Merge pull request #463 from katy-sadowski/katy__test_cleanup

Reorganize test files

NEWS.md

@@ -78,6 +78,10 @@ This release includes:
 
   - The `outputFolder` parameter for the `executeDqChecks` function is now REQUIRED and no longer has a default value.  **This may be a breaking change for users who have not specified this parameter in their script to run DQD.**
 
+### Removal of measurement plausibility checks
+
+  - Most plausibleValueLow and plausibleValueHigh measurement values were removed from the concept check threshold files, due to feedback from the community that many of these ranges included plausible values and as such were causing unexpected check failures. An initiative is planned to reinterrogate these ranges and add them back once the team has higher confidence that they will only flag legitimately implausible values 
+
 ### Integrated testing was also added and the package was refactored on the backend
 
 DataQualityDashboard 1.4.1

tests/testthat/setup.R

@@ -20,46 +20,3 @@ remove_sql_comments <- function(sql) {
   sql4 <- gsub("@@@@ .+? @@@@", " ", sql3, ) # remove multi-line comments
   sql5 <- gsub("\\s+", " ", sql4) # remove multiple spaces
 }
-
-# dbms <- getOption("dbms", default = "sqlite")
-# if (dbms == "sqlite") {
-# connectionDetails <- Eunomia::getEunomiaConnectionDetails()
-# cdmDatabaseSchema <- "main"
-# resultsDatabaseSchema <- "main"
-# cdmVersion <- 5
-# }
-# if (dbms == "postgresql") {
-#   DatabaseConnector::downloadJdbcDrivers("postgresql", pathToDriver = jdbcDriverFolder)
-#   connectionDetails <- createConnectionDetails(dbms = "postgresql",
-#                                                user = Sys.getenv("CDM5_POSTGRESQL_USER"),
-#                                                password = URLdecode(Sys.getenv("CDM5_POSTGRESQL_PASSWORD")),
-#                                                server = Sys.getenv("CDM5_POSTGRESQL_SERVER"),
-#                                                pathToDriver = jdbcDriverFolder)
-#
-#   cdmDatabaseSchema <- Sys.getenv("CDM5_POSTGRESQL_CDM_SCHEMA")
-#   cdmVersion <- 5
-# }
-# if (dbms == "sql server") {
-#   DatabaseConnector::downloadJdbcDrivers("sql server", pathToDriver = jdbcDriverFolder)
-#   connectionDetails <- createConnectionDetails(dbms = "sql server",
-#                                                user = Sys.getenv("CDM5_SQL_SERVER_USER"),
-#                                                password = URLdecode(Sys.getenv("CDM5_SQL_SERVER_PASSWORD")),
-#                                                server = Sys.getenv("CDM5_SQL_SERVER_SERVER"),
-#                                                pathToDriver = jdbcDriverFolder)
-#   cdmDatabaseSchema <- Sys.getenv("CDM5_SQL_SERVER_CDM_SCHEMA")
-#   cdmVersion <- 5
-# }
-# if (dbms == "oracle") {
-#   DatabaseConnector::downloadJdbcDrivers("oracle", pathToDriver = jdbcDriverFolder)
-#   connectionDetails <- createConnectionDetails(dbms = "oracle",
-#                                                user = Sys.getenv("CDM5_ORACLE_USER"),
-#                                                password = URLdecode(Sys.getenv("CDM5_ORACLE_PASSWORD")),
-#                                                server = Sys.getenv("CDM5_ORACLE_SERVER"),
-#                                                pathToDriver = jdbcDriverFolder)
-#   cdmDatabaseSchema <- Sys.getenv("CDM5_ORACLE_CDM_SCHEMA")
-#
-#   # Restore temp schema setting after tests complete
-#   oldTempSchema <- getOption("sqlRenderTempEmulationSchema")
-#   options("sqlRenderTempEmulationSchema" = Sys.getenv("CDM5_ORACLE_OHDSI_SCHEMA"))
-#   cdmVersion <- 5
-# }

tests/testthat/test-execute.R → tests/testthat/test-executeDqChecks.R

@@ -1,11 +1,5 @@
 library(testthat)
 
