Release v0.0.4

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: Strategus
 Type: Package
 Title: Coordinating and Executing Analytics Using HADES Modules
-Version: 0.0.3
-Date: 2023-03-10
+Version: 0.0.4
+Date: 2023-03-29
 Authors@R: c(
 	person("Martijn", "Schuemie", email = "[email protected]", role = c("aut", "cre")),
 	person("Anthony", "Sena", email = "[email protected]", role = c("aut")),
@@ -32,11 +32,12 @@ Imports:
   tibble,
   SqlRender (>= 1.11.0)
 Suggests:
-    testthat (>= 3.0.0),
-    fs,
-    knitr,
-    rmarkdown,
-    Eunomia
+  testthat (>= 3.0.0),
+  fs,
+  knitr,
+  rmarkdown,
+  Eunomia,
+  withr
 Remotes:
   ohdsi/CohortGenerator,
   ohdsi/Eunomia

NEWS.md

@@ -1,3 +1,10 @@
+Strategus 0.0.4
+===============
+
+- Add DB Platform Tests (#53)
+- Add error handling for missing/empty tables (#54)
+- Remove uniqueness check for module table prefix (#55)
+
 Strategus 0.0.3
 ===============
 

R/DatabaseMetaData.R

@@ -34,6 +34,21 @@ createDatabaseMetaData <- function(executionSettings, keyringName = NULL) {
   connection <- DatabaseConnector::connect(connectionDetails)
   on.exit(DatabaseConnector::disconnect(connection))
 
+  # Verify the CDM tables required by this function exist prior to
+  # querying. Then we can stop the processing and provide an informative
+  # message to the user.
+  requiredTables <- c("cdm_source", "vocabulary", "observation_period")
+  cdmTableList <- DatabaseConnector::getTableNames(
+    connection = connection,
+    databaseSchema = executionSettings$cdmDatabaseSchema
+  )
+
+
+  if (!length(cdmTableList[which(x = cdmTableList %in% requiredTables)]) == length(requiredTables)) {
+    missingCdmTables <- requiredTables[!(requiredTables %in% cdmTableList)]
+    stop(sprintf("FATAL ERROR: Your OMOP CDM is missing the following required tables: %s", paste(missingCdmTables, collapse = ", ")))
+  }
+
   resultsDataModel <- CohortGenerator::readCsv(
     file = system.file("databaseMetaDataRdms.csv", package = "Strategus"),
     warnOnCaseMismatch = FALSE
@@ -47,6 +62,11 @@ createDatabaseMetaData <- function(executionSettings, keyringName = NULL) {
     cdm_database_schema = executionSettings$cdmDatabaseSchema
   )
 
+  # Verify that the cdmSource table has information
+  if (nrow(cdmSource) == 0) {
+    stop("FATAL ERROR: The CDM_SOURCE table in your OMOP CDM is empty. Please populate this table with information about your CDM and organization. For more information, please see: https://ohdsi.github.io/CommonDataModel/cdm53.html#CDM_SOURCE")
+  }
+
   # Restrict the cdmSource columns to those that are
   # expected in the resultsDataModel
   cdmSource <- cdmSource[, which(names(cdmSource) %in% SqlRender::snakeCaseToCamelCase(resultsDataModel$columnName))]
@@ -67,6 +87,12 @@ createDatabaseMetaData <- function(executionSettings, keyringName = NULL) {
     cdm_database_schema = executionSettings$cdmDatabaseSchema
   )
 
+  # Verify that the vocabulary_version is found
+  if (nrow(vocabVersion) == 0) {
+    stop("FATAL ERROR: The VOCABULARY table in your OMOP CDM is missing the version. Please verify that your process for loading the vocabulary included an entry in the vocabulary table with vocabulary_id == 'None'")
+  }
+
+
   sql <- "SELECT MAX(observation_period_end_date) as max_obs_period_end_date
   FROM @cdm_database_schema.observation_period;"
   observationPeriodMax <- renderTranslateQuerySql(
@@ -76,6 +102,11 @@ createDatabaseMetaData <- function(executionSettings, keyringName = NULL) {
     cdm_database_schema = executionSettings$cdmDatabaseSchema
   )
 
+  # Verify that the MAX(observation_period_end_date) is a valid date
+  if (is.na(observationPeriodMax$maxObsPeriodEndDate)) {
+    stop("FATAL ERROR: The OBSERVATION_PERIOD table in your OMOP CDM lacks a maximum observation_period_end_date. This may be a result of an error in the ETL as each person in the OMOP CDM must have an observation period with a valid start and end date.")
+  }
+
   databaseId <- digest::digest2int(paste(cdmSource$cdmSourceName, cdmSource$cdmReleaseDate))
   database <- cdmSource %>%
     mutate(

R/ModuleInstantiation.R

@@ -73,29 +73,6 @@ ensureAllModulesInstantiated <- function(analysisSpecifications) {
     stop(message)
   }
 
-  # Check for colliding result table prefixes
-  moduleTablePrefixes <- getModuleTablePrefixes(moduleList = modules)
-  if (nrow(moduleTablePrefixes) != length(unique(moduleTablePrefixes$tablePrefix))) {
-    moduleTablePrefixesInConflict <- moduleTablePrefixes %>%
-      group_by(.data$tablePrefix) %>%
-      summarise(totalCount = n()) %>%
-      filter(.data$totalCount > 1)
-
-    message <- paste(
-      c(
-        "Detected colliding result table prefixes:",
-        sprintf(
-          "- Module '%s' (v'%s') table prefix: '%s'",
-          moduleTablePrefixesInConflict$moduleName,
-          moduleTablePrefixesInConflict$moduleVersion,
-          moduleTablePrefixesInConflict$tablePrefix
-        )
-      ),
-      collapse = "\n"
-    )
-    stop(message)
-  }
-
   return(modules)
 }