diff --git a/lib/galaxy/tools/parameters/grouping.py b/lib/galaxy/tools/parameters/grouping.py index b4f71073ee0..36517ff6d09 100644 --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -100,8 +100,7 @@ class UploadDataset( Group ): self.file_type_to_ext = { 'auto':self.default_file_type } self.metadata_ref = 'files_metadata' def get_file_base_name( self, context ): - log.debug('### uploadDataset get base name context = %s' % str(context)) - fd = context.get('files_metadata|base_name','?') + fd = context.get('files_metadata|base_name','Galaxy_Composite_file') return fd def get_file_type( self, context ): return context.get( self.file_type_name, self.default_file_type ) @@ -295,14 +294,16 @@ class UploadDataset( Group ): temp_name, is_multi_byte = sniff.stream_to_file( StringIO.StringIO( d_type.generate_primary_file( dataset ) ), prefix='upload_auto_primary_file' ) dataset.primary_file = temp_name dataset.space_to_tab = False - dataset.precreated_name = dataset.name = dataset.metadata['base_name'] # was 'Uploaded Composite Dataset (%s)' % ( file_type ) + dsn = dataset.metadata.get('base_name','Uploaded Composite Dataset (%s)' % file_type) + dataset.precreated_name = dataset.name = dsn else: file_bunch, warnings = get_one_filename( groups_incoming[ 0 ] ) writable_files_offset = 1 dataset.primary_file = file_bunch.path dataset.space_to_tab = file_bunch.space_to_tab - dataset.precreated_name = dataset.metadata['base_name'] # file_bunch.precreated_name - dataset.name = file_bunch.precreated_name + dsn = dataset.metadata.get('base_name',file_bunch.precreated_name) + dataset.precreated_name = dsn + dataset.name = dsn dataset.warnings.extend( file_bunch.warnings ) if dataset.primary_file is None:#remove this before finish, this should create an empty dataset raise Exception( 'No primary dataset file was available for composite upload' ) diff --git a/lib/galaxy/web/controllers/dataset.py b/lib/galaxy/web/controllers/dataset.py index b951c9b9231..6690864295c 100644 --- a/lib/galaxy/web/controllers/dataset.py +++ b/lib/galaxy/web/controllers/dataset.py @@ -246,7 +246,6 @@ class DatasetInterface( BaseController, UsesAnnotations, UsesHistoryDatasetAssoc ext = data.extension path = data.file_name fname = os.path.split(path)[-1] - basename = data.metadata.base_name efp = data.extra_files_path htmlname = os.path.splitext(outfname)[0] if not htmlname.endswith(ext): diff --git a/static/images/Armitagep_manhattan.png b/static/images/Armitagep_manhattan.png index 91065a38189..16244b06472 100644 Binary files a/static/images/Armitagep_manhattan.png and b/static/images/Armitagep_manhattan.png differ diff --git a/static/images/Armitagep_qqplot.png b/static/images/Armitagep_qqplot.png index 384419cd0a9..2e4ee961b82 100644 Binary files a/static/images/Armitagep_qqplot.png and b/static/images/Armitagep_qqplot.png differ