Merge pull request #36 from OHDSI/ibms-tests-updates

new tests added

docs/IBM_CCAE_MDCR/Test Cases/R/ConditionOccurrenceTests.R

@@ -126,18 +126,33 @@ createConditionOccurrenceTests <- function () {
   # expect_condition_occurrence(person_id = patient$person_id, condition_concept_id = '195587', condition_status_concept_id = '32908', condition_start_date = '2012-08-02', condition_type_concept_id = '32854')
   expect_condition_occurrence(person_id = patient$person_id, condition_concept_id = '195587', condition_start_date = '2012-07-01', condition_type_concept_id = '32854')
   expect_condition_occurrence(person_id = patient$person_id, condition_concept_id = '195587', condition_start_date = '2012-08-02', condition_type_concept_id = '32854')
+
+  patient <- createPatient()
+  encounter <- createEncounter()
+  declareTest(id = patient$person_id, "Event date is outside of observation_period, condition_occurrence record created. Id is PERSON_ID")
+  add_enrollment_detail(enrolid=patient$enrolid, dtend = '2012-12-31', dtstart = '2012-01-01')
+  add_inpatient_services(enrolid = patient$enrolid, svcdate = '2022-08-02', tsvcdat = '2022-08-02', dx4='57411', dxver='9')
+  expect_condition_occurrence(person_id = patient$person_id, condition_concept_id = '195587', condition_start_date = '2022-08-02', condition_type_concept_id = '32854')
+
+  patient <- createPatient()
+  encounter <- createEncounter()
+  declareTest(id = patient$person_id, "Condition_occurrence record default end_date is NULL. Id is PERSON_ID")
+  add_enrollment_detail(enrolid=patient$enrolid, dtend = '2012-12-31', dtstart = '2012-01-01')
+  add_inpatient_services(enrolid = patient$enrolid, svcdate = '2022-08-03', dx4='57411', dxver='9')
+  expect_condition_occurrence(person_id = patient$person_id, condition_concept_id = '195587', condition_start_date = '2022-08-03', condition_end_date = NULL)
+
 
-  if (truvenType == "MDCD")
+  if (tolower(frameworkType) == "mdcd")
   {
     patient <- createPatient()
     encounter <- createEncounter()
     declareTest(id = patient$person_id, "Patient has diagnosis in dx1 in ltc. Id is PERSON_ID")
     add_enrollment_detail(enrolid=patient$enrolid, dtend = '2012-12-31', dtstart = '2012-01-01')
-    add_long_term_care(enrolid = patient$enrolid, dx1 = 'v901', dxver = '9', svcdate = '2012-11-05', tsvcdat = '2012-11-10')
+    add_long_term_care(enrolid = patient$enrolid, dx1 = 'v9001', dxver = '9', svcdate = '2012-11-05', tsvcdat = '2012-11-10')
     expect_condition_occurrence(person_id = patient$person_id, condition_concept_id = '46270117', condition_type_concept_id = '38004277')
   }
 
-  if (truvenType == "CCAE")
+  if (tolower(frameworkType) == "ccae")
   {
     patient <- createPatient()
     encounter <- createEncounter()

docs/IBM_CCAE_MDCR/Test Cases/R/CostTests.R

@@ -68,7 +68,7 @@ createCostTests <- function () {
   # event_ID <- lookup_procedure_occurrence(fetchField = "procedure_occurrence_id", person_id = patient$person_id)
   # expect_cost(cost_event_id = event_ID , revenue_code_concept_id = 0)
   #
-  # if (Sys.getenv("truvenType") == "MDCD")
+  # if (Sys.getenv("frameworkType") == "MDCD")
   # {
   #   patient <- createPatient()
   #   encounter <- createEncounter()

docs/IBM_CCAE_MDCR/Test Cases/R/DeathTests.R

@@ -3,6 +3,32 @@ createDeathTests <- function () {
 
   set_defaults_enrollment_detail(mhsacovg = '0')
 
