Merge branch 'test-extraction-scenerios' of github.com:onaio/fhir-too…

…ling into test-extraction-scenerios

efsity-cli/build.gradle.kts

@@ -18,7 +18,7 @@ repositories {
 
 group = "org.smartregister"
 
-version = "2.3.12-SNAPSHOT"
+version = "2.3.13-SNAPSHOT"
 
 description = "fhircore-tooling (efsity)"
 

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

@@ -83,6 +83,12 @@ public class QuestionnaireResponseGeneratorCommand implements Runnable {
       defaultValue = ".")
   private String outputFilePath;
 
+  @CommandLine.Option(
+      names = {"-ih", "--ignore-hidden"},
+      description = "Ignore hidden questions when generating responses",
+      defaultValue = "true")
+  private boolean ignoreHiddenQuestions;
+
   private static final Random random = new Random();
   private static final Faker faker = new Faker();
 
@@ -99,7 +105,8 @@ public void run() {
             fhir_base_url,
             apiKey,
             aiModel,
-            maxTokens);
+            maxTokens,
+            ignoreHiddenQuestions);
       } catch (IOException e) {
         throw new RuntimeException(e);
       }
@@ -127,7 +134,8 @@ public static void generateResponse(
       String fhir_base_url,
       String apiKey,
       String aiModel,
-      String maxTokens)
+      String maxTokens,
+      boolean ignoreHiddenQuestions)
       throws IOException {
     long start = System.currentTimeMillis();
 
@@ -141,7 +149,7 @@ public static void generateResponse(
 
     String questionnaireResponseString =
         (Objects.equals(mode, "populate"))
-            ? populateMode(questionnaireData, fhir_base_url, extrasPath)
+            ? populateMode(questionnaireData, fhir_base_url, extrasPath, ignoreHiddenQuestions)
             : aiMode(questionnaireData, apiKey, aiModel, maxTokens);
 
     // Write response to file
@@ -321,9 +329,15 @@ static JSONObject generateAnswer(
     }
   }
 
-  static JSONArray getAnswers(JSONArray questions, JSONArray responses, JSONObject extras) {
+  static JSONArray getAnswers(
+      JSONArray questions, JSONArray responses, JSONObject extras, boolean ignoreHiddenQuestions) {
     for (int i = 0; i < questions.length(); i++) {
       JSONObject current_question = questions.getJSONObject(i);
+
+      if (ignoreHiddenQuestions && isHiddenQuestion(current_question)) {
+        continue;
+      }
+
       String question_type = current_question.getString("type");
       String link_id = current_question.getString("linkId");
 
@@ -335,15 +349,38 @@ static JSONArray getAnswers(JSONArray questions, JSONArray responses, JSONObject
         if (current_question.has("item")) {
           JSONArray group_questions = current_question.getJSONArray("item");
           JSONArray group_responses = responses.getJSONObject(i).getJSONArray("item");
-          getAnswers(group_questions, group_responses, extras);
+          getAnswers(group_questions, group_responses, extras, ignoreHiddenQuestions);
         }
       }
       responses.getJSONObject(i).put("answer", answer_arr);
     }
     return responses;
   }
 
-  static String populateMode(String questionnaireData, String fhir_base_url, String extrasPath)
+  static boolean isHiddenQuestion(JSONObject question) {
+    boolean isHidden = false;
+
+    if (question.has("extension")) {
+      JSONArray extensions = question.getJSONArray("extension");
+      for (int i = 0; i < extensions.length(); i++) {
+        JSONObject extension = extensions.getJSONObject(i);
+        if (extension
+            .getString("url")
+            .equals("http://hl7.org/fhir/StructureDefinition/questionnaire-hidden")) {
+          isHidden = extension.optBoolean("valueBoolean", true);
+          break;
+        }
+      }
+    }
+
+    return isHidden;
+  }
+
+  static String populateMode(
+      String questionnaireData,
+      String fhir_base_url,
+      String extrasPath,
+      boolean ignoreHiddenQuestions)
       throws IOException {
     JSONObject resource = new JSONObject(questionnaireData);
     String questionnaire_id = resource.getString("id");
@@ -377,7 +414,6 @@ static String populateMode(String questionnaireData, String fhir_base_url, Strin
     String populate_endpoint =
         String.join("/", fhir_base_url, resourceType, questionnaire_id, "$populate");
     List<String> result = HttpClient.postRequest(params.toString(), populate_endpoint, null);
-
     JSONObject questionnaire_response = new JSONObject(result.get(1));
     FctUtils.printError("Debug: response from questionnaireResponse: " + questionnaire_response);
 
