Removing one of the pairing rules assertions: Generating FHIR-HF with…

… an undefined onsetDate, when HF was reported on a follow-up assessment, and the assessment date is not available. Address issue #19

fhirvalidation/sampleinputs/input-p11111.json

@@ -0,0 +1,71 @@
+{
+    "project_pseudo_id": {"1a":"11111"},
+    "variant_id": {},
+
+    "date": {"1a":"1992-5","1b":"1995-5","1c":"1997-5","2a":"2001-5","2b":"2002-5","3a":"2003-5","3b":"2005-5"},    
+    "age": {"1a":"22"},
+    "gender": {"1a":"MALE"},
+    "zip_code": {"1a":"11111"},
+    "date_of_death": {"global":"2010-2"},
+    "date_of_inclusion": {"global":"1991-2"},
+
+    "albumin_result_all_m_1" :{ "1a": "51"},
+
+    "creatinine_result_all_m_1":{ "1a": "79.2", "2a":"106.1"},
+    "hemoglobin_result_all_m_1" :{ "1a": "11.1", "2a":"12"},
+
+    "ethnicity_category_adu_q_1":{"1b":"3"},        
+    "hba1cconc_result_all_m_1":{ "1a": "43", "2a":"44"},
+
+    "hypertension_startage_adu_q_1":{"1a":"","3a":"23","3b":"23"},
+    "hypertension_presence_adu_q_1":{"1a":"2","3a":"1","3b":"1"},
+
+    "stroke_startage_adu_q_1":{ "1a": "12" },
+    "stroke_presence_adu_q_1": { "1a": "1" },
+    "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_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"},
+
+    "bp_entrytype_all_m_1":         {"1a":"2","2a":"2"},
+    "bp_bandsize_all_m_1":          {"1a":"1","2a":"1","3a":"1"},
+    "bp_arm_all_m_1":                           {"3a":"2"},
+    "bpavg_systolic_all_m_1":       {"1a":"130","2a":"130"},
+    "bpavg_diastolic_all_m_1":      {"1a":"140","2a":"140"},
+    "bpavg_arterial_all_m_1":       {"1a":"113","2a":"113"},
+
+    "hdlchol_result_all_m_1":       {"1a":"0.31","2a":"0.22"},
+    "ldlchol_result_all_m_1":       {"1a":"0.41","2a":"0.42"},
+    "cholesterol_result_all_m_1":   {"1a":"0.51","2a":"0.52"},
+
+    "heartattack_startage_adu_q_1": {"1a":"33"},
+    "angioplasty_bypass_adu_q_1_a":  {"1a":"1","3a":"1","3b":"1"},
+    "heartattack_presence_adu_q_1": {"1a":"1"},
+    "heartattack_followup_adu_q_1":     {"1b":"2","1c":"2","2a":"2","3a":"2","3b":"2"},
+    "angioplasty_bypass_adu_q_1":   {"1a":"1","3a":"1","3b":"1"},
+
+    "heartfailure_startage_adu_q_1":{ "1a": "" },
+    "heartfailure_presence_adu_q_1": { "1a": "2" },
+    "heartfailure_followup_adu_q_1":{"2a":"2","3a":"2","3b":"2"},
+
+    "carotid_stenosis_adu_q_1":     {"1a":"1"},
+    "claudication_followup_adu_q_1":            {"2a":"2","3a":"2","3b":"2"},
+    "cvd_followup_adu_q_1":             {"1b":"2","1c":"2","2a":"2","3a":"2","3b":"2"},
+
+    "current_smoker_adu_c_2": { "1a": "0", "1b": "0", "1c": "0", "2a": "0", "2b": "0", "3a": "0" },
+    "smoking_startage_adu_c_2": { "1a": "5", "1b": "5", "1c": "5", "2a": "5", "2b": "5", "3a": "5" },
+    "ex_smoker_adu_c_2": { "1a": "1", "1b": "1", "1c": "1", "2a": "1", "2b": "1", "3a": "1" },
+    "smoking_endage_adu_c_2": { "1a": "8", "1b": "8", "1c": "8", "2a": "8", "2b": "8", "3a": "8"},
+    "ever_smoker_adu_c_2": { "1a": "1", "1b": "1", "1c": "1", "2a": "1", "2b": "1", "3a": "1"},
+    "total_frequency_adu_c_1": { "1a": "", "1b": "", "1c": "", "2a": "", "2b": "", "3a": ""},
+    "packyears_cumulative_adu_c_2": { "1a": "", "1b": "", "1c": "", "2a": "", "2b": "", "3a": ""}
+
+
+
+}
+

