README.md

# iric-data

IRIC Data Portal development effort

## Clients:
R: https://gitlab.iric.ca/bioinfo_iric/riricdata
Python: https://gitlab.iric.ca/bioinfo_iric/pyiricdata

## Dependencies
- Python (> 3.6)
- PostgreSQL (> 9.4)
- Node (> 6.12)

## New DEV installation

```bash
# Clone repo and install pypi packages
cd <somewhere>
git clone git@gitlab.iric.ca:bioinfo_iric/iric-data.git
cd iric-data

# Create a virtenv, py3
module add python/3.6.7
python -m venv .venv

# Activate venv
source .venv/bin/activate
pip install --upgrade pip # update pip version to latest

pip install -r requirements.txt

# Install node modules
module add node
npm install

# run default gulp job to generate CSS/JS resources
gulp
# NB: gulp will keep running in "listening" mode, so open a new shell to keep going
```

```SQL
# DB setup
## (login to postgresql server)
CREATE USER iric_data_user WITH PASSWORD 's0me_new_p4ssword';
CREATE DATABASE iric_data_dev;
GRANT ALL PRIVILEGES ON DATABASE iric_data_dev TO iric_data_user;
```

```bash
## Project requires the hstore extension be activated on the project's database
### Need to be admin on postgresql
\c iric_data_dev
CREATE EXTENSION IF NOT EXISTS hstore;
# END DB setup

# update .env to local settings
cp .env.example .env
# Make edits to .env file (including db user passwd !)
```

### Run project locally

```SQL
# If you need to drop the DB tables
# login postgreSQL server and connect to db
DROP OWNED BY iric_data_user;
```

```bash
# with active virtenv

## Initial deploy:
python manage.py migrate
python manage.py populate_iric

## If NOT initial deploy (safe to run if no migrations exist)
python manage.py migrate portal

# Add initial (super) user
python manage.py createsuperuser

# Run without SSL
python manage.py runserver
# Site is now accessible at:
# http://127.0.0.1:8000
```

## Deploy

```bash
git pull origin master
gulp prod
source .venv/bin/activate
python manage.py collectstatic
python manage.py migrate portal
touch iric_data/wsgi.py
```

## Initial Deploy

```bash
# as adsoft, setup environment
sudo yum remove mod_wsgi
sudo yum install python34-devel
sudo pip3 install mod_wsgi
sudo mod_wsgi-express install-module
sudoedit /etc/httpd/conf.d/aa.conf

cd /var/www/private
git clone git@gitlab.iric.ca:bioinfo_iric/iric-data.git
cd
python3 -m venv .venv_local
source /var/www/private/iric-data/.venv/bin/activate
pip install --upgrade pip
pip install -r requirements.txt

module add node
npm install
gulp prod

cp .env.example .env
# edit .env file

python manage.py migrate

sudo systemctl restart httpd
```

## Translations

Make sure your virtual environment is active

```bash
django-admin makemessages -l fr
emacs portal/locale/fr/LC_MESSAGES/django.po # (or install gettext extension of choice)
django-admin compilemessages
```

## DB Migrations
[Django documentation](https://docs.djangoproject.com/en/2.2/ref/django-admin/#migrate)
tl;dr
```bash
python manage.py migrate portal [migration_name]
```
If migration_name is omitted, **ALL** migrations will be applied.
Specify a migration_name to apply migrations **up to that one and no further**.
This can be used to un-apply a migration.


## API Endpoints

Returns list of datafiles based on dataset id, key and/or values present in annotation :
 - api/v1/datafiles/list/json/lookup-key/str:key/
 - api/v1/datafiles/list/json/lookup-key/str:key/str:dataset/
 - api/v1/datafiles/list/json/lookup-value/str:value/
 - api/v1/datafiles/list/json/lookup-value/str:value/str:dataset/
 - api/v1/datafiles/list/json/lookup-key-value/str:key/str:value/
 - api/v1/datafiles/list/json/lookup-key-value/str:key/str:value/str:dataset
 - api/v1/datafiles/list/json/lookup-dataset/str:dataset

Returns annotation for given datafile :
 - api/v1/datafiles/json/annotation/int:pk
 - api/v1/datafiles/json/annotation/slug:iric_data_id

Returns metadata for given datafile :
 - api/v1/datafiles/json/metadata/int:pk
 - api/v1/datafiles/json/metadata/slug:iric_data_id

Returns list of datasets :
 - api/v1/admin/str:sim/datasets/list/json/
 - api/v1/my-datasets/list/json/


## Links to various resources used in this project

[Private Storage](https://pypi.org/project/django-private-storage/)
[PostgreSQL HStore](https://docs.djangoproject.com/en/2.2/ref/contrib/postgres/fields/#hstorefield)