+  if (tolower(frameworkType) != "mdcd")
+  {
+	  patient <- createPatient()
+	  encounter <- createEncounter()
+	  declareTest(id = patient$person_id, "Date of death visit end date. Id is PERSON_ID.")
+	  add_enrollment_detail(enrolid=patient$enrolid, dtend = '2015-12-31', dtstart = '2012-01-01', mhsacovg = 0)
+	  add_inpatient_services(enrolid=patient$enrolid, year = '2013',  svcdate = '2013-01-06', tsvcdat='2013-01-09')
+	  add_outpatient_services(enrolid = patient$enrolid, year = '2013', svcdate = '2013-01-07',tsvcdat = '2013-01-07', dx1 = '7981', dxver = '9', fachdid = encounter$caseid)
+	  add_facility_header(enrolid=patient$enrolid, svcdate = '2013-01-07', tsvcdat = '2013-01-07', dx9 = '7981', fachdid = encounter$caseid, dxver='9')
+	  expect_death(person_id = patient$person_id, death_date = '2013-01-09')
+
+	  patient <- createPatient()
+	  encounter <- createEncounter()
+	  add_enrollment_detail(enrolid=patient$enrolid, dtend = '2016-12-31', dtstart = '2012-01-01', mhsacovg = '0')
+	  declareTest(id = patient$person_id, "ICD10 Death and Death Type Correct. Id is PERSON_ID.")
+	  add_inpatient_services(enrolid=patient$enrolid, year = '2016', svcdate = '2016-01-06', tsvcdat='2016-01-09', dxver = '0', dx1='I461')
+	  expect_death(person_id = patient$person_id, death_type_concept_id = '32812')
+
+	  patient <- createPatient()
+	  encounter <- createEncounter()
+	  add_enrollment_detail(enrolid=patient$enrolid, dtend = '2015-12-31', dtstart = '2012-01-01', mhsacovg = '0')
+	  declareTest(id = patient$person_id, "ICD9 Death and Death Type Correct. Id is PERSON_ID.")
+	  add_inpatient_services(enrolid=patient$enrolid, year = '2013', svcdate = '2013-01-06', tsvcdat='2013-01-09', dxver = '9', dx1='798')
+	  expect_death(person_id = patient$person_id, death_type_concept_id = '32812')
+  }
+
   patient <- createPatient()
   encounter <- createEncounter()
   add_enrollment_detail(enrolid=patient$enrolid, dtend = '2013-02-01', dtstart = '2012-01-01', mhsacovg = '0')
@@ -25,40 +51,4 @@ createDeathTests <- function () {
   add_outpatient_services(enrolid=patient$enrolid, year = '2013', svcdate = '2013-03-12')
   expect_no_death(person_id=patient$enrolid)
 
-
-  if (truvenType == "MDCD")
-  {
-    patient <- createPatient()
-    encounter <- createEncounter()
-    declareTest(id = patient$person_id, "Patient has icd9 death cord in ltc, death record created. Id is PERSON_ID.")
-    add_enrollment_detail(enrolid=patient$enrolid, dtend = '2012-12-31', dtstart = '2012-01-01')
-    add_long_term_care(enrolid = patient$enrolid, dx1 = '798', dxver = '9', svcdate = '2012-11-02', tsvcdat = '2012-11-22')
-    expect_no_death(person_id = patient$person_id)
-  }
-  else
-  {
-    patient <- createPatient()
-    encounter <- createEncounter()
-    declareTest(id = patient$person_id, "Date of death visit end date. Id is PERSON_ID.")
-    add_enrollment_detail(enrolid=patient$enrolid, dtend = '2015-12-31', dtstart = '2012-01-01', mhsacovg = 0)
-    add_inpatient_services(enrolid=patient$enrolid, year = '2013',  svcdate = '2013-01-06', tsvcdat='2013-01-09')
-    add_outpatient_services(enrolid = patient$enrolid, year = '2013', svcdate = '2013-01-07',tsvcdat = '2013-01-07', dx1 = '7981', dxver = '9', fachdid = encounter$caseid)
-    add_facility_header(enrolid=patient$enrolid, svcdate = '2013-01-07', tsvcdat = '2013-01-07', dx9 = '7981', fachdid = encounter$caseid, dxver='9')
-    expect_death(person_id = patient$person_id, death_date = '2013-01-09')
-
-    patient <- createPatient()
-    encounter <- createEncounter()
-    add_enrollment_detail(enrolid=patient$enrolid, dtend = '2016-12-31', dtstart = '2012-01-01', mhsacovg = '0')
-    declareTest(id = patient$person_id, "ICD10 Death and Death Type Correct. Id is PERSON_ID.")
-    add_inpatient_services(enrolid=patient$enrolid, year = '2016', svcdate = '2016-01-06', tsvcdat='2016-01-09', dxver = '0', dx1='I461')
-    expect_death(person_id = patient$person_id, death_type_concept_id = '32812')
-
-    patient <- createPatient()
-    encounter <- createEncounter()
-    add_enrollment_detail(enrolid=patient$enrolid, dtend = '2015-12-31', dtstart = '2012-01-01', mhsacovg = '0')
-    declareTest(id = patient$person_id, "ICD9 Death and Death Type Correct. Id is PERSON_ID.")
-    add_inpatient_services(enrolid=patient$enrolid, year = '2013', svcdate = '2013-01-06', tsvcdat='2013-01-09', dxver = '9', dx1='798')
-    expect_death(person_id = patient$person_id, death_type_concept_id = '32812')
-  }
-
 }

