From ce6b45613df0c19175b5104c0996e20ef42e671f Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 3 Mar 2015 20:27:15 -0500
Subject: [PATCH 01/88] Add argument to tool parameters.

 - Expose via the API to help command-line construction.
 - Default the name of a parameter to be this (minus dashes) if name is not otherwise found.
---
 lib/galaxy/tools/parameters/basic.py | 20 +++++++++++++++-----
 test/api/test_tools.py               |  2 +-
 2 files changed, 16 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 888019d0346..4213c528a3c 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -37,14 +37,15 @@ class ToolParameter( object, Dictifiable ):
     moment but in the future should encapsulate more complex parameters (lists
     of valid choices, validation logic, ...)
     """
-    dict_collection_visible_keys = ( 'name', 'type', 'label', 'help' )
+    dict_collection_visible_keys = ( 'name', 'argument', 'type', 'label', 'help' )
 
     def __init__( self, tool, input_source, context=None ):
         input_source = ensure_input_source(input_source)
         self.tool = tool
         self.refresh_on_change = False
         self.refresh_on_change_values = []
-        self.name = input_source.get("name")
+        self.argument = input_source.get("argument")
+        self.name = ToolParameter.parse_name( input_source )
         self.type = input_source.get("type")
         self.hidden = input_source.get("hidden", False)
         self.is_dynamic = False
@@ -224,9 +225,7 @@ class ToolParameter( object, Dictifiable ):
     @classmethod
     def build( cls, tool, param ):
         """Factory method to create parameter of correct type"""
-        param_name = param.get( "name" )
-        if not param_name:
-            raise ValueError( "Tool parameter '%s' requires a 'name'" % (param_name ) )
+        param_name = cls.parse_name( param )
         param_type = param.get("type")
         if not param_type:
             raise ValueError( "Tool parameter '%s' requires a 'type'" % ( param_name ) )
@@ -235,6 +234,17 @@ class ToolParameter( object, Dictifiable ):
         else:
             return parameter_types[param_type]( tool, param )
 
+    @classmethod
+    def parse_name(cls, input_source):
+        name = input_source.get("name", None)
+        if name is None:
+            argument = input_source.get("argument")
+            if argument:
+                name = argument.lstrip("-")
+            else:
+                raise ValueError("Tool parameter must specify a name.")
+        return name
+
 
 class TextToolParameter( ToolParameter ):
     """
diff --git a/test/api/test_tools.py b/test/api/test_tools.py
index e1b5485ce5b..cecf7e763ca 100644
--- a/test/api/test_tools.py
+++ b/test/api/test_tools.py
@@ -58,7 +58,7 @@ class ToolsTestCase( api.ApiTestCase ):
         self._assert_has_keys( case2, "value", "inputs" )
         case2_inputs = case2[ "inputs" ]
         assert len( case2_inputs ) == 1
-        self._assert_has_keys( case2_inputs[ 0 ], 'name', 'type', 'label', 'help' )
+        self._assert_has_keys( case2_inputs[ 0 ], 'name', 'type', 'label', 'help', 'argument' )
         assert case2_inputs[ 0 ][ "name" ] == "seed"
 
     def _show_valid_tool( self, tool_id ):

From f1c036e746fcd746842b6174e3a7927649b6e1a1 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 23 Mar 2015 15:31:23 -0400
Subject: [PATCH 02/88] ToolForm: Add section tag

---
 client/galaxy/scripts/mvc/form/form-data.js |   7 +-
 lib/galaxy/tools/__init__.py                |  46 +-
 lib/galaxy/tools/parameters/grouping.py     |  54 +++
 static/maps/mvc/form/form-data.js.map       |   2 +-
 static/scripts/mvc/form/form-data.js        |   2 +-
 templates/webapps/galaxy/tool_form.mako     | 469 +-------------------
 6 files changed, 124 insertions(+), 456 deletions(-)

diff --git a/client/galaxy/scripts/mvc/form/form-data.js b/client/galaxy/scripts/mvc/form/form-data.js
index 5e1f23ce1fb..0562d97fbf9 100644
--- a/client/galaxy/scripts/mvc/form/form-data.js
+++ b/client/galaxy/scripts/mvc/form/form-data.js
@@ -96,9 +96,9 @@ return Backbone.Model.extend({
                                 convert(job_input_id, head[input.id + '-section-' + selectedCase]);
                             }
                             break;
-                        // handle custom sub sections
+                        // handle sections
                         case 'section':
-                            convert('', node);
+                            convert(job_input_id, node);
                             break;
                         default:
                             // get field
@@ -191,6 +191,9 @@ return Backbone.Model.extend({
                             search (index, node.cases[selectedCase].inputs);
                         }
                         break;
+                    case 'section':
+                        search (index, node.inputs);
+                        break;
                     default:
                         var input_id = self.map_dict[index];
                         if (input_id) {
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index dd50e17e2ae..448c4a2b4ca 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -40,7 +40,7 @@ from galaxy.tools.parameters.basic import (BaseURLToolParameter,
                                            DataToolParameter, DataCollectionToolParameter, HiddenToolParameter, LibraryDatasetToolParameter,
                                            SelectToolParameter, ToolParameter, UnvalidatedValue,
                                            IntegerToolParameter, FloatToolParameter)
-from galaxy.tools.parameters.grouping import Conditional, ConditionalWhen, Repeat, UploadDataset
+from galaxy.tools.parameters.grouping import Conditional, ConditionalWhen, Repeat, Section, UploadDataset
 from galaxy.tools.parameters.input_translation import ToolInputTranslator
 from galaxy.tools.parameters.output import ToolOutputActionGroup
 from galaxy.tools.parameters.validation import LateValidationError
@@ -972,6 +972,14 @@ class Tool( object, Dictifiable ):
                         case.inputs = odict()
                         group.cases.append( case )
                 rval[group.name] = group
+            elif input_type == "section":
+                group = Section()
+                group.name = input_source.get( "name" )
+                group.title = input_source.get( "title" )
+                group.help = input_source.get( "help", None )
+                page_source = input_source.parse_nested_inputs_source()
+                group.inputs = self.parse_input_elem( page_source, enctypes, context )
+                rval[group.name] = group
             elif input_type == "upload_dataset":
                 elem = input_source.elem()
                 group = UploadDataset()
@@ -1505,6 +1513,20 @@ class Tool( object, Dictifiable ):
                     group_state['__current_case__'] = current_case
                     # Store the value of the test element
                     group_state[ input.test_param.name ] = value
+            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 )
+                group_errors = self.populate_state( trans,
+                                                    input.inputs,
+                                                    group_state,
+                                                    incoming,
+                                                    history,
+                                                    source,
+                                                    prefix=group_prefix,
+                                                    context=context )
+                if group_errors:
+                    errors[ input.name ] = group_errors
             elif isinstance( input, UploadDataset ):
                 group_state = state[input.name]
                 group_errors = []
@@ -1714,6 +1736,22 @@ class Tool( object, Dictifiable ):
                 group_state['__current_case__'] = current_case
                 # Store the value of the test element
                 group_state[ input.test_param.name ] = value
+            elif isinstance( input, Section ):
+                group_state = state[input.name]
+                group_old_errors = old_errors.get( input.name, {} )
+                group_prefix = "%s|" % ( key )
+                group_errors = self.update_state( trans,
+                                                  input.inputs,
+                                                  group_state,
+                                                  incoming,
+                                                  prefix=group_prefix,
+                                                  context=context,
+                                                  source=source,
+                                                  update_only=update_only,
+                                                  old_errors=group_old_errors,
+                                                  item_callback=item_callback )
+                if group_errors:
+                    errors[ input.name ] = group_errors
             elif isinstance( input, UploadDataset ):
                 group_state = state[input.name]
                 group_errors = []
@@ -2416,6 +2454,10 @@ class Tool( object, Dictifiable ):
                             errors[test_param_key] = 'The selected case is unavailable/invalid.'
                             pass
                     group_state[input.test_param.name] = value
+                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)
                 else:
                     default_value = incoming.get(key, state.get(input.name, None))
                     value, error = check_state(trans, input, default_value, context)
@@ -2448,6 +2490,8 @@ class Tool( object, Dictifiable ):
                         if '__current_case__' in group_state:
                             i = group_state['__current_case__']
                             iterate(tool_dict['cases'][i]['inputs'], input.cases[i].inputs, group_state, other_values)
+                elif input.type == 'section':
+                    iterate( tool_dict['inputs'], input.inputs, group_state, other_values )
                 else:
                     # create input dictionary, try to pass other_values if to_dict function supports it e.g. dynamic options
                     try:
diff --git a/lib/galaxy/tools/parameters/grouping.py b/lib/galaxy/tools/parameters/grouping.py
index 30b9dfa6c4c..5a1706579b0 100644
--- a/lib/galaxy/tools/parameters/grouping.py
+++ b/lib/galaxy/tools/parameters/grouping.py
@@ -129,6 +129,60 @@ class Repeat( Group ):
         repeat_dict[ "inputs" ] = map( input_to_dict, self.inputs.values() )
         return repeat_dict
 
+class Section( Group ):
+
+    dict_collection_visible_keys = ( 'name', 'type', 'title', 'help')
+
+    type = "section"
+    def __init__( self ):
+        Group.__init__( self )
+        self.title = None
+        self.inputs = None
+        self.help = None
+    @property
+    def title_plural( self ):
+        return inflector.pluralize( self.title )
+    def label( self ):
+        return "Section (%s)" % self.title
+    def value_to_basic( self, value, app ):
+        rval = {}
+        for input in self.inputs.itervalues():
+            rval[ input.name ] = input.value_to_basic( value[input.name], app )
+        return rval
+    def value_from_basic( self, value, app, ignore_errors=False ):
+        rval = []
+        try:
+            for i, d in enumerate( value ):
+                rval_dict = {}
+                for input in self.inputs.itervalues():
+                    if ignore_errors and input.name not in d:
+                        pass
+                    else:
+                        rval_dict[ input.name ] = input.value_from_basic( d[input.name], app, ignore_errors )
+                rval.append( rval_dict )
+        except Exception, e:
+            if not ignore_errors:
+                raise e
+        return rval
+    def visit_inputs( self, prefix, value, callback ):
+        for i, d in enumerate( value ):
+            for input in self.inputs.itervalues():
+                new_prefix = prefix + "%s_%d|" % ( self.name, i )
+                if isinstance( input, ToolParameter ):
+                    callback( new_prefix, input, d[input.name], parent = d )
+                else:
+                    input.visit_inputs( new_prefix, d[input.name], callback )
+    def get_initial_value( self, trans, context, history=None ):
+        rval = {}
+        for input in self.inputs.itervalues():
+            rval[ input.name ] = input.get_initial_value( trans, context, history=history )
+        return rval
+    def to_dict( self, trans, view='collection', value_mapper=None ):
+        section_dict = super( Section, self ).to_dict( trans, view=view, value_mapper=value_mapper )
+        def input_to_dict( input ):
+            return input.to_dict( trans, view=view, value_mapper=value_mapper )
+        section_dict[ "inputs" ] = map( input_to_dict, self.inputs.values() )
+        return section_dict
 
 class UploadDataset( Group ):
     type = "upload_dataset"
diff --git a/static/maps/mvc/form/form-data.js.map b/static/maps/mvc/form/form-data.js.map
index 84e2565dde4..7522cbb5ded 100644
--- a/static/maps/mvc/form/form-data.js.map
+++ b/static/maps/mvc/form/form-data.js.map
@@ -1 +1 @@
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\ No newline at end of file
+{"version":3,"file":"form-data.js","sources":["../../../src/mvc/form/form-data.js"],"names":["define","Backbone","Model","extend","initialize","app","this","checksum","sum","i","field_list","field","JSON","stringify","value","create","add","job_input_id","input_id","input_value","self","map_dict","result_dict","convert","identifier","head","index","node","input","name","type","section_label","block_indices","block_prefix","block_label","pos","indexOf","length","push","parseInt","substr","sort","a","b","id","test_param","selectedCase","matchCase","undefined","ignore","payload","p_id","dict","_iterate","section","$el","match","truevalue","falsevalue","cases","matchModel","model","callback","search","j","cache","inputs","result","matchResponse","response","new_id","separator","Array","parent","children","$","each","child","attr","hasClass","input_list"],"mappings":"AAGAA,QAAQ,eAAgB,WACxB,MAAOC,UAASC,MAAMC,QAElBC,WAAY,SAASC,GACjBC,KAAKD,IAAMA,GAKfE,SAAU,WACN,GAAIC,GAAM,EACV,KAAK,GAAIC,KAAKH,MAAKD,IAAIK,WAAY,CAC/B,GAAIC,GAAQL,KAAKD,IAAIK,WAAWD,EAChCD,IAAOI,KAAKC,UAAUF,EAAMG,OAASH,EAAMG,SAE/C,MAAON,IAKXO,OAAQ,WAWJ,QAASC,GAAIC,EAAcC,EAAUC,GACjCC,EAAKC,SAASJ,GAAgBC,EAC9BI,EAAYL,GAAgBE,EAIhC,QAASI,GAAQC,EAAYC,GACzB,IAAK,GAAIC,KAASD,GAAM,CACpB,GAAIE,GAAOF,EAAKC,EAChB,IAAIC,EAAKC,MAAO,CAEZ,GAAIA,GAAQD,EAAKC,MAGbX,EAAeO,CAOnB,QANkB,IAAdA,IACAP,GAAgB,KAEpBA,GAAgBW,EAAMC,KAGdD,EAAME,MAEV,IAAK,SAED,GAAIC,GAAgB,WAGhBC,KACAC,EAAe,IACnB,KAAK,GAAIC,KAAeP,GAAM,CAC1B,GAAIQ,GAAMD,EAAYE,QAAQL,EACnB,KAAPI,IACAA,GAAOJ,EAAcM,OACrBL,EAAcM,KAAKC,SAASL,EAAYM,OAAOL,KAC1CF,IACDA,EAAeC,EAAYM,OAAO,EAAGL,KAMjDH,EAAcS,KAAK,SAASC,EAAEC,GAAK,MAAOD,GAAIC,GAG9C,IAAIjB,GAAQ,CACZ,KAAK,GAAIjB,KAAKuB,GACVT,EAAQN,EAAe,IAAMS,IAASC,EAAKM,EAAeD,EAAcvB,IAE5E,MAEJ,KAAK,cAED,GAAIK,GAAQM,EAAKf,IAAIK,WAAWkB,EAAMgB,IAAI9B,OAG1CE,GAAKC,EAAe,IAAMW,EAAMiB,WAAWhB,KAAMD,EAAMgB,GAAI9B,EAG3D,IAAIgC,GAAe1B,EAAK2B,UAAUnB,EAAOd,EACrB,KAAhBgC,GACAvB,EAAQN,EAAcQ,EAAKG,EAAMgB,GAAK,YAAcE,GAExD,MAEJ,KAAK,UACDvB,EAAQN,EAAcU,EACtB,MACJ,SAEI,GAAIhB,GAAQS,EAAKf,IAAIK,WAAWkB,EAAMgB,GACtC,IAAIjC,GAASA,EAAMG,MAAO,CAEtB,GAAIA,GAAQH,EAAMG,OAGlB,KAAqBkC,SAAjBpB,EAAMqB,QAAwBrB,EAAMqB,QAAUnC,KAE9CE,EAAKC,EAAcW,EAAMgB,GAAI9B,GAGzBc,EAAMsB,SACN,IAAK,GAAIC,KAAQvB,GAAMsB,QACnBlC,EAAKmC,EAAMvB,EAAMgB,GAAIhB,EAAMsB,QAAQC,QA5FvE,GAAI/B,GAAOd,KAGP8C,IACJ9C,MAAK+C,SAAS/C,KAAKD,IAAIiD,QAAQC,IAAKH,EAGpC,IAAI9B,KAmGJ,OAlGAhB,MAAKe,YA+FLE,EAAQ,GAAI6B,GAGL9B,GAKXkC,MAAO,SAAUvC,GACb,MAAOX,MAAKe,UAAYf,KAAKe,SAASJ,IAK1C8B,UAAW,SAASnB,EAAOd,GAEM,WAAzBc,EAAMiB,WAAWf,OAEbhB,EADS,QAATA,EACQc,EAAMiB,WAAWY,WAAa,OAE9B7B,EAAMiB,WAAWa,YAAc,QAK/C,KAAK,GAAIjD,KAAKmB,GAAM+B,MAChB,GAAI/B,EAAM+B,MAAMlD,GAAGK,OAASA,EACxB,MAAOL,EAKf,OAAO,IAKXmD,WAAY,SAASC,EAAOC,GAQxB,QAASC,GAAQnB,EAAInB,GACjB,IAAK,GAAIhB,KAAKgB,GAAM,CAChB,GAAIE,GAAOF,EAAKhB,GACZiB,EAAQC,EAAKE,IAIjB,QAHU,IAANe,IACAlB,EAAQkB,EAAK,IAAMlB,GAEfC,EAAKG,MACT,IAAK,SACD,IAAK,GAAIkC,KAAKrC,GAAKsC,MACfF,EAAQrC,EAAQ,IAAMsC,EAAGrC,EAAKsC,MAAMD,GAExC,MACJ,KAAK,cACD,GAAIlD,GAAQa,EAAKkB,YAAclB,EAAKkB,WAAW/B,MAC3CgC,EAAe1B,EAAK2B,UAAUpB,EAAMb,EACpB,KAAhBgC,GACAiB,EAAQrC,EAAOC,EAAKgC,MAAMb,GAAcoB,OAE5C,MACJ,KAAK,UACDH,EAAQrC,EAAOC,EAAKuC,OACpB,MACJ,SACI,GAAIhD,GAAWE,EAAKC,SAASK,EACzBR,IACA4C,EAAS5C,EAAUS,KAhCvC,GAAIwC,MAGA/C,EAAOd,IAuCX,OAHAyD,GAAO,GAAIF,EAAMK,QAGVC,GAKXC,cAAe,SAASC,GAQpB,QAASN,GAAQnB,EAAInB,GACjB,GAAoB,gBAATA,GAAmB,CAC1B,GAAIP,GAAWE,EAAKC,SAASuB,EACzB1B,KACAiD,EAAOjD,GAAYO,OAGvB,KAAK,GAAIhB,KAAKgB,GAAM,CAChB,GAAI6C,GAAS7D,CACb,IAAW,KAAPmC,EAAW,CACX,GAAI2B,GAAY,GACZ9C,aAAgB+C,SAChBD,EAAY,KAEhBD,EAAS1B,EAAK2B,EAAYD,EAE9BP,EAAQO,EAAQ7C,EAAKhB,KAtBjC,GAAI0D,MAGA/C,EAAOd,IA4BX,OAHAyD,GAAO,GAAIM,GAGJF,GAKXd,SAAU,SAASoB,EAAQrB,GAEvB,GAAIhC,GAAOd,KACPoE,EAAWC,EAAEF,GAAQC,UACzBA,GAASE,KAAK,WAEV,GAAIC,GAAQvE,KAGRsC,EAAK+B,EAAEE,GAAOC,KAAK,KAGvB,IAAIH,EAAEE,GAAOE,SAAS,eAAgB,CAElC3B,EAAKR,KAGL,IAAIhB,GAAQR,EAAKf,IAAI2E,WAAWpC,EAC5BhB,KACAwB,EAAKR,IACDhB,MAAQA,IAKhBR,EAAKiC,SAASwB,EAAOzB,EAAKR,QAE1BxB,GAAKiC,SAASwB,EAAOzB"}
\ No newline at end of file
diff --git a/static/scripts/mvc/form/form-data.js b/static/scripts/mvc/form/form-data.js
index 79473f6f824..3e74c8c30a6 100644
--- a/static/scripts/mvc/form/form-data.js
+++ b/static/scripts/mvc/form/form-data.js
@@ -1,2 +1,2 @@
-define(["utils/utils"],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},checksum:function(){var a="";for(var b in this.app.field_list){var c=this.app.field_list[b];a+=JSON.stringify(c.value&&c.value())}return a},create:function(){function a(a,b,d){c.map_dict[a]=b,e[a]=d}function b(d,e){for(var f in e){var g=e[f];if(g.input){var h=g.input,i=d;switch(""!=d&&(i+="|"),i+=h.name,h.type){case"repeat":var j="section-",k=[],l=null;for(var m in g){var n=m.indexOf(j);-1!=n&&(n+=j.length,k.push(parseInt(m.substr(n))),l||(l=m.substr(0,n)))}k.sort(function(a,b){return a-b});var f=0;for(var o in k)b(i+"_"+f++,g[l+k[o]]);break;case"conditional":var p=c.app.field_list[h.id].value();a(i+"|"+h.test_param.name,h.id,p);var q=c.matchCase(h,p);-1!=q&&b(i,e[h.id+"-section-"+q]);break;case"section":b("",g);break;default:var r=c.app.field_list[h.id];if(r&&r.value){var p=r.value();if((void 0===h.ignore||h.ignore!=p)&&(a(i,h.id,p),h.payload))for(var s in h.payload)a(s,h.id,h.payload[s])}}}}}var c=this,d={};this._iterate(this.app.section.$el,d);var e={};return this.map_dict={},b("",d),e},match:function(a){return this.map_dict&&this.map_dict[a]},matchCase:function(a,b){"boolean"==a.test_param.type&&(b="true"==b?a.test_param.truevalue||"true":a.test_param.falsevalue||"false");for(var c in a.cases)if(a.cases[c].value==b)return c;return-1},matchModel:function(a,b){function c(a,d){for(var f in d){var g=d[f],h=g.name;switch(""!=a&&(h=a+"|"+h),g.type){case"repeat":for(var i in g.cache)c(h+"_"+i,g.cache[i]);break;case"conditional":var j=g.test_param&&g.test_param.value,k=e.matchCase(g,j);-1!=k&&c(h,g.cases[k].inputs);break;default:var l=e.map_dict[h];l&&b(l,g)}}}var d={},e=this;return c("",a.inputs),d},matchResponse:function(a){function b(a,e){if("string"==typeof e){var f=d.map_dict[a];f&&(c[f]=e)}else for(var g in e){var h=g;if(""!==a){var i="|";e instanceof Array&&(i="_"),h=a+i+h}b(h,e[g])}}var c={},d=this;return b("",a),c},_iterate:function(a,b){var c=this,d=$(a).children();d.each(function(){var a=this,d=$(a).attr("id");if($(a).hasClass("section-row")){b[d]={};var e=c.app.input_list[d];e&&(b[d]={input:e}),c._iterate(a,b[d])}else c._iterate(a,b)})}})});
+define(["utils/utils"],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},checksum:function(){var a="";for(var b in this.app.field_list){var c=this.app.field_list[b];a+=JSON.stringify(c.value&&c.value())}return a},create:function(){function a(a,b,d){c.map_dict[a]=b,e[a]=d}function b(d,e){for(var f in e){var g=e[f];if(g.input){var h=g.input,i=d;switch(""!=d&&(i+="|"),i+=h.name,h.type){case"repeat":var j="section-",k=[],l=null;for(var m in g){var n=m.indexOf(j);-1!=n&&(n+=j.length,k.push(parseInt(m.substr(n))),l||(l=m.substr(0,n)))}k.sort(function(a,b){return a-b});var f=0;for(var o in k)b(i+"_"+f++,g[l+k[o]]);break;case"conditional":var p=c.app.field_list[h.id].value();a(i+"|"+h.test_param.name,h.id,p);var q=c.matchCase(h,p);-1!=q&&b(i,e[h.id+"-section-"+q]);break;case"section":b(i,g);break;default:var r=c.app.field_list[h.id];if(r&&r.value){var p=r.value();if((void 0===h.ignore||h.ignore!=p)&&(a(i,h.id,p),h.payload))for(var s in h.payload)a(s,h.id,h.payload[s])}}}}}var c=this,d={};this._iterate(this.app.section.$el,d);var e={};return this.map_dict={},b("",d),e},match:function(a){return this.map_dict&&this.map_dict[a]},matchCase:function(a,b){"boolean"==a.test_param.type&&(b="true"==b?a.test_param.truevalue||"true":a.test_param.falsevalue||"false");for(var c in a.cases)if(a.cases[c].value==b)return c;return-1},matchModel:function(a,b){function c(a,d){for(var f in d){var g=d[f],h=g.name;switch(""!=a&&(h=a+"|"+h),g.type){case"repeat":for(var i in g.cache)c(h+"_"+i,g.cache[i]);break;case"conditional":var j=g.test_param&&g.test_param.value,k=e.matchCase(g,j);-1!=k&&c(h,g.cases[k].inputs);break;case"section":c(h,g.inputs);break;default:var l=e.map_dict[h];l&&b(l,g)}}}var d={},e=this;return c("",a.inputs),d},matchResponse:function(a){function b(a,e){if("string"==typeof e){var f=d.map_dict[a];f&&(c[f]=e)}else for(var g in e){var h=g;if(""!==a){var i="|";e instanceof Array&&(i="_"),h=a+i+h}b(h,e[g])}}var c={},d=this;return b("",a),c},_iterate:function(a,b){var c=this,d=$(a).children();d.each(function(){var a=this,d=$(a).attr("id");if($(a).hasClass("section-row")){b[d]={};var e=c.app.input_list[d];e&&(b[d]={input:e}),c._iterate(a,b[d])}else c._iterate(a,b)})}})});
 //# sourceMappingURL=../../../maps/mvc/form/form-data.js.map
\ No newline at end of file
diff --git a/templates/webapps/galaxy/tool_form.mako b/templates/webapps/galaxy/tool_form.mako
index 9f7d986b62e..69e173f9acf 100644
--- a/templates/webapps/galaxy/tool_form.mako
+++ b/templates/webapps/galaxy/tool_form.mako
@@ -3,455 +3,22 @@
 ${h.js("libs/bibtex", "libs/jquery/jquery-ui")}
 ${h.css('base', 'jquery-ui/smoothness/jquery-ui')}
 
-## skip new tool form code if disabled
-%if util.string_as_bool(trans.app.config.get('toolform_upgrade',  True)):
-    <%
-        ## TEMPORARY: create tool dictionary in mako while both tool forms are in use.
-        ## This avoids making two separate requests since the classic form requires the mako anyway.
-        params = dict(trans.request.params)
-        params['__dataset_id__'] = params.get('id', None)
-        self.form_config = tool.to_json(trans, params)
-        self.form_config.update({
-            'id'                : tool.id,
-            'job_id'            : trans.security.encode_id( job.id ) if job else None,
-            'history_id'        : trans.security.encode_id( trans.history.id )
-        })
-    %>
-    <script>
-        require(['mvc/tools/tools-form'], function(ToolsForm){
-            $(function(){
-                var form = new ToolsForm.View(${ h.dumps(self.form_config) });
-            });
+<%
+    ## TEMPORARY: create tool dictionary in mako while both tool forms are in use.
+    ## This avoids making two separate requests since the classic form requires the mako anyway.
+    params = dict(trans.request.params)
+    params['__dataset_id__'] = params.get('id', None)
+    self.form_config = tool.to_json(trans, params)
+    self.form_config.update({
+        'id'                : tool.id,
+        'job_id'            : trans.security.encode_id( job.id ) if job else None,
+        'history_id'        : trans.security.encode_id( trans.history.id )
+    })
+%>
+<script>
+    require(['mvc/tools/tools-form'], function(ToolsForm){
+        $(function(){
+            var form = new ToolsForm.View(${ h.dumps(self.form_config) });
         });
-    </script>
-    <div id="tool-form-classic" style="display: none;">
-%else:
-    <div id="tool-form-classic">
-%endif
-
-    <%namespace file="/message.mako" import="render_msg" />
-    <%namespace file="/base_panels.mako" import="overlay" />
-
-    <% import galaxy.util %>
-
-    <%def name="stylesheets()">
-        ${h.css( "autocomplete_tagging", "base", "library" )}
-        <style type="text/css">
-            html, body {
-                background-color: #fff;
-            }
-        </style>
-    </%def>
-
-    <%def name="javascripts()">
-        ${parent.javascripts()}
-        ${h.js( "galaxy.panels", "libs/jquery/jstorage" )}
-        ${h.js( "libs/bibtex" )}
-        <script type="text/javascript">
-            require( [ "galaxy.tools" ] );
-            window.enhanced_galaxy_tools = true;
-        </script>
-        <script type="text/javascript">
-        $(function() {
-            $(window).bind("refresh_on_change", function() {
-                $(':file').each( function() {
-                    var file = $(this);
-                    var file_value = file.val();
-                    if (file_value) {
-                        // disable file input, since we don't want to upload the file on refresh
-                        var file_name = $(this).attr("name");
-                        file.attr( { name: 'replaced_file_input_' + file_name, disabled: true } );
-                        // create a new hidden field which stores the filename and has the original name of the file input
-                        var new_file_input = $(document.createElement('input'));
-                        new_file_input.attr( { "type": "hidden", "value": file_value, "name": file_name } );
-                        file.after(new_file_input);
-                    }
-                });
-            });
-
-            // For drilldown parameters: add expand/collapse buttons and collapse initially-collapsed elements
-            $( 'div.drilldown-container' ).each( function() {
-                $(this).find('span.form-toggle' ).each( function() {
-                    var show_hide_click_elt = $(this);
-                    var group_id = show_hide_click_elt.attr('id').substring( 0, show_hide_click_elt.attr('id').lastIndexOf( '-click' ) );
-                    $('#' + group_id + '-container').each( function() {
-                        var show_hide_elt = $(this);
-                        if (  show_hide_click_elt.hasClass( 'toggle-expand' ) ) {
-                            show_hide_elt.hide();
-                        }
-                        show_hide_click_elt.click( function() {
-                            if ( show_hide_click_elt.hasClass("toggle") ){
-                                show_hide_click_elt.addClass("toggle-expand");
-                                show_hide_click_elt.removeClass("toggle");
-                                show_hide_elt.slideUp( 'fast' );
-                            }
-                            else {
-                                show_hide_click_elt.addClass("toggle");
-                                show_hide_click_elt.removeClass("toggle-expand");
-                                show_hide_elt.slideDown( 'fast' );
-                            }
-                        });
-                    });
-                });
-            });
-
-            $(".add-librarydataset").click(function() {
-                var link = $(this);
-                $.ajax({
-                    url: "/visualization/list_libraries",
-                    error: function(xhr, ajaxOptions, thrownError) { alert( "Grid failed" ); console.log(xhr, ajaxOptions, thrownError); },
-                    success: function(table_html) {
-                        show_modal(
-                            "Select Library Dataset",
-                            table_html, {
-                                "Cancel": function() {
-                                    hide_modal();
-                                },
-                                "Select": function() {
-                                    var names = [];
-                                    var ids = [];
-                                    counter = 1;
-                                    $('input[name=ldda_ids]:checked').each(function() {
-                                        var name = $.trim( $(this).siblings("label").text() );
-                                        var id = $(this).val();
-                                        names.push( counter + ". " + name );
-                                        counter += 1;
-                                        ids.push(id);
-                                    });
-                                    link.html( names.join("<br/>") );
-                                    link.siblings("input[type=hidden]").val( ids.join("||") );
-                                    hide_modal();
-                                }
-                            }
-                        );
-                    }
-                });
-            });
-        });
-
-        %if not add_frame.debug:
-            if( window.name != "galaxy_main" ) {
-                location.replace( '${h.url_for( controller='root', action='index', tool_id=tool.id )}' );
-            }
-        %endif
-
-        </script>
-
-    </%def>
-
-    <%def name="do_inputs( inputs, tool_state, errors, prefix, other_values=None )">
-        <%
-        from galaxy.util.expressions import ExpressionContext
-        other_values = ExpressionContext( tool_state, other_values )
-        %>
-        %for input_index, input in enumerate( inputs.itervalues() ):
-            %if not input.visible:
-                <% pass %>
-            %elif input.type == "repeat":
-              <div class="repeat-group">
-                  <div class="form-title-row"><strong>${input.title_plural}</strong>
-                  %if input.help:
-                      <div class="toolParamHelp" style="clear: both;">
-                          ${input.help}
-                      </div>
-                  %endif
-                  </div>
-                  <%
-                  repeat_state = tool_state[input.name]
-                  num_repeats = len( repeat_state )
-                  %>
-                  %for i in range( num_repeats ):
-                    <div class="repeat-group-item">
-                        <%
-                        if input.name in errors:
-                            rep_errors = errors[input.name][i]
-                        else:
-                            rep_errors = dict()
-                        index = repeat_state[i]['__index__']
-                        %>
-                        <div class="form-title-row"><strong>${input.title} ${i + 1}</strong></div>
-                        ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )}
-                        %if input.min < num_repeats:
-                            <div class="form-row"><input type="submit" class="btn" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div>
-                        %endif
-                    </div>
-                    %if rep_errors.has_key( '__index__' ):
-                        <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}">&nbsp;<span style="vertical-align: middle;">${rep_errors['__index__']}</span></div>
-                    %endif
-                  %endfor
-                  %if input.max > num_repeats:
-                      <div class="form-row"><input type="submit" class="btn" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div>
-                  %endif
-              </div>
-            %elif input.type == "conditional":
-                <%
-                group_state = tool_state[input.name]
-                group_errors = errors.get( input.name, {} )
-                current_case = group_state['__current_case__']
-                group_prefix = prefix + input.name + "|"
-                %>
-                %if input.value_ref_in_group:
-                    ${row_for_param( group_prefix, input.test_param, group_state, group_errors, other_values )}
-                %endif
-                ${do_inputs( input.cases[current_case].inputs, group_state, group_errors, group_prefix, other_values )}
-            %elif input.type == "upload_dataset":
-                %if input.get_datatype( trans, other_values ).composite_type is None: #have non-composite upload appear as before
-                    <%
-                    if input.name in errors:
-                        rep_errors = errors[input.name][0]
-                    else:
-                        rep_errors = dict()
-                    %>
-                  ${do_inputs( input.inputs, tool_state[input.name][0], rep_errors, prefix + input.name + "_" + str( 0 ) + "|", other_values )}
-                %else:
-                    <div class="repeat-group">
-                        <div class="form-title-row"><strong>${input.group_title( other_values )}</strong></div>
-                        <%
-                        repeat_state = tool_state[input.name]
-                        %>
-                        %for i in range( len( repeat_state ) ):
-                          <div class="repeat-group-item">
-                          <%
-                          if input.name in errors:
-                              rep_errors = errors[input.name][i]
-                          else:
-                              rep_errors = dict()
-                          index = repeat_state[i]['__index__']
-                          %>
-                          <div class="form-title-row"><strong>File Contents for ${input.title_by_index( trans, i, other_values )}</strong></div>
-                          ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )}
-                          ##<div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div>
-                          </div>
-                        %endfor
-                        ##<div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div>
-                    </div>
-                %endif
-            %else:
-                ${row_for_param( prefix, input, tool_state, errors, other_values )}
-            %endif
-        %endfor
-    </%def>
-
-    <%def name="row_for_param( prefix, param, parent_state, parent_errors, other_values )">
-        <%
-        if parent_errors.has_key( param.name ):
-            cls = "form-row form-row-error"
-        else:
-            cls = "form-row"
-
-        field = param.get_html_field( trans, parent_state[ param.name ], other_values )
-        field.refresh_on_change = param.refresh_on_change
-
-        # Field may contain characters submitted by user and these characters may
-        # be unicode; handle non-ascii characters gracefully.
-        field_html = field.get_html( prefix )
-        if type( field_html ) is not unicode:
-            field_html = unicode( field_html, 'utf-8', 'replace' )
-
-        if param.type == "hidden":
-            return field_html
-        %>
-        <div class="${cls}">
-            ${label_for_param( param )}
-            ${input_for_param( param, field_html )}
-            ${errors_for_param( param, parent_errors )}
-            ${help_for_param( param )}
-            <div style="clear: both;"></div>
-        </div>
-    </%def>
-
-    <%def name="input_for_param( param, field_html )">
-        <div class="form-row-input">${field_html}</div>
-    </%def>
-
-    <%def name="label_for_param( param )">
-        <% label = param.get_label()%>
-        %if label:
-            <label for="${param.name}">${label}:</label>
-        %endif
-    </%def>
-
-    <%def name="errors_for_param( param, parent_errors )">
-        %if parent_errors.has_key( param.name ):
-            <div class="form-row-error-message">
-                <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}">&nbsp;<span style="vertical-align: middle;">${parent_errors[param.name]}</span></div>
-            </div>
-        %endif
-    </%def>
-
-    <%def name="help_for_param( param )">
-        %if param.help:
-            <div class="toolParamHelp" style="clear: both;">
-                ${param.help}
-            </div>
-        %endif
-    </%def>
-
-    <%def name="row_for_rerun()">
-        %if trans.app.config.track_jobs_in_database and tool_state.rerun_remap_job_id is not None:
-            <div id="remap-row" class="form-row">
-                <input type="checkbox" name="rerun_remap_job_id" value="${tool_state.rerun_remap_job_id}"> Resume dependencies from this job
-                <div class="toolParamHelp" style="clear: both;">
-                    The previous run of this tool failed and other tools were waiting for it to finish successfully, use this option to resume those tools using the outputs of this tool run.
-                </div>
-            </div>
-            <div style="clear: both;"></div>
-        %endif
-    </%def>
-
-    <% overlay(visible=False) %>
-
-    %if add_frame.from_noframe:
-        <div class="warningmessage">
-            <strong>Welcome to Galaxy</strong>
-            <hr/>
-            It appears that you found this tool from a link outside of Galaxy.
-            If you're not familiar with Galaxy, please consider visiting the
-            <a href="${h.url_for( controller='root' )}" target="_top">welcome page</a>.
-            To learn more about what Galaxy is and what it can do for you, please visit
-            the <a href="${add_frame.wiki_url}" target="_top">Galaxy wiki</a>.
-        </div>
-        <br/>
-    %endif
-
-    <%
-        # Render an error message if a dynamically generated select list is missing a required
-        # index file or entry in the tool_data_table_conf.xml file.
-        message = ""
-        params_with_missing_data_table_entry = tool.params_with_missing_data_table_entry
-        params_with_missing_index_file = tool.params_with_missing_index_file
-        if params_with_missing_data_table_entry:
-            param = params_with_missing_data_table_entry[0]
-            message += "Data table named '%s' is required by tool but not configured.  " % param.options.missing_tool_data_table_name
-        if tool.params_with_missing_index_file:
-            param = params_with_missing_index_file[0]
-            message += "Index file named '%s' is required by tool but not available.  " % param.options.missing_index_file
-
-        # Handle calculating the redirect url for the special case where we have nginx proxy
-        # upload and need to do url_for on the redirect portion of the tool action.
-        try:
-            tool_url = h.url_for(tool.action)
-        except AttributeError:
-            assert len(tool.action) == 2
-            tool_url = tool.action[0] + h.url_for(tool.action[1])
-    %>
-
-    <%
-        # Name of the tool in lower case
-        low_tool_name = tool.name.lower()
-    %>
-
-    %if tool_id_version_message:
-        ${render_msg( tool_id_version_message, 'warning' )}
-    %endif
-
-    <div class="toolForm" id="${tool.id}">
-        <form id="tool_form" name="tool_form" action="${tool_url}" enctype="${tool.enctype}" target="${tool.target}" method="${tool.method}">
-            %if tool.has_multiple_pages:
-                <div class="toolFormTitle">${tool.name} (step ${tool_state.page+1} of ${tool.npages})
-            %elif not tool_version_select_field:
-                <div class="toolFormTitle">${tool.name} (Galaxy tool version ${tool.version})
-            %else:
-                <div class="toolFormTitle">${tool.name} ${tool_version_select_field.get_html()}
-            %endif
-            ## Show information button with underlying requirements and their versions
-            %if tool.requirements:
-                <a href="#" class="icon-btn" title="Underlying versions" tabindex="0" data-toggle="popover" data-placement="bottom" data-content=
-                "
-                %for i, requirement in enumerate( tool.requirements ):
-                    ${ requirement.name } ${ ('v ' + requirement.version ) if requirement.version else ' ' } ${ '' if i + 1 == len( tool.requirements ) else ' | ' } 
-                %endfor
-                "
-                 onclick="$(function () {
-                              $( '[ data-toggle=\'popover\' ]' ).popover();
-                              $( this ).popover( 'show' );
-                          })">
-                    <span class="fa fa-info-circle"></span>
-                </a>
-            %endif
-
-            <span class="pull-right">
-            %if trans.app.config.biostar_url:
-                    ## BioStar links
-                    Help from Biostar
-                    <div class="icon-btn-group">
-                        <a href="${h.url_for( controller='biostar', action='biostar_tool_tag_redirect', tool_id=tool.id )}"
-                            target="_blank" class="icon-btn" title="Search for this tool" data-toggle="tooltip" data-placement="bottom"><span class="fa fa-search"></span></a>
-                        <a href="${h.url_for( controller='biostar', action='biostar_tool_question_redirect', tool_id=tool.id )}"
-                            target="_blank" class="icon-btn" title="Ask a question about this tool" data-toggle="tooltip" data-placement="bottom"><span class="fa fa-question-circle"></a>
-                    </div>
-            %endif
-                <div class="icon-btn-group">
-                    <a href="#" data-link="${h.url_for( controller='root', action='index', tool_id=tool.id, qualified=True )}"
-                        class="icon-btn tool-share-link" title="Share this tool" data-toggle="tooltip" data-placement="bottom"><span class="fa fa-share"></span></a>
-                </div>
-            </span>
-            </div>
-            <div class="toolFormBody">
-                <input type="hidden" name="refresh" value="refresh">
-                <input type="hidden" name="tool_id" value="${tool.id}">
-                <input type="hidden" name="tool_state" value="${util.object_to_string( tool_state.encode( tool, app ) )}">
-                %if tool.display_by_page[tool_state.page]:
-                    ${trans.fill_template_string( tool.display_by_page[tool_state.page], context=tool.get_param_html_map( trans, tool_state.page, tool_state.inputs ) )}
-                    ${row_for_rerun()}
-                    <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute">
-                %else:
-                    ${do_inputs( tool.inputs_by_page[ tool_state.page ], tool_state.inputs, errors, "" )}
-                    %if tool_state.page == tool.last_page:
-                        ${row_for_rerun()}
-                    %endif
-                    <div class="form-row form-actions">
-                        %if tool_state.page == tool.last_page:
-                            <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute">
-                        %else:
-                            <input type="submit" class="btn btn-primary" name="runtool_btn" value="Next step">
-                        %endif
-                    </div>
-                %endif
-            </div>
-        </form>
-    </div>
-    %if tool.help:
-        <div class="toolHelp">
-            <div class="toolHelpBody">
-                <%
-                    if tool.has_multiple_pages:
-                        tool_help = tool.help_by_page[tool_state.page]
-                    else:
-                        tool_help = tool.help
-
-                    # Help is Mako template, so render using current static path.
-                    tool_help = tool_help.render( static_path=h.url_for( '/static' ), host_url=h.url_for('/', qualified=True) )
-
-                    # Convert to unicode to display non-ascii characters.
-                    if type( tool_help ) is not unicode:
-                        tool_help = unicode( tool_help, 'utf-8')
-                %>
-                ${tool_help}
-            </div>
-        </div>
-    %endif
-    %if tool.tool_shed_repository:
-        <% tool_url = tool.tool_shed_repository.get_sharable_url( tool.app ) %>
-        %if tool_url:
-            <br/>
-            ${ render_msg( 'This tool was installed from a ToolShed, you may be able to find additional information by following this link: <a href="%s" target="_blank">%s</a>' % ( tool_url, tool_url ), 'info' ) }
-        %endif
-    %endif
-    %if tool.citations:
-        <script>
-        require(["mvc/citation/citation-model", "mvc/citation/citation-view"
-        ], function( citationModel, citationView ){
-            $(function() {
-                var citations = new citationModel.ToolCitationCollection();
-                citations.tool_id = "${tool.id}";
-                var citation_list_view = new citationView.CitationListView({ collection: citations } );
-                citation_list_view.render();
-                citations.fetch();
-            } );
-        } );
-        </script>
-        <div id="citations">
-        </div>
-    %endif
-</div>
+    });
+</script>
\ No newline at end of file

From 6b86b8c86fec2413920062e10ded240c47725dd0 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 23 Mar 2015 15:41:32 -0400
Subject: [PATCH 03/88] Parameters: Add expanded attribute to section input
 parameter

---
 client/galaxy/scripts/mvc/form/form-section.js | 2 +-
 lib/galaxy/tools/__init__.py                   | 1 +
 lib/galaxy/tools/parameters/grouping.py        | 3 ++-
 static/maps/mvc/form/form-section.js.map       | 2 +-
 static/scripts/mvc/form/form-section.js        | 2 +-
 5 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/client/galaxy/scripts/mvc/form/form-section.js b/client/galaxy/scripts/mvc/form/form-section.js
index f2f4a22785c..3c1c2092451 100644
--- a/client/galaxy/scripts/mvc/form/form-section.js
+++ b/client/galaxy/scripts/mvc/form/form-section.js
@@ -286,7 +286,7 @@ define(['utils/utils',
             });
 
             // show sub section if requested
-            if (input_def.expand) {
+            if (input_def.expanded) {
                 portlet.$header.trigger('click');
             }
 
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 448c4a2b4ca..90ba49ea38a 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -977,6 +977,7 @@ class Tool( object, Dictifiable ):
                 group.name = input_source.get( "name" )
                 group.title = input_source.get( "title" )
                 group.help = input_source.get( "help", None )
+                group.expanded = input_source.get_bool( "expanded", False )
                 page_source = input_source.parse_nested_inputs_source()
                 group.inputs = self.parse_input_elem( page_source, enctypes, context )
                 rval[group.name] = group
diff --git a/lib/galaxy/tools/parameters/grouping.py b/lib/galaxy/tools/parameters/grouping.py
index 5a1706579b0..7950e1f1d2c 100644
--- a/lib/galaxy/tools/parameters/grouping.py
+++ b/lib/galaxy/tools/parameters/grouping.py
@@ -131,7 +131,7 @@ class Repeat( Group ):
 
 class Section( Group ):
 
-    dict_collection_visible_keys = ( 'name', 'type', 'title', 'help')
+    dict_collection_visible_keys = ( 'name', 'type', 'title', 'help', 'expanded')
 
     type = "section"
     def __init__( self ):
@@ -139,6 +139,7 @@ class Section( Group ):
         self.title = None
         self.inputs = None
         self.help = None
+        self.expanded = False
     @property
     def title_plural( self ):
         return inflector.pluralize( self.title )
diff --git a/static/maps/mvc/form/form-section.js.map b/static/maps/mvc/form/form-section.js.map
index ef2d993e2e6..d1aaf3aeb6e 100644
--- a/static/maps/mvc/form/form-section.js.map
+++ b/static/maps/mvc/form/form-section.js.map
@@ -1 +1 @@
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\ No newline at end of file
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\ No newline at end of file
diff --git a/static/scripts/mvc/form/form-section.js b/static/scripts/mvc/form/form-section.js
index f6549141b0b..befc9ba0519 100644
--- a/static/scripts/mvc/form/form-section.js
+++ b/static/scripts/mvc/form/form-section.js
@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-portlet","mvc/form/form-repeat","mvc/form/form-input","mvc/form/form-parameters"],function(a,b,c,d,e,f,g){var h=Backbone.View.extend({initialize:function(a,c){this.app=a,this.inputs=c.inputs,c.cls="ui-table-plain",c.cls_tr="section-row",this.table=new b.View(c),this.parameters=new g(a,c),this.setElement(this.table.$el),this.render()},render:function(){this.table.delAll();for(var a in this.inputs)this.add(this.inputs[a])},add:function(b){var c=jQuery.extend(!0,{},b);c.id=b.id=a.uid(),this.app.input_list[c.id]=c;var d=c.type;switch(d){case"conditional":this._addConditional(c);break;case"repeat":this._addRepeat(c);break;case"section":this._addSection(c);break;default:this._addRow(c)}},_addConditional:function(a){var b=this;a.test_param.id=a.id;var c=this._addRow(a.test_param);c.options.onchange=function(c){var d=b.app.data.matchCase(a,c);for(var e in a.cases){var f=a.cases[e],g=a.id+"-section-"+e,h=b.table.get(g),i=!1;for(var j in f.inputs)if(!f.inputs[j].hidden){i=!0;break}e==d&&i?h.fadeIn("fast"):h.hide()}b.app.trigger("change")};for(var d in a.cases){var e=a.id+"-section-"+d,f=new h(this.app,{inputs:a.cases[d].inputs});f.$el.addClass("ui-table-section"),this.table.add(f.$el),this.table.append(e)}c.trigger("change")},_addRepeat:function(a){function b(b){var e=a.id+"-section-"+d++,f=new h(c.app,{inputs:b});g.add({id:e,$el:f.$el,ondel:function(){g.del(e),c.app.trigger("change")}})}for(var c=this,d=0,g=new e.View({title:a.title,title_new:a.title,min:a.min,max:a.max,onnew:function(){b(a.inputs),c.app.trigger("change")}}),i=a.min,j=_.size(a.cache),k=0;k<Math.max(j,i);k++){var l=null;l=j>k?a.cache[k]:a.inputs,b(l)}var m=new f(this.app,{label:a.title,help:a.help,field:g});this.table.add(m.$el),this.table.append(a.id)},_addSection:function(a){var b=this,e=new h(b.app,{inputs:a.inputs}),f=new c.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"}),g=new d.View({title:a.title,cls:"ui-portlet-section",operations:{button_visible:f}});g.append(e.$el),g.append($("<div/>").addClass("ui-table-form-info").html(a.help));var i=!1;g.$content.hide(),g.$header.css("cursor","pointer"),g.$header.on("click",function(){i?(i=!1,g.$content.hide(),f.setIcon("fa-eye-slash")):(i=!0,g.$content.fadeIn("fast"),f.setIcon("fa-eye"))}),a.expand&&g.$header.trigger("click"),this.table.add(g.$el),this.table.append(a.id)},_addRow:function(a){var b=a.id,c=this.parameters.create(a);this.app.field_list[b]=c;var d=new f(this.app,{label:a.label,default_value:a.default_value,optional:a.optional,help:a.help,field:c});return this.app.element_list[b]=d,this.table.add(d.$el),this.table.append(b),a.hidden&&this.table.get(b).hide(),c}});return{View:h}});
+define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-portlet","mvc/form/form-repeat","mvc/form/form-input","mvc/form/form-parameters"],function(a,b,c,d,e,f,g){var h=Backbone.View.extend({initialize:function(a,c){this.app=a,this.inputs=c.inputs,c.cls="ui-table-plain",c.cls_tr="section-row",this.table=new b.View(c),this.parameters=new g(a,c),this.setElement(this.table.$el),this.render()},render:function(){this.table.delAll();for(var a in this.inputs)this.add(this.inputs[a])},add:function(b){var c=jQuery.extend(!0,{},b);c.id=b.id=a.uid(),this.app.input_list[c.id]=c;var d=c.type;switch(d){case"conditional":this._addConditional(c);break;case"repeat":this._addRepeat(c);break;case"section":this._addSection(c);break;default:this._addRow(c)}},_addConditional:function(a){var b=this;a.test_param.id=a.id;var c=this._addRow(a.test_param);c.options.onchange=function(c){var d=b.app.data.matchCase(a,c);for(var e in a.cases){var f=a.cases[e],g=a.id+"-section-"+e,h=b.table.get(g),i=!1;for(var j in f.inputs)if(!f.inputs[j].hidden){i=!0;break}e==d&&i?h.fadeIn("fast"):h.hide()}b.app.trigger("change")};for(var d in a.cases){var e=a.id+"-section-"+d,f=new h(this.app,{inputs:a.cases[d].inputs});f.$el.addClass("ui-table-section"),this.table.add(f.$el),this.table.append(e)}c.trigger("change")},_addRepeat:function(a){function b(b){var e=a.id+"-section-"+d++,f=new h(c.app,{inputs:b});g.add({id:e,$el:f.$el,ondel:function(){g.del(e),c.app.trigger("change")}})}for(var c=this,d=0,g=new e.View({title:a.title,title_new:a.title,min:a.min,max:a.max,onnew:function(){b(a.inputs),c.app.trigger("change")}}),i=a.min,j=_.size(a.cache),k=0;k<Math.max(j,i);k++){var l=null;l=j>k?a.cache[k]:a.inputs,b(l)}var m=new f(this.app,{label:a.title,help:a.help,field:g});this.table.add(m.$el),this.table.append(a.id)},_addSection:function(a){var b=this,e=new h(b.app,{inputs:a.inputs}),f=new c.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"}),g=new d.View({title:a.title,cls:"ui-portlet-section",operations:{button_visible:f}});g.append(e.$el),g.append($("<div/>").addClass("ui-table-form-info").html(a.help));var i=!1;g.$content.hide(),g.$header.css("cursor","pointer"),g.$header.on("click",function(){i?(i=!1,g.$content.hide(),f.setIcon("fa-eye-slash")):(i=!0,g.$content.fadeIn("fast"),f.setIcon("fa-eye"))}),a.expanded&&g.$header.trigger("click"),this.table.add(g.$el),this.table.append(a.id)},_addRow:function(a){var b=a.id,c=this.parameters.create(a);this.app.field_list[b]=c;var d=new f(this.app,{label:a.label,default_value:a.default_value,optional:a.optional,help:a.help,field:c});return this.app.element_list[b]=d,this.table.add(d.$el),this.table.append(b),a.hidden&&this.table.get(b).hide(),c}});return{View:h}});
 //# sourceMappingURL=../../../maps/mvc/form/form-section.js.map
\ No newline at end of file

From 8608f1e439cdd3d8f7c9289d5cbd42d3f070f059 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 23 Mar 2015 16:12:25 -0400
Subject: [PATCH 04/88] Use context when deriving the initial value, fix visit
 inputs

---
 lib/galaxy/tools/parameters/grouping.py | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/tools/parameters/grouping.py b/lib/galaxy/tools/parameters/grouping.py
index 7950e1f1d2c..f0947f7ac99 100644
--- a/lib/galaxy/tools/parameters/grouping.py
+++ b/lib/galaxy/tools/parameters/grouping.py
@@ -166,17 +166,16 @@ class Section( Group ):
                 raise e
         return rval
     def visit_inputs( self, prefix, value, callback ):
-        for i, d in enumerate( value ):
-            for input in self.inputs.itervalues():
-                new_prefix = prefix + "%s_%d|" % ( self.name, i )
-                if isinstance( input, ToolParameter ):
-                    callback( new_prefix, input, d[input.name], parent = d )
-                else:
-                    input.visit_inputs( new_prefix, d[input.name], callback )
+        for input in self.inputs.itervalues():
+            if isinstance( input, ToolParameter ):
+                callback( prefix, input, value[input.name], parent = value )
+            else:
+                input.visit_inputs( prefix, value[input.name], callback )
     def get_initial_value( self, trans, context, history=None ):
         rval = {}
-        for input in self.inputs.itervalues():
-            rval[ input.name ] = input.get_initial_value( trans, context, history=history )
+        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 )
         return rval
     def to_dict( self, trans, view='collection', value_mapper=None ):
         section_dict = super( Section, self ).to_dict( trans, view=view, value_mapper=value_mapper )

From 006347c36565da6df6aabb08d52a17dd135a2b12 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 23 Mar 2015 16:29:54 -0400
Subject: [PATCH 05/88] Add value_from_basic for sections

---
 lib/galaxy/tools/parameters/grouping.py | 13 ++++---------
 1 file changed, 4 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/tools/parameters/grouping.py b/lib/galaxy/tools/parameters/grouping.py
index f0947f7ac99..000b4d72eeb 100644
--- a/lib/galaxy/tools/parameters/grouping.py
+++ b/lib/galaxy/tools/parameters/grouping.py
@@ -151,16 +151,11 @@ class Section( Group ):
             rval[ input.name ] = input.value_to_basic( value[input.name], app )
         return rval
     def value_from_basic( self, value, app, ignore_errors=False ):
-        rval = []
+        rval = {}
         try:
-            for i, d in enumerate( value ):
-                rval_dict = {}
-                for input in self.inputs.itervalues():
-                    if ignore_errors and input.name not in d:
-                        pass
-                    else:
-                        rval_dict[ input.name ] = input.value_from_basic( d[input.name], app, ignore_errors )
-                rval.append( rval_dict )
+            for input in self.inputs.itervalues():
+                if not ignore_errors or input.name in value:
+                    rval[ input.name ] = input.value_from_basic( value[ input.name ], app, ignore_errors )
         except Exception, e:
             if not ignore_errors:
                 raise e

From 6adf74b668c03e3b0069b8ccebf0f9c2f48c6c25 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 23 Mar 2015 17:03:28 -0400
Subject: [PATCH 06/88] Add section handling to params_to_incoming and
 visit_input_values

---
 lib/galaxy/tools/parameters/__init__.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/lib/galaxy/tools/parameters/__init__.py b/lib/galaxy/tools/parameters/__init__.py
index 6c7ee3ebe19..73fcc26bb1e 100644
--- a/lib/galaxy/tools/parameters/__init__.py
+++ b/lib/galaxy/tools/parameters/__init__.py
@@ -33,6 +33,11 @@ def visit_input_values( inputs, input_values, callback, name_prefix="", label_pr
             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 )
+        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 )
         else:
             new_value = callback( input,
                                   input_values[input.name],
@@ -124,6 +129,10 @@ def params_to_incoming( incoming, inputs, input_values, app, name_prefix="", to_
             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 )
+        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 )
         else:
             value = input_values.get( input.name )
             if to_html:

From 9b282d9d0464c5aaadfde112f01f9be0876a7962 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 23 Mar 2015 17:20:34 -0400
Subject: [PATCH 07/88] Add sections to tool evaluator

---
 lib/galaxy/tools/evaluation.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/evaluation.py b/lib/galaxy/tools/evaluation.py
index bfe7fecf37d..05760d60a76 100644
--- a/lib/galaxy/tools/evaluation.py
+++ b/lib/galaxy/tools/evaluation.py
@@ -22,7 +22,7 @@ from galaxy.tools.parameters.basic import (
     LibraryDatasetToolParameter,
     SelectToolParameter,
 )
-from galaxy.tools.parameters.grouping import Conditional, Repeat
+from galaxy.tools.parameters.grouping import Conditional, Repeat, Section
 from galaxy.jobs.datasets import dataset_path_rewrites
 
 import logging
@@ -143,6 +143,9 @@ class ToolEvaluator( object ):
                     values = input_values[ input.name ]
                     current = values["__current_case__"]
                     do_walk( input.cases[current].inputs, values )
+                elif isinstance( input, Section ):
+                    values = input_values[ input.name ]
+                    do_walk( input.inputs, values )
                 else:
                     func( input_values, input )
 

From 672ffd1e6df1e76cfba42d0e3e0ffed981da972a Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 23 Mar 2015 17:25:13 -0400
Subject: [PATCH 08/88] Add section to wrap_values

---
 lib/galaxy/tools/parameters/wrapped.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/lib/galaxy/tools/parameters/wrapped.py b/lib/galaxy/tools/parameters/wrapped.py
index 473799b5076..ea610b06976 100644
--- a/lib/galaxy/tools/parameters/wrapped.py
+++ b/lib/galaxy/tools/parameters/wrapped.py
@@ -8,6 +8,7 @@ from galaxy.tools.parameters.basic import (
 from galaxy.tools.parameters.grouping import (
     Repeat,
     Conditional,
+    Section
 )
 PARAMS_UNWRAPPED = object()
 
@@ -44,6 +45,9 @@ class WrappedParameters( object ):
                 values = input_values[ input.name ]
                 current = values[ "__current_case__" ]
                 self.wrap_values( input.cases[current].inputs, values, skip_missing_values=skip_missing_values )
+            elif isinstance( input, Section ):
+                values = input_values[ input.name ]
+                self.wrap_values( input.inputs, values, skip_missing_values=skip_missing_values )
             elif isinstance( input, DataToolParameter ) and input.multiple:
                 input_values[ input.name ] = \
                     galaxy.tools.DatasetListWrapper( input_values[ input.name ],

From 3b263a8df4ec1a845242336dd61f11d8888c0460 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 23 Mar 2015 20:04:49 -0400
Subject: [PATCH 09/88] Tool testing sections.

 - Add example tool for testing (section.xml).
 - Implement popular flat group style test cases for section elements (first example in section.xml).
 - Implement nested groupping style test cases for section elements (section example in section.xml).
---
 lib/galaxy/tools/parser/xml.py              |  7 ++++
 lib/galaxy/tools/test.py                    | 14 ++++++-
 test/functional/tools/samples_tool_conf.xml |  1 +
 test/functional/tools/section.xml           | 43 +++++++++++++++++++++
 4 files changed, 64 insertions(+), 1 deletion(-)
 create mode 100644 test/functional/tools/section.xml

diff --git a/lib/galaxy/tools/parser/xml.py b/lib/galaxy/tools/parser/xml.py
index b77c33b21ba..5654be40b4f 100644
--- a/lib/galaxy/tools/parser/xml.py
+++ b/lib/galaxy/tools/parser/xml.py
@@ -418,6 +418,13 @@ def __expand_input_elems( root_elem, prefix="" ):
         __pull_up_params( root_elem, cond_elem )
         root_elem.remove( cond_elem )
 
+    section_elems = root_elem.findall( 'section' )
+    for section_elem in section_elems:
+        new_prefix = __prefix_join( prefix, section_elem.get( "name" ) )
+        __expand_input_elems( section_elem, new_prefix )
+        __pull_up_params( root_elem, section_elem )
+        root_elem.remove( section_elem )
+
 
 def __append_prefix_to_params( elem, prefix ):
     for param_elem in elem.findall( 'param' ):
diff --git a/lib/galaxy/tools/test.py b/lib/galaxy/tools/test.py
index aa4f9f1dbca..e8cee330e3e 100644
--- a/lib/galaxy/tools/test.py
+++ b/lib/galaxy/tools/test.py
@@ -166,7 +166,12 @@ class ToolTestBuilder( object ):
                         # an infinite loop - hence the "case_value is not None"
                         # check.
                         expanded_inputs[ case_context.for_state() ] = expanded_case_value
-
+            elif isinstance( value, galaxy.tools.parameters.grouping.Section ):
+                context = ParamContext( name=value.name, parent_context=parent_context )
+                for r_name, r_value in value.inputs.iteritems():
+                    expanded_input = self.__process_raw_inputs( { context.for_state(): r_value }, raw_inputs, parent_context=context )
+                    if expanded_input:
+                        expanded_inputs.update( expanded_input )
             elif isinstance( value, galaxy.tools.parameters.grouping.Repeat ):
                 repeat_index = 0
                 while True:
@@ -364,6 +369,13 @@ def expand_input_elems( root_elem, prefix="" ):
         __pull_up_params( root_elem, cond_elem )
         root_elem.remove( cond_elem )
 
+    section_elems = root_elem.findall( 'section' )
+    for section_elem in section_elems:
+        new_prefix = __prefix_join( prefix, section_elem.get( "name" ) )
+        expand_input_elems( section_elem, new_prefix )
+        __pull_up_params( root_elem, section_elem )
+        root_elem.remove( section_elem )
+
 
 def __append_prefix_to_params( elem, prefix ):
     for param_elem in elem.findall( 'param' ):
diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
index 2632fe565fe..3b2f1a204a8 100644
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -28,6 +28,7 @@
   <tool file="column_param.xml" />
   <tool file="column_multi_param.xml" />
   <tool file="special_params.xml" />
+  <tool file="section.xml" />
   <tool file="top_level_data.xml" />
   <tool file="validation_default.xml" />
   <tool file="validation_sanitizer.xml" />
diff --git a/test/functional/tools/section.xml b/test/functional/tools/section.xml
new file mode 100644
index 00000000000..29bb7fe10e3
--- /dev/null
+++ b/test/functional/tools/section.xml
@@ -0,0 +1,43 @@
+<tool id="section" name="section">
+    <command>
+        echo "$int.inttest"   >> $out_file1; 
+        echo "$float.floattest" >> $out_file1; 
+    </command>
+    <inputs>
+        <section name="int" title="Integer Section" expanded="true">
+            <param name="inttest" value="1" type="integer" />
+        </section>
+        <section name="float" title="Float Section" expanded="false">
+            <param name="floattest" value="1.0" type="float" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="inttest" value="12456" />
+            <param name="floattest" value="6.789" />
+            <output name="out_file1">
+                <assert_contents>
+                    <has_line line="12456" />
+                    <has_line line="6.789" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <section name="int">
+                <param name="inttest" value="12456" />
+            </section>
+            <section name="float">
+                <param name="floattest" value="6.789" />
+            </section>
+            <output name="out_file1">
+                <assert_contents>
+                    <has_line line="12456" />
+                    <has_line line="6.789" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>

From 49f45d3fcee6621a3617a5278e8e8678976eb356 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 25 Mar 2015 22:54:54 -0400
Subject: [PATCH 10/88] Ui: Add top margin to section element

---
 static/style/blue/base.css    | 56 +++++++++++++++++------------------
 static/style/src/less/ui.less |  1 +
 2 files changed, 29 insertions(+), 28 deletions(-)

diff --git a/static/style/blue/base.css b/static/style/blue/base.css
index 207da8938da..5edc7a740dd 100644
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -41,7 +41,7 @@ html{font-size:62.5%;-webkit-tap-highlight-color:rgba(0,0,0,0)}
 body{font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;font-size:12px;line-height:1.428571429;color:#333;background-color:#fff}
 input,button,select,textarea{font-family:inherit;font-size:inherit;line-height:inherit}
 button,input,select[multiple],textarea{background-image:none}
-a{color:#303030;text-decoration:none}a:hover,a:focus{color:#0a0a0a;text-decoration:underline}
+a{color:#5f6990;text-decoration:none}a:hover,a:focus{color:#404862;text-decoration:underline}
 a:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px}
 img{vertical-align:middle}
 .img-responsive{display:block;max-width:100%;height:auto}
@@ -114,13 +114,13 @@ address{display:block;margin-bottom:17px;font-style:normal;line-height:1.4285714
 .col-xs-12{width:100%}
 @media (min-width:768px){.container{max-width:750px} .col-sm-1,.col-sm-2,.col-sm-3,.col-sm-4,.col-sm-5,.col-sm-6,.col-sm-7,.col-sm-8,.col-sm-9,.col-sm-10,.col-sm-11{float:left} .col-sm-1{width:8.333333333333332%} .col-sm-2{width:16.666666666666664%} .col-sm-3{width:25%} .col-sm-4{width:33.33333333333333%} .col-sm-5{width:41.66666666666667%} .col-sm-6{width:50%} .col-sm-7{width:58.333333333333336%} .col-sm-8{width:66.66666666666666%} .col-sm-9{width:75%} .col-sm-10{width:83.33333333333334%} .col-sm-11{width:91.66666666666666%} .col-sm-12{width:100%} .col-sm-push-1{left:8.333333333333332%} .col-sm-push-2{left:16.666666666666664%} .col-sm-push-3{left:25%} .col-sm-push-4{left:33.33333333333333%} .col-sm-push-5{left:41.66666666666667%} .col-sm-push-6{left:50%} .col-sm-push-7{left:58.333333333333336%} .col-sm-push-8{left:66.66666666666666%} .col-sm-push-9{left:75%} .col-sm-push-10{left:83.33333333333334%} .col-sm-push-11{left:91.66666666666666%} .col-sm-pull-1{right:8.333333333333332%} .col-sm-pull-2{right:16.666666666666664%} .col-sm-pull-3{right:25%} .col-sm-pull-4{right:33.33333333333333%} .col-sm-pull-5{right:41.66666666666667%} .col-sm-pull-6{right:50%} .col-sm-pull-7{right:58.333333333333336%} .col-sm-pull-8{right:66.66666666666666%} .col-sm-pull-9{right:75%} .col-sm-pull-10{right:83.33333333333334%} .col-sm-pull-11{right:91.66666666666666%} .col-sm-offset-1{margin-left:8.333333333333332%} .col-sm-offset-2{margin-left:16.666666666666664%} .col-sm-offset-3{margin-left:25%} .col-sm-offset-4{margin-left:33.33333333333333%} .col-sm-offset-5{margin-left:41.66666666666667%} .col-sm-offset-6{margin-left:50%} .col-sm-offset-7{margin-left:58.333333333333336%} .col-sm-offset-8{margin-left:66.66666666666666%} .col-sm-offset-9{margin-left:75%} .col-sm-offset-10{margin-left:83.33333333333334%} .col-sm-offset-11{margin-left:91.66666666666666%}}@media (min-width:992px){.container{max-width:970px} 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 th{text-align:left}
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-.table thead>tr>th{vertical-align:bottom;border-bottom:2px solid #d6b161}
+.table{width:100%;margin-bottom:17px}.table thead>tr>th,.table tbody>tr>th,.table tfoot>tr>th,.table thead>tr>td,.table tbody>tr>td,.table tfoot>tr>td{padding:8px;line-height:1.428571429;vertical-align:top;border-top:1px solid #bfbfbf}
+.table thead>tr>th{vertical-align:bottom;border-bottom:2px solid #bfbfbf}
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-.table tbody+tbody{border-top:2px solid #d6b161}
+.table tbody+tbody{border-top:2px solid #bfbfbf}
 .table .table{background-color:#fff}
 .table-condensed thead>tr>th,.table-condensed tbody>tr>th,.table-condensed tfoot>tr>th,.table-condensed thead>tr>td,.table-condensed tbody>tr>td,.table-condensed tfoot>tr>td{padding:5px}
-.table-bordered{border:1px solid #d6b161}.table-bordered>thead>tr>th,.table-bordered>tbody>tr>th,.table-bordered>tfoot>tr>th,.table-bordered>thead>tr>td,.table-bordered>tbody>tr>td,.table-bordered>tfoot>tr>td{border:1px solid #d6b161}
+.table-bordered{border:1px solid #bfbfbf}.table-bordered>thead>tr>th,.table-bordered>tbody>tr>th,.table-bordered>tfoot>tr>th,.table-bordered>thead>tr>td,.table-bordered>tbody>tr>td,.table-bordered>tfoot>tr>td{border:1px solid #bfbfbf}
 .table-bordered>thead>tr>th,.table-bordered>thead>tr>td{border-bottom-width:2px}
 .table-striped>tbody>tr:nth-child(odd)>td,.table-striped>tbody>tr:nth-child(odd)>th{background-color:#f9f9f9}
 .table-hover>tbody>tr:hover>td,.table-hover>tbody>tr:hover>th{background-color:#f5f5f5}
@@ -133,7 +133,7 @@ table td[class*="col-"],table th[class*="col-"]{float:none;display:table-cell}
 .table-hover>tbody>tr>td.danger:hover,.table-hover>tbody>tr>th.danger:hover,.table-hover>tbody>tr.danger:hover>td,.table-hover>tbody>tr.danger:hover>th{background-color:#f7b0ae;border-color:#c61913}
 .table>thead>tr>td.warning,.table>tbody>tr>td.warning,.table>tfoot>tr>td.warning,.table>thead>tr>th.warning,.table>tbody>tr>th.warning,.table>tfoot>tr>th.warning,.table>thead>tr.warning>td,.table>tbody>tr.warning>td,.table>tfoot>tr.warning>td,.table>thead>tr.warning>th,.table>tbody>tr.warning>th,.table>tfoot>tr.warning>th{background-color:#fce1ba;border-color:#e28709}
 .table-hover>tbody>tr>td.warning:hover,.table-hover>tbody>tr>th.warning:hover,.table-hover>tbody>tr.warning:hover>td,.table-hover>tbody>tr.warning:hover>th{background-color:#fbd6a2;border-color:#c97908}
-@media (max-width:768px){.table-responsive{width:100%;margin-bottom:15px;overflow-y:hidden;overflow-x:scroll;-ms-overflow-style:-ms-autohiding-scrollbar;border:1px solid #d6b161;-webkit-overflow-scrolling:touch}.table-responsive>.table{margin-bottom:0;background-color:#fff}.table-responsive>.table>thead>tr>th,.table-responsive>.table>tbody>tr>th,.table-responsive>.table>tfoot>tr>th,.table-responsive>.table>thead>tr>td,.table-responsive>.table>tbody>tr>td,.table-responsive>.table>tfoot>tr>td{white-space:nowrap} .table-responsive>.table-bordered{border:0}.table-responsive>.table-bordered>thead>tr>th:first-child,.table-responsive>.table-bordered>tbody>tr>th:first-child,.table-responsive>.table-bordered>tfoot>tr>th:first-child,.table-responsive>.table-bordered>thead>tr>td:first-child,.table-responsive>.table-bordered>tbody>tr>td:first-child,.table-responsive>.table-bordered>tfoot>tr>td:first-child{border-left:0} .table-responsive>.table-bordered>thead>tr>th:last-child,.table-responsive>.table-bordered>tbody>tr>th:last-child,.table-responsive>.table-bordered>tfoot>tr>th:last-child,.table-responsive>.table-bordered>thead>tr>td:last-child,.table-responsive>.table-bordered>tbody>tr>td:last-child,.table-responsive>.table-bordered>tfoot>tr>td:last-child{border-right:0} .table-responsive>.table-bordered>thead>tr:last-child>th,.table-responsive>.table-bordered>tbody>tr:last-child>th,.table-responsive>.table-bordered>tfoot>tr:last-child>th,.table-responsive>.table-bordered>thead>tr:last-child>td,.table-responsive>.table-bordered>tbody>tr:last-child>td,.table-responsive>.table-bordered>tfoot>tr:last-child>td{border-bottom:0}}fieldset{padding:0;margin:0;border:0}
+@media (max-width:768px){.table-responsive{width:100%;margin-bottom:15px;overflow-y:hidden;overflow-x:scroll;-ms-overflow-style:-ms-autohiding-scrollbar;border:1px solid #bfbfbf;-webkit-overflow-scrolling:touch}.table-responsive>.table{margin-bottom:0;background-color:#fff}.table-responsive>.table>thead>tr>th,.table-responsive>.table>tbody>tr>th,.table-responsive>.table>tfoot>tr>th,.table-responsive>.table>thead>tr>td,.table-responsive>.table>tbody>tr>td,.table-responsive>.table>tfoot>tr>td{white-space:nowrap} .table-responsive>.table-bordered{border:0}.table-responsive>.table-bordered>thead>tr>th:first-child,.table-responsive>.table-bordered>tbody>tr>th:first-child,.table-responsive>.table-bordered>tfoot>tr>th:first-child,.table-responsive>.table-bordered>thead>tr>td:first-child,.table-responsive>.table-bordered>tbody>tr>td:first-child,.table-responsive>.table-bordered>tfoot>tr>td:first-child{border-left:0} .table-responsive>.table-bordered>thead>tr>th:last-child,.table-responsive>.table-bordered>tbody>tr>th:last-child,.table-responsive>.table-bordered>tfoot>tr>th:last-child,.table-responsive>.table-bordered>thead>tr>td:last-child,.table-responsive>.table-bordered>tbody>tr>td:last-child,.table-responsive>.table-bordered>tfoot>tr>td:last-child{border-right:0} .table-responsive>.table-bordered>thead>tr:last-child>th,.table-responsive>.table-bordered>tbody>tr:last-child>th,.table-responsive>.table-bordered>tfoot>tr:last-child>th,.table-responsive>.table-bordered>thead>tr:last-child>td,.table-responsive>.table-bordered>tbody>tr:last-child>td,.table-responsive>.table-bordered>tfoot>tr:last-child>td{border-bottom:0}}fieldset{padding:0;margin:0;border:0}
 legend{display:block;width:100%;padding:0;margin-bottom:17px;font-size:18px;line-height:inherit;color:#333;border:0;border-bottom:1px solid #bfbfbf}
 label{display:inline-block;margin-bottom:5px;font-weight:bold}
 input[type="search"]{-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box}
@@ -148,7 +148,7 @@ output{display:block;padding-top:5px;font-size:12px;line-height:1.428571429;colo
 .form-control::-moz-placeholder{color:#999}
 .form-control:-ms-input-placeholder{color:#999}
 .form-control::-webkit-input-placeholder{color:#999}
-.form-control{display:block;width:100%;height:27px;padding:4px 10px;font-size:12px;line-height:1.428571429;color:#555;vertical-align:middle;background-color:#fff;border:1px solid #aaa;border-radius:3px;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);-webkit-transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s;transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s}.form-control:focus{border-color:#66afe9;outline:0;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6)}
+.form-control{display:block;width:100%;height:27px;padding:4px 10px;font-size:12px;line-height:1.428571429;color:#555;vertical-align:middle;background-color:#fff;border:1px solid #bfbfbf;border-radius:3px;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);-webkit-transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s;transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s}.form-control:focus{border-color:#66afe9;outline:0;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6)}
 .form-control[disabled],.form-control[readonly],fieldset[disabled] .form-control{cursor:not-allowed;background-color:#eee}
 textarea.form-control{height:auto}
 .form-group{margin-bottom:15px}
@@ -202,9 +202,9 @@ textarea.input-lg{height:auto}
 .btn-info{color:#fff;background-color:#3186a0;border-color:#010304}.btn-info:hover,.btn-info:focus,.btn-info:active,.btn-info.active,.open .dropdown-toggle.btn-info{color:#fff;background-color:#276c81;border-color:#000}
 .btn-info:active,.btn-info.active,.open .dropdown-toggle.btn-info{background-image:none}
 .btn-info.disabled,.btn-info[disabled],fieldset[disabled] .btn-info,.btn-info.disabled:hover,.btn-info[disabled]:hover,fieldset[disabled] .btn-info:hover,.btn-info.disabled:focus,.btn-info[disabled]:focus,fieldset[disabled] .btn-info:focus,.btn-info.disabled:active,.btn-info[disabled]:active,fieldset[disabled] .btn-info:active,.btn-info.disabled.active,.btn-info[disabled].active,fieldset[disabled] .btn-info.active{background-color:#3186a0;border-color:#010304}
-.btn-link{color:#303030;font-weight:normal;cursor:pointer;border-radius:0}.btn-link,.btn-link:active,.btn-link[disabled],fieldset[disabled] .btn-link{background-color:transparent;-webkit-box-shadow:none;box-shadow:none}
+.btn-link{color:#5f6990;font-weight:normal;cursor:pointer;border-radius:0}.btn-link,.btn-link:active,.btn-link[disabled],fieldset[disabled] .btn-link{background-color:transparent;-webkit-box-shadow:none;box-shadow:none}
 .btn-link,.btn-link:hover,.btn-link:focus,.btn-link:active{border-color:transparent}
-.btn-link:hover,.btn-link:focus{color:#0a0a0a;text-decoration:underline;background-color:transparent}
+.btn-link:hover,.btn-link:focus{color:#404862;text-decoration:underline;background-color:transparent}
 .btn-link[disabled]:hover,fieldset[disabled] .btn-link:hover,.btn-link[disabled]:focus,fieldset[disabled] .btn-link:focus{color:#999;text-decoration:none}
 .btn-lg{padding:8px 14px;font-size:15px;line-height:1.33;border-radius:5px}
 .btn-sm,.btn-xs{padding:3px 8px;font-size:11px;line-height:1.5;border-radius:2px}
@@ -486,7 +486,7 @@ textarea.input-group-lg>.form-control,textarea.input-group-lg>.input-group-addon
 textarea.input-group-sm>.form-control,textarea.input-group-sm>.input-group-addon,textarea.input-group-sm>.input-group-btn>.btn{height:auto}
 .input-group-addon,.input-group-btn,.input-group .form-control{display:table-cell}.input-group-addon:not(:first-child):not(:last-child),.input-group-btn:not(:first-child):not(:last-child),.input-group .form-control:not(:first-child):not(:last-child){border-radius:0}
 .input-group-addon,.input-group-btn{width:1%;white-space:nowrap;vertical-align:middle}
-.input-group-addon{padding:4px 10px;font-size:12px;font-weight:normal;line-height:1;text-align:center;background-color:#eee;border:1px solid #aaa;border-radius:3px}.input-group-addon.input-sm{padding:3px 8px;font-size:11px;border-radius:2px}
+.input-group-addon{padding:4px 10px;font-size:12px;font-weight:normal;line-height:1;text-align:center;background-color:#eee;border:1px solid #bfbfbf;border-radius:3px}.input-group-addon.input-sm{padding:3px 8px;font-size:11px;border-radius:2px}
 .input-group-addon.input-lg{padding:8px 14px;font-size:15px;border-radius:5px}
 .input-group-addon input[type="radio"],.input-group-addon input[type="checkbox"]{margin-top:0}
 .input-group .form-control:first-child,.input-group-addon:first-child,.input-group-btn:first-child>.btn,.input-group-btn:first-child>.dropdown-toggle,.input-group-btn:last-child>.btn:not(:last-child):not(.dropdown-toggle){border-bottom-right-radius:0;border-top-right-radius:0}
@@ -502,7 +502,7 @@ textarea.input-group-sm>.form-control,textarea.input-group-sm>.input-group-addon
 .nav:after{clear:both}
 .nav>li{position:relative;display:block}.nav>li>a{position:relative;display:block;padding:4px 10px}.nav>li>a:hover,.nav>li>a:focus{text-decoration:none;background-color:#eee}
 .nav>li.disabled>a{color:#999}.nav>li.disabled>a:hover,.nav>li.disabled>a:focus{color:#999;text-decoration:none;background-color:transparent;cursor:not-allowed}
-.nav .open>a,.nav .open>a:hover,.nav .open>a:focus{background-color:#eee;border-color:#303030}
+.nav .open>a,.nav .open>a:hover,.nav .open>a:focus{background-color:#eee;border-color:#5f6990}
 .nav .nav-divider{height:1px;margin:7.5px 0;overflow:hidden;background-color:#e5e5e5}
 .nav>li>a>img{max-width:none}
 .nav-tabs{border-bottom:1px solid #bfbfbf}.nav-tabs>li{float:left;margin-bottom:-1px}.nav-tabs>li>a{margin-right:2px;line-height:1.428571429;border:1px solid transparent;border-radius:3px 3px 0 0}.nav-tabs>li>a:hover{border-color:#eee #eee #bfbfbf}
@@ -526,8 +526,8 @@ textarea.input-group-sm>.form-control,textarea.input-group-sm>.input-group-addon
 .tabbable:after{clear:both}
 .tab-content>.tab-pane,.pill-content>.pill-pane{display:none}
 .tab-content>.active,.pill-content>.active{display:block}
-.nav .caret{border-top-color:#303030;border-bottom-color:#303030}
-.nav a:hover .caret{border-top-color:#0a0a0a;border-bottom-color:#0a0a0a}
+.nav .caret{border-top-color:#5f6990;border-bottom-color:#5f6990}
+.nav a:hover .caret{border-top-color:#404862;border-bottom-color:#404862}
 .nav-tabs .dropdown-menu{margin-top:-1px;border-top-right-radius:0;border-top-left-radius:0}
 .navbar{position:relative;z-index:1000;min-height:33px;margin-bottom:17px;border:1px solid transparent}.navbar:before,.navbar:after{content:" ";display:table;}
 .navbar:after{clear:both}
@@ -617,7 +617,7 @@ textarea.input-group-sm>.form-control,textarea.input-group-sm>.input-group-addon
 .badge{display:inline-block;min-width:10px;padding:3px 7px;font-size:11px;font-weight:bold;color:#fff;line-height:1;vertical-align:baseline;white-space:nowrap;text-align:center;background-color:#999;border-radius:10px}.badge:empty{display:none}
 a.badge:hover,a.badge:focus{color:#fff;text-decoration:none;cursor:pointer}
 .btn .badge{position:relative;top:-1px}
-a.list-group-item.active>.badge,.nav-pills>.active>a>.badge{color:#303030;background-color:#fff}
+a.list-group-item.active>.badge,.nav-pills>.active>a>.badge{color:#5f6990;background-color:#fff}
 .nav-pills>li>a>.badge{margin-left:3px}
 .jumbotron{padding:30px;margin-bottom:30px;font-size:18px;font-weight:200;line-height:2.1428571435;color:inherit;background-color:#eee}.jumbotron h1{line-height:1;color:inherit}
 .jumbotron p{line-height:1.4}
@@ -672,7 +672,7 @@ a.list-group-item:hover,a.list-group-item:focus{text-decoration:none;background-
 .panel>.list-group .list-group-item:last-child{border-bottom:0}
 .panel-heading+.list-group .list-group-item:first-child{border-top-width:0}
 .panel>.table{margin-bottom:0}
-.panel>.panel-body+.table{border-top:1px solid #d6b161}
+.panel>.panel-body+.table{border-top:1px solid #bfbfbf}
 .panel-heading{padding:10px 15px;border-bottom:1px solid transparent;border-top-right-radius:2px;border-top-left-radius:2px}
 .panel-title{margin-top:0;margin-bottom:0;font-size:14px}.panel-title>a{color:inherit}
 .panel-footer{padding:10px 15px;background-color:#f5f5f5;border-top:1px solid #bfbfbf;border-bottom-right-radius:2px;border-bottom-left-radius:2px}
@@ -1442,7 +1442,7 @@ html[dir="rtl"] .select2-container-multi .select2-search-choice-close{left:auto;
 .ui-portlet .portlet-backdrop,.ui-portlet-limited .portlet-backdrop,.ui-portlet-narrow .portlet-backdrop{display:none;z-index:10;position:absolute;top:0px;width:100%;height:100%;opacity:0.2;background:#fff;cursor:not-allowed}
 .ui-portlet-repeat,.ui-portlet-section,.ui-portlet-section{border:none;border-left:solid 3px #ebd9b2;border-radius:5px;margin-bottom:5px}.ui-portlet-repeat .portlet-header,.ui-portlet-section .portlet-header{background:#ebd9b2;border-radius:5px;border-bottom-left-radius:0px;border-top-left-radius:0px;padding:0px 2px}.ui-portlet-repeat .portlet-header .portlet-title-text,.ui-portlet-section .portlet-header .portlet-title-text{vertical-align:middle;line-height:20px !important}
 .ui-portlet-repeat .portlet-content,.ui-portlet-section .portlet-content{padding-right:0px}
-.ui-portlet-section{border-left:solid 3px #dfe5f9}.ui-portlet-section .portlet-header{background:#dfe5f9;border-bottom:solid #b4c2f1 1px}
+.ui-portlet-section{margin-top:5px;border-left:solid 3px #dfe5f9}.ui-portlet-section .portlet-header{background:#dfe5f9;border-bottom:solid #b4c2f1 1px}
 .ui-portlet-narrow{border:none}.ui-portlet-narrow .portlet-header{border-radius:3px}.ui-portlet-narrow .portlet-header .portlet-operations .ui-button-icon{margin-left:3px}
 .ui-portlet-narrow .ui-portlet-repeat .portlet-header,.ui-portlet-narrow .ui-portlet-section .portlet-header{border-radius:5px;border-bottom-left-radius:0px;border-top-left-radius:0px}
 .ui-portlet-narrow .portlet-content{padding:0px}
@@ -1450,7 +1450,7 @@ html[dir="rtl"] .select2-container-multi .select2-search-choice-close{left:auto;
 .ui-portlet-limited,.ui-portlet-narrow,.ui-portlet-narrow{max-width:900px}
 .ui-popover{max-width:700px;display:none}.ui-popover .popover-close{position:absolute;right:10px;top:7px;font-size:1.2em;cursor:pointer}
 .ui-popover .popover-title{padding:4px 10px}
-.ui-input,.ui-input-basic,.ui-textarea,.ui-options .ui-options-list,.ui-form-slider .ui-form-slider-text,.ui-select .select2-container-multi .select2-choices,.ui-select select,.ui-select .select2-container .select2-choice{width:100%;display:block;height:27px;padding:4px 10px;font-size:12px;line-height:1.428571429;color:#555;border:1px solid #aaa;border-radius:3px;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);background-image:none;background:transparent;-webkit-appearance:none;-moz-border-radius:3px}.ui-input[disabled],.ui-input[readonly],fieldset[disabled] .ui-input{cursor:not-allowed;background-color:#eee}
+.ui-input,.ui-input-basic,.ui-textarea,.ui-options .ui-options-list,.ui-form-slider .ui-form-slider-text,.ui-select .select2-container-multi .select2-choices,.ui-select select,.ui-select .select2-container .select2-choice{width:100%;display:block;height:27px;padding:4px 10px;font-size:12px;line-height:1.428571429;color:#555;border:1px solid #bfbfbf;border-radius:3px;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);background-image:none;background:transparent;-webkit-appearance:none;-moz-border-radius:3px}.ui-input[disabled],.ui-input[readonly],fieldset[disabled] .ui-input{cursor:not-allowed;background-color:#eee}
 .ui-input-basic,.ui-select select,.ui-select .select2-container .select2-choice,.ui-select select,.ui-select .select2-container .select2-choice{-webkit-box-shadow:inset 0 -1px 1px rgba(0,0,0,0.075);box-shadow:inset 0 -1px 1px rgba(0,0,0,0.075)}
 .ui-textarea{height:100px !important}
 .ui-options .ui-options-list{height:100% !important}.ui-options .ui-options-list input[type=checkbox],.ui-options .ui-options-list input[type=radio]{display:none}
@@ -1476,11 +1476,11 @@ html[dir="rtl"] .select2-container-multi .select2-search-choice-close{left:auto;
 .ui-select .select2-container-multi .select2-choices{padding:0px}
 .ui-select-multiple select{height:80px !important;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075)}
 .ui-select-content .ui-options{float:left;padding-top:2px}
-.select2-container .select2-choice,.select2-container .select2-choices{border:1px solid #aaa}
-.select2-dropdown-open .select2-choice,.select2-dropdown-open .select2-choices{border:1px solid #aaa;border-bottom-left-radius:0px ;border-bottom-right-radius:0px}
-.select2-dropdown-open.select2-drop-above .select2-choice,.select2-dropdown-open.select2-drop-above .select2-choices{border:1px solid #aaa;border-top-left-radius:0px;border-top-right-radius:0px}
-.select2-drop-active{border:1px solid #aaa;border-radius:3px;border-top-left-radius:0px;border-top-right-radius:0px}.select2-drop-active .select2-search{padding-top:5px}
-.select2-drop.select2-drop-above.select2-drop-active{border:1px solid #aaa;border-radius:3px;border-bottom-left-radius:0px;border-bottom-right-radius:0px}.select2-drop.select2-drop-above.select2-drop-active .select2-search{padding-top:0px}
+.select2-container .select2-choice,.select2-container .select2-choices{border:1px solid #bfbfbf}
+.select2-dropdown-open .select2-choice,.select2-dropdown-open .select2-choices{border:1px solid #bfbfbf;border-bottom-left-radius:0px ;border-bottom-right-radius:0px}
+.select2-dropdown-open.select2-drop-above .select2-choice,.select2-dropdown-open.select2-drop-above .select2-choices{border:1px solid #bfbfbf;border-top-left-radius:0px;border-top-right-radius:0px}
+.select2-drop-active{border:1px solid #bfbfbf;border-radius:3px;border-top-left-radius:0px;border-top-right-radius:0px}.select2-drop-active .select2-search{padding-top:5px}
+.select2-drop.select2-drop-above.select2-drop-active{border:1px solid #bfbfbf;border-radius:3px;border-bottom-left-radius:0px;border-bottom-right-radius:0px}.select2-drop.select2-drop-above.select2-drop-active .select2-search{padding-top:0px}
 .libraryRow{background-color:#ebd9b2}
 .datasetHighlighted{background-color:#f9f9f9}
 .libraryItemDeleted-True{font-style:italic}
@@ -1832,7 +1832,7 @@ div.form-row-error-message{width:300px;float:left;color:red;font-weight:bold;pad
 select{padding:2px;font-size:12px;line-height:1.428571429}
 select,input,textarea{font:inherit}
 .form-row select,.form-row textarea,.form-row input[type="text"],.form-row input[type="file"],.form-row input[type="password"]{max-width:90%}
-textarea,input[type="text"],input[type="password"]{font-size:12px;line-height:1.428571429;border:1px solid #aaa;padding:3px}
+textarea,input[type="text"],input[type="password"]{font-size:12px;line-height:1.428571429;border:1px solid #bfbfbf;padding:3px}
 input[type="submit"],button{display:inline-block;padding:4px 10px;margin-bottom:0;font-size:12px;font-weight:normal;line-height:1.428571429;text-align:center;vertical-align:middle;cursor:pointer;border:1px solid transparent;border-radius:3px;white-space:nowrap;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;white-space:normal;color:#333;background-color:#f2f2f2;border-color:#bfbfbf}input[type="submit"]:focus,button:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px}
 input[type="submit"]:hover,button:hover,input[type="submit"]:focus,button:focus{color:#333;text-decoration:none}
 input[type="submit"]:active,button:active,input[type="submit"].active,button.active{outline:0;background-image:none;-webkit-box-shadow:inset 0 3px 5px rgba(0,0,0,0.125);box-shadow:inset 0 3px 5px rgba(0,0,0,0.125)}
@@ -1843,7 +1843,7 @@ input[type="submit"].disabled,button.disabled,input[type="submit"][disabled],but
 input[type="submit"].btn-primary,button.btn-primary{color:#fff;background-color:#5f6990;border-color:#0e0f15}input[type="submit"].btn-primary:hover,button.btn-primary:hover,input[type="submit"].btn-primary:focus,button.btn-primary:focus,input[type="submit"].btn-primary:active,button.btn-primary:active,input[type="submit"].btn-primary.active,button.btn-primary.active,.open .dropdown-toggleinput[type="submit"].btn-primary,.open .dropdown-togglebutton.btn-primary{color:#fff;background-color:#4e5777;border-color:#000}
 input[type="submit"].btn-primary:active,button.btn-primary:active,input[type="submit"].btn-primary.active,button.btn-primary.active,.open .dropdown-toggleinput[type="submit"].btn-primary,.open .dropdown-togglebutton.btn-primary{background-image:none}
 input[type="submit"].btn-primary.disabled,button.btn-primary.disabled,input[type="submit"].btn-primary[disabled],button.btn-primary[disabled],fieldset[disabled] input[type="submit"].btn-primary,fieldset[disabled] button.btn-primary,input[type="submit"].btn-primary.disabled:hover,button.btn-primary.disabled:hover,input[type="submit"].btn-primary[disabled]:hover,button.btn-primary[disabled]:hover,fieldset[disabled] input[type="submit"].btn-primary:hover,fieldset[disabled] button.btn-primary:hover,input[type="submit"].btn-primary.disabled:focus,button.btn-primary.disabled:focus,input[type="submit"].btn-primary[disabled]:focus,button.btn-primary[disabled]:focus,fieldset[disabled] input[type="submit"].btn-primary:focus,fieldset[disabled] button.btn-primary:focus,input[type="submit"].btn-primary.disabled:active,button.btn-primary.disabled:active,input[type="submit"].btn-primary[disabled]:active,button.btn-primary[disabled]:active,fieldset[disabled] input[type="submit"].btn-primary:active,fieldset[disabled] button.btn-primary:active,input[type="submit"].btn-primary.disabled.active,button.btn-primary.disabled.active,input[type="submit"].btn-primary[disabled].active,button.btn-primary[disabled].active,fieldset[disabled] input[type="submit"].btn-primary.active,fieldset[disabled] button.btn-primary.active{background-color:#5f6990;border-color:#0e0f15}
-.search-query{display:inline-block;padding:4px;font-size:12px;line-height:1.428571429;color:#555;border:1px solid #aaa;padding-left:14px !important;padding-right:14px;margin-bottom:0;-webkit-border-radius:14px;-moz-border-radius:14px;border-radius:14px;max-width:auto}
+.search-query{display:inline-block;padding:4px;font-size:12px;line-height:1.428571429;color:#555;border:1px solid #bfbfbf;padding-left:14px !important;padding-right:14px;margin-bottom:0;-webkit-border-radius:14px;-moz-border-radius:14px;border-radius:14px;max-width:auto}
 .search-query:focus{border-color:rgba(24,132,218,0.8);-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075),0 0 8px rgba(82,168,236,0.6);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075),0 0 8px rgba(82,168,236,0.6);outline:0;outline:thin dotted \9;}
 .search-spinner{position:absolute;display:none;right:6px;top:9px}
 #search-clear-btn{position:absolute;right:6px;top:9px;display:block;font-size:1.4em !important;text-decoration:none;color:#888;display:inline-block;font:normal normal normal 14px/1 FontAwesome;font-size:inherit;text-rendering:auto;-moz-osx-font-smoothing:grayscale;font-family:FontAwesome;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale}#search-clear-btn:before{content:"\f057"}
@@ -1884,9 +1884,9 @@ table.tabletip{width:100%;border-collapse:collapse;text-align:left}
 table.tabletip th{white-space:nowrap;border-bottom:1px solid #444;padding-right:3px}
 table.tabletip td{border-bottom:1px solid #ddd}
 table.tabletip tbody tr:hover td{background-color:#eee}
-table.colored{border-top:solid #d6b161 1px;border-bottom:solid #d6b161 1px}
+table.colored{border-top:solid #bfbfbf 1px;border-bottom:solid #bfbfbf 1px}
 table.colored td,table.colored th{text-align:left;padding:5px;line-height:1.428571429}
-table.colored tr.header{background:#ebd9b2;color:#000;background-repeat:repeat-x;background-position:top;border-bottom:solid #d6b161 1px;font-weight:bold}
+table.colored tr.header{background:#ebd9b2;color:#000;background-repeat:repeat-x;background-position:top;border-bottom:solid #bfbfbf 1px;font-weight:bold}
 table.colored tr{background:#fff}
 table.colored tr.odd_row{background:#f9f9f9}
 div.debug{margin:10px;padding:5px;background:#FFFF99;border:solid #FFFF33 1px;color:black}
@@ -1897,7 +1897,7 @@ div.debug{margin:10px;padding:5px;background:#FFFF99;border:solid #FFFF33 1px;co
 .grid tbody td,.ui-table tbody td,.ui-table-plain tbody td{line-height:1.428571429;border-top:solid #DDDDDD 1px;border-bottom:solid #DDDDDD 1px;padding:5px}
 .grid tbody td:empty{padding:0}
 .grid thead tr{height:2em}
-.grid thead th{line-height:1.428571429;background:#ebd9b2;color:#000;border-top:solid #d6b161 1px;border-bottom:solid #d6b161 1px;padding:5px;text-align:left;white-space:nowrap}
+.grid thead th{line-height:1.428571429;background:#ebd9b2;color:#000;border-top:solid #bfbfbf 1px;border-bottom:solid #bfbfbf 1px;padding:5px;text-align:left;white-space:nowrap}
 .grid tfoot td{background-color:#F8F8F8;border-top:solid #DDDDDD 1px;border-bottom:solid #DDDDDD 1px;padding:5px}
 .grid .current{background-color:#EEEEFF}
 .count-box{min-width:1.1em;padding:5px;border-width:1px;border-style:solid;text-align:center;display:inline-block}
@@ -2265,7 +2265,7 @@ pre.peek table,pre.peek th,pre.peek tr,pre.peek td{font-family:Monaco,Menlo,Cons
 .collection-creator .footer .actions .other-options>*{display:none;margin-left:4px}
 .search-input .search-query{width:100%;padding-right:24px}
 .search-input .search-clear,.search-input .search-loading{position:relative;display:inline-block;float:right;margin-top:-24px;margin-right:4px;font-size:1.4em;line-height:23px;color:grey}
-.search-input .search-clear:hover{color:#303030}
+.search-input .search-clear:hover{color:#5f6990}
 .dataset-choice{border:1px solid lightgrey;border-radius:3px;overflow:hidden;padding:10px 8px 8px 8px}.dataset-choice:hover{border-color:black;cursor:pointer}.dataset-choice:hover>*{cursor:pointer}
 .dataset-choice .prompt{margin-right:8px}.dataset-choice .prompt:after{content:':'}
 .dataset-choice .prompt:empty{display:none}
diff --git a/static/style/src/less/ui.less b/static/style/src/less/ui.less
index ef8b2d0acb5..adf9a0fe5b2 100644
--- a/static/style/src/less/ui.less
+++ b/static/style/src/less/ui.less
@@ -272,6 +272,7 @@
 
 .ui-portlet-section {
     &:extend(.ui-portlet-repeat all);
+    margin-top: @ui-margin-vertical;
     border-left: solid 3px @side-panel-bg;
     .portlet-header {
         background: @side-panel-bg;

From 0279d6010ab4f72146582ae0277f2873f3150221 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 25 Mar 2015 22:56:09 -0400
Subject: [PATCH 11/88] Repack styles, packing fails sometimes

