Merged in jmchilton/galaxy-central-fork-1 (pull request #389)

Small Column Parameter Enhancements

lib/galaxy/tools/parameters/basic.py

@@ -1096,7 +1096,13 @@ class ColumnListParameter( SelectToolParameter ):
         self.accept_default = string_as_bool( elem.get( "accept_default", False ))
         self.data_ref = elem.get( "data_ref", None )
         self.ref_input = None
+        # Legacy style default value specification...
         self.default_value = elem.get( "default_value", None )
+        if self.default_value is None:
+            # Newer style... more in line with other parameters.
+            self.default_value = elem.get( "value", None )
+        if self.default_value is not None:
+            self.default_value = ColumnListParameter._strip_c( self.default_value )
         self.is_dynamic = True
         self.usecolnames = string_as_bool( elem.get( "use_header_names", False ))
 
@@ -1105,10 +1111,6 @@ class ColumnListParameter( SelectToolParameter ):
         Label convention prepends column number with a 'c', but tool uses the integer. This
         removes the 'c' when entered into a workflow.
         """
-        def _strip_c( column ):
-            if column.startswith( 'c' ):
-                column = column.strip().lower()[1:]
-            return column
         if self.multiple:
             #split on newline and ,
             if value:
@@ -1120,16 +1122,22 @@ class ColumnListParameter( SelectToolParameter ):
                         column2 = column2.strip()
                         if column2:
                             column_list.append( column2 )
-                value = map( _strip_c, column_list )
+                value = map( ColumnListParameter._strip_c, column_list )
             else:
                 value = []
         else:
             if value:
-                value = _strip_c( value )
+                value = ColumnListParameter._strip_c( value )
             else:
                 value = None
         return super( ColumnListParameter, self ).from_html( value, trans, context )
 
+    @staticmethod
+    def _strip_c(column):
+        if column.startswith( 'c' ):
+            column = column.strip().lower()[1:]
+        return column
+
     def get_column_list( self, trans, other_values ):
         """
         Generate a select list containing the columns of the associated

test/unit/tools/test_column_parameters.py

@@ -0,0 +1,97 @@
+""" Tests for tool parameters, more tests exist in test_data_parameters.py and
+test_select_parameters.py.
+"""
+
+from unittest import TestCase
+from galaxy.tools.parameters import basic
+from galaxy.util import bunch
+from galaxy import model
+from elementtree.ElementTree import XML
+
+import tools_support
+
+
+class DataColumnParameterTestCase( TestCase, tools_support.UsesApp ):
+
+    def test_from_html(self):
+        value = self.param.from_html("3", self.trans, { "input_tsv": self.build_ready_hda()  } )
+        assert value == "3"
+
+    def test_from_html_strips_c(self):
+        value = self.param.from_html("c1", self.trans, { "input_tsv": self.build_ready_hda()  } )
+        assert value == "1"
+
+    def test_multiple_from_html(self):
+        self.multiple = True
+        value = self.param.from_html("1,2,3", self.trans, { "input_tsv": self.build_ready_hda()  } )
+        assert value == ["1", "2", "3"]
+
+    def test_multiple_from_html_with_c(self):
+        self.multiple = True
+        value = self.param.from_html("c1,c2,c3", self.trans, { "input_tsv": self.build_ready_hda()  } )
+        assert value == ["1", "2", "3"]
+
+    def test_get_initial_value_default(self):
+        self.assertEqual( '1', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda()  } ) )
+
+    def test_get_initial_value_override_legacy(self):
+        self.other_attributes = "default_value='2'"
+        self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) )
+
+    def test_get_initial_value_override_newstyle(self):
+        self.other_attributes = "value='2'"
+        self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) )
+
+    def test_get_initial_value_override_newstyle_strips_c(self):
+        self.other_attributes = "value='c2'"
+        self.assertEqual( '2', self.param.get_initial_value( self.trans, { "input_tsv": self.build_ready_hda() } ) )
+
+    def setUp( self ):
+        self.setup_app( mock_model=False )
+        self.mock_tool = bunch.Bunch(
+            app=self.app,
+            tool_type="default",
+        )
+        self.test_history = model.History()
+        self.app.model.context.add( self.test_history )
+        self.app.model.context.flush()
+        self.trans = bunch.Bunch(
+            app=self.app,
+            get_history=lambda: self.test_history,
+            get_current_user_roles=lambda: [],
+            workflow_building_mode=False,
+            webapp=bunch.Bunch( name="galaxy" ),
+        )
+
+        self.type = "data_column"
+        self.other_attributes = ""
+        self.set_data_ref = "input_tsv"
+        self.multiple = False
+        self.optional = False
+        self._param = None
+
+    def build_ready_hda(self):
+        hist = model.History()
+        self.app.model.context.add( hist )
+        ready_hda = hist.add_dataset( model.HistoryDatasetAssociation( extension='interval', create_dataset=True, sa_session=self.app.model.context ) )
+        ready_hda.set_dataset_state( 'ok' )
+        return ready_hda
+
+    @property
+    def param( self ):
+        if not self._param:
+            multi_text = ""
+            if self.multiple:
+                multi_text = 'multiple="True"'
+            optional_text = ""
+            if self.optional:
+                optional_text = 'optional="True"'
+            data_ref_text = ""
+            if self.set_data_ref:
+                data_ref_text = 'data_ref="input_tsv"'
+            template_xml = '''<param name="my_name" type="%s" %s %s %s %s></param>'''
+            self.param_xml = XML( template_xml % ( self.type, data_ref_text, multi_text, optional_text, self.other_attributes ) )
+            self._param = basic.ColumnListParameter( self.mock_tool, self.param_xml )
+            self._param.ref_input = bunch.Bunch(formats=[model.datatypes_registry.get_datatype_by_extension("tabular")])
+
+        return self._param