Merge pull request #3 from dfleming9/feature/upgrade-to-schema-v6

Add support for v6 schema
aehrc · Sep 30, 2024 · 5558d3d · 5558d3d
2 parents a0bd428 + 9a8e62c
commit 5558d3d
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Showing 7 changed files with 229 additions and 197 deletions.
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,45 @@
+# Compiled class file
+*.class
+
+# Log file
+*.log
+
+# BlueJ files
+*.ctxt
+
+# Mobile Tools for Java (J2ME)
+.mtj.tmp/
+
+# Package Files #
+*.jar
+*.war
+*.nar
+*.ear
+*.zip
+*.tar.gz
+*.rar
+
+# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
+hs_err_pid*
+replay_pid*
+
+# maven
+/target/
+
+# output
+/output/**
+
+# upload
+/upload/**
+
+# mac crud
+.DS_Store
+
+# vscode
+.vscode
+
+# secrets
+*.secret.properties
+
+# excel outputs
+*.xlsx
diff --git a/pom.xml b/pom.xml
@@ -7,7 +7,7 @@
 
   <groupId>au.csiro</groupId>
   <artifactId>labcodeset-fhir-transform</artifactId>
-  <version>1.0.1</version>
+  <version>1.1.0</version>
   <packaging>jar</packaging>
 
   <name>Nederlandse Labcodeset XML to FHIR Terminology Transforms</name>

diff --git a/src/main/java/au/csiro/fhir/transforms/generators/LabcodesetResourceGenerator.java b/src/main/java/au/csiro/fhir/transforms/generators/LabcodesetResourceGenerator.java
@@ -23,6 +23,9 @@
 import org.hl7.fhir.r4.model.MetadataResource;
 import org.hl7.fhir.r4.model.Resource;
 import org.hl7.fhir.r4.model.ValueSet;
+
+import au.csiro.fhir.transform.xml.nl.labcodeset.LabConcept;
+import au.csiro.fhir.transform.xml.nl.labcodeset.LabConcept.Materials.Material;
 import au.csiro.fhir.transform.xml.nl.labcodeset.MaterialDefinition;
 import au.csiro.fhir.transform.xml.nl.labcodeset.Publication;
 import au.csiro.fhir.transform.xml.nl.labcodeset.UnitDefinition;
@@ -56,7 +59,7 @@ public class LabcodesetResourceGenerator {
   private Publication pub;
   private File outputDir;
   private String labcodesetVersion;
-  private Map<String, MaterialDefinition> materialMap = new HashMap<>();
+  private Map<String, Material> materialMap = new HashMap<>();
   private Map<String, UnitDefinition> unitMap = new HashMap<>();
 
   private TerminologyClient terminologyClient;
@@ -93,8 +96,10 @@ public LabcodesetResourceGenerator(File labcodesetFile, File outputDir, String l
 
     this.labcodesetVersion = pub.getEffectiveDate().split("-")[0];
 
-    for (MaterialDefinition material : pub.getMaterials().getMaterial()) {
-      materialMap.put(material.getId(), material);
+    for (LabConcept concept : pub.getLabConcepts().getLabConcept()) {
+      for (Material material : concept.getMaterials().getMaterial()) {
+        materialMap.put(material.getCode(), material);
+      }
     }
 
     for (UnitDefinition unit : pub.getUnits().getUnit()) {
@@ -150,7 +155,7 @@ private void generateMaterialResources(Bundle bundle) {
   }
 
   private void generateUcumResources(Bundle bundle) {
-    UcumResourceGenerator ucumResourceGenerator = new UcumResourceGenerator(labcodesetVersion, loincVersion, unitMap, materialMap);
+    UcumResourceGenerator ucumResourceGenerator = new UcumResourceGenerator(labcodesetVersion, loincVersion, unitMap);
 
     CodeSystem ucumCodeSystem = ucumResourceGenerator.createUcumCodeSystem(pub);
     outputResource(ucumCodeSystem, UCUM_CS_FILENAME);
@@ -165,7 +170,7 @@ private void generateUcumResources(Bundle bundle) {
 
   private void generateLoincResources(Bundle bundle) {
     LoincResourceGenerator loincResourceGenerator =
-        new LoincResourceGenerator(labcodesetVersion, loincVersion, terminologyClient, unitMap, materialMap);
+        new LoincResourceGenerator(labcodesetVersion, loincVersion, terminologyClient, unitMap);
 
