-
Notifications
You must be signed in to change notification settings - Fork 2
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Bumped version number, merged in master #139
- Loading branch information
Showing
7 changed files
with
180 additions
and
41 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,105 @@ | ||
| # Check missingness | ||
|
|
||
| check_arg_missingness <- function(database, col, col_value){ | ||
| if(rlang::is_missing(database) | rlang::is_missing(col) | rlang::is_missing(col_value)) | ||
| cli::cli_abort(c( | ||
| "x" = "`database`, `col` or `col_value` must be supplied!" | ||
| ) | ||
| ) | ||
| } | ||
|
|
||
| # Check if table name exists | ||
| # Note that users can supply the $traits table to database, for that reason table can be NA | ||
| # First check if table is NA | ||
|
|
||
| check_table_name_exists <- function(database, table){ | ||
| if(!is.na(table) & !tibble::is_tibble(database)){ # database is NOT $traits and `table` is supplied | ||
| if(! names(database) %in% table |> any()){ # Does any names of the tables in database contain `table` | ||
| cli::cli_abort( | ||
| c( | ||
| "x" = "`{table}` is not a valid table name", | ||
| "i" = "Check `names(database)` and try again!" | ||
| ) | ||
| ) | ||
| } | ||
| } | ||
| } | ||
|
|
||
| # Check if col exists in specified table when database is traits.build object | ||
| check_col_exists_in_table <- function(database, table, col){ | ||
| # If traits table supplied and no table is specified | ||
| if(tibble::is_tibble(database)){ | ||
| if(! names(database) %in% col |> any()){ # Does any names in table contain `col` | ||
| cli::cli_abort(c( | ||
| "x" = "`{col}` is not a valid column name in the `traits` table", | ||
| "i" = "Check `names(database$traits)` and try again!" | ||
| ) | ||
| ) | ||
| } | ||
| } else( | ||
| if(! names(database[[table]]) %in% col |> any()){ # Does any names in table contain `col` | ||
| cli::cli_abort(c( | ||
| "x" = "`{col}` is not a valid column name in the `{table}` table", | ||
| "i" = "Check `names(database${table})` and try again!" | ||
| ) | ||
| ) | ||
| } | ||
| ) | ||
| } | ||
|
|
||
| # Check if col_value exists in the col after attempted extraction | ||
| # Accommodating for multiple values supplied AND partial matching | ||
|
|
||
| check_col_value_exists <- function(ret, table, col, col_value){ | ||
| if(tibble::is_tibble(ret)){ | ||
| if(nrow(ret) == 0) | ||
| cli::cli_abort(c( | ||
| "x" = "`{col_value}` is not a valid value in `{col}` column of the `traits` table", | ||
| "i" = "Check spelling of `{col_value}` and try again!" | ||
| ) | ||
| ) | ||
| } else( | ||
|
|
||
| if(nrow(ret$traits) == 0) | ||
| cli::cli_abort(c( | ||
| "x" = "`{col_value}` is not a valid value in `{col}` column of the `{table}` table", | ||
| "i" = "Check spelling of `{col_value}` and try again!" | ||
| ) | ||
| ) | ||
| ) | ||
| } | ||
|
|
||
| # | ||
| # # Get possible col values | ||
| # available_values <- database[[table]][col] |> dplyr::pull() |> unique() | ||
| # | ||
| # # Check if there are non-matches | ||
| # if(length(col_value) > 1) | ||
| # concat_col_value <- paste(col_value, collapse = "|") | ||
| # | ||
| # partial_matches <- stringr::str_detect(available_values, concat_col_value) | ||
| # | ||
| # if(length(partial_matches) > 1) | ||
| # | ||
| # # Prompt user which one is non-match | ||
| # if(length(no_match) >= 1){ | ||
| # cli::cli_warn(c("x" = "`{no_match}` is not a valid value in `{col}` of the `{table}` table")) | ||
| # } | ||
|
|
||
| # # Check if col_value exists in the col | ||
| # # Accommodating for multiple values supplied | ||
| # | ||
| # # Get possible col values | ||
| # available_values <- database[[table]][col] |> dplyr::pull() |> unique() | ||
| # | ||
| # # Check if there are non-matches | ||
| # no_match <- col_value[which(! col_value %in% available_values)] | ||
| # | ||
| # # Identify matches | ||
| # matches <- col_value[which(col_value %in% available_values)] | ||
| # | ||
| # # Prompt user which one is non-match | ||
| # if(length(no_match) > 0){ | ||
| # cli::cli_warn("`{no_match}` is not a valid value in `{col}` of the `{table}` table") | ||
| # cli::cli_alert_success("Continuing data extraction for {.val {matches}}") | ||
| # } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file was deleted.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,28 @@ | ||
|
|
||
|
|
||
| test_database_structure <- function(database, taxa = NA, dataset_id = NA, n_row = NA) { | ||
|
|
||
| table_names <- c("traits", "locations", "contexts", "methods", "excluded_data", "taxonomic_updates", "taxa", "contributors", | ||
| "sources", "definitions", "schema", "metadata", "build_info") | ||
|
|
||
| testthat::expect_type(database, "list") | ||
| testthat::expect_equal(class(database), "traits.build") | ||
|
|
||
| testthat::expect_equal(names(database), table_names) | ||
|
|
||
| testthat::expect_contains(database$traits$taxon_name |> unique(), database$taxa$taxon_name |> unique()) | ||
| testthat::expect_contains(database$traits$dataset_id |> unique(), database$methods$dataset_id |> unique()) | ||
| testthat::expect_contains(paste(database$traits$dataset_id, database$traits$trait_name) |> unique(), paste(database$methods$dataset_id, database$methods$trait_name) |> unique()) | ||
|
|
||
| if(!is.na(taxa)) { | ||
| testthat::expect_contains(database$traits$taxon_name |> unique(), taxa |> unique()) | ||
| } | ||
|
|
||
| if(!is.na(dataset_id)) { | ||
| testthat::expect_contains(database$traits$dataset_id |> unique(), dataset_id |> unique()) | ||
| } | ||
|
|
||
| if(!is.na(n_row)) { | ||
| testthat::expect_equal(database$traits |> nrow(), n_row) | ||
| } | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters