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1
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2 def load_microbial_data( GALAXY_DATA_INDEX_DIR, sep='\t' ):
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3 # FIXME: this function is duplicated in the DynamicOptions class. It is used here only to
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4 # set data.name in exec_after_process().
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5 microbe_info= {}
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6 orgs = {}
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7
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8 filename = "%s/microbial_data.loc" % GALAXY_DATA_INDEX_DIR
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9 for i, line in enumerate( open( filename ) ):
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10 line = line.rstrip( '\r\n' )
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11 if line and not line.startswith( '#' ):
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12 fields = line.split( sep )
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13 #read each line, if not enough fields, go to next line
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14 try:
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15 info_type = fields.pop(0)
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16 if info_type.upper() == "ORG":
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17 #ORG 12521 Clostridium perfringens SM101 bacteria Firmicutes CP000312,CP000313,CP000314,CP000315 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=12521
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18 org_num = fields.pop(0)
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19 name = fields.pop(0)
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20 kingdom = fields.pop(0)
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21 group = fields.pop(0)
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22 chromosomes = fields.pop(0)
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23 info_url = fields.pop(0)
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24 link_site = fields.pop(0)
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25 if org_num not in orgs:
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26 orgs[ org_num ] = {}
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27 orgs[ org_num ][ 'chrs' ] = {}
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28 orgs[ org_num ][ 'name' ] = name
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29 orgs[ org_num ][ 'kingdom' ] = kingdom
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30 orgs[ org_num ][ 'group' ] = group
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31 orgs[ org_num ][ 'chromosomes' ] = chromosomes
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32 orgs[ org_num ][ 'info_url' ] = info_url
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33 orgs[ org_num ][ 'link_site' ] = link_site
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34 elif info_type.upper() == "CHR":
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35 #CHR 12521 CP000315 Clostridium perfringens phage phiSM101, complete genome 38092 110684521 CP000315.1
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36 org_num = fields.pop(0)
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37 chr_acc = fields.pop(0)
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38 name = fields.pop(0)
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39 length = fields.pop(0)
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40 gi = fields.pop(0)
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41 gb = fields.pop(0)
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42 info_url = fields.pop(0)
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43 chr = {}
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44 chr[ 'name' ] = name
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45 chr[ 'length' ] = length
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46 chr[ 'gi' ] = gi
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47 chr[ 'gb' ] = gb
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48 chr[ 'info_url' ] = info_url
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49 if org_num not in orgs:
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50 orgs[ org_num ] = {}
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51 orgs[ org_num ][ 'chrs' ] = {}
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52 orgs[ org_num ][ 'chrs' ][ chr_acc ] = chr
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53 elif info_type.upper() == "DATA":
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54 #DATA 12521_12521_CDS 12521 CP000315 CDS bed /home/djb396/alignments/playground/bacteria/12521/CP000315.CDS.bed
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55 uid = fields.pop(0)
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56 org_num = fields.pop(0)
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57 chr_acc = fields.pop(0)
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58 feature = fields.pop(0)
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59 filetype = fields.pop(0)
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60 path = fields.pop(0)
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61 data = {}
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62 data[ 'filetype' ] = filetype
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63 data[ 'path' ] = path
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64 data[ 'feature' ] = feature
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65
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66 if org_num not in orgs:
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67 orgs[ org_num ] = {}
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68 orgs[ org_num ][ 'chrs' ] = {}
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69 if 'data' not in orgs[ org_num ][ 'chrs' ][ chr_acc ]:
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70 orgs[ org_num ][ 'chrs' ][ chr_acc ][ 'data' ] = {}
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71 orgs[ org_num ][ 'chrs' ][ chr_acc ][ 'data' ][ uid ] = data
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72 else: continue
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73 except: continue
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74 for org_num in orgs:
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75 org = orgs[ org_num ]
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76 if org[ 'kingdom' ] not in microbe_info:
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77 microbe_info[ org[ 'kingdom' ] ] = {}
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78 if org_num not in microbe_info[ org[ 'kingdom' ] ]:
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79 microbe_info[ org[ 'kingdom' ] ][org_num] = org
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80 return microbe_info
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81
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82 #post processing, set build for data and add additional data to history
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83 from galaxy import datatypes, config, jobs, tools
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84 from shutil import copyfile
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85
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86 def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
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87 base_dataset = out_data.items()[0][1]
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88 history = base_dataset.history
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89 if history == None:
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90 print "unknown history!"
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91 return
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92 kingdom = param_dict.get( 'kingdom', None )
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93 #group = param_dict.get( 'group', None )
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94 org = param_dict.get( 'org', None )
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95
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96 #if not (kingdom or group or org):
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97 if not (kingdom or org):
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98 print "Parameters are not available."
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99 #workflow passes galaxy.tools.parameters.basic.UnvalidatedValue instead of values
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100 if isinstance( kingdom, tools.parameters.basic.UnvalidatedValue ):
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101 kingdom = kingdom.value
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102 if isinstance( org, tools.parameters.basic.UnvalidatedValue ):
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103 org = org.value
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104
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105 GALAXY_DATA_INDEX_DIR = app.config.tool_data_path
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106 microbe_info = load_microbial_data( GALAXY_DATA_INDEX_DIR, sep='\t' )
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107 new_stdout = ""
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108 split_stdout = stdout.split("\n")
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109 basic_name = ""
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110 for line in split_stdout:
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111 fields = line.split("\t")
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112 if fields[0] == "#File1":
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113 description = fields[1]
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114 chr = fields[2]
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115 dbkey = fields[3]
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116 file_type = fields[4]
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117 name, data = out_data.items()[0]
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118 data.set_size()
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119 basic_name = data.name
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120 data.name = data.name + " (" + microbe_info[kingdom][org]['chrs'][chr]['data'][description]['feature'] +" for " + microbe_info[kingdom][org]['name'] + ":" + chr + ")"
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121 data.dbkey = dbkey
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122 data.info = data.name
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123 data = app.datatypes_registry.change_datatype( data, file_type )
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124 data.init_meta()
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125 data.set_peek()
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126 app.model.context.add( data )
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127 app.model.context.flush()
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128 elif fields[0] == "#NewFile":
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129 description = fields[1]
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130 chr = fields[2]
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131 dbkey = fields[3]
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132 filepath = fields[4]
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133 file_type = fields[5]
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134 newdata = app.model.HistoryDatasetAssociation( create_dataset = True, sa_session = app.model.context ) #This import should become a library
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135 newdata.set_size()
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136 newdata.extension = file_type
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137 newdata.name = basic_name + " (" + microbe_info[kingdom][org]['chrs'][chr]['data'][description]['feature'] +" for "+microbe_info[kingdom][org]['name']+":"+chr + ")"
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138 app.model.context.add( newdata )
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139 app.model.context.flush()
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140 app.security_agent.copy_dataset_permissions( base_dataset.dataset, newdata.dataset )
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141 history.add_dataset( newdata )
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142 app.model.context.add( history )
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143 app.model.context.flush()
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144 try:
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145 copyfile(filepath,newdata.file_name)
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146 newdata.info = newdata.name
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147 newdata.state = jobs.JOB_OK
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148 except:
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149 newdata.info = "The requested file is missing from the system."
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150 newdata.state = jobs.JOB_ERROR
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151 newdata.dbkey = dbkey
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152 newdata.init_meta()
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153 newdata.set_peek()
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154 app.model.context.flush()
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