Release 1.13

backend/README.md

@@ -16,7 +16,16 @@ sudo apt-get install python3 python3-dev
 sudo apt-get install -y libssl-dev libffi-dev
 ```
 
-#### PostgreSQL
+#### Using Docker
+You can use Docker to run the two primary dependencies for this project:  Postgres, and ElasticSearch
+
+1. create a directory at  ~/docker/volumes/stardrive
+2. chmod 777 ~/docker/volumes/stardrive/elasticsearch
+3. spin it all up, with docker-compose up
+* Optionally set up a run configuration in PyCharm
+
+####  Not Using Docker
+###### PostgreSQL
 * MacOS:
 [Download and install Postgres.app](https://postgresapp.com). This will install `postgres`, along with the command-line tools, including `psql`, `pg_ctl`, and others. Then update your `PATH` variable to look in the Postgres.app `bin` directory for the relevant Postgres CLI tools.
 ```BASH
@@ -27,28 +36,8 @@ export PATH="/Applications/Postgres.app/Contents/Versions/latest/bin:$PATH"
 ```BASH
 apt-get install postgresql postgresql-client libpq-dev
 ```
-
+###### Database Setup
-#### ElasticSearch
+*NOTE:* Docker will do this automatically, only necissary if you are doing it locally.
-We are currently using version 6, and should look at upgrading this in the future when my hair isn't on fire.
-
-* Debian/Ubuntu: https://medium.com/@pierangelo1982/how-to-install-elasticsearch-6-on-ubuntu-64316dc2de1c
-
-#### Angular
-```BASH
-npm install -g @angular/cli
-```
-
-### Project Setup
-* Please use Python 3's virtual environment setup, and install the dependencies in requirements.txt
-```bash
-cd backend
-python3 -m venv python-env
-source python-env/bin/activate
-pip3 install -r requirements.txt
-```
-
-## Database Setup
-### Create a Database
 *NOTE:* The configuration is currently set up to use "ed_pass" as a password.  You will be promoted to enter a password when you connect.
 * MacOS:
 ```BASH
@@ -68,6 +57,34 @@ exit
 ```
 If you are using Ubuntu you will likely need to [enable PSQL](https://help.ubuntu.com/community/PostgreSQL#Managing_users_and_rights) to manage its own users.
 
+
+###### ElasticSearch
+We are currently using version 6, and should look at upgrading this in the future when my hair isn't on fire.
+
+* Debian/Ubuntu: https://medium.com/@pierangelo1982/how-to-install-elasticsearch-6-on-ubuntu-64316dc2de1c
+
+
+#### Angular
+You will need the angular command line utilities to run the front end.
+```BASH
+npm install -g @angular/cli
+```
+
+### Project Setup
+* Please use Python 3's virtual environment setup, and install the dependencies in requirements.txt
+```bash
+cd backend
+python3 -m venv python-env
+source python-env/bin/activate
+pip3 install -r requirements.txt
+```
+
+## Add a config file
+In the `backend` directory, execute the following command:
+```BASH
+mkdir instance && cp -r config instance/config && cp instance/config/default.py instance/config.py
+```
+
 ### Update the Database
 You will need to update your database each time you return to do a pull to make sure all the migrations are run. In the `backend` directory, execute the following command:
 ```BASH
@@ -95,41 +112,9 @@ This will pull in initial values into the database.
 flask initdb
 ```
 
-## Add a config file
-In the `backend` directory, execute the following command:
-```BASH
-mkdir instance && cp -r config instance/config && cp instance/config/default.py instance/config.py
-```
 
 ## Run the app
-Execute the following at the top level of the repository to start PostgreSQL, flask, and Angular all in one command:
+* Strongly suggest you set up run configurations for this in PyCharm and WebStorm
-```BASH
-./start.sh
-```
-
-Or you can run these 3 commands separately:
-
-Database:
-```BASH
-./start-db.sh
-```
-
-Backend:
-```BASH
-./start-backend.sh
-```
-
-Frontend:
-```BASH
-./start-frontend.sh
-```
-
-Alternatively, you could start each of the services individually, using the commands below.
