Add hda agent generation to dynamic options

galaxyproject · Aug 1, 2016 · bccf3d5 · bccf3d5
1 parent b34757b
commit bccf3d5
Show file tree

Hide file tree

Showing 2 changed files with 18 additions and 6 deletions.
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
@@ -3299,9 +3299,17 @@ def type_id( cls ):
         return (( type_coerce( cls.content_type, types.Unicode ) + u'-' +
                   type_coerce( cls.id, types.Unicode ) ).label( 'type_id' ))
 
-    def to_hda_agent( self ):
-        if len( self.collection.dataset_elements ) > 0:
-            return self.collection.dataset_elements[ 0 ].dataset_instance
+    def to_hda_agent( self, multiple=False ):
+        rval = []
+        for dataset in self.collection.dataset_elements:
+            rval.append( dataset.dataset_instance )
+            if multiple is False:
+                break
+        if len( rval ) > 0:
+            if multiple:
+                return rval
+            else:
+                return rval[ 0 ]
 
     def to_dict( self, view='collection' ):
         dict_value = dict(

diff --git a/lib/galaxy/tools/parameters/dynamic_options.py b/lib/galaxy/tools/parameters/dynamic_options.py
@@ -7,7 +7,7 @@
 import os
 import validation
 from galaxy.util import string_as_bool
-from galaxy.model import User
+from galaxy.model import User, HistoryDatasetAssociation, HistoryDatasetCollectionAssociation
 import galaxy.tools
 
 log = logging.getLogger(__name__)
@@ -125,10 +125,12 @@ def compare_meta_value( file_value, dataset_value ):
                 return dataset_value in file_value.split( self.separator )
             return file_value == dataset_value
         ref = other_values.get( self.ref_name, None )
+        if isinstance( ref, HistoryDatasetCollectionAssociation ):
+            ref = ref.to_hda_agent( self.multiple )
         is_data = isinstance( ref, galaxy.tools.wrappers.DatasetFilenameWrapper )
         is_data_list = isinstance( ref, galaxy.tools.wrappers.DatasetListWrapper ) or isinstance( ref, list )
         is_data_or_data_list = is_data or is_data_list
-        if not isinstance( ref, self.dynamic_option.tool_param.tool.app.model.HistoryDatasetAssociation ) and not is_data_or_data_list:
+        if not isinstance( ref, HistoryDatasetAssociation ) and not is_data_or_data_list:
             return []  # not a valid dataset
 
         if is_data_list:
@@ -398,7 +400,9 @@ def compare_value( option_value, filter_value ):
                 value = other_values.get( self.ref_name )
             else:
                 data_ref = other_values.get( self.meta_ref )
-                if not isinstance( data_ref, self.dynamic_option.tool_param.tool.app.model.HistoryDatasetAssociation ) and not isinstance( data_ref, galaxy.tools.wrappers.DatasetFilenameWrapper ):
+                if isinstance( data_ref, HistoryDatasetCollectionAssociation ):
+                    data_ref = data_ref.to_hda_agent()
+                if not isinstance( data_ref, HistoryDatasetAssociation ) and not isinstance( data_ref, galaxy.tools.wrappers.DatasetFilenameWrapper ):
                     return options  # cannot modify options
                 value = data_ref.metadata.get( self.metadata_key, None )
         return [ ( disp_name, optval, selected ) for disp_name, optval, selected in options if not compare_value( optval, value ) ]