From f05c9518be52ecaa9cb13885aeec3f57054e976a Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 15 Jan 2016 18:38:38 -0500
Subject: [PATCH 01/33] Remove unvalidated values

---
 lib/galaxy/tools/parameters/basic.py          | 47 ++++---------------
 .../tools/parameters/dynamic_options.py       |  2 +-
 2 files changed, 11 insertions(+), 38 deletions(-)

diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 2822a185d803..5043adbf9774 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -885,12 +885,8 @@ def get_options( self, trans, other_values ):
             return self.static_options
 
     def get_legal_values( self, trans, other_values ):
-        def _get_UnvalidatedValue_value( value ):
-            if isinstance( value, UnvalidatedValue ):
-                return value.value
-            return value
         if self.options:
-            return map( _get_UnvalidatedValue_value, set( v for _, v, _ in self.options.get_options( trans, other_values ) ) )
+            return set( v for _, v, _ in self.options.get_options( trans, other_values ) )
         elif self.dynamic_options:
             try:
                 call_other_values = self._get_dynamic_options_call_other_values( trans, other_values )
@@ -906,8 +902,6 @@ def get_html_field( self, trans=None, value=None, context={} ):
         # specifying the value as text for now.
         options = list(self.get_options( trans, context ))
         if len(list(options)) == 0 and (trans is None or trans.workflow_building_mode):
-            if isinstance( value, UnvalidatedValue ):
-                value = value.value
             if self.multiple:
                 if value is None:
                     value = ""
@@ -919,13 +913,8 @@ def get_html_field( self, trans=None, value=None, context={} ):
         if value is not None:
             if not isinstance( value, list ):
                 value = [ value ]
-            # We could have an unvalidated value here when e.g. running a workflow.
-            value = [ val.value if isinstance( val, UnvalidatedValue ) else val for val in value ]
         field = form_builder.SelectField( self.name, self.multiple, self.display, self.refresh_on_change, refresh_on_change_values=self.refresh_on_change_values )
         for text, optval, selected in options:
-            if isinstance( optval, UnvalidatedValue ):
-                optval = optval.value
-                text = "%s (unvalidated)" % text
             if value:
                 selected = ( optval in value )
             field.add_option( text, optval, selected )
@@ -947,7 +936,7 @@ def from_html( self, value, trans=None, context={} ):
                         # in interpreting values but also is needed because many browsers
                         # use \r\n to separate lines.
                         value = value.split()
-            return UnvalidatedValue( value )
+            return value
         if not legal_values and self.optional:
             return None
         if not legal_values:
@@ -1000,9 +989,7 @@ def to_param_dict_string( self, value, other_values={}, value_map=DEFAULT_VALUE_
         return value
 
     def value_to_basic( self, value, app ):
-        if isinstance( value, UnvalidatedValue ):
-            return { "__class__": "UnvalidatedValue", "value": value.value }
-        elif isinstance( value, RuntimeValue ):
+        if isinstance( value, RuntimeValue ):
             # Need to handle runtime value's ourself since delegating to the
             # parent method causes the value to be turned into a string, which
             # breaks multiple selection
@@ -1010,14 +997,15 @@ def value_to_basic( self, value, app ):
         return value
 
     def value_from_basic( self, value, app, ignore_errors=False ):
+        # Backward compatibility for unvalidated values already stored in databases
         if isinstance( value, dict ) and value.get( "__class__", None ) == "UnvalidatedValue":
-            return UnvalidatedValue( value["value"] )
+            return value[ "value" ]
         return super( SelectToolParameter, self ).value_from_basic( value, app, ignore_errors=ignore_errors )
 
     def get_initial_value( self, trans, context, history=None ):
         options = list( self.get_options( trans, context ) )
         if len(options) == 0 and (trans is None or trans.workflow_building_mode):
-            return UnvalidatedValue( None )
+            return None
         value = [ optval for _, optval, selected in options if selected ]
         if len( value ) == 0:
             if not self.optional and not self.multiple and options:
@@ -1031,11 +1019,6 @@ def get_initial_value( self, trans, context, history=None ):
         return value
 
     def value_to_display_text( self, value, app ):
-        if isinstance( value, UnvalidatedValue ):
-            suffix = "\n(value not yet validated)"
-            value = value.value
-        else:
-            suffix = ""
         if not isinstance( value, list ):
             value = [ value ]
         # FIXME: Currently only translating values back to labels if they
@@ -1048,7 +1031,7 @@ def value_to_display_text( self, value, app ):
             for t, v, s in options:
                 if v in value:
                     rval.append( t )
-        return "\n".join( rval ) + suffix
+        return "\n".join( rval )
 
     def get_dependencies( self ):
         """
@@ -1547,8 +1530,6 @@ def get_html_field( self, trans=None, value=None, other_values={} ):
         # specifying the value as text for now.
         options = self.get_options( trans, value, other_values )
         if len(list(options)) == 0 and (trans is None or trans.workflow_building_mode):
-            if isinstance( value, UnvalidatedValue ):
-                value = value.value
             if self.multiple:
                 if value is None:
                     value = ""
@@ -1567,7 +1548,7 @@ def from_html( self, value, trans=None, other_values={} ):
                     value = None
                 else:
                     value = value.split( "\n" )
-            return UnvalidatedValue( value )
+            return value
         if not value and not self.optional:
             raise ValueError( "An invalid option was selected for %s, 'None', please verify" % (self.name) )
         if not value:
@@ -1634,7 +1615,7 @@ def recurse_options( initial_values, options ):
         # More working around dynamic options for workflow
         options = self.get_options( trans=trans, other_values=context )
         if len(list(options)) == 0 and (trans is None or trans.workflow_building_mode):
-            return UnvalidatedValue( None )
+            return None
         initial_values = []
         recurse_options( initial_values, options )
         if len( initial_values ) == 0:
@@ -1650,12 +1631,6 @@ def get_option_display( value, options ):
                 if rval:
                     return rval
             return None  # not found
-
-        if isinstance( value, UnvalidatedValue ):
-            suffix = "\n(value not yet validated)"
-            value = value.value
-        else:
-            suffix = ""
         if not value:
             value = []
         elif not isinstance( value, list ):
@@ -1674,7 +1649,7 @@ def get_option_display( value, options ):
             rval = []
             for val in value:
                 rval.append( get_option_display( val, self.options ) or val )
-        return "\n".join( map( str, rval ) ) + suffix
+        return "\n".join( map( str, rval ) )
 
     def get_dependencies( self ):
         """
@@ -2656,7 +2631,6 @@ def _allow_workflow_parameters_in_context(trans):
     drill_down=DrillDownSelectToolParameter
 )
 
-
 class UnvalidatedValue( object ):
     """
     Wrapper to mark a value that has not been validated
@@ -2667,7 +2641,6 @@ def __init__( self, value ):
     def __str__( self ):
         return str( self.value )
 
-
 class RuntimeValue( object ):
     """
     Wrapper to note a value that is not yet set, but will be required at
diff --git a/lib/galaxy/tools/parameters/dynamic_options.py b/lib/galaxy/tools/parameters/dynamic_options.py
index e6cb93350fd5..e33cec7780f7 100644
--- a/lib/galaxy/tools/parameters/dynamic_options.py
+++ b/lib/galaxy/tools/parameters/dynamic_options.py
@@ -148,7 +148,7 @@ def compare_meta_value( file_value, dataset_value ):
             meta_value = ref.metadata.get( self.key, None )
 
         if meta_value is None:  # assert meta_value is not None, "Required metadata value '%s' not found in referenced dataset" % self.key
-            return [ ( disp_name, basic.UnvalidatedValue( optval ), selected ) for disp_name, optval, selected in options ]
+            return [ ( disp_name, optval, selected ) for disp_name, optval, selected in options ]
 
         if self.column is not None:
             rval = []

From 89ba002475695d09542dbe85886c6d69e6f54307 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sat, 16 Jan 2016 16:27:07 -0500
Subject: [PATCH 02/33] Remove late validation handling

---
 lib/galaxy/tools/__init__.py            | 80 +++----------------------
 lib/galaxy/tools/evaluation.py          |  9 ++-
 lib/galaxy/tools/parameters/__init__.py | 29 +++++----
 lib/galaxy/tools/parameters/basic.py    | 34 ++++++-----
 4 files changed, 50 insertions(+), 102 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 06035765aa03..0fb65d78e703 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1741,58 +1741,6 @@ def check_and_update_param_values_helper( self, inputs, values, trans, messages,
                         if update_values:
                             values[ input.name ] = input.get_initial_value( trans, context )
 
-    def handle_unvalidated_param_values( self, input_values, app ):
-        """
-        Find any instances of `UnvalidatedValue` within input_values and
-        validate them (by calling `ToolParameter.from_html` and
-        `ToolParameter.validate`).
-        """
-        # No validation is done when check_values is False
-        if not self.check_values:
-            return
-        self.handle_unvalidated_param_values_helper( self.inputs, input_values, app )
-
-    def handle_unvalidated_param_values_helper( self, inputs, input_values, app, context=None, prefix="" ):
-        """
-        Recursive helper for `handle_unvalidated_param_values`
-        """
-        context = ExpressionContext( input_values, context )
-        for input in inputs.itervalues():
-            if isinstance( input, Repeat ):
-                for i, d in enumerate( input_values[ input.name ] ):
-                    rep_prefix = prefix + "%s %d > " % ( input.title, i + 1 )
-                    self.handle_unvalidated_param_values_helper( input.inputs, d, app, context, rep_prefix )
-            elif isinstance( input, Conditional ):
-                values = input_values[ input.name ]
-                current = values["__current_case__"]
-                # NOTE: The test param doesn't need to be checked since
-                #       there would be no way to tell what case to use at
-                #       workflow build time. However I'm not sure if we are
-                #       actually preventing such a case explicately.
-                self.handle_unvalidated_param_values_helper( input.cases[current].inputs, values, app, context, prefix )
-            else:
-                # Regular tool parameter
-                value = input_values[ input.name ]
-                if isinstance( value, UnvalidatedValue ):
-                    try:
-                        # Convert from html representation
-                        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 )
-                        # Do any further validation on the value
-                        input.validate( value, None )
-                    except Exception, e:
-                        # Wrap an re-raise any generated error so we can
-                        # generate a more informative message
-                        message = "Failed runtime validation of %s%s (%s)" \
-                            % ( prefix, input.label, e )
-                        raise LateValidationError( message )
-                    input_values[ input.name ] = value
-
     def handle_job_failure_exception( self, e ):
         """
         Called by job.fail when an exception is generated to allow generation
@@ -2152,12 +2100,6 @@ def to_json(self, trans, kwd={}, job=None, workflow_mode=False):
 
         # convert value to jsonifiable value
         def jsonify(v):
-            if isinstance(v, UnvalidatedValue):
-                v = v.value
-                while isinstance( v, UnvalidatedValue ):
-                    v = v.value
-                return v
-
             # check if value is numeric
             isnumber = False
             try:
@@ -2219,29 +2161,21 @@ def sanitize(dict, key='value'):
             dict[key] = value
 
         # check the current state of a value and update it if necessary
-        def check_state(trans, input, value, context):
+        def check_state( trans, input, value, context ):
             error = 'State validation failed.'
-
-            # handle unvalidated values
-            if isinstance(value, galaxy.tools.parameters.basic.DummyDataset):
+            if isinstance( value, galaxy.tools.parameters.basic.DummyDataset ):
                 return [ None, None ]
-            elif isinstance(value, galaxy.tools.parameters.basic.RuntimeValue):
+            elif isinstance( value, galaxy.tools.parameters.basic.RuntimeValue ):
                 return [ { '__class__' : 'RuntimeValue' }, None ]
             elif isinstance( value, dict ):
-                if value.get('__class__') == 'RuntimeValue':
+                if value.get( '__class__' ) == 'RuntimeValue':
                     return [ value, None ]
-
-            # validate value content
             try:
-                # resolves the inconsistent definition of boolean parameters (see base.py) without modifying shared code
-                if input.type == 'boolean' and isinstance(value, basestring):
-                    value, error = [string_as_bool(value), None]
-                else:
-                    value, error = check_param(trans, input, value, context, history=history, workflow_building_mode=workflow_mode)
+                value, error = check_param( trans, input, value, context, history=history, boolean_fix=True, workflow_building_mode=workflow_mode )
             except Exception, err:
-                log.error('Checking parameter %s failed. %s', input.name, str(err))
+                log.error( 'Checking parameter %s failed. %s', input.name, str( err ) )
                 pass
-            return [value, error]
+            return [ value, error ]
 
         # populates state with incoming url parameters
         def populate_state(trans, inputs, state, errors, incoming, prefix="", context=None ):
diff --git a/lib/galaxy/tools/evaluation.py b/lib/galaxy/tools/evaluation.py
index 3b53819c95e5..2e6633f4110d 100644
--- a/lib/galaxy/tools/evaluation.py
+++ b/lib/galaxy/tools/evaluation.py
@@ -21,7 +21,7 @@
     DataCollectionToolParameter,
     SelectToolParameter,
 )
-from galaxy.tools.parameters import wrapped_json
+from galaxy.tools.parameters import wrapped_json, visit_input_values
 from galaxy.tools.parameters.grouping import Conditional, Repeat, Section
 from galaxy.tools import global_tool_errors
 from galaxy.jobs.datasets import dataset_path_rewrites
@@ -52,8 +52,11 @@ def set_compute_environment( self, compute_environment, get_special=None ):
         job = self.job
         incoming = dict( [ ( p.name, p.value ) for p in job.parameters ] )
         incoming = self.tool.params_from_strings( incoming, self.app )
-        # Do any validation that could not be done at job creation
-        self.tool.handle_unvalidated_param_values( incoming, self.app )
+        def validate_inputs( input, value, prefixed_name, prefixed_label, context ):
+            value = input.from_html( value, None, context )
+            input.validate( value, None )
+        visit_input_values ( self.tool.inputs, incoming, validate_inputs, details=True )
+
         # Restore input / output data lists
         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 ] )
diff --git a/lib/galaxy/tools/parameters/__init__.py b/lib/galaxy/tools/parameters/__init__.py
index 67e5bf6f060f..bbfaf26a6a7b 100644
--- a/lib/galaxy/tools/parameters/__init__.py
+++ b/lib/galaxy/tools/parameters/__init__.py
@@ -5,11 +5,12 @@
 from basic import DataCollectionToolParameter, DataToolParameter, SelectToolParameter
 from grouping import Conditional, Repeat, Section, UploadDataset
 from galaxy.util.json import dumps, json_fix, loads
+from galaxy.util.expressions import ExpressionContext
 
 REPLACE_ON_TRUTHY = object()
 
 
-def visit_input_values( inputs, input_values, callback, name_prefix="", label_prefix="", no_replacement_value=REPLACE_ON_TRUTHY ):
+def visit_input_values( inputs, input_values, callback, name_prefix="", label_prefix="", no_replacement_value=REPLACE_ON_TRUTHY, context=None, details=False ):
     """
     Given a tools parameter definition (`inputs`) and a specific set of
     parameter `values`, call `callback` for each non-grouping parameter,
@@ -22,30 +23,35 @@ def visit_input_values( inputs, input_values, callback, name_prefix="", label_pr
            Repeat and Group. This tracks labels and those do not. It would
            be nice to unify all the places that recursively visit inputs.
     """
+    context = ExpressionContext( input_values, context )
     for input in inputs.itervalues():
         if isinstance( input, Repeat ) or isinstance( input, UploadDataset ):
             for i, d in enumerate( input_values[ input.name ] ):
                 index = d['__index__']
                 new_name_prefix = name_prefix + "%s_%d|" % ( input.name, index )
                 new_label_prefix = label_prefix + "%s %d > " % ( input.title, i + 1 )
-                visit_input_values( input.inputs, d, callback, new_name_prefix, new_label_prefix, no_replacement_value=no_replacement_value )
+                visit_input_values( input.inputs, d, callback, new_name_prefix, new_label_prefix, no_replacement_value=no_replacement_value, context=context, details=details )
         elif isinstance( input, Conditional ):
             values = input_values[ input.name ]
             current = values["__current_case__"]
             label_prefix = label_prefix
             new_name_prefix = name_prefix + input.name + "|"
-            visit_input_values( input.cases[current].inputs, values, callback, new_name_prefix, label_prefix, no_replacement_value=no_replacement_value )
+            visit_input_values( input.cases[current].inputs, values, callback, new_name_prefix, label_prefix, no_replacement_value=no_replacement_value, context=context, details=details )
         elif isinstance( input, Section ):
             values = input_values[ input.name ]
             label_prefix = label_prefix
             new_name_prefix = name_prefix + input.name + "|"
-            visit_input_values( input.inputs, values, callback, new_name_prefix, label_prefix, no_replacement_value=no_replacement_value )
+            visit_input_values( input.inputs, values, callback, new_name_prefix, label_prefix, no_replacement_value=no_replacement_value, context=context, details=details )
         else:
-            new_value = callback( input,
-                                  input_values[input.name],
-                                  prefixed_name=name_prefix + input.name,
-                                  prefixed_label=label_prefix + input.label )
-
+            args = {
+                'input'             : input,
+                'value'             : input_values[input.name],
+                'prefixed_name'     : name_prefix + input.name,
+                'prefixed_label'    : label_prefix + input.label
+            }
+            if details:
+                args[ 'context' ] = context
+            new_value = callback( **args )
             if no_replacement_value is REPLACE_ON_TRUTHY:
                 replace = bool(new_value)
             else:
@@ -54,7 +60,7 @@ def visit_input_values( inputs, input_values, callback, name_prefix="", label_pr
                 input_values[input.name] = new_value
 
 
-def check_param( trans, param, incoming_value, param_values, source='html', history=None, workflow_building_mode=False ):
+def check_param( trans, param, incoming_value, param_values, source='html', boolean_fix=False, history=None, workflow_building_mode=False ):
     """
     Check the value of a single parameter `param`. The value in
     `incoming_value` is converted from its HTML encoding and validated.
@@ -65,6 +71,9 @@ def check_param( trans, param, incoming_value, param_values, source='html', hist
     value = incoming_value
     error = None
     try:
+        # resolves the inconsistent definition of boolean parameters (see base.py) without modifying shared code
+        if boolean_fix and param.type == 'boolean' and isinstance( value, basestring ):
+            return [ string_as_bool( value ), None ]
         if history is None:
             history = trans.history
         if value is not None or isinstance( param, DataToolParameter ) or isinstance( param, DataCollectionToolParameter ):
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 5043adbf9774..f92e283c20e3 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -1962,7 +1962,9 @@ def dataset_collector( datasets ):
             return most_recent_dataset[0]
         return ''
 
-    def from_html( self, value, trans, other_values={} ):
+    def from_html( self, value, trans, other_values={}, app=None ):
+        if app is None:
+            app = trans.app
         # Can't look at history in workflow mode, skip validation and such,
         # although, this should never be called in workflow mode right?
         if trans.workflow_building_mode:
@@ -1979,44 +1981,44 @@ def from_html( self, value, trans, other_values={} ):
             for single_value in value:
                 if isinstance( single_value, dict ) and 'src' in single_value and 'id' in single_value:
                     if single_value['src'] == 'hda':
-                        rval.append(trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.app.security.decode_id(single_value['id']) ))
+                        rval.append(app.sa_session.query( app.model.HistoryDatasetAssociation ).get( app.security.decode_id(single_value['id']) ))
                     elif single_value['src'] == 'hdca':
                         found_hdca = True
-                        decoded_id = trans.app.security.decode_id( single_value[ 'id' ] )
-                        rval.append( trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( decoded_id ) )
+                        decoded_id = app.security.decode_id( single_value[ 'id' ] )
+                        rval.append( app.sa_session.query( app.model.HistoryDatasetCollectionAssociation ).get( decoded_id ) )
                     else:
                         raise ValueError("Unknown input source %s passed to job submission API." % single_value['src'])
-                elif isinstance( single_value, trans.app.model.HistoryDatasetCollectionAssociation ):
+                elif isinstance( single_value, app.model.HistoryDatasetCollectionAssociation ):
                     rval.append( single_value )
-                elif isinstance( single_value, trans.app.model.HistoryDatasetAssociation ):
+                elif isinstance( single_value, app.model.HistoryDatasetAssociation ):
                     rval.append( single_value )
                 else:
-                    rval.append( trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( single_value ) )
+                    rval.append( app.sa_session.query( app.model.HistoryDatasetAssociation ).get( single_value ) )
             if found_hdca:
                 for val in rval:
-                    if not isinstance( val, trans.app.model.HistoryDatasetCollectionAssociation ):
+                    if not isinstance( val, app.model.HistoryDatasetCollectionAssociation ):
                         raise ValueError( "If collections are supplied to multiple data input parameter, only collections may be used." )
-        elif isinstance( value, trans.app.model.HistoryDatasetAssociation ):
+        elif isinstance( value, app.model.HistoryDatasetAssociation ):
             rval = value
         elif isinstance( value, dict ) and 'src' in value and 'id' in value:
             if value['src'] == 'hda':
-                rval = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.app.security.decode_id(value['id']) )
+                rval = trans.sa_session.query( app.model.HistoryDatasetAssociation ).get( app.security.decode_id(value['id']) )
             elif value['src'] == 'hdca':
-                decoded_id = trans.app.security.decode_id( value[ 'id' ] )
-                rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( decoded_id )
+                decoded_id = app.security.decode_id( value[ 'id' ] )
+                rval = app.sa_session.query( app.model.HistoryDatasetCollectionAssociation ).get( decoded_id )
             else:
                 raise ValueError("Unknown input source %s passed to job submission API." % value['src'])
         elif str( value ).startswith( "__collection_reduce__|" ):
             encoded_ids = [ v[ len( "__collection_reduce__|" ): ] for v in str( value ).split(",") ]
-            decoded_ids = map( trans.app.security.decode_id, encoded_ids )
+            decoded_ids = map( app.security.decode_id, encoded_ids )
             rval = []
             for decoded_id in decoded_ids:
-                hdca = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( decoded_id )
+                hdca = app.sa_session.query( app.model.HistoryDatasetCollectionAssociation ).get( decoded_id )
                 rval.append( hdca )
-        elif isinstance( value, trans.app.model.HistoryDatasetCollectionAssociation ):
+        elif isinstance( value, app.model.HistoryDatasetCollectionAssociation ):
             rval = value
         else:
-            rval = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( value )
+            rval = app.sa_session.query( app.model.HistoryDatasetAssociation ).get( value )
         if isinstance( rval, list ):
             values = rval
         else:

From 49026134443e49c81d5b071817bb7a018357f945 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 21 Jan 2016 20:45:22 -0500
Subject: [PATCH 03/33] Use bunch instead of trans

---
 lib/galaxy/tools/evaluation.py          |   4 -
 lib/galaxy/tools/parameters/__init__.py |  11 +-
 lib/galaxy/tools/parameters/basic.py    | 180 +++++++++---------------
 lib/galaxy/util/dbkeys.py               |   6 +-
 4 files changed, 75 insertions(+), 126 deletions(-)

diff --git a/lib/galaxy/tools/evaluation.py b/lib/galaxy/tools/evaluation.py
index 2e6633f4110d..bfad5ed5d43d 100644
--- a/lib/galaxy/tools/evaluation.py
+++ b/lib/galaxy/tools/evaluation.py
@@ -52,10 +52,6 @@ def set_compute_environment( self, compute_environment, get_special=None ):
         job = self.job
         incoming = dict( [ ( p.name, p.value ) for p in job.parameters ] )
         incoming = self.tool.params_from_strings( incoming, self.app )
-        def validate_inputs( input, value, prefixed_name, prefixed_label, context ):
-            value = input.from_html( value, None, context )
-            input.validate( value, None )
-        visit_input_values ( self.tool.inputs, incoming, validate_inputs, details=True )
 
         # Restore input / output data lists
         inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] )
diff --git a/lib/galaxy/tools/parameters/__init__.py b/lib/galaxy/tools/parameters/__init__.py
index bbfaf26a6a7b..fec62c68063a 100644
--- a/lib/galaxy/tools/parameters/__init__.py
+++ b/lib/galaxy/tools/parameters/__init__.py
@@ -6,6 +6,7 @@
 from grouping import Conditional, Repeat, Section, UploadDataset
 from galaxy.util.json import dumps, json_fix, loads
 from galaxy.util.expressions import ExpressionContext
+from galaxy.util.bunch import Bunch
 
 REPLACE_ON_TRUTHY = object()
 
@@ -68,6 +69,12 @@ def check_param( trans, param, incoming_value, param_values, source='html', bool
     previous parameters (this may actually be an ExpressionContext
     when dealing with grouping scenarios).
     """
+    request_context = Bunch(
+        user                    = trans.user,
+        history                 = trans.history,
+        user_ftp_dir            = trans.user_ftp_dir,
+        workflow_building_mode  = workflow_building_mode
+    )
     value = incoming_value
     error = None
     try:
@@ -79,9 +86,9 @@ def check_param( trans, param, incoming_value, param_values, source='html', bool
         if value is not None or isinstance( param, DataToolParameter ) or isinstance( param, DataCollectionToolParameter ):
             # Convert value from HTML representation
             if source == 'html':
-                value = param.from_html( value, trans, param_values )
+                value = param.from_html( value, request_context, param_values )
             else:
-                value = param.from_json( value, trans, param_values )
+                value = param.from_json( value, request_context, param_values )
             # Allow the value to be converted if necessary
             filtered_value = param.filter_value( value, trans, param_values )
             # Then do any further validation on the value
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index f92e283c20e3..bddc085d009e 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -51,6 +51,7 @@ class ToolParameter( object, Dictifiable ):
 
     def __init__( self, tool, input_source, context=None ):
         input_source = ensure_input_source(input_source)
+        self.app = tool.app
         self.tool = tool
         self.refresh_on_change = False
         self.refresh_on_change_values = []
@@ -97,7 +98,7 @@ def get_label( self ):
     def get_html_field( self, trans=None, value=None, other_values={} ):
         raise TypeError( "Abstract Method" )
 