     CodeSystem loincSupplement = loincResourceGenerator.createLoincCodeSystemSupplement(pub);
     bundle.addEntry().setResource(loincSupplement);

diff --git a/src/main/java/au/csiro/fhir/transforms/generators/LoincResourceGenerator.java b/src/main/java/au/csiro/fhir/transforms/generators/LoincResourceGenerator.java
@@ -34,8 +34,6 @@
 import au.csiro.fhir.transform.xml.nl.labcodeset.LabConcept.Units;
 import au.csiro.fhir.transform.xml.nl.labcodeset.LoincAxis;
 import au.csiro.fhir.transform.xml.nl.labcodeset.LoincConcept;
-import au.csiro.fhir.transform.xml.nl.labcodeset.MaterialDefinition;
-import au.csiro.fhir.transform.xml.nl.labcodeset.MaterialOrMethodStatus;
 import au.csiro.fhir.transform.xml.nl.labcodeset.Publication;
 import au.csiro.fhir.transform.xml.nl.labcodeset.UnitDefinition;
 import au.csiro.fhir.transforms.utility.Constants;
@@ -73,23 +71,20 @@ public class LoincResourceGenerator {
   private String loincVersion;
   private TerminologyClient terminologyClient;
   private Map<String, UnitDefinition> unitMap;
-  private Map<String, MaterialDefinition> materialsMap;
 
   /**
    * @param labcodesetVersion version of the Labcodeset being transformed
    * @param loincVersion LOINC version the Labcodeset file should be used with
    * @param terminologyClient {@link TerminologyClient} that can be used to lookup details of LOINC
    *        codes
    * @param unitMap Map of the unit references and their details in the Labcodeset file
-   * @param materialsMap Map of the materials references and their details in the Labcodeset file
    */
   public LoincResourceGenerator(String labcodesetVersion, String loincVersion, TerminologyClient terminologyClient,
-      Map<String, UnitDefinition> unitMap, Map<String, MaterialDefinition> materialsMap) {
+      Map<String, UnitDefinition> unitMap) {
     this.labcodesetVersion = labcodesetVersion;
     this.loincVersion = loincVersion;
     this.terminologyClient = terminologyClient;
     this.unitMap = unitMap;
-    this.materialsMap = materialsMap;
   }
 
   /**
@@ -163,20 +158,9 @@ private void setUnitProperties(Units units, ConceptDefinitionComponent concept)
   private void setMaterialProperties(Materials materials, ConceptDefinitionComponent concept) {
     if (materials != null && materials.getMaterial() != null) {
       for (Material material : materials.getMaterial()) {
-        if (material.getStatus() != null && !material.getStatus().equals(MaterialOrMethodStatus.ACTIVE)) {
-          System.err.println("All materials should be active, yet material " + material.getRef() + " on code " + concept.getCode() + " is "
-              + material.getStatus());
-        }
-
-        MaterialDefinition materialDefinition = materialsMap.get(material.getRef());
-
-        if (materialDefinition != null) {
-          concept.addProperty(new ConceptPropertyComponent(new CodeType(LABCODESET_MATERIAL_PROPERTY),
-              new Coding(Constants.SCT_CS_URI, materialDefinition.getCode().toString(),
-                  terminologyClient.getSnomedDisplay(materialDefinition.getCode().toString(), materialDefinition.getDisplayName()))));
-        } else {
-          System.err.println("Could not find material for reference " + material.getRef() + " - omitting this property!");
-        }
+        concept.addProperty(new ConceptPropertyComponent(new CodeType(LABCODESET_MATERIAL_PROPERTY),
+            new Coding(Constants.SCT_CS_URI, material.getCode().toString(),
+                terminologyClient.getSnomedDisplay(material.getCode().toString(), material.getDisplayName()))));
       }
     }
   }

diff --git a/src/main/java/au/csiro/fhir/transforms/generators/MaterialsResourceGenerator.java b/src/main/java/au/csiro/fhir/transforms/generators/MaterialsResourceGenerator.java
@@ -20,8 +20,6 @@
 import org.hl7.fhir.r4.model.ValueSet.ValueSetComposeComponent;
 import au.csiro.fhir.transform.xml.nl.labcodeset.LabConcept;
 import au.csiro.fhir.transform.xml.nl.labcodeset.LabConcept.Materials.Material;
-import au.csiro.fhir.transform.xml.nl.labcodeset.MaterialDefinition;
-import au.csiro.fhir.transform.xml.nl.labcodeset.MaterialOrMethodStatus;
 import au.csiro.fhir.transform.xml.nl.labcodeset.Publication;
 import au.csiro.fhir.transforms.utility.Constants;
 import au.csiro.fhir.transforms.utility.TerminologyClient;
@@ -43,7 +41,7 @@ public class MaterialsResourceGenerator {
   private String labcodesetVersion;
   private String loincVersion;
   private TerminologyClient terminologyClient;
-  private Map<String, MaterialDefinition> materialsMap;
+  private Map<String, Material> materialsMap;
 
