Multiple eRSD Tranformer updates (#530)

* Multiple eRSD Tranformer updates - releaseLabel extension added - date and effectivePeriod added to manifest library * Fixed test data
cqframework · Jun 6, 2024 · 92c4c94 · 92c4c94
1 parent 3babcd0
commit 92c4c94
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Showing 4 changed files with 80 additions and 7 deletions.
diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/casereporting/transformer/ErsdTransformer.java b/tooling/src/main/java/org/opencds/cqf/tooling/casereporting/transformer/ErsdTransformer.java
@@ -20,6 +20,7 @@
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.util.ArrayList;
+import java.util.Date;
 import java.util.HashSet;
 import java.util.List;
 
@@ -35,10 +36,12 @@ public class ErsdTransformer extends Operation {
     private final String usPhTriggeringValueSetLibraryProfileUrl = "https://hl7.org/fhir/us/ecr/StructureDefinition/us-ph-triggering-valueset-library";
     private final String usPhTriggeringValueSetProfileUrl = "https://hl7.org/fhir/us/ecr/StructureDefinition/us-ph-triggering-valueset";
     private final String valueSetStewardExtensionUrl = "https://hl7.org/fhir/StructureDefinition/valueset-steward";
-
+    private final String artifactReleaseLabelExtensionUrl = "https://hl7.org/fhir/StructureDefinition/artifact-releaseLabel";
     private PlanDefinition v2PlanDefinition;
     private String version;
     private Period effectivePeriod;
+    private Date artifactsDate;
+    private String releaseLabel;
 
     public ErsdTransformer() {
         ctx = FhirContext.forR4();
@@ -144,6 +147,10 @@ private PlanDefinition getV2PlanDefinition(String pathToPlanDefinition) {
         if (pathToPlanDefinition != null && !pathToPlanDefinition.isEmpty()) {
             planDef = (PlanDefinition)IOUtils.readResource(pathToPlanDefinition, ctx, true);
             planDef.setEffectivePeriod(this.effectivePeriod);
+            Extension releaseLabelExtension = new Extension();
+            releaseLabelExtension.setUrl(artifactReleaseLabelExtensionUrl);
+            releaseLabelExtension.setValue(new StringType(this.releaseLabel));
+            planDef.addExtension(releaseLabelExtension);
         }
 
         return planDef;
@@ -192,6 +199,11 @@ else if (bundleFile.getName().endsWith("xml")) {
                     && ((Library)x.getResource()).getUrl().equals(RCTCLIBRARYURL)).findFirst().get().getResource();
 
         this.effectivePeriod = rctc.getEffectivePeriod();
+        this.artifactsDate = rctc.getDate();
+        Extension releaseLabelExtension = rctc.getExtensionByUrl(artifactReleaseLabelExtensionUrl);
+        if (releaseLabelExtension != null) {
+            this.releaseLabel = releaseLabelExtension.getValueAsPrimitive().getValueAsString();
+        }
 
         if (rctc.hasVersion()) {
             this.version = rctc.getVersion();
@@ -204,19 +216,29 @@ else if (bundleFile.getName().endsWith("xml")) {
 
     private Library createSpecificationLibrary() {
         Library specificationLibrary = new Library();
-        specificationLibrary.setId(new IdType("Library", "SpecificationLibrary", "1.0.0"));
+        specificationLibrary.setId(new IdType("Library", "SpecificationLibrary"));
         specificationLibrary.getMeta().addProfile(usPhSpecificationLibraryProfileUrl);
+
+        Extension releaseLabelExtension = new Extension();
+        releaseLabelExtension.setUrl(artifactReleaseLabelExtensionUrl);
+        releaseLabelExtension.setValue(new StringType(this.releaseLabel));
+        specificationLibrary.addExtension(releaseLabelExtension);
+
+        if (this.effectivePeriod != null) {
+            specificationLibrary.setEffectivePeriod(this.effectivePeriod);
+        }
+        specificationLibrary.setUrl("https://ersd.aimsplatform.org/fhir/Library/SpecificationLibrary");
+        specificationLibrary.setVersion(this.version);
         specificationLibrary.setName("SpecificationLibrary");
         specificationLibrary.setTitle("Specification Library");
-        specificationLibrary.setVersion(this.version);
-        specificationLibrary.setDescription(
-                "Defines the asset-collection library containing the US Public Health specification assets.");
         specificationLibrary.setStatus(PublicationStatus.ACTIVE);
         specificationLibrary.setExperimental(false);
-        specificationLibrary.setPublisher(PUBLISHER);
-        specificationLibrary.setUrl("https://ersd.aimsplatform.org/fhir/Library/SpecificationLibrary");
         specificationLibrary.setType(new CodeableConcept(
                 new Coding("https://terminology.hl7.org/CodeSystem/library-type", "asset-collection", null)));
+        specificationLibrary.setDate(this.artifactsDate);
+        specificationLibrary.setPublisher(PUBLISHER);
+        specificationLibrary.setDescription(
+                "Defines the asset-collection library containing the US Public Health specification assets.");
 