@@ -387,7 +423,8 @@ static String populateMode(String questionnaireData, String fhir_base_url, Strin
     if (questionnaire_response.has("item")) {
       JSONArray response = (JSONArray) questionnaire_response.get("item");
       JSONArray questions = resource.getJSONArray("item");
-      JSONArray response_with_answers = getAnswers(questions, response, extras);
+      JSONArray response_with_answers =
+          getAnswers(questions, response, extras, ignoreHiddenQuestions);
       questionnaire_response.put("item", response_with_answers);
     }
     return String.valueOf(questionnaire_response);

efsity-cli/src/main/java/org/smartregister/command/TranslateCommand.java

@@ -235,12 +235,16 @@ public void run() {
     Objects.requireNonNull(inputFilePath, "Input file path cannot be null");
 
     if (inputFilePath.endsWith("configs") || inputFilePath.endsWith("fhir_content")) {
+
       return inputFilePath.resolve("translation");
+
     }
     if (inputFilePath.toString().endsWith(".json")) {
       Path parent = inputFilePath.getParent();
       if (parent == null || parent.getParent() == null) {
+
         throw new IllegalArgumentException("Invalid file path for: " + inputFilePath);
+
       }
       return parent.getParent().resolve("translation");
     }

efsity-cli/src/main/java/org/smartregister/command/ValidateStructureMapCommand.java

@@ -127,7 +127,8 @@ void validateStructureMap(String inputFilePath, String structureMapFilePath, boo
           "http://localhost:8080/fhir",
           "",
           "",
-          "");
+          "",
+          true);
 
       // Extract Resources using the StructureMap and the generated QuestionnaireResponse
       String generatedQuestionnaireResponsePath =

efsity-cli/src/test/java/org/smartregister/command/QuestionnaireResponseGeneratorCommandTest.java

@@ -5,6 +5,7 @@
 import java.time.LocalDate;
 import java.time.LocalDateTime;
 import org.json.JSONArray;
+import org.json.JSONException;
 import org.json.JSONObject;
 import org.junit.jupiter.api.Test;
 
