Mercurial > repos > yating-l > hubarchivecreator

annotate hubArchiveCreator.py @ 55:ba9997c847dc draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b2894a39921adaa6a93b12523820b61a78e11f20-dirty
author yating-l
date Wed, 17 May 2017 13:16:57 -0400
parents 4a58094b051e
children 4ca7cbf2d9b8
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1 #!/usr/bin/python
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2 # -*- coding: utf8 -*-
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3
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4 """
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5 This Galaxy tool permits to prepare your files to be ready for
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6 Assembly Hub visualization.
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7 Program test arguments:
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8 hubArchiveCreator.py -g test-data/augustusDbia3.gff3 -f test-data/dbia3.fa -d . -u ./tools -o output.html
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9 """
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10
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11 import argparse
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12 import collections
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13 import json
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14 import logging
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15 import os
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16 import sys
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17
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18 # Internal dependencies
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19 from Bam import Bam
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20 from BedSimpleRepeats import BedSimpleRepeats
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21 from BedSpliceJunctions import BedSpliceJunctions
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22 from Bed import Bed
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23 from cytoBand import cytoBand
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24 from BigWig import BigWig
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25 from util.Fasta import Fasta
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26 from util.Filters import TraceBackFormatter
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27 from Gff3 import Gff3
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28 from Gtf import Gtf
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29 from Psl import Psl
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30 from TrackHub import TrackHub
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31 from bigPsl import bigPsl
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32 from BedBlastAlignments import BedBlastAlignments
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33 from BigBed import BigBed
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34
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35 # TODO: Verify each subprocessed dependency is accessible [gff3ToGenePred, genePredToBed, twoBitInfo, faToTwoBit, bedToBigBed, sort
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37
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38 def main(argv):
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39 # Command Line parsing init
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40 parser = argparse.ArgumentParser(description='Create a foo.txt inside the given folder.')
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41
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42 # Reference genome mandatory
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43 parser.add_argument('-f', '--fasta', help='Fasta file of the reference genome')
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44
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45 # GFF3 Management
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46 parser.add_argument('--gff3', action='append', help='GFF3 format')
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47
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48 # GTF Management
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49 parser.add_argument('--gtf', action='append', help='GTF format')
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50
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51 # Bed4+12 (TrfBig)
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52 parser.add_argument('--bedSimpleRepeats', action='append', help='Bed4+12 format, using simpleRepeats.as')
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53
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54 # Bed12+1 (regtools)
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55 parser.add_argument('--bedSpliceJunctions', action='append', help='Bed12+1 format, using spliceJunctions.as')
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56
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57 # Generic Bed (Blastx transformed to bed)
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58 parser.add_argument('--bed', action='append', help='Bed generic format')
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59
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60 #cytoBandIdeo
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61 parser.add_argument('--cytoBand', action='append', help='Cytoband Track, using cytoBandIdeo.as')
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62
51
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63 # BigPsl (blat alignment)
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64 parser.add_argument('--bigpsl', action='append', help='bigPsl format, using bigPsl.as')
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65
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66 # Bed12+12 (tblastn alignment)
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67 parser.add_argument('--bedBlastAlignments', action='append', help='Bed12+12 format, using bigPsl.as')
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68
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69 # BigWig Management
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70 parser.add_argument('--bigwig', action='append', help='BigWig format')
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72 # Bam Management
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73 parser.add_argument('--bam', action='append', help='Bam format')
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74
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75 # Psl Management
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76 parser.add_argument('--psl', action='append', help='Psl format')
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77
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78 # BigBed Management
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79 parser.add_argument('--bigbed', action='append', help='BigBed format')
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80
11
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81 # TODO: Check if the running directory can have issues if we run the tool outside
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82 parser.add_argument('-d', '--directory',
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83 help='Running tool directory, where to find the templates. Default is running directory')
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84 parser.add_argument('-u', '--ucsc_tools_path',
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85 help='Directory where to find the executables needed to run this tool')
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86 parser.add_argument('-e', '--extra_files_path',
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87 help='Name, in galaxy, of the output folder. Where you would want to build the Track Hub Archive')
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88 parser.add_argument('-o', '--output', help='Name of the HTML summarizing the content of the Track Hub Archive')
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89
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90 parser.add_argument('-j', '--data_json', help='Json containing the metadata of the inputs')
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91
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92 parser.add_argument('--user_email', help='Email of the user who launched the Hub Archive Creation')
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93
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94 parser.add_argument('--genome_name', help='UCSC Genome Browser assembly ID')
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95
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96 parser.add_argument('--debug_mode', action='store_true', help='Allow more details about the errors')
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97
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98 # Begin init variables
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99
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100 toolDirectory = '.'
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101 extra_files_path = '.'
