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Merge pull request #394 from PredictiveEcology/inputPaths
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try to get `inputPaths` back to full functionality
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@eliotmcintire
eliotmcintire authored Jun 10, 2024
2 parents 65913d3 + 7974146 commit 96460a0
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ URL:
https://reproducible.predictiveecology.org,
https://github.com/PredictiveEcology/reproducible
Date: 2024-06-06
Version: 2.1.1
Version: 2.1.1.9000
Authors@R:
c(person(given = "Eliot J B",
family = "McIntire",
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220 changes: 156 additions & 64 deletions R/preProcess.R
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Original file line number Diff line number Diff line change
Expand Up @@ -385,69 +385,79 @@ preProcess <- function(targetFile = NULL, url = NULL, archive = NULL, alsoExtrac
# Change the destinationPath to the reproducible.inputPaths temporarily, so
# download happens there. Later it will be linked to the user destinationPath
if (!is.null(reproducible.inputPaths)) {
# may already have been changed above
outCheck <- if (!is.null(targetFilePath)) {
!file.exists(targetFilePath)
} else {
TRUE
} ## if NULL, it doesn't exist and we want to proceed
if (isTRUE(outCheck)) { # skip if it already existed locally
if (is.null(destinationPathUser)) {
destinationPathUser <- destinationPath
}
on.exit(
{
destinationPath <- destinationPathUser
},
add = TRUE
)

if (!identical(destinationPath, reproducible.inputPaths)) {
# CHANGE destinationPath FOR REMAINDER OF THIS FUNCTION
neededFilesNew <- makeRelative(neededFiles, destinationPath)
targetFilePathNew <- makeRelative(targetFilePath, destinationPath)
destinationPathNew <- reproducible.inputPaths[1]
archiveExistInDestDir <- if (!isNULLorNA(archive)) {
file.exists(archive)
} else {
FALSE
}
existInDestDir <- if (!isNULLorNA(neededFiles)) {
file.exists(neededFiles)
} else {
FALSE
}
if (any(existInDestDir)) {
from <- neededFiles[existInDestDir]
to <- makeAbsolute(neededFilesNew[existInDestDir],
absoluteBase = destinationPathNew
)
linkOrCopyUpdateOnly(from, to, verbose = verbose)
}
if (any(archiveExistInDestDir)) {
from <- archive[archiveExistInDestDir]
to <- makeAbsolute(makeRelative(archive[archiveExistInDestDir], destinationPath),
absoluteBase = destinationPathNew
)
linkOrCopyUpdateOnly(from, to, verbose = verbose - 1)
}
targetPath <- targetFilePathNew
destinationPath <- destinationPathNew
neededFiles <- neededFilesNew
}

if (isTRUE(any(grepl(archive, pattern = destinationPathUser)))) {
# might have a "." as destinationPath -- messes with grepl
patt <- if (grepl("^\\.", destinationPathUser)) {
gsub("^\\.", "^\\\\.", destinationPathUser)
} else {
destinationPathUser
}
archive <- gsub(archive, pattern = patt, replacement = destinationPath)
}
targetFilePath <- makeAbsolute(targetFilePath, destinationPath)
neededFiles <- makeAbsolute(neededFiles, destinationPath)
}
outs <- copyFromDPtoReproducibleIPs(targetFilePath, destinationPathUser, destinationPath,
reproducible.inputPaths, neededFiles, archive, checkSums,
checkSumFilePath = checkSumFilePath, verbose)
on.exit(
{
destinationPath <- destinationPathUser
},
add = TRUE
)
list2env(outs, environment()) # "neededFiles" "targetFilePath" "destinationPath" "archive"
# # may already have been changed above
# outCheck <- if (!is.null(targetFilePath)) {
# !file.exists(targetFilePath)
# } else {
# TRUE
# } ## if NULL, it doesn't exist and we want to proceed
# if (isTRUE(outCheck)) { # skip if it already existed locally
# if (is.null(destinationPathUser)) {
# destinationPathUser <- destinationPath
# }
# on.exit(
# {
# destinationPath <- destinationPathUser
# },
# add = TRUE
# )
#
# if (!identical(destinationPath, reproducible.inputPaths)) {
# # CHANGE destinationPath FOR REMAINDER OF THIS FUNCTION
# neededFilesNew <- makeRelative(neededFiles, destinationPath)
# targetFilePathNew <- makeRelative(targetFilePath, destinationPath)
# destinationPathNew <- reproducible.inputPaths[1]
# archiveExistInDestDir <- if (!isNULLorNA(archive)) {
# file.exists(archive)
# } else {
# FALSE
# }
# existInDestDir <- if (!isNULLorNA(neededFiles)) {
# file.exists(neededFiles)
# } else {
# FALSE
# }
# if (any(existInDestDir)) {
# from <- neededFiles[existInDestDir]
# to <- makeAbsolute(neededFilesNew[existInDestDir],
# absoluteBase = destinationPathNew
# )
# linkOrCopyUpdateOnly(from, to, verbose = verbose)
# }
# if (any(archiveExistInDestDir)) {
# from <- archive[archiveExistInDestDir]
# to <- makeAbsolute(makeRelative(archive[archiveExistInDestDir], destinationPath),
# absoluteBase = destinationPathNew
# )
# linkOrCopyUpdateOnly(from, to, verbose = verbose)
# }
# targetPath <- targetFilePathNew
# destinationPath <- destinationPathNew
# neededFiles <- neededFilesNew
# }
#
# if (isTRUE(any(grepl(archive, pattern = destinationPathUser)))) {
# # might have a "." as destinationPath -- messes with grepl
# patt <- if (grepl("^\\.", destinationPathUser)) {
# gsub("^\\.", "^\\\\.", destinationPathUser)
# } else {
# destinationPathUser
# }
# archive <- gsub(archive, pattern = patt, replacement = destinationPath)
# }
# targetFilePath <- makeAbsolute(targetFilePath, destinationPath)
# neededFiles <- makeAbsolute(neededFiles, destinationPath)
# }
}

