detect merge conflicts

.gitignore

@@ -1,3 +1,8 @@
 __pycache__
 *.py[cod]
 .DS_Store
+
+# Elastic Beanstalk Files
+.elasticbeanstalk/*
+!.elasticbeanstalk/*.cfg.yml
+!.elasticbeanstalk/*.global.yml

README.md

@@ -1,80 +1,19 @@
-# Achoo
-Achoo uses a Raspberry Pi to predict if my son will need his inhaler on any given day using weather, pollen, and air quality data. If the prediction for a given day is above a specified threshold, the Pi will email his school nurse, and myself, notifying her that he may need preemptive treatment. **TUTORIAL COMING SOON**
-
-Prompted by [this](https://www.reddit.com/r/Python/comments/70udwq/what_routine_tasks_do_you_automate_with_programs/) reddit post. Lots of great ideas in there.
-
-**UPDATE: 09/27/2017**
-
-My goal is to have this repo completely decoupled from any UI and instead act as a restful-like API that could be consumed by any UI. Achoo's default UI is housed [here](https://github.com/tmthyjames/AchooUI).
-
-**UPDATE**
-
-I will be updating this readme fairly often for the next week or two to make sure the code and instructions are as readable as possible.
-
-## Environment setup
-
-First, you'll want to declare a few environment variables:
-
-`ACHOO_FROM_EMAIL` - the sender's email address.<br/>
-`ACHOO_TO_EMAIL` - the email addresses to send the alerts to.<br/>
-`ACHOO_GMAIL_PASSWORD` - to send emails (if you don't already have one) you'll need to register an app with gmail.<br/>
-`ACHOO_DARK_SKY_API_KEY` - for the weather data, I'm using [Dark Sky](https://darksky.net/dev). You get 1,000 free hits a day. Their pricing is really affordable.<br/>
-`ACHOO_DARK_SKY_LOCATION` - The latitude, longitude for the location you'll be tracking. <br/>
-`ACHOO_POLLEN_ZIPCODE` - The zipcode you'll be tracking.<br/>
-`ACHOO_DB_USERNAME` - the PostgreSQL username (or other database).<br/>
-`ACHOO_DB_PASSWORD` - PostgreSQL password.<br/>
-`ACHOO_DB_DATABASE` - Name of the database (default: `achoo`).<br/>
-`ACHOO_DB_PORT` - Port number (default: `5432`).<br/>
-
-## Achoo workflow
+![logo](app/static/img/ACHOO-FINAL.png)
 
-For now, the work flow is reflected in the bash script that runs daily:
 
-```bash
-#!/bin/bash
+**UPDATE: 01/10/2018**
 
-Rscript app/models/exe/r/train_model.r &&
+I have released Achoo beta version 0.1! Check it out at [achoo.us](https://achoo.us). Also, check out the [blog post about it](https://tmthyjames.github.io/tools/prediction/Achoo-beta-0.1/). Most of the info below is now obsolete and will be replaced shortly as Achoo is now a web app for users instead of just a repo for devs :) 
 
-python app/munging/get_allergy_data.py &&
-python app/munging/get_weather_data.py &&
-python app/munging/get_air_data.py &&
-
-Rscript app/models/exe/r/run_model.r &&
-
-python app/munging/get_results.py
-```
-
-1) Train the model (this assumes we have data, so I'll upload some test data that I've been using)
-2) Get all weather, allergy, and air quality data
-3) Run the model (this will write the results to the database after every run)
-4) Retrieve the results (this is the step that sends the email if the prediction is greater than X).
-
-This bash script currently runs as a cron job.
-
-**THIS IS LIKELY TO CHANGE SOON.**
-
-To record the inhaler/breathing treatment data, you'll run `treatment_tracker.py` from your Raspberry Pi like this:
-
-```bash
-$ python treatment_tracker.py &
-```
-
-I have two buttons on my Pi: one for his breathing treatment, the other for his inhaler (pics and a blog post coming soon).
-
-### Outstanding questions
+Achoo uses a Raspberry Pi to predict if my son will need his inhaler on any given day using weather, pollen, and air quality data. If the prediction for a given day is above a specified threshold, the Pi will email his school nurse, and myself, notifying her that he may need preemptive treatment. **TUTORIAL COMING SOON**
 
-1) Is there a better way than using a cron job?<br/>
-2) The Raspberry Pi isn't ideal. Maybe we should be using [Nomie 2](https://itunes.apple.com/us/app/nomie-2/id1190618299?mt=8) to record events? (HT to [sujins](https://www.reddit.com/user/sujins) for this suggestion). I'd like to make it easy for the user to add their own method and their own host for storing data.<br/>
-3) I have a feeling many users will want to easily add their own models (Nueral Networks, GBMs, GLMs, etc.). What is the best way for users to add their own models?<br/>
-4) Should we support two languages? Currently I'm using Python and R.<br/>
-5) I still have a lot of architectural concerns about this project so far, but I'm hoping things will be more smooth as a couple weeks' worth of development pass.<br/>
-6) **LONG TERM**: How to make this non-developer friendly? How can the typical person with allergies/asthma make use of this day-to-day? Can we make this a mobile app? I think this is my end goal.<br/>
+Prompted by [this](https://www.reddit.com/r/Python/comments/70udwq/what_routine_tasks_do_you_automate_with_programs/) reddit post. Lots of great ideas in there.
 
