IKDT-1181 Revise readme

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:
-   <source.zip>, <source.version>, 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 <module>loinc-reasoner</module>
+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:
+   - <source.zip>
 
-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
+   ```
+

loinc-owl-transform/pom.xml

@@ -31,6 +31,7 @@
                         </goals>
                         <configuration>
                             <dataStore>${dataStoreLocation}/${dataStore}</dataStore>
+                            <isolate>false</isolate>
                         </configuration>
                     </execution>
                 </executions>

loinc-reasoner/pom.xml

@@ -32,6 +32,7 @@
                         <configuration>
                             <dataStore>${dataStoreLocation}/${dataStore}</dataStore>
                             <reasonerType>${reasoner-type}</reasonerType>
+                            <isolate>false</isolate>
                         </configuration>
                     </execution>
                 </executions>

loinc-starterdata/pom.xml

@@ -85,6 +85,7 @@
                                     <include>**/*-${tinkar-starter-data.classifier}.zip</include>
                                 </includes>
                             </fileset>
+                            <isolate>false</isolate>
                         </configuration>
                         <id>load-data</id>
                         <phase>install</phase>

pom.xml

@@ -73,7 +73,7 @@
         <tinkar-starter-data.groupId>dev.ikm.data.tinkar</tinkar-starter-data.groupId>
         <tinkar-starter-data.artifactId>tinkar-starter-data</tinkar-starter-data.artifactId>
         <tinkar-starter-data.classifier>unreasoned-pb</tinkar-starter-data.classifier>
-        <tinkar-starter-data.version>20250813</tinkar-starter-data.version>
+        <tinkar-starter-data.version>20250915</tinkar-starter-data.version>
         <!-- reasoner options (ElkOwlReasoner, ElkSnomedReasoner, HybridReasoner)-->
         <reasoner-type>ElkSnomedReasoner</reasoner-type>
     </properties>