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Fix to scatterplot to use non-dictionary hda

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This commit is contained in:
Carl Eberhard
2013-05-21 10:58:08 -04:00
parent 7f61cabe0d
commit d98e75dcde
1 changed files with 2 additions and 40 deletions
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lib/galaxy/webapps/galaxy/controllers/visualization.py
+2 -40
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@@ -883,48 +883,10 @@ class VisualizationController( BaseUIController, SharableMixin, UsesAnnotations,
"""
Returns a page that controls and renders a scatteplot graph.
"""
# Get HDA.
hda = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True )
hda_dict = hda.get_api_value()
hda_dict[ 'id' ] = dataset_id
if( ( hda_dict[ 'metadata_column_names' ] == None )
and ( hasattr( hda.datatype, 'column_names' ) ) ):
hda_dict[ 'metadata_column_names' ] = hda.datatype.column_names
# try to get the first line (assuming it's a header)
#TODO: doesn't belong here
try:
num_comment_lines = 1
if hda_dict[ 'metadata_comment_lines' ]:
num_comment_lines = hda_dict[ 'metadata_comment_lines' ]
infile = open( hda.file_name )
for index, line in enumerate( infile ):
if 'comment_lines' not in hda_dict:
hda_dict[ 'comment_lines' ] = []
hda_dict[ 'comment_lines' ].append( line )
if index >= num_comment_lines:
break
infile.close()
except Exception, exc:
if infile:
infile.close()
log.error( str( exc ) )
history_id = trans.security.encode_id( hda.history.id )
#TODO: add column data
# Read data.
#data_provider = ColumnDataProvider( original_dataset=hda, **kwargs )
#data = data_provider.get_data()
# Return plot.
return trans.fill_template_mako( "visualization/scatterplot.mako",
hda=hda_dict,
historyID=history_id,
kwargs=kwargs )
hda=hda,
query_args=kwargs )
@web.expose
def phyloviz( self, trans, dataset_id, tree_index=0, **kwargs ):