How to set up gpf-testing-instances in development mode

• Make sure that you have read access to the directory with the collection data:

  ls -l /mnt/cephfs/seqpipe/duckdb_testing_instances_storage/
  

  If you can’t read the directory, ask the administrator to give you access.

• Clone the gpf-testing-instances repository:

  git clone git@github.com:iossifovlab/gpf-testing-instances.git
  

• Enter into the repository directory and source the environment setup script:

  cd gpf-testing-instances
  source ./seqpipe_setenv.sh
  

• Activate your GPF conda environment

• Prepare to run the Django development server:

  • Run the migrations

    wdaemanage.py migrate
    

  • Create an admin user

    wdaemanage.py user_create admin@iossifovlab.com -p secret -g any_dataset:admin
    

  • Create an OAuth2 application for the frontend

    wdaemanage.py createapplication --user 1 \
        --redirect-uris "http://localhost:4200/login" \
        --name "GPF Genotypes and Phenotypes in Families" \
        --client-id gpfjs  public authorization-code --skip-authorization
    

  • Create an OAuth2 application for the REST based tests

    wdaemanage.py createapplication \
        confidential client-credentials \
        --user 1 \
        --redirect-uris "http://localhost:8000/login" \
        --name "testing rest client app1" \
        --client-id resttest1 \
        --client-secret secret \
        --skip-authorization
    

  • Run the development server

    wdaemanage.py runserver
    

• Enter into your GPFjs source directory and run the Angular development server

  cd gpfjs
  npm install
  ng serve
  

• Open your browser and navigate to http://localhost:4200