WIP: Validate StructureMap (#281)

* Create validateStructureMap command * Add parseCompositionFile function * Add a function that parses the composition file * Update the QRgeneration and call it from validateStructureMap command * Add a folder for saving the QRs * Fix failing Validation test class * Add structueMap validation against QRs * Remove default values for SM command * Add extractedResources sub folder * Add the extractedResources from the bundle to the directory * Add validation code for the project * Fix spotless * Fix failing path * Add FctValidation for questionnaireToStructureMapId Mapping * Add test cases for validateStructureMap * Use questionnaireProcessor * Update validate Structuremap for project * Finalize tests * Add documentation * Fix structureMap path --------- Co-authored-by: sharon2719 <[email protected]> Co-authored-by: Sharon Akinyi <[email protected]>
onaio · Oct 23, 2024 · a70d0cb · a70d0cb
1 parent 6493f4c
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diff --git a/efsity/.gitignore b/efsity/.gitignore
@@ -9,3 +9,5 @@ fhircore-tooling.iml
 # build files
 bin
 target
+
+generatedResources
diff --git a/efsity/README.md b/efsity/README.md
@@ -172,6 +172,38 @@ $ 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.
 
+### Validating Questionnaires and  StructureMap 
+The tool supports two validation modes:
+
+**1.Single mode** - Validates a single StructureMap and questionnaire.
+**2.Project mode** - Validates all project files, including multiple questionnaires and StructureMaps.
+
+The tool maps each questionnaire to the specified StructureMap, then generates the corresponding `QuestionnaireResponse`. Once generated, a bundle is created with the related resources (e.g., Patient, Condition).
+
+To run the tool, ensure the following:
+
+1. Install h`api=fhir-jpaserver-starter`.
+2. In `src/main/resources/application.yaml`, set `hapi: fhir`: to `true`.
+3. Run the command: `mvn spring-boot:run`
+
+The server will be accessible at http://localhost:8080/fhir, and the `CapabilityStatement` can be found at http://localhost:8080/fhir/metadata.
+**Options**
+```
+-i or --input            Path to the project questionnaire folder to be validated.
+-q or --questionnaire     Path to a single questionnaire file to be validated.
+-v or --validate          (Optional) Boolean flag to validate FHIR resources before publishing. Default is `false`.
+-sm or --structure-map    Path to the folder containing StructureMaps. Nested directories are supported.
+
+```
+
+```console (single-mode)
+$  fct validateStructureMap -q ~/Workspace/fhir-resources/<project>/questionnaire-folder/resource.json -sm ~/Workspace/fhir-resources/coda/structure_map-folder/coda-child-structure-map.txt
+```
+
+```console (project-mode)
+$  fct validateStructureMap -i ~/Workspace/fhir-resources/<project>/questionnaire-folder/ -sm ~/Workspace/fhir-resources/coda/structure_map-folder/`
+```
+
 ### Localization
 Tool that supports localization by the use of the translation extension
 

diff --git a/efsity/src/main/java/org/smartregister/Main.java b/efsity/src/main/java/org/smartregister/Main.java
@@ -21,7 +21,8 @@
       TranslateCommand.class,
       QuestionnaireResponseGeneratorCommand.class,
       ValidateFileStructureCommand.class,
-      PublishFhirResourcesCommand.class
+      PublishFhirResourcesCommand.class,
+      ValidateStructureMapCommand.class,
     })
 public class Main implements Runnable {
   public static void main(String[] args) {

diff --git a/efsity/src/main/java/org/smartregister/command/QuestionnaireResponseGeneratorCommand.java b/efsity/src/main/java/org/smartregister/command/QuestionnaireResponseGeneratorCommand.java
@@ -91,7 +91,15 @@ public void run() {
     validateOptions();
     if (inputFilePath != null) {
       try {
-        generateResponse(inputFilePath, mode, extrasPath, fhir_base_url, apiKey);
+        generateResponse(
+            inputFilePath,
+            mode,
+            outputFilePath,
+            extrasPath,
+            fhir_base_url,
+            apiKey,
+            aiModel,
+            maxTokens);
       } catch (IOException e) {
         throw new RuntimeException(e);
       }
@@ -111,8 +119,15 @@ private void validateOptions() {
     }
   }
 
-  private void generateResponse(
-      String inputFilePath, String mode, String extrasPath, String fhir_base_url, String apiKey)
+  public static void generateResponse(
+      String inputFilePath,
+      String mode,
+      String outputFilePath,
+      String extrasPath,
+      String fhir_base_url,
+      String apiKey,
+      String aiModel,
+      String maxTokens)
       throws IOException {
     long start = System.currentTimeMillis();
 
