Merge pull request #48 from OHDSI/unit_tests_PREMIER

fix unit test PREMIER
OHDSI · Feb 15, 2024 · 49d7b5b · 49d7b5b
2 parents 6e39119 + 1429c2e
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diff --git a/.gitignore b/.gitignore
@@ -342,5 +342,4 @@ docs/IBM_CCAE_MDCR/Test Cases/extras/config.csv
 # Pages files to test changes
 _site
 .Rproj.user
-
-
+ETL-LambdaBuilder.Rproj
diff --git a/docs/PREMIER/ARCHIVE/Premier_ETL_CDM_V5.doc b/docs/PREMIER/ARCHIVE/Premier_ETL_CDM_V5.doc
diff --git a/docs/PREMIER/ARCHIVE/Premier_ETL_CDM_V5_2.doc b/docs/PREMIER/ARCHIVE/Premier_ETL_CDM_V5_2.doc
diff --git a/docs/PREMIER/Premier_ETL_CDM_V5_3.doc b/docs/PREMIER/Premier_ETL_CDM_V5_3.doc
diff --git a/docs/PREMIER/Test Cases/.Rbuildignore b/docs/PREMIER/Test Cases/.Rbuildignore
@@ -0,0 +1,2 @@
+^.*\.Rproj$
+^\.Rproj\.user$
diff --git a/docs/PREMIER/Test Cases/.gitignore b/docs/PREMIER/Test Cases/.gitignore
@@ -0,0 +1,8 @@
+.Rproj.user
+.Rhistory
+*.RData
+.Ruserdata
+*errorReport.txt
+*.Rprofile
+/inst/sql/sql_server/insert.sql
+/inst/sql/sql_server/test.sql
diff --git a/docs/PREMIER/Test Cases/DESCRIPTION b/docs/PREMIER/Test Cases/DESCRIPTION
@@ -0,0 +1,14 @@
+Package: PremierTests
+Type: Package
+Title: Configures Test Cases for Premier
+Version: 0.1.0
+Author: Chris Knoll
+Maintainer: Chris Knoll <[email protected]>
+Description: Executes test case inserts and validates results.
+License: None
+LazyData: TRUE
+Depends:
+    SqlRender,
+    DatabaseConnector
+Roxygen: list(wrap = TRUE)
+RoxygenNote: 6.0.1
diff --git a/docs/PREMIER/Test Cases/NAMESPACE b/docs/PREMIER/Test Cases/NAMESPACE
@@ -0,0 +1,4 @@
+# Generated by roxygen2: do not edit by hand
+
+export(generateInsertSql)
+export(generateTestSql)
diff --git a/docs/PREMIER/Test Cases/PremierTests.Rproj b/docs/PREMIER/Test Cases/PremierTests.Rproj
@@ -0,0 +1,20 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,namespace
diff --git a/docs/PREMIER/Test Cases/R/ConditionOccurrenceTests.R b/docs/PREMIER/Test Cases/R/ConditionOccurrenceTests.R
@@ -0,0 +1,67 @@
+createConditionOccurrenceTests <- function () {
+
+
+  # PATICD_DIAG.ICD_CODE ICD9CM
+  patient <- createPatient();
+  visit <- createVisit();
+  declareTest(description="ICD9CM record from PATICD_DIAG to condition_occurrence table", id = patient$person_id);
+  add_pat(medrec_key   = patient$medrec_key,
+          pat_key      = visit$pat_key,
+          adm_date     = "2005-01-01",
+          disc_date    = "2005-01-01");
+  add_patbill(pat_key  = visit$pat_key);
+  add_paticd_diag(pat_key     = visit$pat_key,
+                  icd_code    = "112.89",
+                  icd_version = 9);
+  expect_condition_occurrence(person_id              = patient$person_id,
+                              visit_occurrence_id    = visit$visit_occurrence_id,
+                              condition_concept_id   = 433968,
+                              condition_start_date   = "2005-01-01",
+                              condition_source_value = '112.89');
+
+  # PATICD_DIAG.ICD_CODE ICD10CM
+  patient <- createPatient();
+  visit <- createVisit();
+  declareTest(description="ICD10CM record from PATICD_DIAG to condition_occurrence table", id = patient$person_id);
+  add_pat(medrec_key   = patient$medrec_key,
+          pat_key      = visit$pat_key,
+          adm_date     = "2004-03-01",
+          disc_date    = "2004-03-01");
+  add_patbill(pat_key  = visit$pat_key);
+  add_paticd_diag(pat_key     = visit$pat_key,
+                  icd_code    = "M05.421",
+                  icd_version = 10);
+  expect_condition_occurrence(person_id              = patient$person_id,
+                              visit_occurrence_id    = visit$visit_occurrence_id,
+                              condition_concept_id   = 4116440,
+                              condition_start_date   = "2004-03-01",
+                              condition_source_value = "M05.421");
+  expect_condition_occurrence(person_id              = patient$person_id,
+                              visit_occurrence_id    = visit$visit_occurrence_id,
+                              condition_concept_id   = 4107913, #map to multiple concepts?
