From cb14d9ca47faf1299efab47f355613a6f05f18f7 Mon Sep 17 00:00:00 2001 From: Greg Liebowitz Date: Fri, 19 Sep 2025 11:26:52 -0400 Subject: [PATCH] IKDT-1181 Revise readme --- README-origin.md | 41 --------------------- README.md | 65 +++++++++++++++++++++------------- loinc-origin/.mvn/jvm.config | 0 loinc-origin/.mvn/maven.config | 0 loinc-owl-transform/pom.xml | 1 + loinc-reasoner/pom.xml | 1 + loinc-starterdata/pom.xml | 1 + pom.xml | 2 +- 8 files changed, 45 insertions(+), 66 deletions(-) delete mode 100644 README-origin.md delete mode 100644 loinc-origin/.mvn/jvm.config delete mode 100644 loinc-origin/.mvn/maven.config diff --git a/README-origin.md b/README-origin.md deleted file mode 100644 index b9c920d..0000000 --- a/README-origin.md +++ /dev/null @@ -1,41 +0,0 @@ -# loinc-data - -### Team Ownership - Product Owner -Data Team - -## Getting Started - -Follow these instructions to generate a loinc data ORIGIN dataset: - -1. Clone the [loinc-data repository](https://github.com/ikmdev/loinc-data) - -```bash -git clone [Rep URL] -``` - -2. Change local directory to `loinc-data\loinc-origin` - -3. Ensure the loinc-data/pom.xml contains the proper tags containing source filename for the files such as: - , , etc. - -4. Enter the following command to build the ORIGIN dataset: - -```bash -mvn clean install -U "-DMaven.build.cache.enable=false" -``` - -5. Enter the following command to deploy the ORIGIN dataset to Nexus: - -```bash -mvn deploy -f loinc-origin -DdeployToNexus=true -Dmaven.deploy.skip=true -Dmaven.build.cache.enabled=false -Ptinkarbuild -DrepositoryId=nexus-snapshot -``` - -6. On Nexus, you will find the artifact at the following maven coordinates: - -```bash - - dev.ikm.data.loinc - loinc-origin - Loinc_2.81+1.0.0-20250911.162901-1 - -``` diff --git a/README.md b/README.md index c576a1d..c67dddf 100644 --- a/README.md +++ b/README.md @@ -1,42 +1,59 @@ -# loinc-data +# LOINC Pipeline -### Team Ownership - Product Owner -Data Team +**Prerequisites** -## Getting Started +* JDK 24+ +* Maven 3.9.9+ +* Nexus Repository (optional) -Follow these instructions to generate a loinc dataset: +**Clone Project and Configure Maven Settings** 1. Clone the [loinc-data repository](https://github.com/ikmdev/loinc-data) -```bash -git clone [Rep URL] -``` + ``` + git clone https://github.com/ikmdev/loinc-data.git + ``` -2. Change local directory to `loinc-data` +2. Configure Maven settings.xml based on the [provided sample](https://ikmdev.atlassian.net/wiki/spaces/IKDT/pages/1036648449/Centralized+Documentation+for+Maven+Settings+File+Configuration). -3. Download Loinc file from LOINC site: https://loinc.org/downloads/ +3. Change local directory to `loinc-data` -4. Place the downloaded Loinc_*_.zip in your local Downloads directory. +**Run Origin Packaging** -5. Ensure the loinc-data/pom.xml contains the proper tags containing source filename for the downloaded files such as: - , , etc. +The following source data is required for this pipeline and can be obtained from LOINC: -6. Create a ~/Solor directory and ensure ~/Solor/generated-data does not exist or is empty. +* Loinc_2.81.zip -7. You can create a reasoned or unreasoned dataset by either including or commenting out the loinc-data/pom.xml loinc-reasoner +More information can be found on: https://loinc.org/downloads/ -8. Enter the following command to build the dataset: +1. Place the downloaded ZIPs in your ~/Downloads directory. -```bash -mvn clean install -U "-DMaven.build.cache.enable=false" -``` +2. Ensure the properties defined in loinc-data/pom.xml are set to the correct file names: + - -9. Enter the following command to deploy the dataset: +3. Run origin packaging and deployment. -```bash -mvn deploy -f loinc-export "-DdeployToNexus=true" "-Dmaven.deploy.skip=true" "-Dmaven.build.cache.enabled=false" -``` + To deploy origin artifact to a shared Nexus repository, run the following command, specifying the repository ID and URL in `-DaltDeploymentRepository` + ``` + mvn clean deploy -f loinc-origin -Ptinkarbuild -DaltDeploymentRepository=tinkar-snapshot::https://nexus.tinkar.org/repository/maven-snapshots/ -Dmaven.build.cache.enabled=false + ``` -- NOTE. This repo is built on top of an unreasoned spined array DB from snomed-ct-data. Therefore, make sure you have it built before running step #8. + To install origin artifact to a local M2 repository, run the following command: + ``` + mvn clean install -f loinc-origin -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. Build the pipeline with the following command: + ``` + mvn clean install -U -Ptinkarbuild -Dmaven.build.cache.enabled=false + ``` + +2. Deploy transformed data artifacts to Nexus, run the following command: + ``` + mvn deploy -f loinc-export -Ptinkarbuild -DaltDeploymentRepository=tinkar-snapshot::https://nexus.tinkar.org/repository/maven-snapshots/ -Dmaven.build.cache.enabled=false + ``` + diff --git a/loinc-origin/.mvn/jvm.config b/loinc-origin/.mvn/jvm.config deleted file mode 100644 index e69de29..0000000 diff --git a/loinc-origin/.mvn/maven.config b/loinc-origin/.mvn/maven.config deleted file mode 100644 index e69de29..0000000 diff --git a/loinc-owl-transform/pom.xml b/loinc-owl-transform/pom.xml index 5ba1215..981036c 100644 --- a/loinc-owl-transform/pom.xml +++ b/loinc-owl-transform/pom.xml @@ -31,6 +31,7 @@ ${dataStoreLocation}/${dataStore} + false diff --git a/loinc-reasoner/pom.xml b/loinc-reasoner/pom.xml index 6fd7960..88b5243 100644 --- a/loinc-reasoner/pom.xml +++ b/loinc-reasoner/pom.xml @@ -32,6 +32,7 @@ ${dataStoreLocation}/${dataStore} ${reasoner-type} + false diff --git a/loinc-starterdata/pom.xml b/loinc-starterdata/pom.xml index 01a3cd6..977f4b6 100644 --- a/loinc-starterdata/pom.xml +++ b/loinc-starterdata/pom.xml @@ -85,6 +85,7 @@ **/*-${tinkar-starter-data.classifier}.zip + false load-data install diff --git a/pom.xml b/pom.xml index c70e193..06dec81 100644 --- a/pom.xml +++ b/pom.xml @@ -73,7 +73,7 @@ dev.ikm.data.tinkar tinkar-starter-data unreasoned-pb - 20250813 + 20250915 ElkSnomedReasoner