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102
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103 # Get the args passed in parameter
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104 args = parser.parse_args()
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105
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106 extra_files_path = args.extra_files_path
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107 toolDirectory = args.directory
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108
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109 #### Logging management ####
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110 # If we are in Debug mode, also print in stdout the debug dump
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111
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112 configure_logger(extra_files_path=extra_files_path, debug=args.debug_mode)
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113
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114 #### END Logging management ####
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115
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116 array_inputs_reference_genome = json.loads(args.fasta)
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117
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118 # TODO: Replace these with the object Fasta
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119 input_fasta_file = array_inputs_reference_genome["false_path"]
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120 input_fasta_file_name = sanitize_name_input(array_inputs_reference_genome["name"])
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121 genome_name = sanitize_name_input(args.genome_name)
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122
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123 reference_genome = Fasta(input_fasta_file,
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124 input_fasta_file_name, genome_name)
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125
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126 user_email = args.user_email
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127
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128
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129 # TODO: Use a class to have a better management of the structure of these inputs
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130 # These inputs are populated in the Galaxy Wrapper xml and are in this format:
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131 # ARRAY[DICT{FILE_PATH: DICT{NAME: NAME_VALUE, EXTRA_DATA: EXTRA_DATA_VALUE}}]
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132 # EXTRA_DATA could be anything, for example the index of a BAM => {"index", FILE_PATH}
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133 array_inputs_bam = args.bam
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134 array_inputs_bed_generic = args.bed
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135 array_inputs_bed_cytoBand = args.cytoBand
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136 array_inputs_bed_simple_repeats = args.bedSimpleRepeats
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137 array_inputs_bed_splice_junctions = args.bedSpliceJunctions
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138 array_inputs_bigwig = args.bigwig
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139 array_inputs_gff3 = args.gff3
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140 array_inputs_gtf = args.gtf
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141 array_inputs_psl = args.psl
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142 array_inputs_bigpsl = args.bigpsl
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143 array_inputs_bed_blast_alignments = args.bedBlastAlignments
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144 array_inputs_bigbed = args.bigbed
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145
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146 outputFile = args.output
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147
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148 json_inputs_data = args.data_json
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149
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150 # TODO: Instead use a class to properly store the objects, with object_hook
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151 inputs_data = json.loads(json_inputs_data)
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152 # We remove the spaces in ["name"] of inputs_data
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153 sanitize_name_inputs(inputs_data)
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154
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155 # TODO: Check here all the binaries / tools we need. Exception if missing
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156
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157 # Create the Track Hub folder
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158 trackHub = TrackHub(reference_genome, user_email, outputFile, extra_files_path, toolDirectory)
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159
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160 all_datatype_dictionary = {}
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161
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162 for (inputs, datatype_class) in [
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163 (array_inputs_bam, Bam),
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164 (array_inputs_bed_generic, Bed),
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165 (array_inputs_bed_cytoBand, cytoBand),
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166 (array_inputs_bigwig, BigWig),
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167 (array_inputs_bed_simple_repeats, BedSimpleRepeats),
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168 (array_inputs_bed_splice_junctions, BedSpliceJunctions),
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169 (array_inputs_gff3, Gff3),
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170 (array_inputs_gtf, Gtf),
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171 (array_inputs_psl, Psl),
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172 (array_inputs_bigpsl, bigPsl),
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173 (array_inputs_bed_blast_alignments, BedBlastAlignments),
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174 (array_inputs_bigbed, BigBed)]:
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175 if inputs:
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176 all_datatype_dictionary.update(create_ordered_datatype_objects(datatype_class, inputs, inputs_data))
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177
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178 # Create Ordered Dictionary to add the tracks in the tool form order
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179 all_datatype_ordered_dictionary = collections.OrderedDict(all_datatype_dictionary)
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180
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181 logging.debug("----- End of all_datatype_dictionary processing -----")
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182 logging.debug("all_datatype_ordered_dictionary keys are: {0}".format(all_datatype_ordered_dictionary.values()))
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183
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184 logging.debug("----- Beginning of Track adding processing -----")
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185 for index, datatypeObject in all_datatype_ordered_dictionary.iteritems():
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186 trackHub.addTrack(datatypeObject.track.trackDb)
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187 logging.debug("----- End of Track adding processing -----")
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188
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189 # We process all the modifications to create the zip file
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190 #trackHub.createZip()
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191
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192 # We terminate le process and so create a HTML file summarizing all the files
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193 trackHub.terminate()
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194
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195 logging.debug('#### End of HubArchiveCreator Debug Mode: Bye! ####')
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196
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197 sys.exit(0)
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198
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199
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200 def sanitize_name_input(string_to_sanitize):
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201 """
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202 Sanitize the string passed in parameter by replacing '/' and ' ' by '_'
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203
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204 :param string_to_sanitize:
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205 :return :
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206
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207 :Example:
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208
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209 >>> sanitize_name_input('this/is an//example')
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210 this_is_an__example
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211 """
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212 return string_to_sanitize \
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213 .replace("/", "_") \
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214 .replace(" ", "_")
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215
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216
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217 def sanitize_name_inputs(inputs_data):
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218 """
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219 Sanitize value of the keys "name" of the dictionary passed in parameter.
