Query Tool

The query tool is a React application, developed in TypeScript using a variety of tools including Vite, Cypress, and MUI.

Quickstart | Local Installation | Usage | Testing | License

Please refer to our official documentation for more detailed information on how to use the query tool.

Quickstart

The query tool is hosted at https://query.neurobagel.org/ and interfaces with Neurobagel federation API.

Local Installation

To run the query tool locally, you have two options:

1. Use our docker image
2. Do a manual install from the cloned git repo.

but before proceeding with either you need to set the environment variables.

Mandatory configuration

Environment variable	Type	Required	Default value if not set	Example
NB_API_QUERY_URL	string	Yes	-	https://federate.neurobagel.org/
NB_QUERY_APP_BASE_PATH	string	No	/	/query/
NB_ENABLE_AUTH	boolean	No	false	false
NB_QUERY_CLIENT_ID	string	Yes (if NB_ENABLE_AUTH is set to true)	-	46923719231972-dhsahgasl3123.apps.googleusercontent.com

NB_API_QUERY_URL

You'll need to set the NB_API_QUERY_URL environment variable required to run the query tool. NB_API_QUERY_URL is the Neurobagel API URL that the query tool uses to send requests to for results.

NB_QUERY_APP_BASE_PATH

If you are using a custom configuration where the query tool is accessible via a path other than the root (/), you need to set the NB_QUERY_APP_BASE_PATH to your custom path. This ensures that the query tool is correctly rendered and accessible at the specified URL

NB_ENABLE_AUTH

If the API you'd like to send queries to requires authentication, you need to set NB_ENABLE_AUTH to true as it is false by default. This will enable authentication flow of the app.

NB_QUERY_CLIENT_ID

If the NB_ENABLE_AUTH is set to true (it is false by default), you need to provide a valid client ID for the authentication. At the moment, query tool uses Google for authentication, so you need to obtain a client ID from Google developer console. See documentation for more information.

Set the environment variables

To set environment variables, create a .env file in the root directory and add the environment variables there. If you're running a neurobagel node-API locally on your machine (following the instructions here), your .env file would look something like this:

NB_API_QUERY_URL=http://localhost:8000/

if you're using the remote api, your .env file would look something like this:

NB_API_QUERY_URL=https://federate.neurobagel.org/

if you're using a remote api with authentication, your .env file would look something like this:

NB_API_QUERY_URL=https://federate.neurobagel.org/
NB_ENABLE_AUTH=true
NB_QUERY_CLIENT_ID=46923719231972-dhsahgasl3123.apps.googleusercontent.com

⚠️ The protocol matters here. If you wish to use the Neurobagel remote API, ensure your NB_API_QUERY_URL uses https instead of http.

Docker installation

To obtain the query tool docker image, simply run the following command in your terminal:

docker pull neurobagel/query_tool:latest

This Docker image includes the latest release of the query tool and a minimal http server to serve the static tool.

To launch the query tool Docker container and pass in the .env file you have created, simply run

docker run -p 5173:5173 --env-file=.env neurobagel/query_tool:latest

Then you can access the query tool at http://localhost:5173

Note: the query tool is listening on port 5173 inside the docker container, replace port 5173 by the port you would like to expose to the host. For example if you'd like to run the tool on port 8000 of your machine you can run the following command:

docker run -p 8000:5173 --env-file=.env neurobagel/query_tool:latest

Manual installation

To install the query tool directly, you'll need node package manager (npm) and Node.js. You can find the instructions on installing npm and node in the official documentation.

Once you have npm and node installed, you'll need to install the dependencies outlined in the package.json file. You can do so by running the following command:

npm install

To launch the tool in developer mode run the following command:

npm run dev

You can also build and then run the tool from (production) build of the application by running the following command:

npm run build && npm run preview

You can verify the tool is running by watching for the` info messages from Vite regarding environment, rendering, and what port the tool is running on in your terminal.

Developer setup

Having installed the dependencies, run the following command to enable husky pre-commit and post-merge hooks:

npx husky install

Docker compose testing environment for development

Since the query tool relies on other neurobagel tools to function, their presence is often required during development. To facilitate this, a docker compose containing a complete testing environment has been created. To use it follow the steps below:

1. Install recipes and neurobagel_examples submodules:

git submodule init
git submodule update

2. Pull the latest images and bring up the stack using the test profile:

docker compose --profile test pull && docker compose --profile test up -d

NOTE: Make sure your .env file in the root directory doesn't contain any of the environment variables used in the docker compose file as it will conflict with the configuration, since docker compose will try to use .env by default.

Usage

To define a cohort, set your inclusion criteria using the following:

• Age: Minimum and/or maximum age (in years) of participant that should be included in the results.
• Sex: Sex of participant that should be included in the results.
• Diagnosis: Diagnosis of participant that should be included in the results
• Healthy control: Whether healthy participants should be included in the results. Once healthy control checkbox is selected, diagnosis field will be disabled since a participant cannot be both a healthy control and have a diagnosis.
• Minimum number of imaging sessions: Minimum number of imaging sessions that participant should have to be included in the results.
• Minimum number of phenotypic sessions: Minimum number of phenotypic sessions that participant should have to be included in the results.
• Assessment tool: Non-imaging assessment completed by participant that should be included in the results.
• Imaging modality: Imaging modality of participant scans that should be included in the results.
• Pipeline name: Name of the pipeline used to process subject scans.
• Pipeline version: Version of the pipeline used to process subject scans.

Once you've defined your criteria, submit them as a query and the query tool will display the results.
The query tool offers two different TSV files for results:

• cohort participant results TSV contains: dataset name, portal uri, number of matching subjects, subject id, session id, session file path, session type, age, sex, diagnosis, assessment, number of matching phenotypic sessions, number of matching imaging sessions, session imaging modality, session completed pipelines, dataset imaging modality, and dataset pipelines

• cohort participant machine results TSV contains: dataset name, dataset portal uri, subject id, session id, session file path, session type, number of matching phenotypic sessions, number of matching imaging sessions, session imaging modality, session completed pipelines, dataset imaging modality, and dataset pipeline

You can refer to the neurobagel documentation to see what the outputs of the query tool look like and how they are structured. You can also download the raw example output files here.

Testing

The query tool utilizes Cypress framework for testing.

To run the tests execute the following command:

npx cypress open

License

The query tool is released under the terms of the MIT License