Merge branch 'main' into 289-fix-list

.github/pull_request_template.md

@@ -4,5 +4,5 @@ Fixes #[issue number] or Closes #[issue number]
 
 **Engineer Checklist**
 - [ ] I have run `./gradlew spotlessApply` to check my code follows the project's style guide
-- [ ] I have built and run the efsity jar to verify my change fixes the issue and/or does not break the application 
+- [ ] I have built using the command `./gradlew clean assemble` and run the efsity jar to verify my change fixes the issue and does not break the application 
 

README.md

@@ -4,6 +4,7 @@ A repo to hold our FHIR content and configuration creation tools and scripts.
 
 - [cleaner](https://github.com/onaio/fhircore-tooling/tree/main/cleaner)
 - [efsity](https://github.com/onaio/fhircore-tooling/tree/main/efsity)
+- [efsity-ide](https://github.com/onaio/fhircore-tooling/tree/main/efsity-ide)
 - [importer](https://github.com/onaio/fhircore-tooling/tree/main/importer)
 - [sm-gen](https://github.com/onaio/fhircore-tooling/tree/main/sm-gen)
 - [uploader](https://github.com/onaio/fhircore-tooling/tree/main/uploader)

efsity/build.gradle.kts

@@ -18,7 +18,7 @@ repositories {
 
 group = "org.smartregister"
 
-version = "2.3.8-SNAPSHOT"
+version = "2.3.9-SNAPSHOT"
 
 description = "fhircore-tooling (efsity)"
 
@@ -83,7 +83,8 @@ dependencies {
   implementation(deps.picocli)
   implementation(deps.xstream)
   implementation(deps.icu4j)
-  implementation(deps.javafaker)
+  implementation(deps.javafaker) { exclude(group = "org.yaml") }
+  implementation(deps.snakeyaml)
 
   testImplementation(kotlin("test"))
   testImplementation("junit:junit:4.13.2")

efsity/libs.versions.toml

@@ -2,7 +2,7 @@
 buildConfig-version="4.1.2"
 caffeine-version="2.9.3"
 common-compress-version="1.22"
-cql-version="2.11.0"
+cql-version="3.3.2"
 gson-version="2.10.1"
 hapi-fhir-core-version="5.6.106"
 hapi-fhir-utilities-version="3.8.0"
@@ -15,6 +15,7 @@ jsonschemafriend-version="0.12.2"
 kotlin-stdlib="1.8.22"
 opencds-cql-version="2.4.0"
 project-build-sourceEncoding="UTF-8"
+snakeyaml-version="2.3"
 spotless-version ="6.20.0"
 xstream="1.4.20"
 icu4j-version = "75.1"
@@ -46,6 +47,7 @@ jackson-core = { module = "com.fasterxml.jackson.core:jackson-core", version.ref
 jackson-databind = { module = "com.fasterxml.jackson.core:jackson-databind", version.ref = "jackson-version" }
 javafaker = { module = "com.github.javafaker:javafaker", version.ref = "javafaker-version"}
 picocli = { module = "info.picocli:picocli", version.ref = "info-picocli-version" }
+snakeyaml = { module="org.yaml:snakeyaml", version.ref ="snakeyaml-version"}
 xstream = { module = "com.thoughtworks.xstream:xstream", version.ref = "xstream" }
 icu4j = { module="com.ibm.icu:icu4j", version.ref = "icu4j-version" }
 

efsity/src/main/java/org/smartregister/command/QuestionnaireResponseGeneratorCommand.java

@@ -174,15 +174,15 @@ public static LocalDate generateRandomDate() {
     LocalDate startDate = LocalDate.of(1960, 1, 1);
     LocalDate endDate = LocalDate.of(2023, 12, 31);
     long daysBetween = ChronoUnit.DAYS.between(startDate, endDate);
-    long randomDays = random.nextLong(daysBetween + 1);
+    long randomDays = (long) getRandomNumber(daysBetween + 1);
     return startDate.plusDays(randomDays);
   }
 
   public static LocalDateTime generateRandomDateTime() {
     LocalDateTime startDateTime = LocalDateTime.of(2000, 1, 1, 0, 0);
     LocalDateTime endDateTime = LocalDateTime.of(2024, 12, 31, 23, 59);
     long secondsBetween = ChronoUnit.SECONDS.between(startDateTime, endDateTime);
-    long randomSeconds = random.nextLong(secondsBetween + 1);
+    long randomSeconds = (long) getRandomNumber(secondsBetween + 1);
     return startDateTime.plusSeconds(randomSeconds);
   }
 