---
 static/style/blue/base.css | 54 +++++++++++++++++++-------------------
 1 file changed, 27 insertions(+), 27 deletions(-)

diff --git a/static/style/blue/base.css b/static/style/blue/base.css
index 5edc7a740dd..27c0ed68afc 100644
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -41,7 +41,7 @@ html{font-size:62.5%;-webkit-tap-highlight-color:rgba(0,0,0,0)}
 body{font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;font-size:12px;line-height:1.428571429;color:#333;background-color:#fff}
 input,button,select,textarea{font-family:inherit;font-size:inherit;line-height:inherit}
 button,input,select[multiple],textarea{background-image:none}
-a{color:#5f6990;text-decoration:none}a:hover,a:focus{color:#404862;text-decoration:underline}
+a{color:#303030;text-decoration:none}a:hover,a:focus{color:#0a0a0a;text-decoration:underline}
 a:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px}
 img{vertical-align:middle}
 .img-responsive{display:block;max-width:100%;height:auto}
@@ -114,13 +114,13 @@ address{display:block;margin-bottom:17px;font-style:normal;line-height:1.4285714
 .col-xs-12{width:100%}
 @media (min-width:768px){.container{max-width:750px} .col-sm-1,.col-sm-2,.col-sm-3,.col-sm-4,.col-sm-5,.col-sm-6,.col-sm-7,.col-sm-8,.col-sm-9,.col-sm-10,.col-sm-11{float:left} .col-sm-1{width:8.333333333333332%} .col-sm-2{width:16.666666666666664%} .col-sm-3{width:25%} .col-sm-4{width:33.33333333333333%} .col-sm-5{width:41.66666666666667%} .col-sm-6{width:50%} .col-sm-7{width:58.333333333333336%} .col-sm-8{width:66.66666666666666%} .col-sm-9{width:75%} .col-sm-10{width:83.33333333333334%} .col-sm-11{width:91.66666666666666%} .col-sm-12{width:100%} .col-sm-push-1{left:8.333333333333332%} .col-sm-push-2{left:16.666666666666664%} .col-sm-push-3{left:25%} .col-sm-push-4{left:33.33333333333333%} .col-sm-push-5{left:41.66666666666667%} .col-sm-push-6{left:50%} .col-sm-push-7{left:58.333333333333336%} .col-sm-push-8{left:66.66666666666666%} .col-sm-push-9{left:75%} .col-sm-push-10{left:83.33333333333334%} .col-sm-push-11{left:91.66666666666666%} .col-sm-pull-1{right:8.333333333333332%} .col-sm-pull-2{right:16.666666666666664%} .col-sm-pull-3{right:25%} .col-sm-pull-4{right:33.33333333333333%} .col-sm-pull-5{right:41.66666666666667%} .col-sm-pull-6{right:50%} .col-sm-pull-7{right:58.333333333333336%} .col-sm-pull-8{right:66.66666666666666%} .col-sm-pull-9{right:75%} .col-sm-pull-10{right:83.33333333333334%} .col-sm-pull-11{right:91.66666666666666%} .col-sm-offset-1{margin-left:8.333333333333332%} .col-sm-offset-2{margin-left:16.666666666666664%} .col-sm-offset-3{margin-left:25%} .col-sm-offset-4{margin-left:33.33333333333333%} .col-sm-offset-5{margin-left:41.66666666666667%} .col-sm-offset-6{margin-left:50%} .col-sm-offset-7{margin-left:58.333333333333336%} .col-sm-offset-8{margin-left:66.66666666666666%} .col-sm-offset-9{margin-left:75%} .col-sm-offset-10{margin-left:83.33333333333334%} .col-sm-offset-11{margin-left:91.66666666666666%}}@media (min-width:992px){.container{max-width:970px} .col-md-1,.col-md-2,.col-md-3,.col-md-4,.col-md-5,.col-md-6,.col-md-7,.col-md-8,.col-md-9,.col-md-10,.col-md-11{float:left} .col-md-1{width:8.333333333333332%} .col-md-2{width:16.666666666666664%} .col-md-3{width:25%} .col-md-4{width:33.33333333333333%} .col-md-5{width:41.66666666666667%} .col-md-6{width:50%} .col-md-7{width:58.333333333333336%} .col-md-8{width:66.66666666666666%} .col-md-9{width:75%} .col-md-10{width:83.33333333333334%} .col-md-11{width:91.66666666666666%} .col-md-12{width:100%} .col-md-push-0{left:auto} .col-md-push-1{left:8.333333333333332%} .col-md-push-2{left:16.666666666666664%} .col-md-push-3{left:25%} .col-md-push-4{left:33.33333333333333%} .col-md-push-5{left:41.66666666666667%} .col-md-push-6{left:50%} .col-md-push-7{left:58.333333333333336%} .col-md-push-8{left:66.66666666666666%} .col-md-push-9{left:75%} .col-md-push-10{left:83.33333333333334%} .col-md-push-11{left:91.66666666666666%} .col-md-pull-0{right:auto} .col-md-pull-1{right:8.333333333333332%} .col-md-pull-2{right:16.666666666666664%} .col-md-pull-3{right:25%} .col-md-pull-4{right:33.33333333333333%} .col-md-pull-5{right:41.66666666666667%} .col-md-pull-6{right:50%} .col-md-pull-7{right:58.333333333333336%} .col-md-pull-8{right:66.66666666666666%} .col-md-pull-9{right:75%} .col-md-pull-10{right:83.33333333333334%} .col-md-pull-11{right:91.66666666666666%} .col-md-offset-0{margin-left:0} .col-md-offset-1{margin-left:8.333333333333332%} .col-md-offset-2{margin-left:16.666666666666664%} .col-md-offset-3{margin-left:25%} .col-md-offset-4{margin-left:33.33333333333333%} .col-md-offset-5{margin-left:41.66666666666667%} .col-md-offset-6{margin-left:50%} .col-md-offset-7{margin-left:58.333333333333336%} .col-md-offset-8{margin-left:66.66666666666666%} .col-md-offset-9{margin-left:75%} .col-md-offset-10{margin-left:83.33333333333334%} .col-md-offset-11{margin-left:91.66666666666666%}}@media (min-width:1200px){.container{max-width:1170px} .col-lg-1,.col-lg-2,.col-lg-3,.col-lg-4,.col-lg-5,.col-lg-6,.col-lg-7,.col-lg-8,.col-lg-9,.col-lg-10,.col-lg-11{float:left} .col-lg-1{width:8.333333333333332%} .col-lg-2{width:16.666666666666664%} .col-lg-3{width:25%} .col-lg-4{width:33.33333333333333%} .col-lg-5{width:41.66666666666667%} .col-lg-6{width:50%} .col-lg-7{width:58.333333333333336%} .col-lg-8{width:66.66666666666666%} .col-lg-9{width:75%} .col-lg-10{width:83.33333333333334%} .col-lg-11{width:91.66666666666666%} .col-lg-12{width:100%} .col-lg-push-0{left:auto} .col-lg-push-1{left:8.333333333333332%} .col-lg-push-2{left:16.666666666666664%} .col-lg-push-3{left:25%} .col-lg-push-4{left:33.33333333333333%} .col-lg-push-5{left:41.66666666666667%} .col-lg-push-6{left:50%} .col-lg-push-7{left:58.333333333333336%} .col-lg-push-8{left:66.66666666666666%} .col-lg-push-9{left:75%} .col-lg-push-10{left:83.33333333333334%} .col-lg-push-11{left:91.66666666666666%} .col-lg-pull-0{right:auto} .col-lg-pull-1{right:8.333333333333332%} .col-lg-pull-2{right:16.666666666666664%} .col-lg-pull-3{right:25%} .col-lg-pull-4{right:33.33333333333333%} .col-lg-pull-5{right:41.66666666666667%} .col-lg-pull-6{right:50%} .col-lg-pull-7{right:58.333333333333336%} .col-lg-pull-8{right:66.66666666666666%} .col-lg-pull-9{right:75%} .col-lg-pull-10{right:83.33333333333334%} .col-lg-pull-11{right:91.66666666666666%} .col-lg-offset-0{margin-left:0} .col-lg-offset-1{margin-left:8.333333333333332%} .col-lg-offset-2{margin-left:16.666666666666664%} .col-lg-offset-3{margin-left:25%} .col-lg-offset-4{margin-left:33.33333333333333%} .col-lg-offset-5{margin-left:41.66666666666667%} .col-lg-offset-6{margin-left:50%} .col-lg-offset-7{margin-left:58.333333333333336%} .col-lg-offset-8{margin-left:66.66666666666666%} .col-lg-offset-9{margin-left:75%} .col-lg-offset-10{margin-left:83.33333333333334%} .col-lg-offset-11{margin-left:91.66666666666666%}}table{max-width:100%;background-color:transparent}
 th{text-align:left}
-.table{width:100%;margin-bottom:17px}.table thead>tr>th,.table tbody>tr>th,.table tfoot>tr>th,.table thead>tr>td,.table tbody>tr>td,.table tfoot>tr>td{padding:8px;line-height:1.428571429;vertical-align:top;border-top:1px solid #bfbfbf}
-.table thead>tr>th{vertical-align:bottom;border-bottom:2px solid #bfbfbf}
+.table{width:100%;margin-bottom:17px}.table thead>tr>th,.table tbody>tr>th,.table tfoot>tr>th,.table thead>tr>td,.table tbody>tr>td,.table tfoot>tr>td{padding:8px;line-height:1.428571429;vertical-align:top;border-top:1px solid #d6b161}
+.table thead>tr>th{vertical-align:bottom;border-bottom:2px solid #d6b161}
 .table caption+thead tr:first-child th,.table colgroup+thead tr:first-child th,.table thead:first-child tr:first-child th,.table caption+thead tr:first-child td,.table colgroup+thead tr:first-child td,.table thead:first-child tr:first-child td{border-top:0}
-.table tbody+tbody{border-top:2px solid #bfbfbf}
+.table tbody+tbody{border-top:2px solid #d6b161}
 .table .table{background-color:#fff}
 .table-condensed thead>tr>th,.table-condensed tbody>tr>th,.table-condensed tfoot>tr>th,.table-condensed thead>tr>td,.table-condensed tbody>tr>td,.table-condensed tfoot>tr>td{padding:5px}
-.table-bordered{border:1px solid #bfbfbf}.table-bordered>thead>tr>th,.table-bordered>tbody>tr>th,.table-bordered>tfoot>tr>th,.table-bordered>thead>tr>td,.table-bordered>tbody>tr>td,.table-bordered>tfoot>tr>td{border:1px solid #bfbfbf}
+.table-bordered{border:1px solid #d6b161}.table-bordered>thead>tr>th,.table-bordered>tbody>tr>th,.table-bordered>tfoot>tr>th,.table-bordered>thead>tr>td,.table-bordered>tbody>tr>td,.table-bordered>tfoot>tr>td{border:1px solid #d6b161}
 .table-bordered>thead>tr>th,.table-bordered>thead>tr>td{border-bottom-width:2px}
 .table-striped>tbody>tr:nth-child(odd)>td,.table-striped>tbody>tr:nth-child(odd)>th{background-color:#f9f9f9}
 .table-hover>tbody>tr:hover>td,.table-hover>tbody>tr:hover>th{background-color:#f5f5f5}
@@ -133,7 +133,7 @@ table td[class*="col-"],table th[class*="col-"]{float:none;display:table-cell}
 .table-hover>tbody>tr>td.danger:hover,.table-hover>tbody>tr>th.danger:hover,.table-hover>tbody>tr.danger:hover>td,.table-hover>tbody>tr.danger:hover>th{background-color:#f7b0ae;border-color:#c61913}
 .table>thead>tr>td.warning,.table>tbody>tr>td.warning,.table>tfoot>tr>td.warning,.table>thead>tr>th.warning,.table>tbody>tr>th.warning,.table>tfoot>tr>th.warning,.table>thead>tr.warning>td,.table>tbody>tr.warning>td,.table>tfoot>tr.warning>td,.table>thead>tr.warning>th,.table>tbody>tr.warning>th,.table>tfoot>tr.warning>th{background-color:#fce1ba;border-color:#e28709}
 .table-hover>tbody>tr>td.warning:hover,.table-hover>tbody>tr>th.warning:hover,.table-hover>tbody>tr.warning:hover>td,.table-hover>tbody>tr.warning:hover>th{background-color:#fbd6a2;border-color:#c97908}
-@media (max-width:768px){.table-responsive{width:100%;margin-bottom:15px;overflow-y:hidden;overflow-x:scroll;-ms-overflow-style:-ms-autohiding-scrollbar;border:1px solid #bfbfbf;-webkit-overflow-scrolling:touch}.table-responsive>.table{margin-bottom:0;background-color:#fff}.table-responsive>.table>thead>tr>th,.table-responsive>.table>tbody>tr>th,.table-responsive>.table>tfoot>tr>th,.table-responsive>.table>thead>tr>td,.table-responsive>.table>tbody>tr>td,.table-responsive>.table>tfoot>tr>td{white-space:nowrap} .table-responsive>.table-bordered{border:0}.table-responsive>.table-bordered>thead>tr>th:first-child,.table-responsive>.table-bordered>tbody>tr>th:first-child,.table-responsive>.table-bordered>tfoot>tr>th:first-child,.table-responsive>.table-bordered>thead>tr>td:first-child,.table-responsive>.table-bordered>tbody>tr>td:first-child,.table-responsive>.table-bordered>tfoot>tr>td:first-child{border-left:0} .table-responsive>.table-bordered>thead>tr>th:last-child,.table-responsive>.table-bordered>tbody>tr>th:last-child,.table-responsive>.table-bordered>tfoot>tr>th:last-child,.table-responsive>.table-bordered>thead>tr>td:last-child,.table-responsive>.table-bordered>tbody>tr>td:last-child,.table-responsive>.table-bordered>tfoot>tr>td:last-child{border-right:0} .table-responsive>.table-bordered>thead>tr:last-child>th,.table-responsive>.table-bordered>tbody>tr:last-child>th,.table-responsive>.table-bordered>tfoot>tr:last-child>th,.table-responsive>.table-bordered>thead>tr:last-child>td,.table-responsive>.table-bordered>tbody>tr:last-child>td,.table-responsive>.table-bordered>tfoot>tr:last-child>td{border-bottom:0}}fieldset{padding:0;margin:0;border:0}
+@media (max-width:768px){.table-responsive{width:100%;margin-bottom:15px;overflow-y:hidden;overflow-x:scroll;-ms-overflow-style:-ms-autohiding-scrollbar;border:1px solid #d6b161;-webkit-overflow-scrolling:touch}.table-responsive>.table{margin-bottom:0;background-color:#fff}.table-responsive>.table>thead>tr>th,.table-responsive>.table>tbody>tr>th,.table-responsive>.table>tfoot>tr>th,.table-responsive>.table>thead>tr>td,.table-responsive>.table>tbody>tr>td,.table-responsive>.table>tfoot>tr>td{white-space:nowrap} .table-responsive>.table-bordered{border:0}.table-responsive>.table-bordered>thead>tr>th:first-child,.table-responsive>.table-bordered>tbody>tr>th:first-child,.table-responsive>.table-bordered>tfoot>tr>th:first-child,.table-responsive>.table-bordered>thead>tr>td:first-child,.table-responsive>.table-bordered>tbody>tr>td:first-child,.table-responsive>.table-bordered>tfoot>tr>td:first-child{border-left:0} .table-responsive>.table-bordered>thead>tr>th:last-child,.table-responsive>.table-bordered>tbody>tr>th:last-child,.table-responsive>.table-bordered>tfoot>tr>th:last-child,.table-responsive>.table-bordered>thead>tr>td:last-child,.table-responsive>.table-bordered>tbody>tr>td:last-child,.table-responsive>.table-bordered>tfoot>tr>td:last-child{border-right:0} .table-responsive>.table-bordered>thead>tr:last-child>th,.table-responsive>.table-bordered>tbody>tr:last-child>th,.table-responsive>.table-bordered>tfoot>tr:last-child>th,.table-responsive>.table-bordered>thead>tr:last-child>td,.table-responsive>.table-bordered>tbody>tr:last-child>td,.table-responsive>.table-bordered>tfoot>tr:last-child>td{border-bottom:0}}fieldset{padding:0;margin:0;border:0}
 legend{display:block;width:100%;padding:0;margin-bottom:17px;font-size:18px;line-height:inherit;color:#333;border:0;border-bottom:1px solid #bfbfbf}
 label{display:inline-block;margin-bottom:5px;font-weight:bold}
 input[type="search"]{-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box}
@@ -148,7 +148,7 @@ output{display:block;padding-top:5px;font-size:12px;line-height:1.428571429;colo
 .form-control::-moz-placeholder{color:#999}
 .form-control:-ms-input-placeholder{color:#999}
 .form-control::-webkit-input-placeholder{color:#999}
-.form-control{display:block;width:100%;height:27px;padding:4px 10px;font-size:12px;line-height:1.428571429;color:#555;vertical-align:middle;background-color:#fff;border:1px solid #bfbfbf;border-radius:3px;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);-webkit-transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s;transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s}.form-control:focus{border-color:#66afe9;outline:0;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6)}
+.form-control{display:block;width:100%;height:27px;padding:4px 10px;font-size:12px;line-height:1.428571429;color:#555;vertical-align:middle;background-color:#fff;border:1px solid #aaa;border-radius:3px;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);-webkit-transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s;transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s}.form-control:focus{border-color:#66afe9;outline:0;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6)}
 .form-control[disabled],.form-control[readonly],fieldset[disabled] .form-control{cursor:not-allowed;background-color:#eee}
 textarea.form-control{height:auto}
 .form-group{margin-bottom:15px}
@@ -202,9 +202,9 @@ textarea.input-lg{height:auto}
 .btn-info{color:#fff;background-color:#3186a0;border-color:#010304}.btn-info:hover,.btn-info:focus,.btn-info:active,.btn-info.active,.open .dropdown-toggle.btn-info{color:#fff;background-color:#276c81;border-color:#000}
 .btn-info:active,.btn-info.active,.open .dropdown-toggle.btn-info{background-image:none}
 .btn-info.disabled,.btn-info[disabled],fieldset[disabled] .btn-info,.btn-info.disabled:hover,.btn-info[disabled]:hover,fieldset[disabled] .btn-info:hover,.btn-info.disabled:focus,.btn-info[disabled]:focus,fieldset[disabled] .btn-info:focus,.btn-info.disabled:active,.btn-info[disabled]:active,fieldset[disabled] .btn-info:active,.btn-info.disabled.active,.btn-info[disabled].active,fieldset[disabled] .btn-info.active{background-color:#3186a0;border-color:#010304}
-.btn-link{color:#5f6990;font-weight:normal;cursor:pointer;border-radius:0}.btn-link,.btn-link:active,.btn-link[disabled],fieldset[disabled] .btn-link{background-color:transparent;-webkit-box-shadow:none;box-shadow:none}
+.btn-link{color:#303030;font-weight:normal;cursor:pointer;border-radius:0}.btn-link,.btn-link:active,.btn-link[disabled],fieldset[disabled] .btn-link{background-color:transparent;-webkit-box-shadow:none;box-shadow:none}
 .btn-link,.btn-link:hover,.btn-link:focus,.btn-link:active{border-color:transparent}
-.btn-link:hover,.btn-link:focus{color:#404862;text-decoration:underline;background-color:transparent}
+.btn-link:hover,.btn-link:focus{color:#0a0a0a;text-decoration:underline;background-color:transparent}
 .btn-link[disabled]:hover,fieldset[disabled] .btn-link:hover,.btn-link[disabled]:focus,fieldset[disabled] .btn-link:focus{color:#999;text-decoration:none}
 .btn-lg{padding:8px 14px;font-size:15px;line-height:1.33;border-radius:5px}
 .btn-sm,.btn-xs{padding:3px 8px;font-size:11px;line-height:1.5;border-radius:2px}
@@ -486,7 +486,7 @@ textarea.input-group-lg>.form-control,textarea.input-group-lg>.input-group-addon
 textarea.input-group-sm>.form-control,textarea.input-group-sm>.input-group-addon,textarea.input-group-sm>.input-group-btn>.btn{height:auto}
 .input-group-addon,.input-group-btn,.input-group .form-control{display:table-cell}.input-group-addon:not(:first-child):not(:last-child),.input-group-btn:not(:first-child):not(:last-child),.input-group .form-control:not(:first-child):not(:last-child){border-radius:0}
 .input-group-addon,.input-group-btn{width:1%;white-space:nowrap;vertical-align:middle}
-.input-group-addon{padding:4px 10px;font-size:12px;font-weight:normal;line-height:1;text-align:center;background-color:#eee;border:1px solid #bfbfbf;border-radius:3px}.input-group-addon.input-sm{padding:3px 8px;font-size:11px;border-radius:2px}
+.input-group-addon{padding:4px 10px;font-size:12px;font-weight:normal;line-height:1;text-align:center;background-color:#eee;border:1px solid #aaa;border-radius:3px}.input-group-addon.input-sm{padding:3px 8px;font-size:11px;border-radius:2px}
 .input-group-addon.input-lg{padding:8px 14px;font-size:15px;border-radius:5px}
 .input-group-addon input[type="radio"],.input-group-addon input[type="checkbox"]{margin-top:0}
 .input-group .form-control:first-child,.input-group-addon:first-child,.input-group-btn:first-child>.btn,.input-group-btn:first-child>.dropdown-toggle,.input-group-btn:last-child>.btn:not(:last-child):not(.dropdown-toggle){border-bottom-right-radius:0;border-top-right-radius:0}
@@ -502,7 +502,7 @@ textarea.input-group-sm>.form-control,textarea.input-group-sm>.input-group-addon
 .nav:after{clear:both}
 .nav>li{position:relative;display:block}.nav>li>a{position:relative;display:block;padding:4px 10px}.nav>li>a:hover,.nav>li>a:focus{text-decoration:none;background-color:#eee}
 .nav>li.disabled>a{color:#999}.nav>li.disabled>a:hover,.nav>li.disabled>a:focus{color:#999;text-decoration:none;background-color:transparent;cursor:not-allowed}
-.nav .open>a,.nav .open>a:hover,.nav .open>a:focus{background-color:#eee;border-color:#5f6990}
+.nav .open>a,.nav .open>a:hover,.nav .open>a:focus{background-color:#eee;border-color:#303030}
 .nav .nav-divider{height:1px;margin:7.5px 0;overflow:hidden;background-color:#e5e5e5}
 .nav>li>a>img{max-width:none}
 .nav-tabs{border-bottom:1px solid #bfbfbf}.nav-tabs>li{float:left;margin-bottom:-1px}.nav-tabs>li>a{margin-right:2px;line-height:1.428571429;border:1px solid transparent;border-radius:3px 3px 0 0}.nav-tabs>li>a:hover{border-color:#eee #eee #bfbfbf}
@@ -526,8 +526,8 @@ textarea.input-group-sm>.form-control,textarea.input-group-sm>.input-group-addon
 .tabbable:after{clear:both}
 .tab-content>.tab-pane,.pill-content>.pill-pane{display:none}
 .tab-content>.active,.pill-content>.active{display:block}
-.nav .caret{border-top-color:#5f6990;border-bottom-color:#5f6990}
-.nav a:hover .caret{border-top-color:#404862;border-bottom-color:#404862}
+.nav .caret{border-top-color:#303030;border-bottom-color:#303030}
+.nav a:hover .caret{border-top-color:#0a0a0a;border-bottom-color:#0a0a0a}
 .nav-tabs .dropdown-menu{margin-top:-1px;border-top-right-radius:0;border-top-left-radius:0}
 .navbar{position:relative;z-index:1000;min-height:33px;margin-bottom:17px;border:1px solid transparent}.navbar:before,.navbar:after{content:" ";display:table;}
 .navbar:after{clear:both}
@@ -617,7 +617,7 @@ textarea.input-group-sm>.form-control,textarea.input-group-sm>.input-group-addon
 .badge{display:inline-block;min-width:10px;padding:3px 7px;font-size:11px;font-weight:bold;color:#fff;line-height:1;vertical-align:baseline;white-space:nowrap;text-align:center;background-color:#999;border-radius:10px}.badge:empty{display:none}
 a.badge:hover,a.badge:focus{color:#fff;text-decoration:none;cursor:pointer}
 .btn .badge{position:relative;top:-1px}
-a.list-group-item.active>.badge,.nav-pills>.active>a>.badge{color:#5f6990;background-color:#fff}
+a.list-group-item.active>.badge,.nav-pills>.active>a>.badge{color:#303030;background-color:#fff}
 .nav-pills>li>a>.badge{margin-left:3px}
 .jumbotron{padding:30px;margin-bottom:30px;font-size:18px;font-weight:200;line-height:2.1428571435;color:inherit;background-color:#eee}.jumbotron h1{line-height:1;color:inherit}
 .jumbotron p{line-height:1.4}
@@ -672,7 +672,7 @@ a.list-group-item:hover,a.list-group-item:focus{text-decoration:none;background-
 .panel>.list-group .list-group-item:last-child{border-bottom:0}
 .panel-heading+.list-group .list-group-item:first-child{border-top-width:0}
 .panel>.table{margin-bottom:0}
-.panel>.panel-body+.table{border-top:1px solid #bfbfbf}
+.panel>.panel-body+.table{border-top:1px solid #d6b161}
 .panel-heading{padding:10px 15px;border-bottom:1px solid transparent;border-top-right-radius:2px;border-top-left-radius:2px}
 .panel-title{margin-top:0;margin-bottom:0;font-size:14px}.panel-title>a{color:inherit}
 .panel-footer{padding:10px 15px;background-color:#f5f5f5;border-top:1px solid #bfbfbf;border-bottom-right-radius:2px;border-bottom-left-radius:2px}
@@ -1450,7 +1450,7 @@ html[dir="rtl"] .select2-container-multi .select2-search-choice-close{left:auto;
 .ui-portlet-limited,.ui-portlet-narrow,.ui-portlet-narrow{max-width:900px}
 .ui-popover{max-width:700px;display:none}.ui-popover .popover-close{position:absolute;right:10px;top:7px;font-size:1.2em;cursor:pointer}
 .ui-popover .popover-title{padding:4px 10px}
-.ui-input,.ui-input-basic,.ui-textarea,.ui-options .ui-options-list,.ui-form-slider .ui-form-slider-text,.ui-select .select2-container-multi .select2-choices,.ui-select select,.ui-select .select2-container .select2-choice{width:100%;display:block;height:27px;padding:4px 10px;font-size:12px;line-height:1.428571429;color:#555;border:1px solid #bfbfbf;border-radius:3px;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);background-image:none;background:transparent;-webkit-appearance:none;-moz-border-radius:3px}.ui-input[disabled],.ui-input[readonly],fieldset[disabled] .ui-input{cursor:not-allowed;background-color:#eee}
+.ui-input,.ui-input-basic,.ui-textarea,.ui-options .ui-options-list,.ui-form-slider .ui-form-slider-text,.ui-select .select2-container-multi .select2-choices,.ui-select select,.ui-select .select2-container .select2-choice{width:100%;display:block;height:27px;padding:4px 10px;font-size:12px;line-height:1.428571429;color:#555;border:1px solid #aaa;border-radius:3px;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);background-image:none;background:transparent;-webkit-appearance:none;-moz-border-radius:3px}.ui-input[disabled],.ui-input[readonly],fieldset[disabled] .ui-input{cursor:not-allowed;background-color:#eee}
 .ui-input-basic,.ui-select select,.ui-select .select2-container .select2-choice,.ui-select select,.ui-select .select2-container .select2-choice{-webkit-box-shadow:inset 0 -1px 1px rgba(0,0,0,0.075);box-shadow:inset 0 -1px 1px rgba(0,0,0,0.075)}
 .ui-textarea{height:100px !important}
 .ui-options .ui-options-list{height:100% !important}.ui-options .ui-options-list input[type=checkbox],.ui-options .ui-options-list input[type=radio]{display:none}
@@ -1476,11 +1476,11 @@ html[dir="rtl"] .select2-container-multi .select2-search-choice-close{left:auto;
 .ui-select .select2-container-multi .select2-choices{padding:0px}
 .ui-select-multiple select{height:80px !important;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075)}
 .ui-select-content .ui-options{float:left;padding-top:2px}
-.select2-container .select2-choice,.select2-container .select2-choices{border:1px solid #bfbfbf}
-.select2-dropdown-open .select2-choice,.select2-dropdown-open .select2-choices{border:1px solid #bfbfbf;border-bottom-left-radius:0px ;border-bottom-right-radius:0px}
-.select2-dropdown-open.select2-drop-above .select2-choice,.select2-dropdown-open.select2-drop-above .select2-choices{border:1px solid #bfbfbf;border-top-left-radius:0px;border-top-right-radius:0px}
-.select2-drop-active{border:1px solid #bfbfbf;border-radius:3px;border-top-left-radius:0px;border-top-right-radius:0px}.select2-drop-active .select2-search{padding-top:5px}
-.select2-drop.select2-drop-above.select2-drop-active{border:1px solid #bfbfbf;border-radius:3px;border-bottom-left-radius:0px;border-bottom-right-radius:0px}.select2-drop.select2-drop-above.select2-drop-active .select2-search{padding-top:0px}
+.select2-container .select2-choice,.select2-container .select2-choices{border:1px solid #aaa}
+.select2-dropdown-open .select2-choice,.select2-dropdown-open .select2-choices{border:1px solid #aaa;border-bottom-left-radius:0px ;border-bottom-right-radius:0px}
+.select2-dropdown-open.select2-drop-above .select2-choice,.select2-dropdown-open.select2-drop-above .select2-choices{border:1px solid #aaa;border-top-left-radius:0px;border-top-right-radius:0px}
+.select2-drop-active{border:1px solid #aaa;border-radius:3px;border-top-left-radius:0px;border-top-right-radius:0px}.select2-drop-active .select2-search{padding-top:5px}
+.select2-drop.select2-drop-above.select2-drop-active{border:1px solid #aaa;border-radius:3px;border-bottom-left-radius:0px;border-bottom-right-radius:0px}.select2-drop.select2-drop-above.select2-drop-active .select2-search{padding-top:0px}
 .libraryRow{background-color:#ebd9b2}
 .datasetHighlighted{background-color:#f9f9f9}
 .libraryItemDeleted-True{font-style:italic}
@@ -1832,7 +1832,7 @@ div.form-row-error-message{width:300px;float:left;color:red;font-weight:bold;pad
 select{padding:2px;font-size:12px;line-height:1.428571429}
 select,input,textarea{font:inherit}
 .form-row select,.form-row textarea,.form-row input[type="text"],.form-row input[type="file"],.form-row input[type="password"]{max-width:90%}
-textarea,input[type="text"],input[type="password"]{font-size:12px;line-height:1.428571429;border:1px solid #bfbfbf;padding:3px}
+textarea,input[type="text"],input[type="password"]{font-size:12px;line-height:1.428571429;border:1px solid #aaa;padding:3px}
 input[type="submit"],button{display:inline-block;padding:4px 10px;margin-bottom:0;font-size:12px;font-weight:normal;line-height:1.428571429;text-align:center;vertical-align:middle;cursor:pointer;border:1px solid transparent;border-radius:3px;white-space:nowrap;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;white-space:normal;color:#333;background-color:#f2f2f2;border-color:#bfbfbf}input[type="submit"]:focus,button:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px}
 input[type="submit"]:hover,button:hover,input[type="submit"]:focus,button:focus{color:#333;text-decoration:none}
 input[type="submit"]:active,button:active,input[type="submit"].active,button.active{outline:0;background-image:none;-webkit-box-shadow:inset 0 3px 5px rgba(0,0,0,0.125);box-shadow:inset 0 3px 5px rgba(0,0,0,0.125)}
@@ -1843,7 +1843,7 @@ input[type="submit"].disabled,button.disabled,input[type="submit"][disabled],but
 input[type="submit"].btn-primary,button.btn-primary{color:#fff;background-color:#5f6990;border-color:#0e0f15}input[type="submit"].btn-primary:hover,button.btn-primary:hover,input[type="submit"].btn-primary:focus,button.btn-primary:focus,input[type="submit"].btn-primary:active,button.btn-primary:active,input[type="submit"].btn-primary.active,button.btn-primary.active,.open .dropdown-toggleinput[type="submit"].btn-primary,.open .dropdown-togglebutton.btn-primary{color:#fff;background-color:#4e5777;border-color:#000}
 input[type="submit"].btn-primary:active,button.btn-primary:active,input[type="submit"].btn-primary.active,button.btn-primary.active,.open .dropdown-toggleinput[type="submit"].btn-primary,.open .dropdown-togglebutton.btn-primary{background-image:none}
 input[type="submit"].btn-primary.disabled,button.btn-primary.disabled,input[type="submit"].btn-primary[disabled],button.btn-primary[disabled],fieldset[disabled] input[type="submit"].btn-primary,fieldset[disabled] button.btn-primary,input[type="submit"].btn-primary.disabled:hover,button.btn-primary.disabled:hover,input[type="submit"].btn-primary[disabled]:hover,button.btn-primary[disabled]:hover,fieldset[disabled] input[type="submit"].btn-primary:hover,fieldset[disabled] button.btn-primary:hover,input[type="submit"].btn-primary.disabled:focus,button.btn-primary.disabled:focus,input[type="submit"].btn-primary[disabled]:focus,button.btn-primary[disabled]:focus,fieldset[disabled] input[type="submit"].btn-primary:focus,fieldset[disabled] button.btn-primary:focus,input[type="submit"].btn-primary.disabled:active,button.btn-primary.disabled:active,input[type="submit"].btn-primary[disabled]:active,button.btn-primary[disabled]:active,fieldset[disabled] input[type="submit"].btn-primary:active,fieldset[disabled] button.btn-primary:active,input[type="submit"].btn-primary.disabled.active,button.btn-primary.disabled.active,input[type="submit"].btn-primary[disabled].active,button.btn-primary[disabled].active,fieldset[disabled] input[type="submit"].btn-primary.active,fieldset[disabled] button.btn-primary.active{background-color:#5f6990;border-color:#0e0f15}
-.search-query{display:inline-block;padding:4px;font-size:12px;line-height:1.428571429;color:#555;border:1px solid #bfbfbf;padding-left:14px !important;padding-right:14px;margin-bottom:0;-webkit-border-radius:14px;-moz-border-radius:14px;border-radius:14px;max-width:auto}
+.search-query{display:inline-block;padding:4px;font-size:12px;line-height:1.428571429;color:#555;border:1px solid #aaa;padding-left:14px !important;padding-right:14px;margin-bottom:0;-webkit-border-radius:14px;-moz-border-radius:14px;border-radius:14px;max-width:auto}
 .search-query:focus{border-color:rgba(24,132,218,0.8);-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075),0 0 8px rgba(82,168,236,0.6);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075),0 0 8px rgba(82,168,236,0.6);outline:0;outline:thin dotted \9;}
 .search-spinner{position:absolute;display:none;right:6px;top:9px}
 #search-clear-btn{position:absolute;right:6px;top:9px;display:block;font-size:1.4em !important;text-decoration:none;color:#888;display:inline-block;font:normal normal normal 14px/1 FontAwesome;font-size:inherit;text-rendering:auto;-moz-osx-font-smoothing:grayscale;font-family:FontAwesome;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale}#search-clear-btn:before{content:"\f057"}
@@ -1884,9 +1884,9 @@ table.tabletip{width:100%;border-collapse:collapse;text-align:left}
 table.tabletip th{white-space:nowrap;border-bottom:1px solid #444;padding-right:3px}
 table.tabletip td{border-bottom:1px solid #ddd}
 table.tabletip tbody tr:hover td{background-color:#eee}
-table.colored{border-top:solid #bfbfbf 1px;border-bottom:solid #bfbfbf 1px}
+table.colored{border-top:solid #d6b161 1px;border-bottom:solid #d6b161 1px}
 table.colored td,table.colored th{text-align:left;padding:5px;line-height:1.428571429}
-table.colored tr.header{background:#ebd9b2;color:#000;background-repeat:repeat-x;background-position:top;border-bottom:solid #bfbfbf 1px;font-weight:bold}
+table.colored tr.header{background:#ebd9b2;color:#000;background-repeat:repeat-x;background-position:top;border-bottom:solid #d6b161 1px;font-weight:bold}
 table.colored tr{background:#fff}
 table.colored tr.odd_row{background:#f9f9f9}
 div.debug{margin:10px;padding:5px;background:#FFFF99;border:solid #FFFF33 1px;color:black}
@@ -1897,7 +1897,7 @@ div.debug{margin:10px;padding:5px;background:#FFFF99;border:solid #FFFF33 1px;co
 .grid tbody td,.ui-table tbody td,.ui-table-plain tbody td{line-height:1.428571429;border-top:solid #DDDDDD 1px;border-bottom:solid #DDDDDD 1px;padding:5px}
 .grid tbody td:empty{padding:0}
 .grid thead tr{height:2em}
-.grid thead th{line-height:1.428571429;background:#ebd9b2;color:#000;border-top:solid #bfbfbf 1px;border-bottom:solid #bfbfbf 1px;padding:5px;text-align:left;white-space:nowrap}
+.grid thead th{line-height:1.428571429;background:#ebd9b2;color:#000;border-top:solid #d6b161 1px;border-bottom:solid #d6b161 1px;padding:5px;text-align:left;white-space:nowrap}
 .grid tfoot td{background-color:#F8F8F8;border-top:solid #DDDDDD 1px;border-bottom:solid #DDDDDD 1px;padding:5px}
 .grid .current{background-color:#EEEEFF}
 .count-box{min-width:1.1em;padding:5px;border-width:1px;border-style:solid;text-align:center;display:inline-block}
@@ -2265,7 +2265,7 @@ pre.peek table,pre.peek th,pre.peek tr,pre.peek td{font-family:Monaco,Menlo,Cons
 .collection-creator .footer .actions .other-options>*{display:none;margin-left:4px}
 .search-input .search-query{width:100%;padding-right:24px}
 .search-input .search-clear,.search-input .search-loading{position:relative;display:inline-block;float:right;margin-top:-24px;margin-right:4px;font-size:1.4em;line-height:23px;color:grey}
-.search-input .search-clear:hover{color:#5f6990}
+.search-input .search-clear:hover{color:#303030}
 .dataset-choice{border:1px solid lightgrey;border-radius:3px;overflow:hidden;padding:10px 8px 8px 8px}.dataset-choice:hover{border-color:black;cursor:pointer}.dataset-choice:hover>*{cursor:pointer}
 .dataset-choice .prompt{margin-right:8px}.dataset-choice .prompt:after{content:':'}
 .dataset-choice .prompt:empty{display:none}

From a3cdf22e9f4fb8f61d9be20652b2aa3132808165 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 25 Mar 2015 23:03:03 -0400
Subject: [PATCH 12/88] Add minimal handling for sections to tool shed tool
 form preview

---
 templates/webapps/tool_shed/repository/tool_form.mako | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/templates/webapps/tool_shed/repository/tool_form.mako b/templates/webapps/tool_shed/repository/tool_form.mako
index 7025cf4e920..c3f86cd4d4d 100644
--- a/templates/webapps/tool_shed/repository/tool_form.mako
+++ b/templates/webapps/tool_shed/repository/tool_form.mako
@@ -21,7 +21,7 @@
             %for input_index, input in enumerate( inputs.itervalues() ):
                 %if not input.visible:
                     <% pass %>
-                %elif input.type == "repeat":
+                %elif input.type in ["repeat", "section"]:
                     <div class="repeat-group">
                         <div class="form-title-row">
                             <b>${input.title_plural}</b>

From c3f30fbdc5ed5b76889521453aa44da051357e00 Mon Sep 17 00:00:00 2001
From: Carl Eberhard <carlfeberhard@gmail.com>
Date: Sun, 29 Mar 2015 19:58:12 -0400
Subject: [PATCH 13/88] Managers: refactor hda manager into dataset/dataset
 assoc/etc., begin to expand rbac security for datasets, expand tests

---
 lib/galaxy/managers/annotatable.py            |  35 +-
 lib/galaxy/managers/base.py                   |  82 +--
 lib/galaxy/managers/datasets.py               | 526 +++++++++++++-----
 lib/galaxy/managers/hdas.py                   | 384 +++----------
 lib/galaxy/managers/histories.py              |  25 +-
 lib/galaxy/managers/roles.py                  |  59 +-
 lib/galaxy/managers/sharable.py               |  27 +-
 lib/galaxy/managers/taggable.py               |  40 ++
 lib/galaxy/managers/users.py                  |  29 +-
 lib/galaxy/model/mapping.py                   |  17 +-
 lib/galaxy/webapps/galaxy/api/lda_datasets.py |   8 +-
 lib/galaxy/webapps/galaxy/api/libraries.py    |   2 +-
 test/unit/managers/test_DatasetManager.py     | 264 +++++++--
 test/unit/managers/test_HistoryManager.py     |  12 +-
 test/unit/managers/test_ModelManager.py       |  20 +
 15 files changed, 927 insertions(+), 603 deletions(-)

diff --git a/lib/galaxy/managers/annotatable.py b/lib/galaxy/managers/annotatable.py
index 0b1e4332cc0..3cd1a367882 100644
--- a/lib/galaxy/managers/annotatable.py
+++ b/lib/galaxy/managers/annotatable.py
@@ -13,20 +13,20 @@ class AnnotatableManagerMixin( object ):
     # TODO: most of this seems to be covered by item_attrs.UsesAnnotations
     # TODO: use these below (serializer/deserializer)
     def user_annotation( self, trans, item, user ):
-        return item.get_item_annotation_str( self.app.model.context, user, item )
+        return item.get_item_annotation_str( self.session(), user, item )
 
     def owner_annotation( self, trans, item ):
         return self.user_annotation( trans, item, item.user )
 
     def delete_annotation( self, trans, item, user ):
-        return item.delete_item_annotation( self.app.model.context, user, item )
+        return item.delete_item_annotation( self.session(), user, item )
 
     def annotate( self, trans, item, user, annotation ):
         if annotation is None:
             self.delete_annotation( self, trans, item, user )
             return None
 
-        annotation_obj = item.add_item_annotation( self.app.model.context, user, item, annotation )
+        annotation_obj = item.add_item_annotation( self.session(), user, item, annotation )
         return annotation_obj.annotation
 
     #def by_user( self, trans, user, **kwargs ):
@@ -71,3 +71,32 @@ class AnnotatableDeserializerMixin( object ):
 
         annotated_item = item.add_item_annotation( sa_session, user, item, val )
         return annotated_item.annotation
+
+
+# TODO: I'm not entirely convinced this (or tags) are a good idea for filters since they involve a/the user
+class AnnotatableFilterMixin( object ):
+
+    def _owner_annotation( self, item ):
+        """
+        Get the annotation by the item's owner.
+        """
+        if not item.user:
+            return None
+        for annotation in item.annotations:
+            if annotation.user == item.user:
+                return annotation.annotation
+        return None
+
+    def filter_annotation_contains( self, item, val ):
+        """
+        Test whether `val` is in the owner's annotation.
+        """
+        owner_annotation = self._owner_annotation( item )
+        if owner_annotation is None:
+            return False
+        return val in owner_annotation
+
+    def _add_parsers( self ):
+        self.fn_filter_parsers.update({
+            'annotation'    : { 'op': { 'has': self.filter_annotation_contains, } },
+        })
diff --git a/lib/galaxy/managers/base.py b/lib/galaxy/managers/base.py
index e66f7a27533..51540ef209f 100644
--- a/lib/galaxy/managers/base.py
+++ b/lib/galaxy/managers/base.py
@@ -486,6 +486,14 @@ class ModelDeserializingError( exceptions.ObjectAttributeInvalidException ):
     pass
 
 
+class SkipAttribute( Exception ):
+    """
+    Raise this inside a serializer to prevent the returned dictionary from having
+    a the associated key or value for this attribute.
+    """
+    pass
+
+
 class ModelSerializer( object ):
     """
     Turns models into JSONable dicts.
@@ -563,12 +571,31 @@ class ModelSerializer( object ):
         for key in keys:
             # check both serializers and serializable keys
             if key in self.serializers:
-                returned[ key ] = self.serializers[ key ]( trans, item, key )
+                try:
+                    returned[ key ] = self.serializers[ key ]( trans, item, key )
+                except SkipAttribute, skip:
+                    # dont add this key if the deserializer threw this
+                    pass
             elif key in self.serializable_keyset:
                 returned[ key ] = self.default_serializer( trans, item, key )
             # ignore bad/unreg keys
         return returned
 
+    def skip( self, msg='skipped' ):
+        """
+        To be called from inside a serializer to skip it.
+
+        Handy for config checks, information hiding, etc.
+        """
+        raise SkipAttribute( msg )
+
+    def _remap_from( self, original_key ):
+        if original_key in self.serializers:
+            return self.serializers[ original_key ]
+        if original_key in self.serializable_keyset:
+            return lambda t, i, k: self.default_serializer( t, i, original_key )
+        raise KeyError( 'serializer not found for remap: ' + original_key )
+
     def default_serializer( self, trans, item, key ):
         """
         Serialize the `item`'s attribute named `key`.
@@ -589,6 +616,7 @@ class ModelSerializer( object ):
         Serialize an id attribute of `item`.
         """
         id = getattr( item, key )
+        # Note: it may not be best to encode the id at this layer
         return self.app.security.encode_id( id ) if id is not None else None
 
     # serializing to a view where a view is a predefied list of keys to serialize
@@ -854,6 +882,7 @@ class ModelFilterParser( object ):
         """
         Set up, extend, or alter `orm_filter_parsers` and `fn_filter_parsers`.
         """
+        # note: these are the default filters for all models
         self.orm_filter_parsers.update({
             # (prob.) applicable to all models
             'id'            : { 'op': ( 'in' ), 'val': self.parse_id_list },
@@ -971,57 +1000,6 @@ class ModelFilterParser( object ):
 
     # --- more parsers! yay!
 #TODO: These should go somewhere central - we've got ~6 parser modules/sections now
-    #TODO: to annotatable
-    def _owner_annotation( self, item ):
-        """
-        Get the annotation by the item's owner.
-        """
-        if not item.user:
-            return None
-        for annotation in item.annotations:
-            if annotation.user == item.user:
-                return annotation.annotation
-        return None
-
-    def filter_annotation_contains( self, item, val ):
-        """
-        Test whether `val` is in the owner's annotation.
-        """
-        owner_annotation = self._owner_annotation( item )
-        if owner_annotation is None:
-            return False
-        return val in owner_annotation
-
-    #TODO: to taggable
-    def _tag_str_gen( self, item ):
-        """
-        Return a list of strings built from the item's tags.
-        """
-        #TODO: which user is this? all?
-        for tag in item.tags:
-            tag_str = tag.user_tname
-            if tag.value is not None:
-                tag_str += ":" + tag.user_value
-            yield tag_str
-
-    def filter_has_partial_tag( self, item, val ):
-        """
-        Return True if any tag partially contains `val`.
-        """
-        for tag_str in self._tag_str_gen( item ):
-            if val in tag_str:
-                return True
-        return False
-
-    def filter_has_tag( self, item, val ):
-        """
-        Return True if any tag exactly equals `val`.
-        """
-        for tag_str in self._tag_str_gen( item ):
-            if val == tag_str:
-                return True
-        return False
-
     def parse_bool( self, bool_string ):
         """
         Parse a boolean from a string.
diff --git a/lib/galaxy/managers/datasets.py b/lib/galaxy/managers/datasets.py
index 802845d8063..a85b52a1f6f 100644
--- a/lib/galaxy/managers/datasets.py
+++ b/lib/galaxy/managers/datasets.py
@@ -1,12 +1,16 @@
 """
 Manager and Serializer for Datasets.
 """
+import json
+
 from galaxy import model
 from galaxy import exceptions
+import galaxy.datatypes.metadata
 
 from galaxy.managers import base
 from galaxy.managers import secured
 from galaxy.managers import deletable
+from galaxy.managers import rbac_secured
 from galaxy.managers import users
 
 import logging
@@ -24,47 +28,27 @@ class DatasetManager( base.ModelManager, secured.AccessibleManagerMixin, deletab
 
     def __init__( self, app ):
         super( DatasetManager, self ).__init__( app )
+        self.permissions = DatasetRBACPermissions( app )
         # need for admin test
         self.user_manager = users.UserManager( app )
 
-    def create( self, trans, flush=True, **kwargs ):
+    def create( self, trans, manage_roles=None, access_roles=None, flush=True, **kwargs ):
         """
         Create and return a new Dataset object.
         """
         # default to NEW state on new datasets
         kwargs.update( dict( state=( kwargs.get( 'state', model.Dataset.states.NEW ) ) ) )
         dataset = model.Dataset( **kwargs )
+        self.session().add( dataset )
+
+        self.permissions.set( dataset, manage_roles, access_roles, flush=False )
 
-        self.app.model.context.add( dataset )
         if flush:
-            self.app.model.context.flush()
+            self.session().flush()
         return dataset
 
-    # def copy( self, dataset, **kwargs ):
-    #    """
-    #    Clone, update, and return the given dataset.
-    #    """
-    #    pass
-
-    # def to_hda( self, trans, dataset, history, **kwargs ):
-    #    """
-    #    Create an hda from this dataset.
-    #    """
-    #    pass
-
-    # def to_ldda( self, trans, dataset, library_folder, **kwargs ):
-    #    """
-    #    Create an ldda from this dataset.
-    #    """
-    #    pass
-
-    # TODO: this may be more conv. somewhere else
-    # TODO: how to allow admin bypass?
-    def error_unless_dataset_purge_allowed( self, trans, item, msg=None ):
-        if not self.app.config.allow_user_dataset_purge:
-            msg = msg or 'This instance does not allow user dataset purging'
-            raise exceptions.ConfigDoesNotAllowException( msg )
-        return item
+    def copy( self, dataset, **kwargs ):
+        raise galaxy.exceptions.NotImplemented( 'Datasets cannot be copied' )
 
     def purge( self, trans, dataset, flush=True ):
         """
@@ -77,11 +61,19 @@ class DatasetManager( base.ModelManager, secured.AccessibleManagerMixin, deletab
 
         # the following also marks dataset as purged and deleted
         dataset.full_delete()
-        self.app.model.context.add( dataset )
+        self.session().add( dataset )
         if flush:
-            self.app.model.context.flush()
+            self.session().flush()
         return dataset
 
+    # TODO: this may be more conv. somewhere else
+    # TODO: how to allow admin bypass?
+    def error_unless_dataset_purge_allowed( self, trans, item, msg=None ):
+        if not self.app.config.allow_user_dataset_purge:
+            msg = msg or 'This instance does not allow user dataset purging'
+            raise exceptions.ConfigDoesNotAllowException( msg )
+        return item
+
     # .... accessibility
     # datasets can implement the accessible interface, but accessibility is checked in an entirely different way
     #   than those resources that have a user attribute (histories, pages, etc.)
@@ -91,117 +83,74 @@ class DatasetManager( base.ModelManager, secured.AccessibleManagerMixin, deletab
         """
         if self.user_manager.is_admin( trans, user ):
             return True
-        if self.has_access_permission( trans, dataset, user ):
+        if self.has_access_permission( dataset, user ):
             return True
         return False
 
-    def has_access_permission( self, trans, dataset, user ):
+    def has_access_permission( self, dataset, user ):
         """
         Return T/F if the user has role-based access to the dataset.
         """
         roles = user.all_roles() if user else []
         return self.app.security_agent.can_access_dataset( roles, dataset )
 
-    # TODO: these need work
-    def _access_permission( self, trans, dataset, user=None, role=None ):
-        """
-        Return most recent DatasetPermissions for the dataset and user.
-        """
-        security_agent = self.app.security_agent
-        access_action = security_agent.permitted_actions.DATASET_ACCESS.action
-
-        # get a list of role ids to check access for (defaulting to all_roles)
-        user_roles = [ role ] if role else user.all_roles()
-        user_role_ids = [ r.id for r in user_roles ]
-        query = ( self.app.model.context.query( model.DatasetPermissions )
-                  .filter( model.DatasetPermissions.action == access_action )
-                  .filter( model.DatasetPermissions.dataset == dataset )
-                  .filter( model.DatasetPermissions.role_id.in_( user_role_ids ) ) )
-        # TODO:?? most recent?
-        return query.first()
-
-    def _create_access_permission( self, trans, dataset, role, flush=True ):
-        """
-        Create a new DatasetPermissions for the given dataset and role.
-        """
-        access_action = self.app.security_agent.permitted_actions.DATASET_ACCESS.action
-        permission = model.DatasetPermissions( access_action, dataset, role )
-        self.app.model.context.add( permission )
-        if flush:
-            self.app.model.context.flush()
-        return permission
-
-    # def give_access_permission( self, trans, dataset, user, flush=True ):
-    #    """
-    #    """
-    #    # for now, use the user's private role
-    #    security_agent = self.app.security_agent
-    #    user_role = security_agent.get_private_user_role( user )
-    #
-    #    existing_permission = self._access_permission( trans, dataset, role=user_role )
-    #    print 'existing access_perm:', existing_permission
-    #    if existing_permission:
-    #        return dataset
-    #
-    #    permission = self._create_access_permission( trans, dataset, user_role )
-    #    print 'access_roles:', [ role.name for role in dataset.get_access_roles( trans ) ]
-    #
-    #    #access_action = security_agent.permitted_actions.DATASET_ACCESS.action
-    #    #access_action = security_agent.get_action( access_action )
-    #    #permissions = { access_action : [ user_role ] }
-    #    #security_agent.set_dataset_permission( dataset, permissions )
-    #
-    #    #self.app.model.context.add( dataset )
-    #    #if flush:
-    #    #    self.app.model.context.flush()
-    #
-    #    dbl_chk = self._access_permission( trans, dataset, role=user_role )
-    #    print 'access_perm:', dbl_chk
-    #
-    #    return dataset
-
-    # def remove_access_permission( self, trans, dataset, user ):
-    #    """
-    #    """
-    #    pass
-
-    # .... manage/modify
-    # def has_manage_permission( self, trans, dataset, user ):
-    #    """
-    #    """
-    #    pass
-    #
-    # def give_manage_permission( self, trans, dataset, user ):
-    #    """
-    #    """
-    #    pass
-    #
-    # def remove_manage_permission( self, trans, dataset, user ):
-    #    """
-    #    """
-    #    pass
-
     # TODO: implement above for groups
     # TODO: datatypes?
-
     # .... data, object_store
 
 
+class DatasetRBACPermissions( object ):
+
+    def __init__( self, app ):
+        self.app = app
+        self.access = rbac_secured.AccessDatasetRBACPermission( app )
+        self.manage = rbac_secured.ManageDatasetRBACPermission( app )
+
+    # TODO: temporary facade over security_agent
+    def available_roles( self, trans, dataset, controller='root' ):
+        return self.app.security_agent.get_legitimate_roles( trans, dataset, controller )
+
+    def get( self, dataset, flush=True ):
+        manage = self.manage.by_dataset( dataset )
+        access = self.access.by_dataset( dataset )
+        return ( manage, access )
+
+    def set( self, dataset, manage_roles, access_roles, flush=True ):
+        manage = self.manage.set( dataset, manage_roles or [], flush=False )
+        access = self.access.set( dataset, access_roles or [], flush=flush )
+        return ( manage, access )
+
+    def set_public_with_single_manager( self, dataset, user, flush=True ):
+        manage = self.manage.grant( dataset, user, flush=flush )
+        access = self.access.clear( dataset, flush=False )
+        return ( [ manage ], [] )
+
+    def set_private_to_one_user( self, dataset, user, flush=True ):
+        manage = self.manage.grant( user, flush=False )
+        access = self.access.set_private( dataset, user, flush=flush )
+        return ( [ manage ], access )
+
+
 class DatasetSerializer( base.ModelSerializer, deletable.PurgableSerializerMixin ):
 
     def __init__( self, app ):
         super( DatasetSerializer, self ).__init__( app )
+        self.dataset_manager = DatasetManager( app )
 
         self.default_view = 'summary'
         self.add_view( 'summary', [
             'id',
-            'create_time', 'update_time',
+            'create_time',
+            'update_time',
             'state',
-            'deleted', 'purged', 'purgable',
+            'deleted',
+            'purged',
+            'purgable',
             # 'object_store_id',
             # 'external_filename',
             # 'extra_files_path',
-            'file_size', 'total_size',
+            'file_size',
+            'total_size',
             'uuid',
         ])
         # could do visualizations and/or display_apps
@@ -211,23 +160,74 @@ class DatasetSerializer( base.ModelSerializer, deletable.PurgableSerializerMixin
         deletable.PurgableSerializerMixin.add_serializers( self )
 
         self.serializers.update({
-            'id': self.serialize_id,
-            'create_time': self.serialize_date,
-            'update_time': self.serialize_date,
-            'uuid': lambda t, i, k: str( i.uuid ) if i.uuid else None,
+            'id'            : self.serialize_id,
+            'create_time'   : self.serialize_date,
+            'update_time'   : self.serialize_date,
+
+            'uuid'          : lambda t, i, k: str( i.uuid ) if i.uuid else None,
+            'file_name'     : self.serialize_file_name,
+            'extra_files_path' : self.serialize_extra_files_path,
+            'permissions'   : self.serialize_permissions,
+
+            'total_size'    : lambda t, i, k: int( i.get_total_size() ),
+            'file_size'     : lambda t, i, k: int( i.get_size() )
         })
 
+    def serialize_file_name( self, trans, dataset, key ):
+        """
+        If the config allows or the user is admin, return the file name
+        of the file that contains this dataset's data.
+        """
+        # TODO: allow admin
+        # conifg due to cost of operation
+        if not self.app.config.expose_dataset_path:
+            self.skip()
+        return dataset.file_name
+
+    def serialize_extra_files_path( self, trans, dataset, key ):
+        """
+        If the config allows or the user is admin, return the file path.
+        """
+        # TODO: allow admin
+        # conifg due to cost of operation
+        if not self.app.config.expose_dataset_path:
+            self.skip()
+        return dataset.extra_files_path
+
+    def serialize_permissions( self, trans, dataset, key ):
+        """
+        """
+        permissions = {}
+# TODO: use rbac permissions?
+        return permissions
+
 
 class DatasetDeserializer( base.ModelDeserializer, deletable.PurgableDeserializerMixin ):
     model_manager_class = DatasetManager
 
     def add_deserializers( self ):
         super( DatasetDeserializer, self ).add_deserializers()
+        # not much to set here besides permissions and purged/deleted
         deletable.PurgableDeserializerMixin.add_deserializers( self )
 
+        self.deserializers.update({
+            'permissions' : self.deserialize_permissions,
+        })
+
+    def deserialize_permissions( self, trans, dataset, key, value ):
+        """
+        """
+        permissions = {}
+# TODO: test if different - it's an expensive op
+# TODO: validation will be tricky
+# TODO: use rbac permissions?
+        return permissions
+
 
 # ============================================================================= AKA DatasetInstanceManager
-class DatasetAssociationManager( base.ModelManager, secured.AccessibleManagerMixin, deletable.PurgableManagerMixin ):
+class DatasetAssociationManager( base.ModelManager,
+                                 secured.AccessibleManagerMixin,
+                                 deletable.PurgableManagerMixin ):
     """
     DatasetAssociation/DatasetInstances are intended to be working
     proxies to a Dataset, associated with either a library or a
@@ -248,25 +248,219 @@ class DatasetAssociationManager( base.ModelManager, secured.AccessibleManagerMix
         # defer to the dataset
         return self.dataset_manager.is_accessible( trans, dataset_assoc.dataset, user )
 
-    # def metadata( self, trans, dataset_assoc ):
-    #    """
-    #    Return the metadata collection.
-    #    """
-    #    # get metadata
-    #    pass
+    def purge( self, trans, dataset_assoc, flush=True ):
+        """
+        Purge this DatasetInstance and the dataset underlying it.
+        """
+        # error here if disallowed - before jobs are stopped
+        # TODO: this check may belong in the controller
+        self.dataset_manager.error_unless_dataset_purge_allowed( trans, dataset_assoc )
+        super( DatasetAssociationManager, self ).purge( trans, dataset_assoc, flush=flush )
 
-    # def is_being_used( self, trans, dataset_assoc ):
-    #    """
-    #    """
-    #    #TODO: check history_associations, library_associations
-    #    pass
+        # stop any jobs outputing the dataset_assoc
+        if dataset_assoc.creating_job_associations:
+            job = dataset_assoc.creating_job_associations[0].job
+            if not job.finished:
+                # signal to stop the creating job
+                job.mark_deleted( self.app.config.track_jobs_in_database )
+                self.app.job_manager.job_stop_queue.put( job.id )
+
+        # more importantly, purge underlying dataset as well
+        if dataset_assoc.dataset.user_can_purge:
+            self.dataset_manager.purge( trans, dataset_assoc.dataset )
+        return dataset_assoc
+
+    def by_user( self, trans, user ):
+        """
+        """
+        raise galaxy.exceptions.NotImplemented( 'Abstract Method' )
+
+    # def creating_job( self, trans, dataset_assoc ):
+    #     # TODO: this would be even better if outputs and inputs were the underlying datasets
+    #     # TODO: is this needed? Can't you use the dataset_assoc.creating_job attribute? When is this None?
+    #     job = None
+    #     for job_output_assoc in dataset_assoc.creating_job_associations:
+    #         job = job_output_assoc.job
+    #         break
+    #     return job
+
+    # def stop_creating_job( self, dataset_assoc ):
+    #     """
+    #     Stops an dataset_assoc's creating job if all the job's other outputs are deleted.
+    #     """
+    #     RUNNING_STATES = (
+    #         self.app.model.Job.states.QUEUED,
+    #         self.app.model.Job.states.RUNNING,
+    #         self.app.model.Job.states.NEW
+    #     )
+    #     if dataset_assoc.parent_id is None and len( dataset_assoc.creating_job_associations ) > 0:
+    #         # Mark associated job for deletion
+    #         job = dataset_assoc.creating_job_associations[0].job
+    #         if job.state in RUNNING_STATES:
+    #             # Are *all* of the job's other output datasets deleted?
+    #             if job.check_if_output_datasets_deleted():
+    #                 job.mark_deleted( self.app.config.track_jobs_in_database )
+    #                 self.app.job_manager.job_stop_queue.put( job.id )
+    #                 return True
+    #     return False
 
 
-class DatasetAssociationSerializer( base.ModelSerializer, deletable.PurgableSerializerMixin ):
+class _UnflattenedMetadataDatasetAssociationSerializer( base.ModelSerializer,
+                                                        deletable.PurgableSerializerMixin ):
+
+    def __init__( self, app ):
+        self.dataset_serializer = DatasetSerializer( app )
+        super( _UnflattenedMetadataDatasetAssociationSerializer, self ).__init__( app )
+
+    def add_serializers( self ):
+        super( _UnflattenedMetadataDatasetAssociationSerializer, self ).add_serializers()
+        deletable.PurgableSerializerMixin.add_serializers( self )
+
+        self.serializers.update({
+            'id'            : self.serialize_id,
+            'create_time'   : self.serialize_date,
+            'update_time'   : self.serialize_date,
+
+            # underlying dataset
+            'dataset'       : lambda t, i, k: self.dataset_serializer.serialize_to_view( t, i.dataset, view='summary' ),
+            'dataset_id'    : self._proxy_to_dataset( key='id' ),
+            #TODO: why is this named uuid!? The da doesn't have a uuid - it's the underlying dataset's uuid!
+            'uuid'          : self._proxy_to_dataset( key='uuid' ),
+            # 'dataset_uuid'  : self._proxy_to_dataset( key='uuid' ),
+            'file_name'     : self._proxy_to_dataset( serializer=self.dataset_serializer.serialize_file_name ),
+            'extra_files_path' : self._proxy_to_dataset( serializer=self.dataset_serializer.serialize_extra_files_path ),
+            'permissions'   : self._proxy_to_dataset( serializer=self.dataset_serializer.serialize_permissions),
+            # TODO: do the sizes proxy accurately/in the same way?
+            'size'          : lambda t, i, k: int( i.get_size() ),
+            'file_size'     : lambda t, i, k: self.serializers[ 'size' ]( t, i, k ),
+            'nice_size'     : lambda t, i, k: i.get_size( nice_size=True ),
+
+            # common to lddas and hdas - from mapping.py
+            'copied_from_history_dataset_association_id'        : self.serialize_id,
+            'copied_from_library_dataset_dataset_association_id': self.serialize_id,
+            'info'          : lambda t, i, k: i.info.strip() if isinstance( i.info, basestring ) else i.info,
+            'blurb'         : lambda t, i, k: i.blurb,
+            'peek'          : lambda t, i, k: i.display_peek() if i.peek and i.peek != 'no peek' else None,
+
+            'meta_files'    : self.serialize_meta_files,
+            'metadata'      : self.serialize_metadata,
+
+            'parent_id'     : self.serialize_id,
+            'designation'   : lambda t, i, k: i.designation,
+
+            # 'extended_metadata'     : self.serialize_extended_metadata,
+            # 'extended_metadata_id'  : self.serialize_id,
+
+            # remapped
+            'genome_build'  : lambda t, i, k: i.dbkey,
+
+            # derived (not mapped) attributes
+            'data_type'     : lambda t, i, k: i.datatype.__class__.__module__ + '.' + i.datatype.__class__.__name__,
+
+            # TODO: conversions
+            # TODO: metadata/extra files
+        })
+        # this an abstract superclass, so no views created
+        # because of that: we need to add a few keys that will use the default serializer
+        self.serializable_keyset.update([ 'name', 'state', 'tool_version', 'extension', 'visible', 'dbkey' ])
+
+    def _proxy_to_dataset( self, serializer=None, key=None ):
+        if key:
+            serializer = self.dataset_serializer.serializers.get( key )
+        if serializer:
+            return lambda t, i, k: serializer( t, i.dataset, key or k )
+        raise TypeError( 'kwarg serializer or key needed')
+
+    def serialize_meta_files( self, trans, dataset_assoc, key ):
+        """
+        Cycle through meta files and return them as a list of dictionaries.
+        """
+        meta_files = []
+        for meta_type in dataset_assoc.metadata.spec.keys():
+            if isinstance( dataset_assoc.metadata.spec[ meta_type ].param, galaxy.datatypes.metadata.FileParameter ):
+                meta_files.append( dict( file_type=meta_type ) )
+        return meta_files
+
+    def serialize_metadata( self, trans, dataset_assoc, key, excluded=None ):
+        """
+        Cycle through metadata and return as dictionary.
+        """
+        # dbkey is a repeat actually (metadata_dbkey == genome_build)
+        # excluded = [ 'dbkey' ] if excluded is None else excluded
+        excluded = [] if excluded is None else excluded
+
+        metadata = {}
+        for name, spec in dataset_assoc.metadata.spec.items():
+            if name in excluded:
+                continue
+            val = dataset_assoc.metadata.get( name )
+            # NOTE: no files
+            if isinstance( val, model.MetadataFile ):
+                # only when explicitly set: fetching filepaths can be expensive
+                if not self.app.config.expose_dataset_path:
+                    continue
+                val = val.file_name
+            # TODO:? possibly split this off?
+            # If no value for metadata, look in datatype for metadata.
+            elif val is None and hasattr( dataset_assoc.datatype, name ):
+                val = getattr( dataset_assoc.datatype, name )
+            metadata[ name ] = val
+
+        return metadata
+
+
+class DatasetAssociationSerializer( _UnflattenedMetadataDatasetAssociationSerializer ):
+    # TODO: remove this class - metadata should be a sub-object instead as in the superclass
 
     def add_serializers( self ):
         super( DatasetAssociationSerializer, self ).add_serializers()
-        deletable.PurgableSerializerMixin.add_serializers( self )
+        # remove the single nesting key here
+        del self.serializers[ 'metadata' ]
+
+    def serialize( self, trans, dataset_assoc, keys ):
+        """
+        Override to add metadata as flattened keys on the serialized DatasetInstance.
+        """
+        # if 'metadata' isn't removed from keys here serialize will retrieve the un-serializable MetadataCollection
+        # TODO: remove these when metadata is sub-object
+        KEYS_HANDLED_SEPARATELY = ( 'metadata', )
+        left_to_handle = self.pluck_from_list( keys, KEYS_HANDLED_SEPARATELY )
+        serialized = super( DatasetAssociationSerializer, self ).serialize( trans, dataset_assoc, keys )
+
+        # add metadata directly to the dict instead of as a sub-object
+        if 'metadata' in left_to_handle:
+            metadata = self.prefixed_metadata( trans, dataset_assoc )
+            serialized.update( metadata )
+        return serialized
+
+    # TODO: this is more util/gen. use
+    def pluck_from_list( self, l, elems ):
+        """
+        Removes found elems from list l and returns list of found elems if found.
+        """
+        found = []
+        for elem in elems:
+            try:
+                index = l.index( elem )
+                found.append( l.pop( index ) )
+            except ValueError:
+                pass
+        return found
+
+    def prefixed_metadata( self, trans, dataset_assoc ):
+        """
+        Adds (a prefixed version of) the DatasetInstance metadata to the dict,
+        prefixing each key with 'metadata_'.
+        """
+        # build the original, nested dictionary
+        metadata = self.serialize_metadata( trans, dataset_assoc, 'metadata' )
+
+        # prefix each key within and return
+        prefixed = {}
+        for key, val in metadata.items():
+            prefixed_key = 'metadata_' + key
+            prefixed[ prefixed_key ] = val
+        return prefixed
 
 
 class DatasetAssociationDeserializer( base.ModelDeserializer, deletable.PurgableDeserializerMixin ):
@@ -275,15 +469,75 @@ class DatasetAssociationDeserializer( base.ModelDeserializer, deletable.Purgable
         super( DatasetAssociationDeserializer, self ).add_deserializers()
         deletable.PurgableDeserializerMixin.add_deserializers( self )
 
+        self.deserializers.update({
+            'name'          : self.deserialize_basestring,
+            'info'          : self.deserialize_basestring,
+        })
+        self.deserializable_keyset.update( self.deserializers.keys() )
+
+    def deserialize_metadata( self, trans, dataset_assoc, metadata_key, metadata_dict ):
+        """
+        """
+        self.validate.type( metadata_key, metadata_dict, dict )
+        returned = {}
+        for key, val in metadata_dict.items():
+            returned[ key ] = self.deserialize_metadatum( trans, dataset_assoc, key, val )
+        return returned
+
+    def deserialize_metadatum( self, trans, dataset_assoc, key, val ):
+        """
+        """
+        if key not in dataset_assoc.datatype.metadata_spec:
+            return
+        metadata_specification = dataset_assoc.datatype.metadata_spec[ key ]
+        if metadata_specification.get( 'readonly' ):
+            return
+        unwrapped_val = metadata_specification.unwrap( val )
+        setattr( dataset_assoc.metadata, key, unwrapped_val )
+        # ...?
+        return unwrapped_val
+
 
 class DatasetAssociationFilters( base.ModelFilterParser, deletable.PurgableFiltersMixin ):
 
+    def _datatype_from_string( class_str ):
+        """
+        """
+        return self.app.datatypes_registry.get_datatype_class_by_name( class_str )
+
     def _add_parsers( self ):
         super( DatasetAssociationFilters, self )._add_parsers()
         deletable.PurgableFiltersMixin._add_parsers( self )
 
         self.orm_filter_parsers.update({
-            'name': { 'op': ( 'eq', 'contains', 'like' ) },
-            'state': { 'op': ( 'eq', 'in' ) },
+            'name'      : { 'op': ( 'eq', 'contains', 'like' ) },
+            'state'     : { 'op': ( 'eq', 'in' ) },
+            'visible'   : { 'op': ( 'eq' ), 'val': self.parse_bool },
+            'genome_build' : { 'op': ( 'eq', 'contains', 'like' ) },
         })
-        # self.fn_filter_parsers.update({})
+        self.fn_filter_parsers.update({
+            'data_type' : {
+                'op': {
+                    'eq' : self.eq_datatype,
+                    'is' : self.is_datatype
+                }
+            }
+        })
+
+    def eq_datatype( self, dataset_assoc, class_str ):
+        """
+        """
+        comparison_class = self._datatype_from_string( class_str )
+        return ( comparison_class
+             and dataset_assoc.datatype.__class__ == comparison_class )
+
+    def is_datatype( self, dataset_assoc, class_strs ):
+        """
+        """
+        comparison_classes = []
+        for class_str in class_strs.split( ',' ):
+            datatype_class = self._datatype_from_string( class_str )
+            if datatype_class:
+                comparison_classes.append( datatype_class )
+        return ( comparison_classes
+             and isinstance( dataset_assoc.datatype, comparison_classes ) )
diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py
index d3305439187..d50c7ce0c45 100644
--- a/lib/galaxy/managers/hdas.py
+++ b/lib/galaxy/managers/hdas.py
@@ -11,7 +11,6 @@ import gettext
 from galaxy import model
 from galaxy import exceptions
 from galaxy import datatypes
-import galaxy.datatypes.metadata
 from galaxy import objectstore
 
 from galaxy.managers import datasets
@@ -91,9 +90,9 @@ class HDAManager( datasets.DatasetAssociationManager,
             history.add_dataset( hda )
         #TODO:?? some internal sanity check here (or maybe in add_dataset) to make sure hids are not duped?
 
-        self.app.model.context.add( hda )
+        self.session().add( hda )
         if flush:
-            self.app.model.context.flush()
+            self.session().flush()
         return hda
 
     def copy( self, trans, hda, history=None, **kwargs ):
@@ -125,15 +124,15 @@ class HDAManager( datasets.DatasetAssociationManager,
         # TODO: update from kwargs?
 
         # Need to set after flushed, as MetadataFiles require dataset.id
-        self.app.model.context.add( copy )
-        self.app.model.context.flush()
+        self.session().add( copy )
+        self.session().flush()
         copy.metadata = hda.metadata
 
         # In some instances peek relies on dataset_id, i.e. gmaj.zip for viewing MAFs
         if not hda.datatype.copy_safe_peek:
             copy.set_peek()
 
-        self.app.model.context.flush()
+        self.session().flush()
         return copy
 
     def copy_ldda( self, trans, history, ldda, **kwargs ):
@@ -142,40 +141,18 @@ class HDAManager( datasets.DatasetAssociationManager,
         """
         return ldda.to_history_dataset_association( history, add_to_history=True )
 
-    # TODO: stub
-    # def is_a_copy( self, trans, hda ):
-    #     pass
-
-    # TODO: stub
-    # def copied_from( self, trans, hda ):
-    #     pass
-
-    # TODO: stub
-    # def by_user( self, trans, user ):
-    #     pass
-
+    # .... deletion and purging
     def purge( self, trans, hda, flush=True ):
         """
         Purge this HDA and the dataset underlying it.
         """
-        # error here if disallowed - before jobs are stopped
-        # TODO: poss. move to DatasetAssociationManager
-        self.dataset_manager.error_unless_dataset_purge_allowed( trans, hda )
+        super( HDAManager, self ).purge( trans, hda, flush=flush )
+        # decreate the user's space used
         if trans.user:
             trans.user.total_disk_usage -= hda.quota_amount( trans.user )
-        super( HDAManager, self ).purge( trans, hda, flush=flush )
-        if hda.creating_job_associations:
-            job = hda.creating_job_associations[0].job
-            if not job.finished:
-                # signal to stop the creating job
-                job.mark_deleted( self.app.config.track_jobs_in_database )
-                self.app.job_manager.job_stop_queue.put( job.id )
-
-        # more importantly, purge dataset as well
-        if hda.dataset.user_can_purge:
-            self.dataset_manager.purge( trans, hda.dataset )
         return hda
 
+    # .... states
     def error_if_uploading( self, trans, hda ):
         """
         Raise error if HDA is still uploading.
@@ -185,83 +162,22 @@ class HDAManager( datasets.DatasetAssociationManager,
             raise exceptions.Conflict( "Please wait until this dataset finishes uploading" )
         return hda
 
-    # .... via history
-    # def by_history_id( self, trans, history_id, filters=None, **kwargs ):
-    #    history_id_filter = self.model_class.history_id == history_id
-    #    filters = self._munge_filters( history_id_filter, filters )
-    #    return self.list( trans, filters=filters, **kwargs )
-
-    # def by_history( self, trans, history, filters=None, **kwargs ):
-    #    return history.datasets
-
-    # .... associated
-    def creating_job( self, trans, hda ):
-        # TODO: is this needed? Can't you use the hda.creating_job attribute? When is this None?
-        job = None
-        for job_output_assoc in hda.creating_job_associations:
-            job = job_output_assoc.job
-            break
-        return job
-
-    # .... serialization
-    def get_display_apps( self, trans, hda ):
+    def data_conversion_status( self, trans, hda ):
         """
-        Return dictionary containing new-style display app urls.
+        Returns a message if dataset is not ready to be used in visualization.
         """
-        display_apps = []
-        for display_app in hda.get_display_applications( trans ).itervalues():
+        # this is a weird syntax and return val
+        if not hda:
+            return hda.conversion_messages.NO_DATA
+        if hda.state == model.Job.states.ERROR:
+            return hda.conversion_messages.ERROR
+        if hda.state != model.Job.states.OK:
+            return hda.conversion_messages.PENDING
+        return None
 
-            app_links = []
-            for link_app in display_app.links.itervalues():
-                app_links.append({
-                    'target': link_app.url.get( 'target_frame', '_blank' ),
-                    'href': link_app.get_display_url( hda, trans ),
-                    'text': gettext.gettext( link_app.name )
-                })
-            if app_links:
-                display_apps.append( dict( label=display_app.name, links=app_links ) )
-
-        return display_apps
-
-    def get_old_display_applications( self, trans, hda ):
-        """
-        Return dictionary containing old-style display app urls.
-        """
-        display_apps = []
-        if not self.app.config.enable_old_display_applications:
-            return display_apps
-
-        for display_app in hda.datatype.get_display_types():
-            target_frame, display_links = hda.datatype.get_display_links( hda,
-                                                                          display_app,
-                                                                          self.app,
-                                                                          trans.request.base )
-
-            if len( display_links ) > 0:
-                display_label = hda.datatype.get_display_label( display_app )
-
-                app_links = []
-                for display_name, display_link in display_links:
-                    app_links.append({
-                        'target': target_frame,
-                        'href': display_link,
-                        'text': gettext.gettext( display_name )
-                    })
-                if app_links:
-                    display_apps.append( dict( label=display_label, links=app_links ) )
-
-        return display_apps
-
-    def get_visualizations( self, trans, hda ):
-        """
-        Return a list of dictionaries with links to visualization pages
-        for those visualizations that apply to this hda.
-        """
-        # use older system if registry is off in the config
-        if not self.app.visualizations_registry:
-            return hda.get_visualizations()
-        return self.app.visualizations_registry.get_visualizations( trans, hda )
+    # .... associated job
 
+    # .... data
     # TODO: to data provider or Text datatype directly
     def text_data( self, dataset, preview=True ):
         """
@@ -283,41 +199,9 @@ class HDAManager( datasets.DatasetAssociationManager,
                 dataset_data = None
         return truncated, dataset_data
 
-    # this is a weird syntax and return val
-    def data_conversion_status( self, trans, hda ):
-        """
-        Returns a message if dataset is not ready to be used in visualization.
-        """
-        if not hda:
-            return hda.conversion_messages.NO_DATA
-        if hda.state == model.Job.states.ERROR:
-            return hda.conversion_messages.ERROR
-        if hda.state != model.Job.states.OK:
-            return hda.conversion_messages.PENDING
-        return None
 
-    def stop_creating_job( self, hda ):
-        """
-        Stops an HDA's creating job if all the job's other outputs are deleted.
-        """
-        RUNNING_STATES = (
-            self.app.model.Job.states.QUEUED,
-            self.app.model.Job.states.RUNNING,
-            self.app.model.Job.states.NEW
-        )
-        if hda.parent_id is None and len( hda.creating_job_associations ) > 0:
-            # Mark associated job for deletion
-            job = hda.creating_job_associations[0].job
-            if job.state in RUNNING_STATES:
-                # Are *all* of the job's other output datasets deleted?
-                if job.check_if_output_datasets_deleted():
-                    job.mark_deleted( self.app.config.track_jobs_in_database )
-                    self.app.job_manager.job_stop_queue.put( job.id )
-                    return True
-        return False
-
-
-class HDASerializer( datasets.DatasetAssociationSerializer,
+class HDASerializer( # datasets._UnflattenedMetadataDatasetAssociationSerializer,
+                     datasets.DatasetAssociationSerializer,
                      taggable.TaggableSerializerMixin,
                      annotatable.AnnotatableSerializerMixin ):
     # TODO: inherit from datasets.DatasetAssociationSerializer
@@ -330,6 +214,7 @@ class HDASerializer( datasets.DatasetAssociationSerializer,
         self.default_view = 'summary'
         self.add_view( 'summary', [
             'id', 'name',
+            'type_id',
             'history_id', 'hid',
             # why include if model_class is there?
             'history_content_type',
@@ -349,17 +234,15 @@ class HDASerializer( datasets.DatasetAssociationSerializer,
             # remapped
             'genome_build', 'misc_info', 'misc_blurb',
             'file_ext', 'file_size',
+            'file_path',
 
             'create_time', 'update_time',
             'metadata', 'meta_files', 'data_type',
             'peek',
 
-            #TODO: why is this named uuid!? The hda doesn't have a uuid - it's the underlying dataset's uuid!
             'uuid',
-            # should be:
-            #'dataset_uuid',
+            'permissions',
 
-            'file_path',
             'display_apps',
             'display_types',
             'visualizations',
@@ -389,53 +272,23 @@ class HDASerializer( datasets.DatasetAssociationSerializer,
 
         self.serializers.update({
             'model_class'   : lambda *a: 'HistoryDatasetAssociation',
-            # TODO: accessible needs to go away
-            'accessible'    : lambda *a: True,
-
-            'id'            : self.serialize_id,
-            'history_id'    : self.serialize_id,
             'history_content_type': lambda *a: 'dataset',
-            'dataset_id'    : self.serialize_id,
             'hda_ldda'      : lambda *a: 'hda',
+            'type_id'       : self.serialize_type_id,
+
+            'history_id'    : self.serialize_id,
 
             # remapped
-            'info'          : lambda t, i, k: i.info.strip() if isinstance( i.info, basestring ) else i.info,
-            'misc_info'     : lambda t, i, k: self.serializers[ 'info' ]( t, i, k ),
-            'misc_blurb'    : lambda t, i, k: i.blurb,
-            'genome_build'  : lambda t, i, k: i.dbkey,
-            'file_ext'      : lambda t, i, k: i.extension,
-            'file_size'     : lambda t, i, k: self.serializers[ 'size' ]( t, i, k ),
-
-            'create_time'   : self.serialize_date,
-            'update_time'   : self.serialize_date,
-            'copied_from_history_dataset_association_id'        : self.serialize_id,
-            'copied_from_library_dataset_dataset_association_id': self.serialize_id,
+            'misc_info'     : self._remap_from( 'info' ),
+            'misc_blurb'    : self._remap_from( 'blurb' ),
+            'file_ext'      : self._remap_from( 'extension' ),
+            'file_path'     : self._remap_from( 'file_name' ),
 
             'resubmitted'   : lambda t, i, k: i._state == t.app.model.Dataset.states.RESUBMITTED,
 
-            'meta_files'    : self.serialize_meta_files,
-            'file_path'     : self.serialize_file_path,
-
-            'size'          : lambda t, i, k: int( i.get_size() ),
-            'nice_size'     : lambda t, i, k: i.get_size( nice_size=True ),
-            'data_type'     : lambda t, i, k: i.datatype.__class__.__module__ + '.' + i.datatype.__class__.__name__,
-            'peek'          : lambda t, i, k: i.display_peek() if i.peek and i.peek != 'no peek' else None,
-
-            # currently we send this sub-obj flattened (see serialize and add_flattened_metadata below)
-            # 'metadata'      : self.serialize_metadata,
-            #   make it available here under a different key
-            'metadata_dict' : self.serialize_metadata,
-
-            'parent_id'     : self.serialize_id,
-            'annotation'    : self.serialize_annotation,
-            'tags'          : self.serialize_tags,
-
-            'display_apps'  : lambda t, i, k: self.hda_manager.get_display_apps( t, i ),
-            'display_types' : lambda t, i, k: self.hda_manager.get_old_display_applications( t, i ),
-            'visualizations': lambda t, i, k: self.hda_manager.get_visualizations( t, i ),
-
-            'dataset_uuid'  : lambda t, i, k: str( i.dataset.uuid ) if i.dataset.uuid else None,
-            'uuid'          : lambda t, i, k: self.serializers[ 'dataset_uuid' ]( t, i, k ),
+            'display_apps'  : self.serialize_display_apps,
+            'display_types' : self.serialize_old_display_applications,
+            'visualizations': self.serialize_visualization_links,
 
             # 'url'   : url_for( 'history_content_typed', history_id=encoded_history_id, id=encoded_id, type="dataset" ),
             # TODO: this intermittently causes a routes.GenerationException - temp use the legacy route to prevent this
@@ -443,111 +296,76 @@ class HDASerializer( datasets.DatasetAssociationSerializer,
             #   see also: https://sentry.galaxyproject.org/galaxy/galaxy-main/group/20769/events/9352883/
             'url'           : lambda t, i, k: self.url_for( 'history_content',
                 history_id=t.security.encode_id( i.history_id ), id=t.security.encode_id( i.id ) ),
-
             'urls'          : self.serialize_urls,
+
+            # TODO: backwards compat: need to go away
             'download_url'  : lambda t, i, k: self.url_for( 'history_contents_display',
                 history_id=t.security.encode_id( i.history.id ),
                 history_content_id=t.security.encode_id( i.id ) ),
-
+            'parent_id'     : self.serialize_id,
+            'accessible'    : lambda *a: True,
             'api_type'      : lambda *a: 'file',
             'type'          : lambda *a: 'file'
         })
 
-    def serialize( self, trans, hda, keys ):
-        """
-        Override to add metadata as flattened keys on the serialized HDA.
-        """
-        # if 'metadata' isn't removed from keys here serialize will retrieve the un-serializable MetadataCollection
-        # TODO: remove these when metadata is sub-object
-        KEYS_HANDLED_SEPARATELY = ( 'metadata', )
-        left_to_handle = self.pluck_from_list( keys, KEYS_HANDLED_SEPARATELY )
-        serialized = super( HDASerializer, self ).serialize( trans, hda, keys )
+    def serialize_type_id( self, trans, hda, key ):
+        return 'dataset-' + self.serializers[ 'id' ]( trans, hda, 'id' )
 
-        if 'metadata' in left_to_handle:
-            # we currently add metadata directly to the dict instead of as a sub-object
-            metadata = self.prefixed_metadata( trans, hda )
-            serialized.update( metadata )
-        return serialized
+    def serialize_display_apps( self, trans, hda, key ):
+        """
+        Return dictionary containing new-style display app urls.
+        """
+        display_apps = []
+        for display_app in hda.get_display_applications( trans ).itervalues():
 
-    # TODO: this is more util/gen. use
-    def pluck_from_list( self, l, elems ):
-        """
-        Removes found elems from list l and returns list of found elems if found.
-        """
-        found = []
-        for elem in elems:
-            try:
-                index = l.index( elem )
-                found.append( l.pop( index ) )
-            except ValueError:
-                pass
-        return found
+            app_links = []
+            for link_app in display_app.links.itervalues():
+                app_links.append({
+                    'target': link_app.url.get( 'target_frame', '_blank' ),
+                    'href': link_app.get_display_url( hda, trans ),
+                    'text': gettext.gettext( link_app.name )
+                })
+            if app_links:
+                display_apps.append( dict( label=display_app.name, links=app_links ) )
 
-    def prefixed_metadata( self, trans, hda ):
-        """
-        Adds (a prefixed version of) the hda metadata to the dict, prefixing each key
-        with 'metadata_'.
-        """
-        metadata = self.serialize_metadata( trans, hda, 'metadata' )
-        # TODO: this is factored out for removal - metadata should be a sub-object instead:
-        #   i.e.  'metadata' : self.serialize_metadata,
-        prefixed = {}
-        for key, val in metadata.items():
-            prefixed_key = 'metadata_' + key
-            prefixed[ prefixed_key ] = val
-        return prefixed
+        return display_apps
 
-    def serialize_metadata( self, trans, hda, key, excluded=None ):
+    def serialize_old_display_applications( self, trans, hda, key ):
         """
-        Cycle through metadata and return as dictionary.
+        Return dictionary containing old-style display app urls.
         """
-        # dbkey is a repeat actually (metadata_dbkey == genome_build)
-        # excluded = [ 'dbkey' ] if excluded is None else excluded
-        excluded = [] if excluded is None else excluded
+        display_apps = []
+        if not self.app.config.enable_old_display_applications:
+            return display_apps
 
-        metadata = {}
-        for name, spec in hda.metadata.spec.items():
-            if name in excluded:
-                continue
-            val = hda.metadata.get( name )
-            # NOTE: no files
-            if isinstance( val, model.MetadataFile ):
-                # only when explicitly set: fetching filepaths can be expensive
-                if not self.app.config.expose_dataset_path:
-                    continue
-                val = val.file_name
-            # TODO:? possibly split this off?
-            # If no value for metadata, look in datatype for metadata.
-            elif val is None and hasattr( hda.datatype, name ):
-                val = getattr( hda.datatype, name )
-            metadata[ name ] = val
+        display_link_fn = hda.datatype.get_display_links
+        for display_app in hda.datatype.get_display_types():
+            target_frame, display_links = display_link_fn( hda, display_app, self.app, trans.request.base )
 
-        return metadata
+            if len( display_links ) > 0:
+                display_label = hda.datatype.get_display_label( display_app )
 
-    # add to serialize_metadata above
-    def serialize_meta_files( self, trans, hda, key ):
-        """
-        Cycle through meta files and return them as a list of dictionaries.
-        """
-        meta_files = []
-        for meta_type in hda.metadata.spec.keys():
-            if isinstance( hda.metadata.spec[ meta_type ].param, galaxy.datatypes.metadata.FileParameter ):
-                meta_files.append( dict( file_type=meta_type ) )
-        return meta_files
+                app_links = []
+                for display_name, display_link in display_links:
+                    app_links.append({
+                        'target': target_frame,
+                        'href': display_link,
+                        'text': gettext.gettext( display_name )
+                    })
+                if app_links:
+                    display_apps.append( dict( label=display_label, links=app_links ) )
 
-    # def file_info #TODO
-    # TODO: and to dataset instead (passing through object store)
-    def serialize_file_path( self, trans, hda, key ):
+        return display_apps
+
+    def serialize_visualization_links( self, trans, hda, key ):
         """
-        Return the `file_name` of the HDA if the config exposes it, None otherwise.
+        Return a list of dictionaries with links to visualization pages
+        for those visualizations that apply to this hda.
         """
-        # TODO: allow admin
-        if self.app.config.expose_dataset_path:
-            try:
-                return hda.file_name
-            except objectstore.ObjectNotFound:
-                log.exception( 'objectstore.ObjectNotFound, HDA %s.', hda.id )
-        return None
+        # use older system if registry is off in the config
+        if not self.app.visualizations_registry:
+            return hda.get_visualizations()
+        return self.app.visualizations_registry.get_visualizations( trans, hda )
 
     def serialize_urls( self, trans, hda, key ):
         """
@@ -590,40 +408,20 @@ class HDADeserializer( datasets.DatasetAssociationDeserializer,
         annotatable.AnnotatableDeserializerMixin.add_deserializers( self )
 
         self.deserializers.update({
-            'name'          : self.deserialize_basestring,
             'visible'       : self.deserialize_bool,
-
             # remapped
             'genome_build'  : lambda t, i, k, v: self.deserialize_genome_build( t, i, 'dbkey', v ),
             'misc_info'     : lambda t, i, k, v: self.deserialize_basestring( t, i, 'info', v ),
-
-            # TODO: mixin: deletable
-            'deleted'       : self.deserialize_bool,
-            # sharable
-            'published'     : self.deserialize_bool,
-            'importable'    : self.deserialize_bool,
-
         })
         self.deserializable_keyset.update( self.deserializers.keys() )
 
 
-class HDAFilters( datasets.DatasetAssociationFilters ):
+class HDAFilters( datasets.DatasetAssociationFilters,
+                  taggable.TaggableFilterMixin,
+                  annotatable.AnnotatableFilterMixin ):
     model_class = model.HistoryDatasetAssociation
 
     def _add_parsers( self ):
         super( HDAFilters, self )._add_parsers()
-
-        self.fn_filter_parsers.update({
-            # TODO: filter_string_attr_contains, filter_string_attr_eq
-            # 'dbkey' : { 'op': { 'has' : self.filter_annotation_contains, } },
-
-            # TODO: add this in annotatable mixin
-            'annotation': { 'op': { 'has': self.filter_annotation_contains, } },
-            # TODO: add this in taggable mixin
-            'tag': {
-                'op': {
-                    'eq': self.filter_has_tag,
-                    'has': self.filter_has_partial_tag,
-                }
-            }
-        })
+        taggable.TaggableFilterMixin._add_parsers( self )
+        annotatable.AnnotatableFilterMixin._add_parsers( self )
diff --git a/lib/galaxy/managers/histories.py b/lib/galaxy/managers/histories.py
index c50f69d5827..9b379e92740 100644
--- a/lib/galaxy/managers/histories.py
+++ b/lib/galaxy/managers/histories.py
@@ -342,33 +342,20 @@ class HistoryDeserializer( sharable.SharableModelDeserializer, deletable.Purgabl
         deletable.PurgableDeserializerMixin.add_deserializers( self )
 
         self.deserializers.update({
-            'name': self.deserialize_basestring,
-            'genome_build': self.deserialize_genome_build,
+            'name'          : self.deserialize_basestring,
+            'genome_build'  : self.deserialize_genome_build,
         })
 
 
-class HistoryFilters( sharable.SharableModelFilters, deletable.PurgableFiltersMixin ):
+class HistoryFilters( sharable.SharableModelFilters,
+                      deletable.PurgableFiltersMixin ):
     model_class = model.History
 
     def _add_parsers( self ):
         super( HistoryFilters, self )._add_parsers()
         deletable.PurgableFiltersMixin._add_parsers( self )
-
         self.orm_filter_parsers.update({
             # history specific
-            'name': { 'op': ( 'eq', 'contains', 'like' ) },
-            'genome_build': { 'op': ( 'eq', 'contains', 'like' ) },
-        })
-
-        # TODO: I'm not entirely convinced this (or tags) are a good idea for filters since they involve a/the user
-        self.fn_filter_parsers.update({
-            # TODO: add this in annotatable mixin
-            'annotation': { 'op': { 'has': self.filter_annotation_contains, } },
-            # TODO: add this in taggable mixin
-            'tag': {
-                'op': {
-                    'eq': self.filter_has_tag,
-                    'has': self.filter_has_partial_tag,
-                }
-            }
+            'name'          : { 'op': ( 'eq', 'contains', 'like' ) },
+            'genome_build'  : { 'op': ( 'eq', 'contains', 'like' ) },
         })
diff --git a/lib/galaxy/managers/roles.py b/lib/galaxy/managers/roles.py
index 80bbbced422..1cae158d922 100644
--- a/lib/galaxy/managers/roles.py
+++ b/lib/galaxy/managers/roles.py
@@ -2,40 +2,49 @@
 Manager and Serializer for Roles.
 """
 
-import galaxy.web
-from galaxy import exceptions
-from galaxy.model import orm
-from sqlalchemy.orm.exc import MultipleResultsFound
-from sqlalchemy.orm.exc import NoResultFound
+from sqlalchemy.orm import exc as sqlalchemy_exceptions
+
+import galaxy.exceptions
+from galaxy import model
+from galaxy.managers import base
 
 import logging
 log = logging.getLogger( __name__ )
 
 
 # =============================================================================
-class RoleManager( object ):
+class RoleManager( base.ModelManager ):
     """
-    Interface/service object for interacting with folders.
+    Business logic for roles.
     """
+    model_class = model.Role
+    foreign_key_name = 'role'
 
-    def get( self, trans, decoded_role_id):
-      """
-      Method loads the role from the DB based on the given role id.
+    user_assoc = model.UserRoleAssociation
+    group_assoc = model.GroupRoleAssociation
 
-      :param  decoded_role_id:      id of the role to load from the DB
-      :type   decoded_role_id:      int
+    def __init__( self, app ):
+        super( RoleManager, self ).__init__( app )
 
-      :returns:   the loaded Role object
-      :rtype:     Role
+    def get( self, trans, decoded_role_id ):
+        """
+        Method loads the role from the DB based on the given role id.
 
-      :raises: InconsistentDatabase, RequestParameterInvalidException, InternalServerError
-      """
-      try:
-          role = trans.sa_session.query( trans.app.model.Role ).filter( trans.model.Role.table.c.id == decoded_role_id ).one()
-      except MultipleResultsFound:
-          raise exceptions.InconsistentDatabase( 'Multiple roles found with the same id.' )
-      except NoResultFound:
-          raise exceptions.RequestParameterInvalidException( 'No role found with the id provided.' )
-      except Exception, e:
-          raise exceptions.InternalServerError( 'Error loading from the database.' + str(e) )
-      return role
+        :param  decoded_role_id:      id of the role to load from the DB
+        :type   decoded_role_id:      int
+
+        :returns:   the loaded Role object
+        :rtype:     Role
+
+        :raises: InconsistentDatabase, RequestParameterInvalidException, InternalServerError
+        """
+        try:
+            role = ( self.session().query( self.model_class )
+                        .filter( self.model_class.id == decoded_role_id ).one() )
+        except sqlalchemy_exceptions.MultipleResultsFound:
+            raise galaxy.exceptions.InconsistentDatabase( 'Multiple roles found with the same id.' )
+        except sqlalchemy_exceptions.NoResultFound:
+            raise galaxy.exceptions.RequestParameterInvalidException( 'No role found with the id provided.' )
+        except Exception, e:
+            raise galaxy.exceptions.InternalServerError( 'Error loading from the database.' + str(e) )
+        return role
diff --git a/lib/galaxy/managers/sharable.py b/lib/galaxy/managers/sharable.py
index 96b1cc68117..4f253baaaf6 100644
--- a/lib/galaxy/managers/sharable.py
+++ b/lib/galaxy/managers/sharable.py
@@ -162,7 +162,7 @@ class SharableModelManager( base.ModelManager, secured.OwnableManagerMixin, secu
         Create a share for the given user.
         """
         user_share_assoc = self.user_share_model()
-        self.app.model.context.add( user_share_assoc )
+        self.session().add( user_share_assoc )
         self.associate( trans, user_share_assoc, item )
         user_share_assoc.user = user
 
@@ -171,7 +171,7 @@ class SharableModelManager( base.ModelManager, secured.OwnableManagerMixin, secu
             self.create_unique_slug( trans, item )
 
         if flush:
-            self.app.model.context.flush()
+            self.session().flush()
         return user_share_assoc
 
     def unshare_with( self, trans, item, user, flush=True ):
@@ -182,9 +182,9 @@ class SharableModelManager( base.ModelManager, secured.OwnableManagerMixin, secu
             return map( lambda user: self.unshare_with( trans, item, user, flush=False ), user )
         # Look for and delete sharing relation for user.
         user_share_assoc = self.get_share_assocs( trans, item, user=user )[0]
-        self.app.model.context.delete( user_share_assoc )
+        self.session().delete( user_share_assoc )
         if flush:
-            self.app.model.context.flush()
+            self.session().flush()
         return user_share_assoc
 
     #def _query_shared_with( self, trans, user, filters=None, **kwargs ):
@@ -216,7 +216,7 @@ class SharableModelManager( base.ModelManager, secured.OwnableManagerMixin, secu
 
         item.slug = new_slug
         if flush:
-            self.app.model.context.flush()
+            self.session().flush()
         return item
 
     def is_valid_slug( self, slug ):
@@ -227,12 +227,12 @@ class SharableModelManager( base.ModelManager, secured.OwnableManagerMixin, secu
         return VALID_SLUG_RE.match( slug )
 
     def _existing_set_of_slugs( self, trans, user ):
-        query = ( self.app.model.context.query( self.model_class.slug )
+        query = ( self.session().query( self.model_class.slug )
                     .filter_by( user=user ) )
         return set( query.all() )
 
     def _slug_exists( self, trans, user, slug ):
-        query = ( self.app.model.context.query( self.model_class.slug )
+        query = ( self.session().query( self.model_class.slug )
                     .filter_by( user=user, slug=slug ) )
         return query.count() != 0
 
@@ -269,7 +269,7 @@ class SharableModelManager( base.ModelManager, secured.OwnableManagerMixin, secu
         # add integer to end.
         new_slug = slug_base
         count = 1
-        while ( self.app.model.context.query( item.__class__ )
+        while ( self.session().query( item.__class__ )
                     .filter_by( user=item.user, slug=new_slug, importable=True )
                     .count() != 0 ):
             # Slug taken; choose a new slug based on count. This approach can
@@ -284,9 +284,9 @@ class SharableModelManager( base.ModelManager, secured.OwnableManagerMixin, secu
         Set a new, unique slug on the item.
         """
         item.slug = self.get_unique_slug( trans, item )
-        self.app.model.context.add( item )
+        self.session().add( item )
         if flush:
-            self.app.model.context.flush()
+            self.session().flush()
         return item
 
     #def by_slug( self, trans, user, **kwargs ):
@@ -391,10 +391,15 @@ class SharableModelDeserializer( base.ModelDeserializer,
     #def deserialize_user_shares():
 
 
-class SharableModelFilters( base.ModelFilterParser ):
+class SharableModelFilters( base.ModelFilterParser,
+                      taggable.TaggableFilterMixin,
+                      annotatable.AnnotatableFilterMixin ):
 
     def _add_parsers( self ):
         super( SharableModelFilters, self )._add_parsers()
+        taggable.TaggableFilterMixin._add_parsers( self )
+        annotatable.AnnotatableFilterMixin._add_parsers( self )
+
         self.orm_filter_parsers.update({
             'importable'    : { 'op': ( 'eq' ), 'val': self.parse_bool },
             'published'     : { 'op': ( 'eq' ), 'val': self.parse_bool },
diff --git a/lib/galaxy/managers/taggable.py b/lib/galaxy/managers/taggable.py
index e0ec6427579..cdea2bac55e 100644
--- a/lib/galaxy/managers/taggable.py
+++ b/lib/galaxy/managers/taggable.py
@@ -64,3 +64,43 @@ class TaggableDeserializerMixin( object ):
         #TODO:!! does the creation of new_tags_list mean there are now more and more unused tag rows in the db?
         return item.tags
 
+class TaggableFilterMixin( object ):
+
+    def _tag_str_gen( self, item ):
+        """
+        Return a list of strings built from the item's tags.
+        """
+        #TODO: which user is this? all?
+        for tag in item.tags:
+            tag_str = tag.user_tname
+            if tag.value is not None:
+                tag_str += ":" + tag.user_value
+            yield tag_str
+
+    def filter_has_partial_tag( self, item, val ):
+        """
+        Return True if any tag partially contains `val`.
+        """
+        for tag_str in self._tag_str_gen( item ):
+            if val in tag_str:
+                return True
+        return False
+
+    def filter_has_tag( self, item, val ):
+        """
+        Return True if any tag exactly equals `val`.
+        """
+        for tag_str in self._tag_str_gen( item ):
+            if val == tag_str:
+                return True
+        return False
+
+    def _add_parsers( self ):
+        self.fn_filter_parsers.update({
+            'tag': {
+                'op': {
+                    'eq'    : self.filter_has_tag,
+                    'has'   : self.filter_has_partial_tag,
+                }
+            }
+        })
diff --git a/lib/galaxy/managers/users.py b/lib/galaxy/managers/users.py
index 3f581b2558f..f06af0f2307 100644
--- a/lib/galaxy/managers/users.py
+++ b/lib/galaxy/managers/users.py
@@ -50,9 +50,9 @@ class UserManager( base.ModelManager, deletable.PurgableManagerMixin ):
             # Activation is off, every new user is active by default.
             user.active = True
 
-        self.app.model.context.add( user )
+        self.session().add( user )
         try:
-            self.app.model.context.flush()
+            self.session().flush()
             #TODO:?? flush needed for permissions below? If not, make optional
         except sqlalchemy.exc.IntegrityError, db_err:
             raise exceptions.Conflict( db_err.message )
@@ -142,7 +142,7 @@ class UserManager( base.ModelManager, deletable.PurgableManagerMixin ):
         Raise an error if `user` is anonymous.
         """
         if user is None:
-            #TODO: code is correct (403), but should be named AuthenticationRequired (401 and 403 are flipped)
+            #TODO: code is correct (401) but should be named AuthenticationRequired (401 and 403 are flipped)
             raise exceptions.AuthenticationFailed( msg, **kwargs )
         return user
 
@@ -164,7 +164,7 @@ class UserManager( base.ModelManager, deletable.PurgableManagerMixin ):
         """
         Return this most recent APIKey for this user or None if none have been created.
         """
-        query = ( self.app.model.context.query( model.APIKeys )
+        query = ( self.session().query( model.APIKeys )
                     .filter_by( user=user )
                     .order_by( sqlalchemy.desc( model.APIKeys.create_time ) ) )
         all = query.all()
@@ -187,15 +187,20 @@ class UserManager( base.ModelManager, deletable.PurgableManagerMixin ):
             return existing
         return self.create_api_key( self, trans, user )
 
-    # ---- roles
-    def private_role( self, trans, user ):
-        """
-        Return the security agent's private role for `user`.
-        """
-        #TODO: not sure we need to go through sec agent... it's just the first role of type private
+    # ---- preferences
+
+
+    # ---- roles and permissions
+    def private_role( self, user ):
         return self.app.security_agent.get_private_user_role( user )
 
-    def quota( self, trans, user ):
+    def sharing_roles( self, user ):
+        return self.app.security_agent.get_sharing_roles( user )
+
+    def default_permissions( self, user ):
+        return self.app.security_agent.user_get_default_permissions( user )
+
+    def quota( self, user ):
         #TODO: use quota manager
         return self.app.quota_agent.get_percent( user=user )
 
@@ -214,7 +219,7 @@ class UserManager( base.ModelManager, deletable.PurgableManagerMixin ):
         # create a union of subqueries for each for this user - getting only the tname and user_value
         all_tags_query = None
         for tag_model in tag_models:
-            subq = ( self.app.model.context.query( tag_model.user_tname, tag_model.user_value )
+            subq = ( self.session().query( tag_model.user_tname, tag_model.user_value )
                         .filter( tag_model.user == trans.user ) )
             all_tags_query = subq if all_tags_query is None else all_tags_query.union( subq )
 
diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py
index 50041ff4f69..55ab8c1019e 100644
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -103,7 +103,6 @@ model.HistoryDatasetAssociation.table = Table( "history_dataset_association", me
     Column( "state", TrimmedString( 64 ), index=True, key="_state" ),
     Column( "copied_from_history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), nullable=True ),
     Column( "copied_from_library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), nullable=True ),
-    Column( "hid", Integer ),
     Column( "name", TrimmedString( 255 ) ),
     Column( "info", TrimmedString( 255 ) ),
     Column( "blurb", TrimmedString( 255 ) ),
@@ -114,12 +113,14 @@ model.HistoryDatasetAssociation.table = Table( "history_dataset_association", me
     Column( "parent_id", Integer, ForeignKey( "history_dataset_association.id" ), nullable=True ),
     Column( "designation", TrimmedString( 255 ) ),
     Column( "deleted", Boolean, index=True, default=False ),
-    Column( "purged", Boolean, index=True, default=False ),
     Column( "visible", Boolean ),
+    Column( "extended_metadata_id", Integer, ForeignKey( "extended_metadata.id" ), index=True ),
+    # differs from ldda
+    Column( "hid", Integer ),
+    Column( "purged", Boolean, index=True, default=False ),
     Column( "hidden_beneath_collection_instance_id", ForeignKey( "history_dataset_collection_association.id" ), nullable=True ),
-    Column( "extended_metadata_id", Integer,
-        ForeignKey( "extended_metadata.id" ), index=True )
-    )
+)
+
 
 model.Dataset.table = Table( "dataset", metadata,
     Column( "id", Integer, primary_key=True ),
@@ -322,11 +323,11 @@ model.LibraryDatasetDatasetAssociation.table = Table( "library_dataset_dataset_a
     Column( "designation", TrimmedString( 255 ) ),
     Column( "deleted", Boolean, index=True, default=False ),
     Column( "visible", Boolean ),
+    Column( "extended_metadata_id", Integer, ForeignKey( "extended_metadata.id" ), index=True ),
+    # differs from hda
     Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
     Column( "message", TrimmedString( 255 ) ),
-    Column( "extended_metadata_id", Integer,
-        ForeignKey( "extended_metadata.id" ), index=True )
-    )
+)
 
 
 model.ExtendedMetadata.table = Table("extended_metadata", metadata,
diff --git a/lib/galaxy/webapps/galaxy/api/lda_datasets.py b/lib/galaxy/webapps/galaxy/api/lda_datasets.py
index 9bb7418ad9b..97569b7a4da 100644
--- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py
+++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py
@@ -33,7 +33,7 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ):
     def __init__( self, app ):
         super( LibraryDatasetsController, self ).__init__( app )
         self.folder_manager = folders.FolderManager()
-        self.role_manager = roles.RoleManager()
+        self.role_manager = roles.RoleManager( app )
 
     @expose_api_anonymous
     def show( self, trans, id, **kwd ):
@@ -402,7 +402,7 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ):
         """
         load( self, trans, **kwd ):
         * POST /api/libraries/datasets
-        Load dataset from the given source into the library. 
+        Load dataset from the given source into the library.
         Source can be:
             user directory - root folder specified in galaxy.ini as "$user_library_import_dir"
                 example path: path/to/galaxy/$user_library_import_dir/user@example.com/{user can browse everything here}
@@ -410,7 +410,7 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ):
             (admin)import directory - root folder specified in galaxy ini as "$library_import_dir"
                 example path: path/to/galaxy/$library_import_dir/{admin can browse everything here}
             (admin)any absolute or relative path - option allowed with "allow_library_path_paste" in galaxy.ini
-         
+
         :param  encoded_folder_id:      the encoded id of the folder to import dataset(s) to
         :type   encoded_folder_id:      an encoded id string
         :param  source:                 source the datasets should be loaded form
@@ -427,7 +427,7 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ):
         :type   dbkey:                  str
 
         :returns:   dict containing information about the created upload job
-        :rtype:     dictionary        
+        :rtype:     dictionary
         """
 
         kwd[ 'space_to_tab' ] = 'False'
diff --git a/lib/galaxy/webapps/galaxy/api/libraries.py b/lib/galaxy/webapps/galaxy/api/libraries.py
index aaf777707a1..e1cee57fd9b 100644
--- a/lib/galaxy/webapps/galaxy/api/libraries.py
+++ b/lib/galaxy/webapps/galaxy/api/libraries.py
@@ -18,7 +18,7 @@ class LibrariesController( BaseAPIController ):
         super( LibrariesController, self ).__init__( app )
         self.folder_manager = folders.FolderManager()
         self.library_manager = libraries.LibraryManager()
-        self.role_manager = roles.RoleManager()
+        self.role_manager = roles.RoleManager( app )
 
     @expose_api_anonymous
     def index( self, trans, **kwd ):
diff --git a/test/unit/managers/test_DatasetManager.py b/test/unit/managers/test_DatasetManager.py
index df3dfc4b772..6cc56f7615f 100644
--- a/test/unit/managers/test_DatasetManager.py
+++ b/test/unit/managers/test_DatasetManager.py
@@ -5,6 +5,7 @@ import sys
 import os
 import pprint
 import unittest
+import json
 
 __GALAXY_ROOT__ = os.getcwd() + '/../../../'
 sys.path.insert( 1, __GALAXY_ROOT__ + 'lib' )
@@ -19,7 +20,8 @@ from galaxy.util.bunch import Bunch
 
 import mock
 from test_ModelManager import BaseTestCase
-from galaxy.managers.datasets import DatasetManager
+from galaxy.managers.datasets import (
+    DatasetManager, DatasetRBACPermissions, DatasetSerializer, DatasetDeserializer )
 from galaxy.managers.datasets import DatasetAssociationManager
 from galaxy.managers.histories import HistoryManager
 from galaxy.managers.hdas import HDAManager
@@ -70,7 +72,7 @@ class DatasetManagerTestCase( BaseTestCase ):
     def test_delete( self ):
         item1 = self.dataset_mgr.create( self.trans )
 
-        self.log( "should be able to delete and undelete an hda" )
+        self.log( "should be able to delete and undelete a dataset" )
         self.assertFalse( item1.deleted )
         self.assertEqual( self.dataset_mgr.delete( self.trans, item1 ), item1 )
         self.assertTrue( item1.deleted )
@@ -81,53 +83,221 @@ class DatasetManagerTestCase( BaseTestCase ):
         self.trans.app.config.allow_user_dataset_purge = True
         item1 = self.dataset_mgr.create( self.trans )
 
-        self.log( "should purge an hda if config does allow" )
+        self.log( "should purge a dataset if config does allow" )
         self.assertFalse( item1.purged )
         self.assertEqual( self.dataset_mgr.purge( self.trans, item1 ), item1 )
         self.assertTrue( item1.purged )
 
+        self.log( "should delete a dataset when purging" )
+        self.assertTrue( item1.deleted )
+
     def test_purge_not_allowed( self ):
         self.trans.app.config.allow_user_dataset_purge = False
         item1 = self.dataset_mgr.create( self.trans )
 
-        self.log( "should raise an error when purging an hda if config does not allow" )
+        self.log( "should raise an error when purging a dataset if config does not allow" )
         self.assertFalse( item1.purged )
         self.assertRaises( exceptions.ConfigDoesNotAllowException, self.dataset_mgr.purge, self.trans, item1 )
         self.assertFalse( item1.purged )
 
-    ##TODO: I'm unclear as to how these work, so I'm kicking this down the road a bit....
-    #def test_access_permission( self ):
-    #    owner = self.user_mgr.create( self.trans, **user2_data )
-    #    dataset = self.dataset_mgr.create( self.trans )
-    #    # giving one user access permission makes it non-public, removing access for anyone else
-    #    self.dataset_mgr.give_access_permission( self.trans, dataset, owner )
-    #
-    #    user3 = self.user_mgr.create( self.trans, **user3_data )
-    #    user4 = self.user_mgr.create( self.trans,
-    #        email='user4@user4.user4', username='user4', password=default_password )
-    #
-    #    self.assertTrue( self.dataset_mgr.has_access_permission( self.trans, dataset, owner ) )
-    #    self.assertFalse( self.dataset_mgr.has_access_permission( self.trans, dataset, user3 ) )
-    #    self.assertFalse( self.dataset_mgr.has_access_permission( self.trans, dataset, user4 ) )
-    #
-    #    # should be able to progressively add more roles without removing the previous
-    #    self.dataset_mgr.give_access_permission( self.trans, dataset, user3 )
-    #    self.assertTrue( self.dataset_mgr.has_access_permission( self.trans, dataset, user3 ) )
-    #    self.assertTrue( self.dataset_mgr.has_access_permission( self.trans, dataset, owner ) )
-    #    self.assertFalse( self.dataset_mgr.has_access_permission( self.trans, dataset, user4 ) )
-    #
-    #    #self.assertTrue( self.dataset_mgr.is_accessible( self.trans, dataset, owner ) )
-    #    #self.assertFalse( self.dataset_mgr.is_accessible( self.trans, dataset, non_owner ) )
-
-    def test_accessible( self ):
-        owner = self.user_mgr.create( self.trans, **user2_data )
-        non_owner = self.user_mgr.create( self.trans, **user3_data )
-
+    def test_create_with_no_permissions( self ):
+        self.log( "should be able to create a new Dataset without any permissions" )
         dataset = self.dataset_mgr.create( self.trans )
 
-        self.log( "(by default, dataset permissions are lax) should be accessible to all" )
-        for user in self.user_mgr.list( self.trans ):
-            self.assertTrue( self.dataset_mgr.is_accessible( self.trans, dataset, user ) )
+        permissions = self.dataset_mgr.permissions.get( dataset )
+        self.assertIsInstance( permissions, tuple )
+        self.assertEqual( len( permissions ), 2 )
+        manage_permissions, access_permissions = permissions
+        self.assertEqual( manage_permissions, [] )
+        self.assertEqual( access_permissions, [] )
+
+        user3 = self.user_mgr.create( self.trans, **user3_data )
+        self.log( "a dataset without permissions shouldn't be manageable to just anyone" )
+        self.assertFalse( self.dataset_mgr.permissions.manage.is_permitted( dataset, user3 ) )
+        self.log( "a dataset without permissions should be accessible" )
+        self.assertTrue( self.dataset_mgr.permissions.access.is_permitted( dataset, user3 ) )
+
+    def test_create_public_dataset( self ):
+        self.log( "should be able to create a new Dataset and give it some permissions that actually, you know, might work if there's any justice in this universe" )
+        owner = self.user_mgr.create( self.trans, **user2_data )
+        owner_private_role = self.user_mgr.private_role( owner )
+        dataset = self.dataset_mgr.create( self.trans, manage_roles=[ owner_private_role ] )
+
+        permissions = self.dataset_mgr.permissions.get( dataset )
+        self.assertIsInstance( permissions, tuple )
+        self.assertEqual( len( permissions ), 2 )
+        manage_permissions, access_permissions = permissions
+        self.assertIsInstance( manage_permissions, list )
+        self.assertIsInstance( manage_permissions[0], model.DatasetPermissions )
+        self.assertEqual( access_permissions, [] )
+
+        user3 = self.user_mgr.create( self.trans, **user3_data )
+        self.log( "a public dataset should be manageable to it's owner" )
+        self.assertTrue( self.dataset_mgr.permissions.manage.is_permitted( dataset, owner ) )
+        self.log( "a public dataset shouldn't be manageable to just anyone" )
+        self.assertFalse( self.dataset_mgr.permissions.manage.is_permitted( dataset, user3 ) )
+        self.log( "a public dataset should be accessible" )
+        self.assertTrue( self.dataset_mgr.permissions.access.is_permitted( dataset, user3 ) )
+
+    def test_create_private_dataset( self ):
+        self.log( "should be able to create a new Dataset and give it some permissions that actually, you know, might work if there's any justice in this universe" )
+        owner = self.user_mgr.create( self.trans, **user2_data )
+        owner_private_role = self.user_mgr.private_role( owner )
+        dataset = self.dataset_mgr.create( self.trans,
+            manage_roles=[ owner_private_role ], access_roles=[ owner_private_role ] )
+
+        permissions = self.dataset_mgr.permissions.get( dataset )
+        self.assertIsInstance( permissions, tuple )
+        self.assertEqual( len( permissions ), 2 )
+        manage_permissions, access_permissions = permissions
+        self.assertIsInstance( manage_permissions, list )
+        self.assertIsInstance( manage_permissions[0], model.DatasetPermissions )
+        self.assertIsInstance( access_permissions, list )
+        self.assertIsInstance( access_permissions[0], model.DatasetPermissions )
+
+        self.log( "a private dataset should be manageable by it's owner" )
+        self.assertTrue( self.dataset_mgr.permissions.manage.is_permitted( dataset, owner ) )
+        self.log( "a private dataset should be accessible to it's owner" )
+        self.assertTrue( self.dataset_mgr.permissions.access.is_permitted( dataset, owner ) )
+
+        user3 = self.user_mgr.create( self.trans, **user3_data )
+        self.log( "a private dataset shouldn't be manageable to just anyone" )
+        self.assertFalse( self.dataset_mgr.permissions.manage.is_permitted( dataset, user3 ) )
+        self.log( "a private dataset shouldn't be accessible to just anyone" )
+        self.assertFalse( self.dataset_mgr.permissions.access.is_permitted( dataset, user3 ) )
+
+
+# =============================================================================
+class DatasetRBACPermissionsTestCase( BaseTestCase ):
+
+    def set_up_managers( self ):
+        super( DatasetRBACPermissionsTestCase, self ).set_up_managers()
+        self.dataset_mgr = DatasetManager( self.app )
+
+    # def test_manage( self ):
+    #     self.log( "should be able to create a new Dataset" )
+    #     dataset1 = self.dataset_mgr.create( self.trans )
+    #     self.assertIsInstance( dataset1, model.Dataset )
+    #     self.assertEqual( dataset1, self.trans.sa_session.query( model.Dataset ).get( dataset1.id ) )
+    #
+
+
+# =============================================================================
+# web.url_for doesn't work well in the framework
+testable_url_for = lambda *a, **k: '(fake url): %s, %s' % ( a, k )
+DatasetSerializer.url_for = staticmethod( testable_url_for )
+
+class DatasetSerializerTestCase( BaseTestCase ):
+
+    def set_up_managers( self ):
+        super( DatasetSerializerTestCase, self ).set_up_managers()
+        self.dataset_mgr = DatasetManager( self.app )
+        self.dataset_serializer = DatasetSerializer( self.app )
+
+    def test_views( self ):
+        dataset = self.dataset_mgr.create( self.trans )
+
+        self.log( 'should have a summary view' )
+        summary_view = self.dataset_serializer.serialize_to_view( self.trans, dataset, view='summary' )
+        self.assertKeys( summary_view, self.dataset_serializer.views[ 'summary' ] )
+
+        self.log( 'should have the summary view as default view' )
+        default_view = self.dataset_serializer.serialize_to_view( self.trans, dataset, default_view='summary' )
+        self.assertKeys( summary_view, self.dataset_serializer.views[ 'summary' ] )
+
+        self.log( 'should have a serializer for all serializable keys' )
+        need_no_serializers = ( basestring, bool, type( None ) )
+        for key in self.dataset_serializer.serializable_keyset:
+            instantiated_attribute = getattr( dataset, key, None )
+            if not ( ( key in self.dataset_serializer.serializers )
+                  or ( isinstance( instantiated_attribute, need_no_serializers ) ) ):
+                self.fail( 'no serializer for: %s (%s)' % ( key, instantiated_attribute ) )
+        else:
+            self.assertTrue( True, 'all serializable keys have a serializer' )
+
+    def test_views_and_keys( self ):
+        dataset = self.dataset_mgr.create( self.trans )
+
+        self.log( 'should be able to use keys with views' )
+        serialized = self.dataset_serializer.serialize_to_view( self.trans, dataset,
+            view='summary', keys=[ 'permissions' ] )
+        self.assertKeys( serialized,
+            self.dataset_serializer.views[ 'summary' ] + [ 'permissions' ] )
+
+        self.log( 'should be able to use keys on their own' )
+        serialized = self.dataset_serializer.serialize_to_view( self.trans, dataset,
+            keys=[ 'purgable', 'file_size' ] )
+        self.assertKeys( serialized, [ 'purgable', 'file_size' ] )
+
+    def test_serialize_permissions( self ):
+        dataset = self.dataset_mgr.create( self.trans )
+        self.log( 'serialized permissions should be well formed' )
+
+    def test_serializers( self ):
+        user2 = self.user_mgr.create( self.trans, **user2_data )
+        dataset = self.dataset_mgr.create( self.trans )
+        all_keys = self.dataset_serializer.serializable_keyset
+        serialized = self.dataset_serializer.serialize( self.trans, dataset, all_keys )
+
+        self.log( 'everything serialized should be of the proper type' )
+        self.assertEncodedId( serialized[ 'id' ] )
+        self.assertDate( serialized[ 'create_time' ] )
+        self.assertDate( serialized[ 'update_time' ] )
+
+        self.assertUUID( serialized[ 'uuid' ] )
+        self.assertIsInstance( serialized[ 'state' ], basestring )
+        self.assertIsInstance( serialized[ 'deleted' ], bool )
+        self.assertIsInstance( serialized[ 'purged' ], bool )
+        self.assertIsInstance( serialized[ 'purgable' ], bool )
+
+        # # TODO: no great way to do these with mocked dataset
+        # self.assertIsInstance( serialized[ 'file_size' ], int )
+        # self.assertIsInstance( serialized[ 'total_size' ], int )
+
+        self.log( 'serialized should jsonify well' )
+        self.assertIsInstance( json.dumps( serialized ), basestring )
+
+
+# =============================================================================
+class DatasetDeserializerTestCase( BaseTestCase ):
+
+    def set_up_managers( self ):
+        super( DatasetDeserializerTestCase, self ).set_up_managers()
+        self.dataset_mgr = DatasetManager( self.app )
+        self.dataset_deserializer = DatasetDeserializer( self.app )
+
+    def test_deserialize_delete( self ):
+        dataset = self.dataset_mgr.create( self.trans )
+
+        self.log( 'should raise when deserializing deleted from non-bool' )
+        self.assertFalse( dataset.deleted )
+        self.assertRaises( exceptions.RequestParameterInvalidException,
+            self.dataset_deserializer.deserialize, self.trans, dataset, data={ 'deleted': None }, flush=True )
+        self.assertFalse( dataset.deleted )
+        self.log( 'should be able to deserialize deleted from True' )
+        self.dataset_deserializer.deserialize( self.trans, dataset, data={ 'deleted': True }, flush=True )
+        self.assertTrue( dataset.deleted )
+        self.log( 'should be able to reverse by deserializing deleted from False' )
+        self.dataset_deserializer.deserialize( self.trans, dataset, data={ 'deleted': False }, flush=True )
+        self.assertFalse( dataset.deleted )
+
+    def test_deserialize_purge( self ):
+        dataset = self.dataset_mgr.create( self.trans )
+
+        self.log( 'should raise when deserializing purged from non-bool' )
+        self.assertRaises( exceptions.RequestParameterInvalidException,
+            self.dataset_deserializer.deserialize, self.trans, dataset, data={ 'purged': None }, flush=True )
+        self.assertFalse( dataset.purged )
+        self.log( 'should be able to deserialize purged from True' )
+        self.dataset_deserializer.deserialize( self.trans, dataset, data={ 'purged': True }, flush=True )
+        self.assertTrue( dataset.purged )
+        # TODO: should this raise an error?
+        self.log( 'should NOT be able to deserialize purged from False (will remain True)' )
+        self.dataset_deserializer.deserialize( self.trans, dataset, data={ 'purged': False }, flush=True )
+        self.assertTrue( dataset.purged )
+
+    # def test_deserialize_permissions( self ):
+    #     pass
 
 
 # =============================================================================
@@ -135,10 +305,32 @@ class DatasetAssociationManagerTestCase( BaseTestCase ):
 
     def set_up_managers( self ):
         super( DatasetAssociationManagerTestCase, self ).set_up_managers()
-        self.dataset_mgr = DatasetAssociationManager( self.app )
+        self.dataset_assoc_mgr = HDAManager( self.app )
         self.hda_mgr = HDAManager( self.app )
         self.history_mgr = HistoryManager( self.app )
 
+    def test_purge_allowed( self ):
+        self.trans.app.config.allow_user_dataset_purge = True
+        item1 = self.dataset_assoc_mgr.create( self.trans )
+
+        self.log( "should purge a dataset assoc if config does allow" )
+        self.assertFalse( item1.purged )
+        self.assertEqual( self.dataset_assoc_mgr.purge( self.trans, item1 ), item1 )
+        self.assertTrue( item1.purged )
+
+        # not necc. true for dataset assocs
+        # self.log( "should delete a dataset assoc when purging" )
+        # self.assertTrue( item1.deleted )
+
+    def test_purge_not_allowed( self ):
+        self.trans.app.config.allow_user_dataset_purge = False
+        item1 = self.dataset_assoc_mgr.create( self.trans )
+
+        self.log( "should raise an error when purging a dataset assoc if config does not allow" )
+        self.assertFalse( item1.purged )
+        self.assertRaises( exceptions.ConfigDoesNotAllowException, self.dataset_assoc_mgr.purge, self.trans, item1 )
+        self.assertFalse( item1.purged )
+
     #def test_metadata( self ):
     #    owner = self.user_mgr.create( self.trans, **user2_data )
     #    history1 = self.history_mgr.create( self.trans, name='history1', user=owner )
diff --git a/test/unit/managers/test_HistoryManager.py b/test/unit/managers/test_HistoryManager.py
index db7d777a4df..9d9048d9e0a 100644
--- a/test/unit/managers/test_HistoryManager.py
+++ b/test/unit/managers/test_HistoryManager.py
@@ -5,6 +5,7 @@ import sys
 import os
 import pprint
 import unittest
+import json
 
 __GALAXY_ROOT__ = os.getcwd() + '/../../../'
 sys.path.insert( 1, __GALAXY_ROOT__ + 'lib' )
@@ -398,11 +399,16 @@ class HistorySerializerTestCase( BaseTestCase ):
     def test_history_serializers( self ):
         user2 = self.user_mgr.create( self.trans, **user2_data )
         history1 = self.history_mgr.create( self.trans, name='history1', user=user2 )
-        
-        serialized = self.history_serializer.serialize( self.trans, history1, [ 'size', 'nice_size' ])
+        all_keys = self.history_serializer.serializable_keyset
+        serialized = self.history_serializer.serialize( self.trans, history1, all_keys )
+
+        self.log( 'everything serialized should be of the proper type' )
         self.assertIsInstance( serialized[ 'size' ], int )
         self.assertIsInstance( serialized[ 'nice_size' ], basestring )
 
+        self.log( 'serialized should jsonify well' )
+        self.assertIsInstance( json.dumps( serialized ), basestring )
+
     def test_contents( self ):
         user2 = self.user_mgr.create( self.trans, **user2_data )
         history1 = self.history_mgr.create( self.trans, name='history1', user=user2 )
@@ -464,7 +470,7 @@ class HistoryFiltersTestCase( BaseTestCase ):
         self.assertEqual( len( filters ), 3 )
 
         self.log( 'values should be parsed' )
-        self.assertEqual( filters[1].right.value, True )
+        self.assertIsInstance( filters[1].right, sqlalchemy.sql.elements.True_ )
 
     def test_parse_filters_invalid_filters( self ):
         self.log( 'should error on non-column attr')
diff --git a/test/unit/managers/test_ModelManager.py b/test/unit/managers/test_ModelManager.py
index e53adc0efaf..355d98b6262 100644
--- a/test/unit/managers/test_ModelManager.py
+++ b/test/unit/managers/test_ModelManager.py
@@ -86,6 +86,26 @@ class BaseTestCase( unittest.TestCase ):
         else:
             self.assertTrue( True, 'keys found in object' )
 
+    def assertEncodedId( self, item ):
+        if not isinstance( item, basestring ):
+            self.fail( 'Non-string: ' + type( item ) )
+        # TODO: len mod 8 and hex re
+        self.assertTrue( True, 'is id: ' + item )
+
+    def assertDate( self, item ):
+        if not isinstance( item, basestring ):
+            self.fail( 'Non-string: ' + type( item ) )
+        # TODO: no great way to parse this fully (w/o python-dateutil)
+        # TODO: re?
+        self.assertTrue( True, 'is date: ' + item )
+
+    def assertUUID( self, item ):
+        if not isinstance( item, basestring ):
+            self.fail( 'Non-string: ' + type( item ) )
+        # TODO: re for d4d76d69-80d4-4ed7-80c7-211ebcc1a358
+        self.assertTrue( True, 'is uuid: ' + item )
+
+
 
 # =============================================================================
 if __name__ == '__main__':

From 530a92ef64370fbc21cc502b190f9a558c30a141 Mon Sep 17 00:00:00 2001
From: Carl Eberhard <carlfeberhard@gmail.com>
Date: Sun, 29 Mar 2015 19:59:03 -0400
Subject: [PATCH 14/88] Managers: include rbac_secured module for datasets

