Skip to content

Latest commit

 

History

History
186 lines (153 loc) · 8.18 KB

README.md

File metadata and controls

186 lines (153 loc) · 8.18 KB
Raw

odmltables-for-ldh

odMLtables - Local Data Hub Extension

OdMLtables is a graphical user interfacte that allows to convert odML structures to and from table representations. This extension of the odMLtables GUI supports semi-automatic uploading of odML-meta-data of microneurography recordings to the Local Data Hubs by NFDI4Health. The Local Data Hubs can be installed using Docker Deployment LDH. More information about the LDH can be found on Local Data Hub - Homepage

The current version supports the streaming to the LDHs only for odML-files that comply to the Experiment and Recording template, which can be found in the odMLtablesForMNG repository.

odMLtables provides a set of functions to simplify the setup, maintenance and usage of a metadata management structure using odML.

In addition to the Python API, odMLtables provides its main functionality also via a graphical user interface.

Publications

The concept that the odMLtabled for LDH follows, has been presented as a poster at MIE2024. The poster and corresponding abstract can be found under the related publications folder.

Step-by-Step Guide on How to use the GUI!

Step Description Image
Step 1: Starting Page Open the odMLtables application. Click on Upload to Local Data Hubs to start uploading your data. Starting Page
Step 2: Connect to Local Data Hub Enter the Local Data Hub URL and API token. These credentials are necessary to connect and interact with your LDH. Connect to Local Data Hub
Step 3: Select or Create a Project Select an existing project or create a new one by clicking on Create New Project and filling in the necessary details. Select Project
Create New Project
Step 4: File Selection Choose the odML file for upload by selecting Browse for odML File to Publish. This step is mandatory to proceed. File Selection
Step 5: Data Field Selection Select which data fields you want to share. This step allows for editing your choices before final confirmation. Data Field Selection - Original
Data Field Selection - Edited
Step 6: Review Data Examine your data selections in a table format, making any last-minute changes by checking or unchecking fields as necessary. Review Data - Original
Review Data - Edited
Step 7: Save and Finalize Confirm your selections and specify where to save the cleaned odML and its CSV version within your project directory on the LDH. Configure File Saving
Step 8: Specify Dataset URL Provide a link to your dataset if it is publicly available, or indicate if access requires authorization from the dataset authors. Specify Dataset URL
Step 9: Review and Confirm Data Submission Finalize the submission by reviewing and editing project details, dataset descriptions, and metadata as necessary. Review and Confirm Data SubmissionEditing Possible in the Description
Step 10: Publication Summary View links to the project page, summary data file, and the odML data file, which can be accessed directly through the provided links. Publication Summary

Setup

To integrate and use the odML GUI with LDH, follow the instructions below:

Prerequisites

Ensure you have the odML GUI installed. You can download it from the official odML GitHub repository.

Step-by-Step Guide

  1. Download odML GUI:

    • Clone the odML GUI repository: 
      git clone https://gitlab.com/BI_Koeln/odml-gui-for-ldh.git
cd odml-gui-for-ldh

  2. Set Up the Python Environment:

    • Create a Python virtual environment: 
      python -m venv venv
    • Activate the virtual environment:
      • On Windows: 
        venv\Scripts\activate
      • On macOS/Linux: 
        source venv/bin/activate

  3. Install Required Packages:

    • Install the required packages from requirements_gui.txt: 
      pip install -r requirements_gui.txt

  4. Run the odML GUI Application:

    • Start the GUI application: 
      python odmltables-gui.py

Step-by-Step guide to Create an API in NFDI4Health

  • First Go to http://localhost:3000/.
Image Step-by-Step Guide
Step 1 Navigate to your user profile: Open the user interface and click on your profile name to access options related to your account and projects.
Step 2 Viewing project membership: Check the "Trial Projects I am a member of" section to see your current project memberships.
Step 3 Access user details: On your profile page, you can view your details such as location, expertise, and join date.
Manage API tokens: Go to the API tokens section from your profile to view or manage your tokens.
Step 5 Creating a new API token: Click on "New API Token" to create a new token for API access.
Step 6 Configure new API token: Enter a title for your new API token to help identify its purpose.
Step 7 Complete token creation: After entering the title, click "Create" to generate your new API token.
Step 8 Copy the generated API token: Once created, make sure to copy your new API token as it will not be shown again.

Dependencies

This extension is based on the original odMLtables modified by the odMLtablesForMNG extension. Which are based on odML.

License

BSD-3-Clause license