Metadata Summary Fetcher

DT4H toolbox component returning the summary metadata file associated to AI-ready tabular dataset generated by onFeast REST API.

When integrated at the DataTools4Heart platform as one of the federated tools operated by the central federated manager (FEM), the Metadata Summary Fetcher acts effectively as a middleware able to access the onFHIR services, only exposed locally on the federated data nodes (FDN). The fetcher does a localhost HTTP query to the onFeast REST endpoint, who returns the summary metadata JSON file of a given dataset id.

Pre-conditions

The Metadata Summary Fetcher is mean to interact with other components of DT4H platform:

• onFHIR REST endpoint/s (one or more), generating and returning the summary metadata file
• central federated manager (FEM), executing the tool on the FDNs and setting up its parameters

Build and install

The tool is implemented as a docker container. You can either:

• Pull the image from the DT4H docker registry

TOKEN=<token>
echo "$TOKEN" | docker login registry.gitlab.bsc.es -u <username> --password-stdin
docker pull https://gitlab.bsc.es/fl/dt4h_summary_materializer

• Build the image from the Dockerfile

git clone https://github.com/DataTools4Heart/onFHIR_metadata_fetcher
docker build --tag onFHIR_metadata_fetcher:v1.0 . 

Usage

Configure the following parameters to build the appropiate docker run command.

Environemt variables:

• FILE_ID: dataset identifier
• EXECUTION_DIR: Working directory within the FDN sandbox where the outcomes of the tool execution (logs, tool outfiles, etc.) are going to be generated
• NODE_NAME: Name of the federated data node (FDN)
• GET_URL_[NODE_NAME]: URL onFeast API endpoint generating the summary metadata file

Data volumes:

• EXECUTION_DIR