BacMet

Getting started

To get started running this project you need to get through the following steps:

• Install docker and docker compose or other container runtime alternatives
• Perform Data import
• Start the app
• View the app on http://localhost:5000/

Data import

The original data should be fetched from the server at Chalmers and be put in a directory called data-import, replicating the directory structure on the Chalmers server (see below).

The data is imported into the persistent SQLite database /data/database.db in the database container when the service is brought up and the database is missing or empty.

The data can be reimported by removing the database’s Docker volume and restarting the service. This will cause the database to be recreated and the data to be imported:

docker compose --profile load-data down -v
docker compose --profile load-data up database

The database will also be recreated and the data reimported if the environment variable DATABASE_REINIT has a non-empty value when the service is started.

DATABASE_REINIT=1 docker compose --profile load-data up database

Fetching updated data

Fetching the data is easiest done using rsync:

rsync --progress --stats -h -ia --delete \
    user@server:/remote-path/NBIS/ data-import/

Expected layout of data-import directory

data-import
├── 1-Experimentally_validated
│   ├── 1-BacMet_experimentally_validated_database_3.0.csv
│   ├── 2-BacMet_compound_CAS_numbers.csv
│   └── Experimentally_validated_PDB_files.zip
├── 2-Predicted_database
│   ├── 1-Predicted_unique_homologues.zip
│   ├── 2-Predicted_unique_homologous_sequences.zip     # (not used)
│   └── 3-Predicted_groups.zip
└── 3-Sensitivity_distributions
    ├── MIC_Biocides.zip
    ├── MIC_metals.zip
    └── MIC_other_compounds.zip

4 directories, 9 files

Start the app

The app can be started in a production-like environment or in an environment tuned for convenient development. When you are switching between environments it is important to remember to rebuild the container so either use the build command or add the flag --build.

Start production-like environment

The production-like environment will copy all necessary app related code and assets into the container in order to create a self contained deployable container.

docker compose up --build

Start development environment

The development environment will mount the app directory and automatically reload code when it is changed.

docker compose -f docker-compose.yml -f docker-compose.dev.yml up --build