   /**
    * @param labcodesetVersion version of the Labcodeset being transformed
@@ -53,7 +51,7 @@ public class MaterialsResourceGenerator {
    * @param materialsMap Map of the materials references and their details in the Labcodeset file
    */
   public MaterialsResourceGenerator(String labcodesetVersion, String loincVersion, TerminologyClient terminologyClient,
-      Map<String, MaterialDefinition> materialsMap) {
+      Map<String, Material> materialsMap) {
     this.labcodesetVersion = labcodesetVersion;
     this.loincVersion = loincVersion;
     this.terminologyClient = terminologyClient;
@@ -70,7 +68,7 @@ public ValueSet createMaterialsValueSet(Publication pub) {
     ValueSet valueSet = new ValueSet();
     String identifier = "Labconcepts-materials-" + labcodesetVersion;
     valueSet.setId(identifier);
-    valueSet.setName(identifier).setVersion(labcodesetVersion).setTitle(LABCODESET_MATERIALS_VS_TITLE).setStatus(PublicationStatus.DRAFT)
+    valueSet.setName(identifier).setVersion(labcodesetVersion).setTitle(LABCODESET_MATERIALS_VS_TITLE).setStatus(PublicationStatus.ACTIVE)
         .setUrl(LABCODESET_MATERIALS_VS_URI).setDescription(LABCODESET_MATERIALS_VS_DESCRIPTION).setExperimental(false)
         .setPublisher(Constants.LABCODESET_RESOURCE_PUBLISHER).setCopyright(Constants.LABCODESET_RESOURCE_COPYRIGHT)
         .setLanguage(Constants.DUTCH_LANGUAGE_CODE);
@@ -82,11 +80,8 @@ public ValueSet createMaterialsValueSet(Publication pub) {
     conceptSet.setSystem(Constants.SCT_CS_URI);
     conceptSet.setVersion(Constants.NL_SCT_EDITION);
 
-    for (MaterialDefinition material : pub.getMaterials().getMaterial()) {
-      if (material.getStatus() != null && !material.getStatus().equals(MaterialOrMethodStatus.ACTIVE)) {
-        System.err.println("All materials should be active, yet material " + material.getCode() + " is " + material.getStatus());
-      }
-
+    for (Map.Entry<String, Material> entry : materialsMap.entrySet()) {
+      Material material = entry.getValue();
       ConceptReferenceComponent con = new ConceptReferenceComponent();
 
       con.setCode(material.getCode().toString());
@@ -128,11 +123,6 @@ public ConceptMap createMaterialsConceptMap(Publication pub) {
 
       if (labConcept.getMaterials() != null) {
         for (Material material : labConcept.getMaterials().getMaterial()) {
-          if (material.getStatus() != null && !material.getStatus().equals(MaterialOrMethodStatus.ACTIVE)) {
-            System.err.println("All materials should be active, yet material " + material.getRef() + " on code "
-                + labConcept.getLoincConcept().getLoincNum() + " is " + material.getStatus());
-          }
-
           SourceElementComponent element = new SourceElementComponent();
           element.setCode(labConcept.getLoincConcept().getLoincNum());
           if (labConcept.getLoincConcept().getTranslation() != null
@@ -143,7 +133,7 @@ public ConceptMap createMaterialsConceptMap(Publication pub) {
           }
 
           TargetElementComponent targetElement = new TargetElementComponent();
-          MaterialDefinition cachedMaterial = materialsMap.get(material.getRef());
+          Material cachedMaterial = materialsMap.get(material.getCode());
           targetElement.setCode(cachedMaterial.getCode().toString());
           targetElement.setDisplay(terminologyClient.getSnomedDisplay(targetElement.getCode(), cachedMaterial.getDisplayName()));
           targetElement.setEquivalence(ConceptMapEquivalence.RELATEDTO);

diff --git a/src/main/java/au/csiro/fhir/transforms/generators/UcumResourceGenerator.java b/src/main/java/au/csiro/fhir/transforms/generators/UcumResourceGenerator.java
@@ -25,7 +25,6 @@
 import org.hl7.fhir.r4.model.ValueSet.ValueSetComposeComponent;
 import au.csiro.fhir.transform.xml.nl.labcodeset.LabConcept;
 import au.csiro.fhir.transform.xml.nl.labcodeset.LabConcept.Units;
-import au.csiro.fhir.transform.xml.nl.labcodeset.MaterialDefinition;
 import au.csiro.fhir.transform.xml.nl.labcodeset.Publication;
 import au.csiro.fhir.transform.xml.nl.labcodeset.UnitDefinition;
 import au.csiro.fhir.transforms.utility.Constants;
@@ -56,10 +55,8 @@ public class UcumResourceGenerator {
    * @param terminologyClient {@link TerminologyClient} that can be used to lookup details of LOINC
    *        codes
    * @param unitMap Map of the unit references and their details in the Labcodeset file
-   * @param materialsMap Map of the materials references and their details in the Labcodeset file
    */
-  public UcumResourceGenerator(String labcodesetVersion, String loincVersion, Map<String, UnitDefinition> unitMap,
-      Map<String, MaterialDefinition> materialsMap) {
+  public UcumResourceGenerator(String labcodesetVersion, String loincVersion, Map<String, UnitDefinition> unitMap) {
     this.labcodesetVersion = labcodesetVersion;
     this.loincVersion = loincVersion;
     this.unitMap = unitMap;