Add Google Doc link.

.gitignore

@@ -0,0 +1,3 @@
+*.swp
+*.sqlite
+__pycache__

README.md

@@ -0,0 +1,113 @@
+# Fenceless Grazing System API Server
+
+This is the repository for the API server component of the Fenceless
+Grazing System. This server is written in Python using the Flask
+microframework, and uses the SQLAlchemy ORM to interact with the SQLite
+database.
+
+## Getting the Dependencies
+
+The API server depends on several packages to operate properly, which
+will likely not be installed by default on your system. There are two
+ways to get the required dependencies: using Python's
+`virtualenv` (standard in the Python ecosystem), or using Nix (only if you are into that kind of thing).
+
+### Getting the Dependencies with `virtualenv`
+
+First, create a virtual environment (this only has to be done once):
+
+```Bash
+virtualenv venv
+```
+
+Once the virtual environment has been created, activate it using the
+following command:
+
+```Bash
+source venv/bin/activate
+```
+
+This effectively creates an independent Python environment, into
+which you can install packages without affecting your entire
+system. You can now install the packages from the `requirements.txt` file:
+
+```Bash
+pip install -r requirements.txt
+```
+
+With this, you should have all the necessary dependencies.
+
+### Getting the Dependencies with Nix
+
+Below is the Nix expression I use daily to work on
+this application:
+
+```Nix
+with import <nixpkgs> {};
+
+mkShell {
+    buildInputs = [ (python3.withPackages (ps: with ps; [ flask flask_sqlalchemy pyjwt bcrypt geopy pip ])) ];
+}
+```
+
+Note that some packages (`geopy` in particular) are currently unstable; the expressions from stable Nixpkgs
+may not provide a working derivation. When using the `nixpkgs-unstable`, I have no such issues.
+
+## Setting Up
+The application requires the `DB_LOC` environment variable to be set to indicate the location
+of the database that the server should use:
+
+```Bash
+export DB_LOC=database.sqlite
+```
+
+Additionally, Flask uses the `FLASK_APP` environment variable to determine the entry point
+of a web application
+
+```Bash
+# Here, fgs represents the fgs/ directory in the repository's root.
+export FLASK_APP=fgs
+```
+
+Finally, on first run, you need to create the tables in the application's database.
+This can be done as follows:
+
+```Python
+flask shell
+# Imports, among other things, the db variable, which is the handle for the SQLAlchemy ORM.
+from fgs import *
+
+# SQLAlchemy needs to be aware of the various tables in our database
+from fgs.model import *
+
+# Creates all tables
+db.create_all()
+
+# It also helps to set up a user and a couple of collars:
+user = User(username='user', password='password')
+collar1 = Collar(name='Sample Collar', active=True)
+collar2 = Collar(name='Another Collar', active=True)
+
+# To add the newly created objects to the database, use
+# db.session.add and db.session.commit
+db.session.add(user)
+db.session.add(collar1)
+db.session.add(collar2)
+db.session.commit()
+
+# You can now press Ctrl-D to exit the Flask shell. 
+```
+
+Once the database has been created, you can start the server
+with:
+
+```Bash
+flask run
+```
+
+## Next Steps
+Once the server is up and running, consider setting up the
+[app](https://dev.danilafe.com/CS-46X/app), which is able
+interact with this API server. Additionally, check out the
+[cow description language](https://dev.danilafe.com/CS-46X/cdl)
+if you want to generate mock data for the API server's database.

REVIEW.md

@@ -0,0 +1,12 @@
+# Code Review Changes
+
+Original tables with verbatim feedback can be found in [this Google Doc](https://docs.google.com/document/d/19d5U-ieQyGVVNQjj0rUouzIqF53evEP6yss-wyqNXiQ/edit?usp=sharing).
+
+|Comment|Adjustment|
+|-------|----------|
+|The `models.py` file is too difficult to understand.| `models.py` updated with Python docstrings.|
+|The code in general is not commented.| Every function in the codebase commented with Python docstring to explain usage and implementation. Some comments added to functions longer than a few lines.|
+|It's difficult to set up the server software.| `requirements.txt` file updated with all packages; `default.nix` provided via `README.md` to provide alternative installation method.|
+|No README file.| README file added with installation and configuration instructions.|
+|No unit tests.| Developed [cow description language](https://dev.danilafe.com.CS-46x/cdl.git) to test database access (tests still need to be run manually, due to time constraints).
+|Unrolled list of variables can be converted to list.| Unrolled fields kept to maintain isomorphism with hardware, where unrolling variables is necessary due to hardware and radio limitations. Methods written to limit the need for manually accessing `coord*x` and `coord*y` variables.|