-test_that("listDqChecks works", {
-  checks <- listDqChecks()
-  expect_equal(length(checks), 4)
-  expect_true(all(sapply(checks, is.data.frame)))
-})
-
 test_that("Execute a single DQ check on Synthea/Eunomia", {
   outputFolder <- tempfile("dqd_")
   on.exit(unlink(outputFolder, recursive = TRUE))
@@ -43,7 +37,6 @@ test_that("Execute all TABLE checks on Synthea/Eunomia", {
   expect_true(nrow(results$CheckResults) > 0)
 })
 
-
 test_that("Execute FIELD checks on Synthea/Eunomia", {
   outputFolder <- tempfile("dqd_")
   on.exit(unlink(outputFolder, recursive = TRUE))
@@ -185,44 +178,6 @@ test_that("Check invalid cdm version", {
   )
 })
 
-test_that("Write JSON results", {
-  outputFolder <- tempfile("dqd_")
-  on.exit(unlink(outputFolder, recursive = TRUE))
-
-  expect_warning(
-    results <- executeDqChecks(
-      connectionDetails = connectionDetailsEunomia,
-      cdmDatabaseSchema = cdmDatabaseSchemaEunomia,
-      resultsDatabaseSchema = resultsDatabaseSchemaEunomia,
-      cdmSourceName = "Eunomia",
-      checkNames = "measurePersonCompleteness",
-      outputFolder = outputFolder,
-      writeToTable = FALSE
-    ),
-    regexp = "^Missing check names.*"
-  )
-
-  jsonPath <- list.files(outputFolder, ".json", full.names = TRUE)
-  csvPath <- file.path(outputFolder, "results.csv")
-  writeJsonResultsToCsv(
-    jsonPath = jsonPath,
-    csvPath = csvPath
-  )
-  expect_true(file.exists(csvPath))
-
-  DataQualityDashboard::writeJsonResultsToTable(
-    connectionDetails = connectionDetailsEunomia,
-    resultsDatabaseSchema = resultsDatabaseSchemaEunomia,
-    jsonFilePath = jsonPath,
-    writeTableName = "dqd_results"
-  )
-  connection <- DatabaseConnector::connect(connectionDetailsEunomia)
-  on.exit(DatabaseConnector::disconnect(connection), add = TRUE)
-  tableNames <- DatabaseConnector::getTableNames(connection = connection, databaseSchema = resultsDatabaseSchemaEunomia)
-  expect_true("dqd_results" %in% tolower(tableNames))
-  DatabaseConnector::renderTranslateExecuteSql(connection, "DROP TABLE @database_schema.dqd_results;", database_schema = resultsDatabaseSchemaEunomia)
-})
-
 test_that("Execute DQ checks and write to table", {
   outputFolder <- tempfile("dqd_")
   on.exit(unlink(outputFolder, recursive = TRUE))
@@ -247,33 +202,6 @@ test_that("Execute DQ checks and write to table", {
   DatabaseConnector::renderTranslateExecuteSql(connection, "DROP TABLE @database_schema.dqd_results;", database_schema = resultsDatabaseSchemaEunomia)
 })
 
-test_that("Execute reEvaluateThresholds on Synthea/Eunomia", {
-  outputFolder <- tempfile("dqd_")
-  on.exit(unlink(outputFolder, recursive = TRUE))
-
-  expect_warning(
-    results <- executeDqChecks(
-      connectionDetails = connectionDetailsEunomia,
-      cdmDatabaseSchema = cdmDatabaseSchemaEunomia,
-      resultsDatabaseSchema = resultsDatabaseSchemaEunomia,
-      cdmSourceName = "Eunomia",
-      checkNames = "measurePersonCompleteness",
-      outputFolder = outputFolder,
-      writeToTable = F
-    ),
-    regexp = "^Missing check names.*"
-  )
-
-  jsonPath <- list.files(outputFolder, ".json", full.names = TRUE)
-
-  results2 <- reEvaluateThresholds(
-    jsonFilePath = jsonPath,
-    outputFolder = outputFolder,
-    outputFile = "reEvaluated.txt"
-  )
-  expect_is(results2, "list")
-})
-
 test_that("Execute DQ checks using sqlOnly=TRUE and sqlOnlyUnionCount=4 and sqlOnlyIncrementalInsert=TRUE", {
   outputFolder <- tempfile("dqd_")
   on.exit(unlink(outputFolder, recursive = TRUE))

