diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 451b88d..81d9b5a 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -3,5 +3,5 @@ pkgdown: 2.0.7 pkgdown_sha: ~ articles: DPchecker: DPchecker.html -last_built: 2024-01-16T17:59Z +last_built: 2024-01-26T16:31Z diff --git a/docs/reference/run_congruence_checks.html b/docs/reference/run_congruence_checks.html index 43fcca9..4c20c6f 100644 --- a/docs/reference/run_congruence_checks.html +++ b/docs/reference/run_congruence_checks.html @@ -165,75 +165,7 @@

Examples#> #> ✔ All data files are listed in metadata and all metadata files names refer to #> data files. -#> Called from: eval(expr, p) -#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#524: data_tbl <- EML::eml_get(metadata, "dataTable") -#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#526: if ("attributeList" %in% names(data_tbl)) { -#> data_tbl <- list(data_tbl) -#> } -#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#531: metadata_attrs <- lapply(data_tbl, function(tbl) { -#> arcticdatautils::eml_get_simple(tbl, "attributeName") -#> }) -#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#532: metadata_attrs$`@context` <- NULL -#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#535: data_files <- list.files(path = directory, pattern = ".csv") -#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#538: table_names <- NULL -#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#539: for (i in 1:length(seq_along(data_files))) { -#> tbl_nam <- data_tbl[[i]][["physical"]][["objectName"]] -#> table_names <- append(table_names, tbl_nam) -#> } -#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#540: tbl_nam <- data_tbl[[i]][["physical"]][["objectName"]] -#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#541: table_names <- append(table_names, tbl_nam) -#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#540: tbl_nam <- data_tbl[[i]][["physical"]][["objectName"]] -#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#541: table_names <- append(table_names, tbl_nam) -#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#540: tbl_nam <- data_tbl[[i]][["physical"]][["objectName"]] -#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#541: table_names <- append(table_names, tbl_nam) -#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#544: names(metadata_attrs) <- table_names -#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#547: data_colnames <- sapply(data_files, function(data_file) { -#> names(readr::read_csv(file.path(directory, data_file), n_max = 1, -#> show_col_types = FALSE)) -#> }, USE.NAMES = TRUE, simplify = FALSE) -#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#550: if (!(all(names(data_colnames) %in% names(metadata_attrs)) & -#> all(names(metadata_attrs) %in% names(data_colnames)))) { -#> cli::cli_abort(c(x = "Mismatch in data file column names and the attributes listed in metadata.")) -#> } -#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#555: mismatches <- sapply(data_files, function(data_file) { -#> meta_cols <- metadata_attrs[[data_file]] -#> data_cols <- data_colnames[[data_file]] -#> if (length(meta_cols) == length(data_cols) && all(meta_cols == -#> data_cols)) { -#> return(NULL) -#> } -#> else if (all(meta_cols %in% data_cols) && all(data_cols %in% -#> meta_cols)) { -#> return(c(` ` = paste0("--> {.file ", data_file, "}: Metadata column order does not match data column order"))) -#> } -#> else { -#> missing_from_meta <- data_cols[!(data_cols %in% meta_cols)] -#> if (length(missing_from_meta) > 0) { -#> missing_from_meta <- paste0("----Missing from metadata: ", -#> paste0("{.field ", missing_from_meta, "}", collapse = ", ")) -#> names(missing_from_meta) <- " " -#> } -#> missing_from_data <- meta_cols[!(meta_cols %in% data_cols)] -#> if (length(missing_from_data) > 0) { -#> missing_from_data <- paste0("----Missing from data file: ", -#> paste0("{.field ", missing_from_data, "}", collapse = ", ")) -#> names(missing_from_data) <- " " -#> } -#> msg <- c(` ` = paste0("--> {.file ", data_file, "}:"), -#> missing_from_meta, missing_from_data) -#> return(msg) -#> } -#> }, USE.NAMES = FALSE, simplify = FALSE) -#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#579: mismatches <- purrr::discard(mismatches, is.null) %>% unlist() -#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#583: if (!is.null(mismatches)) { -#> cli::cli_abort(c(x = "Column mismatch between data and metadata.", -#> mismatches)) -#> } else { -#> cli::cli_inform(c(v = "All columns in data match all columns in metadata.")) -#> } -#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#586: cli::cli_inform(c(v = "All columns in data match all columns in metadata.")) #> ✔ All columns in data match all columns in metadata. -#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#589: return(invisible(metadata)) #> subscript out of bounds #> ✔ Columns indicated as numeric in metadata contain only numeric values and #> valid missing value codes. diff --git a/docs/reference/test_fields_match.html b/docs/reference/test_fields_match.html index 87d4526..a2a1717 100644 --- a/docs/reference/test_fields_match.html +++ b/docs/reference/test_fields_match.html @@ -80,75 +80,7 @@

Examples
dir <- DPchecker_example("BICY_veg")
 #> Data are provided for example use only. Do not assume that they are complete, accurate, or up to date.