@@ -299,4 +300,232 @@ void testGenerateDefaultAnswer() {
     assertNotNull(answer);
     assertTrue(answer.isEmpty());
   }
+
+  @Test
+  void testIsHiddenQuestion_hiddenExtensionTrue() {
+    JSONObject question = new JSONObject();
+    JSONArray extensions = new JSONArray();
+    JSONObject hiddenExtension = new JSONObject();
+    hiddenExtension.put("url", "http://hl7.org/fhir/StructureDefinition/questionnaire-hidden");
+    hiddenExtension.put("valueBoolean", true);
+    extensions.put(hiddenExtension);
+    question.put("extension", extensions);
+
+    assertTrue(QuestionnaireResponseGeneratorCommand.isHiddenQuestion(question));
+  }
+
+  @Test
+  void testIsHiddenQuestion_hiddenExtensionFalse() {
+    JSONObject question = new JSONObject();
+    JSONArray extensions = new JSONArray();
+    JSONObject hiddenExtension = new JSONObject();
+    hiddenExtension.put("url", "http://hl7.org/fhir/StructureDefinition/questionnaire-hidden");
+    hiddenExtension.put("valueBoolean", false);
+    extensions.put(hiddenExtension);
+    question.put("extension", extensions);
+
+    assertFalse(QuestionnaireResponseGeneratorCommand.isHiddenQuestion(question));
+  }
+
+  @Test
+  void testIsHiddenQuestion_noHiddenExtension() {
+    JSONObject question = new JSONObject();
+    JSONArray extensions = new JSONArray();
+    JSONObject otherExtension = new JSONObject();
+    otherExtension.put("url", "http://example.com/other-extension");
+    otherExtension.put("valueBoolean", true);
+    extensions.put(otherExtension);
+    question.put("extension", extensions);
+
+    assertFalse(QuestionnaireResponseGeneratorCommand.isHiddenQuestion(question));
+  }
+
+  @Test
+  void testIsHiddenQuestion_noExtensions() {
+    JSONObject question = new JSONObject();
+    assertFalse(QuestionnaireResponseGeneratorCommand.isHiddenQuestion(question));
+  }
+
+  @Test
+  void testIsHiddenQuestion_hiddenExtensionNoValueBoolean() {
+    JSONObject question = new JSONObject();
+    JSONArray extensions = new JSONArray();
+    JSONObject hiddenExtension = new JSONObject();
+    hiddenExtension.put("url", "http://hl7.org/fhir/StructureDefinition/questionnaire-hidden");
+    extensions.put(hiddenExtension);
+    question.put("extension", extensions);
+
+    assertTrue(QuestionnaireResponseGeneratorCommand.isHiddenQuestion(question));
+  }
+
+  @Test
+  void testGetAnswers_simpleQuestion() {
+    JSONArray questions = new JSONArray();
+    JSONObject question = new JSONObject();
+    question.put("type", "string");
+    question.put("linkId", "exampleLinkId");
+    questions.put(question);
+
+    JSONArray responses = new JSONArray();
+    JSONObject response = new JSONObject();
+    responses.put(response);
+
+    JSONObject extras = new JSONObject();
+
+    JSONArray updatedResponses =
+        QuestionnaireResponseGeneratorCommand.getAnswers(questions, responses, extras, false);
+
+    assertNotNull(updatedResponses);
+    assertTrue(updatedResponses.getJSONObject(0).has("answer"));
+    assertTrue(
+        updatedResponses
+            .getJSONObject(0)
+            .getJSONArray("answer")
+            .getJSONObject(0)
+            .has("valueString"));
+  }
+
+  @Test
+  void testGetAnswers_groupQuestion() {
+    JSONArray questions = new JSONArray();
+    JSONObject groupQuestion = new JSONObject();
+    groupQuestion.put("type", "group");
+    groupQuestion.put("linkId", "group1");
+    JSONArray nestedQuestions = new JSONArray();
+    JSONObject nestedQuestion = new JSONObject();
+    nestedQuestion.put("type", "integer");
+    nestedQuestion.put("linkId", "nested1");
+    nestedQuestions.put(nestedQuestion);
+    groupQuestion.put("item", nestedQuestions);
+    questions.put(groupQuestion);
+
+    JSONArray responses = new JSONArray();
+    JSONObject groupResponse = new JSONObject();
+    groupResponse.put("item", new JSONArray().put(new JSONObject()));
+    responses.put(groupResponse);
+
+    JSONObject extras = new JSONObject();
+
+    JSONArray updatedResponses =
+        QuestionnaireResponseGeneratorCommand.getAnswers(questions, responses, extras, false);
+