+                              condition_start_date   = "2004-03-01",
+                              condition_source_value = "M05.421");
+
+  #PRI_SEC flag to condition_status_concept_id
+  pri_sec_vals <- data.frame(
+    icd_pri_sec = c('A', 'P', 'S'),
+    concept_id = c('32890', '32902', '32908'));
+
+  for (i in 1:nrow(pri_sec_vals))
+  {
+    pri_sec_val <- pri_sec_vals[i,]
+    patient <- createPatient();
+    visit <- createVisit();
+    declareTest(description=paste0("PATICD_DIAG.ICD_PRI_SEC = ", pri_sec_val$icd_pri_sec, " to CONDITION_STATUS_CONCEPT_ID = ", pri_sec_val$concept_id),
+                id = patient$person_id);
+    add_pat(medrec_key   = patient$medrec_key,
+            pat_key      = visit$pat_key);
+    add_paticd_diag(pat_key = visit$pat_key,
+                    icd_pri_sec = as.character(pri_sec_val$icd_pri_sec));
+    expect_condition_occurrence(person_id                     = patient$person_id,
+                                visit_occurrence_id           = visit$visit_occurrence_id,
+                                condition_status_concept_id   = pri_sec_val$concept_id,
+                                condition_status_source_value = pri_sec_val$icd_pri_sec);
+  }
+
+}
diff --git a/docs/PREMIER/Test Cases/R/CostTests.R b/docs/PREMIER/Test Cases/R/CostTests.R
@@ -0,0 +1,121 @@
+createCostTests <- function () {
+
+  patient <- createPatient()
+  visit <- createVisit()
+  declareTest(description="Cost record from drug_exposure", id = patient$person_id);
+  add_pat(medrec_key = patient$medrec_key,
+          pat_key    = visit$pat_key);
+  add_patbill(pat_key       = visit$pat_key,
+              std_chg_code  = 250250038820000,
+              bill_charges  = 500.50,
+              bill_cost     = 300.75);
+  add_chgmstr(std_chg_code  = 250250038820000,
+              sum_dept_desc = "PHARMACY",
+              std_dept_desc = "PHARMACY");
+  expect_drug_exposure(person_id       = patient$person_id,
+                       drug_concept_id = 19042590);
+  expect_cost(cost_domain_id            = "Drug",
+              total_charge              = 500.50,
+              total_cost                = 300.75,
+              revenue_code_concept_id   = 38003147,
+              revenue_code_source_value = "PHARMACY / PHARMACY");
+
+
+  patient <- createPatient()
+  visit <- createVisit()
+  declareTest(description="Cost record from procedure_occurrence", id = patient$person_id);
+  add_pat(medrec_key = patient$medrec_key,
+          pat_key    = visit$pat_key);
+  add_patbill(pat_key       = visit$pat_key,
+              std_chg_code  = 33840,
+              bill_charges  = 29374.99,
+              bill_cost     = 13572.76);
+  add_chgmstr(std_chg_code  = 33840,
+              sum_dept_desc = "OR",
+              std_dept_desc = "SURGERY");
+  expect_procedure_occurrence(person_id            = patient$person_id,
+                              procedure_concept_id = 2107402);
+  expect_cost(cost_domain_id            = "Procedure",
+              total_charge              = 29374.99,
+              total_cost                = 13572.76,
+              revenue_code_concept_id   = 38003208,
+              revenue_code_source_value = "OR / SURGERY");
+
+
+  patient <- createPatient()
+  visit <- createVisit()
+  declareTest(description="Cost record from device_exposure", id = patient$person_id);
+  add_pat(medrec_key = patient$medrec_key,
+          pat_key    = visit$pat_key);
+  add_patbill(pat_key       = visit$pat_key,
+              std_chg_code  = 270275000120000,
+              bill_charges  = 499.99,
+              bill_cost     = 99.99);
+  add_chgmstr(std_chg_code  = 270275000120000,
+              sum_dept_desc = "SUPPLY",
+              std_dept_desc = "CENTRAL SUPPLY");
+  expect_device_exposure(person_id         = patient$person_id,
+                         device_concept_id = 4236068);
+  expect_cost(cost_domain_id            = "Device",
+              total_charge              = 499.99,
+              total_cost                = 99.99,
+              revenue_code_concept_id   = 38003163,
+              revenue_code_source_value = "SUPPLY / CENTRAL SUPPLY");
+
+
+  patient <- createPatient()
+  visit <- createVisit()
+  declareTest(description="Cost record from observation", id = patient$person_id);
+  add_pat(medrec_key = patient$medrec_key,
+          pat_key    = visit$pat_key);
+  add_patbill(pat_key       = visit$pat_key,
+              std_chg_code  = 110214000620000,
+              bill_charges  = 2347.77,
+              bill_cost     = 2000.00);
+  add_chgmstr(std_chg_code  = 110214000620000,
+              sum_dept_desc = "OTHER",
+              std_dept_desc = "DIALYSIS");
+  expect_observation(person_id              = patient$person_id,
+                     observation_concept_id = 4227255);
+  expect_cost(cost_domain_id            = "Observation",
+              total_charge              = 2347.77,
