG        = bool(os.environ.get('HARENA_LOGGER_FLASK_DEBUG',         False))
+
+    HARENA_LOGGER_MONGODB_HOST       = os.environ.get('HARENA_LOGGER_MONGODB_HOST',        'localhost')
+    HARENA_LOGGER_MONGODB_PORT       = int(os.environ.get('HARENA_LOGGER_MONGODB_PORT',         27017))
+    HARENA_LOGGER_MONGODB_DB         = os.environ.get('HARENA_LOGGER_MONGODB_DB',      'harena_logger')
+    HARENA_LOGGER_MONGODB_COLLECTION = os.environ.get('HARENA_LOGGER_MONGODB_COLLECTION', 'executions')

modules/relayer/src/server.py

@@ -1,11 +1,13 @@
 import os
 import json
-from flask import Flask, request, jsonify
-from flask_restful import Resource, Api
 import paho.mqtt.client as paho
 import random
 import pymongo
 import time
+from flask import Flask, request, jsonify
+from flask_restful import Resource, Api
+from config import Config
+from flask_cors import CORS
 
 
 class IndexResource(Resource):
@@ -22,72 +24,65 @@ def get(self):
       return message
 
 
-
 class HarenaMessageResource(Resource):
 
     def __init__(self, broker, mongodb_collection):
-      self.broker = broker
-      self.mongodb_collection = mongodb_collection
+        self.broker = broker
+        self.mongodb_collection = mongodb_collection
 
     def post(self):
-      message = request.get_json()
-      print(json.dumps(message))
-      topic   = message['topic']
-      payload = message['payload']
+        message = request.get_json()
+        print(json.dumps(message))
+        topic   = message['topic']
+        payload = message['payload']
 
-      message['timestamp'] = "{}".format(int(round(time.time() * 1000)))
+        message['timestamp'] = "{}".format(int(round(time.time() * 1000)))
 
-      broker_publishing_flag = self.broker.publish(topic,json.dumps(payload))
-      mongodb_insertion_flag = self.mongodb_collection.insert(message)
+        broker_publishing_flag = self.broker.publish(topic,json.dumps(payload))
+        mongodb_insertion_flag = self.mongodb_collection.insert_one(message)
 
-      return 'Message published successfully',201
+        return 'Message published successfully', 201
 
     def get(self):
-      docs = self.mongodb_collection.find().sort([("timestamp", pymongo.DESCENDING)])
+        docs = self.mongodb_collection.find().sort([("timestamp", pymongo.DESCENDING)])
 
-      items = []
+        items = []
 
-      for doc in docs:
-        doc['_id'] = str(doc['_id'])
-        items.append(doc)
+        for doc in docs:
+            doc['_id'] = str(doc['_id'])
+            items.append(doc)
 
-      return jsonify({'execution_stream':items})
+        return jsonify({'execution_stream':items})
 
     def delete(self):
-      self.mongodb_collection.delete_many({})
-
-      return 'Messages in the execution stream deleted successfully'
-
+        self.mongodb_collection.delete_many({})
+        data = {"message":'Messages in the execution stream deleted successfully'}
 
+        return jsonify(data)
 
 
 if __name__ == '__main__':
-
-      web_app = Flask(__name__)
-      api     = Api(web_app)
-
-      config     = {}
-      config['broker_host']        = os.environ.get('HARENA_LOGGER_BROKER_HOST', 'localhost')
-      config['broker_port']        = int(os.environ.get('HARENA_LOGGER_BROKER_PORT', 1883))
 
-      config['flask_host']         = os.environ.get('HARENA_LOGGER_FLASK_HOST',  '0.0.0.0')
-      config['flask_port']         = int(os.environ.get('HARENA_LOGGER_FLASK_PORT',  5000))
-      config['flask_debug']        = bool(os.environ.get('HARENA_LOGGER_FLASK_DEBUG', False))
+    web_app = Flask(__name__)
+    web_app.config.from_object(Config)
+    CORS(web_app)
+    api     = Api(web_app)
 
-      config['mongodb_host']       = os.environ.get('HARENA_LOGGER_MONGODB_HOST',       'localhost')
-      config['mongodb_port']       = int(os.environ.get('HARENA_LOGGER_MONGODB_PORT',       27017))
-      config['mongodb_db']         = os.environ.get('HARENA_LOGGER_MONGODB_DB',         'harena_logger')
-      config['mongodb_collection'] = os.environ.get('HARENA_LOGGER_MONGODB_COLLECTION', 'executions')
+    mongodb_client     = pymongo.MongoClient("mongodb://{0}:{1}/"
+        .format(web_app.config['HARENA_LOGGER_MONGODB_HOST'], \
+        web_app.config['HARENA_LOGGER_MONGODB_PORT']))
 
-      mongodb_client     = pymongo.MongoClient("mongodb://{0}:{1}/".format(config['mongodb_host'],config['mongodb_port']))
-      mongodb_db         = mongodb_client[config['mongodb_db']]
-      mongodb_collection = mongodb_db[    config['mongodb_collection']]
+    mongodb_db         = mongodb_client[web_app.config['HARENA_LOGGER_MONGODB_DB']]
+    mongodb_collection = mongodb_db[web_app.config['HARENA_LOGGER_MONGODB_COLLECTION']]
 
-      broker = paho.Client("publisher{0}".format(random.randint(0,99999999)) )
-      broker.connect(config['broker_host'],config['broker_port'])  
-      broker.reconnect_delay_set(min_delay=1, max_delay=20)
+    broker = paho.Client("publisher{0}".format(random.randint(0,99999999)) )
+    broker.connect(web_app.config['HARENA_LOGGER_BROKER_HOST'],
+                   web_app.config['HARENA_LOGGER_BROKER_PORT'])
+    broker.reconnect_delay_set(min_delay=1, max_delay=20)
 
-      api.add_resource(IndexResource,         '/',       resource_class_args=[broker,mongodb_client])
-      api.add_resource(HarenaMessageResource, '/message',resource_class_args=[broker,mongodb_collection])
+    api.add_resource(IndexResource,         '/',       resource_class_args=[broker,mongodb_client])
+    api.add_resource(HarenaMessageResource, '/message',resource_class_args=[broker,mongodb_collection])
 
-      web_app.run(host=config['flask_host'], port=config['flask_port'],debug=config['flask_debug'])
+    web_app.run(host=web_app.config['HARENA_LOGGER_FLASK_HOST'],
+                port=web_app.config['HARENA_LOGGER_FLASK_PORT'],
+                debug=web_app.config['HARENA_LOGGER_FLASK_DEBUG'])