---
 lib/galaxy/managers/rbac_secured.py | 255 ++++++++++++++++++++++++++++
 1 file changed, 255 insertions(+)
 create mode 100644 lib/galaxy/managers/rbac_secured.py

diff --git a/lib/galaxy/managers/rbac_secured.py b/lib/galaxy/managers/rbac_secured.py
new file mode 100644
index 00000000000..1391c1c4cc1
--- /dev/null
+++ b/lib/galaxy/managers/rbac_secured.py
@@ -0,0 +1,255 @@
+from galaxy import security
+import galaxy.exceptions
+from galaxy import model
+from galaxy.managers import users
+
+import logging
+log = logging.getLogger( __name__ )
+
+class RBACPermissionFailedException( galaxy.exceptions.InsufficientPermissionsException ): pass
+
+class RBACPermission( object ):
+    """
+    Base class for wrangling/controlling the permissions ORM models (*Permissions, Roles)
+    that control which users can perform certain actions on their associated models
+    (Libraries, Datasets).
+    """
+
+    permissions_class = None
+    permission_failed_error_class = RBACPermissionFailedException
+
+    def __init__( self, app ):
+        self.app = app
+        self.user_manager = users.UserManager( app )
+
+    def session( self ):
+        return self.app.model.context
+
+    # TODO: implement group
+    # TODO: how does admin play into this?
+    def is_permitted( self, item, user ):
+        raise NotImplementedError( "abstract parent class" )
+
+    def error_unless_permitted( self, item, user ):
+        if not self.is_permitted( item, user ):
+            error_info = dict( model_class=item.__class__, id=getattr( item, 'id', None ) )
+            raise self.permission_failed_error_class( **error_info )
+
+    def grant( self, item, user, flush=True ):
+        raise NotImplementedError( "abstract parent class" )
+
+    def revoke( self, item, user, flush=True ):
+        raise NotImplementedError( "abstract parent class" )
+
+    def _role_is_permitted( self, item, role ):
+        raise NotImplementedError( "abstract parent class" )
+
+    def _error_unless_role_permitted( self, item, role ):
+        if not self._role_is_permitted( item, role ):
+            error_info = dict( model_class=item.__class__, id=getattr( item, 'id', None ) )
+            raise self.permission_failed_error_class( **error_info )
+
+    def _grant_role( self, item, role, flush=True ):
+        raise NotImplementedError( "abstract parent class" )
+
+    def _revoke_role( self, item, role, flush=True ):
+        raise NotImplementedError( "abstract parent class" )
+
+class DatasetRBACPermission( RBACPermission ):
+    """
+    Base class for the manage and access RBAC permissions used by dataset security.
+
+    The DatasetPermissions used by the RBAC agent are associations between a Dataset
+    and a single Role.
+
+    DatasetPermissions are typed (but not polymorphic themselves) by a string 'action'.
+    There are two types:
+        - manage permissions : can a role manage the permissions on a dataset
+        - access : can a role read/look at/copy a dataset
+    """
+    permissions_class = model.DatasetPermissions
+    action_name = None
+
+    # ---- double secrect probation
+    def __assert_action( self ):
+        if not self.action_name:
+            raise NotImplementedError( "abstract parent class" + " needs action_name" )
+
+    # ---- interface
+    def by_dataset( self, dataset ):
+        self.__assert_action()
+        all_permissions = self._all_types_by_dataset( dataset )
+        return filter( lambda p: p.action == self.action_name, all_permissions )
+
+#TODO: list?
+    def by_roles( self, dataset, roles ):
+        permissions = self.by_dataset( dataset )
+        return filter( lambda p: p.role in roles, permissions )
+
+    def by_role( self, dataset, role ):
+        permissions = self.by_dataset( dataset )
+        found = filter( lambda p: p.role == role, permissions )
+        if not found:
+            return None
+        if len( found ) > 1:
+            raise galaxy.exceptions.InconsistentDatabase( dataset=dataset.id, role=role.id )
+        return found[0]
+
+    def set( self, dataset, roles, flush=True ):
+        # NOTE: this removes all previous permissions of this type
+        self.clear( dataset, flush=False )
+        permissions = []
+        for role in roles:
+            permissions.append( self._create( dataset, role, flush=False ) )
+        if flush:
+            self.session().flush()
+        return permissions
+
+    def clear( self, dataset, flush=True ):
+        permissions = self.by_dataset( dataset )
+        return self._delete( permissions, flush=flush )
+
+    # ---- private
+    def _create( self, dataset, role, flush=True ):
+        permission = self.permissions_class( self.action_name, dataset, role )
+        self.session().add( permission )
+        if flush:
+            self.session().flush()
+        return permission
+
+    def _roles( self, dataset ):
+        return [ permission.role for permission in self.by_dataset( dataset ) ]
+
+    def _all_types_by_dataset( self, dataset ):
+        return dataset.actions
+
+    # as a general rule, DatasetPermissions are considered disposable
+    #   and there is no reason to update the models
+
+#TODO: list?
+    def _delete( self, permissions, flush=True ):
+        for permission in permissions:
+            self.session().delete( permission )
+            if flush:
+                self.session().flush()
+
+    def _revoke_role( self, dataset, role, flush=True ):
+        role_permissions = self.by_roles( dataset, [ role ] )
+        return self._delete( role_permissions, flush=flush )
+
+
+def iterable_has_all( iterable, has_these ):
+    for item in has_these:
+        if item not in iterable:
+            return False
+    return True
+
+
+class DatasetManagePermissionFailedException( RBACPermissionFailedException ): pass
+
+
+class ManageDatasetRBACPermission( DatasetRBACPermission ):
+    """
+    A class that controls the dataset permissions that control
+    who can manage that dataset's permissions.
+
+    When checking permissions for a user, if any of the user's roles
+    have permission on the dataset
+    """
+    # TODO: We may also be able to infer/record the dataset 'owner' as well.
+    action_name = security.RBACAgent.permitted_actions.DATASET_MANAGE_PERMISSIONS.action
+    permission_failed_error_class = DatasetManagePermissionFailedException
+
+    # ---- interface
+    def is_permitted( self, dataset, user ):
+        # anonymous users cannot manage permissions on datasets
+        if self.user_manager.is_anonymous( user ):
+            return False
+        for role in user.all_roles():
+            if self._role_is_permitted( dataset, role ):
+                return True
+        return False
+
+    def grant( self, dataset, user, flush=True ):
+        private_role = self._user_private_role( user )
+        return self._grant_role( dataset, private_role, flush=flush )
+
+    def revoke( self, dataset, user, flush=True ):
+        private_role = self._user_private_role( user )
+        return self._revoke_role( dataset, private_role, flush=flush )
+
+    # ---- private
+    def _role_is_permitted( self, dataset, role ):
+        return role in self._roles( dataset )
+
+    def _user_private_role( self, user ):
+        # error with 401 if no user
+        self.user_manager.error_if_anonymous( user )
+        return self.user_manager.private_role( user )
+
+    def _grant_role( self, dataset, role, flush=True ):
+        existing = self.by_role( dataset, role )
+        if existing:
+            return existing
+        return self._create( dataset, role, flush=flush )
+
+    def _revoke_role( self, dataset, role, flush=True ):
+        permission = self.by_roles( dataset, [ role ] )
+        return self._delete( [ permission ], flush=flush )
+
+
+class DatasetAccessPermissionFailedException( RBACPermissionFailedException ): pass
+
+
+class AccessDatasetRBACPermission( DatasetRBACPermission ):
+    """
+    A class to manage access permissions on a dataset.
+
+    An user must have all the Roles of all the access permissions associated
+    with a dataset in order to access it.
+    """
+    action_name = security.RBACAgent.permitted_actions.DATASET_ACCESS.action
+    permission_failed_error_class = DatasetAccessPermissionFailedException
+
+    # ---- interface
+    def is_permitted( self, dataset, user ):
+        current_roles = self._roles( dataset )
+        # NOTE: that because of short circuiting this allows
+        #   anonymous access to public datasets
+        return ( self._is_public_from_roles( current_roles )
+              or self._user_has_all_roles( user, current_roles ) )
+
+    def grant( self, item, user ):
+        pass
+        # not so easy
+        # need to check for a sharing role
+        # then add the new user to it
+
+    def revoke( self, item, user ):
+        pass
+        # not so easy
+
+    # TODO: these are a lil off message
+    def is_public( self, dataset ):
+        current_roles = self._roles( dataset )
+        return self._is_public_from_roles( current_roles )
+
+    def set_private( self, dataset, user, flush=True ):
+        private_role = self.user_manager.private_role( user )
+        return self.set( dataset, [ private_role ], flush=flush )
+
+    # ---- private
+    def _is_public_from_roles( self, roles ):
+        return len( roles ) == 0
+
+    def _user_has_all_roles( self, user, roles ):
+        user_roles = []
+        if not self.user_manager.is_anonymous( user ):
+            user_roles = user.all_roles()
+        return iterable_has_all( user_roles, roles )
+
+    def _role_is_permitted( self, dataset, role ):
+        current_roles = self._roles( dataset )
+        return ( self._is_public_from_roles( current_roles )
+            # if there's only one role and this is it, let em in
+            or ( ( len( current_roles ) == 1 ) and ( role == current_roles[0] ) ) )

From ba9c8b50b4624782d42f05ca54fd7b8559836964 Mon Sep 17 00:00:00 2001
From: Carl Eberhard <carlfeberhard@gmail.com>
Date: Mon, 30 Mar 2015 15:03:11 -0400
Subject: [PATCH 15/88] Managers, containers: initial outline

---
 lib/galaxy/managers/containers.py | 150 ++++++++++++++++++++++++++++++
 1 file changed, 150 insertions(+)
 create mode 100644 lib/galaxy/managers/containers.py

diff --git a/lib/galaxy/managers/containers.py b/lib/galaxy/managers/containers.py
new file mode 100644
index 00000000000..5a0ab396e5e
--- /dev/null
+++ b/lib/galaxy/managers/containers.py
@@ -0,0 +1,150 @@
+"""
+Manager mixins to unify the interface into things that can contain: Datasets
+and other (nested) containers.
+
+(e.g. DatasetCollections, Histories, LibraryFolders)
+
+Histories should be DatasetCollections.
+Libraries should be DatasetCollections.
+"""
+
+import operator
+
+import galaxy.exceptions
+import galaxy.util
+
+from galaxy.managers import base
+
+import logging
+log = logging.getLogger( __name__ )
+
+
+# ====
+class ContainerManagerMixin( object ):
+    """
+    A class that tracks/contains two types of items:
+        1) some non-container object (such as datasets)
+        2) other sub-containers nested within this one
+
+    Levels of nesting are not considered here; In other words,
+    each of the methods below only work on the first level of
+    nesting.
+    """
+    # TODO: this should be an open mapping (not just 2)
+    #: the classes that can be contained
+    contained_class = None
+    subcontainer_class = None
+    #: how any contents lists produced are ordered
+    order_contents_on = None
+
+    # ---- interface
+    def contents( self, container ):
+        """
+        Returns both types of contents: filtered and in some order.
+        """
+        iters = []
+        iters.append( self.contained( container ) )
+        iters.append( self.subcontainers( container ) )
+        return galaxy.util.merge_sorted_iterables( self.order_contents_on, *iters )
+
+    def contained( self, container ):
+        """
+        Returns non-container objects.
+        """
+        return self._filter_contents( container, self.contained_class, **kwds )
+
+    def subcontainers( self, container ):
+        """
+        Returns only the containers within this one.
+        """
+        return self._filter_contents( container, self.subcontainer_class, **kwds )
+
+    # ---- private
+    def _filter_contents( self, container, content_class, **kwds ):
+        # TODO: use list (or by_history etc.)
+        container_filter = self._filter_to_contained( container, content_class )
+        query = self.session().query( content_class ).filter( container_filter )
+        return query
+
+    def _filter_to_contained( self, container, content_class ):
+        raise galaxy.exceptions.NotImplemented( 'Abstract class' )
+
+    def _get_content_manager( self, content_class ):
+        raise galaxy.exceptions.NotImplemented( 'Abstract class' )
+
+
+class HistoryAsContainerManagerMixin( ContainerManagerMixin ):
+
+    contained_class = model.HistoryDatasetAssociation
+    subcontainer_class = model.HistoryDatasetCollectionAssociation
+    order_contents_on = operator.attrgetter( 'hid' )
+
+    def _filter_to_contained( self, container, content_class ):
+        return content_class.history == container
+
+    def _get_content_manager( self, content_class ):
+        # type snifffing is inevitable
+        if   content_class == model.HistoryDatasetAssociation:
+            return self.hda_manager
+        elif content_class == model.HistoryDatasetCollectionAssociation:
+            return self.hdca_manager
+        raise TypeError( 'Unknown contents class: ' + str( content_class ) )
+
+
+class LibraryFolderAsContainerManagerMixin( ContainerManagerMixin ):
+    # can contain two types of subcontainer: LibraryFolder, LibraryDatasetCollectionAssociation
+    # has as the top level container: Library
+
+    contained_class = model.LibraryDatasetAssociation
+    subcontainer_class = model.LibraryFolder
+    # subcontainer_class = model.LibraryDatasetCollectionAssociation
+    order_contents_on = operator.attrgetter( 'create_time' )
+
+    def _filter_to_contained( self, container, content_class ):
+        if content_class == subcontainer_class:
+            return subcontainer_class.parent == container
+        return contained_class.folder == container
+
+    def _get_content_manager( self, content_class ):
+        # type snifffing is inevitable
+        if   content_class == model.LibraryDatasetAssociation:
+            return self.lda_manager
+        elif content_class == model.LibraryFolder:
+            return self.folder_manager
+        raise TypeError( 'Unknown contents class: ' + str( content_class ) )
+
+
+class DatasetCollectionAsContainerManagerMixin( ContainerManagerMixin ):
+
+    # (note: unlike the other collections, dc's wrap both contained and subcontainers in this class)
+    contained_class = model.DatasetCollectionElement
+    subcontainer_class = model.DatasetCollection
+    order_contents_on = operator.attrgetter( 'element_index' )
+
+    def _filter_to_contained( self, container, content_class ):
+        return content_class.collection == container
+
+    def _get_content_manager( self, content_class ):
+        # type snifffing is inevitable
+        if   content_class == model.DatasetCollectionElement:
+            return self.collection_manager
+        elif content_class == model.DatasetCollection:
+            return self.collection_manager
+        raise TypeError( 'Unknown contents class: ' + str( content_class ) )
+
+
+# ====
+class ContainableModelMixin:
+    """
+    Mixin for that which goes in a container.
+    """
+
+    # ---- interface
+    def parent_container( self, containable ):
+        """
+        Return this item's parent container or None if unrecorded.
+        """
+        raise galaxy.exceptions.NotImplemented( 'Abstract class' )
+
+    def set_parent_container( self, containable, new_parent_container ):
+        raise galaxy.exceptions.NotImplemented( 'Abstract class' )

From e5bf7822d1ffe8c2f3f6271c183d247cbfaa61e6 Mon Sep 17 00:00:00 2001
From: Carl Eberhard <carlfeberhard@gmail.com>
Date: Mon, 30 Mar 2015 15:21:04 -0400
Subject: [PATCH 16/88] Managers, containers: type sniff using isinstance and
 not class equality

---
 lib/galaxy/managers/containers.py | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/lib/galaxy/managers/containers.py b/lib/galaxy/managers/containers.py
index 5a0ab396e5e..aba6edf1612 100644
--- a/lib/galaxy/managers/containers.py
+++ b/lib/galaxy/managers/containers.py
@@ -69,7 +69,7 @@ class ContainerManagerMixin( object ):
     def _filter_to_contained( self, container, content_class ):
         raise galaxy.exceptions.NotImplemented( 'Abstract class' )
 
-    def _get_content_manager( self, content_class ):
+    def _content_manager( self, content_class ):
         raise galaxy.exceptions.NotImplemented( 'Abstract class' )
 
 
@@ -82,11 +82,11 @@ class HistoryAsContainerManagerMixin( ContainerManagerMixin ):
     def _filter_to_contained( self, container, content_class ):
         return content_class.history == container
 
-    def _get_content_manager( self, content_class ):
+    def _content_manager( self, content ):
         # type snifffing is inevitable
-        if   content_class == model.HistoryDatasetAssociation:
+        if   isinstance( content, model.HistoryDatasetAssociation ):
             return self.hda_manager
-        elif content_class == model.HistoryDatasetCollectionAssociation:
+        elif isinstance( content, model.HistoryDatasetCollectionAssociation ):
             return self.hdca_manager
         raise TypeError( 'Unknown contents class: ' + str( content_class ) )
 
@@ -105,11 +105,11 @@ class LibraryFolderAsContainerManagerMixin( ContainerManagerMixin ):
             return subcontainer_class.parent == container
         return contained_class.folder == container
 
-    def _get_content_manager( self, content_class ):
+    def _content_manager( self, content ):
         # type snifffing is inevitable
-        if   content_class == model.LibraryDatasetAssociation:
+        if   isinstance( content, model.LibraryDatasetAssociation ):
             return self.lda_manager
-        elif content_class == model.LibraryFolder:
+        elif isinstance( content, model.LibraryFolder ):
             return self.folder_manager
         raise TypeError( 'Unknown contents class: ' + str( content_class ) )
 
@@ -124,11 +124,11 @@ class DatasetCollectionAsContainerManagerMixin( ContainerManagerMixin ):
     def _filter_to_contained( self, container, content_class ):
         return content_class.collection == container
 
-    def _get_content_manager( self, content_class ):
+    def _content_manager( self, content ):
         # type snifffing is inevitable
-        if   content_class == model.DatasetCollectionElement:
+        if   isinstance( content, model.DatasetCollectionElement ):
             return self.collection_manager
-        elif content_class == model.DatasetCollection:
+        elif isinstance( content, model.DatasetCollection ):
             return self.collection_manager
         raise TypeError( 'Unknown contents class: ' + str( content_class ) )
 

From 188ff0076f04ddd321b6fd882d5249c2dcecdc7e Mon Sep 17 00:00:00 2001
From: Carl Eberhard <carlfeberhard@gmail.com>
Date: Mon, 30 Mar 2015 18:00:13 -0400
Subject: [PATCH 17/88] Managers, Users: corrections and refactoring, expansion
 of tests

---
 lib/galaxy/managers/users.py              |  30 +++---
 test/unit/managers/mock.py                |  13 ++-
 test/unit/managers/test_HistoryManager.py |   1 -
 test/unit/managers/test_ModelManager.py   |  12 ++-
 test/unit/managers/test_UserManager.py    | 121 +++++++++++++++++++++-
 5 files changed, 153 insertions(+), 24 deletions(-)

diff --git a/lib/galaxy/managers/users.py b/lib/galaxy/managers/users.py
index f06af0f2307..c204f1ad63f 100644
--- a/lib/galaxy/managers/users.py
+++ b/lib/galaxy/managers/users.py
@@ -260,7 +260,7 @@ class UserSerializer( base.ModelSerializer, deletable.PurgableSerializerMixin ):
 
             'total_disk_usage',
             'nice_total_disk_usage',
-            'quota_percent'
+            'quota_percent',
 
             #'deleted',
             #'purged',
@@ -284,13 +284,24 @@ class UserSerializer( base.ModelSerializer, deletable.PurgableSerializerMixin ):
             'is_admin'      : lambda t, i, k: self.user_manager.is_admin( t, i ),
 
             'total_disk_usage' : lambda t, i, k: float( i.total_disk_usage ),
-            'quota_percent' : lambda t, i, k: self.user_manager.quota( t, i ),
+            'quota_percent' : lambda t, i, k: self.user_manager.quota( i ),
 
             'tags_used'     : lambda t, i, k: self.user_manager.tags_used( t, i ),
             #TODO: 'has_requests' is more apt
             'requests'      : lambda t, i, k: self.user_manager.has_requests( t, i )
         })
 
+
+class CurrentUserSerializer( UserSerializer ):
+
+    def serialize( self, trans, user, keys ):
+        """
+        Override to return at least some usage info if user is anonymous.
+        """
+        if self.user_manager.is_anonymous( user ):
+            return self.serialize_current_anonymous_user( trans, user, keys )
+        return super( UserSerializer, self ).serialize( trans, user, keys )
+
     def serialize_current_anonymous_user( self, trans, user, keys ):
         # use the current history if any to get usage stats for trans' anonymous user
         #TODO: might be better as sep. Serializer class
@@ -304,7 +315,7 @@ class UserSerializer( base.ModelSerializer, deletable.PurgableSerializerMixin ):
         # a very small subset of keys available
         values = {
             'id'                    : None,
-            'total_disk_usage'      : int( usage ),
+            'total_disk_usage'      : float( usage ),
             'nice_total_disk_usage' : util.nice_size( usage ),
             'quota_percent'         : percent,
         }
@@ -314,25 +325,16 @@ class UserSerializer( base.ModelSerializer, deletable.PurgableSerializerMixin ):
                 serialized[ key ] = values[ key ]
         return serialized
 
-    def serialize( self, trans, user, keys ):
-        """
-        Override to return at least some usage info if user is anonymous.
-        """
-        if self.user_manager.is_anonymous( user ):
-            return self.serialize_current_anonymous_user( trans, user, keys )
-        return super( UserSerializer, self ).serialize( trans, user, keys )
 
-
-class AdminUserFilters( base.ModelFilterParser, deletable.PurgableFiltersMixin ):
+class AdminUserFilterParser( base.ModelFilterParser, deletable.PurgableFiltersMixin ):
     model_class = model.User
 
     def _add_parsers( self ):
-        super( AdminUserFilters, self )._add_parsers()
+        super( AdminUserFilterParser, self )._add_parsers()
         deletable.PurgableFiltersMixin._add_parsers( self )
 
         #PRECONDITION: user making the query has been verified as an admin
         self.orm_filter_parsers.update({
-            'name'          : { 'op': ( 'eq', 'contains', 'like' ) },
             'email'         : { 'op': ( 'eq', 'contains', 'like' ) },
             'username'      : { 'op': ( 'eq', 'contains', 'like' ) },
             'active'        : { 'op': ( 'eq' ) },
diff --git a/test/unit/managers/mock.py b/test/unit/managers/mock.py
index 8d349b84cac..adc67c6a52d 100644
--- a/test/unit/managers/mock.py
+++ b/test/unit/managers/mock.py
@@ -16,6 +16,8 @@ from galaxy import objectstore
 from galaxy.model import mapping
 from galaxy.util.bunch import Bunch
 
+from galaxy.managers import tags
+from galaxy import quota
 
 # =============================================================================
 class OpenObject( object ):
@@ -29,6 +31,8 @@ class MockApp( object ):
         self.model = mapping.init( "/tmp", "sqlite:///:memory:", create_tables=True, object_store=self.object_store )
         self.security_agent = self.model.security_agent
         self.visualizations_registry = MockVisualizationsRegistry()
+        self.tag_handler = tags.GalaxyTagManager( self )
+        self.quota_agent = quota.QuotaAgent( self.model )
 
 class MockAppConfig( Bunch ):
     def __init__( self, **kwargs ):
@@ -53,10 +57,15 @@ class MockWebapp( object ):
     def __init__( self, **kwargs ):
         self.name = kwargs.get( 'name', 'galaxy' )
 
+class MockVisualizationsRegistry( object ):
+    def get_visualizations( self, trans, target ):
+        return []
+
 class MockTrans( object ):
     def __init__( self, user=None, history=None, **kwargs ):
 
         self.app = MockApp( **kwargs )
+        self.model = self.app.model
         self.webapp = MockWebapp( **kwargs )
         self.sa_session = self.app.model.session
 
@@ -91,7 +100,3 @@ class MockTrans( object ):
         template = template_lookup.get_template( filename )
         template.output_encoding = 'utf-8'
         return template.render( **kwargs )
-
-class MockVisualizationsRegistry( object ):
-    def get_visualizations( self, trans, target ):
-        return []
diff --git a/test/unit/managers/test_HistoryManager.py b/test/unit/managers/test_HistoryManager.py
index 9d9048d9e0a..70a817cf4c9 100644
--- a/test/unit/managers/test_HistoryManager.py
+++ b/test/unit/managers/test_HistoryManager.py
@@ -316,7 +316,6 @@ testable_url_for = lambda *a, **k: '(fake url): %s, %s' % ( a, k )
 HistorySerializer.url_for = staticmethod( testable_url_for )
 hdas.HDASerializer.url_for = staticmethod( testable_url_for )
 
-
 class HistorySerializerTestCase( BaseTestCase ):
 
     def set_up_managers( self ):
diff --git a/test/unit/managers/test_ModelManager.py b/test/unit/managers/test_ModelManager.py
index 355d98b6262..611dcc4ae68 100644
--- a/test/unit/managers/test_ModelManager.py
+++ b/test/unit/managers/test_ModelManager.py
@@ -88,23 +88,29 @@ class BaseTestCase( unittest.TestCase ):
 
     def assertEncodedId( self, item ):
         if not isinstance( item, basestring ):
-            self.fail( 'Non-string: ' + type( item ) )
+            self.fail( 'Non-string: ' + str( type( item ) ) )
         # TODO: len mod 8 and hex re
         self.assertTrue( True, 'is id: ' + item )
 
     def assertDate( self, item ):
         if not isinstance( item, basestring ):
-            self.fail( 'Non-string: ' + type( item ) )
+            self.fail( 'Non-string: ' + str( type( item ) ) )
         # TODO: no great way to parse this fully (w/o python-dateutil)
         # TODO: re?
         self.assertTrue( True, 'is date: ' + item )
 
     def assertUUID( self, item ):
         if not isinstance( item, basestring ):
-            self.fail( 'Non-string: ' + type( item ) )
+            self.fail( 'Non-string: ' + str( type( item ) ) )
         # TODO: re for d4d76d69-80d4-4ed7-80c7-211ebcc1a358
         self.assertTrue( True, 'is uuid: ' + item )
 
+    def assertORMFilter( self, item, msg=None ):
+        if not isinstance( item, sqlalchemy.sql.elements.BinaryExpression ):
+            self.fail( 'Not an orm filter: ' + str( type( item ) ) )
+        # TODO: re for d4d76d69-80d4-4ed7-80c7-211ebcc1a358
+        self.assertTrue( True, msg or ( 'is an orm filter: ' + item ) )
+
 
 
 # =============================================================================
diff --git a/test/unit/managers/test_UserManager.py b/test/unit/managers/test_UserManager.py
index 5b78fae5bdf..6d8666e3a13 100644
--- a/test/unit/managers/test_UserManager.py
+++ b/test/unit/managers/test_UserManager.py
@@ -5,6 +5,7 @@ import sys
 import os
 import pprint
 import unittest
+import json
 
 __GALAXY_ROOT__ = os.getcwd() + '/../../../'
 sys.path.insert( 1, __GALAXY_ROOT__ + 'lib' )
@@ -19,14 +20,15 @@ from galaxy.util.bunch import Bunch
 
 import mock
 from test_ModelManager import BaseTestCase
+from galaxy.managers import users
+from galaxy.managers import histories
 
 
 # =============================================================================
-admin_email = 'admin@admin.admin'
-admin_users = admin_email
 default_password = '123456'
 user2_data = dict( email='user2@user2.user2', username='user2', password=default_password )
 user3_data = dict( email='user3@user3.user3', username='user3', password=default_password )
+user4_data = dict( email='user4@user4.user4', username='user4', password=default_password )
 
 
 # =============================================================================
@@ -130,6 +132,121 @@ class UserManagerTestCase( BaseTestCase ):
         self.assertEqual( self.user_mgr.valid_api_key( self.trans, user2 ).key, user2_api_key_2 )
 
 
+# =============================================================================
+class UserSerializerTestCase( BaseTestCase ):
+
+    def set_up_managers( self ):
+        super( UserSerializerTestCase, self ).set_up_managers()
+        self.user_serializer = users.UserSerializer( self.app )
+
+    def test_views( self ):
+        user = self.user_mgr.create( self.trans, **user2_data )
+
+        self.log( 'should have a summary view' )
+        summary_view = self.user_serializer.serialize_to_view( self.trans, user, view='summary' )
+        self.assertKeys( summary_view, self.user_serializer.views[ 'summary' ] )
+
+        self.log( 'should have the summary view as default view' )
+        default_view = self.user_serializer.serialize_to_view( self.trans, user, default_view='summary' )
+        self.assertKeys( summary_view, self.user_serializer.views[ 'summary' ] )
+
+        self.log( 'should have a serializer for all serializable keys' )
+        need_no_serializers = ( basestring, bool, type( None ) )
+        for key in self.user_serializer.serializable_keyset:
+            instantiated_attribute = getattr( user, key, None )
+            if not ( ( key in self.user_serializer.serializers )
+                  or ( isinstance( instantiated_attribute, need_no_serializers ) ) ):
+                self.fail( 'no serializer for: %s (%s)' % ( key, instantiated_attribute ) )
+        else:
+            self.assertTrue( True, 'all serializable keys have a serializer' )
+
+    def test_views_and_keys( self ):
+        user = self.user_mgr.create( self.trans, **user2_data )
+
+        self.log( 'should be able to use keys with views' )
+        serialized = self.user_serializer.serialize_to_view( self.trans, user,
+            view='summary', keys=[ 'create_time' ] )
+        self.assertKeys( serialized,
+            self.user_serializer.views[ 'summary' ] + [ 'create_time' ] )
+
+        self.log( 'should be able to use keys on their own' )
+        serialized = self.user_serializer.serialize_to_view( self.trans, user,
+            keys=[ 'tags_used', 'is_admin' ] )
+        self.assertKeys( serialized, [ 'tags_used', 'is_admin' ] )
+
+    def test_serializers( self ):
+        user = self.user_mgr.create( self.trans, **user2_data )
+        all_keys = self.user_serializer.serializable_keyset
+        serialized = self.user_serializer.serialize( self.trans, user, all_keys )
+        # pprint.pprint( serialized )
+
+        self.log( 'everything serialized should be of the proper type' )
+        self.assertEncodedId( serialized[ 'id' ] )
+        self.assertDate( serialized[ 'create_time' ] )
+        self.assertDate( serialized[ 'update_time' ] )
+        self.assertIsInstance( serialized[ 'deleted' ], bool )
+        self.assertIsInstance( serialized[ 'purged' ], bool )
+
+        # self.assertIsInstance( serialized[ 'active' ], bool )
+        self.assertIsInstance( serialized[ 'is_admin' ], bool )
+        self.assertIsInstance( serialized[ 'total_disk_usage' ], float )
+        self.assertIsInstance( serialized[ 'nice_total_disk_usage' ], basestring )
+        self.assertIsInstance( serialized[ 'quota_percent' ], ( type( None ), float ) )
+        self.assertIsInstance( serialized[ 'tags_used' ], list )
+        self.assertIsInstance( serialized[ 'requests' ], list )
+
+        self.log( 'serialized should jsonify well' )
+        self.assertIsInstance( json.dumps( serialized ), basestring )
+
+
+class CurrentUserSerializerTestCase( BaseTestCase ):
+
+    def set_up_managers( self ):
+        super( CurrentUserSerializerTestCase, self ).set_up_managers()
+        self.history_manager = histories.HistoryManager( self.app )
+        self.user_serializer = users.CurrentUserSerializer( self.app )
+
+    def test_anonymous( self ):
+        anonym = None
+        # need a history here for total_disk_usage
+        self.trans.set_history( self.history_manager.create( self.trans ) )
+
+        self.log( 'should be able to serialize anonymous user' )
+        serialized = self.user_serializer.serialize_to_view( self.trans, anonym, view='detailed' )
+        self.assertKeys( serialized,
+            [ 'id', 'total_disk_usage', 'nice_total_disk_usage', 'quota_percent' ] )
+
+        self.log( 'anonymous\'s id should be None' )
+        self.assertEqual( serialized[ 'id' ], None )
+        self.log( 'everything serialized should be of the proper type' )
+        self.assertIsInstance( serialized[ 'total_disk_usage' ], float )
+        self.assertIsInstance( serialized[ 'nice_total_disk_usage' ], basestring )
+        self.assertIsInstance( serialized[ 'quota_percent' ], ( type( None ), float ) )
+
+        self.log( 'serialized should jsonify well' )
+        self.assertIsInstance( json.dumps( serialized ), basestring )
+
+
+# =============================================================================
+class AdminUserFilterParserTestCase( BaseTestCase ):
+
+    def set_up_managers( self ):
+        super( AdminUserFilterParserTestCase, self ).set_up_managers()
+        self.filter_parser = users.AdminUserFilterParser( self.app )
+
+    def test_parsable( self ):
+        self.log( 'the following filters should be parsable' )
+        self.assertORMFilter( self.filter_parser.parse_filter( 'email', 'eq', 'wot' ) )
+        self.assertORMFilter( self.filter_parser.parse_filter( 'email', 'contains', 'wot' ) )
+        self.assertORMFilter( self.filter_parser.parse_filter( 'email', 'like', 'wot' ) )
+        self.assertORMFilter( self.filter_parser.parse_filter( 'username', 'eq', 'wot' ) )
+        self.assertORMFilter( self.filter_parser.parse_filter( 'username', 'contains', 'wot' ) )
+        self.assertORMFilter( self.filter_parser.parse_filter( 'username', 'like', 'wot' ) )
+        self.assertORMFilter( self.filter_parser.parse_filter( 'active', 'eq', True ) )
+        self.assertORMFilter( self.filter_parser.parse_filter( 'disk_usage', 'le', 500000.00 ) )
+        self.assertORMFilter( self.filter_parser.parse_filter( 'disk_usage', 'ge', 500000.00 ) )
+
+
 # =============================================================================
 if __name__ == '__main__':
     # or more generally, nosetests test_resourcemanagers.py -s -v

From 9f1be65937fd49f05d74fd6ab32ff47f22834434 Mon Sep 17 00:00:00 2001
From: Carl Eberhard <carlfeberhard@gmail.com>
Date: Tue, 31 Mar 2015 11:15:49 -0400
Subject: [PATCH 18/88] Managers: re-add dataset assoc job methods, move
 primary id serialization into base serializer, minor fixes and refactoring,
 expand tests

---
 lib/galaxy/managers/base.py               |   5 +-
 lib/galaxy/managers/datasets.py           |  61 ++--
 lib/galaxy/managers/deletable.py          |   1 +
 lib/galaxy/managers/hdas.py               |  48 +--
 test/unit/managers/test_DatasetManager.py |  66 +---
 test/unit/managers/test_HDAManager.py     | 372 +++++++++++++++++++++-
 test/unit/managers/test_HistoryManager.py |  12 +-
 test/unit/managers/test_ModelManager.py   |  19 +-
 test/unit/managers/test_UserManager.py    |  10 +-
 9 files changed, 469 insertions(+), 125 deletions(-)

diff --git a/lib/galaxy/managers/base.py b/lib/galaxy/managers/base.py
index 51540ef209f..999d770f0b8 100644
--- a/lib/galaxy/managers/base.py
+++ b/lib/galaxy/managers/base.py
@@ -542,8 +542,9 @@ class ModelSerializer( object ):
         Register a map of attribute keys -> serializing functions that will serialize
         the attribute.
         """
-        # to be overridden in subclasses
-        pass
+        self.serializers.update({
+            'id' : self.serialize_id,
+        })
 
     def add_view( self, view_name, key_list, include_keys_from=None ):
         """
diff --git a/lib/galaxy/managers/datasets.py b/lib/galaxy/managers/datasets.py
index a85b52a1f6f..3275782b1b7 100644
--- a/lib/galaxy/managers/datasets.py
+++ b/lib/galaxy/managers/datasets.py
@@ -160,7 +160,6 @@ class DatasetSerializer( base.ModelSerializer, deletable.PurgableSerializerMixin
         deletable.PurgableSerializerMixin.add_serializers( self )
 
         self.serializers.update({
-            'id'            : self.serialize_id,
             'create_time'   : self.serialize_date,
             'update_time'   : self.serialize_date,
 
@@ -275,34 +274,35 @@ class DatasetAssociationManager( base.ModelManager,
         """
         raise galaxy.exceptions.NotImplemented( 'Abstract Method' )
 
-    # def creating_job( self, trans, dataset_assoc ):
-    #     # TODO: this would be even better if outputs and inputs were the underlying datasets
-    #     # TODO: is this needed? Can't you use the dataset_assoc.creating_job attribute? When is this None?
-    #     job = None
-    #     for job_output_assoc in dataset_assoc.creating_job_associations:
-    #         job = job_output_assoc.job
-    #         break
-    #     return job
+    def creating_job( self, trans, dataset_assoc ):
+        # TODO: is this needed? Can't you use the dataset_assoc.creating_job attribute? When is this None?
+        # TODO: this would be even better if outputs and inputs were the underlying datasets
+        job = None
+        for job_output_assoc in dataset_assoc.creating_job_associations:
+            job = job_output_assoc.job
+            break
+        return job
 
-    # def stop_creating_job( self, dataset_assoc ):
-    #     """
-    #     Stops an dataset_assoc's creating job if all the job's other outputs are deleted.
-    #     """
-    #     RUNNING_STATES = (
-    #         self.app.model.Job.states.QUEUED,
-    #         self.app.model.Job.states.RUNNING,
-    #         self.app.model.Job.states.NEW
-    #     )
-    #     if dataset_assoc.parent_id is None and len( dataset_assoc.creating_job_associations ) > 0:
-    #         # Mark associated job for deletion
-    #         job = dataset_assoc.creating_job_associations[0].job
-    #         if job.state in RUNNING_STATES:
-    #             # Are *all* of the job's other output datasets deleted?
-    #             if job.check_if_output_datasets_deleted():
-    #                 job.mark_deleted( self.app.config.track_jobs_in_database )
-    #                 self.app.job_manager.job_stop_queue.put( job.id )
-    #                 return True
-    #     return False
+    def stop_creating_job( self, dataset_assoc ):
+        """
+        Stops an dataset_assoc's creating job if all the job's other outputs are deleted.
+        """
+        # TODO: use in purge above
+        RUNNING_STATES = (
+            self.app.model.Job.states.QUEUED,
+            self.app.model.Job.states.RUNNING,
+            self.app.model.Job.states.NEW
+        )
+        if dataset_assoc.parent_id is None and len( dataset_assoc.creating_job_associations ) > 0:
+            # Mark associated job for deletion
+            job = dataset_assoc.creating_job_associations[0].job
+            if job.state in RUNNING_STATES:
+                # Are *all* of the job's other output datasets deleted?
+                if job.check_if_output_datasets_deleted():
+                    job.mark_deleted( self.app.config.track_jobs_in_database )
+                    self.app.job_manager.job_stop_queue.put( job.id )
+                    return True
+        return False
 
 
 class _UnflattenedMetadataDatasetAssociationSerializer( base.ModelSerializer,
@@ -317,7 +317,6 @@ class _UnflattenedMetadataDatasetAssociationSerializer( base.ModelSerializer,
         deletable.PurgableSerializerMixin.add_serializers( self )
 
         self.serializers.update({
-            'id'            : self.serialize_id,
             'create_time'   : self.serialize_date,
             'update_time'   : self.serialize_date,
 
@@ -498,7 +497,7 @@ class DatasetAssociationDeserializer( base.ModelDeserializer, deletable.Purgable
         return unwrapped_val
 
 
-class DatasetAssociationFilters( base.ModelFilterParser, deletable.PurgableFiltersMixin ):
+class DatasetAssociationFilterParser( base.ModelFilterParser, deletable.PurgableFiltersMixin ):
 
     def _datatype_from_string( class_str ):
         """
@@ -506,7 +505,7 @@ class DatasetAssociationFilters( base.ModelFilterParser, deletable.PurgableFilte
         return self.app.datatypes_registry.get_datatype_class_by_name( class_str )
 
     def _add_parsers( self ):
-        super( DatasetAssociationFilters, self )._add_parsers()
+        super( DatasetAssociationFilterParser, self )._add_parsers()
         deletable.PurgableFiltersMixin._add_parsers( self )
 
         self.orm_filter_parsers.update({
diff --git a/lib/galaxy/managers/deletable.py b/lib/galaxy/managers/deletable.py
index b8090e84016..2d1dd5af2cc 100644
--- a/lib/galaxy/managers/deletable.py
+++ b/lib/galaxy/managers/deletable.py
@@ -103,6 +103,7 @@ class PurgableDeserializerMixin( DeletableDeserializerMixin ):
         new_purged = self.validate.bool( key, val )
         if new_purged == item.purged:
             return item.purged
+        # do we want to error if something attempts to 'unpurge'?
         if new_purged:
             self.manager.purge( trans, item, flush=False )
         return item.purged
diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py
index d50c7ce0c45..fc111de0e8c 100644
--- a/lib/galaxy/managers/hdas.py
+++ b/lib/galaxy/managers/hdas.py
@@ -164,40 +164,40 @@ class HDAManager( datasets.DatasetAssociationManager,
 
     def data_conversion_status( self, trans, hda ):
         """
-        Returns a message if dataset is not ready to be used in visualization.
+        Returns a message if an hda is not ready to be used in visualization.
         """
+        HDA_model = model.HistoryDatasetAssociation
         # this is a weird syntax and return val
         if not hda:
-            return hda.conversion_messages.NO_DATA
+            return HDA_model.conversion_messages.NO_DATA
         if hda.state == model.Job.states.ERROR:
-            return hda.conversion_messages.ERROR
+            return HDA_model.conversion_messages.ERROR
         if hda.state != model.Job.states.OK:
-            return hda.conversion_messages.PENDING
+            return HDA_model.conversion_messages.PENDING
         return None
 
     # .... associated job
 
     # .... data
     # TODO: to data provider or Text datatype directly
-    def text_data( self, dataset, preview=True ):
+    def text_data( self, hda, preview=True ):
         """
         Get data from text file, truncating if necessary.
         """
+        # 1 MB
+        MAX_PEEK_SIZE = 1000000
+
         truncated = False
-        dataset_data = None
-        if os.path.exists( dataset.file_name ):
-            if isinstance( dataset.datatype, datatypes.data.Text ):
-                max_peek_size = 1000000  # 1 MB
-                if preview and os.stat( dataset.file_name ).st_size > max_peek_size:
-                    dataset_data = open( dataset.file_name ).read( max_peek_size )
-                    truncated = True
-                else:
-                    dataset_data = open( dataset.file_name ).read( max_peek_size )
-                    truncated = False
-            else:
-                # For now, cannot get data from non-text datasets.
-                dataset_data = None
-        return truncated, dataset_data
+        hda_data = None
+        # For now, cannot get data from non-text datasets.
+        if not isinstance( hda.datatype, datatypes.data.Text ):
+            return truncated, hda_data
+        if not os.path.exists( hda.file_name ):
+            return truncated, hda_data
+
+        truncated = preview and os.stat( hda.file_name ).st_size > MAX_PEEK_SIZE
+        hda_data = open( hda.file_name ).read( max_peek_size )
+        return truncated, hda_data
 
 
 class HDASerializer( # datasets._UnflattenedMetadataDatasetAssociationSerializer,
@@ -372,7 +372,7 @@ class HDASerializer( # datasets._UnflattenedMetadataDatasetAssociationSerializer
         Return web controller urls useful for this HDA.
         """
         url_for = self.url_for
-        encoded_id = self.security.encode_id( hda.id )
+        encoded_id = self.app.security.encode_id( hda.id )
         urls = {
             'purge'         : url_for( controller='dataset', action='purge_async', dataset_id=encoded_id ),
             'display'       : url_for( controller='dataset', action='display', dataset_id=encoded_id, preview=True ),
@@ -416,12 +416,12 @@ class HDADeserializer( datasets.DatasetAssociationDeserializer,
         self.deserializable_keyset.update( self.deserializers.keys() )
 
 
-class HDAFilters( datasets.DatasetAssociationFilters,
-                  taggable.TaggableFilterMixin,
-                  annotatable.AnnotatableFilterMixin ):
+class HDAFilterParser( datasets.DatasetAssociationFilterParser,
+                       taggable.TaggableFilterMixin,
+                       annotatable.AnnotatableFilterMixin ):
     model_class = model.HistoryDatasetAssociation
 
     def _add_parsers( self ):
-        super( HDAFilters, self )._add_parsers()
+        super( HDAFilterParser, self )._add_parsers()
         taggable.TaggableFilterMixin._add_parsers( self )
         annotatable.AnnotatableFilterMixin._add_parsers( self )
diff --git a/test/unit/managers/test_DatasetManager.py b/test/unit/managers/test_DatasetManager.py
index 6cc56f7615f..9a3a6a7480c 100644
--- a/test/unit/managers/test_DatasetManager.py
+++ b/test/unit/managers/test_DatasetManager.py
@@ -1,11 +1,10 @@
-#!/usr/bin/env python
+# -*- coding: utf-8 -*-
 """
 """
 import sys
 import os
 import pprint
 import unittest
-import json
 
 __GALAXY_ROOT__ = os.getcwd() + '/../../../'
 sys.path.insert( 1, __GALAXY_ROOT__ + 'lib' )
@@ -206,11 +205,10 @@ class DatasetSerializerTestCase( BaseTestCase ):
         self.assertKeys( summary_view, self.dataset_serializer.views[ 'summary' ] )
 
         self.log( 'should have a serializer for all serializable keys' )
-        need_no_serializers = ( basestring, bool, type( None ) )
         for key in self.dataset_serializer.serializable_keyset:
             instantiated_attribute = getattr( dataset, key, None )
             if not ( ( key in self.dataset_serializer.serializers )
-                  or ( isinstance( instantiated_attribute, need_no_serializers ) ) ):
+                  or ( isinstance( instantiated_attribute, self.TYPES_NEEDING_NO_SERIALIZERS ) ) ):
                 self.fail( 'no serializer for: %s (%s)' % ( key, instantiated_attribute ) )
         else:
             self.assertTrue( True, 'all serializable keys have a serializer' )
@@ -236,7 +234,7 @@ class DatasetSerializerTestCase( BaseTestCase ):
     def test_serializers( self ):
         user2 = self.user_mgr.create( self.trans, **user2_data )
         dataset = self.dataset_mgr.create( self.trans )
-        all_keys = self.dataset_serializer.serializable_keyset
+        all_keys = list( self.hda_serializer.serializable_keyset )
         serialized = self.dataset_serializer.serialize( self.trans, dataset, all_keys )
 
         self.log( 'everything serialized should be of the proper type' )
@@ -255,7 +253,7 @@ class DatasetSerializerTestCase( BaseTestCase ):
         # self.assertIsInstance( serialized[ 'total_size' ], int )
 
         self.log( 'serialized should jsonify well' )
-        self.assertIsInstance( json.dumps( serialized ), basestring )
+        self.assertIsJsonifyable( serialized )
 
 
 # =============================================================================
@@ -272,13 +270,13 @@ class DatasetDeserializerTestCase( BaseTestCase ):
         self.log( 'should raise when deserializing deleted from non-bool' )
         self.assertFalse( dataset.deleted )
         self.assertRaises( exceptions.RequestParameterInvalidException,
-            self.dataset_deserializer.deserialize, self.trans, dataset, data={ 'deleted': None }, flush=True )
+            self.dataset_deserializer.deserialize, self.trans, dataset, data={ 'deleted': None } )
         self.assertFalse( dataset.deleted )
         self.log( 'should be able to deserialize deleted from True' )
-        self.dataset_deserializer.deserialize( self.trans, dataset, data={ 'deleted': True }, flush=True )
+        self.dataset_deserializer.deserialize( self.trans, dataset, data={ 'deleted': True } )
         self.assertTrue( dataset.deleted )
         self.log( 'should be able to reverse by deserializing deleted from False' )
-        self.dataset_deserializer.deserialize( self.trans, dataset, data={ 'deleted': False }, flush=True )
+        self.dataset_deserializer.deserialize( self.trans, dataset, data={ 'deleted': False } )
         self.assertFalse( dataset.deleted )
 
     def test_deserialize_purge( self ):
@@ -286,14 +284,14 @@ class DatasetDeserializerTestCase( BaseTestCase ):
 
         self.log( 'should raise when deserializing purged from non-bool' )
         self.assertRaises( exceptions.RequestParameterInvalidException,
-            self.dataset_deserializer.deserialize, self.trans, dataset, data={ 'purged': None }, flush=True )
+            self.dataset_deserializer.deserialize, self.trans, dataset, data={ 'purged': None } )
         self.assertFalse( dataset.purged )
         self.log( 'should be able to deserialize purged from True' )
-        self.dataset_deserializer.deserialize( self.trans, dataset, data={ 'purged': True }, flush=True )
+        self.dataset_deserializer.deserialize( self.trans, dataset, data={ 'purged': True } )
         self.assertTrue( dataset.purged )
         # TODO: should this raise an error?
         self.log( 'should NOT be able to deserialize purged from False (will remain True)' )
-        self.dataset_deserializer.deserialize( self.trans, dataset, data={ 'purged': False }, flush=True )
+        self.dataset_deserializer.deserialize( self.trans, dataset, data={ 'purged': False } )
         self.assertTrue( dataset.purged )
 
     # def test_deserialize_permissions( self ):
@@ -301,44 +299,12 @@ class DatasetDeserializerTestCase( BaseTestCase ):
 
 
 # =============================================================================
-class DatasetAssociationManagerTestCase( BaseTestCase ):
-
-    def set_up_managers( self ):
-        super( DatasetAssociationManagerTestCase, self ).set_up_managers()
-        self.dataset_assoc_mgr = HDAManager( self.app )
-        self.hda_mgr = HDAManager( self.app )
-        self.history_mgr = HistoryManager( self.app )
-
-    def test_purge_allowed( self ):
-        self.trans.app.config.allow_user_dataset_purge = True
-        item1 = self.dataset_assoc_mgr.create( self.trans )
-
-        self.log( "should purge a dataset assoc if config does allow" )
-        self.assertFalse( item1.purged )
-        self.assertEqual( self.dataset_assoc_mgr.purge( self.trans, item1 ), item1 )
-        self.assertTrue( item1.purged )
-
-        # not necc. true for dataset assocs
-        # self.log( "should delete a dataset assoc when purging" )
-        # self.assertTrue( item1.deleted )
-
-    def test_purge_not_allowed( self ):
-        self.trans.app.config.allow_user_dataset_purge = False
-        item1 = self.dataset_assoc_mgr.create( self.trans )
-
-        self.log( "should raise an error when purging a dataset assoc if config does not allow" )
-        self.assertFalse( item1.purged )
-        self.assertRaises( exceptions.ConfigDoesNotAllowException, self.dataset_assoc_mgr.purge, self.trans, item1 )
-        self.assertFalse( item1.purged )
-
-    #def test_metadata( self ):
-    #    owner = self.user_mgr.create( self.trans, **user2_data )
-    #    history1 = self.history_mgr.create( self.trans, name='history1', user=owner )
-    #    dataset1 = self.dataset_mgr.create( self.trans )
-    #
-    #    self.log( "should be able to create a new HDA with a specified history and dataset" )
-    #    hda1 = self.hda_mgr.create( self.trans, history=history1, dataset=dataset1, hid=1 )
-
+# NOTE: that we test the DatasetAssociation* classes in either test_HDAManager or test_LDAManager
+# (as part of those subclasses):
+#   DatasetAssociationManager,
+#   DatasetAssociationSerializer,
+#   DatasetAssociationDeserializer,
+#   DatasetAssociationFilterParser
 
 # =============================================================================
 if __name__ == '__main__':
diff --git a/test/unit/managers/test_HDAManager.py b/test/unit/managers/test_HDAManager.py
index 1911d3a74b4..9e1eb159f73 100644
--- a/test/unit/managers/test_HDAManager.py
+++ b/test/unit/managers/test_HDAManager.py
@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import sys
 import os
 import pprint
@@ -18,7 +19,7 @@ import mock
 from test_ModelManager import BaseTestCase
 from galaxy.managers.histories import HistoryManager
 from galaxy.managers.datasets import DatasetManager
-from galaxy.managers.hdas import HDAManager
+from galaxy.managers import hdas
 
 
 # =============================================================================
@@ -26,15 +27,24 @@ default_password = '123456'
 user2_data = dict( email='user2@user2.user2', username='user2', password=default_password )
 user3_data = dict( email='user3@user3.user3', username='user3', password=default_password )
 
-
-# =============================================================================
-class HDAManagerTestCase( BaseTestCase ):
+class HDATestCase( BaseTestCase ):
 
     def set_up_managers( self ):
-        super( HDAManagerTestCase, self ).set_up_managers()
+        super( HDATestCase, self ).set_up_managers()
+        self.hda_mgr = hdas.HDAManager( self.app )
         self.history_mgr = HistoryManager( self.app )
         self.dataset_mgr = DatasetManager( self.app )
-        self.hda_mgr = HDAManager( self.app )
+
+    def _create_vanilla_hda( self, user_data=None ):
+        user_data = user_data or user2_data
+        owner = self.user_mgr.create( self.trans, **user_data )
+        history1 = self.history_mgr.create( self.trans, name='history1', user=owner )
+        dataset1 = self.dataset_mgr.create( self.trans )
+        return self.hda_mgr.create( self.trans, history=history1, dataset=dataset1 )
+
+
+# =============================================================================
+class HDAManagerTestCase( HDATestCase ):
 
     def test_base( self ):
         hda_model = model.HistoryDatasetAssociation
@@ -211,6 +221,356 @@ class HDAManagerTestCase( BaseTestCase ):
         self.assertRaises( exceptions.ItemOwnershipException,
             self.hda_mgr.error_unless_owner, self.trans, item1, non_owner )
 
+    def test_error_if_uploading( self ):
+        owner = self.user_mgr.create( self.trans, **user2_data )
+        history1 = self.history_mgr.create( self.trans, name='history1', user=owner )
+        dataset1 = self.dataset_mgr.create( self.trans )
+        hda = self.hda_mgr.create( self.trans, history=history1, dataset=dataset1 )
+
+        hda.state = model.Dataset.states.OK
+        self.log( "should not raise an error when calling error_if_uploading and in a non-uploading state" )
+        self.assertEqual( self.hda_mgr.error_if_uploading( self.trans, hda ), hda )
+
+        hda.state = model.Dataset.states.UPLOAD
+        self.log( "should raise an error when calling error_if_uploading and in the uploading state" )
+        self.assertRaises( exceptions.Conflict,
+            self.hda_mgr.error_if_uploading, self.trans, hda )
+
+    def test_data_conversion_status( self ):
+        owner = self.user_mgr.create( self.trans, **user2_data )
+        history1 = self.history_mgr.create( self.trans, name='history1', user=owner )
+        dataset1 = self.dataset_mgr.create( self.trans )
+        hda = self.hda_mgr.create( self.trans, history=history1, dataset=dataset1 )
+
+        self.log( "data conversion status should reflect state" )
+        self.assertEqual( self.hda_mgr.data_conversion_status( self.trans, None ),
+            hda.conversion_messages.NO_DATA )
+        hda.state = model.Dataset.states.ERROR
+        self.assertEqual( self.hda_mgr.data_conversion_status( self.trans, hda ),
+            hda.conversion_messages.ERROR )
+        hda.state = model.Dataset.states.QUEUED
+        self.assertEqual( self.hda_mgr.data_conversion_status( self.trans, hda ),
+            hda.conversion_messages.PENDING )
+        hda.state = model.Dataset.states.OK
+        self.assertEqual( self.hda_mgr.data_conversion_status( self.trans, hda ), None )
+
+    # def test_text_data( self ):
+
+
+# =============================================================================
+# web.url_for doesn't work well in the framework
+testable_url_for = lambda *a, **k: '(fake url): %s, %s' % ( a, k )
+hdas.HDASerializer.url_for = staticmethod( testable_url_for )
+
+class HDASerializerTestCase( HDATestCase ):
+
+    def set_up_managers( self ):
+        super( HDASerializerTestCase, self ).set_up_managers()
+        self.hda_serializer = hdas.HDASerializer( self.app )
+
+    def test_views( self ):
+        hda = self._create_vanilla_hda()
+
+        self.log( 'should have a summary view' )
+        summary_view = self.hda_serializer.serialize_to_view( self.trans, hda, view='summary' )
+        self.assertKeys( summary_view, self.hda_serializer.views[ 'summary' ] )
+
+        self.log( 'should have the summary view as default view' )
+        default_view = self.hda_serializer.serialize_to_view( self.trans, hda, default_view='summary' )
+        self.assertKeys( summary_view, self.hda_serializer.views[ 'summary' ] )
+
+        # self.log( 'should have a detailed view' )
+        # detailed_view = self.hda_serializer.serialize_to_view( self.trans, hda, view='detailed' )
+        # self.assertKeys( detailed_view, self.hda_serializer.views[ 'detailed' ] )
+
+        # self.log( 'should have a extended view' )
+        # extended_view = self.hda_serializer.serialize_to_view( self.trans, hda, view='extended' )
+        # self.assertKeys( extended_view, self.hda_serializer.views[ 'extended' ] )
+
+        self.log( 'should have a inaccessible view' )
+        inaccessible_view = self.hda_serializer.serialize_to_view( self.trans, hda, view='inaccessible' )
+        self.assertKeys( inaccessible_view, self.hda_serializer.views[ 'inaccessible' ] )
+
+        # skip metadata for this test
+        def is_metadata( key ):
+            return ( key == 'metadata'
+                  or key.startswith( 'metadata_' ) )
+
+        self.log( 'should have a serializer for all serializable keys' )
+        for key in self.hda_serializer.serializable_keyset:
+            instantiated_attribute = getattr( hda, key, None )
+            if not ( ( key in self.hda_serializer.serializers )
+                  or ( isinstance( instantiated_attribute, self.TYPES_NEEDING_NO_SERIALIZERS ) )
+                  or ( is_metadata( key ) ) ):
+                self.fail( 'no serializer for: %s (%s)' % ( key, instantiated_attribute ) )
+        else:
+            self.assertTrue( True, 'all serializable keys have a serializer' )
+
+    def test_views_and_keys( self ):
+        hda = self._create_vanilla_hda()
+
+        self.log( 'should be able to use keys with views' )
+        serialized = self.hda_serializer.serialize_to_view( self.trans, hda,
+            view='summary', keys=[ 'uuid' ] )
+        self.assertKeys( serialized,
+            self.hda_serializer.views[ 'summary' ] + [ 'uuid' ] )
+
+        self.log( 'should be able to use keys on their own' )
+        serialized = self.hda_serializer.serialize_to_view( self.trans, hda,
+            keys=[ 'file_path', 'visualizations' ] )
+        self.assertKeys( serialized, [ 'file_path', 'visualizations' ] )
+
+    def test_serializers( self ):
+        hda = self._create_vanilla_hda()
+        all_keys = list( self.hda_serializer.serializable_keyset )
+        serialized = self.hda_serializer.serialize( self.trans, hda, all_keys )
+
+        self.log( 'everything serialized should be of the proper type' )
+        # base
+        self.assertEncodedId( serialized[ 'id' ] )
+        self.assertDate( serialized[ 'create_time' ] )
+        self.assertDate( serialized[ 'update_time' ] )
+
+        # dataset association
+        self.assertIsInstance( serialized[ 'dataset' ], dict )
+        self.assertEncodedId( serialized[ 'dataset_id' ] )
+        self.assertUUID( serialized[ 'uuid' ] )
+        self.assertIsInstance( serialized[ 'file_name' ], basestring )
+        self.assertIsInstance( serialized[ 'extra_files_path' ], basestring )
+        self.assertIsInstance( serialized[ 'permissions' ], dict )
+        self.assertIsInstance( serialized[ 'size' ], int )
+        self.assertIsInstance( serialized[ 'file_size' ], int )
+        self.assertIsInstance( serialized[ 'nice_size' ], basestring )
+        # TODO: these should be tested w/copy
+        self.assertNullableEncodedId( serialized[ 'copied_from_history_dataset_association_id'] )
+        self.assertNullableEncodedId( serialized[ 'copied_from_library_dataset_dataset_association_id'] )
+        self.assertNullableBasestring( serialized[ 'info' ] )
+        self.assertNullableBasestring( serialized[ 'blurb' ] )
+        self.assertNullableBasestring( serialized[ 'peek' ] )
+        self.assertIsInstance( serialized[ 'meta_files' ], list )
+        self.assertNullableEncodedId( serialized[ 'parent_id'] )
+        self.assertEqual( serialized[ 'designation' ], None )
+        self.assertIsInstance( serialized[ 'genome_build' ], basestring )
+        self.assertIsInstance( serialized[ 'data_type' ], basestring )
+
+        # hda
+        self.assertEncodedId( serialized[ 'history_id' ] )
+        self.assertEqual( serialized[ 'type_id' ], 'dataset-' + serialized[ 'id' ] )
+
+        self.assertIsInstance( serialized[ 'resubmitted' ], bool )
+        self.assertIsInstance( serialized[ 'display_apps' ], list )
+        self.assertIsInstance( serialized[ 'display_types' ], list )
+        self.assertIsInstance( serialized[ 'visualizations' ], list )
+
+        # remapped
+        self.assertNullableBasestring( serialized[ 'misc_info' ] )
+        self.assertNullableBasestring( serialized[ 'misc_blurb' ] )
+        self.assertNullableBasestring( serialized[ 'file_ext' ] )
+        self.assertNullableBasestring( serialized[ 'file_path' ] )
+
+        # identities
+        self.assertEqual( serialized[ 'model_class' ], 'HistoryDatasetAssociation' )
+        self.assertEqual( serialized[ 'history_content_type' ], 'dataset' )
+        self.assertEqual( serialized[ 'hda_ldda' ], 'hda' )
+        self.assertEqual( serialized[ 'accessible' ], True )
+        self.assertEqual( serialized[ 'api_type' ], 'file' )
+        self.assertEqual( serialized[ 'type' ], 'file' )
+
+        self.assertIsInstance( serialized[ 'url' ], basestring )
+        self.assertIsInstance( serialized[ 'urls' ], dict )
+        self.assertIsInstance( serialized[ 'download_url' ], basestring )
+
+        self.log( 'serialized should jsonify well' )
+        self.assertIsJsonifyable( serialized )
+
+
+# =============================================================================
+class HDADeserializerTestCase( HDATestCase ):
+
+    def set_up_managers( self ):
+        super( HDADeserializerTestCase, self ).set_up_managers()
+        self.hda_deserializer = hdas.HDADeserializer( self.app )
+
+    def test_deserialize_delete( self ):
+        hda = self._create_vanilla_hda()
+
+        self.log( 'should raise when deserializing deleted from non-bool' )
+        self.assertFalse( hda.deleted )
+        self.assertRaises( exceptions.RequestParameterInvalidException,
+            self.hda_deserializer.deserialize, self.trans, hda, data={ 'deleted': None } )
+        self.assertFalse( hda.deleted )
+        self.log( 'should be able to deserialize deleted from True' )
+        self.hda_deserializer.deserialize( self.trans, hda, data={ 'deleted': True } )
+        self.assertTrue( hda.deleted )
+        self.log( 'should be able to reverse by deserializing deleted from False' )
+        self.hda_deserializer.deserialize( self.trans, hda, data={ 'deleted': False } )
+        self.assertFalse( hda.deleted )
+
+    def test_deserialize_purge( self ):
+        hda = self._create_vanilla_hda()
+
+        self.log( 'should raise when deserializing purged from non-bool' )
+        self.assertRaises( exceptions.RequestParameterInvalidException,
+            self.hda_deserializer.deserialize, self.trans, hda, data={ 'purged': None } )
+        self.assertFalse( hda.purged )
+        self.log( 'should be able to deserialize purged from True' )
+        self.hda_deserializer.deserialize( self.trans, hda, data={ 'purged': True } )
+        self.assertTrue( hda.purged )
+        # TODO: should this raise an error?
+        self.log( 'should NOT be able to deserialize purged from False (will remain True)' )
+        self.hda_deserializer.deserialize( self.trans, hda, data={ 'purged': False } )
+        self.assertTrue( hda.purged )
+
+    def test_deserialize_visible( self ):
+        hda = self._create_vanilla_hda()
+
+        self.log( 'should raise when deserializing from non-bool' )
+        self.assertTrue( hda.visible )
+        self.assertRaises( exceptions.RequestParameterInvalidException,
+            self.hda_deserializer.deserialize, self.trans, hda, data={ 'visible': 'None' } )
+        self.assertTrue( hda.visible )
+        self.log( 'should be able to deserialize from False' )
+        self.hda_deserializer.deserialize( self.trans, hda, data={ 'visible': False } )
+        self.assertFalse( hda.visible )
+        self.log( 'should be able to reverse by deserializing from True' )
+        self.hda_deserializer.deserialize( self.trans, hda, data={ 'visible': True } )
+        self.assertTrue( hda.visible )
+
+    def test_deserialize_genome_build( self ):
+        hda = self._create_vanilla_hda()
+
+        self.assertIsInstance( hda.dbkey, basestring )
+        self.log( 'should deserialize to "?" from None' )
+        self.hda_deserializer.deserialize( self.trans, hda, data={ 'genome_build': None } )
+        self.assertEqual( hda.dbkey, '?' )
+        self.log( 'should raise when deserializing from non-string' )
+        self.assertRaises( exceptions.RequestParameterInvalidException,
+            self.hda_deserializer.deserialize, self.trans, hda, data={ 'genome_build': 12 } )
+        self.log( 'should be able to deserialize from unicode' )
+        date_palm = u'نخيل التمر'
+        self.hda_deserializer.deserialize( self.trans, hda, data={ 'genome_build': date_palm } )
+        self.assertEqual( hda.dbkey, date_palm )
+        self.log( 'should be deserializable from empty string' )
+        self.hda_deserializer.deserialize( self.trans, hda, data={ 'genome_build': '' } )
+        self.assertEqual( hda.dbkey, '' )
+
+
+# # =============================================================================
+# # web.url_for doesn't work well in the framework
+# testable_url_for = lambda *a, **k: '(fake url): %s, %s' % ( a, k )
+# DatasetSerializer.url_for = staticmethod( testable_url_for )
+
+# class DatasetAssociationSerializerTestCase( BaseTestCase ):
+
+#     def set_up_managers( self ):
+#         super( DatasetAssociationSerializerTestCase, self ).set_up_managers()
+#         self.dataset_assoc_mgr = DatasetAssociationManager( self.app )
+#         self.dataset_assoc_serializer = DatasetAssocationSerializer( self.app )
+
+#     def test_views( self ):
+#         dataset_assoc = self.dataset_mgr.create( self.trans )
+
+#         self.log( 'should have a summary view' )
+#         summary_view = self.dataset_serializer.serialize_to_view( self.trans, dataset, view='summary' )
+#         self.assertKeys( summary_view, self.dataset_serializer.views[ 'summary' ] )
+
+#         self.log( 'should have the summary view as default view' )
+#         default_view = self.dataset_serializer.serialize_to_view( self.trans, dataset, default_view='summary' )
+#         self.assertKeys( summary_view, self.dataset_serializer.views[ 'summary' ] )
+
+#         self.log( 'should have a serializer for all serializable keys' )
+#         for key in self.dataset_serializer.serializable_keyset:
+#             instantiated_attribute = getattr( dataset, key, None )
+#             if not ( ( key in self.dataset_serializer.serializers )
+#                   or ( isinstance( instantiated_attribute, self.TYPES_NEEDING_NO_SERIALIZERS ) ) ):
+#                 self.fail( 'no serializer for: %s (%s)' % ( key, instantiated_attribute ) )
+#         else:
+#             self.assertTrue( True, 'all serializable keys have a serializer' )
+
+#     def test_views_and_keys( self ):
+#         dataset = self.dataset_mgr.create( self.trans )
+
+#         self.log( 'should be able to use keys with views' )
+#         serialized = self.dataset_serializer.serialize_to_view( self.trans, dataset,
+#             view='summary', keys=[ 'permissions' ] )
+#         self.assertKeys( serialized,
+#             self.dataset_serializer.views[ 'summary' ] + [ 'permissions' ] )
+
+#         self.log( 'should be able to use keys on their own' )
+#         serialized = self.dataset_serializer.serialize_to_view( self.trans, dataset,
+#             keys=[ 'purgable', 'file_size' ] )
+#         self.assertKeys( serialized, [ 'purgable', 'file_size' ] )
+
+#     def test_serialize_permissions( self ):
+#         dataset = self.dataset_mgr.create( self.trans )
+#         self.log( 'serialized permissions should be well formed' )
+
+#     def test_serializers( self ):
+#         user2 = self.user_mgr.create( self.trans, **user2_data )
+#         dataset = self.dataset_mgr.create( self.trans )
+#         all_keys = list( self.hda_serializer.serializable_keyset )
+#         serialized = self.dataset_serializer.serialize( self.trans, dataset, all_keys )
+
+#         self.log( 'everything serialized should be of the proper type' )
+#         self.assertEncodedId( serialized[ 'id' ] )
+#         self.assertDate( serialized[ 'create_time' ] )
+#         self.assertDate( serialized[ 'update_time' ] )
+
+#         self.assertUUID( serialized[ 'uuid' ] )
+#         self.assertIsInstance( serialized[ 'state' ], basestring )
+#         self.assertIsInstance( serialized[ 'deleted' ], bool )
+#         self.assertIsInstance( serialized[ 'purged' ], bool )
+#         self.assertIsInstance( serialized[ 'purgable' ], bool )
+
+#         # # TODO: no great way to do these with mocked dataset
+#         # self.assertIsInstance( serialized[ 'file_size' ], int )
+#         # self.assertIsInstance( serialized[ 'total_size' ], int )
+
+#         self.log( 'serialized should jsonify well' )
+#         self.assertIsJsonifyable( serialized )
+
+
+# # =============================================================================
+# class DatasetAssocationDeserializerTestCase( BaseTestCase ):
+
+#     def set_up_managers( self ):
+#         super( DatasetAssocationDeserializerTestCase, self ).set_up_managers()
+#         self.dataset_mgr = DatasetAssocationManager( self.app )
+#         self.dataset_deserializer = DatasetAssocationDeserializer( self.app )
+
+#     def test_deserialize_delete( self ):
+#         dataset = self.dataset_mgr.create( self.trans )
+
+#         self.log( 'should raise when deserializing deleted from non-bool' )
+#         self.assertFalse( dataset.deleted )
+#         self.assertRaises( exceptions.RequestParameterInvalidException,
+#             self.dataset_deserializer.deserialize, self.trans, dataset, data={ 'deleted': None } )
+#         self.assertFalse( dataset.deleted )
+#         self.log( 'should be able to deserialize deleted from True' )
+#         self.dataset_deserializer.deserialize( self.trans, dataset, data={ 'deleted': True } )
+#         self.assertTrue( dataset.deleted )
+#         self.log( 'should be able to reverse by deserializing deleted from False' )
+#         self.dataset_deserializer.deserialize( self.trans, dataset, data={ 'deleted': False } )
+#         self.assertFalse( dataset.deleted )
+
+#     def test_deserialize_purge( self ):
+#         dataset = self.dataset_mgr.create( self.trans )
+
+#         self.log( 'should raise when deserializing purged from non-bool' )
+#         self.assertRaises( exceptions.RequestParameterInvalidException,
+#             self.dataset_deserializer.deserialize, self.trans, dataset, data={ 'purged': None } )
+#         self.assertFalse( dataset.purged )
+#         self.log( 'should be able to deserialize purged from True' )
+#         self.dataset_deserializer.deserialize( self.trans, dataset, data={ 'purged': True } )
+#         self.assertTrue( dataset.purged )
+#         # TODO: should this raise an error?
+#         self.log( 'should NOT be able to deserialize purged from False (will remain True)' )
+#         self.dataset_deserializer.deserialize( self.trans, dataset, data={ 'purged': False } )
+#         self.assertTrue( dataset.purged )
+
+#     # def test_deserialize_permissions( self ):
+#     #     pass
+
 
 # =============================================================================
 if __name__ == '__main__':
diff --git a/test/unit/managers/test_HistoryManager.py b/test/unit/managers/test_HistoryManager.py
index 70a817cf4c9..a83e1411c89 100644
--- a/test/unit/managers/test_HistoryManager.py
+++ b/test/unit/managers/test_HistoryManager.py
@@ -1,11 +1,10 @@
-#!/usr/bin/env python
+# -*- coding: utf-8 -*-
 """
 """
 import sys
 import os
 import pprint
 import unittest
-import json
 
 __GALAXY_ROOT__ = os.getcwd() + '/../../../'
 sys.path.insert( 1, __GALAXY_ROOT__ + 'lib' )
@@ -341,11 +340,10 @@ class HistorySerializerTestCase( BaseTestCase ):
         self.assertKeys( summary_view, self.history_serializer.views[ 'summary' ] )
 
         self.log( 'should have a serializer for all serializable keys' )
-        need_no_serializers = ( basestring, bool, type( None ) )
         for key in self.history_serializer.serializable_keyset:
             instantiated_attribute = getattr( history1, key, None )
             if not ( ( key in self.history_serializer.serializers )
-                  or ( isinstance( instantiated_attribute, need_no_serializers ) ) ):
+                  or ( isinstance( instantiated_attribute, self.TYPES_NEEDING_NO_SERIALIZERS ) ) ):
                 self.fail( 'no serializer for: %s (%s)' % ( key, instantiated_attribute ) )
         else:
             self.assertTrue( True, 'all serializable keys have a serializer' )
@@ -398,7 +396,7 @@ class HistorySerializerTestCase( BaseTestCase ):
     def test_history_serializers( self ):
         user2 = self.user_mgr.create( self.trans, **user2_data )
         history1 = self.history_mgr.create( self.trans, name='history1', user=user2 )
-        all_keys = self.history_serializer.serializable_keyset
+        all_keys = list( self.hda_serializer.serializable_keyset )
         serialized = self.history_serializer.serialize( self.trans, history1, all_keys )
 
         self.log( 'everything serialized should be of the proper type' )
@@ -438,6 +436,10 @@ class HistorySerializerTestCase( BaseTestCase ):
         serialized = self.history_serializer.serialize( self.trans, history1, [ 'contents' ] )
         self.assertHasKeys( serialized[ 'contents' ][0], [ 'id', 'name', 'peek', 'create_time' ])
 
+        self.log( 'serialized should jsonify well' )
+        self.assertIsJsonifyable( serialized )
+
+
 # =============================================================================
 class HistoryDeserializerTestCase( BaseTestCase ):
 
diff --git a/test/unit/managers/test_ModelManager.py b/test/unit/managers/test_ModelManager.py
index 611dcc4ae68..bab2682e434 100644
--- a/test/unit/managers/test_ModelManager.py
+++ b/test/unit/managers/test_ModelManager.py
@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 """
 """
 from __future__ import print_function
@@ -7,6 +6,7 @@ import sys
 import os
 import pprint
 import unittest
+import json
 
 __GALAXY_ROOT__ = os.getcwd() + '/../../../'
 sys.path.insert( 1, __GALAXY_ROOT__ + 'lib' )
@@ -76,6 +76,8 @@ class BaseTestCase( unittest.TestCase ):
         print( *args, **kwargs )
 
     # ---- additional test types
+    TYPES_NEEDING_NO_SERIALIZERS = ( basestring, bool, type( None ), int, float )
+
     def assertKeys( self, obj, key_list ):
         self.assertEqual( sorted( obj.keys() ), sorted( key_list ) )
 
@@ -86,12 +88,24 @@ class BaseTestCase( unittest.TestCase ):
         else:
             self.assertTrue( True, 'keys found in object' )
 
+    def assertNullableBasestring( self, item ):
+        if not isinstance( item, ( basestring, type( None ) ) ):
+            self.fail( 'Non-nullable basestring: ' + str( type( item ) ) )
+        # TODO: len mod 8 and hex re
+        self.assertTrue( True, 'is nullable basestring: ' + str( item ) )
+
     def assertEncodedId( self, item ):
         if not isinstance( item, basestring ):
             self.fail( 'Non-string: ' + str( type( item ) ) )
         # TODO: len mod 8 and hex re
         self.assertTrue( True, 'is id: ' + item )
 
+    def assertNullableEncodedId( self, item ):
+        if item is None:
+            self.assertTrue( True, 'nullable id is None' )
+        else:
+            self.assertEncodedId( item )
+
     def assertDate( self, item ):
         if not isinstance( item, basestring ):
             self.fail( 'Non-string: ' + str( type( item ) ) )
@@ -111,6 +125,9 @@ class BaseTestCase( unittest.TestCase ):
         # TODO: re for d4d76d69-80d4-4ed7-80c7-211ebcc1a358
         self.assertTrue( True, msg or ( 'is an orm filter: ' + item ) )
 
+    def assertIsJsonifyable( self, item ):
+        # TODO: use galaxy's override
+        self.assertIsInstance( json.dumps( item ), basestring )
 
 
 # =============================================================================
diff --git a/test/unit/managers/test_UserManager.py b/test/unit/managers/test_UserManager.py
index 6d8666e3a13..f48e03f6855 100644
--- a/test/unit/managers/test_UserManager.py
+++ b/test/unit/managers/test_UserManager.py
@@ -1,11 +1,10 @@
-#!/usr/bin/env python
+# -*- coding: utf-8 -*-
 """
 """
 import sys
 import os
 import pprint
 import unittest
-import json
 
 __GALAXY_ROOT__ = os.getcwd() + '/../../../'
 sys.path.insert( 1, __GALAXY_ROOT__ + 'lib' )
@@ -151,11 +150,10 @@ class UserSerializerTestCase( BaseTestCase ):
         self.assertKeys( summary_view, self.user_serializer.views[ 'summary' ] )
 
         self.log( 'should have a serializer for all serializable keys' )
-        need_no_serializers = ( basestring, bool, type( None ) )
         for key in self.user_serializer.serializable_keyset:
             instantiated_attribute = getattr( user, key, None )
             if not ( ( key in self.user_serializer.serializers )
-                  or ( isinstance( instantiated_attribute, need_no_serializers ) ) ):
+                  or ( isinstance( instantiated_attribute, self.TYPES_NEEDING_NO_SERIALIZERS ) ) ):
                 self.fail( 'no serializer for: %s (%s)' % ( key, instantiated_attribute ) )
         else:
             self.assertTrue( True, 'all serializable keys have a serializer' )
@@ -176,7 +174,7 @@ class UserSerializerTestCase( BaseTestCase ):
 
     def test_serializers( self ):
         user = self.user_mgr.create( self.trans, **user2_data )
-        all_keys = self.user_serializer.serializable_keyset
+        all_keys = list( self.hda_serializer.serializable_keyset )
         serialized = self.user_serializer.serialize( self.trans, user, all_keys )
         # pprint.pprint( serialized )
 
@@ -196,7 +194,7 @@ class UserSerializerTestCase( BaseTestCase ):
         self.assertIsInstance( serialized[ 'requests' ], list )
 
         self.log( 'serialized should jsonify well' )
-        self.assertIsInstance( json.dumps( serialized ), basestring )
+        self.assertIsJsonifyable( serialized )
 
 
 class CurrentUserSerializerTestCase( BaseTestCase ):

From f8c6725c4201272f9764086aaf7614c1dceaf395 Mon Sep 17 00:00:00 2001
From: Carl Eberhard <carlfeberhard@gmail.com>
Date: Tue, 31 Mar 2015 15:35:17 -0400
Subject: [PATCH 19/88] Managers, filters: allow remapping of attribute keys;
 expand tests

---
 lib/galaxy/managers/base.py               |  38 ++++-
 lib/galaxy/managers/datasets.py           |  21 ++-
 test/unit/managers/test_DatasetManager.py |   2 +-
 test/unit/managers/test_HDAManager.py     | 177 +++++++++-------------
 test/unit/managers/test_HistoryManager.py |   4 +-
 test/unit/managers/test_ModelManager.py   |   8 +-
 test/unit/managers/test_UserManager.py    |   4 +-
 7 files changed, 124 insertions(+), 130 deletions(-)

diff --git a/lib/galaxy/managers/base.py b/lib/galaxy/managers/base.py
index 999d770f0b8..cd6c0e514dd 100644
--- a/lib/galaxy/managers/base.py
+++ b/lib/galaxy/managers/base.py
@@ -886,7 +886,8 @@ class ModelFilterParser( object ):
         # note: these are the default filters for all models
         self.orm_filter_parsers.update({
             # (prob.) applicable to all models
-            'id'            : { 'op': ( 'in' ), 'val': self.parse_id_list },
+            'id'            : { 'op': ( 'in' ) },
+            'encoded_id'    : { 'column' : 'id', 'op': ( 'in' ), 'val': self.parse_id_list },
             # dates can be directly passed through the orm into a filter (no need to parse into datetime object)
             'create_time'   : { 'op': ( 'le', 'ge' ) },
             'update_time'   : { 'op': ( 'le', 'ge' ) },
@@ -925,7 +926,7 @@ class ModelFilterParser( object ):
         # by convention, assume most val parsers raise ValueError
         except ValueError, val_err:
             raise exceptions.RequestParameterInvalidException( 'unparsable value for filter',
-                column=attr, operation=op, value=val )
+                column=attr, operation=op, value=val, ValueError=str( val_err ) )
 
         # if neither of the above work, raise an error with how-to info
         #TODO: send back all valid filter keys in exception for added user help
@@ -934,6 +935,7 @@ class ModelFilterParser( object ):
     # ---- fn filters
     def _parse_fn_filter( self, attr, op, val ):
         """
+        Attempt to parse a non-ORM filter function.
         """
         # fn_filter_list is a dict: fn_filter_list[ attr ] = { 'opname1' : opfn1, 'opname2' : opfn2, etc. }
 
@@ -957,18 +959,33 @@ class ModelFilterParser( object ):
     # ---- ORM filters
     def _parse_orm_filter( self, attr, op, val ):
         """
+        Attempt to parse a ORM-based filter.
+
+        Using SQLAlchemy, this would yield a sql.elements.BinaryExpression.
         """
         # orm_filter_list is a dict: orm_filter_list[ attr ] = <list of allowed ops>
-        # attr must be a whitelisted column
-        column = self.model_class.table.columns.get( attr )
         column_map = self.orm_filter_parsers.get( attr, None )
-        if column is None or not column_map:
+        if not column_map:
+            # no column mapping (not whitelisted)
             return None
+        # attr must be a whitelisted column by attr name or by key passed in column_map
+        # note: column_map[ 'column' ] takes precedence
+        column = self.model_class.table.columns.get( attr )
+        if 'column' in column_map:
+            remap_to = column_map[ 'column' ]
+            column = self.model_class.table.columns.get( remap_to )
+        if column is None:
+            # no orm column
+            return None
+
         # op must be whitelisted: contained in the list orm_filter_list[ attr ][ 'op' ]
         allowed_ops = column_map.get( 'op' )
         if op not in allowed_ops:
             return None
         op = self._convert_op_string_to_fn( column, op )
+        if not op:
+            return None
+
         # parse the val from string using the 'val' parser if present (otherwise, leave as string)
         val_parser = column_map.get( 'val', None )
         if val_parser:
@@ -993,12 +1010,21 @@ class ModelFilterParser( object ):
             fn_name = 'in_'
 
         # get the column fn using the op_string and error if not a callable attr
-        #TODO: special case 'not in' - or disallow?
+        # TODO: special case 'not in' - or disallow?
         op_fn = getattr( column, fn_name, None )
         if not op_fn or not callable( op_fn ):
             return None
         return op_fn
 
+    # ---- preset fn_filters: dictionaries of standard filter ops for standard datatypes
+    def string_standard_ops( self, key ):
+        return {
+            'op' : {
+                'eq'        : lambda i, v: v == getattr( i, key ),
+                'contains'  : lambda i, v: v in getattr( i, key ),
+            }
+        }
+
     # --- more parsers! yay!
 #TODO: These should go somewhere central - we've got ~6 parser modules/sections now
     def parse_bool( self, bool_string ):
diff --git a/lib/galaxy/managers/datasets.py b/lib/galaxy/managers/datasets.py
index 3275782b1b7..f9f68300851 100644
--- a/lib/galaxy/managers/datasets.py
+++ b/lib/galaxy/managers/datasets.py
@@ -499,43 +499,42 @@ class DatasetAssociationDeserializer( base.ModelDeserializer, deletable.Purgable
 
 class DatasetAssociationFilterParser( base.ModelFilterParser, deletable.PurgableFiltersMixin ):
 
-    def _datatype_from_string( class_str ):
-        """
-        """
-        return self.app.datatypes_registry.get_datatype_class_by_name( class_str )
-
     def _add_parsers( self ):
         super( DatasetAssociationFilterParser, self )._add_parsers()
         deletable.PurgableFiltersMixin._add_parsers( self )
 
         self.orm_filter_parsers.update({
             'name'      : { 'op': ( 'eq', 'contains', 'like' ) },
-            'state'     : { 'op': ( 'eq', 'in' ) },
+            'state'     : { 'column' : '_state', 'op': ( 'eq', 'in' ) },
             'visible'   : { 'op': ( 'eq' ), 'val': self.parse_bool },
-            'genome_build' : { 'op': ( 'eq', 'contains', 'like' ) },
         })
         self.fn_filter_parsers.update({
+            'genome_build' : self.string_standard_ops( 'dbkey' ),
             'data_type' : {
                 'op': {
                     'eq' : self.eq_datatype,
-                    'is' : self.is_datatype
+                    'isinstance' : self.isinstance_datatype
                 }
             }
         })
 
     def eq_datatype( self, dataset_assoc, class_str ):
         """
+        Is the `dataset_assoc` datatype equal to the registered datatype `class_str`?
         """
-        comparison_class = self._datatype_from_string( class_str )
+        comparison_class = self.app.datatypes_registry.get_datatype_class_by_name( class_str )
         return ( comparison_class
              and dataset_assoc.datatype.__class__ == comparison_class )
 
-    def is_datatype( self, dataset_assoc, class_strs ):
+    def isinstance_datatype( self, dataset_assoc, class_strs ):
         """
+        Is the `dataset_assoc` datatype derived from any of the registered
+        datatypes in the comma separated string `class_strs`?
         """
+        parse_datatype_fn = self.app.datatypes_registry.get_datatype_class_by_name
         comparison_classes = []
         for class_str in class_strs.split( ',' ):
-            datatype_class = self._datatype_from_string( class_str )
+            datatype_class = parse_datatype_fn( class_str )
             if datatype_class:
                 comparison_classes.append( datatype_class )
         return ( comparison_classes
diff --git a/test/unit/managers/test_DatasetManager.py b/test/unit/managers/test_DatasetManager.py
index 9a3a6a7480c..f33fba84d64 100644
--- a/test/unit/managers/test_DatasetManager.py
+++ b/test/unit/managers/test_DatasetManager.py
@@ -234,7 +234,7 @@ class DatasetSerializerTestCase( BaseTestCase ):
     def test_serializers( self ):
         user2 = self.user_mgr.create( self.trans, **user2_data )
         dataset = self.dataset_mgr.create( self.trans )
-        all_keys = list( self.hda_serializer.serializable_keyset )
+        all_keys = list( self.dataset_serializer.serializable_keyset )
         serialized = self.dataset_serializer.serialize( self.trans, dataset, all_keys )
 
         self.log( 'everything serialized should be of the proper type' )
diff --git a/test/unit/managers/test_HDAManager.py b/test/unit/managers/test_HDAManager.py
index 9e1eb159f73..a588325f42c 100644
--- a/test/unit/managers/test_HDAManager.py
+++ b/test/unit/managers/test_HDAManager.py
@@ -454,122 +454,87 @@ class HDADeserializerTestCase( HDATestCase ):
         self.hda_deserializer.deserialize( self.trans, hda, data={ 'genome_build': '' } )
         self.assertEqual( hda.dbkey, '' )
 
+    def test_deserialize_name( self ):
+        hda = self._create_vanilla_hda()
 
-# # =============================================================================
-# # web.url_for doesn't work well in the framework
-# testable_url_for = lambda *a, **k: '(fake url): %s, %s' % ( a, k )
-# DatasetSerializer.url_for = staticmethod( testable_url_for )
+        self.log( 'should raise when deserializing from non-string' )
+        self.assertRaises( exceptions.RequestParameterInvalidException,
+            self.hda_deserializer.deserialize, self.trans, hda, data={ 'name': True } )
+        self.log( 'should raise when deserializing from None' )
+        self.assertRaises( exceptions.RequestParameterInvalidException,
+            self.hda_deserializer.deserialize, self.trans, hda, data={ 'name': None } )
+        # self.log( 'should deserialize to empty string from None' )
+        # self.hda_deserializer.deserialize( self.trans, hda, data={ 'name': None } )
+        # self.assertEqual( hda.name, '' )
+        self.log( 'should be able to deserialize from unicode' )
+        olive = u'ελιά'
+        self.hda_deserializer.deserialize( self.trans, hda, data={ 'name': olive } )
+        self.assertEqual( hda.name, olive )
+        self.log( 'should be deserializable from empty string' )
+        self.hda_deserializer.deserialize( self.trans, hda, data={ 'name': '' } )
+        self.assertEqual( hda.name, '' )
 
-# class DatasetAssociationSerializerTestCase( BaseTestCase ):
+    def test_deserialize_info( self ):
+        hda = self._create_vanilla_hda()
 
-#     def set_up_managers( self ):
-#         super( DatasetAssociationSerializerTestCase, self ).set_up_managers()
-#         self.dataset_assoc_mgr = DatasetAssociationManager( self.app )
-#         self.dataset_assoc_serializer = DatasetAssocationSerializer( self.app )
-
-#     def test_views( self ):
-#         dataset_assoc = self.dataset_mgr.create( self.trans )
-
-#         self.log( 'should have a summary view' )
-#         summary_view = self.dataset_serializer.serialize_to_view( self.trans, dataset, view='summary' )
-#         self.assertKeys( summary_view, self.dataset_serializer.views[ 'summary' ] )
-
-#         self.log( 'should have the summary view as default view' )
-#         default_view = self.dataset_serializer.serialize_to_view( self.trans, dataset, default_view='summary' )
-#         self.assertKeys( summary_view, self.dataset_serializer.views[ 'summary' ] )
-
-#         self.log( 'should have a serializer for all serializable keys' )
-#         for key in self.dataset_serializer.serializable_keyset:
-#             instantiated_attribute = getattr( dataset, key, None )
-#             if not ( ( key in self.dataset_serializer.serializers )
-#                   or ( isinstance( instantiated_attribute, self.TYPES_NEEDING_NO_SERIALIZERS ) ) ):
-#                 self.fail( 'no serializer for: %s (%s)' % ( key, instantiated_attribute ) )
-#         else:
-#             self.assertTrue( True, 'all serializable keys have a serializer' )
-
-#     def test_views_and_keys( self ):
-#         dataset = self.dataset_mgr.create( self.trans )
-
-#         self.log( 'should be able to use keys with views' )
-#         serialized = self.dataset_serializer.serialize_to_view( self.trans, dataset,
-#             view='summary', keys=[ 'permissions' ] )
-#         self.assertKeys( serialized,
-#             self.dataset_serializer.views[ 'summary' ] + [ 'permissions' ] )
-
-#         self.log( 'should be able to use keys on their own' )
-#         serialized = self.dataset_serializer.serialize_to_view( self.trans, dataset,
-#             keys=[ 'purgable', 'file_size' ] )
-#         self.assertKeys( serialized, [ 'purgable', 'file_size' ] )
-
-#     def test_serialize_permissions( self ):
-#         dataset = self.dataset_mgr.create( self.trans )
-#         self.log( 'serialized permissions should be well formed' )
-
-#     def test_serializers( self ):
-#         user2 = self.user_mgr.create( self.trans, **user2_data )
-#         dataset = self.dataset_mgr.create( self.trans )
-#         all_keys = list( self.hda_serializer.serializable_keyset )
-#         serialized = self.dataset_serializer.serialize( self.trans, dataset, all_keys )
-
-#         self.log( 'everything serialized should be of the proper type' )
-#         self.assertEncodedId( serialized[ 'id' ] )
-#         self.assertDate( serialized[ 'create_time' ] )
-#         self.assertDate( serialized[ 'update_time' ] )
-
-#         self.assertUUID( serialized[ 'uuid' ] )
-#         self.assertIsInstance( serialized[ 'state' ], basestring )
-#         self.assertIsInstance( serialized[ 'deleted' ], bool )
-#         self.assertIsInstance( serialized[ 'purged' ], bool )
-#         self.assertIsInstance( serialized[ 'purgable' ], bool )
-
-#         # # TODO: no great way to do these with mocked dataset
-#         # self.assertIsInstance( serialized[ 'file_size' ], int )
-#         # self.assertIsInstance( serialized[ 'total_size' ], int )
-
-#         self.log( 'serialized should jsonify well' )
-#         self.assertIsJsonifyable( serialized )
+        self.log( 'should raise when deserializing from non-string' )
+        self.assertRaises( exceptions.RequestParameterInvalidException,
+            self.hda_deserializer.deserialize, self.trans, hda, data={ 'info': True } )
+        self.log( 'should raise when deserializing from None' )
+        self.assertRaises( exceptions.RequestParameterInvalidException,
+            self.hda_deserializer.deserialize, self.trans, hda, data={ 'info': None } )
+        self.log( 'should be able to deserialize from unicode' )
+        rice = u'飯'
+        self.hda_deserializer.deserialize( self.trans, hda, data={ 'info': rice } )
+        self.assertEqual( hda.info, rice )
+        self.log( 'should be deserializable from empty string' )
+        self.hda_deserializer.deserialize( self.trans, hda, data={ 'info': '' } )
+        self.assertEqual( hda.info, '' )
 
 
-# # =============================================================================
-# class DatasetAssocationDeserializerTestCase( BaseTestCase ):
+# =============================================================================
+class HDAFilterParserTestCase( HDATestCase ):
 
-#     def set_up_managers( self ):
-#         super( DatasetAssocationDeserializerTestCase, self ).set_up_managers()
-#         self.dataset_mgr = DatasetAssocationManager( self.app )
-#         self.dataset_deserializer = DatasetAssocationDeserializer( self.app )
+    def set_up_managers( self ):
+        super( HDAFilterParserTestCase, self ).set_up_managers()
+        self.filter_parser = hdas.HDAFilterParser( self.app )
 
-#     def test_deserialize_delete( self ):
-#         dataset = self.dataset_mgr.create( self.trans )
+    def test_parsable( self ):
+        self.log( 'the following filters should be parsable' )
+        # base
+        self.assertORMFilter( self.filter_parser.parse_filter( 'id', 'in', [ 1, 2 ] ) )
+        encoded_id_string = ','.join([ self.app.security.encode_id( id_ ) for id_ in [ 1, 2 ] ] )
+        self.assertORMFilter( self.filter_parser.parse_filter( 'encoded_id', 'in', encoded_id_string ) )
+        self.assertORMFilter( self.filter_parser.parse_filter( 'create_time', 'le', '2015-03-15' ) )
+        self.assertORMFilter( self.filter_parser.parse_filter( 'create_time', 'ge', '2015-03-15' ) )
+        self.assertORMFilter( self.filter_parser.parse_filter( 'update_time', 'le', '2015-03-15' ) )
+        self.assertORMFilter( self.filter_parser.parse_filter( 'update_time', 'ge', '2015-03-15' ) )
+        # purgable
+        self.assertORMFilter( self.filter_parser.parse_filter( 'deleted', 'eq', True ) )
+        self.assertORMFilter( self.filter_parser.parse_filter( 'purged', 'eq', True ) )
+        # dataset asociation
+        self.assertORMFilter( self.filter_parser.parse_filter( 'name', 'eq', 'wot' ) )
+        self.assertORMFilter( self.filter_parser.parse_filter( 'name', 'contains', 'wot' ) )
+        self.assertORMFilter( self.filter_parser.parse_filter( 'name', 'like', 'wot' ) )
+        self.assertORMFilter( self.filter_parser.parse_filter( 'state', 'eq', 'ok' ) )
+        self.assertORMFilter( self.filter_parser.parse_filter( 'state', 'in', [ 'queued', 'running' ] ) )
+        self.assertORMFilter( self.filter_parser.parse_filter( 'visible', 'eq', True ) )
+        self.assertFnFilter( self.filter_parser.parse_filter( 'genome_build', 'eq', 'wot' ) )
+        self.assertFnFilter( self.filter_parser.parse_filter( 'genome_build', 'contains', 'wot' ) )
+        self.assertFnFilter( self.filter_parser.parse_filter( 'data_type', 'eq', 'wot' ) )
+        self.assertFnFilter( self.filter_parser.parse_filter( 'data_type', 'isinstance', 'wot' ) )
+        # taggable
+        self.assertFnFilter( self.filter_parser.parse_filter( 'tag', 'eq', 'wot' ) )
+        self.assertFnFilter( self.filter_parser.parse_filter( 'tag', 'has', 'wot' ) )
+        # annotatable
+        self.assertFnFilter( self.filter_parser.parse_filter( 'annotation', 'has', 'wot' ) )
 
-#         self.log( 'should raise when deserializing deleted from non-bool' )
-#         self.assertFalse( dataset.deleted )
-#         self.assertRaises( exceptions.RequestParameterInvalidException,
-#             self.dataset_deserializer.deserialize, self.trans, dataset, data={ 'deleted': None } )
-#         self.assertFalse( dataset.deleted )
-#         self.log( 'should be able to deserialize deleted from True' )
-#         self.dataset_deserializer.deserialize( self.trans, dataset, data={ 'deleted': True } )
-#         self.assertTrue( dataset.deleted )
-#         self.log( 'should be able to reverse by deserializing deleted from False' )
-#         self.dataset_deserializer.deserialize( self.trans, dataset, data={ 'deleted': False } )
-#         self.assertFalse( dataset.deleted )
 
-#     def test_deserialize_purge( self ):
-#         dataset = self.dataset_mgr.create( self.trans )
+    def test_genome_build_filters( self ):
+        pass
 
-#         self.log( 'should raise when deserializing purged from non-bool' )
-#         self.assertRaises( exceptions.RequestParameterInvalidException,
-#             self.dataset_deserializer.deserialize, self.trans, dataset, data={ 'purged': None } )
-#         self.assertFalse( dataset.purged )
-#         self.log( 'should be able to deserialize purged from True' )
-#         self.dataset_deserializer.deserialize( self.trans, dataset, data={ 'purged': True } )
-#         self.assertTrue( dataset.purged )
-#         # TODO: should this raise an error?
-#         self.log( 'should NOT be able to deserialize purged from False (will remain True)' )
-#         self.dataset_deserializer.deserialize( self.trans, dataset, data={ 'purged': False } )
-#         self.assertTrue( dataset.purged )
-
-#     # def test_deserialize_permissions( self ):
-#     #     pass
+    def test_data_type_filters( self ):
+        pass
 
 
 # =============================================================================
diff --git a/test/unit/managers/test_HistoryManager.py b/test/unit/managers/test_HistoryManager.py
index a83e1411c89..a3feca6e819 100644
--- a/test/unit/managers/test_HistoryManager.py
+++ b/test/unit/managers/test_HistoryManager.py
@@ -396,7 +396,7 @@ class HistorySerializerTestCase( BaseTestCase ):
     def test_history_serializers( self ):
         user2 = self.user_mgr.create( self.trans, **user2_data )
         history1 = self.history_mgr.create( self.trans, name='history1', user=user2 )
-        all_keys = list( self.hda_serializer.serializable_keyset )
+        all_keys = list( self.history_serializer.serializable_keyset )
         serialized = self.history_serializer.serialize( self.trans, history1, all_keys )
 
         self.log( 'everything serialized should be of the proper type' )
@@ -404,7 +404,7 @@ class HistorySerializerTestCase( BaseTestCase ):
         self.assertIsInstance( serialized[ 'nice_size' ], basestring )
 
         self.log( 'serialized should jsonify well' )
-        self.assertIsInstance( json.dumps( serialized ), basestring )
+        self.assertIsJsonifyable( serialized )
 
     def test_contents( self ):
         user2 = self.user_mgr.create( self.trans, **user2_data )
diff --git a/test/unit/managers/test_ModelManager.py b/test/unit/managers/test_ModelManager.py
index bab2682e434..a25b3f0a771 100644
--- a/test/unit/managers/test_ModelManager.py
+++ b/test/unit/managers/test_ModelManager.py
@@ -122,8 +122,12 @@ class BaseTestCase( unittest.TestCase ):
     def assertORMFilter( self, item, msg=None ):
         if not isinstance( item, sqlalchemy.sql.elements.BinaryExpression ):
             self.fail( 'Not an orm filter: ' + str( type( item ) ) )
-        # TODO: re for d4d76d69-80d4-4ed7-80c7-211ebcc1a358
-        self.assertTrue( True, msg or ( 'is an orm filter: ' + item ) )
+        self.assertTrue( True, msg or ( 'is an orm filter: ' + str( item ) ) )
+
+    def assertFnFilter( self, item, msg=None ):
+        if not item or not callable( item ):
+            self.fail( 'Not a fn filter: ' + str( type( item ) ) )
+        self.assertTrue( True, msg or ( 'is a fn filter: ' + str( item ) ) )
 
     def assertIsJsonifyable( self, item ):
         # TODO: use galaxy's override
diff --git a/test/unit/managers/test_UserManager.py b/test/unit/managers/test_UserManager.py
index f48e03f6855..f6f77e4bd3c 100644
--- a/test/unit/managers/test_UserManager.py
+++ b/test/unit/managers/test_UserManager.py
@@ -174,7 +174,7 @@ class UserSerializerTestCase( BaseTestCase ):
 
     def test_serializers( self ):
         user = self.user_mgr.create( self.trans, **user2_data )
-        all_keys = list( self.hda_serializer.serializable_keyset )
+        all_keys = list( self.user_serializer.serializable_keyset )
         serialized = self.user_serializer.serialize( self.trans, user, all_keys )
         # pprint.pprint( serialized )
 
@@ -222,7 +222,7 @@ class CurrentUserSerializerTestCase( BaseTestCase ):
         self.assertIsInstance( serialized[ 'quota_percent' ], ( type( None ), float ) )
 
         self.log( 'serialized should jsonify well' )
-        self.assertIsInstance( json.dumps( serialized ), basestring )
+        self.assertIsJsonifyable( serialized )
 
 
 # =============================================================================

From fafea361ac05f8787d271ebab1b777294592b46b Mon Sep 17 00:00:00 2001
From: Carl Eberhard <carlfeberhard@gmail.com>
Date: Wed, 1 Apr 2015 15:21:25 -0400
Subject: [PATCH 20/88] Managers: remove trans param as much as possible (this
 results in some clunky use of current_history kwarg)

---
 lib/galaxy/managers/annotatable.py            |  12 +-
 lib/galaxy/managers/base.py                   |  38 +-
 lib/galaxy/managers/collections.py            |   6 +-
 lib/galaxy/managers/datasets.py               |  45 +-
 lib/galaxy/managers/deletable.py              |  12 +-
 lib/galaxy/managers/hdas.py                   |  65 +--
 lib/galaxy/managers/histories.py              | 207 +++++----
 lib/galaxy/managers/secured.py                |  34 +-
 lib/galaxy/managers/sharable.py               | 126 +++---
 lib/galaxy/managers/users.py                  |  60 +--
 lib/galaxy/visualization/registry.py          |   2 +-
 lib/galaxy/webapps/galaxy/api/annotations.py  |   6 +-
 .../webapps/galaxy/api/configuration.py       |   2 +-
 .../webapps/galaxy/api/dataset_collections.py |   2 +-
 lib/galaxy/webapps/galaxy/api/datasets.py     |  10 +-
 .../webapps/galaxy/api/extended_metadata.py   |   6 +-
 .../webapps/galaxy/api/folder_contents.py     |   6 +-
 lib/galaxy/webapps/galaxy/api/histories.py    |  30 +-
 .../webapps/galaxy/api/history_contents.py    |  29 +-
 lib/galaxy/webapps/galaxy/api/jobs.py         |   2 +-
 .../webapps/galaxy/api/library_contents.py    |   4 +-
 lib/galaxy/webapps/galaxy/api/provenance.py   |   2 +-
 lib/galaxy/webapps/galaxy/api/tools.py        |   8 +-
 lib/galaxy/webapps/galaxy/api/workflows.py    |   8 +-
 .../webapps/galaxy/controllers/dataset.py     |  34 +-
 .../webapps/galaxy/controllers/history.py     |  54 +--
 lib/galaxy/webapps/galaxy/controllers/page.py |   6 +-
 .../galaxy/controllers/visualization.py       |   6 +-
 lib/galaxy/workflow/run_request.py            |   2 +-
 test/unit/managers/test_CollectionManager.py  |  48 +--
 test/unit/managers/test_DatasetManager.py     | 110 ++---
 test/unit/managers/test_HDAManager.py         | 242 ++++++-----
 test/unit/managers/test_HistoryManager.py     | 393 +++++++++---------
 test/unit/managers/test_ModelManager.py       |   5 +-
 test/unit/managers/test_UserManager.py        |  88 ++--
 35 files changed, 883 insertions(+), 827 deletions(-)

diff --git a/lib/galaxy/managers/annotatable.py b/lib/galaxy/managers/annotatable.py
index 3cd1a367882..dacbf31bf86 100644
--- a/lib/galaxy/managers/annotatable.py
+++ b/lib/galaxy/managers/annotatable.py
@@ -12,18 +12,18 @@ class AnnotatableManagerMixin( object ):
 
     # TODO: most of this seems to be covered by item_attrs.UsesAnnotations
     # TODO: use these below (serializer/deserializer)
-    def user_annotation( self, trans, item, user ):
+    def user_annotation( self, item, user ):
         return item.get_item_annotation_str( self.session(), user, item )
 
-    def owner_annotation( self, trans, item ):
-        return self.user_annotation( trans, item, item.user )
+    def owner_annotation( self, item ):
+        return self.user_annotation( item, item.user )
 
-    def delete_annotation( self, trans, item, user ):
+    def delete_annotation( self, item, user ):
         return item.delete_item_annotation( self.session(), user, item )
 
-    def annotate( self, trans, item, user, annotation ):
+    def annotate( self, item, user, annotation ):
         if annotation is None:
-            self.delete_annotation( self, trans, item, user )
+            self.delete_annotation( item, user )
             return None
 
         annotation_obj = item.add_item_annotation( self.session(), user, item, annotation )
diff --git a/lib/galaxy/managers/base.py b/lib/galaxy/managers/base.py
index cd6c0e514dd..2e3d210af93 100644
--- a/lib/galaxy/managers/base.py
+++ b/lib/galaxy/managers/base.py
@@ -179,7 +179,7 @@ class ModelManager( object ):
         return item
 
     # .... query foundation wrapper
-    def query( self, trans, eagerloads=True, filters=None, order_by=None, limit=None, offset=None, **kwargs ):
+    def query( self, eagerloads=True, filters=None, order_by=None, limit=None, offset=None, **kwargs ):
         """
         Return a basic query from model_class, filters, order_by, and limit and offset.
 
@@ -258,11 +258,11 @@ class ModelManager( object ):
         return query
 
     # .... query resolution
-    def one( self, trans, **kwargs ):
+    def one( self, **kwargs ):
         """
         Sends kwargs to build the query and returns one and only one model.
         """
-        query = self.query( trans, **kwargs )
+        query = self.query( **kwargs )
         return self._one_with_recast_errors( query )
 
     def _one_with_recast_errors( self, query ):
@@ -292,33 +292,33 @@ class ModelManager( object ):
             return None
 
     #NOTE: at this layer, all ids are expected to be decoded and in int form
-    def by_id( self, trans, id, **kwargs ):
+    def by_id( self, id, **kwargs ):
         """
         Gets a model by primary id.
         """
         id_filter = self.model_class.id == id
-        return self.one( trans, filters=id_filter, **kwargs )
+        return self.one( filters=id_filter, **kwargs )
 
     # .... multirow queries
-    def _orm_list( self, trans, query=None, **kwargs ):
+    def _orm_list( self, query=None, **kwargs ):
         """
         Sends kwargs to build the query return all models found.
         """
-        query = query or self.query( trans, **kwargs )
+        query = query or self.query( **kwargs )
         return query.all()
 
-    #def list( self, trans, query=None, filters=None, order_by=None, limit=None, offset=None, **kwargs ):
-    def list( self, trans, filters=None, order_by=None, limit=None, offset=None, **kwargs ):
+    #def list( self, query=None, filters=None, order_by=None, limit=None, offset=None, **kwargs ):
+    def list( self, filters=None, order_by=None, limit=None, offset=None, **kwargs ):
         """
         Returns all objects matching the given filters
         """
         orm_filters, fn_filters = self._split_filters( filters )
         if not fn_filters:
             # if no fn_filtering required, we can use the 'all orm' version with limit offset
-            return self._orm_list( trans, filters=orm_filters, order_by=order_by, limit=limit, offset=offset, **kwargs )
+            return self._orm_list( filters=orm_filters, order_by=order_by, limit=limit, offset=offset, **kwargs )
 
         # fn filters will change the number of items returnable by limit/offset - remove them here from the orm query
-        query = self.query( trans, filters=orm_filters, order_by=order_by, limit=None, offset=None, **kwargs )
+        query = self.query( filters=orm_filters, order_by=order_by, limit=None, offset=None, **kwargs )
         items = query.all()
 
         # apply limit, offset after SQL filtering
@@ -381,12 +381,12 @@ class ModelManager( object ):
             yield item
             yielded += 1
 
-    def by_ids( self, trans, ids, filters=None, **kwargs ):
+    def by_ids( self, ids, filters=None, **kwargs ):
         """
         Returns an in-order list of models with the matching ids in `ids`.
         """
         ids_filter = self.model_class.id.in_( ids )
-        found = self.list( trans, filters=self._munge_filters( ids_filter, filters ), **kwargs )
+        found = self.list( filters=self._munge_filters( ids_filter, filters ), **kwargs )
         # TODO: this does not order by the original 'ids' array
 
         # ...could use get (supposedly since found are in the session, the db won't be hit twice)
@@ -420,7 +420,7 @@ class ModelManager( object ):
                 in_order.append( item_dict[ id ] )
         return in_order
 
-    def create( self, trans, flush=True, *args, **kwargs ):
+    def create( self, flush=True, *args, **kwargs ):
         """
         Generically create a new model.
         """
@@ -431,13 +431,13 @@ class ModelManager( object ):
             self.session().flush()
         return item
 
-    def copy( self, trans, item, **kwargs ):
+    def copy( self, item, **kwargs ):
         """
         Clone or copy an item.
         """
         raise exceptions.NotImplemented( 'Abstract method' )
 
-    def update( self, trans, item, new_values, flush=True, **kwargs ):
+    def update( self, item, new_values, flush=True, **kwargs ):
         """
         Given a dictionary of new values, update `item` and return it.
 
@@ -452,7 +452,7 @@ class ModelManager( object ):
         return item
 
     # TODO: yagni?
-    def associate( self, trans, associate_with, item, foreign_key_name=None ):
+    def associate( self, associate_with, item, foreign_key_name=None ):
         """
         Generically associate `item` with `associate_with` based on `foreign_key_name`.
         """
@@ -460,7 +460,7 @@ class ModelManager( object ):
         setattr( associate_with, foreign_key_name, item )
         return item
 
-    def query_associated( self, trans, associated_model_class, item, foreign_key_name=None ):
+    def query_associated( self, associated_model_class, item, foreign_key_name=None ):
         """
         Generically query other items that have been associated with this `item`.
         """
@@ -469,7 +469,7 @@ class ModelManager( object ):
         return self.session().query( associated_model_class ).filter( foreign_key == item )
 
     # a rename of sql DELETE to differentiate from the Galaxy notion of mark_as_deleted
-    # def destroy( self, trans, item, **kwargs ):
+    # def destroy( self, item, **kwargs ):
     #    return item
 
 
diff --git a/lib/galaxy/managers/collections.py b/lib/galaxy/managers/collections.py
index ccdf0c16900..b129ff5d61e 100644
--- a/lib/galaxy/managers/collections.py
+++ b/lib/galaxy/managers/collections.py
@@ -277,7 +277,7 @@ class DatasetCollectionManager( object ):
 
         if src_type == 'hda':
             decoded_id = int( trans.app.security.decode_id( encoded_id ) )
-            element = self.hda_manager.get_accessible( trans, decoded_id, trans.user )
+            element = self.hda_manager.get_accessible( decoded_id, trans.user )
         elif src_type == 'ldda':
             element = self.ldda_manager.get( trans, encoded_id )
         elif src_type == 'hdca':
@@ -312,9 +312,9 @@ class DatasetCollectionManager( object ):
         instance_id = int( trans.app.security.decode_id( id ) )
         collection_instance = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( instance_id )
         if check_ownership:
-            self.history_manager.error_unless_owner( trans, collection_instance.history, trans.user )
+            self.history_manager.error_unless_owner( collection_instance.history, trans.user, current_history=trans.history )
         if check_accessible:
-            self.history_manager.error_unless_accessible( trans, collection_instance.history, trans.user )
+            self.history_manager.error_unless_accessible( collection_instance.history, trans.user, current_history=trans.history )
         return collection_instance
 
     def __get_library_collection_instance( self, trans, id, check_ownership=False, check_accessible=True ):
diff --git a/lib/galaxy/managers/datasets.py b/lib/galaxy/managers/datasets.py
index f9f68300851..e8b94af3cc5 100644
--- a/lib/galaxy/managers/datasets.py
+++ b/lib/galaxy/managers/datasets.py
@@ -32,7 +32,7 @@ class DatasetManager( base.ModelManager, secured.AccessibleManagerMixin, deletab
         # need for admin test
         self.user_manager = users.UserManager( app )
 
-    def create( self, trans, manage_roles=None, access_roles=None, flush=True, **kwargs ):
+    def create( self, manage_roles=None, access_roles=None, flush=True, **kwargs ):
         """
         Create and return a new Dataset object.
         """
@@ -50,14 +50,14 @@ class DatasetManager( base.ModelManager, secured.AccessibleManagerMixin, deletab
     def copy( self, dataset, **kwargs ):
         raise galaxy.exceptions.NotImplemented( 'Datasets cannot be copied' )
 
-    def purge( self, trans, dataset, flush=True ):
+    def purge( self, dataset, flush=True ):
         """
         Remove the object_store/file for this dataset from storage and mark
         as purged.
 