-    def get_html( self, trans=None, value=None, other_values={}):
+    def get_html( self, trans=None, value=None, other_values={} ):
         """
         Returns the html widget corresponding to the parameter.
         Optionally attempt to retain the current value specific by 'value'
@@ -355,15 +356,15 @@ def get_html_field( self, trans=None, value=None, other_values={} ):
             value = str( value )
         return super( IntegerToolParameter, self ).get_html_field( trans=trans, value=value, other_values=other_values )
 
-    def from_html( self, value, trans=None, other_values={} ):
+    def from_html( self, value, trans, other_values={} ):
         try:
             return int( value )
         except:
-            if contains_workflow_parameter(value) and _allow_workflow_parameters_in_context(trans):
+            if contains_workflow_parameter( value ) and trans.workflow_building_mode:
                 return value
             if not value and self.optional:
                 return ""
-            if _allow_workflow_parameters_in_context(trans):
+            if trans.workflow_building_mode:
                 raise ValueError( "An integer or workflow parameter e.g. ${name} is required" )
             else:
                 raise ValueError( "An integer is required" )
@@ -434,15 +435,15 @@ def get_html_field( self, trans=None, value=None, other_values={} ):
             value = str( value )
         return super( FloatToolParameter, self ).get_html_field( trans=trans, value=value, other_values=other_values )
 
-    def from_html( self, value, trans=None, other_values={} ):
+    def from_html( self, value, trans, other_values={} ):
         try:
             return float( value )
         except:
-            if contains_workflow_parameter(value) and _allow_workflow_parameters_in_context(trans):
+            if contains_workflow_parameter( value ) and trans.workflow_building_mode:
                 return value
             if not value and self.optional:
                 return ""
-            if _allow_workflow_parameters_in_context(trans):
+            if trans and trans.workflow_building_mode:
                 raise ValueError( "A real number or workflow parameter e.g. ${name} is required" )
             else:
                 raise ValueError( "A real number is required" )
@@ -559,7 +560,7 @@ def from_html( self, value, trans=None, other_values={} ):
         # Middleware or proxies may encode files in special ways (TODO: this
         # should be pluggable)
         if type( value ) == dict:
-            upload_store = self.tool.app.config.nginx_upload_store
+            upload_store = self.app.config.nginx_upload_store
             assert upload_store, \
                 "Request appears to have been processed by nginx_upload_module \
                 but Galaxy is not configured to recognize it"
@@ -634,7 +635,7 @@ def get_html_field( self, trans=None, value=None, other_values={}  ):
             user_ftp_dir = None
         else:
             user_ftp_dir = trans.user_ftp_dir
-        return form_builder.FTPFileField( self.name, user_ftp_dir, trans.app.config.ftp_upload_site, value=value )
+        return form_builder.FTPFileField( self.name, user_ftp_dir, self.app.config.ftp_upload_site, value=value )
 
     def to_param_dict_string( self, value, other_values={} ):
         if value is '':
@@ -646,7 +647,7 @@ def to_param_dict_string( self, value, other_values={} ):
             return lst[ 0 ]
 
     def from_html( self, value, trans=None, other_values={} ):
-        return self.to_python( value, trans.app, validate=True )
+        return self.to_python( value, self.app, validate=True )
 
     def to_string( self, value, app ):
         return self.to_python( value, app )
@@ -742,7 +743,7 @@ def get_initial_value( self, trans, context, history=None ):
     def get_html_field( self, trans=None, value=None, other_values={} ):
         return form_builder.HiddenField( self.name, self._get_value() )
 
-    def from_html( self, value=None, trans=None, context={} ):
+    def from_html( self, value=None, trans=None, other_values={} ):
         return self._get_value()
 
     def _get_value( self ):
@@ -901,7 +902,7 @@ def get_html_field( self, trans=None, value=None, context={} ):
         # Dynamic options are not yet supported in workflow, allow
         # specifying the value as text for now.
         options = list(self.get_options( trans, context ))
-        if len(list(options)) == 0 and (trans is None or trans.workflow_building_mode):
+        if len(list(options)) == 0 and trans.workflow_building_mode:
             if self.multiple:
                 if value is None:
                     value = ""
@@ -920,9 +921,9 @@ def get_html_field( self, trans=None, value=None, context={} ):
             field.add_option( text, optval, selected )
         return field
 
-    def from_html( self, value, trans=None, context={} ):
-        legal_values = self.get_legal_values( trans, context )
-        if len(list(legal_values)) == 0 and (trans is None or trans.workflow_building_mode):
+    def from_html( self, value, trans, other_values={} ):
+        legal_values = self.get_legal_values( trans, other_values )
+        if len(list(legal_values)) == 0 and trans.workflow_building_mode:
             if self.multiple:
                 # While it is generally allowed that a select value can be '',
                 # we do not allow this to be the case in a dynamically
@@ -1004,7 +1005,7 @@ def value_from_basic( self, value, app, ignore_errors=False ):
 
     def get_initial_value( self, trans, context, history=None ):
         options = list( self.get_options( trans, context ) )
-        if len(options) == 0 and (trans is None or trans.workflow_building_mode):
+        if len(options) == 0 and trans.workflow_building_mode:
             return None
         value = [ optval for _, optval, selected in options if selected ]
         if len( value ) == 0:
@@ -1150,7 +1151,7 @@ def _get_dbkey_names( self, trans=None ):
         if not self.tool:
             # Hack for unit tests, since we have no tool
             return util.read_dbnames( None )
-        return self.tool.app.genome_builds.get_genome_build_names( trans=trans )
+        return self.app.genome_builds.get_genome_build_names( trans=trans )
 
 
 class ColumnListParameter( SelectToolParameter ):
@@ -1196,7 +1197,7 @@ def __init__( self, tool, input_source ):
         self.is_dynamic = True
         self.usecolnames = input_source.get_bool( "use_header_names", False )
 
-    def from_html( self, value, trans=None, context={} ):
+    def from_html( self, value, trans, other_values={} ):
         """
         Label convention prepends column number with a 'c', but tool uses the integer. This
         removes the 'c' when entered into a workflow.
@@ -1220,7 +1221,7 @@ def from_html( self, value, trans=None, context={} ):
                 value = ColumnListParameter._strip_c( value )
             else:
                 value = None
-        return super( ColumnListParameter, self ).from_html( value, trans, context )
+        return super( ColumnListParameter, self ).from_html( value, trans, other_values )
 
     @staticmethod
     def _strip_c(column):
@@ -1529,7 +1530,7 @@ def get_html_field( self, trans=None, value=None, other_values={} ):
         # Dynamic options are not yet supported in workflow, allow
         # specifying the value as text for now.
         options = self.get_options( trans, value, other_values )
-        if len(list(options)) == 0 and (trans is None or trans.workflow_building_mode):
+        if len(list(options)) == 0 and trans.workflow_building_mode:
             if self.multiple:
                 if value is None:
                     value = ""
@@ -1540,9 +1541,9 @@ def get_html_field( self, trans=None, value=None, other_values={} ):
                 return form_builder.TextField( self.name, value=(value or "") )
         return form_builder.DrillDownField( self.name, self.multiple, self.display, self.refresh_on_change, options, value, refresh_on_change_values=self.refresh_on_change_values )
 
-    def from_html( self, value, trans=None, other_values={} ):
+    def from_html( self, value, trans, other_values={} ):
         legal_values = self.get_legal_values( trans, other_values )
-        if len(list(legal_values)) == 0 and (trans is None or trans.workflow_building_mode):
+        if len( list( legal_values ) ) == 0 and trans.workflow_building_mode:
             if self.multiple:
                 if value == '':  # No option selected
                     value = None
@@ -1554,14 +1555,14 @@ def from_html( self, value, trans=None, other_values={} ):
         if not value:
             return None
         if not isinstance( value, list ):
-            value = [value]
+            value = [ value ]
         if not( self.repeat ) and len( value ) > 1:
             assert self.multiple, "Multiple values provided but parameter %s is not expecting multiple values" % self.name
         rval = []
         assert legal_values, "Parameter %s requires a value, but has no legal values defined" % self.name
         for val in value:
             if val not in legal_values:
-                raise ValueError( "An invalid option was selected for %s, %r, please verify" % (self.name, val))
+                raise ValueError( "An invalid option was selected for %s, %r, please verify" % ( self.name, val ) )
             rval.append( val )
         return rval
 
@@ -1614,7 +1615,7 @@ def recurse_options( initial_values, options ):
                 recurse_options( initial_values, option['options'] )
         # More working around dynamic options for workflow
         options = self.get_options( trans=trans, other_values=context )
-        if len(list(options)) == 0 and (trans is None or trans.workflow_building_mode):
+        if len(list(options)) == 0 and trans.workflow_building_mode:
             return None
         initial_values = []
         recurse_options( initial_values, options )
@@ -1709,7 +1710,7 @@ def _datatypes_registery( self, trans, tool ):
             if trans:
                 # Must account for "Input Dataset" types, which while not a tool still need access to the real registry.
                 # A handle to the transaction (and thus app) will be given by the module.
-                datatypes_registry = trans.app.datatypes_registry
+                datatypes_registry = self.app.datatypes_registry
             else:
                 # This occurs for things such as unit tests
                 import galaxy.datatypes.registry
@@ -1867,7 +1868,7 @@ def value_modifier(value):
             name = history_dataset_collection.name
             hid = str( history_dataset_collection.hid )
             hidden_text = ""  # TODO
-            id = value_modifier( dataset_matcher.trans.security.encode_id( history_dataset_collection.id ) )
+            id = value_modifier( self.app.security.encode_id( history_dataset_collection.id ) )
             selected = value and history_dataset_collection in value
             text = "%s:%s %s" % ( hid, hidden_text, name )
             field.add_option( text, id, selected )
@@ -1933,7 +1934,7 @@ def get_initial_value_from_history_prevent_repeats( self, trans, context, alread
               happens twice (here and when generating HTML).
         """
         # Can't look at history in workflow mode. Tool shed has no histories.
-        if trans is None or trans.workflow_building_mode or trans.webapp.name == 'tool_shed':
+        if trans.workflow_building_mode or trans.webapp.name == 'tool_shed':
             return DummyDataset()
         history = self._get_history( trans, history )
         dataset_matcher = DatasetMatcher( trans, self, None, context )
@@ -1962,16 +1963,14 @@ def dataset_collector( datasets ):
             return most_recent_dataset[0]
         return ''
 
-    def from_html( self, value, trans, other_values={}, app=None ):
-        if app is None:
-            app = trans.app
+    def from_html( self, value, trans, other_values={} ):
         # Can't look at history in workflow mode, skip validation and such,
         # although, this should never be called in workflow mode right?
         if trans.workflow_building_mode:
             return None
         if not value and not self.optional:
             raise ValueError( "History does not include a dataset of the required format / build" )
-        if value in [None, "None", '']:
+        if value in [ None, "None", '' ]:
             return None
         if isinstance( value, str ) and value.find( "," ) > 0:
             value = [ int( value_part ) for value_part in value.split( "," ) ]
@@ -1981,44 +1980,44 @@ def from_html( self, value, trans, other_values={}, app=None ):
             for single_value in value:
                 if isinstance( single_value, dict ) and 'src' in single_value and 'id' in single_value:
                     if single_value['src'] == 'hda':
-                        rval.append(app.sa_session.query( app.model.HistoryDatasetAssociation ).get( app.security.decode_id(single_value['id']) ))
+                        rval.append( self.app.model.context.query( self.app.model.HistoryDatasetAssociation ).get( self.app.security.decode_id(single_value['id']) ))
                     elif single_value['src'] == 'hdca':
                         found_hdca = True
-                        decoded_id = app.security.decode_id( single_value[ 'id' ] )
-                        rval.append( app.sa_session.query( app.model.HistoryDatasetCollectionAssociation ).get( decoded_id ) )
+                        decoded_id = self.app.security.decode_id( single_value[ 'id' ] )
+                        rval.append( self.app.model.context.query( self.app.model.HistoryDatasetCollectionAssociation ).get( decoded_id ) )
                     else:
                         raise ValueError("Unknown input source %s passed to job submission API." % single_value['src'])
-                elif isinstance( single_value, app.model.HistoryDatasetCollectionAssociation ):
+                elif isinstance( single_value, self.app.model.HistoryDatasetCollectionAssociation ):
                     rval.append( single_value )
-                elif isinstance( single_value, app.model.HistoryDatasetAssociation ):
+                elif isinstance( single_value, self.app.model.HistoryDatasetAssociation ):
                     rval.append( single_value )
                 else:
-                    rval.append( app.sa_session.query( app.model.HistoryDatasetAssociation ).get( single_value ) )
+                    rval.append( self.app.model.context.query( self.app.model.HistoryDatasetAssociation ).get( single_value ) )
             if found_hdca:
                 for val in rval:
-                    if not isinstance( val, app.model.HistoryDatasetCollectionAssociation ):
+                    if not isinstance( val, self.app.model.HistoryDatasetCollectionAssociation ):
                         raise ValueError( "If collections are supplied to multiple data input parameter, only collections may be used." )
-        elif isinstance( value, app.model.HistoryDatasetAssociation ):
+        elif isinstance( value, self.app.model.HistoryDatasetAssociation ):
             rval = value
         elif isinstance( value, dict ) and 'src' in value and 'id' in value:
             if value['src'] == 'hda':
-                rval = trans.sa_session.query( app.model.HistoryDatasetAssociation ).get( app.security.decode_id(value['id']) )
+                rval = self.app.model.context.query( self.app.model.HistoryDatasetAssociation ).get( self.app.security.decode_id(value['id']) )
             elif value['src'] == 'hdca':
-                decoded_id = app.security.decode_id( value[ 'id' ] )
-                rval = app.sa_session.query( app.model.HistoryDatasetCollectionAssociation ).get( decoded_id )
+                decoded_id = self.app.security.decode_id( value[ 'id' ] )
+                rval = self.app.model.context.query( self.app.model.HistoryDatasetCollectionAssociation ).get( decoded_id )
             else:
                 raise ValueError("Unknown input source %s passed to job submission API." % value['src'])
         elif str( value ).startswith( "__collection_reduce__|" ):
             encoded_ids = [ v[ len( "__collection_reduce__|" ): ] for v in str( value ).split(",") ]
-            decoded_ids = map( app.security.decode_id, encoded_ids )
+            decoded_ids = map( self.app.security.decode_id, encoded_ids )
             rval = []
             for decoded_id in decoded_ids:
-                hdca = app.sa_session.query( app.model.HistoryDatasetCollectionAssociation ).get( decoded_id )
+                hdca = self.app.model.context.query( self.app.model.HistoryDatasetCollectionAssociation ).get( decoded_id )
                 rval.append( hdca )
-        elif isinstance( value, app.model.HistoryDatasetCollectionAssociation ):
+        elif isinstance( value, self.app.model.HistoryDatasetCollectionAssociation ):
             rval = value
         else:
-            rval = app.sa_session.query( app.model.HistoryDatasetAssociation ).get( value )
+            rval = self.app.model.context.query( self.app.model.HistoryDatasetAssociation ).get( value )
         if isinstance( rval, list ):
             values = rval
         else:
@@ -2204,7 +2203,7 @@ def to_dict( self, trans, view='collection', value_mapper=None, other_values={}
             if match:
                 m = match.hda
                 d['options']['hda'].append({
-                    'id'            : trans.security.encode_id( m.id ),
+                    'id'            : self.app.security.encode_id( m.id ),
                     'hid'           : m.hid,
                     'name'          : m.name if m.visible else '(hidden) %s' % m.name,
                     'src'           : 'hda'
@@ -2215,7 +2214,7 @@ def to_dict( self, trans, view='collection', value_mapper=None, other_values={}
         for hdca in history.active_dataset_collections:
             if dataset_collection_matcher.hdca_match( hdca, reduction=multiple ):
                 d['options']['hdca'].append({
-                    'id'            : trans.security.encode_id( hdca.id ),
+                    'id'            : self.app.security.encode_id( hdca.id ),
                     'hid'           : hdca.hid,
                     'name'          : hdca.name,
                     'src'           : 'hdca'
@@ -2250,7 +2249,7 @@ def collection_types( self ):
         return self._collection_types
 
     def _history_query( self, trans ):
-        dataset_collection_type_descriptions = trans.app.dataset_collections_service.collection_type_descriptions
+        dataset_collection_type_descriptions = self.app.dataset_collections_service.collection_type_descriptions
         return history_query.HistoryQuery.from_parameter( self, dataset_collection_type_descriptions )
 
     def get_html_field( self, trans=None, value=None, other_values={} ):
@@ -2273,7 +2272,7 @@ def get_html_field( self, trans=None, value=None, other_values={} ):
         return self._switch_fields( fields, default_field=default_field )
 
     def match_collections( self, trans, history, dataset_matcher ):
-        dataset_collections = trans.app.dataset_collections_service.history_dataset_collections( history, self._history_query( trans ) )
+        dataset_collections = self.app.dataset_collections_service.history_dataset_collections( history, self._history_query( trans ) )
         dataset_collection_matcher = DatasetCollectionMatcher( dataset_matcher )
 
         for dataset_collection_instance in dataset_collections:
@@ -2317,8 +2316,8 @@ def _get_select_dataset_collection_field( self, trans, history, multiple=False,
             name = history_dataset_collection.name
             hid = str( history_dataset_collection.hid )
             hidden_text = ""  # TODO
-            subcollection_type = self._history_query( trans ).can_map_over( history_dataset_collection ).collection_type
-            id = "%s|%s" % ( dataset_matcher.trans.security.encode_id( history_dataset_collection.id ), subcollection_type )
+            subcollection_type = self._history_query( trans ).collection_type_description.collection_type
+            id = "%s|%s" % ( self.app.security.encode_id( history_dataset_collection.id ), subcollection_type )
             text = "%s:%s %s" % ( hid, hidden_text, name )
 
             field.add_option( text, id, False )
@@ -2332,30 +2331,30 @@ def from_html( self, value, trans, other_values={} ):
             return None
         if isinstance( value, str ) and value.find( "," ) > 0:
             value = [ int( value_part ) for value_part in value.split( "," ) ]
-        elif isinstance( value, trans.app.model.HistoryDatasetCollectionAssociation ):
+        elif isinstance( value, self.app.model.HistoryDatasetCollectionAssociation ):
             rval = value
-        elif isinstance( value, trans.app.model.DatasetCollectionElement ):
+        elif isinstance( value, self.app.model.DatasetCollectionElement ):
             # When mapping over nested collection - this paramter will recieve
             # a DatasetCollectionElement instead of a
             # HistoryDatasetCollectionAssociation.
             rval = value
         elif isinstance( value, dict ) and 'src' in value and 'id' in value:
             if value['src'] == 'hdca':
-                rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( trans.app.security.decode_id(value['id']) )
+                rval = self.app.model.context.query( self.app.model.HistoryDatasetCollectionAssociation ).get( self.app.security.decode_id(value['id']) )
         elif isinstance( value, list ):
             if len( value ) > 0:
                 value = value[0]
                 if isinstance( value, dict ) and 'src' in value and 'id' in value:
                     if value['src'] == 'hdca':
-                        rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( trans.app.security.decode_id(value['id']) )
+                        rval = self.app.model.context.query( self.app.model.HistoryDatasetCollectionAssociation ).get( self.app.security.decode_id(value['id']) )
         elif isinstance( value, basestring ):
             if value.startswith( "dce:" ):
-                rval = trans.sa_session.query( trans.app.model.DatasetCollectionElement ).get( value[ len( "dce:"): ] )
+                rval = self.app.model.context.query( self.app.model.DatasetCollectionElement ).get( value[ len( "dce:"): ] )
             elif value.startswith( "hdca:" ):
-                rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( value[ len( "hdca:"): ] )
+                rval = self.app.model.context.query( self.app.model.HistoryDatasetCollectionAssociation ).get( value[ len( "hdca:"): ] )
             else:
-                rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( value )
-        if rval and isinstance( rval, trans.app.model.HistoryDatasetCollectionAssociation ):
+                rval = self.app.model.context.query( self.app.model.HistoryDatasetCollectionAssociation ).get( value )
+        if rval and isinstance( rval, self.app.model.HistoryDatasetCollectionAssociation ):
             if rval.deleted:
                 raise ValueError( "The previously selected dataset collection has been deleted" )
             # TODO: Handle error states, implement error states ...
@@ -2424,7 +2423,7 @@ def to_dict( self, trans, view='collection', value_mapper=None, other_values=Non
         # append directly matched collections
         for hdca in self.match_collections( trans, history, dataset_matcher ):
             d['options']['hdca'].append({
-                'id': trans.security.encode_id( hdca.id ),
+                'id': self.app.security.encode_id( hdca.id ),
                 'hid': hdca.hid,
                 'name': hdca.name,
                 'src': 'hdca'
@@ -2434,7 +2433,7 @@ def to_dict( self, trans, view='collection', value_mapper=None, other_values=Non
         for hdca in self.match_multirun_collections( trans, history, dataset_matcher ):
             subcollection_type = self._history_query( trans ).can_map_over( hdca ).collection_type
             d['options']['hdca'].append({
-                'id': trans.security.encode_id( hdca.id ),
+                'id': self.app.security.encode_id( hdca.id ),
                 'hid': hdca.hid,
                 'name': hdca.name,
                 'src': 'hdca',
@@ -2483,7 +2482,7 @@ def get_initial_value( self, trans, context, history=None ):
         return None
 
     def from_html( self, value, trans, other_values={} ):
-        return self.to_python( value, trans.app, other_values=other_values, validate=True )
+        return self.to_python( value, self.app, other_values=other_values, validate=True )
 
     def to_param_dict_string( self, value, other_values={} ):
         if value is None:
@@ -2560,59 +2559,6 @@ def to_dict( self, trans, view='collection', value_mapper=None, other_values=Non
         d['multiple'] = self.multiple
         return d
 
-
-def _allow_workflow_parameters_in_context(trans):
-    return trans is None or trans.workflow_building_mode
-
-
-# class RawToolParameter( ToolParameter ):
-#     """
-#     Completely nondescript parameter, HTML representation is provided as text
-#     contents.
-#
-#     >>> p = RawToolParameter( None, XML(
-#     ... '''
-#     ... <param name="blah" type="raw">
-#     ... <![CDATA[<span id="$name">Some random stuff</span>]]>
-#     ... </param>
-#     ... ''' ) )
-#     >>> print p.name
-#     blah
-#     >>> print p.get_html().strip()
-#     <span id="blah">Some random stuff</span>
-#     """
-#     def __init__( self, tool, elem ):
-#         ToolParameter.__init__( self, tool, elem )
-#         self.template = string.Template( elem.text )
-#     def get_html( self, prefix="" ):
-#         context = dict( self.__dict__ )
-#         context.update( dict( prefix=prefix ) )
-#         return self.template.substitute( context )
-
-# class HistoryIDParameter( ToolParameter ):
-#     """
-#     Parameter that takes a name value, makes history.id available.
-#
-#     FIXME: This is a hack (esp. if hidden params are a hack) but in order to
-#            have the history accessable at the job level, it is necessary
-#            I also probably wrote this docstring test thing wrong.
-#
-#     >>> from galaxy.model import History
-#     >>> from galaxy.util.bunch import Bunch
-#     >>> hist = History( id=1 )
-#     >>> p = HistoryIDParameter( None, XML( '<param name="blah" type="history"/>' ) )
-#     >>> print p.name
-#     blah
-#     >>> html_string = '<input type="hidden" name="blah" value="%d">' % hist.id
-#     >>> assert p.get_html( trans=Bunch( history=hist ) ) == html_string
-#     """
-#     def __init__( self, tool, elem ):
-#         ToolParameter.__init__( self, tool, elem )
-#     def get_html( self, trans, value=None, other_values={} ):
-#         assert trans.history is not None, "HistoryIDParameter requires a history"
-#         self.html = form_builder.HiddenField( self.name, trans.history.id ).get_html()
-#         return self.html
-
 parameter_types = dict(
     text=TextToolParameter,
     integer=IntegerToolParameter,
diff --git a/lib/galaxy/util/dbkeys.py b/lib/galaxy/util/dbkeys.py
index 216e7cb6d388..8aa66bbf8c7f 100644
--- a/lib/galaxy/util/dbkeys.py
+++ b/lib/galaxy/util/dbkeys.py
@@ -33,7 +33,7 @@ def get_genome_build_names( self, trans=None ):
                 # It does allow one-off, history specific dbkeys to be created by a user. But we are not filtering,
                 # so a len file will be listed twice (as the build name and again as dataset name),
                 # if custom dbkey creation/conversion occurred within the current history.
-                datasets = trans.sa_session.query( self._app.model.HistoryDatasetAssociation ) \
+                datasets = self._app.model.context.query( self._app.model.HistoryDatasetAssociation ) \
                                 .filter_by( deleted=False, history_id=trans.history.id, extension="len" )
                 for dataset in datasets:
                     rval.append( ( dataset.dbkey, "%s (%s) [History]" % ( dataset.name, dataset.dbkey ) ) )
@@ -72,11 +72,11 @@ def get_chrom_info( self, dbkey, trans=None, custom_build_hack_get_len_from_fast
                     # fasta-to-len converter.
                     if 'fasta' in custom_build_dict and custom_build_hack_get_len_from_fasta_conversion:
                         # Build is defined by fasta; get len file, which is obtained from converting fasta.
-                        build_fasta_dataset = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( custom_build_dict[ 'fasta' ] )
+                        build_fasta_dataset = self._app.model.context.query( self._app.model.HistoryDatasetAssociation ).get( custom_build_dict[ 'fasta' ] )
                         chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name
                     elif 'len' in custom_build_dict:
                         # Build is defined by len file, so use it.
-                        chrom_info = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( custom_build_dict[ 'len' ] ).file_name
+                        chrom_info = self._app.model.context.query( self._app.model.HistoryDatasetAssociation ).get( custom_build_dict[ 'len' ] ).file_name
         # Check Data table
         if not chrom_info:
             dbkey_table = self._app.tool_data_tables.get( self._data_table_name, None )