 test_fields_match(dir)
-#> Called from: eval(expr, p)
-#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#524: data_tbl <- EML::eml_get(metadata, "dataTable")
-#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#526: if ("attributeList" %in% names(data_tbl)) {
-#>     data_tbl <- list(data_tbl)
-#> }
-#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#531: metadata_attrs <- lapply(data_tbl, function(tbl) {
-#>     arcticdatautils::eml_get_simple(tbl, "attributeName")
-#> })
-#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#532: metadata_attrs$`@context` <- NULL
-#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#535: data_files <- list.files(path = directory, pattern = ".csv")
-#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#538: table_names <- NULL
-#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#539: for (i in 1:length(seq_along(data_files))) {
-#>     tbl_nam <- data_tbl[[i]][["physical"]][["objectName"]]
-#>     table_names <- append(table_names, tbl_nam)
-#> }
-#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#540: tbl_nam <- data_tbl[[i]][["physical"]][["objectName"]]
-#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#541: table_names <- append(table_names, tbl_nam)
-#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#540: tbl_nam <- data_tbl[[i]][["physical"]][["objectName"]]
-#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#541: table_names <- append(table_names, tbl_nam)
-#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#540: tbl_nam <- data_tbl[[i]][["physical"]][["objectName"]]
-#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#541: table_names <- append(table_names, tbl_nam)
-#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#544: names(metadata_attrs) <- table_names
-#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#547: data_colnames <- sapply(data_files, function(data_file) {
-#>     names(readr::read_csv(file.path(directory, data_file), n_max = 1, 
-#>         show_col_types = FALSE))
-#> }, USE.NAMES = TRUE, simplify = FALSE)
-#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#550: if (!(all(names(data_colnames) %in% names(metadata_attrs)) & 
-#>     all(names(metadata_attrs) %in% names(data_colnames)))) {
-#>     cli::cli_abort(c(x = "Mismatch in data file column names and the attributes listed in metadata."))
-#> }
-#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#555: mismatches <- sapply(data_files, function(data_file) {
-#>     meta_cols <- metadata_attrs[[data_file]]
-#>     data_cols <- data_colnames[[data_file]]
-#>     if (length(meta_cols) == length(data_cols) && all(meta_cols == 
-#>         data_cols)) {
-#>         return(NULL)
-#>     }
-#>     else if (all(meta_cols %in% data_cols) && all(data_cols %in% 
-#>         meta_cols)) {
-#>         return(c(` ` = paste0("--> {.file ", data_file, "}: Metadata column order does not match data column order")))
-#>     }
-#>     else {
-#>         missing_from_meta <- data_cols[!(data_cols %in% meta_cols)]
-#>         if (length(missing_from_meta) > 0) {
-#>             missing_from_meta <- paste0("----Missing from metadata: ", 
-#>                 paste0("{.field ", missing_from_meta, "}", collapse = ", "))
-#>             names(missing_from_meta) <- " "
-#>         }
-#>         missing_from_data <- meta_cols[!(meta_cols %in% data_cols)]
-#>         if (length(missing_from_data) > 0) {
-#>             missing_from_data <- paste0("----Missing from data file: ", 
-#>                 paste0("{.field ", missing_from_data, "}", collapse = ", "))
-#>             names(missing_from_data) <- " "
-#>         }
-#>         msg <- c(` ` = paste0("--> {.file ", data_file, "}:"), 
-#>             missing_from_meta, missing_from_data)
-#>         return(msg)
-#>     }
-#> }, USE.NAMES = FALSE, simplify = FALSE)
-#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#579: mismatches <- purrr::discard(mismatches, is.null) %>% unlist()
-#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#583: if (!is.null(mismatches)) {
-#>     cli::cli_abort(c(x = "Column mismatch between data and metadata.", 
-#>         mismatches))
-#> } else {
-#>     cli::cli_inform(c(v = "All columns in data match all columns in metadata."))
-#> }
-#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#586: cli::cli_inform(c(v = "All columns in data match all columns in metadata."))
 #> ✔ All columns in data match all columns in metadata.
-#> debug at C:/Users/rlbaker/Documents/RDev/DPchecker_devspace/R/tabular_data_congruence.R#589: return(invisible(metadata))