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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,49 @@ | ||
| checkMilestoneFolders = function(metadatadir, partNumber) { | ||
| if (partNumber == 1) return() | ||
| # This function checks whether expected output folder(s) exists | ||
| # If not, it creates them | ||
| # Further it check whether folders with expected content are empty. | ||
| # If yesm it gives error. | ||
| paths = c(paste0(metadatadir, "/meta/basic"), | ||
| paste0(metadatadir, "/meta/ms2.out"), | ||
| paste0(metadatadir, "/meta/ms3.out"), | ||
| paste0(metadatadir, "/meta/ms4.out"), | ||
| paste0(metadatadir, "/meta/ms5.out")) | ||
| sleepqc = paste0(metadatadir, "/meta/sleep.qc") | ||
|
|
||
| # Make sure folders exists | ||
| for (i in 1:partNumber) { | ||
| if (!dir.exists(paths[i])) { | ||
| dir.create(file.path(paths[i]), recursive = TRUE) | ||
| } | ||
| } | ||
| if (partNumber >= 3) { | ||
| if (!dir.exists(sleepqc)) { | ||
| dir.create(file.path(sleepqc), recursive = TRUE) | ||
| } | ||
| } | ||
|
|
||
| # Make sure preceding parts have files | ||
| if (partNumber == 2) { | ||
| expectedParts = 1 | ||
| } else if (partNumber == 3) { | ||
| expectedParts = 2 | ||
| } else if (partNumber == 4) { | ||
| expectedParts = 3 | ||
| } else if (partNumber == 5) { | ||
| expectedParts = c(2, 3, 4) | ||
| } | ||
|
|
||
| # Give error when no data was found in the expected parts | ||
| warnAbout = NULL | ||
| for (i in expectedParts) { | ||
| N = length(dir(paths[i])) | ||
| if (N == 0) { | ||
| warnAbout = c(warnAbout, i) | ||
| } | ||
| } | ||
| if (length(warnAbout) > 0) { | ||
| stop(paste0("\nNo milestone data found for part(s) ", paste0(warnAbout, collapse = " and "), | ||
| ". Run this/these first before running part ", partNumber, "."), call. = FALSE) | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,28 @@ | ||
| \name{checkMilestoneFolders} | ||
| \alias{checkMilestoneFolders} | ||
| \title{ | ||
| Checks for existence of folders to process | ||
| } | ||
| \description{ | ||
| Checks whether milestone folders exist, create them if needed, | ||
| and check whether folders are not empty. Only done for part 1 to 5 | ||
| and not part 6, which is different and handled inside \link{g.part6}. | ||
| } | ||
| \usage{ | ||
| checkMilestoneFolders(metadatadir, partNumber) | ||
| } | ||
| \arguments{ | ||
| \item{metadatadir}{ | ||
| Character, path to root of outputfolder. | ||
| } | ||
| \item{partNumber}{ | ||
| Numeric, number from the set 2, 3, 4 or 5. | ||
| } | ||
| } | ||
| \value{ | ||
| No value is produced | ||
| } | ||
| \keyword{internal} | ||
| \author{ | ||
| Vincent T van Hees <v.vanhees@accelting.com> | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,9 @@ | ||
| library(GGIR) | ||
| context("checkMilestoneFolders") | ||
| test_that("checkMilestoneFolders creates expected folders and gives expected warnings", { | ||
| test_folder = "test_milestone_folders" | ||
| dir.create(test_folder) | ||
| expect_error(checkMilestoneFolders(test_folder, partNumber = 5)) | ||
| expect_true(dir.exists(paste0(test_folder, "/meta/ms5.out"))) | ||
| if (dir.exists(test_folder)) unlink(test_folder, recursive = TRUE) | ||
| }) |