From 12f2571d975ca89548259e1322882e87dbb5b17e Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 22 Jan 2016 15:09:55 -0500
Subject: [PATCH 04/33] Use self.app in tools

---
 lib/galaxy/tools/__init__.py | 28 ++++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 0fb65d78e703..6ef7eafadb77 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1734,7 +1734,7 @@ def check_and_update_param_values_helper( self, inputs, values, trans, messages,
                                 ck_param = False
                             # this will fail when a parameter's type has changed to a non-compatible one: e.g. conditional group changed to dataset input
                             if ck_param:
-                                input.value_from_basic( input.value_to_basic( value, trans.app ), trans.app, ignore_errors=False )
+                                input.value_from_basic( input.value_to_basic( value, self.app ), self.app, ignore_errors=False )
                     except:
                         log.info("Parameter validation failed.", exc_info=True)
                         messages[ input.name ] = "Value no longer valid for '%s%s', replacing with default" % ( prefix, input.label )
@@ -2058,7 +2058,7 @@ def to_dict( self, trans, link_details=False, io_details=False ):
         # Add input and output details.
         if io_details:
             tool_dict[ 'inputs' ] = [ input.to_dict( trans ) for input in self.inputs.values() ]
-            tool_dict[ 'outputs' ] = [ output.to_dict( app=trans.app ) for output in self.outputs.values() ]
+            tool_dict[ 'outputs' ] = [ output.to_dict( app=self.app ) for output in self.outputs.values() ]
 
         tool_dict[ 'panel_section_id' ], tool_dict[ 'panel_section_name' ] = self.get_panel_section()
 
@@ -2087,11 +2087,11 @@ def to_json(self, trans, kwd={}, job=None, workflow_mode=False):
         tool_message = ''
         if job:
             try:
-                job_params = job.get_param_values( trans.app, ignore_errors=True )
+                job_params = job.get_param_values( self.app, ignore_errors=True )
                 self.check_and_update_param_values( job_params, trans, update_values=False )
                 self._map_source_to_history( trans, self.inputs, job_params, history )
                 tool_message = self._compare_tool_version(trans, job)
-                params_to_incoming( kwd, self.inputs, job_params, trans.app, to_html=False )
+                params_to_incoming( kwd, self.inputs, job_params, self.app, to_html=False )
             except Exception, e:
                 raise exceptions.MessageException( str( e ) )
 
@@ -2109,17 +2109,17 @@ def jsonify(v):
                 pass
 
             # fix hda parsing
-            if isinstance(v, trans.app.model.HistoryDatasetAssociation):
+            if isinstance(v, self.app.model.HistoryDatasetAssociation):
                 return {
                     'id'  : trans.security.encode_id(v.id),
                     'src' : 'hda'
                 }
-            elif isinstance(v, trans.app.model.HistoryDatasetCollectionAssociation):
+            elif isinstance(v, self.app.model.HistoryDatasetCollectionAssociation):
                 return {
                     'id'  : trans.security.encode_id(v.id),
                     'src' : 'hdca'
                 }
-            elif isinstance(v, trans.app.model.LibraryDatasetDatasetAssociation):
+            elif isinstance(v, self.app.model.LibraryDatasetDatasetAssociation):
                 return {
                     'id'  : trans.security.encode_id(v.id),
                     'name': v.name,
@@ -2244,7 +2244,7 @@ def iterate(group_inputs, inputs, state_inputs, other_values=None):
                         test_param = tool_dict['test_param']
                         test_param['default_value'] = jsonify(input.test_param.get_initial_value(trans, other_values, history=history))
                         test_param['value'] = jsonify(group_state.get(test_param['name'], test_param['default_value']))
-                        test_param['text_value'] = input.test_param.value_to_display_text(test_param['value'], trans.app)
+                        test_param['text_value'] = input.test_param.value_to_display_text(test_param['value'], self.app)
                         for i in range(len( tool_dict['cases'] ) ):
                             current_state = {}
                             if i == group_state.get('__current_case__', None):
@@ -2274,7 +2274,7 @@ def iterate(group_inputs, inputs, state_inputs, other_values=None):
                     tool_dict['value'] = state_inputs.get(input.name, tool_dict['default_value'])
 
                     # add text value
-                    tool_dict[ 'text_value' ] = input.value_to_display_text( tool_dict[ 'value' ], trans.app )
+                    tool_dict[ 'text_value' ] = input.value_to_display_text( tool_dict[ 'value' ], self.app )
 
                     # sanitize values
                     sanitize(tool_dict, 'value')
@@ -2353,14 +2353,14 @@ def sanitize_state(state):
         # add toolshed url
         sharable_url = None
         if self.tool_shed_repository:
-            sharable_url = self.tool_shed_repository.get_sharable_url( trans.app )
+            sharable_url = self.tool_shed_repository.get_sharable_url( self.app )
 
         # add additional properties
         tool_model.update({
             'id'            : self.id,
             'help'          : tool_help,
             'citations'     : tool_citations,
-            'biostar_url'   : trans.app.config.biostar_url,
+            'biostar_url'   : self.app.config.biostar_url,
             'sharable_url'  : sharable_url,
             'message'       : tool_message,
             'versions'      : tool_versions,
@@ -2407,10 +2407,10 @@ def _map_source_to_history(self, trans, tool_inputs, params, history):
         def map_to_history(value):
             id = None
             source = None
-            if isinstance(value, trans.app.model.HistoryDatasetAssociation):
+            if isinstance(value, self.app.model.HistoryDatasetAssociation):
                 id = value.dataset.id
                 source = hda_source_dict
-            elif isinstance(value, trans.app.model.HistoryDatasetCollectionAssociation):
+            elif isinstance(value, self.app.model.HistoryDatasetCollectionAssociation):
                 id = value.collection.id
                 source = hdca_source_dict
             else:
@@ -2430,7 +2430,7 @@ def map_to_history(value):
         def mapping_callback( input, value, prefixed_name, prefixed_label ):
             if isinstance( value, UnvalidatedValue ):
                 try:
-                    return input.to_html_value( value.value, trans.app )
+                    return input.to_html_value( value.value, self.app )
                 except Exception, e:
                     # Need to determine when (if ever) the to_html_value call could fail.
                     log.debug( "Failed to use input.to_html_value to determine value of unvalidated parameter, defaulting to string: %s" % ( e ) )

From 52b6881f017e38ea5969c5adb70b5c83d6753cd3 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 22 Jan 2016 18:02:29 -0500
Subject: [PATCH 05/33] Revise history handling

---
 lib/galaxy/tools/__init__.py            |  6 +---
 lib/galaxy/tools/parameters/basic.py    | 42 ++++++++++++-------------
 lib/galaxy/tools/parameters/grouping.py | 20 ++++++------
 3 files changed, 32 insertions(+), 36 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 6ef7eafadb77..0550da3ddd7a 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1485,11 +1485,7 @@ def update_state( self, trans, inputs, state, incoming, source='html', prefix=""
                         # load default initial value
                         if not test_param_error:
                             test_param_error = str( e )
-                        if trans is not None:
-                            history = trans.get_history()
-                        else:
-                            history = None
-                        value = input.test_param.get_initial_value( trans, context, history=history )
+                        value = input.test_param.get_initial_value( trans, context )
                         current_case = input.get_current_case( value, trans )
                 case_changed = current_case != old_current_case
                 if case_changed:
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index bddc085d009e..2e1fe8940c7b 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -115,13 +115,13 @@ def from_html( self, value, trans=None, other_values={} ):
     def from_json( self, value, trans=None, other_values={} ):
         return self.from_html( value, trans, other_values )
 
-    def get_initial_value( self, trans, context, history=None ):
+    def get_initial_value( self, trans, context ):
         """
         Return the starting value of the parameter
         """
         return None
 
-    def get_initial_value_from_history_prevent_repeats( self, trans, context, already_used, history=None ):
+    def get_initial_value_from_history_prevent_repeats( self, trans, context, already_used ):
         """
         Get the starting value for the parameter, but if fetching from the history, try
         to find a value that has not yet been used. already_used is a list of objects that
@@ -129,7 +129,7 @@ def get_initial_value_from_history_prevent_repeats( self, trans, context, alread
         if a value has already been chosen from the history. This is to support the capability to
         choose each dataset once
         """
-        return self.get_initial_value(trans, context, history=history)
+        return self.get_initial_value( trans, context )
 
     def get_required_enctype( self ):
         """
@@ -297,7 +297,7 @@ def validate( self, value, history=None, workflow_building_mode=False ):
         if not ( workflow_building_mode and contains_workflow_parameter(value, search=search) ):
             return super( TextToolParameter, self ).validate( value, history )
 
-    def get_initial_value( self, trans, context, history=None ):
+    def get_initial_value( self, trans, context ):
         return self.value
 
     def to_dict( self, trans, view='collection', value_mapper=None, other_values={} ):
@@ -379,7 +379,7 @@ def to_python( self, value, app ):
                 return None
             raise err
 
-    def get_initial_value( self, trans, context, history=None ):
+    def get_initial_value( self, trans, context ):
         if self.value:
             return int( self.value )
         else:
@@ -458,7 +458,7 @@ def to_python( self, value, app ):
                 return None
             raise err
 
-    def get_initial_value( self, trans, context, history=None ):
+    def get_initial_value( self, trans, context ):
         try:
             return float( self.value )
         except:
@@ -511,7 +511,7 @@ def to_html_value( self, value, app ):
     def to_python( self, value, app ):
         return ( value in [ 'True', 'true' ])
 
-    def get_initial_value( self, trans, context, history=None ):
+    def get_initial_value( self, trans, context ):
         return self.checked
 
     def to_param_dict_string( self, value, other_values={} ):
@@ -601,7 +601,7 @@ def to_python( self, value, app ):
         else:
             raise Exception( "FileToolParameter cannot be persisted" )
 
-    def get_initial_value( self, trans, context, history=None ):
+    def get_initial_value( self, trans, context ):
         return None
 
 
@@ -618,7 +618,7 @@ def __init__( self, tool, input_source ):
         self.multiple = input_source.get_bool( 'multiple', True )
         self.user_ftp_dir = ''
 
-    def get_initial_value( self, trans, context, history=None ):
+    def get_initial_value( self, trans, context ):
         if trans is not None:
             if trans.user is not None:
                 self.user_ftp_dir = "%s/" % trans.user_ftp_dir
@@ -700,7 +700,7 @@ def __init__( self, tool, input_source ):
     def get_html_field( self, trans=None, value=None, other_values={} ):
         return form_builder.HiddenField( self.name, self.value )
 
-    def get_initial_value( self, trans, context, history=None ):
+    def get_initial_value( self, trans, context ):
         return self.value
 
     def get_label( self ):
@@ -723,7 +723,7 @@ def __init__( self, tool, input_source ):
     def get_html_field( self, trans=None, value=None, other_values={} ):
         return form_builder.HiddenField( self.name, self.value )
 
-    def get_initial_value( self, trans, context, history=None ):
+    def get_initial_value( self, trans, context ):
         return self.value.lower()
 
 
@@ -737,7 +737,7 @@ def __init__( self, tool, input_source ):
         super( BaseURLToolParameter, self ).__init__( tool, input_source )
         self.value = input_source.get( 'value', '' )
 
-    def get_initial_value( self, trans, context, history=None ):
+    def get_initial_value( self, trans, context ):
         return self._get_value()
 
     def get_html_field( self, trans=None, value=None, other_values={} ):
@@ -1003,7 +1003,7 @@ def value_from_basic( self, value, app, ignore_errors=False ):
             return value[ "value" ]
         return super( SelectToolParameter, self ).value_from_basic( value, app, ignore_errors=ignore_errors )
 
-    def get_initial_value( self, trans, context, history=None ):
+    def get_initial_value( self, trans, context ):
         options = list( self.get_options( trans, context ) )
         if len(options) == 0 and trans.workflow_building_mode:
             return None
@@ -1311,7 +1311,7 @@ def get_options( self, trans, other_values ):
                     options.append( ( 'Column: ' + col, col, False ) )
         return options
 
-    def get_initial_value( self, trans, context, history=None ):
+    def get_initial_value( self, trans, context ):
         if self.default_value is not None:
             return self.default_value
         return SelectToolParameter.get_initial_value( self, trans, context )
@@ -1607,7 +1607,7 @@ def recurse_option( option_list, option ):
                 rval = sanitize_param( rval )
         return rval
 
-    def get_initial_value( self, trans, context, history=None ):
+    def get_initial_value( self, trans, context ):
         def recurse_options( initial_values, options ):
             for option in options:
                 if option['selected']:
@@ -1925,10 +1925,10 @@ def dataset_collector( hdas, parent_hid ):
         for item in dataset_collector( history.active_datasets_children_and_roles, None ):
             yield item
 
-    def get_initial_value( self, trans, context, history=None ):
-        return self.get_initial_value_from_history_prevent_repeats(trans, context, None, history=history)
+    def get_initial_value( self, trans, context ):
+        return self.get_initial_value_from_history_prevent_repeats(trans, context, None )
 
-    def get_initial_value_from_history_prevent_repeats( self, trans, context, already_used, history=None ):
+    def get_initial_value_from_history_prevent_repeats( self, trans, context, already_used ):
         """
         NOTE: This is wasteful since dynamic options and dataset collection
               happens twice (here and when generating HTML).
@@ -1936,7 +1936,7 @@ def get_initial_value_from_history_prevent_repeats( self, trans, context, alread
         # Can't look at history in workflow mode. Tool shed has no histories.
         if trans.workflow_building_mode or trans.webapp.name == 'tool_shed':
             return DummyDataset()
-        history = self._get_history( trans, history )
+        history = self._get_history( trans )
         dataset_matcher = DatasetMatcher( trans, self, None, context )
         if self.optional:
             return None
@@ -2458,7 +2458,7 @@ def __init__( self, tool, elem ):
         self.type = "hidden_data"
         self.hidden = True
 
-    def get_initial_value( self, trans, context, history=None ):
+    def get_initial_value( self, trans, context ):
         return None
 
     def get_html_field( self, trans=None, value=None, other_values={} ):
@@ -2478,7 +2478,7 @@ def __init__( self, tool, input_source, context=None ):
     def get_html_field( self, trans=None, value=None, other_values={} ):
         return form_builder.LibraryField( self.name, value=value, trans=trans )
 
-    def get_initial_value( self, trans, context, history=None ):
+    def get_initial_value( self, trans, context ):
         return None
 
     def from_html( self, value, trans, other_values={} ):
diff --git a/lib/galaxy/tools/parameters/grouping.py b/lib/galaxy/tools/parameters/grouping.py
index ecd006b934a7..8998dc897b25 100644
--- a/lib/galaxy/tools/parameters/grouping.py
+++ b/lib/galaxy/tools/parameters/grouping.py
@@ -43,7 +43,7 @@ def value_from_basic( self, value, app, ignore_errors=False ):
         """
         return value
 
-    def get_initial_value( self, trans, context, history=None ):
+    def get_initial_value( self, trans, context ):
         """
         Return the initial state/value for this group
         """
@@ -120,12 +120,12 @@ def visit_inputs( self, prefix, value, callback ):
                 else:
                     input.visit_inputs( new_prefix, d[input.name], callback )
 
-    def get_initial_value( self, trans, context, history=None ):
+    def get_initial_value( self, trans, context ):
         rval = []
         for i in range( self.default ):
             rval_dict = { '__index__': i}
             for input in self.inputs.itervalues():
-                rval_dict[ input.name ] = input.get_initial_value( trans, context, history=history )
+                rval_dict[ input.name ] = input.get_initial_value( trans, context )
             rval.append( rval_dict )
         return rval
 
@@ -182,11 +182,11 @@ def visit_inputs( self, prefix, value, callback ):
             else:
                 input.visit_inputs( prefix, value[input.name], callback )
 
-    def get_initial_value( self, trans, context, history=None ):
+    def get_initial_value( self, trans, context ):
         rval = {}
         child_context = ExpressionContext( rval, context )
         for child_input in self.inputs.itervalues():
-            rval[ child_input.name ] = child_input.get_initial_value( trans, child_context, history=history )
+            rval[ child_input.name ] = child_input.get_initial_value( trans, child_context )
         return rval
 
     def to_dict( self, trans, view='collection', value_mapper=None ):
@@ -296,14 +296,14 @@ def visit_inputs( self, prefix, value, callback ):
                 else:
                     input.visit_inputs( new_prefix, d[input.name], callback )
 
-    def get_initial_value( self, trans, context, history=None ):
+    def get_initial_value( self, trans, context ):
         d_type = self.get_datatype( trans, context )
         rval = []
         for i, ( composite_name, composite_file ) in enumerate( d_type.writable_files.iteritems() ):
             rval_dict = {}
             rval_dict['__index__'] = i  # create __index__
             for input in self.inputs.itervalues():
-                rval_dict[ input.name ] = input.get_initial_value( trans, context, history=history )  # input.value_to_basic( d[input.name], app )
+                rval_dict[ input.name ] = input.get_initial_value( trans, context )
             rval.append( rval_dict )
         return rval
 
@@ -611,12 +611,12 @@ def visit_inputs( self, prefix, value, callback ):
             else:
                 input.visit_inputs( prefix, value[input.name], callback )
 
-    def get_initial_value( self, trans, context, history=None ):
+    def get_initial_value( self, trans, context ):
         # State for a conditional is a plain dictionary.
         rval = {}
         # Get the default value for the 'test element' and use it
         # to determine the current case
-        test_value = self.test_param.get_initial_value( trans, context, history=history )
+        test_value = self.test_param.get_initial_value( trans, context )
         current_case = self.get_current_case( test_value, trans )
         # Store the current case in a special value
         rval['__current_case__'] = current_case
@@ -625,7 +625,7 @@ def get_initial_value( self, trans, context, history=None ):
         # Fill in state for selected case
         child_context = ExpressionContext( rval, context )
         for child_input in self.cases[current_case].inputs.itervalues():
-            rval[ child_input.name ] = child_input.get_initial_value( trans, child_context, history=history )
+            rval[ child_input.name ] = child_input.get_initial_value( trans, child_context )
         return rval
 
     def to_dict( self, trans, view='collection', value_mapper=None ):

From 34f46c98c7bdace6af9126b44534fd41c9121002 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 22 Jan 2016 18:04:05 -0500
Subject: [PATCH 06/33] Remove comments

---
 lib/galaxy/tools/parameters/grouping.py | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/lib/galaxy/tools/parameters/grouping.py b/lib/galaxy/tools/parameters/grouping.py
index 8998dc897b25..1942d78670ae 100644
--- a/lib/galaxy/tools/parameters/grouping.py
+++ b/lib/galaxy/tools/parameters/grouping.py
@@ -323,11 +323,9 @@ def get_file_name( file_name ):
                 if not dataset_info:
                     dataset_info = 'uploaded file'
                 return Bunch( type='file', path=data_file['local_filename'], name=dataset_name )
-                # return 'file', data_file['local_filename'], get_file_name( data_file.filename ), dataset_name, dataset_info
             except:
                 # The uploaded file should've been persisted by the upload tool action
                 return Bunch( type=None, path=None, name=None )
-                # return None, None, None, None, None
 
         def get_url_paste_urls_or_filename( group_incoming, override_name=None, override_info=None ):
             url_paste_file = group_incoming.get( 'url_paste', None )
@@ -347,7 +345,6 @@ def get_url_paste_urls_or_filename( group_incoming, override_name=None, override
                             if not dataset_info:
                                 dataset_info = 'uploaded url'
                             yield Bunch( type='url', path=line, name=dataset_name )
-                            # yield ( 'url', line, precreated_name, dataset_name, dataset_info )
                 else:
                     dataset_name = dataset_info = precreated_name = 'Pasted Entry'  # we need to differentiate between various url pastes here
                     if override_name:
@@ -355,7 +352,6 @@ def get_url_paste_urls_or_filename( group_incoming, override_name=None, override
                     if override_info:
                         dataset_info = override_info
                     yield Bunch( type='file', path=url_paste_file, name=precreated_name )
-                    # yield ( 'file', url_paste_file, precreated_name, dataset_name, dataset_info )
 
         def get_one_filename( context ):
             data_file = context['file_data']

From 7eb6cc7b8247689d1bfef12c99a9514610bbd0bb Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 22 Jan 2016 18:44:18 -0500
Subject: [PATCH 07/33] Revise validate signature

---
 lib/galaxy/tools/parameters/__init__.py   |  8 +++-----
 lib/galaxy/tools/parameters/validation.py | 24 +++++++++++------------
 2 files changed, 15 insertions(+), 17 deletions(-)

diff --git a/lib/galaxy/tools/parameters/__init__.py b/lib/galaxy/tools/parameters/__init__.py
index fec62c68063a..e9f4563cfe27 100644
--- a/lib/galaxy/tools/parameters/__init__.py
+++ b/lib/galaxy/tools/parameters/__init__.py
@@ -81,8 +81,6 @@ def check_param( trans, param, incoming_value, param_values, source='html', bool
         # resolves the inconsistent definition of boolean parameters (see base.py) without modifying shared code
         if boolean_fix and param.type == 'boolean' and isinstance( value, basestring ):
             return [ string_as_bool( value ), None ]
-        if history is None:
-            history = trans.history
         if value is not None or isinstance( param, DataToolParameter ) or isinstance( param, DataCollectionToolParameter ):
             # Convert value from HTML representation
             if source == 'html':
@@ -90,12 +88,12 @@ def check_param( trans, param, incoming_value, param_values, source='html', bool
             else:
                 value = param.from_json( value, request_context, param_values )
             # Allow the value to be converted if necessary
-            filtered_value = param.filter_value( value, trans, param_values )
+            filtered_value = param.filter_value( value, request_context, param_values )
             # Then do any further validation on the value
-            param.validate( filtered_value, history, workflow_building_mode=workflow_building_mode )
+            param.validate( filtered_value, request_context )
         elif value is None and isinstance( param, SelectToolParameter ):
             # An empty select list or column list
-            param.validate( value, history, workflow_building_mode=workflow_building_mode )
+            param.validate( value, request_context )
     except ValueError, e:
         error = str( e )
     return value, error
diff --git a/lib/galaxy/tools/parameters/validation.py b/lib/galaxy/tools/parameters/validation.py
index e84156a9bc6d..c4bf76a9e8f9 100644
--- a/lib/galaxy/tools/parameters/validation.py
+++ b/lib/galaxy/tools/parameters/validation.py
@@ -28,7 +28,7 @@ def from_element( cls, param, elem ):
         assert type is not None, "Required 'type' attribute missing from validator"
         return validator_types[type].from_element( param, elem )
 
-    def validate( self, value, history=None ):
+    def validate( self, value, trans=None ):
         raise TypeError( "Abstract Method" )
 
 
@@ -61,7 +61,7 @@ def __init__( self, message, expression ):
         # the sre module.
         self.expression = expression
 
-    def validate( self, value, history=None ):
+    def validate( self, value, trans=None ):
         if re.match( self.expression, value ) is None:
             raise ValueError( self.message )
 
@@ -95,7 +95,7 @@ def __init__( self, message, expression, substitute_value_in_message ):
         # Save compiled expression, code objects are thread safe (right?)
         self.expression = compile( expression, '<string>', 'eval' )
 
-    def validate( self, value, history=None ):
+    def validate( self, value, trans=None ):
         if not( eval( self.expression, dict( value=value ) ) ):
             message = self.message
             if self.substitute_value_in_message:
@@ -156,7 +156,7 @@ def __init__( self, message, range_min, range_max, exclude_min=False, exclude_ma
             op2 = '<'
         self.message = message or "Value must be %s %s and %s %s" % ( op1, self_min_str, op2, self_max_str )
 
-    def validate( self, value, history=None ):
+    def validate( self, value, trans=None ):
         if self.exclude_min:
             if not self.min < float( value ):
                 raise ValueError( self.message )
@@ -207,7 +207,7 @@ def __init__( self, message, length_min, length_max ):
         self.min = length_min
         self.max = length_max
 
-    def validate( self, value, history=None ):
+    def validate( self, value, trans=None ):
         if self.min is not None and len( value ) < self.min:
             raise ValueError( self.message or ( "Must have length of at least %d" % self.min ) )
         if self.max is not None and len( value ) > self.max:
@@ -226,7 +226,7 @@ def __init__( self, message=None ):
     def from_element( cls, param, elem ):
         return cls( elem.get( 'message', None ) )
 
-    def validate( self, value, history=None ):
+    def validate( self, value, trans=None ):
         if value and value.state != model.Dataset.states.OK:
             if self.message is None:
                 self.message = "The selected dataset is still being generated, select another dataset or wait until it is completed"
@@ -248,7 +248,7 @@ def __init__( self, message=None, check="", skip="" ):
     def from_element( cls, param, elem ):
         return cls( message=elem.get( 'message', None ), check=elem.get( 'check', "" ), skip=elem.get( 'skip', "" ) )
 
