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Adding renv.lock helper functions (#116)
* Fix module check and results upload bugs * Add helper functions and update test module * Adding tests * Add renv.lock file validation helper * Add local module renv.lock validator script to extras * Add dev modules for testing * Update analysis spec to use newly released modules * Update module reference file
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,225 @@ | ||
| #' Compare two renv.lock files | ||
| #' | ||
| #' @description | ||
| #' Used to compare renv.lock files and return the results in a data.frame. | ||
| #' The return value will include a "full join" representation of the packages | ||
| #' across the two lock files. | ||
| #' | ||
| #' @param filename1 The first renv.lock file name | ||
| #' | ||
| #' @param filename2 The second renv.lock file name | ||
| #' | ||
| #' @return | ||
| #' A data.frame with the comparison of the rev.lock files | ||
| #' | ||
| #' @export | ||
| compareLockFiles <- function(filename1, filename2) { | ||
| # Read the lock files | ||
| lockfile1 <- renv::lockfile_read( | ||
| file = filename1 | ||
| ) | ||
|
|
||
| lockfile2 <- renv::lockfile_read( | ||
| file = filename2 | ||
| ) | ||
|
|
||
| # Compare lock files | ||
| lockfile1Packages <- lockFileToDataFrame(lockfile1) | ||
| names(lockfile1Packages) <- paste0("lockfile1", names(lockfile1Packages)) | ||
| lockfile2Packages <- lockFileToDataFrame(lockfile2) | ||
| names(lockfile2Packages) <- paste0("lockfile2", names(lockfile2Packages)) | ||
| mergedLockFilePackages <- merge( | ||
| x = lockfile1Packages, | ||
| y = lockfile2Packages, | ||
| by.x = "lockfile1Name", | ||
| by.y = "lockfile2Name", | ||
| all = TRUE | ||
| ) | ||
| return(mergedLockFilePackages) | ||
| } | ||
|
|
||
| #' Synchronize renv.lock files and overwrite the target file | ||
| #' (read the description) | ||
| #' | ||
| #' @description | ||
| #' Used to synchronize the values from the "source of truth" renv.lock file to | ||
| #' the target renv.lock file. Packages are compared (by name) and if the version | ||
| #' of the package in the "source of truth" is greater the one found in the | ||
| #' target, the target renv.lock file will be updated. This function will | ||
| #' automatically update the target file. | ||
| #' | ||
| #' Version comparison is handled by the `semver` package and since most packages | ||
| #' use semantic versioning. When a package does not use semantic versioning, | ||
| #' a warning is provided so the user can review. | ||
| #' | ||
| #' @param sourceOfTruthLockFileName The renv.lock file to use as the source of | ||
| #' truth | ||
| #' | ||
| #' @param targetLockFileName The target renv.lock file that will be synced with | ||
| #' the source of truth | ||
| #' | ||
| #' @return | ||
| #' A data.frame containing the different packages and their version that | ||
| #' were involved in the synchronization process | ||
| #' | ||
| #' @export | ||
| syncLockFile <- function(sourceOfTruthLockFileName, targetLockFileName) { | ||
| findPackageByName <- function(list, packageName) { | ||
| index <- which(sapply(list, function(x) x$Package == packageName)) | ||
| return(index) | ||
| } | ||
|
|
||
| # Read the lock files | ||
| sourceOfTruthLockFile <- renv::lockfile_read( | ||
| file = sourceOfTruthLockFileName | ||
| ) | ||
| targetLockFile <- renv::lockfile_read( | ||
| file = targetLockFileName | ||
| ) | ||
|
|
||
| # Compare the lock files to get the differences in package versions | ||
| comparedLockFiles <- compareLockFiles( | ||
| filename1 = sourceOfTruthLockFileName, | ||
| filename2 = targetLockFileName | ||
| ) | ||
| verDiffs <- comparedLockFiles[!is.na(comparedLockFiles$lockfile2Version) & | ||
| comparedLockFiles$lockfile1Version != comparedLockFiles$lockfile2Version,] | ||
| verDiffs <- verDiffs[!is.na(verDiffs$lockfile1Name),] | ||
|
|
||
| if (nrow(verDiffs) == 0) { | ||
| rlang::inform("Lock files are already in sync.") | ||
| return(invisible(NULL)) | ||
| } | ||
|
|
||
| # Update the target lock file based on the source of truth | ||
| for (i in 1:nrow(verDiffs)) { | ||