fhirvalidation/sampleinputs/input-p675432-hf-followup-missing-date.json

@@ -0,0 +1,71 @@
+{
+    "project_pseudo_id": {"1a":"675432"},
+    "variant_id": {},
+
+    "date": {"1a":"1992-5","1b":"1995-5","1c":"1997-5","2a":"2001-5","2b":"2002-5","3a":"","3b":"2005-5"},
+
+    "age": {"1a":"22"},
+    "gender": {"1a":"MALE"},
+    "zip_code": {"1a":"11111"},
+    "date_of_death": {"global":"2010-2"},
+    "date_of_inclusion": {"global":"1991-2"},
+
+    "albumin_result_all_m_1" :{ "1a": "51"},
+    "creatinine_result_all_m_1":{ "1a": "79.2", "2a":"106.1"},
+    "ethnicity_category_adu_q_1":{"1b":"3"},
+    "hemoglobin_result_all_m_1" :{ "1a": "11.1", "2a":"12"},
+    "hba1cconc_result_all_m_1":{ "1a": "43", "2a":"44"},
+
+    "hypertension_startage_adu_q_1":{"1a":"","3a":"23","3b":"23"},
+    "hypertension_presence_adu_q_1":{"1a":"2","3a":"1","3b":"1"},
+
+    "stroke_startage_adu_q_1":{ "1a": "12" },
+    "stroke_presence_adu_q_1": { "1a": "1" },
+    "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_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"},
+
+    "bp_entrytype_all_m_1":         {"1a":"2","2a":"2"},
+    "bp_bandsize_all_m_1":          {"1a":"1","2a":"1","3a":"1"},
+    "bp_arm_all_m_1":                           {"3a":"2"},
+    "bpavg_systolic_all_m_1":       {"1a":"130","2a":"130"},
+    "bpavg_diastolic_all_m_1":      {"1a":"140","2a":"140"},
+    "bpavg_arterial_all_m_1":       {"1a":"113","2a":"113"},
+
+    "hdlchol_result_all_m_1":       {"1a":"0.31","2a":"0.22"},
+    "ldlchol_result_all_m_1":       {"1a":"0.41","2a":"0.42"},
+    "cholesterol_result_all_m_1":   {"1a":"0.51","2a":"0.52"},
+
+    "heartattack_startage_adu_q_1": {"1a":"33"},
+    "angioplasty_bypass_adu_q_1_a":  {"1a":"1","3a":"1","3b":"1"},
+    "heartattack_presence_adu_q_1": {"1a":"1"},
+    "heartattack_followup_adu_q_1":     {"1b":"2","1c":"2","2a":"2","3a":"2","3b":"2"},
+    "angioplasty_bypass_adu_q_1":   {"1a":"1","3a":"1","3b":"1"},
+
+    "heartfailure_startage_adu_q_1":{ "1a": "" },
+    "heartfailure_presence_adu_q_1": { "1a": "2" },
+    "heartfailure_followup_adu_q_1":{"2a":"2","3a":"1","3b":"2"},
+
+    "carotid_stenosis_adu_q_1":     {"1a":"1"},
+    "claudication_followup_adu_q_1":            {"2a":"2","3a":"2","3b":"2"},
+    "cvd_followup_adu_q_1":             {"1b":"2","1c":"2","2a":"2","3a":"2","3b":"2"},
+
+    "current_smoker_adu_c_2": { "1a": "0", "1b": "0", "1c": "0", "2a": "0", "2b": "0", "3a": "0" },
+    "smoking_startage_adu_c_2": { "1a": "5", "1b": "5", "1c": "5", "2a": "5", "2b": "5", "3a": "5" },
+    "ex_smoker_adu_c_2": { "1a": "1", "1b": "1", "1c": "1", "2a": "1", "2b": "1", "3a": "1" },
+    "smoking_endage_adu_c_2": { "1a": "8", "1b": "8", "1c": "8", "2a": "8", "2b": "8", "3a": "8"},
+    "ever_smoker_adu_c_2": { "1a": "1", "1b": "1", "1c": "1", "2a": "1", "2b": "1", "3a": "1"},
+    "total_frequency_adu_c_1": { "1a": "", "1b": "", "1c": "", "2a": "", "2b": "", "3a": ""},
+    "packyears_cumulative_adu_c_2": { "1a": "", "1b": "", "1c": "", "2a": "", "2b": "", "3a": ""}
+
+
+
+}
+