-    def validate( self, value, history=None ):
+    def validate( self, value, trans=None ):
         if value:
             if not isinstance( value, model.DatasetInstance ):
                 raise ValueError( 'A non-dataset value was provided.' )
@@ -274,7 +274,7 @@ def __init__( self, message=None ):
     def from_element( cls, param, elem ):
         return cls( elem.get( 'message', None ) )
 
-    def validate( self, value, history=None ):
+    def validate( self, value, trans=None ):
         # if value is None, we cannot validate
         if value:
             dbkey = value.metadata.dbkey
@@ -294,7 +294,7 @@ def __init__( self, message=None ):
     def from_element( cls, param, elem ):
         return cls( elem.get( 'message', None ) )
 
-    def validate( self, value, history=None ):
+    def validate( self, value, trans=None ):
         if value is None:
             if self.message is None:
                 self.message = "No options available for selection"
@@ -311,7 +311,7 @@ def __init__( self, message=None ):
     def from_element( cls, param, elem ):
         return cls( elem.get( 'message', None ) )
 
-    def validate( self, value, history=None ):
+    def validate( self, value, trans=None ):
         if value == '':
             if self.message is None:
                 self.message = "Field requires a value"
@@ -349,7 +349,7 @@ def __init__( self, filename, metadata_name, metadata_column, message="Value for
                 if metadata_column < len( fields ):
                     self.valid_values.append( fields[metadata_column].strip() )
 
-    def validate( self, value, history=None ):
+    def validate( self, value, trans=None ):
         if not value:
             return
         if hasattr( value, "metadata" ):
@@ -401,7 +401,7 @@ def _load_values( self ):
             if self._metadata_column < len( fields ):
                 self.valid_values.append( fields[ self._metadata_column ] )
 
-    def validate( self, value, history=None ):
+    def validate( self, value, trans=None ):
         if not value:
             return
         if hasattr( value, "metadata" ):

From a272bff066516019ca74ee0012b2ae6fe02c21bc Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 22 Jan 2016 18:52:59 -0500
Subject: [PATCH 08/33] Use consistently other_values

---
 lib/galaxy/tools/__init__.py         |  8 ++---
 lib/galaxy/tools/parameters/basic.py | 52 ++++++++++++++--------------
 2 files changed, 30 insertions(+), 30 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 0550da3ddd7a..dfbf36124ce8 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1066,7 +1066,7 @@ def fill_in_new_state( self, trans, inputs, state, context=None, history=None ):
         """
         context = ExpressionContext( state, context )
         for input in inputs.itervalues():
-            state[ input.name ] = input.get_initial_value( trans, context, history=history )
+            state[ input.name ] = input.get_initial_value( trans, context )
 
     def get_param_html_map( self, trans, page=0, other_values={} ):
         """
@@ -2177,7 +2177,7 @@ def check_state( trans, input, value, context ):
         def populate_state(trans, inputs, state, errors, incoming, prefix="", context=None ):
             context = ExpressionContext(state, context)
             for input in inputs.itervalues():
-                state[input.name] = input.get_initial_value(trans, context, history=history)
+                state[input.name] = input.get_initial_value(trans, context)
                 key = prefix + input.name
                 if input.type == 'repeat':
                     group_state = state[input.name]
@@ -2238,7 +2238,7 @@ def iterate(group_inputs, inputs, state_inputs, other_values=None):
                     tool_dict = input.to_dict(trans)
                     if 'test_param' in tool_dict:
                         test_param = tool_dict['test_param']
-                        test_param['default_value'] = jsonify(input.test_param.get_initial_value(trans, other_values, history=history))
+                        test_param['default_value'] = jsonify(input.test_param.get_initial_value(trans, other_values))
                         test_param['value'] = jsonify(group_state.get(test_param['name'], test_param['default_value']))
                         test_param['text_value'] = input.test_param.value_to_display_text(test_param['value'], self.app)
                         for i in range(len( tool_dict['cases'] ) ):
@@ -2260,7 +2260,7 @@ def iterate(group_inputs, inputs, state_inputs, other_values=None):
 
                     # backup default value
                     try:
-                        tool_dict['default_value'] = input.get_initial_value(trans, other_values, history=history)
+                        tool_dict['default_value'] = input.get_initial_value(trans, other_values)
                     except Exception:
                         tool_dict['default_value'] = None
                         log.exception('tools::to_json() - Getting initial value failed %s.' % input.name)
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 2e1fe8940c7b..b797613fb4cc 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -115,13 +115,13 @@ def from_html( self, value, trans=None, other_values={} ):
     def from_json( self, value, trans=None, other_values={} ):
         return self.from_html( value, trans, other_values )
 
-    def get_initial_value( self, trans, context ):
+    def get_initial_value( self, trans, other_values ):
         """
         Return the starting value of the parameter
         """
         return None
 
-    def get_initial_value_from_history_prevent_repeats( self, trans, context, already_used ):
+    def get_initial_value_from_history_prevent_repeats( self, trans, other_values, already_used ):
         """
         Get the starting value for the parameter, but if fetching from the history, try
         to find a value that has not yet been used. already_used is a list of objects that
@@ -129,7 +129,7 @@ def get_initial_value_from_history_prevent_repeats( self, trans, context, alread
         if a value has already been chosen from the history. This is to support the capability to
         choose each dataset once
         """
-        return self.get_initial_value( trans, context )
+        return self.get_initial_value( trans, other_values )
 
     def get_required_enctype( self ):
         """
@@ -297,7 +297,7 @@ def validate( self, value, history=None, workflow_building_mode=False ):
         if not ( workflow_building_mode and contains_workflow_parameter(value, search=search) ):
             return super( TextToolParameter, self ).validate( value, history )
 
-    def get_initial_value( self, trans, context ):
+    def get_initial_value( self, trans, other_values ):
         return self.value
 
     def to_dict( self, trans, view='collection', value_mapper=None, other_values={} ):
@@ -379,7 +379,7 @@ def to_python( self, value, app ):
                 return None
             raise err
 
-    def get_initial_value( self, trans, context ):
+    def get_initial_value( self, trans, other_values ):
         if self.value:
             return int( self.value )
         else:
@@ -458,7 +458,7 @@ def to_python( self, value, app ):
                 return None
             raise err
 
-    def get_initial_value( self, trans, context ):
+    def get_initial_value( self, trans, other_values ):
         try:
             return float( self.value )
         except:
@@ -511,7 +511,7 @@ def to_html_value( self, value, app ):
     def to_python( self, value, app ):
         return ( value in [ 'True', 'true' ])
 
-    def get_initial_value( self, trans, context ):
+    def get_initial_value( self, trans, other_values ):
         return self.checked
 
     def to_param_dict_string( self, value, other_values={} ):
@@ -601,7 +601,7 @@ def to_python( self, value, app ):
         else:
             raise Exception( "FileToolParameter cannot be persisted" )
 
-    def get_initial_value( self, trans, context ):
+    def get_initial_value( self, trans, other_values ):
         return None
 
 
@@ -618,7 +618,7 @@ def __init__( self, tool, input_source ):
         self.multiple = input_source.get_bool( 'multiple', True )
         self.user_ftp_dir = ''
 
-    def get_initial_value( self, trans, context ):
+    def get_initial_value( self, trans, other_values ):
         if trans is not None:
             if trans.user is not None:
                 self.user_ftp_dir = "%s/" % trans.user_ftp_dir
@@ -700,7 +700,7 @@ def __init__( self, tool, input_source ):
     def get_html_field( self, trans=None, value=None, other_values={} ):
         return form_builder.HiddenField( self.name, self.value )
 
-    def get_initial_value( self, trans, context ):
+    def get_initial_value( self, trans, other_values ):
         return self.value
 
     def get_label( self ):
@@ -723,7 +723,7 @@ def __init__( self, tool, input_source ):
     def get_html_field( self, trans=None, value=None, other_values={} ):
         return form_builder.HiddenField( self.name, self.value )
 
-    def get_initial_value( self, trans, context ):
+    def get_initial_value( self, trans, other_values ):
         return self.value.lower()
 
 
@@ -737,7 +737,7 @@ def __init__( self, tool, input_source ):
         super( BaseURLToolParameter, self ).__init__( tool, input_source )
         self.value = input_source.get( 'value', '' )
 
-    def get_initial_value( self, trans, context ):
+    def get_initial_value( self, trans, other_values ):
         return self._get_value()
 
     def get_html_field( self, trans=None, value=None, other_values={} ):
@@ -898,10 +898,10 @@ def get_legal_values( self, trans, other_values ):
         else:
             return self.legal_values
 
-    def get_html_field( self, trans=None, value=None, context={} ):
+    def get_html_field( self, trans=None, value=None, other_values={} ):
         # Dynamic options are not yet supported in workflow, allow
         # specifying the value as text for now.
-        options = list(self.get_options( trans, context ))
+        options = list(self.get_options( trans, other_values ))
         if len(list(options)) == 0 and trans.workflow_building_mode:
             if self.multiple:
                 if value is None:
@@ -1003,8 +1003,8 @@ def value_from_basic( self, value, app, ignore_errors=False ):
             return value[ "value" ]
         return super( SelectToolParameter, self ).value_from_basic( value, app, ignore_errors=ignore_errors )
 
-    def get_initial_value( self, trans, context ):
-        options = list( self.get_options( trans, context ) )
+    def get_initial_value( self, trans, other_values ):
+        options = list( self.get_options( trans, other_values ) )
         if len(options) == 0 and trans.workflow_building_mode:
             return None
         value = [ optval for _, optval, selected in options if selected ]
@@ -1311,10 +1311,10 @@ def get_options( self, trans, other_values ):
                     options.append( ( 'Column: ' + col, col, False ) )
         return options
 
-    def get_initial_value( self, trans, context ):
+    def get_initial_value( self, trans, other_values ):
         if self.default_value is not None:
             return self.default_value
-        return SelectToolParameter.get_initial_value( self, trans, context )
+        return SelectToolParameter.get_initial_value( self, trans, other_values )
 
     def get_legal_values( self, trans, other_values ):
         return set( self.get_column_list( trans, other_values ) )
@@ -1607,14 +1607,14 @@ def recurse_option( option_list, option ):
                 rval = sanitize_param( rval )
         return rval
 
-    def get_initial_value( self, trans, context ):
+    def get_initial_value( self, trans, other_values ):
         def recurse_options( initial_values, options ):
             for option in options:
                 if option['selected']:
                     initial_values.append( option['value'] )
                 recurse_options( initial_values, option['options'] )
         # More working around dynamic options for workflow
-        options = self.get_options( trans=trans, other_values=context )
+        options = self.get_options( trans=trans, other_values=other_values )
         if len(list(options)) == 0 and trans.workflow_building_mode:
             return None
         initial_values = []
@@ -1925,10 +1925,10 @@ def dataset_collector( hdas, parent_hid ):
         for item in dataset_collector( history.active_datasets_children_and_roles, None ):
             yield item
 
-    def get_initial_value( self, trans, context ):
-        return self.get_initial_value_from_history_prevent_repeats(trans, context, None )
+    def get_initial_value( self, trans, other_values ):
+        return self.get_initial_value_from_history_prevent_repeats(trans, other_values, None )
 
-    def get_initial_value_from_history_prevent_repeats( self, trans, context, already_used ):
+    def get_initial_value_from_history_prevent_repeats( self, trans, other_values, already_used ):
         """
         NOTE: This is wasteful since dynamic options and dataset collection
               happens twice (here and when generating HTML).
@@ -1937,7 +1937,7 @@ def get_initial_value_from_history_prevent_repeats( self, trans, context, alread
         if trans.workflow_building_mode or trans.webapp.name == 'tool_shed':
             return DummyDataset()
         history = self._get_history( trans )
-        dataset_matcher = DatasetMatcher( trans, self, None, context )
+        dataset_matcher = DatasetMatcher( trans, self, None, other_values )
         if self.optional:
             return None
         most_recent_dataset = []
@@ -2458,7 +2458,7 @@ def __init__( self, tool, elem ):
         self.type = "hidden_data"
         self.hidden = True
 
-    def get_initial_value( self, trans, context ):
+    def get_initial_value( self, trans, other_values ):
         return None
 
     def get_html_field( self, trans=None, value=None, other_values={} ):
@@ -2478,7 +2478,7 @@ def __init__( self, tool, input_source, context=None ):
     def get_html_field( self, trans=None, value=None, other_values={} ):
         return form_builder.LibraryField( self.name, value=value, trans=trans )
 
-    def get_initial_value( self, trans, context ):
+    def get_initial_value( self, trans, other_values ):
         return None
 
     def from_html( self, value, trans, other_values={} ):

From 550102915866ab4448a3e8a070437c80772320da Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 22 Jan 2016 20:05:11 -0500
Subject: [PATCH 09/33] Revise validate signature

---
 lib/galaxy/tools/parameters/basic.py | 24 +++++++++++-------------
 1 file changed, 11 insertions(+), 13 deletions(-)

diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index b797613fb4cc..d738746d105d 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -210,11 +210,11 @@ def to_param_dict_string( self, value, other_values={} ):
                 value = sanitize_param( value )
         return value
 
-    def validate( self, value, history=None, workflow_building_mode=False ):
+    def validate( self, value, trans ):
         if value == "" and self.optional:
             return
         for validator in self.validators:
-            validator.validate( value, history )
+            validator.validate( value, trans )
 
     def to_dict( self, trans, view='collection', value_mapper=None, other_values={} ):
         """ to_dict tool parameter. This can be overridden by subclasses. """
@@ -292,10 +292,10 @@ def to_html_value( self, value, app ):
         else:
             return self.to_string( value, app )
 
-    def validate( self, value, history=None, workflow_building_mode=False ):
+    def validate( self, value, trans ):
         search = self.type == "text"
-        if not ( workflow_building_mode and contains_workflow_parameter(value, search=search) ):
-            return super( TextToolParameter, self ).validate( value, history )
+        if not ( trans.workflow_building_mode and contains_workflow_parameter(value, search=search) ):
+            return super( TextToolParameter, self ).validate( value, trans )
 
     def get_initial_value( self, trans, other_values ):
         return self.value
@@ -1683,13 +1683,11 @@ class BaseDataToolParameter( ToolParameter ):
     def __init__( self, tool, input_source, trans ):
         super(BaseDataToolParameter, self).__init__( tool, input_source )
 
-    def _get_history( self, trans, history=None ):
+    def _get_history( self, trans ):
         class_name = self.__class__.__name__
         assert trans is not None, "%s requires a trans" % class_name
-        if history is None:
-            history = trans.get_history()
-        assert history is not None, "%s requires a history" % class_name
-        return history
+        assert trans.history is not None, "%s requires a history" % class_name
+        return trans.history
 
     def _ensure_selection( self, field ):
         set_selected = field.get_selected( return_label=True, return_value=True, multi=False ) is not None
@@ -2090,14 +2088,14 @@ def value_to_display_text( self, value, app ):
                 pass
         return "No dataset"
 
-    def validate( self, value, history=None, workflow_building_mode=False ):
+    def validate( self, value, trans=None ):
         dataset_count = 0
         for validator in self.validators:
             def do_validate( v ):
                 if validator.requires_dataset_metadata and v and v.dataset.state != galaxy.model.Dataset.states.OK:
                     return
                 else:
-                    validator.validate( v, history )
+                    validator.validate( v, trans )
 
             if value and self.multiple:
                 if not isinstance( value, list ):
@@ -2402,7 +2400,7 @@ def value_to_display_text( self, value, app ):
             display_text = "No dataset collection."
         return display_text
 
-    def validate( self, value, history=None, workflow_building_mode=False ):
+    def validate( self, value, trans ):
         return True  # TODO
 
     def to_dict( self, trans, view='collection', value_mapper=None, other_values=None ):

From 4b6172299e2adc4edd117c505e5c7ddcde38c24b Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sun, 24 Jan 2016 14:08:59 -0500
Subject: [PATCH 10/33] Use workcontext

---
 lib/galaxy/tools/evaluation.py          | 11 ++++
 lib/galaxy/tools/parameters/__init__.py |  8 +--
 lib/galaxy/tools/parameters/basic.py    | 70 ++++++++++++-------------
 lib/galaxy/work/context.py              |  3 +-
 4 files changed, 52 insertions(+), 40 deletions(-)

diff --git a/lib/galaxy/tools/evaluation.py b/lib/galaxy/tools/evaluation.py
index bfad5ed5d43d..8bdb2d83a97b 100644
--- a/lib/galaxy/tools/evaluation.py
+++ b/lib/galaxy/tools/evaluation.py
@@ -53,6 +53,17 @@ def set_compute_environment( self, compute_environment, get_special=None ):
         incoming = dict( [ ( p.name, p.value ) for p in job.parameters ] )
         incoming = self.tool.params_from_strings( incoming, self.app )
 
+        # Regular parameter validation
+        #def validate_inputs( input, value, prefixed_name, prefixed_label, context ):
+        #    value = input.from_html( value, Bunch(
+        #        user                    = job.history.user,
+        #        history                 = job.history,
+        #        ##user_ftp_dir            = trans.user_ftp_dir,
+        #        workflow_building_mode  = False
+        #    ), context )
+        #    input.validate( value, None )
+        #visit_input_values ( self.tool.inputs, incoming, validate_inputs, details=True )
+
         # Restore input / output data lists
         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 ] )
diff --git a/lib/galaxy/tools/parameters/__init__.py b/lib/galaxy/tools/parameters/__init__.py
index e9f4563cfe27..fd63b4363896 100644
--- a/lib/galaxy/tools/parameters/__init__.py
+++ b/lib/galaxy/tools/parameters/__init__.py
@@ -6,7 +6,7 @@
 from grouping import Conditional, Repeat, Section, UploadDataset
 from galaxy.util.json import dumps, json_fix, loads
 from galaxy.util.expressions import ExpressionContext
-from galaxy.util.bunch import Bunch
+from galaxy.work.context import WorkRequestContext
 
 REPLACE_ON_TRUTHY = object()
 
@@ -69,10 +69,10 @@ def check_param( trans, param, incoming_value, param_values, source='html', bool
     previous parameters (this may actually be an ExpressionContext
     when dealing with grouping scenarios).
     """
-    request_context = Bunch(
+    request_context = WorkRequestContext(
+        app                     = trans.app,
         user                    = trans.user,
-        history                 = trans.history,
-        user_ftp_dir            = trans.user_ftp_dir,
+        history                 = history or trans.history,
         workflow_building_mode  = workflow_building_mode
     )
     value = incoming_value
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index d738746d105d..3ab296f1f373 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -560,7 +560,7 @@ def from_html( self, value, trans=None, other_values={} ):
         # Middleware or proxies may encode files in special ways (TODO: this
         # should be pluggable)
         if type( value ) == dict:
-            upload_store = self.app.config.nginx_upload_store
+            upload_store = trans.app.config.nginx_upload_store
             assert upload_store, \
                 "Request appears to have been processed by nginx_upload_module \
                 but Galaxy is not configured to recognize it"
@@ -635,7 +635,7 @@ def get_html_field( self, trans=None, value=None, other_values={}  ):
             user_ftp_dir = None
         else:
             user_ftp_dir = trans.user_ftp_dir
-        return form_builder.FTPFileField( self.name, user_ftp_dir, self.app.config.ftp_upload_site, value=value )
+        return form_builder.FTPFileField( self.name, user_ftp_dir, trans.app.config.ftp_upload_site, value=value )
 
     def to_param_dict_string( self, value, other_values={} ):
         if value is '':
@@ -1151,7 +1151,7 @@ def _get_dbkey_names( self, trans=None ):
         if not self.tool:
             # Hack for unit tests, since we have no tool
             return util.read_dbnames( None )
-        return self.app.genome_builds.get_genome_build_names( trans=trans )
+        return trans.app.genome_builds.get_genome_build_names( trans=trans )
 
 
 class ColumnListParameter( SelectToolParameter ):
@@ -1708,7 +1708,7 @@ def _datatypes_registery( self, trans, tool ):
             if trans:
                 # Must account for "Input Dataset" types, which while not a tool still need access to the real registry.
                 # A handle to the transaction (and thus app) will be given by the module.
-                datatypes_registry = self.app.datatypes_registry
+                datatypes_registry = trans.app.datatypes_registry
             else:
                 # This occurs for things such as unit tests
                 import galaxy.datatypes.registry
@@ -1866,7 +1866,7 @@ def value_modifier(value):
             name = history_dataset_collection.name
             hid = str( history_dataset_collection.hid )
             hidden_text = ""  # TODO
-            id = value_modifier( self.app.security.encode_id( history_dataset_collection.id ) )
+            id = value_modifier( dataset_matcher.app.security.encode_id( history_dataset_collection.id ) )
             selected = value and history_dataset_collection in value
             text = "%s:%s %s" % ( hid, hidden_text, name )
             field.add_option( text, id, selected )
@@ -1978,44 +1978,44 @@ def from_html( self, value, trans, other_values={} ):
             for single_value in value:
                 if isinstance( single_value, dict ) and 'src' in single_value and 'id' in single_value:
                     if single_value['src'] == 'hda':
-                        rval.append( self.app.model.context.query( self.app.model.HistoryDatasetAssociation ).get( self.app.security.decode_id(single_value['id']) ))
+                        rval.append( trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.app.security.decode_id(single_value['id']) ))
                     elif single_value['src'] == 'hdca':
                         found_hdca = True
-                        decoded_id = self.app.security.decode_id( single_value[ 'id' ] )
-                        rval.append( self.app.model.context.query( self.app.model.HistoryDatasetCollectionAssociation ).get( decoded_id ) )
+                        decoded_id = trans.app.security.decode_id( single_value[ 'id' ] )
+                        rval.append( trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( decoded_id ) )
                     else:
                         raise ValueError("Unknown input source %s passed to job submission API." % single_value['src'])
-                elif isinstance( single_value, self.app.model.HistoryDatasetCollectionAssociation ):
+                elif isinstance( single_value, trans.app.model.HistoryDatasetCollectionAssociation ):
                     rval.append( single_value )
-                elif isinstance( single_value, self.app.model.HistoryDatasetAssociation ):
+                elif isinstance( single_value, trans.app.model.HistoryDatasetAssociation ):
                     rval.append( single_value )
                 else:
-                    rval.append( self.app.model.context.query( self.app.model.HistoryDatasetAssociation ).get( single_value ) )
+                    rval.append( trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( single_value ) )
             if found_hdca:
                 for val in rval:
-                    if not isinstance( val, self.app.model.HistoryDatasetCollectionAssociation ):
+                    if not isinstance( val, trans.app.model.HistoryDatasetCollectionAssociation ):
                         raise ValueError( "If collections are supplied to multiple data input parameter, only collections may be used." )
-        elif isinstance( value, self.app.model.HistoryDatasetAssociation ):
+        elif isinstance( value, trans.app.model.HistoryDatasetAssociation ):
             rval = value
         elif isinstance( value, dict ) and 'src' in value and 'id' in value:
             if value['src'] == 'hda':
-                rval = self.app.model.context.query( self.app.model.HistoryDatasetAssociation ).get( self.app.security.decode_id(value['id']) )
+                rval = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.app.security.decode_id(value['id']) )
             elif value['src'] == 'hdca':
-                decoded_id = self.app.security.decode_id( value[ 'id' ] )
-                rval = self.app.model.context.query( self.app.model.HistoryDatasetCollectionAssociation ).get( decoded_id )
+                decoded_id = trans.app.security.decode_id( value[ 'id' ] )
+                rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( decoded_id )
             else:
                 raise ValueError("Unknown input source %s passed to job submission API." % value['src'])
         elif str( value ).startswith( "__collection_reduce__|" ):
             encoded_ids = [ v[ len( "__collection_reduce__|" ): ] for v in str( value ).split(",") ]
-            decoded_ids = map( self.app.security.decode_id, encoded_ids )
+            decoded_ids = map( trans.app.security.decode_id, encoded_ids )
             rval = []
             for decoded_id in decoded_ids:
-                hdca = self.app.model.context.query( self.app.model.HistoryDatasetCollectionAssociation ).get( decoded_id )
+                hdca = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( decoded_id )
                 rval.append( hdca )
-        elif isinstance( value, self.app.model.HistoryDatasetCollectionAssociation ):
+        elif isinstance( value, trans.app.model.HistoryDatasetCollectionAssociation ):
             rval = value
         else:
-            rval = self.app.model.context.query( self.app.model.HistoryDatasetAssociation ).get( value )
+            rval = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( value )
         if isinstance( rval, list ):
             values = rval
         else:
@@ -2201,7 +2201,7 @@ def to_dict( self, trans, view='collection', value_mapper=None, other_values={}
             if match:
                 m = match.hda
                 d['options']['hda'].append({
-                    'id'            : self.app.security.encode_id( m.id ),
+                    'id'            : trans.app.security.encode_id( m.id ),
                     'hid'           : m.hid,
                     'name'          : m.name if m.visible else '(hidden) %s' % m.name,
                     'src'           : 'hda'
@@ -2212,7 +2212,7 @@ def to_dict( self, trans, view='collection', value_mapper=None, other_values={}
         for hdca in history.active_dataset_collections:
             if dataset_collection_matcher.hdca_match( hdca, reduction=multiple ):
                 d['options']['hdca'].append({
-                    'id'            : self.app.security.encode_id( hdca.id ),
+                    'id'            : trans.app.security.encode_id( hdca.id ),
                     'hid'           : hdca.hid,
                     'name'          : hdca.name,
                     'src'           : 'hdca'
@@ -2247,7 +2247,7 @@ def collection_types( self ):
         return self._collection_types
 
