RxNorm Pipeline

Prerequisites

• JDK 24+
• Maven 3.9.9+
• Nexus Repository (optional)
• SnomedCt Pipeline Artifact (see snomed-ct-data repository)

Clone Project and Configure Maven Settings

1. Clone the rxnorm-data repository

   git clone https://github.com/ikmdev/rxnorm-data.git
   

2. Configure Maven settings.xml based on the provided sample.

3. Change local directory to rxnorm-data

Run Origin Packaging

The following source data is required for this pipeline:

• Pilot-Defined-RxNorm-with-SNCT-classes-2024-04-10-with-custom-annotations.owl

More information can be found on National Library of Medicine (RxNorm-in-OWL/RxNorm Files): https://www.nlm.nih.gov/research/umls/rxnorm/index.html

1. Place the downloaded file in your ~/Downloads directory.

2. Ensure the properties defined in rxnorm-data/pom.xml are set to the correct file names:

   • <source.zip>

3. Run origin packaging and deployment.

   To deploy origin artifact to a shared Nexus repository, run the following command, specifying the repository ID and URL in -DaltDeploymentRepository

   mvn clean deploy --projects rxnorm-origin --also-make -Ptinkarbuild -DaltDeploymentRepository=tinkar-snapshot::https://nexus.tinkar.org/repository/maven-snapshots/ -Dmaven.build.cache.enabled=false
   

   To install origin artifact to a local M2 repository, run the following command:

   mvn clean install --projects rxnorm-origin --also-make -Ptinkarbuild,generateDataLocal -Dmaven.build.cache.enabled=false
   

Run Transformation Pipeline

The transformation pipeline can be built after origin data is available in Nexus or a local M2 repository.

1. Ensure the rxnorm-data/pom.xml contains the proper tags containing source filename for the downloaded files such as: <source.zip>, <source.version>, <snomedct.version>, , etc.

2. Build the pipeline with the following command:

   mvn clean install -U -Ptinkarbuild -Dmaven.build.cache.enabled=false
   

3. Deploy transformed data artifacts to Nexus, run the following command:

   mvn deploy --projects rxnorm-export --also-make -Ptinkarbuild -DaltDeploymentRepository=tinkar-snapshot::https://nexus.tinkar.org/repository/maven-snapshots/ -Dmaven.build.cache.enabled=false