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1 #!/usr/bin/env python
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2 import sys
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3 import os
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4 import tempfile
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5 import shutil
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6 import optparse
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7 import urllib2
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8 import subprocess
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9 from ftplib import FTP
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10 import tarfile
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11 import zipfile
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12 import gzip
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13 import bz2
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14
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15 from galaxy.util.json import from_json_string, to_json_string
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16
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17 CHUNK_SIZE = 2**20 #1mb
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18
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19 def cleanup_before_exit( tmp_dir ):
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20 if tmp_dir and os.path.exists( tmp_dir ):
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21 shutil.rmtree( tmp_dir )
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22
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23
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24 def stop_err(msg):
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25 sys.stderr.write(msg)
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26 sys.exit(1)
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27
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28
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29 def _get_files_in_ftp_path( ftp, path ):
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30 path_contents = []
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31 ftp.retrlines( 'MLSD %s' % ( path ), path_contents.append )
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32 return [ line.split( ';' )[ -1 ].lstrip() for line in path_contents ]
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33
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34
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35 def _get_stream_readers_for_tar( file_obj, tmp_dir ):
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36 fasta_tar = tarfile.open( fileobj=file_obj, mode='r:*' )
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37 return [ fasta_tar.extractfile( member ) for member in fasta_tar.getmembers() ]
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38
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39
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40 def _get_stream_readers_for_zip( file_obj, tmp_dir ):
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41 fasta_zip = zipfile.ZipFile( file_obj, 'r' )
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42 rval = []
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43 for member in fasta_zip.namelist():
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44 fasta_zip.extract( member, tmp_dir )
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45 rval.append( open( os.path.join( tmp_dir, member ), 'rb' ) )
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46 return rval
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47
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48
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49 def _get_stream_readers_for_gzip( file_obj, tmp_dir ):
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50 return [ gzip.GzipFile( fileobj=file_obj, mode='rb' ) ]
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51
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52
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53 def _get_stream_readers_for_bz2( file_obj, tmp_dir ):
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54 return [ bz2.BZ2File( file_obj.name, 'rb' ) ]
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55
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56
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57 def download_from_ncbi( data_manager_dict, params, target_directory, database_id, database_name ):
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58 NCBI_FTP_SERVER = 'ftp.ncbi.nlm.nih.gov'
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59 NCBI_DOWNLOAD_PATH = '/blast/db/FASTA/'
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60 COMPRESSED_EXTENSIONS = [ ( '.tar.gz', _get_stream_readers_for_tar ), ( '.tar.bz2', _get_stream_readers_for_tar ), ( '.zip', _get_stream_readers_for_zip ), ( '.gz', _get_stream_readers_for_gzip ), ( '.bz2', _get_stream_readers_for_bz2 ) ]
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61
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62 ncbi_identifier = params['param_dict']['reference_source']['requested_identifier']
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63 ftp = FTP( NCBI_FTP_SERVER )
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64 ftp.login()
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65
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66 path_contents = _get_files_in_ftp_path( ftp, NCBI_DOWNLOAD_PATH )
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67
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68 ncbi_file_name = None
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69 get_stream_reader = None
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70 ext = None
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71 for ext, get_stream_reader in COMPRESSED_EXTENSIONS:
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72 if "%s%s" % ( ncbi_identifier, ext ) in path_contents:
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73 ncbi_file_name = "%s%s%s" % ( NCBI_DOWNLOAD_PATH, ncbi_identifier, ext )
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74 break
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75
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76 if not ncbi_file_name:
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77 raise Exception( 'Unable to determine filename for NCBI database for %s: %s' % ( ncbi_identifier, path_contents ) )
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78
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79 tmp_dir = tempfile.mkdtemp( prefix='tmp-data-manager-ncbi-' )
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80 ncbi_fasta_filename = os.path.join( tmp_dir, "%s%s" % ( ncbi_identifier, ext ) )
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81
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82 fasta_base_filename = "%s.fa" % database_id
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83 fasta_filename = os.path.join( target_directory, fasta_base_filename )
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84 fasta_writer = open( fasta_filename, 'wb+' )
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85
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86 tmp_extract_dir = os.path.join ( tmp_dir, 'extracted_fasta' )
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87 os.mkdir( tmp_extract_dir )
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88
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89 tmp_fasta = open( ncbi_fasta_filename, 'wb+' )
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90
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91 ftp.retrbinary( 'RETR %s' % ncbi_file_name, tmp_fasta.write )
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92
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93 tmp_fasta.flush()
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94 tmp_fasta.seek( 0 )
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95
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96 fasta_readers = get_stream_reader( tmp_fasta, tmp_extract_dir )
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97
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98 data_table_entry = _stream_fasta_to_file( fasta_readers, target_directory, database_id, database_name, params )
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99 _add_data_table_entry( data_manager_dict, data_table_entry )
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100
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101 for fasta_reader in fasta_readers:
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102 fasta_reader.close()
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103 tmp_fasta.close()
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104 cleanup_before_exit( tmp_dir )
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105
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106
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107 def download_from_url( data_manager_dict, params, target_directory, database_id, database_name ):
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108 #TODO: we should automatically do decompression here
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109 urls = filter( bool, map( lambda x: x.strip(), params['param_dict']['reference_source']['user_url'].split( '\n' ) ) )
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110 fasta_reader = [ urllib2.urlopen( url ) for url in urls ]
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111
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112 data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, database_id, database_name, params )
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113 _add_data_table_entry( data_manager_dict, data_table_entry )
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114
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115
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116 def download_from_history( data_manager_dict, params, target_directory, database_id, database_name ):
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117 #TODO: allow multiple FASTA input files
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118 input_filename = params['param_dict']['reference_source']['input_fasta']
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119 if isinstance( input_filename, list ):
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120 fasta_reader = [ open( filename, 'rb' ) for filename in input_filename ]
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121 else:
