Release v0.2.0 prep (#117)

* Run styler * Update copyright year * Rebuild vignettes and pkg docs * Regenerate docs
OHDSI · Jan 26, 2024 · bda6bef · bda6bef
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diff --git a/DESCRIPTION b/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")),
@@ -47,7 +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
diff --git a/NEWS.md b/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
 ===============
 

diff --git a/R/DatabaseMetaData.R b/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
 #

diff --git a/R/Execution.R b/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
 #
@@ -72,18 +72,21 @@ execute <- function(analysisSpecifications,
       FUN = function(tableName) {
         sql <- SqlRender::render(
           sql = "CREATE TABLE @table;",
-          table =  tableName
+          table = tableName
+        )
+        tryCatch(
+          {
+            SqlRender::translate(
+              sql = sql,
+              targetDialect = connectionDetails$dbms
+            )
+            return(TRUE)
+          },
+          warning = function(w) {
+            warning(w)
+            return(FALSE)
+          }
         )
-        tryCatch({
-          SqlRender::translate(
-            sql = sql,
-            targetDialect = connectionDetails$dbms
-          )
-          return(TRUE)
-        }, warning = function(w) {
-          warning(w)
-          return(FALSE)
-        })
       }
     )
 

diff --git a/R/ModuleEnv.R b/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
 #

diff --git a/R/ModuleInstantiation.R b/R/ModuleInstantiation.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
 #
@@ -87,9 +87,11 @@ ensureAllModulesInstantiated <- function(analysisSpecifications, forceVerificati
     )
     moduleInstallStatus[[length(moduleInstallStatus) + 1]] <- status
   }
-  attr(modules, 'moduleInstallStatus') <- moduleInstallStatus
+  attr(modules, "moduleInstallStatus") <- moduleInstallStatus
 
-  installStatus <- unlist(lapply(moduleInstallStatus, FUN = function(x) { x$moduleInstalled }))
+  installStatus <- unlist(lapply(moduleInstallStatus, FUN = function(x) {
+    x$moduleInstalled
+  }))
   if (!all(installStatus)) {
     problemModules <- moduleInstallStatus[!installStatus]
     message("There were ", length(problemModules), " issue(s) found with your Strategus modules!")
@@ -159,7 +161,7 @@ verifyModuleInstallation <- function(module, version, silent = FALSE, forceVerif
       verifyModuleInstallationReturnValue(
         moduleFolder = moduleFolder,
         moduleInstalled = FALSE
-        )
+      )
     )
   }
 
@@ -207,7 +209,7 @@ verifyModuleInstallation <- function(module, version, silent = FALSE, forceVerif
         verifyModuleInstallationReturnValue(
           moduleFolder = moduleFolder,
           moduleInstalled = TRUE
-          )
+        )
       )
     }
   }
@@ -230,12 +232,13 @@ verifyModuleInstallation <- function(module, version, silent = FALSE, forceVerif
       packages <- sort(union(renv::dependencies(quiet = TRUE)$Package, "renv"))
       packages <- sort(unique(c(library, lockfile, packages)))
       projectStatus$packages <- packages
-      saveRDS(object = list(
-        library = library,
-        lockfile = lockfile,
-        packages = packages
+      saveRDS(
+        object = list(
+          library = library,
+          lockfile = lockfile,
+          packages = packages
         ),
-        file="projectStatus.rds"
+        file = "projectStatus.rds"
       )
     },
     moduleFolder = moduleFolder

diff --git a/R/RenvHelpers.R b/R/RenvHelpers.R
@@ -83,8 +83,8 @@ syncLockFile <- function(sourceOfTruthLockFileName, targetLockFileName) {
     filename2 = targetLockFileName
   )
   verDiffs <- comparedLockFiles[!is.na(comparedLockFiles$lockfile2Version) &
-                                  comparedLockFiles$lockfile1Version != comparedLockFiles$lockfile2Version,]
-  verDiffs <- verDiffs[!is.na(verDiffs$lockfile1Name),]
+    comparedLockFiles$lockfile1Version != comparedLockFiles$lockfile2Version, ]
+  verDiffs <- verDiffs[!is.na(verDiffs$lockfile1Name), ]
 
   if (nrow(verDiffs) == 0) {
     rlang::inform("Lock files are already in sync.")
@@ -93,32 +93,32 @@ syncLockFile <- function(sourceOfTruthLockFileName, targetLockFileName) {
 