         :raises exceptions.ConfigDoesNotAllowException: if the instance doesn't allow
         """
-        self.error_unless_dataset_purge_allowed( trans, dataset )
+        self.error_unless_dataset_purge_allowed( dataset )
 
         # the following also marks dataset as purged and deleted
         dataset.full_delete()
@@ -68,20 +68,19 @@ class DatasetManager( base.ModelManager, secured.AccessibleManagerMixin, deletab
 
     # TODO: this may be more conv. somewhere else
     # TODO: how to allow admin bypass?
-    def error_unless_dataset_purge_allowed( self, trans, item, msg=None ):
+    def error_unless_dataset_purge_allowed( self, msg=None ):
         if not self.app.config.allow_user_dataset_purge:
             msg = msg or 'This instance does not allow user dataset purging'
             raise exceptions.ConfigDoesNotAllowException( msg )
-        return item
 
     # .... accessibility
     # datasets can implement the accessible interface, but accessibility is checked in an entirely different way
     #   than those resources that have a user attribute (histories, pages, etc.)
-    def is_accessible( self, trans, dataset, user ):
+    def is_accessible( self, dataset, user, **kwargs ):
         """
         Is this dataset readable/viewable to user?
         """
-        if self.user_manager.is_admin( trans, user ):
+        if self.user_manager.is_admin( user ):
             return True
         if self.has_access_permission( dataset, user ):
             return True
@@ -99,6 +98,8 @@ class DatasetManager( base.ModelManager, secured.AccessibleManagerMixin, deletab
     # .... data, object_store
 
 
+# TODO: SecurityAgentDatasetRBACPermissions( object ):
+
 class DatasetRBACPermissions( object ):
 
     def __init__( self, app ):
@@ -126,7 +127,7 @@ class DatasetRBACPermissions( object ):
         return ( [ manage ], [] )
 
     def set_private_to_one_user( self, dataset, user, flush=True ):
-        manage = self.manage.grant( user, flush=False )
+        manage = self.manage.grant( dataset, user, flush=False )
         access = self.access.set_private( dataset, user, flush=flush )
         return ( [ manage ], access )
 
@@ -240,21 +241,21 @@ class DatasetAssociationManager( base.ModelManager,
         super( DatasetAssociationManager, self ).__init__( app )
         self.dataset_manager = DatasetManager( app )
 
-    def is_accessible( self, trans, dataset_assoc, user ):
+    def is_accessible( self, dataset_assoc, user, **kwargs ):
         """
         Is this DA accessible to `user`?
         """
         # defer to the dataset
-        return self.dataset_manager.is_accessible( trans, dataset_assoc.dataset, user )
+        return self.dataset_manager.is_accessible( dataset_assoc.dataset, user )
 
-    def purge( self, trans, dataset_assoc, flush=True ):
+    def purge( self, dataset_assoc, flush=True ):
         """
         Purge this DatasetInstance and the dataset underlying it.
         """
         # error here if disallowed - before jobs are stopped
         # TODO: this check may belong in the controller
-        self.dataset_manager.error_unless_dataset_purge_allowed( trans, dataset_assoc )
-        super( DatasetAssociationManager, self ).purge( trans, dataset_assoc, flush=flush )
+        self.dataset_manager.error_unless_dataset_purge_allowed()
+        super( DatasetAssociationManager, self ).purge( dataset_assoc, flush=flush )
 
         # stop any jobs outputing the dataset_assoc
         if dataset_assoc.creating_job_associations:
@@ -266,15 +267,15 @@ class DatasetAssociationManager( base.ModelManager,
 
         # more importantly, purge underlying dataset as well
         if dataset_assoc.dataset.user_can_purge:
-            self.dataset_manager.purge( trans, dataset_assoc.dataset )
+            self.dataset_manager.purge( dataset_assoc.dataset )
         return dataset_assoc
 
-    def by_user( self, trans, user ):
+    def by_user( self, user ):
         """
         """
         raise galaxy.exceptions.NotImplemented( 'Abstract Method' )
 
-    def creating_job( self, trans, dataset_assoc ):
+    def creating_job( self, dataset_assoc ):
         # TODO: is this needed? Can't you use the dataset_assoc.creating_job attribute? When is this None?
         # TODO: this would be even better if outputs and inputs were the underlying datasets
         job = None
@@ -423,17 +424,17 @@ class DatasetAssociationSerializer( _UnflattenedMetadataDatasetAssociationSerial
         # if 'metadata' isn't removed from keys here serialize will retrieve the un-serializable MetadataCollection
         # TODO: remove these when metadata is sub-object
         KEYS_HANDLED_SEPARATELY = ( 'metadata', )
-        left_to_handle = self.pluck_from_list( keys, KEYS_HANDLED_SEPARATELY )
+        left_to_handle = self._pluck_from_list( keys, KEYS_HANDLED_SEPARATELY )
         serialized = super( DatasetAssociationSerializer, self ).serialize( trans, dataset_assoc, keys )
 
         # add metadata directly to the dict instead of as a sub-object
         if 'metadata' in left_to_handle:
-            metadata = self.prefixed_metadata( trans, dataset_assoc )
+            metadata = self._prefixed_metadata( trans, dataset_assoc )
             serialized.update( metadata )
         return serialized
 
     # TODO: this is more util/gen. use
-    def pluck_from_list( self, l, elems ):
+    def _pluck_from_list( self, l, elems ):
         """
         Removes found elems from list l and returns list of found elems if found.
         """
@@ -446,7 +447,7 @@ class DatasetAssociationSerializer( _UnflattenedMetadataDatasetAssociationSerial
                 pass
         return found
 
-    def prefixed_metadata( self, trans, dataset_assoc ):
+    def _prefixed_metadata( self, trans, dataset_assoc ):
         """
         Adds (a prefixed version of) the DatasetInstance metadata to the dict,
         prefixing each key with 'metadata_'.
@@ -469,8 +470,8 @@ class DatasetAssociationDeserializer( base.ModelDeserializer, deletable.Purgable
         deletable.PurgableDeserializerMixin.add_deserializers( self )
 
         self.deserializers.update({
-            'name'          : self.deserialize_basestring,
-            'info'          : self.deserialize_basestring,
+            'name' : self.deserialize_basestring,
+            'info' : self.deserialize_basestring,
         })
         self.deserializable_keyset.update( self.deserializers.keys() )
 
diff --git a/lib/galaxy/managers/deletable.py b/lib/galaxy/managers/deletable.py
index 2d1dd5af2cc..6618fba1156 100644
--- a/lib/galaxy/managers/deletable.py
+++ b/lib/galaxy/managers/deletable.py
@@ -19,13 +19,13 @@ class DeletableManagerMixin( object ):
     removed by an admin/script.
     """
 
-    def delete( self, trans, item, flush=True, **kwargs ):
+    def delete( self, item, flush=True, **kwargs ):
         """
         Mark as deleted and return.
         """
         return self._session_setattr( item, 'deleted', True, flush=flush )
 
-    def undelete( self, trans, item, flush=True, **kwargs ):
+    def undelete( self, item, flush=True, **kwargs ):
         """
         Mark as not deleted and return.
         """
@@ -53,9 +53,9 @@ class DeletableDeserializerMixin( object ):
             return item.deleted
         # TODO:?? flush=False?
         if new_deleted:
-            self.manager.delete( trans, item, flush=False )
+            self.manager.delete( item, flush=False )
         else:
-            self.manager.undelete( trans, item, flush=False )
+            self.manager.undelete( item, flush=False )
         return item.deleted
 
 
@@ -74,7 +74,7 @@ class PurgableManagerMixin( DeletableManagerMixin ):
     file).
     """
 
-    def purge( self, trans, item, flush=True, **kwargs ):
+    def purge( self, item, flush=True, **kwargs ):
         """
         Mark as purged and return.
 
@@ -105,7 +105,7 @@ class PurgableDeserializerMixin( DeletableDeserializerMixin ):
             return item.purged
         # do we want to error if something attempts to 'unpurge'?
         if new_purged:
-            self.manager.purge( trans, item, flush=False )
+            self.manager.purge( item, flush=False )
         return item.purged
 
 
diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py
index fc111de0e8c..51b64cf4f19 100644
--- a/lib/galaxy/managers/hdas.py
+++ b/lib/galaxy/managers/hdas.py
@@ -47,28 +47,35 @@ class HDAManager( datasets.DatasetAssociationManager,
         self.user_manager = users.UserManager( app )
 
     # .... security and permissions
-    def is_accessible( self, trans, hda, user ):
+    def is_accessible( self, hda, user, **kwargs ):
         """
         Override to allow owners (those that own the associated history).
         """
-        if self.is_owner( trans, hda, user ):
-            return True
-        return super( HDAManager, self ).is_accessible( trans, hda, user )
+        # this, apparently, is not True:
+        #   if I have a copy of a dataset and anyone who manages permissions on it revokes my access
+        #   I can not access that dataset even if it's in my history
+        # if self.is_owner( hda, user, **kwargs ):
+        #     return True
+        return super( HDAManager, self ).is_accessible( hda, user )
 
-    def is_owner( self, trans, hda, user ):
+    def is_owner( self, hda, user, current_history=None, **kwargs ):
         """
         Use history to see if current user owns HDA.
         """
         history = hda.history
+        if self.user_manager.is_admin( user ):
+            return True
+        # allow anonymous user to access current history
         # TODO: some dup here with historyManager.is_owner but prevents circ import
-        if self.user_manager.is_admin( trans, user ):
-            return True
-        if self.user_manager.is_anonymous( user ) and history == trans.get_history():
-            return True
+        # TODO: awkward kwarg (which is my new band name); this may not belong here - move to controller?
+        if self.user_manager.is_anonymous( user ):
+            if current_history and history == current_history:
+                return True
+            return False
         return history.user == user
 
     # .... create and copy
-    def create( self, trans, history=None, dataset=None, flush=True, **kwargs ):
+    def create( self, history=None, dataset=None, flush=True, **kwargs ):
         """
         Create a new hda optionally passing in it's history and dataset.
 
@@ -77,25 +84,22 @@ class HDAManager( datasets.DatasetAssociationManager,
         """
         if not dataset:
             kwargs[ 'create_dataset' ] = True
-        hda = super( HDAManager, self ).create( trans,
-                                                flush=flush,
-                                                history=history,
-                                                dataset=dataset,
-                                                sa_session=self.app.model.context, **kwargs )
+        hda = model.HistoryDatasetAssociation( history=history, dataset=dataset,
+            sa_session=self.app.model.context, **kwargs )
 
         if history:
-            # TODO Probably Bug:  set_hid is never used, and should be passed
-            # to history.add_dataset here.
+# TODO Probably Bug:  set_hid is never used, and should be passed
+# to history.add_dataset here.
             set_hid = not ( 'hid' in kwargs )
             history.add_dataset( hda )
-        #TODO:?? some internal sanity check here (or maybe in add_dataset) to make sure hids are not duped?
+#TODO:?? some internal sanity check here (or maybe in add_dataset) to make sure hids are not duped?
 
         self.session().add( hda )
         if flush:
             self.session().flush()
         return hda
 
-    def copy( self, trans, hda, history=None, **kwargs ):
+    def copy( self, hda, history=None, **kwargs ):
         """
         Copy and return the given HDA.
         """
@@ -135,25 +139,25 @@ class HDAManager( datasets.DatasetAssociationManager,
         self.session().flush()
         return copy
 
-    def copy_ldda( self, trans, history, ldda, **kwargs ):
+    def copy_ldda( self, history, ldda, **kwargs ):
         """
         Copy this HDA as a LDDA and return.
         """
         return ldda.to_history_dataset_association( history, add_to_history=True )
 
     # .... deletion and purging
-    def purge( self, trans, hda, flush=True ):
+    def purge( self, hda, current_user=None, flush=True ):
         """
         Purge this HDA and the dataset underlying it.
         """
-        super( HDAManager, self ).purge( trans, hda, flush=flush )
-        # decreate the user's space used
-        if trans.user:
-            trans.user.total_disk_usage -= hda.quota_amount( trans.user )
+        super( HDAManager, self ).purge( hda, flush=flush )
+        # decrease the user's space used
+        if current_user:
+            current_user.total_disk_usage -= hda.quota_amount( current_user )
         return hda
 
     # .... states
-    def error_if_uploading( self, trans, hda ):
+    def error_if_uploading( self, hda ):
         """
         Raise error if HDA is still uploading.
         """
@@ -162,18 +166,17 @@ class HDAManager( datasets.DatasetAssociationManager,
             raise exceptions.Conflict( "Please wait until this dataset finishes uploading" )
         return hda
 
-    def data_conversion_status( self, trans, hda ):
+    def data_conversion_status( self, hda ):
         """
         Returns a message if an hda is not ready to be used in visualization.
         """
-        HDA_model = model.HistoryDatasetAssociation
         # this is a weird syntax and return val
         if not hda:
-            return HDA_model.conversion_messages.NO_DATA
+            return self.model_class.conversion_messages.NO_DATA
         if hda.state == model.Job.states.ERROR:
-            return HDA_model.conversion_messages.ERROR
+            return self.model_class.conversion_messages.ERROR
         if hda.state != model.Job.states.OK:
-            return HDA_model.conversion_messages.PENDING
+            return self.model_class.conversion_messages.PENDING
         return None
 
     # .... associated job
diff --git a/lib/galaxy/managers/histories.py b/lib/galaxy/managers/histories.py
index 9b379e92740..e5b21a96ea6 100644
--- a/lib/galaxy/managers/histories.py
+++ b/lib/galaxy/managers/histories.py
@@ -9,7 +9,7 @@ from galaxy import model
 from galaxy.managers import sharable
 from galaxy.managers import deletable
 from galaxy.managers import hdas
-from galaxy.managers.collections_util import dictify_dataset_collection_instance
+from galaxy.managers import collections_util
 
 import logging
 log = logging.getLogger( __name__ )
@@ -32,7 +32,7 @@ class HistoryManager( sharable.SharableModelManager, deletable.PurgableManagerMi
 
         self.hda_manager = hdas.HDAManager( app )
 
-    def copy( self, trans, history, user, **kwargs ):
+    def copy( self, history, user, **kwargs ):
         """
         Copy and return the given `history`.
         """
@@ -40,60 +40,62 @@ class HistoryManager( sharable.SharableModelManager, deletable.PurgableManagerMi
 
     # .... sharable
     # overriding to handle anonymous users' current histories in both cases
-    def by_user( self, trans, user, **kwargs ):
+    def by_user( self, user, current_history=None, **kwargs ):
         """
         Get all the histories for a given user (allowing anon users' theirs)
         ordered by update time.
         """
         # handle default and/or anonymous user (which still may not have a history yet)
         if self.user_manager.is_anonymous( user ):
-            current_history = self.get_current( trans )
             return [ current_history ] if current_history else []
+        return super( HistoryManager, self ).by_user( user, **kwargs )
 
-        return super( HistoryManager, self ).by_user( trans, user, **kwargs )
-
-    def is_owner( self, trans, history, user ):
+    def is_owner( self, history, user, current_history=None, **kwargs ):
         """
         True if the current user is the owner of the given history.
         """
         # anon users are only allowed to view their current history
-        if self.user_manager.is_anonymous( user ) and history == self.get_current( trans ):
-            return True
-        return super( HistoryManager, self ).is_owner( trans, history, user )
+        if self.user_manager.is_anonymous( user ):
+            if current_history and history == current_history:
+                return True
+            return False
+        return super( HistoryManager, self ).is_owner( history, user )
 
-    # TODO: possibly to sharable
-    def most_recent( self, trans, user, filters=None, **kwargs ):
+    # TODO: possibly to sharable or base
+    def most_recent( self, user, filters=None, current_history=None, **kwargs ):
         """
         Return the most recently update history for the user.
 
         If user is anonymous, return the current history. If the user is anonymous
         and the current history is deleted, return None.
         """
-        # TODO: trans
-        if not user:
-            current_history = self.get_current( trans )
+        if self.user_manager.is_anonymous( user ):
             return None if ( not current_history or current_history.deleted ) else current_history
         desc_update_time = self.model_class.table.c.update_time
         filters = self._munge_filters( filters, self.model_class.user_id == user.id )
         # TODO: normalize this return value
-        return self.query( trans, filters=filters, order_by=desc_update_time, limit=1, **kwargs ).first()
+        return self.query( filters=filters, order_by=desc_update_time, limit=1, **kwargs ).first()
 
     # .... purgable
-    def purge( self, trans, history, flush=True, **kwargs ):
+    def purge( self, history, flush=True, **kwargs ):
         """
         Purge this history and all HDAs, Collections, and Datasets inside this history.
         """
-        self.hda_manager.dataset_manager.error_unless_dataset_purge_allowed( trans, history )
+        self.hda_manager.dataset_manager.error_unless_dataset_purge_allowed()
 
         # First purge all the datasets
         for hda in history.datasets:
             if not hda.purged:
-                self.hda_manager.purge( trans, hda, flush=True )
+                self.hda_manager.purge( hda, flush=True )
 
         # Now mark the history as purged
-        super( HistoryManager, self ).purge( trans, history, flush=flush, **kwargs )
+        super( HistoryManager, self ).purge( history, flush=flush, **kwargs )
 
     # .... current
+    # TODO: make something to bypass the anon user + current history permissions issue
+    # def is_current_users_current_history( self, history, trans ):
+    #     pass
+
     def get_current( self, trans ):
         """
         Return the current history.
@@ -113,10 +115,9 @@ class HistoryManager( sharable.SharableModelManager, deletable.PurgableManagerMi
         """
         Set the current history by an id.
         """
-        return self.set_current( trans, self.by_id( trans, history_id ) )
+        return self.set_current( trans, self.by_id( history_id ) )
 
-    # .... serialization
-    # TODO: move to serializer (i.e. history with contents attr)
+# TODO: replace or move to serializer
     def _get_history_data( self, trans, history ):
         """
         Returns a dictionary containing ``history`` and ``contents``, serialized
@@ -129,6 +130,7 @@ class HistoryManager( sharable.SharableModelManager, deletable.PurgableManagerMi
         contents_dictionaries = []
         try:
             history_dictionary = history_serializer.serialize_to_view( trans, history, view='detailed' )
+
             for content in history.contents_iter( types=[ 'dataset', 'dataset_collection' ] ):
                 contents_dict = {}
                 if isinstance( content, model.HistoryDatasetAssociation ):
@@ -160,79 +162,6 @@ class HistoryManager( sharable.SharableModelManager, deletable.PurgableManagerMi
         return { 'history': history_dictionary,
                  'contents': contents_dictionaries }
 
-    # remove this
-    def get_state_counts( self, trans, history, exclude_deleted=True, exclude_hidden=False ):
-        """
-        Return a dictionary keyed to possible dataset states and valued with the number
-        of datasets in this history that have those states.
-        """
-        # TODO: the default flags above may not make a lot of sense (T,T?)
-        state_counts = {}
-        for state in model.Dataset.states.values():
-            state_counts[ state ] = 0
-
-        # TODO:?? collections and coll. states?
-        for hda in history.datasets:
-            if exclude_deleted and hda.deleted:
-                continue
-            if exclude_hidden and not hda.visible:
-                continue
-            state_counts[ hda.state ] = state_counts[ hda.state ] + 1
-        return state_counts
-
-    # remove this
-    def get_state_ids( self, trans, history ):
-        """
-        Return a dictionary keyed to possible dataset states and valued with lists
-        containing the ids of each HDA in that state.
-        """
-        state_ids = {}
-        for state in model.Dataset.states.values():
-            state_ids[ state ] = []
-
-        # TODO:?? collections and coll. states?
-        for hda in history.datasets:
-            # TODO: do not encode ids at this layer
-            encoded_id = self.app.security.encode_id( hda.id )
-            state_ids[ hda.state ].append( encoded_id )
-        return state_ids
-
-    # TODO: remove this (is state used/useful?)
-    def get_history_state( self, trans, history ):
-        """
-        Returns the history state based on the states of the HDAs it contains.
-        """
-        states = model.Dataset.states
-
-        # (default to ERROR)
-        state = states.ERROR
-
-        # TODO: history_state and state_counts are classically calc'd at the same time
-        #   so this is rel. ineff. - if we keep this...
-        hda_state_counts = self.get_state_counts( trans, history, exclude_deleted=False )
-        num_hdas = sum( hda_state_counts.values() )
-        if num_hdas == 0:
-            state = states.NEW
-
-        else:
-            if ( hda_state_counts[ states.RUNNING ] > 0
-                 or hda_state_counts[ states.SETTING_METADATA ] > 0
-                 or hda_state_counts[ states.UPLOAD ] > 0 ):
-                state = states.RUNNING
-            # TODO: this method may be more useful if we *also* polled the histories jobs here too
-
-            elif hda_state_counts[ states.QUEUED ] > 0:
-                state = states.QUEUED
-
-            elif ( hda_state_counts[ states.ERROR ] > 0
-                   or hda_state_counts[ states.FAILED_METADATA ] > 0 ):
-                state = states.ERROR
-
-            elif hda_state_counts[ states.OK ] == num_hdas:
-                state = states.OK
-
-        return state
-
 
 class HistorySerializer( sharable.SharableModelSerializer, deletable.PurgableSerializerMixin ):
     """
@@ -289,7 +218,7 @@ class HistorySerializer( sharable.SharableModelSerializer, deletable.PurgableSer
             'update_time'   : self.serialize_date,
             'size'          : lambda t, i, k: int( i.get_disk_size() ),
             'nice_size'     : lambda t, i, k: i.get_disk_size( nice_size=True ),
-            'state'         : lambda t, i, k: self.history_manager.get_history_state( t, i ),
+            'state'         : self.serialize_history_state,
 
             'url'           : lambda t, i, k: self.url_for( 'history', id=t.security.encode_id( i.id ) ),
             'contents_url'  : lambda t, i, k: self.url_for( 'history_contents',
@@ -298,11 +227,79 @@ class HistorySerializer( sharable.SharableModelSerializer, deletable.PurgableSer
             'empty'         : lambda t, i, k: ( len( i.datasets ) + len( i.dataset_collections ) ) <= 0,
             'count'         : lambda trans, item, key: len( item.datasets ),
             'hdas'          : lambda t, i, k: [ t.security.encode_id( hda.id ) for hda in i.datasets ],
-            'state_details' : lambda t, i, k: self.history_manager.get_state_counts( t, i ),
-            'state_ids'     : lambda t, i, k: self.history_manager.get_state_ids( t, i ),
+            'state_details' : self.serialize_state_counts,
+            'state_ids'     : self.serialize_state_ids,
             'contents'      : self.serialize_contents
         })
 
+    # remove this
+    def serialize_state_ids( self, trans, history, key ):
+        """
+        Return a dictionary keyed to possible dataset states and valued with lists
+        containing the ids of each HDA in that state.
+        """
+        state_ids = {}
+        for state in model.Dataset.states.values():
+            state_ids[ state ] = []
+
+        # TODO:?? collections and coll. states?
+        for hda in history.datasets:
+            # TODO: do not encode ids at this layer
+            encoded_id = self.app.security.encode_id( hda.id )
+            state_ids[ hda.state ].append( encoded_id )
+        return state_ids
+
+    # remove this
+    def serialize_state_counts( self, trans, history, key, exclude_deleted=True, exclude_hidden=False ):
+        """
+        Return a dictionary keyed to possible dataset states and valued with the number
+        of datasets in this history that have those states.
+        """
+        # TODO: the default flags above may not make a lot of sense (T,T?)
+        state_counts = {}
+        for state in model.Dataset.states.values():
+            state_counts[ state ] = 0
+
+        # TODO:?? collections and coll. states?
+        for hda in history.datasets:
+            if exclude_deleted and hda.deleted:
+                continue
+            if exclude_hidden and not hda.visible:
+                continue
+            state_counts[ hda.state ] = state_counts[ hda.state ] + 1
+        return state_counts
+
+    # TODO: remove this (is state used/useful?)
+    def serialize_history_state( self, trans, history, key ):
+        """
+        Returns the history state based on the states of the HDAs it contains.
+        """
+        states = model.Dataset.states
+        # (default to ERROR)
+        state = states.ERROR
+        # TODO: history_state and state_counts are classically calc'd at the same time
+        #   so this is rel. ineff. - if we keep this...
+        hda_state_counts = self.serialize_state_counts( trans, history, 'counts', exclude_deleted=False )
+        num_hdas = sum( hda_state_counts.values() )
+        if num_hdas == 0:
+            state = states.NEW
+
+        else:
+            if ( hda_state_counts[ states.RUNNING ] > 0
+                 or hda_state_counts[ states.SETTING_METADATA ] > 0
+                 or hda_state_counts[ states.UPLOAD ] > 0 ):
+                state = states.RUNNING
+            # TODO: this method may be more useful if we *also* polled the histories jobs here too
+            elif hda_state_counts[ states.QUEUED ] > 0:
+                state = states.QUEUED
+            elif ( hda_state_counts[ states.ERROR ] > 0
+                   or hda_state_counts[ states.FAILED_METADATA ] > 0 ):
+                state = states.ERROR
+            elif hda_state_counts[ states.OK ] == num_hdas:
+                state = states.OK
+
+        return state
+
     def serialize_contents( self, trans, history, *args ):
         contents_dictionaries = []
         for content in history.contents_iter( types=[ 'dataset', 'dataset_collection' ] ):
@@ -310,21 +307,19 @@ class HistorySerializer( sharable.SharableModelSerializer, deletable.PurgableSer
             if isinstance( content, model.HistoryDatasetAssociation ):
                 contents_dict = self.hda_serializer.serialize_to_view( trans, content, view='detailed' )
             elif isinstance( content, model.HistoryDatasetCollectionAssociation ):
-                contents_dict = self.serialize_collection( trans, content )
+                contents_dict = self._serialize_collection( trans, content )
             contents_dictionaries.append( contents_dict )
         return contents_dictionaries
 
-    def serialize_collection( self, trans, collection ):
+    def _serialize_collection( self, trans, collection ):
         service = self.app.dataset_collections_service
         dataset_collection_instance = service.get_dataset_collection_instance(
             trans=trans,
             instance_type='history',
-            id=self.security.encode_id( collection.id ),
+            id=self.app.security.encode_id( collection.id ),
         )
-        return dictify_dataset_collection_instance( dataset_collection_instance,
-                                                    security=self.app.security,
-                                                    parent=dataset_collection_instance.history,
-                                                    view="element" )
+        return collections_util.dictify_dataset_collection_instance( dataset_collection_instance,
+            security=self.app.security, parent=dataset_collection_instance.history, view="element" )
 
 
 class HistoryDeserializer( sharable.SharableModelDeserializer, deletable.PurgableDeserializerMixin ):
diff --git a/lib/galaxy/managers/secured.py b/lib/galaxy/managers/secured.py
index dd6825b4bc3..aada0b0025a 100644
--- a/lib/galaxy/managers/secured.py
+++ b/lib/galaxy/managers/secured.py
@@ -16,35 +16,35 @@ class AccessibleManagerMixin( object ):
     """
 
     # don't want to override by_id since consumers will also want to fetch w/o any security checks
-    def is_accessible( self, trans, item, user ):
+    def is_accessible( self, item, user, **kwargs ):
         """
         Return True if the item accessible to user.
         """
         # override in subclasses
         raise exceptions.NotImplemented( "Abstract interface Method" )
 
-    def get_accessible( self, trans, id, user, **kwargs ):
+    def get_accessible( self, id, user, **kwargs ):
         """
         Return the item with the given id if it's accessible to user,
         otherwise raise an error.
 
         :raises exceptions.ItemAccessibilityException:
         """
-        item = self.by_id( trans, id )
-        return self.error_unless_accessible( trans, item, user )
+        item = self.by_id( id )
+        return self.error_unless_accessible( item, user, **kwargs )
 
-    def error_unless_accessible( self, trans, item, user ):
+    def error_unless_accessible( self, item, user, **kwargs ):
         """
         Raise an error if the item is NOT accessible to user, otherwise return the item.
 
         :raises exceptions.ItemAccessibilityException:
         """
-        if self.is_accessible( trans, item, user ):
+        if self.is_accessible( item, user, **kwargs ):
             return item
         raise exceptions.ItemAccessibilityException( "%s is not accessible by user" % ( self.model_class.__name__ ) )
 
     # TODO:?? are these even useful?
-    def list_accessible( self, trans, user, **kwargs ):
+    def list_accessible( self, user, **kwargs ):
         """
         Return a list of items accessible to the user, raising an error if ANY
         are inaccessible.
@@ -56,7 +56,7 @@ class AccessibleManagerMixin( object ):
         # items = ModelManager.list( self, trans, **kwargs )
         # return [ self.error_unless_accessible( trans, item, user ) for item in items ]
 
-    def filter_accessible( self, trans, user, **kwargs ):
+    def filter_accessible( self, user, **kwargs ):
         """
         Return a list of items accessible to the user.
         """
@@ -76,34 +76,34 @@ class OwnableManagerMixin( object ):
     This can also be thought of as write/edit privileges.
     """
 
-    def is_owner( self, trans, item, user ):
+    def is_owner( self, item, user, **kwargs ):
         """
         Return True if user owns the item.
         """
         # override in subclasses
         raise exceptions.NotImplemented( "Abstract interface Method" )
 
-    def get_owned( self, trans, id, user, **kwargs ):
+    def get_owned( self, id, user, **kwargs ):
         """
         Return the item with the given id if owned by the user,
         otherwise raise an error.
 
         :raises exceptions.ItemOwnershipException:
         """
-        item = self.by_id( trans, id )
-        return self.error_unless_owner( trans, item, user )
+        item = self.by_id( id )
+        return self.error_unless_owner( item, user, **kwargs )
 
-    def error_unless_owner( self, trans, item, user ):
+    def error_unless_owner( self, item, user, **kwargs ):
         """
         Raise an error if the item is NOT owned by user, otherwise return the item.
 
         :raises exceptions.ItemAccessibilityException:
         """
-        if self.is_owner( trans, item, user ):
+        if self.is_owner( item, user, **kwargs ):
             return item
         raise exceptions.ItemOwnershipException( "%s is not owned by user" % ( self.model_class.__name__ ) )
 
-    def list_owned( self, trans, user, **kwargs ):
+    def list_owned( self, user, **kwargs ):
         """
         Return a list of items owned by the user, raising an error if ANY
         are not.
@@ -114,9 +114,9 @@ class OwnableManagerMixin( object ):
         # just alias to by_user (easier/same thing)
         #return self.by_user( trans, user, **kwargs )
 
-    def filter_owned( self, trans, user, **kwargs ):
+    def filter_owned( self, user, **kwargs ):
         """
         Return a list of items owned by the user.
         """
         # just alias to list_owned
-        return self.list_owned( trans, user, **kwargs )
+        return self.list_owned( user, **kwargs )
diff --git a/lib/galaxy/managers/sharable.py b/lib/galaxy/managers/sharable.py
index 4f253baaaf6..19c1b3033e4 100644
--- a/lib/galaxy/managers/sharable.py
+++ b/lib/galaxy/managers/sharable.py
@@ -42,30 +42,26 @@ class SharableModelManager( base.ModelManager, secured.OwnableManagerMixin, secu
         self.user_manager = users.UserManager( app )
 
     # .... has a user
-    def by_user( self, trans, user, filters=None, **kwargs ):
+    def by_user( self, user, filters=None, **kwargs ):
         """
         Return list for all items (of model_class type) associated with the given
         `user`.
         """
         user_filter = self.model_class.user_id == user.id
         filters=self._munge_filters( user_filter, filters )
-        return self.list( trans, filters=filters, **kwargs )
+        return self.list( filters=filters, **kwargs )
 
-    # .... owned model interface
-    def is_owner( self, trans, item, user ):
+    # .... owned/accessible interfaces
+    def is_owner( self, item, user, **kwargs ):
         """
         Return true if this sharable belongs to `user` (or `user` is an admin).
         """
-        if self.user_manager.is_anonymous( user ):
-            # note: this needs to be overridden in the case of anon users and session.current_history
-            return False
         # ... effectively a good fit to have this here, but not semantically
-        if self.user_manager.is_admin( trans, user ):
+        if self.user_manager.is_admin( user ):
             return True
         return item.user == user
 
-    # .... accessible interface
-    def is_accessible( self, trans, item, user ):
+    def is_accessible( self, item, user, **kwargs ):
         """
         If the item is importable, is owned by `user`, or (the valid) `user`
         is in 'users shared with' list for the item: return True.
@@ -73,7 +69,7 @@ class SharableModelManager( base.ModelManager, secured.OwnableManagerMixin, secu
         if item.importable:
             return True
         # note: owners always have access - checking for accessible implicitly checks for ownership
-        if self.is_owner( trans, item, user ):
+        if self.is_owner( item, user, **kwargs ):
             return True
         if self.user_manager.is_anonymous( user ):
             return False
@@ -82,16 +78,16 @@ class SharableModelManager( base.ModelManager, secured.OwnableManagerMixin, secu
         return False
 
     # .... importable
-    def make_importable( self, trans, item, flush=True ):
+    def make_importable( self, item, flush=True ):
         """
         Makes item accessible--viewable and importable--and sets item's slug.
         Does not flush/commit changes, however. Item must have name, user,
         importable, and slug attributes.
         """
-        self.create_unique_slug( trans, item, flush=False )
+        self.create_unique_slug( item, flush=False )
         return self._session_setattr( item, 'importable', True, flush=flush )
 
-    def make_non_importable( self, trans, item, flush=True ):
+    def make_non_importable( self, item, flush=True ):
         """
         Makes item accessible--viewable and importable--and sets item's slug.
         Does not flush/commit changes, however. Item must have name, user,
@@ -99,110 +95,112 @@ class SharableModelManager( base.ModelManager, secured.OwnableManagerMixin, secu
         """
         # item must be unpublished if non-importable
         if item.published:
-            self.unpublish( trans, item, flush=False )
+            self.unpublish( item, flush=False )
         return self._session_setattr( item, 'importable', False, flush=flush )
 
     # .... published
-    def publish( self, trans, item, flush=True ):
+    def publish( self, item, flush=True ):
         """
         Set both the importable and published flags on `item` to True.
         """
         # item must be importable to be published
         if not item.importable:
-            self.make_importable( trans, item, flush=False )
+            self.make_importable( item, flush=False )
         return self._session_setattr( item, 'published', True, flush=flush )
 
-    def unpublish( self, trans, item, flush=True ):
+    def unpublish( self, item, flush=True ):
         """
         Set the published flag on `item` to False.
         """
         return self._session_setattr( item, 'published', False, flush=flush )
 
-    #def _query_published( self, trans, filters=None, **kwargs ):
-    #    """
-    #    """
-    #    published_filter = self.model_class.published == True
-    #    filters = self._munge_filters( published_filter, filters )
-    #    return self.list( trans, filters=filters, **kwargs )
-    #
-    #def list_published( self, trans, **kwargs ):
-    #    """
-    #    """
-    #    query = self._query_published( trans, user, **kwargs )
-    #    return self.list( trans, query=query, **kwargs )
+    def _query_published( self, filters=None, **kwargs ):
+       """
+       Query all published items.
+       """
+       published_filter = self.model_class.published == True
+       filters = self._munge_filters( published_filter, filters )
+       return self.list( filters=filters, **kwargs )
+
+    def list_published( self, **kwargs ):
+       """
+       Return a list of all published items.
+       """
+       query = self._query_published( user, **kwargs )
+       return self.list( query=query, **kwargs )
 
     # .... user sharing
     # sharing is often done via a 3rd table btwn a User and an item -> a <Item>UserShareAssociation
-    def get_share_assocs( self, trans, item, user=None ):
+    def get_share_assocs( self, item, user=None ):
         """
         Get the UserShareAssociations for the `item`.
 
         Optionally send in `user` to test for a single match.
         """
-        query = self.query_associated( trans, self.user_share_model, item )
+        query = self.query_associated( self.user_share_model, item )
         if user is not None:
             query = query.filter_by( user=user )
         return query.all()
 
-    def share_with( self, trans, item, user, flush=True ):
+    def share_with( self, item, user, flush=True ):
         """
         Get or create a share for the given user (or users if `user` is a list).
         """
         # allow user to be a list and call recursivly
         if isinstance( user, list ):
-            return map( lambda user: self.share_with( trans, item, user, flush=False ), user )
+            return map( lambda user: self.share_with( item, user, flush=False ), user )
         # get or create
-        existing = self.get_share_assocs( trans, item, user=user )
+        existing = self.get_share_assocs( item, user=user )
         if existing:
             return existing.pop( 0 )
-        return self._create_user_share_assoc( trans, item, user, flush=flush )
+        return self._create_user_share_assoc( item, user, flush=flush )
 
-    def _create_user_share_assoc( self, trans, item, user, flush=True ):
+    def _create_user_share_assoc( self, item, user, flush=True ):
         """
         Create a share for the given user.
         """
         user_share_assoc = self.user_share_model()
         self.session().add( user_share_assoc )
-        self.associate( trans, user_share_assoc, item )
+        self.associate( user_share_assoc, item )
         user_share_assoc.user = user
 
         # ensure an item slug so shared users can access
         if not item.slug:
-            self.create_unique_slug( trans, item )
+            self.create_unique_slug( item )
 
         if flush:
             self.session().flush()
         return user_share_assoc
 
-    def unshare_with( self, trans, item, user, flush=True ):
+    def unshare_with( self, item, user, flush=True ):
         """
         Delete a user share (or list of shares) from the database.
         """
         if isinstance( user, list ):
-            return map( lambda user: self.unshare_with( trans, item, user, flush=False ), user )
+            return map( lambda user: self.unshare_with( item, user, flush=False ), user )
         # Look for and delete sharing relation for user.
-        user_share_assoc = self.get_share_assocs( trans, item, user=user )[0]
+        user_share_assoc = self.get_share_assocs( item, user=user )[0]
         self.session().delete( user_share_assoc )
         if flush:
             self.session().flush()
         return user_share_assoc
 
-    #def _query_shared_with( self, trans, user, filters=None, **kwargs ):
+    #def _query_shared_with( self, user, filters=None, **kwargs ):
     ##TODO:
     #    """
     #    """
     #    pass
 
-    #def list_shared_with( self, trans, user, **kwargs ):
+    #def list_shared_with( self, user, **kwargs ):
     #    """
     #    """
-    #    query = self._query_shared_with( trans, user, **kwargs )
-    #    return self.list( trans, query=query, **kwargs )
+    #    query = self._query_shared_with( user, **kwargs )
+    #    return self.list( query=query, **kwargs )
 
     # .... slugs
     # slugs are human readable strings often used to link to sharable resources (replacing ids)
     #TODO: as validator, deserializer, etc. (maybe another object entirely?)
-    def set_slug( self, trans, item, new_slug, flush=True ):
+    def set_slug( self, item, new_slug, user, flush=True ):
         """
         Validate and set the new slug for `item`.
         """
@@ -211,7 +209,7 @@ class SharableModelManager( base.ModelManager, secured.OwnableManagerMixin, secu
             raise exceptions.RequestParameterInvalidException( "Invalid slug", slug=new_slug )
 
         # error if slug is already in use
-        if self._slug_exists( trans, trans.user, new_slug ):
+        if self._slug_exists( user, new_slug ):
             raise exceptions.Conflict( "Slug already exists", slug=new_slug )
 
         item.slug = new_slug
@@ -226,12 +224,12 @@ class SharableModelManager( base.ModelManager, secured.OwnableManagerMixin, secu
         VALID_SLUG_RE = re.compile( "^[a-z0-9\-]+$" )
         return VALID_SLUG_RE.match( slug )
 
-    def _existing_set_of_slugs( self, trans, user ):
+    def _existing_set_of_slugs( self, user ):
         query = ( self.session().query( self.model_class.slug )
                     .filter_by( user=user ) )
-        return set( query.all() )
+        return list( set( query.all() ) )
 
-    def _slug_exists( self, trans, user, slug ):
+    def _slug_exists( self, user, slug ):
         query = ( self.session().query( self.model_class.slug )
                     .filter_by( user=user, slug=slug ) )
         return query.count() != 0
@@ -246,13 +244,13 @@ class SharableModelManager( base.ModelManager, secured.OwnableManagerMixin, secu
             slug_base = slug_base[:-1]
         return slug_base
 
-    def _default_slug_base( self, trans, item ):
+    def _default_slug_base( self, item ):
         # override in subclasses
         if hasattr( item, 'title' ):
             return item.title.lower()
         return item.name.lower()
 
-    def get_unique_slug( self, trans, item ):
+    def get_unique_slug( self, item ):
         """
         Returns a slug that is unique among user's importable items
         for item's class.
@@ -261,7 +259,7 @@ class SharableModelManager( base.ModelManager, secured.OwnableManagerMixin, secu
 
         # Setup slug base.
         if cur_slug is None or cur_slug == "":
-            slug_base = self._slugify( self._default_slug_base( trans, item ) )
+            slug_base = self._slugify( self._default_slug_base( item ) )
         else:
             slug_base = cur_slug
 
@@ -279,28 +277,28 @@ class SharableModelManager( base.ModelManager, secured.OwnableManagerMixin, secu
 
         return new_slug
 
-    def create_unique_slug( self, trans, item, flush=True ):
+    def create_unique_slug( self, item, flush=True ):
         """
         Set a new, unique slug on the item.
         """
-        item.slug = self.get_unique_slug( trans, item )
+        item.slug = self.get_unique_slug( item )
         self.session().add( item )
         if flush:
             self.session().flush()
         return item
 
-    #def by_slug( self, trans, user, **kwargs ):
+    #def by_slug( self, user, **kwargs ):
     #    """
     #    """
     #    pass
 
     # .... display
-    #def display_by_username_and_slug( self, trans, username, slug ):
+    #def display_by_username_and_slug( self, username, slug ):
     #    """ Display item by username and slug. """
 
-    #def set_public_username( self, trans, id, username, **kwargs ):
+    #def set_public_username( self, id, username, **kwargs ):
     #    """ Set user's public username and delegate to sharing() """
-    #def sharing( self, trans, id, **kwargs ):
+    #def sharing( self, id, **kwargs ):
     #    """ Handle item sharing. """
 
 
@@ -364,9 +362,9 @@ class SharableModelDeserializer( base.ModelDeserializer,
             return val
 
         if val:
-            self.manager.publish( trans, item, flush=False )
+            self.manager.publish( item, flush=False )
         else:
-            self.manager.unpublish( trans, item, flush=False )
+            self.manager.unpublish( item, flush=False )
         return item.published
 
     def deserialize_importable( self, trans, item, key, val ):
@@ -377,9 +375,9 @@ class SharableModelDeserializer( base.ModelDeserializer,
             return val
 
         if val:
-            self.manager.make_importable( trans, item, flush=False )
+            self.manager.make_importable( item, flush=False )
         else:
-            self.manager.make_non_importable( trans, item, flush=False )
+            self.manager.make_non_importable( item, flush=False )
         return item.published
 
     #def deserialize_slug( self, trans, item, val ):
diff --git a/lib/galaxy/managers/users.py b/lib/galaxy/managers/users.py
index c204f1ad63f..360191c7e50 100644
--- a/lib/galaxy/managers/users.py
+++ b/lib/galaxy/managers/users.py
@@ -31,7 +31,7 @@ class UserManager( base.ModelManager, deletable.PurgableManagerMixin ):
     #TODO: incorporate security/validate_user_input.py
     #TODO: incorporate UsesFormDefinitionsMixin?
 
-    def create( self, trans, **kwargs ):
+    def create( self, webapp_name=None, **kwargs ):
         """
         Create a new user.
         """
@@ -39,7 +39,7 @@ class UserManager( base.ModelManager, deletable.PurgableManagerMixin ):
         email = kwargs[ 'email' ]
         username = kwargs[ 'username' ]
         password = kwargs[ 'password' ]
-        self._error_on_duplicate_email( trans, email )
+        self._error_on_duplicate_email( email )
 
         user = model.User( email=email, password=password )
         user.username = username
@@ -60,72 +60,71 @@ class UserManager( base.ModelManager, deletable.PurgableManagerMixin ):
         # can throw an sqlalx.IntegrityError if username not unique
 
         self.app.security_agent.create_private_user_role( user )
-        #TODO: trans
-        if trans.webapp.name == 'galaxy':
+        if webapp_name == 'galaxy':
             # We set default user permissions, before we log in and set the default history permissions
             permissions = self.app.config.new_user_dataset_access_role_default_private
             self.app.security_agent.user_set_default_permissions( user, default_access_private=permissions )
         return user
 
-    def _error_on_duplicate_email( self, trans, email ):
+    def _error_on_duplicate_email( self, email ):
         """
         Check for a duplicate email and raise if found.
 
         :raises exceptions.Conflict: if any are found
         """
         #TODO: remove this check when unique=True is added to the email column
-        if self.by_email( trans, email ) is not None:
+        if self.by_email( email ) is not None:
             raise exceptions.Conflict( 'Email must be unique', email=email )
 
     # ---- filters
-    def by_email( self, trans, email, filters=None, **kwargs ):
+    def by_email( self, email, filters=None, **kwargs ):
         """
         Find a user by their email.
         """
         filters = self._munge_filters( self.model_class.email == email, filters )
         try:
 #TODO: use one_or_none
-            return super( UserManager, self ).one( trans, filters=filters, **kwargs )
+            return super( UserManager, self ).one( filters=filters, **kwargs )
         except exceptions.ObjectNotFound, not_found:
             return None
 
-    def by_email_like( self, trans, email_with_wildcards, filters=None, order_by=None, **kwargs ):
+    def by_email_like( self, email_with_wildcards, filters=None, order_by=None, **kwargs ):
         """
         Find a user searching with SQL wildcards.
         """
         filters = self._munge_filters( self.model_class.email.like( email_with_wildcards ), filters )
         order_by = order_by or ( model.User.email, )
-        return super( UserManager, self ).list( trans, filters=filters, order_by=order_by, **kwargs )
+        return super( UserManager, self ).list( filters=filters, order_by=order_by, **kwargs )
 
     # ---- admin
-    def is_admin( self, trans, user ):
+    def is_admin( self, user ):
         """
         Return True if this user is an admin.
         """
-        admin_emails = self._admin_emails( trans )
+        admin_emails = self._admin_emails()
         return user and admin_emails and user.email in admin_emails
 
-    def _admin_emails( self, trans ):
+    def _admin_emails( self ):
         """
         Return a list of admin email addresses from the config file.
         """
         return [ email.strip() for email in self.app.config.get( "admin_users", "" ).split( "," ) ]
 
-    def admins( self, trans, filters=None, **kwargs ):
+    def admins( self, filters=None, **kwargs ):
         """
         Return a list of admin Users.
         """
-        filters = self._munge_filters( self.model_class.email.in_( self._admin_emails( trans ) ), filters )
-        return super( UserManager, self ).list( trans, filters=filters, **kwargs )
+        filters = self._munge_filters( self.model_class.email.in_( self._admin_emails() ), filters )
+        return super( UserManager, self ).list( filters=filters, **kwargs )
 
-    def error_unless_admin( self, trans, user, msg="Administrators only", **kwargs ):
+    def error_unless_admin( self, user, msg="Administrators only", **kwargs ):
         """
         Raise an error if `user` is not an admin.
 
         :raises exceptions.AdminRequiredException: if `user` is not an admin.
         """
         # useful in admin only methods
-        if not self.is_admin( trans, user ):
+        if not self.is_admin( user ):
             raise exceptions.AdminRequiredException( msg, **kwargs )
         return user
 
@@ -137,7 +136,7 @@ class UserManager( base.ModelManager, deletable.PurgableManagerMixin ):
         # define here for single point of change and make more readable
         return user is None
 
-    def error_if_anonymous( self, trans, user, msg="Log-in required", **kwargs ):
+    def error_if_anonymous( self, user, msg="Log-in required", **kwargs ):
         """
         Raise an error if `user` is anonymous.
         """
@@ -149,10 +148,11 @@ class UserManager( base.ModelManager, deletable.PurgableManagerMixin ):
     # ---- current
     def current_user( self, trans ):
         # define here for single point of change and make more readable
+        # TODO: trans
         return trans.user
 
     # ---- api keys
-    def create_api_key( self, trans, user ):
+    def create_api_key( self, user ):
         """
         Create and return an API key for `user`.
         """
@@ -160,7 +160,7 @@ class UserManager( base.ModelManager, deletable.PurgableManagerMixin ):
         return api_keys.ApiKeyManager( self.app ).create_api_key( user )
 
     #TODO: possibly move to ApiKeyManager
-    def valid_api_key( self, trans, user ):
+    def valid_api_key( self, user ):
         """
         Return this most recent APIKey for this user or None if none have been created.
         """
@@ -177,15 +177,15 @@ class UserManager( base.ModelManager, deletable.PurgableManagerMixin ):
         #return query.first()
 
     #TODO: possibly move to ApiKeyManager
-    def get_or_create_valid_api_key( self, trans, user ):
+    def get_or_create_valid_api_key( self, user ):
         """
         Return this most recent APIKey for this user or create one if none have been
         created.
         """
-        existing = self.valid_api_key( trans, user )
+        existing = self.valid_api_key( user )
         if existing:
             return existing
-        return self.create_api_key( self, trans, user )
+        return self.create_api_key( self, user )
 
     # ---- preferences
 
@@ -204,7 +204,7 @@ class UserManager( base.ModelManager, deletable.PurgableManagerMixin ):
         #TODO: use quota manager
         return self.app.quota_agent.get_percent( user=user )
 
-    def tags_used( self, trans, user, tag_models=None ):
+    def tags_used( self, user, tag_models=None ):
         """
         Return a list of distinct 'user_tname:user_value' strings that the
         given user has used.
@@ -220,7 +220,7 @@ class UserManager( base.ModelManager, deletable.PurgableManagerMixin ):
         all_tags_query = None
         for tag_model in tag_models:
             subq = ( self.session().query( tag_model.user_tname, tag_model.user_value )
-                        .filter( tag_model.user == trans.user ) )
+                        .filter( tag_model.user == user ) )
             all_tags_query = subq if all_tags_query is None else all_tags_query.union( subq )
 
         # if nothing init'd the query, bail
@@ -232,7 +232,7 @@ class UserManager( base.ModelManager, deletable.PurgableManagerMixin ):
         tags = [( ( name + ':' + val ) if val else name ) for name, val in tags ]
         return sorted( tags )
 
-    def has_requests( self, trans, user ):
+    def has_requests( self, user, trans ):
         """
         """
         if self.is_anonymous( user ):
@@ -281,14 +281,14 @@ class UserSerializer( base.ModelSerializer, deletable.PurgableSerializerMixin ):
             'id'            : self.serialize_id,
             'create_time'   : self.serialize_date,
             'update_time'   : self.serialize_date,
-            'is_admin'      : lambda t, i, k: self.user_manager.is_admin( t, i ),
+            'is_admin'      : lambda t, i, k: self.user_manager.is_admin( i ),
 
             'total_disk_usage' : lambda t, i, k: float( i.total_disk_usage ),
             'quota_percent' : lambda t, i, k: self.user_manager.quota( i ),
 
-            'tags_used'     : lambda t, i, k: self.user_manager.tags_used( t, i ),
+            'tags_used'     : lambda t, i, k: self.user_manager.tags_used( i ),
             #TODO: 'has_requests' is more apt
-            'requests'      : lambda t, i, k: self.user_manager.has_requests( t, i )
+            'requests'      : lambda t, i, k: self.user_manager.has_requests( i, t )
         })
 
 
diff --git a/lib/galaxy/visualization/registry.py b/lib/galaxy/visualization/registry.py
index d94841aa4ef..053862a4137 100644
--- a/lib/galaxy/visualization/registry.py
+++ b/lib/galaxy/visualization/registry.py
@@ -961,7 +961,7 @@ class ResourceParser( object ):
 
         elif param_type == 'dataset':
             decoded_dataset_id = trans.security.decode_id( query_param )
-            parsed_param = controller.hda_manager.get_accessible( trans, decoded_dataset_id, trans.user )
+            parsed_param = controller.hda_manager.get_accessible( decoded_dataset_id, trans.user )
 
         elif param_type == 'hda_or_ldda':
             encoded_dataset_id = query_param
diff --git a/lib/galaxy/webapps/galaxy/api/annotations.py b/lib/galaxy/webapps/galaxy/api/annotations.py
index b621bf55b9d..d0dbd931d80 100644
--- a/lib/galaxy/webapps/galaxy/api/annotations.py
+++ b/lib/galaxy/webapps/galaxy/api/annotations.py
@@ -63,7 +63,7 @@ class HistoryAnnotationsController(BaseAnnotationsController):
 
     def _get_item_from_id(self, trans, idstr):
         decoded_idstr = self.decode_id( idstr )
-        history = self.history_manager.get_accessible( trans, decoded_idstr, trans.user )
+        history = self.history_manager.get_accessible( decoded_idstr, trans.user, current_history=trans.history )
         return history
 
 
@@ -77,8 +77,8 @@ class HistoryContentAnnotationsController( BaseAnnotationsController ):
 
     def _get_item_from_id(self, trans, idstr):
         decoded_idstr = self.decode_id( idstr )
-        hda = self.hda_manager.get_accessible( trans, decoded_idstr, trans.user )
-        hda = self.hda_manager.error_if_uploading( trans, hda )
+        hda = self.hda_manager.get_accessible( decoded_idstr, trans.user )
+        hda = self.hda_manager.error_if_uploading( hda )
         return hda
 
 
diff --git a/lib/galaxy/webapps/galaxy/api/configuration.py b/lib/galaxy/webapps/galaxy/api/configuration.py
index d9ff5fcb1cb..240b8037778 100644
--- a/lib/galaxy/webapps/galaxy/api/configuration.py
+++ b/lib/galaxy/webapps/galaxy/api/configuration.py
@@ -29,7 +29,7 @@ class ConfigurationController( BaseAPIController ):
 
         Note: a more complete list is returned if the user is an admin.
         """
-        is_admin = self.user_manager.is_admin( trans, trans.user )
+        is_admin = self.user_manager.is_admin( trans.user )
         serialization_params = self._parse_serialization_params( kwd, 'all' )
         return self.get_config_dict( trans, is_admin, **serialization_params )
 
diff --git a/lib/galaxy/webapps/galaxy/api/dataset_collections.py b/lib/galaxy/webapps/galaxy/api/dataset_collections.py
index 2f489618752..9d25976dffd 100644
--- a/lib/galaxy/webapps/galaxy/api/dataset_collections.py
+++ b/lib/galaxy/webapps/galaxy/api/dataset_collections.py
@@ -45,7 +45,7 @@ class DatasetCollectionsController(
         if instance_type == "history":
             history_id = payload.get( 'history_id' )
             history_id = self.decode_id( history_id )
-            history = self.history_manager.get_owned( trans, history_id, trans.user )
+            history = self.history_manager.get_owned( history_id, trans.user, current_history=trans.history )
             create_params[ "parent" ] = history
         elif instance_type == "library":
             folder_id = payload.get( 'folder_id' )
diff --git a/lib/galaxy/webapps/galaxy/api/datasets.py b/lib/galaxy/webapps/galaxy/api/datasets.py
index 0b870c6e366..dabfd8d384e 100644
--- a/lib/galaxy/webapps/galaxy/api/datasets.py
+++ b/lib/galaxy/webapps/galaxy/api/datasets.py
@@ -80,7 +80,7 @@ class DatasetsController( BaseAPIController, UsesVisualizationMixin ):
         """
         Returns state of dataset.
         """
-        msg = self.hda_manager.data_conversion_status( trans, dataset )
+        msg = self.hda_manager.data_conversion_status( dataset )
         if not msg:
             msg = dataset.conversion_messages.DATA
 
@@ -91,7 +91,7 @@ class DatasetsController( BaseAPIController, UsesVisualizationMixin ):
         Init-like method that returns state of dataset's converted datasets.
         Returns valid chroms for that dataset as well.
         """
-        msg = self.hda_manager.data_conversion_status( trans, dataset )
+        msg = self.hda_manager.data_conversion_status( dataset )
         if msg:
             return msg
 
@@ -140,7 +140,7 @@ class DatasetsController( BaseAPIController, UsesVisualizationMixin ):
             return dataset.conversion_messages.NO_DATA
 
         # Dataset check.
-        msg = self.hda_manager.data_conversion_status( trans, dataset )
+        msg = self.hda_manager.data_conversion_status( dataset )
         if msg:
             return msg
 
@@ -233,7 +233,7 @@ class DatasetsController( BaseAPIController, UsesVisualizationMixin ):
         be slow because indexes need to be created.
         """
         # Dataset check.
-        msg = self.hda_manager.data_conversion_status( trans, dataset )
+        msg = self.hda_manager.data_conversion_status( dataset )
         if msg:
             return msg
 
@@ -280,7 +280,7 @@ class DatasetsController( BaseAPIController, UsesVisualizationMixin ):
 
         rval = ''
         try:
-            hda = self.hda_manager.get_accessible( trans, decoded_content_id, trans.user )
+            hda = self.hda_manager.get_accessible( decoded_content_id, trans.user )
 
             if raw:
                 if filename and filename != 'index':
diff --git a/lib/galaxy/webapps/galaxy/api/extended_metadata.py b/lib/galaxy/webapps/galaxy/api/extended_metadata.py
index 4d2db859af0..6d168d184e0 100644
--- a/lib/galaxy/webapps/galaxy/api/extended_metadata.py
+++ b/lib/galaxy/webapps/galaxy/api/extended_metadata.py
@@ -71,7 +71,7 @@ class HistoryDatasetExtendMetadataController(BaseExtendedMetadataController):
     def _get_item_from_id(self, trans, idstr, check_writable=True):
         decoded_idstr = self.decode_id( idstr )
         if check_writable:
-            return self.hda_manager.get_owned( trans, decoded_idstr, trans.user )
+            return self.hda_manager.get_owned( decoded_idstr, trans.user, current_history=trans.history )
         else:
-            hda = self.hda_manager.get_accessible( trans, decoded_idstr, trans.user )
-            return self.hda_manager.error_if_uploading( trans, hda )
+            hda = self.hda_manager.get_accessible( decoded_idstr, trans.user )
+            return self.hda_manager.error_if_uploading( hda )
diff --git a/lib/galaxy/webapps/galaxy/api/folder_contents.py b/lib/galaxy/webapps/galaxy/api/folder_contents.py
index 780cf63e4a7..e5693c1f9f3 100644
--- a/lib/galaxy/webapps/galaxy/api/folder_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py
@@ -130,7 +130,7 @@ class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrary
 
         # Check whether user can modify the current folder
         can_modify_folder = is_admin or trans.app.security_agent.can_modify_library_item( current_user_roles, folder )
-        
+
         parent_library_id = None
         if folder.parent_library is not None:
             parent_library_id = trans.security.encode_id( folder.parent_library.id )
@@ -268,8 +268,8 @@ class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrary
         rval = {}
         try:
             decoded_hda_id = self.decode_id( from_hda_id )
-            hda = self.hda_manager.get_owned( trans, decoded_hda_id, trans.user )
-            hda = self.hda_manager.error_if_uploading( trans, hda )
+            hda = self.hda_manager.get_owned( decoded_hda_id, trans.user, current_history=trans.history )
+            hda = self.hda_manager.error_if_uploading( hda )
             folder = self.get_library_folder( trans, encoded_folder_id_16, check_accessible=True )
 
             library = folder.parent_library
diff --git a/lib/galaxy/webapps/galaxy/api/histories.py b/lib/galaxy/webapps/galaxy/api/histories.py
index 813ef96da83..c1ccd60e95e 100644
--- a/lib/galaxy/webapps/galaxy/api/histories.py
+++ b/lib/galaxy/webapps/galaxy/api/histories.py
@@ -116,7 +116,7 @@ class HistoriesController( BaseAPIController, ExportsHistoryMixin, ImportsHistor
 
         #TODO: eventually make order_by a param as well
         order_by = sqlalchemy.desc( self.app.model.History.create_time )
-        histories = self.history_manager.list( trans, filters=filters, order_by=order_by, limit=limit, offset=offset )
+        histories = self.history_manager.list( filters=filters, order_by=order_by, limit=limit, offset=offset )
 
         rval = []
         for history in histories:
@@ -174,10 +174,10 @@ class HistoriesController( BaseAPIController, ExportsHistoryMixin, ImportsHistor
         deleted = string_as_bool( deleted )
 
         if history_id == "most_recently_used":
-            history = self.history_manager.most_recent( trans, trans.user,
-                filters=( self.app.model.History.deleted == False ) )
+            history = self.history_manager.most_recent( trans.user,
+                filters=( self.app.model.History.deleted == False ), current_history=trans.history )
         else:
-            history = self.history_manager.get_accessible( trans, self.decode_id( history_id ), trans.user )
+            history = self.history_manager.get_accessible( self.decode_id( history_id ), trans.user, current_history=trans.history )
 
         return self.history_serializer.serialize_to_view( trans, history,
             **self._parse_serialization_params( kwd, 'detailed' ) )
@@ -186,7 +186,7 @@ class HistoriesController( BaseAPIController, ExportsHistoryMixin, ImportsHistor
     def citations( self, trans, history_id, **kwd ):
         """
         """
-        history = self.history_manager.get_accessible( trans, self.decode_id( history_id ), trans.user )
+        history = self.history_manager.get_accessible( self.decode_id( history_id ), trans.user, current_history=trans.history )
         tool_ids = set([])
         for dataset in history.datasets:
             job = dataset.creating_job
@@ -234,13 +234,13 @@ class HistoriesController( BaseAPIController, ExportsHistoryMixin, ImportsHistor
         # if a history id was passed, copy that history
         if copy_this_history_id:
             decoded_id = self.decode_id( copy_this_history_id )
-            original_history = self.history_manager.get_accessible( trans, decoded_id, trans.user )
+            original_history = self.history_manager.get_accessible( decoded_id, trans.user, current_history=trans.history )
             hist_name = hist_name or ( "Copy of '%s'" % original_history.name )
             new_history = original_history.copy( name=hist_name, target_user=trans.user )
 
         # otherwise, create a new empty history
         else:
-            new_history = self.history_manager.create( trans, user=trans.user, name=hist_name )
+            new_history = self.history_manager.create( user=trans.user, name=hist_name )
 
         trans.sa_session.add( new_history )
         trans.sa_session.flush()
@@ -279,10 +279,10 @@ class HistoriesController( BaseAPIController, ExportsHistoryMixin, ImportsHistor
         if kwd.get( 'payload', None ):
             purge = string_as_bool( kwd['payload'].get( 'purge', False ) )
 
-        history = self.history_manager.get_owned( trans, self.decode_id( history_id ), trans.user )
-        self.history_manager.delete( trans, history )
+        history = self.history_manager.get_owned( self.decode_id( history_id ), trans.user, current_history=trans.history )
+        self.history_manager.delete( history )
         if purge:
-            self.history_manager.purge( trans, history )
+            self.history_manager.purge( history )
 
         return self.history_serializer.serialize_to_view( trans, history,
             **self._parse_serialization_params( kwd, 'detailed' ) )
@@ -304,8 +304,8 @@ class HistoriesController( BaseAPIController, ExportsHistoryMixin, ImportsHistor
         :returns:   'OK' if the history was undeleted
         """
         history_id = id
-        history = self.history_manager.get_owned( trans, self.decode_id( history_id ), trans.user )
-        self.history_manager.undelete( trans, history )
+        history = self.history_manager.get_owned( self.decode_id( history_id ), trans.user, current_history=trans.history )
+        self.history_manager.undelete( history )
 
         return self.history_serializer.serialize_to_view( trans, history,
             **self._parse_serialization_params( kwd, 'detailed' ) )
@@ -333,7 +333,7 @@ class HistoriesController( BaseAPIController, ExportsHistoryMixin, ImportsHistor
             any values that were different from the original and, therefore, updated
         """
         #TODO: PUT /api/histories/{encoded_history_id} payload = { rating: rating } (w/ no security checks)
-        history = self.history_manager.get_owned( trans, self.decode_id( id ), trans.user )
+        history = self.history_manager.get_owned( self.decode_id( id ), trans.user, current_history=trans.history )
 
         self.history_deserializer.deserialize( trans, history, payload )
         return self.history_serializer.serialize_to_view( trans, history,
@@ -355,7 +355,7 @@ class HistoriesController( BaseAPIController, ExportsHistoryMixin, ImportsHistor
         """
         # PUT instead of POST because multiple requests should just result
         # in one object being created.
-        history = self.history_manager.get_accessible( trans, self.decode_id( id ), trans.user )
+        history = self.history_manager.get_accessible( self.decode_id( id ), trans.user, current_history=trans.history )
         jeha = history.latest_export
         up_to_date = jeha and jeha.up_to_date
         if 'force' in kwds:
@@ -388,7 +388,7 @@ class HistoriesController( BaseAPIController, ExportsHistoryMixin, ImportsHistor
         """
         # Seems silly to put jeha_id in here, but want GET to be immuatable?
         # and this is being accomplished this way.
-        history = self.history_manager.get_accessible( trans, self.decode_id( id ), trans.user )
+        history = self.history_manager.get_accessible( self.decode_id( id ), trans.user, current_history=trans.history )
         matching_exports = filter( lambda e: trans.security.encode_id( e.id ) == jeha_id, history.exports )
         if not matching_exports:
             raise exceptions.ObjectNotFound()
diff --git a/lib/galaxy/webapps/galaxy/api/history_contents.py b/lib/galaxy/webapps/galaxy/api/history_contents.py
index 6b8118f9501..eecf2533c6e 100644
--- a/lib/galaxy/webapps/galaxy/api/history_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/history_contents.py
@@ -68,7 +68,7 @@ class HistoryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
         """
         rval = []
 
-        history = self.history_manager.get_accessible( trans, self.decode_id( history_id ), trans.user )
+        history = self.history_manager.get_accessible( self.decode_id( history_id ), trans.user, current_history=trans.history )
 
         # Allow passing in type or types - for continuity rest of methods
         # take in type - but this one can be passed multiple types and
@@ -132,7 +132,7 @@ class HistoryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
         :rtype:     dict
         :returns:   dictionary containing detailed HDA information
         """
-        history = self.history_manager.get_accessible( trans, self.decode_id( history_id ), trans.user )
+        history = self.history_manager.get_accessible( self.decode_id( history_id ), trans.user, current_history=trans.history )
 
         contents_type = kwd.get('type', 'dataset')
         if contents_type == 'dataset':
@@ -143,7 +143,7 @@ class HistoryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
             return self.__handle_unknown_contents_type( trans, contents_type )
 
     def __show_dataset( self, trans, id, **kwd ):
-        hda = self.hda_manager.get_accessible( trans, self.decode_id( id ), trans.user )
+        hda = self.hda_manager.get_accessible( self.decode_id( id ), trans.user )
         return self.hda_serializer.serialize_to_view( trans, hda,
             **self._parse_serialization_params( kwd, 'detailed' ) )
 
@@ -214,7 +214,8 @@ class HistoryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
         # TODO: Flush out create new collection documentation above, need some
         # examples. See also bioblend and API tests for specific examples.
 
-        history = self.history_manager.get_owned( trans, self.decode_id( history_id ), trans.user )
+        history = self.history_manager.get_owned( self.decode_id( history_id ), trans.user,
+            current_history=trans.history )
 
         type = payload.get( 'type', 'dataset' )
         if type == 'dataset':
@@ -247,9 +248,9 @@ class HistoryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
         # copy an existing, accessible hda
         elif source == 'hda':
             unencoded_hda_id = self.decode_id( content )
-            original = self.hda_manager.get_accessible( trans, unencoded_hda_id, trans.user )
+            original = self.hda_manager.get_accessible( unencoded_hda_id, trans.user )
             # check for access on history that contains the original hda as well
-            self.history_manager.error_unless_accessible( trans, original.history, trans.user )
+            self.history_manager.error_unless_accessible( original.history, trans.user, current_history=trans.history )
             data_copy = original.copy( copy_children=True )
             hda = history.add_dataset( data_copy )
 
@@ -319,10 +320,10 @@ class HistoryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
         # anon user: ensure that history ids match up and the history is the current,
         #   check for uploading, and use only the subset of attribute keys manipulatable by anon users
         if trans.user == None:
-            hda = self.hda_manager.by_id( trans, self.decode_id( id ) )
+            hda = self.hda_manager.by_id( self.decode_id( id ) )
             if hda.history != trans.history:
                 raise exceptions.AuthenticationRequired( 'API authentication required for this request' )
-            hda = self.hda_manager.error_if_uploading( trans, hda )
+            hda = self.hda_manager.error_if_uploading( hda )
 
             anon_allowed_payload = {}
             if 'deleted' in payload:
@@ -333,12 +334,12 @@ class HistoryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
 
         # logged in user: use full payload, check state if deleting, and make sure the history is theirs
         else:
-            hda = self.hda_manager.get_owned( trans, self.decode_id( id ), trans.user )
+            hda = self.hda_manager.get_owned( self.decode_id( id ), trans.user, current_history=trans.history )
 
             # only check_state if not deleting, otherwise cannot delete uploading files
             check_state = not payload.get( 'deleted', False )
             if check_state:
-                hda = self.hda_manager.error_if_uploading( trans, hda )
+                hda = self.hda_manager.error_if_uploading( hda )
 
         # make the actual changes
         #TODO: is this if still needed?
@@ -399,13 +400,13 @@ class HistoryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
             # payload takes priority
             purge = util.string_as_bool( kwd['payload'].get( 'purge', purge ) )
 
-        hda = self.hda_manager.get_owned( trans, self.decode_id( id ), trans.user )
-        self.hda_manager.error_if_uploading( trans, hda )
+        hda = self.hda_manager.get_owned( self.decode_id( id ), trans.user, current_history=trans.history )
+        self.hda_manager.error_if_uploading( hda )
 
         if purge:
-            self.hda_manager.purge( trans, hda )
+            self.hda_manager.purge( hda )
         else:
-            self.hda_manager.delete( trans, hda )
+            self.hda_manager.delete( hda )
         return self.hda_serializer.serialize_to_view( trans, hda,
             **self._parse_serialization_params( kwd, 'detailed' ) )
 
diff --git a/lib/galaxy/webapps/galaxy/api/jobs.py b/lib/galaxy/webapps/galaxy/api/jobs.py
index 4bd0cdbc662..193179dc9e2 100644
--- a/lib/galaxy/webapps/galaxy/api/jobs.py
+++ b/lib/galaxy/webapps/galaxy/api/jobs.py
@@ -262,7 +262,7 @@ class JobController( BaseAPIController, UsesLibraryMixinItems ):
                 if 'id' in v:
                     if 'src' not in v or v[ 'src' ] == 'hda':
                         hda_id = self.decode_id( v['id'] )
-                        dataset = self.hda_manager.get_accessible( trans, hda_id, trans.user )
+                        dataset = self.hda_manager.get_accessible( hda_id, trans.user )
                     else:
                         dataset = self.get_library_dataset_dataset_association( trans, v['id'] )
                     if dataset is None:
diff --git a/lib/galaxy/webapps/galaxy/api/library_contents.py b/lib/galaxy/webapps/galaxy/api/library_contents.py
index 55dff652056..d0e05dd8c15 100644
--- a/lib/galaxy/webapps/galaxy/api/library_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/library_contents.py
@@ -304,8 +304,8 @@ class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
             # check permissions on (all three?) resources: hda, library, folder
             # TODO: do we really need the library??
             from_hda_id = self.decode_id( from_hda_id )
-            hda = self.hda_manager.get_owned( trans, from_hda_id, trans.user )
-            hda = self.hda_manager.error_if_uploading( trans, hda )
+            hda = self.hda_manager.get_owned( from_hda_id, trans.user, current_history=trans.history )
+            hda = self.hda_manager.error_if_uploading( hda )
             # library = self.get_library( trans, library_id, check_accessible=True )
             folder = self.get_library_folder( trans, folder_id, check_accessible=True )
 
diff --git a/lib/galaxy/webapps/galaxy/api/provenance.py b/lib/galaxy/webapps/galaxy/api/provenance.py
index 1a6678b39e3..4b9500833d2 100644
--- a/lib/galaxy/webapps/galaxy/api/provenance.py
+++ b/lib/galaxy/webapps/galaxy/api/provenance.py
@@ -41,7 +41,7 @@ class BaseProvenanceController( BaseAPIController ):
     def _get_provenance( self, trans, item_class_name, item_id, follow=True ):
         provenance_item = self.get_object( trans, item_id, item_class_name, check_ownership=False, check_accessible=False)
         if item_class_name == "HistoryDatasetAssociation":
-            self.hda_manager.error_unless_accessible( trans, provenance_item, trans.user )
+            self.hda_manager.error_unless_accessible( provenance_item, trans.user )
         else:
             self.security_check( trans, provenance_item, check_accessible=True )
         out = self._get_record( trans, provenance_item, follow )
diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py
index a6687438040..25bd7a38ae9 100644
--- a/lib/galaxy/webapps/galaxy/api/tools.py
+++ b/lib/galaxy/webapps/galaxy/api/tools.py
@@ -241,7 +241,7 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin ):
         history_id = payload.get("history_id", None)
         if history_id:
             decoded_id = self.decode_id( history_id )
-            target_history = self.history_manager.get_owned( trans, decoded_id, trans.user )
+            target_history = self.history_manager.get_owned( decoded_id, trans.user, current_history=trans.history )
         else:
             target_history = None
 
@@ -387,9 +387,9 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin ):
 
         # Dataset check.
         decoded_dataset_id = self.decode_id( payload.get( 'target_dataset_id' ) )
-        original_dataset = self.hda_manager.get_accessible( trans, decoded_dataset_id, user=trans.user )
-        original_dataset = self.hda_manager.error_if_uploading( trans, original_dataset )
-        msg = self.hda_manager.data_conversion_status( trans, original_dataset )
+        original_dataset = self.hda_manager.get_accessible( decoded_dataset_id, user=trans.user )
+        original_dataset = self.hda_manager.error_if_uploading( original_dataset )
+        msg = self.hda_manager.data_conversion_status( original_dataset )
         if msg:
             return msg
 
diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index 69086100b0a..41445ea65e8 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -152,7 +152,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         if 'from_history_id' in payload:
             from_history_id = payload.get( 'from_history_id' )
             from_history_id = self.decode_id( from_history_id )
-            history = self.history_manager.get_accessible( trans, from_history_id, trans.user )
+            history = self.history_manager.get_accessible( from_history_id, trans.user, current_history=trans.history )
 
             job_ids = map( self.decode_id, payload.get( 'job_ids', [] ) )
             dataset_ids = payload.get( 'dataset_ids', [] )
@@ -318,10 +318,10 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         tool_version    = payload.get( 'tool_version', None )
         tool_inputs     = payload.get( 'inputs', None )
         annotation      = payload.get( 'annotation', '' )
-        
+
         # load tool
         tool = self._get_tool( tool_id, tool_version=tool_version, user=trans.user )
-        
+
         # initialize module
         trans.workflow_building_mode = True
         module = module_factory.from_dict( trans, {
@@ -329,7 +329,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
             'tool_id'       : tool.id,
             'tool_state'    : None
         } )
-        
+
         # create tool model and default tool state (if missing)
         tool_model = module.tool.to_json(trans, tool_inputs, is_dynamic=False)
         module.state.inputs = copy.deepcopy(tool_model['state_inputs'])
diff --git a/lib/galaxy/webapps/galaxy/controllers/dataset.py b/lib/galaxy/webapps/galaxy/controllers/dataset.py
index 992e2ac5900..e12ad1c4280 100644
--- a/lib/galaxy/webapps/galaxy/controllers/dataset.py
+++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py
@@ -529,8 +529,8 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesItemRatings, Uses
     def get_name_and_link_async( self, trans, id=None ):
         """ Returns dataset's name and link. """
         decoded_id = self.decode_id( id )
-        dataset = self.hda_manager.get_accessible( trans, decoded_id, trans.user )
-        dataset = self.hda_manager.error_if_uploading( trans, dataset )
+        dataset = self.hda_manager.get_accessible( decoded_id, trans.user )
+        dataset = self.hda_manager.error_if_uploading( dataset )
         return_dict = { "name" : dataset.name, "link" : url_for( controller='dataset', action="display_by_username_and_slug", username=dataset.history.user.username, slug=trans.security.encode_id( dataset.id ) ) }
         return return_dict
 
@@ -538,8 +538,8 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesItemRatings, Uses
     def get_embed_html_async( self, trans, id ):
         """ Returns HTML for embedding a dataset in a page. """
         decoded_id = self.decode_id( id )
-        dataset = self.hda_manager.get_accessible( trans, decoded_id, trans.user )
-        dataset = self.hda_manager.error_if_uploading( trans, dataset )
+        dataset = self.hda_manager.get_accessible( decoded_id, trans.user )
+        dataset = self.hda_manager.error_if_uploading( dataset )
         if dataset:
             return "Embedded Dataset '%s'" % dataset.name
 
@@ -556,8 +556,8 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesItemRatings, Uses
         """ Rate a dataset asynchronously and return updated community data. """
 
         decoded_id = self.decode_id( id )
-        dataset = self.hda_manager.get_accessible( trans, decoded_id, trans.user )
-        dataset = self.hda_manager.error_if_uploading( trans, dataset )
+        dataset = self.hda_manager.get_accessible( decoded_id, trans.user )
+        dataset = self.hda_manager.error_if_uploading( dataset )
         if not dataset:
             return trans.show_error_message( "The specified dataset does not exist." )
 
@@ -571,8 +571,8 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesItemRatings, Uses
         """ Display dataset by username and slug; because datasets do not yet have slugs, the slug is the dataset's id. """
         id = slug
         decoded_id = self.decode_id( id )
-        dataset = self.hda_manager.get_accessible( trans, decoded_id, trans.user )
-        dataset = self.hda_manager.error_if_uploading( trans, dataset )
+        dataset = self.hda_manager.get_accessible( decoded_id, trans.user )
+        dataset = self.hda_manager.error_if_uploading( dataset )
         if dataset:
             # Filename used for composite types.
             if filename:
@@ -614,8 +614,8 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesItemRatings, Uses
         """ Returns item content in HTML format. """
 
         decoded_id = self.decode_id( id )
-        dataset = self.hda_manager.get_accessible( trans, decoded_id, trans.user )
-        dataset = self.hda_manager.error_if_uploading( trans, dataset )
+        dataset = self.hda_manager.get_accessible( decoded_id, trans.user )
+        dataset = self.hda_manager.error_if_uploading( dataset )
         if dataset is None:
             raise web.httpexceptions.HTTPNotFound()
         truncated, dataset_data = self.hda_manager.text_data( dataset, preview=True )
@@ -627,8 +627,8 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesItemRatings, Uses
     def annotate_async( self, trans, id, new_annotation=None, **kwargs ):
         #TODO:?? why is this an access check only?
         decoded_id = self.decode_id( id )
-        dataset = self.hda_manager.get_accessible( trans, decoded_id, trans.user )
-        dataset = self.hda_manager.error_if_uploading( trans, dataset )
+        dataset = self.hda_manager.get_accessible( decoded_id, trans.user )
+        dataset = self.hda_manager.error_if_uploading( dataset )
         if not dataset:
             web.httpexceptions.HTTPNotFound()
         if dataset and new_annotation:
@@ -641,8 +641,8 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesItemRatings, Uses
     @web.expose
     def get_annotation_async( self, trans, id ):
         decoded_id = self.decode_id( id )
-        dataset = self.hda_manager.get_accessible( trans, decoded_id, trans.user )
-        dataset = self.hda_manager.error_if_uploading( trans, dataset )
+        dataset = self.hda_manager.get_accessible( decoded_id, trans.user )
+        dataset = self.hda_manager.error_if_uploading( dataset )
         if not dataset:
             web.httpexceptions.HTTPNotFound()
         annotation = self.get_item_annotation_str( trans.sa_session, trans.user, dataset )
@@ -1023,7 +1023,7 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesItemRatings, Uses
         user = trans.get_user()
         if source_history is not None:
             decoded_source_history_id = self.decode_id( source_history )
-            history = self.history_manager.get_owned( trans, decoded_source_history_id, trans.user )
+            history = self.history_manager.get_owned( decoded_source_history_id, trans.user, current_history=trans.history )
             current_history = trans.get_history()
         else:
             history = current_history = trans.get_history()
@@ -1129,8 +1129,8 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesItemRatings, Uses
                     error_msg = error_msg + "You do not have permission to add datasets to %i requested histories.  " % ( len( target_histories ) )
             for dataset_id in dataset_ids:
                 decoded_id = self.decode_id( dataset_id )
-                data = self.hda_manager.get_accessible( trans, decoded_id, trans.user )
-                data = self.hda_manager.error_if_uploading( trans, data )
+                data = self.hda_manager.get_accessible( decoded_id, trans.user )
+                data = self.hda_manager.error_if_uploading( data )
 
                 if data is None:
                     error_msg = error_msg + "You tried to copy a dataset that does not exist or that you do not have access to.  "
diff --git a/lib/galaxy/webapps/galaxy/controllers/history.py b/lib/galaxy/webapps/galaxy/controllers/history.py
index 727b0a2e7f3..7b5b807ac39 100644
--- a/lib/galaxy/webapps/galaxy/controllers/history.py
+++ b/lib/galaxy/webapps/galaxy/controllers/history.py
@@ -254,7 +254,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
                 return self.rename( trans, **kwargs )
             if operation == "view":
                 decoded_id = self.decode_id( kwargs.get( 'id', None ) )
-                history = self.history_manager.get_owned( trans, decoded_id, trans.user )
+                history = self.history_manager.get_owned( decoded_id, trans.user, current_history=trans.history )
                 return trans.response.send_redirect( url_for( controller='history',
                                                               action='view',
                                                               id=kwargs['id'],
@@ -268,7 +268,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
             # Load the histories and ensure they all belong to the current user
             histories = []
             for history_id in history_ids:
-                history = self.history_manager.get_owned( trans, self.decode_id( history_id ), trans.user )
+                history = self.history_manager.get_owned( self.decode_id( history_id ), trans.user, current_history=trans.history )
                 if history:
                     # Ensure history is owned by current user
                     if history.user_id != None and trans.user:
@@ -313,7 +313,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
                     if history_ids:
                         histories = []
                         for history_id in history_ids:
-                            history = self.history_manager.get_owned( trans, self.decode_id( history_id ), trans.user )
+                            history = self.history_manager.get_owned( self.decode_id( history_id ), trans.user, current_history=trans.history )
                             if history.importable:
                                 history.importable = False
                             histories.append( history )
@@ -439,7 +439,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
             operation = kwargs['operation'].lower()
             if operation == "view":
                 # Display history.
-                history = self.history_manager.get_accessible( trans, self.decode_id( ids[0] ), trans.user )
+                history = self.history_manager.get_accessible( self.decode_id( ids[0] ), trans.user, current_history=trans.history )
                 return self.display_by_username_and_slug( trans, history.user.username, history.slug )
             elif operation == "copy":
                 if not ids:
@@ -455,7 +455,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
                 for id in ids:
                     # No need to check security, association below won't yield a
                     # hit if this user isn't having the history shared with her.
-                    history = self.history_manager.by_id( trans, self.decode_id( id ) )
+                    history = self.history_manager.by_id( self.decode_id( id ) )
                     # Current user is the user with which the histories were shared
                     association = ( trans.sa_session.query( trans.app.model.HistoryUserShareAssociation )
                                         .filter_by( user=trans.user, history=history ).one() )
@@ -555,7 +555,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
         unencoded_history_id = trans.history.id
         if id:
             unencoded_history_id = self.decode_id( id )
-        history_to_view = self.history_manager.get_accessible( trans, unencoded_history_id, trans.user )
+        history_to_view = self.history_manager.get_accessible( unencoded_history_id, trans.user, current_history=trans.history )
 
         history_data = self.history_manager._get_history_data( trans, history_to_view )
         history_dictionary = history_data[ 'history' ]
@@ -595,7 +595,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
         hda_dictionaries   = []
         user_is_owner = False
         try:
-            history_to_view = self.history_manager.get_accessible( trans, self.decode_id( id ), trans.user )
+            history_to_view = self.history_manager.get_accessible( self.decode_id( id ), trans.user, current_history=trans.history )
             user_is_owner = history_to_view.user == trans.user
 
             # include all datasets: hidden, deleted, and purged
@@ -641,7 +641,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
         current_history_id = trans.security.encode_id( current_history.id ) if current_history else None
 
         history_dictionaries = []
-        for history in self.history_manager.by_user( trans, trans.user, filters=deleted_filter ):
+        for history in self.history_manager.by_user( trans.user, filters=deleted_filter ):
             history_dictionary = self.history_serializer.serialize_to_view( trans, history, view='detailed' )
             history_dictionaries.append( history_dictionary )
 
@@ -661,7 +661,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
         if history is None:
            raise web.httpexceptions.HTTPNotFound()
         # Security check raises error if user cannot access history.
-        self.history_manager.error_unless_accessible( trans, history, trans.user )
+        self.history_manager.error_unless_accessible( history, trans.user, current_history=trans.history )
 
         # Get rating data.
         user_item_rating = 0
@@ -701,7 +701,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
         if id:
             ids = galaxy.util.listify( id )
             if ids:
-                histories = [ self.history_manager.get_accessible( trans, self.decode_id( history_id ), trans.user )
+                histories = [ self.history_manager.get_accessible( self.decode_id( history_id ), trans.user, current_history=trans.history )
                               for history_id in ids ]
         elif not histories:
             histories = [ trans.history ]
@@ -771,7 +771,9 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
             send_to_err = err_msg
             histories = []
             for history_id in id:
-                histories.append( self.history_manager.get_owned( trans, self.decode_id( history_id ), trans.user ) )
+                history_id = self.decode_id( history_id )
+                history = self.history_manager.get_owned( history_id, trans.user, current_history=trans.history )
+                histories.append( history )
             return trans.fill_template( "/history/share.mako",
                                         histories=histories,
                                         email=email,
@@ -894,7 +896,9 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
         ids = galaxy.util.listify( ids )
         histories = []
         for history_id in ids:
-            histories.append( self.history_manager.get_owned( trans, self.decode_id( history_id ), trans.user ) )
+            history_id = self.decode_id( history_id )
+            history = self.history_manager.get_owned( history_id, trans.user, current_history=trans.history )
+            histories.append(  )
         return histories
 
     def _get_users( self, trans, user, emails_or_ids ):
@@ -908,14 +912,14 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
             send_to_user = None
             if '@' in string:
                 email_address = string
-                send_to_user = self.user_manager.by_email( trans, email_address,
+                send_to_user = self.user_manager.by_email( email_address,
                     filters=[ trans.app.model.User.table.c.deleted == False ] )
 
             else:
                 user_id = string
                 try:
                     decoded_user_id = self.decode_id( string )
-                    send_to_user = self.user_manager.by_id( trans, decoded_user_id )
+                    send_to_user = self.user_manager.by_id( decoded_user_id )
                     if send_to_user.deleted:
                         send_to_user = None
                 #TODO: in an ideal world, we would let this bubble up to web.expose which would handle it
@@ -1144,7 +1148,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
                     trans.app.job_manager.job_stop_queue.put( job.id )
 
         # Regardless of whether it was previously deleted, get the most recent history or create a new one.
-        most_recent_history = self.history_manager.most_recent( trans, user=trans.user )
+        most_recent_history = self.history_manager.most_recent( user=trans.user )
         if most_recent_history:
             trans.set_history( most_recent_history )
             return trans.show_ok_message( "History deleted, your most recent history is now active",
@@ -1188,7 +1192,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
     @web.json
     def rate_async( self, trans, id, rating ):
         """ Rate a history asynchronously and return updated community data. """
-        history = self.history_manager.get_accessible( trans, self.decode_id( id ), trans.user )
+        history = self.history_manager.get_accessible( self.decode_id( id ), trans.user, current_history=trans.history )
         if not history:
             return trans.show_error_message( "The specified history does not exist." )
         # Rate history.
@@ -1232,7 +1236,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
         # Get history to export.
         #
         if id:
-            history = self.history_manager.get_accessible( trans, self.decode_id( id ), trans.user )
+            history = self.history_manager.get_accessible( self.decode_id( id ), trans.user, current_history=trans.history )
         else:
             # Use current history.
             history = trans.history
@@ -1265,7 +1269,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
     @web.require_login( "get history name and link" )
     def get_name_and_link_async( self, trans, id=None ):
         """ Returns history's name and link. """
-        history = self.history_manager.get_accessible( trans, self.decode_id( id ), trans.user )
+        history = self.history_manager.get_accessible( self.decode_id( id ), trans.user, current_history=trans.history )
         if self.create_item_slug( trans.sa_session, history ):
             trans.sa_session.flush()
         return_dict = {
@@ -1279,7 +1283,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
     @web.require_login( "set history's accessible flag" )
     def set_accessible_async( self, trans, id=None, accessible=False ):
         """ Set history's importable attribute and slug. """
-        history = self.history_manager.get_owned( trans, self.decode_id( id ), trans.user )
+        history = self.history_manager.get_owned( self.decode_id( id ), trans.user, current_history=trans.history )
         # Only set if importable value would change; this prevents a change in the update_time unless attribute really changed.
         importable = accessible in ['True', 'true', 't', 'T'];
         if history and history.importable != importable:
@@ -1327,11 +1331,11 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
         # Do import.
         if not id:
             return trans.show_error_message( "You must specify a history you want to import.<br>You can %s." % referer_message, use_panels=True )
-        import_history = self.history_manager.by_id( trans, self.decode_id( id ) )
+        import_history = self.history_manager.by_id( self.decode_id( id ) )
         if not import_history:
             return trans.show_error_message( "The specified history does not exist.<br>You can %s." % referer_message, use_panels=True )
         # History is importable if user is admin or it's accessible. TODO: probably want to have app setting to enable admin access to histories.
-        if not self.history_manager.is_accessible( trans, import_history, trans.user ):
+        if not self.history_manager.is_accessible( import_history, trans.user, current_history=trans.history ):
             return trans.show_error_message( "You cannot access this history.<br>You can %s." % referer_message, use_panels=True )
         if user:
             #dan: I can import my own history.
@@ -1397,7 +1401,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
         histories = []
 
         for history_id in id:
-            history = self.history_manager.get_owned( trans, self.decode_id( history_id ), trans.user )
+            history = self.history_manager.get_owned( self.decode_id( history_id ), trans.user, current_history=trans.history )
             if history and history.user_id == user.id:
                 histories.append( history )
         if not name or len( histories ) != len( name ):
@@ -1454,7 +1458,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
             ids = galaxy.util.listify( id )
             histories = []
             for history_id in ids:
-                history = self.history_manager.get_accessible( trans, self.decode_id( history_id ), trans.user )
+                history = self.history_manager.get_accessible( self.decode_id( history_id ), trans.user, current_history=trans.history )
                 histories.append( history )
         user = trans.get_user()
         for history in histories:
@@ -1491,7 +1495,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
         return trans.response.send_redirect( url_for( "/" ) )
 
     def get_item( self, trans, id ):
-        return self.history_manager.get_owned( trans, self.decode_id( id ), trans.user )
+        return self.history_manager.get_owned( self.decode_id( id ), trans.user, current_history=trans.history )
         #TODO: override of base ui controller?
 
     def history_data( self, trans, history ):
@@ -1506,7 +1510,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
         """
         """
         try:
-            history = self.history_manager.get_owned( trans, self.decode_id( id ), trans.user )
+            history = self.history_manager.get_owned( self.decode_id( id ), trans.user, current_history=trans.history )
             trans.set_history( history )
             return self.history_serializer.serialize_to_view( trans, history, view='detailed' )
         except exceptions.MessageException, msg_exc:
diff --git a/lib/galaxy/webapps/galaxy/controllers/page.py b/lib/galaxy/webapps/galaxy/controllers/page.py
index 47b83675efe..3d04a2351be 100644
--- a/lib/galaxy/webapps/galaxy/controllers/page.py
+++ b/lib/galaxy/webapps/galaxy/controllers/page.py
@@ -748,7 +748,7 @@ class PageController( BaseUIController, SharableMixin,
         # TODO: should be moved to history controller and/or called via ajax from the template
         decoded_id = self.decode_id( id )
         # histories embedded in pages are set to importable when embedded, check for access here
-        history = self.history_manager.get_accessible( trans, decoded_id, trans.user )
+        history = self.history_manager.get_accessible( decoded_id, trans.user, current_history=trans.history )
 
         # create ownership flag for template, dictify models
         # note: adding original annotation since this is published - get_dict returns user-based annos
@@ -798,8 +798,8 @@ class PageController( BaseUIController, SharableMixin,
 
         elif item_class == model.HistoryDatasetAssociation:
             decoded_id = self.decode_id( item_id )
-            dataset = self.hda_manager.get_accessible( trans, decoded_id, trans.user )
-            dataset = self.hda_manager.error_if_uploading( trans, dataset )
+            dataset = self.hda_manager.get_accessible( decoded_id, trans.user )
+            dataset = self.hda_manager.error_if_uploading( dataset )
 
             dataset.annotation = self.get_item_annotation_str( trans.sa_session, dataset.history.user, dataset )
             if dataset:
diff --git a/lib/galaxy/webapps/galaxy/controllers/visualization.py b/lib/galaxy/webapps/galaxy/controllers/visualization.py
index 990fb5882d3..1d5da3d1a76 100644
--- a/lib/galaxy/webapps/galaxy/controllers/visualization.py
+++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py
@@ -871,7 +871,7 @@ class VisualizationController( BaseUIController, SharableMixin, UsesVisualizatio
             dbkey = None
             if new_dataset_id:
                 decoded_id = self.decode_id( new_dataset_id )
-                hda = self.hda_manager.get_owned( trans, decoded_id, trans.user )
+                hda = self.hda_manager.get_owned( decoded_id, trans.user, current_history=trans.user )
                 dbkey = hda.dbkey
                 if dbkey == '?':
                     dbkey = kwargs.get( "dbkey", None )
@@ -981,7 +981,7 @@ class VisualizationController( BaseUIController, SharableMixin, UsesVisualizatio
             viz = self.get_visualization( trans, id )
             viz_config = self.get_visualization_config( trans, viz )
             decoded_id = self.decode_id( viz_config[ 'dataset_id' ] )
-            dataset = self.hda_manager.get_owned( trans, decoded_id, trans.user )
+            dataset = self.hda_manager.get_owned( decoded_id, trans.user, current_history=trans.history )
         else:
             # Loading new visualization.
             dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id )
@@ -1016,7 +1016,7 @@ class VisualizationController( BaseUIController, SharableMixin, UsesVisualizatio
         # get the hda if we can, then its data using the phyloviz parsers
         if dataset_id:
             decoded_id = self.decode_id( dataset_id )
-            hda = self.hda_manager.get_accessible( trans, decoded_id, trans.user )
+            hda = self.hda_manager.get_accessible( decoded_id, trans.user )
             hda = self.hda_manager.error_if_uploading( hda )
         else:
             return trans.show_message( "Phyloviz couldn't find a dataset_id" )
diff --git a/lib/galaxy/workflow/run_request.py b/lib/galaxy/workflow/run_request.py
index 3def2dcb6e3..260eb29a622 100644
--- a/lib/galaxy/workflow/run_request.py
+++ b/lib/galaxy/workflow/run_request.py
@@ -196,7 +196,7 @@ def build_workflow_run_config( trans, workflow, payload ):
         # Passing an existing history to use.
         encoded_history_id = history_param[ 8: ]
         history_id = __decode_id( trans, encoded_history_id, model_type="history" )
-        history = history_manager.get_owned( trans, history_id, trans.user )
+        history = history_manager.get_owned( history_id, trans.user, current_history=trans.history )
     else:
         # Send workflow outputs to new history.
         history = app.model.History(name=history_param, user=trans.user)
diff --git a/test/unit/managers/test_CollectionManager.py b/test/unit/managers/test_CollectionManager.py
index 427da4b53bd..cbc0eecc53d 100644
--- a/test/unit/managers/test_CollectionManager.py
+++ b/test/unit/managers/test_CollectionManager.py
@@ -36,10 +36,10 @@ class DatasetCollectionManagerTestCase( BaseTestCase ):
 
     def set_up_managers( self ):
         super( DatasetCollectionManagerTestCase, self ).set_up_managers()
-        self.dataset_mgr = DatasetManager( self.app )
-        self.hda_mgr = HDAManager( self.app )
-        self.history_mgr = HistoryManager( self.app )
-        self.collection_mgr = DatasetCollectionManager( self.app )
+        self.dataset_manager = DatasetManager( self.app )
+        self.hda_manager = HDAManager( self.app )
+        self.history_manager = HistoryManager( self.app )
+        self.collection_manager = DatasetCollectionManager( self.app )
 
     def build_element_identifiers( self, elements ):
         identifier_list = []
@@ -54,20 +54,20 @@ class DatasetCollectionManagerTestCase( BaseTestCase ):
         return identifier_list
 
     def test_create_simple_list( self ):
-        owner = self.user_mgr.create( self.trans, **user2_data )
+        owner = self.user_manager.create( **user2_data )
 
-        history = self.history_mgr.create( self.trans, name='history1', user=owner )
+        history = self.history_manager.create( name='history1', user=owner )
 
-        hda1 = self.hda_mgr.create( self.trans, name='one',
-            history=history, dataset=self.dataset_mgr.create( self.trans ) )
-        hda2 = self.hda_mgr.create( self.trans, name='two',
-            history=history, dataset=self.dataset_mgr.create( self.trans ) )
-        hda3 = self.hda_mgr.create( self.trans, name='three',
-            history=history, dataset=self.dataset_mgr.create( self.trans ) )
+        hda1 = self.hda_manager.create( name='one',
+            history=history, dataset=self.dataset_manager.create() )
+        hda2 = self.hda_manager.create( name='two',
+            history=history, dataset=self.dataset_manager.create() )
+        hda3 = self.hda_manager.create( name='three',
+            history=history, dataset=self.dataset_manager.create() )
 
         self.log( "should be able to create a new Collection via ids" )
         element_identifiers = self.build_element_identifiers( [ hda1, hda2, hda3 ] )
-        hdca = self.collection_mgr.create( self.trans, history, 'test collection', 'list',
+        hdca = self.collection_manager.create( self.trans, history, 'test collection', 'list',
                                            element_identifiers=element_identifiers )
         self.assertIsInstance( hdca, model.HistoryDatasetCollectionAssociation )
         self.assertEqual( hdca.name, 'test collection' )
@@ -117,26 +117,26 @@ class DatasetCollectionManagerTestCase( BaseTestCase ):
 
         self.log( "should be able to create a new Collection via objects" )
         elements = dict( one=hda1, two=hda2, three=hda3 )
-        hdca2 = self.collection_mgr.create( self.trans, history, 'test collection 2', 'list', elements=elements )
+        hdca2 = self.collection_manager.create( self.trans, history, 'test collection 2', 'list', elements=elements )
         self.assertIsInstance( hdca2, model.HistoryDatasetCollectionAssociation )
 
     def test_update_from_dict( self ):
-        owner = self.user_mgr.create( self.trans, **user2_data )
+        owner = self.user_manager.create( **user2_data )
 
-        history = self.history_mgr.create( self.trans, name='history1', user=owner )
+        history = self.history_manager.create( name='history1', user=owner )
 
-        hda1 = self.hda_mgr.create( self.trans, name='one',
-            history=history, dataset=self.dataset_mgr.create( self.trans ) )
-        hda2 = self.hda_mgr.create( self.trans, name='two',
-            history=history, dataset=self.dataset_mgr.create( self.trans ) )
-        hda3 = self.hda_mgr.create( self.trans, name='three',
-            history=history, dataset=self.dataset_mgr.create( self.trans ) )
+        hda1 = self.hda_manager.create( name='one',
+            history=history, dataset=self.dataset_manager.create() )
+        hda2 = self.hda_manager.create( name='two',
+            history=history, dataset=self.dataset_manager.create() )
+        hda3 = self.hda_manager.create( name='three',
+            history=history, dataset=self.dataset_manager.create() )
 
         elements = dict( one=hda1, two=hda2, three=hda3 )
-        hdca = self.collection_mgr.create( self.trans, history, 'test collection', 'list', elements=elements )
+        hdca = self.collection_manager.create( self.trans, history, 'test collection', 'list', elements=elements )
 
         self.log( "should be set from a dictionary" )
-        self.collection_mgr._set_from_dict( self.trans, hdca, {
+        self.collection_manager._set_from_dict( self.trans, hdca, {
             'deleted'   : True,
             'visible'   : False,
             'name'      : 'New Name',
diff --git a/test/unit/managers/test_DatasetManager.py b/test/unit/managers/test_DatasetManager.py
index f33fba84d64..2bf50a1fcd4 100644
--- a/test/unit/managers/test_DatasetManager.py
+++ b/test/unit/managers/test_DatasetManager.py
@@ -37,54 +37,54 @@ class DatasetManagerTestCase( BaseTestCase ):
 
     def set_up_managers( self ):
         super( DatasetManagerTestCase, self ).set_up_managers()
-        self.dataset_mgr = DatasetManager( self.app )
+        self.dataset_manager = DatasetManager( self.app )
 
     def test_create( self ):
         self.log( "should be able to create a new Dataset" )
-        dataset1 = self.dataset_mgr.create( self.trans )
+        dataset1 = self.dataset_manager.create()
         self.assertIsInstance( dataset1, model.Dataset )
         self.assertEqual( dataset1, self.trans.sa_session.query( model.Dataset ).get( dataset1.id ) )
 
     def test_base( self ):
-        dataset1 = self.dataset_mgr.create( self.trans )
-        dataset2 = self.dataset_mgr.create( self.trans )
+        dataset1 = self.dataset_manager.create()
+        dataset2 = self.dataset_manager.create()
 
         self.log( "should be able to query" )
         datasets = self.trans.sa_session.query( model.Dataset ).all()
-        self.assertEqual( self.dataset_mgr.list( self.trans ), datasets )
-        self.assertEqual( self.dataset_mgr.one( self.trans, filters=( model.Dataset.id == dataset1.id ) ), dataset1 )
-        self.assertEqual( self.dataset_mgr.by_id( self.trans, dataset1.id ), dataset1 )
-        self.assertEqual( self.dataset_mgr.by_ids( self.trans, [ dataset2.id, dataset1.id ] ), [ dataset2, dataset1 ] )
+        self.assertEqual( self.dataset_manager.list(), datasets )
+        self.assertEqual( self.dataset_manager.one( filters=( model.Dataset.id == dataset1.id ) ), dataset1 )
+        self.assertEqual( self.dataset_manager.by_id( dataset1.id ), dataset1 )
+        self.assertEqual( self.dataset_manager.by_ids( [ dataset2.id, dataset1.id ] ), [ dataset2, dataset1 ] )
 
         self.log( "should be able to limit and offset" )
-        self.assertEqual( self.dataset_mgr.list( self.trans, limit=1 ), datasets[0:1] )
-        self.assertEqual( self.dataset_mgr.list( self.trans, offset=1 ), datasets[1:] )
-        self.assertEqual( self.dataset_mgr.list( self.trans, limit=1, offset=1 ), datasets[1:2] )
+        self.assertEqual( self.dataset_manager.list( limit=1 ), datasets[0:1] )
+        self.assertEqual( self.dataset_manager.list( offset=1 ), datasets[1:] )
+        self.assertEqual( self.dataset_manager.list( limit=1, offset=1 ), datasets[1:2] )
 
-        self.assertEqual( self.dataset_mgr.list( self.trans, limit=0 ), [] )
-        self.assertEqual( self.dataset_mgr.list( self.trans, offset=3 ), [] )
+        self.assertEqual( self.dataset_manager.list( limit=0 ), [] )
+        self.assertEqual( self.dataset_manager.list( offset=3 ), [] )
 
         self.log( "should be able to order" )
-        self.assertEqual( self.dataset_mgr.list( self.trans, order_by=sqlalchemy.desc( model.Dataset.create_time ) ),
+        self.assertEqual( self.dataset_manager.list( order_by=sqlalchemy.desc( model.Dataset.create_time ) ),
             [ dataset2, dataset1 ] )
 
     def test_delete( self ):
-        item1 = self.dataset_mgr.create( self.trans )
+        item1 = self.dataset_manager.create()
 
         self.log( "should be able to delete and undelete a dataset" )
         self.assertFalse( item1.deleted )
-        self.assertEqual( self.dataset_mgr.delete( self.trans, item1 ), item1 )
+        self.assertEqual( self.dataset_manager.delete( item1 ), item1 )
         self.assertTrue( item1.deleted )
-        self.assertEqual( self.dataset_mgr.undelete( self.trans, item1 ), item1 )
+        self.assertEqual( self.dataset_manager.undelete( item1 ), item1 )
         self.assertFalse( item1.deleted )
 
     def test_purge_allowed( self ):
         self.trans.app.config.allow_user_dataset_purge = True
-        item1 = self.dataset_mgr.create( self.trans )
+        item1 = self.dataset_manager.create()
 
         self.log( "should purge a dataset if config does allow" )
         self.assertFalse( item1.purged )
-        self.assertEqual( self.dataset_mgr.purge( self.trans, item1 ), item1 )
+        self.assertEqual( self.dataset_manager.purge( item1 ), item1 )
         self.assertTrue( item1.purged )
 
         self.log( "should delete a dataset when purging" )
@@ -92,37 +92,37 @@ class DatasetManagerTestCase( BaseTestCase ):
 
     def test_purge_not_allowed( self ):
         self.trans.app.config.allow_user_dataset_purge = False
-        item1 = self.dataset_mgr.create( self.trans )
+        item1 = self.dataset_manager.create()
 
         self.log( "should raise an error when purging a dataset if config does not allow" )
         self.assertFalse( item1.purged )
-        self.assertRaises( exceptions.ConfigDoesNotAllowException, self.dataset_mgr.purge, self.trans, item1 )
+        self.assertRaises( exceptions.ConfigDoesNotAllowException, self.dataset_manager.purge, item1 )
         self.assertFalse( item1.purged )
 
     def test_create_with_no_permissions( self ):
         self.log( "should be able to create a new Dataset without any permissions" )
-        dataset = self.dataset_mgr.create( self.trans )
+        dataset = self.dataset_manager.create()
 
-        permissions = self.dataset_mgr.permissions.get( dataset )
+        permissions = self.dataset_manager.permissions.get( dataset )
         self.assertIsInstance( permissions, tuple )
         self.assertEqual( len( permissions ), 2 )
         manage_permissions, access_permissions = permissions
         self.assertEqual( manage_permissions, [] )
         self.assertEqual( access_permissions, [] )
 
-        user3 = self.user_mgr.create( self.trans, **user3_data )
+        user3 = self.user_manager.create( **user3_data )
         self.log( "a dataset without permissions shouldn't be manageable to just anyone" )
-        self.assertFalse( self.dataset_mgr.permissions.manage.is_permitted( dataset, user3 ) )
+        self.assertFalse( self.dataset_manager.permissions.manage.is_permitted( dataset, user3 ) )
         self.log( "a dataset without permissions should be accessible" )
-        self.assertTrue( self.dataset_mgr.permissions.access.is_permitted( dataset, user3 ) )
+        self.assertTrue( self.dataset_manager.permissions.access.is_permitted( dataset, user3 ) )
 
     def test_create_public_dataset( self ):
         self.log( "should be able to create a new Dataset and give it some permissions that actually, you know, might work if there's any justice in this universe" )
-        owner = self.user_mgr.create( self.trans, **user2_data )
-        owner_private_role = self.user_mgr.private_role( owner )
-        dataset = self.dataset_mgr.create( self.trans, manage_roles=[ owner_private_role ] )
+        owner = self.user_manager.create( **user2_data )
+        owner_private_role = self.user_manager.private_role( owner )
+        dataset = self.dataset_manager.create( manage_roles=[ owner_private_role ] )
 
-        permissions = self.dataset_mgr.permissions.get( dataset )
+        permissions = self.dataset_manager.permissions.get( dataset )
         self.assertIsInstance( permissions, tuple )
         self.assertEqual( len( permissions ), 2 )
         manage_permissions, access_permissions = permissions
@@ -130,22 +130,22 @@ class DatasetManagerTestCase( BaseTestCase ):
         self.assertIsInstance( manage_permissions[0], model.DatasetPermissions )
         self.assertEqual( access_permissions, [] )
 
-        user3 = self.user_mgr.create( self.trans, **user3_data )
+        user3 = self.user_manager.create( **user3_data )
         self.log( "a public dataset should be manageable to it's owner" )
-        self.assertTrue( self.dataset_mgr.permissions.manage.is_permitted( dataset, owner ) )
+        self.assertTrue( self.dataset_manager.permissions.manage.is_permitted( dataset, owner ) )
         self.log( "a public dataset shouldn't be manageable to just anyone" )
-        self.assertFalse( self.dataset_mgr.permissions.manage.is_permitted( dataset, user3 ) )
+        self.assertFalse( self.dataset_manager.permissions.manage.is_permitted( dataset, user3 ) )
         self.log( "a public dataset should be accessible" )
-        self.assertTrue( self.dataset_mgr.permissions.access.is_permitted( dataset, user3 ) )
+        self.assertTrue( self.dataset_manager.permissions.access.is_permitted( dataset, user3 ) )
 
     def test_create_private_dataset( self ):
         self.log( "should be able to create a new Dataset and give it some permissions that actually, you know, might work if there's any justice in this universe" )
-        owner = self.user_mgr.create( self.trans, **user2_data )
-        owner_private_role = self.user_mgr.private_role( owner )
-        dataset = self.dataset_mgr.create( self.trans,
+        owner = self.user_manager.create( **user2_data )
+        owner_private_role = self.user_manager.private_role( owner )
+        dataset = self.dataset_manager.create(
             manage_roles=[ owner_private_role ], access_roles=[ owner_private_role ] )
 
-        permissions = self.dataset_mgr.permissions.get( dataset )
+        permissions = self.dataset_manager.permissions.get( dataset )
         self.assertIsInstance( permissions, tuple )
         self.assertEqual( len( permissions ), 2 )
         manage_permissions, access_permissions = permissions
@@ -155,15 +155,15 @@ class DatasetManagerTestCase( BaseTestCase ):
         self.assertIsInstance( access_permissions[0], model.DatasetPermissions )
 
         self.log( "a private dataset should be manageable by it's owner" )
-        self.assertTrue( self.dataset_mgr.permissions.manage.is_permitted( dataset, owner ) )
+        self.assertTrue( self.dataset_manager.permissions.manage.is_permitted( dataset, owner ) )
         self.log( "a private dataset should be accessible to it's owner" )
-        self.assertTrue( self.dataset_mgr.permissions.access.is_permitted( dataset, owner ) )
+        self.assertTrue( self.dataset_manager.permissions.access.is_permitted( dataset, owner ) )
 
-        user3 = self.user_mgr.create( self.trans, **user3_data )
+        user3 = self.user_manager.create( **user3_data )
         self.log( "a private dataset shouldn't be manageable to just anyone" )
-        self.assertFalse( self.dataset_mgr.permissions.manage.is_permitted( dataset, user3 ) )
+        self.assertFalse( self.dataset_manager.permissions.manage.is_permitted( dataset, user3 ) )
         self.log( "a private dataset shouldn't be accessible to just anyone" )
-        self.assertFalse( self.dataset_mgr.permissions.access.is_permitted( dataset, user3 ) )
+        self.assertFalse( self.dataset_manager.permissions.access.is_permitted( dataset, user3 ) )
 
 
 # =============================================================================
@@ -171,13 +171,13 @@ class DatasetRBACPermissionsTestCase( BaseTestCase ):
 
     def set_up_managers( self ):
         super( DatasetRBACPermissionsTestCase, self ).set_up_managers()
-        self.dataset_mgr = DatasetManager( self.app )
+        self.dataset_manager = DatasetManager( self.app )
 
     # def test_manage( self ):
     #     self.log( "should be able to create a new Dataset" )
-    #     dataset1 = self.dataset_mgr.create( self.trans )
+    #     dataset1 = self.dataset_manager.create()
     #     self.assertIsInstance( dataset1, model.Dataset )
-    #     self.assertEqual( dataset1, self.trans.sa_session.query( model.Dataset ).get( dataset1.id ) )
+    #     self.assertEqual( dataset1, self.app.model.context.query( model.Dataset ).get( dataset1.id ) )
     #
 
 
@@ -190,11 +190,11 @@ class DatasetSerializerTestCase( BaseTestCase ):
 
     def set_up_managers( self ):
         super( DatasetSerializerTestCase, self ).set_up_managers()
-        self.dataset_mgr = DatasetManager( self.app )
+        self.dataset_manager = DatasetManager( self.app )
         self.dataset_serializer = DatasetSerializer( self.app )
 
     def test_views( self ):
-        dataset = self.dataset_mgr.create( self.trans )
+        dataset = self.dataset_manager.create()
 
         self.log( 'should have a summary view' )
         summary_view = self.dataset_serializer.serialize_to_view( self.trans, dataset, view='summary' )
@@ -214,7 +214,7 @@ class DatasetSerializerTestCase( BaseTestCase ):
             self.assertTrue( True, 'all serializable keys have a serializer' )
 
     def test_views_and_keys( self ):
-        dataset = self.dataset_mgr.create( self.trans )
+        dataset = self.dataset_manager.create()
 
         self.log( 'should be able to use keys with views' )
         serialized = self.dataset_serializer.serialize_to_view( self.trans, dataset,
@@ -228,12 +228,12 @@ class DatasetSerializerTestCase( BaseTestCase ):
         self.assertKeys( serialized, [ 'purgable', 'file_size' ] )
 
     def test_serialize_permissions( self ):
-        dataset = self.dataset_mgr.create( self.trans )
+        dataset = self.dataset_manager.create()
         self.log( 'serialized permissions should be well formed' )
 
     def test_serializers( self ):
-        user2 = self.user_mgr.create( self.trans, **user2_data )
-        dataset = self.dataset_mgr.create( self.trans )
+        user2 = self.user_manager.create( **user2_data )
+        dataset = self.dataset_manager.create()
         all_keys = list( self.dataset_serializer.serializable_keyset )
         serialized = self.dataset_serializer.serialize( self.trans, dataset, all_keys )
 
@@ -261,11 +261,11 @@ class DatasetDeserializerTestCase( BaseTestCase ):
 
     def set_up_managers( self ):
         super( DatasetDeserializerTestCase, self ).set_up_managers()
-        self.dataset_mgr = DatasetManager( self.app )
+        self.dataset_manager = DatasetManager( self.app )
         self.dataset_deserializer = DatasetDeserializer( self.app )
 
     def test_deserialize_delete( self ):
-        dataset = self.dataset_mgr.create( self.trans )
+        dataset = self.dataset_manager.create()
 
         self.log( 'should raise when deserializing deleted from non-bool' )
         self.assertFalse( dataset.deleted )
@@ -280,7 +280,7 @@ class DatasetDeserializerTestCase( BaseTestCase ):
         self.assertFalse( dataset.deleted )
 
     def test_deserialize_purge( self ):
-        dataset = self.dataset_mgr.create( self.trans )
+        dataset = self.dataset_manager.create()
 
         self.log( 'should raise when deserializing purged from non-bool' )
         self.assertRaises( exceptions.RequestParameterInvalidException,
diff --git a/test/unit/managers/test_HDAManager.py b/test/unit/managers/test_HDAManager.py
index a588325f42c..6ad03ac27a1 100644
--- a/test/unit/managers/test_HDAManager.py
+++ b/test/unit/managers/test_HDAManager.py
@@ -31,16 +31,16 @@ class HDATestCase( BaseTestCase ):
 
     def set_up_managers( self ):
         super( HDATestCase, self ).set_up_managers()
-        self.hda_mgr = hdas.HDAManager( self.app )
-        self.history_mgr = HistoryManager( self.app )
-        self.dataset_mgr = DatasetManager( self.app )
+        self.hda_manager = hdas.HDAManager( self.app )
+        self.history_manager = HistoryManager( self.app )
+        self.dataset_manager = DatasetManager( self.app )
 
     def _create_vanilla_hda( self, user_data=None ):
         user_data = user_data or user2_data
-        owner = self.user_mgr.create( self.trans, **user_data )
-        history1 = self.history_mgr.create( self.trans, name='history1', user=owner )
-        dataset1 = self.dataset_mgr.create( self.trans )
-        return self.hda_mgr.create( self.trans, history=history1, dataset=dataset1 )
+        owner = self.user_manager.create( **user_data )
+        history1 = self.history_manager.create( name='history1', user=owner )
+        dataset1 = self.dataset_manager.create()
+        return self.hda_manager.create( history=history1, dataset=dataset1 )
 
 
 # =============================================================================
@@ -48,40 +48,40 @@ class HDAManagerTestCase( HDATestCase ):
 
     def test_base( self ):
         hda_model = model.HistoryDatasetAssociation
-        owner = self.user_mgr.create( self.trans, **user2_data )
-        history1 = self.history_mgr.create( self.trans, name='history1', user=owner )
-        hda1 = self.hda_mgr.create( self.trans, history=history1, hid=1 )
-        hda2 = self.hda_mgr.create( self.trans, history=history1, hid=2 )
-        hda3 = self.hda_mgr.create( self.trans, history=history1, hid=3 )
+        owner = self.user_manager.create( **user2_data )
+        history1 = self.history_manager.create( name='history1', user=owner )
+        hda1 = self.hda_manager.create( history=history1, hid=1 )
+        hda2 = self.hda_manager.create( history=history1, hid=2 )
+        hda3 = self.hda_manager.create( history=history1, hid=3 )
 
         self.log( "should be able to query" )
         hdas = self.trans.sa_session.query( hda_model ).all()
-        self.assertEqual( self.hda_mgr.list( self.trans ), hdas )
-        self.assertEqual( self.hda_mgr.one( self.trans, filters=( hda_model.id == hda1.id ) ), hda1 )
-        self.assertEqual( self.hda_mgr.by_id( self.trans, hda1.id ), hda1 )
-        self.assertEqual( self.hda_mgr.by_ids( self.trans, [ hda2.id, hda1.id ] ), [ hda2, hda1 ] )
+        self.assertEqual( self.hda_manager.list(), hdas )
+        self.assertEqual( self.hda_manager.one( filters=( hda_model.id == hda1.id ) ), hda1 )
+        self.assertEqual( self.hda_manager.by_id( hda1.id ), hda1 )
+        self.assertEqual( self.hda_manager.by_ids( [ hda2.id, hda1.id ] ), [ hda2, hda1 ] )
 
         self.log( "should be able to limit and offset" )
-        self.assertEqual( self.hda_mgr.list( self.trans, limit=1 ), hdas[0:1] )
-        self.assertEqual( self.hda_mgr.list( self.trans, offset=1 ), hdas[1:] )
-        self.assertEqual( self.hda_mgr.list( self.trans, limit=1, offset=1 ), hdas[1:2] )
+        self.assertEqual( self.hda_manager.list( limit=1 ), hdas[0:1] )
+        self.assertEqual( self.hda_manager.list( offset=1 ), hdas[1:] )
+        self.assertEqual( self.hda_manager.list( limit=1, offset=1 ), hdas[1:2] )
 
-        self.assertEqual( self.hda_mgr.list( self.trans, limit=0 ), [] )
-        self.assertEqual( self.hda_mgr.list( self.trans, offset=3 ), [] )
+        self.assertEqual( self.hda_manager.list( limit=0 ), [] )
+        self.assertEqual( self.hda_manager.list( offset=3 ), [] )
 
         self.log( "should be able to order" )
-        self.assertEqual( self.hda_mgr.list( self.trans, order_by=sqlalchemy.desc( hda_model.create_time ) ),
+        self.assertEqual( self.hda_manager.list( order_by=sqlalchemy.desc( hda_model.create_time ) ),
             [ hda3, hda2, hda1 ] )
 
     def test_create( self ):
-        owner = self.user_mgr.create( self.trans, **user2_data )
-        non_owner = self.user_mgr.create( self.trans, **user3_data )
+        owner = self.user_manager.create( **user2_data )
+        non_owner = self.user_manager.create( **user3_data )
 