| index <- findPackageByName(targetLockFile$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,]$lockfile1Version | ||
| targetVersion <- targetLockFile$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, "]") | ||
| ) | ||
| 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, "]") | ||
| ) | ||
| } | ||
| } else { | ||
| rlang::warn(paste0("Package: [", verDiffs[i,]$lockfile1Name, "] - version number could not be parsed. Please inspect manually as it may require an upgrade.")) | ||
| } | ||
| }, error = function(err) { | ||
| rlang::inform("An error occurred:", str(err), "\n") | ||
| }) | ||
| } | ||
|
|
||
| # Save the updated lock file | ||
| renv::lockfile_write( | ||
| lockfile = targetLockFile, | ||
| file = targetLockFileName | ||
| ) | ||
|
|
||
| return(invisible(verDiffs)) | ||
| } | ||
|
|
||
| #' Validate an renv.lock file to ensure it is ready for use by Strategus | ||
| #' | ||
| #' @description | ||
| #' Will check an renv.lock file for a module to verify that it only references | ||
| #' tagged packages and includes the packages required by Strategus. It will | ||
| #' also check for suggested packages that are useful for testing, such as | ||
| #' RSQLite. | ||
| #' | ||
| #' @param filename The renv.lock file to validate | ||
| #' | ||
| #' @export | ||
| validateLockFile <- function(filename) { | ||
| # Read the lock file | ||
| lockFile <- renv::lockfile_read( | ||
| file = filename | ||
| ) | ||
| # Create a data.frame from the renv.lock file | ||
| df <- lockFileToDataFrame( | ||
| lf = lockFile | ||
| ) | ||
|
|
||
| # Check that the mandatory dependencies are met | ||
| message("Checking mandatory packages...", appendLF = F) | ||
| if (length(mandatoryPackages()) != nrow(df[df$Name %in% mandatoryPackages(),])) { | ||
| missingPkgs <- setdiff(mandatoryPackages(), df[df$Name %in% mandatoryPackages(),]$Name) | ||
| message("FAILED!") | ||
| message(" -- Missing the mandatory packages: ", paste(missingPkgs, collapse = ", ")) | ||
| message(" Please record these missing dependencies in your renv.lock file.") | ||
| } else { | ||
| message("PASSED!") | ||
| } | ||
|
|
||
| # 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(),]$Name) | ||
| message("WARNING!") | ||
| message(" -- Missing the suggested packages: ", paste(missingPkgs, collapse = ", ")) | ||
| message(" This is an optional set of dependencies so you may decide if you wish to have them in your renv.lock file.") | ||
| } else { | ||
| message("PASSED!") | ||
| } | ||
|
|
||
| # Check that we're using declared versions of all packages | ||
| message("Checking all package using tagged versions in RemoteRef...", appendLF = F) | ||
| # Start by filtering out the CRAN Repository entries | ||
| dfFiltered <- df[tolower(df$Source) != "repository",] | ||
| 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),] | ||
| for (i in 1:nrow(problemPkgs)) { | ||
| message(paste0(" -- Package: ", problemPkgs$Name[[i]], "; RemoteRef: ", problemPkgs$RemoteRef[[i]])) | ||
| } | ||
| message(" Please ensure you are only including tagged versions of package dependencies in your renv.lock file.") | ||
| } else { | ||
| message("PASSED!") | ||
| } | ||
| } | ||
|
|
||
| mandatoryPackages <- function() { | ||
| return(c( | ||
| "CohortGenerator", | ||
| "DatabaseConnector", | ||
| "keyring", | ||
| "ParallelLogger", | ||
| "renv", | ||
| "SqlRender" | ||
| )) | ||
| } | ||
|
|
||
| suggestedPacakges <- function() { | ||
| return(c("RSQLite")) | ||
| } | ||
|
|
||
|
|
||
| # internal function to read lock file into data frame | ||
| lockFileToDataFrame <- function(lf) { | ||
| df <- data.frame() | ||
| for (i in 1:length(lf$Packages)) { | ||
| df <- rbind( | ||
| df, | ||
| data.frame( | ||
| Name = lf$Packages[[i]]$Package, | ||
| Version = lf$Packages[[i]]$Version, | ||
| Source = lf$Packages[[i]]$Source, | ||
| RemoteRef = ifelse(is.null(lf$Packages[[i]]$RemoteRef), yes = NA, no = lf$Packages[[i]]$RemoteRef) | ||
| ) | ||
| ) | ||
| } | ||
| return(df) | ||
| } | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,4 @@ | ||
| SettingsFunctions.R | ||
|
|
||
| extras/ | ||
| /tests/ |
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