fgs/flatten.py

@@ -0,0 +1,83 @@
+from fgs.model import *
+import itertools
+
+def flatten(points):
+    """
+    This function is used to convert
+    a list of points of arbitrary length into
+    a BoundingBox, which only has a fixed number
+    of fields (all of which are hardcoded variable names.
+    """
+
+    # To convert an index to a variable namne, we define
+    # a list of setters, where the 1st setter changes the
+    # coord0 field, and so on.
+    def set0x(b, v): b.coord0x = v
+    def set1x(b, v): b.coord1x = v
+    def set2x(b, v): b.coord2x = v
+    def set3x(b, v): b.coord3x = v
+    def set4x(b, v): b.coord4x = v
+    def set5x(b, v): b.coord5x = v
+    def set6x(b, v): b.coord6x = v
+    def set7x(b, v): b.coord7x = v
+    def set8x(b, v): b.coord8x = v
+    def set9x(b, v): b.coord9x = v
+
+    def set0y(b, v): b.coord0y = v
+    def set1y(b, v): b.coord1y = v
+    def set2y(b, v): b.coord2y = v
+    def set3y(b, v): b.coord3y = v
+    def set4y(b, v): b.coord4y = v
+    def set5y(b, v): b.coord5y = v
+    def set6y(b, v): b.coord6y = v
+    def set7y(b, v): b.coord7y = v
+    def set8y(b, v): b.coord8y = v
+    def set9y(b, v): b.coord9y = v
+
+    setters_x = [ set0x, set1x, set2x, set3x, set4x, set5x, set6x, set7x, set8x, set9x ]
+    setters_y = [ set0y, set1y, set2y, set3y, set4y, set5y, set6y, set7y, set8y, set9y ]
+
+    boundary = BoundingBox()
+    boundary.num_points = len(points)
+    for (point, set_x, set_y) in zip(points, setters_x, setters_y):
+        set_x(boundary, float(point['longitude']))
+        set_y(boundary, float(point['latitude']))
+    return boundary
+
+def unflatten(boundary):
+    """
+    This function is used to convert a grazing boundary,
+    which has 10 hardcoded vertex fields, to
+    an arbitrary list of points.
+    """
+    if boundary is None: return []
+
+    getters_x = [
+            lambda b: b.coord0x,
+            lambda b: b.coord1x,
+            lambda b: b.coord2x,
+            lambda b: b.coord3x,
+            lambda b: b.coord4x,
+            lambda b: b.coord5x,
+            lambda b: b.coord6x,
+            lambda b: b.coord7x,
+            lambda b: b.coord8x,
+            lambda b: b.coord9x
+        ]
+    getters_y = [
+            lambda b: b.coord0y,
+            lambda b: b.coord1y,
+            lambda b: b.coord2y,
+            lambda b: b.coord3y,
+            lambda b: b.coord4y,
+            lambda b: b.coord5y,
+            lambda b: b.coord6y,
+            lambda b: b.coord7y,
+            lambda b: b.coord8y,
+            lambda b: b.coord9y
+        ]
+    
+    points = []
+    for i in range(boundary.num_points):
+        points.append({'longitude': str(getters_x[i](boundary)), 'latitude': str(getters_y[i](boundary))})
+    return points

fgs/jwt.py

@@ -5,11 +5,20 @@ from .model import User
 from functools import wraps
 
 def get_jwt(self):
+    """
+    Extension method for the User class to
+    compute the user's JSON Web Token
+    """
     return jwt.encode({'id': self.id}, app.secret_key, algorithm='HS256')
 
