Setup your own

Running the application

To quickly get something running download the (latest) version of the application from http://download.systemsbiology.nl/unlock/ and download the fairds-latest.jar file.

To start the program in a terminal (Linux/Mac) or Command Prompt/Powershell in Windows by typing: java -jar fairds-latest.jar

When you see the following line, the application has started…

Started Application in 3.666 seconds (process running for 6.147)

Now you can access the application using your browser at http://localhost:8083

(The application is now only accessible from your own device)

Here you can generate your templates and validate your metadata. Or you can work on your own metadata packages, see: Templates

Using docker

When you want to use the application through docker the following command can be used:

Mac:

docker run -v $PWD/fairds_storage:/fairds_storage -it -p 8083:8083 docker-registry.wur.nl/m-unlock/docker/fairds:latest

Linux:

docker run -v $PWD/fairds_storage:/fairds_storage -it -p 8083:8083 docker-registry.wur.nl/m-unlock/docker/fairds:latest

Windows:

docker run -v “%cd%”/fairds_storage:/fairds_storage -it -p 8083:8083 docker-registry.wur.nl/m-unlock/docker/fairds:latest

This command will mount the current directory into the fairds_storage folder inside the docker to ensure that all files are stored locally.

Configuring the application

After the inital startup of the application a fairds_storage folder will be created in the current directory. This folder contains the configuration file for the application, the metadata file to ensure term standardisation and additional folders for various modules (if enabled).

fairds_storage
fairds_storage/bioprojects
fairds_storage/bioprojects/raw
fairds_storage/config.yaml
fairds_storage/metadata.xlsx
fairds_storage/validation

The config.yaml file contains the configuration for the application. You can edit this file to change the settings of the application. The following settings can be changed:

# Menus enabled in the FAIR Data Station
menus:
  about: true
  configurator: true
  validator: true
  bioprojects: true
  ena: true
  terms: true
  irods: true
  api: true

The first section of the configuration file contains the menus that are enabled in the FAIR Data Station. You can enable or disable the menus by setting the value to true or false.

counter:
  goat: '<script data-goatcounter="https://fairds.goatcounter.com/count" async src="//gc.zgo.at/count.js"></script>'

The counter section contains the code for the GoatCounter, which is used to track the usage of the FAIR Data Station. You can remove this section if you do not want to use GoatCounter or you can change it for your own instnace.

params:
  irods_investigation_directory: /{ZONE}/home/

The irods_investigation_directory parameter defines the root path for new investigations in iRODS, where {ZONE} is a placeholder that automatically resolves to the user’s zone after login, allowing zone-specific directory creation under (in this case) /home/.

irods_storage:
  tags:
    request for archive:
      attribute: "archive_status"
      value: "archive_requested"

This part of the YAML defines configurable archive request tags for iRODS. Each tag corresponds to a button in the iRODS archiving UI. When clicked, the button sets iRODS metadata using the specified attribute, value, and optionally units. In this example, the “request for archive” button will set archive_status = archive_requested on the selected data.

view:
  validation:
    investigation_identifier: "e.g. NWO_UNLOCK"
    investigation_title: "e.g. Synergies between biological and ozonisation processes for micropollutant removal"
    investigation_description: "e.g. investigation into optimizing micropollutant removal from wastewater treatment plant effluent using biological treatment and ozonation"
    study_identifier: "e.g. BO3B-BR1"
    study_title: "e.g. Optimizing conditions using bioreactors."
    study_description: "e.g. What type of bioreactors are best at removing organic matter from wastewater treatment plant effluent. And what conditions can optimize these processes."

The view section contains the example values for the investigation and study identifiers, titles, and descriptions. These values are used in the validation module to show to users what is expected in these fields. You can change these values to your own examples.

irods:
  - label: UNLOCK
    host: data.m-unlock.nl
    port: 1247
    zone: unlock
    authscheme: PAM
    ssl: CS_NEG_REQUIRE

  - label: Vrije Universiteit Amsterdam
    host: data.yoda.vu.nl
    port: 1247
    zone: vu
    authscheme: PAM
    ssl: CS_NEG_REQUIRE
...

The irods section contains the iRODS servers that are configured for the FAIR Data Station. You can add or remove iRODS servers by adding or removing the entries in this section. Each entry contains the label, host, port, zone, authscheme, and ssl settings for the iRODS server.