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220
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221 Because sometimes output from Galaxy, or even just file name, from user inputs, have spaces.
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222 Also, it can contain '/' character and could break the use of os.path function.
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223
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224 :param inputs_data: dict[string, dict[string, string]]
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225 """
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226 for key in inputs_data:
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227 inputs_data[key]["name"] = sanitize_name_input(inputs_data[key]["name"])
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228
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229
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230 def create_ordered_datatype_objects(ExtensionClass, array_inputs, inputs_data):
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231 """
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232 Function which executes the creation all the necessary files / folders for a special Datatype, for TrackHub
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233 and update the dictionary of datatype
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234
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235 :param ExtensionClass:
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236 :param array_inputs:
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237 :param inputs_data:
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238 :type ExtensionClass: Datatype
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239 :type array_inputs: list[string]
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240 :type inputs_data: dict
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241 :rtype: dict
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242 """
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243
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244 datatype_dictionary = {}
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245
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246 # TODO: Optimize this double loop
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247 for input_false_path in array_inputs:
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248 for key, data_value in inputs_data.items():
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249 if key == input_false_path:
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250 logging.debug("input_false_path: " + input_false_path)
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251 logging.debug("data_value: " + str(data_value))
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252 extensionObject = ExtensionClass(input_false_path, data_value)
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253 datatype_dictionary.update({data_value["order_index"]: extensionObject})
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254 return datatype_dictionary
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255
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256 def configure_logger(extra_files_path=None, debug=False):
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257 if not extra_files_path:
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258 raise Exception("Extra files path is not set. Stopping the application")
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259
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260
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261 # All case log: log everything in a .log file
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262 logger_file_name = ''.join([__name__, '.log'])
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263 logging_file_path = os.path.join(extra_files_path, logger_file_name)
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264
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265 logging.basicConfig(filename=logging_file_path, level=logging.DEBUG)
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266
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267 log_stdout = logging.StreamHandler(sys.stdout)
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268 if not debug:
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269 configure_logger_user(log_stdout)
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270 else:
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271 configure_logger_dev(log_stdout)
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272
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273 # stderr configuration
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274 configure_logger_stderr()
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275
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276 logging.debug('#### Welcome in HubArchiveCreator Debug Mode ####\n')
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277
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278 def configure_logger_user(log_stdout=None):
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279 """
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280 User Logger is defined as following:
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281 - User needs to have WARN, ERROR and CRITICAL but well formatted / without traceback
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282 in STDOUT
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283 - Still access to full, brute and traceback for errors
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284 in STDERR
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285 - And further access to debug if needed
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286 in .log
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287
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288 """
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289
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290 if not log_stdout:
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291 raise Exception("No log_stdout given. Stopping the application")
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292
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293 # stdout for INFO / WARN / ERROR / CRITICAL
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294 log_stdout.setLevel(logging.INFO)
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295
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296 formatter = TraceBackFormatter('%(message)s')
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297
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298 log_stdout.setFormatter(formatter)
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299
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300 logging.getLogger().addHandler(log_stdout)
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301
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302 def configure_logger_dev(log_stdout=None):
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303 """
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304 Dev Logger is defined as following:
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305 - Dev needs to have WARN, ERROR and CRITICAL but well formatted / without traceback, in stdout
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306 - Still access to full, brute and traceback in stderr for errors
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307 - And further access to debug if needed
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308
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309 """
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310 if not log_stdout:
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311 raise Exception("No log_stdout given. Stopping the application")
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312 log_format = '%(message)s'
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313
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314 # stdout and stderr and both identical for INFO / WARN / ERROR / CRITICAL
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315 log_stdout.setLevel(logging.DEBUG)
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316
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317 formatter = logging.Formatter(log_format)
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318
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319 log_stdout.setFormatter(formatter)
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320
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321 logging.getLogger().addHandler(log_stdout)
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322
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323 def configure_logger_stderr():
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324 """
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325 Configure what should be logged in stderr
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326 """
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327 log_error = logging.StreamHandler(sys.stderr)
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328 log_error.setLevel(logging.ERROR)
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329 log_error_format = '%(message)s'
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330
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331 formatter_error = logging.Formatter(log_error_format)
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332
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333 log_error.setFormatter(formatter_error)
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334
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335 logging.getLogger().addHandler(log_error)
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336
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337 if __name__ == "__main__":
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338 logging.getLogger(__name__)
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339 main(sys.argv)