Merge pull request #54 from OHDSI/mdcd-framework-refresh

framework refreshed with latest ScanReport

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

@@ -159,14 +159,14 @@ createConditionOccurrenceTests <- function () {
     declareTest(id = patient$person_id, "HRA mapped to condition/drug the END_DATE is NULL. Id is PERSON_ID")
     add_enrollment_detail(enrolid=patient$enrolid, dtend = '2012-12-31', dtstart = '2012-01-01')
     add_health_risk_assessment(enrolid = patient$enrolid, survdate = '2012-03-12', cc_backpain = "1")
-    expect_condition_occurrence(person_id = patient$person_id, condition_concept_id = '134736', condition_status_concept_id = 0, condition_start_date = '2012-03-12', condition_end_date = NULL)#, condition_type_concept_id = '32850')
+    expect_condition_occurrence(person_id = patient$person_id, condition_concept_id = '134736', condition_status_concept_id = NULL, condition_start_date = '2012-03-12', condition_end_date = NULL)#, condition_type_concept_id = '32850')
 
     patient <- createPatient()
     encounter <- createEncounter()  
     declareTest(id = patient$person_id, "Patient has 1 in CC_ASTHMA column, condition_source_value=Self-reported Asthma. Id is PERSON_ID")
     add_enrollment_detail(enrolid=patient$enrolid, dtend = '2012-12-31', dtstart = '2012-01-01')
     add_health_risk_assessment(enrolid = patient$enrolid, survdate = '2012-09-13', cc_asthma = '1')
-    expect_condition_occurrence(person_id = patient$person_id, condition_concept_id = '317009', condition_source_value = 'CC_ASTHMA', condition_status_concept_id = 0, condition_start_date = '2012-09-13')#, condition_type_concept_id = '32850')
+    expect_condition_occurrence(person_id = patient$person_id, condition_concept_id = '317009', condition_source_value = 'CC_ASTHMA', condition_status_concept_id = NULL, condition_start_date = '2012-09-13')#, condition_type_concept_id = '32850')
 
   }
 }

docs/IBM_CCAE_MDCR/Test Cases/extras/IBMMDCD_TestingFramework.R

@@ -118,7 +118,7 @@ initFramework <- function() {
   defaults$thergrp <- '08'
   defaults$version <- '10'
   defaults$year <- '2017'
-  defaults$gpi <- '44201010103410'
+
   assign('drug_claims', defaults, envir = frameworkContext$defaultValues)
 
   defaults <- list()
@@ -709,7 +709,7 @@ set_defaults_version <- function(version_id, version_date) {
   invisible(defaults)
 }
 
-set_defaults_drug_claims <- function(awp, boe, cap, cob, coins, copay, dawind, daysupp, deaclas, deduct, dispfee, dobyr, drugcovg, enrolid, generid, genind, ingcost, maintin, mas, mcasenum, medicare, metqty, mhsacovg, ndcnum, netpay, pay, pddate, pharmid, plantyp, qty, refill, seqnum, sex, stdrace, svcdate, thercls, thergrp, version, year, gpi) {
+set_defaults_drug_claims <- function(awp, boe, cap, cob, coins, copay, dawind, daysupp, deaclas, deduct, dispfee, dobyr, drugcovg, enrolid, generid, genind, ingcost, maintin, mas, mcasenum, medicare, metqty, mhsacovg, ndcnum, netpay, pay, pddate, pharmid, plantyp, qty, refill, seqnum, sex, stdrace, svcdate, thercls, thergrp, version, year) {
   defaults <- get('drug_claims', envir = frameworkContext$defaultValues)
   if (!missing(awp)) {
     defaults$awp <- awp
@@ -828,9 +828,6 @@ set_defaults_drug_claims <- function(awp, boe, cap, cob, coins, copay, dawind, d
   if (!missing(year)) {
     defaults$year <- year
   }
-  if (!missing(gpi)) {
-    defaults$gpi <- gpi
-  }
   assign('drug_claims', defaults, envir = frameworkContext$defaultValues)
   invisible(defaults)
 }
@@ -2516,7 +2513,7 @@ add_version <- function(version_id, version_date) {
   invisible(NULL)
 }
 
-add_drug_claims <- function(awp, boe, cap, cob, coins, copay, dawind, daysupp, deaclas, deduct, dispfee, dobyr, drugcovg, enrolid, generid, genind, ingcost, maintin, mas, mcasenum, medicare, metqty, mhsacovg, ndcnum, netpay, pay, pddate, pharmid, plantyp, qty, refill, seqnum, sex, stdrace, svcdate, thercls, thergrp, version, year, gpi) {
+add_drug_claims <- function(awp, boe, cap, cob, coins, copay, dawind, daysupp, deaclas, deduct, dispfee, dobyr, drugcovg, enrolid, generid, genind, ingcost, maintin, mas, mcasenum, medicare, metqty, mhsacovg, ndcnum, netpay, pay, pddate, pharmid, plantyp, qty, refill, seqnum, sex, stdrace, svcdate, thercls, thergrp, version, year) {
   defaults <- get('drug_claims', envir = frameworkContext$defaultValues)
   fields <- c()
   values <- c()
@@ -2831,15 +2828,7 @@ add_drug_claims <- function(awp, boe, cap, cob, coins, copay, dawind, daysupp, d
   }
   fields <- c(fields, "year")
   values <- c(values, if (is.null(year)) "NULL" else if (is(year, "subQuery")) paste0("(", as.character(year), ")") else paste0("'", as.character(year), "'"))
-
-  if (missing(gpi)) {
-    gpi <- defaults$gpi
-  } else {
-    frameworkContext$sourceFieldsTested <- c(frameworkContext$sourceFieldsTested, 'drug_claims.gpi')
-  }
-  fields <- c(fields, "_gpi")
-  values <- c(values, if (is.null(gpi)) "NULL" else if (is(gpi, "subQuery")) paste0("(", as.character(gpi), ")") else paste0("'", as.character(gpi), "'"))
-
+
   inserts <- list(testId = frameworkContext$testId, testDescription = frameworkContext$testDescription, table = "drug_claims", fields = fields, values = values)
   frameworkContext$inserts[[length(frameworkContext$inserts) + 1]] <- inserts
   invisible(NULL)