Add structure map generation tool to efsity

efsity/.gitignore

@@ -9,3 +9,5 @@ fhircore-tooling.iml
 # build files
 bin
 target
+generated-structure-map.txt
+generated-json-map.json

efsity/README.md

@@ -172,6 +172,36 @@ $ fct validateFileStructure -i ~/Workspace/fhir-resources/<project> -s ~/path/to
 If the file structure matches the schema then a positive result is printed to the terminal, otherwise an error 
 is thrown showing the issue.
 
+### Generating a structure map
+To generate a Structure Map, you need to provide the questionnaire, the configuration path, and the questionnaire response path. The output will be based on the specified inputs
+```console
+$ fct generateStructureMap --questionnaire /path/to/questionnaire.json --configPath /path/to/config/StructureMap.xls --questionnaireResponsePath /path/to/questionnaire-response.json
+```
+This process will generate two output files: a .map file and its JSON equivalent
+**Options**
+```
+-q or --questionnaire                 Path to the Questionnaire JSON file.
+-c or --configPath                    Path to the Structure Map configuration file (XLS format).
+-qr or --questionnaireResponsePath    Path to the Questionnaire Response JSON file.
+```
+**Sample Configuration File**
+
+To help users get started with the Structure Map generation process, we provide a sample configuration file in XLS format. You can download the sample from the link below:
+
+[Download Sample Structure Map Configuration (XLS)](https://github.com/onaio/fhir-tooling/blob/main/sm-gen/src/main/resources/StructureMap%20XLS.xls)
+
+Alternatively, if you have cloned the repository, the sample file can be found in the following path:
+
+console
+```
+/path/to/your/repository/src/main/resources/StructureMapXLS.xls
+```
+
+This sample XLS form includes the required structure and format to define mappings between questionnaire fields and FHIR resources. You can customize it according to your specific needs.
+
+For more documentation please refer to this  [documentation](https://github.com/onaio/fhir-tooling/blob/main/efsity/Structure_map_gen.md)
+
+
 ### Localization
 Tool that supports localization by the use of the translation extension
 

efsity/Structure_map_gen.md

@@ -0,0 +1,38 @@
+# StructureMap tooling
+
+The StructureMap Tooling is a utility designed to generate Structure Maps for FHIR (Fast Healthcare Interoperability Resources) transformations. Structure Maps are used to define how one FHIR resource is transformed into another. This tooling leverages the HL7 FHIRPath language to provide support for creating and managing these transformations.
+
+## Features
+**FHIRPath Engine**: Utilizes the FHIRPath engine to evaluate and transform FHIR resources.
+
+**Transformation Support**: Provides services to support the transformation process, ensuring that resources are accurately converted according to the specified Structure Map.
+
+**Automation**: Simplifies the process of generating Structure Maps through automated tooling.
+
+## Files
+**FhirPathEngineHostServices.kt**: Contains services for hosting and running the FHIRPath engine.
+
+**Main.kt**: The entry point of the application. It orchestrates the process of reading input, processing it through the FHIRPath engine, and generating the Structure Map.
+
+**TransformSupportServices.kt**: Provides additional support services required for the transformation process.
+
+**Utils.kt**: Contains the main logic for generating the Structure Maps using the FHIRPath engine and transformation support services.
+
+## Prerequisites
+- Questionnaire JSON
+- XLS form with the required information based on the questionnaire
+
+### Installation
+1. Clone the Repository:
+
+```console
+git clone https://github.com/your-repo/structuremap-tooling.git
+cd structuremap-tooling
+```
+2. Once the `structuremap-tooling` folder, click on run.
+3. A prompt will appear on the CLI `Kindly enter the XLS filepath`: Enter the absolute path of the file's location. Click `Enter`
+4. Another prompt will appear on the CLI `Kindly enter the questionnaire filepath`: Enter the absolute path of the file's location. Click `Enter`
+5. The structureMap will be generated in the CLI and two complete files in the folder containing the `.json` and `.map` files
+
+## Contributing
+Contributions are welcome! Please open an issue or submit a pull request for any enhancements or bug fixes.