         UsageContext reportingUsageContext =
             new UsageContext(

diff --git a/...ng/src/test/java/org/opencds/cqf/tooling/casereporting/transformer/ErsdTransformerIT.java b/...ng/src/test/java/org/opencds/cqf/tooling/casereporting/transformer/ErsdTransformerIT.java
@@ -4,6 +4,7 @@
 import ca.uhn.fhir.parser.JsonParser;
 import ca.uhn.fhir.parser.XmlParser;
 import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.Library;
 import org.hl7.fhir.r4.model.UsageContext;
 import org.hl7.fhir.r4.model.ValueSet;
 import org.opencds.cqf.tooling.parameter.TransformErsdParameters;
@@ -149,4 +150,43 @@ public void testErsdTransformerEmergentPriorityUseContextPreserved() throws Exce
 
         logger.info("Transform");
     }
+
+    @Test
+    public void testErsdTransformerManifestElementPresence() throws Exception {
+        TransformErsdParameters params = new TransformErsdParameters();
+        params.pathToBundle = "src/test/resources/casereporting/transformer/eRSDv1bundle.json";
+        params.outputPath = "src/test/resources/casereporting/transformer/output";
+        String outputBundleFileName = "rctc-release-2022-10-19-Bundle-rctc.json";
+        params.pathToV2PlanDefinition = "src/test/resources/casereporting/transformer/eRSDv2PlanDefinition/plandefinition-us-ecr-specification.json";
+
+        Bundle outputBundle = transformBundle(params, outputBundleFileName);
+
+        assertNotNull(outputBundle);
+        Library manifestLibrary;
+        manifestLibrary = (Library)outputBundle.getEntry().stream().filter(x -> x.hasResource()
+                && x.getResource().fhirType().equals("Library")
+                && x.getResource().getId().equals("https://ersd.aimsplatform.org/fhir/Library/SpecificationLibrary")).findFirst().get().getResource();
+
+        assertNotNull(manifestLibrary);
+
+        List<UsageContext> useContexts = manifestLibrary.getUseContext();
+        UsageContext reportingUseContext = useContexts.stream().filter(x -> x.hasCode()
+                && x.getCode().getCode().equals("reporting")
+                && x.hasValueCodeableConcept()
+                && x.getValueCodeableConcept().getCodingFirstRep().getCode().equals("triggering")).findFirst().get();
+        assertNotNull(reportingUseContext);
+
+        UsageContext specificationTypeUseContext = useContexts.stream().filter(x -> x.hasCode()
+                && x.getCode().getCode().equals("reporting")
+                && x.hasValueCodeableConcept()
+                && x.getValueCodeableConcept().getCodingFirstRep().getCode().equals("triggering")).findFirst().get();
+        assertNotNull(specificationTypeUseContext);
+
+        assertNotNull(manifestLibrary.getDate());
+        assertNotNull(manifestLibrary.getEffectivePeriod());
+        assertNotNull(manifestLibrary.getEffectivePeriod().getStart());
+        assertNotNull(manifestLibrary.getExtensionByUrl("https://hl7.org/fhir/StructureDefinition/artifact-releaseLabel"));
+
+        logger.info("Transform");
+    }
 }
diff --git a/tooling/src/test/resources/casereporting/transformer/eRSDv1bundle.json b/tooling/src/test/resources/casereporting/transformer/eRSDv1bundle.json
@@ -512,6 +512,12 @@
             "https://hl7.org/fhir/us/ecr/StructureDefinition/ersd-valueset-library"
           ]
         },
+        "extension": [          
+          {
+            "url": "https://hl7.org/fhir/StructureDefinition/artifact-releaseLabel",
+            "valueString": "2022-10-19"
+          }
+        ],
         "url": "https://ersd.aimsplatform.org/fhir/Library/rctc",
         "identifier": [
           {
@@ -531,6 +537,7 @@
             }
           ]
         },
+        "date": "2024-04-02T12:19:03-04:00",
         "description": "Release Description: This release includes code updates for the existing 132 conditions and adds codes for 41 new conditions: Agricultural Chemicals (Fertilizer) Poisoning Asbestosis Byssinosis Carbapenem-resistant Acinetobacter baumannii (CRAB) Carbapenem-resistant Pseudomonas aeruginosa (CRPA) Catheter-associated Urinary Tract Infection (CAUTI) Central Line-associated Bloodstream Infection (CLABSI) Chemical Pneumonitis Clostridium perfringens Infection Coal Workers Pneumoconiosis (CWP) Cysticercosis Drowning and Submersion Encephalitis Farmer's Lung Granuloma Inguinale (Donovanosis) Guillain-Barre Syndrome Gunshot Wound Head Injury Hepatitis G Virus Infection Herpes, Genital Herpes, Neonatal Leishmaniasis Louse-borne relapsing fever (LBRF) Lymphatic Filariasis Motor Vehicle Injury Multisystem Inflammatory Syndrome (MIS) Non-Polio Enterovirus Infection Nontuberculous Mycobacteria Infection, Pulmonary Ophthalmia Neonatorum Orthopoxvirus Disease Reye's Syndrome Rheumatic Fever Rotavirus Disease Scabies Staphylococcal Enterotoxin B Poisoning Suicide Surgical Site Infection (SSI) Taeniasis Toxoplasmosis Ventilator-associated Event (VAE) Vesicular Stomatitis",
         "purpose": "Triggers for initiating decision support for electronic case reports",
         "effectivePeriod": {