docs/IBM_CCAE_MDCR/Test Cases/R/DrugExposureTests.R

@@ -43,6 +43,13 @@ createDrugExposureTests <- function () {
   add_enrollment_detail(enrolid=patient$enrolid, dtend = '2012-12-31', dtstart = '2012-01-01')
   add_drug_claims(enrolid = patient$enrolid, ndcnum = '13533063670', year = '2012', svcdate = '2012-01-17')
   expect_drug_exposure(person_id = patient$person_id, drug_concept_id = '46275250', drug_exposure_start_date = '2012-01-17')
+
+  patient <- createPatient()
+  encounter <- createEncounter()
+  declareTest(id = patient$person_id, "Drug exposure quantity - if not populated in source, leave it NULL. Id is PERSON_ID. Id is PERSON_ID.")
+  add_enrollment_detail(enrolid=patient$enrolid, dtend = '2012-12-31', dtstart = '2012-01-01')
+  add_drug_claims(enrolid = patient$enrolid, ndcnum = '13533063670', year = '2012', svcdate = '2012-01-19', metqty = NULL)
+  expect_drug_exposure(person_id = patient$person_id, drug_concept_id = '46275250', drug_exposure_start_date = '2012-01-19', quantity = NULL)
 
   patient <- createPatient()
   encounter <- createEncounter()
@@ -65,16 +72,12 @@ createDrugExposureTests <- function () {
   add_drug_claims(enrolid = patient$enrolid, ndcnum = '00069100101', year = '2014', svcdate = '2014-09-18')
   expect_drug_exposure(person_id = patient$person_id, drug_source_concept_id = '45332969')
 
-  if (Sys.getenv("truvenType") == "CCAE")
-  {
-    patient <- createPatient()
-    encounter <- createEncounter()
-    declareTest(id = patient$person_id, "HRA Drug still has a DRUG_EXPOSURE_END_DATE (HIX-1433). Id is PERSON_ID.")
-    add_enrollment_detail(enrolid=patient$enrolid, dtend = '2012-12-31', dtstart = '2012-01-01')
-    add_health_risk_assessment(enrolid = patient$enrolid, survdate = '2012-05-25', flu_shot = '1')
-    expect_drug_exposure(person_id = patient$person_id, drug_exposure_end_date = '2012-05-25', drug_concept_id = '4214838')
-
-  }
+  patient <- createPatient()
+  encounter <- createEncounter()
+  declareTest(id = patient$person_id, "Event date is outside of observation_period, drug_exposure record created. Id is PERSON_ID")
+  add_enrollment_detail(enrolid=patient$enrolid, dtend = '2014-12-31', dtstart = '2014-01-01')
+  add_drug_claims(enrolid = patient$enrolid, ndcnum = '00069100101', year = '2019', svcdate = '2019-09-18')
+  expect_drug_exposure(person_id = patient$person_id, drug_exposure_start_date = '2019-09-18')
 }
 
 

docs/IBM_CCAE_MDCR/Test Cases/R/LocationTests.R

@@ -1,7 +1,7 @@
 #' @export
 createLocationTests <- function () {
 
-if (truvenType != "MDCD")  {
+if (tolower(frameworkType) != "mdcd")  {
 
   patient<-createPatient()
   declareTest(id = patient$person_id, "Location record generated for egeoloc 11. Id is PERSON_ID")

docs/IBM_CCAE_MDCR/Test Cases/R/MeasurementTests.R

@@ -2,7 +2,7 @@
 createMeasurementTests <- function () {
 
 
-  if (truvenType != "MDCD")
+  if (tolower(frameworkType) != "mdcd")
   {
 
   patient <- createPatient()
@@ -73,11 +73,25 @@ createMeasurementTests <- function () {
 
   patient <- createPatient()
   encounter <- createEncounter()
-  declareTest(id = patient$person_id, "If you do not get a map from UCUM for UNIT_CONCEPT_ID then try JNJ_UNITS (HIX-1419). Id is PERSON_ID.")
+  declareTest(id = patient$person_id, "For UNIT_CONCEPT_ID UCUM lookup should not be used, use JNJ_UNITS istead. Id is PERSON_ID.")
   add_enrollment_detail(enrolid=patient$enrolid, dtend = '2012-12-31', dtstart = '2012-01-01')
   add_lab(enrolid = patient$enrolid, year='2012', svcdate = '2012-04-06', loinccd = '56789-1', result = '100', resunit = 'lbs.')
   expect_measurement(person_id = patient$person_id, unit_concept_id = '8739')
 