@@ -193,7 +193,7 @@ public static JSONObject generateChoiceValue(JSONArray questions, String link_id
       if (Objects.equals(current_id, link_id)) {
         if (current_object.has("answerOption")) {
           JSONArray answer_options = current_object.getJSONArray("answerOption");
-          int random_index = random.nextInt(answer_options.length());
+          int random_index = (int) getRandomNumber(answer_options.length() + 1);
           return answer_options.getJSONObject(random_index).getJSONObject("valueCoding");
         }
       }
@@ -226,7 +226,7 @@ public static JSONObject generateQuantityValue(JSONArray questions, String link_
       }
     }
     JSONObject quantityAnswer = new JSONObject();
-    quantityAnswer.put("value", random.nextInt(minValue, maxValue));
+    quantityAnswer.put("value", getRandomNumber(minValue, maxValue));
     quantityAnswer.put("unit", unit);
     quantityAnswer.put("system", "http://unitsofmeasure.org");
     quantityAnswer.put("code", unit);
@@ -236,7 +236,7 @@ public static JSONObject generateQuantityValue(JSONArray questions, String link_
   public static JSONObject generateReferenceValue() {
     List<String> exampleResourceTypes =
         Arrays.asList("Patient", "Practitioner", "Location", "Immunization");
-    int randomPick = random.nextInt(0, exampleResourceTypes.size());
+    int randomPick = (int) getRandomNumber(0, exampleResourceTypes.size());
     JSONObject reference = new JSONObject();
     reference.put(
         "reference",
@@ -269,10 +269,11 @@ static JSONObject generateAnswer(
     switch (type.toLowerCase()) {
       case "string":
         return answer.put(
-            "valueString", result != null ? result.toString() : "FakeString" + random.nextInt(100));
+            "valueString",
+            result != null ? result.toString() : "FakeString" + getRandomNumber(100));
       case "integer":
         return answer.put(
-            "valueInteger", result instanceof Integer ? (Integer) result : random.nextInt(100));
+            "valueInteger", result instanceof Integer ? (Integer) result : getRandomNumber(100));
       case "boolean":
         return answer.put(
             "valueBoolean", result instanceof Boolean ? (Boolean) result : random.nextBoolean());
@@ -296,7 +297,7 @@ static JSONObject generateAnswer(
       case "text":
         return answer.put(
             "valueString",
-            result != null ? result.toString() : "This is a fake text" + random.nextInt(100));
+            result != null ? result.toString() : "This is a fake text" + getRandomNumber(100));
       case "reference":
         return answer.put("valueReference", generateReferenceValue());
       default:
@@ -439,6 +440,21 @@ private static String aiGenerated(
     }
   }
 
+  public static <T extends Number> double getRandomNumber(T bound) {
+    return random.nextDouble() * bound.doubleValue();
+  }
+
+  public static <T extends Number> double getRandomNumber(T origin, T bound) {
+    double originValue = origin.doubleValue();
+    double boundValue = bound.doubleValue();
+
+    if (originValue >= boundValue) {
+      throw new IllegalArgumentException("Origin must be less than bound");
+    }
+
+    return originValue + random.nextDouble() * (boundValue - originValue);
+  }
+
   public static class Constants {
     public static final String QUESTIONNAIRE_RESPONSE_SUFFIX = "-response.json";
   }

efsity/src/main/kotlin/org/smartregister/external/CqlToLibraryConvertServices.kt

@@ -3,11 +3,9 @@ package org.smartregister.external
 
 import com.ibm.icu.impl.Assert.fail
 import org.cqframework.cql.cql2elm.CqlTranslator
-import org.cqframework.cql.cql2elm.CqlTranslatorOptions
 import org.cqframework.cql.cql2elm.LibraryManager
 import org.cqframework.cql.cql2elm.ModelManager
 import org.cqframework.cql.cql2elm.quick.FhirLibrarySourceProvider
-import org.fhir.ucum.UcumEssenceService
 import org.hl7.fhir.r4.model.Attachment
 import org.hl7.fhir.r4.model.Enumerations
 import org.hl7.fhir.r4.model.Library
@@ -49,21 +47,14 @@ class CqlToLibraryConvertServices {
    * @param cqlText the CQL Library
    * @return a [CqlTranslator] object that contains the elm representation of the library inside it.
    */
-  private fun compile(cqlText: String): CqlTranslator {
+  fun compile(cqlText: String): CqlTranslator {
     val modelManager = ModelManager()
     val libraryManager =
       LibraryManager(modelManager).apply {
         librarySourceLoader.registerProvider(FhirLibrarySourceProvider())
       }
 