+              total_cost                = 2000.00,
+              revenue_code_concept_id   = 38003458,
+              revenue_code_source_value = "OTHER / DIALYSIS");
+
+
+  patient <- createPatient()
+  visit <- createVisit()
+  declareTest(description="Cost record from measurement", id = patient$person_id);
+  add_pat(medrec_key = patient$medrec_key,
+          pat_key    = visit$pat_key);
+  add_patbill(pat_key       = visit$pat_key,
+              std_chg_code  = 85013,
+              bill_charges  = 79.99,
+              bill_cost     = 19.50);
+  add_chgmstr(std_chg_code  = 85013,
+              sum_dept_desc = "LAB",
+              std_dept_desc = "LABORATORY");
+  expect_measurement(person_id            = patient$person_id,
+                     measurement_concept_id = 4016241);
+  expect_cost(cost_domain_id            = "Measurement",
+              total_charge              = 79.99,
+              total_cost                = 19.50,
+              revenue_code_concept_id   = 38003172,
+              revenue_code_source_value = "LAB / LABORATORY");
+
+
+  patient <- createPatient();
+  visit <- createVisit();
+  declareTest(description="MS_DRG record (1 digit) to cost table", id = patient$person_id);
+  add_pat(medrec_key   = patient$medrec_key,
+          pat_key      = visit$pat_key,
+          adm_date     = "2005-01-01",
+          disc_date    = "2005-01-01",
+          ms_drg       = 1);
+  add_patbill(pat_key  = visit$pat_key);
+  expect_count_cost(drg_concept_id      = 38000887, #drg=001
+              drg_source_value    = "001",
+			  rowCount = 1);
+
+}
diff --git a/docs/PREMIER/Test Cases/R/DeathTests.R b/docs/PREMIER/Test Cases/R/DeathTests.R
@@ -0,0 +1,79 @@
+createDeathTests <- function ()
+{
+
+  # note death.death_date = visit_occurrence.visit_end_date
+
+  patient <- createPatient();
+  visit <- createVisit();
+  declareTest(description = "Death from PAT.DISC_STATUS without PATICD.ICD_CODE death codes", id = patient$person_id);
+  add_pat(medrec_key   = patient$medrec_key,
+          pat_key      = visit$pat_key,
+          adm_date     = "2010-10-01",
+          disc_date    = "2010-10-04",
+          disc_status  = 20);
+  add_patbill(pat_key  = visit$pat_key)
+  expect_death(person_id             = patient$person_id,
+               death_type_concept_id = 32812,
+               death_date            = '2010-10-04');
+
+
+  patient <- createPatient();
+  visit <- createVisit();
+  declareTest(description = "Death from PAT.DISC_STATUS with PATICD.ICD_CODE death code, use DISC_STATUS", id = patient$person_id);
+  add_pat(medrec_key   = patient$medrec_key,
+          pat_key      = visit$pat_key,
+          adm_date     = "2010-10-01",
+          disc_date    = "2010-10-04",
+          disc_status  = 20);
+  add_patbill(pat_key  = visit$pat_key)
+  add_paticd_diag(pat_key     = visit$pat_key,
+                  icd_version = 10,
+                  icd_code    = "G93.82")
+  expect_death(person_id             = patient$person_id,
+               death_type_concept_id = 32812,
+               death_date            = '2010-10-04');
+
+
+  patient <- createPatient();
+  visit <- createVisit();
+  declareTest(description = "Death PATICD.ICD_CODE death code", id = patient$person_id);
+  add_pat(medrec_key   = patient$medrec_key,
+          pat_key      = visit$pat_key,
+          adm_date     = "2010-10-01",
+          disc_date    = "2010-10-04",
+          disc_status  = 99);
+  add_patbill(pat_key  = visit$pat_key);
+  add_paticd_diag(pat_key     = visit$pat_key,
+                  icd_version = 10,
+                  icd_code    = "G93.82");
+  expect_death(person_id             = patient$person_id,
+               death_type_concept_id = 32875,
+               death_date            = '2010-10-04');
+
+
+  patient <- createPatient();
+  visit1 <- createVisit();
+  visit2 <- createVisit();
+  declareTest(description = "No records populated >32 days after death", id = patient$person_id);
+  add_pat(medrec_key   = patient$medrec_key,
+          pat_key      = visit1$pat_key,
+          adm_date     = "2010-10-01",
+          disc_date    = "2010-10-04",
+          disc_status  = 20);
+  add_patbill(pat_key  = visit1$pat_key);
+  add_pat(medrec_key   = patient$medrec_key,
+          pat_key      = visit2$pat_key,
+          adm_date     = "2011-01-01",
+          disc_date    = "2011-01-01",
+          disc_status  = 99);
+  add_patbill(pat_key  = visit2$pat_key);
+  expect_death(person_id             = patient$person_id,
+               death_type_concept_id = 32812,
+               death_date            = '2010-10-04');
+  expect_no_visit_occurrence(person_id           = patient$person_id,
+                             visit_occurrence_id = visit2$visit_occurrence_id,
+                             visit_start_date    = '2011-01-01',
+                             visit_end_date      = '2011-01-01')
+
+}
+