diff util/santitizer.py @ 29:7e8a8b732db3 draft

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/santitizer.py	Wed May 16 18:04:20 2018 -0400
@@ -0,0 +1,61 @@
+#!/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(' ', '_')