NLP2FHIR-Docker

The NLP2FHIR-Docker project was created to ease the burden of building the NLP2FHIR project. This project builds the multiple software projects required as dependencies for running the GUI in the NLP2FHIR project. This is done by creating a Docker container to build the projects and place the resources and artifacts on a volume (directory) on the user’s system. Additionally, there is a script that is produced to start the NLP2FHIR-GUI using the correct classpath.

Details

Prerequisites

To run this project, you will need the following:

• Git installed to download this project.
• Docker installed.
• This project also requires you to have a UMLS license.

After cloning the project, cd to the NLP2FHIR-Docker directory. In this directory, you will need to supply two additional directories (UMLS and SNOMEDCT_US). Both of these resources require you to have a UMLS license. As such, it is the responsibility of the user to manually download the UMLS and SNOMEDCT_US.

• UMLS Directory - The MRCONSO.RRF file from a copy of the UMLS must be placed in the UMLS directory in the NLP2FHIR-Docker directory.
• SNOMEDCT_US Directory - The SNOMEDCT US Edition resource files (located at <SNOWMEDCT_US download dir>/Full/Terminology/*) must be placed in the SNOMEDCT_US directory in the NLP2FHIR-Docker directory.

The directory structure should look like this:

• NLP2FHIR-Docker/UMLS
• NLP2FHIR-Docker/SNOMEDCT_US

Build

Mac/Linux OS

• Run the ./build.sh command to start the build process.

Windows OS

• Run the ./build_win.bat command to start the build process.

The Docker container will do the following tasks:

• Verify that the user has the directory NLP2FHIR-Docker/UMLS.
• Verify that the user has the directory NLP2FHIR-Docker/SNOMEDCT_US.
• Create an NLP2FHIR-Docker/target directory that will contain all of the necessary build resources, build artifacts and run scripts.
• Build the MedTagger project and gather the artifacts and resources.
• Build the MedTime project and gather the artifacts and resources.
• Build the MedXN project and gather the artifacts and resources.
• Build the UMLS_VTS project and gather the artifacts and resources.
• Build the UIMA-Stream-Server project and gather the artifacts and resources.
• Download the cTAKES project, unzip it and gather the resources.
• Build the NLP2FHIR project and gather the artifacts.
• Create a run script to run the NLP2FHIR-GUI.

Run

After the build command has completed, there will be a target directory.
cd to this target directory.

Mac/Linux OS

• Run the run_nlp2fir-gui_linux.sh command to launch the NLP2FHIR-GUI.

Windows OS

• Run the run_nlp2fir-gui_linux.sh command to launch the NLP2FHIR-GUI.