Mercurial > repos > yating-l > jbrowsearchivecreator

annotate util/santitizer.py @ 50:804e7217f27c draft default tip

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planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 3afab1eb0da4823419945c523a1d37cd5973e7f6-dirty
author yating-l
date Fri, 20 Jul 2018 11:38:01 -0400
parents 31a41ce128cc
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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1 #!/usr/bin/python
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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2 # -*- coding: utf8 -*-
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4 """
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5 This class handles the subprocess calls of the different tools used
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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6 in HubArchiveCreator
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7 """
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9 import logging
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10 import os
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11 import subprocess
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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12 import sys
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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13 import string
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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14 import tempfile
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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17 def prefixTrackName(filename):
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18 """
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19 santitize trackName. Because track name must begin with a letter and
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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20 contain only the following chars: [a-zA-Z0-9_].
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21 See the "track" Common settings at:
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22 https://genome.ucsc.edu/goldenpath/help/trackDb/trackDbHub.html#bigPsl_-_Pairwise_Alignments
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23 skip the santitization for cytoBandIdeo track
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24 """
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25 if filename == 'cytoBandIdeo':
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26 return filename
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27 valid_chars = "_%s%s" % (string.ascii_letters, string.digits)
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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28 sanitize_name = ''.join([c if c in valid_chars else '_' for c in filename])
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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29 sanitize_name = "gonramp_" + sanitize_name
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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30 return sanitize_name
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32 def sanitize_name_input(string_to_sanitize):
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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33 """
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34 Sanitize the string passed in parameter by replacing '/' and ' ' by '_'
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36 :param string_to_sanitize:
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37 :return :
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39 :Example:
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41 >>> sanitize_name_input('this/is an//example')
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42 this_is_an__example
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43 """
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44 return string_to_sanitize \
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45 .replace("/", "_") \
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46 .replace(" ", "_")
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48 def sanitize_name_inputs(inputs_data):
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49 """
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50 Sanitize value of the keys "name" of the dictionary passed in parameter.
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52 Because sometimes output from Galaxy, or even just file name, from user inputs, have spaces.
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53 Also, it can contain '/' character and could break the use of os.path function.
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55 :param inputs_data: dict[string, dict[string, string]]
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56 """
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57 for key in inputs_data:
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58 inputs_data[key]["name"] = sanitize_name_input(inputs_data[key]["name"])
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60 def sanitize_group_name(group_name):
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61 return group_name.lower().replace(' ', '_')
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63 def sanitize_name(input_name):
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64 """
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65 Galaxy will name all the files and dirs as *.dat,
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66 the function can replace '.' to '_' for the dirs
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67 """
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68 validChars = "_-%s%s" % (string.ascii_letters, string.digits)
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69 sanitized_name = ''.join([c if c in validChars else '_' for c in input_name])
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70 return "gonramp_" + sanitized_name