-
-### Start PostgreSQL
-```BASH
-pg_ctl -D /usr/local/var/postgres start
-```
 
 ### Start the backend app
 In the `backend` directory, execute the following command:
@@ -144,12 +129,6 @@ npm install
 ng serve
 ```
 
-### Stopping the app
-Execute the following at the top level of the repository to stop all running services:
-```BASH
-./stop.sh
-```
-
 ### Setting up Mailtrap
 To test email integration set up an account with [Mailtrap](https://mailtrap.io/)
 In your instance config, set your sname and password.

backend/app/__init__.py

@@ -40,6 +40,10 @@ if "MIRRORING" in os.environ and os.environ["MIRRORING"] == "true":
 # Database Configuration
 app.config['SQLALCHEMY_TRACK_MODIFICATIONS'] = False
 db = SQLAlchemy(app)
+""":type: sqlalchemy.orm.SQLAlchemy"""
+
+session = db.session
+""":type: sqlalchemy.orm.Session"""
 
 # Enable CORS
 if app.config["CORS_ENABLED"]:
@@ -49,6 +53,7 @@ if app.config["CORS_ENABLED"]:
 
 # Flask-Marshmallow provides HATEOAS links
 ma = Marshmallow(app)
+""":type: flask_marshmallow.Marshmallow"""
 
 # Database Migrations
 migrate = Migrate(app, db, compare_type=True)
@@ -210,6 +215,24 @@ def loadstudies():
     data_loader.load_studies()
 
 
+@app.cli.command()
+def loadusers():
+    """Used for loading new users into the database"""
+    click.echo('Loading users, not clearing out existing ones')
+    from app import data_loader
+    data_loader = data_loader.DataLoader()
+    data_loader.load_users()
+
+
+@app.cli.command()
+def loadparticipants():
+    """Used for loading new participants into the database"""
+    click.echo('Loading participants, not clearing out existing ones')
+    from app import data_loader
+    data_loader = data_loader.DataLoader()
+    data_loader.load_participants()
+
+
 @app.cli.command()
 def run_full_export():
     """Remove all data and recreate it from the example data files"""

backend/app/model/questionnaires/chain_questionnaire.py

@@ -3,9 +3,9 @@ from sqlalchemy import func
 from sqlalchemy.ext.declarative import declared_attr
 
 from app import db, ma
+from app.export_service import ExportService
 from app.model.questionnaires.chain_session import ChainSessionSchema, ChainSession
 from app.schema.model_schema import ModelSchema
-from app.export_service import ExportService
 
 
 class ChainQuestionnaire(db.Model):
@@ -68,4 +68,5 @@ class ChainQuestionnaireSchema(ModelSchema):
             "time_on_task_ms",
             "sessions",
         )
+
     sessions = ma.Nested(ChainSessionSchema, many=True)

backend/app/model/questionnaires/chain_session.py

@@ -28,9 +28,7 @@ class ChainSession(db.Model):
         db.ForeignKey('chain_questionnaire.id')
     )
 
-    @declared_attr
+    date = db.Column(
-    def date(cls):
-        return db.Column(
             db.DateTime(timezone=True),
             info={
                 "display_order": 1,
@@ -42,9 +40,7 @@ class ChainSession(db.Model):
             },
         )
 
-    @declared_attr
+    completed = db.Column(
-    def completed(cls):
-        return db.Column(
             db.Boolean,
             info={
                 "display_order": 2,
@@ -60,9 +56,7 @@ class ChainSession(db.Model):
             },
         )
 
-    @declared_attr
+    session_type = db.Column(
-    def session_type(cls):
-        return db.Column(
             db.String,
             info={
                 "display_order": 2,
@@ -79,11 +73,9 @@ class ChainSession(db.Model):
             },
         )
 
-    @declared_attr
+    step_attempts = db.relationship(
-    def step_attempts(cls):
-        return db.relationship(
             "ChainSessionStep",
-            backref=db.backref(cls.__tablename__, lazy=True),
+            backref='chain_session',
             cascade="all, delete-orphan",
             passive_deletes=True
         )
@@ -104,6 +96,7 @@ class ChainSession(db.Model):
         }
         return field_groups
 
+
 class ChainSessionSchema(ModelSchema):
     @pre_load
     def set_field_session(self, data, **kwargs):