+    assertNotNull(updatedResponses);
+    JSONObject nestedResponse =
+        updatedResponses.getJSONObject(0).getJSONArray("item").getJSONObject(0);
+    assertTrue(nestedResponse.has("answer"));
+    assertTrue(nestedResponse.getJSONArray("answer").getJSONObject(0).has("valueInteger"));
+  }
+
+  @Test
+  void testGetAnswers_ignoreHiddenQuestions() {
+    JSONArray questions = new JSONArray();
+    JSONObject hiddenQuestion = new JSONObject();
+    hiddenQuestion.put("type", "boolean");
+    hiddenQuestion.put("linkId", "hidden1");
+    JSONArray extensions = new JSONArray();
+    JSONObject hiddenExtension = new JSONObject();
+    hiddenExtension.put("url", "http://hl7.org/fhir/StructureDefinition/questionnaire-hidden");
+    hiddenExtension.put("valueBoolean", true);
+    extensions.put(hiddenExtension);
+    hiddenQuestion.put("extension", extensions);
+    questions.put(hiddenQuestion);
+
+    JSONArray responses = new JSONArray();
+    responses.put(new JSONObject());
+
+    JSONObject extras = new JSONObject();
+
+    JSONArray updatedResponses =
+        QuestionnaireResponseGeneratorCommand.getAnswers(questions, responses, extras, true);
+
+    assertNotNull(updatedResponses);
+    assertFalse(updatedResponses.getJSONObject(0).has("answer"));
+  }
+
+  @Test
+  void testGetAnswers_includeHiddenQuestions() {
+    JSONArray questions = new JSONArray();
+    JSONObject hiddenQuestion = new JSONObject();
+    hiddenQuestion.put("type", "boolean");
+    hiddenQuestion.put("linkId", "hidden1");
+    JSONArray extensions = new JSONArray();
+    JSONObject hiddenExtension = new JSONObject();
+    hiddenExtension.put("url", "http://hl7.org/fhir/StructureDefinition/questionnaire-hidden");
+    hiddenExtension.put("valueBoolean", true);
+    extensions.put(hiddenExtension);
+    hiddenQuestion.put("extension", extensions);
+    questions.put(hiddenQuestion);
+
+    JSONArray responses = new JSONArray();
+    responses.put(new JSONObject());
+
+    JSONObject extras = new JSONObject();
+
+    JSONArray updatedResponses =
+        QuestionnaireResponseGeneratorCommand.getAnswers(questions, responses, extras, false);
+
+    assertNotNull(updatedResponses);
+    assertTrue(updatedResponses.getJSONObject(0).has("answer"));
+    assertTrue(
+        updatedResponses
+            .getJSONObject(0)
+            .getJSONArray("answer")
+            .getJSONObject(0)
+            .has("valueBoolean"));
+  }
+
+  @Test
+  void testGetAnswers_noExtras() {
+    JSONArray questions = new JSONArray();
+    JSONObject question = new JSONObject();
+    question.put("type", "decimal");
+    question.put("linkId", "decimal1");
+    questions.put(question);
+
+    JSONArray responses = new JSONArray();
+    responses.put(new JSONObject());
+
+    JSONArray updatedResponses =
+        QuestionnaireResponseGeneratorCommand.getAnswers(questions, responses, null, false);
+
+    assertNotNull(updatedResponses);
+    assertTrue(updatedResponses.getJSONObject(0).has("answer"));
+    assertTrue(
+        updatedResponses
+            .getJSONObject(0)
+            .getJSONArray("answer")
+            .getJSONObject(0)
+            .has("valueDecimal"));
+  }
+
+  @Test
+  void testGetAnswers_emptyQuestionnaire() {
+    JSONArray questions = new JSONArray();
+    JSONArray responses = new JSONArray();
+    JSONObject extras = new JSONObject();
+
+    JSONArray updatedResponses =
+        QuestionnaireResponseGeneratorCommand.getAnswers(questions, responses, extras, false);
+
+    assertNotNull(updatedResponses);
+    assertEquals(0, updatedResponses.length());
+  }
+
+  @Test
+  void testGetAnswers_mismatchedQuestionsAndResponses() {
+    JSONArray questions = new JSONArray();
+    JSONObject question = new JSONObject();
+    question.put("type", "text");
+    question.put("linkId", "text1");
+    questions.put(question);
+
+    JSONArray responses = new JSONArray();
+
+    JSONObject extras = new JSONObject();
+
+    assertThrows(
+        JSONException.class,
+        () ->
+            QuestionnaireResponseGeneratorCommand.getAnswers(questions, responses, extras, false));
+  }
 }