CSVCLEAN(1) csvkit CSVCLEAN(1)

csvclean - csvclean Documentation

Reports and fixes common errors in a CSV file.

  • 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).

•
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

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: 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.

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

Christopher Groskopf and contributors

2016, Christopher Groskopf and James McKinney

July 12, 2024 2.0.1