@@ -115,12 +108,28 @@ class ChainSessionSchema(ModelSchema):
         fields = (
             "id",
             "last_updated",
+            "participant_id",
+            "user_id",
             "time_on_task_ms",
             "date",
             "completed",
             "session_type",
+            "chain_questionnaire_id",
             "step_attempts",
-            "chain_questionnaire_id"
         )
 
-    step_attempts = ma.Nested(ChainSessionStepSchema, many=True)
+    step_attempts = fields.Nested(ChainSessionStepSchema, many=True)
+    participant_id = fields.Method('get_participant_id', dump_only=True)
+    user_id = fields.Method('get_user_id', dump_only=True)
+
+    def get_participant_id(self, obj):
+        if obj is None:
+            return missing
+
+        return obj.chain_questionnaire.participant_id
+
+    def get_user_id(self, obj):
+        if obj is None:
+            return missing
+
+        return obj.chain_questionnaire.user_id

backend/app/model/questionnaires/chain_session_step.py

@@ -1,13 +1,13 @@
-from marshmallow import missing, pre_load
+from marshmallow import fields, missing
 from sqlalchemy import func
 from sqlalchemy.ext.declarative import declared_attr
 
-from app import db, ma
+from app import db
-from app.schema.model_schema import ModelSchema
 from app.export_service import ExportService
 from app.model.chain_step import ChainStep
 from app.model.questionnaires.challenging_behavior import ChallengingBehavior, ChallengingBehaviorSchema
 from app.schema.chain_step_schema import ChainStepSchema
+from app.schema.model_schema import ModelSchema
 
 
 class ChainSessionStep(db.Model):
@@ -37,7 +37,10 @@ class ChainSessionStep(db.Model):
         except:
             pass
 
-        return db.Column("chain_step_id", db.Integer, db.ForeignKey('chain_step.id'), info={
+        return db.Column(
+            "chain_step_id",
+            db.Integer,
+            db.ForeignKey('chain_step.id'), info={
                 "display_order": 1,
                 "type": "select",
                 "template_options": {
@@ -290,8 +293,10 @@ class ChainSessionStepSchema(ModelSchema):
         fields = (
             "id",
             "last_updated",
+            "participant_id",
+            "user_id",
+            "chain_session_id",
             "chain_step_id",
-            "chain_step",
             "date",
             "session_type",
             "was_focus_step",
@@ -303,11 +308,14 @@ class ChainSessionStepSchema(ModelSchema):
             "had_challenging_behavior",
             "reason_step_incomplete",
             "challenging_behaviors",
-            "chain_session_id"
+            "chain_step",
         )
-    challenging_behaviors = ma.Nested(ChallengingBehaviorSchema, many=True)
+
-    chain_step = ma.Method('get_chain_step', dump_only=True)
+    participant_id = fields.Method('get_participant_id', dump_only=True)
-    session_type = ma.Method('get_session_type', dump_only=True)
+    user_id = fields.Method('get_user_id', dump_only=True)
+    challenging_behaviors = fields.Nested(ChallengingBehaviorSchema, many=True)
+    chain_step = fields.Method('get_chain_step', dump_only=True)
+    session_type = fields.Method('get_session_type', dump_only=True)
 
     def get_chain_step(self, obj):
         if obj is None:
@@ -320,5 +328,16 @@ class ChainSessionStepSchema(ModelSchema):
         if obj is None:
             return missing
 
-        if hasattr(obj, 'chain_session'):
         return obj.chain_session.session_type
+
+    def get_participant_id(self, obj):
+        if obj is None:
+            return missing
+
+        return obj.chain_session.chain_questionnaire.participant_id
+
+    def get_user_id(self, obj):
+        if obj is None:
+            return missing
+
+        return obj.chain_session.chain_questionnaire.user_id

backend/app/resources/Auth.py

@@ -5,7 +5,7 @@ import datetime
 
 from itsdangerous import URLSafeTimedSerializer, BadSignature, SignatureExpired
 from sqlalchemy import func
-from app import app, RestException, db, auth, email_service
