Merge pull request #21 from MyDigiTwinNL/fix/removing_assertion_fu_diab_undefined_date

Generating FHIR-Diabetes with undefined onsetdate, instead of assertion failing when the date cannot be calculated

Author: hcadavid

…ut-p675432-hf-followup-missing-date.json …75432-hf-diab-followup-missing-date.jsonfhirvalidation/sampleinputs/input-p675432-hf-followup-missing-date.json renamed to fhirvalidation/sampleinputs/input-p675432-hf-diab-followup-missing-date.json fhirvalidation/sampleinputs/input-p675432-hf-followup-missing-date.json renamed to fhirvalidation/sampleinputs/input-p675432-hf-diab-followup-missing-date.json

@@ -24,13 +24,13 @@
     "stroke_followup_adu_q_1":{"2a":"2","3a":"2","3b":"2"},
 
 
-    "diabetes_presence_adu_q_1":    {"1a":"1"},
-    "diabetes_startage_adu_q_1":    {"1a":"28"},
-    "diabetes_followup_adu_q_1":        {"1b":"2","1c":"2","2a":"2","3a":"2","3b":"2"},
+    "diabetes_presence_adu_q_1":    {"1a":"2"},
+    "diabetes_startage_adu_q_1":    {"1a":""},
+    "diabetes_followup_adu_q_1":        {"1b":"2","1c":"2","2a":"2","3a":"1","3b":"2"},
     "diabetes_type_adu_q_1":        {"1a":"2"},
     "diabetes_type_adu_q_1_a":      {"1a":""},
     "t1d_followup_adu_q_1":                 {"2a":"2","3a":"2","3b":"2"},
-    "t2d_followup_adu_q_1":                 {"2a":"2","3a":"2","3b":"2"},
+    "t2d_followup_adu_q_1":                 {"2a":"2","3a":"1","3b":"2"},
 
     "bp_entrytype_all_m_1":         {"1a":"2","2a":"2"},
     "bp_bandsize_all_m_1":          {"1a":"1","2a":"1","3a":"1"},

src/__tests__/diabetes.test.ts

@@ -53,6 +53,38 @@ test('diabetes clinical status, when reported positive in a follow-up, diabetes
 
 
 
+test('assertion test: diabetes clinical status, when reported positive in a follow-up, but no diabetes type is defined', () => {
+
+  const input = {
+    "diabetes_presence_adu_q_1": { "1a": "2" },
+    "diabetes_followup_adu_q_1": { "1b": "2", "1c": "2", "2a": "2", "3a": "1", "3b": "2" },
+    "diabetes_startage_adu_q_1": { "1a": "" },
+    "diabetes_type_adu_q_1":     { "1a": "2" },
+    "diabetes_type_adu_q_1_a":   { "1a": "" },
+    "t1d_followup_adu_q_1":                            { "2a": "2", "3a": "2", "3b": "2" },
+    "t2d_followup_adu_q_1":                            { "2a": "2", "3a": "2", "3b": "2" },    
+    "date": {"1a":"1992-5","1b":"1995-5","1c":"1997-5",/*date1*/"2a":"2001-5",/*date2*/"3a":"2003-5","3b":"2005-5"},
+    "age": { "1a": "22" },
+  }
+
+  try{
+    InputSingleton.getInstance().setInput(input);
+    expect(diabetesmf.clinicalStatus()).toBe(clinicalStatusSNOMEDCodeList.active);
+    expect(diabetesmf.isPresent()).toBe(true);
+    expect(diabetesmf.code()).toBe(conditionsSNOMEDCodeList.diabetes_mellitus_type_1);
+    expect(diabetesmf.onsetDateTime()).toBe("2002-05");
+    //execution shouldn't reach this point
+    throw new Error('Transformation should have failed with an UnexpectedInputException');
+  }
+  catch(error){
+    if (!(error instanceof UnexpectedInputException)) throw new Error('Transformation should have failed with an UnexpectedInputException');
+  }
+
+});
+
+
+
+
 test('diabetes clinical status, when reported positive in a follow-up after multiple skipped assessments, diabetes type 1', () => {
 
   const input = {
@@ -75,11 +107,11 @@ test('diabetes clinical status, when reported positive in a follow-up after mult
 
 });
 
