davidshumway/maldidb

Overview

• Mass data import from SQLite
• Search and browse data
• User and group management
• Pipelines:
  • Bin peaks and cosine scoring for search and dendrograms
  • Replicates to collapsed spectra
  • Preprocessing
  • Upload spectra files

Docker install with docker-compose

 git clone https://github.com/davidshumway/maldidb
 cd ./maldidb/
 # Use project.env.template to create project.env
 cp project.env.template project.env

Edit project.env to include the following:

POSTGRES_USER=<database user>
POSTGRES_PASSWORD=<database password>
POSTGRES_DB=<database name>
DATABASE=postgres
DATABASE_HOST=postgresdb
DATABASE_PORT=5432
SECRET_KEY=<any key>

Update docker-compose.yaml to point to R01 data files, if present, or remove the R01 volume, if not present:

  - /home/ubuntu/r01data:/home/app/r01data/

Finally, build and run the project:

docker-compose up --build

PostgreSQL does not need to be installed on the system beforehand unless performing a manual installaion.

Running docker-compose up --build the first time may take 15-30 minutes to complete. However, successive builds should complete within 15-30 seconds.

Manual install

Install prerequisites

• R
• IDBacApp (R library)
• PostgreSQL
  • Run psql and create an initial database:

 CREATE DATABASE <database>;
 CREATE USER <user> WITH PASSWORD '<password>';
 ALTER ROLE <user> SET client_encoding TO 'utf8';
 ALTER ROLE <user> SET default_transaction_isolation TO 'read committed';
 ALTER ROLE <user> SET timezone TO 'UTC';
 GRANT ALL PRIVILEGES ON DATABASE <database> TO <user>;

Clone repository and start a test server

 git clone https://github.com/davidshumway/maldidb
 cd ./maldidb
 # Use project.env.template to create project.env
 # and input settings used in psql. 
 # DATABASE_HOST should be set to "localhost"
 # rather than postgresdb.
 cp project.env.template project.env
 nano project.env
 # Initialize environment variables and virtualenv
 source project.env
 sudo pip3 install virtualenv
 virtualenv venv -p python3
 source venv/bin/activate
 cd ./maldidb
 pip install -r requirements.txt
 # Run server
 python manage.py makemigrations
 python manage.py migrate

In maldidb/soMedia/settings.py, set Debug = False.

Execute python manage.py runserver to run the project. The site should now be available in a browser at http://localhost:8000/.

A graph diagram of the application's models may be generated using ./manage.py graph_models -a -g -o models.png.

The environment variables in project.env may not work unless export ... is added to the file. For example:

POSTGRES_USER=<database user>
POSTGRES_PASSWORD=<database password>
POSTGRES_DB=<database name>
DATABASE=postgres
DATABASE_HOST=postgresdb
DATABASE_PORT=5432
SECRET_KEY=<any key>
export POSTGRES_USER=$POSTGRES_USER
export POSTGRES_PASSWORD=$POSTGRES_PASSWORD
export POSTGRES_DB=$POSTGRES_DB
export DATABASE=$DATABASE
export DATABASE_HOST=$DATABASE_HOST
export DATABASE_PORT=$DATABASE_PORT
export SECRET_KEY=$SECRET_KEY