-### Here's my Pi setup
+### Here's my Pi setup (obsolete as this is all done through the app now)
 
 Blue button is for inhaler (first line of defense)
 
 red button is for breathing treatment (second line of defense; use this one if his symptoms are really bad)
 
-![From the top](img/IMG_5919.JPG)
+![From the top](app/static/img/IMG_5919.JPG)
 

SETUP.md

@@ -0,0 +1,72 @@
+# Achoo Environment Setup
+
+### Dependencies:
+
+You will need the following installed on your OS of choice to run Achoo:
+ * Python 3
+ * R
+ * PostgreSQL
+ * PostGIS with command line tools
+
+We recommend using a [virtualenv](https://docs.python.org/3/library/venv.html) to manage Python dependencies.
+
+To install the Python dependencies, run the following from the project root:
+
+`pip install -r requirements.txt`
+
+
+# Flask
+### Environment Variables:
+
+Variable Name | Value
+--- | ---
+`ACHOO_SECRET_KEY` | [Key for signing things](http://flask.pocoo.org/docs/0.12/api/#flask.Flask.secret_key), set to strong random value.
+`ACHOO_PG_CONN_STR` | [SQLAlchemy database URI (PostgreSQL)](http://docs.sqlalchemy.org/en/latest/core/engines.html#database-urls). Something like `postgresql://user@localhost:5432/achoo`.
+`ACHOO_GOOGLE_MAPS_API_KEY` | [Google Maps API Key](https://developers.google.com/maps/documentation/javascript/get-api-key).
+
+### Bootstrap the Database for the first time
+
+From the application root directory, run the following in a python interpreter to create the database and tables:
+
+```python
+from app.models.models import db
+db.create_all()
+```
+
+Initialize PostGIS:
+
+```bash
+psql achoo
+CREATE EXTENSION postgis;
+\q
+```
+
+Download and import GIS shapefiles and clean up:
+
+```bash
+mkdir gisdata
+cd gisdata
+wget http://www2.census.gov/geo/tiger/GENZ2016/shp/cb_2016_us_zcta510_500k.zip
+unzip cb_2016_us_zcta510_500k.zip
+shp2pgsql cb_2016_us_zcta510_500k.shp > gisdata.sql
+psql achoo < gisdata.sql
+cd ..
+rm -r gisdata
+```
+
+### Run the Web Application
+
+```bash
+python3 application.py
+```
+
+Or:
+
+```bash
+export FLASK_PATH=/path/to/Achoo/application.py
+flask run --reload
+```
+
+
+# Analytics
+TODO

app/__init__.py

@@ -0,0 +1,7 @@
+from flask import Flask
+import os
+
+application = Flask(__name__)
+application.config['SECRET_KEY'] = os.environ['ACHOO_SECRET_KEY']
+application.config['SQLALCHEMY_DATABASE_URI'] = os.environ['ACHOO_PG_CONN_STR']
+application.config['SQLALCHEMY_TRACK_MODIFICATIONS'] = False

ui/app/api/api.py → app/api/api.py

@@ -3,12 +3,38 @@
 from flask import request, url_for
 from flask_login import current_user, login_user
 
+from sqlalchemy import bindparam
+from sqlalchemy.sql import text
+from sqlalchemy.exc import DataError
+
 import requests
 import json
 
 # models
 from app.models.models import User, db, bcrypt, Treatment
 
+
+def get_zipcode_from_coords(lat=-86.725573627, lng=36.227447713):
+
+    # bindparams casts the input to SQLAlchemy types,
+    # throws DataError if types are wrong.
+    statement = text("""
+        select geom.geoid10 
+        from cb_2016_us_zcta510_500k geom 
+        where ST_Contains(geom.geom, ST_MakePoint(:lng, :lat))
+    """).bindparams(
+        bindparam('lng', value=lng, type_=db.Float),
+        bindparam('lat', value=lat, type_=db.Float)
+    )
+
+    try:
+        result = db.engine.execute(statement).first()
+    except DataError:
+        return None
+
+    if result:
+        return result[0]
+
 class Prediction(Resource):
 
     def get(self):
@@ -18,6 +44,7 @@ def post(self):
         capture_data = request.get_json()
         latitude = capture_data.get('coords').get('latitude')
         longitude = capture_data.get('coords').get('longitude')
+        zipcode = get_zipcode_from_coords(latitude, longitude)
         timestamp = capture_data.get('timestamp')
         treatment = capture_data.get('treatment')
         accuracy = capture_data.get('accuracy')
@@ -28,7 +55,8 @@ def post(self):
             lat=latitude,
             lng=longitude,
             treatment=treatment,
-            accuracy=accuracy
+            accuracy=accuracy,
+            zipcode=zipcode
         )
         db.session.add(treatment)
         db.session.commit()

app/config.py

@@ -0,0 +1,8 @@
+import os
+
+ENV = os.environ.get('ACHOO_DEBUG')
+
+class Config(object):
+    MSG = '(beta)'
+    VERSION = '0.1'
+    DEBUG = True if ENV == 'local' else False

ui/app/models/models.py → app/models/models.py

@@ -3,10 +3,10 @@
 from flask_bcrypt import Bcrypt
 from werkzeug.security import generate_password_hash, check_password_hash
 from flask_login import UserMixin
-from app import app
+from app import application
 
-db = SQLAlchemy(app)
-bcrypt = Bcrypt(app)
+db = SQLAlchemy(application)
+bcrypt = Bcrypt(application)
 
 
 class User(UserMixin, db.Model):
@@ -34,9 +34,10 @@ class Treatment(UserMixin, db.Model):
     __tablename__ = 'treatment'
     id = db.Column(db.Integer, primary_key=True)
     userid = db.Column(db.Integer, nullable=False)
-    timestamp = db.Column(db.Integer, nullable=False)
+    timestamp = db.Column(db.BigInteger, nullable=False)
     lng = db.Column(db.Float)
     lat = db.Column(db.Float)
     treatment = db.Column(db.String(100), nullable=False)
     accuracy = db.Column(db.Integer)
+    zipcode = db.Column(db.String(10))