Unverified Commit 4768d3d1 authored by Nicola Soranzo's avatar Nicola Soranzo
Browse files

Drop Python helper script from sort1 tool 

Also:
- Incidentally address the deprecation of the `argparse.FileType` type
  converter in Python 3.14 , see
  https://docs.python.org/3.14/whatsnew/3.14.html#deprecated
  https://github.com/galaxyproject/galaxy/issues/16854
- Drop the now unnecessary Python requirement.
- Use CDATA.
parent 2fa7b43a

tools/filters/sorter.py

deleted100644 → 0
+0 −71
Original line number Diff line number Diff line 
"""

Sorts tabular data on one or more columns. All comments of the file are collected

and placed at the beginning of the sorted output file.

"""



# 03/05/2013 guerler



import argparse

import subprocess

import sys





def stop_err(msg):

    sys.exit(msg)





def main():

    # define options

    parser = argparse.ArgumentParser(description=__doc__)

    parser.add_argument("-i", "--input", type=argparse.FileType("r"), help="Tabular file to be sorted")

    parser.add_argument("-o", "--output", type=argparse.FileType("w"), help="Sorted output file")

    parser.add_argument("-k", "--key", action="append", help="Key (see manual for bash/sort)")

    parser.add_argument("-H", "--header_lines", type=int, help="Number of header lines to ignore")



    # parse

    args = parser.parse_args()



    try:

        # retrieve options

        input_fh = args.input

        output_fh = args.output

        header_lines = args.header_lines

        key_args = []

        for k in args.key:

            key_args.extend(["-k", k])



        # sed header

        if header_lines > 0:

            sed_header = ["sed", "-n", f"1,{header_lines:d}p"]

            subprocess.check_call(sed_header, stdin=input_fh, stdout=output_fh)

            input_fh.seek(0)



        # grep comments

        grep_comments = ["grep", "^#"]

        exit_code = subprocess.call(grep_comments, stdin=input_fh, stdout=output_fh)

        input_fh.seek(0)

        if exit_code not in [0, 1]:

            stop_err("Searching for comment lines failed")



        # grep and sort columns

        if header_lines > 0:

            sed_cmd = ["sed", f"1,{header_lines:d}d"]

            sed_header_restore = subprocess.Popen(sed_cmd, stdin=input_fh, stdout=subprocess.PIPE)

            pipe_stdin = sed_header_restore.stdout

        else:

            pipe_stdin = input_fh

        grep = subprocess.Popen(["grep", "^[^#]"], stdin=pipe_stdin, stdout=subprocess.PIPE)

        sort = subprocess.Popen(["sort", "-f", "-t", "\t"] + key_args, stdin=grep.stdout, stdout=output_fh)

        # wait for commands to complete

        sort.communicate()

        assert sort.returncode == 0, f"sort pipeline exited with non-zero exit code: {sort.returncode:d}"



    except Exception as ex:

        stop_err("Error running sorter.py\n" + str(ex))



    # exit

    sys.exit(0)





if __name__ == "__main__":

    main()

tools/filters/sorter.xml

+17 −11
Original line number Diff line number Diff line 
<tool id="sort1" name="Sort" version="1.2.0">

    <description>data in ascending or descending order</description>

    <requirements>

        <requirement type="package" version="3.8">python</requirement>

        <requirement type="package" version="2.14">grep</requirement>

        <requirement type="package" version="4.4">sed</requirement>

        <requirement type="package" version="8.31">coreutils</requirement>

    </requirements>

    <command detect_errors="exit_code">

python '$__tool_directory__/sorter.py'



--input='$input'

--output='$out_file1'

    <command detect_errors="exit_code"><![CDATA[

## Sorts tabular data on one or more columns. All comments of the file are

## collected and placed at the beginning of the sorted output file.

#if $header_lines > 0:

    sed -n 1,${header_lines}p '$input' > '$out_file1' &&

#end if

grep '^#' '$input' >> '$out_file1';

#if $header_lines > 0:

    sed 1,${header_lines}d '$input' |

#else:

    < '$input'

#end if

grep '^[^#]' | sort -f -t \$'\t'



#if (str($style) == 'num'):

    #set $style = 'n'
@@ -22,8 +29,7 @@ python '$__tool_directory__/sorter.py' 


#set $order = '' if (str($order) == 'ASC') else 'r'



--key=${column},${column}${style}${order}



-k ${column},${column}${style}${order}



#for $col in $column_set:

    #set $other_column = str($col.other_column)
@@ -37,10 +43,10 @@ python '$__tool_directory__/sorter.py' 
    #end if



    #set $other_order = '' if (str($col.other_order) == "ASC") else 'r'

    --key=${other_column},${other_column}${other_style}${other_order}

    -k ${other_column},${other_column}${other_style}${other_order}

#end for

--header $header_lines

    </command>

>> '$out_file1'

    ]]></command>

    <inputs>

        <param format="tabular" name="input" type="data" label="Sort Dataset" />

        <param name="column" label="on column" type="data_column" data_ref="input" accept_default="true"/>