-        history1 = self.history_mgr.create( self.trans, name='history1', user=owner )
-        dataset1 = self.dataset_mgr.create( self.trans )
+        history1 = self.history_manager.create( name='history1', user=owner )
+        dataset1 = self.dataset_manager.create()
 
         self.log( "should be able to create a new HDA with a specified history and dataset" )
-        hda1 = self.hda_mgr.create( self.trans, history=history1, dataset=dataset1 )
+        hda1 = self.hda_manager.create( history=history1, dataset=dataset1 )
         self.assertIsInstance( hda1, model.HistoryDatasetAssociation )
         self.assertEqual( hda1, self.trans.sa_session.query( model.HistoryDatasetAssociation ).get( hda1.id ) )
         self.assertEqual( hda1.history, history1 )
@@ -89,27 +89,27 @@ class HDAManagerTestCase( HDATestCase ):
         self.assertEqual( hda1.hid, 1 )
 
         self.log( "should be able to create a new HDA with only a specified history and no dataset" )
-        hda2 = self.hda_mgr.create( self.trans, history=history1 )
+        hda2 = self.hda_manager.create( history=history1 )
         self.assertIsInstance( hda2, model.HistoryDatasetAssociation )
         self.assertIsInstance( hda2.dataset, model.Dataset )
         self.assertEqual( hda2.history, history1 )
         self.assertEqual( hda2.hid, 2 )
 
         self.log( "should be able to create a new HDA with no history and no dataset" )
-        hda3 = self.hda_mgr.create( self.trans, hid=None )
+        hda3 = self.hda_manager.create( hid=None )
         self.assertIsInstance( hda3, model.HistoryDatasetAssociation )
         self.assertIsInstance( hda3.dataset, model.Dataset, msg="dataset will be auto created" )
         self.assertIsNone( hda3.history, msg="history will be None" )
         self.assertEqual( hda3.hid, None, msg="should allow setting hid to None (or any other value)" )
 
     def test_copy_from_hda( self ):
-        owner = self.user_mgr.create( self.trans, **user2_data )
-        history1 = self.history_mgr.create( self.trans, name='history1', user=owner )
-        dataset1 = self.dataset_mgr.create( self.trans )
-        hda1 = self.hda_mgr.create( self.trans, history=history1, dataset=dataset1 )
+        owner = self.user_manager.create( **user2_data )
+        history1 = self.history_manager.create( name='history1', user=owner )
+        dataset1 = self.dataset_manager.create()
+        hda1 = self.hda_manager.create( history=history1, dataset=dataset1 )
 
         self.log( "should be able to copy an HDA" )
-        hda2 = self.hda_mgr.copy( self.trans, hda1, history=history1 )
+        hda2 = self.hda_manager.copy( hda1, history=history1 )
         self.assertIsInstance( hda2, model.HistoryDatasetAssociation )
         self.assertEqual( hda2, self.trans.sa_session.query( model.HistoryDatasetAssociation ).get( hda2.id ) )
         self.assertEqual( hda2.name, hda1.name )
@@ -118,141 +118,193 @@ class HDAManagerTestCase( HDATestCase ):
         self.assertNotEqual( hda2, hda1 )
 
     #def test_copy_from_ldda( self ):
-    #    owner = self.user_mgr.create( self.trans, **user2_data )
-    #    history1 = self.history_mgr.create( self.trans, name='history1', user=owner )
+    #    owner = self.user_manager.create( **user2_data )
+    #    history1 = self.history_manager.create( name='history1', user=owner )
     #
     #    self.log( "should be able to copy an HDA" )
-    #    hda2 = self.hda_mgr.copy_ldda( self.trans, history1, hda1 )
+    #    hda2 = self.hda_manager.copy_ldda( history1, hda1 )
 
     def test_delete( self ):
-        owner = self.user_mgr.create( self.trans, **user2_data )
-        history1 = self.history_mgr.create( self.trans, name='history1', user=owner )
-        dataset1 = self.dataset_mgr.create( self.trans )
-        item1 = self.hda_mgr.create( self.trans, history=history1, dataset=dataset1 )
+        owner = self.user_manager.create( **user2_data )
+        history1 = self.history_manager.create( name='history1', user=owner )
+        dataset1 = self.dataset_manager.create()
+        item1 = self.hda_manager.create( history=history1, dataset=dataset1 )
 
         self.log( "should be able to delete and undelete an hda" )
         self.assertFalse( item1.deleted )
-        self.assertEqual( self.hda_mgr.delete( self.trans, item1 ), item1 )
+        self.assertEqual( self.hda_manager.delete( item1 ), item1 )
         self.assertTrue( item1.deleted )
-        self.assertEqual( self.hda_mgr.undelete( self.trans, item1 ), item1 )
+        self.assertEqual( self.hda_manager.undelete( item1 ), item1 )
         self.assertFalse( item1.deleted )
 
     def test_purge_allowed( self ):
         self.trans.app.config.allow_user_dataset_purge = True
 
-        owner = self.user_mgr.create( self.trans, **user2_data )
-        history1 = self.history_mgr.create( self.trans, name='history1', user=owner )
-        dataset1 = self.dataset_mgr.create( self.trans )
-        item1 = self.hda_mgr.create( self.trans, history=history1, dataset=dataset1 )
+        owner = self.user_manager.create( **user2_data )
+        history1 = self.history_manager.create( name='history1', user=owner )
+        dataset1 = self.dataset_manager.create()
+        item1 = self.hda_manager.create( history=history1, dataset=dataset1 )
 
         self.log( "should purge an hda if config does allow" )
         self.assertFalse( item1.purged )
-        self.assertEqual( self.hda_mgr.purge( self.trans, item1 ), item1 )
+        self.assertEqual( self.hda_manager.purge( item1 ), item1 )
         self.assertTrue( item1.purged )
 
     def test_purge_not_allowed( self ):
         self.trans.app.config.allow_user_dataset_purge = False
 
-        owner = self.user_mgr.create( self.trans, **user2_data )
-        history1 = self.history_mgr.create( self.trans, name='history1', user=owner )
-        dataset1 = self.dataset_mgr.create( self.trans )
-        item1 = self.hda_mgr.create( self.trans, history=history1, dataset=dataset1 )
+        owner = self.user_manager.create( **user2_data )
+        history1 = self.history_manager.create( name='history1', user=owner )
+        dataset1 = self.dataset_manager.create()
+        item1 = self.hda_manager.create( history=history1, dataset=dataset1 )
 
         self.log( "should raise an error when purging an hda if config does not allow" )
         self.assertFalse( item1.purged )
-        self.assertRaises( exceptions.ConfigDoesNotAllowException, self.hda_mgr.purge, self.trans, item1 )
+        self.assertRaises( exceptions.ConfigDoesNotAllowException, self.hda_manager.purge, item1 )
         self.assertFalse( item1.purged )
 
     def test_ownable( self ):
-        owner = self.user_mgr.create( self.trans, **user2_data )
-        non_owner = self.user_mgr.create( self.trans, **user3_data )
+        owner = self.user_manager.create( **user2_data )
+        non_owner = self.user_manager.create( **user3_data )
 
-        history1 = self.history_mgr.create( self.trans, name='history1', user=owner )
-        dataset1 = self.dataset_mgr.create( self.trans )
-        item1 = self.hda_mgr.create( self.trans, history1, dataset1 )
+        history1 = self.history_manager.create( name='history1', user=owner )
+        dataset1 = self.dataset_manager.create()
+        item1 = self.hda_manager.create( history1, dataset1 )
 
         self.log( "should be able to poll whether a given user owns an item" )
-        self.assertTrue(  self.hda_mgr.is_owner( self.trans, item1, owner ) )
-        self.assertFalse( self.hda_mgr.is_owner( self.trans, item1, non_owner ) )
+        self.assertTrue(  self.hda_manager.is_owner( item1, owner ) )
+        self.assertFalse( self.hda_manager.is_owner( item1, non_owner ) )
 
         self.log( "should raise an error when checking ownership with non-owner" )
         self.assertRaises( exceptions.ItemOwnershipException,
-            self.hda_mgr.error_unless_owner, self.trans, item1, non_owner )
+            self.hda_manager.error_unless_owner, item1, non_owner )
 
         self.log( "should raise an error when checking ownership with anonymous" )
         self.assertRaises( exceptions.ItemOwnershipException,
-            self.hda_mgr.error_unless_owner, self.trans, item1, None )
+            self.hda_manager.error_unless_owner, item1, None )
 
         self.log( "should not raise an error when checking ownership with owner" )
-        self.assertEqual( self.hda_mgr.error_unless_owner( self.trans, item1, owner ), item1 )
+        self.assertEqual( self.hda_manager.error_unless_owner( item1, owner ), item1 )
 
         self.log( "should not raise an error when checking ownership with admin" )
-        self.assertEqual( self.hda_mgr.error_unless_owner( self.trans, item1, self.admin_user ), item1 )
+        self.assertEqual( self.hda_manager.error_unless_owner( item1, self.admin_user ), item1 )
 
     def test_accessible( self ):
-        owner = self.user_mgr.create( self.trans, **user2_data )
-        non_owner = self.user_mgr.create( self.trans, **user3_data )
+        owner = self.user_manager.create( **user2_data )
+        non_owner = self.user_manager.create( **user3_data )
 
-        history1 = self.history_mgr.create( self.trans, name='history1', user=owner )
-        dataset1 = self.dataset_mgr.create( self.trans )
-        item1 = self.hda_mgr.create( self.trans, history1, dataset1 )
+        history1 = self.history_manager.create( name='history1', user=owner )
+        dataset1 = self.dataset_manager.create()
+        item1 = self.hda_manager.create( history1, dataset1 )
 
         self.log( "(by default, dataset permissions are lax) should be accessible to all" )
-        for user in self.user_mgr.list( self.trans ):
-            self.assertTrue( self.hda_mgr.is_accessible( self.trans, item1, user ) )
+        for user in self.user_manager.list():
+            self.assertTrue( self.hda_manager.is_accessible( item1, user ) )
 
-        #TODO: set perms on underlying dataset and then test accessible
+        self.log( "after setting a dataset to private (one user) permissions, access should be allowed for that user" )
+        # for this test, set restrictive access permissions
+        self.dataset_manager.permissions.set_private_to_one_user( dataset1, owner )
+        accessible = self.hda_manager.get_accessible( item1.id, owner, current_history=self.trans.history )
+        self.assertEqual( accessible, item1 )
 
-    def test_anon( self ):
+        self.log( "after setting a dataset to private (one user) permissions, "
+                + "access should be not allowed for other users" )
+        self.assertRaises( exceptions.ItemAccessibilityException,
+            self.hda_manager.get_accessible, item1.id, non_owner, current_history=self.trans.history )
+
+        self.log( "a copy of a restricted dataset in another users history should be inaccessible even to "
+                + "the histories owner" )
+        history2 = self.history_manager.create( name='history2', user=non_owner )
+        self.trans.set_history( history2 )
+        item2 = self.hda_manager.copy( item1, history=history2 )
+        self.assertIsInstance( item2, model.HistoryDatasetAssociation )
+        self.assertRaises( exceptions.ItemAccessibilityException,
+            self.hda_manager.get_accessible, item2.id, non_owner, current_history=self.trans.history )
+
+        self.log( "a restricted dataset cannot be accessed by anonymous users" )
+        anon_user = None
+        self.trans.set_user( anon_user )
+        history3 = self.history_manager.create( name='anon_history', user=anon_user )
+        self.trans.set_history( history2 )
+        self.assertRaises( exceptions.ItemAccessibilityException,
+            self.hda_manager.get_accessible, item1.id, anon_user, current_history=self.trans.history )
+
+    def test_anon_ownership( self ):
         anon_user = None
         self.trans.set_user( anon_user )
 
-        history1 = self.history_mgr.create( self.trans, name='anon_history', user=anon_user )
+        history1 = self.history_manager.create( name='anon_history', user=anon_user )
         self.trans.set_history( history1 )
-        dataset1 = self.dataset_mgr.create( self.trans )
-        item1 = self.hda_mgr.create( self.trans, history1, dataset1 )
+        dataset1 = self.dataset_manager.create()
+        item1 = self.hda_manager.create( history1, dataset1 )
 
-        self.log( "should not raise an error when checking ownership/access on anonymous' own dataset" )
-        self.assertTrue( self.hda_mgr.is_accessible( self.trans, item1, anon_user ) )
-        self.assertEqual( self.hda_mgr.error_unless_owner( self.trans, item1, anon_user ), item1 )
+        self.log( "should not raise an error when checking ownership on anonymous' own dataset" )
+        # need to pass the current history for comparison
+        self.assertTrue( self.hda_manager.is_owner( item1, anon_user, current_history=self.trans.history ) )
+        item = self.hda_manager.error_unless_owner( item1, anon_user, current_history=self.trans.history )
+        self.assertEqual( item, item1 )
+        item = self.hda_manager.get_owned( item1.id, anon_user, current_history=self.trans.history )
+        self.assertEqual( item, item1 )
 
         self.log( "should raise an error when checking ownership on anonymous' dataset with other user" )
-        non_owner = self.user_mgr.create( self.trans, **user3_data )
+        non_owner = self.user_manager.create( **user3_data )
+        self.assertFalse( self.hda_manager.is_owner( item1, non_owner ) )
         self.assertRaises( exceptions.ItemOwnershipException,
-            self.hda_mgr.error_unless_owner, self.trans, item1, non_owner )
+            self.hda_manager.error_unless_owner, item1, non_owner )
+        self.assertRaises( exceptions.ItemOwnershipException,
+            self.hda_manager.get_owned, item1.id, non_owner )
+
+    def test_anon_accessibility( self ):
+        anon_user = None
+        self.trans.set_user( anon_user )
+
+        history1 = self.history_manager.create( name='anon_history', user=anon_user )
+        self.trans.set_history( history1 )
+        dataset1 = self.dataset_manager.create()
+        item1 = self.hda_manager.create( history1, dataset1 )
+
+        # datasets are public by default
+        self.assertTrue( self.hda_manager.is_accessible( item1, anon_user ) )
+        # for this test, set restrictive access permissions
+        dataset_owner = self.user_manager.create( **user3_data )
+        self.dataset_manager.permissions.set_private_to_one_user( dataset1, dataset_owner )
+
+        self.log( "anonymous users should not be able to access datasets within their own histories if "
+                + "permissions do not allow" )
+        self.assertFalse( self.hda_manager.is_accessible( item1, anon_user ) )
+        self.assertRaises( exceptions.ItemAccessibilityException,
+            self.hda_manager.error_unless_accessible, item1, anon_user )
+
+        self.log( "those users with access permissions should still be allowed access to datasets "
+                + "within anon users' histories" )
+        self.assertTrue( self.hda_manager.is_accessible( item1, dataset_owner ) )
 
     def test_error_if_uploading( self ):
-        owner = self.user_mgr.create( self.trans, **user2_data )
-        history1 = self.history_mgr.create( self.trans, name='history1', user=owner )
-        dataset1 = self.dataset_mgr.create( self.trans )
-        hda = self.hda_mgr.create( self.trans, history=history1, dataset=dataset1 )
+        hda = self._create_vanilla_hda()
 
         hda.state = model.Dataset.states.OK
         self.log( "should not raise an error when calling error_if_uploading and in a non-uploading state" )
-        self.assertEqual( self.hda_mgr.error_if_uploading( self.trans, hda ), hda )
+        self.assertEqual( self.hda_manager.error_if_uploading( hda ), hda )
 
         hda.state = model.Dataset.states.UPLOAD
         self.log( "should raise an error when calling error_if_uploading and in the uploading state" )
         self.assertRaises( exceptions.Conflict,
-            self.hda_mgr.error_if_uploading, self.trans, hda )
+            self.hda_manager.error_if_uploading, hda )
 
     def test_data_conversion_status( self ):
-        owner = self.user_mgr.create( self.trans, **user2_data )
-        history1 = self.history_mgr.create( self.trans, name='history1', user=owner )
-        dataset1 = self.dataset_mgr.create( self.trans )
-        hda = self.hda_mgr.create( self.trans, history=history1, dataset=dataset1 )
+        hda = self._create_vanilla_hda()
 
         self.log( "data conversion status should reflect state" )
-        self.assertEqual( self.hda_mgr.data_conversion_status( self.trans, None ),
+        self.assertEqual( self.hda_manager.data_conversion_status( None ),
             hda.conversion_messages.NO_DATA )
         hda.state = model.Dataset.states.ERROR
-        self.assertEqual( self.hda_mgr.data_conversion_status( self.trans, hda ),
+        self.assertEqual( self.hda_manager.data_conversion_status( hda ),
             hda.conversion_messages.ERROR )
         hda.state = model.Dataset.states.QUEUED
-        self.assertEqual( self.hda_mgr.data_conversion_status( self.trans, hda ),
+        self.assertEqual( self.hda_manager.data_conversion_status( hda ),
             hda.conversion_messages.PENDING )
         hda.state = model.Dataset.states.OK
-        self.assertEqual( self.hda_mgr.data_conversion_status( self.trans, hda ), None )
+        self.assertEqual( self.hda_manager.data_conversion_status( hda ), None )
 
     # def test_text_data( self ):
 
diff --git a/test/unit/managers/test_HistoryManager.py b/test/unit/managers/test_HistoryManager.py
index a3feca6e819..8cad26c8839 100644
--- a/test/unit/managers/test_HistoryManager.py
+++ b/test/unit/managers/test_HistoryManager.py
@@ -39,14 +39,14 @@ class HistoryManagerTestCase( BaseTestCase ):
 
     def set_up_managers( self ):
         super( HistoryManagerTestCase, self ).set_up_managers()
-        self.history_mgr = HistoryManager( self.app )
+        self.history_manager = HistoryManager( self.app )
 
     def test_base( self ):
-        user2 = self.user_mgr.create( self.trans, **user2_data )
-        user3 = self.user_mgr.create( self.trans, **user3_data )
+        user2 = self.user_manager.create( **user2_data )
+        user3 = self.user_manager.create( **user3_data )
 
         self.log( "should be able to create a new history" )
-        history1 = self.history_mgr.create( self.trans, name='history1', user=user2 )
+        history1 = self.history_manager.create( name='history1', user=user2 )
         self.assertIsInstance( history1, model.History )
         self.assertEqual( history1.name, 'history1' )
         self.assertEqual( history1.user, user2 )
@@ -57,7 +57,7 @@ class HistoryManagerTestCase( BaseTestCase ):
             self.trans.sa_session.query( model.History ).filter( model.History.user == user2 ).one() )
 
         self.log( "should be able to copy a history" )
-        history2 = self.history_mgr.copy( self.trans, history1, user=user3 )
+        history2 = self.history_manager.copy( history1, user=user3 )
         self.assertIsInstance( history2, model.History )
         self.assertEqual( history2.user, user3 )
         self.assertEqual( history2, self.trans.sa_session.query( model.History ).get( history2.id ) )
@@ -66,184 +66,184 @@ class HistoryManagerTestCase( BaseTestCase ):
 
         self.log( "should be able to query" )
         histories = self.trans.sa_session.query( model.History ).all()
-        self.assertEqual( self.history_mgr.one( self.trans, filters=( model.History.id == history1.id ) ), history1 )
-        self.assertEqual( self.history_mgr.list( self.trans ), histories )
-        self.assertEqual( self.history_mgr.by_id( self.trans, history1.id ), history1 )
-        self.assertEqual( self.history_mgr.by_ids( self.trans, [ history2.id, history1.id ] ), [ history2, history1 ] )
+        self.assertEqual( self.history_manager.one( filters=( model.History.id == history1.id ) ), history1 )
+        self.assertEqual( self.history_manager.list(), histories )
+        self.assertEqual( self.history_manager.by_id( history1.id ), history1 )
+        self.assertEqual( self.history_manager.by_ids( [ history2.id, history1.id ] ), [ history2, history1 ] )
 
         self.log( "should be able to limit and offset" )
-        self.assertEqual( self.history_mgr.list( self.trans, limit=1 ), histories[0:1] )
-        self.assertEqual( self.history_mgr.list( self.trans, offset=1 ), histories[1:] )
-        self.assertEqual( self.history_mgr.list( self.trans, limit=1, offset=1 ), histories[1:2] )
+        self.assertEqual( self.history_manager.list( limit=1 ), histories[0:1] )
+        self.assertEqual( self.history_manager.list( offset=1 ), histories[1:] )
+        self.assertEqual( self.history_manager.list( limit=1, offset=1 ), histories[1:2] )
 
-        self.assertEqual( self.history_mgr.list( self.trans, limit=0 ), [] )
-        self.assertEqual( self.history_mgr.list( self.trans, offset=3 ), [] )
+        self.assertEqual( self.history_manager.list( limit=0 ), [] )
+        self.assertEqual( self.history_manager.list( offset=3 ), [] )
 
         self.log( "should be able to order" )
-        history3 = self.history_mgr.create( self.trans, name="history3", user=user2 )
+        history3 = self.history_manager.create( name="history3", user=user2 )
         name_first_then_time = ( model.History.name, sqlalchemy.desc( model.History.create_time ) )
-        self.assertEqual( self.history_mgr.list( self.trans, order_by=name_first_then_time ),
+        self.assertEqual( self.history_manager.list( order_by=name_first_then_time ),
             [ history2, history1, history3 ] )
 
     def test_has_user( self ):
-        owner = self.user_mgr.create( self.trans, **user2_data )
-        non_owner = self.user_mgr.create( self.trans, **user3_data )
+        owner = self.user_manager.create( **user2_data )
+        non_owner = self.user_manager.create( **user3_data )
 
-        item1 = self.history_mgr.create( self.trans, user=owner )
-        item2 = self.history_mgr.create( self.trans, user=owner )
-        item3 = self.history_mgr.create( self.trans, user=non_owner )
+        item1 = self.history_manager.create( user=owner )
+        item2 = self.history_manager.create( user=owner )
+        item3 = self.history_manager.create( user=non_owner )
 
         self.log( "should be able to list items by user" )
-        user_histories = self.history_mgr.by_user( self.trans, owner )
+        user_histories = self.history_manager.by_user( owner )
         self.assertEqual( user_histories, [ item1, item2 ] )
 
     def test_ownable( self ):
-        owner = self.user_mgr.create( self.trans, **user2_data )
-        non_owner = self.user_mgr.create( self.trans, **user3_data )
+        owner = self.user_manager.create( **user2_data )
+        non_owner = self.user_manager.create( **user3_data )
 
-        item1 = self.history_mgr.create( self.trans, user=owner )
+        item1 = self.history_manager.create( user=owner )
 
         self.log( "should be able to poll whether a given user owns an item" )
-        self.assertTrue(  self.history_mgr.is_owner( self.trans, item1, owner ) )
-        self.assertFalse( self.history_mgr.is_owner( self.trans, item1, non_owner ) )
+        self.assertTrue(  self.history_manager.is_owner( item1, owner ) )
+        self.assertFalse( self.history_manager.is_owner( item1, non_owner ) )
 
         self.log( "should raise an error when checking ownership with non-owner" )
         self.assertRaises( exceptions.ItemOwnershipException,
-            self.history_mgr.error_unless_owner, self.trans, item1, non_owner )
+            self.history_manager.error_unless_owner, item1, non_owner )
         self.assertRaises( exceptions.ItemOwnershipException,
-            self.history_mgr.get_owned, self.trans, item1.id, non_owner )
+            self.history_manager.get_owned, item1.id, non_owner )
 
         self.log( "should not raise an error when checking ownership with owner" )
-        self.assertEqual( self.history_mgr.error_unless_owner( self.trans, item1, owner ), item1 )
-        self.assertEqual( self.history_mgr.get_owned( self.trans, item1.id, owner ), item1 )
+        self.assertEqual( self.history_manager.error_unless_owner( item1, owner ), item1 )
+        self.assertEqual( self.history_manager.get_owned( item1.id, owner ), item1 )
 
         self.log( "should not raise an error when checking ownership with admin" )
-        self.assertTrue( self.history_mgr.is_owner( self.trans, item1, self.admin_user ) )
-        self.assertEqual( self.history_mgr.error_unless_owner( self.trans, item1, self.admin_user ), item1 )
-        self.assertEqual( self.history_mgr.get_owned( self.trans, item1.id, self.admin_user ), item1 )
+        self.assertTrue( self.history_manager.is_owner( item1, self.admin_user ) )
+        self.assertEqual( self.history_manager.error_unless_owner( item1, self.admin_user ), item1 )
+        self.assertEqual( self.history_manager.get_owned( item1.id, self.admin_user ), item1 )
 
     def test_accessible( self ):
-        owner = self.user_mgr.create( self.trans, **user2_data )
-        item1 = self.history_mgr.create( self.trans, user=owner )
+        owner = self.user_manager.create( **user2_data )
+        item1 = self.history_manager.create( user=owner )
 
-        non_owner = self.user_mgr.create( self.trans, **user3_data )
+        non_owner = self.user_manager.create( **user3_data )
 
         self.log( "should be inaccessible by default except to owner" )
-        self.assertTrue( self.history_mgr.is_accessible( self.trans, item1, owner ) )
-        self.assertTrue( self.history_mgr.is_accessible( self.trans, item1, self.admin_user ) )
-        self.assertFalse( self.history_mgr.is_accessible( self.trans, item1, non_owner ) )
+        self.assertTrue( self.history_manager.is_accessible( item1, owner ) )
+        self.assertTrue( self.history_manager.is_accessible( item1, self.admin_user ) )
+        self.assertFalse( self.history_manager.is_accessible( item1, non_owner ) )
 
         self.log( "should raise an error when checking accessibility with non-owner" )
         self.assertRaises( exceptions.ItemAccessibilityException,
-            self.history_mgr.error_unless_accessible, self.trans, item1, non_owner )
+            self.history_manager.error_unless_accessible, item1, non_owner )
         self.assertRaises( exceptions.ItemAccessibilityException,
-            self.history_mgr.get_accessible, self.trans, item1.id, non_owner )
+            self.history_manager.get_accessible, item1.id, non_owner )
 
         self.log( "should not raise an error when checking ownership with owner" )
-        self.assertEqual( self.history_mgr.error_unless_accessible( self.trans, item1, owner ), item1 )
-        self.assertEqual( self.history_mgr.get_accessible( self.trans, item1.id, owner ), item1 )
+        self.assertEqual( self.history_manager.error_unless_accessible( item1, owner ), item1 )
+        self.assertEqual( self.history_manager.get_accessible( item1.id, owner ), item1 )
 
         self.log( "should not raise an error when checking ownership with admin" )
-        self.assertTrue( self.history_mgr.is_accessible( self.trans, item1, self.admin_user ) )
-        self.assertEqual( self.history_mgr.error_unless_accessible( self.trans, item1, self.admin_user ), item1 )
-        self.assertEqual( self.history_mgr.get_accessible( self.trans, item1.id, self.admin_user ), item1 )
+        self.assertTrue( self.history_manager.is_accessible( item1, self.admin_user ) )
+        self.assertEqual( self.history_manager.error_unless_accessible( item1, self.admin_user ), item1 )
+        self.assertEqual( self.history_manager.get_accessible( item1.id, self.admin_user ), item1 )
 
     def test_importable( self ):
-        owner = self.user_mgr.create( self.trans, **user2_data )
+        owner = self.user_manager.create( **user2_data )
         self.trans.set_user( owner )
-        non_owner = self.user_mgr.create( self.trans, **user3_data )
+        non_owner = self.user_manager.create( **user3_data )
 
-        item1 = self.history_mgr.create( self.trans, user=owner )
+        item1 = self.history_manager.create( user=owner )
 
         self.log( "should not be importable by default" )
         self.assertFalse( item1.importable )
         self.assertIsNone( item1.slug )
 
         self.log( "should be able to make importable (accessible by link) to all users" )
-        accessible = self.history_mgr.make_importable( self.trans, item1 )
+        accessible = self.history_manager.make_importable( item1 )
         self.assertEqual( accessible, item1 )
         self.assertIsNotNone( accessible.slug )
         self.assertTrue( accessible.importable )
 
-        for user in self.user_mgr.list( self.trans ):
-            self.assertTrue( self.history_mgr.is_accessible( self.trans, accessible, user ) )
+        for user in self.user_manager.list():
+            self.assertTrue( self.history_manager.is_accessible( accessible, user ) )
 
         self.log( "should be able to make non-importable/inaccessible again" )
-        inaccessible = self.history_mgr.make_non_importable( self.trans, accessible )
+        inaccessible = self.history_manager.make_non_importable( accessible )
         self.assertEqual( inaccessible, accessible )
         self.assertIsNotNone( inaccessible.slug )
         self.assertFalse( inaccessible.importable )
 
-        self.assertTrue( self.history_mgr.is_accessible( self.trans, inaccessible, owner ) )
-        self.assertFalse( self.history_mgr.is_accessible( self.trans, inaccessible, non_owner ) )
-        self.assertTrue( self.history_mgr.is_accessible( self.trans, inaccessible, self.admin_user ) )
+        self.assertTrue( self.history_manager.is_accessible( inaccessible, owner ) )
+        self.assertFalse( self.history_manager.is_accessible( inaccessible, non_owner ) )
+        self.assertTrue( self.history_manager.is_accessible( inaccessible, self.admin_user ) )
 
     def test_published( self ):
-        owner = self.user_mgr.create( self.trans, **user2_data )
+        owner = self.user_manager.create( **user2_data )
         self.trans.set_user( owner )
-        non_owner = self.user_mgr.create( self.trans, **user3_data )
+        non_owner = self.user_manager.create( **user3_data )
 
-        item1 = self.history_mgr.create( self.trans, user=owner )
+        item1 = self.history_manager.create( user=owner )
 
         self.log( "should not be published by default" )
         self.assertFalse( item1.published )
         self.assertIsNone( item1.slug )
 
         self.log( "should be able to publish (listed publicly) to all users" )
-        published = self.history_mgr.publish( self.trans, item1 )
+        published = self.history_manager.publish( item1 )
         self.assertEqual( published, item1 )
         self.assertTrue( published.published )
         # note: publishing sets importable to true as well
         self.assertTrue( published.importable )
         self.assertIsNotNone( published.slug )
 
-        for user in self.user_mgr.list( self.trans ):
-            self.assertTrue( self.history_mgr.is_accessible( self.trans, published, user ) )
+        for user in self.user_manager.list():
+            self.assertTrue( self.history_manager.is_accessible( published, user ) )
 
         self.log( "should be able to make non-importable/inaccessible again" )
-        unpublished = self.history_mgr.unpublish( self.trans, published )
+        unpublished = self.history_manager.unpublish( published )
         self.assertEqual( unpublished, published )
         self.assertFalse( unpublished.published )
         # note: unpublishing does not make non-importable, you must explicitly do that separately
         self.assertTrue( published.importable )
-        self.history_mgr.make_non_importable( self.trans, unpublished )
+        self.history_manager.make_non_importable( unpublished )
         self.assertFalse( published.importable )
         # note: slug still remains after unpublishing
         self.assertIsNotNone( unpublished.slug )
 
-        self.assertTrue( self.history_mgr.is_accessible( self.trans, unpublished, owner ) )
-        self.assertFalse( self.history_mgr.is_accessible( self.trans, unpublished, non_owner ) )
-        self.assertTrue( self.history_mgr.is_accessible( self.trans, unpublished, self.admin_user ) )
+        self.assertTrue( self.history_manager.is_accessible( unpublished, owner ) )
+        self.assertFalse( self.history_manager.is_accessible( unpublished, non_owner ) )
+        self.assertTrue( self.history_manager.is_accessible( unpublished, self.admin_user ) )
 
     def test_sharable( self ):
-        owner = self.user_mgr.create( self.trans, **user2_data )
+        owner = self.user_manager.create( **user2_data )
         self.trans.set_user( owner )
-        item1 = self.history_mgr.create( self.trans, user=owner )
+        item1 = self.history_manager.create( user=owner )
 
-        non_owner = self.user_mgr.create( self.trans, **user3_data )
-        #third_party = self.user_mgr.create( self.trans, **user4_data )
+        non_owner = self.user_manager.create( **user3_data )
+        #third_party = self.user_manager.create( **user4_data )
 
         self.log( "should be unshared by default" )
-        self.assertEqual( self.history_mgr.get_share_assocs( self.trans, item1 ), [] )
+        self.assertEqual( self.history_manager.get_share_assocs( item1 ), [] )
         self.assertEqual( item1.slug, None )
 
         self.log( "should be able to share with specific users" )
-        share_assoc = self.history_mgr.share_with( self.trans, item1, non_owner )
+        share_assoc = self.history_manager.share_with( item1, non_owner )
         self.assertIsInstance( share_assoc, model.HistoryUserShareAssociation )
-        self.assertTrue( self.history_mgr.is_accessible( self.trans, item1, non_owner ) )
+        self.assertTrue( self.history_manager.is_accessible( item1, non_owner ) )
         self.assertEqual(
-            len( self.history_mgr.get_share_assocs( self.trans, item1 ) ), 1 )
+            len( self.history_manager.get_share_assocs( item1 ) ), 1 )
         self.assertEqual(
-            len( self.history_mgr.get_share_assocs( self.trans, item1, user=non_owner ) ), 1 )
+            len( self.history_manager.get_share_assocs( item1, user=non_owner ) ), 1 )
         self.assertIsInstance( item1.slug, basestring )
 
         self.log( "should be able to unshare with specific users" )
-        share_assoc = self.history_mgr.unshare_with( self.trans, item1, non_owner )
+        share_assoc = self.history_manager.unshare_with( item1, non_owner )
         self.assertIsInstance( share_assoc, model.HistoryUserShareAssociation )
-        self.assertFalse( self.history_mgr.is_accessible( self.trans, item1, non_owner ) )
-        self.assertEqual( self.history_mgr.get_share_assocs( self.trans, item1 ), [] )
+        self.assertFalse( self.history_manager.is_accessible( item1, non_owner ) )
+        self.assertEqual( self.history_manager.get_share_assocs( item1 ), [] )
         self.assertEqual(
-            self.history_mgr.get_share_assocs( self.trans, item1, user=non_owner ), [] )
+            self.history_manager.get_share_assocs( item1, user=non_owner ), [] )
 
     #TODO: test slug formation
 
@@ -252,61 +252,64 @@ class HistoryManagerTestCase( BaseTestCase ):
         self.trans.set_user( anon_user )
 
         self.log( "should not allow access and owner for anon user on a history by another anon user (None)" )
-        anon_history1 = self.history_mgr.create( self.trans, user=None )
-        self.assertFalse( self.history_mgr.is_owner( self.trans, anon_history1, anon_user ) )
-        self.assertFalse( self.history_mgr.is_accessible( self.trans, anon_history1, anon_user ) )
+        anon_history1 = self.history_manager.create( user=None )
+        # do not set the trans.history!
+        self.assertFalse( self.history_manager.is_owner( anon_history1, anon_user, current_history=self.trans.history ) )
+        self.assertFalse( self.history_manager.is_accessible( anon_history1, anon_user, current_history=self.trans.history ) )
 
         self.log( "should allow access and owner for anon user on a history if it's the session's current history" )
-        anon_history2 = self.history_mgr.create( self.trans, user=anon_user )
+        anon_history2 = self.history_manager.create( user=anon_user )
         self.trans.set_history( anon_history2 )
-        self.assertTrue( self.history_mgr.is_owner( self.trans, anon_history2, anon_user ) )
-        self.assertTrue( self.history_mgr.is_accessible( self.trans, anon_history2, anon_user ) )
+        self.assertTrue( self.history_manager.is_owner( anon_history2, anon_user, current_history=self.trans.history ) )
+        self.assertTrue( self.history_manager.is_accessible( anon_history2, anon_user, current_history=self.trans.history ) )
 
         self.log( "should not allow owner or access for anon user on someone elses history" )
-        owner = self.user_mgr.create( self.trans, **user2_data )
-        someone_elses = self.history_mgr.create( self.trans, user=owner )
-        self.assertFalse( self.history_mgr.is_owner( self.trans, someone_elses, anon_user ) )
-        self.assertFalse( self.history_mgr.is_accessible( self.trans, someone_elses, anon_user ) )
+        owner = self.user_manager.create( **user2_data )
+        someone_elses = self.history_manager.create( user=owner )
+        self.assertFalse( self.history_manager.is_owner( someone_elses, anon_user, current_history=self.trans.history ) )
+        self.assertFalse( self.history_manager.is_accessible( someone_elses, anon_user, current_history=self.trans.history ) )
 
         self.log( "should allow access for anon user if the history is published or importable" )
-        self.history_mgr.make_importable( self.trans, someone_elses )
-        self.assertTrue( self.history_mgr.is_accessible( self.trans, someone_elses, anon_user ) )
-        self.history_mgr.publish( self.trans, someone_elses )
-        self.assertTrue( self.history_mgr.is_accessible( self.trans, someone_elses, anon_user ) )
+        self.history_manager.make_importable( someone_elses )
+        self.assertTrue( self.history_manager.is_accessible( someone_elses, anon_user, current_history=self.trans.history ) )
+        self.history_manager.publish( someone_elses )
+        self.assertTrue( self.history_manager.is_accessible( someone_elses, anon_user, current_history=self.trans.history ) )
 
     def test_delete_and_purge( self ):
-        user2 = self.user_mgr.create( self.trans, **user2_data )
+        user2 = self.user_manager.create( **user2_data )
         self.trans.set_user( user2 )
 
-        history1 = self.history_mgr.create( self.trans, name='history1', user=user2 )
+        history1 = self.history_manager.create( name='history1', user=user2 )
         self.trans.set_history( history1 )
 
+        self.log( "should allow deletion and undeletion" )
         self.assertFalse( history1.deleted )
 
-        self.history_mgr.delete( self.trans, history1 )
+        self.history_manager.delete(  history1 )
         self.assertTrue( history1.deleted )
 
-        self.history_mgr.undelete( self.trans, history1 )
+        self.history_manager.undelete( history1 )
         self.assertFalse( history1.deleted )
 
-        history2 = self.history_mgr.create( self.trans, name='history2', user=user2 )
-        self.history_mgr.purge( self.trans, history1 )
-        self.assertTrue( history1.purged )
+        self.log( "should allow purging" )
+        history2 = self.history_manager.create( name='history2', user=user2 )
+        self.history_manager.purge( history2 )
+        self.assertTrue( history2.purged )
 
-    def test_histories( self ):
-        user2 = self.user_mgr.create( self.trans, **user2_data )
+    def test_current( self ):
+        user2 = self.user_manager.create( **user2_data )
         self.trans.set_user( user2 )
 
-        history1 = self.history_mgr.create( self.trans, name='history1', user=user2 )
+        history1 = self.history_manager.create( name='history1', user=user2 )
         self.trans.set_history( history1 )
-        history2 = self.history_mgr.create( self.trans, name='history2', user=user2 )
+        history2 = self.history_manager.create( name='history2', user=user2 )
 
         self.log( "should be able to set or get the current history for a user" )
-        self.assertEqual( self.history_mgr.get_current( self.trans ), history1 )
-        self.assertEqual( self.history_mgr.set_current( self.trans, history2 ), history2 )
-        self.assertEqual( self.history_mgr.get_current( self.trans ), history2 )
-        self.assertEqual( self.history_mgr.set_current_by_id( self.trans, history1.id ), history1 )
-        self.assertEqual( self.history_mgr.get_current( self.trans ), history1 )
+        self.assertEqual( self.history_manager.get_current( self.trans ), history1 )
+        self.assertEqual( self.history_manager.set_current( self.trans, history2 ), history2 )
+        self.assertEqual( self.history_manager.get_current( self.trans ), history2 )
+        self.assertEqual( self.history_manager.set_current_by_id( self.trans, history1.id ), history1 )
+        self.assertEqual( self.history_manager.get_current( self.trans ), history1 )
 
 
 # =============================================================================
@@ -319,13 +322,13 @@ class HistorySerializerTestCase( BaseTestCase ):
 
     def set_up_managers( self ):
         super( HistorySerializerTestCase, self ).set_up_managers()
-        self.history_mgr = HistoryManager( self.app )
-        self.hda_mgr = hdas.HDAManager( self.app )
+        self.history_manager = HistoryManager( self.app )
+        self.hda_manager = hdas.HDAManager( self.app )
         self.history_serializer = HistorySerializer( self.app )
 
     def test_views( self ):
-        user2 = self.user_mgr.create( self.trans, **user2_data )
-        history1 = self.history_mgr.create( self.trans, name='history1', user=user2 )
+        user2 = self.user_manager.create( **user2_data )
+        history1 = self.history_manager.create( name='history1', user=user2 )
 
         self.log( 'should have a summary view' )
         summary_view = self.history_serializer.serialize_to_view( self.trans, history1, view='summary' )
@@ -349,8 +352,8 @@ class HistorySerializerTestCase( BaseTestCase ):
             self.assertTrue( True, 'all serializable keys have a serializer' )
 
     def test_views_and_keys( self ):
-        user2 = self.user_mgr.create( self.trans, **user2_data )
-        history1 = self.history_mgr.create( self.trans, name='history1', user=user2 )
+        user2 = self.user_manager.create( **user2_data )
+        history1 = self.history_manager.create( name='history1', user=user2 )
 
         self.log( 'should be able to use keys with views' )
         serialized = self.history_serializer.serialize_to_view( self.trans, history1,
@@ -364,8 +367,8 @@ class HistorySerializerTestCase( BaseTestCase ):
         self.assertKeys( serialized, [ 'state_ids', 'user_id' ] )
 
     def test_sharable( self ):
-        user2 = self.user_mgr.create( self.trans, **user2_data )
-        history1 = self.history_mgr.create( self.trans, name='history1', user=user2 )
+        user2 = self.user_manager.create( **user2_data )
+        history1 = self.history_manager.create( name='history1', user=user2 )
 
         self.log( 'should have a serializer for all SharableModel keys' )
         sharable_attrs = [ 'user_id', 'username_and_slug', 'importable', 'published', 'slug' ]
@@ -373,8 +376,8 @@ class HistorySerializerTestCase( BaseTestCase ):
         self.assertKeys( serialized, sharable_attrs )
 
     def test_purgable( self ):
-        user2 = self.user_mgr.create( self.trans, **user2_data )
-        history1 = self.history_mgr.create( self.trans, name='history1', user=user2 )
+        user2 = self.user_manager.create( **user2_data )
+        history1 = self.history_manager.create( name='history1', user=user2 )
 
         self.log( 'deleted and purged should be returned in their default states' )
         keys = [ 'deleted', 'purged' ]
@@ -383,19 +386,19 @@ class HistorySerializerTestCase( BaseTestCase ):
         self.assertEqual( serialized[ 'purged' ], False )
 
         self.log( 'deleted and purged should return their current state' )
-        self.history_mgr.delete( self.trans, history1 )
+        self.history_manager.delete( history1 )
         serialized = self.history_serializer.serialize( self.trans, history1, keys )
         self.assertEqual( serialized[ 'deleted' ], True )
         self.assertEqual( serialized[ 'purged' ], False )
 
-        self.history_mgr.purge( self.trans, history1 )
+        self.history_manager.purge( history1 )
         serialized = self.history_serializer.serialize( self.trans, history1, keys )
         self.assertEqual( serialized[ 'deleted' ], True )
         self.assertEqual( serialized[ 'purged' ], True )
 
     def test_history_serializers( self ):
-        user2 = self.user_mgr.create( self.trans, **user2_data )
-        history1 = self.history_mgr.create( self.trans, name='history1', user=user2 )
+        user2 = self.user_manager.create( **user2_data )
+        history1 = self.history_manager.create( name='history1', user=user2 )
         all_keys = list( self.history_serializer.serializable_keyset )
         serialized = self.history_serializer.serialize( self.trans, history1, all_keys )
 
@@ -407,8 +410,8 @@ class HistorySerializerTestCase( BaseTestCase ):
         self.assertIsJsonifyable( serialized )
 
     def test_contents( self ):
-        user2 = self.user_mgr.create( self.trans, **user2_data )
-        history1 = self.history_mgr.create( self.trans, name='history1', user=user2 )
+        user2 = self.user_manager.create( **user2_data )
+        history1 = self.history_manager.create( name='history1', user=user2 )
 
         self.log( 'a history with no contents should be properly reflected in empty, etc.' )
         keys = [ 'empty', 'count', 'state_ids', 'state_details', 'state', 'hdas' ]
@@ -421,8 +424,8 @@ class HistorySerializerTestCase( BaseTestCase ):
         self.assertIsInstance( serialized[ 'hdas' ], list )
 
         self.log( 'a history with contents should be properly reflected in empty, etc.' )
-        hda1 = self.hda_mgr.create( self.trans, history=history1, hid=1 )
-        self.hda_mgr.update( self.trans, hda1, dict( state='ok' ) )
+        hda1 = self.hda_manager.create( history=history1, hid=1 )
+        self.hda_manager.update( hda1, dict( state='ok' ) )
 
         serialized = self.history_serializer.serialize( self.trans, history1, keys )
         self.assertEqual( serialized[ 'state' ], 'ok' )
@@ -440,16 +443,16 @@ class HistorySerializerTestCase( BaseTestCase ):
         self.assertIsJsonifyable( serialized )
 
 
-# =============================================================================
-class HistoryDeserializerTestCase( BaseTestCase ):
+# # =============================================================================
+# class HistoryDeserializerTestCase( BaseTestCase ):
 
-    def set_up_managers( self ):
-        super( HistoryDeserializerTestCase, self ).set_up_managers()
-        self.history_mgr = HistoryManager( self.app )
-        self.history_deserializer = HistoryDeserializer( self.app )
+#     def set_up_managers( self ):
+#         super( HistoryDeserializerTestCase, self ).set_up_managers()
+#         self.history_manager = HistoryManager( self.app )
+#         self.history_deserializer = HistoryDeserializer( self.app )
 
-    def test_base( self ):
-        pass
+#     def test_base( self ):
+#         pass
 
 
 # =============================================================================
@@ -457,7 +460,7 @@ class HistoryFiltersTestCase( BaseTestCase ):
 
     def set_up_managers( self ):
         super( HistoryFiltersTestCase, self ).set_up_managers()
-        self.history_mgr = HistoryManager( self.app )
+        self.history_manager = HistoryManager( self.app )
         self.filter_parser = HistoryFilters( self.app )
 
     # ---- functional and orm filter splitting and resolution
@@ -496,47 +499,47 @@ class HistoryFiltersTestCase( BaseTestCase ):
         ])
 
     def test_orm_filter_parsing( self ):
-        user2 = self.user_mgr.create( self.trans, **user2_data )
-        history1 = self.history_mgr.create( self.trans, name='history1', user=user2 )
-        history2 = self.history_mgr.create( self.trans, name='history2', user=user2 )
-        history3 = self.history_mgr.create( self.trans, name='history3', user=user2 )
+        user2 = self.user_manager.create( **user2_data )
+        history1 = self.history_manager.create( name='history1', user=user2 )
+        history2 = self.history_manager.create( name='history2', user=user2 )
+        history3 = self.history_manager.create( name='history3', user=user2 )
 
         filters = self.filter_parser.parse_filters([
             ( 'name', 'like', 'history%' ),
         ])
-        histories = self.history_mgr.list( self.trans, filters=filters )
+        histories = self.history_manager.list( filters=filters )
         #for h in histories:
         #    print h.name
         self.assertEqual( histories, [ history1, history2, history3 ])
 
         filters = self.filter_parser.parse_filters([ ( 'name', 'like', '%2' ), ])
-        self.assertEqual( self.history_mgr.list( self.trans, filters=filters ), [ history2 ])
+        self.assertEqual( self.history_manager.list( filters=filters ), [ history2 ])
 
         filters = self.filter_parser.parse_filters([ ( 'name', 'eq', 'history2' ), ])
-        self.assertEqual( self.history_mgr.list( self.trans, filters=filters ), [ history2 ])
+        self.assertEqual( self.history_manager.list( filters=filters ), [ history2 ])
 
-        self.history_mgr.update( self.trans, history1, dict( deleted=True ) )
+        self.history_manager.update( history1, dict( deleted=True ) )
         filters = self.filter_parser.parse_filters([ ( 'deleted', 'eq', 'True' ), ])
-        self.assertEqual( self.history_mgr.list( self.trans, filters=filters ), [ history1 ])
+        self.assertEqual( self.history_manager.list( filters=filters ), [ history1 ])
         filters = self.filter_parser.parse_filters([ ( 'deleted', 'eq', 'False' ), ])
-        self.assertEqual( self.history_mgr.list( self.trans, filters=filters ), [ history2, history3 ])
-        self.assertEqual( self.history_mgr.list( self.trans ), [ history1, history2, history3 ])
+        self.assertEqual( self.history_manager.list( filters=filters ), [ history2, history3 ])
+        self.assertEqual( self.history_manager.list(), [ history1, history2, history3 ])
 
-        self.history_mgr.update( self.trans, history3, dict( deleted=True ) )
-        self.history_mgr.update( self.trans, history1, dict( importable=True ) )
-        self.history_mgr.update( self.trans, history2, dict( importable=True ) )
+        self.history_manager.update( history3, dict( deleted=True ) )
+        self.history_manager.update( history1, dict( importable=True ) )
+        self.history_manager.update( history2, dict( importable=True ) )
         filters = self.filter_parser.parse_filters([
             ( 'deleted', 'eq', 'True' ),
             ( 'importable', 'eq', 'True' ),
         ])
-        self.assertEqual( self.history_mgr.list( self.trans, filters=filters ), [ history1 ])
-        self.assertEqual( self.history_mgr.list( self.trans ), [ history1, history2, history3 ])
+        self.assertEqual( self.history_manager.list( filters=filters ), [ history1 ])
+        self.assertEqual( self.history_manager.list(), [ history1, history2, history3 ])
 
     def test_fn_filter_parsing( self ):
-        user2 = self.user_mgr.create( self.trans, **user2_data )
-        history1 = self.history_mgr.create( self.trans, name='history1', user=user2 )
-        history2 = self.history_mgr.create( self.trans, name='history2', user=user2 )
-        history3 = self.history_mgr.create( self.trans, name='history3', user=user2 )
+        user2 = self.user_manager.create( **user2_data )
+        history1 = self.history_manager.create( name='history1', user=user2 )
+        history2 = self.history_manager.create( name='history2', user=user2 )
+        history3 = self.history_manager.create( name='history3', user=user2 )
 
         filters = self.filter_parser.parse_filters([ ( 'annotation', 'has', 'no play' ), ])
         anno_filter = filters[0]
@@ -547,15 +550,15 @@ class HistoryFiltersTestCase( BaseTestCase ):
         self.assertTrue( anno_filter( history3 ) )
         self.assertFalse( anno_filter( history2 ) )
 
-        self.assertEqual( self.history_mgr.list( self.trans, filters=filters ), [ history3 ])
+        self.assertEqual( self.history_manager.list( filters=filters ), [ history3 ])
 
         self.log( 'should allow combinations of orm and fn filters' )
-        self.history_mgr.update( self.trans, history3, dict( importable=True ) )
-        self.history_mgr.update( self.trans, history2, dict( importable=True ) )
+        self.history_manager.update( history3, dict( importable=True ) )
+        self.history_manager.update( history2, dict( importable=True ) )
         history1.add_item_annotation( self.trans.sa_session, user2, history1, "All work and no play" )
         self.trans.sa_session.flush()
 
-        shining_examples = self.history_mgr.list( self.trans, filters=self.filter_parser.parse_filters([
+        shining_examples = self.history_manager.list( filters=self.filter_parser.parse_filters([
             ( 'importable', 'eq', 'True' ),
             ( 'annotation', 'has', 'no play' ),
         ]))
@@ -586,15 +589,15 @@ class HistoryFiltersTestCase( BaseTestCase ):
         """
         Test limit and offset in conjunction with both orm and fn filtering.
         """
-        user2 = self.user_mgr.create( self.trans, **user2_data )
-        history1 = self.history_mgr.create( self.trans, name='history1', user=user2 )
-        history2 = self.history_mgr.create( self.trans, name='history2', user=user2 )
-        history3 = self.history_mgr.create( self.trans, name='history3', user=user2 )
-        history4 = self.history_mgr.create( self.trans, name='history4', user=user2 )
+        user2 = self.user_manager.create( **user2_data )
+        history1 = self.history_manager.create( name='history1', user=user2 )
+        history2 = self.history_manager.create( name='history2', user=user2 )
+        history3 = self.history_manager.create( name='history3', user=user2 )
+        history4 = self.history_manager.create( name='history4', user=user2 )
 
-        self.history_mgr.delete( self.trans, history1 )
-        self.history_mgr.delete( self.trans, history2 )
-        self.history_mgr.delete( self.trans, history3 )
+        self.history_manager.delete( history1 )
+        self.history_manager.delete( history2 )
+        self.history_manager.delete( history3 )
 
         test_annotation = "testing"
         history2.add_item_annotation( self.trans.sa_session, user2, history2, test_annotation )
@@ -608,50 +611,50 @@ class HistoryFiltersTestCase( BaseTestCase ):
         deleted_and_annotated = [ history2, history3 ]
 
         self.log( "no offset, no limit should work" )
-        self.assertEqual( self.history_mgr.list( self.trans, offset=None, limit=None ), all_histories )
-        self.assertEqual( self.history_mgr.list( self.trans ), all_histories )
+        self.assertEqual( self.history_manager.list( offset=None, limit=None ), all_histories )
+        self.assertEqual( self.history_manager.list(), all_histories )
         self.log( "no offset, limit should work" )
-        self.assertEqual( self.history_mgr.list( self.trans, limit=2 ), [ history1, history2 ] )
+        self.assertEqual( self.history_manager.list( limit=2 ), [ history1, history2 ] )
         self.log( "offset, no limit should work" )
-        self.assertEqual( self.history_mgr.list( self.trans, offset=1 ), [ history2, history3, history4 ] )
+        self.assertEqual( self.history_manager.list( offset=1 ), [ history2, history3, history4 ] )
         self.log( "offset, limit should work" )
-        self.assertEqual( self.history_mgr.list( self.trans, offset=1, limit=1 ), [ history2 ] )
+        self.assertEqual( self.history_manager.list( offset=1, limit=1 ), [ history2 ] )
 
         self.log( "zero limit should return empty list" )
-        self.assertEqual( self.history_mgr.list( self.trans, limit=0 ), [] )
+        self.assertEqual( self.history_manager.list( limit=0 ), [] )
         self.log( "past len offset should return empty list" )
-        self.assertEqual( self.history_mgr.list( self.trans, offset=len( all_histories ) ), [] )
+        self.assertEqual( self.history_manager.list( offset=len( all_histories ) ), [] )
         self.log( "negative limit should return full list" )
-        self.assertEqual( self.history_mgr.list( self.trans, limit=-1 ), all_histories )
+        self.assertEqual( self.history_manager.list( limit=-1 ), all_histories )
         self.log( "negative offset should return full list" )
-        self.assertEqual( self.history_mgr.list( self.trans, offset=-1 ), all_histories )
+        self.assertEqual( self.history_manager.list( offset=-1 ), all_histories )
 
         filters = [ model.History.deleted == True ]
         self.log( "orm filtered, no offset, no limit should work" )
-        found = self.history_mgr.list( self.trans, filters=filters )
+        found = self.history_manager.list( filters=filters )
         self.assertEqual( found, [ history1, history2, history3 ] )
         self.log( "orm filtered, no offset, limit should work" )
-        found = self.history_mgr.list( self.trans, filters=filters, limit=2 )
+        found = self.history_manager.list( filters=filters, limit=2 )
         self.assertEqual( found, [ history1, history2 ] )
         self.log( "orm filtered, offset, no limit should work" )
-        found = self.history_mgr.list( self.trans, filters=filters, offset=1 )
+        found = self.history_manager.list( filters=filters, offset=1 )
         self.assertEqual( found, [ history2, history3 ] )
         self.log( "orm filtered, offset, limit should work" )
-        found = self.history_mgr.list( self.trans, filters=filters, offset=1, limit=1 )
+        found = self.history_manager.list( filters=filters, offset=1, limit=1 )
         self.assertEqual( found, [ history2 ] )
 
         filters = self.filter_parser.parse_filters([ ( 'annotation', 'has', test_annotation ) ])
         self.log( "fn filtered, no offset, no limit should work" )
-        found = self.history_mgr.list( self.trans, filters=filters )
+        found = self.history_manager.list( filters=filters )
         self.assertEqual( found, [ history2, history3, history4 ] )
         self.log( "fn filtered, no offset, limit should work" )
-        found = self.history_mgr.list( self.trans, filters=filters, limit=2 )
+        found = self.history_manager.list( filters=filters, limit=2 )
         self.assertEqual( found, [ history2, history3 ] )
         self.log( "fn filtered, offset, no limit should work" )
-        found = self.history_mgr.list( self.trans, filters=filters, offset=1 )
+        found = self.history_manager.list( filters=filters, offset=1 )
         self.assertEqual( found, [ history3, history4 ] )
         self.log( "fn filtered, offset, limit should work" )
-        found = self.history_mgr.list( self.trans, filters=filters, offset=1, limit=1 )
+        found = self.history_manager.list( filters=filters, offset=1, limit=1 )
         self.assertEqual( found, [ history3 ] )
 
         filters = self.filter_parser.parse_filters([
@@ -659,29 +662,29 @@ class HistoryFiltersTestCase( BaseTestCase ):
             ( 'annotation', 'has', test_annotation )
         ])
         self.log( "orm and fn filtered, no offset, no limit should work" )
-        found = self.history_mgr.list( self.trans, filters=filters )
+        found = self.history_manager.list( filters=filters )
         self.assertEqual( found, [ history2, history3 ] )
         self.log( "orm and fn filtered, no offset, limit should work" )
-        found = self.history_mgr.list( self.trans, filters=filters, limit=1 )
+        found = self.history_manager.list( filters=filters, limit=1 )
         self.assertEqual( found, [ history2 ] )
         self.log( "orm and fn filtered, offset, no limit should work" )
-        found = self.history_mgr.list( self.trans, filters=filters, offset=1 )
+        found = self.history_manager.list( filters=filters, offset=1 )
         self.assertEqual( found, [ history3 ] )
         self.log( "orm and fn filtered, offset, limit should work" )
-        found = self.history_mgr.list( self.trans, filters=filters, offset=1, limit=1 )
+        found = self.history_manager.list( filters=filters, offset=1, limit=1 )
         self.assertEqual( found, [ history3 ] )
 
         self.log( "orm and fn filtered, zero limit should return empty list" )
-        found = self.history_mgr.list( self.trans, filters=filters, limit=0 )
+        found = self.history_manager.list( filters=filters, limit=0 )
         self.assertEqual( found, [] )
         self.log( "orm and fn filtered, past len offset should return empty list" )
-        found = self.history_mgr.list( self.trans, filters=filters, offset=len( deleted_and_annotated ) )
+        found = self.history_manager.list( filters=filters, offset=len( deleted_and_annotated ) )
         self.assertEqual( found, [] )
         self.log( "orm and fn filtered, negative limit should return full list" )
-        found = self.history_mgr.list( self.trans, filters=filters, limit=-1 )
+        found = self.history_manager.list( filters=filters, limit=-1 )
         self.assertEqual( found, deleted_and_annotated )
         self.log( "orm and fn filtered, negative offset should return full list" )
-        found = self.history_mgr.list( self.trans, filters=filters, offset=-1 )
+        found = self.history_manager.list( filters=filters, offset=-1 )
         self.assertEqual( found, deleted_and_annotated )
 
 
diff --git a/test/unit/managers/test_ModelManager.py b/test/unit/managers/test_ModelManager.py
index a25b3f0a771..fbaf0eb68af 100644
--- a/test/unit/managers/test_ModelManager.py
+++ b/test/unit/managers/test_ModelManager.py
@@ -61,11 +61,10 @@ class BaseTestCase( unittest.TestCase ):
         self.app = self.trans.app
 
     def set_up_managers( self ):
-        self.user_mgr = UserManager( self.app )
+        self.user_manager = UserManager( self.app )
 
     def set_up_trans( self ):
-        self.admin_user = self.user_mgr.create( self.trans,
-            email=admin_email, username='admin', password=default_password )
+        self.admin_user = self.user_manager.create( email=admin_email, username='admin', password=default_password )
         self.trans.set_user( self.admin_user )
         self.trans.set_history( None )
 
diff --git a/test/unit/managers/test_UserManager.py b/test/unit/managers/test_UserManager.py
index f6f77e4bd3c..34c3b818c9c 100644
--- a/test/unit/managers/test_UserManager.py
+++ b/test/unit/managers/test_UserManager.py
@@ -39,96 +39,96 @@ class UserManagerTestCase( BaseTestCase ):
 
     def test_base( self ):
         self.log( "should be able to create a user" )
-        user2 = self.user_mgr.create( self.trans, **user2_data )
+        user2 = self.user_manager.create( **user2_data )
         self.assertIsInstance( user2, model.User )
         self.assertIsNotNone( user2.id )
         self.assertEqual( user2.email, user2_data[ 'email' ] )
         self.assertEqual( user2.password, default_password )
 
-        user3 = self.user_mgr.create( self.trans, **user3_data )
+        user3 = self.user_manager.create( **user3_data )
 
         self.log( "should be able to query" )
         users = self.trans.sa_session.query( model.User ).all()
-        self.assertEqual( self.user_mgr.list( self.trans ), users )
+        self.assertEqual( self.user_manager.list(), users )
 
-        self.assertEqual( self.user_mgr.by_id( self.trans, user2.id ), user2 )
-        self.assertEqual( self.user_mgr.by_ids( self.trans, [ user3.id, user2.id ] ), [ user3, user2 ] )
+        self.assertEqual( self.user_manager.by_id( user2.id ), user2 )
+        self.assertEqual( self.user_manager.by_ids( [ user3.id, user2.id ] ), [ user3, user2 ] )
 
         self.log( "should be able to limit and offset" )
-        self.assertEqual( self.user_mgr.list( self.trans, limit=1 ), users[0:1] )
-        self.assertEqual( self.user_mgr.list( self.trans, offset=1 ), users[1:] )
-        self.assertEqual( self.user_mgr.list( self.trans, limit=1, offset=1 ), users[1:2] )
+        self.assertEqual( self.user_manager.list( limit=1 ), users[0:1] )
+        self.assertEqual( self.user_manager.list( offset=1 ), users[1:] )
+        self.assertEqual( self.user_manager.list( limit=1, offset=1 ), users[1:2] )
 
-        self.assertEqual( self.user_mgr.list( self.trans, limit=0 ), [] )
-        self.assertEqual( self.user_mgr.list( self.trans, offset=3 ), [] )
+        self.assertEqual( self.user_manager.list( limit=0 ), [] )
+        self.assertEqual( self.user_manager.list( offset=3 ), [] )
 
         self.log( "should be able to order" )
-        self.assertEqual( self.user_mgr.list( self.trans, order_by=( sqlalchemy.desc( model.User.create_time ) ) ),
+        self.assertEqual( self.user_manager.list( order_by=( sqlalchemy.desc( model.User.create_time ) ) ),
             [ user3, user2, self.admin_user ] )
 
     def test_invalid_create( self ):
-        user2 = self.user_mgr.create( self.trans, **user2_data )
+        user2 = self.user_manager.create( **user2_data )
 
         self.log( "emails must be unique" )
-        self.assertRaises( exceptions.Conflict, self.user_mgr.create,
-            self.trans, **dict( email='user2@user2.user2', username='user2a', password=default_password ) )
+        self.assertRaises( exceptions.Conflict, self.user_manager.create,
+            **dict( email='user2@user2.user2', username='user2a', password=default_password ) )
         self.log( "usernames must be unique" )
-        self.assertRaises( exceptions.Conflict, self.user_mgr.create,
-            self.trans, **dict( email='user2a@user2.user2', username='user2', password=default_password ) )
+        self.assertRaises( exceptions.Conflict, self.user_manager.create,
+            **dict( email='user2a@user2.user2', username='user2', password=default_password ) )
 
     def test_email_queries( self ):
-        user2 = self.user_mgr.create( self.trans, **user2_data )
-        user3 = self.user_mgr.create( self.trans, **user3_data )
+        user2 = self.user_manager.create( **user2_data )
+        user3 = self.user_manager.create( **user3_data )
 
         self.log( "should be able to query by email" )
-        self.assertEqual( self.user_mgr.by_email( self.trans, user2_data[ 'email' ] ), user2 )
+        self.assertEqual( self.user_manager.by_email( user2_data[ 'email' ] ), user2 )
 
         #note: sorted by email alpha
         users = self.trans.sa_session.query( model.User ).all()
-        self.assertEqual( self.user_mgr.by_email_like( self.trans, '%@%' ), [ self.admin_user, user2, user3 ] )
+        self.assertEqual( self.user_manager.by_email_like( '%@%' ), [ self.admin_user, user2, user3 ] )
 
     def test_admin( self ):
-        user2 = self.user_mgr.create( self.trans, **user2_data )
-        user3 = self.user_mgr.create( self.trans, **user3_data )
+        user2 = self.user_manager.create( **user2_data )
+        user3 = self.user_manager.create( **user3_data )
 
         self.log( "should be able to test whether admin" )
-        self.assertTrue( self.user_mgr.is_admin( self.trans, self.admin_user ) )
-        self.assertFalse( self.user_mgr.is_admin( self.trans, user2 ) )
-        self.assertEqual( self.user_mgr.admins( self.trans ), [ self.admin_user ] )
-        self.assertRaises( exceptions.AdminRequiredException, self.user_mgr.error_unless_admin, self.trans, user2 )
-        self.assertEqual( self.user_mgr.error_unless_admin( self.trans, self.admin_user ), self.admin_user )
+        self.assertTrue( self.user_manager.is_admin( self.admin_user ) )
+        self.assertFalse( self.user_manager.is_admin( user2 ) )
+        self.assertEqual( self.user_manager.admins(), [ self.admin_user ] )
+        self.assertRaises( exceptions.AdminRequiredException, self.user_manager.error_unless_admin, user2 )
+        self.assertEqual( self.user_manager.error_unless_admin( self.admin_user ), self.admin_user )
 
     def test_anonymous( self ):
         anon = None
-        user2 = self.user_mgr.create( self.trans, **user2_data )
+        user2 = self.user_manager.create( **user2_data )
 
         self.log( "should be able to tell if a user is anonymous" )
-        self.assertRaises( exceptions.AuthenticationFailed, self.user_mgr.error_if_anonymous, self.trans, anon )
-        self.assertEqual( self.user_mgr.error_if_anonymous( self.trans, user2 ), user2 )
+        self.assertRaises( exceptions.AuthenticationFailed, self.user_manager.error_if_anonymous, anon )
+        self.assertEqual( self.user_manager.error_if_anonymous( user2 ), user2 )
 
     def test_current( self ):
-        user2 = self.user_mgr.create( self.trans, **user2_data )
-        user3 = self.user_mgr.create( self.trans, **user3_data )
+        user2 = self.user_manager.create( **user2_data )
+        user3 = self.user_manager.create( **user3_data )
 
         self.log( "should be able to tell if a user is the current (trans) user" )
-        self.assertEqual( self.user_mgr.current_user( self.trans ), self.admin_user )
-        self.assertNotEqual( self.user_mgr.current_user( self.trans ), user2 )
+        self.assertEqual( self.user_manager.current_user( self.trans ), self.admin_user )
+        self.assertNotEqual( self.user_manager.current_user( self.trans ), user2 )
 
     def test_api_keys( self ):
-        user2 = self.user_mgr.create( self.trans, **user2_data )
-        user3 = self.user_mgr.create( self.trans, **user3_data )
+        user2 = self.user_manager.create( **user2_data )
+        user3 = self.user_manager.create( **user3_data )
 
         self.log( "should return None if no APIKey has been created" )
-        self.assertEqual( self.user_mgr.valid_api_key( self.trans, user2 ), None )
+        self.assertEqual( self.user_manager.valid_api_key( user2 ), None )
 
         self.log( "should be able to generate and retrieve valid api key" )
-        user2_api_key = self.user_mgr.create_api_key( self.trans, user2 )
+        user2_api_key = self.user_manager.create_api_key( user2 )
         self.assertIsInstance( user2_api_key, basestring )
-        self.assertEqual( self.user_mgr.valid_api_key( self.trans, user2 ).key, user2_api_key )
+        self.assertEqual( self.user_manager.valid_api_key( user2 ).key, user2_api_key )
 
         self.log( "should return the most recent (i.e. most valid) api key" )
-        user2_api_key_2 = self.user_mgr.create_api_key( self.trans, user2 )
-        self.assertEqual( self.user_mgr.valid_api_key( self.trans, user2 ).key, user2_api_key_2 )
+        user2_api_key_2 = self.user_manager.create_api_key( user2 )
+        self.assertEqual( self.user_manager.valid_api_key( user2 ).key, user2_api_key_2 )
 
 
 # =============================================================================
@@ -139,7 +139,7 @@ class UserSerializerTestCase( BaseTestCase ):
         self.user_serializer = users.UserSerializer( self.app )
 
     def test_views( self ):
-        user = self.user_mgr.create( self.trans, **user2_data )
+        user = self.user_manager.create( **user2_data )
 
         self.log( 'should have a summary view' )
         summary_view = self.user_serializer.serialize_to_view( self.trans, user, view='summary' )
@@ -159,7 +159,7 @@ class UserSerializerTestCase( BaseTestCase ):
             self.assertTrue( True, 'all serializable keys have a serializer' )
 
     def test_views_and_keys( self ):
-        user = self.user_mgr.create( self.trans, **user2_data )
+        user = self.user_manager.create( **user2_data )
 
         self.log( 'should be able to use keys with views' )
         serialized = self.user_serializer.serialize_to_view( self.trans, user,
@@ -173,7 +173,7 @@ class UserSerializerTestCase( BaseTestCase ):
         self.assertKeys( serialized, [ 'tags_used', 'is_admin' ] )
 
     def test_serializers( self ):
-        user = self.user_mgr.create( self.trans, **user2_data )
+        user = self.user_manager.create( **user2_data )
         all_keys = list( self.user_serializer.serializable_keyset )
         serialized = self.user_serializer.serialize( self.trans, user, all_keys )
         # pprint.pprint( serialized )

From c1f721086f5169ddd452aee73f7423536e11b976 Mon Sep 17 00:00:00 2001
From: Carl Eberhard <carlfeberhard@gmail.com>
Date: Thu, 2 Apr 2015 13:49:03 -0400
Subject: [PATCH 21/88] Managers: attempt to extract trans from de/serializers

---
 lib/galaxy/managers/annotatable.py            | 29 +++----
 lib/galaxy/managers/base.py                   | 51 ++++++------
 lib/galaxy/managers/configuration.py          | 74 +++++++++--------
 lib/galaxy/managers/datasets.py               | 59 +++++++-------
 lib/galaxy/managers/deletable.py              |  6 +-
 lib/galaxy/managers/hdas.py                   | 41 +++++-----
 lib/galaxy/managers/histories.py              | 41 +++++-----
 lib/galaxy/managers/ratable.py                |  4 +-
 lib/galaxy/managers/sharable.py               | 10 +--
 lib/galaxy/managers/taggable.py               |  8 +-
 lib/galaxy/managers/users.py                  | 24 +++---
 .../webapps/galaxy/api/configuration.py       | 79 +------------------
 lib/galaxy/webapps/galaxy/api/datasets.py     |  3 +-
 lib/galaxy/webapps/galaxy/api/histories.py    | 30 ++++---
 .../webapps/galaxy/api/history_contents.py    | 20 ++---
 .../webapps/galaxy/controllers/history.py     | 11 +--
 test/unit/managers/test_DatasetManager.py     | 22 +++---
 test/unit/managers/test_HDAManager.py         | 60 +++++++-------
 test/unit/managers/test_HistoryManager.py     | 26 +++---
 test/unit/managers/test_UserManager.py        | 14 ++--
 20 files changed, 279 insertions(+), 333 deletions(-)

diff --git a/lib/galaxy/managers/annotatable.py b/lib/galaxy/managers/annotatable.py
index dacbf31bf86..7f9a32f7d3f 100644
--- a/lib/galaxy/managers/annotatable.py
+++ b/lib/galaxy/managers/annotatable.py
@@ -29,7 +29,7 @@ class AnnotatableManagerMixin( object ):
         annotation_obj = item.add_item_annotation( self.session(), user, item, annotation )
         return annotation_obj.annotation
 
-    #def by_user( self, trans, user, **kwargs ):
+    #def by_user( self, user, **kwargs ):
     #    pass
 
 
@@ -38,13 +38,11 @@ class AnnotatableSerializerMixin( object ):
     def add_serializers( self ):
         self.serializers[ 'annotation' ] = self.serialize_annotation
 
-    def serialize_annotation( self, trans, item, key ):
+    def serialize_annotation( self, item, key, user=None, **context ):
         """
         Get and serialize an `item`'s annotation.
         """
         # user = item.user
-        #TODO: trans
-        user = trans.user
         sa_session = self.app.model.context
         returned = item.get_item_annotation_str( sa_session, user, item )
         return returned
@@ -55,22 +53,25 @@ class AnnotatableDeserializerMixin( object ):
     def add_deserializers( self ):
         self.deserializers[ 'annotation' ] = self.deserialize_annotation
 
-    def deserialize_annotation( self, trans, item, key, val ):
+    def deserialize_annotation( self, item, key, val, user=None, **context ):
         """
         Make sure `val` is a valid annotation and assign it, deleting any existing
         if `val` is None.
         """
+        print '-' * 20
+        print item
+        print key
+        print val
+        print user
         val = self.validate.nullable_basestring( key, val )
+        # sa_session = self.app.model.context
+        # if val is None:
+        #     item.delete_item_annotation( sa_session, user, item )
+        #     return None
 
-        sa_session = self.app.model.context
-        #TODO: trans
-        user = trans.user
-        if val is None:
-            item.delete_item_annotation( sa_session, user, item )
-            return None
-
-        annotated_item = item.add_item_annotation( sa_session, user, item, val )
-        return annotated_item.annotation
+        # annotated_item = item.add_item_annotation( sa_session, user, item, val )
+        # return annotated_item.annotation
+        return self.manager.annotate( item, user, val )
 
 
 # TODO: I'm not entirely convinced this (or tags) are a good idea for filters since they involve a/the user
diff --git a/lib/galaxy/managers/base.py b/lib/galaxy/managers/base.py
index 2e3d210af93..f659c82a82c 100644
--- a/lib/galaxy/managers/base.py
+++ b/lib/galaxy/managers/base.py
@@ -500,7 +500,7 @@ class ModelSerializer( object ):
 
     Maintains a map of requestable keys and the Callable() serializer functions
     that should be called for those keys.
-    E.g. { 'x' : lambda trans, item, key: item.x, ... }
+    E.g. { 'x' : lambda item, key: item.x, ... }
 
     Note: if a key to serialize is not listed in the Serializer.serializable_keyset
     or serializers, it will not be returned.
@@ -509,7 +509,7 @@ class ModelSerializer( object ):
         my_serializer = MySerializer( app )
         ...
         keys_to_serialize = [ 'id', 'name', 'attr1', 'attr2', ... ]
-        item_dict = MySerializer.serialize( trans, my_item, keys_to_serialize )
+        item_dict = MySerializer.serialize( my_item, keys_to_serialize )
     """
     #: 'service' to use for getting urls - use class var to allow overriding when testing
     url_for = staticmethod( routes.url_for )
@@ -559,7 +559,7 @@ class ModelSerializer( object ):
         self.serializable_keyset.update( key_list )
         return key_list
 
-    def serialize( self, trans, item, keys ):
+    def serialize( self, item, keys, **context ):
         """
         Serialize the model `item` to a dictionary.
 
@@ -567,18 +567,18 @@ class ModelSerializer( object ):
         built from each key in `keys` that also exists in `serializers` and
         values of calling the keyed/named serializers on item.
         """
-        # main interface fn for converting a model to a dict
+        # TODO: constrain context to current_user/whos_asking when that's all we need (trans)
         returned = {}
         for key in keys:
             # check both serializers and serializable keys
             if key in self.serializers:
                 try:
-                    returned[ key ] = self.serializers[ key ]( trans, item, key )
+                    returned[ key ] = self.serializers[ key ]( item, key, **context )
                 except SkipAttribute, skip:
                     # dont add this key if the deserializer threw this
                     pass
             elif key in self.serializable_keyset:
-                returned[ key ] = self.default_serializer( trans, item, key )
+                returned[ key ] = self.default_serializer( item, key, **context )
             # ignore bad/unreg keys
         return returned
 
@@ -594,10 +594,10 @@ class ModelSerializer( object ):
         if original_key in self.serializers:
             return self.serializers[ original_key ]
         if original_key in self.serializable_keyset:
-            return lambda t, i, k: self.default_serializer( t, i, original_key )
+            return lambda i, k, **c: self.default_serializer( i, original_key, **c )
         raise KeyError( 'serializer not found for remap: ' + original_key )
 
-    def default_serializer( self, trans, item, key ):
+    def default_serializer( self, item, key, **context ):
         """
         Serialize the `item`'s attribute named `key`.
         """
@@ -605,14 +605,14 @@ class ModelSerializer( object ):
         return getattr( item, key )
 
     # serializers for common galaxy objects
-    def serialize_date( self, trans, item, key ):
+    def serialize_date( self, item, key, **context ):
         """
         Serialize a date attribute of `item`.
         """
         date = getattr( item, key )
         return date.isoformat() if date is not None else None
 
-    def serialize_id( self, trans, item, key ):
+    def serialize_id( self, item, key, **context ):
         """
         Serialize an id attribute of `item`.
         """
@@ -621,7 +621,7 @@ class ModelSerializer( object ):
         return self.app.security.encode_id( id ) if id is not None else None
 
     # serializing to a view where a view is a predefied list of keys to serialize
-    def serialize_to_view( self, trans, item, view=None, keys=None, default_view=None ):
+    def serialize_to_view( self, item, view=None, keys=None, default_view=None, **context ):
         """
         Use a predefined list of keys (the string `view`) and any additional keys
         listed in `keys`.
@@ -647,7 +647,7 @@ class ModelSerializer( object ):
             elif default_view:
                 all_keys = self._view_to_keys( default_view )
 
-        return self.serialize( trans, item, all_keys )
+        return self.serialize( item, all_keys, **context )
 
     def _view_to_keys( self, view=None ):
         """
@@ -697,16 +697,17 @@ class ModelDeserializer( object ):
         # to be overridden in subclasses
         pass
 
-    def deserialize( self, trans, item, data, flush=True ):
+    def deserialize( self, item, data, flush=True, **context ):
         """
         Convert an incoming serialized dict into values that can be
         directly assigned to an item's attributes and assign them
         """
+        # TODO: constrain context to current_user/whos_asking when that's all we need (trans)
         sa_session = self.app.model.context
         new_dict = {}
         for key, val in data.items():
             if key in self.deserializers:
-                new_dict[ key ] = self.deserializers[ key ]( trans, item, key, val )
+                new_dict[ key ] = self.deserializers[ key ]( item, key, val, **context )
             # !important: don't error on unreg. keys -- many clients will add weird ass keys onto the model
 
         # TODO:?? add and flush here or in manager?
@@ -717,7 +718,7 @@ class ModelDeserializer( object ):
         return new_dict
 
     # ... common deserializers for primitives
-    def default_deserializer( self, trans, item, key, val ):
+    def default_deserializer( self, item, key, val, **context ):
         """
         If the incoming `val` is different than the `item` value change it
         and, in either case, return the value.
@@ -729,28 +730,28 @@ class ModelDeserializer( object ):
             setattr( item, key, val )
         return val
 
-    def deserialize_basestring( self, trans, item, key, val ):
+    def deserialize_basestring( self, item, key, val, **context ):
         val = self.validate.basestring( key, val )
-        return self.default_deserializer( trans, item, key, val )
+        return self.default_deserializer( item, key, val, **context )
 
-    def deserialize_bool( self, trans, item, key, val ):
+    def deserialize_bool( self, item, key, val, **context ):
         val = self.validate.bool( key, val )
-        return self.default_deserializer( trans, item, key, val )
+        return self.default_deserializer( item, key, val, **context )
 
-    def deserialize_int( self, trans, item, key, val, min=None, max=None ):
+    def deserialize_int( self, item, key, val, min=None, max=None, **context ):
         val = self.validate.int_range( key, val, min, max )
-        return self.default_deserializer( trans, item, key, val )
+        return self.default_deserializer( item, key, val, **context )
 
-    #def deserialize_date( self, trans, item, key, val ):
+    #def deserialize_date( self, item, key, val ):
     #   #TODO: parse isoformat date into date object
 
     # ... common deserializers for Galaxy
-    def deserialize_genome_build( self, trans, item, key, val ):
+    def deserialize_genome_build( self, item, key, val, **context ):
         """
         Make sure `val` is a valid dbkey and assign it.
         """
         val = self.validate.genome_build( key, val )
-        return self.default_deserializer( trans, item, key, val )
+        return self.default_deserializer( item, key, val, **context )
 
 
 class ModelValidator( object ):
@@ -830,7 +831,7 @@ class ModelValidator( object ):
         # IOW: fallback to string validation
         return self.basestring( key, val )
 
-    # def slug( self, trans, item, key, val ):
+    # def slug( self, item, key, val ):
     #    """validate slug"""
     #    pass
 
diff --git a/lib/galaxy/managers/configuration.py b/lib/galaxy/managers/configuration.py
index b85b2f94c3f..7c844053eff 100644
--- a/lib/galaxy/managers/configuration.py
+++ b/lib/galaxy/managers/configuration.py
@@ -15,6 +15,7 @@ import logging
 log = logging.getLogger( __name__ )
 
 
+#TODO: for lack of a manager file for the config. May well be better in config.py? Circ imports?
 class ConfigSerializer( base.ModelSerializer ):
 
     def __init__( self, app ):
@@ -23,61 +24,64 @@ class ConfigSerializer( base.ModelSerializer ):
         self.default_view = 'all'
         self.add_view( 'all', self.serializers.keys() )
 
-    def default_serializer( self, trans, config, key ):
-        return config.get( key, None )
-
-    def _defaults_to( self, default ):
-        return lambda t, i, k: i.get( k, default )
+    def default_serializer( self, config, key ):
+        return getattr( config, key, None )
 
     def add_serializers( self ):
+        def _defaults_to( default ):
+            return lambda i, k, **c: getattr( i, k, default )
+
         self.serializers = {
             #TODO: this is available from user data, remove
-            'is_admin_user'             : lambda *a: False,
+            'is_admin_user'             : lambda *a, **c: False,
 
-            'brand'                     : lambda t, i, k: i.get( k, "" ),
+            'brand'                     : _defaults_to( '' ),
             #TODO: this doesn't seem right
-            'logo_url'                  : lambda t, i, k: web.url_for( i.get( k, '/') ),
-            'terms_url'                 : lambda t, i, k: i.get( k, "" ),
+            'logo_url'                  : lambda i, k, **c: self.url_for( i.get( k, '/' ) ),
+            'terms_url'                 : _defaults_to( '' ),
 
             #TODO: don't hardcode here - hardcode defaults once in config.py
-            'wiki_url'                  : self._defaults_to( "http://galaxyproject.org/" ),
-            'search_url'                : self._defaults_to( "http://galaxyproject.org/search/usegalaxy/" ),
-            'mailing_lists'             : self._defaults_to( "http://wiki.galaxyproject.org/MailingLists" ),
-            'screencasts_url'           : self._defaults_to( "http://vimeo.com/galaxyproject" ),
-            'citation_url'              : self._defaults_to( "http://wiki.galaxyproject.org/CitingGalaxy" ),
-            'support_url'               : self._defaults_to( "http://wiki.galaxyproject.org/Support" ),
-            'lims_doc_url'              : self._defaults_to( "http://main.g2.bx.psu.edu/u/rkchak/p/sts" ),
-            'biostar_url'               : lambda t, i, k: i.biostar_url,
-            'biostar_url_redirect'      : lambda *a: web.url_for( controller='biostar', action='biostar_redirect',
-                                                                qualified=True ),
+            'wiki_url'                  : _defaults_to( "http://galaxyproject.org/" ),
+            'search_url'                : _defaults_to( "http://galaxyproject.org/search/usegalaxy/" ),
+            'mailing_lists'             : _defaults_to( "http://wiki.galaxyproject.org/MailingLists" ),
+            'screencasts_url'           : _defaults_to( "http://vimeo.com/galaxyproject" ),
+            'citation_url'              : _defaults_to( "http://wiki.galaxyproject.org/CitingGalaxy" ),
+            'support_url'               : _defaults_to( "http://wiki.galaxyproject.org/Support" ),
+            'lims_doc_url'              : _defaults_to( "http://main.g2.bx.psu.edu/u/rkchak/p/sts" ),
+            'biostar_url'               : _defaults_to( '' ),
+            'biostar_url_redirect'      : lambda *a, **c: self.url_for( controller='biostar', action='biostar_redirect',
+                                                                   qualified=True ),
 
-            'allow_user_creation'       : lambda t, i, k: i.allow_user_creation,
-            'use_remote_user'           : lambda t, i, k: i.use_remote_user,
-            'remote_user_logout_href'   : lambda t, i, k: i.remote_user_logout_href,
-            'enable_cloud_launch'       : self._defaults_to( False ),
-            'datatypes_disable_auto'    : self._defaults_to( False ),
-            'allow_user_dataset_purge'  : self._defaults_to( False ),
-            'enable_unique_workflow_defaults' : self._defaults_to( False ),
+            'allow_user_creation'       : lambda i, k, **c: i.allow_user_creation,
+            'use_remote_user'           : _defaults_to( None ),
+            'remote_user_logout_href'   : _defaults_to( '' ),
+            'enable_cloud_launch'       : _defaults_to( False ),
+            'datatypes_disable_auto'    : _defaults_to( False ),
+            'allow_user_dataset_purge'  : _defaults_to( False ),
+            'enable_unique_workflow_defaults' : _defaults_to( False ),
 
-            'nginx_upload_path'         : self._defaults_to( web.url_for( controller='api', action='tools' ) ),
-            'ftp_upload_dir'            : self._defaults_to( None ),
-            'ftp_upload_site'           : self._defaults_to( None ),
+            'nginx_upload_path'         : _defaults_to( self.url_for( controller='api', action='tools' ) ),
+            'ftp_upload_dir'            : _defaults_to( None ),
+            'ftp_upload_site'           : _defaults_to( None ),
+            'version_major'             : _defaults_to( None ),
         }
 
 
 class AdminConfigSerializer( ConfigSerializer ):
-    """Config attributes viewable by admin users"""
+    # config attributes viewable by admin users
 
     def add_serializers( self ):
         super( AdminConfigSerializer, self ).add_serializers()
+        def _defaults_to( default ):
+            return lambda i, k, **c: getattr( i, k, default )
 
         self.serializers.update({
             #TODO: this is available from user data, remove
             'is_admin_user'             : lambda *a: True,
 
-            'library_import_dir'        : self._defaults_to( None ),
-            'user_library_import_dir'   : self._defaults_to( None ),
-            'allow_library_path_paste'  : self._defaults_to( None ),
-            'allow_user_creation'       : self._defaults_to( False ),
-            'allow_user_deletion'       : self._defaults_to( False ),
+            'library_import_dir'        : _defaults_to( None ),
+            'user_library_import_dir'   : _defaults_to( None ),
+            'allow_library_path_paste'  : _defaults_to( False ),
+            'allow_user_creation'       : _defaults_to( False ),
+            'allow_user_deletion'       : _defaults_to( False ),
         })
diff --git a/lib/galaxy/managers/datasets.py b/lib/galaxy/managers/datasets.py
index e8b94af3cc5..e6e0f92a606 100644
--- a/lib/galaxy/managers/datasets.py
+++ b/lib/galaxy/managers/datasets.py
@@ -111,6 +111,7 @@ class DatasetRBACPermissions( object ):
     def available_roles( self, trans, dataset, controller='root' ):
         return self.app.security_agent.get_legitimate_roles( trans, dataset, controller )
 
+    # TODO: not enough by a long shot
     def get( self, dataset, flush=True ):
         manage = self.manage.by_dataset( dataset )
         access = self.access.by_dataset( dataset )
@@ -121,6 +122,7 @@ class DatasetRBACPermissions( object ):
         access = self.access.set( dataset, access_roles or [], flush=flush )
         return ( manage, access )
 
+    # ---- conv. settings
     def set_public_with_single_manager( self, dataset, user, flush=True ):
         manage = self.manage.grant( dataset, user, flush=flush )
         access = self.access.clear( dataset, flush=False )
@@ -164,16 +166,16 @@ class DatasetSerializer( base.ModelSerializer, deletable.PurgableSerializerMixin
             'create_time'   : self.serialize_date,
             'update_time'   : self.serialize_date,
 
-            'uuid'          : lambda t, i, k: str( i.uuid ) if i.uuid else None,
+            'uuid'          : lambda i, k, **c: str( i.uuid ) if i.uuid else None,
             'file_name'     : self.serialize_file_name,
             'extra_files_path' : self.serialize_extra_files_path,
             'permissions'   : self.serialize_permissions,
 
-            'total_size'    : lambda t, i, k: int( i.get_total_size() ),
-            'file_size'     : lambda t, i, k: int( i.get_size() )
+            'total_size'    : lambda i, k, **c: int( i.get_total_size() ),
+            'file_size'     : lambda i, k, **c: int( i.get_size() )
         })
 
-    def serialize_file_name( self, trans, dataset, key ):
+    def serialize_file_name( self, dataset, key, **context ):
         """
         If the config allows or the user is admin, return the file name
         of the file that contains this dataset's data.
@@ -184,7 +186,7 @@ class DatasetSerializer( base.ModelSerializer, deletable.PurgableSerializerMixin
             self.skip()
         return dataset.file_name
 
-    def serialize_extra_files_path( self, trans, dataset, key ):
+    def serialize_extra_files_path( self, dataset, key, **context ):
         """
         If the config allows or the user is admin, return the file path.
         """
@@ -194,7 +196,7 @@ class DatasetSerializer( base.ModelSerializer, deletable.PurgableSerializerMixin
             self.skip()
         return dataset.extra_files_path
 
-    def serialize_permissions( self, trans, dataset, key ):
+    def serialize_permissions( self, dataset, key, **context ):
         """
         """
         permissions = {}
@@ -214,7 +216,7 @@ class DatasetDeserializer( base.ModelDeserializer, deletable.PurgableDeserialize
             'permissions' : self.deserialize_permissions,
         })
 
-    def deserialize_permissions( self, trans, dataset, key, value ):
+    def deserialize_permissions( self, dataset, key, value, **context ):
         """
         """
         permissions = {}
@@ -322,7 +324,7 @@ class _UnflattenedMetadataDatasetAssociationSerializer( base.ModelSerializer,
             'update_time'   : self.serialize_date,
 
             # underlying dataset
-            'dataset'       : lambda t, i, k: self.dataset_serializer.serialize_to_view( t, i.dataset, view='summary' ),
+            'dataset'       : lambda i, k, **c: self.dataset_serializer.serialize_to_view( i.dataset, view='summary', **c ),
             'dataset_id'    : self._proxy_to_dataset( key='id' ),
             #TODO: why is this named uuid!? The da doesn't have a uuid - it's the underlying dataset's uuid!
             'uuid'          : self._proxy_to_dataset( key='uuid' ),
@@ -331,31 +333,31 @@ class _UnflattenedMetadataDatasetAssociationSerializer( base.ModelSerializer,
             'extra_files_path' : self._proxy_to_dataset( serializer=self.dataset_serializer.serialize_extra_files_path ),
             'permissions'   : self._proxy_to_dataset( serializer=self.dataset_serializer.serialize_permissions),
             # TODO: do the sizes proxy accurately/in the same way?
-            'size'          : lambda t, i, k: int( i.get_size() ),
-            'file_size'     : lambda t, i, k: self.serializers[ 'size' ]( t, i, k ),
-            'nice_size'     : lambda t, i, k: i.get_size( nice_size=True ),
+            'size'          : lambda i, k, **c: int( i.get_size() ),
+            'file_size'     : lambda i, k, **c: self.serializers[ 'size' ]( i, k, **c ),
+            'nice_size'     : lambda i, k, **c: i.get_size( nice_size=True ),
 
             # common to lddas and hdas - from mapping.py
             'copied_from_history_dataset_association_id'        : self.serialize_id,
             'copied_from_library_dataset_dataset_association_id': self.serialize_id,
-            'info'          : lambda t, i, k: i.info.strip() if isinstance( i.info, basestring ) else i.info,
-            'blurb'         : lambda t, i, k: i.blurb,
-            'peek'          : lambda t, i, k: i.display_peek() if i.peek and i.peek != 'no peek' else None,
+            'info'          : lambda i, k, **c: i.info.strip() if isinstance( i.info, basestring ) else i.info,
+            'blurb'         : lambda i, k, **c: i.blurb,
+            'peek'          : lambda i, k, **c: i.display_peek() if i.peek and i.peek != 'no peek' else None,
 
             'meta_files'    : self.serialize_meta_files,
             'metadata'      : self.serialize_metadata,
 
             'parent_id'     : self.serialize_id,
-            'designation'   : lambda t, i, k: i.designation,
+            'designation'   : lambda i, k, **c: i.designation,
 
             # 'extended_metadata'     : self.serialize_extended_metadata,
             # 'extended_metadata_id'  : self.serialize_id,
 
             # remapped
-            'genome_build'  : lambda t, i, k: i.dbkey,
+            'genome_build'  : lambda i, k, **c: i.dbkey,
 
             # derived (not mapped) attributes
-            'data_type'     : lambda t, i, k: i.datatype.__class__.__module__ + '.' + i.datatype.__class__.__name__,
+            'data_type'     : lambda i, k, **c: i.datatype.__class__.__module__ + '.' + i.datatype.__class__.__name__,
 
             # TODO: conversions
             # TODO: metadata/extra files
@@ -368,10 +370,10 @@ class _UnflattenedMetadataDatasetAssociationSerializer( base.ModelSerializer,
         if key:
             serializer = self.dataset_serializer.serializers.get( key )
         if serializer:
-            return lambda t, i, k: serializer( t, i.dataset, key or k )
+            return lambda i, k, **c: serializer( i.dataset, key or k, **c )
         raise TypeError( 'kwarg serializer or key needed')
 
-    def serialize_meta_files( self, trans, dataset_assoc, key ):
+    def serialize_meta_files( self, dataset_assoc, key, **context ):
         """
         Cycle through meta files and return them as a list of dictionaries.
         """
@@ -381,7 +383,7 @@ class _UnflattenedMetadataDatasetAssociationSerializer( base.ModelSerializer,
                 meta_files.append( dict( file_type=meta_type ) )
         return meta_files
 
-    def serialize_metadata( self, trans, dataset_assoc, key, excluded=None ):
+    def serialize_metadata( self, dataset_assoc, key, excluded=None, **context ):
         """
         Cycle through metadata and return as dictionary.
         """
@@ -417,7 +419,7 @@ class DatasetAssociationSerializer( _UnflattenedMetadataDatasetAssociationSerial
         # remove the single nesting key here
         del self.serializers[ 'metadata' ]
 
-    def serialize( self, trans, dataset_assoc, keys ):
+    def serialize( self, dataset_assoc, keys, **context ):
         """
         Override to add metadata as flattened keys on the serialized DatasetInstance.
         """
@@ -425,11 +427,11 @@ class DatasetAssociationSerializer( _UnflattenedMetadataDatasetAssociationSerial
         # TODO: remove these when metadata is sub-object
         KEYS_HANDLED_SEPARATELY = ( 'metadata', )
         left_to_handle = self._pluck_from_list( keys, KEYS_HANDLED_SEPARATELY )
-        serialized = super( DatasetAssociationSerializer, self ).serialize( trans, dataset_assoc, keys )
+        serialized = super( DatasetAssociationSerializer, self ).serialize( dataset_assoc, keys, **context )
 
         # add metadata directly to the dict instead of as a sub-object
         if 'metadata' in left_to_handle:
-            metadata = self._prefixed_metadata( trans, dataset_assoc )
+            metadata = self._prefixed_metadata( dataset_assoc )
             serialized.update( metadata )
         return serialized
 
@@ -447,13 +449,13 @@ class DatasetAssociationSerializer( _UnflattenedMetadataDatasetAssociationSerial
                 pass
         return found
 
-    def _prefixed_metadata( self, trans, dataset_assoc ):
+    def _prefixed_metadata( self, dataset_assoc ):
         """
         Adds (a prefixed version of) the DatasetInstance metadata to the dict,
         prefixing each key with 'metadata_'.
         """
         # build the original, nested dictionary
-        metadata = self.serialize_metadata( trans, dataset_assoc, 'metadata' )
+        metadata = self.serialize_metadata( dataset_assoc, 'metadata' )
 
         # prefix each key within and return
         prefixed = {}
@@ -475,16 +477,17 @@ class DatasetAssociationDeserializer( base.ModelDeserializer, deletable.Purgable
         })
         self.deserializable_keyset.update( self.deserializers.keys() )
 
-    def deserialize_metadata( self, trans, dataset_assoc, metadata_key, metadata_dict ):
+# TODO: untested
+    def deserialize_metadata( self, dataset_assoc, metadata_key, metadata_dict, **context ):
         """
         """
         self.validate.type( metadata_key, metadata_dict, dict )
         returned = {}
         for key, val in metadata_dict.items():
-            returned[ key ] = self.deserialize_metadatum( trans, dataset_assoc, key, val )
+            returned[ key ] = self.deserialize_metadatum( dataset_assoc, key, val, **context )
         return returned
 
-    def deserialize_metadatum( self, trans, dataset_assoc, key, val ):
+    def deserialize_metadatum( self, dataset_assoc, key, val, **context ):
         """
         """
         if key not in dataset_assoc.datatype.metadata_spec:
diff --git a/lib/galaxy/managers/deletable.py b/lib/galaxy/managers/deletable.py
index 6618fba1156..dc55eea5baf 100644
--- a/lib/galaxy/managers/deletable.py
+++ b/lib/galaxy/managers/deletable.py
@@ -18,7 +18,6 @@ class DeletableManagerMixin( object ):
     that they are no longer needed, should not be displayed, or may be actually
     removed by an admin/script.
     """
-
     def delete( self, item, flush=True, **kwargs ):
         """
         Mark as deleted and return.
@@ -44,7 +43,7 @@ class DeletableDeserializerMixin( object ):
     def add_deserializers( self ):
         self.deserializers[ 'deleted' ] = self.deserialize_deleted
 
-    def deserialize_deleted( self, trans, item, key, val ):
+    def deserialize_deleted( self, item, key, val, **context ):
         """
         Delete or undelete `item` based on `val` then return `item.deleted`.
         """
@@ -73,7 +72,6 @@ class PurgableManagerMixin( DeletableManagerMixin ):
     purging is often removal of some additional, non-db resource (e.g. a dataset's
     file).
     """
-
     def purge( self, item, flush=True, **kwargs ):
         """
         Mark as purged and return.
@@ -96,7 +94,7 @@ class PurgableDeserializerMixin( DeletableDeserializerMixin ):
         DeletableDeserializerMixin.add_deserializers( self )
         self.deserializers[ 'purged' ] = self.deserialize_purged
 
-    def deserialize_purged( self, trans, item, key, val ):
+    def deserialize_purged( self, item, key, val, **context ):
         """
         If `val` is True, purge `item` and return `item.purged`.
         """
diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py
index 51b64cf4f19..7aee71aba9d 100644
--- a/lib/galaxy/managers/hdas.py
+++ b/lib/galaxy/managers/hdas.py
@@ -274,9 +274,9 @@ class HDASerializer( # datasets._UnflattenedMetadataDatasetAssociationSerializer
         annotatable.AnnotatableSerializerMixin.add_serializers( self )
 
         self.serializers.update({
-            'model_class'   : lambda *a: 'HistoryDatasetAssociation',
-            'history_content_type': lambda *a: 'dataset',
-            'hda_ldda'      : lambda *a: 'hda',
+            'model_class'   : lambda *a, **c: 'HistoryDatasetAssociation',
+            'history_content_type': lambda *a, **c: 'dataset',
+            'hda_ldda'      : lambda *a, **c: 'hda',
             'type_id'       : self.serialize_type_id,
 
             'history_id'    : self.serialize_id,
@@ -287,7 +287,7 @@ class HDASerializer( # datasets._UnflattenedMetadataDatasetAssociationSerializer
             'file_ext'      : self._remap_from( 'extension' ),
             'file_path'     : self._remap_from( 'file_name' ),
 
-            'resubmitted'   : lambda t, i, k: i._state == t.app.model.Dataset.states.RESUBMITTED,
+            'resubmitted'   : lambda i, k, **c: i._state == model.Dataset.states.RESUBMITTED,
 
             'display_apps'  : self.serialize_display_apps,
             'display_types' : self.serialize_old_display_applications,
@@ -297,24 +297,25 @@ class HDASerializer( # datasets._UnflattenedMetadataDatasetAssociationSerializer
             # TODO: this intermittently causes a routes.GenerationException - temp use the legacy route to prevent this
             #   see also: https://trello.com/c/5d6j4X5y
             #   see also: https://sentry.galaxyproject.org/galaxy/galaxy-main/group/20769/events/9352883/
-            'url'           : lambda t, i, k: self.url_for( 'history_content',
-                history_id=t.security.encode_id( i.history_id ), id=t.security.encode_id( i.id ) ),
+            'url'           : lambda i, k, **c: self.url_for( 'history_content',
+                history_id=self.app.security.encode_id( i.history_id ),
+                id=self.app.security.encode_id( i.id ) ),
             'urls'          : self.serialize_urls,
 
             # TODO: backwards compat: need to go away
-            'download_url'  : lambda t, i, k: self.url_for( 'history_contents_display',
-                history_id=t.security.encode_id( i.history.id ),
-                history_content_id=t.security.encode_id( i.id ) ),
+            'download_url'  : lambda i, k, **c: self.url_for( 'history_contents_display',
+                history_id=self.app.security.encode_id( i.history.id ),
+                history_content_id=self.app.security.encode_id( i.id ) ),
             'parent_id'     : self.serialize_id,
-            'accessible'    : lambda *a: True,
-            'api_type'      : lambda *a: 'file',
-            'type'          : lambda *a: 'file'
+            'accessible'    : lambda *a, **c: True,
+            'api_type'      : lambda *a, **c: 'file',
+            'type'          : lambda *a, **c: 'file'
         })
 
-    def serialize_type_id( self, trans, hda, key ):
-        return 'dataset-' + self.serializers[ 'id' ]( trans, hda, 'id' )
+    def serialize_type_id( self, hda, key, **context ):
+        return 'dataset-' + self.serializers[ 'id' ]( hda, 'id' )
 
-    def serialize_display_apps( self, trans, hda, key ):
+    def serialize_display_apps( self, hda, key, trans=None, **context ):
         """
         Return dictionary containing new-style display app urls.
         """
@@ -333,7 +334,7 @@ class HDASerializer( # datasets._UnflattenedMetadataDatasetAssociationSerializer
 
         return display_apps
 
-    def serialize_old_display_applications( self, trans, hda, key ):
+    def serialize_old_display_applications( self, hda, key, trans=None, **context ):
         """
         Return dictionary containing old-style display app urls.
         """
@@ -360,7 +361,7 @@ class HDASerializer( # datasets._UnflattenedMetadataDatasetAssociationSerializer
 
         return display_apps
 
-    def serialize_visualization_links( self, trans, hda, key ):
+    def serialize_visualization_links( self, hda, key, trans=None, **context ):
         """
         Return a list of dictionaries with links to visualization pages
         for those visualizations that apply to this hda.
@@ -370,7 +371,7 @@ class HDASerializer( # datasets._UnflattenedMetadataDatasetAssociationSerializer
             return hda.get_visualizations()
         return self.app.visualizations_registry.get_visualizations( trans, hda )
 
-    def serialize_urls( self, trans, hda, key ):
+    def serialize_urls( self, hda, key, **context ):
         """
         Return web controller urls useful for this HDA.
         """
@@ -413,8 +414,8 @@ class HDADeserializer( datasets.DatasetAssociationDeserializer,
         self.deserializers.update({
             'visible'       : self.deserialize_bool,
             # remapped
-            'genome_build'  : lambda t, i, k, v: self.deserialize_genome_build( t, i, 'dbkey', v ),
-            'misc_info'     : lambda t, i, k, v: self.deserialize_basestring( t, i, 'info', v ),
+            'genome_build'  : lambda i, k, v, **c: self.deserialize_genome_build( i, 'dbkey', v ),
+            'misc_info'     : lambda i, k, v, **c: self.deserialize_basestring( i, 'info', v ),
         })
         self.deserializable_keyset.update( self.deserializers.keys() )
 
diff --git a/lib/galaxy/managers/histories.py b/lib/galaxy/managers/histories.py
index e5b21a96ea6..d365911a38e 100644
--- a/lib/galaxy/managers/histories.py
+++ b/lib/galaxy/managers/histories.py
@@ -129,12 +129,14 @@ class HistoryManager( sharable.SharableModelManager, deletable.PurgableManagerMi
         history_dictionary = {}
         contents_dictionaries = []
         try:
-            history_dictionary = history_serializer.serialize_to_view( trans, history, view='detailed' )
+            history_dictionary = history_serializer.serialize_to_view( history, view='detailed',
+                user=trans.user, trans=trans )
 
             for content in history.contents_iter( types=[ 'dataset', 'dataset_collection' ] ):
                 contents_dict = {}
                 if isinstance( content, model.HistoryDatasetAssociation ):
-                    contents_dict = hda_serializer.serialize_to_view( trans, content, view='detailed' )
+                    contents_dict = hda_serializer.serialize_to_view( content, view='detailed',
+                        user=trans.user, trans=trans )
                 elif isinstance( content, model.HistoryDatasetCollectionAssociation ):
                     try:
                         service = self.app.dataset_collections_service
@@ -212,28 +214,28 @@ class HistorySerializer( sharable.SharableModelSerializer, deletable.PurgableSer
         deletable.PurgableSerializerMixin.add_serializers( self )
 
         self.serializers.update({
-            'model_class'   : lambda *a: 'History',
+            'model_class'   : lambda *a, **c: 'History',
             'id'            : self.serialize_id,
             'create_time'   : self.serialize_date,
             'update_time'   : self.serialize_date,
-            'size'          : lambda t, i, k: int( i.get_disk_size() ),
-            'nice_size'     : lambda t, i, k: i.get_disk_size( nice_size=True ),
+            'size'          : lambda i, k, **c: int( i.get_disk_size() ),
+            'nice_size'     : lambda i, k, **c: i.get_disk_size( nice_size=True ),
             'state'         : self.serialize_history_state,
 
-            'url'           : lambda t, i, k: self.url_for( 'history', id=t.security.encode_id( i.id ) ),
-            'contents_url'  : lambda t, i, k: self.url_for( 'history_contents',
-                history_id=t.security.encode_id( i.id ) ),
+            'url'           : lambda i, k, **c: self.url_for( 'history', id=self.app.security.encode_id( i.id ) ),
+            'contents_url'  : lambda i, k, **c: self.url_for( 'history_contents',
+                history_id=self.app.security.encode_id( i.id ) ),
 
-            'empty'         : lambda t, i, k: ( len( i.datasets ) + len( i.dataset_collections ) ) <= 0,
-            'count'         : lambda trans, item, key: len( item.datasets ),
-            'hdas'          : lambda t, i, k: [ t.security.encode_id( hda.id ) for hda in i.datasets ],
+            'empty'         : lambda i, k, **c: ( len( i.datasets ) + len( i.dataset_collections ) ) <= 0,
+            'count'         : lambda i, k, **c: len( i.datasets ),
+            'hdas'          : lambda i, k, **c: [ self.app.security.encode_id( hda.id ) for hda in i.datasets ],
             'state_details' : self.serialize_state_counts,
             'state_ids'     : self.serialize_state_ids,
             'contents'      : self.serialize_contents
         })
 
     # remove this
-    def serialize_state_ids( self, trans, history, key ):
+    def serialize_state_ids( self, history, key, **context ):
         """
         Return a dictionary keyed to possible dataset states and valued with lists
         containing the ids of each HDA in that state.
@@ -250,7 +252,7 @@ class HistorySerializer( sharable.SharableModelSerializer, deletable.PurgableSer
         return state_ids
 
     # remove this
-    def serialize_state_counts( self, trans, history, key, exclude_deleted=True, exclude_hidden=False ):
+    def serialize_state_counts( self, history, key, exclude_deleted=True, exclude_hidden=False, **context ):
         """
         Return a dictionary keyed to possible dataset states and valued with the number
         of datasets in this history that have those states.
@@ -270,7 +272,7 @@ class HistorySerializer( sharable.SharableModelSerializer, deletable.PurgableSer
         return state_counts
 
     # TODO: remove this (is state used/useful?)
-    def serialize_history_state( self, trans, history, key ):
+    def serialize_history_state( self, history, key, **context ):
         """
         Returns the history state based on the states of the HDAs it contains.
         """
@@ -279,7 +281,7 @@ class HistorySerializer( sharable.SharableModelSerializer, deletable.PurgableSer
         state = states.ERROR
         # TODO: history_state and state_counts are classically calc'd at the same time
         #   so this is rel. ineff. - if we keep this...
-        hda_state_counts = self.serialize_state_counts( trans, history, 'counts', exclude_deleted=False )
+        hda_state_counts = self.serialize_state_counts( history, 'counts', exclude_deleted=False, **context )
         num_hdas = sum( hda_state_counts.values() )
         if num_hdas == 0:
             state = states.NEW
@@ -300,17 +302,18 @@ class HistorySerializer( sharable.SharableModelSerializer, deletable.PurgableSer
 
         return state
 
-    def serialize_contents( self, trans, history, *args ):
+    def serialize_contents( self, history, *args, **context ):
         contents_dictionaries = []
         for content in history.contents_iter( types=[ 'dataset', 'dataset_collection' ] ):
             contents_dict = {}
             if isinstance( content, model.HistoryDatasetAssociation ):
-                contents_dict = self.hda_serializer.serialize_to_view( trans, content, view='detailed' )
-            elif isinstance( content, model.HistoryDatasetCollectionAssociation ):
-                contents_dict = self._serialize_collection( trans, content )
+                contents_dict = self.hda_serializer.serialize_to_view( content, view='detailed', **context )
+            # elif isinstance( content, model.HistoryDatasetCollectionAssociation ):
+            #     contents_dict = self._serialize_collection( trans, content )
             contents_dictionaries.append( contents_dict )
         return contents_dictionaries
 
+    # TODO: remove trans
     def _serialize_collection( self, trans, collection ):
         service = self.app.dataset_collections_service
         dataset_collection_instance = service.get_dataset_collection_instance(
diff --git a/lib/galaxy/managers/ratable.py b/lib/galaxy/managers/ratable.py
index b6682a58222..21e6e0f3884 100644
--- a/lib/galaxy/managers/ratable.py
+++ b/lib/galaxy/managers/ratable.py
@@ -26,12 +26,12 @@ class RatableSerializerMixin( object ):
         self.serializers[ 'user_rating' ] = self.serialize_user_rating
         self.serializers[ 'community_rating' ] = self.serialize_community_rating
 
-    def serialize_user_rating( self, trans, item, key ):
+    def serialize_user_rating( self, item, key, user=None, **context ):
         """
         """
         pass
 
-    def serialize_community_rating( self, trans, item, key ):
+    def serialize_community_rating( self, item, key, **context ):
         """
         """
         pass
diff --git a/lib/galaxy/managers/sharable.py b/lib/galaxy/managers/sharable.py
index 19c1b3033e4..56af2106aa0 100644
--- a/lib/galaxy/managers/sharable.py
+++ b/lib/galaxy/managers/sharable.py
@@ -321,13 +321,13 @@ class SharableModelSerializer( base.ModelSerializer,
             'importable', 'published', 'slug'
         ])
 
-    def serialize_username_and_slug( self, trans, item, key ):
+    def serialize_username_and_slug( self, item, key, **context ):
         if not ( item.user and item.slug and self.SINGLE_CHAR_ABBR ):
             return None
 #TODO: self.url_for
         return ( '/' ).join(( 'u', item.user.username, self.SINGLE_CHAR_ABBR, item.slug ) )
 
-    #def published_url( self, trans, item, key ):
+    #def published_url( self, item, key, **context ):
     #    """
     #    """
     #    url = url_for(controller='history', action="display_by_username_and_slug",
@@ -354,7 +354,7 @@ class SharableModelDeserializer( base.ModelDeserializer,
             'importable'    : self.deserialize_importable,
         })
 
-    def deserialize_published( self, trans, item, key, val ):
+    def deserialize_published( self, item, key, val, **context ):
         """
         """
         val = self.validate.bool( key, val )
@@ -367,7 +367,7 @@ class SharableModelDeserializer( base.ModelDeserializer,
             self.manager.unpublish( item, flush=False )
         return item.published
 
-    def deserialize_importable( self, trans, item, key, val ):
+    def deserialize_importable( self, item, key, val, **context ):
         """
         """
         val = self.validate.bool( key, val )
@@ -380,7 +380,7 @@ class SharableModelDeserializer( base.ModelDeserializer,
             self.manager.make_non_importable( item, flush=False )
         return item.published
 
-    #def deserialize_slug( self, trans, item, val ):
+    #def deserialize_slug( self, item, val, **context ):
     #    """
     #    """
     #    #TODO: call manager.set_slug
diff --git a/lib/galaxy/managers/taggable.py b/lib/galaxy/managers/taggable.py
index cdea2bac55e..7ecfe971304 100644
--- a/lib/galaxy/managers/taggable.py
+++ b/lib/galaxy/managers/taggable.py
@@ -15,7 +15,7 @@ class TaggableManagerMixin( object ):
 
     #TODO: most of this can be done by delegating to the TagManager?
 
-    #def by_user( self, trans, user, **kwargs ):
+    #def by_user( self, user, **kwargs ):
     #    pass
 
 
@@ -24,7 +24,7 @@ class TaggableSerializerMixin( object ):
     def add_serializers( self ):
         self.serializers[ 'tags' ] = self.serialize_tags
 
-    def serialize_tags( self, trans, item, key ):
+    def serialize_tags( self, item, key, **context ):
         """
         Return tags as a list of strings.
         """
@@ -45,7 +45,7 @@ class TaggableDeserializerMixin( object ):
     def add_deserializers( self ):
         self.deserializers[ 'tags' ] = self.deserialize_tags
 
-    def deserialize_tags( self, trans, item, key, val ):
+    def deserialize_tags( self, item, key, val, user=None, **context ):
         """
         Make sure `val` is a valid list of tag strings and assign them.
 