diff --git a/tooling/src/test/resources/casereporting/transformer/eRSDv1bundle.xml b/tooling/src/test/resources/casereporting/transformer/eRSDv1bundle.xml
@@ -1479,6 +1479,9 @@
             <meta>
                <profile value="https://hl7.org/fhir/us/ecr/StructureDefinition/ersd-valueset-library"></profile>
             </meta>
+            <extension url="https://hl7.org/fhir/StructureDefinition/artifact-releaseLabel">
+               <valueString value="2022-10-19"></valueString>
+            </extension>
             <url value="https://ersd.aimsplatform.org/fhir/Library/rctc"></url>
             <identifier>
                <system value="urn:ietf:rfc:3986"></system>
@@ -1494,6 +1497,7 @@
                   <code value="asset-collection"></code>
                </coding>
             </type>
+            <date value="2024-04-02T12:19:03-04:00"></date>
             <description value="Release Description: This release includes code updates for the existing 132 conditions and adds codes for 41 new conditions: Agricultural Chemicals (Fertilizer) Poisoning Asbestosis Byssinosis Carbapenem-resistant Acinetobacter baumannii (CRAB) Carbapenem-resistant Pseudomonas aeruginosa (CRPA) Catheter-associated Urinary Tract Infection (CAUTI) Central Line-associated Bloodstream Infection (CLABSI) Chemical Pneumonitis Clostridium perfringens Infection Coal Workers Pneumoconiosis (CWP) Cysticercosis Drowning and Submersion Encephalitis Farmer's Lung Granuloma Inguinale (Donovanosis) Guillain-Barre Syndrome Gunshot Wound Head Injury Hepatitis G Virus Infection Herpes, Genital Herpes, Neonatal Leishmaniasis Louse-borne relapsing fever (LBRF) Lymphatic Filariasis Motor Vehicle Injury Multisystem Inflammatory Syndrome (MIS) Non-Polio Enterovirus Infection Nontuberculous Mycobacteria Infection, Pulmonary Ophthalmia Neonatorum Orthopoxvirus Disease Reye's Syndrome Rheumatic Fever Rotavirus Disease Scabies Staphylococcal Enterotoxin B Poisoning Suicide Surgical Site Infection (SSI) Taeniasis Toxoplasmosis Ventilator-associated Event (VAE) Vesicular Stomatitis"></description>
             <purpose value="Triggers for initiating decision support for electronic case reports"></purpose>
             <effectivePeriod>