# HG changeset patch
# User blankenberg
# Date 1422302056 18000
# Node ID 0e5299e77334f4e09f90160f340dcd150c53cb70
# Parent  d59e1d23b38862177107dca40eeda1a914c860e4
Uploaded

diff -r d59e1d23b388 -r 0e5299e77334 data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py
--- a/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py	Wed Jul 02 00:35:38 2014 -0400
+++ b/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py	Mon Jan 26 14:54:16 2015 -0500
@@ -14,7 +14,7 @@
 import gzip
 import bz2
 
-from galaxy.util.json import from_json_string, to_json_string
+from json import loads, dumps
 
 
 CHUNK_SIZE = 2**20 #1mb
@@ -55,7 +55,7 @@
 
 def _get_stream_readers_for_tar( file_obj, tmp_dir ):
     fasta_tar = tarfile.open( fileobj=file_obj, mode='r:*' )
-    return [ fasta_tar.extractfile( member ) for member in fasta_tar.getmembers() ]
+    return filter( lambda x: x is not None, [ fasta_tar.extractfile( member ) for member in fasta_tar.getmembers() ] )
 
 def _get_stream_readers_for_zip( file_obj, tmp_dir ):
     fasta_zip = zipfile.ZipFile( file_obj, 'r' )
@@ -177,7 +177,6 @@
 
 def download_from_ucsc( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ):
     UCSC_FTP_SERVER = 'hgdownload.cse.ucsc.edu'
-    UCSC_CHROM_FA_FILENAME = 'chromFa'
     UCSC_DOWNLOAD_PATH = '/goldenPath/%s/bigZips/'
     COMPRESSED_EXTENSIONS = [ ( '.tar.gz', _get_stream_readers_for_tar ), ( '.tar.bz2', _get_stream_readers_for_tar ), ( '.zip', _get_stream_readers_for_zip ), ( '.fa.gz', _get_stream_readers_for_gzip ), ( '.fa.bz2', _get_stream_readers_for_bz2 ) ]
     
@@ -186,6 +185,8 @@
         email = 'anonymous@example.com'
 
     ucsc_dbkey = params['param_dict']['reference_source']['requested_dbkey'] or dbkey
+    UCSC_CHROM_FA_FILENAMES = [ '%s.chromFa' % ucsc_dbkey, 'chromFa' ]
+    
     ftp = FTP( UCSC_FTP_SERVER )
     ftp.login( 'anonymous', email )
     
@@ -195,9 +196,13 @@
     ucsc_file_name = None
     get_stream_reader = None
     ext = None
-    for ext, get_stream_reader in COMPRESSED_EXTENSIONS:
-        if "%s%s" % ( UCSC_CHROM_FA_FILENAME, ext ) in path_contents:
-            ucsc_file_name = "%s%s%s" % ( ucsc_path, UCSC_CHROM_FA_FILENAME, ext )
+    ucsc_chrom_fa_filename = None
+    for ucsc_chrom_fa_filename in UCSC_CHROM_FA_FILENAMES:
+        for ext, get_stream_reader in COMPRESSED_EXTENSIONS:
+            if "%s%s" % ( ucsc_chrom_fa_filename, ext ) in path_contents:
+                ucsc_file_name = "%s%s%s" % ( ucsc_path, ucsc_chrom_fa_filename, ext )
+                break
+        if ucsc_file_name:
             break
     
     if not ucsc_file_name:
@@ -205,7 +210,7 @@
     
     
     tmp_dir = tempfile.mkdtemp( prefix='tmp-data-manager-ucsc-' )
-    ucsc_fasta_filename = os.path.join( tmp_dir, "%s%s" % ( UCSC_CHROM_FA_FILENAME, ext ) )
+    ucsc_fasta_filename = os.path.join( tmp_dir, "%s%s" % ( ucsc_chrom_fa_filename, ext ) )
     
     fasta_base_filename = "%s.fa" % sequence_id
     fasta_filename = os.path.join( target_directory, fasta_base_filename )
@@ -237,7 +242,7 @@
     
     requested_identifier = params['param_dict']['reference_source']['requested_identifier']
     url = NCBI_DOWNLOAD_URL % requested_identifier
-    fasta_reader = urllib2.urlopen( url )
+    fasta_readers = urllib2.urlopen( url )
     