 User.get_jwt = get_jwt
 
 def jwt_required(f):
+    """
+    Decorator for routes in the views module,
+    returning a bad request error if the "Authorization"
+    header is not set with a valid authentication token.
+    """
     @wraps(f)
     def decorated_function(*args, **kwargs):
         if 'Authorization' not in request.headers:

fgs/model.py

@@ -2,12 +2,35 @@ from . import db
 import bcrypt
 
 class Collar(db.Model):
+    """
+    Table representing a collar device.
+
+    The collar has the following columns:
+        name - the collar's human-readable name.
+        active - whether or not the collar should be shown to users.
+        data_points - the list of coordinates transmitted by this collar.
+        boundary - the collar's valid grazing boundary (can be null)
+    """
     id = db.Column(db.Integer, primary_key=True)
     name = db.Column(db.String)
     active = db.Column(db.Boolean)
     data_points = db.relationship('DataPoint')
+    boundary = db.relationship("BoundingBox", uselist=False)
 
 class DataPoint(db.Model):
+    """
+    A data point transmitted by the collar.
+
+    The data point has the following attributes; though they
+    were specified in the design document, currently, only the latitude,
+    longitude, and datetime (along with the collar ID) are used.
+        collar_id - the identifier of the collar that generated this point.
+        longitude - the collar's longitude.
+        latitude - the collar's latitude.
+        battery_level - the collar's battery level, between 0 and 1.
+        datetime - the time when this data point was collected.
+        outside - whether or not the collar is outside the grazing boundary.
+    """
     id = db.Column(db.Integer, primary_key=True)
     collar_id = db.Column(db.Integer, db.ForeignKey('collar.id'))
     longitude = db.Column(db.Float(precision=10))
@@ -25,24 +48,95 @@ class DataPoint(db.Model):
                 }
 
 class StimulusActivation(db.Model):
+    """
+    A report made by the collar when it attempts
+    to get the animal to move back into the grazing area.
+
+    The report has the following attributes:
+        collar_id - the collar that reported the attempt.
+        longitude - the collar's longitude at the time of the attempt.
+        latitude - the collar's latitude at the time of the attempt.
+        volume_level - the volume level of the sound the collar emitted.
+        voltage_level - the voltage of the electric shock the collar emitted.
+        datetime - the time at which the attempt was made.
+    """
     id = db.Column(db.Integer, primary_key=True)
+    collar_id = db.Column(db.Integer, db.ForeignKey('collar.id'))
     longitude = db.Column(db.Float(precision=10))
     latitude = db.Column(db.Float(precision=10))
     volume_level = db.Column(db.Integer)
     voltage_level = db.Column(db.Integer)
+    datetime = db.Column(db.DateTime)
+
+
+class BoundingBox(db.Model):
+    """
+    A polygon bounding box represent the valid grazing area.
+
+    To more closely match the collar's hardware limitation,
+    this table has exactly 10 vertex points. These points
+    are converted to and from lists of coordinates
+    by the unflatten and flatten functions, respectively.
+    Other than the coodinates, the polygon has the following
+    attributes:
+        collar_id - the identifier of the collar whose grazing area this is.
+        num_points - the number of points (from 0) that are actually used in this polygon.
+    """
+    id = db.Column(db.Integer, primary_key=True)
+    collar_id = db.Column(db.Integer, db.ForeignKey('collar.id'))
+    num_points = db.Column(db.Integer)
+    needs_push = db.Column(db.Boolean)
+    coord0x = db.Column(db.Float(precision=10))
+    coord0y = db.Column(db.Float(precision=10))
+    coord1x = db.Column(db.Float(precision=10))
+    coord1y = db.Column(db.Float(precision=10))
+    coord2x = db.Column(db.Float(precision=10))
+    coord2y = db.Column(db.Float(precision=10))
+    coord3x = db.Column(db.Float(precision=10))
+    coord3y = db.Column(db.Float(precision=10))
+    coord4x = db.Column(db.Float(precision=10))
+    coord4y = db.Column(db.Float(precision=10))
+    coord5x = db.Column(db.Float(precision=10))
+    coord5y = db.Column(db.Float(precision=10))
+    coord6x = db.Column(db.Float(precision=10))
+    coord6y = db.Column(db.Float(precision=10))
+    coord7x = db.Column(db.Float(precision=10))
+    coord7y = db.Column(db.Float(precision=10))
+    coord8x = db.Column(db.Float(precision=10))
+    coord8y = db.Column(db.Float(precision=10))
+    coord9x = db.Column(db.Float(precision=10))
+    coord9y = db.Column(db.Float(precision=10))
 
