IFS4205 Team 1

Notes

• After installing dependecies, use pip3 freeze > requirements.txt to update the file so others can download the new dependencies.

Directory Structure

ifs4205team1
├── adminlogin
│   ├── anonymise.py
│   ├── anonymise_helper.py
│   ├── forms.py
│   ├── static
│   │   └── astyle.css
│   ├── templates
│   ├── urls.py
│   ├── views.py
├── adminusers
│   ├── templates
│   ├── forms.py
│   ├── urls.py
│   ├── views.py
├── core
│   ├── fixtures
│   │   ├── initial_core.json
│   │   ├── initial_users.json
│   │   └── test_users.json
│   ├── management
│   │   ├── commands
│   │   │   ├── clear_users.py
│   │   │   ├── initusers.py
│   │   │   ├── load_csv.py
│   │   │   ├── load_users_csv.py
│   │   └── files
│   │       ├── images.csv
│   │       ├── test_users.csv
│   │       ├── test_users_less.csv
│   │       ├── time_series.csv
│   │       └── videos.csv
│   ├── models.py
├── healthcarelogin
│   ├── templates
│   │   ├── healthcare_change_password_complete.html
│   │   ├── healthcare_change_password.html
│   │   ├── healthcare_dashboard.html
│   │   ├── healthcare_edit_settings.html
│   │   ├── healthcare_login.html
│   │   ├── healthcare_qr.html
│   │   ├── healthcare_settings.html
│   │   └── healthcare_token_register.html
│   ├── urls.py
│   └── views.py
├── healthcarenotes
│   ├── forms.py
│   ├── templates
│   │   ├── create_healthcare_note_for_patient.html
│   │   ├── create_healthcare_note.html
│   │   ├── edit_healthcare_note.html
│   │   ├── edit_healthcare_note_permission.html
│   │   ├── show_all_healthcare_notes.html
│   │   └── show_healthcare_note.html
│   ├── urls.py
│   └── views.py
├── healthcarepatients
│   ├── forms.py
│   ├── templates
│   │   ├── new_patient_images_record.html
│   │   ├── new_patient_readings_record.html
│   │   ├── new_patient_record.html
│   │   ├── new_patient_timeseries_record.html
│   │   ├── new_patient_videos_record.html
│   │   ├── show_all_patients.html
│   │   ├── show_patient.html
│   │   ├── show_patient_record.html
│   │   ├── show_patient_records.html
│   │   └── transfer_patient.html
│   ├── urls.py
│   └── views.py
├── ifs4205team1
│   ├── config
│   │   └── settings
│   │       ├── base.py
│   │       ├── development.py
│   │       ├── production.py
│   │       └── testing.py
│   ├── templates
│   │   └── protected_record.html
│   ├── urls.py
│   ├── views.py
│   └── wsgi.py
├── manage.py
├── media
│   ├── images
│   ├── timeseries
│   └── videos
├── mobileregister
│   ├── forms.py
│   ├── templates
│   │   ├── repeat_register.html
│   │   ├── success_register.html
│   │   ├── user_login.html
│   │   └── user_register.html
│   ├── urls.py
│   └── views.py
├── patienthealthcare
│   ├── fixtures
│   │   └── initial_notes.json
│   ├── management
│   │   └── commands
│   │       └── initnotes.py
│   ├── templates
│   │   ├── show_all_notes.html
│   │   └── show_note.html
│   ├── urls.py
│   └── views.py
├── patientlogin
│   ├── forms.py
│   ├── templates
│   │   ├── patient_change_password_complete.html
│   │   ├── patient_change_password.html
│   │   ├── patient_dashboard.html
│   │   ├── patient_edit_settings.html
│   │   ├── patient_login.html
│   │   ├── patient_qr.html
│   │   ├── patient_settings.html
│   │   └── patient_token_register.html
│   ├── urls.py
│   └── views.py
├── patientrecords
│   ├── fixtures
│   │   ├── initial_data_readings.json
│   │   ├── initial_data_readingsperm.tar.xz
│   │   └── initial_records.json
│   ├── forms.py
│   ├── management
│   │   ├── commands
│   │   │   ├── clear_records.py
│   │   │   ├── generate_records.py
│   │   │   ├── initrecords.py
│   │   └── files
│   │       ├── diagnosis_random.csv
│   │       ├── diagnosis_random_less.csv
│   │       ├── readings.csv
│   │       └── readings_less.csv
│   ├── models.py
│   ├── templates
│   │   ├── edit_permission.html
│   │   ├── new_documents_record.html
│   │   ├── new_images_record.html
│   │   ├── new_readings_record.html
│   │   ├── new_record.html
│   │   ├── new_timeseries_record.html
│   │   ├── new_videos_record.html
│   │   ├── show_all_records.html
│   │   └── show_record.html
│   ├── templatetags
│   │   ├── app_filters.py
│   ├── tests
│   │   └── test_views.py
│   ├── urls.py
│   └── views.py
├── requirements.txt
├── researcherlogin
│   ├── forms.py
│   ├── templates
│   │   ├── researcher_change_password_complete.html
│   │   ├── researcher_change_password.html
│   │   ├── researcher_dashboard.html
│   │   ├── researcher_edit_settings.html
│   │   ├── researcher_login.html
│   │   ├── researcher_qr.html
│   │   ├── researcher_settings.html
│   │   └── researcher_token_register.html
│   ├── urls.py
│   └── views.py
├── researcherquery
│   ├── fixtures
│   │   └── initial_saferecords.json
│   ├── forms.py
│   ├── management
│   │   └── commands
│   │       ├── init_saferecords.py
│   ├── models.py
│   ├── router.py
│   ├── static
│   │   └── researcherstyle.css
│   ├── templates
│   │   └── search_records.html
│   ├── templatetags
│   │   ├── app_filters.py
│   ├── urls.py
│   └── views.py
├── templates
│   ├── admin_base.html
│   ├── base.html
│   ├── healthcare_base.html
│   ├── home.html
│   ├── patient_base.html
│   └── researcher_base.html
└── userlogs
    ├── models.py
    ├── router.py

