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Replace find_gridfile() with more generic find_varfile() function
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,7 +1,7 @@ | ||
| Package: lpjmlkit | ||
| Type: Package | ||
| Title: Toolkit for Basic LPJmL Handling | ||
| Version: 1.5.0 | ||
| Version: 1.6.0 | ||
| Authors@R: c( | ||
| person("Jannes", "Breier", , "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9055-6904")), | ||
| person("Sebastian","Ostberg", , "[email protected]", role = "aut", comment = c(ORCID = "0000-0002-2368-7015")), | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,82 @@ | ||
| #' Search for a variable file in a directory | ||
| #' | ||
| #' Function to search for a file containing a specific variable in a specific | ||
| #' directory. | ||
| #' | ||
| #' @param searchdir Directory where to look for the variable file. | ||
| #' @param variable Single character string containing the variable to search for | ||
| #' @param strict Boolean. If set to `TRUE`, file must be named "variable.**", | ||
| #' where "**" is one or two file extensions with 3 or 4 characters, e.g. | ||
| #' "grid.bin.json" if `variable = "grid"`. If set to `FALSE`, the function | ||
| #' will first try to match the strict pattern. If unsuccessful, any filename | ||
| #' that starts with "variable" will be matched. | ||
| #' @return Character string with the file name of a matched file, including the | ||
| #' full path. | ||
| #' | ||
| #' @details This function looks for file names in `searchdir` that match the | ||
| #' `pattern` parameter in its [`list.files()`] call. Files of type "meta" are | ||
| #' preferred. Files of type "clm" are also accepted. The function returns an | ||
| #' error if no suitable file or multiple files are found. | ||
| #' @export | ||
| find_varfile <- function(searchdir, variable = "grid", strict = FALSE) { | ||
| if (length(variable) != 1 || !is.character(variable)) { | ||
| stop(col_var("variable"), " must be a single character string") | ||
| } | ||
| # This will only match file names "variable.*", where * is one or two file | ||
| # extensions with 3 or 4 characters, e.g. "grid.bin" or "grid.bin.json". | ||
| var_files <- list.files( | ||
| path = searchdir, | ||
| pattern = paste0("^", variable, "(\\.[[:alpha:]]{3,4})+$"), | ||
| full.names = TRUE | ||
| ) | ||
| if (length(var_files) > 0) { | ||
| var_types <- sapply(var_files, detect_io_type) # nolint:undesirable_function_linter. | ||
| # Prefer "meta" file_type if present | ||
| if (length(which(var_types == "meta")) == 1) { | ||
| filename <- var_files[match("meta", var_types)] | ||
| } else if (length(which(var_types == "clm")) == 1) { | ||
| # Second priority "clm" file_type | ||
| filename <- var_files[match("clm", var_types)] | ||
| } else if (strict) { | ||
| # Stop if either multiple files per file type or not the right type have | ||
| # been detected | ||
| stop( | ||
| "Cannot detect ", col_var(variable), " file automatically." | ||
| ) | ||
| } | ||
| } else if (strict) { | ||
| # Stop if no file name matching pattern detected | ||
| stop( | ||
| "Cannot detect ", col_var(variable), " file automatically." | ||
| ) | ||
| } else { | ||
| # Less strict pattern matching any file name that starts with "grid*". | ||
| var_files <- list.files( | ||
| path = searchdir, | ||
| pattern = paste0("^", variable), | ||
| full.names = TRUE | ||
| ) | ||
| if (length(var_files) > 0) { | ||
| var_types <- sapply(var_files, detect_io_type) # nolint:undesirable_function_linter. | ||
| # Prefer "meta" file_type if present | ||
| if (length(which(var_types == "meta")) == 1) { | ||
| filename <- var_files[match("meta", var_types)] | ||
| } else if (length(which(var_types == "clm")) == 1) { | ||
| # Second priority "clm" file_type | ||
| filename <- var_files[match("clm", var_types)] | ||
| } else { | ||
| # Stop if either multiple files per file type or not the right type have | ||
| # been detected | ||
| stop( | ||
| "Cannot detect ", col_var(variable), " file automatically." | ||
| ) | ||
| } | ||
| } else { | ||
| # Stop if no file name matching pattern detected | ||
| stop( | ||
| "Cannot detect ", col_var(variable), " file automatically." | ||
| ) | ||
| } | ||
| } | ||
| filename | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,16 @@ | ||
| test_that("test find_varfile", { | ||
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| # grid file in directory matching search pattern | ||
| expect_match( | ||
| find_varfile("../testdata/output", "grid"), | ||
| "testdata/output/grid.bin.json" | ||
| ) | ||
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| # Error due to missing grid file | ||
| expect_error( | ||
| find_varfile(".", "grid"), | ||
| "Cannot detect grid file automatically" | ||
| ) | ||
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| }) | ||
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