+from app import app, RestException, db, auth, email_service, session
 from app.model.email_log import EmailLog
 from app.model.user import User
 from flask import g, request, Blueprint, jsonify
@@ -24,7 +24,7 @@ def confirm_email(email_token):
     except:
         raise RestException(RestException.EMAIL_TOKEN_INVALID)
 
-    user = User.query.filter_by(email=email).first_or_404()
+    user = session.query(User).filter_by(email=email).first_or_404()
     user.email_verified = True
     db.session.add(user)
     db.session.commit()
@@ -42,7 +42,7 @@ def login_password():
         raise RestException(RestException.INVALID_INPUT)
 
     email = request_data['email']
-    user = User.query.filter(func.lower(User.email) == email.lower()).first()
+    user = session.query(User).filter(func.lower(User.email) == email.lower()).first()
     schema = UserSchema(many=False)
 
     if user is None:
@@ -71,7 +71,7 @@ def login_password():
 def forgot_password():
     request_data = request.get_json()
     email = request_data['email']
-    user = User.query.filter(func.lower(User.email) == email.lower()).first()
+    user = session.query(User).filter(func.lower(User.email) == func.lower(email)).first()
 
     if user:
         tracking_code = email_service.reset_email(user)
@@ -101,7 +101,7 @@ def reset_password():
     except BadSignature:
         raise RestException(RestException.TOKEN_INVALID)
 
-    user = User.query.filter(func.lower(User.email) == email.lower()).first_or_404()
+    user = session.query(User).filter(func.lower(User.email) == email.lower()).first_or_404()
     user.token_url = ''
     user.email_verified = True
     user.password = password
@@ -118,7 +118,7 @@ def verify_token(token):
     try:
         resp = User.decode_auth_token(token)
         if resp:
-            g.user = User.query.filter_by(id=resp).first()
+            g.user = session.query(User).filter_by(id=resp).first()
     except:
         g.user = None
 

backend/example_data/users.csv

@@ -4,3 +4,4 @@ id,email,password,role
 3,ajlouie@gmail.com,Total Perspective Vortex 56,admin
 4,aaron@sartography.com,Zarquon Disaster Area 78,user
 5,kenna@sartography.com,Example Password Runner 2019,admin
+6,alicia@sartography.com,Example Password billybob 55,admin

backend/requirements.txt

@@ -16,6 +16,7 @@ googlemaps==3.0.2
 marshmallow-enum==1.5.1
 marshmallow==3.8.0
 marshmallow_sqlalchemy==0.23.1
+sqlalchemy==1.3.18
 mod-wsgi==4.7.1
 nose2==0.6.0
 nose==1.3.7

frontend/3rdpartylicenses.txt

@@ -80,7 +80,7 @@ MIT
 MIT
 The MIT License
 
-Copyright (c) 2020 Google LLC.
+Copyright (c) 2021 Google LLC.
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -139,7 +139,7 @@ MIT
 MIT
 The MIT License
 
-Copyright (c) 2020 Google LLC.
+Copyright (c) 2021 Google LLC.
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -202,7 +202,7 @@ MIT
 
 core-js
 MIT
-Copyright (c) 2014-2020 Denis Pushkarev
+Copyright (c) 2014-2021 Denis Pushkarev
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -223,30 +223,6 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 THE SOFTWARE.
 
 
-css-loader
-MIT
-Copyright JS Foundation and other contributors
-
-Permission is hereby granted, free of charge, to any person obtaining
-a copy of this software and associated documentation files (the
-'Software'), to deal in the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to
-the following conditions:
-
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
-IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
-CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
-TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
-SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-
-
 geolib
 MIT
 MIT License
@@ -489,6 +465,7 @@ all code is your original work. `</legalese>`
 
 ## Marked
 
+Copyright (c) 2018+, MarkedJS (https://github.com/markedjs/)
 Copyright (c) 2011-2018, Christopher Jeffrey (https://github.com/chjj/)
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
@@ -555,6 +532,7 @@ SOFTWARE.