   # Update the target lock file based on the source of truth
   for (i in 1:nrow(verDiffs)) {
-    index <- findPackageByName(targetLockFile$Packages, verDiffs[i,]$lockfile1Name)
+    index <- findPackageByName(targetLockFile$Packages, verDiffs[i, ]$lockfile1Name)
     tryCatch(expr = {
       semverPattern <- "^\\d+\\.\\d+\\.\\d+(?:-[0-9A-Za-z-]+(?:\\.[0-9A-Za-z-]+)*)?(?:\\+[0-9A-Za-z-]+)?$"
-      sourceOfTruthVersion <- verDiffs[i,]$lockfile1Version
+      sourceOfTruthVersion <- verDiffs[i, ]$lockfile1Version
       targetVersion <- targetLockFile$Packages[[index]]$Version
       if (grepl(semverPattern, sourceOfTruthVersion) && grepl(semverPattern, targetVersion)) {
         sourceOfTruthVersion <- semver::parse_version(sourceOfTruthVersion)
         targetVersion <- semver::parse_version(targetVersion)
         if (sourceOfTruthVersion > targetVersion) {
           rlang::inform(
-            message = paste(verDiffs[i,]$lockfile1Name, "[", targetVersion, "->", sourceOfTruthVersion, "]")
+            message = paste(verDiffs[i, ]$lockfile1Name, "[", targetVersion, "->", sourceOfTruthVersion, "]")
           )
-          targetLockFile$Packages[[index]]$Version <- verDiffs[i,]$lockfile1Version
-          if (!is.na(verDiffs[i,]$lockfile1RemoteRef)) {
-            targetLockFile$Packages[[index]]$RemoteRef <- verDiffs[i,]$lockfile1RemoteRef
+          targetLockFile$Packages[[index]]$Version <- verDiffs[i, ]$lockfile1Version
+          if (!is.na(verDiffs[i, ]$lockfile1RemoteRef)) {
+            targetLockFile$Packages[[index]]$RemoteRef <- verDiffs[i, ]$lockfile1RemoteRef
           }
         } else {
           rlang::inform(
-            message = paste(verDiffs[i,]$lockfile1Name, "[ SKIPPING - ", targetVersion, ">", sourceOfTruthVersion, "]")
+            message = paste(verDiffs[i, ]$lockfile1Name, "[ SKIPPING - ", targetVersion, ">", sourceOfTruthVersion, "]")
           )
         }
       } else {
-        rlang::warn(paste0("Package: [", verDiffs[i,]$lockfile1Name, "] - version number could not be parsed. Please inspect manually as it may require an upgrade."))
+        rlang::warn(paste0("Package: [", verDiffs[i, ]$lockfile1Name, "] - version number could not be parsed. Please inspect manually as it may require an upgrade."))
       }
     }, error = function(err) {
-      rlang::inform("An error occurred:", str(err), "\n")
+      rlang::inform("An error occurred:", utils::str(err), "\n")
     })
   }
 
@@ -154,8 +154,8 @@ validateLockFile <- function(filename) {
 
   # Check that the mandatory dependencies are met
   message("Checking mandatory packages...", appendLF = F)
-  if (length(mandatoryPackages()) != nrow(df[df$Name %in% mandatoryPackages(),])) {
-    missingPkgs <- setdiff(mandatoryPackages(), df[df$Name %in% mandatoryPackages(),]$Name)
+  if (length(mandatoryPackages()) != nrow(df[df$Name %in% mandatoryPackages(), ])) {
+    missingPkgs <- setdiff(mandatoryPackages(), df[df$Name %in% mandatoryPackages(), ]$Name)
     message("FAILED!")
     message(" -- Missing the mandatory packages: ", paste(missingPkgs, collapse = ", "))
     message(" Please record these missing dependencies in your renv.lock file.")
@@ -165,8 +165,8 @@ validateLockFile <- function(filename) {
 
   # Check for suggested packages
   message("Checking suggested packages...", appendLF = F)
-  if (length(suggestedPacakges()) != nrow(df[df$Name %in% suggestedPacakges(),])) {
-    missingPkgs <- setdiff(suggestedPacakges(), df[df$Name %in% suggestedPacakges(),]$Name)
+  if (length(suggestedPacakges()) != nrow(df[df$Name %in% suggestedPacakges(), ])) {
+    missingPkgs <- setdiff(suggestedPacakges(), df[df$Name %in% suggestedPacakges(), ]$Name)
     message("WARNING!")
     message(" -- Missing the suggested packages: ", paste(missingPkgs, collapse = ", "))
     message(" This is an optional set of dependencies so you may decide if you wish to have them in your renv.lock file.")
@@ -177,10 +177,10 @@ validateLockFile <- function(filename) {
   # Check that we're using declared versions of all packages
   message("Checking all package using tagged versions in RemoteRef...", appendLF = F)
   # Start by filtering out the CRAN Repository entries
-  dfFiltered <- df[tolower(df$Source) != "repository",]
+  dfFiltered <- df[tolower(df$Source) != "repository", ]
   if (!all(grepl("^(v)?\\d+(\\.\\d+){2}$", dfFiltered$RemoteRef))) {
     message("FAILED! Please check the following packages:")
-    problemPkgs <- dfFiltered[!grepl("^(v)?\\d+(\\.\\d+){2}$", dfFiltered$RemoteRef),]
+    problemPkgs <- dfFiltered[!grepl("^(v)?\\d+(\\.\\d+){2}$", dfFiltered$RemoteRef), ]
     for (i in 1:nrow(problemPkgs)) {
       message(paste0(" -- Package: ", problemPkgs$Name[[i]], "; RemoteRef: ", problemPkgs$RemoteRef[[i]]))
     }
@@ -190,6 +190,9 @@ validateLockFile <- function(filename) {
   }
 }
 
+#' List of mandatory packages for a Strategus module
+#'
+#' @keywords internal
 mandatoryPackages <- function() {
   return(c(
     "CohortGenerator",
@@ -201,12 +204,17 @@ mandatoryPackages <- function() {
   ))
 }
 
+#' List of suggested packages for a Strategus module
+#'
+#' @keywords internal
 suggestedPacakges <- function() {
   return(c("RSQLite"))
 }
 
 
-# internal function to read lock file into data frame
+#' Convert a lock file to a data.frame
+#'
+#' @keywords internal
 lockFileToDataFrame <- function(lf) {
   df <- data.frame()
   for (i in 1:length(lf$Packages)) {
@@ -222,4 +230,3 @@ lockFileToDataFrame <- function(lf) {
   }
   return(df)
 }
-
diff --git a/R/ResultModelCreation.R b/R/ResultModelCreation.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
 #

diff --git a/R/ResultsUpload.R b/R/ResultsUpload.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
 #

diff --git a/R/RunModule.R b/R/RunModule.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
 #

diff --git a/R/Settings.R b/R/Settings.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
 #

diff --git a/R/Strategus.R b/R/Strategus.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
 #

diff --git a/docs/404.html b/docs/404.html