@@ -53,8 +53,6 @@ class TaggableDeserializerMixin( object ):
         """
         new_tags_list = self.validate.basestring_list( key, val )
         #TODO: have to assume trans.user here...
-        #TODO: trans
-        user = trans.user
         #TODO: duped from tags manager - de-dupe when moved to taggable mixin
         tag_handler = self.app.tag_handler
         tag_handler.delete_item_tags( user, item )
diff --git a/lib/galaxy/managers/users.py b/lib/galaxy/managers/users.py
index 360191c7e50..8d68f8d3a98 100644
--- a/lib/galaxy/managers/users.py
+++ b/lib/galaxy/managers/users.py
@@ -281,36 +281,38 @@ class UserSerializer( base.ModelSerializer, deletable.PurgableSerializerMixin ):
             'id'            : self.serialize_id,
             'create_time'   : self.serialize_date,
             'update_time'   : self.serialize_date,
-            'is_admin'      : lambda t, i, k: self.user_manager.is_admin( i ),
+            'is_admin'      : lambda i, k, **c: self.user_manager.is_admin( i ),
 
-            'total_disk_usage' : lambda t, i, k: float( i.total_disk_usage ),
-            'quota_percent' : lambda t, i, k: self.user_manager.quota( i ),
+            'total_disk_usage' : lambda i, k, **c: float( i.total_disk_usage ),
+            'quota_percent' : lambda i, k, **c: self.user_manager.quota( i ),
 
-            'tags_used'     : lambda t, i, k: self.user_manager.tags_used( i ),
+            'tags_used'     : lambda i, k, **c: self.user_manager.tags_used( i ),
             #TODO: 'has_requests' is more apt
-            'requests'      : lambda t, i, k: self.user_manager.has_requests( i, t )
+            'requests'      : lambda i, k, trans=None, **c: self.user_manager.has_requests( i, trans )
         })
 
 
 class CurrentUserSerializer( UserSerializer ):
 
-    def serialize( self, trans, user, keys ):
+    def serialize( self, user, keys, **kwargs ):
         """
         Override to return at least some usage info if user is anonymous.
         """
+# hmmm.
+        kwargs[ 'current_user' ] = user
         if self.user_manager.is_anonymous( user ):
-            return self.serialize_current_anonymous_user( trans, user, keys )
-        return super( UserSerializer, self ).serialize( trans, user, keys )
+            return self.serialize_current_anonymous_user( user, keys, **kwargs )
+        return super( UserSerializer, self ).serialize( user, keys, **kwargs )
 
-    def serialize_current_anonymous_user( self, trans, user, keys ):
+    def serialize_current_anonymous_user( self, user, keys, trans=None, **kwargs ):
         # use the current history if any to get usage stats for trans' anonymous user
         #TODO: might be better as sep. Serializer class
         history = trans.history
         if not history:
             raise exceptions.AuthenticationRequired( 'No history for anonymous user usage stats' );
 
-        usage = trans.app.quota_agent.get_usage( trans, history=trans.history )
-        percent = trans.app.quota_agent.get_percent( trans=trans, usage=usage )
+        usage = self.app.quota_agent.get_usage( trans, history=trans.history )
+        percent = self.app.quota_agent.get_percent( trans=trans, usage=usage )
 
         # a very small subset of keys available
         values = {
diff --git a/lib/galaxy/webapps/galaxy/api/configuration.py b/lib/galaxy/webapps/galaxy/api/configuration.py
index 240b8037778..2f2ccd74037 100644
--- a/lib/galaxy/webapps/galaxy/api/configuration.py
+++ b/lib/galaxy/webapps/galaxy/api/configuration.py
@@ -9,6 +9,7 @@ from galaxy.web import require_admin
 from galaxy.web.base.controller import BaseAPIController
 
 from galaxy.managers import base
+from galaxy.managers import configuration
 
 import logging
 log = logging.getLogger( __name__ )
@@ -18,8 +19,8 @@ class ConfigurationController( BaseAPIController ):
 
     def __init__( self, app ):
         super( ConfigurationController, self ).__init__( app )
-        self.config_serializer = ConfigSerializer( app )
-        self.admin_config_serializer = AdminConfigSerializer( app )
+        self.config_serializer = configuration.ConfigSerializer( app )
+        self.admin_config_serializer = configuration.AdminConfigSerializer( app )
 
     @expose_api_anonymous_and_sessionless
     def index( self, trans, **kwd ):
@@ -57,8 +58,7 @@ class ConfigurationController( BaseAPIController ):
             #TODO: this should probably just be under a different route: 'admin/configuration'
             serializer = self.admin_config_serializer
 
-        serialized = serializer.serialize_to_view( trans, self.app.config,
-                                                   view=view, keys=keys, default_view=default_view )
+        serialized = serializer.serialize_to_view( self.app.config, view=view, keys=keys, default_view=default_view )
         return serialized
 
     @expose_api
@@ -85,77 +85,6 @@ class ConfigurationController( BaseAPIController ):
         return rval
 
 
-#TODO: for lack of a manager file for the config. May well be better in config.py? Circ imports?
-class ConfigSerializer( base.ModelSerializer ):
-
-    def __init__( self, app ):
-        super( ConfigSerializer, self ).__init__( app )
-
-        self.default_view = 'all'
-        self.add_view( 'all', self.serializers.keys() )
-
-    def default_serializer( self, trans, config, key ):
-        return getattr( config, key, None )
-
-    def add_serializers( self ):
-        def _defaults_to( default ):
-            return lambda t, i, k: getattr( i, k, default )
-
-        self.serializers = {
-            #TODO: this is available from user data, remove
-            'is_admin_user'             : lambda *a: False,
-
-            'brand'                     : _defaults_to( '' ),
-            #TODO: this doesn't seem right
-            'logo_url'                  : lambda t, i, k: self.url_for( i.get( k, '/' ) ),
-            'terms_url'                 : _defaults_to( '' ),
-
-            #TODO: don't hardcode here - hardcode defaults once in config.py
-            'wiki_url'                  : _defaults_to( "http://galaxyproject.org/" ),
-            'search_url'                : _defaults_to( "http://galaxyproject.org/search/usegalaxy/" ),
-            'mailing_lists'             : _defaults_to( "http://wiki.galaxyproject.org/MailingLists" ),
-            'screencasts_url'           : _defaults_to( "http://vimeo.com/galaxyproject" ),
-            'citation_url'              : _defaults_to( "http://wiki.galaxyproject.org/CitingGalaxy" ),
-            'support_url'               : _defaults_to( "http://wiki.galaxyproject.org/Support" ),
-            'lims_doc_url'              : _defaults_to( "http://main.g2.bx.psu.edu/u/rkchak/p/sts" ),
-            'biostar_url'               : _defaults_to( '' ),
-            'biostar_url_redirect'      : lambda *a: self.url_for( controller='biostar', action='biostar_redirect',
-                                                                   qualified=True ),
-
-            'use_remote_user'           : _defaults_to( None ),
-            'remote_user_logout_href'   : _defaults_to( '' ),
-            'enable_cloud_launch'       : _defaults_to( False ),
-            'datatypes_disable_auto'    : _defaults_to( False ),
-            'allow_user_dataset_purge'  : _defaults_to( False ),
-            'enable_unique_workflow_defaults' : _defaults_to( False ),
-
-            'nginx_upload_path'         : _defaults_to( self.url_for( controller='api', action='tools' ) ),
-            'ftp_upload_dir'            : _defaults_to( None ),
-            'ftp_upload_site'           : _defaults_to( None ),
-            'version_major'             : _defaults_to( None ),
-        }
-
-
-class AdminConfigSerializer( ConfigSerializer ):
-    # config attributes viewable by admin users
-
-    def add_serializers( self ):
-        super( AdminConfigSerializer, self ).add_serializers()
-        def _defaults_to( default ):
-            return lambda t, i, k: getattr( i, k, default )
-
-        self.serializers.update({
-            #TODO: this is available from user data, remove
-            'is_admin_user'             : lambda *a: True,
-
-            'library_import_dir'        : _defaults_to( None ),
-            'user_library_import_dir'   : _defaults_to( None ),
-            'allow_library_path_paste'  : _defaults_to( False ),
-            'allow_user_creation'       : _defaults_to( False ),
-            'allow_user_deletion'       : _defaults_to( False ),
-        })
-
-
 def _tool_conf_to_dict(conf):
     return dict(
         config_filename=conf['config_filename'],
diff --git a/lib/galaxy/webapps/galaxy/api/datasets.py b/lib/galaxy/webapps/galaxy/api/datasets.py
index dabfd8d384e..0f24ba1e2ce 100644
--- a/lib/galaxy/webapps/galaxy/api/datasets.py
+++ b/lib/galaxy/webapps/galaxy/api/datasets.py
@@ -66,7 +66,8 @@ class DatasetsController( BaseAPIController, UsesVisualizationMixin ):
             else:
                 # Default: return dataset as dict.
                 if hda_ldda == 'hda':
-                    return self.hda_serializer.serialize_to_view( trans, dataset, view=kwd.get( 'view', 'detailed' ) )
+                    return self.hda_serializer.serialize_to_view( dataset,
+                        view=kwd.get( 'view', 'detailed' ), user=trans.user, trans=trans )
                 else:
                     rval = dataset.to_dict()
 
diff --git a/lib/galaxy/webapps/galaxy/api/histories.py b/lib/galaxy/webapps/galaxy/api/histories.py
index c1ccd60e95e..f1753be7982 100644
--- a/lib/galaxy/webapps/galaxy/api/histories.py
+++ b/lib/galaxy/webapps/galaxy/api/histories.py
@@ -103,8 +103,11 @@ class HistoriesController( BaseAPIController, ExportsHistoryMixin, ImportsHistor
         current_user = self.user_manager.current_user( trans )
         if self.user_manager.is_anonymous( current_user ):
             current_history = self.history_manager.get_current( trans )
+            if not current_history:
+                return []
             #note: ignores filters, limit, offset
-            return [ self.history_serializer.serialize_to_view( trans, current_history, **serialization_params ) ]
+            return [ self.history_serializer.serialize_to_view( current_history,
+                     user=current_user, trans=trans, **serialization_params ) ]
 
         filters = []
         # support the old default of not-returning/filtering-out deleted histories
@@ -120,7 +123,8 @@ class HistoriesController( BaseAPIController, ExportsHistoryMixin, ImportsHistor
 
         rval = []
         for history in histories:
-            history_dict = self.history_serializer.serialize_to_view( trans, history, **serialization_params )
+            history_dict = self.history_serializer.serialize_to_view( history,
+                user=trans.user, trans=trans, **serialization_params )
             rval.append( history_dict )
         return rval
 
@@ -179,8 +183,8 @@ class HistoriesController( BaseAPIController, ExportsHistoryMixin, ImportsHistor
         else:
             history = self.history_manager.get_accessible( self.decode_id( history_id ), trans.user, current_history=trans.history )
 
-        return self.history_serializer.serialize_to_view( trans, history,
-            **self._parse_serialization_params( kwd, 'detailed' ) )
+        return self.history_serializer.serialize_to_view( history,
+            user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) )
 
     @expose_api_anonymous
     def citations( self, trans, history_id, **kwd ):
@@ -245,8 +249,8 @@ class HistoriesController( BaseAPIController, ExportsHistoryMixin, ImportsHistor
         trans.sa_session.add( new_history )
         trans.sa_session.flush()
 
-        return self.history_serializer.serialize_to_view( trans, new_history,
-            **self._parse_serialization_params( kwd, 'detailed' ) )
+        return self.history_serializer.serialize_to_view( new_history,
+            user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) )
 
     @expose_api
     def delete( self, trans, id, **kwd ):
@@ -284,8 +288,8 @@ class HistoriesController( BaseAPIController, ExportsHistoryMixin, ImportsHistor
         if purge:
             self.history_manager.purge( history )
 
-        return self.history_serializer.serialize_to_view( trans, history,
-            **self._parse_serialization_params( kwd, 'detailed' ) )
+        return self.history_serializer.serialize_to_view( history,
+            user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) )
 
     @expose_api
     def undelete( self, trans, id, **kwd ):
@@ -307,8 +311,8 @@ class HistoriesController( BaseAPIController, ExportsHistoryMixin, ImportsHistor
         history = self.history_manager.get_owned( self.decode_id( history_id ), trans.user, current_history=trans.history )
         self.history_manager.undelete( history )
 
-        return self.history_serializer.serialize_to_view( trans, history,
-            **self._parse_serialization_params( kwd, 'detailed' ) )
+        return self.history_serializer.serialize_to_view( history,
+            user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) )
 
     @expose_api
     def update( self, trans, id, payload, **kwd ):
@@ -335,9 +339,9 @@ class HistoriesController( BaseAPIController, ExportsHistoryMixin, ImportsHistor
         #TODO: PUT /api/histories/{encoded_history_id} payload = { rating: rating } (w/ no security checks)
         history = self.history_manager.get_owned( self.decode_id( id ), trans.user, current_history=trans.history )
 
-        self.history_deserializer.deserialize( trans, history, payload )
-        return self.history_serializer.serialize_to_view( trans, history,
-            **self._parse_serialization_params( kwd, 'detailed' ) )
+        self.history_deserializer.deserialize( history, payload, user=trans.user, trans=trans )
+        return self.history_serializer.serialize_to_view( history,
+            user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) )
 
     @expose_api
     def archive_export( self, trans, id, **kwds ):
diff --git a/lib/galaxy/webapps/galaxy/api/history_contents.py b/lib/galaxy/webapps/galaxy/api/history_contents.py
index eecf2533c6e..95817c72131 100644
--- a/lib/galaxy/webapps/galaxy/api/history_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/history_contents.py
@@ -102,7 +102,7 @@ class HistoryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
 
             if isinstance( content, trans.app.model.HistoryDatasetAssociation ):
                 view = 'detailed' if detailed else 'summary'
-                hda_dict = self.hda_serializer.serialize_to_view( trans, content, view=view )
+                hda_dict = self.hda_serializer.serialize_to_view( content, view=view, user=trans.user, trans=trans )
                 rval.append( hda_dict )
 
             elif isinstance( content, trans.app.model.HistoryDatasetCollectionAssociation ):
@@ -144,8 +144,8 @@ class HistoryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
 
     def __show_dataset( self, trans, id, **kwd ):
         hda = self.hda_manager.get_accessible( self.decode_id( id ), trans.user )
-        return self.hda_serializer.serialize_to_view( trans, hda,
-            **self._parse_serialization_params( kwd, 'detailed' ) )
+        return self.hda_serializer.serialize_to_view( hda,
+            user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) )
 
     def __show_dataset_collection( self, trans, id, history_id, **kwd ):
         try:
@@ -257,8 +257,8 @@ class HistoryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
         trans.sa_session.flush()
         if not hda:
             return None
-        return self.hda_serializer.serialize_to_view( trans, hda,
-            **self._parse_serialization_params( kwd, 'detailed' ) )
+        return self.hda_serializer.serialize_to_view( hda,
+            user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) )
 
     def __create_dataset_collection( self, trans, history, payload, **kwd ):
         source = kwd.get("source", "new_collection")
@@ -344,12 +344,12 @@ class HistoryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
         # make the actual changes
         #TODO: is this if still needed?
         if hda and isinstance( hda, trans.model.HistoryDatasetAssociation ):
-            self.hda_deserializer.deserialize( trans, hda, payload )
+            self.hda_deserializer.deserialize( hda, payload, user=trans.user, trans=trans )
             #TODO: this should be an effect of deleting the hda
             if payload.get( 'deleted', False ):
                 self.hda_manager.stop_creating_job( hda )
-            return self.hda_serializer.serialize_to_view( trans, hda,
-                **self._parse_serialization_params( kwd, 'detailed' ) )
+            return self.hda_serializer.serialize_to_view( hda,
+                user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) )
 
         return {}
 
@@ -407,8 +407,8 @@ class HistoryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
             self.hda_manager.purge( hda )
         else:
             self.hda_manager.delete( hda )
-        return self.hda_serializer.serialize_to_view( trans, hda,
-            **self._parse_serialization_params( kwd, 'detailed' ) )
+        return self.hda_serializer.serialize_to_view( hda,
+            user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) )
 
     def __handle_unknown_contents_type( self, trans, contents_type ):
         raise exceptions.UnknownContentsType('Unknown contents type: %s' % type)
diff --git a/lib/galaxy/webapps/galaxy/controllers/history.py b/lib/galaxy/webapps/galaxy/controllers/history.py
index 7b5b807ac39..617bb8ede97 100644
--- a/lib/galaxy/webapps/galaxy/controllers/history.py
+++ b/lib/galaxy/webapps/galaxy/controllers/history.py
@@ -642,7 +642,8 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
 
         history_dictionaries = []
         for history in self.history_manager.by_user( trans.user, filters=deleted_filter ):
-            history_dictionary = self.history_serializer.serialize_to_view( trans, history, view='detailed' )
+            history_dictionary = self.history_serializer.serialize_to_view( history,
+                view='detailed', user=trans.user, trans=trans )
             history_dictionaries.append( history_dictionary )
 
         return trans.fill_template_mako( "history/view_multiple.mako",
@@ -1501,7 +1502,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
     def history_data( self, trans, history ):
         """
         """
-        return self.history_serializer.serialize_to_view( trans, history, view='detailed' )
+        return self.history_serializer.serialize_to_view( history, view='detailed', user=trans.user, trans=trans )
 
     #TODO: combine these next two - poss. with a redirect flag
     #@web.require_login( "switch to a history" )
@@ -1512,7 +1513,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
         try:
             history = self.history_manager.get_owned( self.decode_id( id ), trans.user, current_history=trans.history )
             trans.set_history( history )
-            return self.history_serializer.serialize_to_view( trans, history, view='detailed' )
+            return self.history_serializer.serialize_to_view( history, view='detailed', user=trans.user, trans=trans )
         except exceptions.MessageException, msg_exc:
             trans.response.status = msg_exc.err_code.code
             return { 'err_msg': msg_exc.err_msg, 'err_code': msg_exc.err_code.code }
@@ -1522,13 +1523,13 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
         """
         """
         history = trans.get_history( create=True )
-        return self.history_serializer.serialize_to_view( trans, history, view='detailed' )
+        return self.history_serializer.serialize_to_view( history, view='detailed', user=trans.user, trans=trans )
 
     @web.json
     def create_new_current( self, trans, name=None ):
         """
         """
         new_history = trans.new_history( name )
-        return self.history_serializer.serialize_to_view( trans, new_history, view='detailed' )
+        return self.history_serializer.serialize_to_view( new_history, view='detailed', user=trans.user, trans=trans )
 
     #TODO: /history/current to do all of the above: if ajax, return json; if post, read id and set to current
diff --git a/test/unit/managers/test_DatasetManager.py b/test/unit/managers/test_DatasetManager.py
index 2bf50a1fcd4..e902bd14510 100644
--- a/test/unit/managers/test_DatasetManager.py
+++ b/test/unit/managers/test_DatasetManager.py
@@ -197,11 +197,11 @@ class DatasetSerializerTestCase( BaseTestCase ):
         dataset = self.dataset_manager.create()
 
         self.log( 'should have a summary view' )
-        summary_view = self.dataset_serializer.serialize_to_view( self.trans, dataset, view='summary' )
+        summary_view = self.dataset_serializer.serialize_to_view( dataset, view='summary' )
         self.assertKeys( summary_view, self.dataset_serializer.views[ 'summary' ] )
 
         self.log( 'should have the summary view as default view' )
-        default_view = self.dataset_serializer.serialize_to_view( self.trans, dataset, default_view='summary' )
+        default_view = self.dataset_serializer.serialize_to_view( dataset, default_view='summary' )
         self.assertKeys( summary_view, self.dataset_serializer.views[ 'summary' ] )
 
         self.log( 'should have a serializer for all serializable keys' )
@@ -217,13 +217,13 @@ class DatasetSerializerTestCase( BaseTestCase ):
         dataset = self.dataset_manager.create()
 
         self.log( 'should be able to use keys with views' )
-        serialized = self.dataset_serializer.serialize_to_view( self.trans, dataset,
+        serialized = self.dataset_serializer.serialize_to_view( dataset,
             view='summary', keys=[ 'permissions' ] )
         self.assertKeys( serialized,
             self.dataset_serializer.views[ 'summary' ] + [ 'permissions' ] )
 
         self.log( 'should be able to use keys on their own' )
-        serialized = self.dataset_serializer.serialize_to_view( self.trans, dataset,
+        serialized = self.dataset_serializer.serialize_to_view( dataset,
             keys=[ 'purgable', 'file_size' ] )
         self.assertKeys( serialized, [ 'purgable', 'file_size' ] )
 
@@ -235,7 +235,7 @@ class DatasetSerializerTestCase( BaseTestCase ):
         user2 = self.user_manager.create( **user2_data )
         dataset = self.dataset_manager.create()
         all_keys = list( self.dataset_serializer.serializable_keyset )
-        serialized = self.dataset_serializer.serialize( self.trans, dataset, all_keys )
+        serialized = self.dataset_serializer.serialize( dataset, all_keys )
 
         self.log( 'everything serialized should be of the proper type' )
         self.assertEncodedId( serialized[ 'id' ] )
@@ -270,13 +270,13 @@ class DatasetDeserializerTestCase( BaseTestCase ):
         self.log( 'should raise when deserializing deleted from non-bool' )
         self.assertFalse( dataset.deleted )
         self.assertRaises( exceptions.RequestParameterInvalidException,
-            self.dataset_deserializer.deserialize, self.trans, dataset, data={ 'deleted': None } )
+            self.dataset_deserializer.deserialize, dataset, data={ 'deleted': None } )
         self.assertFalse( dataset.deleted )
         self.log( 'should be able to deserialize deleted from True' )
-        self.dataset_deserializer.deserialize( self.trans, dataset, data={ 'deleted': True } )
+        self.dataset_deserializer.deserialize( dataset, data={ 'deleted': True } )
         self.assertTrue( dataset.deleted )
         self.log( 'should be able to reverse by deserializing deleted from False' )
-        self.dataset_deserializer.deserialize( self.trans, dataset, data={ 'deleted': False } )
+        self.dataset_deserializer.deserialize( dataset, data={ 'deleted': False } )
         self.assertFalse( dataset.deleted )
 
     def test_deserialize_purge( self ):
@@ -284,14 +284,14 @@ class DatasetDeserializerTestCase( BaseTestCase ):
 
         self.log( 'should raise when deserializing purged from non-bool' )
         self.assertRaises( exceptions.RequestParameterInvalidException,
-            self.dataset_deserializer.deserialize, self.trans, dataset, data={ 'purged': None } )
+            self.dataset_deserializer.deserialize, dataset, data={ 'purged': None } )
         self.assertFalse( dataset.purged )
         self.log( 'should be able to deserialize purged from True' )
-        self.dataset_deserializer.deserialize( self.trans, dataset, data={ 'purged': True } )
+        self.dataset_deserializer.deserialize( dataset, data={ 'purged': True } )
         self.assertTrue( dataset.purged )
         # TODO: should this raise an error?
         self.log( 'should NOT be able to deserialize purged from False (will remain True)' )
-        self.dataset_deserializer.deserialize( self.trans, dataset, data={ 'purged': False } )
+        self.dataset_deserializer.deserialize( dataset, data={ 'purged': False } )
         self.assertTrue( dataset.purged )
 
     # def test_deserialize_permissions( self ):
diff --git a/test/unit/managers/test_HDAManager.py b/test/unit/managers/test_HDAManager.py
index 6ad03ac27a1..6e7d51c17da 100644
--- a/test/unit/managers/test_HDAManager.py
+++ b/test/unit/managers/test_HDAManager.py
@@ -324,23 +324,23 @@ class HDASerializerTestCase( HDATestCase ):
         hda = self._create_vanilla_hda()
 
         self.log( 'should have a summary view' )
-        summary_view = self.hda_serializer.serialize_to_view( self.trans, hda, view='summary' )
+        summary_view = self.hda_serializer.serialize_to_view( hda, view='summary' )
         self.assertKeys( summary_view, self.hda_serializer.views[ 'summary' ] )
 
         self.log( 'should have the summary view as default view' )
-        default_view = self.hda_serializer.serialize_to_view( self.trans, hda, default_view='summary' )
+        default_view = self.hda_serializer.serialize_to_view( hda, default_view='summary' )
         self.assertKeys( summary_view, self.hda_serializer.views[ 'summary' ] )
 
         # self.log( 'should have a detailed view' )
-        # detailed_view = self.hda_serializer.serialize_to_view( self.trans, hda, view='detailed' )
+        # detailed_view = self.hda_serializer.serialize_to_view( hda, view='detailed' )
         # self.assertKeys( detailed_view, self.hda_serializer.views[ 'detailed' ] )
 
         # self.log( 'should have a extended view' )
-        # extended_view = self.hda_serializer.serialize_to_view( self.trans, hda, view='extended' )
+        # extended_view = self.hda_serializer.serialize_to_view( hda, view='extended' )
         # self.assertKeys( extended_view, self.hda_serializer.views[ 'extended' ] )
 
         self.log( 'should have a inaccessible view' )
-        inaccessible_view = self.hda_serializer.serialize_to_view( self.trans, hda, view='inaccessible' )
+        inaccessible_view = self.hda_serializer.serialize_to_view( hda, view='inaccessible' )
         self.assertKeys( inaccessible_view, self.hda_serializer.views[ 'inaccessible' ] )
 
         # skip metadata for this test
@@ -362,20 +362,20 @@ class HDASerializerTestCase( HDATestCase ):
         hda = self._create_vanilla_hda()
 
         self.log( 'should be able to use keys with views' )
-        serialized = self.hda_serializer.serialize_to_view( self.trans, hda,
+        serialized = self.hda_serializer.serialize_to_view( hda,
             view='summary', keys=[ 'uuid' ] )
         self.assertKeys( serialized,
             self.hda_serializer.views[ 'summary' ] + [ 'uuid' ] )
 
         self.log( 'should be able to use keys on their own' )
-        serialized = self.hda_serializer.serialize_to_view( self.trans, hda,
+        serialized = self.hda_serializer.serialize_to_view( hda,
             keys=[ 'file_path', 'visualizations' ] )
         self.assertKeys( serialized, [ 'file_path', 'visualizations' ] )
 
     def test_serializers( self ):
         hda = self._create_vanilla_hda()
         all_keys = list( self.hda_serializer.serializable_keyset )
-        serialized = self.hda_serializer.serialize( self.trans, hda, all_keys )
+        serialized = self.hda_serializer.serialize( hda, all_keys )
 
         self.log( 'everything serialized should be of the proper type' )
         # base
@@ -449,13 +449,13 @@ class HDADeserializerTestCase( HDATestCase ):
         self.log( 'should raise when deserializing deleted from non-bool' )
         self.assertFalse( hda.deleted )
         self.assertRaises( exceptions.RequestParameterInvalidException,
-            self.hda_deserializer.deserialize, self.trans, hda, data={ 'deleted': None } )
+            self.hda_deserializer.deserialize, hda, { 'deleted': None } )
         self.assertFalse( hda.deleted )
         self.log( 'should be able to deserialize deleted from True' )
-        self.hda_deserializer.deserialize( self.trans, hda, data={ 'deleted': True } )
+        self.hda_deserializer.deserialize( hda, { 'deleted': True } )
         self.assertTrue( hda.deleted )
         self.log( 'should be able to reverse by deserializing deleted from False' )
-        self.hda_deserializer.deserialize( self.trans, hda, data={ 'deleted': False } )
+        self.hda_deserializer.deserialize( hda, { 'deleted': False } )
         self.assertFalse( hda.deleted )
 
     def test_deserialize_purge( self ):
@@ -463,14 +463,14 @@ class HDADeserializerTestCase( HDATestCase ):
 
         self.log( 'should raise when deserializing purged from non-bool' )
         self.assertRaises( exceptions.RequestParameterInvalidException,
-            self.hda_deserializer.deserialize, self.trans, hda, data={ 'purged': None } )
+            self.hda_deserializer.deserialize, hda, { 'purged': None } )
         self.assertFalse( hda.purged )
         self.log( 'should be able to deserialize purged from True' )
-        self.hda_deserializer.deserialize( self.trans, hda, data={ 'purged': True } )
+        self.hda_deserializer.deserialize( hda, { 'purged': True } )
         self.assertTrue( hda.purged )
         # TODO: should this raise an error?
         self.log( 'should NOT be able to deserialize purged from False (will remain True)' )
-        self.hda_deserializer.deserialize( self.trans, hda, data={ 'purged': False } )
+        self.hda_deserializer.deserialize( hda, { 'purged': False } )
         self.assertTrue( hda.purged )
 
     def test_deserialize_visible( self ):
@@ -479,13 +479,13 @@ class HDADeserializerTestCase( HDATestCase ):
         self.log( 'should raise when deserializing from non-bool' )
         self.assertTrue( hda.visible )
         self.assertRaises( exceptions.RequestParameterInvalidException,
-            self.hda_deserializer.deserialize, self.trans, hda, data={ 'visible': 'None' } )
+            self.hda_deserializer.deserialize, hda, { 'visible': 'None' } )
         self.assertTrue( hda.visible )
         self.log( 'should be able to deserialize from False' )
-        self.hda_deserializer.deserialize( self.trans, hda, data={ 'visible': False } )
+        self.hda_deserializer.deserialize( hda, { 'visible': False } )
         self.assertFalse( hda.visible )
         self.log( 'should be able to reverse by deserializing from True' )
-        self.hda_deserializer.deserialize( self.trans, hda, data={ 'visible': True } )
+        self.hda_deserializer.deserialize( hda, { 'visible': True } )
         self.assertTrue( hda.visible )
 
     def test_deserialize_genome_build( self ):
@@ -493,17 +493,17 @@ class HDADeserializerTestCase( HDATestCase ):
 
         self.assertIsInstance( hda.dbkey, basestring )
         self.log( 'should deserialize to "?" from None' )
-        self.hda_deserializer.deserialize( self.trans, hda, data={ 'genome_build': None } )
+        self.hda_deserializer.deserialize( hda, { 'genome_build': None } )
         self.assertEqual( hda.dbkey, '?' )
         self.log( 'should raise when deserializing from non-string' )
         self.assertRaises( exceptions.RequestParameterInvalidException,
-            self.hda_deserializer.deserialize, self.trans, hda, data={ 'genome_build': 12 } )
+            self.hda_deserializer.deserialize, hda, { 'genome_build': 12 } )
         self.log( 'should be able to deserialize from unicode' )
         date_palm = u'نخيل التمر'
-        self.hda_deserializer.deserialize( self.trans, hda, data={ 'genome_build': date_palm } )
+        self.hda_deserializer.deserialize( hda, { 'genome_build': date_palm } )
         self.assertEqual( hda.dbkey, date_palm )
         self.log( 'should be deserializable from empty string' )
-        self.hda_deserializer.deserialize( self.trans, hda, data={ 'genome_build': '' } )
+        self.hda_deserializer.deserialize( hda, { 'genome_build': '' } )
         self.assertEqual( hda.dbkey, '' )
 
     def test_deserialize_name( self ):
@@ -511,19 +511,19 @@ class HDADeserializerTestCase( HDATestCase ):
 
         self.log( 'should raise when deserializing from non-string' )
         self.assertRaises( exceptions.RequestParameterInvalidException,
-            self.hda_deserializer.deserialize, self.trans, hda, data={ 'name': True } )
+            self.hda_deserializer.deserialize, hda, { 'name': True } )
         self.log( 'should raise when deserializing from None' )
         self.assertRaises( exceptions.RequestParameterInvalidException,
-            self.hda_deserializer.deserialize, self.trans, hda, data={ 'name': None } )
+            self.hda_deserializer.deserialize, hda, { 'name': None } )
         # self.log( 'should deserialize to empty string from None' )
-        # self.hda_deserializer.deserialize( self.trans, hda, data={ 'name': None } )
+        # self.hda_deserializer.deserialize( hda, { 'name': None } )
         # self.assertEqual( hda.name, '' )
         self.log( 'should be able to deserialize from unicode' )
         olive = u'ελιά'
-        self.hda_deserializer.deserialize( self.trans, hda, data={ 'name': olive } )
+        self.hda_deserializer.deserialize( hda, { 'name': olive } )
         self.assertEqual( hda.name, olive )
         self.log( 'should be deserializable from empty string' )
-        self.hda_deserializer.deserialize( self.trans, hda, data={ 'name': '' } )
+        self.hda_deserializer.deserialize( hda, { 'name': '' } )
         self.assertEqual( hda.name, '' )
 
     def test_deserialize_info( self ):
@@ -531,16 +531,16 @@ class HDADeserializerTestCase( HDATestCase ):
 
         self.log( 'should raise when deserializing from non-string' )
         self.assertRaises( exceptions.RequestParameterInvalidException,
-            self.hda_deserializer.deserialize, self.trans, hda, data={ 'info': True } )
+            self.hda_deserializer.deserialize, hda, { 'info': True } )
         self.log( 'should raise when deserializing from None' )
         self.assertRaises( exceptions.RequestParameterInvalidException,
-            self.hda_deserializer.deserialize, self.trans, hda, data={ 'info': None } )
+            self.hda_deserializer.deserialize, hda, { 'info': None } )
         self.log( 'should be able to deserialize from unicode' )
         rice = u'飯'
-        self.hda_deserializer.deserialize( self.trans, hda, data={ 'info': rice } )
+        self.hda_deserializer.deserialize( hda, { 'info': rice } )
         self.assertEqual( hda.info, rice )
         self.log( 'should be deserializable from empty string' )
-        self.hda_deserializer.deserialize( self.trans, hda, data={ 'info': '' } )
+        self.hda_deserializer.deserialize( hda, { 'info': '' } )
         self.assertEqual( hda.info, '' )
 
 
diff --git a/test/unit/managers/test_HistoryManager.py b/test/unit/managers/test_HistoryManager.py
index 8cad26c8839..b727b3dddff 100644
--- a/test/unit/managers/test_HistoryManager.py
+++ b/test/unit/managers/test_HistoryManager.py
@@ -331,15 +331,15 @@ class HistorySerializerTestCase( BaseTestCase ):
         history1 = self.history_manager.create( name='history1', user=user2 )
 
         self.log( 'should have a summary view' )
-        summary_view = self.history_serializer.serialize_to_view( self.trans, history1, view='summary' )
+        summary_view = self.history_serializer.serialize_to_view( history1, view='summary' )
         self.assertKeys( summary_view, self.history_serializer.views[ 'summary' ] )
 
         self.log( 'should have a detailed view' )
-        detailed_view = self.history_serializer.serialize_to_view( self.trans, history1, view='detailed' )
+        detailed_view = self.history_serializer.serialize_to_view( history1, view='detailed' )
         self.assertKeys( detailed_view, self.history_serializer.views[ 'detailed' ] )
 
         self.log( 'should have the summary view as default view' )
-        default_view = self.history_serializer.serialize_to_view( self.trans, history1, default_view='summary' )
+        default_view = self.history_serializer.serialize_to_view( history1, default_view='summary' )
         self.assertKeys( summary_view, self.history_serializer.views[ 'summary' ] )
 
         self.log( 'should have a serializer for all serializable keys' )
@@ -356,13 +356,13 @@ class HistorySerializerTestCase( BaseTestCase ):
         history1 = self.history_manager.create( name='history1', user=user2 )
 
         self.log( 'should be able to use keys with views' )
-        serialized = self.history_serializer.serialize_to_view( self.trans, history1,
+        serialized = self.history_serializer.serialize_to_view( history1,
             view='summary', keys=[ 'state_ids', 'user_id' ] )
         self.assertKeys( serialized,
             self.history_serializer.views[ 'summary' ] + [ 'state_ids', 'user_id' ] )
 
         self.log( 'should be able to use keys on their own' )
-        serialized = self.history_serializer.serialize_to_view( self.trans, history1,
+        serialized = self.history_serializer.serialize_to_view( history1,
             keys=[ 'state_ids', 'user_id' ] )
         self.assertKeys( serialized, [ 'state_ids', 'user_id' ] )
 
@@ -372,7 +372,7 @@ class HistorySerializerTestCase( BaseTestCase ):
 
         self.log( 'should have a serializer for all SharableModel keys' )
         sharable_attrs = [ 'user_id', 'username_and_slug', 'importable', 'published', 'slug' ]
-        serialized = self.history_serializer.serialize( self.trans, history1, sharable_attrs )
+        serialized = self.history_serializer.serialize( history1, sharable_attrs )
         self.assertKeys( serialized, sharable_attrs )
 
     def test_purgable( self ):
@@ -381,18 +381,18 @@ class HistorySerializerTestCase( BaseTestCase ):
 
         self.log( 'deleted and purged should be returned in their default states' )
         keys = [ 'deleted', 'purged' ]
-        serialized = self.history_serializer.serialize( self.trans, history1, keys )
+        serialized = self.history_serializer.serialize( history1, keys )
         self.assertEqual( serialized[ 'deleted' ], False )
         self.assertEqual( serialized[ 'purged' ], False )
 
         self.log( 'deleted and purged should return their current state' )
         self.history_manager.delete( history1 )
-        serialized = self.history_serializer.serialize( self.trans, history1, keys )
+        serialized = self.history_serializer.serialize( history1, keys )
         self.assertEqual( serialized[ 'deleted' ], True )
         self.assertEqual( serialized[ 'purged' ], False )
 
         self.history_manager.purge( history1 )
-        serialized = self.history_serializer.serialize( self.trans, history1, keys )
+        serialized = self.history_serializer.serialize( history1, keys )
         self.assertEqual( serialized[ 'deleted' ], True )
         self.assertEqual( serialized[ 'purged' ], True )
 
@@ -400,7 +400,7 @@ class HistorySerializerTestCase( BaseTestCase ):
         user2 = self.user_manager.create( **user2_data )
         history1 = self.history_manager.create( name='history1', user=user2 )
         all_keys = list( self.history_serializer.serializable_keyset )
-        serialized = self.history_serializer.serialize( self.trans, history1, all_keys )
+        serialized = self.history_serializer.serialize( history1, all_keys )
 
         self.log( 'everything serialized should be of the proper type' )
         self.assertIsInstance( serialized[ 'size' ], int )
@@ -415,7 +415,7 @@ class HistorySerializerTestCase( BaseTestCase ):
 
         self.log( 'a history with no contents should be properly reflected in empty, etc.' )
         keys = [ 'empty', 'count', 'state_ids', 'state_details', 'state', 'hdas' ]
-        serialized = self.history_serializer.serialize( self.trans, history1, keys )
+        serialized = self.history_serializer.serialize( history1, keys )
         self.assertEqual( serialized[ 'state' ], 'new' )
         self.assertEqual( serialized[ 'empty' ], True )
         self.assertEqual( serialized[ 'count' ], 0 )
@@ -427,7 +427,7 @@ class HistorySerializerTestCase( BaseTestCase ):
         hda1 = self.hda_manager.create( history=history1, hid=1 )
         self.hda_manager.update( hda1, dict( state='ok' ) )
 
-        serialized = self.history_serializer.serialize( self.trans, history1, keys )
+        serialized = self.history_serializer.serialize( history1, keys )
         self.assertEqual( serialized[ 'state' ], 'ok' )
         self.assertEqual( serialized[ 'empty' ], False )
         self.assertEqual( serialized[ 'count' ], 1 )
@@ -436,7 +436,7 @@ class HistorySerializerTestCase( BaseTestCase ):
         self.assertIsInstance( serialized[ 'hdas' ], list )
         self.assertIsInstance( serialized[ 'hdas' ][0], basestring )
 
-        serialized = self.history_serializer.serialize( self.trans, history1, [ 'contents' ] )
+        serialized = self.history_serializer.serialize( history1, [ 'contents' ] )
         self.assertHasKeys( serialized[ 'contents' ][0], [ 'id', 'name', 'peek', 'create_time' ])
 
         self.log( 'serialized should jsonify well' )
diff --git a/test/unit/managers/test_UserManager.py b/test/unit/managers/test_UserManager.py
index 34c3b818c9c..843f4f0630c 100644
--- a/test/unit/managers/test_UserManager.py
+++ b/test/unit/managers/test_UserManager.py
@@ -142,11 +142,11 @@ class UserSerializerTestCase( BaseTestCase ):
         user = self.user_manager.create( **user2_data )
 
         self.log( 'should have a summary view' )
-        summary_view = self.user_serializer.serialize_to_view( self.trans, user, view='summary' )
+        summary_view = self.user_serializer.serialize_to_view( user, view='summary' )
         self.assertKeys( summary_view, self.user_serializer.views[ 'summary' ] )
 
         self.log( 'should have the summary view as default view' )
-        default_view = self.user_serializer.serialize_to_view( self.trans, user, default_view='summary' )
+        default_view = self.user_serializer.serialize_to_view( user, default_view='summary' )
         self.assertKeys( summary_view, self.user_serializer.views[ 'summary' ] )
 
         self.log( 'should have a serializer for all serializable keys' )
@@ -162,20 +162,20 @@ class UserSerializerTestCase( BaseTestCase ):
         user = self.user_manager.create( **user2_data )
 
         self.log( 'should be able to use keys with views' )
-        serialized = self.user_serializer.serialize_to_view( self.trans, user,
+        serialized = self.user_serializer.serialize_to_view( user,
             view='summary', keys=[ 'create_time' ] )
         self.assertKeys( serialized,
             self.user_serializer.views[ 'summary' ] + [ 'create_time' ] )
 
         self.log( 'should be able to use keys on their own' )
-        serialized = self.user_serializer.serialize_to_view( self.trans, user,
+        serialized = self.user_serializer.serialize_to_view( user,
             keys=[ 'tags_used', 'is_admin' ] )
         self.assertKeys( serialized, [ 'tags_used', 'is_admin' ] )
 
     def test_serializers( self ):
         user = self.user_manager.create( **user2_data )
         all_keys = list( self.user_serializer.serializable_keyset )
-        serialized = self.user_serializer.serialize( self.trans, user, all_keys )
+        serialized = self.user_serializer.serialize( user, all_keys, trans=self.trans )
         # pprint.pprint( serialized )
 
         self.log( 'everything serialized should be of the proper type' )
@@ -207,10 +207,10 @@ class CurrentUserSerializerTestCase( BaseTestCase ):
     def test_anonymous( self ):
         anonym = None
         # need a history here for total_disk_usage
-        self.trans.set_history( self.history_manager.create( self.trans ) )
+        self.trans.set_history( self.history_manager.create() )
 
         self.log( 'should be able to serialize anonymous user' )
-        serialized = self.user_serializer.serialize_to_view( self.trans, anonym, view='detailed' )
+        serialized = self.user_serializer.serialize_to_view( anonym, view='detailed', trans=self.trans )
         self.assertKeys( serialized,
             [ 'id', 'total_disk_usage', 'nice_total_disk_usage', 'quota_percent' ] )
 

From 660cfcbdf88b5aa48bef998c980460ccd9f06716 Mon Sep 17 00:00:00 2001
From: David Trudgian <david.trudgian@utsouthwestern.edu>
Date: Thu, 2 Apr 2015 13:01:49 -0500
Subject: [PATCH 22/88] Initial attempt at LDAP login with username - WIP

---
 config/galaxy.ini.sample                      |  2 +-
 lib/galaxy/auth/__init__.py                   | 49 +++++++++-------
 lib/galaxy/auth/providers/__init__.py         | 12 ++--
 lib/galaxy/auth/providers/alwaysreject.py     |  4 +-
 .../{activedirectory.py => ldap_ad.py}        | 58 +++++++++++--------
 lib/galaxy/auth/providers/localdb.py          |  4 +-
 lib/galaxy/security/validate_user_input.py    |  4 +-
 .../webapps/galaxy/controllers/mobile.py      | 14 +++--
 lib/galaxy/webapps/galaxy/controllers/user.py | 26 +++++----
 templates/user/login.mako                     |  4 +-
 10 files changed, 99 insertions(+), 78 deletions(-)
 rename lib/galaxy/auth/providers/{activedirectory.py => ldap_ad.py} (60%)

diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample
index 3ddf929677b..69b2b925ae9 100644
--- a/config/galaxy.ini.sample
+++ b/config/galaxy.ini.sample
@@ -856,7 +856,7 @@ use_interactive = True
 #openid_consumer_cache_path = database/openid_consumer_cache
 
 # XML config file that allows the use of different authentication providers
-# (e.g. Active Directory) instead or in addition to local authentication
+# (e.g. LDAP) instead or in addition to local authentication
 # (.sample is used if default does not exist).
 #auth_config_file = config/auth_conf.xml
 
diff --git a/lib/galaxy/auth/__init__.py b/lib/galaxy/auth/__init__.py
index 116229659a1..aa4efc6f498 100644
--- a/lib/galaxy/auth/__init__.py
+++ b/lib/galaxy/auth/__init__.py
@@ -20,19 +20,23 @@ log = logging.getLogger(__name__)
 
 # <auth>
 #     <authenticator>
-#         <type>activedirectory</type>
-#         <filter>'[username]'.endswith('@students.latrobe.edu.au')</filter>
+#         <type>ldap_ad</type>
+#         <filter>'[login]'.endswith('@students.latrobe.edu.au')</filter>
 #         <options>
 #             <auto-register>True</auto-register>
 #             <server>ldap://STUDENTS.ltu.edu.au</server>
-#             [<search-filter>(&amp;(objectClass=user)(mail={username}))</search-filter>
+#             [<search-filter>(&amp;(objectClass=user)(mail={login}))</search-filter>
 #             <search-base>dc=STUDENTS,dc=ltu,dc=edu,dc=au</search-base>
 #             <search-user>jsmith</search-user>
 #             <search-password>mysecret</search-password>
-#             <search-fields>sAMAccountName</search-fields>]
+#             <search-fields>sAMAccountName,mail</search-fields>]
 #             <bind-user>{sAMAccountName}@STUDENTS.ltu.edu.au</bind-user>
 #             <bind-password>{password}</bind-password>
 #             <auto-register-username>{sAMAccountName}</auto-register-username>
+#	      <auto-register-email>{mail}</auto-register-email>
+#	   <!-- To allow login with username instead of email
+#	      <login-use-username>True</login-use-username>
+#	   -->
 #         </options>
 #     </authenticator>
 #     ...
@@ -80,18 +84,18 @@ class AuthManager(object):
             authenticators.append(authenticator)
         self.authenticators = authenticators
 
-    def check_registration_allowed(self, email, password):
-        """Checks if the provided email is allowed to register."""
+    def check_registration_allowed(self, login, password):
+        """Checks if the provided email/username is allowed to register."""
         message = ''
         status = 'done'
-        for provider, options in self.active_authenticators(email, password):
+        for provider, options in self.active_authenticators(login, password):
             allow_reg = _get_tri_state(options, 'allow-register', True)
             if allow_reg is None:  # i.e. challenge
-                auth_result, msg = provider.authenticate(email, password, options)
+                auth_result, msg = provider.authenticate(login, password, options)
                 if auth_result is True:
                     break
                 if auth_result is None:
-                    message = 'Invalid email address or password'
+                    message = 'Invalid email address/username or password'
                     status = 'error'
                     break
             elif allow_reg is True:
@@ -102,16 +106,17 @@ class AuthManager(object):
                 break
         return message, status
 
-    def check_auto_registration(self, trans, email, password):
+    def check_auto_registration(self, trans, login, password):
         """
-        Checks the email/password using auth providers in order. If a match is
-        found, returns the 'auto-register' option for that provider.
+        Checks the username/email & password using auth providers in order.
+        If a match is found, returns the 'auto-register' option for that provider.
         """
-        for provider, options in self.active_authenticators(email, password):
+        for provider, options in self.active_authenticators(login, password):
             if provider is None:
                 log.debug( "Unable to find module: %s" % options )
             else:
-                auth_result, auto_username = provider.authenticate(email, password, options)
+                auth_result, auto_email, auto_username = provider.authenticate(login, password, options)
+                auto_email    = str(auto_email).lower()
                 auto_username = str(auto_username).lower()
                 if auth_result is True:
                     # make username unique
@@ -124,16 +129,16 @@ class AuthManager(object):
                             i += 1
                         else:
                             break  # end for loop if we can't make a unique username
-                    log.debug( "Email: %s, auto-register with username: %s" % (email, auto_username) )
-                    return (_get_bool(options, 'auto-register', False), auto_username)
+                    log.debug( "Email: %s, auto-register with username: %s" % (auto_email, auto_username) )
+                    return (_get_bool(options, 'auto-register', False), auto_email, auto_username)
                 elif auth_result is None:
-                    log.debug( "Email: %s, stopping due to failed non-continue" % (email) )
+                    log.debug( "Email: %s, Username %s, stopping due to failed non-continue" % (auto_email, auto_username) )
                     break  # end authentication (skip rest)
         return (False, '')
 
     def check_password(self, user, password):
-        """Checks the email/password using auth providers."""
-        for provider, options in self.active_authenticators(user.email, password):
+        """Checks the username/email and password using auth providers."""
+        for provider, options in self.active_authenticators(user, password):
             if provider is None:
                 log.debug( "Unable to find module: %s" % options )
             else:
@@ -148,7 +153,7 @@ class AuthManager(object):
         """Checks that auth provider allows password changes and current_password
         matches.
         """
-        for provider, options in self.active_authenticators(user.email, current_password):
+        for provider, options in self.active_authenticators(user, current_password):
             if provider is None:
                 log.debug( "Unable to find module: %s" % options )
             else:
@@ -162,7 +167,7 @@ class AuthManager(object):
                     return (False, 'Password change not supported')
         return (False, 'Invalid current password')
 
-    def active_authenticators(self, username, password):
+    def active_authenticators(self, login, password):
         """Yields AuthProvider instances for the provided configfile that match the
         filters.
         """
@@ -170,7 +175,7 @@ class AuthManager(object):
             for authenticator in self.authenticators:
                 filter_template = authenticator.filter_template
                 if filter_template:
-                    filter_str = filter_template.format(username=username, password=password)
+                    filter_str = filter_template.format(login=login, password=password)
                     passed_filter = eval(filter_str, {"__builtins__": None}, {'str': str})
                     if not passed_filter:
                         continue  # skip to next
diff --git a/lib/galaxy/auth/providers/__init__.py b/lib/galaxy/auth/providers/__init__.py
index 724192007ce..5552193f257 100644
--- a/lib/galaxy/auth/providers/__init__.py
+++ b/lib/galaxy/auth/providers/__init__.py
@@ -16,23 +16,23 @@ class AuthProvider(object):
         """ Short string providing labelling this plugin """
 
     @abc.abstractmethod
-    def authenticate(self, username, password, options):
+    def authenticate(self, login, password, options):
         """
         Check that the username and password are correct.
 
         NOTE: Used within auto-registration to check it is ok to register this
         user.
 
-        :param  username: the users email address
-        :type   username: str
+        :param  login: the users email address
+        :type   login: str
         :param  password: the plain text password they typed
         :type   password: str
         :param  options: options provided in auth_config_file
         :type   options: dict
         :returns:   True: accept user, False: reject user and None: reject user
-            and don't try any other providers.  str is the username to register
-            with if accepting
-        :rtype:     (bool, str)
+            and don't try any other providers.  str, str is the email and
+            username to register with if accepting
+        :rtype:     (bool, str, str)
         """
 
     @abc.abstractmethod
diff --git a/lib/galaxy/auth/providers/alwaysreject.py b/lib/galaxy/auth/providers/alwaysreject.py
index a9cb54faf94..a2c27b6293a 100644
--- a/lib/galaxy/auth/providers/alwaysreject.py
+++ b/lib/galaxy/auth/providers/alwaysreject.py
@@ -16,11 +16,11 @@ class AlwaysReject(AuthProvider):
     """
     plugin_type = 'alwaysreject'
 
-    def authenticate(self, username, password, options):
+    def authenticate(self, login, password, options):
         """
         See abstract method documentation.
         """
-        return (None, '')
+        return (None, '', '')
 
     def authenticate_user(self, user, password, options):
         """
diff --git a/lib/galaxy/auth/providers/activedirectory.py b/lib/galaxy/auth/providers/ldap_ad.py
similarity index 60%
rename from lib/galaxy/auth/providers/activedirectory.py
rename to lib/galaxy/auth/providers/ldap_ad.py
index 8f77a9703aa..76986ca33dd 100644
--- a/lib/galaxy/auth/providers/activedirectory.py
+++ b/lib/galaxy/auth/providers/ldap_ad.py
@@ -4,34 +4,37 @@ Created on 15/07/2014
 @author: Andrew Robinson
 """
 
+import logging
+
 from galaxy.exceptions import ConfigurationError
 from ..providers import AuthProvider
+from galaxy.util import string_as_bool
+from galaxy.auth import _get_bool
 
-import logging
 log = logging.getLogger(__name__)
 
 
 def _get_subs(d, k, params):
     if k not in d:
-        raise ConfigurationError("Missing '%s' parameter in Active Directory options" % k)
+        raise ConfigurationError("Missing '%s' parameter in LDAP options" % k)
     return str(d[k]).format(**params)
 
 
-class ActiveDirectory(AuthProvider):
+class LDAPAD(AuthProvider):
     """
-    Attempts to authenticate users against an Active Directory server.
+    Attempts to authenticate users against an LDAP server.
 
-    If options include search-fields then it will attempt to search the AD for
-    those fields first.  After that it will bind to the AD with the username
+    If options include search-fields then it will attempt to search LDAP for
+    those fields first.  After that it will bind to LDAP with the username
     (formatted as specified).
     """
-    plugin_type = 'activedirectory'
+    plugin_type = 'ldap_ad'
 
-    def authenticate(self, username, password, options):
+    def authenticate(self, login, password, options):
         """
         See abstract method documentation.
         """
-        log.debug("Username: %s" % username)
+        log.debug("Login: %s" % login)
         log.debug("Options: %s" % options)
 
         failure_mode = False  # reject but continue
@@ -41,11 +44,11 @@ class ActiveDirectory(AuthProvider):
         try:
             import ldap
         except:
-            log.debug("User: %s, ACTIVEDIRECTORY: False (no ldap)" % (username))
+            log.debug("Login: %s, LDAP: False (could not load ldap module)" % (login))
             return (failure_mode, '')
 
-        # do AD search (if required)
-        params = {'username': username, 'password': password}
+        # do LDAP search (if required)
+        params = {'login': login, 'password': password}
         if 'search-fields' in options:
             try:
                 # setup connection
@@ -54,7 +57,8 @@ class ActiveDirectory(AuthProvider):
                 l.protocol_version = 3
 
                 if 'search-user' in options:
-                    l.simple_bind_s(_get_subs(options, 'search-user', params), _get_subs(options, 'search-password', params))
+                    l.simple_bind_s(_get_subs(options, 'search-user', params),
+                                    _get_subs(options, 'search-password', params))
                 else:
                     l.simple_bind_s()
 
@@ -62,13 +66,14 @@ class ActiveDirectory(AuthProvider):
 
                 # setup search
                 attributes = [_.strip().format(**params) for _ in options['search-fields'].split(',')]
-                result = l.search(_get_subs(options, 'search-base', params), scope, _get_subs(options, 'search-filter', params), attributes)
+                result = l.search(_get_subs(options, 'search-base', params), scope,
+                                  _get_subs(options, 'search-filter', params), attributes)
 
                 # parse results
                 _, suser = l.result(result, 60)
                 dn, attrs = suser[0]
-                log.debug(("AD dn: %s" % dn))
-                log.debug(("AD Search attributes: %s" % attrs))
+                log.debug(("LDAP dn: %s" % dn))
+                log.debug(("LDAP Search attributes: %s" % attrs))
                 if hasattr(attrs, 'has_key'):
                     for attr in attributes:
                         if attr in attrs:
@@ -77,8 +82,8 @@ class ActiveDirectory(AuthProvider):
                             params[attr] = ""
                 params['dn'] = dn
             except Exception:
-                log.exception('ACTIVEDIRECTORY Search Exception for User: %s' % username)
-                return (failure_mode, '')
+                log.exception('LDAP Search Exception for login: %s' % login)
+                return (failure_mode, '', '')
         # end search
 
         # bind as user to check their credentials
@@ -89,17 +94,22 @@ class ActiveDirectory(AuthProvider):
             l.protocol_version = 3
             l.simple_bind_s(_get_subs(options, 'bind-user', params), _get_subs(options, 'bind-password', params))
         except Exception:
-            log.exception('ACTIVEDIRECTORY Authenticate Exception for User %s' % username)
-            return (failure_mode, '')
+            log.exception('LDAP Authentication Exception for login %s' % login)
+            return (failure_mode, '', '')
 
-        log.debug("User: %s, ACTIVEDIRECTORY: True" % (username))
-        return (True, _get_subs(options, 'auto-register-username', params))
+        log.debug("Login: %s, LDAP: True" % (login))
+        return (True,
+                _get_subs(options, 'auto-register-email', params),
+                _get_subs(options, 'auto-register-username', params))
 
     def authenticate_user(self, user, password, options):
         """
         See abstract method documentation.
         """
-        return self.authenticate(user.email, password, options)[0]
 
+	if _get_bool(options, 'login-use-username', False):
+            return self.authenticate(user.username, password, options)[0]
+	else:
+	    return self.authenticate(user.email, password, options)[0]
 
-__all__ = ['ActiveDirectory']
+__all__ = ['LDAPAD']
diff --git a/lib/galaxy/auth/providers/localdb.py b/lib/galaxy/auth/providers/localdb.py
index 5f01e6e5208..718889acad0 100644
--- a/lib/galaxy/auth/providers/localdb.py
+++ b/lib/galaxy/auth/providers/localdb.py
@@ -13,11 +13,11 @@ class LocalDB(AuthProvider):
     """Authenticate users against the local Galaxy database (as per usual)."""
     plugin_type = 'localdb'
 
-    def authenticate(self, username, password, options):
+    def authenticate(self, login, password, options):
         """
         See abstract method documentation.
         """
-        return (False, '')  # it can never auto-create based of localdb (chicken-egg)
+        return (False, '', '')  # it can never auto-create based of localdb (chicken-egg)
 
     def authenticate_user(self, user, password, options):
         """
diff --git a/lib/galaxy/security/validate_user_input.py b/lib/galaxy/security/validate_user_input.py
index 0c15cacdc01..96c676c89e0 100644
--- a/lib/galaxy/security/validate_user_input.py
+++ b/lib/galaxy/security/validate_user_input.py
@@ -37,7 +37,7 @@ def validate_email( trans, email, user=None, check_dup=True ):
 
 
 def validate_publicname( trans, publicname, user=None ):
-    # User names must be at least four characters in length and contain only lower-case
+    # User names must be at least three characters in length and contain only lower-case
     # letters, numbers, and the '-' character.
     if user and user.username == publicname:
         return ''
@@ -45,7 +45,7 @@ def validate_publicname( trans, publicname, user=None ):
         if len( publicname ) < 3:
             return "Public name must be at least 3 characters in length"
     else:
-        if len( publicname ) < 4:
+        if len( publicname ) < 3:
             return "Public name must be at least 4 characters in length"
     if len( publicname ) > 255:
         return "Public name cannot be more than 255 characters in length"
diff --git a/lib/galaxy/webapps/galaxy/controllers/mobile.py b/lib/galaxy/webapps/galaxy/controllers/mobile.py
index 592d424046a..b0fa11cbd19 100644
--- a/lib/galaxy/webapps/galaxy/controllers/mobile.py
+++ b/lib/galaxy/webapps/galaxy/controllers/mobile.py
@@ -53,17 +53,21 @@ class Mobile( BaseUIController ):
         # trans.log_event( "User logged out" )
         # trans.handle_user_logout()
 
-    def __login( self, trans, email="", password="" ):
+    def __login(self, trans, login="", password=""):
         return trans.response.send_redirect( web.url_for(controller='root', action='index' ) )
         # error = password_error = None
-        # user = trans.sa_session.query( model.User ).filter_by( email = email ).first()
+        # user = trans.sa_session.query( model.User ).filter(or_(
+        #    email == login,
+        #    username == login
+        # )).first()
         # if not user:
-        #     autoreg = galaxy.auth.check_auto_registration(trans, email, password, trans.app.config.auth_config_file)
+        #     autoreg = galaxy.auth.check_auto_registration(trans, login, password, trans.app.config.auth_config_file)
         #     if autoreg[0]:
         #         kwd = {}
-        #         kwd['username'] = autoreg[1]
+        #         kwd['email'] = autoreg[1]
+        #         kwd['username'] = autoreg[2]
         #         params = util.Params( kwd )
-        #         message = validate_email( trans, email )
+        #         message = validate_email( trans, kwd['email'] )
         #         if not message:
         #             message, status, user, success = self.__register( trans, 'user', False, **kwd )
         #             if success:
diff --git a/lib/galaxy/webapps/galaxy/controllers/user.py b/lib/galaxy/webapps/galaxy/controllers/user.py
index 6077e340672..bea04c02c2e 100644
--- a/lib/galaxy/webapps/galaxy/controllers/user.py
+++ b/lib/galaxy/webapps/galaxy/controllers/user.py
@@ -14,7 +14,7 @@ from datetime import datetime, timedelta
 from galaxy import model
 from galaxy import util
 from galaxy import web
-from galaxy.model.orm import and_
+from galaxy.model.orm import and_, or_
 from galaxy.security.validate_user_input import (transform_publicname,
                                                  validate_email,
                                                  validate_password,
@@ -467,7 +467,7 @@ class User( BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Creat
         status = kwd.get( 'status', 'done' )
         header = ''
         user = trans.user
-        email = kwd.get( 'email', '' )
+        login = kwd.get( 'login', '' )
         if user:
             # Already logged in.
             redirect_url = redirect
@@ -496,7 +496,7 @@ class User( BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Creat
                 else:
                     header = REQUIRE_LOGIN_TEMPLATE % ( "Galaxy tool shed", "" )
         return trans.fill_template( '/user/login.mako',
-                                    email=email,
+                                    login=login,
                                     header=header,
                                     use_panels=use_panels,
                                     redirect_url=redirect_url,
@@ -510,21 +510,23 @@ class User( BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Creat
 
     def __validate_login( self, trans, **kwd ):
         """Validates numerous cases that might happen during the login time."""
-        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'error' )
-        email = kwd.get( 'email', '' )
+        login = kwd.get( 'login', '' )
         password = kwd.get( 'password', '' )
-        username = kwd.get( 'username', '' )
         redirect = kwd.get( 'redirect', trans.request.referer ).strip()
         success = False
-        user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email == email ).first()
+        user = trans.sa_session.query( trans.app.model.User ).filter(or_(
+            trans.app.model.User.table.c.email == login,
+            trans.app.model.User.table.c.username == login
+        )).first()
         log.debug("trans.app.config.auth_config_file: %s" % trans.app.config.auth_config_file)
         if not user:
-            autoreg = trans.app.auth_manager.check_auto_registration(trans, email, password)
+            autoreg = trans.app.auth_manager.check_auto_registration(trans, login, password)
             if autoreg[0]:
-                kwd['username'] = autoreg[1]
+                kwd['email'] = autoreg[1]
+                kwd['username'] = autoreg[2]
                 params = util.Params( kwd )
-                message = validate_email( trans, email )  #self.__validate( trans, params, email, password, password, username )
+                message = validate_email( trans, kwd['email'] )  #self.__validate( trans, params, email, password, password, username )
                 if not message:
                     message, status, user, success = self.__register( trans, 'user', False, **kwd )
                     if success:
@@ -552,11 +554,11 @@ class User( BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Creat
         elif trans.app.config.user_activation_on and not user.active:  # activation is ON and the user is INACTIVE
             if ( trans.app.config.activation_grace_period != 0 ):  # grace period is ON
                 if self.is_outside_grace_period( trans, user.create_time ):  # User is outside the grace period. Login is disabled and he will have the activation email resent.
-                    message, status = self.resend_verification_email( trans, email, username )
+                    message, status = self.resend_verification_email( trans, user.email, user.username )
                 else:  # User is within the grace period, let him log in.
                     message, success, status = self.proceed_login( trans, user, redirect )
             else:  # Grace period is off. Login is disabled and user will have the activation email resent.
-                message, status = self.resend_verification_email( trans, email, username )
+                message, status = self.resend_verification_email( trans, user.email, user.username )
         else:  # activation is OFF
             message, success, status = self.proceed_login( trans, user, redirect )
         return ( message, status, user, success )
diff --git a/templates/user/login.mako b/templates/user/login.mako
index 26358f5e062..91c58604597 100644
--- a/templates/user/login.mako
+++ b/templates/user/login.mako
@@ -80,8 +80,8 @@ def inherit(context):
         <div class="toolFormTitle">Login</div>
         <form name="login" id="login" action="${form_action}" method="post" >
             <div class="form-row">
-                <label>Email address:</label>
-                <input type="text" name="email" value="${email | h}" size="40"/>
+                <label>Username / Email Address:</label>
+                <input type="text" name="login" value="${login | h}" size="40"/>
                 <input type="hidden" name="redirect" value="${redirect | h}" size="40"/>
             </div>
             <div class="form-row">

From ceeff0a03c8ca1b30934edc28054aa7764520c8e Mon Sep 17 00:00:00 2001
From: Carl Eberhard <carlfeberhard@gmail.com>
Date: Thu, 2 Apr 2015 14:22:26 -0400
Subject: [PATCH 23/88] Fix to c1f7210: remove print statements and minor fixes

---
 lib/galaxy/managers/annotatable.py | 12 ------------
 lib/galaxy/managers/datasets.py    |  1 +
 lib/galaxy/managers/hdas.py        |  9 ++-------
 lib/galaxy/managers/sharable.py    |  7 ++++---
 lib/galaxy/managers/users.py       |  3 ---
 test/casperjs/spaceghost.js        |  2 +-
 6 files changed, 8 insertions(+), 26 deletions(-)

diff --git a/lib/galaxy/managers/annotatable.py b/lib/galaxy/managers/annotatable.py
index 7f9a32f7d3f..af2dfbac802 100644
--- a/lib/galaxy/managers/annotatable.py
+++ b/lib/galaxy/managers/annotatable.py
@@ -58,19 +58,7 @@ class AnnotatableDeserializerMixin( object ):
         Make sure `val` is a valid annotation and assign it, deleting any existing
         if `val` is None.
         """
-        print '-' * 20
-        print item
-        print key
-        print val
-        print user
         val = self.validate.nullable_basestring( key, val )
-        # sa_session = self.app.model.context
-        # if val is None:
-        #     item.delete_item_annotation( sa_session, user, item )
-        #     return None
-
-        # annotated_item = item.add_item_annotation( sa_session, user, item, val )
-        # return annotated_item.annotation
         return self.manager.annotate( item, user, val )
 
 
diff --git a/lib/galaxy/managers/datasets.py b/lib/galaxy/managers/datasets.py
index e6e0f92a606..198753c6b0f 100644
--- a/lib/galaxy/managers/datasets.py
+++ b/lib/galaxy/managers/datasets.py
@@ -277,6 +277,7 @@ class DatasetAssociationManager( base.ModelManager,
         """
         raise galaxy.exceptions.NotImplemented( 'Abstract Method' )
 
+    # .... associated job
     def creating_job( self, dataset_assoc ):
         # TODO: is this needed? Can't you use the dataset_assoc.creating_job attribute? When is this None?
         # TODO: this would be even better if outputs and inputs were the underlying datasets
diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py
index 7aee71aba9d..7f26c960e9f 100644
--- a/lib/galaxy/managers/hdas.py
+++ b/lib/galaxy/managers/hdas.py
@@ -88,11 +88,8 @@ class HDAManager( datasets.DatasetAssociationManager,
             sa_session=self.app.model.context, **kwargs )
 
         if history:
-# TODO Probably Bug:  set_hid is never used, and should be passed
-# to history.add_dataset here.
-            set_hid = not ( 'hid' in kwargs )
-            history.add_dataset( hda )
-#TODO:?? some internal sanity check here (or maybe in add_dataset) to make sure hids are not duped?
+            history.add_dataset( hda, set_hid=( 'hid' not in kwargs ) )
+        #TODO:?? some internal sanity check here (or maybe in add_dataset) to make sure hids are not duped?
 
         self.session().add( hda )
         if flush:
@@ -179,8 +176,6 @@ class HDAManager( datasets.DatasetAssociationManager,
             return self.model_class.conversion_messages.PENDING
         return None
 
-    # .... associated job
-
     # .... data
     # TODO: to data provider or Text datatype directly
     def text_data( self, hda, preview=True ):
diff --git a/lib/galaxy/managers/sharable.py b/lib/galaxy/managers/sharable.py
index 56af2106aa0..791e460e403 100644
--- a/lib/galaxy/managers/sharable.py
+++ b/lib/galaxy/managers/sharable.py
@@ -317,6 +317,7 @@ class SharableModelSerializer( base.ModelSerializer,
             'user_id'           : self.serialize_id,
             'username_and_slug' : self.serialize_username_and_slug
         })
+        # these use the default serializer but must still be white-listed
         self.serializable_keyset.update([
             'importable', 'published', 'slug'
         ])
@@ -324,13 +325,13 @@ class SharableModelSerializer( base.ModelSerializer,
     def serialize_username_and_slug( self, item, key, **context ):
         if not ( item.user and item.slug and self.SINGLE_CHAR_ABBR ):
             return None
-#TODO: self.url_for
         return ( '/' ).join(( 'u', item.user.username, self.SINGLE_CHAR_ABBR, item.slug ) )
 
-    #def published_url( self, item, key, **context ):
+    # def serialize_username_and_slug( self, item, key, **context ):
     #    """
     #    """
-    #    url = url_for(controller='history', action="display_by_username_and_slug",
+    #     #TODO: replace the above with this
+    #    url = self.url_for(controller='history', action="display_by_username_and_slug",
     #        username=item.user.username, slug=item.slug )
     #    return url
 
diff --git a/lib/galaxy/managers/users.py b/lib/galaxy/managers/users.py
index 8d68f8d3a98..4b4a8fcf003 100644
--- a/lib/galaxy/managers/users.py
+++ b/lib/galaxy/managers/users.py
@@ -168,9 +168,6 @@ class UserManager( base.ModelManager, deletable.PurgableManagerMixin ):
                     .filter_by( user=user )
                     .order_by( sqlalchemy.desc( model.APIKeys.create_time ) ) )
         all = query.all()
-        for a in all:
-            print a.user.username, a.key, a.create_time
-        print all
         if len( all ):
             return all[0]
         return None
diff --git a/test/casperjs/spaceghost.js b/test/casperjs/spaceghost.js
index d8f8bcf7e9f..a1dfa1cadc9 100644
--- a/test/casperjs/spaceghost.js
+++ b/test/casperjs/spaceghost.js
@@ -532,7 +532,7 @@ SpaceGhost.prototype.openHomePage = function openHomePage( then, delay ){
             },
             then,
             function openHomePageTimeout(){
-                throw new GalaxyError( 'Homepage timed out' );
+                throw new GalaxyError( 'Homepage timed out - are you sure your instance is running?' );
             },
             delay
         );

From a8a7c0ee37f50c2f1a0682f6c3d2f01f02ab4d5b Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 2 Apr 2015 10:00:30 -0400
Subject: [PATCH 24/88] Allow configuration of port infrastructure services
 should access Galaxy via.

For dynamic scenarios when a galaxy_infrastructure_url cannot be known ahead of time - but the port is. See comments in config.ini.sample for more information.
---
 config/galaxy.ini.sample                        | 9 +++++++++
 lib/galaxy/config.py                            | 8 +++++---
 lib/galaxy/web/base/interactive_environments.py | 3 ++-
 3 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample
index 3ddf929677b..d3b8e2edca0 100644
--- a/config/galaxy.ini.sample
+++ b/config/galaxy.ini.sample
@@ -476,6 +476,15 @@ nglims_config_file = tool-data/nglims.yaml
 # IPython Docker container for communicating back with Galaxy via the API.
 #galaxy_infrastructure_url = http://localhost:8080
 
+# If the above URL cannot be determined ahead of time in dynamic environments
+# but the port which should be used to access Galaxy can be - this should be
+# set to prevent Galaxy from having to guess. For example if Galaxy is sitting
+# behind a proxy with REMOTE_USER enabled - infrastructure shouldn't talk to
+# Python processes directly and this should be set to 80 or 443, etc.... If
+# unset this file will be read for a server block defining a port
+# corresponding to the webapp.
+#galaxy_infrastructure_web_port = 8080
+
 # The URL of the page to display in Galaxy's middle pane when loaded.  This can
 # be an absolute or relative URL.
 #welcome_url = /static/welcome.html
diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py
index a7f9863d0ad..7e4a4e75003 100644
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -356,6 +356,8 @@ class Configuration( object ):
 
         # Default URL (with schema http/https) of the Galaxy instance within the
         # local network - used to remotely communicate with the Galaxy API.
+        web_port = kwargs.get("galaxy_infrastructure_web_port", None)
+        self.galaxy_infrastructure_web_port = web_port
         galaxy_infrastructure_url = kwargs.get( 'galaxy_infrastructure_url', None )
         galaxy_infrastructure_url_set = True
         if galaxy_infrastructure_url is None:
@@ -363,9 +365,9 @@ class Configuration( object ):
             # so dependending on the context a better default can be used (
             # request url in a web thread, Docker parent in IE stuff, etc...)
             galaxy_infrastructure_url = "http://localhost"
-            port = self.guess_galaxy_port()
-            if port:
-                galaxy_infrastructure_url += ":%s" % (port)
+            web_port = self.galaxy_infrastructure_web_port or self.guess_galaxy_port()
+            if web_port:
+                galaxy_infrastructure_url += ":%s" % (web_port)
             galaxy_infrastructure_url_set = False
         if "HOST_IP" in galaxy_infrastructure_url:
             galaxy_infrastructure_url = string.Template(galaxy_infrastructure_url).safe_substitute({
diff --git a/lib/galaxy/web/base/interactive_environments.py b/lib/galaxy/web/base/interactive_environments.py
index 63a8954ac4f..041f6b0ee8b 100644
--- a/lib/galaxy/web/base/interactive_environments.py
+++ b/lib/galaxy/web/base/interactive_environments.py
@@ -86,7 +86,8 @@ class InteractiveEnviornmentRequest(object):
             conf_file['galaxy_url'] = self.attr.galaxy_config.galaxy_infrastructure_url.rstrip('/') + '/'
         else:
             conf_file['galaxy_url'] = request.application_url.rstrip('/') + '/'
-            conf_file['galaxy_paster_port'] = self.attr.galaxy_config.guess_galaxy_port()
+            web_port = self.attr.galaxy_config.galaxy_infrastructure_web_port
+            conf_file['galaxy_paster_port'] = web_port or self.attr.galaxy_config.guess_galaxy_port()
 
         if self.attr.PASSWORD_AUTH:
             # Generate a random password + salt

From df165fd830767bc4f040ae9f633f7f83ea097063 Mon Sep 17 00:00:00 2001
From: Carl Eberhard <carlfeberhard@gmail.com>
Date: Thu, 2 Apr 2015 15:13:53 -0400
Subject: [PATCH 25/88] Fix to re-add some things lost in the merge

---
 lib/galaxy/managers/base.py |  2 +-
 lib/galaxy/managers/hdas.py | 20 +++++++++++++++++++-
 2 files changed, 20 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/managers/base.py b/lib/galaxy/managers/base.py
index 953ec0e9782..c93063db519 100644
--- a/lib/galaxy/managers/base.py
+++ b/lib/galaxy/managers/base.py
@@ -730,7 +730,7 @@ class ModelDeserializer( object ):
             setattr( item, key, val )
         return val
 
-    def deserialize_basestring( self, item, key, val, convert_none_to_empty=True, **context ):
+    def deserialize_basestring( self, item, key, val, convert_none_to_empty=False, **context ):
         val = '' if ( convert_none_to_empty and val is None ) else self.validate.basestring( key, val )
         return self.default_deserializer( item, key, val, **context )
 
diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py
index 9534e08022a..71e3f2eb532 100644
--- a/lib/galaxy/managers/hdas.py
+++ b/lib/galaxy/managers/hdas.py
@@ -172,6 +172,23 @@ class HDAManager( datasets.DatasetAssociationManager,
             .filter( model.JobStateHistory.state == job_states.RESUBMITTED ) )
         return self.app.model.context.query( query.exists() ).scalar()
 
+    def _job_state_history_query( self, hda ):
+        """
+        Return a query of the job's state history for the job that created this hda.
+        """
+        session = self.app.model.context
+        JobToOutputDatasetAssociation = model.JobToOutputDatasetAssociation
+        JobStateHistory = model.JobStateHistory
+
+        # TODO: this does not play well with copied hdas
+        # NOTE: don't eagerload (JODA will load the hda were using!)
+        hda_id = hda.id
+        query = ( session.query( JobToOutputDatasetAssociation, JobStateHistory )
+            .filter( JobToOutputDatasetAssociation.dataset_id == hda_id )
+            .filter( JobStateHistory.job_id == JobToOutputDatasetAssociation.job_id )
+            .enable_eagerloads( False ) )
+        return query
+
     def data_conversion_status( self, hda ):
         """
         Returns a message if an hda is not ready to be used in visualization.
@@ -420,7 +437,8 @@ class HDADeserializer( datasets.DatasetAssociationDeserializer,
             'visible'       : self.deserialize_bool,
             # remapped
             'genome_build'  : lambda i, k, v, **c: self.deserialize_genome_build( i, 'dbkey', v ),
-            'misc_info'     : lambda i, k, v, **c: self.deserialize_basestring( i, 'info', v ),
+            'misc_info'     : lambda i, k, v, **c: self.deserialize_basestring( i, 'info', v,
+                convert_none_to_empty=True ),
         })
         self.deserializable_keyset.update( self.deserializers.keys() )
 

From b9fc715dd56d399643c929c101b45c968de4294c Mon Sep 17 00:00:00 2001
From: Carl Eberhard <carlfeberhard@gmail.com>
Date: Thu, 2 Apr 2015 17:16:46 -0400
Subject: [PATCH 26/88] Fix url for DatasetAssociationCollection (and expansion
 of datasets in dataset-choice.js)

---
 client/galaxy/scripts/mvc/dataset/dataset-model.js | 7 ++++++-
 static/maps/mvc/dataset/dataset-model.js.map       | 2 +-
 static/scripts/mvc/dataset/dataset-model.js        | 2 +-
 3 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/client/galaxy/scripts/mvc/dataset/dataset-model.js b/client/galaxy/scripts/mvc/dataset/dataset-model.js
index b563965cedf..6c38e09f54d 100644
--- a/client/galaxy/scripts/mvc/dataset/dataset-model.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-model.js
@@ -57,7 +57,7 @@ var DatasetAssociation = Backbone.Model.extend( BASE_MVC.LoggableMixin ).extend(
 
         this._setUpListeners();
     },
-    
+
     /** returns misc. web urls for rendering things like re-run, display, etc. */
     _generateUrls : function(){
 //TODO: would be nice if the API did this
@@ -251,6 +251,11 @@ var DatasetAssociationCollection = Backbone.Collection.extend( BASE_MVC.Loggable
     urlRoot : (( window.galaxy_config && galaxy_config.root )?( galaxy_config.root ):( '/' ))
         + 'api/datasets',
 
+    /** url fn */
+    url : function(){
+        return this.urlRoot
+    },
+
     // ........................................................................ common queries
     /** Get the ids of every item in this collection
      *  @returns array of encoded ids
diff --git a/static/maps/mvc/dataset/dataset-model.js.map b/static/maps/mvc/dataset/dataset-model.js.map
index 23f361a2975..a451c4f1ac5 100644
--- a/static/maps/mvc/dataset/dataset-model.js.map
+++ b/static/maps/mvc/dataset/dataset-model.js.map
@@ -1 +1 @@
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diff --git a/static/scripts/mvc/dataset/dataset-model.js b/static/scripts/mvc/dataset/dataset-model.js
index 715a159df44..76ee5214d46 100644
--- a/static/scripts/mvc/dataset/dataset-model.js
+++ b/static/scripts/mvc/dataset/dataset-model.js
@@ -1,2 +1,2 @@
-define(["mvc/dataset/states","mvc/base-mvc","utils/localization"],function(a,b,c){var d=b.SearchableModelMixin,e=Backbone.Model.extend(b.LoggableMixin).extend(b.mixin(d,{defaults:{state:a.NEW,deleted:!1,purged:!1,name:"(unnamed dataset)",accessible:!0,data_type:"",file_ext:"",file_size:0,meta_files:[],misc_blurb:"",misc_info:"",tags:[]},initialize:function(b,c){this.debug(this+"(Dataset).initialize",b,c),this.get("accessible")||this.set("state",a.NOT_VIEWABLE),this.urls=this._generateUrls(),this._setUpListeners()},_generateUrls:function(){var a=this.get("id");if(!a)return{};var b={purge:"datasets/"+a+"/purge_async",display:"datasets/"+a+"/display/?preview=True",edit:"datasets/"+a+"/edit",download:"datasets/"+a+"/display?to_ext="+this.get("file_ext"),report_error:"dataset/errors?id="+a,rerun:"tool_runner/rerun?id="+a,show_params:"datasets/"+a+"/show_params",visualization:"visualization",meta_download:"dataset/get_metadata_file?hda_id="+a+"&metadata_name="},c=window.galaxy_config&&galaxy_config.root?galaxy_config.root:"/";return _.each(b,function(a,d){b[d]=c+a}),this.urls=b,b},_setUpListeners:function(){this.on("change:state",function(a,b){this.log(this+" has changed state:",a,b),this.inReadyState()&&this.trigger("state:ready",a,b,this.previous("state"))}),this.on("change:id change:file_ext",function(){this._generateUrls()})},toJSON:function(){var a=Backbone.Model.prototype.toJSON.call(this);return _.extend(a,{urls:this.urls})},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},inReadyState:function(){var b=_.contains(a.READY_STATES,this.get("state"));return this.isDeletedOrPurged()||b},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return this.get("file_size")>0},fetch:function(a){var b=this;return Backbone.Model.prototype.fetch.call(this,a).always(function(){b._generateUrls()})},"delete":function(a){return this.get("deleted")?jQuery.when():this.save({deleted:!0},a)},undelete:function(a){return!this.get("deleted")||this.get("purged")?jQuery.when():this.save({deleted:!1},a)},purge:function(a){if(this.get("purged"))return jQuery.when();a=a||{},a.url=this.urls.purge;var b=this,d=jQuery.ajax(a);return d.done(function(){b.set({deleted:!0,purged:!0})}),d.fail(function(d){var e=c("Unable to purge dataset"),f="Removal of datasets by users is not allowed in this Galaxy instance";d.responseJSON&&d.responseJSON.error?e=d.responseJSON.error:-1!==d.responseText.indexOf(f)&&(e=f),d.responseText=e,b.trigger("error",b,d,a,c(e),{error:e})}),d},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},toString:function(){var a=this.get("id")||"";return this.get("name")&&(a='"'+this.get("name")+'",'+a),"Dataset("+a+")"}})),f=Backbone.Collection.extend(b.LoggableMixin).extend({model:e,urlRoot:(window.galaxy_config&&galaxy_config.root?galaxy_config.root:"/")+"api/datasets",ids:function(){return this.map(function(a){return a.get("id")})},notReady:function(){return this.filter(function(a){return!a.inReadyState()})},haveDetails:function(){return this.all(function(a){return a.hasDetails()})},ajaxQueue:function(a,b){var c=jQuery.Deferred(),d=this.length,e=[];if(!d)return c.resolve([]),c;var f=this.chain().reverse().map(function(g,h){return function(){var i=a.call(g,b);i.done(function(a){c.notify({curr:h,total:d,response:a,model:g})}),i.always(function(a){e.push(a),f.length?f.shift()():c.resolve(e)})}}).value();return f.shift()(),c},matches:function(a){return this.filter(function(b){return b.matches(a)})},toString:function(){return["DatasetAssociationCollection(",this.length,")"].join("")}});return{DatasetAssociation:e,DatasetAssociationCollection:f}});
+define(["mvc/dataset/states","mvc/base-mvc","utils/localization"],function(a,b,c){var d=b.SearchableModelMixin,e=Backbone.Model.extend(b.LoggableMixin).extend(b.mixin(d,{defaults:{state:a.NEW,deleted:!1,purged:!1,name:"(unnamed dataset)",accessible:!0,data_type:"",file_ext:"",file_size:0,meta_files:[],misc_blurb:"",misc_info:"",tags:[]},initialize:function(b,c){this.debug(this+"(Dataset).initialize",b,c),this.get("accessible")||this.set("state",a.NOT_VIEWABLE),this.urls=this._generateUrls(),this._setUpListeners()},_generateUrls:function(){var a=this.get("id");if(!a)return{};var b={purge:"datasets/"+a+"/purge_async",display:"datasets/"+a+"/display/?preview=True",edit:"datasets/"+a+"/edit",download:"datasets/"+a+"/display?to_ext="+this.get("file_ext"),report_error:"dataset/errors?id="+a,rerun:"tool_runner/rerun?id="+a,show_params:"datasets/"+a+"/show_params",visualization:"visualization",meta_download:"dataset/get_metadata_file?hda_id="+a+"&metadata_name="},c=window.galaxy_config&&galaxy_config.root?galaxy_config.root:"/";return _.each(b,function(a,d){b[d]=c+a}),this.urls=b,b},_setUpListeners:function(){this.on("change:state",function(a,b){this.log(this+" has changed state:",a,b),this.inReadyState()&&this.trigger("state:ready",a,b,this.previous("state"))}),this.on("change:id change:file_ext",function(){this._generateUrls()})},toJSON:function(){var a=Backbone.Model.prototype.toJSON.call(this);return _.extend(a,{urls:this.urls})},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},inReadyState:function(){var b=_.contains(a.READY_STATES,this.get("state"));return this.isDeletedOrPurged()||b},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return this.get("file_size")>0},fetch:function(a){var b=this;return Backbone.Model.prototype.fetch.call(this,a).always(function(){b._generateUrls()})},"delete":function(a){return this.get("deleted")?jQuery.when():this.save({deleted:!0},a)},undelete:function(a){return!this.get("deleted")||this.get("purged")?jQuery.when():this.save({deleted:!1},a)},purge:function(a){if(this.get("purged"))return jQuery.when();a=a||{},a.url=this.urls.purge;var b=this,d=jQuery.ajax(a);return d.done(function(){b.set({deleted:!0,purged:!0})}),d.fail(function(d){var e=c("Unable to purge dataset"),f="Removal of datasets by users is not allowed in this Galaxy instance";d.responseJSON&&d.responseJSON.error?e=d.responseJSON.error:-1!==d.responseText.indexOf(f)&&(e=f),d.responseText=e,b.trigger("error",b,d,a,c(e),{error:e})}),d},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},toString:function(){var a=this.get("id")||"";return this.get("name")&&(a='"'+this.get("name")+'",'+a),"Dataset("+a+")"}})),f=Backbone.Collection.extend(b.LoggableMixin).extend({model:e,urlRoot:(window.galaxy_config&&galaxy_config.root?galaxy_config.root:"/")+"api/datasets",url:function(){return this.urlRoot},ids:function(){return this.map(function(a){return a.get("id")})},notReady:function(){return this.filter(function(a){return!a.inReadyState()})},haveDetails:function(){return this.all(function(a){return a.hasDetails()})},ajaxQueue:function(a,b){var c=jQuery.Deferred(),d=this.length,e=[];if(!d)return c.resolve([]),c;var f=this.chain().reverse().map(function(g,h){return function(){var i=a.call(g,b);i.done(function(a){c.notify({curr:h,total:d,response:a,model:g})}),i.always(function(a){e.push(a),f.length?f.shift()():c.resolve(e)})}}).value();return f.shift()(),c},matches:function(a){return this.filter(function(b){return b.matches(a)})},toString:function(){return["DatasetAssociationCollection(",this.length,")"].join("")}});return{DatasetAssociation:e,DatasetAssociationCollection:f}});
 //# sourceMappingURL=../../../maps/mvc/dataset/dataset-model.js.map
\ No newline at end of file

From 3bca8799b5ee12878bc9751461ba570942032e9c Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 3 Apr 2015 11:46:17 -0400
Subject: [PATCH 27/88] [STABLE] Revise re-run mapping of datasets and
 collections for imported and copied history items. The previous method (from
 tool_runner.py) had difficulties with consistently hashing history items
 which caused issues for imported datasets. We fixed that, however now
 datasets copied back to the same history are shown instead of the original
 dataset.

---
 lib/galaxy/tools/__init__.py | 63 +++++++++++++++++++++---------------
 1 file changed, 37 insertions(+), 26 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index cd9cd2b5dc8..f613efdc480 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2590,28 +2590,44 @@ class Tool( object, Dictifiable ):
         # dataset used; parameter should be the analygous dataset in the
         # current history.
         history = trans.get_history()
-        hda_source_dict = {} # Mapping from HDA in history to source HDAs.
+
+        # Create index for hdas.
+        hda_source_dict = {}
         for hda in history.datasets:
-            source_hda = hda.copied_from_history_dataset_association
-            while source_hda:
-                if source_hda.dataset.id not in hda_source_dict or source_hda.hid == hda.hid:
-                    hda_source_dict[ source_hda.dataset.id ] = hda
-                source_hda = source_hda.copied_from_history_dataset_association
+            key = '%s_%s' % (hda.hid, hda.dataset.id)
+            hda_source_dict[ hda.dataset.id ] = hda_source_dict[ key ] = hda
 
         # Ditto for dataset collections.
         hdca_source_dict = {}
         for hdca in history.dataset_collections:
-            source_hdca = hdca.copied_from_history_dataset_collection_association
-            while source_hdca:
-                if source_hdca.collection.id not in hdca_source_dict or source_hdca.hid == hdca.hid:
-                    hdca_source_dict[ source_hdca.collection.id ] = hdca
-                source_hdca = source_hdca.copied_from_history_dataset_collection_association
+            key = '%s_%s' % (hdca.hid, hdca.collection.id)
+            hdca_source_dict[ hda.collection.id ] = hdca_source_dict[ key ] = hdca
+
+        # Map dataset or collection to current history
+        def map_to_history(value):
+            id = None
+            source = None
+            if isinstance(value, trans.app.model.HistoryDatasetAssociation):
+                id = value.dataset.id
+                source = hda_source_dict
+            elif isinstance(value, trans.app.model.HistoryDatasetCollectionAssociation):
+                id = value.collection.id
+                source = hdca_source_dict
+            else:
+                return None
+            key = '%s_%s' % (value.hid, id)
+            if key in source:
+                return source[ key ]
+            elif id in source:
+                return source[ id ]
+            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 rerun_callback( input, value, prefixed_name, prefixed_label ):
+        def mapping_callback( input, value, prefixed_name, prefixed_label ):
             if isinstance( value, UnvalidatedValue ):
                 try:
                     return input.to_html_value( value.value, trans.app )
@@ -2623,22 +2639,17 @@ class Tool( object, Dictifiable ):
                 if isinstance(value,list):
                     values = []
                     for val in value:
-                        if isinstance(val, trans.app.model.HistoryDatasetAssociation):
-                            if val.dataset.id in hda_source_dict:
-                                values.append( hda_source_dict[ val.dataset.id ] )
-                            else:
-                                values.append( val )
+                        new_val = map_to_history( val )
+                        if new_val:
+                            values.append( new_val )
+                        else:
+                            values.append( val )
                     return values
-                if isinstance(value, trans.app.model.HistoryDatasetAssociation):
-                    if value.dataset.id in hda_source_dict:
-                        return hda_source_dict[ value.dataset.id ]
-                if isinstance(value, trans.app.model.HistoryDatasetCollectionAssociation):
-                    if value.collection.id in hdca_source_dict:
-                        return hdca_source_dict[ value.collection.id ]
+                else:
+                    return map_to_history( value )
             elif isinstance( input, DataCollectionToolParameter ):
-                if value.collection.id in hdca_source_dict:
-                    return hdca_source_dict[ value.collection.id ]
-        visit_input_values( tool_inputs, params, rerun_callback )
+                return map_to_history( value )
+        visit_input_values( tool_inputs, params, mapping_callback )
 
     def _compare_tool_version( self, trans, job ):
         """

From 3d92202402f628d5b47ba2fefa1811d82a15c460 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan.blankenberg@gmail.com>
Date: Fri, 3 Apr 2015 14:39:40 -0400
Subject: [PATCH 28/88] Fixes for displaying certain valid tool interfaces in
 the ToolShed.

---
 lib/galaxy/util/dbkeys.py          | 2 +-
 lib/galaxy/web/framework/webapp.py | 3 ++-
 lib/tool_shed/util/tool_util.py    | 7 +++++++
 3 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/util/dbkeys.py b/lib/galaxy/util/dbkeys.py
index 9bf7d09e8e3..c537d6999ec 100644
--- a/lib/galaxy/util/dbkeys.py
+++ b/lib/galaxy/util/dbkeys.py
@@ -38,7 +38,7 @@ class GenomeBuilds( object ):
                 for dataset in datasets:
                     rval.append( ( dataset.dbkey, "%s (%s) [History]" % ( dataset.name, dataset.dbkey ) ) )
             user = trans.user
-            if user and 'dbkeys' in user.preferences:
+            if user and hasattr( user, 'preferences' ) and 'dbkeys' in user.preferences:
                 user_keys = loads( user.preferences['dbkeys'] )
                 for key, chrom_dict in user_keys.iteritems():
                     rval.append( ( key, "%s (%s) [Custom]" % ( chrom_dict['name'], key ) ) )
diff --git a/lib/galaxy/web/framework/webapp.py b/lib/galaxy/web/framework/webapp.py
index 2a852eeb7c4..49f350590bc 100644
--- a/lib/galaxy/web/framework/webapp.py
+++ b/lib/galaxy/web/framework/webapp.py
@@ -668,7 +668,8 @@ class GalaxyWebTransaction( base.DefaultWebTransaction,
         """
         history = None
         if self.galaxy_session:
-            history = self.galaxy_session.current_history
+            if hasattr( self.galaxy_session, 'current_history' ):
+                history = self.galaxy_session.current_history
         if not history and util.string_as_bool( create ):
             history = self.new_history()
         return history
diff --git a/lib/tool_shed/util/tool_util.py b/lib/tool_shed/util/tool_util.py
index 2f907cf4014..10fec0e2f5c 100644
--- a/lib/tool_shed/util/tool_util.py
+++ b/lib/tool_shed/util/tool_util.py
@@ -237,12 +237,19 @@ def new_state( trans, tool, invalid=False ):
     if invalid:
         # We're attempting to display a tool in the tool shed that has been determined to have errors, so is invalid.
         return state
+    try:
+        # Attempt to generate the tool state using the standard Galaxy-side code
+        return tool.new_state( trans )
+    except Exception, e:
+        # Fall back to building tool state as below
+        log.debug( 'Failed to build tool state for tool "%s" using standard method, will try to fall back on custom method: %s', tool.id, e )
     inputs = tool.inputs_by_page[ 0 ]
     context = ExpressionContext( state.inputs, parent=None )
     for input in inputs.itervalues():
         try:
             state.inputs[ input.name ] = input.get_initial_value( trans, context )
         except:
+            # FIXME: not all values should be an empty list
             state.inputs[ input.name ] = []
     return state
 

From 204314a7801f362691519d7a039d6a2daa0371e0 Mon Sep 17 00:00:00 2001
From: David Trudgian <dave@trudgian.net>
Date: Fri, 3 Apr 2015 21:55:15 -0500
Subject: [PATCH 29/88] Fix some PEP8 complaints and comments

---
 lib/galaxy/auth/__init__.py                | 13 +++++++------
 lib/galaxy/auth/providers/__init__.py      |  4 ++--
 lib/galaxy/auth/providers/ldap_ad.py       | 17 ++++++++++-------
 lib/galaxy/security/validate_user_input.py |  4 +++-
 4 files changed, 22 insertions(+), 16 deletions(-)

diff --git a/lib/galaxy/auth/__init__.py b/lib/galaxy/auth/__init__.py
index aa4efc6f498..ad2d2b6fcbd 100644
--- a/lib/galaxy/auth/__init__.py
+++ b/lib/galaxy/auth/__init__.py
@@ -27,16 +27,17 @@ log = logging.getLogger(__name__)
 #             <server>ldap://STUDENTS.ltu.edu.au</server>
 #             [<search-filter>(&amp;(objectClass=user)(mail={login}))</search-filter>
 #             <search-base>dc=STUDENTS,dc=ltu,dc=edu,dc=au</search-base>
+#             <!-- If search-user not specified will bind anonymously to LDAP for search -->
 #             <search-user>jsmith</search-user>
 #             <search-password>mysecret</search-password>
 #             <search-fields>sAMAccountName,mail</search-fields>]
 #             <bind-user>{sAMAccountName}@STUDENTS.ltu.edu.au</bind-user>
 #             <bind-password>{password}</bind-password>
 #             <auto-register-username>{sAMAccountName}</auto-register-username>
-#	      <auto-register-email>{mail}</auto-register-email>
-#	   <!-- To allow login with username instead of email
-#	      <login-use-username>True</login-use-username>
-#	   -->
+#             <auto-register-email>{mail}</auto-register-email>
+#      <!-- To allow login with username instead of email
+#            <login-use-username>True</login-use-username>
+#      -->
 #         </options>
 #     </authenticator>
 #     ...
@@ -48,7 +49,7 @@ class AuthManager(object):
     def __init__(self, app):
         self.__app = app
         import galaxy.auth.providers
-        self.__plugins_dict = plugin_config.plugins_dict( galaxy.auth.providers, 'plugin_type' )
+        self.__plugins_dict = plugin_config.plugins_dict(galaxy.auth.providers, 'plugin_type' )
         auth_config_file = app.config.auth_config_file
         self.__init_authenticators(auth_config_file)
 
@@ -116,7 +117,7 @@ class AuthManager(object):
                 log.debug( "Unable to find module: %s" % options )
             else:
                 auth_result, auto_email, auto_username = provider.authenticate(login, password, options)
-                auto_email    = str(auto_email).lower()
+                auto_email = str(auto_email).lower()
                 auto_username = str(auto_username).lower()
                 if auth_result is True:
                     # make username unique
diff --git a/lib/galaxy/auth/providers/__init__.py b/lib/galaxy/auth/providers/__init__.py
index 5552193f257..fd200c01db4 100644
--- a/lib/galaxy/auth/providers/__init__.py
+++ b/lib/galaxy/auth/providers/__init__.py
@@ -23,7 +23,7 @@ class AuthProvider(object):
         NOTE: Used within auto-registration to check it is ok to register this
         user.
 
-        :param  login: the users email address
+        :param  login: the user's email address or username
         :type   login: str
         :param  password: the plain text password they typed
         :type   password: str
@@ -44,7 +44,7 @@ class AuthProvider(object):
         NOTE: used on normal login to check authentication and update user
         details if required.
 
-        :param  username: the users email address
+        :param  username: the user's email address or username
         :type   username: str
         :param  password: the plain text password they typed
         :type   password: str
diff --git a/lib/galaxy/auth/providers/ldap_ad.py b/lib/galaxy/auth/providers/ldap_ad.py
index 76986ca33dd..b4b6c87a8fd 100644
--- a/lib/galaxy/auth/providers/ldap_ad.py
+++ b/lib/galaxy/auth/providers/ldap_ad.py
@@ -8,7 +8,6 @@ import logging
 
 from galaxy.exceptions import ConfigurationError
 from ..providers import AuthProvider
-from galaxy.util import string_as_bool
 from galaxy.auth import _get_bool
 
 log = logging.getLogger(__name__)
@@ -21,6 +20,7 @@ def _get_subs(d, k, params):
 
 
 class LDAPAD(AuthProvider):
+
     """
     Attempts to authenticate users against an LDAP server.
 
@@ -44,7 +44,8 @@ class LDAPAD(AuthProvider):
         try:
             import ldap
         except:
-            log.debug("Login: %s, LDAP: False (could not load ldap module)" % (login))
+            log.debug(
+                "Login: %s, LDAP: False (could not load ldap module)" % (login))
             return (failure_mode, '')
 
         # do LDAP search (if required)
@@ -65,7 +66,8 @@ class LDAPAD(AuthProvider):
                 scope = ldap.SCOPE_SUBTREE
 
                 # setup search
-                attributes = [_.strip().format(**params) for _ in options['search-fields'].split(',')]
+                attributes = [_.strip().format(**params)
+                              for _ in options['search-fields'].split(',')]
                 result = l.search(_get_subs(options, 'search-base', params), scope,
                                   _get_subs(options, 'search-filter', params), attributes)
 
@@ -92,7 +94,8 @@ class LDAPAD(AuthProvider):
             ldap.set_option(ldap.OPT_REFERRALS, 0)
             l = ldap.initialize(_get_subs(options, 'server', params))
             l.protocol_version = 3
-            l.simple_bind_s(_get_subs(options, 'bind-user', params), _get_subs(options, 'bind-password', params))
+            l.simple_bind_s(_get_subs(
+                options, 'bind-user', params), _get_subs(options, 'bind-password', params))
         except Exception:
             log.exception('LDAP Authentication Exception for login %s' % login)
             return (failure_mode, '', '')
@@ -107,9 +110,9 @@ class LDAPAD(AuthProvider):
         See abstract method documentation.
         """
 
-	if _get_bool(options, 'login-use-username', False):
+        if _get_bool(options, 'login-use-username', False):
             return self.authenticate(user.username, password, options)[0]
-	else:
-	    return self.authenticate(user.email, password, options)[0]
+        else:
+            return self.authenticate(user.email, password, options)[0]
 
 __all__ = ['LDAPAD']
diff --git a/lib/galaxy/security/validate_user_input.py b/lib/galaxy/security/validate_user_input.py
index 96c676c89e0..59cbb6a5640 100644
--- a/lib/galaxy/security/validate_user_input.py
+++ b/lib/galaxy/security/validate_user_input.py
@@ -45,8 +45,10 @@ def validate_publicname( trans, publicname, user=None ):
         if len( publicname ) < 3:
             return "Public name must be at least 3 characters in length"
     else:
+        # DCT - TODO - Simplify logic if 3 chars is okay for publicname for
+        # galaxy as well as toolshed
         if len( publicname ) < 3:
-            return "Public name must be at least 4 characters in length"
+            return "Public name must be at least 3 characters in length"
     if len( publicname ) > 255:
         return "Public name cannot be more than 255 characters in length"
     if not( VALID_PUBLICNAME_RE.match( publicname ) ):

From 0cb2e7548faa1394f567d64fa6f0d14e2aaff9b9 Mon Sep 17 00:00:00 2001
From: David Trudgian <dave@trudgian.net>
Date: Fri, 3 Apr 2015 22:06:17 -0500
Subject: [PATCH 30/88] 3 char for username in user info and registration

Assuming 3 character username is okay, update the info and registration
forms. NB - username regex in register.mako already allowed 3 char. In
info.mako was 4 char.
---
 templates/user/info.mako     | 8 ++++----
 templates/user/register.mako | 6 +++---
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/templates/user/info.mako b/templates/user/info.mako
index 7447085a722..5ecc1847c7a 100644
--- a/templates/user/info.mako
+++ b/templates/user/info.mako
@@ -9,7 +9,7 @@
 
             function validateString(test_string, type) {
                 var mail_re = /^(([^<>()[\]\\.,;:\s@\"]+(\.[^<>()[\]\\.,;:\s@\"]+)*)|(\".+\"))@((\[[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}\])|(([a-zA-Z\-0-9]+\.)+[a-zA-Z]{2,}))$/;
-                var username_re = /^[a-z0-9\-]{4,255}$/;
+                var username_re = /^[a-z0-9\-]{3,255}$/;
                 if (type === 'email') {
                     return mail_re.test(test_string);
                 } else if (type === 'username'){
@@ -47,7 +47,7 @@
             $( '#login_info' ).bind( 'submit', function( e ) {
                 var error_text_email= 'Please enter your valid email address.';
                 var error_text_email_long= 'Email cannot be more than 255 characters in length.';
-                var error_text_username_characters = 'Public name must contain only lowercase letters, numbers and "-". It also has to be shorter than 255 characters but longer than 3.';
+                var error_text_username_characters = 'Public name must contain only lowercase letters, numbers and "-". It also has to be shorter than 255 characters but longer than 2.';
                 var email = $( '#email_input' ).val();
                 var name = $( '#name_input' ).val();
                 var validForm = true;
@@ -108,7 +108,7 @@
                         <input type="text" id="name_input" name="username" size="40" value="${username | h}"/>
                         <div class="toolParamHelp" style="clear: both;">
                             Your public name provides a means of identifying you publicly within this tool shed. Public
-                            names must be at least four characters in length and contain only lower-case letters, numbers,
+                            names must be at least three characters in length and contain only lower-case letters, numbers,
                             and the '-' character.  You cannot change your public name after you have created a repository
                             in this tool shed.
                         </div>
@@ -117,7 +117,7 @@
                     <input type="text" id="name_input" name="username" size="40" value="${username | h}"/>
                     <div class="toolParamHelp" style="clear: both;">
                         Your public name is an optional identifier that will be used to generate addresses for information
-                        you share publicly. Public names must be at least four characters in length and contain only lower-case
+                        you share publicly. Public names must be at least three characters in length and contain only lower-case
                         letters, numbers, and the '-' character.
                     </div>
                 %endif
diff --git a/templates/user/register.mako b/templates/user/register.mako
index 549d8f77d7b..68393e1b703 100644
--- a/templates/user/register.mako
+++ b/templates/user/register.mako
@@ -96,7 +96,7 @@ def inherit(context):
 
     			var error_text_email= 'Please enter your valid email address';
     			var error_text_email_long= 'Email cannot be more than 255 characters in length';
-    			var error_text_username_characters = 'Public name must contain only lowercase letters, numbers and "-". It also has to be shorter than 255 characters but longer than 3.';
+    			var error_text_username_characters = 'Public name must contain only lowercase letters, numbers and "-". It also has to be shorter than 255 characters but longer than 2.';
     			var error_text_password_short = 'Please use a password of at least 6 characters';
     			var error_text_password_match = "Passwords don't match";
 
@@ -141,13 +141,13 @@ def inherit(context):
                 %if t.webapp.name == 'galaxy':
                     <div class="toolParamHelp" style="clear: both;">
                         Your public name is an identifier that will be used to generate addresses for information
-                        you share publicly. Public names must be at least four characters in length and contain only lower-case
+                        you share publicly. Public names must be at least three characters in length and contain only lower-case
                         letters, numbers, and the '-' character.
                     </div>
                 %else:
                     <div class="toolParamHelp" style="clear: both;">
                         Your public name provides a means of identifying you publicly within this tool shed. Public
-                        names must be at least four characters in length and contain only lower-case letters, numbers,
+                        names must be at least three characters in length and contain only lower-case letters, numbers,
                         and the '-' character.  You cannot change your public name after you have created a repository
                         in this tool shed.
                     </div>

From 62c66d3c92b39cb820454b56a4c3d17e0e88ec5f Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan.blankenberg@gmail.com>
Date: Thu, 26 Mar 2015 10:47:58 -0400
Subject: [PATCH 31/88] Re-enable IGV local external display application by
 default. Add hg38 as available genome. We should probably update this view to
 either allow any genome or to function like the current web_link_main.

---
 tool-data/shared/igv/igv_build_sites.txt.sample | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tool-data/shared/igv/igv_build_sites.txt.sample b/tool-data/shared/igv/igv_build_sites.txt.sample
index ce3f18f16b6..e19b0b6d25b 100644
--- a/tool-data/shared/igv/igv_build_sites.txt.sample
+++ b/tool-data/shared/igv/igv_build_sites.txt.sample
@@ -1,4 +1,4 @@
 #site_id	site_name	site_url	dbkey	ivg_build_name
 web_link_main	web current	http://www.broadinstitute.org/igv/projects/current/igv.php	hg_g1k_v37	b37
 #web_jnlp_1.5	web 1.5	http://www.broadinstitute.org/igvdata/jws/prod	hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum	hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum
-#local_default	local	http://localhost:60151/load	hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum	hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum
+local_default	local	http://localhost:60151/load	hg38,hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum	hg38,hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum

From 6fee45fbfda52146faec6f89ebb59de068f4541d Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 6 Apr 2015 11:37:47 -0400
Subject: [PATCH 32/88] Bugfixes for runtime parameter handling in the workflow
 run form.

The behavior of these forms was modified in PR 433 (https://bitbucket.org/galaxy/galaxy-central/pull-request/433/fix-allow-editing-workflows-on-the-fly-for/diff# - not merged by me :| ) - so that the entire workflow would be submitted as runtime parameters on each submission.

In addition to this causing bugs related to unvalidated parameters https://trello.com/c/72WuZ8mu and other problems with select parameters (e.g. http://dev.list.galaxyproject.org/Workflow-bug-when-loc-entries-are-missing-tc4666875.html) - I just discovered it would also cause the modified value to be submitted even if the user opts to undo the selection of a runtime workflow parameter and restore the previous selection (i.e. the form would show the original value but the new value would be submitted).

This PR restores the previous behavior of giving the submitted form elements a unique name so every value in the workflow is not replaced as part of the submission - fixing the former problem. The new technique also fixes the other problem as well.
---
 templates/webapps/galaxy/workflow/run.mako | 19 ++++++++++++++-----
 1 file changed, 14 insertions(+), 5 deletions(-)

diff --git a/templates/webapps/galaxy/workflow/run.mako b/templates/webapps/galaxy/workflow/run.mako
index b70f07142dd..dfcdd9ec189 100644
--- a/templates/webapps/galaxy/workflow/run.mako
+++ b/templates/webapps/galaxy/workflow/run.mako
@@ -154,11 +154,11 @@
 
          $(".workflow-edit-button").on("click",function(){
                 var state = $(this).attr("name");
-                var stepToolBox = $(this).parent().find('input:not([class]):not([type="hidden"]), select:not([class])');
-                var labels = $(this).parent().find('label');
+                var stepToolBox = $(this).parent().parent().find('.editable-param').find('input:not([class]):not([type="hidden"]), select:not([class])');
+                var labels = $(this).parent().parent().find('.editable-param').find('label');
                 var split_name = stepToolBox.attr("name").split("|");
                 var step_id = split_name[0];
-                var step_name = split_name.slice(1, split_name.length).join("|");
+                var step_name = split_name.slice(2, split_name.length).join("|");
                 var hidden_html = "<input type='hidden' name='"+step_id+"|__runtime__"+step_name+"' value='true' />";
                 var html = "";
                 if (state === "edit"){
@@ -179,9 +179,9 @@
                 }
                 else{
                     $(this).parent().find(".editable").hide();
+                    $(this).parent().find(".editable").empty();
                     $(this).parent().parent().find(".uneditable_field").show();
                     $(this).attr("name", "edit");
-                    stepToolBox.hide();
                     readyParameter($(this));
                 }
             }).each(function(i, icon) {
@@ -281,6 +281,9 @@
     .editable {
         display: none;
     }
+    .editable-param {
+        display: none;
+    }
 
     .workflow-edit-button-editing {
         color: black;
@@ -448,11 +451,17 @@ if wf_parms:
                     </span>
                     <span class="editable_field">
                         <span class="editable">
-                            ${param.get_html_field( t, value, other_values).get_html( str(step.id) + "|"+ prefix )}
                         </span>
 
                         <i class="fa workflow-edit-button"></i>
                     </span>
+                    <span class="editable-param">
+                        <!-- Pristine variant of param, this will be cloned
+                             and modified when the user opts to make this
+                             editable.
+                        -->
+                        ${param.get_html_field( t, value, other_values).get_html( str(step.id) + "|"+ "editable" + "|" + prefix )}
+                    </span>
                 </span>
                 %endif
             %endif

From 4a6484593f6cf376ae210f21595fccca808b1312 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 6 Apr 2015 13:03:47 -0400
Subject: [PATCH 33/88] Add a line to run_test.sh help detailing how to run a
 single API test.

---
 run_tests.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/run_tests.sh b/run_tests.sh
index 8b5dc93f61a..f9cd194c635 100755
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -13,6 +13,7 @@ cat <<EOF
 '${0##*/} -sid ccc'                 for testing one section with sid 'ccc' ('ccc' is the string after 'section::')
 '${0##*/} -list'                    for listing all the tool ids
 '${0##*/} -api'                     for running all the test scripts in the ./test/api directory
+'${0##*/} -api test/api/<file>.py:<class>.<test_name>'    for running one specific API test
 '${0##*/} -toolshed'                for running all the test scripts in the ./test/tool_shed/functional directory
 '${0##*/} -toolshed testscriptname' for running one test script named testscriptname in the .test/tool_shed/functional directory
 '${0##*/} -workflow test.xml'       for running a workflow test case as defined by supplied workflow xml test file (experimental)

From 9bf00daaae9c5ef5b4a4b614868da1c9b9447187 Mon Sep 17 00:00:00 2001
From: Matt Shirley <mdshw5@gmail.com>
Date: Mon, 6 Apr 2015 13:34:19 -0400
Subject: [PATCH 34/88] Add NCBI SRA datatype mdshw5/sra-tools-galaxy#1

Note that the ncbi/sra-tools [wiki](https://github.com/ncbi/sra-tools/wiki/HowTo:-Access-SRA-Data) discourages users downloading SRA data  using anything other than `prefetch`, `ascp`, or the "on-demand" fetching built in to all newer toolkit versions. However, it is still a common occurrence for Galaxy users to email me asking how to upload a ".sra" file into their history.

Support for SRA datatypes also partially mitigates the problem of shared caching for the `prefetch` and "on-demand" download methods of the toolkit.

CC: @jmchilton
---
 lib/galaxy/datatypes/binary.py | 37 ++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index 4fe54baabff..42f80cacc84 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -753,3 +753,40 @@ class Xlsx(Binary):
 
 Binary.register_sniffable_binary_format("xlsx", "xlsx", Xlsx)
 
+
+class Sra( Binary ):
+    """ Sequence Read Archive (SRA) datatype originally from mdshw5/sra-tools-galaxy"""
+    file_ext = 'sra'
+
+    def __init__( self, **kwd ):
+        Binary.__init__( self, **kwd )
+
+    def sniff( self, filename ):
+        """ The first 8 bytes of any NCBI sra file is 'NCBI.sra', and the file is binary.
+        For details about the format, see http://www.ncbi.nlm.nih.gov/books/n/helpsra/SRA_Overview_BK/#SRA_Overview_BK.4_SRA_Data_Structure
+        """
+        try:
+            header = open(filename).read(8)
+            if binascii.b2a_hex(header) == binascii.hexlify('NCBI.sra'):
+                return True
+            else:
+                return False
+        except:
+            return False
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        if not dataset.dataset.purged:
+            dataset.peek  = 'Binary sra file'
+            dataset.blurb = data.nice_size(dataset.get_size())
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+    def display_peek(self, dataset):
+        try:
+            return dataset.peek
+        except:
+            return 'Binary sra file (%s)' % (data.nice_size(dataset.get_size()))
+
+Binary.register_sniffable_binary_format('sra', 'sra', Sra)
+

From fb3d622041bf589bc2b7d7dc737fa80f2eeb6a87 Mon Sep 17 00:00:00 2001
From: Carl Eberhard <carlfeberhard@gmail.com>
Date: Mon, 6 Apr 2015 13:44:21 -0400
Subject: [PATCH 35/88] Fix: datasets.purge_async/_purge to allow purging hdas
 within non-current histories

---
 lib/galaxy/webapps/galaxy/controllers/dataset.py | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/controllers/dataset.py b/lib/galaxy/webapps/galaxy/controllers/dataset.py
index 071bbbf3c13..b71ca7352b9 100644
--- a/lib/galaxy/webapps/galaxy/controllers/dataset.py
+++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py
@@ -852,22 +852,24 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesItemRatings, Uses
         status = 'done'
         try:
             id = trans.app.security.decode_id( dataset_id )
-            history = trans.get_history()
             user = trans.get_user()
             hda = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( id )
             # Invalid HDA
             assert hda, 'Invalid history dataset ID'
+
             # Walk up parent datasets to find the containing history
+            history = trans.get_history()
             topmost_parent = hda
             while topmost_parent.parent:
                 topmost_parent = topmost_parent.parent
-            assert topmost_parent in history.datasets, "Data does not belong to current history"
             # If the user is anonymous, make sure the HDA is owned by the current session.
             if not user:
-                assert trans.galaxy_session.current_history_id == trans.history.id, 'Invalid history dataset ID'
+                current_history_id = trans.galaxy_session.current_history_id
+                assert topmost_parent.history.id == current_history_id, 'Data does not belong to current user'
             # If the user is known, make sure the HDA is owned by the current user.
             else:
-                assert topmost_parent.history.user == trans.user, 'Invalid history dataset ID'
+                assert topmost_parent.history.user == user, 'Data does not belong to current user'
+
             # Ensure HDA is deleted
             hda.deleted = True
             # HDA is purgeable
@@ -890,8 +892,8 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesItemRatings, Uses
                 except:
                     log.exception( 'Unable to purge dataset (%s) on purge of HDA (%s):' % ( hda.dataset.id, hda.id ) )
             trans.sa_session.flush()
-        except Exception:
-            msg = 'HDA purge failed (encoded: %s, decoded: %s)' % ( dataset_id, id )
+        except Exception, exc:
+            msg = 'HDA purge failed (encoded: %s, decoded: %s): %s' % ( dataset_id, id, exc )
             log.exception( msg )
             trans.log_event( msg )
             message = 'Dataset removal from disk failed'

From f6299976f3acedf404561dcfa7406918d7dcc8b1 Mon Sep 17 00:00:00 2001
From: Matt Shirley <mdshw5@gmail.com>
Date: Mon, 6 Apr 2015 15:01:04 -0400
Subject: [PATCH 36/88] Checkout proper branch...

