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1 #!/usr/bin/env python
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2 #
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3
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4 import sys
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5 import os
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6 import subprocess
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7 import tempfile
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8 import optparse
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9 import urllib2
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10 import gzip
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11 import shutil
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12
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13 from galaxy.util.json import from_json_string, to_json_string
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14
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15 # Download file from specified URL and put into local subdir
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16
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17 if __name__ == '__main__':
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18 #Parse Command Line
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19 parser = optparse.OptionParser()
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20 options,args = parser.parse_args()
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21 print "options: %s" % options
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22 print "args : %s" % args
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23 if len(args) != 2:
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24 p.error("Need to supply JSON file name and description text")
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25
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26 # Read the JSON supplied from the data manager tool
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27 # Results from this program will be returned via the
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28 # same file
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29 jsonfile = args[0]
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30 params = from_json_string(open(jsonfile).read() )
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31 print "%s" % params
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32
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33 # Extract the data from the input JSON
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34 # See https://wiki.galaxyproject.org/Admin/Tools/DataManagers/HowTo/Define?highlight=%28\bAdmin%2FTools%2FDataManagers\b%29
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35 # for example of JSON
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36 #
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37 # We want the values set in the data manager XML
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38 dbkey = params['param_dict']['dbkey']
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39 description = args[1].strip()
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40 identifier = params['param_dict']['unique_id'].strip()
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41 # Where to put the output file
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42 # Nb we have to make this ourselves, it doesn't exist by default
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43 target_dir = params['output_data'][0]['extra_files_path']
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44 os.mkdir(target_dir)
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45
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46 method = params['param_dict']['reference_source']['reference_source_selector']
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47
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48 # Dictionary for returning to data manager
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49 data_manager_dict = {}
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50 data_manager_dict['data_tables'] = dict()
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51
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52 # Download from URL
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53 if method == 'web':
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54 url = params['param_dict']['reference_source']['annotation_url']
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55 print "Downloading: %s" % url
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56 annotation_file_name = os.path.basename(url)
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57 annotation_file_path = os.path.join(target_dir,annotation_file_name)
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58 print "Annotation file name: %s" % annotation_file_name
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59 print "Annotation file path: %s" % annotation_file_path
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60 open(annotation_file_path,'wb').write(urllib2.urlopen(url).read())
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61 if annotation_file_name.endswith('.gz'):
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62 # Uncompress
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63 uncompressed_file = annotation_file_path[:-3]
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64 open(uncompressed_file,'wb').write(gzip.open(annotation_file_path,'rb').read())
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65 # Remove gzipped file
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66 os.remove(annotation_file_path)
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67 annotation_file_name = os.path.basename(uncompressed_file)
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68 annotation_file_path = uncompressed_file
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69 # Update the identifier and description
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70 if not identifier:
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71 identifier = "%s_ceas_web" % dbkey
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72 if not description:
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73 description = "%s (%s)" % (os.path.splitext(annotation_file_name)[0],dbkey)
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74 # Update the output dictionary
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75 data_manager_dict['data_tables']['ceas_annotations'] = {
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76 'value': identifier,
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77 'dbkey': dbkey,
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78 'name': description,
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79 'path': annotation_file_name,
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80 }
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81 elif method == 'server':
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82 # Pull in a file from the server
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83 filename = params['param_dict']['reference_source']['annotation_filename']
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84 create_symlink = params['param_dict']['reference_source']['create_symlink']
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85 print "Canonical gene list file name: %s" % filename
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86 print "Create symlink: %s" % create_symlink
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87 target_filename = os.path.join(target_dir,os.path.basename(filename))
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88 if create_symlink == 'copy_file':
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89 shutil.copyfile(filename,target_filename)
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90 else:
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91 os.symlink(filename,target_filename)
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92 # Update the identifier and description
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93 if not identifier:
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94 identifier = "%s_%s" % (dbkey,
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95 os.path.splitext(os.path.basename(filename))[0])
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96 if not description:
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97 description = "%s: %s" % (dbkey,
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98 os.path.splitext(os.path.basename(filename))[0])
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99 # Update the output dictionary
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100 data_manager_dict['data_tables']['ceas_annotations'] = {
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101 'value': identifier,
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102 'dbkey': dbkey,
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103 'name': description,
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104 'path': os.path.basename(filename),
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105 }
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106 elif method == 'from_wig':
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107 # Make a reference file from a wig file
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108 wig_file = params['param_dict']['reference_source']['wig_file']
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109 gene_annotation = params['param_dict']['reference_source']['gene_annotation']
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110 target_filename = os.path.join(target_dir,"%s_%s.%s" % (dbkey,
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111 os.path.basename(wig_file),
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112 gene_annotation))
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113 print "Wig file: %s" % wig_file
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114 print "Gene annotation: %s" % gene_annotation
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115 print "Output file: %s" % os.path.basename(target_filename)
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116 # Make a working directory
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117 working_dir = tempfile.mkdtemp()
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118 # Collect stderr in a file for reporting later
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119 stderr_filen = tempfile.NamedTemporaryFile().name
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120 # Build the command to run
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121 cmd = "build_genomeBG -d %s -g %s -w %s -o %s" % (dbkey,
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122 gene_annotation,
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123 wig_file,
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124 target_filename)
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125 print "Running %s" % cmd
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126 proc = subprocess.Popen(args=cmd,shell=True,cwd=working_dir,
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127 stderr=open(stderr_filen,'wb'))
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128 proc.wait()
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129 # Copy stderr to stdout
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130 with open(stderr_filen,'r') as fp:
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131 sys.stdout.write(fp.read())
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132 # Update identifier and description
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133 if not identifier:
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134 identifier = "%s_%s_%s" % (dbkey,
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135 gene_annotation,
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136 os.path.basename(wig_file))
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137 if not description:
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138 description = "%s %s from %s" % (dbkey,
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139 gene_annotation,
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140 os.path.basename(wig_file))
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141 # Update the output dictionary
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142 data_manager_dict['data_tables']['ceas_annotations'] = {
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143 'value': identifier,
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144 'dbkey': dbkey,
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145 'name': description,
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146 'path': os.path.basename(target_filename),
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147 }
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148 else:
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149 raise NotImplementedError("Method '%s' not implemented" % method)
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150
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151 #save info to json file
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152 open(jsonfile,'wb').write(to_json_string(data_manager_dict))
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153
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