Run all of the checks in the eesyscreener package against your data file and associated metadata file. It takes in the paths to the CSV files then reads and parses the files and runs the checks in multiple stages, the function will return early if any check in a stage fails.
Usage
screen_csv(
datapath,
metapath,
datafilename = NULL,
metafilename = NULL,
verbose = FALSE,
stop_on_error = FALSE
)Arguments
- datapath
Path to the data CSV file
- metapath
Path to the meta CSV file
- datafilename
Optional - the name of the data file, if not given it will be assumed from the path
- metafilename
Optional - the name of the metadata file, if not given it will be assumed from the path
- verbose
Logical, if TRUE prints feedback messages to console for every test, if FALSE run silently
- stop_on_error
Logical, if TRUE will stop with an error if the result is "FAIL", and will throw genuine warning if result is "WARNING"
Value
A list containing
A table with the full results of the checks with four columns:
result of the check (PASS / FAIL / ADVISORY)
message giving feedback about the check
group that the check belongs to
name of the check
Overall stage the checks reached
Boolean indicating if the data passed the screening
Boolean indicating if the data is suitable for the API
Examples
# Create temp files for the example
data_path <- file.path(tempdir(), "example.csv")
meta_path <- file.path(tempdir(), "example.meta.csv")
write.csv(example_data, data_path, row.names = FALSE)
write.csv(example_meta, meta_path, row.names = FALSE)
screen_csv(data_path, meta_path)
#> $results_table
#> check result
#> 1 check_filename_data_spaces PASS
#> 2 check_filename_metadata_spaces PASS
#> 3 check_filename_data_special PASS
#> 4 check_filename_metadata_special PASS
#> 5 check_filenames_match PASS
#> 6 col_req_meta PASS
#> 7 col_invalid_meta PASS
#> 8 col_req_data PASS
#> 9 col_to_rows PASS
#> 10 meta_col_type PASS
#> 11 meta_ob_unit PASS
#> 12 meta_col_name PASS
#> 13 meta_col_name PASS
#> 14 time_id_valid PASS
#> 15 check_api_char_limit_column-name PASS
#> message
#> 1 'example.csv' does not have spaces in the filename.
#> 2 'example.meta.csv' does not have spaces in the filename.
#> 3 'example.csv' does not contain any special characters.
#> 4 'example.meta.csv' does not contain any special characters.
#> 5 The names of the files follow the recommended naming convention.
#> 6 All of the required columns are present in the metadata file.
#> 7 There are no invalid columns in the metadata file.
#> 8 All of the required columns are present in the data file.
#> 9 There are an equal number of rows in the metadata file (3) and non-mandatory columns in the data file (3).
#> 10 col_type is always 'Filter' or 'Indicator'.
#> 11 No observational units have been included in the metadata file.
#> 12 The col_name column is completed for every row in the metadata.
#> 13 The indicator_dp column is completed for all indicators.
#> 14 The time_identifier values are all valid.
#> 15 All filter / indicator names are less than or equal to the character limit of 50.
#> guidance_url stage
#> 1 NA filename
#> 2 NA filename
#> 3 NA filename
#> 4 NA filename
#> 5 NA filename
#> 6 NA Precheck columns
#> 7 NA Precheck columns
#> 8 NA Precheck columns
#> 9 NA Precheck columns
#> 10 NA Precheck meta
#> 11 NA Precheck meta
#> 12 NA Precheck meta
#> 13 NA Check meta
#> 14 NA Precheck time
#> 15 NA Check API
#>
#> $overall_stage
#> [1] "Passed"
#>
#> $passed
#> [1] TRUE
#>
#> $api_suitable
#> [1] TRUE
#>
screen_csv(
data_path,
meta_path,
"data.csv",
"data.meta.csv",
verbose = TRUE
)
#> ✔ 'data.csv' does not have spaces in the filename.
#> ✔ 'data.meta.csv' does not have spaces in the filename.
#> ✔ 'data.csv' does not contain any special characters.
#> ✔ 'data.meta.csv' does not contain any special characters.
#> ✔ The names of the files follow the recommended naming convention.
#> ✔ Filenames passed all checks
#> ✔ All of the required columns are present in the metadata file.
#> ✔ There are no invalid columns in the metadata file.
#> ✔ All of the required columns are present in the data file.
#> ✔ There are an equal number of rows in the metadata file (3) and non-mandatory columns in the data file (3).
#> ✔ col_type is always 'Filter' or 'Indicator'.
#> ✔ No observational units have been included in the metadata file.
#> ✔ The col_name column is completed for every row in the metadata.
#> ✔ The indicator_dp column is completed for all indicators.
#> ✔ The time_identifier values are all valid.
#> ✔ All filter / indicator names are less than or equal to the character limit of 50.
#> ✔ Data and metadata passed all checks
#> ✔ Data and metadata passed all checks
#> $results_table
#> check result
#> 1 check_filename_data_spaces PASS
#> 2 check_filename_metadata_spaces PASS
#> 3 check_filename_data_special PASS
#> 4 check_filename_metadata_special PASS
#> 5 check_filenames_match PASS
#> 6 col_req_meta PASS
#> 7 col_invalid_meta PASS
#> 8 col_req_data PASS
#> 9 col_to_rows PASS
#> 10 meta_col_type PASS
#> 11 meta_ob_unit PASS
#> 12 meta_col_name PASS
#> 13 meta_col_name PASS
#> 14 time_id_valid PASS
#> 15 check_api_char_limit_column-name PASS
#> message
#> 1 'data.csv' does not have spaces in the filename.
#> 2 'data.meta.csv' does not have spaces in the filename.
#> 3 'data.csv' does not contain any special characters.
#> 4 'data.meta.csv' does not contain any special characters.
#> 5 The names of the files follow the recommended naming convention.
#> 6 All of the required columns are present in the metadata file.
#> 7 There are no invalid columns in the metadata file.
#> 8 All of the required columns are present in the data file.
#> 9 There are an equal number of rows in the metadata file (3) and non-mandatory columns in the data file (3).
#> 10 col_type is always 'Filter' or 'Indicator'.
#> 11 No observational units have been included in the metadata file.
#> 12 The col_name column is completed for every row in the metadata.
#> 13 The indicator_dp column is completed for all indicators.
#> 14 The time_identifier values are all valid.
#> 15 All filter / indicator names are less than or equal to the character limit of 50.
#> guidance_url stage
#> 1 NA filename
#> 2 NA filename
#> 3 NA filename
#> 4 NA filename
#> 5 NA filename
#> 6 NA Precheck columns
#> 7 NA Precheck columns
#> 8 NA Precheck columns
#> 9 NA Precheck columns
#> 10 NA Precheck meta
#> 11 NA Precheck meta
#> 12 NA Precheck meta
#> 13 NA Check meta
#> 14 NA Precheck time
#> 15 NA Check API
#>
#> $overall_stage
#> [1] "Passed"
#>
#> $passed
#> [1] TRUE
#>
#> $api_suitable
#> [1] TRUE
#>
# Clean up temp files
invisible(file.remove(data_path))
invisible(file.remove(meta_path))