Release v0.2.0

Release v0.2.0

.github/workflows/R_CMD_check_Hades.yaml

@@ -21,10 +21,10 @@ jobs:
       matrix:
         config:
           - {os: windows-latest, r: '4.2.3', rtools: '42', rspm: "https://cloud.r-project.org"}
-          - {os: macOS-latest, r: '4.2.3', rtools: '42', rspm: "https://cloud.r-project.org"}
+          #- {os: macOS-latest, r: '4.2.3', rtools: '42', rspm: "https://cloud.r-project.org"}
           - {os: ubuntu-20.04, r: '4.2.3', rtools: '42', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: windows-latest, r: 'release', rtools: '', rspm: "https://cloud.r-project.org"}
-          #- {os: macOS-latest, r: 'release', rtools: '', rspm: "https://cloud.r-project.org"}
+          - {os: macOS-latest, r: 'release', rtools: '', rspm: "https://cloud.r-project.org"}
           - {os: ubuntu-20.04, r: 'release', rtools: '', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 
     env:

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: Strategus
 Type: Package
 Title: Coordinating and Executing Analytics Using HADES Modules
-Version: 0.1.0
-Date: 2023-10-04
+Version: 0.2.0
+Date: 2023-01-26
 Authors@R: c(
 	person("Martijn", "Schuemie", email = "[email protected]", role = c("aut")),
 	person("Anthony", "Sena", email = "[email protected]", role = c("aut", "cre")),
@@ -32,7 +32,8 @@ Imports:
   methods,
   tibble,
   ResultModelManager (>= 0.3.0),
-  SqlRender (>= 1.11.0)
+  SqlRender (>= 1.11.0),
+  semver
 Suggests:
   testthat (>= 3.0.0),
   fs,
@@ -46,7 +47,7 @@ Remotes:
   ohdsi/Eunomia
 VignetteBuilder: knitr
 NeedsCompilation: no
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)
 Encoding: UTF-8
 Config/testthat/edition: 3

NAMESPACE

@@ -2,6 +2,7 @@
 
 export(addModuleSpecifications)
 export(addSharedResources)
+export(compareLockFiles)
 export(createCdmExecutionSettings)
 export(createEmptyAnalysisSpecificiations)
 export(createResultDataModels)
@@ -11,7 +12,10 @@ export(execute)
 export(getModuleList)
 export(retrieveConnectionDetails)
 export(storeConnectionDetails)
+export(syncLockFile)
 export(unlockKeyring)
+export(validateLockFile)
+export(verifyModuleInstallation)
 import(CohortGenerator)
 import(DatabaseConnector)
 import(dplyr)

NEWS.md

@@ -1,3 +1,14 @@
+Strategus 0.2.0
+===============
+- Add functions for developers to help with renv.lock file validation (#69)
+- Use renv project profiles for modules (#94)
+- Convert relative paths to absolute path before passing to a module (#99)
+- Address missing package dependencies in modules (#99)
+- Throw informative error message when connection detail reference not set in keyring (#100)
+- Validate execution settings (#101)
+- Pass temp emulation schema properly (#76)
+- Remove local library package dependencies (#96)
+
 Strategus 0.1.0
 ===============
 

R/DatabaseMetaData.R

@@ -1,4 +1,4 @@
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of Strategus
 #

R/Execution.R

@@ -1,4 +1,4 @@
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of Strategus
 #
@@ -48,9 +48,10 @@ execute <- function(analysisSpecifications,
   checkmate::assertChoice(x = keyringName, choices = keyringList$keyring, null.ok = TRUE, add = errorMessages)
   checkmate::reportAssertions(collection = errorMessages)
 
-  # Assert that the temp emulation schema is set if required for the dbms
-  # specified by the executionSettings
+  # Validate the execution settings
   if (is(executionSettings, "CdmExecutionSettings")) {
+    # Assert that the temp emulation schema is set if required for the dbms
+    # specified by the executionSettings
     connectionDetails <- retrieveConnectionDetails(
       connectionDetailsReference = executionSettings$connectionDetailsReference,
       keyringName = keyringName
@@ -59,8 +60,48 @@ execute <- function(analysisSpecifications,
       dbms = connectionDetails$dbms,
       tempEmulationSchema = executionSettings$tempEmulationSchema
     )
+
+    # Validate that the table names specified in the execution settings
+    # do not violate the maximum table length. To do this we will render
+    # a query using the execution settings so that SqlRender can provide
+    # the appropriate warning. Only stop execution if we are running on
+    # Oracle; otherwise it is unclear if the table name length will have
+    # an impact
+    cohortTableChecks <- lapply(
+      X = executionSettings$cohortTableNames,
+      FUN = function(tableName) {
+        sql <- SqlRender::render(
+          sql = "CREATE TABLE @table;",
+          table = tableName
+        )
+        tryCatch(
+          {
+            SqlRender::translate(
+              sql = sql,
+              targetDialect = connectionDetails$dbms
+            )
+            return(TRUE)
+          },
+          warning = function(w) {
+            warning(w)
+            return(FALSE)
+          }
+        )
+      }
+    )
+
+    # Since the warning is thrown for all dbms systems, only stop if
+    # we are executing on Oracle
+    if (tolower(connectionDetails$dbms) == "oracle" && !all(unlist(cohortTableChecks))) {
+      stop("Your cohort table names are too long for Oracle. Please update your executionSettings to use shorter cohort table names and try again.")
+    }
   }
+
+  # Validate the modules
   modules <- ensureAllModulesInstantiated(analysisSpecifications)
+  if (isFALSE(modules$allModulesInstalled)) {
+    stop("Stopping execution due to module issues")
+  }
 
