cbpOrganizer

Tool to organize cBioPortal studies for publishing to cBioPortal. This will help cBioPortal study owners prepare and validate their studies. This tool helps to publish cBioPortal studies efficiently.

Stack

• React
• Spring Boot
• Python
• Keycloak

Prerequisites

• Node.js
• Java 8 or higher

Project Structure

Running the Application

1. Clone the repository
2. Navigate to the project directory and run npm install to install dependencies for the frontend
3. Run mvn clean package to build the backend Spring Boot application
4. Start the backend by running java -jar target/cbporganizer-0.0.1-SNAPSHOT.jar
5. Start the frontend by running npm start from the project directory
6. Open http://localhost:3030 in your browser to access the application

Docker

1. Clone the repository
2. Create a .env file in the project directory and add the following environment variables: BACKEND_URL=http://localhost:8080 See .env.example for more details
3. Create a .env file in the 'frontend' directory and add the following environment variables: REACT_APP_API_URL = 'http://localhost:8080/file/' See .env.example for more details
4. In project root folder, run in terminal docker-compose up -d
5. (WIP) The application is not connected to any identify provider, so you can access the backend wit h changing the getUserIdFromSession() method in the FileController.java file to return a hard coded user id. This will be fixed in the future.

Debug

To debug docker container, add the following to the backend Dockerfile:

ENV JAVA_TOOL_OPTIONS="-agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=*:5005"

In the IDE, add a remote debug configuration with the following settings:

- Transport: Socket
- Debugger mode: Attach
- Host: localhost
- Port: 5005

For example, in IntelliJ, select Run -> Edit Configurations -> + -> Remote JVM debug

And make sure it has the follow command line arguments

-agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=*:5005 

Features

• Upload cBioPortal study .tar.gz files to the server
• Validate uploaded files
• View validation results

Uploading Studies

To upload a study, click the "Upload File" button and select the .tar.gz you want to upload.

Validating Studies

To validate a study, select the validate tab, select the study you want to validate, and click the "Validate" button.

Viewing Validation Results

In Result tab, you can view the validation results for the selected study.

Contributing

If you would like to contribute to this project, please create a pull request.

License

This project is licensed under the MIT License. See the LICENSE file for details.