 class User(db.Model):
+    """
+    Database model representing the user. The user's password is stored
+    as a Bcrypt hash, and accessed via the password property.
+
+    The user has the following attributes:
+        username - the username of the user
+        password_hash - the Bcrypt hash stored in the database. This can be set using the password property.
+    """
     id = db.Column(db.Integer, primary_key=True)
     username = db.Column(db.String)
     password_hash = db.Column(db.String)
 
     def get_password(self):
+        """
+        Returns the user's encrypted password.
+        """
         return self.password_hash
 
     def set_password(self, password):
+        """
+        Encrypts and updates the user's password.
+        """
         self.password_hash = bcrypt.hashpw(password.encode(), bcrypt.gensalt())
 
     def check_password(self, password):
+        """
+        Checks if the given (unencrypted) password
+        matches the user's password hash.
+        """
         return bcrypt.checkpw(password.encode(), self.password_hash)
 
     password = property(get_password, set_password)

fgs/views.py

@@ -1,16 +1,32 @@
 from . import app, db
+from .flatten import flatten, unflatten
 from .jwt import jwt_required
 from .model import *
 from flask import g, jsonify, request, abort
 from sqlalchemy import func
-import geopy.distance
+from geopy.distance import geodesic
+from datetime import datetime, timedelta
 
 @app.route('/')
 def index():
+    """
+    Index function, mostly used to ensure that the API is up and running.
+    Does not require authentication.
+    """
     return 'Hello, world!'
 
 @app.route('/login', methods=['POST'])
 def login():
+    """
+    Authentication function.
+
+    The form data containing the username
+    and password is retrieved and compared against the database; if the
+    username does not exist, or  the password doesn't match,
+    the service responds with a "bad request". A JSON token, unique
+    to the user, is returned when the authentication succeeds. This
+    token can then be used by the routes protected with @jwt_required.
+    """
     username = request.form.get('username')
     password = request.form.get('password')
     if username is None or password is None: abort(400)
@@ -21,11 +37,23 @@ def login():
 @app.route('/me')
 @jwt_required
 def me():
+    """
+    Function used to ensure that a token is valid with the API.
+
+    Simply returns the username of the user to whom the token belongs.
+    """
     return jsonify({ 'username' : g.user.username })
 
 @app.route('/collars')
 @jwt_required
 def collars():
+    """
+    Function to retrieve the initial list of collars, to be shown on
+    the application's main page.
+
+    The response contains the identifier, name, and position of each
+    currently active collar.
+    """
     active_collars = []
     for collar in Collar.query.filter_by(active=True).all():
         max_point = DataPoint.query.filter_by(collar_id=collar.id).\
@@ -41,17 +69,34 @@ def collars():
 @app.route('/collars/stats/distance')
 @jwt_required
 def collars_distance():
+    """
+    One of the functions used for displaying graphs / statistics to the user.
+    Computes the total distance traveled by an animal.
+
+    Returns, for each active collar, the identifier, name,
+    and total distance traveled. The name is included for convenience,
+    to prevent further API requests.
+    """
+
     active_collars = []
     for collar in Collar.query.filter_by(active=True).all():
-        coords = DataPoint.query.filter_by(collar_id=collar.id).\
+        # Can't use SQLAlchemy's data_points field
+        # to further restrict query (without some tinkering, which would hurt elsewhere)
+        data_points = DataPoint.query.filter_by(collar_id=collar.id).\
                 order_by(DataPoint.datetime.desc())
-  
-        distance_kilometers = 0
-        coords_pairs = list(map(lambda e : (e.longitude, e.latitude), coords))
 