-test('diabetes clinical status, with inconsistencies, missing date on the assessment where diabetes is reported', () => {
+test('diabetes clinical status (T1D) reported on a follow up, with missing date on the assessment where was reported', () => {
 
   const input = {
     "diabetes_presence_adu_q_1": { "1a": "2" },
-    "diabetes_followup_adu_q_1": { "1b": "2", "1c": "2", "2a": "2", "3a": "", "3b": "1" },
+    "diabetes_followup_adu_q_1": { "1b": "2", "1c": "2", "2a": "2", "3a": "1", "3b": "2" },
     "diabetes_startage_adu_q_1": { "1a": "" },
     "diabetes_type_adu_q_1":     { "1a": "2" },
     "diabetes_type_adu_q_1_a":   { "1a": "" },
@@ -89,16 +121,13 @@ test('diabetes clinical status, with inconsistencies, missing date on the assess
     "age": { "1a": "22" },
   }
 
-  try{
-    InputSingleton.getInstance().setInput(input);
-    expect(diabetesmf.clinicalStatus()).toBe(clinicalStatusSNOMEDCodeList.active);
-    expect(diabetesmf.isPresent()).toBe(true);
-    expect(diabetesmf.code()).toBe(conditionsSNOMEDCodeList.diabetes_mellitus_type_1);
-    expect(diabetesmf.onsetDateTime()).toBe("2003-05");
-  }
-  catch(error){
-    if (!(error instanceof UnexpectedInputException)) fail('Expected exception')
-  }
+  
+  InputSingleton.getInstance().setInput(input);
+  expect(diabetesmf.clinicalStatus()).toBe(clinicalStatusSNOMEDCodeList.active);
+  expect(diabetesmf.isPresent()).toBe(true);
+  expect(diabetesmf.code()).toBe(conditionsSNOMEDCodeList.diabetes_mellitus_type_1);
+  expect(diabetesmf.onsetDateTime()).toBe(undefined);
+  
 
 
 });

src/lifelines/Diabetes.ts

@@ -90,18 +90,23 @@ const _clinicalStatus = moize((diab_presence:string|undefined,followup_assessmen
  * ------------------------------------------------------------------
  * 
  * @precondition
- *      - date is never a missing value (is a default variable)
  *      - the problem is 'active' (see clinicalStatus function)
  *      - if there is a diabetes report on a follow-up 'diabetes_followup_adu_q_1', there should be a 'yes' value
  *        in either t2d_followup_adu_q_1 or t2d_followup_adu_q_1 (diabetes type)
  * 
  * 
  * @pairingrule
- *      if diabetes_presence_adu_q_1 = yes in 1A => approximate year on which the participant given the age reported  by diabetes_startage_adu_q_1
- *          (undefined if diabetes_startage_adu_q_1 has a missing value)
+ *      if diabetes_presence_adu_q_1 = yes in 1A => 
+ *              if start_age was reported, approximate year of the event given start_age reported (diabetes_startage_adu_q_1) 
+ *                  and the year of the year of the assessment.
+ *              else
+ *                  undefined onset date
  *      else
- *          if there is a 'yes' in any diabetes_followup_adu_q_1 => mean date between the date of the assessment 
- *              where diabetes_followup_adu_q_1 = yes, and the date of the preceding one.
+ *          if there is a 'yes' in any diabetes_followup_adu_q_1 => 
+ *              If the date of the assessment where diabetes_followup_adu_q_1 = yes is available =>
+ *                  mean date between that particular date (when diabetes_followup_adu_q_1 = yes), and the date of the preceding assessment.
+ *              Else
+ *                  return undefined onset date
  *          else
  *              error/precondition violated ('diabetes' is not 'active' if the execution reached this point)
  *              
@@ -135,19 +140,29 @@ export const onsetDateTime = ():string|undefined => {
             return lifelinesDateToISO(lifelinesMeanDate(date1,date2))
         }
         else{
-            throw Error("Unexpected input (precondition violated): no 'yes' values in neither t2d_followup_adu_q_1 nor t2d_followup_adu_q_1")
+            return undefined;            
         }
 
