csvclean - csvkit 2.0.1 documentation

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# csvclean

## Description

Reports and fixes common errors in a CSV file.

### Checks

- Reports rows that have a different number of columns than the header row, if the `--length-mismatch` option is set.

- Reports columns that are empty, if the `--empty-columns` option is set.

Tip

Enable all checks with `--enable-all-checks` (`-a`).

### Fixes

- If a CSV has unquoted cells that contain line breaks, like:

      id,address,country
      1,1 Main St
      Springfield,US
      2,123 Acadia Avenue
      London,GB

  Use `--join-short-rows` to attempt to correct the errors by merging short rows into a single row:

      id,address,country
      1,"1 Main St
      Springfield",US
      2,"123 Acadia Avenue
      London",GB

  To change the string used to join the lines, use `--separator`. For example, with `--separator ", "`:

      id,address,country
      1,"1 Main St, Springfield",US
      2,"123 Acadia Avenue, London",GB

- If a CSV has missing delimiters, like:

      id,name,country
      1,Alice
      2,Bob,CA

  You can add the missing delimiters with `--fill-short-rows`:

      id,name,country
      1,Alice,
      2,Bob,CA

  Tip

  csvcut without options also adds missing delimiters!

  To change the value used to fill short rows, use `--fillvalue`. For example, with `--fillvalue "US"`:

      id,name,country
      1,Alice,US
      2,Bob,CA

See also

`--header-normalize-space` under Usage.

Note

Every csvkit tool does the following:

- Removes optional quote characters, unless the –quoting (-u) option is set to change this behavior

- Changes the field delimiter to a comma, if the input delimiter is set with the –delimiter (-d) or –tabs (-t) options

- Changes the record delimiter to a line feed (LF or `\n`)

- Changes the quote character to a double-quotation mark, if the character is set with the –quotechar (-q) option

- Changes the character encoding to UTF-8, if the input encoding is set with the –encoding (-e) option

### Output

`csvclean` attempts to make the selected fixes. Then:

- If the `--omit-error-rows` option is set, only rows that pass the selected checks are written to standard output. If not, all rows are written to standard output.

- If any checks are enabled, error rows along with line numbers and descriptions are written to standard error. If there are error rows, the exit code is 1.

### Usage

    usage: csvclean [-h] [-d DELIMITER] [-t] [-q QUOTECHAR] [-u {0,1,2,3}] [-b]
                    [-p ESCAPECHAR] [-z FIELD_SIZE_LIMIT] [-e ENCODING] [-S] [-H]
                    [-K SKIP_LINES] [-v] [-l] [--zero] [-V]
                    [FILE]

    Fix common errors in a CSV file.

    positional arguments:
      FILE                  The CSV file to operate on. If omitted, will accept
                            input as piped data via STDIN.

    optional arguments:
      -h, --help            show this help message and exit
      --length-mismatch     Report data rows that are shorter or longer than the
                            header row.
      --empty-columns       Report empty columns as errors.
      -a, --enable-all-checks
                            Enable all error reporting.
      --omit-error-rows     Omit data rows that contain errors, from standard
                            output.
      --label LABEL         Add a "label" column to standard error. Useful in
                            automated workflows.
      --header-normalize-space
                            Strip leading and trailing whitespace and replace
                            sequences of whitespace characters by a single space
                            in the header.
      --join-short-rows     Merges short rows into a single row.
      --separator SEPARATOR
                            The string with which to join short rows. Defaults to
                            a newline.
      --fill-short-rows     Fill short rows with the missing cells.
      --fillvalue FILLVALUE
                            The value with which to fill short rows. Defaults to
                            none.

See also: Arguments common to all tools.

## Examples

Test a file with data rows that are shorter and longer than the header row:

    $ csvclean examples/bad.csv 2> errors.csv
    column_a,column_b,column_c
    0,mixed types.... uh oh,17
    $ cat errors.csv
    line_number,msg,column_a,column_b,column_c
    1,"Expected 3 columns, found 4 columns",1,27,,I'm too long!
    2,"Expected 3 columns, found 2 columns",,I'm too short!

Note

If any data rows are longer than the header row, you need to add columns manually: for example, by adding one or more delimiters (`,`) to the end of the header row. `csvclean` can’t do this, because it is designed to work with standard input, and correcting an error at the start of the CSV data based on an observation later in the CSV data would require holding all the CSV data in memory – which is not an option for large files.

Test a file with empty columns:

    $ csvclean --empty-columns examples/test_empty_columns.csv 2> errors.csv
    a,b,c,,
    a,,,,
    ,,c,,
    ,,,,
    $ cat errors.csv
    line_number,msg,a,b,c,,
    1,"Empty columns named 'b', '', ''! Try: csvcut -C 2,4,5",,,,,

Use csvcut to exclude the empty columns:

    $ csvcut -C 2,4,5 examples/test_empty_columns.csv
    a,c
    a,
    ,c
    ,

To change the line ending from line feed (LF or `\n`) to carriage return and line feed (CRLF or `\r\n`) use:

    csvformat -M $'\r\n' examples/dummy.csv