0.1 core

• commands
  • initusers: Loads inital_users.json fixture into database
  • load_csv: Loads a csv file (test_user.csv) into database
• models.py: User (extended from django.contrib.auth.models.AbstractUser, Patient, Healthcare, Researcher, Admin

0.2 Patient Interface

0.2.1 patientlogin

• views.py: Patients' Login, Settings -related views

0.2.2 patientrecords

• commands
  • initrecords: Loads initial_records.json fixture into database
• models.py: Readings, TimeSeries, Documents, Images, Videos, ReadingsPerm, TimeSeriesPerm, DocumentsPerm, ImagesPerm, VideosPerm, Diagnosis, DiagnosisPerm
• views.py: Patients' Medical Records, Medical Records' Permissions -related views

0.2.3 patienthealthcare

• views.py: Patients' Healthcare Professional Notes -related views

0.3 Healthcare Professional Interface

0.3.1 healthcarelogin

• views.py: Healthcare Professionals' Login, Settings -related views

0.3.2 healthcarepatients

• commands
  • initnotes: Loads initial_notes.json fixture into database
• views.py: Healthcare Professionals' Patients -related views

0.4 Researcher Interface

0.4.1 researcherlogin

• views.py: Researchers' Login, Settings -related views

0.4.2 researcherquery

• models.py: QiInfo, SafeUsers, SafeDiagnosis, SafeReadings, SafeImages, SafeVideos
• views.py: Researchers' Query, Download Anonymised Records -related views

1. Running Django

1.1 Running Django for the First Time

1.1.1 Installing Virtual Environment

1. Install the virtual environment, and virtualenvwrapper to manage the virtual environments

   ~$ pip3 install virtualenv
   ~$ pip3 install virtualenvwrapper
   

2. Create a file to store all virtual environments in the same place

   ~$ mkdir ~/.virtualenvs

3. Add the following at the end of the .bashrc file:

   VIRTUALENVWRAPPER_PYTHON=/usr/local/bin/python3
   export VIRTUALENVWRAPPER_PYTHON
   export WORKON_HOME=$HOME/.virtualenvs
   source /usr/local/bin/virtualenvwrapper.sh
   

   If paths above are incorrect, use which python3 and which virtualenvwrapper.sh to find the correct paths.

4. Reload .bashrc file

   ~$ source ~/.bashrc

5. Navigate to the Django project, and create a new virtual environment

   ~$ mkvirtualenv --python=/usr/local/bin/python3 ifsteam4205env

6. Install dependencies

   ~$ pip3 install -r requirements.txt

1.1.2 Setting Up the Database

The database used is PostgreSQL v10.10.

1. Create a .env file in the ifs4205team1/config/settings folder.

2. Add the following into the .env file:

   export DB_NAME = 'YOUR_DB_NAME'
   export DB_USER = 'YOUR_DB_USER'
   export DB_PASS = 'YOUR_DB_PASS'
   export DB_HOST = 'localhost'
   

3. Make migrations

   ~$ python manage.py makemigrations
   ~$ python manage.py migrate
   

1.1.3 Adding Sample Data into Database

1.1.3.1 Loading Sample Data from Fixtures

1. Run the following commands

   $ python manage.py initusers
   $ python manage.py initrecords
   $ python manage.py initnotes
   

1.1.3.2 Loading Sample Data from CSV File

1. Run the following commands

$ python manage.py load_csv --csvpath="<PATH/TO/CSV>/ifs4205team1/core/management/files/test_users.csv"

Note: A test_users_less.csv with only a few rows of data exists in the same directory for testing purposes.

1.1.4 Populating .env File

1. Add on the following into the .env file:

   export MEDIA_URL = 'MEDIA_URL'
   

1.1.5 Starting Django

1. Start Django

   ~$ python manage.py runserver

1.2 Running Django for the Subsequent Times

1. Start the virtual environment before working on the project

   ~$ workon ifs4205team1env