fhirvalidation/sampleinputs/input-p98765-unreported-hf-startage.json

@@ -0,0 +1,71 @@
+{
+    "project_pseudo_id": {"1a":"98765"},
+    "variant_id": {},
+
+    "date": {"1a":"1992-5","1b":"1995-5","1c":"1997-5","2a":"2001-5","2b":"2002-5","3a":"2003-5","3b":"2005-5"},
+
+    "age": {"1a":"22"},
+    "gender": {"1a":"MALE"},
+    "zip_code": {"1a":"11111"},
+    "date_of_death": {"global":"2010-2"},
+    "date_of_inclusion": {"global":"1991-2"},
+
+    "albumin_result_all_m_1" :{ "1a": "51"},
+    "creatinine_result_all_m_1":{ "1a": "79.2", "2a":"106.1"},
+    "ethnicity_category_adu_q_1":{"1b":"3"},
+    "hemoglobin_result_all_m_1" :{ "1a": "11.1", "2a":"12"},
+    "hba1cconc_result_all_m_1":{ "1a": "43", "2a":"44"},
+
+    "hypertension_startage_adu_q_1":{"1a":"","3a":"23","3b":"23"},
+    "hypertension_presence_adu_q_1":{"1a":"2","3a":"1","3b":"1"},
+
+    "stroke_startage_adu_q_1":{ "1a": "12" },
+    "stroke_presence_adu_q_1": { "1a": "1" },
+    "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_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"},
+
+    "bp_entrytype_all_m_1":         {"1a":"2","2a":"2"},
+    "bp_bandsize_all_m_1":          {"1a":"1","2a":"1","3a":"1"},
+    "bp_arm_all_m_1":                           {"3a":"2"},
+    "bpavg_systolic_all_m_1":       {"1a":"130","2a":"130"},
+    "bpavg_diastolic_all_m_1":      {"1a":"140","2a":"140"},
+    "bpavg_arterial_all_m_1":       {"1a":"113","2a":"113"},
+
+    "hdlchol_result_all_m_1":       {"1a":"0.31","2a":"0.22"},
+    "ldlchol_result_all_m_1":       {"1a":"0.41","2a":"0.42"},
+    "cholesterol_result_all_m_1":   {"1a":"0.51","2a":"0.52"},
+
+    "heartattack_startage_adu_q_1": {"1a":"33"},
+    "angioplasty_bypass_adu_q_1_a":  {"1a":"1","3a":"1","3b":"1"},
+    "heartattack_presence_adu_q_1": {"1a":"1"},
+    "heartattack_followup_adu_q_1":     {"1b":"2","1c":"2","2a":"2","3a":"2","3b":"2"},
+    "angioplasty_bypass_adu_q_1":   {"1a":"1","3a":"1","3b":"1"},
+
+    "heartfailure_startage_adu_q_1":{ "1a": "" },
+    "heartfailure_presence_adu_q_1": { "1a": "1" },
+    "heartfailure_followup_adu_q_1":{"2a":"2","3a":"2","3b":"2"},
+
+    "carotid_stenosis_adu_q_1":     {"1a":"1"},
+    "claudication_followup_adu_q_1":            {"2a":"2","3a":"2","3b":"2"},
+    "cvd_followup_adu_q_1":             {"1b":"2","1c":"2","2a":"2","3a":"2","3b":"2"},
+
+    "current_smoker_adu_c_2": { "1a": "0", "1b": "0", "1c": "0", "2a": "0", "2b": "0", "3a": "0" },
+    "smoking_startage_adu_c_2": { "1a": "5", "1b": "5", "1c": "5", "2a": "5", "2b": "5", "3a": "5" },
+    "ex_smoker_adu_c_2": { "1a": "1", "1b": "1", "1c": "1", "2a": "1", "2b": "1", "3a": "1" },
+    "smoking_endage_adu_c_2": { "1a": "8", "1b": "8", "1c": "8", "2a": "8", "2b": "8", "3a": "8"},
+    "ever_smoker_adu_c_2": { "1a": "1", "1b": "1", "1c": "1", "2a": "1", "2b": "1", "3a": "1"},
+    "total_frequency_adu_c_1": { "1a": "", "1b": "", "1c": "", "2a": "", "2b": "", "3a": ""},
+    "packyears_cumulative_adu_c_2": { "1a": "", "1b": "", "1c": "", "2a": "", "2b": "", "3a": ""}
+
+
+
+}
+