   if (is.null(executionScriptFolder)) {
     executionScriptFolder <- tempfile("strategusTempSettings")
@@ -72,14 +113,16 @@ execute <- function(analysisSpecifications,
     }
     dir.create(executionScriptFolder, recursive = TRUE)
   }
+  # Normalize path to convert from relative to absolute path
+  executionScriptFolder <- normalizePath(executionScriptFolder, mustWork = F)
 
   if (is(executionSettings, "CdmExecutionSettings")) {
     executionSettings$databaseId <- createDatabaseMetaData(
       executionSettings = executionSettings,
       keyringName = keyringName
     )
   }
-  dependencies <- extractDependencies(modules)
+  dependencies <- extractDependencies(modules$modules)
 
 
   fileName <- generateTargetsScript(
@@ -154,11 +197,11 @@ generateTargetsScript <- function(analysisSpecifications, executionSettings, dep
   )
 
   # Store settings objects in the temp folder so they are available in targets
-  analysisSpecificationsFileName <- gsub("\\\\", "/", file.path(executionScriptFolder, "analysisSpecifications.rds"))
+  analysisSpecificationsFileName <- .formatAndNormalizeFilePathForScript(file.path(executionScriptFolder, "analysisSpecifications.rds"))
   saveRDS(analysisSpecifications, analysisSpecificationsFileName)
-  executionSettingsFileName <- gsub("\\\\", "/", file.path(executionScriptFolder, "executionSettings.rds"))
+  executionSettingsFileName <- .formatAndNormalizeFilePathForScript(file.path(executionScriptFolder, "executionSettings.rds"))
   saveRDS(executionSettings, executionSettingsFileName)
-  keyringSettingsFileName <- gsub("\\\\", "/", file.path(executionScriptFolder, "keyringSettings.rds"))
+  keyringSettingsFileName <- .formatAndNormalizeFilePathForScript(file.path(executionScriptFolder, "keyringSettings.rds"))
   saveRDS(list(keyringName = keyringName), keyringSettingsFileName)
 
   # Generate target names by module type
@@ -172,10 +215,10 @@ generateTargetsScript <- function(analysisSpecifications, executionSettings, dep
     )
   }
   moduleToTargetNames <- bind_rows(moduleToTargetNames)
-  moduleToTargetNamesFileName <- gsub("\\\\", "/", file.path(executionScriptFolder, "moduleTargetNames.rds"))
+  moduleToTargetNamesFileName <- .formatAndNormalizeFilePathForScript(file.path(executionScriptFolder, "moduleTargetNames.rds"))
   saveRDS(moduleToTargetNames, moduleToTargetNamesFileName)
 
-  dependenciesFileName <- gsub("\\\\", "/", file.path(executionScriptFolder, "dependencies.rds"))
+  dependenciesFileName <- .formatAndNormalizeFilePathForScript(file.path(executionScriptFolder, "dependencies.rds"))
   saveRDS(dependencies, dependenciesFileName)
 
   execResultsUpload <- all(c(

R/ModuleEnv.R

@@ -1,4 +1,4 @@
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of Strategus
 #
@@ -47,16 +47,13 @@
 #' @param injectVars        list of var names list(name=value) to replace (e.g. replace list(foo = "some string") will
 #'                          find the pattern foo and replace it with the string some string - be careful!
 #' @param tempScriptFile    tempFile to write script to
-#' @param useLocalStrategusLibrary Use the locally installed Strategus library? TRUE will use the Strategus
-#'                          installation from the calling R process.
 #' @param job               run as rstudio job
 #' @param processName       String name for process
 #' @returns NULL invisibly
 withModuleRenv <- function(code,
                            moduleFolder,
                            injectVars = list(),
                            tempScriptFile = tempfile(fileext = ".R"),
-                           useLocalStrategusLibrary = TRUE,
                            job = FALSE,
                            processName = paste(moduleFolder, "_renv_run")) {
   # convert human readable code to a string for writing
@@ -81,19 +78,16 @@ withModuleRenv <- function(code,
     }
   }
 
-  # Enforce attachment of Strategus from calling process - note one inside the renv
-  if (useLocalStrategusLibrary) {
-    script <- c(.getLocalLibraryScipt("Strategus"), script)
-    # Adding Strategus dependencies to the script
-    script <- c(.getLocalLibraryScipt("ParallelLogger"), script)
-    script <- c(.getLocalLibraryScipt("CohortGenerator"), script)
-    script <- c(.getLocalLibraryScipt("DatabaseConnector"), script)
-    script <- c(.getLocalLibraryScipt("keyring"), script)
-    script <- c(.getLocalLibraryScipt("openssl"), script)
-    script <- c(.getLocalLibraryScipt("dplyr"), script)
-    script <- c(.getLocalLibraryScipt("R6"), script)
+  # Turning off verbose output to hide renv output
+  # unless the user has set this option to TRUE.
+  if (!getOption(x = "renv.verbose", default = FALSE)) {
+    options(renv.verbose = FALSE)
   }
 
+  # Import the Strategus functions we need to use in the module scripts
+  script <- c("retrieveConnectionDetails <- ", base::deparse(Strategus::retrieveConnectionDetails), script)
+  script <- c("unlockKeyring <- ", base::deparse(Strategus::unlockKeyring), script)
+
   # Write file and execute script inside an renv
   fileConn <- file(tempScriptFile)
   writeLines(script, fileConn)
@@ -123,3 +117,7 @@ withModuleRenv <- function(code,
     paste0("# option = ", optionName, " - could not be passed to this file, likely because it is a function.")
   }
 }
+
+.formatAndNormalizeFilePathForScript <- function(filePath) {
+  return(gsub("\\\\", "/", normalizePath(path = filePath, mustWork = F)))
+}