diff util/santitizer.py @ 3:6f262a92e8dc draft default tip

planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 91b46f7c891c2466bc5b6a063411cdae75964515-dirty

--- a/util/santitizer.py	Wed Oct 25 12:41:34 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,70 +0,0 @@
-#!/usr/bin/python
-# -*- coding: utf8 -*-
-
-"""
-This class handles the subprocess calls of the different tools used
-in HubArchiveCreator
-"""
-
-import logging
-import os
-import subprocess
-import sys
-import string
-import tempfile
-
-    
-def prefixTrackName(filename):       
-    """
-    santitize trackName. Because track name must begin with a letter and
-    contain only the following chars: [a-zA-Z0-9_].
-    See the "track" Common settings at:
-    https://genome.ucsc.edu/goldenpath/help/trackDb/trackDbHub.html#bigPsl_-_Pairwise_Alignments
-    skip the santitization for cytoBandIdeo track
-    """
-    if filename == 'cytoBandIdeo':
-        return filename
-    valid_chars = "_%s%s" % (string.ascii_letters, string.digits)
-    sanitize_name = ''.join([c if c in valid_chars else '_' for c in filename])
-    sanitize_name = "gonramp_" + sanitize_name
-    return sanitize_name
-
-def sanitize_name_input(string_to_sanitize):
-    """
-    Sanitize the string passed in parameter by replacing '/' and ' ' by '_'
-
-    :param string_to_sanitize:
-    :return :
-
-    :Example:
-
-    >>> sanitize_name_input('this/is an//example')
-    this_is_an__example
-    """
-    return string_to_sanitize \
-            .replace("/", "_") \
-            .replace(" ", "_")
-
-def sanitize_name_inputs(inputs_data):
-    """
-    Sanitize value of the keys "name" of the dictionary passed in parameter.
-
-    Because sometimes output from Galaxy, or even just file name, from user inputs, have spaces.
-    Also, it can contain '/' character and could break the use of os.path function.
-
-    :param inputs_data: dict[string, dict[string, string]]
-    """
-    for key in inputs_data:
-        inputs_data[key]["name"] = sanitize_name_input(inputs_data[key]["name"])
-
-def sanitize_group_name(group_name):
-    return group_name.lower().replace(' ', '_')
-
-def sanitize_name(input_name):
-    """
-    Galaxy will name all the files and dirs as *.dat, 
-    the function can replace '.' to '_' for the dirs
-    """
-    validChars = "_-%s%s" % (string.ascii_letters, string.digits)
-    sanitized_name = ''.join([c if c in validChars else '_' for c in input_name])
-    return "gonramp_" + sanitized_name