     for data_table_name, data_table_entry in _stream_fasta_to_file( fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params ):
         if data_table_entry:
@@ -246,7 +251,7 @@
 def download_from_url( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ):
     #TODO: we should automatically do decompression here
     urls = filter( bool, map( lambda x: x.strip(), params['param_dict']['reference_source']['user_url'].split( '\n' ) ) )
-    fasta_reader = [ urllib2.urlopen( url ) for url in urls ]
+    fasta_readers = [ urllib2.urlopen( url ) for url in urls ]
     
     for data_table_name, data_table_entry in _stream_fasta_to_file( fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params ):
         if data_table_entry:
@@ -256,9 +261,9 @@
     #TODO: allow multiple FASTA input files
     input_filename = params['param_dict']['reference_source']['input_fasta']
     if isinstance( input_filename, list ):
-        fasta_reader = [ open( filename, 'rb' ) for filename in input_filename ]
+        fasta_readers = [ open( filename, 'rb' ) for filename in input_filename ]
     else:
-        fasta_reader = open( input_filename )
+        fasta_readers = open( input_filename )
     
     for data_table_name, data_table_entry in _stream_fasta_to_file( fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params ):
         if data_table_entry:
@@ -271,10 +276,10 @@
         data_table_entries = _create_symlink( input_filename, target_directory, dbkey, dbkey_name, sequence_id, sequence_name )
     else:
         if isinstance( input_filename, list ):
-            fasta_reader = [ open( filename, 'rb' ) for filename in input_filename ]
+            fasta_readers = [ open( filename, 'rb' ) for filename in input_filename ]
         else:
-            fasta_reader = open( input_filename )    
-        data_table_entries = _stream_fasta_to_file( fasta_reader, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params )
+            fasta_readers = open( input_filename )    
+        data_table_entries = _stream_fasta_to_file( fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params )
     for data_table_name, data_table_entry in data_table_entries:
         if data_table_entry:
             _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name )
@@ -391,7 +396,7 @@
     
     filename = args[0]
     
-    params = from_json_string( open( filename ).read() )
+    params = loads( open( filename ).read() )
     target_directory = params[ 'output_data' ][0]['extra_files_path']
     os.mkdir( target_directory )
     data_manager_dict = {}
@@ -405,6 +410,6 @@
     REFERENCE_SOURCE_TO_DOWNLOAD[ params['param_dict']['reference_source']['reference_source_selector'] ]( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name )
     
     #save info to json file
-    open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
+    open( filename, 'wb' ).write( dumps( data_manager_dict ) )
         
 if __name__ == "__main__": main()
diff -r d59e1d23b388 -r 0e5299e77334 data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml
--- a/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml	Wed Jul 02 00:35:38 2014 -0400
+++ b/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml	Mon Jan 26 14:54:16 2015 -0500
@@ -2,9 +2,9 @@
     <description>fetching</description>
     <command interpreter="python">data_manager_fetch_genome_all_fasta_dbkeys.py "${out_file}" 
     #if str( $dbkey_source.dbkey_source_selector ) == 'existing':
-    --dbkey_description ${ dbkey.get_display_text() }
+    --dbkey_description ${ dbkey_source.dbkey.get_display_text() }
     #else
-    --dbkey_description "${ dbkey_source.dbkey_name or dbkey_source.dbkey }"
+    --dbkey_description "${ dbkey_source.dbkey_name or $dbkey_source.dbkey }"
     #end if
     
     </command>
@@ -24,7 +24,6 @@
         </conditional>
         
         <param type="text" name="sequence_name" value="" label="Name of sequence" />
-        <param type="text" name="sequence_desc" value="" label="Description of sequence" />
         <param type="text" name="sequence_id" value="" label="ID for sequence" />
         <conditional name="reference_source">
           <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
@@ -48,7 +47,7 @@
           </when>
           <when value="directory">
             <param type="text" name="fasta_filename" value="" label="Full path to FASTA File on disk" optional="False" />
-            <param type="boolean" name="create_symlink" truevalue="create_symlink" falsevalue="copy_file" label="Create symlink to orignal data instead of copying" checked="False" />
+            <param type="boolean" name="create_symlink" truevalue="create_symlink" falsevalue="copy_file" label="Create symlink to original data instead of copying" checked="False" />
           </when>
         </conditional>
         <conditional name="sorting">