     def _history_query( self, trans ):
-        dataset_collection_type_descriptions = self.app.dataset_collections_service.collection_type_descriptions
+        dataset_collection_type_descriptions = trans.app.dataset_collections_service.collection_type_descriptions
         return history_query.HistoryQuery.from_parameter( self, dataset_collection_type_descriptions )
 
     def get_html_field( self, trans=None, value=None, other_values={} ):
@@ -2270,7 +2270,7 @@ def get_html_field( self, trans=None, value=None, other_values={} ):
         return self._switch_fields( fields, default_field=default_field )
 
     def match_collections( self, trans, history, dataset_matcher ):
-        dataset_collections = self.app.dataset_collections_service.history_dataset_collections( history, self._history_query( trans ) )
+        dataset_collections = trans.app.dataset_collections_service.history_dataset_collections( history, self._history_query( trans ) )
         dataset_collection_matcher = DatasetCollectionMatcher( dataset_matcher )
 
         for dataset_collection_instance in dataset_collections:
@@ -2315,7 +2315,7 @@ def _get_select_dataset_collection_field( self, trans, history, multiple=False,
             hid = str( history_dataset_collection.hid )
             hidden_text = ""  # TODO
             subcollection_type = self._history_query( trans ).collection_type_description.collection_type
-            id = "%s|%s" % ( self.app.security.encode_id( history_dataset_collection.id ), subcollection_type )
+            id = "%s|%s" % ( trans.app.security.encode_id( history_dataset_collection.id ), subcollection_type )
             text = "%s:%s %s" % ( hid, hidden_text, name )
 
             field.add_option( text, id, False )
@@ -2329,30 +2329,30 @@ def from_html( self, value, trans, other_values={} ):
             return None
         if isinstance( value, str ) and value.find( "," ) > 0:
             value = [ int( value_part ) for value_part in value.split( "," ) ]
-        elif isinstance( value, self.app.model.HistoryDatasetCollectionAssociation ):
+        elif isinstance( value, trans.app.model.HistoryDatasetCollectionAssociation ):
             rval = value
-        elif isinstance( value, self.app.model.DatasetCollectionElement ):
+        elif isinstance( value, trans.app.model.DatasetCollectionElement ):
             # When mapping over nested collection - this paramter will recieve
             # a DatasetCollectionElement instead of a
             # HistoryDatasetCollectionAssociation.
             rval = value
         elif isinstance( value, dict ) and 'src' in value and 'id' in value:
             if value['src'] == 'hdca':
-                rval = self.app.model.context.query( self.app.model.HistoryDatasetCollectionAssociation ).get( self.app.security.decode_id(value['id']) )
+                rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( trans.app.security.decode_id(value['id']) )
         elif isinstance( value, list ):
             if len( value ) > 0:
                 value = value[0]
                 if isinstance( value, dict ) and 'src' in value and 'id' in value:
                     if value['src'] == 'hdca':
-                        rval = self.app.model.context.query( self.app.model.HistoryDatasetCollectionAssociation ).get( self.app.security.decode_id(value['id']) )
+                        rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( trans.app.security.decode_id(value['id']) )
         elif isinstance( value, basestring ):
             if value.startswith( "dce:" ):
-                rval = self.app.model.context.query( self.app.model.DatasetCollectionElement ).get( value[ len( "dce:"): ] )
+                rval = trans.sa_session.query( trans.app.model.DatasetCollectionElement ).get( value[ len( "dce:"): ] )
             elif value.startswith( "hdca:" ):
-                rval = self.app.model.context.query( self.app.model.HistoryDatasetCollectionAssociation ).get( value[ len( "hdca:"): ] )
+                rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( value[ len( "hdca:"): ] )
             else:
-                rval = self.app.model.context.query( self.app.model.HistoryDatasetCollectionAssociation ).get( value )
-        if rval and isinstance( rval, self.app.model.HistoryDatasetCollectionAssociation ):
+                rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( value )
+        if rval and isinstance( rval, trans.app.model.HistoryDatasetCollectionAssociation ):
             if rval.deleted:
                 raise ValueError( "The previously selected dataset collection has been deleted" )
             # TODO: Handle error states, implement error states ...
@@ -2421,7 +2421,7 @@ def to_dict( self, trans, view='collection', value_mapper=None, other_values=Non
         # append directly matched collections
         for hdca in self.match_collections( trans, history, dataset_matcher ):
             d['options']['hdca'].append({
-                'id': self.app.security.encode_id( hdca.id ),
+                'id': trans.app.security.encode_id( hdca.id ),
                 'hid': hdca.hid,
                 'name': hdca.name,
                 'src': 'hdca'
@@ -2431,7 +2431,7 @@ def to_dict( self, trans, view='collection', value_mapper=None, other_values=Non
         for hdca in self.match_multirun_collections( trans, history, dataset_matcher ):
             subcollection_type = self._history_query( trans ).can_map_over( hdca ).collection_type
             d['options']['hdca'].append({
-                'id': self.app.security.encode_id( hdca.id ),
+                'id': trans.app.security.encode_id( hdca.id ),
                 'hid': hdca.hid,
                 'name': hdca.name,
                 'src': 'hdca',
diff --git a/lib/galaxy/work/context.py b/lib/galaxy/work/context.py
index 47782440b008..323d5d23661d 100644
--- a/lib/galaxy/work/context.py
+++ b/lib/galaxy/work/context.py
@@ -18,12 +18,13 @@ class WorkRequestContext( ProvidesAppContext, ProvidesUserContext, ProvidesHisto
     objects.
     """
 
-    def __init__( self, app, user=None, history=None ):
+    def __init__( self, app, user=None, history=None, workflow_building_mode=None ):
         self.app = app
         self.security = app.security
         self.__user = user
         self.__history = history
         self.api_inherit_admin = False
+        self.workflow_building_mode = workflow_building_mode
 
     def get_history( self, create=False ):
         if create:

From eaf02029d43620db309e2860d4502e0f830bc2a9 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sun, 24 Jan 2016 14:14:37 -0500
Subject: [PATCH 11/33] Fix remaining self.app, use workcontext app

---
 lib/galaxy/tools/parameters/basic.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 3ab296f1f373..acd3a39cfb21 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -51,7 +51,6 @@ class ToolParameter( object, Dictifiable ):
 
     def __init__( self, tool, input_source, context=None ):
         input_source = ensure_input_source(input_source)
-        self.app = tool.app
         self.tool = tool
         self.refresh_on_change = False
         self.refresh_on_change_values = []
@@ -647,7 +646,7 @@ def to_param_dict_string( self, value, other_values={} ):
             return lst[ 0 ]
 
     def from_html( self, value, trans=None, other_values={} ):
-        return self.to_python( value, self.app, validate=True )
+        return self.to_python( value, trans.app, validate=True )
 
     def to_string( self, value, app ):
         return self.to_python( value, app )
@@ -2480,7 +2479,7 @@ def get_initial_value( self, trans, other_values ):
         return None
 
     def from_html( self, value, trans, other_values={} ):
-        return self.to_python( value, self.app, other_values=other_values, validate=True )
+        return self.to_python( value, trans.app, other_values=other_values, validate=True )
 
     def to_param_dict_string( self, value, other_values={} ):
         if value is None:

From 5a72480719055ac4a6d04ff690f69d5a118b5c81 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sun, 24 Jan 2016 14:21:07 -0500
Subject: [PATCH 12/33] Fix dataset selection

---
 lib/galaxy/tools/parameters/basic.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index acd3a39cfb21..613fad22e517 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -901,7 +901,7 @@ def get_html_field( self, trans=None, value=None, other_values={} ):
         # Dynamic options are not yet supported in workflow, allow
         # specifying the value as text for now.
         options = list(self.get_options( trans, other_values ))
-        if len(list(options)) == 0 and trans.workflow_building_mode:
+        if len( list( options ) ) == 0 and trans.workflow_building_mode:
             if self.multiple:
                 if value is None:
                     value = ""
@@ -1529,7 +1529,7 @@ def get_html_field( self, trans=None, value=None, other_values={} ):
         # Dynamic options are not yet supported in workflow, allow
         # specifying the value as text for now.
         options = self.get_options( trans, value, other_values )
-        if len(list(options)) == 0 and trans.workflow_building_mode:
+        if len( list( options ) ) == 0 and trans.workflow_building_mode:
             if self.multiple:
                 if value is None:
                     value = ""
@@ -1795,7 +1795,7 @@ def __init__( self, tool, input_source, trans=None):
             conv_types = [ tool.app.datatypes_registry.get_datatype_by_extension( conv_extensions.lower() ) ]
             self.conversions.append( ( name, conv_extensions, conv_types ) )
 
-    def get_html_field( self, trans=None, value=None, other_values={} ):
+    def get_html_field( self, trans, value=None, other_values={} ):
         if value is not None:
             if type( value ) != list:
                 value = [ value ]
@@ -1811,7 +1811,7 @@ def get_html_field( self, trans=None, value=None, other_values={} ):
             fields[ "multiselect_single" ] = multi_select
 
             if self.__display_multirun_option():
-                collection_select = self._get_select_dataset_collection_fields( history, dataset_matcher, suffix="", reduction=True )
+                collection_select = self._get_select_dataset_collection_fields( trans, dataset_matcher, suffix="", reduction=True )
                 if collection_select.get_selected(return_value=True):
                     default_field = "multiselect_collection"
                 fields[ "multiselect_collection" ] = collection_select
@@ -1840,12 +1840,12 @@ def get_html_field( self, trans=None, value=None, other_values={} ):
                 multi_dataset_matcher = DatasetMatcher( trans, self, multirun_value, other_values )
                 multi_select = self._get_select_dataset_field( history, multi_dataset_matcher, multiple=True, suffix="|__multirun__" )
                 fields[ "select_multiple" ] = multi_select
-                collection_field = self._get_select_dataset_collection_fields( history, dataset_matcher, multiple=False, reduction=False )
+                collection_field = self._get_select_dataset_collection_fields( trans, dataset_matcher, multiple=False, reduction=False )
                 fields[ "select_collection" ] = collection_field
 
         return self._switch_fields( fields, default_field=default_field )
 
-    def _get_select_dataset_collection_fields( self, history, dataset_matcher, multiple=False, suffix="|__collection_multirun__", reduction=False ):
+    def _get_select_dataset_collection_fields( self, trans, dataset_matcher, multiple=False, suffix="|__collection_multirun__", reduction=False ):
         if not reduction:
             def value_modifier(x):
                 return x
@@ -1861,11 +1861,11 @@ def value_modifier(value):
         field_name = "%s%s" % ( self.name, suffix )
         field = form_builder.SelectField( field_name, multiple, None, self.refresh_on_change, refresh_on_change_values=self.refresh_on_change_values )
 
-        for history_dataset_collection in self.match_collections( history, dataset_matcher, reduction=reduction ):
+        for history_dataset_collection in self.match_collections( trans.history, dataset_matcher, reduction=reduction ):
             name = history_dataset_collection.name
             hid = str( history_dataset_collection.hid )
             hidden_text = ""  # TODO
-            id = value_modifier( dataset_matcher.app.security.encode_id( history_dataset_collection.id ) )
+            id = value_modifier( trans.app.security.encode_id( history_dataset_collection.id ) )
             selected = value and history_dataset_collection in value
             text = "%s:%s %s" % ( hid, hidden_text, name )
             field.add_option( text, id, selected )

From 7cc505019d2b2af938b61efe0e00bd25a13af91b Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sun, 24 Jan 2016 14:24:33 -0500
Subject: [PATCH 13/33] Use sa_session of workcontext

---
 lib/galaxy/util/dbkeys.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/util/dbkeys.py b/lib/galaxy/util/dbkeys.py
index 8aa66bbf8c7f..e57f28e290be 100644
--- a/lib/galaxy/util/dbkeys.py
+++ b/lib/galaxy/util/dbkeys.py
@@ -33,7 +33,7 @@ def get_genome_build_names( self, trans=None ):
                 # It does allow one-off, history specific dbkeys to be created by a user. But we are not filtering,
                 # so a len file will be listed twice (as the build name and again as dataset name),
                 # if custom dbkey creation/conversion occurred within the current history.
-                datasets = self._app.model.context.query( self._app.model.HistoryDatasetAssociation ) \
+                datasets = trans.sa_session.query( self._app.model.HistoryDatasetAssociation ) \
                                 .filter_by( deleted=False, history_id=trans.history.id, extension="len" )
                 for dataset in datasets:
                     rval.append( ( dataset.dbkey, "%s (%s) [History]" % ( dataset.name, dataset.dbkey ) ) )
@@ -72,11 +72,11 @@ def get_chrom_info( self, dbkey, trans=None, custom_build_hack_get_len_from_fast
                     # fasta-to-len converter.
                     if 'fasta' in custom_build_dict and custom_build_hack_get_len_from_fasta_conversion:
                         # Build is defined by fasta; get len file, which is obtained from converting fasta.
-                        build_fasta_dataset = self._app.model.context.query( self._app.model.HistoryDatasetAssociation ).get( custom_build_dict[ 'fasta' ] )
+                        build_fasta_dataset = trans.sa_session.query( self._app.model.HistoryDatasetAssociation ).get( custom_build_dict[ 'fasta' ] )
                         chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name
                     elif 'len' in custom_build_dict:
                         # Build is defined by len file, so use it.
-                        chrom_info = self._app.model.context.query( self._app.model.HistoryDatasetAssociation ).get( custom_build_dict[ 'len' ] ).file_name
+                        chrom_info = trans.sa_session.query( self._app.model.HistoryDatasetAssociation ).get( custom_build_dict[ 'len' ] ).file_name
         # Check Data table
         if not chrom_info:
             dbkey_table = self._app.tool_data_tables.get( self._data_table_name, None )

From b56574115fa9ae32f2d4703f0b257991ad2f4c26 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sun, 24 Jan 2016 14:26:06 -0500
Subject: [PATCH 14/33] Fix trans usage

---
 lib/galaxy/util/dbkeys.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/util/dbkeys.py b/lib/galaxy/util/dbkeys.py
index e57f28e290be..216e7cb6d388 100644
--- a/lib/galaxy/util/dbkeys.py
+++ b/lib/galaxy/util/dbkeys.py
@@ -72,11 +72,11 @@ def get_chrom_info( self, dbkey, trans=None, custom_build_hack_get_len_from_fast
                     # fasta-to-len converter.
                     if 'fasta' in custom_build_dict and custom_build_hack_get_len_from_fasta_conversion:
                         # Build is defined by fasta; get len file, which is obtained from converting fasta.
-                        build_fasta_dataset = trans.sa_session.query( self._app.model.HistoryDatasetAssociation ).get( custom_build_dict[ 'fasta' ] )
+                        build_fasta_dataset = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( custom_build_dict[ 'fasta' ] )
                         chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name
                     elif 'len' in custom_build_dict:
                         # Build is defined by len file, so use it.
-                        chrom_info = trans.sa_session.query( self._app.model.HistoryDatasetAssociation ).get( custom_build_dict[ 'len' ] ).file_name
+                        chrom_info = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( custom_build_dict[ 'len' ] ).file_name
         # Check Data table
         if not chrom_info:
             dbkey_table = self._app.tool_data_tables.get( self._data_table_name, None )

From 93dbf742b36b614bacbb7a806431532567203b70 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sun, 24 Jan 2016 14:30:08 -0500
Subject: [PATCH 15/33] Reinsert last validation

---
 lib/galaxy/tools/evaluation.py | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/tools/evaluation.py b/lib/galaxy/tools/evaluation.py
index 8bdb2d83a97b..34011f157548 100644
--- a/lib/galaxy/tools/evaluation.py
+++ b/lib/galaxy/tools/evaluation.py
@@ -54,15 +54,15 @@ def set_compute_environment( self, compute_environment, get_special=None ):
         incoming = self.tool.params_from_strings( incoming, self.app )
 
         # Regular parameter validation
-        #def validate_inputs( input, value, prefixed_name, prefixed_label, context ):
-        #    value = input.from_html( value, Bunch(
-        #        user                    = job.history.user,
-        #        history                 = job.history,
-        #        ##user_ftp_dir            = trans.user_ftp_dir,
-        #        workflow_building_mode  = False
-        #    ), context )
-        #    input.validate( value, None )
-        #visit_input_values ( self.tool.inputs, incoming, validate_inputs, details=True )
+        def validate_inputs( input, value, prefixed_name, prefixed_label, context ):
+            value = input.from_html( value, Bunch(
+                app                     = app,
+                user                    = job.history.user,
+                history                 = job.history,
+                workflow_building_mode  = False
+            ), context )
+            input.validate( value, None )
+        visit_input_values ( self.tool.inputs, incoming, validate_inputs, details=True )
 
         # Restore input / output data lists
         inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] )

From 7c69227c8cde400df37f5e9390fdd88e51f64f2a Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sun, 24 Jan 2016 15:17:56 -0500
Subject: [PATCH 16/33] Fix db_builds

---
 lib/galaxy/tools/parameters/basic.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 613fad22e517..1a5f31678725 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -1150,7 +1150,7 @@ def _get_dbkey_names( self, trans=None ):
         if not self.tool:
             # Hack for unit tests, since we have no tool
             return util.read_dbnames( None )
-        return trans.app.genome_builds.get_genome_build_names( trans=trans )
+        return self.tool.app.genome_builds.get_genome_build_names( trans=trans )
 
 
 class ColumnListParameter( SelectToolParameter ):

From 269ce36d3f5212b2d98315a67b25cc6db5a3429c Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sun, 24 Jan 2016 17:30:10 -0500
Subject: [PATCH 17/33] Fix check params

---
 lib/galaxy/tools/__init__.py   | 24 ++++++++++++------------
 lib/galaxy/tools/evaluation.py | 17 +++++++++--------
 lib/galaxy/tools/execute.py    |  2 +-
 lib/galaxy/workflow/modules.py |  2 +-
 4 files changed, 23 insertions(+), 22 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index dfbf36124ce8..e4a90f74b702 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1648,17 +1648,17 @@ def params_to_strings( self, params, app ):
     def params_from_strings( self, params, app, ignore_errors=False ):
         return params_from_strings( self.inputs, params, app, ignore_errors )
 
-    def check_and_update_param_values( self, values, trans, update_values=True, allow_workflow_parameters=False ):
+    def check_and_update_param_values( self, values, trans, update_values=True ):
         """
         Check that all parameters have values, and fill in with default
         values where necessary. This could be called after loading values
         from a database in case new parameters have been added.
         """
         messages = {}
-        self.check_and_update_param_values_helper( self.inputs, values, trans, messages, update_values=update_values, allow_workflow_parameters=allow_workflow_parameters )
+        self.check_and_update_param_values_helper( self.inputs, values, trans, messages, update_values=update_values )
         return messages
 
-    def check_and_update_param_values_helper( self, inputs, values, trans, messages, context=None, prefix="", update_values=True, allow_workflow_parameters=False ):
+    def check_and_update_param_values_helper( self, inputs, values, trans, messages, context=None, prefix="", update_values=True ):
         """
         Recursive helper for `check_and_update_param_values_helper`
         """
@@ -1673,7 +1673,7 @@ def check_and_update_param_values_helper( self, inputs, values, trans, messages,
                         messages[ input.name ] = cond_messages
                     test_value = input.test_param.get_initial_value( trans, context )
                     current_case = input.get_current_case( test_value, trans )
-                    self.check_and_update_param_values_helper( input.cases[ current_case ].inputs, {}, trans, cond_messages, context, prefix, allow_workflow_parameters=allow_workflow_parameters )
+                    self.check_and_update_param_values_helper( input.cases[ current_case ].inputs, {}, trans, cond_messages, context, prefix )
                 elif isinstance( input, Repeat ):
                     if input.min:
                         messages[ input.name ] = []
@@ -1681,10 +1681,10 @@ def check_and_update_param_values_helper( self, inputs, values, trans, messages,
                             rep_prefix = prefix + "%s %d > " % ( input.title, i + 1 )
                             rep_dict = dict()
                             messages[ input.name ].append( rep_dict )
-                            self.check_and_update_param_values_helper( input.inputs, {}, trans, rep_dict, context, rep_prefix, allow_workflow_parameters=allow_workflow_parameters )
+                            self.check_and_update_param_values_helper( input.inputs, {}, trans, rep_dict, context, rep_prefix )
                 elif isinstance( input, Section ):
                     messages[ input.name ] = {}
-                    self.check_and_update_param_values_helper( input.inputs, {}, trans, messages[ input.name ], context, prefix, allow_workflow_parameters=allow_workflow_parameters )
+                    self.check_and_update_param_values_helper( input.inputs, {}, trans, messages[ input.name ], context, prefix )
                 else:
                     messages[ input.name ] = "No value found for '%s%s', using default" % ( prefix, input.label )
                 values[ input.name ] = input.get_initial_value( trans, context )
@@ -1693,7 +1693,7 @@ def check_and_update_param_values_helper( self, inputs, values, trans, messages,
                 if isinstance( input, Repeat ):
                     for i, d in enumerate( values[ input.name ] ):
                         rep_prefix = prefix + "%s %d > " % ( input.title, i + 1 )
-                        self.check_and_update_param_values_helper( input.inputs, d, trans, messages, context, rep_prefix, allow_workflow_parameters=allow_workflow_parameters )
+                        self.check_and_update_param_values_helper( input.inputs, d, trans, messages, context, rep_prefix )
                 elif isinstance( input, Conditional ):
                     group_values = values[ input.name ]
                     use_initial_value = False
@@ -1711,22 +1711,22 @@ def check_and_update_param_values_helper( self, inputs, values, trans, messages,
                             messages[ child_input.name ] = "Value no longer valid for '%s%s', replacing with default" % ( prefix, child_input.label )
                     else:
                         current = group_values["__current_case__"]
-                        self.check_and_update_param_values_helper( input.cases[current].inputs, group_values, trans, messages, context, prefix, allow_workflow_parameters=allow_workflow_parameters )
+                        self.check_and_update_param_values_helper( input.cases[current].inputs, group_values, trans, messages, context, prefix )
                 elif isinstance( input, Section ):
                     messages[ input.name ] = {}
-                    self.check_and_update_param_values_helper( input.inputs, values[ input.name ], trans, messages[ input.name ], context, prefix, allow_workflow_parameters=allow_workflow_parameters )
+                    self.check_and_update_param_values_helper( input.inputs, values[ input.name ], trans, messages[ input.name ], context, prefix )
                 else:
                     # Regular tool parameter, no recursion needed
                     try:
                         value = values[ input.name ]
-                        if not allow_workflow_parameters:
+                        if not trans.workflow_building_mode:
                             input.value_from_basic( input.value_to_basic( value, trans.app ), trans.app, ignore_errors=False )
-                            input.validate( value, history=trans.history )
+                            input.validate( value, trans )
                         else:
                             # skip check if is workflow parameters
                             ck_param = True
                             search = input.type in ["text"]
-                            if allow_workflow_parameters and contains_workflow_parameter( values[ input.name ], search=search ):
+                            if trans.workflow_building_mode and contains_workflow_parameter( values[ input.name ], search=search ):
                                 ck_param = False
                             # this will fail when a parameter's type has changed to a non-compatible one: e.g. conditional group changed to dataset input
                             if ck_param:
diff --git a/lib/galaxy/tools/evaluation.py b/lib/galaxy/tools/evaluation.py
index 34011f157548..f23f73f11557 100644
--- a/lib/galaxy/tools/evaluation.py
+++ b/lib/galaxy/tools/evaluation.py
@@ -25,7 +25,7 @@
 from galaxy.tools.parameters.grouping import Conditional, Repeat, Section
 from galaxy.tools import global_tool_errors
 from galaxy.jobs.datasets import dataset_path_rewrites
-
+from galaxy.work.context import WorkRequestContext
 import logging
 log = logging.getLogger( __name__ )
 
@@ -54,14 +54,15 @@ def set_compute_environment( self, compute_environment, get_special=None ):
         incoming = self.tool.params_from_strings( incoming, self.app )
 
         # Regular parameter validation
+        request_context = WorkRequestContext(
+            app                     = self.app,
+            user                    = job.history.user,
+            history                 = job.history,
+            workflow_building_mode  = False
+        )
         def validate_inputs( input, value, prefixed_name, prefixed_label, context ):
-            value = input.from_html( value, Bunch(
-                app                     = app,
-                user                    = job.history.user,
-                history                 = job.history,
-                workflow_building_mode  = False
-            ), context )
-            input.validate( value, None )
+            value = input.from_html( value, request_context, context )
+            input.validate( value, request_context )
         visit_input_values ( self.tool.inputs, incoming, validate_inputs, details=True )
 
         # Restore input / output data lists
diff --git a/lib/galaxy/tools/execute.py b/lib/galaxy/tools/execute.py
index e1763f346156..3a2bc03bc456 100644
--- a/lib/galaxy/tools/execute.py
+++ b/lib/galaxy/tools/execute.py
@@ -39,7 +39,7 @@ def execute_single_job(params):
         # the state we about to execute one last time. Consider whether tool executions
         # should run this as well.
         if workflow_invocation_uuid:
-            messages = tool.check_and_update_param_values( params, trans, update_values=False, allow_workflow_parameters=False )
+            messages = tool.check_and_update_param_values( params, trans, update_values=False )
             if messages:
                 execution_tracker.record_error( messages )
                 return
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index 7ae7aa45925e..37931da7e5b6 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -1080,7 +1080,7 @@ def item_callback( trans, key, input, value, error, old_value, context ):
 
     def check_and_update_state( self ):
         inputs = self.state.inputs
-        return self.tool.check_and_update_param_values( inputs, self.trans, allow_workflow_parameters=True )
+        return self.tool.check_and_update_param_values( inputs, self.trans )
 
     def compute_runtime_state( self, trans, step_updates=None, source="html" ):
         # Warning: This method destructively modifies existing step state.