 
 
 ngx-progressbar
+MIT
 
 regenerator-runtime
 MIT
@@ -825,7 +803,7 @@ zone.js
 MIT
 The MIT License
 
-Copyright (c) 2010-2020 Google LLC. http://angular.io/license
+Copyright (c) 2010-2020 Google LLC. https://angular.io/license
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

frontend/index.html

@@ -6,29 +6,16 @@
   <title>Autism DRIVE</title>
   <base href="/">
 
-  <meta
+  <meta name="viewport" content="width=device-width, initial-scale=1">
-    name="viewport"
-    content="width=device-width, initial-scale=1"
-  >
   <meta property="og:site_name" content="Autism DRIVE"/>
   <meta property="og:type" content="website"/>
   <meta property="og:title" content="Transform Outcomes. Together."/>
-  <meta property="og:description" content="Transform Outcomes. Together. A centralized system for autism research & resources for individuals, families & professionals. " />
+  <meta property="og:description" content="Transform Outcomes. Together. A centralized system for autism research &amp; resources for individuals, families &amp; professionals. "/>
   <meta name="twitter:text:title" content="Transform Outcomes. Together."/>
-  <link
+  <link rel="icon" type="image/x-icon" href="/assets/favicon.ico">
-    rel="icon"
+  <style type="text/css">@font-face{font-family:'Material Icons';font-style:normal;font-weight:400;src:url(https://fonts.gstatic.com/s/materialicons/v83/flUhRq6tzZclQEJ-Vdg-IuiaDsNa.woff) format('woff');}.material-icons{font-family:'Material Icons';font-weight:normal;font-style:normal;font-size:24px;line-height:1;letter-spacing:normal;text-transform:none;display:inline-block;white-space:nowrap;word-wrap:normal;direction:ltr;font-feature-settings:'liga';}@font-face{font-family:'Material Icons';font-style:normal;font-weight:400;src:url(https://fonts.gstatic.com/s/materialicons/v83/flUhRq6tzZclQEJ-Vdg-IuiaDsNcIhQ8tQ.woff2) format('woff2');}.material-icons{font-family:'Material Icons';font-weight:normal;font-style:normal;font-size:24px;line-height:1;letter-spacing:normal;text-transform:none;display:inline-block;white-space:nowrap;word-wrap:normal;direction:ltr;-webkit-font-feature-settings:'liga';-webkit-font-smoothing:antialiased;}</style>
-    type="image/x-icon"
+  <link rel="stylesheet" href="https://use.typekit.net/ato2zta.css">
-    href="/assets/favicon.ico"
+<link rel="stylesheet" href="styles.418eadfe1eb1ee0b2bd8.css"></head>
-  >
-  <link
-    href="https://fonts.googleapis.com/icon?family=Material+Icons"
-    rel="stylesheet"
-  >
-  <link
-    rel="stylesheet"
-    href="https://use.typekit.net/ato2zta.css"
-  >
-<link rel="stylesheet" href="styles.253f70d6ea3ee022e42d.css"></head>
 
 <body>
   <app-root></app-root>
@@ -39,6 +26,6 @@
     var firstScriptTag = document.getElementsByTagName('script')[0];
     firstScriptTag.parentNode.insertBefore(tag, firstScriptTag);
   </script>
-<script src="runtime-es2015.66c79b9d36e7169e27b0.js" type="module"></script><script src="runtime-es5.66c79b9d36e7169e27b0.js" nomodule defer></script><script src="polyfills-es5.5f25760a6e7790d968b4.js" nomodule defer></script><script src="polyfills-es2015.f4693cff282ac90e4596.js" type="module"></script><script src="main-es2015.bf887d12e63744995793.js" type="module"></script><script src="main-es5.bf887d12e63744995793.js" nomodule defer></script></body>
+<script src="runtime-es2015.a4dadbc03350107420a4.js" type="module"></script><script src="runtime-es5.a4dadbc03350107420a4.js" nomodule="" defer=""></script><script src="polyfills-es5.e6fc9488c015b7e85901.js" nomodule="" defer=""></script><script src="polyfills-es2015.2f61e63415c6de3ac93d.js" type="module"></script><script src="main-es2015.68cedc8815d9c8207bb5.js" type="module"></script><script src="main-es5.68cedc8815d9c8207bb5.js" nomodule="" defer=""></script></body>
 
 </html>