-        coord_last = coords_pairs.pop()
+        # Extract longitude and latitude
+        coords_pairs = list(map(lambda e : (e.latitude, e.longitude), data_points))
+
+        # The animal has not traveled at all; skip.
+        if len(coords_pairs) < 1: continue
+
+        # Start with the current location, and work backwards
+        # one data point at a time.
+        distance_kilometers = 0
+        coord_last = coords_pairs.pop(0)
         for coord in coords_pairs:
-            distance_kilometers += geopy.distance.VincentyDistance(coord_last,coord).km
+            distance_kilometers += geodesic(coord_last,coord).km
             coord_last = coord
          
         active_collars.append(
@@ -64,6 +109,11 @@ def collars_distance():
 @app.route('/collars/<int:id>/history')
 @jwt_required
 def collar_history(id):
+    """
+    Function to retrieve the complete history of a collar, sorted newest to oldest.
+
+    Returns a list of coordinates.
+    """
     collar = Collar.query.filter_by(id=id).first()
     if collar is None: abort(404)
 
@@ -76,7 +126,48 @@ def collar_history(id):
 @app.route('/collars/<int:id>/details')
 @jwt_required
 def collar_detail(id):
+    """
+    Function to get the information needed for a single-collar view.
+
+    At the moment, this information includes the collar's name, location,
+    valid grazing area, and how many times it had triggered the 
+    out-of-grazing-area stimulus in the last 24 hours.
+    """
     collar = Collar.query.filter_by(id=id).first()
     if collar is None: abort(404)
 
-    return jsonify({'id': collar.id, 'name': collar.name })
+    # get stimulus activation reports from within last 24 hours
+    since = datetime.now() - timedelta(hours=24)
+    stimulus_points = StimulusActivation.query.\
+            filter_by(collar_id=id).\
+            filter(StimulusActivation.datetime > since).\
+            order_by(StimulusActivation.datetime.desc())
+    n_stimulus = stimulus_points.count() 
+
+    return jsonify({'id': collar.id, 'name': collar.name, 'stimilus': n_stimulus, 'boundary': unflatten(collar.boundary) })
+
+@app.route('/collars/<int:id>/boundary/set', methods=['POST'])
+@jwt_required
+def collar_set_boundary(id):
+    """
+    Function to configure a collar's grazing boundary.
+
+    A grazing boundary is received from the application as a list of
+    vertices; we hide the the 10-point constraint from that part
+    of the system to prevent coupling. However, this means
+    that we need to convert an arbitrary list of points into
+    the flattened BoundingBox instance, which is handled
+    by flatten. Setting a collar boundary removes the old
+    boundary from the database.
+    """
+    collar = Collar.query.filter_by(id=id).first()
+    if collar is None: abort(404)
+
+    new_boundary = flatten(request.json)
+    new_boundary.needs_push = True
+    if collar.boundary is not None:
+        db.session.delete(collar.boundary)
+    collar.boundary = new_boundary
+    db.session.add(new_boundary)
+    db.session.commit()
+    return jsonify({})

requirements.txt

@@ -1,14 +1,22 @@
 bcrypt==3.1.7
-cffi==1.13.2
+cffi==1.14.0
-Click==7.0
+click==7.1.1
+cryptography==2.9.1
+ecdsa==0.14.1
 Flask==1.1.1
 Flask-SQLAlchemy==2.4.1
+geographiclib==1.50
+geopy==2.0.0a0
+greenlet==0.4.15
 itsdangerous==1.1.0
 Jinja2==2.11.1
 MarkupSafe==1.1.1
+msgpack==1.0.0
+packaging==20.1
 pycparser==2.19
 PyJWT==1.7.1
 pynvim==0.4.1
+pyparsing==2.4.6
 six==1.14.0
 SQLAlchemy==1.3.13
 Werkzeug==0.16.1

run.sh

@@ -6,5 +6,6 @@ fi
 
 # Run the Flask and Python server through inlets
 export DB_LOC=$3 
+export FLASK_ENV=development
 inlets client --remote=$1 --upstream=http://127.0.0.1:5000 --token=$2 &
 FLASK_APP=fgs flask run