---
 config/datatypes_conf.xml.sample | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
index 726f231384c..42b874b46cc 100644
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -186,6 +186,7 @@
         <converter file="tabular_to_dbnsfp.xml" target_datatype="snpsiftdbnsfp"/>
     </datatype>
     <datatype extension="sff" type="galaxy.datatypes.binary:Sff" mimetype="application/octet-stream" display_in_upload="true" description="A binary file in 'Standard Flowgram Format' with a '.sff' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Sff"/>
+    <datatype extension="sra" type="galaxy.datatypes.binary:Sra" mimetype="application/octet-stream" display_in_upload="true" description="A binary file archive format from the NCBI Sequence Read Archive with a '.sra' file extension." description_url="http://www.ncbi.nlm.nih.gov/books/n/helpsra/SRA_Overview_BK/#SRA_Overview_BK.4_SRA_Data_Structure"/>
     <datatype extension="svg" type="galaxy.datatypes.images:Image" mimetype="image/svg+xml"/>
     <datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/>
     <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true" description="Any data in tab delimited format (tabular)." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Tabular_.28tab_delimited.29"/>
@@ -285,6 +286,7 @@
     <sniffer type="galaxy.datatypes.binary:SQlite"/>
     <sniffer type="galaxy.datatypes.binary:Bam"/>
     <sniffer type="galaxy.datatypes.binary:Sff"/>
+    <sniffer type="galaxy.datatypes.binary:Sra"/>
     <sniffer type="galaxy.datatypes.xml:Phyloxml"/>
     <sniffer type="galaxy.datatypes.xml:Owl"/>
     <sniffer type="galaxy.datatypes.xml:GenericXml"/>

From 359dceabf83f7470c6766e2a19efd70c930d5df0 Mon Sep 17 00:00:00 2001
From: David Trudgian <david.trudgian@utsouthwestern.edu>
Date: Mon, 6 Apr 2015 14:31:06 -0500
Subject: [PATCH 37/88] Split LDAP from AD auth provider (in name only at
 present) Suggested and supplied by @jmchilton

---
 lib/galaxy/auth/providers/ldap_ad.py | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/auth/providers/ldap_ad.py b/lib/galaxy/auth/providers/ldap_ad.py
index b4b6c87a8fd..491fb0b26e7 100644
--- a/lib/galaxy/auth/providers/ldap_ad.py
+++ b/lib/galaxy/auth/providers/ldap_ad.py
@@ -19,7 +19,7 @@ def _get_subs(d, k, params):
     return str(d[k]).format(**params)
 
 
-class LDAPAD(AuthProvider):
+class LDAP(AuthProvider):
 
     """
     Attempts to authenticate users against an LDAP server.
@@ -28,7 +28,7 @@ class LDAPAD(AuthProvider):
     those fields first.  After that it will bind to LDAP with the username
     (formatted as specified).
     """
-    plugin_type = 'ldap_ad'
+    plugin_type = 'ldap'
 
     def authenticate(self, login, password, options):
         """
@@ -115,4 +115,10 @@ class LDAPAD(AuthProvider):
         else:
             return self.authenticate(user.email, password, options)[0]
 
-__all__ = ['LDAPAD']
+
+class ActiveDirectory(LDAP):
+     """ Effectively just an alias for LDAP auth, but may contain active directory specific
+     logic in the future. """
+     plugin_type = 'activedirectory'
+
+__all__ = ['LDAP', 'ActiveDirectory']

From 42eb4837d8ab8e16fe3673d416d31c6f7ecfd46c Mon Sep 17 00:00:00 2001
From: David Trudgian <david.trudgian@utsouthwestern.edu>
Date: Mon, 6 Apr 2015 14:36:45 -0500
Subject: [PATCH 38/88] Missed PEP8 indent rule again - sorry

---
 lib/galaxy/auth/providers/ldap_ad.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/auth/providers/ldap_ad.py b/lib/galaxy/auth/providers/ldap_ad.py
index 491fb0b26e7..ef2dddb83b8 100644
--- a/lib/galaxy/auth/providers/ldap_ad.py
+++ b/lib/galaxy/auth/providers/ldap_ad.py
@@ -117,8 +117,8 @@ class LDAP(AuthProvider):
 
 
 class ActiveDirectory(LDAP):
-     """ Effectively just an alias for LDAP auth, but may contain active directory specific
-     logic in the future. """
-     plugin_type = 'activedirectory'
+    """ Effectively just an alias for LDAP auth, but may contain active directory specific
+    logic in the future. """
+    plugin_type = 'activedirectory'
 
 __all__ = ['LDAP', 'ActiveDirectory']

From 894cc1cb28462950f56aebec03044383904a3b68 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 6 Apr 2015 17:17:24 -0400
Subject: [PATCH 39/88] Clarify optional test name specification for nose tests
 and add a couple examples.

---
 run_tests.sh | 30 ++++++++++++++++++++----------
 1 file changed, 20 insertions(+), 10 deletions(-)

diff --git a/run_tests.sh b/run_tests.sh
index f9cd194c635..b37103b669b 100755
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -3,30 +3,40 @@
 ./scripts/common_startup.sh
 
 # A good place to look for nose info: http://somethingaboutorange.com/mrl/projects/nose/
-rm -f run_functional_tests.log 
+rm -f run_functional_tests.log
 
 show_help() {
 cat <<EOF
-'${0##*/}'                          for testing all the tools in functional directory
-'${0##*/} aaa'                      for testing one test case of 'aaa' ('aaa' is the file name with path)
+'${0##*/} (test_path)'              for testing all the tools in functional directory
 '${0##*/} -id bbb'                  for testing one tool with id 'bbb' ('bbb' is the tool id)
 '${0##*/} -sid ccc'                 for testing one section with sid 'ccc' ('ccc' is the string after 'section::')
 '${0##*/} -list'                    for listing all the tool ids
-'${0##*/} -api'                     for running all the test scripts in the ./test/api directory
-'${0##*/} -api test/api/<file>.py:<class>.<test_name>'    for running one specific API test
-'${0##*/} -toolshed'                for running all the test scripts in the ./test/tool_shed/functional directory
-'${0##*/} -toolshed testscriptname' for running one test script named testscriptname in the .test/tool_shed/functional directory
+'${0##*/} -api (test_path)'         for running all the test scripts in the ./test/api directory
+'${0##*/} -toolshed (test_path)'    for running all the test scripts in the ./test/tool_shed/functional directory
 '${0##*/} -workflow test.xml'       for running a workflow test case as defined by supplied workflow xml test file (experimental)
-'${0##*/} -framework'               for running through example tool tests testing framework features in test/functional/tools"   
+'${0##*/} -framework'               for running through example tool tests testing framework features in test/functional/tools"
 '${0##*/} -framework -id toolid'    for testing one framework tool (in test/functional/tools/) with id 'toolid'
 '${0##*/} -data_managers -id data_manager_id'    for testing one Data Manager with id 'data_manager_id'
-'${0##*/} -unit'                    for running all unit tests (doctests in lib and tests in test/unit)
-'${0##*/} -unit testscriptath'      running particular tests scripts
+'${0##*/} -unit (test_path)'        for running all unit tests (doctests in lib and tests in test/unit)
 '${0##*/} -qunit'                   for running qunit JavaScript tests
 '${0##*/} -qunit testname'          for running single JavaScript test with given name
 
+
+Nose tests will allow specific tests to be selected per the documentation at
+https://nose.readthedocs.org/en/latest/usage.html#selecting-tests.  These are
+indicated with the optional parameter (test_path).  A few examples are:
+
+Run all TestUserInfo functional tests:
+    ./run_tests.sh test/functional/test_user_info.py:TestUserInfo.test_005_create_user_info_forms
+
+Run a specific API test requiring the framework test tools:
+    ./run_tests.sh -api -with_framework_test_tools test/api/test_tools.py:ToolsTestCase.test_map_over_with_output_format_actions
+
+
 Extra options:
 
+
+
  --verbose_errors      Force some tests produce more verbose error reporting.
  --no_cleanup          Do not delete temp files for Python functional tests (-toolshed, -framework, etc...)
  --report_file         Path of HTML report to produce (for Python Galaxy functional tests).

From af8ddb14a37b38b35d2c2b64286b774dcbc5eb3a Mon Sep 17 00:00:00 2001
From: yhoogstrate <y.hoogstrate@erasmusmc.nl>
Date: Tue, 7 Apr 2015 14:59:29 +0200
Subject: [PATCH 40/88] ScatterPlot No API connection for nested www_root

ScatterPlot makes use of a hardcoded API url which is incorrect for certain server configuratoins. Currently these servers need to be manually configured to link to the correct API URL. This patch creates the correct URL from the parental variable parent.galaxy_config.root and returns "/" if this variable can not be found. More visualisations suffer from this bug and have to be patched as well.
---
 .../visualizations/scatterplot/static/scatterplot-edit.js       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/plugins/visualizations/scatterplot/static/scatterplot-edit.js b/config/plugins/visualizations/scatterplot/static/scatterplot-edit.js
index fc44b025410..be7cc5c296b 100644
--- a/config/plugins/visualizations/scatterplot/static/scatterplot-edit.js
+++ b/config/plugins/visualizations/scatterplot/static/scatterplot-edit.js
@@ -1 +1 @@
-function scatterplot(a,b,c){function d(){var a={v:{},h:{}};return a.v.lines=p.selectAll("line.v-grid-line").data(m.x.ticks(q.x.fn.ticks()[0])),a.v.lines.enter().append("svg:line").classed("grid-line v-grid-line",!0),a.v.lines.attr("x1",m.x).attr("x2",m.x).attr("y1",0).attr("y2",b.height),a.v.lines.exit().remove(),a.h.lines=p.selectAll("line.h-grid-line").data(m.y.ticks(q.y.fn.ticks()[0])),a.h.lines.enter().append("svg:line").classed("grid-line h-grid-line",!0),a.h.lines.attr("x1",0).attr("x2",b.width).attr("y1",m.y).attr("y2",m.y),a.h.lines.exit().remove(),a}function e(){return t.attr("cx",function(a,b){return m.x(j(a,b))}).attr("cy",function(a,b){return m.y(k(a,b))}).style("display","block").filter(function(){var a=d3.select(this).attr("cx"),c=d3.select(this).attr("cy");return 0>a||a>b.width?!0:0>c||c>b.height?!0:!1}).style("display","none")}function f(){$(".chart-info-box").remove(),q.redraw(),e(),s=d(),$(o.node()).trigger("zoom.scatterplot",{scale:n.scale(),translate:n.translate()})}function g(a,c,d){return c+=8,$(['<div class="chart-info-box" style="position: absolute">',void 0!==b.idColumn?"<div>"+d[b.idColumn]+"</div>":"","<div>",j(d),"</div>","<div>",k(d),"</div>","</div>"].join("")).css({top:a,left:c,"z-index":2})}var h=function(a,b){return"translate("+a+","+b+")"},i=function(a,b,c){return"rotate("+a+","+b+","+c+")"},j=function(a){return a[b.xColumn]},k=function(a){return a[b.yColumn]},l={x:{extent:d3.extent(c,j)},y:{extent:d3.extent(c,k)}},m={x:d3.scale.linear().domain(l.x.extent).range([0,b.width]),y:d3.scale.linear().domain(l.y.extent).range([b.height,0])},n=d3.behavior.zoom().x(m.x).y(m.y).scaleExtent([1,30]).scale(b.scale||1).translate(b.translate||[0,0]),o=d3.select(a).attr("class","scatterplot").attr("width","100%").attr("height",b.height+(b.margin.top+b.margin.bottom)),p=o.append("g").attr("class","content").attr("transform",h(b.margin.left,b.margin.top)).call(n);p.append("rect").attr("class","zoom-rect").attr("width",b.width).attr("height",b.height).style("fill","transparent");var q={x:{},y:{}};q.x.fn=d3.svg.axis().orient("bottom").scale(m.x).ticks(b.xTicks).tickFormat(d3.format("s")),q.y.fn=d3.svg.axis().orient("left").scale(m.y).ticks(b.yTicks).tickFormat(d3.format("s")),q.x.g=p.append("g").attr("class","x axis").attr("transform",h(0,b.height)).call(q.x.fn),q.y.g=p.append("g").attr("class","y axis").call(q.y.fn);var r=6;q.x.label=o.append("text").attr("id","x-axis-label").attr("class","axis-label").text(b.xLabel).attr("text-anchor","middle").attr("dominant-baseline","text-after-edge").attr("x",b.width/2+b.margin.left).attr("y",b.height+b.margin.bottom+b.margin.top-r),q.y.label=o.append("text").attr("id","y-axis-label").attr("class","axis-label").text(b.yLabel).attr("text-anchor","middle").attr("dominant-baseline","text-before-edge").attr("x",r).attr("y",b.height/2).attr("transform",i(-90,r,b.height/2)),q.redraw=function(){o.select(".x.axis").call(q.x.fn),o.select(".y.axis").call(q.y.fn)};var s=d(),t=p.selectAll(".glyph").data(c).enter().append("svg:circle").classed("glyph",!0).attr("cx",function(a,b){return m.x(j(a,b))}).attr("cy",function(a,b){return m.y(k(a,b))}).attr("r",0);t.transition().duration(b.animDuration).attr("r",b.datapointSize),e(),n.on("zoom",f),t.on("mouseover",function(a,c){var d=d3.select(this);d.classed("highlight",!0).style("fill","red").style("fill-opacity",1),p.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",d.attr("cx")-b.datapointSize).attr("y1",d.attr("cy")).attr("x2",0).attr("y2",d.attr("cy")).classed("hoverline",!0),d.attr("cy")<b.height&&p.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",d.attr("cx")).attr("y1",+d.attr("cy")+b.datapointSize).attr("x2",d.attr("cx")).attr("y2",b.height).classed("hoverline",!0);var e=this.getBoundingClientRect();$("body").append(g(e.top,e.right,a)),$(o.node()).trigger("mouseover-datapoint.scatterplot",[this,a,c])}),t.on("mouseout",function(){d3.select(this).classed("highlight",!1).style("fill","black").style("fill-opacity",.2),p.selectAll(".hoverline").remove(),$(".chart-info-box").remove()})}this.scatterplot=this.scatterplot||{},this.scatterplot.chartcontrol=Handlebars.template({compiler:[6,">= 2.0.0-beta.1"],main:function(a,b,c,d){var e,f="function",g=b.helperMissing,h=this.escapeExpression;return'<p class="help-text">\n    Use the following controls to how the chart is displayed.\n    The slide controls can be moved by the mouse or, if the \'handle\' is in focus, your keyboard\'s arrow keys.\n    Move the focus between controls by using the tab or shift+tab keys on your keyboard.\n    Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n</p>\n\n<div data-config-key="datapointSize" class="form-input numeric-slider-input">\n    <label for="datapointSize">Size of data point: </label>\n    <div class="slider-output">'+h((e=null!=(e=b.datapointSize||(null!=a?a.datapointSize:a))?e:g,typeof e===f?e.call(a,{name:"datapointSize",hash:{},data:d}):e))+'</div>\n    <div class="slider"></div>\n    <p class="form-help help-text-small">\n        Size of the graphic representation of each data point\n    </p>\n</div>\n\n<div data-config-key="width" class="form-input numeric-slider-input">\n    <label for="width">Chart width: </label>\n    <div class="slider-output">'+h((e=null!=(e=b.width||(null!=a?a.width:a))?e:g,typeof e===f?e.call(a,{name:"width",hash:{},data:d}):e))+'</div>\n    <div class="slider"></div>\n    <p class="form-help help-text-small">\n        (not including chart margins and axes)\n    </p>\n</div>\n\n<div data-config-key="height" class="form-input numeric-slider-input">\n    <label for="height">Chart height: </label>\n    <div class="slider-output">'+h((e=null!=(e=b.height||(null!=a?a.height:a))?e:g,typeof e===f?e.call(a,{name:"height",hash:{},data:d}):e))+'</div>\n    <div class="slider"></div>\n    <p class="form-help help-text-small">\n        (not including chart margins and axes)\n    </p>\n</div>\n\n<div data-config-key="X-axis-label"class="text-input form-input">\n    <label for="X-axis-label">Re-label the X axis: </label>\n    <input type="text" name="X-axis-label" id="X-axis-label" value="'+h((e=null!=(e=b.xLabel||(null!=a?a.xLabel:a))?e:g,typeof e===f?e.call(a,{name:"xLabel",hash:{},data:d}):e))+'" />\n    <p class="form-help help-text-small"></p>\n</div>\n\n<div data-config-key="Y-axis-label" class="text-input form-input">\n    <label for="Y-axis-label">Re-label the Y axis: </label>\n    <input type="text" name="Y-axis-label" id="Y-axis-label" value="'+h((e=null!=(e=b.yLabel||(null!=a?a.yLabel:a))?e:g,typeof e===f?e.call(a,{name:"yLabel",hash:{},data:d}):e))+'" />\n    <p class="form-help help-text-small"></p>\n</div>\n\n<button class="render-button btn btn-primary active">Draw</button>\n'},useData:!0}),this.scatterplot.datacontrol=Handlebars.template({compiler:[6,">= 2.0.0-beta.1"],main:function(a,b,c,d){var e,f,g="function",h=b.helperMissing,i='<p class="help-text">\n    Use the following control to change which columns are used by the chart. Click any cell\n    from the last three rows of the table to select the column for the appropriate data.\n    Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n</p>\n\n<ul class="help-text" style="margin-left: 8px">\n    <li><b>X Column</b>: which column values will be used for the x axis of the chart.</li>\n    <li><b>Y Column</b>: which column values will be used for the y axis of the chart.</li>\n    <li><b>ID Column</b>: an additional column value displayed when the user hovers over a data point.\n    It may be useful to select unique or categorical identifiers here (such as gene ids).\n    </li>\n</ul>\n\n<div class="column-selection">\n    <pre class="peek">';return f=null!=(f=b.peek||(null!=a?a.peek:a))?f:h,e=typeof f===g?f.call(a,{name:"peek",hash:{},data:d}):f,null!=e&&(i+=e),i+'</pre>\n</div>\n\n<p class="help-text help-text-small">\n    <b>Note</b>: If it can be determined from the dataset\'s filetype that a column is not numeric,\n    that column choice may be disabled for either the x or y axis.\n</p>\n\n<button class="render-button btn btn-primary active">Draw</button>\n'},useData:!0}),this.scatterplot.editor=Handlebars.template({compiler:[6,">= 2.0.0-beta.1"],main:function(){return'<div class="scatterplot-editor tabbable tabs-left">\n    <ul class="nav nav-tabs">\n        <li class="active">\n            <a title="Use this tab to change which data are used"\n               href="#data-control" data-toggle="tab">Data Controls</a>\n        </li>\n        <li>\n            <a title="Use this tab to change how the chart is drawn"\n               href="#chart-control" data-toggle="tab" >Chart Controls</a>\n        </li>\n        <li class="disabled">\n            <a title="This tab will display the chart"\n               href="#chart-display" data-toggle="tab">Chart</a>\n        </li>\n        <li class="file-controls">\n<!--            <button class="copy-btn btn btn-default"\n                    title="Save this as a new visualization">Save to new</button>-->\n            <button class="save-btn btn btn-default">Save</button>\n        </li>\n    </ul>\n\n    <div class="tab-content">\n        <div id="data-control" class="scatterplot-config-control tab-pane active">\n        </div>\n    \n        <div id="chart-control" class="scatterplot-config-control tab-pane">\n        </div>\n\n        <div id="chart-display" class="scatterplot-display tab-pane"></div>\n\n    </div>\n</div>\n'},useData:!0});var ScatterplotConfigEditor=Backbone.View.extend({className:"scatterplot-control-form",initialize:function(a){if(this.model||(this.model=new Visualization({type:"scatterplot"})),!a||!a.dataset)throw new Error("ScatterplotConfigEditor requires a dataset");this.dataset=a.dataset,this.display=new ScatterplotDisplay({dataset:a.dataset,model:this.model})},render:function(){this.$el.empty().append(ScatterplotConfigEditor.templates.mainLayout({})),this.model.id&&(this.$el.find(".copy-btn").show(),this.$el.find(".save-btn").text("Update saved")),this.$el.find("[title]").tooltip(),this._render_dataControl(),this._render_chartControls(),this._render_chartDisplay();var a=this.model.get("config");return this.model.id&&_.isFinite(a.xColumn)&&_.isFinite(a.yColumn)&&this.renderChart(),this},_getColumnIndecesByType:function(){var a={numeric:[],text:[],all:[]};return _.each(this.dataset.metadata_column_types||[],function(b,c){"int"===b||"float"===b?a.numeric.push(c):("str"===b||"list"===b)&&a.text.push(c),a.all.push(c)}),a.numeric.length<2&&(a.numeric=[]),a},_render_dataControl:function(a){a=a||this.$el;var b=this,c=this.model.get("config"),d=this._getColumnIndecesByType(),e=a.find(".tab-pane#data-control");return e.html(ScatterplotConfigEditor.templates.dataControl({peek:this.dataset.peek})),e.find(".peek").peekColumnSelector({controls:[{label:"X Column",id:"xColumn",selected:c.xColumn,disabled:d.text},{label:"Y Column",id:"yColumn",selected:c.yColumn,disabled:d.text},{label:"ID Column",id:"idColumn",selected:c.idColumn}]}).on("peek-column-selector.change",function(a,c){b.model.set("config",c)}).on("peek-column-selector.rename",function(){}),e.find("[title]").tooltip(),e},_render_chartControls:function(a){function b(){var a=$(this),b=a.slider("value");c.model.set("config",_.object([[a.parent().data("config-key"),b]])),a.siblings(".slider-output").text(b)}a=a||this.$el;var c=this,d=this.model.get("config"),e=a.find("#chart-control");e.html(ScatterplotConfigEditor.templates.chartControl(d));var f={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};e.find(".numeric-slider-input").each(function(){var a=$(this),c=a.attr("data-config-key"),e=_.extend(f[c],{value:d[c],change:b,slide:b});a.find(".slider").slider(e),a.children(".slider-output").text(d[c])});var g=this.dataset.metadata_column_names||[],h=d.xLabel||g[d.xColumn]||"X",i=d.yLabel||g[d.yColumn]||"Y";return e.find('input[name="X-axis-label"]').val(h).on("change",function(){c.model.set("config",{xLabel:$(this).val()})}),e.find('input[name="Y-axis-label"]').val(i).on("change",function(){c.model.set("config",{yLabel:$(this).val()})}),e.find("[title]").tooltip(),e},_render_chartDisplay:function(a){a=a||this.$el;var b=a.find(".tab-pane#chart-display");return this.display.setElement(b),this.display.render(),b.find("[title]").tooltip(),b},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","click #data-control .render-button":"renderChart","click #chart-control .render-button":"renderChart","click .save-btn":"saveVisualization"},saveVisualization:function(){var a=this;this.model.save().fail(function(b,c,d){console.error(b,c,d),a.trigger("save:error",view),alert("Error loading data:\n"+b.responseText)}).then(function(){a.display.render()})},toggleThirdColumnSelector:function(){this.$el.find('select[name="idColumn"]').parent().toggle()},renderChart:function(){this.$el.find(".nav li.disabled").removeClass("disabled"),this.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show"),this.display.fetchData()},toString:function(){return"ScatterplotConfigEditor("+(this.dataset?this.dataset.id:"")+")"}});ScatterplotConfigEditor.templates={mainLayout:scatterplot.editor,dataControl:scatterplot.datacontrol,chartControl:scatterplot.chartcontrol};var ScatterplotDisplay=Backbone.View.extend({initialize:function(a){this.data=null,this.dataset=a.dataset,this.lineCount=this.dataset.metadata_data_lines||null},fetchData:function(){this.showLoadingIndicator();var a=this,b=this.model.get("config"),c=jQuery.getJSON("/api/datasets/"+this.dataset.id,{data_type:"raw_data",provider:"dataset-column",limit:b.pagination.perPage,offset:b.pagination.currPage*b.pagination.perPage});return c.done(function(b){a.data=b.data,a.trigger("data:fetched",a),a.renderData()}),c.fail(function(b,c,d){console.error(b,c,d),a.trigger("data:error",a),alert("Error loading data:\n"+b.responseText)}),c},showLoadingIndicator:function(){this.$el.find(".scatterplot-data-info").html(['<div class="loading-indicator">','<span class="fa fa-spinner fa-spin"></span>','<span class="loading-indicator-message">loading...</span>',"</div>"].join(""))},template:function(){var a=['<div class="controls clear">','<div class="right">','<p class="scatterplot-data-info"></p>','<button class="stats-toggle-btn">Stats</button>','<button class="rerender-btn">Redraw</button>',"</div>",'<div class="left">','<div class="page-control"></div>',"</div>","</div>","<svg/>",'<div class="stats-display"></div>'].join("");return a},render:function(){return this.$el.addClass("scatterplot-display").html(this.template()),this.data&&this.renderData(),this},renderData:function(){this.renderLeftControls(),this.renderRightControls(),this.renderPlot(this.data),this.getStats()},renderLeftControls:function(){var a=this,b=this.model.get("config");return this.$el.find(".controls .left .page-control").pagination({startingPage:b.pagination.currPage,perPage:b.pagination.perPage,totalDataSize:this.lineCount,currDataSize:this.data.length}).off().on("pagination.page-change",function(c,d){b.pagination.currPage=d,a.model.set("config",{pagination:b.pagination}),a.resetZoom(),a.fetchData()}),this},renderRightControls:function(){var a=this;this.setLineInfo(this.data),this.$el.find(".stats-toggle-btn").off().click(function(){a.toggleStats()}),this.$el.find(".rerender-btn").off().click(function(){a.resetZoom(),a.renderPlot(this.data)})},renderPlot:function(){var a=this,b=this.$el.find("svg");this.toggleStats(!1),b.off().empty().show().on("zoom.scatterplot",function(b,c){a.model.set("config",c)}),scatterplot(b.get(0),this.model.get("config"),this.data)},setLineInfo:function(a,b){if(a){var c=this.model.get("config"),d=this.lineCount||"an unknown total",e=c.pagination.currPage*c.pagination.perPage,f=e+a.length;this.$el.find(".controls p.scatterplot-data-info").text([e+1,"to",f,"of",d].join(" "))}else this.$el.find(".controls p.scatterplot-data-info").html(b||"");return this},resetZoom:function(a,b){return a=void 0!==a?a:1,b=void 0!==b?b:[0,0],this.model.set("config",{scale:a,translate:b}),this},getStats:function(){if(this.data){var a=this,b=this.model.get("config"),c=new Worker("/plugins/visualizations/scatterplot/static/worker-stats.js");c.postMessage({data:this.data,keys:[b.xColumn,b.yColumn]}),c.onerror=function(){c.terminate()},c.onmessage=function(b){a.renderStats(b.data)}}},renderStats:function(a){var b=this.model.get("config"),c=this.$el.find(".stats-display"),d=b.xLabel,e=b.yLabel,f=$("<table/>").addClass("table").append(["<thead><th></th><th>",d,"</th><th>",e,"</th></thead>"].join("")).append(_.map(a,function(a,b){return $(["<tr><td>",b,"</td><td>",a[0],"</td><td>",a[1],"</td></tr>"].join(""))}));c.empty().append(f)},toggleStats:function(a){var b=this.$el.find(".stats-display");a=void 0===a?b.is(":hidden"):a,a?(this.$el.find("svg").hide(),b.show(),this.$el.find(".controls .stats-toggle-btn").text("Plot")):(b.hide(),this.$el.find("svg").show(),this.$el.find(".controls .stats-toggle-btn").text("Stats"))},toString:function(){return"ScatterplotView()"}}),ScatterplotModel=Visualization.extend({defaults:{type:"scatterplot",config:{pagination:{currPage:0,perPage:3e3},width:400,height:400,margin:{top:16,right:16,bottom:40,left:54},xTicks:10,xLabel:"X",yTicks:10,yLabel:"Y",datapointSize:4,animDuration:500,scale:1,translate:[0,0]}}});
\ No newline at end of file
+function scatterplot(a,b,c){function d(){var a={v:{},h:{}};return a.v.lines=p.selectAll("line.v-grid-line").data(m.x.ticks(q.x.fn.ticks()[0])),a.v.lines.enter().append("svg:line").classed("grid-line v-grid-line",!0),a.v.lines.attr("x1",m.x).attr("x2",m.x).attr("y1",0).attr("y2",b.height),a.v.lines.exit().remove(),a.h.lines=p.selectAll("line.h-grid-line").data(m.y.ticks(q.y.fn.ticks()[0])),a.h.lines.enter().append("svg:line").classed("grid-line h-grid-line",!0),a.h.lines.attr("x1",0).attr("x2",b.width).attr("y1",m.y).attr("y2",m.y),a.h.lines.exit().remove(),a}function e(){return t.attr("cx",function(a,b){return m.x(j(a,b))}).attr("cy",function(a,b){return m.y(k(a,b))}).style("display","block").filter(function(){var a=d3.select(this).attr("cx"),c=d3.select(this).attr("cy");return 0>a||a>b.width?!0:0>c||c>b.height?!0:!1}).style("display","none")}function f(){$(".chart-info-box").remove(),q.redraw(),e(),s=d(),$(o.node()).trigger("zoom.scatterplot",{scale:n.scale(),translate:n.translate()})}function g(a,c,d){return c+=8,$(['<div class="chart-info-box" style="position: absolute">',void 0!==b.idColumn?"<div>"+d[b.idColumn]+"</div>":"","<div>",j(d),"</div>","<div>",k(d),"</div>","</div>"].join("")).css({top:a,left:c,"z-index":2})}var h=function(a,b){return"translate("+a+","+b+")"},i=function(a,b,c){return"rotate("+a+","+b+","+c+")"},j=function(a){return a[b.xColumn]},k=function(a){return a[b.yColumn]},l={x:{extent:d3.extent(c,j)},y:{extent:d3.extent(c,k)}},m={x:d3.scale.linear().domain(l.x.extent).range([0,b.width]),y:d3.scale.linear().domain(l.y.extent).range([b.height,0])},n=d3.behavior.zoom().x(m.x).y(m.y).scaleExtent([1,30]).scale(b.scale||1).translate(b.translate||[0,0]),o=d3.select(a).attr("class","scatterplot").attr("width","100%").attr("height",b.height+(b.margin.top+b.margin.bottom)),p=o.append("g").attr("class","content").attr("transform",h(b.margin.left,b.margin.top)).call(n);p.append("rect").attr("class","zoom-rect").attr("width",b.width).attr("height",b.height).style("fill","transparent");var q={x:{},y:{}};q.x.fn=d3.svg.axis().orient("bottom").scale(m.x).ticks(b.xTicks).tickFormat(d3.format("s")),q.y.fn=d3.svg.axis().orient("left").scale(m.y).ticks(b.yTicks).tickFormat(d3.format("s")),q.x.g=p.append("g").attr("class","x axis").attr("transform",h(0,b.height)).call(q.x.fn),q.y.g=p.append("g").attr("class","y axis").call(q.y.fn);var r=6;q.x.label=o.append("text").attr("id","x-axis-label").attr("class","axis-label").text(b.xLabel).attr("text-anchor","middle").attr("dominant-baseline","text-after-edge").attr("x",b.width/2+b.margin.left).attr("y",b.height+b.margin.bottom+b.margin.top-r),q.y.label=o.append("text").attr("id","y-axis-label").attr("class","axis-label").text(b.yLabel).attr("text-anchor","middle").attr("dominant-baseline","text-before-edge").attr("x",r).attr("y",b.height/2).attr("transform",i(-90,r,b.height/2)),q.redraw=function(){o.select(".x.axis").call(q.x.fn),o.select(".y.axis").call(q.y.fn)};var s=d(),t=p.selectAll(".glyph").data(c).enter().append("svg:circle").classed("glyph",!0).attr("cx",function(a,b){return m.x(j(a,b))}).attr("cy",function(a,b){return m.y(k(a,b))}).attr("r",0);t.transition().duration(b.animDuration).attr("r",b.datapointSize),e(),n.on("zoom",f),t.on("mouseover",function(a,c){var d=d3.select(this);d.classed("highlight",!0).style("fill","red").style("fill-opacity",1),p.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",d.attr("cx")-b.datapointSize).attr("y1",d.attr("cy")).attr("x2",0).attr("y2",d.attr("cy")).classed("hoverline",!0),d.attr("cy")<b.height&&p.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",d.attr("cx")).attr("y1",+d.attr("cy")+b.datapointSize).attr("x2",d.attr("cx")).attr("y2",b.height).classed("hoverline",!0);var e=this.getBoundingClientRect();$("body").append(g(e.top,e.right,a)),$(o.node()).trigger("mouseover-datapoint.scatterplot",[this,a,c])}),t.on("mouseout",function(){d3.select(this).classed("highlight",!1).style("fill","black").style("fill-opacity",.2),p.selectAll(".hoverline").remove(),$(".chart-info-box").remove()})}this.scatterplot=this.scatterplot||{},this.scatterplot.chartcontrol=Handlebars.template({compiler:[6,">= 2.0.0-beta.1"],main:function(a,b,c,d){var e,f="function",g=b.helperMissing,h=this.escapeExpression;return'<p class="help-text">\n    Use the following controls to how the chart is displayed.\n    The slide controls can be moved by the mouse or, if the \'handle\' is in focus, your keyboard\'s arrow keys.\n    Move the focus between controls by using the tab or shift+tab keys on your keyboard.\n    Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n</p>\n\n<div data-config-key="datapointSize" class="form-input numeric-slider-input">\n    <label for="datapointSize">Size of data point: </label>\n    <div class="slider-output">'+h((e=null!=(e=b.datapointSize||(null!=a?a.datapointSize:a))?e:g,typeof e===f?e.call(a,{name:"datapointSize",hash:{},data:d}):e))+'</div>\n    <div class="slider"></div>\n    <p class="form-help help-text-small">\n        Size of the graphic representation of each data point\n    </p>\n</div>\n\n<div data-config-key="width" class="form-input numeric-slider-input">\n    <label for="width">Chart width: </label>\n    <div class="slider-output">'+h((e=null!=(e=b.width||(null!=a?a.width:a))?e:g,typeof e===f?e.call(a,{name:"width",hash:{},data:d}):e))+'</div>\n    <div class="slider"></div>\n    <p class="form-help help-text-small">\n        (not including chart margins and axes)\n    </p>\n</div>\n\n<div data-config-key="height" class="form-input numeric-slider-input">\n    <label for="height">Chart height: </label>\n    <div class="slider-output">'+h((e=null!=(e=b.height||(null!=a?a.height:a))?e:g,typeof e===f?e.call(a,{name:"height",hash:{},data:d}):e))+'</div>\n    <div class="slider"></div>\n    <p class="form-help help-text-small">\n        (not including chart margins and axes)\n    </p>\n</div>\n\n<div data-config-key="X-axis-label"class="text-input form-input">\n    <label for="X-axis-label">Re-label the X axis: </label>\n    <input type="text" name="X-axis-label" id="X-axis-label" value="'+h((e=null!=(e=b.xLabel||(null!=a?a.xLabel:a))?e:g,typeof e===f?e.call(a,{name:"xLabel",hash:{},data:d}):e))+'" />\n    <p class="form-help help-text-small"></p>\n</div>\n\n<div data-config-key="Y-axis-label" class="text-input form-input">\n    <label for="Y-axis-label">Re-label the Y axis: </label>\n    <input type="text" name="Y-axis-label" id="Y-axis-label" value="'+h((e=null!=(e=b.yLabel||(null!=a?a.yLabel:a))?e:g,typeof e===f?e.call(a,{name:"yLabel",hash:{},data:d}):e))+'" />\n    <p class="form-help help-text-small"></p>\n</div>\n\n<button class="render-button btn btn-primary active">Draw</button>\n'},useData:!0}),this.scatterplot.datacontrol=Handlebars.template({compiler:[6,">= 2.0.0-beta.1"],main:function(a,b,c,d){var e,f,g="function",h=b.helperMissing,i='<p class="help-text">\n    Use the following control to change which columns are used by the chart. Click any cell\n    from the last three rows of the table to select the column for the appropriate data.\n    Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n</p>\n\n<ul class="help-text" style="margin-left: 8px">\n    <li><b>X Column</b>: which column values will be used for the x axis of the chart.</li>\n    <li><b>Y Column</b>: which column values will be used for the y axis of the chart.</li>\n    <li><b>ID Column</b>: an additional column value displayed when the user hovers over a data point.\n    It may be useful to select unique or categorical identifiers here (such as gene ids).\n    </li>\n</ul>\n\n<div class="column-selection">\n    <pre class="peek">';return f=null!=(f=b.peek||(null!=a?a.peek:a))?f:h,e=typeof f===g?f.call(a,{name:"peek",hash:{},data:d}):f,null!=e&&(i+=e),i+'</pre>\n</div>\n\n<p class="help-text help-text-small">\n    <b>Note</b>: If it can be determined from the dataset\'s filetype that a column is not numeric,\n    that column choice may be disabled for either the x or y axis.\n</p>\n\n<button class="render-button btn btn-primary active">Draw</button>\n'},useData:!0}),this.scatterplot.editor=Handlebars.template({compiler:[6,">= 2.0.0-beta.1"],main:function(){return'<div class="scatterplot-editor tabbable tabs-left">\n    <ul class="nav nav-tabs">\n        <li class="active">\n            <a title="Use this tab to change which data are used"\n               href="#data-control" data-toggle="tab">Data Controls</a>\n        </li>\n        <li>\n            <a title="Use this tab to change how the chart is drawn"\n               href="#chart-control" data-toggle="tab" >Chart Controls</a>\n        </li>\n        <li class="disabled">\n            <a title="This tab will display the chart"\n               href="#chart-display" data-toggle="tab">Chart</a>\n        </li>\n        <li class="file-controls">\n<!--            <button class="copy-btn btn btn-default"\n                    title="Save this as a new visualization">Save to new</button>-->\n            <button class="save-btn btn btn-default">Save</button>\n        </li>\n    </ul>\n\n    <div class="tab-content">\n        <div id="data-control" class="scatterplot-config-control tab-pane active">\n        </div>\n    \n        <div id="chart-control" class="scatterplot-config-control tab-pane">\n        </div>\n\n        <div id="chart-display" class="scatterplot-display tab-pane"></div>\n\n    </div>\n</div>\n'},useData:!0});var ScatterplotConfigEditor=Backbone.View.extend({className:"scatterplot-control-form",initialize:function(a){if(this.model||(this.model=new Visualization({type:"scatterplot"})),!a||!a.dataset)throw new Error("ScatterplotConfigEditor requires a dataset");this.dataset=a.dataset,this.display=new ScatterplotDisplay({dataset:a.dataset,model:this.model})},render:function(){this.$el.empty().append(ScatterplotConfigEditor.templates.mainLayout({})),this.model.id&&(this.$el.find(".copy-btn").show(),this.$el.find(".save-btn").text("Update saved")),this.$el.find("[title]").tooltip(),this._render_dataControl(),this._render_chartControls(),this._render_chartDisplay();var a=this.model.get("config");return this.model.id&&_.isFinite(a.xColumn)&&_.isFinite(a.yColumn)&&this.renderChart(),this},_getColumnIndecesByType:function(){var a={numeric:[],text:[],all:[]};return _.each(this.dataset.metadata_column_types||[],function(b,c){"int"===b||"float"===b?a.numeric.push(c):("str"===b||"list"===b)&&a.text.push(c),a.all.push(c)}),a.numeric.length<2&&(a.numeric=[]),a},_render_dataControl:function(a){a=a||this.$el;var b=this,c=this.model.get("config"),d=this._getColumnIndecesByType(),e=a.find(".tab-pane#data-control");return e.html(ScatterplotConfigEditor.templates.dataControl({peek:this.dataset.peek})),e.find(".peek").peekColumnSelector({controls:[{label:"X Column",id:"xColumn",selected:c.xColumn,disabled:d.text},{label:"Y Column",id:"yColumn",selected:c.yColumn,disabled:d.text},{label:"ID Column",id:"idColumn",selected:c.idColumn}]}).on("peek-column-selector.change",function(a,c){b.model.set("config",c)}).on("peek-column-selector.rename",function(){}),e.find("[title]").tooltip(),e},_render_chartControls:function(a){function b(){var a=$(this),b=a.slider("value");c.model.set("config",_.object([[a.parent().data("config-key"),b]])),a.siblings(".slider-output").text(b)}a=a||this.$el;var c=this,d=this.model.get("config"),e=a.find("#chart-control");e.html(ScatterplotConfigEditor.templates.chartControl(d));var f={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};e.find(".numeric-slider-input").each(function(){var a=$(this),c=a.attr("data-config-key"),e=_.extend(f[c],{value:d[c],change:b,slide:b});a.find(".slider").slider(e),a.children(".slider-output").text(d[c])});var g=this.dataset.metadata_column_names||[],h=d.xLabel||g[d.xColumn]||"X",i=d.yLabel||g[d.yColumn]||"Y";return e.find('input[name="X-axis-label"]').val(h).on("change",function(){c.model.set("config",{xLabel:$(this).val()})}),e.find('input[name="Y-axis-label"]').val(i).on("change",function(){c.model.set("config",{yLabel:$(this).val()})}),e.find("[title]").tooltip(),e},_render_chartDisplay:function(a){a=a||this.$el;var b=a.find(".tab-pane#chart-display");return this.display.setElement(b),this.display.render(),b.find("[title]").tooltip(),b},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","click #data-control .render-button":"renderChart","click #chart-control .render-button":"renderChart","click .save-btn":"saveVisualization"},saveVisualization:function(){var a=this;this.model.save().fail(function(b,c,d){console.error(b,c,d),a.trigger("save:error",view),alert("Error loading data:\n"+b.responseText)}).then(function(){a.display.render()})},toggleThirdColumnSelector:function(){this.$el.find('select[name="idColumn"]').parent().toggle()},renderChart:function(){this.$el.find(".nav li.disabled").removeClass("disabled"),this.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show"),this.display.fetchData()},toString:function(){return"ScatterplotConfigEditor("+(this.dataset?this.dataset.id:"")+")"}});ScatterplotConfigEditor.templates={mainLayout:scatterplot.editor,dataControl:scatterplot.datacontrol,chartControl:scatterplot.chartcontrol};var ScatterplotDisplay=Backbone.View.extend({initialize:function(a){this.data=null,this.dataset=a.dataset,this.lineCount=this.dataset.metadata_data_lines||null},fetchData:function(){this.showLoadingIndicator();var a=this,b=this.model.get("config"),c=jQuery.getJSON(((typeof parent.galaxy_config.root == 'undefined') ? '/' : parent.galaxy_config.root)+"api/datasets/"+this.dataset.id,{data_type:"raw_data",provider:"dataset-column",limit:b.pagination.perPage,offset:b.pagination.currPage*b.pagination.perPage});return c.done(function(b){a.data=b.data,a.trigger("data:fetched",a),a.renderData()}),c.fail(function(b,c,d){console.error(b,c,d),a.trigger("data:error",a),alert("Error loading data:\n"+b.responseText)}),c},showLoadingIndicator:function(){this.$el.find(".scatterplot-data-info").html(['<div class="loading-indicator">','<span class="fa fa-spinner fa-spin"></span>','<span class="loading-indicator-message">loading...</span>',"</div>"].join(""))},template:function(){var a=['<div class="controls clear">','<div class="right">','<p class="scatterplot-data-info"></p>','<button class="stats-toggle-btn">Stats</button>','<button class="rerender-btn">Redraw</button>',"</div>",'<div class="left">','<div class="page-control"></div>',"</div>","</div>","<svg/>",'<div class="stats-display"></div>'].join("");return a},render:function(){return this.$el.addClass("scatterplot-display").html(this.template()),this.data&&this.renderData(),this},renderData:function(){this.renderLeftControls(),this.renderRightControls(),this.renderPlot(this.data),this.getStats()},renderLeftControls:function(){var a=this,b=this.model.get("config");return this.$el.find(".controls .left .page-control").pagination({startingPage:b.pagination.currPage,perPage:b.pagination.perPage,totalDataSize:this.lineCount,currDataSize:this.data.length}).off().on("pagination.page-change",function(c,d){b.pagination.currPage=d,a.model.set("config",{pagination:b.pagination}),a.resetZoom(),a.fetchData()}),this},renderRightControls:function(){var a=this;this.setLineInfo(this.data),this.$el.find(".stats-toggle-btn").off().click(function(){a.toggleStats()}),this.$el.find(".rerender-btn").off().click(function(){a.resetZoom(),a.renderPlot(this.data)})},renderPlot:function(){var a=this,b=this.$el.find("svg");this.toggleStats(!1),b.off().empty().show().on("zoom.scatterplot",function(b,c){a.model.set("config",c)}),scatterplot(b.get(0),this.model.get("config"),this.data)},setLineInfo:function(a,b){if(a){var c=this.model.get("config"),d=this.lineCount||"an unknown total",e=c.pagination.currPage*c.pagination.perPage,f=e+a.length;this.$el.find(".controls p.scatterplot-data-info").text([e+1,"to",f,"of",d].join(" "))}else this.$el.find(".controls p.scatterplot-data-info").html(b||"");return this},resetZoom:function(a,b){return a=void 0!==a?a:1,b=void 0!==b?b:[0,0],this.model.set("config",{scale:a,translate:b}),this},getStats:function(){if(this.data){var a=this,b=this.model.get("config"),c=new Worker("/plugins/visualizations/scatterplot/static/worker-stats.js");c.postMessage({data:this.data,keys:[b.xColumn,b.yColumn]}),c.onerror=function(){c.terminate()},c.onmessage=function(b){a.renderStats(b.data)}}},renderStats:function(a){var b=this.model.get("config"),c=this.$el.find(".stats-display"),d=b.xLabel,e=b.yLabel,f=$("<table/>").addClass("table").append(["<thead><th></th><th>",d,"</th><th>",e,"</th></thead>"].join("")).append(_.map(a,function(a,b){return $(["<tr><td>",b,"</td><td>",a[0],"</td><td>",a[1],"</td></tr>"].join(""))}));c.empty().append(f)},toggleStats:function(a){var b=this.$el.find(".stats-display");a=void 0===a?b.is(":hidden"):a,a?(this.$el.find("svg").hide(),b.show(),this.$el.find(".controls .stats-toggle-btn").text("Plot")):(b.hide(),this.$el.find("svg").show(),this.$el.find(".controls .stats-toggle-btn").text("Stats"))},toString:function(){return"ScatterplotView()"}}),ScatterplotModel=Visualization.extend({defaults:{type:"scatterplot",config:{pagination:{currPage:0,perPage:3e3},width:400,height:400,margin:{top:16,right:16,bottom:40,left:54},xTicks:10,xLabel:"X",yTicks:10,yLabel:"Y",datapointSize:4,animDuration:500,scale:1,translate:[0,0]}}});

From fc51b85d2c47a98b54649ed3aa66d59dc26c1de8 Mon Sep 17 00:00:00 2001
From: yhoogstrate <y.hoogstrate@erasmusmc.nl>
Date: Tue, 7 Apr 2015 15:50:30 +0200
Subject: [PATCH 41/88] Update scatterplot-edit.js

automatically generated by grunt
---
 .../visualizations/scatterplot/static/scatterplot-edit.js       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/plugins/visualizations/scatterplot/static/scatterplot-edit.js b/config/plugins/visualizations/scatterplot/static/scatterplot-edit.js
index be7cc5c296b..5ef5bdc44fc 100644
--- a/config/plugins/visualizations/scatterplot/static/scatterplot-edit.js
+++ b/config/plugins/visualizations/scatterplot/static/scatterplot-edit.js
@@ -1 +1 @@
-function scatterplot(a,b,c){function d(){var a={v:{},h:{}};return a.v.lines=p.selectAll("line.v-grid-line").data(m.x.ticks(q.x.fn.ticks()[0])),a.v.lines.enter().append("svg:line").classed("grid-line v-grid-line",!0),a.v.lines.attr("x1",m.x).attr("x2",m.x).attr("y1",0).attr("y2",b.height),a.v.lines.exit().remove(),a.h.lines=p.selectAll("line.h-grid-line").data(m.y.ticks(q.y.fn.ticks()[0])),a.h.lines.enter().append("svg:line").classed("grid-line h-grid-line",!0),a.h.lines.attr("x1",0).attr("x2",b.width).attr("y1",m.y).attr("y2",m.y),a.h.lines.exit().remove(),a}function e(){return t.attr("cx",function(a,b){return m.x(j(a,b))}).attr("cy",function(a,b){return m.y(k(a,b))}).style("display","block").filter(function(){var a=d3.select(this).attr("cx"),c=d3.select(this).attr("cy");return 0>a||a>b.width?!0:0>c||c>b.height?!0:!1}).style("display","none")}function f(){$(".chart-info-box").remove(),q.redraw(),e(),s=d(),$(o.node()).trigger("zoom.scatterplot",{scale:n.scale(),translate:n.translate()})}function g(a,c,d){return c+=8,$(['<div class="chart-info-box" style="position: absolute">',void 0!==b.idColumn?"<div>"+d[b.idColumn]+"</div>":"","<div>",j(d),"</div>","<div>",k(d),"</div>","</div>"].join("")).css({top:a,left:c,"z-index":2})}var h=function(a,b){return"translate("+a+","+b+")"},i=function(a,b,c){return"rotate("+a+","+b+","+c+")"},j=function(a){return a[b.xColumn]},k=function(a){return a[b.yColumn]},l={x:{extent:d3.extent(c,j)},y:{extent:d3.extent(c,k)}},m={x:d3.scale.linear().domain(l.x.extent).range([0,b.width]),y:d3.scale.linear().domain(l.y.extent).range([b.height,0])},n=d3.behavior.zoom().x(m.x).y(m.y).scaleExtent([1,30]).scale(b.scale||1).translate(b.translate||[0,0]),o=d3.select(a).attr("class","scatterplot").attr("width","100%").attr("height",b.height+(b.margin.top+b.margin.bottom)),p=o.append("g").attr("class","content").attr("transform",h(b.margin.left,b.margin.top)).call(n);p.append("rect").attr("class","zoom-rect").attr("width",b.width).attr("height",b.height).style("fill","transparent");var q={x:{},y:{}};q.x.fn=d3.svg.axis().orient("bottom").scale(m.x).ticks(b.xTicks).tickFormat(d3.format("s")),q.y.fn=d3.svg.axis().orient("left").scale(m.y).ticks(b.yTicks).tickFormat(d3.format("s")),q.x.g=p.append("g").attr("class","x axis").attr("transform",h(0,b.height)).call(q.x.fn),q.y.g=p.append("g").attr("class","y axis").call(q.y.fn);var r=6;q.x.label=o.append("text").attr("id","x-axis-label").attr("class","axis-label").text(b.xLabel).attr("text-anchor","middle").attr("dominant-baseline","text-after-edge").attr("x",b.width/2+b.margin.left).attr("y",b.height+b.margin.bottom+b.margin.top-r),q.y.label=o.append("text").attr("id","y-axis-label").attr("class","axis-label").text(b.yLabel).attr("text-anchor","middle").attr("dominant-baseline","text-before-edge").attr("x",r).attr("y",b.height/2).attr("transform",i(-90,r,b.height/2)),q.redraw=function(){o.select(".x.axis").call(q.x.fn),o.select(".y.axis").call(q.y.fn)};var s=d(),t=p.selectAll(".glyph").data(c).enter().append("svg:circle").classed("glyph",!0).attr("cx",function(a,b){return m.x(j(a,b))}).attr("cy",function(a,b){return m.y(k(a,b))}).attr("r",0);t.transition().duration(b.animDuration).attr("r",b.datapointSize),e(),n.on("zoom",f),t.on("mouseover",function(a,c){var d=d3.select(this);d.classed("highlight",!0).style("fill","red").style("fill-opacity",1),p.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",d.attr("cx")-b.datapointSize).attr("y1",d.attr("cy")).attr("x2",0).attr("y2",d.attr("cy")).classed("hoverline",!0),d.attr("cy")<b.height&&p.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",d.attr("cx")).attr("y1",+d.attr("cy")+b.datapointSize).attr("x2",d.attr("cx")).attr("y2",b.height).classed("hoverline",!0);var e=this.getBoundingClientRect();$("body").append(g(e.top,e.right,a)),$(o.node()).trigger("mouseover-datapoint.scatterplot",[this,a,c])}),t.on("mouseout",function(){d3.select(this).classed("highlight",!1).style("fill","black").style("fill-opacity",.2),p.selectAll(".hoverline").remove(),$(".chart-info-box").remove()})}this.scatterplot=this.scatterplot||{},this.scatterplot.chartcontrol=Handlebars.template({compiler:[6,">= 2.0.0-beta.1"],main:function(a,b,c,d){var e,f="function",g=b.helperMissing,h=this.escapeExpression;return'<p class="help-text">\n    Use the following controls to how the chart is displayed.\n    The slide controls can be moved by the mouse or, if the \'handle\' is in focus, your keyboard\'s arrow keys.\n    Move the focus between controls by using the tab or shift+tab keys on your keyboard.\n    Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n</p>\n\n<div data-config-key="datapointSize" class="form-input numeric-slider-input">\n    <label for="datapointSize">Size of data point: </label>\n    <div class="slider-output">'+h((e=null!=(e=b.datapointSize||(null!=a?a.datapointSize:a))?e:g,typeof e===f?e.call(a,{name:"datapointSize",hash:{},data:d}):e))+'</div>\n    <div class="slider"></div>\n    <p class="form-help help-text-small">\n        Size of the graphic representation of each data point\n    </p>\n</div>\n\n<div data-config-key="width" class="form-input numeric-slider-input">\n    <label for="width">Chart width: </label>\n    <div class="slider-output">'+h((e=null!=(e=b.width||(null!=a?a.width:a))?e:g,typeof e===f?e.call(a,{name:"width",hash:{},data:d}):e))+'</div>\n    <div class="slider"></div>\n    <p class="form-help help-text-small">\n        (not including chart margins and axes)\n    </p>\n</div>\n\n<div data-config-key="height" class="form-input numeric-slider-input">\n    <label for="height">Chart height: </label>\n    <div class="slider-output">'+h((e=null!=(e=b.height||(null!=a?a.height:a))?e:g,typeof e===f?e.call(a,{name:"height",hash:{},data:d}):e))+'</div>\n    <div class="slider"></div>\n    <p class="form-help help-text-small">\n        (not including chart margins and axes)\n    </p>\n</div>\n\n<div data-config-key="X-axis-label"class="text-input form-input">\n    <label for="X-axis-label">Re-label the X axis: </label>\n    <input type="text" name="X-axis-label" id="X-axis-label" value="'+h((e=null!=(e=b.xLabel||(null!=a?a.xLabel:a))?e:g,typeof e===f?e.call(a,{name:"xLabel",hash:{},data:d}):e))+'" />\n    <p class="form-help help-text-small"></p>\n</div>\n\n<div data-config-key="Y-axis-label" class="text-input form-input">\n    <label for="Y-axis-label">Re-label the Y axis: </label>\n    <input type="text" name="Y-axis-label" id="Y-axis-label" value="'+h((e=null!=(e=b.yLabel||(null!=a?a.yLabel:a))?e:g,typeof e===f?e.call(a,{name:"yLabel",hash:{},data:d}):e))+'" />\n    <p class="form-help help-text-small"></p>\n</div>\n\n<button class="render-button btn btn-primary active">Draw</button>\n'},useData:!0}),this.scatterplot.datacontrol=Handlebars.template({compiler:[6,">= 2.0.0-beta.1"],main:function(a,b,c,d){var e,f,g="function",h=b.helperMissing,i='<p class="help-text">\n    Use the following control to change which columns are used by the chart. Click any cell\n    from the last three rows of the table to select the column for the appropriate data.\n    Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n</p>\n\n<ul class="help-text" style="margin-left: 8px">\n    <li><b>X Column</b>: which column values will be used for the x axis of the chart.</li>\n    <li><b>Y Column</b>: which column values will be used for the y axis of the chart.</li>\n    <li><b>ID Column</b>: an additional column value displayed when the user hovers over a data point.\n    It may be useful to select unique or categorical identifiers here (such as gene ids).\n    </li>\n</ul>\n\n<div class="column-selection">\n    <pre class="peek">';return f=null!=(f=b.peek||(null!=a?a.peek:a))?f:h,e=typeof f===g?f.call(a,{name:"peek",hash:{},data:d}):f,null!=e&&(i+=e),i+'</pre>\n</div>\n\n<p class="help-text help-text-small">\n    <b>Note</b>: If it can be determined from the dataset\'s filetype that a column is not numeric,\n    that column choice may be disabled for either the x or y axis.\n</p>\n\n<button class="render-button btn btn-primary active">Draw</button>\n'},useData:!0}),this.scatterplot.editor=Handlebars.template({compiler:[6,">= 2.0.0-beta.1"],main:function(){return'<div class="scatterplot-editor tabbable tabs-left">\n    <ul class="nav nav-tabs">\n        <li class="active">\n            <a title="Use this tab to change which data are used"\n               href="#data-control" data-toggle="tab">Data Controls</a>\n        </li>\n        <li>\n            <a title="Use this tab to change how the chart is drawn"\n               href="#chart-control" data-toggle="tab" >Chart Controls</a>\n        </li>\n        <li class="disabled">\n            <a title="This tab will display the chart"\n               href="#chart-display" data-toggle="tab">Chart</a>\n        </li>\n        <li class="file-controls">\n<!--            <button class="copy-btn btn btn-default"\n                    title="Save this as a new visualization">Save to new</button>-->\n            <button class="save-btn btn btn-default">Save</button>\n        </li>\n    </ul>\n\n    <div class="tab-content">\n        <div id="data-control" class="scatterplot-config-control tab-pane active">\n        </div>\n    \n        <div id="chart-control" class="scatterplot-config-control tab-pane">\n        </div>\n\n        <div id="chart-display" class="scatterplot-display tab-pane"></div>\n\n    </div>\n</div>\n'},useData:!0});var ScatterplotConfigEditor=Backbone.View.extend({className:"scatterplot-control-form",initialize:function(a){if(this.model||(this.model=new Visualization({type:"scatterplot"})),!a||!a.dataset)throw new Error("ScatterplotConfigEditor requires a dataset");this.dataset=a.dataset,this.display=new ScatterplotDisplay({dataset:a.dataset,model:this.model})},render:function(){this.$el.empty().append(ScatterplotConfigEditor.templates.mainLayout({})),this.model.id&&(this.$el.find(".copy-btn").show(),this.$el.find(".save-btn").text("Update saved")),this.$el.find("[title]").tooltip(),this._render_dataControl(),this._render_chartControls(),this._render_chartDisplay();var a=this.model.get("config");return this.model.id&&_.isFinite(a.xColumn)&&_.isFinite(a.yColumn)&&this.renderChart(),this},_getColumnIndecesByType:function(){var a={numeric:[],text:[],all:[]};return _.each(this.dataset.metadata_column_types||[],function(b,c){"int"===b||"float"===b?a.numeric.push(c):("str"===b||"list"===b)&&a.text.push(c),a.all.push(c)}),a.numeric.length<2&&(a.numeric=[]),a},_render_dataControl:function(a){a=a||this.$el;var b=this,c=this.model.get("config"),d=this._getColumnIndecesByType(),e=a.find(".tab-pane#data-control");return e.html(ScatterplotConfigEditor.templates.dataControl({peek:this.dataset.peek})),e.find(".peek").peekColumnSelector({controls:[{label:"X Column",id:"xColumn",selected:c.xColumn,disabled:d.text},{label:"Y Column",id:"yColumn",selected:c.yColumn,disabled:d.text},{label:"ID Column",id:"idColumn",selected:c.idColumn}]}).on("peek-column-selector.change",function(a,c){b.model.set("config",c)}).on("peek-column-selector.rename",function(){}),e.find("[title]").tooltip(),e},_render_chartControls:function(a){function b(){var a=$(this),b=a.slider("value");c.model.set("config",_.object([[a.parent().data("config-key"),b]])),a.siblings(".slider-output").text(b)}a=a||this.$el;var c=this,d=this.model.get("config"),e=a.find("#chart-control");e.html(ScatterplotConfigEditor.templates.chartControl(d));var f={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};e.find(".numeric-slider-input").each(function(){var a=$(this),c=a.attr("data-config-key"),e=_.extend(f[c],{value:d[c],change:b,slide:b});a.find(".slider").slider(e),a.children(".slider-output").text(d[c])});var g=this.dataset.metadata_column_names||[],h=d.xLabel||g[d.xColumn]||"X",i=d.yLabel||g[d.yColumn]||"Y";return e.find('input[name="X-axis-label"]').val(h).on("change",function(){c.model.set("config",{xLabel:$(this).val()})}),e.find('input[name="Y-axis-label"]').val(i).on("change",function(){c.model.set("config",{yLabel:$(this).val()})}),e.find("[title]").tooltip(),e},_render_chartDisplay:function(a){a=a||this.$el;var b=a.find(".tab-pane#chart-display");return this.display.setElement(b),this.display.render(),b.find("[title]").tooltip(),b},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","click #data-control .render-button":"renderChart","click #chart-control .render-button":"renderChart","click .save-btn":"saveVisualization"},saveVisualization:function(){var a=this;this.model.save().fail(function(b,c,d){console.error(b,c,d),a.trigger("save:error",view),alert("Error loading data:\n"+b.responseText)}).then(function(){a.display.render()})},toggleThirdColumnSelector:function(){this.$el.find('select[name="idColumn"]').parent().toggle()},renderChart:function(){this.$el.find(".nav li.disabled").removeClass("disabled"),this.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show"),this.display.fetchData()},toString:function(){return"ScatterplotConfigEditor("+(this.dataset?this.dataset.id:"")+")"}});ScatterplotConfigEditor.templates={mainLayout:scatterplot.editor,dataControl:scatterplot.datacontrol,chartControl:scatterplot.chartcontrol};var ScatterplotDisplay=Backbone.View.extend({initialize:function(a){this.data=null,this.dataset=a.dataset,this.lineCount=this.dataset.metadata_data_lines||null},fetchData:function(){this.showLoadingIndicator();var a=this,b=this.model.get("config"),c=jQuery.getJSON(((typeof parent.galaxy_config.root == 'undefined') ? '/' : parent.galaxy_config.root)+"api/datasets/"+this.dataset.id,{data_type:"raw_data",provider:"dataset-column",limit:b.pagination.perPage,offset:b.pagination.currPage*b.pagination.perPage});return c.done(function(b){a.data=b.data,a.trigger("data:fetched",a),a.renderData()}),c.fail(function(b,c,d){console.error(b,c,d),a.trigger("data:error",a),alert("Error loading data:\n"+b.responseText)}),c},showLoadingIndicator:function(){this.$el.find(".scatterplot-data-info").html(['<div class="loading-indicator">','<span class="fa fa-spinner fa-spin"></span>','<span class="loading-indicator-message">loading...</span>',"</div>"].join(""))},template:function(){var a=['<div class="controls clear">','<div class="right">','<p class="scatterplot-data-info"></p>','<button class="stats-toggle-btn">Stats</button>','<button class="rerender-btn">Redraw</button>',"</div>",'<div class="left">','<div class="page-control"></div>',"</div>","</div>","<svg/>",'<div class="stats-display"></div>'].join("");return a},render:function(){return this.$el.addClass("scatterplot-display").html(this.template()),this.data&&this.renderData(),this},renderData:function(){this.renderLeftControls(),this.renderRightControls(),this.renderPlot(this.data),this.getStats()},renderLeftControls:function(){var a=this,b=this.model.get("config");return this.$el.find(".controls .left .page-control").pagination({startingPage:b.pagination.currPage,perPage:b.pagination.perPage,totalDataSize:this.lineCount,currDataSize:this.data.length}).off().on("pagination.page-change",function(c,d){b.pagination.currPage=d,a.model.set("config",{pagination:b.pagination}),a.resetZoom(),a.fetchData()}),this},renderRightControls:function(){var a=this;this.setLineInfo(this.data),this.$el.find(".stats-toggle-btn").off().click(function(){a.toggleStats()}),this.$el.find(".rerender-btn").off().click(function(){a.resetZoom(),a.renderPlot(this.data)})},renderPlot:function(){var a=this,b=this.$el.find("svg");this.toggleStats(!1),b.off().empty().show().on("zoom.scatterplot",function(b,c){a.model.set("config",c)}),scatterplot(b.get(0),this.model.get("config"),this.data)},setLineInfo:function(a,b){if(a){var c=this.model.get("config"),d=this.lineCount||"an unknown total",e=c.pagination.currPage*c.pagination.perPage,f=e+a.length;this.$el.find(".controls p.scatterplot-data-info").text([e+1,"to",f,"of",d].join(" "))}else this.$el.find(".controls p.scatterplot-data-info").html(b||"");return this},resetZoom:function(a,b){return a=void 0!==a?a:1,b=void 0!==b?b:[0,0],this.model.set("config",{scale:a,translate:b}),this},getStats:function(){if(this.data){var a=this,b=this.model.get("config"),c=new Worker("/plugins/visualizations/scatterplot/static/worker-stats.js");c.postMessage({data:this.data,keys:[b.xColumn,b.yColumn]}),c.onerror=function(){c.terminate()},c.onmessage=function(b){a.renderStats(b.data)}}},renderStats:function(a){var b=this.model.get("config"),c=this.$el.find(".stats-display"),d=b.xLabel,e=b.yLabel,f=$("<table/>").addClass("table").append(["<thead><th></th><th>",d,"</th><th>",e,"</th></thead>"].join("")).append(_.map(a,function(a,b){return $(["<tr><td>",b,"</td><td>",a[0],"</td><td>",a[1],"</td></tr>"].join(""))}));c.empty().append(f)},toggleStats:function(a){var b=this.$el.find(".stats-display");a=void 0===a?b.is(":hidden"):a,a?(this.$el.find("svg").hide(),b.show(),this.$el.find(".controls .stats-toggle-btn").text("Plot")):(b.hide(),this.$el.find("svg").show(),this.$el.find(".controls .stats-toggle-btn").text("Stats"))},toString:function(){return"ScatterplotView()"}}),ScatterplotModel=Visualization.extend({defaults:{type:"scatterplot",config:{pagination:{currPage:0,perPage:3e3},width:400,height:400,margin:{top:16,right:16,bottom:40,left:54},xTicks:10,xLabel:"X",yTicks:10,yLabel:"Y",datapointSize:4,animDuration:500,scale:1,translate:[0,0]}}});
+function scatterplot(a,b,c){function d(){var a={v:{},h:{}};return a.v.lines=p.selectAll("line.v-grid-line").data(m.x.ticks(q.x.fn.ticks()[0])),a.v.lines.enter().append("svg:line").classed("grid-line v-grid-line",!0),a.v.lines.attr("x1",m.x).attr("x2",m.x).attr("y1",0).attr("y2",b.height),a.v.lines.exit().remove(),a.h.lines=p.selectAll("line.h-grid-line").data(m.y.ticks(q.y.fn.ticks()[0])),a.h.lines.enter().append("svg:line").classed("grid-line h-grid-line",!0),a.h.lines.attr("x1",0).attr("x2",b.width).attr("y1",m.y).attr("y2",m.y),a.h.lines.exit().remove(),a}function e(){return t.attr("cx",function(a,b){return m.x(j(a,b))}).attr("cy",function(a,b){return m.y(k(a,b))}).style("display","block").filter(function(a,c){var d=d3.select(this).attr("cx"),e=d3.select(this).attr("cy");return 0>d||d>b.width?!0:0>e||e>b.height?!0:!1}).style("display","none")}function f(a,b,c){$(".chart-info-box").remove(),q.redraw(),e(),s=d(),$(o.node()).trigger("zoom.scatterplot",{scale:n.scale(),translate:n.translate()})}function g(a,c,d){return c+=8,$(['<div class="chart-info-box" style="position: absolute">',void 0!==b.idColumn?"<div>"+d[b.idColumn]+"</div>":"","<div>",j(d),"</div>","<div>",k(d),"</div>","</div>"].join("")).css({top:a,left:c,"z-index":2})}var h=function(a,b){return"translate("+a+","+b+")"},i=function(a,b,c){return"rotate("+a+","+b+","+c+")"},j=function(a,c){return a[b.xColumn]},k=function(a,c){return a[b.yColumn]},l={x:{extent:d3.extent(c,j)},y:{extent:d3.extent(c,k)}},m={x:d3.scale.linear().domain(l.x.extent).range([0,b.width]),y:d3.scale.linear().domain(l.y.extent).range([b.height,0])},n=d3.behavior.zoom().x(m.x).y(m.y).scaleExtent([1,30]).scale(b.scale||1).translate(b.translate||[0,0]),o=d3.select(a).attr("class","scatterplot").attr("width","100%").attr("height",b.height+(b.margin.top+b.margin.bottom)),p=o.append("g").attr("class","content").attr("transform",h(b.margin.left,b.margin.top)).call(n);p.append("rect").attr("class","zoom-rect").attr("width",b.width).attr("height",b.height).style("fill","transparent");var q={x:{},y:{}};q.x.fn=d3.svg.axis().orient("bottom").scale(m.x).ticks(b.xTicks).tickFormat(d3.format("s")),q.y.fn=d3.svg.axis().orient("left").scale(m.y).ticks(b.yTicks).tickFormat(d3.format("s")),q.x.g=p.append("g").attr("class","x axis").attr("transform",h(0,b.height)).call(q.x.fn),q.y.g=p.append("g").attr("class","y axis").call(q.y.fn);var r=6;q.x.label=o.append("text").attr("id","x-axis-label").attr("class","axis-label").text(b.xLabel).attr("text-anchor","middle").attr("dominant-baseline","text-after-edge").attr("x",b.width/2+b.margin.left).attr("y",b.height+b.margin.bottom+b.margin.top-r),q.y.label=o.append("text").attr("id","y-axis-label").attr("class","axis-label").text(b.yLabel).attr("text-anchor","middle").attr("dominant-baseline","text-before-edge").attr("x",r).attr("y",b.height/2).attr("transform",i(-90,r,b.height/2)),q.redraw=function(){o.select(".x.axis").call(q.x.fn),o.select(".y.axis").call(q.y.fn)};var s=d(),t=p.selectAll(".glyph").data(c).enter().append("svg:circle").classed("glyph",!0).attr("cx",function(a,b){return m.x(j(a,b))}).attr("cy",function(a,b){return m.y(k(a,b))}).attr("r",0);t.transition().duration(b.animDuration).attr("r",b.datapointSize),e(),n.on("zoom",f),t.on("mouseover",function(a,c){var d=d3.select(this);d.classed("highlight",!0).style("fill","red").style("fill-opacity",1),p.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",d.attr("cx")-b.datapointSize).attr("y1",d.attr("cy")).attr("x2",0).attr("y2",d.attr("cy")).classed("hoverline",!0),d.attr("cy")<b.height&&p.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",d.attr("cx")).attr("y1",+d.attr("cy")+b.datapointSize).attr("x2",d.attr("cx")).attr("y2",b.height).classed("hoverline",!0);var e=this.getBoundingClientRect();$("body").append(g(e.top,e.right,a)),$(o.node()).trigger("mouseover-datapoint.scatterplot",[this,a,c])}),t.on("mouseout",function(){d3.select(this).classed("highlight",!1).style("fill","black").style("fill-opacity",.2),p.selectAll(".hoverline").remove(),$(".chart-info-box").remove()})}this.scatterplot=this.scatterplot||{},this.scatterplot.chartcontrol=Handlebars.template({compiler:[6,">= 2.0.0-beta.1"],main:function(a,b,c,d){var e,f="function",g=b.helperMissing,h=this.escapeExpression;return'<p class="help-text">\n    Use the following controls to how the chart is displayed.\n    The slide controls can be moved by the mouse or, if the \'handle\' is in focus, your keyboard\'s arrow keys.\n    Move the focus between controls by using the tab or shift+tab keys on your keyboard.\n    Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n</p>\n\n<div data-config-key="datapointSize" class="form-input numeric-slider-input">\n    <label for="datapointSize">Size of data point: </label>\n    <div class="slider-output">'+h((e=null!=(e=b.datapointSize||(null!=a?a.datapointSize:a))?e:g,typeof e===f?e.call(a,{name:"datapointSize",hash:{},data:d}):e))+'</div>\n    <div class="slider"></div>\n    <p class="form-help help-text-small">\n        Size of the graphic representation of each data point\n    </p>\n</div>\n\n<div data-config-key="width" class="form-input numeric-slider-input">\n    <label for="width">Chart width: </label>\n    <div class="slider-output">'+h((e=null!=(e=b.width||(null!=a?a.width:a))?e:g,typeof e===f?e.call(a,{name:"width",hash:{},data:d}):e))+'</div>\n    <div class="slider"></div>\n    <p class="form-help help-text-small">\n        (not including chart margins and axes)\n    </p>\n</div>\n\n<div data-config-key="height" class="form-input numeric-slider-input">\n    <label for="height">Chart height: </label>\n    <div class="slider-output">'+h((e=null!=(e=b.height||(null!=a?a.height:a))?e:g,typeof e===f?e.call(a,{name:"height",hash:{},data:d}):e))+'</div>\n    <div class="slider"></div>\n    <p class="form-help help-text-small">\n        (not including chart margins and axes)\n    </p>\n</div>\n\n<div data-config-key="X-axis-label"class="text-input form-input">\n    <label for="X-axis-label">Re-label the X axis: </label>\n    <input type="text" name="X-axis-label" id="X-axis-label" value="'+h((e=null!=(e=b.xLabel||(null!=a?a.xLabel:a))?e:g,typeof e===f?e.call(a,{name:"xLabel",hash:{},data:d}):e))+'" />\n    <p class="form-help help-text-small"></p>\n</div>\n\n<div data-config-key="Y-axis-label" class="text-input form-input">\n    <label for="Y-axis-label">Re-label the Y axis: </label>\n    <input type="text" name="Y-axis-label" id="Y-axis-label" value="'+h((e=null!=(e=b.yLabel||(null!=a?a.yLabel:a))?e:g,typeof e===f?e.call(a,{name:"yLabel",hash:{},data:d}):e))+'" />\n    <p class="form-help help-text-small"></p>\n</div>\n\n<button class="render-button btn btn-primary active">Draw</button>\n'},useData:!0}),this.scatterplot.datacontrol=Handlebars.template({compiler:[6,">= 2.0.0-beta.1"],main:function(a,b,c,d){var e,f,g="function",h=b.helperMissing,i='<p class="help-text">\n    Use the following control to change which columns are used by the chart. Click any cell\n    from the last three rows of the table to select the column for the appropriate data.\n    Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n</p>\n\n<ul class="help-text" style="margin-left: 8px">\n    <li><b>X Column</b>: which column values will be used for the x axis of the chart.</li>\n    <li><b>Y Column</b>: which column values will be used for the y axis of the chart.</li>\n    <li><b>ID Column</b>: an additional column value displayed when the user hovers over a data point.\n    It may be useful to select unique or categorical identifiers here (such as gene ids).\n    </li>\n</ul>\n\n<div class="column-selection">\n    <pre class="peek">';return f=null!=(f=b.peek||(null!=a?a.peek:a))?f:h,e=typeof f===g?f.call(a,{name:"peek",hash:{},data:d}):f,null!=e&&(i+=e),i+'</pre>\n</div>\n\n<p class="help-text help-text-small">\n    <b>Note</b>: If it can be determined from the dataset\'s filetype that a column is not numeric,\n    that column choice may be disabled for either the x or y axis.\n</p>\n\n<button class="render-button btn btn-primary active">Draw</button>\n'},useData:!0}),this.scatterplot.editor=Handlebars.template({compiler:[6,">= 2.0.0-beta.1"],main:function(a,b,c,d){return'<div class="scatterplot-editor tabbable tabs-left">\n    <ul class="nav nav-tabs">\n        <li class="active">\n            <a title="Use this tab to change which data are used"\n               href="#data-control" data-toggle="tab">Data Controls</a>\n        </li>\n        <li>\n            <a title="Use this tab to change how the chart is drawn"\n               href="#chart-control" data-toggle="tab" >Chart Controls</a>\n        </li>\n        <li class="disabled">\n            <a title="This tab will display the chart"\n               href="#chart-display" data-toggle="tab">Chart</a>\n        </li>\n        <li class="file-controls">\n<!--            <button class="copy-btn btn btn-default"\n                    title="Save this as a new visualization">Save to new</button>-->\n            <button class="save-btn btn btn-default">Save</button>\n        </li>\n    </ul>\n\n    <div class="tab-content">\n        <div id="data-control" class="scatterplot-config-control tab-pane active">\n        </div>\n    \n        <div id="chart-control" class="scatterplot-config-control tab-pane">\n        </div>\n\n        <div id="chart-display" class="scatterplot-display tab-pane"></div>\n\n    </div>\n</div>\n'},useData:!0});var ScatterplotConfigEditor=Backbone.View.extend({className:"scatterplot-control-form",initialize:function(a){if(this.model||(this.model=new Visualization({type:"scatterplot"})),!a||!a.dataset)throw new Error("ScatterplotConfigEditor requires a dataset");this.dataset=a.dataset,this.display=new ScatterplotDisplay({dataset:a.dataset,model:this.model})},render:function(){this.$el.empty().append(ScatterplotConfigEditor.templates.mainLayout({})),this.model.id&&(this.$el.find(".copy-btn").show(),this.$el.find(".save-btn").text("Update saved")),this.$el.find("[title]").tooltip(),this._render_dataControl(),this._render_chartControls(),this._render_chartDisplay();var a=this.model.get("config");return this.model.id&&_.isFinite(a.xColumn)&&_.isFinite(a.yColumn)&&this.renderChart(),this},_getColumnIndecesByType:function(){var a={numeric:[],text:[],all:[]};return _.each(this.dataset.metadata_column_types||[],function(b,c){"int"===b||"float"===b?a.numeric.push(c):("str"===b||"list"===b)&&a.text.push(c),a.all.push(c)}),a.numeric.length<2&&(a.numeric=[]),a},_render_dataControl:function(a){a=a||this.$el;var b=this,c=this.model.get("config"),d=this._getColumnIndecesByType(),e=a.find(".tab-pane#data-control");return e.html(ScatterplotConfigEditor.templates.dataControl({peek:this.dataset.peek})),e.find(".peek").peekColumnSelector({controls:[{label:"X Column",id:"xColumn",selected:c.xColumn,disabled:d.text},{label:"Y Column",id:"yColumn",selected:c.yColumn,disabled:d.text},{label:"ID Column",id:"idColumn",selected:c.idColumn}]}).on("peek-column-selector.change",function(a,c){b.model.set("config",c)}).on("peek-column-selector.rename",function(a,b){}),e.find("[title]").tooltip(),e},_render_chartControls:function(a){function b(){var a=$(this),b=a.slider("value");c.model.set("config",_.object([[a.parent().data("config-key"),b]])),a.siblings(".slider-output").text(b)}a=a||this.$el;var c=this,d=this.model.get("config"),e=a.find("#chart-control");e.html(ScatterplotConfigEditor.templates.chartControl(d));var f={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};e.find(".numeric-slider-input").each(function(){var a=$(this),c=a.attr("data-config-key"),e=_.extend(f[c],{value:d[c],change:b,slide:b});a.find(".slider").slider(e),a.children(".slider-output").text(d[c])});var g=this.dataset.metadata_column_names||[],h=d.xLabel||g[d.xColumn]||"X",i=d.yLabel||g[d.yColumn]||"Y";return e.find('input[name="X-axis-label"]').val(h).on("change",function(){c.model.set("config",{xLabel:$(this).val()})}),e.find('input[name="Y-axis-label"]').val(i).on("change",function(){c.model.set("config",{yLabel:$(this).val()})}),e.find("[title]").tooltip(),e},_render_chartDisplay:function(a){a=a||this.$el;var b=a.find(".tab-pane#chart-display");return this.display.setElement(b),this.display.render(),b.find("[title]").tooltip(),b},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","click #data-control .render-button":"renderChart","click #chart-control .render-button":"renderChart","click .save-btn":"saveVisualization"},saveVisualization:function(){var a=this;this.model.save().fail(function(b,c,d){console.error(b,c,d),a.trigger("save:error",view),alert("Error loading data:\n"+b.responseText)}).then(function(){a.display.render()})},toggleThirdColumnSelector:function(){this.$el.find('select[name="idColumn"]').parent().toggle()},renderChart:function(){this.$el.find(".nav li.disabled").removeClass("disabled"),this.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show"),this.display.fetchData()},toString:function(){return"ScatterplotConfigEditor("+(this.dataset?this.dataset.id:"")+")"}});ScatterplotConfigEditor.templates={mainLayout:scatterplot.editor,dataControl:scatterplot.datacontrol,chartControl:scatterplot.chartcontrol};var ScatterplotDisplay=Backbone.View.extend({initialize:function(a){this.data=null,this.dataset=a.dataset,this.lineCount=this.dataset.metadata_data_lines||null},fetchData:function(){this.showLoadingIndicator();var a=this,b=this.model.get("config"),c=jQuery.getJSON(("undefined"==typeof parent.galaxy_config.root?"/":parent.galaxy_config.root)+"api/datasets/"+this.dataset.id,{data_type:"raw_data",provider:"dataset-column",limit:b.pagination.perPage,offset:b.pagination.currPage*b.pagination.perPage});return c.done(function(b){a.data=b.data,a.trigger("data:fetched",a),a.renderData()}),c.fail(function(b,c,d){console.error(b,c,d),a.trigger("data:error",a),alert("Error loading data:\n"+b.responseText)}),c},showLoadingIndicator:function(){this.$el.find(".scatterplot-data-info").html(['<div class="loading-indicator">','<span class="fa fa-spinner fa-spin"></span>','<span class="loading-indicator-message">loading...</span>',"</div>"].join(""))},template:function(){var a=['<div class="controls clear">','<div class="right">','<p class="scatterplot-data-info"></p>','<button class="stats-toggle-btn">Stats</button>','<button class="rerender-btn">Redraw</button>',"</div>",'<div class="left">','<div class="page-control"></div>',"</div>","</div>","<svg/>",'<div class="stats-display"></div>'].join("");return a},render:function(){return this.$el.addClass("scatterplot-display").html(this.template()),this.data&&this.renderData(),this},renderData:function(){this.renderLeftControls(),this.renderRightControls(),this.renderPlot(this.data),this.getStats()},renderLeftControls:function(){var a=this,b=this.model.get("config");return this.$el.find(".controls .left .page-control").pagination({startingPage:b.pagination.currPage,perPage:b.pagination.perPage,totalDataSize:this.lineCount,currDataSize:this.data.length}).off().on("pagination.page-change",function(c,d){b.pagination.currPage=d,a.model.set("config",{pagination:b.pagination}),a.resetZoom(),a.fetchData()}),this},renderRightControls:function(){var a=this;this.setLineInfo(this.data),this.$el.find(".stats-toggle-btn").off().click(function(){a.toggleStats()}),this.$el.find(".rerender-btn").off().click(function(){a.resetZoom(),a.renderPlot(this.data)})},renderPlot:function(){var a=this,b=this.$el.find("svg");this.toggleStats(!1),b.off().empty().show().on("zoom.scatterplot",function(b,c){a.model.set("config",c)}),scatterplot(b.get(0),this.model.get("config"),this.data)},setLineInfo:function(a,b){if(a){var c=this.model.get("config"),d=this.lineCount||"an unknown total",e=c.pagination.currPage*c.pagination.perPage,f=e+a.length;this.$el.find(".controls p.scatterplot-data-info").text([e+1,"to",f,"of",d].join(" "))}else this.$el.find(".controls p.scatterplot-data-info").html(b||"");return this},resetZoom:function(a,b){return a=void 0!==a?a:1,b=void 0!==b?b:[0,0],this.model.set("config",{scale:a,translate:b}),this},getStats:function(){if(this.data){var a=this,b=this.model.get("config"),c=new Worker("/plugins/visualizations/scatterplot/static/worker-stats.js");c.postMessage({data:this.data,keys:[b.xColumn,b.yColumn]}),c.onerror=function(a){c.terminate()},c.onmessage=function(b){a.renderStats(b.data)}}},renderStats:function(a,b){var c=this.model.get("config"),d=this.$el.find(".stats-display"),e=c.xLabel,f=c.yLabel,g=$("<table/>").addClass("table").append(["<thead><th></th><th>",e,"</th><th>",f,"</th></thead>"].join("")).append(_.map(a,function(a,b){return $(["<tr><td>",b,"</td><td>",a[0],"</td><td>",a[1],"</td></tr>"].join(""))}));d.empty().append(g)},toggleStats:function(a){var b=this.$el.find(".stats-display");a=void 0===a?b.is(":hidden"):a,a?(this.$el.find("svg").hide(),b.show(),this.$el.find(".controls .stats-toggle-btn").text("Plot")):(b.hide(),this.$el.find("svg").show(),this.$el.find(".controls .stats-toggle-btn").text("Stats"))},toString:function(){return"ScatterplotView()"}}),ScatterplotModel=Visualization.extend({defaults:{type:"scatterplot",config:{pagination:{currPage:0,perPage:3e3},width:400,height:400,margin:{top:16,right:16,bottom:40,left:54},xTicks:10,xLabel:"X",yTicks:10,yLabel:"Y",datapointSize:4,animDuration:500,scale:1,translate:[0,0]}}});

From b29ea767d9ebc45e076e852b6f37ec29b80a8f32 Mon Sep 17 00:00:00 2001
From: yhoogstrate <y.hoogstrate@erasmusmc.nl>
Date: Tue, 7 Apr 2015 15:51:55 +0200
Subject: [PATCH 42/88] Update scatterplot-display.js

---
 .../visualizations/scatterplot/src/scatterplot-display.js       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/plugins/visualizations/scatterplot/src/scatterplot-display.js b/config/plugins/visualizations/scatterplot/src/scatterplot-display.js
index 7f36486e09f..0429f1472bb 100644
--- a/config/plugins/visualizations/scatterplot/src/scatterplot-display.js
+++ b/config/plugins/visualizations/scatterplot/src/scatterplot-display.js
@@ -20,7 +20,7 @@ var ScatterplotDisplay = Backbone.View.extend({
         var view = this,
             config = this.model.get( 'config' ),
             //TODO: very tied to datasets - should be generalized eventually
-            xhr = jQuery.getJSON( '/api/datasets/' + this.dataset.id, {
+            xhr = jQuery.getJSON(((typeof parent.galaxy_config.root == 'undefined') ? '/' : parent.galaxy_config.root) + 'api/datasets/' + this.dataset.id, {
                 data_type   : 'raw_data',
                 provider    : 'dataset-column',
                 limit       : config.pagination.perPage,

From 15d26ba942ea340f229299c7e8556a7d12cf4b84 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 7 Apr 2015 10:07:26 -0400
Subject: [PATCH 43/88] Fix example auth definition -- found by Nicola

---
 lib/galaxy/auth/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/auth/__init__.py b/lib/galaxy/auth/__init__.py
index ad2d2b6fcbd..7dbb843b37f 100644
--- a/lib/galaxy/auth/__init__.py
+++ b/lib/galaxy/auth/__init__.py
@@ -20,7 +20,7 @@ log = logging.getLogger(__name__)
 
 # <auth>
 #     <authenticator>
-#         <type>ldap_ad</type>
+#         <type>ldap</type>
 #         <filter>'[login]'.endswith('@students.latrobe.edu.au')</filter>
 #         <options>
 #             <auto-register>True</auto-register>

From 27a78957f64f13e82b19b19a8d74de82c094bbf4 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 7 Apr 2015 10:13:10 -0400
Subject: [PATCH 44/88] Meant to not specify a particular test in the
 TestUserInfo example

---
 run_tests.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/run_tests.sh b/run_tests.sh
index b37103b669b..02edf48ca22 100755
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -27,7 +27,7 @@ https://nose.readthedocs.org/en/latest/usage.html#selecting-tests.  These are
 indicated with the optional parameter (test_path).  A few examples are:
 
 Run all TestUserInfo functional tests:
-    ./run_tests.sh test/functional/test_user_info.py:TestUserInfo.test_005_create_user_info_forms
+    ./run_tests.sh test/functional/test_user_info.py:TestUserInfo
 
 Run a specific API test requiring the framework test tools:
     ./run_tests.sh -api -with_framework_test_tools test/api/test_tools.py:ToolsTestCase.test_map_over_with_output_format_actions

From 6e48df2dc89b58f3bda5b45bef380795bf2501f7 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan.blankenberg@gmail.com>
Date: Tue, 7 Apr 2015 11:35:29 -0400
Subject: [PATCH 45/88] Add a debug message for when dynamic_options (code
 files) encounter exceptions when generating lists of options.

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

diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 052f68d769d..ba4a8928ab1 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -816,7 +816,8 @@ class SelectToolParameter( ToolParameter ):
             call_other_values = self._get_dynamic_options_call_other_values( trans, other_values )
             try:
                 return eval( self.dynamic_options, self.tool.code_namespace, call_other_values )
-            except Exception:
+            except Exception, e:
+                log.debug( "Error determining dynamic options for parameter '%s' in tool '%s':", self.name, self.tool.id, exc_info=e )
                 return []
         else:
             return self.static_options

From 3207302e04e956c84584fac6f9b0bd4663624063 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Tue, 7 Apr 2015 13:11:39 -0400
Subject: [PATCH 46/88] Fix re-run option for data manager tools

---
 templates/webapps/galaxy/tool_form.mako | 1 +
 1 file changed, 1 insertion(+)

diff --git a/templates/webapps/galaxy/tool_form.mako b/templates/webapps/galaxy/tool_form.mako
index 9f7d986b62e..d8dcb5a9c37 100644
--- a/templates/webapps/galaxy/tool_form.mako
+++ b/templates/webapps/galaxy/tool_form.mako
@@ -10,6 +10,7 @@ ${h.css('base', 'jquery-ui/smoothness/jquery-ui')}
         ## This avoids making two separate requests since the classic form requires the mako anyway.
         params = dict(trans.request.params)
         params['__dataset_id__'] = params.get('id', None)
+        params['__job_id__'] = params.get('job_id', None)
         self.form_config = tool.to_json(trans, params)
         self.form_config.update({
             'id'                : tool.id,

From 40b6fd2e8f5f5ef08df481194ad6d2b8b98e7146 Mon Sep 17 00:00:00 2001
From: Martin Cech <cech.marten@gmail.com>
Date: Tue, 7 Apr 2015 16:13:19 -0400
Subject: [PATCH 47/88] fix repo search by explicitly casting response to
 string some change happened recently that broke this, not sure where but
 nothing else is probably affected

---
 lib/galaxy/webapps/tool_shed/api/search.py | 20 ++++++++++++++------
 1 file changed, 14 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/webapps/tool_shed/api/search.py b/lib/galaxy/webapps/tool_shed/api/search.py
index f6d6a152d98..c0db8897b90 100644
--- a/lib/galaxy/webapps/tool_shed/api/search.py
+++ b/lib/galaxy/webapps/tool_shed/api/search.py
@@ -22,12 +22,20 @@ class SearchController ( BaseAPIController ):
         TS config option toolshed_search_on has to be turned on and
         toolshed_whoosh_index_dir has to be specified and existing.
 
-        :param search_term:
-        :param page:
-        :param jsonp:
-        :param callback:
+        :param search_term:   (required)the term to search
+        :type  search_term:   str
 
-        :returns dict:
+        :param page:          (optional)requested page of the search
+        :type  page:          int
+
+        :param jsonp:         (optional)flag whether to use jsonp format response, defaults to False
+        :type  jsonp:         bool
+
+        :param callback:      (optional)name of the function to wrap callback in
+                              used only when jsonp is true, defaults to 'callback'
+        :type  callback:      str
+
+        :returns dict:        object containing list of results and a hostname
         """
         if not self.app.config.toolshed_search_on:
             raise exceptions.ConfigDoesNotAllowException( 'Searching the TS through the API is turned off for this instance.' )
@@ -46,7 +54,7 @@ class SearchController ( BaseAPIController ):
         results[ 'hostname' ] = url_for( '/', qualified = True )
 
         if return_jsonp:
-            response = '%s(%s);' % ( callback, json.dumps( results ) )
+            response = str( '%s(%s);' % ( callback, json.dumps( results ) ) )
         else:
             response = json.dumps( results )
         return response

From 54ccd3e4a4d9890aa181c59bf22eb8fd2423ab8b Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 8 Apr 2015 08:47:10 -0400
Subject: [PATCH 48/88] Fix documentation for real user parameters.

I think what was documented was the ideal case - which would be great if these could be set per destination - but they cannot be so they shouldn't be documented that way.

Documentation broken in https://github.com/galaxyproject/galaxy/commit/9b7775be03728f724c025a83bc7ffa9e28c2c932.
---
 config/galaxy.ini.sample            | 11 +++++++++++
 config/job_conf.xml.sample_advanced |  5 +----
 2 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample
index 0530a37ec94..fcd4d6e73f3 100644
--- a/config/galaxy.ini.sample
+++ b/config/galaxy.ini.sample
@@ -960,6 +960,17 @@ use_interactive = True
 # always, onsuccess, never
 #cleanup_job = always
 
+# For sites where all users in Galaxy match users on the system on which Galaxy
+# runs, the DRMAA job runner can be configured to submit jobs to the DRM as the
+# actual user instead of as the user running the Galaxy server process.  For
+# details on these options, see the documentation at:
+#
+# http://galaxyproject.org/wiki/Admin/Config/Performance/Cluster
+#
+#drmaa_external_runjob_script = scripts/drmaa_external_runner.py
+#drmaa_external_killjob_script = scripts/drmaa_external_killer.py
+#external_chown_script = scripts/external_chown_script.py
+
 # File to source to set up the environment when running jobs.  By default, the
 # environment in which the Galaxy server starts is used when running jobs
 # locally, and the environment set up per the DRM's submission method and
diff --git a/config/job_conf.xml.sample_advanced b/config/job_conf.xml.sample_advanced
index 6219311eb8d..a76879f1e10 100644
--- a/config/job_conf.xml.sample_advanced
+++ b/config/job_conf.xml.sample_advanced
@@ -252,10 +252,7 @@
           -->
         </destination>
         <destination id="real_user_cluster" runner="drmaa">
-            <!-- TODO: The real user options should maybe not be considered runner params. -->
-            <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param>
-            <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param>
-            <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param>
+            <!-- Make sure to setup 3 real user parameters in galaxy.ini. -->
         </destination>
         <destination id="dynamic" runner="dynamic">
             <!-- A destination that represents a method in the dynamic runner. -->

From 497ae712c10f956f0f5607d208c2e4f51c2b5cf1 Mon Sep 17 00:00:00 2001
From: Carl Eberhard <carlfeberhard@gmail.com>
Date: Wed, 8 Apr 2015 10:12:01 -0400
Subject: [PATCH 49/88] Incorporate feedback from linter; Remove
 managers/datasets,pages from pep8_sources

---
 .ci/pep8_sources.txt            | 2 +-
 lib/galaxy/managers/datasets.py | 6 ++----
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/.ci/pep8_sources.txt b/.ci/pep8_sources.txt
index 01ed8dca4cd..4c92802deb3 100644
--- a/.ci/pep8_sources.txt
+++ b/.ci/pep8_sources.txt
@@ -3,7 +3,7 @@ lib/galaxy/config.py
 lib/galaxy/exceptions/error_codes.py
 lib/galaxy/jobs/{__init__,error_level,manager,stock_rules}.py
 lib/galaxy/main.py
-lib/galaxy/managers/{api_keys,citations,collections,collections_util,datasets,folders,pages,tags,workflows}.py
+lib/galaxy/managers/{api_keys,citations,collections,collections_util,folders,tags,workflows}.py
 lib/galaxy/model/orm/{engine_factory,now}.py
 lib/galaxy/model/util.py
 lib/galaxy/model/tool_shed_install/__init__.py
diff --git a/lib/galaxy/managers/datasets.py b/lib/galaxy/managers/datasets.py
index 198753c6b0f..324baa2bc67 100644
--- a/lib/galaxy/managers/datasets.py
+++ b/lib/galaxy/managers/datasets.py
@@ -1,8 +1,6 @@
 """
 Manager and Serializer for Datasets.
 """
-import json
-
 from galaxy import model
 from galaxy import exceptions
 import galaxy.datatypes.metadata
@@ -125,7 +123,7 @@ class DatasetRBACPermissions( object ):
     # ---- conv. settings
     def set_public_with_single_manager( self, dataset, user, flush=True ):
         manage = self.manage.grant( dataset, user, flush=flush )
-        access = self.access.clear( dataset, flush=False )
+        self.access.clear( dataset, flush=False )
         return ( [ manage ], [] )
 
     def set_private_to_one_user( self, dataset, user, flush=True ):
@@ -327,7 +325,7 @@ class _UnflattenedMetadataDatasetAssociationSerializer( base.ModelSerializer,
             # underlying dataset
             'dataset'       : lambda i, k, **c: self.dataset_serializer.serialize_to_view( i.dataset, view='summary', **c ),
             'dataset_id'    : self._proxy_to_dataset( key='id' ),
-            #TODO: why is this named uuid!? The da doesn't have a uuid - it's the underlying dataset's uuid!
+            # TODO: why is this named uuid!? The da doesn't have a uuid - it's the underlying dataset's uuid!
             'uuid'          : self._proxy_to_dataset( key='uuid' ),
             # 'dataset_uuid'  : self._proxy_to_dataset( key='uuid' ),
             'file_name'     : self._proxy_to_dataset( serializer=self.dataset_serializer.serialize_file_name ),

From 137543ea674945e47a95fe548118dfc63e359e77 Mon Sep 17 00:00:00 2001
From: Carl Eberhard <carlfeberhard@gmail.com>
Date: Wed, 8 Apr 2015 10:41:46 -0400
Subject: [PATCH 50/88] Fix container model import and LibraryDataset reference

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

diff --git a/lib/galaxy/managers/containers.py b/lib/galaxy/managers/containers.py
index aba6edf1612..4593e9f8272 100644
--- a/lib/galaxy/managers/containers.py
+++ b/lib/galaxy/managers/containers.py
@@ -10,6 +10,7 @@ Libraries should be DatasetCollections.
 
 import operator
 
+from galaxy import model
 import galaxy.exceptions
 import galaxy.util
 
@@ -95,7 +96,7 @@ class LibraryFolderAsContainerManagerMixin( ContainerManagerMixin ):
     # can contain two types of subcontainer: LibraryFolder, LibraryDatasetCollectionAssociation
     # has as the top level container: Library
 
-    contained_class = model.LibraryDatasetAssociation
+    contained_class = model.LibraryDataset
     subcontainer_class = model.LibraryFolder
     # subcontainer_class = model.LibraryDatasetCollectionAssociation
     order_contents_on = operator.attrgetter( 'create_time' )
@@ -107,7 +108,7 @@ class LibraryFolderAsContainerManagerMixin( ContainerManagerMixin ):
 
     def _content_manager( self, content ):
         # type snifffing is inevitable
-        if   isinstance( content, model.LibraryDatasetAssociation ):
+        if   isinstance( content, model.LibraryDataset ):
             return self.lda_manager
         elif isinstance( content, model.LibraryFolder ):
             return self.folder_manager

From 24b71b7f682105ded0bd6cb24d9cbc9ec380fb55 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 8 Apr 2015 11:50:34 -0400
Subject: [PATCH 51/88] Potential fix for recent uwsgi toolshed database
 issues.  In any event, this current pool disposal is definitely broken (and
 hidden from view due to blanket passing except) in the current
 implementation.

---
 lib/galaxy/webapps/tool_shed/buildapp.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/webapps/tool_shed/buildapp.py b/lib/galaxy/webapps/tool_shed/buildapp.py
index 2f9e191b94b..dfe3dccce10 100644
--- a/lib/galaxy/webapps/tool_shed/buildapp.py
+++ b/lib/galaxy/webapps/tool_shed/buildapp.py
@@ -163,9 +163,9 @@ def app_factory( global_conf, **kwargs ):
             webapp = wrap_in_static( webapp, global_conf, **kwargs )
     # Close any pooled database connections before forking
     try:
-        galaxy.webapps.tool_shed.model.mapping.metadata.engine.connection_provider._pool.dispose()
+        galaxy.webapps.tool_shed.model.mapping.metadata.bind.dispose()
     except:
-        pass
+        log.exception("Unable to dispose of pooled tool_shed model database connections.")
     # Return
     return webapp
 

From 0e030831d031b8ca721537e9d0919e376cf67564 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 8 Apr 2015 11:53:32 -0400
Subject: [PATCH 52/88] Similar fix as the previous -- Galaxy wasn't disposing
 of pooled connections prior to returning webapp and (potential) forking.

---
 lib/galaxy/webapps/galaxy/buildapp.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index 27986d71baa..b124d8b1f7f 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -103,13 +103,13 @@ def app_factory( global_conf, **kwargs ):
             webapp = wrap_in_static( webapp, global_conf, plugin_frameworks=[ app.visualizations_registry ], **kwargs )
     # Close any pooled database connections before forking
     try:
-        galaxy.model.mapping.metadata.engine.connection_provider._pool.dispose()
+        galaxy.model.mapping.metadata.bind.dispose()
     except:
-        pass
+        log.exception("Unable to dispose of pooled galaxy model database connections.")
     try:
-        galaxy.model.tool_shed_install.mapping.metadata.engine.connection_provider._pool.dispose()
+        galaxy.model.tool_shed_install.mapping.metadata.bind.dispose()
     except:
-        pass
+        log.exception("Unable to dispose of pooled toolshed install model database connections.")
 
     if not app.config.is_uwsgi:
         postfork_setup()

From f40e7046e9bb6138934bb317d066e96579953eae Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 8 Apr 2015 13:46:55 -0400
Subject: [PATCH 53/88] Another pool disposal fix, for reports.

---
 lib/galaxy/webapps/reports/buildapp.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/webapps/reports/buildapp.py b/lib/galaxy/webapps/reports/buildapp.py
index b5fc37284b8..1b1965706c6 100644
--- a/lib/galaxy/webapps/reports/buildapp.py
+++ b/lib/galaxy/webapps/reports/buildapp.py
@@ -70,12 +70,13 @@ def app_factory( global_conf, **kwargs ):
         webapp = wrap_in_static( webapp, global_conf, **kwargs )
     # Close any pooled database connections before forking
     try:
-        galaxy.model.mapping.metadata.engine.connection_provider._pool.dispose()
+        galaxy.model.mapping.metadata.bind.dispose()
     except:
-        pass
+        log.exception("Unable to dispose of pooled galaxy model database connections.")
     # Return
     return webapp
 
+
 def wrap_in_middleware( app, global_conf, **local_conf ):
     """Based on the configuration wrap `app` in a set of common and useful middleware."""
     # Merge the global and local configurations

From d6bf6fc2b2f8c14ddfad1e1b4e44b0b006333682 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 8 Apr 2015 11:50:34 -0400
Subject: [PATCH 54/88] Potential fix for recent uwsgi toolshed database
 issues.  In any event, this current pool disposal is definitely broken (and
 hidden from view due to blanket passing except) in the current
 implementation.

---
 lib/galaxy/webapps/tool_shed/buildapp.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/webapps/tool_shed/buildapp.py b/lib/galaxy/webapps/tool_shed/buildapp.py
index 6b63eb276f4..ce26b0cf5e9 100644
--- a/lib/galaxy/webapps/tool_shed/buildapp.py
+++ b/lib/galaxy/webapps/tool_shed/buildapp.py
@@ -153,9 +153,9 @@ def app_factory( global_conf, **kwargs ):
             webapp = wrap_in_static( webapp, global_conf, **kwargs )
     # Close any pooled database connections before forking
     try:
-        galaxy.webapps.tool_shed.model.mapping.metadata.engine.connection_provider._pool.dispose()
+        galaxy.webapps.tool_shed.model.mapping.metadata.bind.dispose()
     except:
-        pass
+        log.exception("Unable to dispose of pooled tool_shed model database connections.")
     # Return
     return webapp
 

From d403c43123b921f28a463ecbb28ccae2f82452c9 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 8 Apr 2015 11:53:32 -0400
Subject: [PATCH 55/88] Similar fix as the previous -- Galaxy wasn't disposing
 of pooled connections prior to returning webapp and (potential) forking.

---
 lib/galaxy/webapps/galaxy/buildapp.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index d7492408b52..4c57821e0f5 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -106,13 +106,13 @@ def app_factory( global_conf, **kwargs ):
         pack_scripts()
     # Close any pooled database connections before forking
     try:
-        galaxy.model.mapping.metadata.engine.connection_provider._pool.dispose()
+        galaxy.model.mapping.metadata.bind.dispose()
     except:
-        pass
+        log.exception("Unable to dispose of pooled galaxy model database connections.")
     try:
-        galaxy.model.tool_shed_install.mapping.metadata.engine.connection_provider._pool.dispose()
+        galaxy.model.tool_shed_install.mapping.metadata.bind.dispose()
     except:
-        pass
+        log.exception("Unable to dispose of pooled toolshed install model database connections.")
 
     if not app.config.is_uwsgi:
         postfork_setup()

From 3ac516291cc8bd9604d8a1053c3bd6bec3968229 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 8 Apr 2015 13:46:55 -0400
Subject: [PATCH 56/88] Another pool disposal fix, for reports.

---
 lib/galaxy/webapps/reports/buildapp.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/webapps/reports/buildapp.py b/lib/galaxy/webapps/reports/buildapp.py
index b5fc37284b8..1b1965706c6 100644
--- a/lib/galaxy/webapps/reports/buildapp.py
+++ b/lib/galaxy/webapps/reports/buildapp.py
@@ -70,12 +70,13 @@ def app_factory( global_conf, **kwargs ):
         webapp = wrap_in_static( webapp, global_conf, **kwargs )
     # Close any pooled database connections before forking
     try:
-        galaxy.model.mapping.metadata.engine.connection_provider._pool.dispose()
+        galaxy.model.mapping.metadata.bind.dispose()
     except:
-        pass
+        log.exception("Unable to dispose of pooled galaxy model database connections.")
     # Return
     return webapp
 
+
 def wrap_in_middleware( app, global_conf, **local_conf ):
     """Based on the configuration wrap `app` in a set of common and useful middleware."""
     # Merge the global and local configurations

From 870770ffe125988d05d510a569633c2741b0a69a Mon Sep 17 00:00:00 2001
From: Martin Cech <cech.marten@gmail.com>
Date: Wed, 8 Apr 2015 14:37:52 -0400
Subject: [PATCH 57/88] add more style exceptions

In order to allow https://github.com/galaxyproject/galaxy/pull/76 to proceed.
---
 setup.cfg | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/setup.cfg b/setup.cfg
index 10a0c4ded0e..da197b9fd48 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,4 +1,7 @@
 [flake8]
-# 201 and 202 are spaces after ( and before ), 501 is line length. These
-# are exceptions allowed (encouraged?) by Galaxy style guidelines.
-ignore = E201,E202,E501
+# These are exceptions allowed (encouraged?) by Galaxy style guidelines.
+# 128 continuation line under-indented for visual indent
+# 201 and 202 are spaces after ( and before )
+# 203 whitespace before ':'
+# 501 is line length
+ignore = E128,E201,E202,E203,E501

From c4c3d3e0650739fa91b1bed549def5e8f495eec6 Mon Sep 17 00:00:00 2001
From: Carl Eberhard <carlfeberhard@gmail.com>
Date: Wed, 8 Apr 2015 17:36:53 -0400
Subject: [PATCH 58/88] Put managers/datasets and pages back in
 pep8_sources.txt

---
 .ci/pep8_sources.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.ci/pep8_sources.txt b/.ci/pep8_sources.txt
index 4c92802deb3..01ed8dca4cd 100644
--- a/.ci/pep8_sources.txt
+++ b/.ci/pep8_sources.txt
@@ -3,7 +3,7 @@ lib/galaxy/config.py
 lib/galaxy/exceptions/error_codes.py
 lib/galaxy/jobs/{__init__,error_level,manager,stock_rules}.py
 lib/galaxy/main.py
-lib/galaxy/managers/{api_keys,citations,collections,collections_util,folders,tags,workflows}.py
+lib/galaxy/managers/{api_keys,citations,collections,collections_util,datasets,folders,pages,tags,workflows}.py
 lib/galaxy/model/orm/{engine_factory,now}.py
 lib/galaxy/model/util.py
 lib/galaxy/model/tool_shed_install/__init__.py

From 08c6f796922215bd7e322f788127ecc4cfabf5c0 Mon Sep 17 00:00:00 2001
From: David Trudgian <dave@trudgian.net>
Date: Wed, 8 Apr 2015 16:59:43 -0500
Subject: [PATCH 59/88] Correct ldap authenticator type in example config

Thanks to @nsoranzo for spotting.
---
 lib/galaxy/auth/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/auth/__init__.py b/lib/galaxy/auth/__init__.py
index ad2d2b6fcbd..7dbb843b37f 100644
--- a/lib/galaxy/auth/__init__.py
+++ b/lib/galaxy/auth/__init__.py
@@ -20,7 +20,7 @@ log = logging.getLogger(__name__)
 
 # <auth>
 #     <authenticator>
-#         <type>ldap_ad</type>
+#         <type>ldap</type>
 #         <filter>'[login]'.endswith('@students.latrobe.edu.au')</filter>
 #         <options>
 #             <auto-register>True</auto-register>

From 027c65a8da1b47cf795e9cd609398e77fb1e9a89 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 8 Apr 2015 22:40:51 -0400
Subject: [PATCH 60/88] Remove unused method form install_environment.

settings is undefined so this is a previous clear sign the method is unused.
---
 .../tool_dependencies/recipe/install_environment.py          | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
index 1c9c132b802..d336c711f42 100644
--- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
@@ -46,11 +46,6 @@ class InstallEnvironment( object ):
         self.install_dir = install_dir
         self.tool_shed_repository_install_dir = tool_shed_repository_install_dir
 
-    def __call__( self ):
-        with settings( warn_only=True, **basic_util.get_env_var_values( self ) ):
-            with prefix( self.__setup_environment() ):
-                yield
-
     def add_env_shell_file_paths( self, paths ):
         for path in paths:
             self.env_shell_file_paths.append( str( path ) )

From b24875679a6001b79f3e2aeb6dbc5fcd4a4b5f2c Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 8 Apr 2015 22:48:13 -0400
Subject: [PATCH 61/88] Remove broken method from library_common.

That method could never have done anything but throw an exception or return [], this commit just assumes that it was always returning [] and updates the one place it was called accordingly. Not sure what widgets are - but I don't think @martenson is implementing them in the data library rewrite.

This method was originally added in f7334104a000f36fd1c5f8f18cf617b399b7ff0f
---
 .../webapps/galaxy/controllers/library_common.py    | 13 +------------
 1 file changed, 1 insertion(+), 12 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/controllers/library_common.py b/lib/galaxy/webapps/galaxy/controllers/library_common.py
index 1a7bfd80f6a..4f530d61dec 100644
--- a/lib/galaxy/webapps/galaxy/controllers/library_common.py
+++ b/lib/galaxy/webapps/galaxy/controllers/library_common.py
@@ -1432,7 +1432,6 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
                 message = 'Select at least one dataset from the list of active datasets in your current history'
                 status = 'error'
                 upload_option = kwd.get( 'upload_option', 'import_from_history' )
-                widgets = self._get_populated_widgets( folder )
                 # Send list of data formats to the upload form so the "extension" select list can be populated dynamically
                 file_formats = trans.app.datatypes_registry.upload_file_formats
                 # Send list of genome builds to the form so the "dbkey" select list can be populated dynamically
@@ -1459,7 +1458,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
                                             last_used_build=last_used_build,
                                             roles_select_list=roles_select_list,
                                             history=history,
-                                            widgets=widgets,
+                                            widgets=[],
                                             template_id=template_id,
                                             space_to_tab=space_to_tab,
                                             link_data_only=link_data_only,
@@ -1515,16 +1514,6 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
                 upload_option_select_list.add_option( option_label, option_value, selected=option_value==upload_option )
         return upload_option_select_list
 
-    def _get_populated_widgets( self, folder ):
-        # See if we have any inherited templates.
-        info_association, inherited = folder.get_info_association( inherited=True )
-        if info_association and info_association.inheritable:
-            widgets = folder.get_template_widgets( trans, get_contents=True )
-            # Retain contents of widget fields when form was submitted via refresh_on_change.
-            return self.populate_widgets_from_kwd( trans, widgets, **kwd )
-        else:
-            return []
-
     @web.expose
     def download_dataset_from_folder( self, trans, cntrller, id, library_id=None, **kwd ):
         """Catches the dataset id and displays file contents as directed"""

From 124243b24e4eae5a305bab39e65800bd182b522b Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 8 Apr 2015 22:52:08 -0400
Subject: [PATCH 62/88] Fix unknown name library_dataset in _check_manage of
 library_common.

Again - was completely broken - couldn't have worked as previously implemented This variant seems to make more sense.
---
 lib/galaxy/webapps/galaxy/controllers/library_common.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/controllers/library_common.py b/lib/galaxy/webapps/galaxy/controllers/library_common.py
index 4f530d61dec..2206c586baa 100644
--- a/lib/galaxy/webapps/galaxy/controllers/library_common.py
+++ b/lib/galaxy/webapps/galaxy/controllers/library_common.py
@@ -2573,8 +2573,8 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
             # Deny access if the user is not an admin and does not have the LIBRARY_MANAGE and DATASET_MANAGE_PERMISSIONS permissions.
             if not ( is_admin or \
                      ( trans.app.security_agent.can_manage_library_item( current_user_roles, item ) and
-                       trans.app.security_agent.can_manage_dataset( current_user_roles, library_dataset.library_dataset_dataset_association.dataset ) ) ):
-                message = "You are not authorized to manage permissions on library dataset (%s)." % escape( library_dataset.name )
+                       trans.app.security_agent.can_manage_dataset( current_user_roles, item.library_dataset_dataset_association.dataset ) ) ):
+                message = "You are not authorized to manage permissions on library dataset (%s)." % escape( item.name )
                 if cntrller == 'api':
                     return 403, message
                 return trans.response.send_redirect( web.url_for( controller='library_common',

From db5bea46a6661bd9d8bc6a2c3bef0aeafc0c07f7 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 8 Apr 2015 22:55:29 -0400
Subject: [PATCH 63/88] Remove broken and seemingly unused method from
 external_services.

Can find no callers for this method in templates, test, or lib. The method is broken anyway (trans not defined).
---
 lib/galaxy/external_services/service.py | 14 --------------
 1 file changed, 14 deletions(-)

diff --git a/lib/galaxy/external_services/service.py b/lib/galaxy/external_services/service.py
index 2bc11848162..fe6fa1ce628 100644
--- a/lib/galaxy/external_services/service.py
+++ b/lib/galaxy/external_services/service.py
@@ -210,19 +210,5 @@ class PopulatedExternalService( object ):
         assert action, 'Action not found: %s' % actions_list
         return action
 
-    def get_action_links( self ):
-        rval = []
-        param_dict = {}
-        param_dict['fields'] = Bunch( **self.service_instance.form_values.content )
-        param_dict['item'] = self.item
-        for item in self.service.items:
-            if isinstance( item, ExternalServiceParameter ):
-                param_dict[ item.name ] = item.get_value( param_dict )
-            elif isinstance( item, ExternalServiceAction ):
-                rval.append( item.get_action_access_link( self.item, trans, param_dict ) )
-            elif isinstance( item, ExternalServiceActionsGroup ):
-                rval.extend( item.populate( self.service_instance, item, param_dict ).get_action_links() )
-            else:
-                raise 'unknown item type found'
     def __nonzero__( self ):
         return self.actions.has_action()

From bf5176664de9e3630edcd9b2580d47ec40ed756f Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 8 Apr 2015 23:02:26 -0400
Subject: [PATCH 64/88] Fix missing import in
 galaxy.webapps.tool_shed.api.repositories.

---
 lib/galaxy/webapps/tool_shed/api/repositories.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/galaxy/webapps/tool_shed/api/repositories.py b/lib/galaxy/webapps/tool_shed/api/repositories.py
index 92fb87f519f..c92070157ef 100644
--- a/lib/galaxy/webapps/tool_shed/api/repositories.py
+++ b/lib/galaxy/webapps/tool_shed/api/repositories.py
@@ -12,6 +12,7 @@ from galaxy import util
 from galaxy import web
 from galaxy.exceptions import RequestParameterMissingException
 from galaxy.exceptions import RequestParameterInvalidException
+from galaxy.exceptions import InsufficientPermissionsException
 from galaxy.exceptions import ActionInputError
 from galaxy.exceptions import ObjectNotFound
 from galaxy.exceptions import MalformedId

From 453dde829eb04128202d9837dae83e893a1676ab Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 8 Apr 2015 23:04:06 -0400
Subject: [PATCH 65/88] Fix unknown name self in tool_shed.scripts.api.export.

---
 lib/tool_shed/scripts/api/export.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/tool_shed/scripts/api/export.py b/lib/tool_shed/scripts/api/export.py
index dea6c5dd211..bfb6c17c74a 100644
--- a/lib/tool_shed/scripts/api/export.py
+++ b/lib/tool_shed/scripts/api/export.py
@@ -25,7 +25,7 @@ def generate_repository_archive_filename( tool_shed_url, name, owner, changeset_
                                           export_repository_dependencies, use_tmp_archive_dir=False ):
     tool_shed = remove_protocol_from_tool_shed_url( tool_shed_url )
     file_type_str = basic_util.get_file_type_str( changeset_revision, file_type )
-    if self.export_repository_dependencies:
+    if export_repository_dependencies:
         repositories_archive_filename = '%s_%s_%s_%s_%s' % ( CAPSULE_WITH_DEPENDENCIES_FILENAME,
                                                              tool_shed,
                                                              name,

From dc256aebf22497cfce57de04e33fd606f97e485e Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 8 Apr 2015 23:06:12 -0400
Subject: [PATCH 66/88] Fix tool shed scripts that log without creating a log.