From 3acdee5143586d0224f896d2bfc5c085e3409349 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sun, 24 Jan 2016 17:58:41 -0500
Subject: [PATCH 18/33] Show validation error for workflow step preparation

---
 lib/galaxy/jobs/runners/__init__.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/jobs/runners/__init__.py b/lib/galaxy/jobs/runners/__init__.py
index 0e6b78607d8d..608aabfa9c5c 100644
--- a/lib/galaxy/jobs/runners/__init__.py
+++ b/lib/galaxy/jobs/runners/__init__.py
@@ -169,9 +169,9 @@ def prepare_job(self, job_wrapper, include_metadata=False, include_work_dir_outp
                 include_metadata=include_metadata,
                 include_work_dir_outputs=include_work_dir_outputs,
             )
-        except:
+        except Exception, e:
             log.exception("(%s) Failure preparing job" % job_id)
-            job_wrapper.fail( "failure preparing job", exception=True )
+            job_wrapper.fail( e.message if hasattr( e, 'message' ) else "Job preparation failed", exception=True )
             return False
 
         if not job_wrapper.runner_command_line:

From b38479c4a49efcf2c56e400b56d1da4f5eb4a02d Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sun, 24 Jan 2016 18:20:20 -0500
Subject: [PATCH 19/33] Remove unvalidated value handling in workflow
 extraction

---
 lib/galaxy/tools/parameters/basic.py | 2 +-
 lib/galaxy/work/context.py           | 2 +-
 lib/galaxy/workflow/extract.py       | 3 ---
 3 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 1a5f31678725..ff4e4254cbbc 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -1614,7 +1614,7 @@ def recurse_options( initial_values, options ):
                 recurse_options( initial_values, option['options'] )
         # More working around dynamic options for workflow
         options = self.get_options( trans=trans, other_values=other_values )
-        if len(list(options)) == 0 and trans.workflow_building_mode:
+        if len( list( options ) ) == 0 and trans.workflow_building_mode:
             return None
         initial_values = []
         recurse_options( initial_values, options )
diff --git a/lib/galaxy/work/context.py b/lib/galaxy/work/context.py
index 323d5d23661d..4252ef9f4a02 100644
--- a/lib/galaxy/work/context.py
+++ b/lib/galaxy/work/context.py
@@ -18,7 +18,7 @@ class WorkRequestContext( ProvidesAppContext, ProvidesUserContext, ProvidesHisto
     objects.
     """
 
-    def __init__( self, app, user=None, history=None, workflow_building_mode=None ):
+    def __init__( self, app, user=None, history=None, workflow_building_mode=False ):
         self.app = app
         self.security = app.security
         self.__user = user
diff --git a/lib/galaxy/workflow/extract.py b/lib/galaxy/workflow/extract.py
index c9309192645f..8971dbb4b6ff 100644
--- a/lib/galaxy/workflow/extract.py
+++ b/lib/galaxy/workflow/extract.py
@@ -317,9 +317,6 @@ def __cleanup_param_values( inputs, values ):
     # Recursively clean data inputs and dynamic selects
     def cleanup( prefix, inputs, values ):
         for key, input in inputs.items():
-            if isinstance( input, ( SelectToolParameter, DrillDownSelectToolParameter ) ):
-                if input.is_dynamic and not isinstance( values[key], UnvalidatedValue ):
-                    values[key] = UnvalidatedValue( values[key] )
             if isinstance( input, DataToolParameter ) or isinstance( input, DataCollectionToolParameter ):
                 tmp = values[key]
                 values[key] = None

From 6939c99f1bb06532e5c4cb4c2a4ef936075b4569 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Sun, 24 Jan 2016 18:29:19 -0500
Subject: [PATCH 20/33] Remove more unvalidated value hacks

---
 lib/galaxy/jobs/__init__.py          |  4 +---
 lib/galaxy/tools/__init__.py         | 13 +------------
 lib/galaxy/tools/imp_exp/__init__.py |  3 ---
 lib/galaxy/tools/parameters/basic.py | 10 ----------
 lib/galaxy/workflow/extract.py       |  3 +--
 5 files changed, 3 insertions(+), 30 deletions(-)

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 4759fa8f1b47..9892732d698b 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -1301,9 +1301,7 @@ def path_rewriter( path ):
             if not data:
                 continue
             input_ext = data.ext
-        # 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
+        # why not re-use self.param_dict here?
         param_dict = dict( [ ( p.name, p.value ) for p in job.parameters ] )
         param_dict = self.tool.params_from_strings( param_dict, self.app )
         # Create generated output children and primary datasets and add to param_dict
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index e4a90f74b702..8668e4bf6b33 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -31,7 +31,7 @@
 from galaxy.tools.parameters import output_collect
 from galaxy.tools.parameters.basic import (BaseURLToolParameter,
                                            DataToolParameter, DataCollectionToolParameter, HiddenToolParameter,
-                                           SelectToolParameter, ToolParameter, UnvalidatedValue,
+                                           SelectToolParameter, ToolParameter,
                                            contains_workflow_parameter)
 from galaxy.tools.parameters.grouping import Conditional, ConditionalWhen, Repeat, Section, UploadDataset
 from galaxy.tools.parameters.input_translation import ToolInputTranslator
@@ -2419,18 +2419,7 @@ def map_to_history(value):
             else:
                 return None
 
-        # Unpack unvalidated values to strings, they'll be validated when the
-        # form is submitted (this happens when re-running a job that was
-        # initially run by a workflow)
-        # This needs to be done recursively through grouping parameters
         def mapping_callback( input, value, prefixed_name, prefixed_label ):
-            if isinstance( value, UnvalidatedValue ):
-                try:
-                    return input.to_html_value( value.value, self.app )
-                except Exception, e:
-                    # Need to determine when (if ever) the to_html_value call could fail.
-                    log.debug( "Failed to use input.to_html_value to determine value of unvalidated parameter, defaulting to string: %s" % ( e ) )
-                    return str( value )
             if isinstance( input, DataToolParameter ):
                 if isinstance(value, list):
                     values = []
diff --git a/lib/galaxy/tools/imp_exp/__init__.py b/lib/galaxy/tools/imp_exp/__init__.py
index 87f65f2f38d6..7db8ae032fa9 100644
--- a/lib/galaxy/tools/imp_exp/__init__.py
+++ b/lib/galaxy/tools/imp_exp/__init__.py
@@ -9,7 +9,6 @@
 
 from galaxy import model
 from galaxy.model.item_attrs import UsesAnnotations
-from galaxy.tools.parameters.basic import UnvalidatedValue
 from galaxy.util.json import dumps, loads
 from galaxy.web.framework.helpers import to_unicode
 
@@ -382,8 +381,6 @@ def default( self, obj ):
                     else:
                         rval['exported'] = True
                     return rval
-                if isinstance( obj, UnvalidatedValue ):
-                    return obj.__str__()
                 return json.JSONEncoder.default( self, obj )
 
         #
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index ff4e4254cbbc..177653645527 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -2576,16 +2576,6 @@ def to_dict( self, trans, view='collection', value_mapper=None, other_values=Non
     drill_down=DrillDownSelectToolParameter
 )
 
-class UnvalidatedValue( object ):
-    """
-    Wrapper to mark a value that has not been validated
-    """
-    def __init__( self, value ):
-        self.value = value
-
-    def __str__( self ):
-        return str( self.value )
-
 class RuntimeValue( object ):
     """
     Wrapper to note a value that is not yet set, but will be required at
diff --git a/lib/galaxy/workflow/extract.py b/lib/galaxy/workflow/extract.py
index 8971dbb4b6ff..901b7e9c1dce 100644
--- a/lib/galaxy/workflow/extract.py
+++ b/lib/galaxy/workflow/extract.py
@@ -8,8 +8,7 @@
     DataToolParameter,
     DataCollectionToolParameter,
     DrillDownSelectToolParameter,
-    SelectToolParameter,
-    UnvalidatedValue
+    SelectToolParameter
 )
 from galaxy.tools.parser import ToolOutputCollectionPart
 from galaxy.tools.parameters.grouping import (

From 539ddd4d90bda5400c3006ab4c574bebd353d280 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 25 Jan 2016 01:00:19 -0500
Subject: [PATCH 21/33] Remove optional parameter from request context
 initialization

---
 lib/galaxy/tools/evaluation.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/tools/evaluation.py b/lib/galaxy/tools/evaluation.py
index f23f73f11557..4ecc14b47f17 100644
--- a/lib/galaxy/tools/evaluation.py
+++ b/lib/galaxy/tools/evaluation.py
@@ -53,12 +53,11 @@ def set_compute_environment( self, compute_environment, get_special=None ):
         incoming = dict( [ ( p.name, p.value ) for p in job.parameters ] )
         incoming = self.tool.params_from_strings( incoming, self.app )
 
-        # Regular parameter validation
+        # Full parameter validation
         request_context = WorkRequestContext(
             app                     = self.app,
             user                    = job.history.user,
-            history                 = job.history,
-            workflow_building_mode  = False
+            history                 = job.history
         )
         def validate_inputs( input, value, prefixed_name, prefixed_label, context ):
             value = input.from_html( value, request_context, context )

From cc2cfe8d6adb264df41e18b4c33781712bb12cbb Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 25 Jan 2016 01:54:39 -0500
Subject: [PATCH 22/33] Use request context instead of trans in to_json

---
 lib/galaxy/tools/__init__.py            | 62 ++++++++++++++-----------
 lib/galaxy/tools/parameters/__init__.py | 19 +++-----
 lib/galaxy/tools/parameters/basic.py    |  2 +-
 3 files changed, 41 insertions(+), 42 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 8668e4bf6b33..be9c608a8e03 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -53,6 +53,7 @@
 from galaxy.web import url_for
 from galaxy.web.form_builder import SelectField
 from galaxy.util.dictifiable import Dictifiable
+from galaxy.work.context import WorkRequestContext
 from tool_shed.util import common_util
 from tool_shed.util import shed_util_common as suc
 
@@ -2076,17 +2077,22 @@ def to_json(self, trans, kwd={}, job=None, workflow_mode=False):
         except Exception, e:
             raise exceptions.MessageException( '[history_id=%s] Failed to retrieve history. %s.' % ( history_id, str( e ) ) )
 
-        # set workflow mode ( TODO: Should be revised/parsed without trans to tool parameters (basic.py) )
-        trans.workflow_building_mode = workflow_mode
+        # build request context
+        request_context = WorkRequestContext(
+            app                     = trans.app,
+            user                    = trans.user,
+            history                 = history,
+            workflow_building_mode  = workflow_mode
+        )
 
         # load job parameters into incoming
         tool_message = ''
         if job:
             try:
                 job_params = job.get_param_values( self.app, ignore_errors=True )
-                self.check_and_update_param_values( job_params, trans, update_values=False )
-                self._map_source_to_history( trans, self.inputs, job_params, history )
-                tool_message = self._compare_tool_version(trans, job)
+                self.check_and_update_param_values( job_params, request_context, update_values=False )
+                self._map_source_to_history( request_context, self.inputs, job_params, history )
+                tool_message = self._compare_tool_version( job )
                 params_to_incoming( kwd, self.inputs, job_params, self.app, to_html=False )
             except Exception, e:
                 raise exceptions.MessageException( str( e ) )
@@ -2157,7 +2163,7 @@ def sanitize(dict, key='value'):
             dict[key] = value
 
         # check the current state of a value and update it if necessary
-        def check_state( trans, input, value, context ):
+        def check_state( input, value, context ):
             error = 'State validation failed.'
             if isinstance( value, galaxy.tools.parameters.basic.DummyDataset ):
                 return [ None, None ]
@@ -2167,17 +2173,17 @@ def check_state( trans, input, value, context ):
                 if value.get( '__class__' ) == 'RuntimeValue':
                     return [ value, None ]
             try:
-                value, error = check_param( trans, input, value, context, history=history, boolean_fix=True, workflow_building_mode=workflow_mode )
+                value, error = check_param( request_context, input, value, context, boolean_fix=True )
             except Exception, err:
                 log.error( 'Checking parameter %s failed. %s', input.name, str( err ) )
                 pass
             return [ value, error ]
 
         # populates state with incoming url parameters
-        def populate_state(trans, inputs, state, errors, incoming, prefix="", context=None ):
+        def populate_state( inputs, state, errors, incoming, prefix="", context=None ):
             context = ExpressionContext(state, context)
             for input in inputs.itervalues():
-                state[input.name] = input.get_initial_value(trans, context)
+                state[input.name] = input.get_initial_value( request_context, context )
                 key = prefix + input.name
                 if input.type == 'repeat':
                     group_state = state[input.name]
@@ -2191,21 +2197,21 @@ def populate_state(trans, inputs, state, errors, incoming, prefix="", context=No
                             new_state = {}
                             new_state['__index__'] = rep_index
                             group_state.append(new_state)
-                            populate_state(trans, input.inputs, new_state, errors, incoming, prefix=rep_name + "|", context=context)
+                            populate_state( input.inputs, new_state, errors, incoming, prefix=rep_name + "|", context=context )
                         rep_index += 1
                 elif input.type == 'conditional':
                     group_state = state[input.name]
                     group_prefix = "%s|" % ( key )
                     test_param_key = group_prefix + input.test_param.name
                     default_value = incoming.get(test_param_key, group_state.get(input.test_param.name, None))
-                    value, error = check_state(trans, input.test_param, default_value, context)
+                    value, error = check_state( input.test_param, default_value, context )
                     if error:
                         errors[test_param_key] = error
                     else:
                         try:
-                            current_case = input.get_current_case(value, trans)
+                            current_case = input.get_current_case( value, request_context )
                             group_state = state[input.name] = {}
-                            populate_state( trans, input.cases[current_case].inputs, group_state, errors, incoming, prefix=group_prefix, context=context)
+                            populate_state( input.cases[current_case].inputs, group_state, errors, incoming, prefix=group_prefix, context=context )
                             group_state['__current_case__'] = current_case
                         except Exception:
                             errors[test_param_key] = 'The selected case is unavailable/invalid.'
@@ -2214,53 +2220,53 @@ def populate_state(trans, inputs, state, errors, incoming, prefix="", context=No
                 elif input.type == 'section':
                     group_state = state[input.name]
                     group_prefix = "%s|" % ( key )
-                    populate_state(trans, input.inputs, group_state, errors, incoming, prefix=group_prefix, context=context)
+                    populate_state( input.inputs, group_state, errors, incoming, prefix=group_prefix, context=context )
                 else:
                     default_value = incoming.get(key, state.get(input.name, None))
-                    value, error = check_state(trans, input, default_value, context)
+                    value, error = check_state( input, default_value, context )
                     if error:
                         errors[key] = error
                     state[input.name] = value
 
         # builds tool model including all attributes
-        def iterate(group_inputs, inputs, state_inputs, other_values=None):
+        def iterate( group_inputs, inputs, state_inputs, other_values=None ):
             other_values = ExpressionContext( state_inputs, other_values )
             for input_index, input in enumerate( inputs.itervalues() ):
                 tool_dict = None
                 group_state = state_inputs.get(input.name, {})
                 if input.type == 'repeat':
-                    tool_dict = input.to_dict(trans)
+                    tool_dict = input.to_dict( request_context )
                     group_cache = tool_dict['cache'] = {}
                     for i in range( len( group_state ) ):
                         group_cache[i] = {}
                         iterate( group_cache[i], input.inputs, group_state[i], other_values )
                 elif input.type == 'conditional':
-                    tool_dict = input.to_dict(trans)
+                    tool_dict = input.to_dict( request_context )
                     if 'test_param' in tool_dict:
                         test_param = tool_dict['test_param']
-                        test_param['default_value'] = jsonify(input.test_param.get_initial_value(trans, other_values))
+                        test_param['default_value'] = jsonify( input.test_param.get_initial_value( request_context, other_values ) )
                         test_param['value'] = jsonify(group_state.get(test_param['name'], test_param['default_value']))
                         test_param['text_value'] = input.test_param.value_to_display_text(test_param['value'], self.app)
                         for i in range(len( tool_dict['cases'] ) ):
                             current_state = {}
                             if i == group_state.get('__current_case__', None):
                                 current_state = group_state
-                            iterate(tool_dict['cases'][i]['inputs'], input.cases[i].inputs, current_state, other_values)
+                            iterate( tool_dict['cases'][i]['inputs'], input.cases[i].inputs, current_state, other_values )
                 elif input.type == 'section':
-                    tool_dict = input.to_dict(trans)
+                    tool_dict = input.to_dict( request_context )
                     iterate( tool_dict['inputs'], input.inputs, group_state, other_values )
                 else:
                     # expand input dictionary, resolve dynamic parameters
                     try:
-                        tool_dict = input.to_dict(trans, other_values=other_values)
+                        tool_dict = input.to_dict( request_context, other_values=other_values )
                     except Exception:
-                        tool_dict = input.to_dict(trans)
+                        tool_dict = input.to_dict( request_context )
                         log.exception('tools::to_json() - Skipping parameter expansion for %s.' % input.name)
                         pass
 
                     # backup default value
                     try:
-                        tool_dict['default_value'] = input.get_initial_value(trans, other_values)
+                        tool_dict['default_value'] = input.get_initial_value( request_context, other_values )
                     except Exception:
                         tool_dict['default_value'] = None
                         log.exception('tools::to_json() - Getting initial value failed %s.' % input.name)
@@ -2305,14 +2311,14 @@ def sanitize_state(state):
         # initialize and populate tool state
         state_inputs = {}
         state_errors = {}
-        populate_state(trans, self.inputs, state_inputs, state_errors, params.__dict__)
+        populate_state( request_context, self.inputs, state_inputs, state_errors, params.__dict__ )
 
         # create basic tool model
-        tool_model = self.to_dict(trans)
+        tool_model = self.to_dict( request_context )
         tool_model['inputs'] = {}
 
         # build tool model and tool state
-        iterate(tool_model['inputs'], self.inputs, state_inputs, '')
+        iterate( request_context, tool_model['inputs'], self.inputs, state_inputs, '' )
 
         # sanitize tool state
         sanitize_state(state_inputs)
@@ -2436,7 +2442,7 @@ def mapping_callback( input, value, prefixed_name, prefixed_label ):
                 return map_to_history( value )
         visit_input_values( tool_inputs, params, mapping_callback )
 
-    def _compare_tool_version( self, trans, job ):
+    def _compare_tool_version( self, job ):
         """
         Compares a tool version with the tool version from a job (from ToolRunner).
         """
diff --git a/lib/galaxy/tools/parameters/__init__.py b/lib/galaxy/tools/parameters/__init__.py
index fd63b4363896..bfdb8061dd33 100644
--- a/lib/galaxy/tools/parameters/__init__.py
+++ b/lib/galaxy/tools/parameters/__init__.py
@@ -6,7 +6,6 @@
 from grouping import Conditional, Repeat, Section, UploadDataset
 from galaxy.util.json import dumps, json_fix, loads
 from galaxy.util.expressions import ExpressionContext
-from galaxy.work.context import WorkRequestContext
 
 REPLACE_ON_TRUTHY = object()
 
@@ -61,7 +60,7 @@ def visit_input_values( inputs, input_values, callback, name_prefix="", label_pr
                 input_values[input.name] = new_value
 
 
-def check_param( trans, param, incoming_value, param_values, source='html', boolean_fix=False, history=None, workflow_building_mode=False ):
+def check_param( trans, param, incoming_value, param_values, source='html', boolean_fix=False ):
     """
     Check the value of a single parameter `param`. The value in
     `incoming_value` is converted from its HTML encoding and validated.
@@ -69,12 +68,6 @@ def check_param( trans, param, incoming_value, param_values, source='html', bool
     previous parameters (this may actually be an ExpressionContext
     when dealing with grouping scenarios).
     """
-    request_context = WorkRequestContext(
-        app                     = trans.app,
-        user                    = trans.user,
-        history                 = history or trans.history,
-        workflow_building_mode  = workflow_building_mode
-    )
     value = incoming_value
     error = None
     try:
@@ -84,16 +77,16 @@ def check_param( trans, param, incoming_value, param_values, source='html', bool
         if value is not None or isinstance( param, DataToolParameter ) or isinstance( param, DataCollectionToolParameter ):
             # Convert value from HTML representation
             if source == 'html':
-                value = param.from_html( value, request_context, param_values )
+                value = param.from_html( value, trans, param_values )
             else:
-                value = param.from_json( value, request_context, param_values )
+                value = param.from_json( value, trans, param_values )
             # Allow the value to be converted if necessary
-            filtered_value = param.filter_value( value, request_context, param_values )
+            filtered_value = param.filter_value( value, trans, param_values )
             # Then do any further validation on the value
-            param.validate( filtered_value, request_context )
+            param.validate( filtered_value, trans )
         elif value is None and isinstance( param, SelectToolParameter ):
             # An empty select list or column list
-            param.validate( value, request_context )
+            param.validate( value, trans )
     except ValueError, e:
         error = str( e )
     return value, error
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 177653645527..c05db4a90e69 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -1931,7 +1931,7 @@ def get_initial_value_from_history_prevent_repeats( self, trans, other_values, a
               happens twice (here and when generating HTML).
         """
         # Can't look at history in workflow mode. Tool shed has no histories.
-        if trans.workflow_building_mode or trans.webapp.name == 'tool_shed':
+        if trans.workflow_building_mode or trans.app.name == 'tool_shed':
             return DummyDataset()
         history = self._get_history( trans )
         dataset_matcher = DatasetMatcher( trans, self, None, other_values )

From a7117574268ab907fb27483a485d5d9e501b7e5e Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 25 Jan 2016 02:12:50 -0500
Subject: [PATCH 23/33] Remove unused error handler, error is handled
 consistently through full validation

---
 lib/galaxy/jobs/__init__.py               |  3 ---
 lib/galaxy/tools/__init__.py              | 13 -------------
 lib/galaxy/tools/parameters/validation.py |  6 ------
 3 files changed, 22 deletions(-)

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 9892732d698b..39a8f166c52f 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -965,9 +965,6 @@ def fail( self, message, exception=False, stdout="", stderr="", exit_code=None )
                 # Get the exception and let the tool attempt to generate
                 # a better message
                 etype, evalue, tb = sys.exc_info()
-                m = self.tool.handle_job_failure_exception( evalue )
-                if m:
-                    message = m
             if self.app.config.outputs_to_working_directory:
                 for dataset_path in self.get_output_fnames():
                     try:
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index be9c608a8e03..e0b018a14a3c 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -35,7 +35,6 @@
                                            contains_workflow_parameter)
 from galaxy.tools.parameters.grouping import Conditional, ConditionalWhen, Repeat, Section, UploadDataset
 from galaxy.tools.parameters.input_translation import ToolInputTranslator
-from galaxy.tools.parameters.validation import LateValidationError
 from galaxy.tools.test import parse_tests
 from galaxy.tools.parser import get_tool_source
 from galaxy.tools.parser.xml import XmlPageSource
@@ -1738,18 +1737,6 @@ def check_and_update_param_values_helper( self, inputs, values, trans, messages,
                         if update_values:
                             values[ input.name ] = input.get_initial_value( trans, context )
 
-    def handle_job_failure_exception( self, e ):
-        """
-        Called by job.fail when an exception is generated to allow generation
-        of a better error message (returning None yields the default behavior)
-        """
-        message = None
-        # If the exception was generated by late validation, use its error
-        # message (contains the parameter name and value)
-        if isinstance( e, LateValidationError ):
-            message = e.message
-        return message
-
     def build_dependency_shell_commands( self, job_directory=None ):
         """Return a list of commands to be run to populate the current environment to include this tools requirements."""
         return self.app.toolbox.dependency_manager.dependency_shell_commands(
diff --git a/lib/galaxy/tools/parameters/validation.py b/lib/galaxy/tools/parameters/validation.py
index c4bf76a9e8f9..d802fd8429e3 100644
--- a/lib/galaxy/tools/parameters/validation.py
+++ b/lib/galaxy/tools/parameters/validation.py
@@ -10,12 +10,6 @@
 log = logging.getLogger( __name__ )
 
 
-class LateValidationError( Exception ):
-
-    def __init__( self, message ):
-        self.message = message
-
-
 class Validator( object ):
     """
     A validator checks that a value meets some conditions OR raises ValueError

From 0ca9c7027b5ee3cd8ba433a4e8bc3e5ad57a5d7f Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 25 Jan 2016 02:18:03 -0500
Subject: [PATCH 24/33] Use request context in handle inputs

---
 lib/galaxy/tools/__init__.py                  | 57 ++++++-------------
 lib/galaxy/tools/evaluation.py                |  9 +--
 lib/galaxy/tools/parameters/__init__.py       |  1 +
 lib/galaxy/tools/parameters/basic.py          |  6 +-
 .../tools/parameters/dynamic_options.py       |  1 -
 lib/galaxy/workflow/extract.py                |  4 +-
 6 files changed, 26 insertions(+), 52 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index e0b018a14a3c..4392b784193c 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1049,17 +1049,17 @@ def check_workflow_compatible( self, tool_source ):
         #       outputs?
         return True
 
-    def new_state( self, trans, history=None ):
+    def new_state( self, trans ):
         """
         Create a new `DefaultToolState` for this tool. It will be initialized
         with default values for inputs.
         """
         state = DefaultToolState()
         state.inputs = {}
-        self.fill_in_new_state( trans, self.inputs, state.inputs, history=history )
+        self.fill_in_new_state( trans, self.inputs, state.inputs )
         return state
 
