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Some genomespace_file_browser tweaks.

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This commit is contained in:
Daniel Blankenberg
2011-10-06 14:22:59 -04:00
parent e8d8d8e7c3
commit 68f2b7656b
2 changed files with 3 additions and 5 deletions
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lib/galaxy/tools/__init__.py
+1
View File
@@ -2028,6 +2028,7 @@ class DataSourceTool( Tool ):
data_dict = dict( out_data_name = out_name,
ext = data.ext,
dataset_id = data.dataset.id,
hda_id = data.id,
file_name = file_name,
extra_files_path = extra_files_path )
tools/data_source/genomespace_file_browser.py
+2 -5
View File
@@ -109,8 +109,8 @@ def download_from_genomespace_file_browser( json_parameter_file ):
assert None not in [ username, token ], "Missing GenomeSpace username or token."
output_filename = datasource_params.get( "output", None )
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 )
file_count = 1
file_url_prefix = "fileUrl"
file_type_prefix = "fileFormat"
metadata_parameter_file = open( json_params['job_config']['TOOL_PROVIDED_JOB_METADATA_FILE'], 'wb' )
@@ -120,19 +120,16 @@ def download_from_genomespace_file_browser( json_parameter_file ):
name = name[len( file_url_prefix ):]
file_numbers.append( int( name ) )
file_numbers.sort()
print 'file_numbers', file_numbers
#print 'datasource_params', datasource_params
for file_num in file_numbers:
url_key = "%s%i" % ( file_url_prefix, file_num )
download_url = datasource_params.get( url_key, None )
if download_url is None:
print 'wtf none', file_num
break
filetype_key = "%s%i" % ( file_type_prefix, file_num )
filetype_url = datasource_params.get( filetype_key, None )
galaxy_ext = get_galaxy_ext_from_genomespace_format_url( url_opener, filetype_url )
if output_filename is None:
output_filename = os.path.join( datasource_params['__new_file_path__'], 'primary_%i_output%i_visible_%s' % ( dataset_id, file_count, galaxy_ext ) )
output_filename = os.path.join( datasource_params['__new_file_path__'], 'primary_%i_output%i_visible_%s' % ( hda_id, file_num, galaxy_ext ) )
else:
if dataset_id is not None:
metadata_parameter_file.write( "%s\n" % simplejson.dumps( dict( type = 'dataset',