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Enhance GenomeSpace import tool to display a better history item name for additional primary datasets.

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This commit is contained in:
Daniel Blankenberg
2012-10-24 12:33:34 -04:00
parent a8dc575445
commit 43dafa165f
1 changed files with 9 additions and 3 deletions
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tools/genomespace/genomespace_importer.py
+9 -3
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@@ -100,7 +100,7 @@ def download_from_genomespace_importer( username, token, json_parameter_file, ge
datasource_params = json_params.get( 'param_dict' )
assert None not in [ username, token ], "Missing GenomeSpace username or token."
output_filename = datasource_params.get( "output_file1", None )
dataset_id = json_params['output_data'][0]['dataset_id']
dataset_id = base_dataset_id = json_params['output_data'][0]['dataset_id']
hda_id = json_params['output_data'][0]['hda_id']
url_opener = get_cookie_opener( username, token )
#load and set genomespace format ids to galaxy exts
@@ -182,12 +182,18 @@ def download_from_genomespace_importer( username, token, json_parameter_file, ge
name = "GenomeSpace importer on %s" % ( filename ) ) ) )
#if using tmp file, move the file to the new file path dir to get scooped up later
if using_temp_file:
original_filename = filename
filename = ''.join( c in VALID_CHARS and c or '-' for c in filename )
while filename in used_filenames:
filename = "-%s" % filename
used_filenames.append( filename )
shutil.move( output_filename, os.path.join( datasource_params['__new_file_path__'], 'primary_%i_%s_visible_%s' % ( hda_id, filename, file_type ) ) )
target_output_filename = os.path.join( datasource_params['__new_file_path__'], 'primary_%i_%s_visible_%s' % ( hda_id, filename, file_type ) )
shutil.move( output_filename, target_output_filename )
metadata_parameter_file.write( "%s\n" % simplejson.dumps( dict( type = 'new_primary_dataset',
base_dataset_id = base_dataset_id,
ext = file_type,
filename = target_output_filename,
name = "GenomeSpace importer on %s" % ( original_filename ) ) ) )
dataset_id = None #only one primary dataset available
output_filename = None #only have one filename available
metadata_parameter_file.close()