 
     }
 
 }
 
-/**
+
+ /* 
+ * 
+ * Helper function for 'onsetDateTime'
  * 
  * @param diabFollowUp 
- * @returns 
- * @precondition there is always a date on the assessment prior to the one where diabetes_followup_adu_q_1 was 'yes'
+ * 
+ * @return
+ *      If the date of the assessment where diabetes_followup_adu_q_1 = yes is available =>
+ *          mean date between that particular date (when diabetes_followup_adu_q_1 = yes), and the date of the preceding assessment.
+ *      Else
+ *          return undefined date
+ * 
+ * @precondition: there is at least one 'yes'/1 on diabetes_followup_adu_q_1
+ * @precondition there is always a date on one of the assessment prior to the one where diabetes_followup_adu_q_1 was 'yes'
  * 
  */
 function findDatesBetweenDiabetesPresenceReport(): [string,string]|undefined{
@@ -160,18 +175,23 @@ function findDatesBetweenDiabetesPresenceReport(): [string,string]|undefined{
     assertIsDefined(diabetesRepWave,`A 'yes' value on diabetes_followup_adu_q_1 was expected`)    
 
     const diabetesRepWaveDate = inputValue("date",diabetesRepWave)
-    assertIsDefined(diabetesRepWaveDate,`A non-null date is expected in the assessment where diabetes_followup_adu_q_1 is reported`)
+    if (diabetesRepWaveDate === undefined){
+        return undefined
+    } 
+    else{
+        //find the previous non-undefined assessment date
+        const assessmentDates:variableAssessments = inputValues('date')            
+        const waves = ['1a','1b','1c','2a','3a','3b'];    
+        const previousWaves = waves.slice(0,waves.indexOf(diabetesRepWave))
+        const previousAssessmentWave = previousWaves.reverse().find((pwave)=>assessmentDates[pwave]!==undefined)
+        
+        assertIsDefined(previousAssessmentWave,`Assessment (with a defined date) expected to exist previous to the one where diabetes_followup_adu_q_1 is reported`)
+
+        const previousAssessmentDate:string = assessmentDates[previousAssessmentWave]!;
+        return [previousAssessmentDate,diabetesRepWaveDate]
+    }
 
-    //find the previous non-undefined assessment date
-    const assessmentDates:variableAssessments = inputValues('date')            
-    const waves = ['1a','1b','1c','2a','3a','3b'];    
-    const previousWaves = waves.slice(0,waves.indexOf(diabetesRepWave))
-    const previousAssessmentWave = previousWaves.reverse().find((pwave)=>assessmentDates[pwave]!==undefined)
-    
-    assertIsDefined(previousAssessmentWave,`Assessment (with a defined date) expected to exist previous to the one where diabetes_followup_adu_q_1 is reported`)
 
-    const previousAssessmentDate:string = assessmentDates[previousAssessmentWave]!;
-    return [previousAssessmentDate,diabetesRepWaveDate]
 
 
   }

src/lifelines/HeartFailure.ts

@@ -154,6 +154,7 @@ const _clinicalStatus = moize((heartfailure_presence:string|undefined,followup_a
  * 
  * 
  * @precondition: there is at least one 'yes'/1 on heartfailure_followup_adu_q_1
+ * @precondition there is always a date on one of the assessment prior to the one where diabetes_followup_adu_q_1 was 'yes'
  * 
  * If the date of the assessment where heartfailure_followup_adu_q_1 = yes is available =>
  *      mean date between that particular date (when heartfailure_followup_adu_q_1 = yes), and the date of the preceding assessment.

src/viewerserver/serversettings.ts

@@ -19,6 +19,6 @@ export const targets:MappingTarget[] = [
     //{ "module": './lifelines/HaemoglobinConcentration', "template": '../../zib-2017-mappings/generic/LabTestResult_Diagnostic_Report.jsonata' },
     //{ "module": './lifelines/HaemoglobinConcentration', "template": '../../zib-2017-mappings/generic/LabTestResult_Observation.jsonata' },
     //{ "module": './lifelines/HaemoglobinConcentration', "template": '../../zib-2017-mappings/generic/LabTestResult_Specimen.jsonata' },
-    { "template": '../../zib-2017-mappings/generic/Condition.jsonata', "module": './lifelines/HeartFailure' },  
+    { "template": '../../zib-2017-mappings/Diabetes.jsonata', "module": './lifelines/Diabetes' },  
 
   ]