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122 fasta_reader = open( input_filename )
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123
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124 data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, database_id, database_name, params )
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125 _add_data_table_entry( data_manager_dict, data_table_entry )
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126
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127
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128 def copy_from_directory( data_manager_dict, params, target_directory, database_id, database_name ):
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129 input_filename = params['param_dict']['reference_source']['fasta_filename']
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130 create_symlink = params['param_dict']['reference_source']['create_symlink'] == 'create_symlink'
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131 if create_symlink:
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132 data_table_entry = _create_symlink( input_filename, target_directory, database_id, database_name )
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133 else:
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134 if isinstance( input_filename, list ):
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135 fasta_reader = [ open( filename, 'rb' ) for filename in input_filename ]
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136 else:
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137 fasta_reader = open( input_filename )
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138 data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, database_id, database_name, params )
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139 _add_data_table_entry( data_manager_dict, data_table_entry )
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140
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141
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142 def _add_data_table_entry( data_manager_dict, data_table_entry ):
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143 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
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144 data_manager_dict['data_tables']['diamond_database'] = data_manager_dict['data_tables'].get( 'diamond_database', [] )
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145 data_manager_dict['data_tables']['diamond_database'].append( data_table_entry )
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146 return data_manager_dict
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147
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148
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149 def _stream_fasta_to_file( fasta_stream, target_directory, database_id, database_name, params, close_stream=True ):
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150 fasta_base_filename = "%s.fa" % database_id
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151 fasta_filename = os.path.join( target_directory, fasta_base_filename )
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152
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153 temp_fasta = tempfile.NamedTemporaryFile( delete=False, suffix=".fasta" )
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154 temp_fasta.close()
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155 fasta_writer = open( temp_fasta.name, 'wb+' )
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156
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157 if isinstance( fasta_stream, list ) and len( fasta_stream ) == 1:
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158 fasta_stream = fasta_stream[0]
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159
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160 if isinstance( fasta_stream, list ):
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161 last_char = None
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162 for fh in fasta_stream:
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163 if last_char not in [ None, '\n', '\r' ]:
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164 fasta_writer.write( '\n' )
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165 while True:
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166 data = fh.read( CHUNK_SIZE )
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167 if data:
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168 fasta_writer.write( data )
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169 last_char = data[-1]
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170 else:
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171 break
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172 if close_stream:
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173 fh.close()
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174 else:
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175 while True:
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176 data = fasta_stream.read( CHUNK_SIZE )
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177 if data:
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178 fasta_writer.write( data )
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179 else:
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180 break
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181 if close_stream:
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182 fasta_stream.close()
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183
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184 fasta_writer.close()
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185
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186 args = [ 'diamond', 'makedb', '--in', temp_fasta.name, '--db', fasta_filename]
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187
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188 tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-diamond-database-builder-stderr" )
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189 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() )
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190 return_code = proc.wait()
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191 if return_code:
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192 tmp_stderr.flush()
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193 tmp_stderr.seek(0)
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194 print >> sys.stderr, "Error building diamond database:"
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195 while True:
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196 chunk = tmp_stderr.read( CHUNK_SIZE )
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197 if not chunk:
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198 break
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199 sys.stderr.write( chunk )
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200 sys.exit( return_code )
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201 tmp_stderr.close()
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202 os.remove( temp_fasta.name )
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203 return dict( value=database_id, name=database_name, db_path="%s.dmnd" % fasta_base_filename )
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204
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205
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206 def _create_symlink( input_filename, target_directory, database_id, database_name ):
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207 fasta_base_filename = "%s.fa" % database_id
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208 fasta_filename = os.path.join( target_directory, fasta_base_filename )
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209 os.symlink( input_filename, fasta_filename )
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210 return dict( value=database_id, name=database_name, db_path=fasta_base_filename )
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211
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212
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213 REFERENCE_SOURCE_TO_DOWNLOAD = dict( ncbi=download_from_ncbi, url=download_from_url, history=download_from_history, directory=copy_from_directory )
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214
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215 def main():
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216 #Parse Command Line
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217 parser = optparse.OptionParser()
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218 parser.add_option( '-d', '--dbkey_description', dest='dbkey_description', action='store', type="string", default=None, help='dbkey_description' )
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219 (options, args) = parser.parse_args()
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220
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221 filename = args[0]
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222
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223 params = from_json_string( open( filename ).read() )
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224 target_directory = params[ 'output_data' ][0]['extra_files_path']
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225 os.mkdir( target_directory )
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226 data_manager_dict = {}
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227
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228 database_id = params['param_dict']['database_id']
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229 database_name = params['param_dict']['database_name']
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230
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231 #Fetch the FASTA
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232 REFERENCE_SOURCE_TO_DOWNLOAD[ params['param_dict']['reference_source']['reference_source_selector'] ]( data_manager_dict, params, target_directory, database_id, database_name )
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233
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234 #save info to json file
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235 open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
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236
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237 if __name__ == "__main__":
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238 main()
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