src/__tests__/heartfailure.ts → src/__tests__/heartfailure.test.ts

@@ -3,6 +3,7 @@ import { heartFailure } from '../lifelines/HeartFailure';
 import { MappingTarget, processInput } from '../mapper'
 import {getSNOMEDCode} from '../codes/codesCollection'
 
+
 test('heartfailure, when reported positive in 1A', () => {
 
   const input = {
@@ -24,6 +25,27 @@ test('heartfailure, when reported positive in 1A', () => {
 });
 
 
+test('heartfailure, when reported positive in 1A, but no start_age was reported', () => {
+
+  const input = {
+    "heartfailure_startage_adu_q_1":{ "1a": "" },
+    "heartfailure_presence_adu_q_1": { "1a": "1" },
+    "heartfailure_followup_adu_q_1":{"1b":"2","1c":"2","2a":"2","3a":"2","3b":"2"},
+    "date": {"1a":"1992-5","1b":"1995-5","1c":"1997-5","2a":"2001-5","2b":"2002-5","3a":"2003-5","3b":"2005-5"},
+    "age": { "1a": "22" }
+  }
+
+  InputSingleton.getInstance().setInput(input);
+
+
+  expect(heartFailure.clinicalStatus()?.display).toBe("Active");
+  expect(heartFailure.isPresent()).toBe(true);
+  expect(heartFailure.code().display).toBe("Heart failure (disorder)");
+  expect(heartFailure.onsetDateTime()).toBe(undefined);
+
+});
+
+
 test('heart failure, when reported in 2A', () => {
 
   const input = {
@@ -43,6 +65,26 @@ test('heart failure, when reported in 2A', () => {
 });
 
 
+test('heart failure, when reported in 2A, but there is no assessment date available for 2A', () => {
+
+  const input = {
+    "heartfailure_startage_adu_q_1":{ "1a": "" },
+    "heartfailure_presence_adu_q_1": { "1a": "2" },
+    "heartfailure_followup_adu_q_1":{"1b":"2","1c":"2","2a":"1","3a":"2","3b":"2"},    
+    "date": {"1a":"1992-5","1b":"","1c":"","2a":"","3a":"","3b":""},
+    "age": { "1a": "22" }
+  }
+
+  InputSingleton.getInstance().setInput(input);
+  expect(heartFailure.clinicalStatus()?.display).toBe("Active");
+  expect(heartFailure.isPresent()).toBe(true);
+  expect(heartFailure.code().display).toBe("Heart failure (disorder)");
+  expect(heartFailure.onsetDateTime()).toBe(undefined);
+
+});
+
+
+
 test('heart failure, when reported right after baseline (1B)', () => {
 
   const input = {
@@ -100,6 +142,26 @@ test('heart failure, when reported in 2A, after skipping multiple assessments',
 });
 