###############################################################
Expand Down Expand Up @@ -581,7 +591,7 @@ preProcess <- function(targetFile = NULL, url = NULL, archive = NULL, alsoExtrac
messagePreProcess("...using file(s) in getOption('reproducible.inputPaths')...",
verbose = verbose)
}
outHLC <- hardLinkOrCopy(from, to, verbose = verbose - 1)
outHLC <- hardLinkOrCopy(from, to, verbose = verbose)
filesExtr[foundInInputPaths] <- to
}
}
Expand Down Expand Up @@ -1868,3 +1878,85 @@ linkOrCopyUpdateOnly <- function(from, to, verbose) {

messageChecksummingAllFiles <- "Checksumming all files in archive"



# may already have been changed above
copyFromDPtoReproducibleIPs <- function(targetFilePath, destinationPathUser, destinationPath,
reproducible.inputPaths, neededFiles, archive, checkSums,
checkSumFilePath, verbose) {
outCheck <- if (!is.null(targetFilePath)) {
!file.exists(targetFilePath)
} else {
TRUE
} ## if NULL, it doesn't exist and we want to proceed
if (isTRUE(outCheck)) { # skip if it already existed locally
if (is.null(destinationPathUser)) {
destinationPathUser <- destinationPath
}
on.exit(
{
destinationPath <- destinationPathUser
},
add = TRUE
)

if (!identical(destinationPath, reproducible.inputPaths)) {
# CHANGE destinationPath FOR REMAINDER OF THIS FUNCTION
neededFilesNew <- makeRelative(neededFiles, destinationPath)
targetFilePathNew <- makeRelative(targetFilePath, destinationPath)
destinationPathNew <- reproducible.inputPaths[1]
archiveExistInDestDir <- if (!isNULLorNA(archive)) {
file.exists(archive)
} else {
FALSE
}
existInDestDir <- if (!isNULLorNA(neededFiles)) {
file.exists(neededFiles)
} else {
FALSE
}
filesToAppendToChecksums <- character()
if (any(existInDestDir)) {
from <- neededFiles[existInDestDir]
to <- makeAbsolute(neededFilesNew[existInDestDir],
absoluteBase = destinationPathNew
)
linkOrCopyUpdateOnly(from, to, verbose = verbose)
filesToAppendToChecksums <- c(filesToAppendToChecksums, to)
}
if (any(archiveExistInDestDir)) {
from <- archive[archiveExistInDestDir]
to <- makeAbsolute(makeRelative(archive[archiveExistInDestDir], destinationPath),
absoluteBase = destinationPathNew
)
linkOrCopyUpdateOnly(from, to, verbose = verbose)
filesToAppendToChecksums <- c(filesToAppendToChecksums, to)
}
if (any(nzchar(filesToAppendToChecksums) %in% TRUE)) {
appendChecksumsTableWithCS(append = TRUE,
checkSumFilePath = file.path(destinationPathNew, basename(checkSumFilePath)),
destinationPathNew,
filesToChecksum = filesToAppendToChecksums, currentFiles = checkSums,
verbose)

}
targetPath <- targetFilePathNew
destinationPath <- destinationPathNew
neededFiles <- neededFilesNew
}

if (isTRUE(any(grepl(archive, pattern = destinationPathUser)))) {
# might have a "." as destinationPath -- messes with grepl
patt <- if (grepl("^\\.", destinationPathUser)) {
gsub("^\\.", "^\\\\.", destinationPathUser)
} else {
destinationPathUser
}
archive <- gsub(archive, pattern = patt, replacement = destinationPath)
}
targetFilePath <- makeAbsolute(targetFilePath, destinationPath)
neededFiles <- makeAbsolute(neededFiles, destinationPath)
}
list(neededFiles = neededFiles, targetFilePath = targetFilePath, destinationPath = destinationPath,
archive = archive)
}
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