+  patient <- createPatient()
+  encounter <- createEncounter()
+  declareTest(id = patient$person_id, "For UNIT_CONCEPT_ID UCUM lookup should not be used, use JNJ_UNITS istead. 586323 concept_id is expected. 9471 is a wrong UCUM derived unit. Id is a PERSON_ID.")
+  add_enrollment_detail(enrolid=patient$enrolid, dtend = '2012-12-31', dtstart = '2012-01-01')
+  add_lab(enrolid = patient$enrolid, year='2012', svcdate = '2012-04-06', loinccd = '56789-1', result = '100', resunit = 'C')
+  expect_measurement(person_id = patient$person_id, unit_concept_id = '586323')
+
+  patient <- createPatient()
+  encounter <- createEncounter()
+  declareTest(id = patient$person_id, "Patient has null in resunit, measurement record have unit_concept_id = NULL and unit_source_concept_id = NULL. Id is PERSON_ID.")
+  add_enrollment_detail(enrolid=patient$enrolid, dtend = '2012-12-31', dtstart = '2012-01-01')
+  add_lab(enrolid = patient$enrolid, year='2012', svcdate = '2012-04-06', loinccd = '56789-1', result = NULL, resunit = NULL)
+  expect_measurement(person_id = patient$person_id, unit_concept_id = NULL, unit_source_concept_id = NULL)
+
   patient <- createPatient()
   encounter <- createEncounter()
   declareTest(id = patient$person_id, "for LOINCs 3142-7, 29463-7, 3141-9 sometimes padded with 0000, strip padding (HIX-1418). Id is PERSON_ID.")
@@ -99,10 +113,17 @@ createMeasurementTests <- function () {
   add_lab(enrolid = patient$enrolid, year='2012', svcdate = '2012-04-06', loinccd = '29463-7', result = '1950000', resunit = 'LBS')
   expect_measurement(person_id = patient$person_id, value_as_number = '195', unit_concept_id = '8739')
 
+
+  patient <- createPatient()
+  encounter <- createEncounter()
+  declareTest(id = patient$person_id, "Event date is outside of observation_period, measurement record created. Id is PERSON_ID")
+  add_enrollment_detail(enrolid=patient$enrolid, dtend = '2012-12-31', dtstart = '2012-01-01')
+  add_lab(enrolid = patient$enrolid, year='2022', svcdate = '2022-04-06', loinccd = '29463-7', result = '1950000', resunit = 'LBS')
+  expect_measurement(person_id = patient$person_id, measurement_date = '2022-04-06')
   }
 
 
-  if (truvenType == "CCAE")
+  if (tolower(frameworkType) == "ccae")
   {
 
     patient <- createPatient()

docs/IBM_CCAE_MDCR/Test Cases/R/ObservationTests.R

@@ -1,7 +1,7 @@
 #' @export
 createObservationTests <- function () {
 
-  if (truvenType == "CCAE")
+  if (tolower(frameworkType) == "ccae")
   {
 
   patient <- createPatient()
@@ -31,6 +31,13 @@ createObservationTests <- function () {
   add_enrollment_detail(enrolid=patient$enrolid, dtend = '2012-12-31', dtstart = '2012-01-01')
   add_health_risk_assessment(enrolid = patient$enrolid, survdate = '2012-05-25', flu_shot = '1')
   expect_observation(person_id = patient$person_id, observation_source_value = 'FLU_SHOT')
+
+  patient <- createPatient()
+  encounter <- createEncounter()  
+  declareTest(id = patient$person_id, "Event date is outside of observation_period, observation record created. Id is PERSON_ID")
+  add_enrollment_detail(enrolid=patient$enrolid, dtend = '2012-12-31', dtstart = '2012-01-01')
+  add_health_risk_assessment(enrolid = patient$enrolid, survdate = '2022-03-14', cgtpkamt = '2')
+  expect_observation(person_id = patient$person_id, observation_source_value = 'CGTPKAMT', value_as_number = '2.00', observation_date = '2022-03-14')
 
