Fixes for dealing with UnvalidatedValues (i.e. when running workflows) and also when passing None trans to dynamic options.

lib/galaxy/jobs/__init__.py

@@ -464,7 +464,7 @@ class JobWrapper( object ):
         # custom post process setup
         inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] )
         out_data = dict( [ ( da.name, da.dataset ) for da in job.output_datasets ] )
-        param_dict = dict( [ ( p.name, p.value ) for p in job.parameters ] ) # why not re-use self.param_dict here?
+        param_dict = dict( [ ( p.name, p.value ) for p in job.parameters ] ) # why not re-use self.param_dict here? ##dunno...probably should, this causes tools.parameters.basic.UnvalidatedValue to be used in following methods instead of validated and transformed values during i.e. running workflows
         param_dict = self.tool.params_from_strings( param_dict, self.app )
         # Check for and move associated_files
         self.tool.collect_associated_files(out_data)

lib/galaxy/tools/__init__.py

@@ -948,7 +948,10 @@ class Tool:
                 # Regular tool parameter
                 value = input_values[ input.name ]
                 if isinstance( value, UnvalidatedValue ):
-                    value = input.from_html( value.value, None, context )
+                    if value.value is None: #if value.value is None, it could not have been submited via html form and therefore .from_html can't be guaranteed to work
+                        value = None
+                    else:
+                        value = input.from_html( value.value, None, context )
                     # Then do any further validation on the value
                     input.validate( value, None )
                     input_values[ input.name ] = value

lib/galaxy/tools/parameters/dynamic_options.py

@@ -102,7 +102,7 @@ class DataMetaFilter( Filter ):
             if self.multiple:
                 return dataset_value in file_value.split( self.separator )
             return file_value == dataset_value
-        assert self.ref_name in other_values or trans.workflow_building_mode, "Required dependency '%s' not found in incoming values" % self.ref_name
+        assert self.ref_name in other_values or ( trans is not None and trans.workflow_building_mode), "Required dependency '%s' not found in incoming values" % self.ref_name
         ref = other_values.get( self.ref_name, None )
         if not isinstance( ref, self.dynamic_option.tool_param.tool.app.model.HistoryDatasetAssociation ):
             return [] #not a valid dataset
@@ -146,9 +146,9 @@ class ParamValueFilter( Filter ):
     def get_dependency_name( self ):
         return self.ref_name
     def filter_options( self, options, trans, other_values ):
-        if trans.workflow_building_mode: return []
+        if trans is not None and trans.workflow_building_mode: return []
+        assert self.ref_name in other_values, "Required dependency '%s' not found in incoming values" % self.ref_name
         ref = str( other_values.get( self.ref_name, None ) )
-        assert ref is not None, "Required dependency '%s' not found in incoming values" % self.ref_name
         rval = []
         for fields in options:
             if ( self.keep and fields[self.column] == ref ) or ( not self.keep and fields[self.column] != ref ):

tools/data_source/microbial_import_code.py

@@ -80,7 +80,7 @@ def load_microbial_data( GALAXY_DATA_INDEX_DIR, sep='\t' ):
     return microbe_info
 
 #post processing, set build for data and add additional data to history
-from galaxy import datatypes, config, jobs 
+from galaxy import datatypes, config, jobs, tools
 from shutil import copyfile
 
 def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
@@ -95,7 +95,12 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr
     #if not (kingdom or group or org):
     if not (kingdom or org):
         print "Parameters are not available."
-    
+    #workflow passes galaxy.tools.parameters.basic.UnvalidatedValue instead of values
+    if isinstance( kingdom, tools.parameters.basic.UnvalidatedValue ):
+        kingdom = kingdom.value
+    if isinstance( org, tools.parameters.basic.UnvalidatedValue ):
+        org = org.value
+    
     GALAXY_DATA_INDEX_DIR = app.config.tool_data_path
     microbe_info = load_microbial_data( GALAXY_DATA_INDEX_DIR, sep='\t' )
     new_stdout = ""