 
+test('heart failure, when reported in 2A, after skipping multiple assessments', () => {
+
+  const input = {
+    "heartfailure_startage_adu_q_1":{ "1a": "" },
+    "heartfailure_presence_adu_q_1": { "1a": "2" },
+    "heartfailure_followup_adu_q_1":{"1b":undefined,"1c":undefined,"2a":"1","3a":"2","3b":"2"},    
+    "date": {"1a":"1992-5","1b":undefined,"1c":undefined,"2a":"2002-5","3a":"2003-5","3b":"2005-5"},
+    "age": { "1a": "22" }
+  }
+
+  InputSingleton.getInstance().setInput(input);
+  expect(heartFailure.clinicalStatus()?.display).toBe("Active");
+  expect(heartFailure.isPresent()).toBe(true);
+  expect(heartFailure.code().display).toBe("Heart failure (disorder)");
+  expect(heartFailure.onsetDateTime()).toBe("1997-05");
+
+});
+
+
+
 
 test('heart failure, when no reported', () => {
 

src/lifelines/HeartFailure.ts

@@ -54,14 +54,20 @@ export const heartFailure:Condition = {
      * ------------------------------------------------------------------
      *
      * @precondition
-     *      - date and age are not missing values (undefined)
      *      - the problem is 'active' (see clinicalStatus function)
      *
      * @pairingrule
-     *      if heartfailure_presence_adu_q_1 = yes in 1A => approximate year on which the participant given the age reported  by heartfailure_startage_adu_q_1
+     *      if heartfailure_presence_adu_q_1 = yes in 1A => 
+     *              if start_age was reported, approximate year of the event given start_age reported (heartfailure_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 heartfailure_followup_adu_q_1 => mean date between the date of the assessment
-     *              where heartfailure_followup_adu_q_1 = yes, and the date of the preceding one.
+     *          if there is a 'yes' in any heartfailure_followup_adu_q_1 => 
+     *              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.
+     *              Else
+     *                  return undefined date
      *          else
      *              error/precondition violated ('heartfailure' is not 'active' if the execution reached this point)
      *
@@ -95,7 +101,7 @@ export const heartFailure:Condition = {
                 return lifelinesDateToISO(lifelinesMeanDate(date1, date2));
             }
             else {
-                throw Error("Unexpected input (precondition violated): no 'yes' values in heartfailure_followup_adu_q_1");
+                return undefined;                
             }
 
 
@@ -147,8 +153,13 @@ const _clinicalStatus = moize((heartfailure_presence:string|undefined,followup_a
  * date                           [X ][X ][X ][X ][X ][X ]
  * 
  * 
- * mean date between the date of the assessment 
- *              where heartfailure_followup_adu_q_1 = yes, and the date of the preceding one.
+ * @precondition: there is at least one 'yes'/1 on heartfailure_followup_adu_q_1
+ * 
+ * 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.
+ * Else
+ *      return undefined date
+ *
  * 
  * 
  * @param diabFollowUp 
@@ -164,16 +175,22 @@ function findDatesBetweenheartfailurePresenceReport(): [string,string]|undefined
     assertIsDefined(heartfailureWave,`A 'yes' value on heartfailure_followup_adu_q_1 was expected`)
 
     const heartfailureWaveDate = inputValue("date",heartfailureWave)
-    assertIsDefined(heartfailureWaveDate,`A non-null date is expected in the assessment where heartfailure_followup_adu_q_1 is reported`)
 
-    //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(heartfailureWave))
-    const previousAssessmentWave = previousWaves.reverse().find((pwave)=>assessmentDates[pwave]!==undefined)
-
-    assertIsDefined(previousAssessmentWave,`Assessment (with a non-null date) expected to exist previous to the one where heartfailure_followup_adu_q_1 is reported`)
+    //If the date of the assessment where the episode was reported is not available, return undefined date
+    if (heartfailureWaveDate === 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(heartfailureWave))
+        const previousAssessmentWave = previousWaves.reverse().find((pwave)=>assessmentDates[pwave]!==undefined)
+
+        assertIsDefined(previousAssessmentWave,`Assessment (with a non-null date) expected to exist previous to the one where heartfailure_followup_adu_q_1 is reported`)
+
+        const previousAssessmentDate:string = assessmentDates[previousAssessmentWave!]!;
+        return [previousAssessmentDate,heartfailureWaveDate]
+    }
 
-    const previousAssessmentDate:string = assessmentDates[previousAssessmentWave!]!;
-    return [previousAssessmentDate,heartfailureWaveDate]
   }