@@ -127,17 +142,17 @@ private void generateResponse(
     String questionnaireResponseString =
         (Objects.equals(mode, "populate"))
             ? populateMode(questionnaireData, fhir_base_url, extrasPath)
-            : aiMode(questionnaireData, apiKey);
+            : aiMode(questionnaireData, apiKey, aiModel, maxTokens);
 
     // Write response to file
     FctUtils.printInfo("Writing response to file");
     String output =
-        Files.isDirectory(Paths.get(this.outputFilePath))
-            ? this.outputFilePath
+        Files.isDirectory(Paths.get(outputFilePath))
+            ? outputFilePath
                 + File.separator
                 + inputFile.getNameWithoutExtension()
                 + Constants.QUESTIONNAIRE_RESPONSE_SUFFIX
-            : this.outputFilePath;
+            : outputFilePath;
 
     FctUtils.writeJsonFile(output, questionnaireResponseString);
     FctUtils.printInfo(
@@ -148,7 +163,7 @@ private void generateResponse(
     FctUtils.printCompletedInDuration(start);
   }
 
-  Boolean checkResource(
+  static Boolean checkResource(
       String questionnaire_id, String resourceType, JSONObject resource, String fhir_base_url)
       throws IOException {
     JSONObject request = new JSONObject();
@@ -305,7 +320,7 @@ static JSONObject generateAnswer(
     }
   }
 
-  JSONArray getAnswers(JSONArray questions, JSONArray responses, JSONObject extras) {
+  static JSONArray getAnswers(JSONArray questions, JSONArray responses, JSONObject extras) {
     for (int i = 0; i < questions.length(); i++) {
       JSONObject current_question = questions.getJSONObject(i);
       String question_type = current_question.getString("type");
@@ -327,7 +342,7 @@ JSONArray getAnswers(JSONArray questions, JSONArray responses, JSONObject extras
     return responses;
   }
 
-  String populateMode(String questionnaireData, String fhir_base_url, String extrasPath)
+  static String populateMode(String questionnaireData, String fhir_base_url, String extrasPath)
       throws IOException {
     JSONObject resource = new JSONObject(questionnaireData);
     String questionnaire_id = resource.getString("id");
@@ -369,7 +384,8 @@ String populateMode(String questionnaireData, String fhir_base_url, String extra
     return String.valueOf(questionnaire_response);
   }
 
-  String aiMode(String questionnaireData, String apiKey) throws IOException {
+  static String aiMode(String questionnaireData, String apiKey, String aiModel, String maxTokens)
+      throws IOException {
     if (true) {
       throw new IllegalStateException("Sorry, the AI mode is temporarily unsupported");
     }
@@ -383,7 +399,7 @@ String aiMode(String questionnaireData, String apiKey) throws IOException {
 
     // Generate response
     String generatedResponseString =
-        aiGenerated(questionnaireJsonString, apiKey, this.aiModel, this.maxTokens);
+        aiGenerated(questionnaireJsonString, apiKey, aiModel, maxTokens);
     JSONObject obj = new JSONObject(generatedResponseString);
     JSONArray choices = obj.getJSONArray("choices");
     String questionnaireResponseString = "";

diff --git a/efsity/src/main/java/org/smartregister/command/StructureMapExtractResourcesCommand.java b/efsity/src/main/java/org/smartregister/command/StructureMapExtractResourcesCommand.java
@@ -42,19 +42,22 @@ public class StructureMapExtractResourcesCommand implements Runnable {
   public void run() {
 
     try {
-      extractResource(qr, sm);
+      extractResource(qr, sm, output);
 
     } catch (IOException e) {
       throw new RuntimeException(e);
     }
   }
 
-  private void extractResource(String qrFilePath, String structureMapFilePath) throws IOException {
+  static void extractResource(String qrFilePath, String structureMapFilePath, String output)
+      throws IOException {
 
     long start = System.currentTimeMillis();
 
-    FctUtils.printInfo(String.format("Questionnaire Response file path \u001b[35m%s\u001b[0m", qr));
-    FctUtils.printInfo(String.format("Structure Map file path \u001b[35m%s\u001b[0m", sm));
+    FctUtils.printInfo(
+        String.format("Questionnaire Response file path \u001b[35m%s\u001b[0m", qrFilePath));
+    FctUtils.printInfo(
+        String.format("Structure Map file path \u001b[35m%s\u001b[0m", structureMapFilePath));
 
     FctFile questionnaireResponse = FctUtils.readFile(qrFilePath);
-Original file line number
+Diff line change
@@ Expand Up / @@ -9,3 +9,5 @@ fhircore-tooling.iml @@
     # build files
     bin
     target
+    generatedResources