-    def fill_in_new_state( self, trans, inputs, state, context=None, history=None ):
+    def fill_in_new_state( self, trans, inputs, state, context=None ):
         """
         Fill in a tool state dictionary with default values for all parameters
         in the dictionary `inputs`. Grouping elements are filled in recursively.
@@ -1068,22 +1068,6 @@ def fill_in_new_state( self, trans, inputs, state, context=None, history=None ):
         for input in inputs.itervalues():
             state[ input.name ] = input.get_initial_value( trans, context )
 
-    def get_param_html_map( self, trans, page=0, other_values={} ):
-        """
-        Return a dictionary containing the HTML representation of each
-        parameter. This is used for rendering display elements. It is
-        currently not compatible with grouping constructs.
-
-        NOTE: This should be considered deprecated, it is only used for tools
-              with `display` elements. These should be eliminated.
-        """
-        rval = dict()
-        for key, param in self.inputs_by_page[page].iteritems():
-            if not isinstance( param, ToolParameter ):
-                raise Exception( "'get_param_html_map' only supported for simple paramters" )
-            rval[key] = param.get_html( trans, other_values=other_values )
-        return rval
-
     def get_param( self, key ):
         """
         Returns the parameter named `key` or None if there is no such
@@ -1128,6 +1112,7 @@ def handle_input( self, trans, incoming, history=None, source='html' ):
         to the form or execute the tool (only if 'execute' was clicked and
         there were no errors).
         """
+        request_context = WorkRequestContext( app=trans.app, user=trans.user, history=history or trans.history )
         rerun_remap_job_id = None
         if 'rerun_remap_job_id' in incoming:
             try:
@@ -1152,7 +1137,7 @@ def handle_input( self, trans, incoming, history=None, source='html' ):
         all_params = []
         validate_input = self.get_hook( 'validate_input' )
         for expanded_incoming in expanded_incomings:
-            expanded_state = self.new_state( trans, history=history )
+            expanded_state = self.new_state( request_context )
             # Process incoming data
             if not self.check_values:
                 # If `self.check_values` is false we don't do any checking or
@@ -1163,7 +1148,7 @@ def handle_input( self, trans, incoming, history=None, source='html' ):
             else:
                 # Update state for all inputs on the current page taking new
                 # values from `incoming`.
-                errors = self.populate_state( trans, self.inputs, expanded_state.inputs, expanded_incoming, history, source=source )
+                errors = self.populate_state( request_context, self.inputs, expanded_state.inputs, expanded_incoming, source=source )
                 # If the tool provides a `validate_input` hook, call it.
                 if validate_input:
                     validate_input( trans, errors, expanded_state.inputs, self.inputs )
@@ -1176,7 +1161,7 @@ def handle_input( self, trans, incoming, history=None, source='html' ):
         if any( all_errors ):
             raise exceptions.MessageException( err_data=all_errors[ 0 ] )
         else:
-            execution_tracker = execute_job( trans, self, all_params, history=history, rerun_remap_job_id=rerun_remap_job_id, collection_info=collection_info )
+            execution_tracker = execute_job( trans, self, all_params, history=request_context.history, rerun_remap_job_id=rerun_remap_job_id, collection_info=collection_info )
             if execution_tracker.successful_jobs:
                 return dict( out_data=execution_tracker.output_datasets,
                              num_jobs=len( execution_tracker.successful_jobs ),
@@ -1219,7 +1204,7 @@ def find_fieldstorage( self, x ):
         elif isinstance(x, list):
             [ self.find_fieldstorage( y ) for y in x ]
 
-    def populate_state( self, trans, inputs, state, incoming, history=None, source="html", prefix="", context=None ):
+    def populate_state( self, trans, inputs, state, incoming, source="html", prefix="", context=None ):
         errors = dict()
         # Push this level onto the context stack
         context = ExpressionContext( state, context )
@@ -1239,14 +1224,13 @@ def populate_state( self, trans, inputs, state, incoming, history=None, source="
                     if rep_index < input.max:
                         new_state = {}
                         new_state['__index__'] = rep_index
-                        self.fill_in_new_state( trans, input.inputs, new_state, context, history=history )
+                        self.fill_in_new_state( trans, input.inputs, new_state, context )
                         group_state.append( new_state )
                         group_errors.append( {} )
                         rep_errors = self.populate_state( trans,
                                                           input.inputs,
                                                           new_state,
                                                           incoming,
-                                                          history,
                                                           source,
                                                           prefix=rep_name + "|",
                                                           context=context )
@@ -1288,12 +1272,11 @@ def populate_state( self, trans, inputs, state, incoming, history=None, source="
                     # Current case has changed, throw away old state
                     group_state = state[input.name] = {}
                     # TODO: we should try to preserve values if we can
-                    self.fill_in_new_state( trans, input.cases[current_case].inputs, group_state, context, history=history )
+                    self.fill_in_new_state( trans, input.cases[current_case].inputs, group_state, context )
                     group_errors = self.populate_state( trans,
                                                         input.cases[current_case].inputs,
                                                         group_state,
                                                         incoming,
-                                                        history,
                                                         source,
                                                         prefix=group_prefix,
                                                         context=context)
@@ -1306,12 +1289,11 @@ def populate_state( self, trans, inputs, state, incoming, history=None, source="
             elif isinstance( input, Section ):
                 group_state = state[input.name]
                 group_prefix = "%s|" % ( key )
-                self.fill_in_new_state( trans, input.inputs, group_state, context, history=history )
+                self.fill_in_new_state( trans, input.inputs, group_state, context )
                 group_errors = self.populate_state( trans,
                                                     input.inputs,
                                                     group_state,
                                                     incoming,
-                                                    history,
                                                     source,
                                                     prefix=group_prefix,
                                                     context=context )
@@ -1344,7 +1326,6 @@ def populate_state( self, trans, inputs, state, incoming, history=None, source="
                                                       input.inputs,
                                                       rep_state,
                                                       incoming,
-                                                      history,
                                                       source,
                                                       prefix=rep_prefix,
                                                       context=context)
@@ -2065,12 +2046,7 @@ def to_json(self, trans, kwd={}, job=None, workflow_mode=False):
             raise exceptions.MessageException( '[history_id=%s] Failed to retrieve history. %s.' % ( history_id, str( e ) ) )
 
         # build request context
-        request_context = WorkRequestContext(
-            app                     = trans.app,
-            user                    = trans.user,
-            history                 = history,
-            workflow_building_mode  = workflow_mode
-        )
+        request_context = WorkRequestContext( app=trans.app, user=trans.user, history=history, workflow_building_mode=workflow_mode )
 
         # load job parameters into incoming
         tool_message = ''
@@ -2078,7 +2054,7 @@ def to_json(self, trans, kwd={}, job=None, workflow_mode=False):
             try:
                 job_params = job.get_param_values( self.app, ignore_errors=True )
                 self.check_and_update_param_values( job_params, request_context, update_values=False )
-                self._map_source_to_history( request_context, self.inputs, job_params, history )
+                self._map_source_to_history( request_context, self.inputs, job_params )
                 tool_message = self._compare_tool_version( job )
                 params_to_incoming( kwd, self.inputs, job_params, self.app, to_html=False )
             except Exception, e:
@@ -2298,14 +2274,14 @@ def sanitize_state(state):
         # initialize and populate tool state
         state_inputs = {}
         state_errors = {}
-        populate_state( request_context, self.inputs, state_inputs, state_errors, params.__dict__ )
+        populate_state( self.inputs, state_inputs, state_errors, params.__dict__ )
 
         # create basic tool model
         tool_model = self.to_dict( request_context )
         tool_model['inputs'] = {}
 
         # build tool model and tool state
-        iterate( request_context, tool_model['inputs'], self.inputs, state_inputs, '' )
+        iterate( tool_model['inputs'], self.inputs, state_inputs, '' )
 
         # sanitize tool state
         sanitize_state(state_inputs)
@@ -2375,10 +2351,11 @@ def _get_job_remap( self, job):
                     pass
         return False
 
-    def _map_source_to_history(self, trans, tool_inputs, params, history):
+    def _map_source_to_history( self, trans, tool_inputs, params ):
         # Need to remap dataset parameters. Job parameters point to original
         # dataset used; parameter should be the analygous dataset in the
         # current history.
+        history = trans.history
 
         # Create index for hdas.
         hda_source_dict = {}
diff --git a/lib/galaxy/tools/evaluation.py b/lib/galaxy/tools/evaluation.py
index 4ecc14b47f17..1934d0936dc1 100644
--- a/lib/galaxy/tools/evaluation.py
+++ b/lib/galaxy/tools/evaluation.py
@@ -54,15 +54,12 @@ def set_compute_environment( self, compute_environment, get_special=None ):
         incoming = self.tool.params_from_strings( incoming, self.app )
 
         # Full parameter validation
-        request_context = WorkRequestContext(
-            app                     = self.app,
-            user                    = job.history.user,
-            history                 = job.history
-        )
+        request_context = WorkRequestContext( app=self.app, user=job.history.user, history=job.history )
+
         def validate_inputs( input, value, prefixed_name, prefixed_label, context ):
             value = input.from_html( value, request_context, context )
             input.validate( value, request_context )
-        visit_input_values ( self.tool.inputs, incoming, validate_inputs, details=True )
+        visit_input_values( self.tool.inputs, incoming, validate_inputs, details=True )
 
         # Restore input / output data lists
         inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] )
diff --git a/lib/galaxy/tools/parameters/__init__.py b/lib/galaxy/tools/parameters/__init__.py
index bfdb8061dd33..6829c3144039 100644
--- a/lib/galaxy/tools/parameters/__init__.py
+++ b/lib/galaxy/tools/parameters/__init__.py
@@ -4,6 +4,7 @@
 
 from basic import DataCollectionToolParameter, DataToolParameter, SelectToolParameter
 from grouping import Conditional, Repeat, Section, UploadDataset
+from galaxy.util import string_as_bool
 from galaxy.util.json import dumps, json_fix, loads
 from galaxy.util.expressions import ExpressionContext
 
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index c05db4a90e69..5f1efe2eaa3f 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -615,6 +615,7 @@ def __init__( self, tool, input_source ):
         input_source = ensure_input_source(input_source)
         ToolParameter.__init__( self, tool, input_source )
         self.multiple = input_source.get_bool( 'multiple', True )
+        self.optional = input_source.parse_optional( True )
         self.user_ftp_dir = ''
 
     def get_initial_value( self, trans, other_values ):
@@ -652,8 +653,6 @@ def to_string( self, value, app ):
         return self.to_python( value, app )
 
     def to_python( self, value, app, validate=False ):
-        if validate and self.tool.app.config.ftp_upload_dir is None:
-            raise ValueError( "The FTP directory is not configured." )
         if not isinstance( value, list ):
             value = [ value ]
         lst = []
@@ -669,6 +668,8 @@ def to_python( self, value, app, validate=False ):
             if not self.optional and validate:
                 raise ValueError( "Please select a valid FTP file." )
             return ''
+        if validate and self.tool.app.config.ftp_upload_dir is None:
+            raise ValueError( "The FTP directory is not configured." )
         return lst
 
     def to_dict( self, trans, view='collection', value_mapper=None, other_values=None ):
@@ -2576,6 +2577,7 @@ def to_dict( self, trans, view='collection', value_mapper=None, other_values=Non
     drill_down=DrillDownSelectToolParameter
 )
 
+
 class RuntimeValue( object ):
     """
     Wrapper to note a value that is not yet set, but will be required at
diff --git a/lib/galaxy/tools/parameters/dynamic_options.py b/lib/galaxy/tools/parameters/dynamic_options.py
index e33cec7780f7..c70a385f27cf 100644
--- a/lib/galaxy/tools/parameters/dynamic_options.py
+++ b/lib/galaxy/tools/parameters/dynamic_options.py
@@ -5,7 +5,6 @@
 
 import logging
 import os
-import basic
 import validation
 from galaxy.util import string_as_bool
 from galaxy.model import User
diff --git a/lib/galaxy/workflow/extract.py b/lib/galaxy/workflow/extract.py
index 901b7e9c1dce..05887a556662 100644
--- a/lib/galaxy/workflow/extract.py
+++ b/lib/galaxy/workflow/extract.py
@@ -6,9 +6,7 @@
 from galaxy import model
 from galaxy.tools.parameters.basic import (
     DataToolParameter,
-    DataCollectionToolParameter,
-    DrillDownSelectToolParameter,
-    SelectToolParameter
+    DataCollectionToolParameter
 )
 from galaxy.tools.parser import ToolOutputCollectionPart
 from galaxy.tools.parameters.grouping import (

From 193c5293d9552d53a2358254fa2a25b236a31511 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 26 Jan 2016 01:25:56 -0500
Subject: [PATCH 25/33] Remove invalid validator from upload.xml

---
 tools/data_source/upload.xml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tools/data_source/upload.xml b/tools/data_source/upload.xml
index 196237fd4141..e28b95dbb56f 100644
--- a/tools/data_source/upload.xml
+++ b/tools/data_source/upload.xml
@@ -34,7 +34,6 @@
     <param name="async_datasets" type="hidden" value="None"/>
     <upload_dataset name="files" title="Specify Files for Dataset" file_type_name="file_type" metadata_ref="files_metadata">
         <param name="file_data" type="file" size="30" label="File" ajax-upload="true" help="TIP: Due to browser limitations, uploading files larger than 2GB is guaranteed to fail.  To upload large files, use the URL method (below) or FTP (if enabled by the site administrator).">
-        <validator type="expression" message="You will need to reselect the file you specified (%s)." substitute_value_in_message="True">not ( ( isinstance( value, unicode ) or isinstance( value, str ) ) and value != "" )</validator> <!-- use validator to post message to user about needing to reselect the file, since most browsers won't accept the value attribute for file inputs -->
       </param>
       <param name="url_paste" type="text" area="true" size="5x35" label="URL/Text" help="Here you may specify a list of URLs (one per line) or paste the contents of a file."/> 
       <param name="ftp_files" type="ftpfile" label="Files uploaded via FTP"/>

From 0fc8726414bfedcc234d7c4738ebff3a1b37e3d4 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 26 Jan 2016 02:17:57 -0500
Subject: [PATCH 26/33] Fix prefixed_label concatenation

---
 lib/galaxy/tools/parameters/__init__.py | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/tools/parameters/__init__.py b/lib/galaxy/tools/parameters/__init__.py
index 6829c3144039..8feabcbb7dc4 100644
--- a/lib/galaxy/tools/parameters/__init__.py
+++ b/lib/galaxy/tools/parameters/__init__.py
@@ -35,20 +35,18 @@ def visit_input_values( inputs, input_values, callback, name_prefix="", label_pr
         elif isinstance( input, Conditional ):
             values = input_values[ input.name ]
             current = values["__current_case__"]
-            label_prefix = label_prefix
             new_name_prefix = name_prefix + input.name + "|"
             visit_input_values( input.cases[current].inputs, values, callback, new_name_prefix, label_prefix, no_replacement_value=no_replacement_value, context=context, details=details )
         elif isinstance( input, Section ):
             values = input_values[ input.name ]
-            label_prefix = label_prefix
             new_name_prefix = name_prefix + input.name + "|"
             visit_input_values( input.inputs, values, callback, new_name_prefix, label_prefix, no_replacement_value=no_replacement_value, context=context, details=details )
         else:
             args = {
                 'input'             : input,
-                'value'             : input_values[input.name],
-                'prefixed_name'     : name_prefix + input.name,
-                'prefixed_label'    : label_prefix + input.label
+                'value'             : input_values[ input.name ],
+                'prefixed_name'     : "%s%s" % ( name_prefix, input.name ),
+                'prefixed_label'    : "%s%s" % ( label_prefix, input.label )
             }
             if details:
                 args[ 'context' ] = context

From 0521644bb37336f31577c8bd73ac1fef6c936016 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 26 Jan 2016 02:58:42 -0500
Subject: [PATCH 27/33] Fix select validator

---
 lib/galaxy/tools/parameters/basic.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 5f1efe2eaa3f..ba5c6fb217ec 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -938,7 +938,7 @@ def from_html( self, value, trans, other_values={} ):
                         # use \r\n to separate lines.
                         value = value.split()
             return value
-        if not legal_values and self.optional:
+        if ( not legal_values or value is None ) and self.optional:
             return None
         if not legal_values:
             raise ValueError( "Parameter %s requires a value, but has no legal values defined." % self.name )

From 8bd4cabdde922f23c06c64f95f50ea4d81caa940 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 26 Jan 2016 03:15:38 -0500
Subject: [PATCH 28/33] Use request context for parameter helper

---
 lib/galaxy/tools/__init__.py   | 17 +++++++++--------
 lib/galaxy/tools/evaluation.py |  2 +-
 lib/galaxy/workflow/modules.py |  2 +-
 3 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 4392b784193c..4b456dd5b5e9 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1629,14 +1629,15 @@ def params_to_strings( self, params, app ):
     def params_from_strings( self, params, app, ignore_errors=False ):
         return params_from_strings( self.inputs, params, app, ignore_errors )
 
-    def check_and_update_param_values( self, values, trans, update_values=True ):
+    def check_and_update_param_values( self, values, trans, update_values=True, workflow_building_mode=False ):
         """
         Check that all parameters have values, and fill in with default
         values where necessary. This could be called after loading values
         from a database in case new parameters have been added.
         """
         messages = {}
-        self.check_and_update_param_values_helper( self.inputs, values, trans, messages, update_values=update_values )
+        request_context = WorkRequestContext( app=trans.app, user=trans.user, history=trans.history, workflow_building_mode=workflow_building_mode )
+        self.check_and_update_param_values_helper( self.inputs, values, request_context, messages, update_values=update_values )
         return messages
 
     def check_and_update_param_values_helper( self, inputs, values, trans, messages, context=None, prefix="", update_values=True ):
@@ -1654,7 +1655,7 @@ def check_and_update_param_values_helper( self, inputs, values, trans, messages,
                         messages[ input.name ] = cond_messages
                     test_value = input.test_param.get_initial_value( trans, context )
                     current_case = input.get_current_case( test_value, trans )
-                    self.check_and_update_param_values_helper( input.cases[ current_case ].inputs, {}, trans, cond_messages, context, prefix )
+                    self.check_and_update_param_values_helper( input.cases[ current_case ].inputs, {}, trans, cond_messages, context, prefix, update_values=update_values )
                 elif isinstance( input, Repeat ):
                     if input.min:
                         messages[ input.name ] = []
@@ -1662,10 +1663,10 @@ def check_and_update_param_values_helper( self, inputs, values, trans, messages,
                             rep_prefix = prefix + "%s %d > " % ( input.title, i + 1 )
                             rep_dict = dict()
                             messages[ input.name ].append( rep_dict )
-                            self.check_and_update_param_values_helper( input.inputs, {}, trans, rep_dict, context, rep_prefix )
+                            self.check_and_update_param_values_helper( input.inputs, {}, trans, rep_dict, context, rep_prefix, update_values=update_values )
                 elif isinstance( input, Section ):
                     messages[ input.name ] = {}
-                    self.check_and_update_param_values_helper( input.inputs, {}, trans, messages[ input.name ], context, prefix )
+                    self.check_and_update_param_values_helper( input.inputs, {}, trans, messages[ input.name ], context, prefix, update_values=update_values )
                 else:
                     messages[ input.name ] = "No value found for '%s%s', using default" % ( prefix, input.label )
                 values[ input.name ] = input.get_initial_value( trans, context )
@@ -1674,7 +1675,7 @@ def check_and_update_param_values_helper( self, inputs, values, trans, messages,
                 if isinstance( input, Repeat ):
                     for i, d in enumerate( values[ input.name ] ):
                         rep_prefix = prefix + "%s %d > " % ( input.title, i + 1 )
-                        self.check_and_update_param_values_helper( input.inputs, d, trans, messages, context, rep_prefix )
+                        self.check_and_update_param_values_helper( input.inputs, d, trans, messages, context, rep_prefix, update_values=update_values )
                 elif isinstance( input, Conditional ):
                     group_values = values[ input.name ]
                     use_initial_value = False
@@ -1692,10 +1693,10 @@ def check_and_update_param_values_helper( self, inputs, values, trans, messages,
                             messages[ child_input.name ] = "Value no longer valid for '%s%s', replacing with default" % ( prefix, child_input.label )
                     else:
                         current = group_values["__current_case__"]
-                        self.check_and_update_param_values_helper( input.cases[current].inputs, group_values, trans, messages, context, prefix )
+                        self.check_and_update_param_values_helper( input.cases[current].inputs, group_values, trans, messages, context, prefix, update_values=update_values )
                 elif isinstance( input, Section ):
                     messages[ input.name ] = {}
-                    self.check_and_update_param_values_helper( input.inputs, values[ input.name ], trans, messages[ input.name ], context, prefix )
+                    self.check_and_update_param_values_helper( input.inputs, values[ input.name ], trans, messages[ input.name ], context, prefix, update_values=update_values )
                 else:
                     # Regular tool parameter, no recursion needed
                     try:
diff --git a/lib/galaxy/tools/evaluation.py b/lib/galaxy/tools/evaluation.py
index 1934d0936dc1..6e845b94b70c 100644
--- a/lib/galaxy/tools/evaluation.py
+++ b/lib/galaxy/tools/evaluation.py
@@ -54,7 +54,7 @@ def set_compute_environment( self, compute_environment, get_special=None ):
         incoming = self.tool.params_from_strings( incoming, self.app )
 
         # Full parameter validation
-        request_context = WorkRequestContext( app=self.app, user=job.history.user, history=job.history )
+        request_context = WorkRequestContext( app=self.app, user=job.history and job.history.user, history=job.history )
 
         def validate_inputs( input, value, prefixed_name, prefixed_label, context ):
             value = input.from_html( value, request_context, context )
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index 37931da7e5b6..4433d6b8b9d5 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -1080,7 +1080,7 @@ def item_callback( trans, key, input, value, error, old_value, context ):
 
     def check_and_update_state( self ):
         inputs = self.state.inputs
-        return self.tool.check_and_update_param_values( inputs, self.trans )
+        return self.tool.check_and_update_param_values( inputs, self.trans, workflow_building_mode=True )
 
     def compute_runtime_state( self, trans, step_updates=None, source="html" ):
         # Warning: This method destructively modifies existing step state.