-    val translator =
-      CqlTranslator.fromText(
-        cqlText,
-        modelManager,
-        libraryManager,
-        UcumEssenceService(this::class.java.getResourceAsStream("/ucum-essence.xml")),
-        *CqlTranslatorOptions.defaultOptions().options.toTypedArray()
-      )
+    val translator = CqlTranslator.fromText(cqlText, libraryManager)
 
     // Helper makes sure the test CQL compiles. Reports an error if it doesn't
     if (this.isStrictMode && translator.errors.isNotEmpty()) {
@@ -84,21 +75,20 @@ class CqlToLibraryConvertServices {
   }
 
   /**
-   * Assembles an ELM Library exported as a JSON in to a FHIRLibrary
+   * Assembles an ELM Library exported as a JSON into a FHIRLibrary
    *
    * @param jsonElmStr the JSON representation of the ELM Library
    * @param libName the Library name
    * @param libVersion the Library Version
    * @return a FHIR Library that includes the ELM Library.
    */
-  private fun assembleFhirLib(
+  fun assembleFhirLib(
     cqlStr: String?,
     jsonElmStr: String?,
     xmlElmStr: String?,
     libName: String,
-    libVersion: String
+    libVersion: String,
   ): Library {
-
     val attachmentCql =
       cqlStr?.let {
         Attachment().apply {
@@ -129,7 +119,7 @@ class CqlToLibraryConvertServices {
       version = libVersion
       status = Enumerations.PublicationStatus.ACTIVE
       experimental = true
-      url = "http://localhost/Library/$libName|$libVersion"
+      url = "http://localhost/Library/$libName"
       attachmentCql?.let { addContent(it) }
       attachmentJson?.let { addContent(it) }
       attachmentXml?.let { addContent(it) }

efsity/src/main/kotlin/org/smartregister/external/FhirCarePlanGeneratorLite.kt

@@ -75,7 +75,7 @@ class FhirCarePlanGeneratorLite {
       )
     )
 
-    if (planDefinition == null || planDefinition.action == null || planDefinition.action.size < 1) {
+    if (planDefinition.action == null || planDefinition.action.size < 1) {
       FctUtils.printWarning("No Actions defined found for the Plan definition")
     } else
       FctUtils.printInfo(

efsity/src/main/kotlin/org/smartregister/external/TransformSupportServices.kt

@@ -1,6 +1,8 @@
 /* (C)2021-2023 */
 package org.smartregister.external
 
+import javax.inject.Inject
+import javax.inject.Singleton
 import org.hl7.fhir.exceptions.FHIRException
 import org.hl7.fhir.r4.context.SimpleWorkerContext
 import org.hl7.fhir.r4.model.AdverseEvent
@@ -22,18 +24,25 @@ import org.hl7.fhir.r4.model.Task
 import org.hl7.fhir.r4.model.Timing
 import org.hl7.fhir.r4.terminologies.ConceptMapEngine
 import org.hl7.fhir.r4.utils.StructureMapUtilities.ITransformerServices
+import org.smartregister.util.FctUtils
 
 /**
- * 3RD PARTY CODE: Copied from
- * https://github.com/opensrp/fhircore/blob/main/android/engine/src/main/java/org/smartregister/fhircore/engine/util/helper/TransformSupportServices.kt
+ * Copied from
+ * https://github.com/hapifhir/org.hl7.fhir.core/blob/master/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/TransformSupportServices.java
+ * and adapted for R4. This class enables us to implement generation of Types and Resources not in
+ * the original Hapi Fhir source code here
+ * https://github.com/hapifhir/org.hl7.fhir.core/blob/master/org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/model/ResourceFactory.java.
+ * The missing Types and Resources are internal model types eg RiskAssessment.Prediction,
+ * Immunization.Reaction
  */
-class TransformSupportServices constructor(private val simpleWorkerContext: SimpleWorkerContext) :
+@Singleton
+class TransformSupportServices @Inject constructor(val simpleWorkerContext: SimpleWorkerContext) :
   ITransformerServices {
 
-  private val outputs: MutableList<Base> = mutableListOf()
+  val outputs: MutableList<Base> = mutableListOf()
 
   override fun log(message: String) {
-    // logger.info(message)
+    FctUtils.printInfo(message)
   }
 
   @Throws(FHIRException::class)