tests/testthat/test-listChecks.R

@@ -0,0 +1,7 @@
+library(testthat)
+
+test_that("listDqChecks works", {
+  checks <- listDqChecks()
+  expect_equal(length(checks), 4)
+  expect_true(all(sapply(checks, is.data.frame)))
+})

tests/testthat/test-reEvaluateThresholds.R

@@ -0,0 +1,28 @@
+library(testthat)
+
+test_that("Execute reEvaluateThresholds on Synthea/Eunomia", {
+  outputFolder <- tempfile("dqd_")
+  on.exit(unlink(outputFolder, recursive = TRUE))
+
+  expect_warning(
+    results <- executeDqChecks(
+      connectionDetails = connectionDetailsEunomia,
+      cdmDatabaseSchema = cdmDatabaseSchemaEunomia,
+      resultsDatabaseSchema = resultsDatabaseSchemaEunomia,
+      cdmSourceName = "Eunomia",
+      checkNames = "measurePersonCompleteness",
+      outputFolder = outputFolder,
+      writeToTable = F
+    ),
+    regexp = "^Missing check names.*"
+  )
+
+  jsonPath <- list.files(outputFolder, ".json", full.names = TRUE)
+
+  results2 <- reEvaluateThresholds(
+    jsonFilePath = jsonPath,
+    outputFolder = outputFolder,
+    outputFile = "reEvaluated.txt"
+  )
+  expect_is(results2, "list")
+})

tests/testthat/test-writeJsonResultsTo.R

@@ -0,0 +1,39 @@
+library(testthat)
+
+test_that("Write JSON results", {
+  outputFolder <- tempfile("dqd_")
+  on.exit(unlink(outputFolder, recursive = TRUE))
+
+  expect_warning(
+    results <- executeDqChecks(
+      connectionDetails = connectionDetailsEunomia,
+      cdmDatabaseSchema = cdmDatabaseSchemaEunomia,
+      resultsDatabaseSchema = resultsDatabaseSchemaEunomia,
+      cdmSourceName = "Eunomia",
+      checkNames = "measurePersonCompleteness",
+      outputFolder = outputFolder,
+      writeToTable = FALSE
+    ),
+    regexp = "^Missing check names.*"
+  )
+
+  jsonPath <- list.files(outputFolder, ".json", full.names = TRUE)
+  csvPath <- file.path(outputFolder, "results.csv")
+  writeJsonResultsToCsv(
+    jsonPath = jsonPath,
+    csvPath = csvPath
+  )
+  expect_true(file.exists(csvPath))
+
+  DataQualityDashboard::writeJsonResultsToTable(
+    connectionDetails = connectionDetailsEunomia,
+    resultsDatabaseSchema = resultsDatabaseSchemaEunomia,
+    jsonFilePath = jsonPath,
+    writeTableName = "dqd_results"
+  )
+  connection <- DatabaseConnector::connect(connectionDetailsEunomia)
+  on.exit(DatabaseConnector::disconnect(connection), add = TRUE)
+  tableNames <- DatabaseConnector::getTableNames(connection = connection, databaseSchema = resultsDatabaseSchemaEunomia)
+  expect_true("dqd_results" %in% tolower(tableNames))
+  DatabaseConnector::renderTranslateExecuteSql(connection, "DROP TABLE @database_schema.dqd_results;", database_schema = resultsDatabaseSchemaEunomia)
+})