   }
 }

docs/IBM_CCAE_MDCR/Test Cases/R/PayerPlanPeriodTests.R

@@ -2,7 +2,7 @@
 #' @export
 createPayerPlanPeriodTests <- function () {
 
-  if (truvenType != "MDCD") {
+  if (tolower(frameworkType) != "mdcd") {
 
   patient<-createPatient()
   declareTest(id = patient$person_id, "Person does not have prescription benefits and is excluded. Id is PERSON_ID.")
@@ -11,7 +11,7 @@ createPayerPlanPeriodTests <- function () {
 
   }
 
-  if (truvenType == "CCAE") {
+  if (tolower(frameworkType) == "ccae") {
     patient<-createPatient()
     declareTest(id = patient$person_id, "Person has a gap of >32 days between enrollment periods with the same payer_source_value; person has two records. Id is PERSON_ID.")
     add_enrollment_detail(enrolid=patient$enrolid, dtstart="2013-01-01", dtend="2013-01-31", datatyp="1", plantyp="6")
@@ -47,7 +47,7 @@ createPayerPlanPeriodTests <- function () {
 
   }
 
-  if (truvenType == "MDCR") {
+  if (tolower(frameworkType) == "mdcr") {
     patient<-createPatient()
     declareTest(id = patient$person_id, "Person has a gap of >32 days between enrollment periods with the same payer_source_value; person has two records. Id is PERSON_ID.")
     add_enrollment_detail(enrolid=patient$enrolid, dtstart="2013-01-01", dtend="2013-01-31", datatyp="1", plantyp="6")
@@ -69,7 +69,7 @@ createPayerPlanPeriodTests <- function () {
     expect_payer_plan_period(person_id=patient$person_id, payer_plan_period_start_date="2012-04-01", payer_plan_period_end_date="2012-04-30", payer_source_value="C Medicare PPO")
   }
 
-  if (truvenType == "MDCD") {
+  if (tolower(frameworkType) == "mdcd") {
 
     patient<-createPatient()
     declareTest(id = patient$person_id, "Person has a gap of >32 days between enrollment periods with the same payer_source_value; person has two records. Id is PERSON_ID.")
@@ -80,7 +80,7 @@ createPayerPlanPeriodTests <- function () {
 
     patient<-createPatient()
     declareTest(id = patient$person_id, "Person does not have prescription benefits and is excluded. Id is PERSON_ID.")
-    add_enrollment_detail(enrolid=patient$enrolid, dtstart="2013-01-01", dtend="2013-01-31", plantyp="6", drugcovg ="0")
+    add_enrollment_detail(enrolid=patient$enrolid, dtstart="2013-01-01", dtend="2013-01-31", plantyp="6", drugcovg ="0", medicare="0")
     expect_no_payer_plan_period(person_id = patient$person_id)
 
     patient<-createPatient()

docs/IBM_CCAE_MDCR/Test Cases/R/PersonTests.R

@@ -50,7 +50,12 @@ createPersonTests <- function () {
   declareTest(id = patient$person_id, "Person with sex=3 is excluded. Id is PERSON_ID.")
   add_enrollment_detail(enrolid=patient$enrolid, sex="3")
   expect_no_person(person_id = patient$person_id)
-
+
+  patient<-createPatient()
+  declareTest(id = patient$person_id, "Person born after current year. Id is PERSON_ID.")
+  add_enrollment_detail(enrolid=patient$enrolid, dobyr="2032")
+  expect_no_person(person_id = patient$person_id)
+
   patient<-createPatient()
   declareTest(id = patient$person_id, "Person has record with sex=3 but last record has sex=1, person is kept. Id is PERSON_ID.")
   add_enrollment_detail(enrolid=patient$enrolid, dtend="2012-01-31", dtstart="2012-01-01", sex="3")
@@ -62,7 +67,7 @@ createPersonTests <- function () {
   add_enrollment_detail(enrolid=patient$enrolid, dtend="2012-04-30", dtstart="2012-04-01", dobyr="2012")
   expect_person(person_id=patient$person_id, year_of_birth="2012", month_of_birth="4", day_of_birth="1")
 
-  if (truvenType != "MDCD")
+  if (tolower(frameworkType) != "mdcd")
   {
     patient<-createPatient()
     declareTest(id = patient$person_id, "Person with Rx benefits is kept. Id is PERSON_ID.")
@@ -81,7 +86,7 @@ createPersonTests <- function () {
     expect_person(person_id=patient$person_id)
   }
 
-  if (truvenType == "MDCD")
+  if (tolower(frameworkType) == "mdcd")
   {
     patient<-createPatient()
     declareTest(id = patient$person_id, "Person with two birth years >2 yrs apart is included because max(DOBYR) > 90. Id is PERSON_ID.")