mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
Daniel Blankenberg
b9e242e4eb
These are now used to store the list of chromosomes for species as well as the index for MAF files. MAF tools have been enhanced to make use of index files when available. TODO: When datasets are purged from disk, these files should also be purged.
68 lines
2.1 KiB
Python
68 lines
2.1 KiB
Python
#!/usr/bin/env python
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#Retreives data from UCSC and stores in a file. UCSC parameters are provided in the input/output file.
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import urllib, sys, os, gzip, tempfile, shutil
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from galaxy import eggs
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#from galaxy.datatypes import data
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from galaxy.util import gzip_magic
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assert sys.version_info[:2] >= ( 2, 4 )
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def stop_err( msg ):
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sys.stderr.write( msg )
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sys.exit()
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def check_gzip( filename ):
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temp = open( filename, "U" )
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magic_check = temp.read( 2 )
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temp.close()
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if magic_check != gzip_magic:
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return False
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return True
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def __main__():
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filename = sys.argv[1]
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params = {}
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for line in open( filename, 'r' ):
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try:
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line = line.strip()
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fields = line.split( '\t' )
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params[ fields[0] ] = fields[1]
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except:
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continue
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URL = params.get( 'URL', None )
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if not URL:
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open( filename, 'w' ).write( "" )
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stop_err( 'The remote data source application has not sent back a URL parameter in the request.' )
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out = open( filename, 'w' )
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CHUNK_SIZE = 2**20 # 1Mb
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try:
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page = urllib.urlopen( URL, urllib.urlencode( params ) )
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except:
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stop_err( 'It appears that the remote data source application is currently off line. Please try again later.' )
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while 1:
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chunk = page.read( CHUNK_SIZE )
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if not chunk:
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break
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out.write( chunk )
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out.close()
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if check_gzip( filename ):
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fd, uncompressed = tempfile.mkstemp()
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gzipped_file = gzip.GzipFile( filename )
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while 1:
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try:
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chunk = gzipped_file.read( CHUNK_SIZE )
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except IOError:
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os.close( fd )
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os.remove( uncompressed )
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gzipped_file.close()
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stop_err( 'Problem uncompressing gzipped data, please try retrieving the data uncompressed.' )
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if not chunk:
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break
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os.write( fd, chunk )
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os.close( fd )
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gzipped_file.close()
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# Replace the gzipped file with the uncompressed file
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shutil.move( uncompressed, filename )
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if __name__ == "__main__": __main__()
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