From b3f3f81a7d0d221e4a698dbd9a586a92cd6662af Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 27 Jan 2016 01:50:05 -0500
Subject: [PATCH 29/33] Remove unused to_html helper

---
 lib/galaxy/tools/__init__.py                  |  2 +-
 lib/galaxy/tools/parameters/__init__.py       | 10 ++++-----
 lib/galaxy/tools/parameters/basic.py          | 22 -------------------
 .../galaxy/workflow/editor_tool_form.mako     |  2 +-
 templates/webapps/galaxy/workflow/run.mako    |  2 +-
 5 files changed, 7 insertions(+), 31 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 4b456dd5b5e9..25789a87c87c 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2057,7 +2057,7 @@ def to_json(self, trans, kwd={}, job=None, workflow_mode=False):
                 self.check_and_update_param_values( job_params, request_context, update_values=False )
                 self._map_source_to_history( request_context, self.inputs, job_params )
                 tool_message = self._compare_tool_version( job )
-                params_to_incoming( kwd, self.inputs, job_params, self.app, to_html=False )
+                params_to_incoming( kwd, self.inputs, job_params, self.app )
             except Exception, e:
                 raise exceptions.MessageException( str( e ) )
 
diff --git a/lib/galaxy/tools/parameters/__init__.py b/lib/galaxy/tools/parameters/__init__.py
index 8feabcbb7dc4..3590a9c5e8d2 100644
--- a/lib/galaxy/tools/parameters/__init__.py
+++ b/lib/galaxy/tools/parameters/__init__.py
@@ -123,7 +123,7 @@ def params_from_strings( params, param_values, app, ignore_errors=False ):
     return rval
 
 
-def params_to_incoming( incoming, inputs, input_values, app, name_prefix="", to_html=True ):
+def params_to_incoming( incoming, inputs, input_values, app, name_prefix="" ):
     """
     Given a tool's parameter definition (`inputs`) and a specific set of
     parameter `input_values` objects, populate `incoming` with the html values.
@@ -135,19 +135,17 @@ def params_to_incoming( incoming, inputs, input_values, app, name_prefix="", to_
             for d in input_values[ input.name ]:
                 index = d['__index__']
                 new_name_prefix = name_prefix + "%s_%d|" % ( input.name, index )
-                params_to_incoming( incoming, input.inputs, d, app, new_name_prefix, to_html=to_html)
+                params_to_incoming( incoming, input.inputs, d, app, new_name_prefix )
         elif isinstance( input, Conditional ):
             values = input_values[ input.name ]
             current = values["__current_case__"]
             new_name_prefix = name_prefix + input.name + "|"
             incoming[ new_name_prefix + input.test_param.name ] = values[ input.test_param.name ]
-            params_to_incoming( incoming, input.cases[current].inputs, values, app, new_name_prefix, to_html=to_html )
+            params_to_incoming( incoming, input.cases[current].inputs, values, app, new_name_prefix )
         elif isinstance( input, Section ):
             values = input_values[ input.name ]
             new_name_prefix = name_prefix + input.name + "|"
-            params_to_incoming( incoming, input.inputs, values, app, new_name_prefix, to_html=to_html )
+            params_to_incoming( incoming, input.inputs, values, app, new_name_prefix )
         else:
             value = input_values.get( input.name )
-            if to_html:
-                value = input.to_html_value( value, app )
             incoming[ name_prefix + input.name ] = value
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index ba5c6fb217ec..3fda7438038f 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -151,10 +151,6 @@ def filter_value( self, value, trans=None, other_values={} ):
         """
         return value
 
-    def to_html_value( self, value, app ):
-        """Convert an object value to the value expected from an html post"""
-        return self.to_string( value, app )
-
     def to_string( self, value, app ):
         """Convert a value to a string representation suitable for persisting"""
         if not isinstance( value, basestring ):
@@ -285,12 +281,6 @@ def to_string( self, value, app ):
             rval = util.smart_str( value )
         return rval
 
-    def to_html_value( self, value, app ):
-        if value is None:
-            return ''
-        else:
-            return self.to_string( value, app )
-
     def validate( self, value, trans ):
         search = self.type == "text"
         if not ( trans.workflow_building_mode and contains_workflow_parameter(value, search=search) ):
@@ -501,12 +491,6 @@ def from_html( self, value, trans=None, other_values={} ):
     def from_json( self, value, trans=None, other_values={} ):
         return string_as_bool( value )
 
-    def to_html_value( self, value, app ):
-        if value:
-            return [ 'true', 'true' ]
-        else:
-            return [ 'true' ]
-
     def to_python( self, value, app ):
         return ( value in [ 'True', 'true' ])
 
@@ -963,12 +947,6 @@ def from_html( self, value, trans, other_values={} ):
                 raise ValueError( "An invalid option was selected for %s, %r, please verify." % ( self.name, value ) )
             return value
 
-    def to_html_value( self, value, app ):
-        if isinstance( value, list ):
-            return value
-        else:
-            return str( value )
-
     def to_param_dict_string( self, value, other_values={}, value_map=DEFAULT_VALUE_MAP ):
         if value is None:
             return "None"
diff --git a/templates/webapps/galaxy/workflow/editor_tool_form.mako b/templates/webapps/galaxy/workflow/editor_tool_form.mako
index 95cd50c75b66..2922f68605ff 100644
--- a/templates/webapps/galaxy/workflow/editor_tool_form.mako
+++ b/templates/webapps/galaxy/workflow/editor_tool_form.mako
@@ -3,7 +3,7 @@
     ## This avoids making two separate requests since the classic form requires the mako anyway.
     from galaxy.tools.parameters import params_to_incoming
     incoming = {}
-    params_to_incoming( incoming, tool.inputs, module.state.inputs, trans.app, to_html=False)
+    params_to_incoming( incoming, tool.inputs, module.state.inputs, trans.app )
     self.form_config = tool.to_json(trans, incoming, workflow_mode=True)
     self.form_config.update({
         'id'                : tool.id,
diff --git a/templates/webapps/galaxy/workflow/run.mako b/templates/webapps/galaxy/workflow/run.mako
index 2e499621ec09..e4d0851687d1 100644
--- a/templates/webapps/galaxy/workflow/run.mako
+++ b/templates/webapps/galaxy/workflow/run.mako
@@ -27,7 +27,7 @@
             elif step.type == 'tool':
                 incoming = {}
                 tool = trans.app.toolbox.get_tool( step.tool_id )
-                params_to_incoming( incoming, tool.inputs, step.state.inputs, trans.app, to_html=False )
+                params_to_incoming( incoming, tool.inputs, step.state.inputs, trans.app )
                 step_model = tool.to_json( trans, incoming, workflow_mode=True )
                 step_model[ 'post_job_actions' ] = [{
                     'short_str'         : ActionBox.get_short_str( pja ),

From 8b6e4c9f2584d5768926836ee08607aeae0bb501 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 27 Jan 2016 01:57:57 -0500
Subject: [PATCH 30/33] Remove unused filter value helper

---
 lib/galaxy/tools/parameters/__init__.py |  4 +---
 lib/galaxy/tools/parameters/basic.py    | 12 ------------
 lib/galaxy/tools/parameters/grouping.py |  2 +-
 3 files changed, 2 insertions(+), 16 deletions(-)

diff --git a/lib/galaxy/tools/parameters/__init__.py b/lib/galaxy/tools/parameters/__init__.py
index 3590a9c5e8d2..a243ce35114d 100644
--- a/lib/galaxy/tools/parameters/__init__.py
+++ b/lib/galaxy/tools/parameters/__init__.py
@@ -79,10 +79,8 @@ def check_param( trans, param, incoming_value, param_values, source='html', bool
                 value = param.from_html( value, trans, param_values )
             else:
                 value = param.from_json( value, trans, param_values )
-            # Allow the value to be converted if necessary
-            filtered_value = param.filter_value( value, trans, param_values )
             # Then do any further validation on the value
-            param.validate( filtered_value, trans )
+            param.validate( value, trans )
         elif value is None and isinstance( param, SelectToolParameter ):
             # An empty select list or column list
             param.validate( value, trans )
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 3fda7438038f..d33c92cf1207 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -144,13 +144,6 @@ def get_dependencies( self ):
         """
         return []
 
-    def filter_value( self, value, trans=None, other_values={} ):
-        """
-        Parse the value returned by the view into a form usable by the tool OR
-        raise a ValueError.
-        """
-        return value
-
     def to_string( self, value, app ):
         """Convert a value to a string representation suitable for persisting"""
         if not isinstance( value, basestring ):
@@ -778,8 +771,6 @@ class SelectToolParameter( ToolParameter ):
     <option value="y">I am Y</option>
     <option value="z" selected>I am Z</option>
     </select>
-    >>> print p.filter_value( "y" )
-    y
 
     >>> p = SelectToolParameter( None, XML(
     ... '''
@@ -1085,9 +1076,6 @@ class GenomeBuildParameter( SelectToolParameter ):
     <option value="hg17">Human May 2004 (NCBI35/hg17) (hg17)</option>
     ...
     </select>
-
-    >>> print p.filter_value( "hg17" )
-    hg17
     """
     def __init__( self, *args, **kwds ):
         super( GenomeBuildParameter, self ).__init__( *args, **kwds )
diff --git a/lib/galaxy/tools/parameters/grouping.py b/lib/galaxy/tools/parameters/grouping.py
index 1942d78670ae..b667daa35f30 100644
--- a/lib/galaxy/tools/parameters/grouping.py
+++ b/lib/galaxy/tools/parameters/grouping.py
@@ -557,7 +557,7 @@ def get_current_case( self, value, trans ):
         if isinstance( value, bool ):
             str_value = self.test_param.to_param_dict_string( value )
         else:
-            str_value = self.test_param.filter_value( value, trans )
+            str_value = value
         # Find the matching case
         for index, case in enumerate( self.cases ):
             if str_value == case.value:

From 27df773c5a8823fff2d0dd68a8bd162147336bed Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 28 Jan 2016 00:23:17 -0500
Subject: [PATCH 31/33] Always display discarded datasets on rerun

---
 lib/galaxy/tools/parameters/basic.py | 22 ++++++++++------------
 1 file changed, 10 insertions(+), 12 deletions(-)

diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index d33c92cf1207..5b8bc258b517 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -2160,29 +2160,27 @@ def to_dict( self, trans, view='collection', value_mapper=None, other_values={}
         if history is None:
             return d
 
+        # build and append a new select option
+        def append( list, id, hid, name, src ):
+            return list.append( { 'id' : trans.app.security.encode_id( id ), 'hid' : hid, 'name' : name, 'src' : src } )
+
         # add datasets
         visible_hda = other_values.get( self.name )
+        has_matched = False
         for hda in history.active_datasets_children_and_roles:
             match = dataset_matcher.hda_match( hda, ensure_visible=visible_hda != hda )
             if match:
                 m = match.hda
-                d['options']['hda'].append({
-                    'id'            : trans.app.security.encode_id( m.id ),
-                    'hid'           : m.hid,
-                    'name'          : m.name if m.visible else '(hidden) %s' % m.name,
-                    'src'           : 'hda'
-                })
+                has_matched = has_matched or visible_hda == m
+                append( d[ 'options' ][ 'hda' ], m.id, m.hid, m.name if m.visible else '(hidden) %s' % m.name, 'hda' )
+        if not has_matched and isinstance( visible_hda, trans.app.model.HistoryDatasetAssociation ):
+            append( d[ 'options' ][ 'hda' ], visible_hda.id, visible_hda.hid, '(unavailable) %s' % visible_hda.name, 'hda' )
 
         # add dataset collections
         dataset_collection_matcher = DatasetCollectionMatcher( dataset_matcher )
         for hdca in history.active_dataset_collections:
             if dataset_collection_matcher.hdca_match( hdca, reduction=multiple ):
-                d['options']['hdca'].append({
-                    'id'            : trans.app.security.encode_id( hdca.id ),
-                    'hid'           : hdca.hid,
-                    'name'          : hdca.name,
-                    'src'           : 'hdca'
-                })
+                append( d[ 'options' ][ 'hdca' ], hdca.id, hdca.hid, hdca.name, 'hdca' )
 
         # sort both lists
         d['options']['hda'] = sorted(d['options']['hda'], key=lambda k: k['hid'], reverse=True)

From f8e3fa51f4b2fbaab54becd869ede40e43c5067a Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 28 Jan 2016 13:12:46 -0500
Subject: [PATCH 32/33] Apply suggested fixes, fix test cases

---
 lib/galaxy/jobs/runners/__init__.py       |  2 +-
 lib/galaxy/tools/parameters/basic.py      | 48 ++++++++++++-----------
 test/unit/tools/test_data_parameters.py   |  1 +
 test/unit/tools/test_evaluation.py        |  5 ++-
 test/unit/tools/test_execution.py         |  1 +
 test/unit/tools/test_select_parameters.py |  4 +-
 test/unit/tools_support.py                |  1 +
 7 files changed, 35 insertions(+), 27 deletions(-)

diff --git a/lib/galaxy/jobs/runners/__init__.py b/lib/galaxy/jobs/runners/__init__.py
index 608aabfa9c5c..ba7f2120d0eb 100644
--- a/lib/galaxy/jobs/runners/__init__.py
+++ b/lib/galaxy/jobs/runners/__init__.py
@@ -169,7 +169,7 @@ def prepare_job(self, job_wrapper, include_metadata=False, include_work_dir_outp
                 include_metadata=include_metadata,
                 include_work_dir_outputs=include_work_dir_outputs,
             )
-        except Exception, e:
+        except Exception as e:
             log.exception("(%s) Failure preparing job" % job_id)
             job_wrapper.fail( e.message if hasattr( e, 'message' ) else "Job preparation failed", exception=True )
             return False
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 5b8bc258b517..715e1993ceb4 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -198,7 +198,7 @@ def to_param_dict_string( self, value, other_values={} ):
                 value = sanitize_param( value )
         return value
 
-    def validate( self, value, trans ):
+    def validate( self, value, trans=None ):
         if value == "" and self.optional:
             return
         for validator in self.validators:
@@ -274,9 +274,9 @@ def to_string( self, value, app ):
             rval = util.smart_str( value )
         return rval
 
-    def validate( self, value, trans ):
+    def validate( self, value, trans=None ):
         search = self.type == "text"
-        if not ( trans.workflow_building_mode and contains_workflow_parameter(value, search=search) ):
+        if not ( trans and trans.workflow_building_mode and contains_workflow_parameter(value, search=search) ):
             return super( TextToolParameter, self ).validate( value, trans )
 
     def get_initial_value( self, trans, other_values ):
@@ -292,15 +292,16 @@ def to_dict( self, trans, view='collection', value_mapper=None, other_values={}
 class IntegerToolParameter( TextToolParameter ):
     """
     Parameter that takes an integer value.
-
+    >>> from galaxy.util.bunch import Bunch
+    >>> trans = Bunch( history=Bunch(), workflow_building_mode=True )
     >>> p = IntegerToolParameter( None, XML( '<param name="blah" type="integer" size="4" value="10" />' ) )
     >>> print p.name
     blah
     >>> print p.get_html()
     <input type="text" name="blah" size="4" value="10">
-    >>> type( p.from_html( "10" ) )
+    >>> type( p.from_html( "10", trans ) )
     <type 'int'>
-    >>> type( p.from_html( "bleh" ) )
+    >>> type( p.from_html( "bleh", trans ) )
     Traceback (most recent call last):
         ...
     ValueError: An integer or workflow parameter e.g. ${name} is required
@@ -371,15 +372,16 @@ def get_initial_value( self, trans, other_values ):
 class FloatToolParameter( TextToolParameter ):
     """
     Parameter that takes a real number value.
-
+    >>> from galaxy.util.bunch import Bunch
+    >>> trans = Bunch( history=Bunch(), workflow_building_mode=True )
     >>> p = FloatToolParameter( None, XML( '<param name="blah" type="float" size="4" value="3.141592" />' ) )
     >>> print p.name
     blah
     >>> print p.get_html()
     <input type="text" name="blah" size="4" value="3.141592">
-    >>> type( p.from_html( "36.1" ) )
+    >>> type( p.from_html( "36.1", trans ) )
     <type 'float'>
-    >>> type( p.from_html( "bleh" ) )
+    >>> type( p.from_html( "bleh", trans ) )
     Traceback (most recent call last):
         ...
     ValueError: A real number or workflow parameter e.g. ${name} is required
@@ -1832,7 +1834,7 @@ def value_modifier(value):
             name = history_dataset_collection.name
             hid = str( history_dataset_collection.hid )
             hidden_text = ""  # TODO
-            id = value_modifier( trans.app.security.encode_id( history_dataset_collection.id ) )
+            id = value_modifier( trans.security.encode_id( history_dataset_collection.id ) )
             selected = value and history_dataset_collection in value
             text = "%s:%s %s" % ( hid, hidden_text, name )
             field.add_option( text, id, selected )
@@ -1944,10 +1946,10 @@ def from_html( self, value, trans, other_values={} ):
             for single_value in value:
                 if isinstance( single_value, dict ) and 'src' in single_value and 'id' in single_value:
                     if single_value['src'] == 'hda':
-                        rval.append( trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.app.security.decode_id(single_value['id']) ))
+                        rval.append( trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id(single_value['id']) ))
                     elif single_value['src'] == 'hdca':
                         found_hdca = True
-                        decoded_id = trans.app.security.decode_id( single_value[ 'id' ] )
+                        decoded_id = trans.security.decode_id( single_value[ 'id' ] )
                         rval.append( trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( decoded_id ) )
                     else:
                         raise ValueError("Unknown input source %s passed to job submission API." % single_value['src'])
@@ -1965,15 +1967,15 @@ def from_html( self, value, trans, other_values={} ):
             rval = value
         elif isinstance( value, dict ) and 'src' in value and 'id' in value:
             if value['src'] == 'hda':
-                rval = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.app.security.decode_id(value['id']) )
+                rval = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id(value['id']) )
             elif value['src'] == 'hdca':
-                decoded_id = trans.app.security.decode_id( value[ 'id' ] )
+                decoded_id = trans.security.decode_id( value[ 'id' ] )
                 rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( decoded_id )
             else:
                 raise ValueError("Unknown input source %s passed to job submission API." % value['src'])
         elif str( value ).startswith( "__collection_reduce__|" ):
             encoded_ids = [ v[ len( "__collection_reduce__|" ): ] for v in str( value ).split(",") ]
-            decoded_ids = map( trans.app.security.decode_id, encoded_ids )
+            decoded_ids = map( trans.security.decode_id, encoded_ids )
             rval = []
             for decoded_id in decoded_ids:
                 hdca = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( decoded_id )
@@ -2162,7 +2164,7 @@ def to_dict( self, trans, view='collection', value_mapper=None, other_values={}
 
         # build and append a new select option
         def append( list, id, hid, name, src ):
-            return list.append( { 'id' : trans.app.security.encode_id( id ), 'hid' : hid, 'name' : name, 'src' : src } )
+            return list.append( { 'id' : trans.security.encode_id( id ), 'hid' : hid, 'name' : name, 'src' : src } )
 
         # add datasets
         visible_hda = other_values.get( self.name )
@@ -2278,8 +2280,8 @@ def _get_select_dataset_collection_field( self, trans, history, multiple=False,
             name = history_dataset_collection.name
             hid = str( history_dataset_collection.hid )
             hidden_text = ""  # TODO
-            subcollection_type = self._history_query( trans ).collection_type_description.collection_type
-            id = "%s|%s" % ( trans.app.security.encode_id( history_dataset_collection.id ), subcollection_type )
+            subcollection_type = self._history_query( trans ).can_map_over( history_dataset_collection ).collection_type
+            id = "%s|%s" % ( trans.security.encode_id( history_dataset_collection.id ), subcollection_type )
             text = "%s:%s %s" % ( hid, hidden_text, name )
 
             field.add_option( text, id, False )
@@ -2302,13 +2304,13 @@ def from_html( self, value, trans, other_values={} ):
             rval = value
         elif isinstance( value, dict ) and 'src' in value and 'id' in value:
             if value['src'] == 'hdca':
-                rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( trans.app.security.decode_id(value['id']) )
+                rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( trans.security.decode_id(value['id']) )
         elif isinstance( value, list ):
             if len( value ) > 0:
                 value = value[0]
                 if isinstance( value, dict ) and 'src' in value and 'id' in value:
                     if value['src'] == 'hdca':
-                        rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( trans.app.security.decode_id(value['id']) )
+                        rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( trans.security.decode_id(value['id']) )
         elif isinstance( value, basestring ):
             if value.startswith( "dce:" ):
                 rval = trans.sa_session.query( trans.app.model.DatasetCollectionElement ).get( value[ len( "dce:"): ] )
@@ -2364,7 +2366,7 @@ def value_to_display_text( self, value, app ):
             display_text = "No dataset collection."
         return display_text
 
-    def validate( self, value, trans ):
+    def validate( self, value, trans=None ):
         return True  # TODO
 
     def to_dict( self, trans, view='collection', value_mapper=None, other_values=None ):
@@ -2385,7 +2387,7 @@ def to_dict( self, trans, view='collection', value_mapper=None, other_values=Non
         # append directly matched collections
         for hdca in self.match_collections( trans, history, dataset_matcher ):
             d['options']['hdca'].append({
-                'id': trans.app.security.encode_id( hdca.id ),
+                'id': trans.security.encode_id( hdca.id ),
                 'hid': hdca.hid,
                 'name': hdca.name,
                 'src': 'hdca'
@@ -2395,7 +2397,7 @@ def to_dict( self, trans, view='collection', value_mapper=None, other_values=Non
         for hdca in self.match_multirun_collections( trans, history, dataset_matcher ):
             subcollection_type = self._history_query( trans ).can_map_over( hdca ).collection_type
             d['options']['hdca'].append({
-                'id': trans.app.security.encode_id( hdca.id ),
+                'id': trans.security.encode_id( hdca.id ),
                 'hid': hdca.hid,
                 'name': hdca.name,
                 'src': 'hdca',
diff --git a/test/unit/tools/test_data_parameters.py b/test/unit/tools/test_data_parameters.py
index c78d05af6994..c847ba164ab5 100644
--- a/test/unit/tools/test_data_parameters.py
+++ b/test/unit/tools/test_data_parameters.py
@@ -154,6 +154,7 @@ def setUp( self ):
             get_current_user_roles=lambda: [],
             workflow_building_mode=False,
             webapp=bunch.Bunch( name="galaxy" ),
+            history=self.test_history,
         )
         self.multiple = False
         self.optional = False
diff --git a/test/unit/tools/test_evaluation.py b/test/unit/tools/test_evaluation.py
index 127a6073c245..63ff8d542f2b 100644
--- a/test/unit/tools/test_evaluation.py
+++ b/test/unit/tools/test_evaluation.py
@@ -149,7 +149,10 @@ def get_field_by_name_for_value( name, value, trans, other_values ):
             assert name == "path"
             return ["/old/path/human"]
 
-        parameter.options = Bunch(get_field_by_name_for_value=get_field_by_name_for_value)
+        def get_options( trans, other_values ):
+            return [ [ "", "/old/path/human", "" ] ]
+
+        parameter.options = Bunch(get_field_by_name_for_value=get_field_by_name_for_value, get_options=get_options)
         self.tool.set_params( {
             "index_path": parameter
         } )
diff --git a/test/unit/tools/test_execution.py b/test/unit/tools/test_execution.py
index c3a2bc8e2af0..df947825084f 100644
--- a/test/unit/tools/test_execution.py
+++ b/test/unit/tools/test_execution.py
@@ -268,6 +268,7 @@ class MockTrans( object ):
     def __init__( self, app, history ):
         self.app = app
         self.history = history
+        self.user = None
         self.history._active_datasets_children_and_roles = filter( lambda hda: hda.active and hda.history == history, self.app.model.context.model_objects[ galaxy.model.HistoryDatasetAssociation ] )
         self.workflow_building_mode = False
         self.webapp = Bunch( name="galaxy" )
diff --git a/test/unit/tools/test_select_parameters.py b/test/unit/tools/test_select_parameters.py
index 0e18010975b8..e4ebe7590bd5 100644
--- a/test/unit/tools/test_select_parameters.py
+++ b/test/unit/tools/test_select_parameters.py
@@ -28,7 +28,7 @@ def test_validated_values_missing_dependency( self ):
     def test_unvalidated_values( self ):
         self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>'''
         self.trans.workflow_building_mode = True
-        assert self.param.from_html("42", self.trans).value == "42"
+        assert self.param.from_html("42", self.trans) == "42"
 
     def test_validated_datasets( self ):
         self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>'''
@@ -42,7 +42,7 @@ def test_validated_datasets( self ):
     def test_unvalidated_datasets( self ):
         self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>'''
         self.trans.workflow_building_mode = True
-        assert isinstance( self.param.from_html( model.HistoryDatasetAssociation(), self.trans, { "input_bam": basic.RuntimeValue() } ).value, model.HistoryDatasetAssociation )
+        assert isinstance( self.param.from_html( model.HistoryDatasetAssociation(), self.trans, { "input_bam": basic.RuntimeValue() } ), model.HistoryDatasetAssociation )
 
     def test_filter_param_value( self ):
         self.options_xml = '''<options from_data_table="test_table"><filter type="param_value" ref="input_bam" column="0" /></options>'''
diff --git a/test/unit/tools_support.py b/test/unit/tools_support.py
index 0249cb2bf88d..3d435ca1f68d 100644
--- a/test/unit/tools_support.py
+++ b/test/unit/tools_support.py
@@ -154,6 +154,7 @@ def __init__(self, model_objects=None):
         self.flushed = False
         self.model_objects = model_objects or defaultdict( lambda: {} )
         self.created_objects = []
+        self.current = self
 
     def expunge_all(self):
         self.expunged_all = True

From 72370b251723eac746bd1720a85df539cd96e78a Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 28 Jan 2016 19:28:57 -0500
Subject: [PATCH 33/33] Fix paused workflow step resubmission

---
 lib/galaxy/tools/actions/__init__.py    |  6 ++++--
 lib/galaxy/tools/parameters/__init__.py | 21 ++++++++++++++++++++-
 2 files changed, 24 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py
index eacae091ddf6..f14fe80168b6 100644
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -6,6 +6,7 @@
 from galaxy import model
 from galaxy.tools.parameters.basic import DataCollectionToolParameter, DataToolParameter
 from galaxy.tools.parameters.wrapped import WrappedParameters
+from galaxy.tools.parameters import update_param
 from galaxy.util import ExecutionTimer
 from galaxy.util.json import dumps
 from galaxy.util.none_like import NoneDataset
@@ -491,9 +492,10 @@ def handle_output( name, output, hidden=None ):
                                 if hda.state == hda.states.PAUSED:
                                     hda.state = hda.states.NEW
                                     hda.info = None
+                            input_values = dict( [ ( p.name, json.loads( p.value ) ) for p in job_to_remap.parameters ] )
+                            update_param( jtid.name, input_values, str( out_data[ jtod.name ].id ) )
                             for p in job_to_remap.parameters:
-                                if p.name == jtid.name and p.value == str(jtod.dataset.id):
-                                    p.value = str(out_data[jtod.name].id)
+                                p.value = json.dumps( input_values[ p.name ] )
                             jtid.dataset = out_data[jtod.name]
                             jtid.dataset.hid = jtod.dataset.hid
                             log.info('Job %s input HDA %s remapped to new HDA %s' % (job_to_remap.id, jtod.dataset.id, jtid.dataset.id))
diff --git a/lib/galaxy/tools/parameters/__init__.py b/lib/galaxy/tools/parameters/__init__.py
index a243ce35114d..2312110130b1 100644
--- a/lib/galaxy/tools/parameters/__init__.py
+++ b/lib/galaxy/tools/parameters/__init__.py
@@ -1,7 +1,7 @@
 """
 Classes encapsulating Galaxy tool parameters.
 """
-
+import re
 from basic import DataCollectionToolParameter, DataToolParameter, SelectToolParameter
 from grouping import Conditional, Repeat, Section, UploadDataset
 from galaxy.util import string_as_bool
@@ -147,3 +147,22 @@ def params_to_incoming( incoming, inputs, input_values, app, name_prefix="" ):
         else:
             value = input_values.get( input.name )
             incoming[ name_prefix + input.name ] = value
+
+
+def update_param( prefixed_name, input_values, new_value ):
+    """
+    Given a prefixed parameter name, e.g. 'parameter_0|parameter_1', update
+    the corresponding input value in a nested input values dictionary.
+    """
+    for key in input_values:
+        match = re.match( '^' + key + '_(\d+)\|(.+)', prefixed_name )
+        if match:
+            index = int( match.group( 1 ) )
+            if isinstance( input_values[ key ], list ) and len( input_values[ key ] ) > index:
+                update_param( match.group( 2 ), input_values[ key ][ index ], new_value )
+        else:
+            match = re.match( '^' + key + '\|(.+)', prefixed_name )
+            if isinstance( input_values[ key ], dict ) and match:
+                update_param( match.group( 1 ), input_values[ key ], new_value )
+            elif prefixed_name == key:
+                input_values[ key ] = new_value