efsity/build.gradle.kts

@@ -83,13 +83,17 @@ dependencies {
   implementation(deps.picocli)
   implementation(deps.xstream)
   implementation(deps.icu4j)
+  implementation(deps.poi)
+  implementation(deps.poiooxml)
   implementation(deps.javafaker) { exclude(group = "org.yaml") }
   implementation(deps.snakeyaml)
   implementation("ca.uhn.hapi.fhir:hapi-fhir-validation:6.8.0")
 
   testImplementation(kotlin("test"))
   testImplementation("junit:junit:4.13.2")
   testImplementation("org.mockito:mockito-inline:3.12.4")
+  testImplementation("io.mockk:mockk:1.13.7")
+  testImplementation("org.mockito.kotlin:mockito-kotlin:4.1.0")
 }
 
 tasks.withType<JavaCompile> { options.encoding = deps.versions.project.build.sourceEncoding.get() }

efsity/libs.versions.toml

@@ -19,6 +19,8 @@ snakeyaml-version="2.3"
 spotless-version ="6.20.0"
 xstream="1.4.20"
 icu4j-version = "75.1"
+poi-version = "4.1.1"
+poi-ooxml-version = "4.1.1"
 
 [libraries]
 caffeine = { module = "com.github.ben-manes.caffeine:caffeine", version.ref = "caffeine-version" }
@@ -50,6 +52,8 @@ 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" }
+poi = { module="org.apache.poi:poi", version.ref = "poi-version" }
+poiooxml = { module="org.apache.poi:poi-ooxml", version.ref = "poi-ooxml-version" }
 
 [bundles]
 cqf-cql = ["cql-to-elm","elm","elm-jackson","model","model-jackson"]

efsity/src/main/java/org/smartregister/Main.java

@@ -21,7 +21,8 @@
       TranslateCommand.class,
       QuestionnaireResponseGeneratorCommand.class,
       ValidateFileStructureCommand.class,
-      PublishFhirResourcesCommand.class
+      PublishFhirResourcesCommand.class,
+      GenerateStructureMapCommand.class
     })
 public class Main implements Runnable {
   public static void main(String[] args) {

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

@@ -0,0 +1,48 @@
+package org.smartregister.command;
+
+import java.io.IOException;
+import org.smartregister.structuremaptool.GenerateStructureMapServiceKt;
+import org.smartregister.util.FctUtils;
+import picocli.CommandLine;
+
+@CommandLine.Command(name = "generateStructureMap")
+public class GenerateStructureMapCommand implements Runnable {
+  @CommandLine.Option(
+      names = {"-q", "--questionnaire"},
+      description = "Questionnaire",
+      required = true)
+  private String questionnairePath;
+
+  @CommandLine.Option(
+      names = {"-c", "--configPath"},
+      description = "StructureMap generation configuration in an excel sheet",
+      required = true)
+  private String configPath;
+
+  @CommandLine.Option(
+      names = {"-qr", "--questionnaireResponsePath"},
+      description = "Questionnaire response",
+      required = true)
+  private String questionnaireResponsePath;
+
+  @Override
+  public void run() {
+    if (configPath != null) {
+      try {
+        generateStructureMap(configPath, questionnairePath, questionnaireResponsePath);
+      } catch (IOException e) {
+        throw new RuntimeException(e);
+      }
+    }
+  }
+
+  public static void generateStructureMap(
+      String configPath, String questionnairePath, String questionnaireResponsePath)
+      throws IOException {
+    long start = System.currentTimeMillis();
+    FctUtils.printInfo("Starting StructureMap generation");
+    GenerateStructureMapServiceKt.main(configPath, questionnairePath, questionnaireResponsePath);
+
+    FctUtils.printCompletedInDuration(start);
+  }
+}

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

@@ -55,6 +55,7 @@ class TransformSupportServices @Inject constructor(val simpleWorkerContext: Simp
   override fun createType(appInfo: Any, name: String): Base {
     return when (name) {
       "RiskAssessment_Prediction" -> RiskAssessmentPredictionComponent()
+      "RiskAssessment\$RiskAssessmentPredictionComponent" -> RiskAssessmentPredictionComponent()
       "Immunization_AppliedProtocol" -> Immunization.ImmunizationProtocolAppliedComponent()
       "Immunization_Reaction" -> Immunization.ImmunizationReactionComponent()
       "EpisodeOfCare_Diagnosis" -> EpisodeOfCare.DiagnosisComponent()