---
 lib/tool_shed/scripts/api/import_capsule.py                 | 3 ++-
 lib/tool_shed/scripts/api/reset_metadata_on_repositories.py | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/lib/tool_shed/scripts/api/import_capsule.py b/lib/tool_shed/scripts/api/import_capsule.py
index 3f9bce80351..e58cc25df82 100644
--- a/lib/tool_shed/scripts/api/import_capsule.py
+++ b/lib/tool_shed/scripts/api/import_capsule.py
@@ -14,7 +14,8 @@ method (they'll have to be created manually, which can be done after the import)
 Here is a working example of how to use this script to install a repository from the test tool shed.
 ./import_capsule.py -a <api key> -u http://localhost:9009 -c capsule_localhost_colon_9009_filter_test1_8923f52d5c6d.tar.gz
 """
-
+import logging
+log = logging.getLogger(__name__)
 import os
 import sys
 import argparse
diff --git a/lib/tool_shed/scripts/api/reset_metadata_on_repositories.py b/lib/tool_shed/scripts/api/reset_metadata_on_repositories.py
index 104689e87ac..fe3a1fcf64e 100644
--- a/lib/tool_shed/scripts/api/reset_metadata_on_repositories.py
+++ b/lib/tool_shed/scripts/api/reset_metadata_on_repositories.py
@@ -11,7 +11,8 @@ usage: reset_metadata_on_repositories.py key <my_writable>
 Here is a working example of how to use this script to reset metadata on certain repositories in a specified Tool Shed.
 python ./reset_metadata_on_repositories.py -a 22be3b -m True -u http://localhost:9009/
 """
-
+import logging
+log = logging.getLogger(__name__)
 import argparse
 import os
 import sys

From 6d49f1ef51017c9534f98729782c4c34764e5f8a Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 8 Apr 2015 23:08:10 -0400
Subject: [PATCH 67/88] Fix undefined variables in
 remote_repository_registry_entry.

---
 lib/tool_shed/scripts/api/remove_repository_registry_entry.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/tool_shed/scripts/api/remove_repository_registry_entry.py b/lib/tool_shed/scripts/api/remove_repository_registry_entry.py
index 5eec6ecfe11..730b3262693 100644
--- a/lib/tool_shed/scripts/api/remove_repository_registry_entry.py
+++ b/lib/tool_shed/scripts/api/remove_repository_registry_entry.py
@@ -26,7 +26,7 @@ def main( options ):
             response_dict = submit( url, data, api_key=api_key, return_formatted=False )
             print response_dict
         else:
-            print "Invalid tool_shed: ", base_tool_shed_url, " name: ", name, " or owner: ", owner, "."
+            print "Invalid tool_shed: ", base_tool_shed_url, " name: ", options.name, " or owner: ", options.owner, "."
     else:
         print "An API key for an admin user in the Tool Shed is required to remove entries from the Tool Shed's repository registry."
 

From 7c9413c13d87699c6d451e930488ffd574e8e6c7 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 8 Apr 2015 23:08:30 -0400
Subject: [PATCH 68/88] Fix undefined name in recently refactored
 yaml_to_workflow.py.

---
 test/api/yaml_to_workflow.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/api/yaml_to_workflow.py b/test/api/yaml_to_workflow.py
index 6771fa252b9..890180ccff5 100644
--- a/test/api/yaml_to_workflow.py
+++ b/test/api/yaml_to_workflow.py
@@ -17,7 +17,7 @@ STEP_TYPE_ALIASES = {
 
 def yaml_to_workflow(has_yaml):
     as_python = yaml.load(has_yaml)
-    return python_to_workflow(as_path)
+    return python_to_workflow(as_python)
 
 
 def python_to_workflow(as_python):

From 577107ec05dcddd43ecf5ab7e3809174b20454dc Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 8 Apr 2015 23:14:57 -0400
Subject: [PATCH 69/88] TraivsCI: More aggressive checks for very broken stuff.

Seems we are far from a consensus on style-based linting - but it should be not controversial that referenced variables should be defined and file syntax should be valid.
---
 .ci/flake8_wrapper.sh | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.ci/flake8_wrapper.sh b/.ci/flake8_wrapper.sh
index e606be9d1d0..63108bc4903 100755
--- a/.ci/flake8_wrapper.sh
+++ b/.ci/flake8_wrapper.sh
@@ -2,6 +2,11 @@
 
 set -e
 
+# Run broad range of checks over specific white-listed files, this uses
+# the default checks defined in setup.cfg.
 while read p; do
     flake8 $(eval echo "$p")
 done <.ci/pep8_sources.txt
+
+# Look for obviously broken stuff lots more places.
+flake8 --select=E901,E902,F821,F822,F823,F831 --exclude lib/galaxy/util/pastescript/serve.py lib/{galaxy,tool_shed} test/{api,unit}

From e84d3225ec9ecb7c222132c195304cfe437ac7e7 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 6 Apr 2015 11:06:48 -0400
Subject: [PATCH 70/88] Add more simple constructs to simple_constructs.xml
 test tool.

These demonstrate different kinds of simple selectors - using them for testing workflow runtime parameter problems.
---
 test/functional/tools/simple_constructs.xml | 24 ++++++++++++++++++---
 1 file changed, 21 insertions(+), 3 deletions(-)

diff --git a/test/functional/tools/simple_constructs.xml b/test/functional/tools/simple_constructs.xml
index b543af03a89..d67c0c282ee 100644
--- a/test/functional/tools/simple_constructs.xml
+++ b/test/functional/tools/simple_constructs.xml
@@ -1,10 +1,13 @@
-<tool id="simple_constructs" name="simple_constructs">
+<tool id="simple_constructs" name="simple_constructs" version="1.0.0">
     <command>
         echo "$p1.p1val"  >> $out_file1;
         echo "$booltest"  >> $out_file1;
         echo "$inttest"   >> $out_file1; 
-        echo "$floattest" >> $out_file1; 
-        cat "$files[0].file"   >> $out_file1;
+        echo "$floattest" >> $out_file1;
+        echo "$radio_select" >> $out_file1;
+        echo "$check_select" >> $out_file1;
+        echo "$drop_select"  >> $out_file1;
+        cat "$files[0].file" >> $out_file1;
     </command>
     <inputs>
         <conditional name="p1">
@@ -19,6 +22,21 @@
         <param name="booltest" truevalue="booltrue" falsevalue="boolfalse" checked="false" type="boolean" />
         <param name="inttest" value="1" type="integer" />
         <param name="floattest" value="1.0" type="float" />
+        <param name="radio_select" type="select" display="radio">
+            <option value="a_radio" selected="true">A Radio</option>
+            <option value="b_radio">B Radio</option>
+            <option value="c_radio">C Radio</option>
+        </param>
+        <param name="check_select" type="select" display="checkboxes" multiple="true">
+            <option value="a_check" selected="true">A Check</option>
+            <option value="b_check">B Check</option>
+            <option value="c_check">C Check</option>
+        </param>
+        <param name="drop_select" type="select">
+            <option value="a_drop" selected="true">A Drop</option>
+            <option value="b_drop">B Drop</option>
+            <option value="c_drop">C Drop</option>
+        </param>
         <repeat name="files" title="Files">
             <param name="file" type="data" format="txt" />
         </repeat>

From fe461599d603baeae1f71ea140b0a12bd0a4cabf Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 9 Apr 2015 09:40:49 -0400
Subject: [PATCH 71/88] Add test tool demonstrating/testing type inheritance.

---
 test/functional/tools/inheritance_simple.xml | 24 ++++++++++++++++++++
 test/functional/tools/samples_tool_conf.xml  |  1 +
 2 files changed, 25 insertions(+)
 create mode 100644 test/functional/tools/inheritance_simple.xml

diff --git a/test/functional/tools/inheritance_simple.xml b/test/functional/tools/inheritance_simple.xml
new file mode 100644
index 00000000000..218e9653112
--- /dev/null
+++ b/test/functional/tools/inheritance_simple.xml
@@ -0,0 +1,24 @@
+<tool id="inheritance_simple" name="inheritance_simple" version="1.0.0">
+    <description>(demonstrates subtypes are usable for parent format)</description>
+    <command>
+        cat $input1 > $out_file1
+    </command>
+    <inputs>
+        <param name="input1" type="data" label="Copy FASTQ" format="fastq" />
+    </inputs>
+    <outputs>
+        <data name="out_file1" format_source="input1" metadata_source="input1"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="1.fastqsanger" ftype="fastqsanger" />
+            <output name="out_file1" file="1.fastqsanger" ftype="fastqsanger" />
+        </test>
+        <test>
+            <param name="input1" value="1.fastqsolexa" ftype="fastqsolexa" />
+            <output name="out_file1" file="1.fastqsolexa" ftype="fastqsolexa" />
+        </test>
+    </tests>
+    <help>
+    </help>
+</tool>
diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
index 0f21dd8d712..f33c1155d44 100644
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -2,6 +2,7 @@
 <toolbox tool_path="${tool_conf_dir}">
   <tool file="upload.xml"/>
   <tool file="simple_constructs.xml" />
+  <tool file="inheritance_simple.xml" />
   <tool file="composite.xml" />
   <tool file="compare_bam_as_sam.xml" />
   <tool file="code_file.xml" />

From fb1048bb093c1b6f0af32fd79c93622dca290a4a Mon Sep 17 00:00:00 2001
From: Carl Eberhard <carlfeberhard@gmail.com>
Date: Thu, 9 Apr 2015 11:05:34 -0400
Subject: [PATCH 72/88] UI, history multipanel: attempt to solve undefined
 context in underscore.debounce<-checkColumnsInView by removing context
 binding

---
 client/galaxy/scripts/mvc/history/multi-panel.js | 4 +++-
 static/maps/mvc/history/multi-panel.js.map       | 2 +-
 static/scripts/mvc/history/multi-panel.js        | 2 +-
 3 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/client/galaxy/scripts/mvc/history/multi-panel.js b/client/galaxy/scripts/mvc/history/multi-panel.js
index 0175267f6fa..cb030684db2 100644
--- a/client/galaxy/scripts/mvc/history/multi-panel.js
+++ b/client/galaxy/scripts/mvc/history/multi-panel.js
@@ -968,7 +968,9 @@ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({
 
         // when scrolling - check for histories now in view: they will fire 'in-view' and queueHdaLoading if necc.
         //TODO:?? might be able to simplify and not use pub-sub
-        var debouncedInView = _.debounce( _.bind( this.checkColumnsInView, this ), 100 );
+        var debouncedInView = _.debounce( function _debouncedInner(){
+            multipanel.checkColumnsInView();
+        }, 100 );
         this.$( '.middle' ).parent().scroll( debouncedInView );
     },
 
diff --git a/static/maps/mvc/history/multi-panel.js.map b/static/maps/mvc/history/multi-panel.js.map
index 6704afd8645..2f26adecb76 100644
--- a/static/maps/mvc/history/multi-panel.js.map
+++ b/static/maps/mvc/history/multi-panel.js.map
@@ -1 +1 @@
-{"version":3,"file":"multi-panel.js","sources":["../../../src/mvc/history/multi-panel.js"],"names":["define","HISTORY_MODEL","HPANEL_EDIT","baseMVC","ajaxQueue","historyCopyDialog","history","options","validateName","name","Galaxy","modal","$","size","$invalidTitle","attr","css","color","margin-top","addClass","text","_l","append","copyHistory","$copyIndicator","copy","fail","alert","always","hide","checkNameAndCopy","val","historyName","get","defaultCopyName","show","_","extend","title","body","join","buttons","Cancel","Copy","focus","select","on","ev","keyCode","HistoryPanelColumn","Backbone","View","LoggableMixin","tagName","className","id","this","model","initialize","purgeAllowed","isUndefined","panel","createPanel","setUpListeners","panelOptions","dragItems","HistoryPanelEdit","_renderEmptyMessage","__patch_renderEmptyMessage","$whereTo","hdaCount","chain","values","flatten","value","length","$emptyMsg","$emptyMessage","isEmpty","hdaViews","contents","empty","searchFor","noneFoundMsg","emptyMsg","column","once","trigger","setUpPanelListeners","listenTo","rendered","inView","viewLeft","viewRight","columnLeft","$el","offset","left","columnRight","width","$panel","render","speed","undefined","modelData","toJSON","html","template","renderPanel","setUpBehaviors","data","isCurrentHistory","currentHistory","controlsLeftTemplate","view","controlsRightTemplate","setElement","$list","before","_renderDropTargetHelp","events","click .switch-to.btn","setAsCurrent","click .delete-history","_delete","xhr","status","error","done","click .undelete-history","undelete","click .purge-history","confirm","purge","click .copy-history","variable","toString","MultiPanelColumns","log","currentHistoryId","Error","columnWidth","borderWidth","columnGap","headerHeight","footerHeight","controlsHeight","order","_initSortOrders","hdaQueue","NamedAjaxQueue","collection","setCollection","histories","columnMap","createColumns","columnOptions","_comparator","getter","a","b","asc","sortOrders","update","fn","h","Date","name-dsc","size-dsc","models","multipanel","stopListening","sortCollection","silent","setUpCollectionListeners","add","addAsCurrentColumn","set-as-current","setCurrentHistory","change:deleted change:purged","handleDeletedHistory","sort","renderColumns","oldCurrentColumn","height","newCurrentColumn","_recalcFirstColumnHeight","includeDeleted","removeColumn","sortOrder","comparator","is","popover","create","current","each","createColumn","config","allow_user_dataset_purge","setUpColumnListeners","sortedFilteredColumns","filters","sortedColumns","filter","filtered","every","map","call","sorted","addColumn","newColumn","queueHdaFetch","widthToRemove","fadeOut","remove","checkColumnsInView","in-view","view:draggable:dragstart","_dropData","JSON","parse","dataTransfer","getData","currentColumnDropTargetOn","view:draggable:dragend","currentColumnDropTargetOff","droptarget:drop","toCopy","json","isCopyable","queue","forEach","content","start","fetch","columnMapLength","Object","keys","fxSpeed","mainTemplate","sortedAndFiltered","$middle","appendTo","delegateEvents","renderColumn","xhrData","ids","storage","dataset_details","renderItems","running","queueHdaFetchDetails","haveDetails","details","renderInfo","msg","click .done.btn","click .create-new.btn","click #include-deleted","click .order .set-order","click #toggle-deleted","click 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\ No newline at end of file
diff --git a/static/scripts/mvc/history/multi-panel.js b/static/scripts/mvc/history/multi-panel.js
index d09120cb6f5..0ef96a512c7 100644
--- a/static/scripts/mvc/history/multi-panel.js
+++ b/static/scripts/mvc/history/multi-panel.js
@@ -1,2 +1,2 @@
-define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/base-mvc","utils/ajax-queue","ui/mode-button","ui/search-input"],function(a,b,c,d){function e(a,b){function c(a){if(!a){if(!Galaxy.modal.$("#invalid-title").size()){var b=$("<p/>").attr("id","invalid-title").css({color:"red","margin-top":"8px"}).addClass("bg-danger").text(_l("Please enter a valid history title"));Galaxy.modal.$(".modal-body").append(b)}return!1}return a}function d(b){var c=$('<p><span class="fa fa-spinner fa-spin"></span> Copying history...</p>').css("margin-top","8px");Galaxy.modal.$(".modal-body").append(c),a.copy(!0,b).fail(function(){alert(_l("History could not be copied. Please contact a Galaxy administrator"))}).always(function(){Galaxy.modal.hide()})}function e(){var a=Galaxy.modal.$("#copy-modal-title").val();c(a)&&d(a)}if(b=b||{},!Galaxy||!Galaxy.modal)return a.copy();var f=a.get("name"),g="Copy of '"+f+"'";Galaxy.modal.show(_.extend({title:_l("Copying history")+' "'+f+'"',body:$(['<label for="copy-modal-title">',_l("Enter a title for the copied history"),":","</label><br />",'<input id="copy-modal-title" class="form-control" style="width: 100%" value="',g,'" />'].join("")),buttons:{Cancel:function(){Galaxy.modal.hide()},Copy:e}},b)),$("#copy-modal-title").focus().select(),$("#copy-modal-title").on("keydown",function(a){13===a.keyCode&&e()})}var f=Backbone.View.extend(c.LoggableMixin).extend({tagName:"div",className:"history-column flex-column flex-row-container",id:function(){return this.model?"history-column-"+this.model.get("id"):""},initialize:function(a){a=a||{},this.purgeAllowed=_.isUndefined(a.purgeAllowed)?!1:a.purgeAllowed,this.panel=a.panel||this.createPanel(a),this.setUpListeners()},createPanel:function(a){a=_.extend({model:this.model,purgeAllowed:this.purgeAllowed,dragItems:!0},a);var c=new b.HistoryPanelEdit(a);return c._renderEmptyMessage=this.__patch_renderEmptyMessage,c},__patch_renderEmptyMessage:function(a){var b=this,c=_.chain(this.model.get("state_ids")).values().flatten().value().length,d=b.$emptyMessage(a);return _.isEmpty(b.hdaViews)?c&&!this.model.contents.length?d.empty().append($('<span class="fa fa-spinner fa-spin"></span> <i>loading datasets...</i>')).show():b.searchFor?d.text(b.noneFoundMsg).show():d.text(b.emptyMsg).show():d.hide(),d},setUpListeners:function(){var a=this;this.once("rendered",function(){a.trigger("rendered:initial",a)}),this.setUpPanelListeners()},setUpPanelListeners:function(){var a=this;this.listenTo(this.panel,{rendered:function(){a.trigger("rendered",a)}},this)},inView:function(a,b){var c=this.$el.offset().left,d=c+this.$el.width();return a>d?!1:c>b?!1:!0},$panel:function(){return this.$(".history-panel")},render:function(a){a=void 0!==a?a:"fast";var b=this.model?this.model.toJSON():{};return this.$el.html(this.template(b)),this.renderPanel(a),this.setUpBehaviors(),this},setUpBehaviors:function(){},template:function(a){return a=_.extend(a||{},{isCurrentHistory:this.currentHistory}),$(['<div class="panel-controls clear flex-row">',this.controlsLeftTemplate({history:a,view:this}),this.controlsRightTemplate({history:a,view:this}),"</div>",'<div class="inner flex-row flex-column-container">','<div id="history-',a.id,'" class="history-column history-panel flex-column"></div>',"</div>"].join(""))},renderPanel:function(a){return a=void 0!==a?a:"fast",this.panel.setElement(this.$panel()).render(a),this.currentHistory&&this.panel.$list().before(this.panel._renderDropTargetHelp()),this},events:{"click .switch-to.btn":function(){this.model.setAsCurrent()},"click .delete-history":function(){var a=this;this.model._delete().fail(function(a,b,c){alert(_l("Could not delete the history")+":\n"+c)}).done(function(){a.render()})},"click .undelete-history":function(){var a=this;this.model.undelete().fail(function(a,b,c){alert(_l("Could not undelete the history")+":\n"+c)}).done(function(){a.render()})},"click .purge-history":function(){if(confirm(_l("This will permanently remove the data. Are you sure?"))){var a=this;this.model.purge().fail(function(a,b,c){alert(_l("Could not purge the history")+":\n"+c)}).done(function(){a.render()})}},"click .copy-history":"copy"},copy:function(){e(this.model)},controlsLeftTemplate:_.template(['<div class="pull-left">',"<% if( data.history.isCurrentHistory ){ %>",'<strong class="current-label">',_l("Current History"),"</strong>","<% } else { %>",'<button class="switch-to btn btn-default">',_l("Switch to"),"</button>","<% } %>","</div>"].join(""),{variable:"data"}),controlsRightTemplate:_.template(['<div class="pull-right">',"<% if( !data.history.purged ){ %>",'<div class="panel-menu btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu pull-right" role="menu">',"<% if( !data.history.deleted ){ %>",'<li><a href="javascript:void(0);" class="copy-history">',_l("Copy"),"</a></li>",'<li><a href="javascript:void(0);" class="delete-history">',_l("Delete"),"</a></li>","<% } else /* if is deleted */ { %>",'<li><a href="javascript:void(0);" class="undelete-history">',_l("Undelete"),"</a></li>","<% } %>","<% if( data.view.purgeAllowed ){ %>",'<li><a href="javascript:void(0);" class="purge-history">',_l("Purge"),"</a></li>","<% } %>","</ul>","</div>","<% } %>","</div>"].join(""),{variable:"data"}),toString:function(){return"HistoryPanelColumn("+(this.panel?this.panel:"")+")"}}),g=Backbone.View.extend(c.LoggableMixin).extend({className:"multi-panel-history",initialize:function(a){if(a=a||{},this.log(this+".init",a),this.$el.addClass(this.className),!a.currentHistoryId)throw new Error(this+" requires a currentHistoryId in the options");this.currentHistoryId=a.currentHistoryId,this.options={columnWidth:312,borderWidth:1,columnGap:8,headerHeight:29,footerHeight:0,controlsHeight:20},this.order=a.order||"update",this._initSortOrders(),this.hdaQueue=new d.NamedAjaxQueue([],!1),this.collection=null,this.setCollection(a.histories||[]),this.columnMap={},this.createColumns(a.columnOptions),this.setUpListeners()},_initSortOrders:function(){function a(a,b){return function(c,d,e){return c.id===e?-1:d.id===e?1:(c=a(c),d=a(d),b.asc?c===d?0:c>d?1:-1:c===d?0:c>d?-1:1)}}return this.sortOrders={update:{text:_l("most recent first"),fn:a(function(a){return new Date(a.get("update_time"))},{asc:!1})},name:{text:_l("name, a to z"),fn:a(function(a){return a.get("name")},{asc:!0})},"name-dsc":{text:_l("name, z to a"),fn:a(function(a){return a.get("name")},{asc:!1})},size:{text:_l("size, large to small"),fn:a(function(a){return a.get("size")},{asc:!1})},"size-dsc":{text:_l("size, small to large"),fn:a(function(a){return a.get("size")},{asc:!0})}},this.sortOrders},setUpListeners:function(){},setCollection:function(a){var b=this;return b.stopListening(b.collection),b.collection=a,b.sortCollection(b.order,{silent:!0}),b.setUpCollectionListeners(),b.trigger("new-collection",b),b},setUpCollectionListeners:function(){var a=this,b=a.collection;a.listenTo(b,{add:a.addAsCurrentColumn,"set-as-current":a.setCurrentHistory,"change:deleted change:purged":a.handleDeletedHistory,sort:function(){a.renderColumns(0)}})},setCurrentHistory:function(a){var b=this.columnMap[this.currentHistoryId];b&&(b.currentHistory=!1,b.$el.height("")),this.currentHistoryId=a.id;var c=this.columnMap[this.currentHistoryId];return c.currentHistory=!0,this.sortCollection(),multipanel._recalcFirstColumnHeight(),c},handleDeletedHistory:function(a){if(a.get("deleted")||a.get("purged")){this.log("handleDeletedHistory",this.collection.includeDeleted,a);var b=this;if(column=b.columnMap[a.id],!column)return;column.model.id===this.currentHistoryId||b.collection.includeDeleted||b.removeColumn(column)}},sortCollection:function(a,b){a=_.isUndefined(a)?this.order:a,a in this.sortOrders||(a="update"),this.order=a;var c=this.currentHistoryId,d=this.sortOrders[a];return this.collection.comparator=function(a,b){return d.fn(a,b,c)},this.$(".current-order").text(d.text),this.$(".more-options").is(":visible")&&this.$(".open-more-options.btn").popover("show"),this.collection.sort(b),this.collection},create:function(){return this.collection.create({current:!0})},createColumns:function(a){a=a||{};var b=this;this.columnMap={},b.collection.each(function(c){var d=b.createColumn(c,a);b.columnMap[c.id]=d})},createColumn:function(a,b){b=_.extend({},b,{model:a,purgeAllowed:Galaxy.config.allow_user_dataset_purge});var c=new f(b);return a.id===this.currentHistoryId&&(c.currentHistory=!0),this.setUpColumnListeners(c),c},sortedFilteredColumns:function(a){if(a=a||this.filters,!a||!a.length)return this.sortedColumns();var b=this;return b.sortedColumns().filter(function(b){var c=b.currentHistory||_.every(a.map(function(a){return a.call(b)}));return c})},sortedColumns:function(){var a=this,b=this.collection.map(function(b){return a.columnMap[b.id]});return b},addColumn:function(a,b){b=void 0!==b?b:!0;var c=this.createColumn(a);return this.columnMap[a.id]=c,b&&this.renderColumns(),c},addAsCurrentColumn:function(a){var b=this,c=this.addColumn(a,!1);return this.setCurrentHistory(a),c.once("rendered",function(){b.queueHdaFetch(c)}),c},removeColumn:function(a,b){if(b=void 0!==b?b:!0,this.log("removeColumn",a),a){var c=this,d=this.options.columnWidth+this.options.columnGap;a.$el.fadeOut("fast",function(){b&&($(this).remove(),c.$(".middle").width(c.$(".middle").width()-d),c.checkColumnsInView(),c._recalcFirstColumnHeight()),c.stopListening(a.panel),c.stopListening(a),delete c.columnMap[a.model.id],a.remove()})}},setUpColumnListeners:function(a){var b=this;b.listenTo(a,{"in-view":b.queueHdaFetch}),b.listenTo(a.panel,{"view:draggable:dragstart":function(a){b._dropData=JSON.parse(a.dataTransfer.getData("text")),b.currentColumnDropTargetOn()},"view:draggable:dragend":function(){b._dropData=null,b.currentColumnDropTargetOff()},"droptarget:drop":function(a,c,e){var f=b._dropData.filter(function(a){return e.model.contents.isCopyable(a)});b._dropData=null;var g=new d.NamedAjaxQueue;f.forEach(function(a){g.add({name:"copy-"+a.id,fn:function(){return e.model.contents.copy(a)}})}),g.start(),g.done(function(){e.model.fetch()})}})},columnMapLength:function(){return Object.keys(this.columnMap).length},render:function(a){a=void 0!==a?a:this.fxSpeed;var b=this;return b.log(b+".render"),b.$el.html(b.mainTemplate(b)),b.renderColumns(a),b.setUpBehaviors(),b.trigger("rendered",b),b},renderColumns:function(a){a=void 0!==a?a:this.fxSpeed;var b=this,c=b.sortedFilteredColumns();b.$(".middle").width(c.length*(this.options.columnWidth+this.options.columnGap)+this.options.columnGap+16);var d=b.$(".middle");return d.empty(),c.forEach(function(c){c.$el.appendTo(d),c.delegateEvents(),b.renderColumn(c,a)}),this.searchFor&&c.length<=1||(b.checkColumnsInView(),this._recalcFirstColumnHeight()),c},renderColumn:function(a,b){return b=void 0!==b?b:this.fxSpeed,a.render(b)},queueHdaFetch:function(a){if(0===a.model.contents.length&&!a.model.get("empty")){var b={},c=_.values(a.panel.storage.get("expandedIds")).join();c&&(b.dataset_details=c),this.hdaQueue.add({name:a.model.id,fn:function(){var c=a.model.contents.fetch({data:b,silent:!0});return c.done(function(){a.panel.renderItems()})}}),this.hdaQueue.running||this.hdaQueue.start()}},queueHdaFetchDetails:function(a){(0===a.model.contents.length&&!a.model.get("empty")||!a.model.contents.haveDetails())&&(this.hdaQueue.add({name:a.model.id,fn:function(){var b=a.model.contents.fetch({data:{details:"all"},silent:!0});return b.done(function(){a.panel.renderItems()})}}),this.hdaQueue.running||this.hdaQueue.start())},renderInfo:function(a){return this.$(".header .header-info").text(a)},events:{"click .done.btn":"close","click .create-new.btn":"create","click #include-deleted":"_clickToggleDeletedHistories","click .order .set-order":"_chooseOrder","click #toggle-deleted":"_clickToggleDeletedDatasets","click #toggle-hidden":"_clickToggleHiddenDatasets"},close:function(){var a="/";Galaxy&&Galaxy.options&&Galaxy.options.root?a=Galaxy.options.root:galaxy_config&&galaxy_config.root&&(a=galaxy_config.root),window.location=a},_clickToggleDeletedHistories:function(a){return this.toggleDeletedHistories($(a.currentTarget).is(":checked"))},toggleDeletedHistories:function(a){window.location=a?Galaxy.options.root+"history/view_multiple?include_deleted_histories=True":Galaxy.options.root+"history/view_multiple"},_clickToggleDeletedDatasets:function(a){return this.toggleDeletedDatasets($(a.currentTarget).is(":checked"))},toggleDeletedDatasets:function(a){a=void 0!==a?a:!1;var b=this;b.sortedFilteredColumns().forEach(function(b,c){_.delay(function(){b.panel.toggleShowDeleted(a,!1)},200*c)})},_clickToggleHiddenDatasets:function(a){return this.toggleHiddenDatasets($(a.currentTarget).is(":checked"))},toggleHiddenDatasets:function(a){a=void 0!==a?a:!1;var b=this;b.sortedFilteredColumns().forEach(function(b,c){_.delay(function(){b.panel.toggleShowHidden(a,!1)},200*c)})},_chooseOrder:function(a){var b=$(a.currentTarget).data("order");this.sortCollection(b)},setUpBehaviors:function(){var a=this;a._moreOptionsPopover(),a.$("#search-histories").searchInput({name:"search-histories",placeholder:_l("search histories"),onsearch:function(b){a.searchFor=b,a.filters=[function(){return this.model.matchesAll(a.searchFor)}],a.renderColumns(0)},onclear:function(){a.searchFor=null,a.filters=[],a.renderColumns(0)}}),a.$("#search-datasets").searchInput({name:"search-datasets",placeholder:_l("search all datasets"),onfirstsearch:function(b){a.hdaQueue.clear(),a.$("#search-datasets").searchInput("toggle-loading"),a.searchFor=b,a.sortedFilteredColumns().forEach(function(c){c.panel.searchItems(b),a.queueHdaFetchDetails(c)}),a.hdaQueue.progress(function(b){a.renderInfo([_l("searching"),b.curr+1,_l("of"),b.total].join(" "))}),a.hdaQueue.deferred.done(function(){a.renderInfo(""),a.$("#search-datasets").searchInput("toggle-loading")})},onsearch:function(b){a.searchFor=b,a.sortedFilteredColumns().forEach(function(a){a.panel.searchItems(b)})},onclear:function(){a.searchFor=null,a.sortedFilteredColumns().forEach(function(a){a.panel.clearSearch()})}}),$(window).resize(function(){a._recalcFirstColumnHeight()});var b=_.debounce(_.bind(this.checkColumnsInView,this),100);this.$(".middle").parent().scroll(b)},_moreOptionsPopover:function(){return this.$(".open-more-options.btn").popover({container:".header",placement:"bottom",html:!0,content:$(this.optionsPopoverTemplate(this))})},_recalcFirstColumnHeight:function(){var a=this.$(".history-column").first(),b=this.$(".middle").height(),c=a.find(".panel-controls").height();a.height(b).find(".inner").height(b-c)},_viewport:function(){var a=this.$(".middle").parent().offset().left;return{left:a,right:a+this.$(".middle").parent().width()}},columnsInView:function(){var a=this._viewport();return this.sortedFilteredColumns().filter(function(b){return b.currentHistory||b.inView(a.left,a.right)})},checkColumnsInView:function(){this.columnsInView().forEach(function(a){a.trigger("in-view",a)})},currentColumnDropTargetOn:function(){var a=this.columnMap[this.currentHistoryId];a&&(a.panel.dataDropped=function(){},a.panel.dropTargetOn())},currentColumnDropTargetOff:function(){var a=this.columnMap[this.currentHistoryId];a&&(a.panel.dataDropped=b.HistoryPanelEdit.prototype.dataDrop,a.panel.dropTarget=!1,a.panel.$(".history-drop-target").remove())},toString:function(){return"MultiPanelColumns("+(this.columns?this.columns.length:0)+")"},mainTemplate:_.template(['<div class="header flex-column-container">','<div class="control-column control-column-left flex-column">','<button class="done btn btn-default" tabindex="1">',_l("Done"),"</button>",'<div id="search-histories" class="search-control"></div>','<div id="search-datasets" class="search-control"></div>','<a class="open-more-options btn btn-default" tabindex="3">','<span class="fa fa-ellipsis-h"></span>',"</a>","</div>",'<div class="control-column control-column-center flex-column">','<div class="header-info">',"</div>","</div>",'<div class="control-column control-column-right flex-column">','<button class="create-new btn btn-default" tabindex="4">',_l("Create new"),"</button> ","</div>","</div>",'<div class="outer-middle flex-row flex-row-container">','<div class="middle flex-column-container flex-row"></div>',"</div>",'<div class="footer flex-column-container">',"</div>"].join(""),{variable:"view"}),optionsPopoverTemplate:_.template(['<div class="more-options">','<div class="order btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">',_l("Order histories by")+" ",'<span class="current-order"><%= view.sortOrders[ view.order ].text %></span> ','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">',"<% _.each( view.sortOrders, function( order, key ){ %>",'<li><a href="javascript:void(0);" class="set-order" data-order="<%= key %>">',"<%= order.text %>","</a></li>","<% }); %>","</ul>","</div>",'<div class="checkbox"><label><input id="include-deleted" type="checkbox"','<%= view.collection.includeDeleted? " checked" : "" %>>',_l("Include deleted histories"),"</label></div>","<hr />",'<div class="checkbox"><label><input id="toggle-deleted" type="checkbox">',_l("Include deleted datasets"),"</label></div>",'<div class="checkbox"><label><input id="toggle-hidden" type="checkbox">',_l("Include hidden datasets"),"</label></div>","</div>"].join(""),{variable:"view"})});return{MultiPanelColumns:g}});
+define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/base-mvc","utils/ajax-queue","ui/mode-button","ui/search-input"],function(a,b,c,d){function e(a,b){function c(a){if(!a){if(!Galaxy.modal.$("#invalid-title").size()){var b=$("<p/>").attr("id","invalid-title").css({color:"red","margin-top":"8px"}).addClass("bg-danger").text(_l("Please enter a valid history title"));Galaxy.modal.$(".modal-body").append(b)}return!1}return a}function d(b){var c=$('<p><span class="fa fa-spinner fa-spin"></span> Copying history...</p>').css("margin-top","8px");Galaxy.modal.$(".modal-body").append(c),a.copy(!0,b).fail(function(){alert(_l("History could not be copied. Please contact a Galaxy administrator"))}).always(function(){Galaxy.modal.hide()})}function e(){var a=Galaxy.modal.$("#copy-modal-title").val();c(a)&&d(a)}if(b=b||{},!Galaxy||!Galaxy.modal)return a.copy();var f=a.get("name"),g="Copy of '"+f+"'";Galaxy.modal.show(_.extend({title:_l("Copying history")+' "'+f+'"',body:$(['<label for="copy-modal-title">',_l("Enter a title for the copied history"),":","</label><br />",'<input id="copy-modal-title" class="form-control" style="width: 100%" value="',g,'" />'].join("")),buttons:{Cancel:function(){Galaxy.modal.hide()},Copy:e}},b)),$("#copy-modal-title").focus().select(),$("#copy-modal-title").on("keydown",function(a){13===a.keyCode&&e()})}var f=Backbone.View.extend(c.LoggableMixin).extend({tagName:"div",className:"history-column flex-column flex-row-container",id:function(){return this.model?"history-column-"+this.model.get("id"):""},initialize:function(a){a=a||{},this.purgeAllowed=_.isUndefined(a.purgeAllowed)?!1:a.purgeAllowed,this.panel=a.panel||this.createPanel(a),this.setUpListeners()},createPanel:function(a){a=_.extend({model:this.model,purgeAllowed:this.purgeAllowed,dragItems:!0},a);var c=new b.HistoryPanelEdit(a);return c._renderEmptyMessage=this.__patch_renderEmptyMessage,c},__patch_renderEmptyMessage:function(a){var b=this,c=_.chain(this.model.get("state_ids")).values().flatten().value().length,d=b.$emptyMessage(a);return _.isEmpty(b.hdaViews)?c&&!this.model.contents.length?d.empty().append($('<span class="fa fa-spinner fa-spin"></span> <i>loading datasets...</i>')).show():b.searchFor?d.text(b.noneFoundMsg).show():d.text(b.emptyMsg).show():d.hide(),d},setUpListeners:function(){var a=this;this.once("rendered",function(){a.trigger("rendered:initial",a)}),this.setUpPanelListeners()},setUpPanelListeners:function(){var a=this;this.listenTo(this.panel,{rendered:function(){a.trigger("rendered",a)}},this)},inView:function(a,b){var c=this.$el.offset().left,d=c+this.$el.width();return a>d?!1:c>b?!1:!0},$panel:function(){return this.$(".history-panel")},render:function(a){a=void 0!==a?a:"fast";var b=this.model?this.model.toJSON():{};return this.$el.html(this.template(b)),this.renderPanel(a),this.setUpBehaviors(),this},setUpBehaviors:function(){},template:function(a){return a=_.extend(a||{},{isCurrentHistory:this.currentHistory}),$(['<div class="panel-controls clear flex-row">',this.controlsLeftTemplate({history:a,view:this}),this.controlsRightTemplate({history:a,view:this}),"</div>",'<div class="inner flex-row flex-column-container">','<div id="history-',a.id,'" class="history-column history-panel flex-column"></div>',"</div>"].join(""))},renderPanel:function(a){return a=void 0!==a?a:"fast",this.panel.setElement(this.$panel()).render(a),this.currentHistory&&this.panel.$list().before(this.panel._renderDropTargetHelp()),this},events:{"click .switch-to.btn":function(){this.model.setAsCurrent()},"click .delete-history":function(){var a=this;this.model._delete().fail(function(a,b,c){alert(_l("Could not delete the history")+":\n"+c)}).done(function(){a.render()})},"click .undelete-history":function(){var a=this;this.model.undelete().fail(function(a,b,c){alert(_l("Could not undelete the history")+":\n"+c)}).done(function(){a.render()})},"click .purge-history":function(){if(confirm(_l("This will permanently remove the data. Are you sure?"))){var a=this;this.model.purge().fail(function(a,b,c){alert(_l("Could not purge the history")+":\n"+c)}).done(function(){a.render()})}},"click .copy-history":"copy"},copy:function(){e(this.model)},controlsLeftTemplate:_.template(['<div class="pull-left">',"<% if( data.history.isCurrentHistory ){ %>",'<strong class="current-label">',_l("Current History"),"</strong>","<% } else { %>",'<button class="switch-to btn btn-default">',_l("Switch to"),"</button>","<% } %>","</div>"].join(""),{variable:"data"}),controlsRightTemplate:_.template(['<div class="pull-right">',"<% if( !data.history.purged ){ %>",'<div class="panel-menu btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu pull-right" role="menu">',"<% if( !data.history.deleted ){ %>",'<li><a href="javascript:void(0);" class="copy-history">',_l("Copy"),"</a></li>",'<li><a href="javascript:void(0);" class="delete-history">',_l("Delete"),"</a></li>","<% } else /* if is deleted */ { %>",'<li><a href="javascript:void(0);" class="undelete-history">',_l("Undelete"),"</a></li>","<% } %>","<% if( data.view.purgeAllowed ){ %>",'<li><a href="javascript:void(0);" class="purge-history">',_l("Purge"),"</a></li>","<% } %>","</ul>","</div>","<% } %>","</div>"].join(""),{variable:"data"}),toString:function(){return"HistoryPanelColumn("+(this.panel?this.panel:"")+")"}}),g=Backbone.View.extend(c.LoggableMixin).extend({className:"multi-panel-history",initialize:function(a){if(a=a||{},this.log(this+".init",a),this.$el.addClass(this.className),!a.currentHistoryId)throw new Error(this+" requires a currentHistoryId in the options");this.currentHistoryId=a.currentHistoryId,this.options={columnWidth:312,borderWidth:1,columnGap:8,headerHeight:29,footerHeight:0,controlsHeight:20},this.order=a.order||"update",this._initSortOrders(),this.hdaQueue=new d.NamedAjaxQueue([],!1),this.collection=null,this.setCollection(a.histories||[]),this.columnMap={},this.createColumns(a.columnOptions),this.setUpListeners()},_initSortOrders:function(){function a(a,b){return function(c,d,e){return c.id===e?-1:d.id===e?1:(c=a(c),d=a(d),b.asc?c===d?0:c>d?1:-1:c===d?0:c>d?-1:1)}}return this.sortOrders={update:{text:_l("most recent first"),fn:a(function(a){return new Date(a.get("update_time"))},{asc:!1})},name:{text:_l("name, a to z"),fn:a(function(a){return a.get("name")},{asc:!0})},"name-dsc":{text:_l("name, z to a"),fn:a(function(a){return a.get("name")},{asc:!1})},size:{text:_l("size, large to small"),fn:a(function(a){return a.get("size")},{asc:!1})},"size-dsc":{text:_l("size, small to large"),fn:a(function(a){return a.get("size")},{asc:!0})}},this.sortOrders},setUpListeners:function(){},setCollection:function(a){var b=this;return b.stopListening(b.collection),b.collection=a,b.sortCollection(b.order,{silent:!0}),b.setUpCollectionListeners(),b.trigger("new-collection",b),b},setUpCollectionListeners:function(){var a=this,b=a.collection;a.listenTo(b,{add:a.addAsCurrentColumn,"set-as-current":a.setCurrentHistory,"change:deleted change:purged":a.handleDeletedHistory,sort:function(){a.renderColumns(0)}})},setCurrentHistory:function(a){var b=this.columnMap[this.currentHistoryId];b&&(b.currentHistory=!1,b.$el.height("")),this.currentHistoryId=a.id;var c=this.columnMap[this.currentHistoryId];return c.currentHistory=!0,this.sortCollection(),multipanel._recalcFirstColumnHeight(),c},handleDeletedHistory:function(a){if(a.get("deleted")||a.get("purged")){this.log("handleDeletedHistory",this.collection.includeDeleted,a);var b=this;if(column=b.columnMap[a.id],!column)return;column.model.id===this.currentHistoryId||b.collection.includeDeleted||b.removeColumn(column)}},sortCollection:function(a,b){a=_.isUndefined(a)?this.order:a,a in this.sortOrders||(a="update"),this.order=a;var c=this.currentHistoryId,d=this.sortOrders[a];return this.collection.comparator=function(a,b){return d.fn(a,b,c)},this.$(".current-order").text(d.text),this.$(".more-options").is(":visible")&&this.$(".open-more-options.btn").popover("show"),this.collection.sort(b),this.collection},create:function(){return this.collection.create({current:!0})},createColumns:function(a){a=a||{};var b=this;this.columnMap={},b.collection.each(function(c){var d=b.createColumn(c,a);b.columnMap[c.id]=d})},createColumn:function(a,b){b=_.extend({},b,{model:a,purgeAllowed:Galaxy.config.allow_user_dataset_purge});var c=new f(b);return a.id===this.currentHistoryId&&(c.currentHistory=!0),this.setUpColumnListeners(c),c},sortedFilteredColumns:function(a){if(a=a||this.filters,!a||!a.length)return this.sortedColumns();var b=this;return b.sortedColumns().filter(function(b){var c=b.currentHistory||_.every(a.map(function(a){return a.call(b)}));return c})},sortedColumns:function(){var a=this,b=this.collection.map(function(b){return a.columnMap[b.id]});return b},addColumn:function(a,b){b=void 0!==b?b:!0;var c=this.createColumn(a);return this.columnMap[a.id]=c,b&&this.renderColumns(),c},addAsCurrentColumn:function(a){var b=this,c=this.addColumn(a,!1);return this.setCurrentHistory(a),c.once("rendered",function(){b.queueHdaFetch(c)}),c},removeColumn:function(a,b){if(b=void 0!==b?b:!0,this.log("removeColumn",a),a){var c=this,d=this.options.columnWidth+this.options.columnGap;a.$el.fadeOut("fast",function(){b&&($(this).remove(),c.$(".middle").width(c.$(".middle").width()-d),c.checkColumnsInView(),c._recalcFirstColumnHeight()),c.stopListening(a.panel),c.stopListening(a),delete c.columnMap[a.model.id],a.remove()})}},setUpColumnListeners:function(a){var b=this;b.listenTo(a,{"in-view":b.queueHdaFetch}),b.listenTo(a.panel,{"view:draggable:dragstart":function(a){b._dropData=JSON.parse(a.dataTransfer.getData("text")),b.currentColumnDropTargetOn()},"view:draggable:dragend":function(){b._dropData=null,b.currentColumnDropTargetOff()},"droptarget:drop":function(a,c,e){var f=b._dropData.filter(function(a){return e.model.contents.isCopyable(a)});b._dropData=null;var g=new d.NamedAjaxQueue;f.forEach(function(a){g.add({name:"copy-"+a.id,fn:function(){return e.model.contents.copy(a)}})}),g.start(),g.done(function(){e.model.fetch()})}})},columnMapLength:function(){return Object.keys(this.columnMap).length},render:function(a){a=void 0!==a?a:this.fxSpeed;var b=this;return b.log(b+".render"),b.$el.html(b.mainTemplate(b)),b.renderColumns(a),b.setUpBehaviors(),b.trigger("rendered",b),b},renderColumns:function(a){a=void 0!==a?a:this.fxSpeed;var b=this,c=b.sortedFilteredColumns();b.$(".middle").width(c.length*(this.options.columnWidth+this.options.columnGap)+this.options.columnGap+16);var d=b.$(".middle");return d.empty(),c.forEach(function(c){c.$el.appendTo(d),c.delegateEvents(),b.renderColumn(c,a)}),this.searchFor&&c.length<=1||(b.checkColumnsInView(),this._recalcFirstColumnHeight()),c},renderColumn:function(a,b){return b=void 0!==b?b:this.fxSpeed,a.render(b)},queueHdaFetch:function(a){if(0===a.model.contents.length&&!a.model.get("empty")){var b={},c=_.values(a.panel.storage.get("expandedIds")).join();c&&(b.dataset_details=c),this.hdaQueue.add({name:a.model.id,fn:function(){var c=a.model.contents.fetch({data:b,silent:!0});return c.done(function(){a.panel.renderItems()})}}),this.hdaQueue.running||this.hdaQueue.start()}},queueHdaFetchDetails:function(a){(0===a.model.contents.length&&!a.model.get("empty")||!a.model.contents.haveDetails())&&(this.hdaQueue.add({name:a.model.id,fn:function(){var b=a.model.contents.fetch({data:{details:"all"},silent:!0});return b.done(function(){a.panel.renderItems()})}}),this.hdaQueue.running||this.hdaQueue.start())},renderInfo:function(a){return this.$(".header .header-info").text(a)},events:{"click .done.btn":"close","click .create-new.btn":"create","click #include-deleted":"_clickToggleDeletedHistories","click .order .set-order":"_chooseOrder","click #toggle-deleted":"_clickToggleDeletedDatasets","click #toggle-hidden":"_clickToggleHiddenDatasets"},close:function(){var a="/";Galaxy&&Galaxy.options&&Galaxy.options.root?a=Galaxy.options.root:galaxy_config&&galaxy_config.root&&(a=galaxy_config.root),window.location=a},_clickToggleDeletedHistories:function(a){return this.toggleDeletedHistories($(a.currentTarget).is(":checked"))},toggleDeletedHistories:function(a){window.location=a?Galaxy.options.root+"history/view_multiple?include_deleted_histories=True":Galaxy.options.root+"history/view_multiple"},_clickToggleDeletedDatasets:function(a){return this.toggleDeletedDatasets($(a.currentTarget).is(":checked"))},toggleDeletedDatasets:function(a){a=void 0!==a?a:!1;var b=this;b.sortedFilteredColumns().forEach(function(b,c){_.delay(function(){b.panel.toggleShowDeleted(a,!1)},200*c)})},_clickToggleHiddenDatasets:function(a){return this.toggleHiddenDatasets($(a.currentTarget).is(":checked"))},toggleHiddenDatasets:function(a){a=void 0!==a?a:!1;var b=this;b.sortedFilteredColumns().forEach(function(b,c){_.delay(function(){b.panel.toggleShowHidden(a,!1)},200*c)})},_chooseOrder:function(a){var b=$(a.currentTarget).data("order");this.sortCollection(b)},setUpBehaviors:function(){var a=this;a._moreOptionsPopover(),a.$("#search-histories").searchInput({name:"search-histories",placeholder:_l("search histories"),onsearch:function(b){a.searchFor=b,a.filters=[function(){return this.model.matchesAll(a.searchFor)}],a.renderColumns(0)},onclear:function(){a.searchFor=null,a.filters=[],a.renderColumns(0)}}),a.$("#search-datasets").searchInput({name:"search-datasets",placeholder:_l("search all datasets"),onfirstsearch:function(b){a.hdaQueue.clear(),a.$("#search-datasets").searchInput("toggle-loading"),a.searchFor=b,a.sortedFilteredColumns().forEach(function(c){c.panel.searchItems(b),a.queueHdaFetchDetails(c)}),a.hdaQueue.progress(function(b){a.renderInfo([_l("searching"),b.curr+1,_l("of"),b.total].join(" "))}),a.hdaQueue.deferred.done(function(){a.renderInfo(""),a.$("#search-datasets").searchInput("toggle-loading")})},onsearch:function(b){a.searchFor=b,a.sortedFilteredColumns().forEach(function(a){a.panel.searchItems(b)})},onclear:function(){a.searchFor=null,a.sortedFilteredColumns().forEach(function(a){a.panel.clearSearch()})}}),$(window).resize(function(){a._recalcFirstColumnHeight()});var b=_.debounce(function(){a.checkColumnsInView()},100);this.$(".middle").parent().scroll(b)},_moreOptionsPopover:function(){return this.$(".open-more-options.btn").popover({container:".header",placement:"bottom",html:!0,content:$(this.optionsPopoverTemplate(this))})},_recalcFirstColumnHeight:function(){var a=this.$(".history-column").first(),b=this.$(".middle").height(),c=a.find(".panel-controls").height();a.height(b).find(".inner").height(b-c)},_viewport:function(){var a=this.$(".middle").parent().offset().left;return{left:a,right:a+this.$(".middle").parent().width()}},columnsInView:function(){var a=this._viewport();return this.sortedFilteredColumns().filter(function(b){return b.currentHistory||b.inView(a.left,a.right)})},checkColumnsInView:function(){this.columnsInView().forEach(function(a){a.trigger("in-view",a)})},currentColumnDropTargetOn:function(){var a=this.columnMap[this.currentHistoryId];a&&(a.panel.dataDropped=function(){},a.panel.dropTargetOn())},currentColumnDropTargetOff:function(){var a=this.columnMap[this.currentHistoryId];a&&(a.panel.dataDropped=b.HistoryPanelEdit.prototype.dataDrop,a.panel.dropTarget=!1,a.panel.$(".history-drop-target").remove())},toString:function(){return"MultiPanelColumns("+(this.columns?this.columns.length:0)+")"},mainTemplate:_.template(['<div class="header flex-column-container">','<div class="control-column control-column-left flex-column">','<button class="done btn btn-default" tabindex="1">',_l("Done"),"</button>",'<div id="search-histories" class="search-control"></div>','<div id="search-datasets" class="search-control"></div>','<a class="open-more-options btn btn-default" tabindex="3">','<span class="fa fa-ellipsis-h"></span>',"</a>","</div>",'<div class="control-column control-column-center flex-column">','<div class="header-info">',"</div>","</div>",'<div class="control-column control-column-right flex-column">','<button class="create-new btn btn-default" tabindex="4">',_l("Create new"),"</button> ","</div>","</div>",'<div class="outer-middle flex-row flex-row-container">','<div class="middle flex-column-container flex-row"></div>',"</div>",'<div class="footer flex-column-container">',"</div>"].join(""),{variable:"view"}),optionsPopoverTemplate:_.template(['<div class="more-options">','<div class="order btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">',_l("Order histories by")+" ",'<span class="current-order"><%= view.sortOrders[ view.order ].text %></span> ','<span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">',"<% _.each( view.sortOrders, function( order, key ){ %>",'<li><a href="javascript:void(0);" class="set-order" data-order="<%= key %>">',"<%= order.text %>","</a></li>","<% }); %>","</ul>","</div>",'<div class="checkbox"><label><input id="include-deleted" type="checkbox"','<%= view.collection.includeDeleted? " checked" : "" %>>',_l("Include deleted histories"),"</label></div>","<hr />",'<div class="checkbox"><label><input id="toggle-deleted" type="checkbox">',_l("Include deleted datasets"),"</label></div>",'<div class="checkbox"><label><input id="toggle-hidden" type="checkbox">',_l("Include hidden datasets"),"</label></div>","</div>"].join(""),{variable:"view"})});return{MultiPanelColumns:g}});
 //# sourceMappingURL=../../../maps/mvc/history/multi-panel.js.map
\ No newline at end of file

From 4f78a9aee36b4a3fdbf82a358d5e3679c3a9c062 Mon Sep 17 00:00:00 2001
From: Carl Eberhard <carlfeberhard@gmail.com>
Date: Thu, 9 Apr 2015 12:34:07 -0400
Subject: [PATCH 73/88] Managers: more travis fixes: missing/misnamed variables

---
 lib/galaxy/managers/containers.py | 26 +++++++++++++-------------
 lib/galaxy/managers/hdas.py       |  2 +-
 lib/galaxy/managers/histories.py  | 11 ++++++-----
 lib/galaxy/managers/sharable.py   |  2 +-
 4 files changed, 21 insertions(+), 20 deletions(-)

diff --git a/lib/galaxy/managers/containers.py b/lib/galaxy/managers/containers.py
index 4593e9f8272..4eae8fe68fd 100644
--- a/lib/galaxy/managers/containers.py
+++ b/lib/galaxy/managers/containers.py
@@ -48,20 +48,20 @@ class ContainerManagerMixin( object ):
         iters.append( self.subcontainers( container ) )
         return galaxy.util.merge_sorted_iterables( self.order_contents_on, *iters )
 
-    def contained( self, container ):
+    def contained( self, container, **kwargs ):
         """
         Returns non-container objects.
         """
-        return self._filter_contents( container, self.contained_class, **kwds )
+        return self._filter_contents( container, self.contained_class, **kwargs )
 
-    def subcontainers( self, container ):
+    def subcontainers( self, container, **kwargs ):
         """
         Returns only the containers within this one.
         """
-        return self._filter_contents( container, self.subcontainer_class, **kwds )
+        return self._filter_contents( container, self.subcontainer_class, **kwargs )
 
     # ---- private
-    def _filter_contents( self, container, content_class, **kwds ):
+    def _filter_contents( self, container, content_class, **kwargs ):
         # TODO: use list (or by_history etc.)
         container_filter = self._filter_to_contained( container, content_class )
         query = self.session().query( content_class ).filter( container_filter )
@@ -70,7 +70,7 @@ class ContainerManagerMixin( object ):
     def _filter_to_contained( self, container, content_class ):
         raise galaxy.exceptions.NotImplemented( 'Abstract class' )
 
-    def _content_manager( self, content_class ):
+    def _content_manager( self, content ):
         raise galaxy.exceptions.NotImplemented( 'Abstract class' )
 
 
@@ -84,12 +84,12 @@ class HistoryAsContainerManagerMixin( ContainerManagerMixin ):
         return content_class.history == container
 
     def _content_manager( self, content ):
-        # type snifffing is inevitable
+        # type sniffing is inevitable
         if   isinstance( content, model.HistoryDatasetAssociation ):
             return self.hda_manager
         elif isinstance( content, model.HistoryDatasetCollectionAssociation ):
             return self.hdca_manager
-        raise TypeError( 'Unknown contents class: ' + str( content_class ) )
+        raise TypeError( 'Unknown contents class: ' + str( content ) )
 
 
 class LibraryFolderAsContainerManagerMixin( ContainerManagerMixin ):
@@ -102,9 +102,9 @@ class LibraryFolderAsContainerManagerMixin( ContainerManagerMixin ):
     order_contents_on = operator.attrgetter( 'create_time' )
 
     def _filter_to_contained( self, container, content_class ):
-        if content_class == subcontainer_class:
-            return subcontainer_class.parent == container
-        return contained_class.folder == container
+        if content_class == self.subcontainer_class:
+            return self.subcontainer_class.parent == container
+        return self.contained_class.folder == container
 
     def _content_manager( self, content ):
         # type snifffing is inevitable
@@ -112,7 +112,7 @@ class LibraryFolderAsContainerManagerMixin( ContainerManagerMixin ):
             return self.lda_manager
         elif isinstance( content, model.LibraryFolder ):
             return self.folder_manager
-        raise TypeError( 'Unknown contents class: ' + str( content_class ) )
+        raise TypeError( 'Unknown contents class: ' + str( content ) )
 
 
 class DatasetCollectionAsContainerManagerMixin( ContainerManagerMixin ):
@@ -131,7 +131,7 @@ class DatasetCollectionAsContainerManagerMixin( ContainerManagerMixin ):
             return self.collection_manager
         elif isinstance( content, model.DatasetCollection ):
             return self.collection_manager
-        raise TypeError( 'Unknown contents class: ' + str( content_class ) )
+        raise TypeError( 'Unknown contents class: ' + str( content ) )
 
 
 # ====
diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py
index 71e3f2eb532..65a6665fdc1 100644
--- a/lib/galaxy/managers/hdas.py
+++ b/lib/galaxy/managers/hdas.py
@@ -220,7 +220,7 @@ class HDAManager( datasets.DatasetAssociationManager,
             return truncated, hda_data
 
         truncated = preview and os.stat( hda.file_name ).st_size > MAX_PEEK_SIZE
-        hda_data = open( hda.file_name ).read( max_peek_size )
+        hda_data = open( hda.file_name ).read( MAX_PEEK_SIZE )
         return truncated, hda_data
 
 
diff --git a/lib/galaxy/managers/histories.py b/lib/galaxy/managers/histories.py
index d365911a38e..b167e07a0e6 100644
--- a/lib/galaxy/managers/histories.py
+++ b/lib/galaxy/managers/histories.py
@@ -140,15 +140,16 @@ class HistoryManager( sharable.SharableModelManager, deletable.PurgableManagerMi
                 elif isinstance( content, model.HistoryDatasetCollectionAssociation ):
                     try:
                         service = self.app.dataset_collections_service
-                        dataset_collection_instance = service.get_dataset_collection_instance(
+                        collection = service.get_dataset_collection_instance(
                             trans=trans,
                             instance_type='history',
                             id=self.app.security.encode_id( content.id ),
                         )
-                        contents_dict = dictify_dataset_collection_instance( dataset_collection_instance,
-                                                                             security=self.app.security,
-                                                                             parent=dataset_collection_instance.history,
-                                                                             view="element" )
+                        serializer = collections_util.dictify_dataset_collection_instance
+                        contents_dict = serializer( collection,
+                                                    security=self.app.security,
+                                                    parent=collection.history,
+                                                    view="element" )
                     except Exception, exc:
                         log.exception( "Error in history API at listing dataset collection: %s", exc )
                         # TODO: return some dict with the error
diff --git a/lib/galaxy/managers/sharable.py b/lib/galaxy/managers/sharable.py
index 791e460e403..8ecb4944c70 100644
--- a/lib/galaxy/managers/sharable.py
+++ b/lib/galaxy/managers/sharable.py
@@ -126,7 +126,7 @@ class SharableModelManager( base.ModelManager, secured.OwnableManagerMixin, secu
        """
        Return a list of all published items.
        """
-       query = self._query_published( user, **kwargs )
+       query = self._query_published( **kwargs )
        return self.list( query=query, **kwargs )
 
     # .... user sharing

From 237c857f8dcd1caf92e20c75b046e19f10810748 Mon Sep 17 00:00:00 2001
From: Carl Eberhard <carlfeberhard@gmail.com>
Date: Thu, 9 Apr 2015 15:03:31 -0400
Subject: [PATCH 74/88] UI, Histories: respect subtitle dataset hiding switch
 and prevent bad autohiding of newly added datasets.

---
 client/galaxy/scripts/mvc/history/history-panel-edit.js | 2 +-
 static/maps/mvc/history/history-panel-edit.js.map       | 2 +-
 static/scripts/mvc/history/history-panel-edit.js        | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/client/galaxy/scripts/mvc/history/history-panel-edit.js b/client/galaxy/scripts/mvc/history/history-panel-edit.js
index ae1de05ef56..7f68f324287 100644
--- a/client/galaxy/scripts/mvc/history/history-panel-edit.js
+++ b/client/galaxy/scripts/mvc/history/history-panel-edit.js
@@ -360,7 +360,7 @@ var HistoryPanelEdit = _super.extend(
      *  @param {Model} the item model to check
      */
     _handleHdaVisibleChange : function( itemModel ){
-        if( itemModel.hidden() && !this.storage.showHidden ){
+        if( itemModel.hidden() && !this.showHidden ){
             this.removeItemView( itemModel );
         }
         this._renderCounts();
diff --git a/static/maps/mvc/history/history-panel-edit.js.map b/static/maps/mvc/history/history-panel-edit.js.map
index dc92a2a1a8b..4f27cc377ab 100644
--- a/static/maps/mvc/history/history-panel-edit.js.map
+++ b/static/maps/mvc/history/history-panel-edit.js.map
@@ -1 +1 @@
-{"version":3,"file":"history-panel-edit.js","sources":["../../../src/mvc/history/history-panel-edit.js"],"names":["define","HPANEL","HISTORY_CONTENTS","STATES","HDA_MODEL","HDA_LI_EDIT","HDCA_LI_EDIT","TAGS","ANNOTATIONS","LIST_COLLECTION_CREATOR","PAIR_COLLECTION_CREATOR","LIST_OF_PAIRS_COLLECTION_CREATOR","faIconButton","PopupMenu","_l","_super","HistoryPanel","HistoryPanelEdit","extend","HDAViewClass","HDAListItemEdit","HDCAViewClass","HDCAListItemEdit","initialize","attributes","prototype","call","this","tagsEditor","annotationEditor","purgeAllowed","annotationEditorShown","tagsEditorShown","_setUpListeners","panel","on","ev","data","dataDropped","dropTargetOff","_renderCounts","_setUpCollectionListeners","collection","_handleHdaDeletionChange","_handleHdaVisibleChange","model","fetch","_setUpModelListeners","updateHistoryDiskSize","_buildNewRender","$newRender","Galaxy","currUser","id","get","_renderTags","_renderAnnotation","renderItems","$whereTo","views","toggleLink","_class","text","join","$el","deleted","where","hidden","visible","msgs","length","push","showDeleted","showHidden","find","html","$where","TagsEditor","el","onshowFirstTime","render","onshow","toggleHDATagEditors","fxSpeed","onhide","$activator","title","classes","faIcon","appendTo","AnnotationEditor","toggleHDAAnnotationEditors","_setUpBehaviors","isAnonymous","nameSelector","attr","tooltip","placement","make_text_editable","on_finish","newName","previousName","save","name","fail","previous","multiselectActions","actions","func","action","HistoryDatasetAssociation","hide","getSelectedModels","ajaxQueue","unhide","undelete","confirm","purge","concat","_collectionActions","createListHDCA","done","refresh","createPairHDCA","createListOfPairsCollection","_attachItems","$list","append","reverse","map","view","_attachView","unshift","prepend","trigger","slideDown","_getItemViewOptions","options","_","itemModel","removeItemView","storage","args","Array","slice","arguments","each","toggle","apply","events","clone","click .show-selectors-btn","click .toggle-deleted-link","toggleShowDeleted","click 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diff --git a/static/scripts/mvc/history/history-panel-edit.js b/static/scripts/mvc/history/history-panel-edit.js
index c7149d46e26..1d10888a343 100644
--- a/static/scripts/mvc/history/history-panel-edit.js
+++ b/static/scripts/mvc/history/history-panel-edit.js
@@ -1,2 +1,2 @@
-define(["mvc/history/history-panel","mvc/history/history-contents","mvc/dataset/states","mvc/history/hda-model","mvc/history/hda-li-edit","mvc/history/hdca-li-edit","mvc/tags","mvc/annotations","mvc/collection/list-collection-creator","mvc/collection/pair-collection-creator","mvc/collection/list-of-pairs-collection-creator","ui/fa-icon-button","mvc/ui/popup-menu","utils/localization"],function(a,b,c,d,e,f,g,h,i,j,k,l,m,n){var o=a.HistoryPanel,p=o.extend({HDAViewClass:e.HDAListItemEdit,HDCAViewClass:f.HDCAListItemEdit,initialize:function(a){a=a||{},o.prototype.initialize.call(this,a),this.tagsEditor=null,this.annotationEditor=null,this.purgeAllowed=a.purgeAllowed||!1,this.annotationEditorShown=a.annotationEditorShown||!1,this.tagsEditorShown=a.tagsEditorShown||!1},_setUpListeners:function(){var a=this;o.prototype._setUpListeners.call(a),a.on("drop",function(b,c){a.dataDropped(c),a.dropTargetOff()}),a.on("view:attached view:removed",function(){a._renderCounts()},a)},_setUpCollectionListeners:function(){return o.prototype._setUpCollectionListeners.call(this),this.collection.on("change:deleted",this._handleHdaDeletionChange,this),this.collection.on("change:visible",this._handleHdaVisibleChange,this),this.collection.on("change:purged",function(){this.model.fetch()},this),this},_setUpModelListeners:function(){return o.prototype._setUpModelListeners.call(this),this.model.on("change:nice_size",this.updateHistoryDiskSize,this),this},_buildNewRender:function(){var a=o.prototype._buildNewRender.call(this);return this.model?(Galaxy&&Galaxy.currUser&&Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")&&(this._renderTags(a),this._renderAnnotation(a)),a):a},renderItems:function(a){var b=o.prototype.renderItems.call(this,a);return this._renderCounts(a),b},_renderCounts:function(a){function b(a,b){return['<a class="',a,'" href="javascript:void(0);">',b,"</a>"].join("")}a=a||this.$el;var c=this.collection.where({deleted:!0}),d=this.collection.where({visible:!1}),e=[];return this.views.length&&e.push([this.views.length,n("shown")].join(" ")),c.length&&e.push(this.showDeleted?b("toggle-deleted-link",n("hide deleted")):[c.length,b("toggle-deleted-link",n("deleted"))].join(" ")),d.length&&e.push(this.showHidden?b("toggle-hidden-link",n("hide hidden")):[d.length,b("toggle-hidden-link",n("hidden"))].join(" ")),a.find("> .controls .subtitle").html(e.join(", "))},_renderTags:function(a){var b=this;this.tagsEditor=new g.TagsEditor({model:this.model,el:a.find(".controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){b.toggleHDATagEditors(!0,b.fxSpeed)},onhide:function(){b.toggleHDATagEditors(!1,b.fxSpeed)},$activator:l({title:n("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(a.find(".controls .actions"))})},_renderAnnotation:function(a){var b=this;this.annotationEditor=new h.AnnotationEditor({model:this.model,el:a.find(".controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){b.toggleHDAAnnotationEditors(!0,b.fxSpeed)},onhide:function(){b.toggleHDAAnnotationEditors(!1,b.fxSpeed)},$activator:l({title:n("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(a.find(".controls .actions"))})},_setUpBehaviors:function(a){if(a=a||this.$el,o.prototype._setUpBehaviors.call(this,a),this.model&&Galaxy.currUser&&!Galaxy.currUser.isAnonymous()&&Galaxy.currUser.id===this.model.get("user_id")){var b=this,c="> .controls .name";a.find(c).attr("title",n("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(a){var d=b.model.get("name");a&&a!==d?(b.$el.find(c).text(a),b.model.save({name:a}).fail(function(){b.$el.find(c).text(b.model.previous("name"))})):b.$el.find(c).text(d)}})}},multiselectActions:function(){var a=this,b=[{html:n("Hide datasets"),func:function(){var b=d.HistoryDatasetAssociation.prototype.hide;a.getSelectedModels().ajaxQueue(b)}},{html:n("Unhide datasets"),func:function(){var b=d.HistoryDatasetAssociation.prototype.unhide;a.getSelectedModels().ajaxQueue(b)}},{html:n("Delete datasets"),func:function(){var b=d.HistoryDatasetAssociation.prototype.delete;a.getSelectedModels().ajaxQueue(b)}},{html:n("Undelete datasets"),func:function(){var b=d.HistoryDatasetAssociation.prototype.undelete;a.getSelectedModels().ajaxQueue(b)}}];return a.purgeAllowed&&b.push({html:n("Permanently delete datasets"),func:function(){if(confirm(n("This will permanently remove the data in your datasets. Are you sure?"))){var b=d.HistoryDatasetAssociation.prototype.purge;a.getSelectedModels().ajaxQueue(b)}}}),b=b.concat(a._collectionActions())},_collectionActions:function(){var a=this;return[{html:n("Build Dataset List"),func:function(){i.createListHDCA(a.getSelectedModels()).done(function(){a.model.refresh()})}},{html:n("Build Dataset Pair"),func:function(){j.createPairHDCA(a.getSelectedModels()).done(function(){a.model.refresh()})}},{html:n("Build List of Dataset Pairs"),func:function(){k.createListOfPairsCollection(a.getSelectedModels()).done(function(){a.model.refresh()})}}]},_attachItems:function(a){return this.$list(a).append(this.views.reverse().map(function(a){return a.$el})),this},_attachView:function(a){var b=this;b.views.unshift(a),b.$list().prepend(a.render(0).$el.hide()),b.trigger("view:attached",a),a.$el.slideDown(b.fxSpeed,function(){b.trigger("view:attached:rendered")})},_getItemViewOptions:function(a){var b=o.prototype._getItemViewOptions.call(this,a);return _.extend(b,{purgeAllowed:this.purgeAllowed,tagsEditorShown:this.tagsEditor&&!this.tagsEditor.hidden,annotationEditorShown:this.annotationEditor&&!this.annotationEditor.hidden}),b},_handleHdaDeletionChange:function(a){a.get("deleted")&&!this.showDeleted&&this.removeItemView(a),this._renderCounts()},_handleHdaVisibleChange:function(a){a.hidden()&&!this.storage.showHidden&&this.removeItemView(a),this._renderCounts()},toggleHDATagEditors:function(){var a=Array.prototype.slice.call(arguments,1);_.each(this.views,function(b){b.tagsEditor&&b.tagsEditor.toggle.apply(b.tagsEditor,a)})},toggleHDAAnnotationEditors:function(){var a=Array.prototype.slice.call(arguments,1);_.each(this.views,function(b){b.annotationEditor&&b.annotationEditor.toggle.apply(b.annotationEditor,a)})},events:_.extend(_.clone(o.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click .toggle-deleted-link":function(){this.toggleShowDeleted()},"click .toggle-hidden-link":function(){this.toggleShowHidden()}}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},dropTargetOn:function(){if(this.dropTarget)return this;this.dropTarget=!0;var a={dragenter:_.bind(this.dragenter,this),dragover:_.bind(this.dragover,this),dragleave:_.bind(this.dragleave,this),drop:_.bind(this.drop,this)},b=this._renderDropTarget();this.$list().before([this._renderDropTargetHelp(),b]);for(var c in a)a.hasOwnProperty(c)&&b.on(c,a[c]);return this},_renderDropTarget:function(){return this.$(".history-drop-target").remove(),$("<div/>").addClass("history-drop-target").css({height:"64px",margin:"0px 10px 10px 10px",border:"1px dashed black","border-radius":"3px"})},_renderDropTargetHelp:function(){return this.$(".history-drop-target-help").remove(),$("<div/>").addClass("history-drop-target-help").css({margin:"10px 10px 4px 10px",color:"grey","font-size":"80%","font-style":"italic"}).text(n("Drag datasets here to copy them to the current history"))},dropTargetOff:function(){if(!this.dropTarget)return this;this.dropTarget=!1;var a=this.$(".history-drop-target").get(0);for(var b in this._dropHandlers)this._dropHandlers.hasOwnProperty(b)&&(console.debug(b,this._dropHandlers[b]),a.off(b,this._dropHandlers[b]));return this.$(".history-drop-target").remove(),this.$(".history-drop-target-help").remove(),this},dropTargetToggle:function(){return this.dropTarget?this.dropTargetOff():this.dropTargetOn(),this},dragenter:function(a){a.preventDefault(),a.stopPropagation(),this.$(".history-drop-target").css("border","2px solid black")},dragover:function(a){a.preventDefault(),a.stopPropagation()},dragleave:function(a){a.preventDefault(),a.stopPropagation(),this.$(".history-drop-target").css("border","1px dashed black")},drop:function(a){a.preventDefault(),a.dataTransfer.dropEffect="move";var b=this,c=a.dataTransfer.getData("text");try{c=JSON.parse(c)}catch(d){this.warn("error parsing JSON from drop:",c)}return this.trigger("droptarget:drop",a,c,b),!1},dataDropped:function(a){var b=this;return _.isObject(a)&&"HistoryDatasetAssociation"===a.model_class&&a.id?b.model.contents.copy(a.id):jQuery.when()},toString:function(){return"HistoryPanelEdit("+(this.model?this.model.get("name"):"")+")"}});return{HistoryPanelEdit:p}});
+define(["mvc/history/history-panel","mvc/history/history-contents","mvc/dataset/states","mvc/history/hda-model","mvc/history/hda-li-edit","mvc/history/hdca-li-edit","mvc/tags","mvc/annotations","mvc/collection/list-collection-creator","mvc/collection/pair-collection-creator","mvc/collection/list-of-pairs-collection-creator","ui/fa-icon-button","mvc/ui/popup-menu","utils/localization"],function(a,b,c,d,e,f,g,h,i,j,k,l,m,n){var o=a.HistoryPanel,p=o.extend({HDAViewClass:e.HDAListItemEdit,HDCAViewClass:f.HDCAListItemEdit,initialize:function(a){a=a||{},o.prototype.initialize.call(this,a),this.tagsEditor=null,this.annotationEditor=null,this.purgeAllowed=a.purgeAllowed||!1,this.annotationEditorShown=a.annotationEditorShown||!1,this.tagsEditorShown=a.tagsEditorShown||!1},_setUpListeners:function(){var a=this;o.prototype._setUpListeners.call(a),a.on("drop",function(b,c){a.dataDropped(c),a.dropTargetOff()}),a.on("view:attached view:removed",function(){a._renderCounts()},a)},_setUpCollectionListeners:function(){return o.prototype._setUpCollectionListeners.call(this),this.collection.on("change:deleted",this._handleHdaDeletionChange,this),this.collection.on("change:visible",this._handleHdaVisibleChange,this),this.collection.on("change:purged",function(){this.model.fetch()},this),this},_setUpModelListeners:function(){return o.prototype._setUpModelListeners.call(this),this.model.on("change:nice_size",this.updateHistoryDiskSize,this),this},_buildNewRender:function(){var a=o.prototype._buildNewRender.call(this);return this.model?(Galaxy&&Galaxy.currUser&&Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")&&(this._renderTags(a),this._renderAnnotation(a)),a):a},renderItems:function(a){var b=o.prototype.renderItems.call(this,a);return this._renderCounts(a),b},_renderCounts:function(a){function b(a,b){return['<a class="',a,'" href="javascript:void(0);">',b,"</a>"].join("")}a=a||this.$el;var c=this.collection.where({deleted:!0}),d=this.collection.where({visible:!1}),e=[];return this.views.length&&e.push([this.views.length,n("shown")].join(" ")),c.length&&e.push(this.showDeleted?b("toggle-deleted-link",n("hide deleted")):[c.length,b("toggle-deleted-link",n("deleted"))].join(" ")),d.length&&e.push(this.showHidden?b("toggle-hidden-link",n("hide hidden")):[d.length,b("toggle-hidden-link",n("hidden"))].join(" ")),a.find("> .controls .subtitle").html(e.join(", "))},_renderTags:function(a){var b=this;this.tagsEditor=new g.TagsEditor({model:this.model,el:a.find(".controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){b.toggleHDATagEditors(!0,b.fxSpeed)},onhide:function(){b.toggleHDATagEditors(!1,b.fxSpeed)},$activator:l({title:n("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(a.find(".controls .actions"))})},_renderAnnotation:function(a){var b=this;this.annotationEditor=new h.AnnotationEditor({model:this.model,el:a.find(".controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){b.toggleHDAAnnotationEditors(!0,b.fxSpeed)},onhide:function(){b.toggleHDAAnnotationEditors(!1,b.fxSpeed)},$activator:l({title:n("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(a.find(".controls .actions"))})},_setUpBehaviors:function(a){if(a=a||this.$el,o.prototype._setUpBehaviors.call(this,a),this.model&&Galaxy.currUser&&!Galaxy.currUser.isAnonymous()&&Galaxy.currUser.id===this.model.get("user_id")){var b=this,c="> .controls .name";a.find(c).attr("title",n("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(a){var d=b.model.get("name");a&&a!==d?(b.$el.find(c).text(a),b.model.save({name:a}).fail(function(){b.$el.find(c).text(b.model.previous("name"))})):b.$el.find(c).text(d)}})}},multiselectActions:function(){var a=this,b=[{html:n("Hide datasets"),func:function(){var b=d.HistoryDatasetAssociation.prototype.hide;a.getSelectedModels().ajaxQueue(b)}},{html:n("Unhide datasets"),func:function(){var b=d.HistoryDatasetAssociation.prototype.unhide;a.getSelectedModels().ajaxQueue(b)}},{html:n("Delete datasets"),func:function(){var b=d.HistoryDatasetAssociation.prototype.delete;a.getSelectedModels().ajaxQueue(b)}},{html:n("Undelete datasets"),func:function(){var b=d.HistoryDatasetAssociation.prototype.undelete;a.getSelectedModels().ajaxQueue(b)}}];return a.purgeAllowed&&b.push({html:n("Permanently delete datasets"),func:function(){if(confirm(n("This will permanently remove the data in your datasets. Are you sure?"))){var b=d.HistoryDatasetAssociation.prototype.purge;a.getSelectedModels().ajaxQueue(b)}}}),b=b.concat(a._collectionActions())},_collectionActions:function(){var a=this;return[{html:n("Build Dataset List"),func:function(){i.createListHDCA(a.getSelectedModels()).done(function(){a.model.refresh()})}},{html:n("Build Dataset Pair"),func:function(){j.createPairHDCA(a.getSelectedModels()).done(function(){a.model.refresh()})}},{html:n("Build List of Dataset Pairs"),func:function(){k.createListOfPairsCollection(a.getSelectedModels()).done(function(){a.model.refresh()})}}]},_attachItems:function(a){return this.$list(a).append(this.views.reverse().map(function(a){return a.$el})),this},_attachView:function(a){var b=this;b.views.unshift(a),b.$list().prepend(a.render(0).$el.hide()),b.trigger("view:attached",a),a.$el.slideDown(b.fxSpeed,function(){b.trigger("view:attached:rendered")})},_getItemViewOptions:function(a){var b=o.prototype._getItemViewOptions.call(this,a);return _.extend(b,{purgeAllowed:this.purgeAllowed,tagsEditorShown:this.tagsEditor&&!this.tagsEditor.hidden,annotationEditorShown:this.annotationEditor&&!this.annotationEditor.hidden}),b},_handleHdaDeletionChange:function(a){a.get("deleted")&&!this.showDeleted&&this.removeItemView(a),this._renderCounts()},_handleHdaVisibleChange:function(a){a.hidden()&&!this.showHidden&&this.removeItemView(a),this._renderCounts()},toggleHDATagEditors:function(){var a=Array.prototype.slice.call(arguments,1);_.each(this.views,function(b){b.tagsEditor&&b.tagsEditor.toggle.apply(b.tagsEditor,a)})},toggleHDAAnnotationEditors:function(){var a=Array.prototype.slice.call(arguments,1);_.each(this.views,function(b){b.annotationEditor&&b.annotationEditor.toggle.apply(b.annotationEditor,a)})},events:_.extend(_.clone(o.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click .toggle-deleted-link":function(){this.toggleShowDeleted()},"click .toggle-hidden-link":function(){this.toggleShowHidden()}}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},dropTargetOn:function(){if(this.dropTarget)return this;this.dropTarget=!0;var a={dragenter:_.bind(this.dragenter,this),dragover:_.bind(this.dragover,this),dragleave:_.bind(this.dragleave,this),drop:_.bind(this.drop,this)},b=this._renderDropTarget();this.$list().before([this._renderDropTargetHelp(),b]);for(var c in a)a.hasOwnProperty(c)&&b.on(c,a[c]);return this},_renderDropTarget:function(){return this.$(".history-drop-target").remove(),$("<div/>").addClass("history-drop-target").css({height:"64px",margin:"0px 10px 10px 10px",border:"1px dashed black","border-radius":"3px"})},_renderDropTargetHelp:function(){return this.$(".history-drop-target-help").remove(),$("<div/>").addClass("history-drop-target-help").css({margin:"10px 10px 4px 10px",color:"grey","font-size":"80%","font-style":"italic"}).text(n("Drag datasets here to copy them to the current history"))},dropTargetOff:function(){if(!this.dropTarget)return this;this.dropTarget=!1;var a=this.$(".history-drop-target").get(0);for(var b in this._dropHandlers)this._dropHandlers.hasOwnProperty(b)&&(console.debug(b,this._dropHandlers[b]),a.off(b,this._dropHandlers[b]));return this.$(".history-drop-target").remove(),this.$(".history-drop-target-help").remove(),this},dropTargetToggle:function(){return this.dropTarget?this.dropTargetOff():this.dropTargetOn(),this},dragenter:function(a){a.preventDefault(),a.stopPropagation(),this.$(".history-drop-target").css("border","2px solid black")},dragover:function(a){a.preventDefault(),a.stopPropagation()},dragleave:function(a){a.preventDefault(),a.stopPropagation(),this.$(".history-drop-target").css("border","1px dashed black")},drop:function(a){a.preventDefault(),a.dataTransfer.dropEffect="move";var b=this,c=a.dataTransfer.getData("text");try{c=JSON.parse(c)}catch(d){this.warn("error parsing JSON from drop:",c)}return this.trigger("droptarget:drop",a,c,b),!1},dataDropped:function(a){var b=this;return _.isObject(a)&&"HistoryDatasetAssociation"===a.model_class&&a.id?b.model.contents.copy(a.id):jQuery.when()},toString:function(){return"HistoryPanelEdit("+(this.model?this.model.get("name"):"")+")"}});return{HistoryPanelEdit:p}});
 //# sourceMappingURL=../../../maps/mvc/history/history-panel-edit.js.map
\ No newline at end of file

From 8254caba549ddb39474827fe2f8de323d7b2d1d7 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@tgac.ac.uk>
Date: Thu, 9 Apr 2015 20:37:03 +0100
Subject: [PATCH 75/88] Update many links which redirect to https.

---
 CONTRIBUTING.md                               |  2 +-
 config/galaxy.ini.sample                      | 60 +++++++++----------
 lib/galaxy/config.py                          |  2 +-
 lib/galaxy/managers/configuration.py          | 10 ++--
 lib/galaxy/web/base/controllers/admin.py      |  2 +-
 .../tool_dependencies/recipe/step_handler.py  |  6 +-
 lib/tool_shed/util/common_util.py             |  2 +-
 templates/webapps/galaxy/galaxy.masthead.mako | 12 ++--
 templates/webapps/tool_shed/base_panels.mako  | 10 ++--
 test/qunit/tests/galaxy-app-base.js           |  4 +-
 10 files changed, 55 insertions(+), 55 deletions(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 7888a623415..4f1503dad1d 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -4,7 +4,7 @@ This document briefly describes how to contribute to the [core
 galaxy project](https://github.com/galaxyproject/galaxy) -
 also checkout our 2013 Galaxy Community
 Conference presentation on the topic
-([video](http://vimeo.com/channels/581875/73486255),
+([video](https://vimeo.com/channels/581875/73486255),
 [presentation](https://wiki.galaxyproject.org/Documents/Presentations/GCC2013?action=AttachFile&do=view&target=BakerContribute.pdf)). For
 information on contributing more broadly to the Galaxy ecosystem and a
 deeper discussion of some of these points - please see the
diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample
index 138f3841b5b..811eee95117 100644
--- a/config/galaxy.ini.sample
+++ b/config/galaxy.ini.sample
@@ -218,7 +218,7 @@ paste.app_factory = galaxy.web.buildapp:app_factory
 #tool_data_path = tool-data
 
 # Directory where Tool Data Table related files will be placed
-# when installed from a ToolShed. Defaults to tool_data_path
+# when installed from a ToolShed. Defaults to tool_data_path.
 #shed_tool_data_path = tool-data
 
 # File containing old-style genome builds
@@ -369,7 +369,7 @@ paste.app_factory = galaxy.web.buildapp:app_factory
 
 # URL of the support resource for the galaxy instance.  Used in activation
 # emails.
-#instance_resource_url = http://wiki.galaxyproject.org/
+#instance_resource_url = https://wiki.galaxyproject.org/
 
 # E-mail domains blacklist is used for filtering out users that are using
 # disposable email address during the registration.  If their address domain
@@ -465,7 +465,7 @@ nglims_config_file = tool-data/nglims.yaml
 # Format string used when showing date and time information.
 # The string may contain:
 # - the directives used by Python time.strftime() function (see
-#   http://docs.python.org/2/library/time.html#time.strftime ),
+#   https://docs.python.org/2/library/time.html#time.strftime ),
 # - $locale (complete format string for the server locale),
 # - $iso8601 (complete format string as specified by ISO 8601 international
 #   standard).
@@ -478,11 +478,11 @@ nglims_config_file = tool-data/nglims.yaml
 
 # If the above URL cannot be determined ahead of time in dynamic environments
 # but the port which should be used to access Galaxy can be - this should be
-# set to prevent Galaxy from having to guess. For example if Galaxy is sitting
+# set to prevent Galaxy from having to guess.  For example if Galaxy is sitting
 # behind a proxy with REMOTE_USER enabled - infrastructure shouldn't talk to
-# Python processes directly and this should be set to 80 or 443, etc.... If
-# unset this file will be read for a server block defining a port
-# corresponding to the webapp.
+# Python processes directly and this should be set to 80 or 443, etc... If
+# unset this file will be read for a server block defining a port corresponding
+# to the webapp.
 #galaxy_infrastructure_web_port = 8080
 
 # The URL of the page to display in Galaxy's middle pane when loaded.  This can
@@ -493,22 +493,22 @@ nglims_config_file = tool-data/nglims.yaml
 #logo_url = /
 
 # The URL linked by the "Wiki" link in the "Help" menu.
-#wiki_url = http://wiki.galaxyproject.org/
+#wiki_url = https://wiki.galaxyproject.org/
 
 # The URL linked by the "Support" link in the "Help" menu.
-#support_url = http://wiki.galaxyproject.org/Support
+#support_url = https://wiki.galaxyproject.org/Support
 
 # The URL linked by the "How to Cite Galaxy" link in the "Help" menu.
-#citation_url = http://wiki.galaxyproject.org/CitingGalaxy
+#citation_url = https://wiki.galaxyproject.org/CitingGalaxy
 
 #The URL linked by the "Search" link in the "Help" menu.
 #search_url = http://galaxyproject.org/search/usegalaxy/
 
 #The URL linked by the "Mailing Lists" link in the "Help" menu.
-#mailing_lists_url = http://wiki.galaxyproject.org/MailingLists
+#mailing_lists_url = https://wiki.galaxyproject.org/MailingLists
 
 #The URL linked by the "Videos" link in the "Help" menu.
-#videos_url = http://vimeo.com/galaxyproject
+#screencasts_url = https://vimeo.com/galaxyproject
 
 # The URL linked by the "Terms and Conditions" link in the "Help" menu, as well
 # as on the user registration and login forms and in the activation emails.
@@ -612,7 +612,7 @@ nglims_config_file = tool-data/nglims.yaml
 # -- Logging and Debugging
 
 # Verbosity of console log messages.  Acceptable values can be found here:
-# http://docs.python.org/library/logging.html#logging-levels
+# https://docs.python.org/2/library/logging.html#logging-levels
 #log_level = DEBUG
 
 # Print database operations to the server log (warning, quite verbose!).
@@ -725,16 +725,16 @@ use_interactive = True
 # -- Toolbox Search
 
 # The following boosts are used to customize this instance's toolbox search.
-# The higher the boost the more importance the scoring algorithm gives to the
-# given field. Section refers to the tool group in the tool panel. Rest of 
+# The higher the boost, the more importance the scoring algorithm gives to the
+# given field.  Section refers to the tool group in the tool panel.  Rest of
 # the fields are tool's attributes.
 # tool_name_boost = 9
 # tool_section_boost = 3
 # tool_description_boost = 2
 # tool_help_boost = 0.5
 
-# Limits the number of results in toolbox search. Can be used to tweak 
-# how many results will appear.
+# Limits the number of results in toolbox search.  Can be used to tweak how many
+# results will appear.
 # tool_search_limit = 20
 
 # -- Users and Security
@@ -814,11 +814,12 @@ use_interactive = True
 # public.
 #new_user_dataset_access_role_default_private = False
 
-# Expose user list. Setting this to true will expose the user list to authenticated users. This
-# makes sharing datasets in smaller galaxy instances much easier as they can type a name/email and
-# have the correct user show up. This makes less sense on large public galaxy instances where
-# that data shouldn't be exposed. For semi-public galaxies, it may make sense to expose just the
-# username and not email, or vice versa.
+# Expose user list.  Setting this to True will expose the user list to
+# authenticated users.  This makes sharing datasets in smaller galaxy instances
+# much easier as they can type a name/email and have the correct user show up.
+# This makes less sense on large public Galaxy instances where that data
+# shouldn't be exposed.  For semi-public Galaxies, it may make sense to expose
+# just the username and not email, or vice versa.
 #expose_user_name = False
 #expose_user_email = False
 
@@ -865,8 +866,8 @@ use_interactive = True
 #openid_consumer_cache_path = database/openid_consumer_cache
 
 # XML config file that allows the use of different authentication providers
-# (e.g. LDAP) instead or in addition to local authentication
-# (.sample is used if default does not exist).
+# (e.g. LDAP) instead or in addition to local authentication (.sample is used
+# if default does not exist).
 #auth_config_file = config/auth_conf.xml
 
 # Optional list of email addresses of API users who can make calls on behalf of
@@ -915,14 +916,14 @@ use_interactive = True
 #expose_dataset_path = False
 
 # Data manager configuration options
-# Allow non-admin users to view available Data Manager options
+# Allow non-admin users to view available Data Manager options.
 #enable_data_manager_user_view = False
 # File where Data Managers are configured (.sample used if default does not
-# exist)
+# exist).
 #data_manager_config_file = config/data_manager_conf.xml
-# File where Tool Shed based Data Managers are configured
+# File where Tool Shed based Data Managers are configured.
 #shed_data_manager_config_file = config/shed_data_manager_conf.xml
-# Directory to store Data Manager based tool-data; defaults to tool_data_path
+# Directory to store Data Manager based tool-data; defaults to tool_data_path.
 #galaxy_data_manager_data_path = tool-data
 
 # -- Job Execution
@@ -990,7 +991,7 @@ use_interactive = True
 # actual user instead of as the user running the Galaxy server process.  For
 # details on these options, see the documentation at:
 #
-# http://galaxyproject.org/wiki/Admin/Config/Performance/Cluster
+# https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
 #
 #drmaa_external_runjob_script = scripts/drmaa_external_runner.py
 #drmaa_external_killjob_script = scripts/drmaa_external_killer.py
@@ -1007,7 +1008,6 @@ use_interactive = True
 # individually.
 #environment_setup_file = None
 
-
 # Optional file containing job resource data entry fields definition.
 # These fields will be presented to users in the tool forms and allow them to
 # overwrite default job resources such as number of processors, memory and
diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py
index 7e4a4e75003..5db75aabd91 100644
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -262,7 +262,7 @@ class Configuration( object ):
         self.message_box_content = kwargs.get( 'message_box_content', None )
         self.message_box_class = kwargs.get( 'message_box_class', 'info' )
         self.support_url = kwargs.get( 'support_url', 'https://wiki.galaxyproject.org/Support' )
-        self.wiki_url = kwargs.get( 'wiki_url', 'http://wiki.galaxyproject.org/' )
+        self.wiki_url = kwargs.get( 'wiki_url', 'https://wiki.galaxyproject.org/' )
         self.blog_url = kwargs.get( 'blog_url', None )
         self.screencasts_url = kwargs.get( 'screencasts_url', None )
         self.library_import_dir = kwargs.get( 'library_import_dir', None )
diff --git a/lib/galaxy/managers/configuration.py b/lib/galaxy/managers/configuration.py
index 7c844053eff..81b22f5f9e0 100644
--- a/lib/galaxy/managers/configuration.py
+++ b/lib/galaxy/managers/configuration.py
@@ -43,11 +43,11 @@ class ConfigSerializer( base.ModelSerializer ):
             #TODO: don't hardcode here - hardcode defaults once in config.py
             'wiki_url'                  : _defaults_to( "http://galaxyproject.org/" ),
             'search_url'                : _defaults_to( "http://galaxyproject.org/search/usegalaxy/" ),
-            'mailing_lists'             : _defaults_to( "http://wiki.galaxyproject.org/MailingLists" ),
-            'screencasts_url'           : _defaults_to( "http://vimeo.com/galaxyproject" ),
-            'citation_url'              : _defaults_to( "http://wiki.galaxyproject.org/CitingGalaxy" ),
-            'support_url'               : _defaults_to( "http://wiki.galaxyproject.org/Support" ),
-            'lims_doc_url'              : _defaults_to( "http://main.g2.bx.psu.edu/u/rkchak/p/sts" ),
+            'mailing_lists'             : _defaults_to( "https://wiki.galaxyproject.org/MailingLists" ),
+            'screencasts_url'           : _defaults_to( "https://vimeo.com/galaxyproject" ),
+            'citation_url'              : _defaults_to( "https://wiki.galaxyproject.org/CitingGalaxy" ),
+            'support_url'               : _defaults_to( "https://wiki.galaxyproject.org/Support" ),
+            'lims_doc_url'              : _defaults_to( "https://usegalaxy.org/u/rkchak/p/sts" ),
             'biostar_url'               : _defaults_to( '' ),
             'biostar_url_redirect'      : lambda *a, **c: self.url_for( controller='biostar', action='biostar_redirect',
                                                                    qualified=True ),
diff --git a/lib/galaxy/web/base/controllers/admin.py b/lib/galaxy/web/base/controllers/admin.py
index e4ca72649dc..349d83df3a5 100644
--- a/lib/galaxy/web/base/controllers/admin.py
+++ b/lib/galaxy/web/base/controllers/admin.py
@@ -1039,7 +1039,7 @@ class Admin( object ):
                 stop_msg += '.'
             for job_id in job_ids:
                 error_msg = "This job was stopped by an administrator: %s  <a href='%s' target='_blank'>Contact support</a> for additional help." \
-                        % ( stop_msg, self.app.config.get("support_url", "http://wiki.galaxyproject.org/Support" ) )
+                        % ( stop_msg, self.app.config.get("support_url", "https://wiki.galaxyproject.org/Support" ) )
                 if trans.app.config.track_jobs_in_database:
                     job = trans.sa_session.query( trans.app.model.Job ).get( job_id )
                     job.stderr = error_msg
diff --git a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
index 4db6d3efb12..5d469b90c50 100644
--- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
@@ -238,7 +238,7 @@ class AssertDirectoryExecutable( RecipeStep ):
             return False
         if os.path.isdir( full_path ):
             # Make sure the owner has execute permission on the directory.
-            # See http://docs.python.org/2/library/stat.html
+            # See https://docs.python.org/2/library/stat.html
             if stat.S_IXUSR & os.stat( full_path )[ stat.ST_MODE ] == 64:
                 return True
         return False
@@ -334,7 +334,7 @@ class AssertFileExecutable( RecipeStep ):
             return False
         if os.path.exists( full_path ):
             # Make sure the owner has execute permission on the file.
-            # See http://docs.python.org/2/library/stat.html
+            # See https://docs.python.org/2/library/stat.html
             if stat.S_IXUSR & os.stat( full_path )[ stat.ST_MODE ] == 64:
                 return True
         return False
@@ -896,7 +896,7 @@ class SetEnvironment( RecipeStep ):
         in the tool_dependencies.xml file in the order discussed here.  The example for this discussion is the
         tool_dependencies.xml file contained in the osra repository, which is available at:
     
-        http://testtoolshed.g2.bx.psu.edu/view/bgruening/osra
+        https://testtoolshed.g2.bx.psu.edu/view/bgruening/osra
     
         The first tag set defines a complex repository dependency like this.  This tag set ensures that changeset
         revision XXX of the repository named package_graphicsmagick_1_3 owned by YYY in the tool shed ZZZ has been
diff --git a/lib/tool_shed/util/common_util.py b/lib/tool_shed/util/common_util.py
index be33e737f9d..caa70774cc8 100644
--- a/lib/tool_shed/util/common_util.py
+++ b/lib/tool_shed/util/common_util.py
@@ -334,7 +334,7 @@ def tool_shed_get( app, tool_shed_url, uri ):
     """Make contact with the tool shed via the uri provided."""
     registry = app.tool_shed_registry
     # urllib2 auto-detects system proxies, when passed a Proxyhandler.
-    # Refer: http://docs.python.org/2/howto/urllib2.html#proxies
+    # Refer: https://docs.python.org/2/howto/urllib2.html#proxies
     proxy = urllib2.ProxyHandler()
     urlopener = urllib2.build_opener( proxy )
     urllib2.install_opener( urlopener )
diff --git a/templates/webapps/galaxy/galaxy.masthead.mako b/templates/webapps/galaxy/galaxy.masthead.mako
index f5061dfa9b4..c89be9adef2 100644
--- a/templates/webapps/galaxy/galaxy.masthead.mako
+++ b/templates/webapps/galaxy/galaxy.masthead.mako
@@ -12,15 +12,15 @@
             'use_remote_user'           : app.config.use_remote_user,
             'remote_user_logout_href'   : app.config.remote_user_logout_href,
             'enable_cloud_launch'       : app.config.get_bool('enable_cloud_launch', False),
-            'lims_doc_url'              : app.config.get("lims_doc_url", "http://main.g2.bx.psu.edu/u/rkchak/p/sts"),
+            'lims_doc_url'              : app.config.get("lims_doc_url", "https://usegalaxy.org/u/rkchak/p/sts"),
             'biostar_url'               : app.config.biostar_url,
             'biostar_url_redirect'      : h.url_for( controller='biostar', action='biostar_redirect', qualified=True ),
-            'support_url'               : app.config.get("support_url", "http://wiki.galaxyproject.org/Support"),
+            'support_url'               : app.config.get("support_url", "https://wiki.galaxyproject.org/Support"),
             'search_url'                : app.config.get("search_url", "http://galaxyproject.org/search/usegalaxy/"),
-            'mailing_lists'             : app.config.get("mailing_lists", "http://wiki.galaxyproject.org/MailingLists"),
-            'screencasts_url'           : app.config.get("screencasts_url", "http://vimeo.com/galaxyproject"),
-            'wiki_url'                  : app.config.get("wiki_url", "http://galaxyproject.org/"),
-            'citation_url'              : app.config.get("citation_url", "http://wiki.galaxyproject.org/CitingGalaxy"),
+            'mailing_lists'             : app.config.get("mailing_lists", "https://wiki.galaxyproject.org/MailingLists"),
+            'screencasts_url'           : app.config.get("screencasts_url", "https://vimeo.com/galaxyproject"),
+            'wiki_url'                  : app.config.get("wiki_url", "https://wiki.galaxyproject.org/"),
+            'citation_url'              : app.config.get("citation_url", "https://wiki.galaxyproject.org/CitingGalaxy"),
             'terms_url'                 : app.config.get("terms_url", ""),
             'allow_user_creation'       : app.config.allow_user_creation,
             'logo_url'                  : h.url_for(app.config.get( 'logo_url', '/')),
diff --git a/templates/webapps/tool_shed/base_panels.mako b/templates/webapps/tool_shed/base_panels.mako
index ed17535b6cd..645bf8fdabe 100644
--- a/templates/webapps/tool_shed/base_panels.mako
+++ b/templates/webapps/tool_shed/base_panels.mako
@@ -90,13 +90,13 @@
                     if qa_url:
                         menu_options = [ [_('Galaxy Q&A'), qa_url, "_blank" ] ]
                     menu_options.extend( [
-                        [_('Tool Shed Wiki'), app.config.get( "wiki_url", "http://wiki.galaxyproject.org/Tool%20Shed" ), "_blank" ],
-                        [_('Support'), app.config.get( "support_url", "http://wiki.galaxyproject.org/Support" ), "_blank" ],
+                        [_('Tool Shed Wiki'), app.config.get( "wiki_url", "https://wiki.galaxyproject.org/ToolShed" ), "_blank" ],
+                        [_('Support'), app.config.get( "support_url", "https://wiki.galaxyproject.org/Support" ), "_blank" ],
                         [_('Search'), app.config.get( "search_url", "http://galaxyproject.org/search/usegalaxy/" ), "_blank" ],
-                        [_('Mailing Lists'), app.config.get( "mailing_lists_url", "http://wiki.galaxyproject.org/MailingLists" ), "_blank" ],
-                        [_('Videos'), app.config.get( "screencasts_url", "http://vimeo.com/galaxyproject" ), "_blank" ],
+                        [_('Mailing Lists'), app.config.get( "mailing_lists_url", "https://wiki.galaxyproject.org/MailingLists" ), "_blank" ],
+                        [_('Videos'), app.config.get( "screencasts_url", "https://vimeo.com/galaxyproject" ), "_blank" ],
                         [_('Wiki'), app.config.get( "wiki_url", "http://galaxyproject.org/" ), "_blank" ],
-                        [_('How to Cite Galaxy'), app.config.get( "citation_url", "http://wiki.galaxyproject.org/CitingGalaxy" ), "_blank" ]
+                        [_('How to Cite Galaxy'), app.config.get( "citation_url", "https://wiki.galaxyproject.org/CitingGalaxy" ), "_blank" ]
                     ] )
                     tab( "help", _("Help"), None, menu_options=menu_options )
                 %>
diff --git a/test/qunit/tests/galaxy-app-base.js b/test/qunit/tests/galaxy-app-base.js
index 3f56be384df..30c2de54b70 100644
--- a/test/qunit/tests/galaxy-app-base.js
+++ b/test/qunit/tests/galaxy-app-base.js
@@ -3,7 +3,7 @@ define( 'bootstrapped-data', function(){
         config  : {
             "allow_user_deletion": false,
             "allow_user_creation": true,
-            "wiki_url": "http://wiki.galaxyproject.org/",
+            "wiki_url": "https://wiki.galaxyproject.org/",
             "ftp_upload_site": null,
             "support_url": "https://wiki.galaxyproject.org/Support",
             "allow_user_dataset_purge": false,
@@ -98,7 +98,7 @@ define([
         ok( app.hasOwnProperty( 'config' ) && typeof app.config === 'object' );
         equal( app.config.allow_user_deletion,  false );
         equal( app.config.allow_user_creation,  true );
-        equal( app.config.wiki_url,             "http://wiki.galaxyproject.org/" );
+        equal( app.config.wiki_url,             "https://wiki.galaxyproject.org/" );
         equal( app.config.ftp_upload_site,      null );
         //...
     });

From e625190219e48caf70666af19d48b0df77c56f26 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 9 Apr 2015 22:18:41 -0400
Subject: [PATCH 76/88] Fix default value handling in new tool form

---
 client/galaxy/scripts/mvc/form/form-input.js | 2 +-
 lib/galaxy/tools/__init__.py                 | 6 +-----
 static/maps/mvc/form/form-input.js.map       | 2 +-
 static/scripts/mvc/form/form-input.js        | 2 +-
 4 files changed, 4 insertions(+), 8 deletions(-)

diff --git a/client/galaxy/scripts/mvc/form/form-input.js b/client/galaxy/scripts/mvc/form/form-input.js
index edb5bcc2c3e..6b3820ce95a 100644
--- a/client/galaxy/scripts/mvc/form/form-input.js
+++ b/client/galaxy/scripts/mvc/form/form-input.js
@@ -34,7 +34,7 @@ define([], function() {
             this.field.skip = false;
             var v = this.field.value && this.field.value();
             this.field.skip = Boolean(options.optional &&
-                                        (v === null || v === '' || v === this.default_value ||
+                                        (v === this.default_value ||
                                          String(v) === String(this.default_value) ||
                                          Number(v) === Number(this.default_value) ||
                                          JSON.stringify(v) === JSON.stringify(this.default_value)));
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 5679539134a..2aafd2dfed0 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2436,16 +2436,12 @@ class Tool( object, Dictifiable ):
                             pass
 
                         # update input value from tool state
-                        tool_dict['value'] = state_inputs.get(input_name, None)
+                        tool_dict['value'] = state_inputs.get(input_name, tool_dict['default_value'])
 
                         # sanitize values
                         sanitize(tool_dict, 'value')
                         sanitize(tool_dict, 'default_value')
 
-                        # use default value
-                        if tool_dict['value'] is None:
-                            tool_dict['value'] = tool_dict['default_value']
-
                 # backup final input dictionary
                 group_inputs[input_index] = tool_dict
 
diff --git a/static/maps/mvc/form/form-input.js.map b/static/maps/mvc/form/form-input.js.map
index a81c028ce12..ec8d9ecfae8 100644
--- a/static/maps/mvc/form/form-input.js.map
+++ b/static/maps/mvc/form/form-input.js.map
@@ -1 +1 @@
-{"version":3,"file":"form-input.js","sources":["../../../src/mvc/form/form-input.js"],"names":["define","Backbone","View","extend","initialize","app","options","this","text_enable","text_disable","cls_enable","cls_disable","field","default_value","setElement","_template","$field","$el","find","$optional","$optional_icon","$error_text","$error","prepend","skip","v","value","Boolean","optional","String","Number","JSON","stringify","_refresh","self","on","trigger","error","text","html","show","addClass","reset","hide","removeClass","_tooltip","fadeIn","title","cls","length","tooltip","placement","attr","tmp","label","help"],"mappings":"AAGAA,UAAW,WACP,MAAOC,UAASC,KAAKC,QACjBC,WAAY,SAASC,EAAKC,GAEtBC,KAAKF,IAAMA,EAGXE,KAAKC,YAAiBH,EAAIC,QAAQE,aAAe,SACjDD,KAAKE,aAAiBJ,EAAIC,QAAQG,cAAgB,UAClDF,KAAKG,WAAiBL,EAAIC,QAAQI,YAAc,oBAChDH,KAAKI,YAAiBN,EAAIC,QAAQK,aAAe,qBAGjDJ,KAAKK,MAAQN,EAAQM,MACrBL,KAAKM,cAAgBP,EAAQO,cAG7BN,KAAKO,WAAWP,KAAKQ,UAAUT,IAG/BC,KAAKS,OAAST,KAAKU,IAAIC,KAAK,wBAC5BX,KAAKY,UAAYZ,KAAKU,IAAIC,KAAK,2BAC/BX,KAAKa,eAAiBb,KAAKU,IAAIC,KAAK,2BAA2BA,KAAK,SACpEX,KAAKc,YAAcd,KAAKU,IAAIC,KAAK,6BACjCX,KAAKe,OAASf,KAAKU,IAAIC,KAAK,wBAG5BX,KAAKS,OAAOO,QAAQhB,KAAKK,MAAMK,KAG/BV,KAAKK,MAAMY,MAAO,CAClB,IAAIC,GAAIlB,KAAKK,MAAMc,OAASnB,KAAKK,MAAMc,OACvCnB,MAAKK,MAAMY,KAAOG,QAAQrB,EAAQsB,WACC,OAANH,GAAoB,KAANA,GAAYA,IAAMlB,KAAKM,eACrCgB,OAAOJ,KAAOI,OAAOtB,KAAKM,gBAC1BiB,OAAOL,KAAOK,OAAOvB,KAAKM,gBAC1BkB,KAAKC,UAAUP,KAAOM,KAAKC,UAAUzB,KAAKM,iBAGvEN,KAAK0B,UAGL,IAAIC,GAAO3B,IACXA,MAAKY,UAAUgB,GAAG,QAAS,WAEvBD,EAAKtB,MAAMY,MAAQU,EAAKtB,MAAMY,KAG9BU,EAAKD,WAGLC,EAAK7B,IAAI+B,QAAQ,aAMzBC,MAAO,SAASC,GACZ/B,KAAKc,YAAYkB,KAAKD,GACtB/B,KAAKe,OAAOkB,OACZjC,KAAKU,IAAIwB,SAAS,aAKtBC,MAAO,WACHnC,KAAKe,OAAOqB,OACZpC,KAAKU,IAAI2B,YAAY,aAKzBX,SAAU,WAEN1B,KAAKa,eAAewB,cAAcH,SAAS,QAGtClC,KAAKK,MAAMY,MAOZjB,KAAKS,OAAO2B,OACZpC,KAAKsC,SAAStC,KAAKC,YAAaD,KAAKG,YAErCH,KAAKK,MAAMc,OAASnB,KAAKK,MAAMc,MAAMnB,KAAKM,iBAR1CN,KAAKS,OAAO8B,OAAO,QACnBvC,KAAKsC,SAAStC,KAAKE,aAAcF,KAAKI,eAa9CkC,SAAU,SAASE,EAAOC,GAClBzC,KAAKY,UAAU8B,QACf1C,KAAKa,eAAeqB,SAASO,GACTE,SAAUC,UAAW,WACrBC,KAAK,sBAAuBL,GAC5BG,QAAQ,YAAYA,QAAQ,SAMxDnC,UAAW,SAAST,GAEhB,GAAI+C,GAAQ,8LA+BZ,OAvBIA,IADA/C,EAAQsB,SACQ,wDAC0BtB,EAAQgD,MAClC,SAEThD,EAAQgD,MAInBD,GAAgB,0CAIhBA,GAAoB,mCAChB/C,EAAQiD,OACRF,GAAoB/C,EAAQiD,MAEhCF,GAAoB,SAGpBA,GAAgB"}
\ No newline at end of file
+{"version":3,"file":"form-input.js","sources":["../../../src/mvc/form/form-input.js"],"names":["define","Backbone","View","extend","initialize","app","options","this","text_enable","text_disable","cls_enable","cls_disable","field","default_value","setElement","_template","$field","$el","find","$optional","$optional_icon","$error_text","$error","prepend","skip","v","value","Boolean","optional","String","Number","JSON","stringify","_refresh","self","on","trigger","error","text","html","show","addClass","reset","hide","removeClass","_tooltip","fadeIn","title","cls","length","tooltip","placement","attr","tmp","label","help"],"mappings":"AAGAA,UAAW,WACP,MAAOC,UAASC,KAAKC,QACjBC,WAAY,SAASC,EAAKC,GAEtBC,KAAKF,IAAMA,EAGXE,KAAKC,YAAiBH,EAAIC,QAAQE,aAAe,SACjDD,KAAKE,aAAiBJ,EAAIC,QAAQG,cAAgB,UAClDF,KAAKG,WAAiBL,EAAIC,QAAQI,YAAc,oBAChDH,KAAKI,YAAiBN,EAAIC,QAAQK,aAAe,qBAGjDJ,KAAKK,MAAQN,EAAQM,MACrBL,KAAKM,cAAgBP,EAAQO,cAG7BN,KAAKO,WAAWP,KAAKQ,UAAUT,IAG/BC,KAAKS,OAAST,KAAKU,IAAIC,KAAK,wBAC5BX,KAAKY,UAAYZ,KAAKU,IAAIC,KAAK,2BAC/BX,KAAKa,eAAiBb,KAAKU,IAAIC,KAAK,2BAA2BA,KAAK,SACpEX,KAAKc,YAAcd,KAAKU,IAAIC,KAAK,6BACjCX,KAAKe,OAASf,KAAKU,IAAIC,KAAK,wBAG5BX,KAAKS,OAAOO,QAAQhB,KAAKK,MAAMK,KAG/BV,KAAKK,MAAMY,MAAO,CAClB,IAAIC,GAAIlB,KAAKK,MAAMc,OAASnB,KAAKK,MAAMc,OACvCnB,MAAKK,MAAMY,KAAOG,QAAQrB,EAAQsB,WACLH,IAAMlB,KAAKM,eACXgB,OAAOJ,KAAOI,OAAOtB,KAAKM,gBAC1BiB,OAAOL,KAAOK,OAAOvB,KAAKM,gBAC1BkB,KAAKC,UAAUP,KAAOM,KAAKC,UAAUzB,KAAKM,iBAGvEN,KAAK0B,UAGL,IAAIC,GAAO3B,IACXA,MAAKY,UAAUgB,GAAG,QAAS,WAEvBD,EAAKtB,MAAMY,MAAQU,EAAKtB,MAAMY,KAG9BU,EAAKD,WAGLC,EAAK7B,IAAI+B,QAAQ,aAMzBC,MAAO,SAASC,GACZ/B,KAAKc,YAAYkB,KAAKD,GACtB/B,KAAKe,OAAOkB,OACZjC,KAAKU,IAAIwB,SAAS,aAKtBC,MAAO,WACHnC,KAAKe,OAAOqB,OACZpC,KAAKU,IAAI2B,YAAY,aAKzBX,SAAU,WAEN1B,KAAKa,eAAewB,cAAcH,SAAS,QAGtClC,KAAKK,MAAMY,MAOZjB,KAAKS,OAAO2B,OACZpC,KAAKsC,SAAStC,KAAKC,YAAaD,KAAKG,YAErCH,KAAKK,MAAMc,OAASnB,KAAKK,MAAMc,MAAMnB,KAAKM,iBAR1CN,KAAKS,OAAO8B,OAAO,QACnBvC,KAAKsC,SAAStC,KAAKE,aAAcF,KAAKI,eAa9CkC,SAAU,SAASE,EAAOC,GAClBzC,KAAKY,UAAU8B,QACf1C,KAAKa,eAAeqB,SAASO,GACTE,SAAUC,UAAW,WACrBC,KAAK,sBAAuBL,GAC5BG,QAAQ,YAAYA,QAAQ,SAMxDnC,UAAW,SAAST,GAEhB,GAAI+C,GAAQ,8LA+BZ,OAvBIA,IADA/C,EAAQsB,SACQ,wDAC0BtB,EAAQgD,MAClC,SAEThD,EAAQgD,MAInBD,GAAgB,0CAIhBA,GAAoB,mCAChB/C,EAAQiD,OACRF,GAAoB/C,EAAQiD,MAEhCF,GAAoB,SAGpBA,GAAgB"}
\ No newline at end of file
diff --git a/static/scripts/mvc/form/form-input.js b/static/scripts/mvc/form/form-input.js
index d09ecf80b65..960b6027068 100644
--- a/static/scripts/mvc/form/form-input.js
+++ b/static/scripts/mvc/form/form-input.js
@@ -1,2 +1,2 @@
-define([],function(){return Backbone.View.extend({initialize:function(a,b){this.app=a,this.text_enable=a.options.text_enable||"Enable",this.text_disable=a.options.text_disable||"Disable",this.cls_enable=a.options.cls_enable||"fa fa-plus-square",this.cls_disable=a.options.cls_disable||"fa fa-minus-square",this.field=b.field,this.default_value=b.default_value,this.setElement(this._template(b)),this.$field=this.$el.find(".ui-table-form-field"),this.$optional=this.$el.find(".ui-table-form-optional"),this.$optional_icon=this.$el.find(".ui-table-form-optional").find(".icon"),this.$error_text=this.$el.find(".ui-table-form-error-text"),this.$error=this.$el.find(".ui-table-form-error"),this.$field.prepend(this.field.$el),this.field.skip=!1;var c=this.field.value&&this.field.value();this.field.skip=Boolean(b.optional&&(null===c||""===c||c===this.default_value||String(c)===String(this.default_value)||Number(c)===Number(this.default_value)||JSON.stringify(c)===JSON.stringify(this.default_value))),this._refresh();var d=this;this.$optional.on("click",function(){d.field.skip=!d.field.skip,d._refresh(),d.app.trigger("change")})},error:function(a){this.$error_text.html(a),this.$error.show(),this.$el.addClass("ui-error")},reset:function(){this.$error.hide(),this.$el.removeClass("ui-error")},_refresh:function(){this.$optional_icon.removeClass().addClass("icon"),this.field.skip?(this.$field.hide(),this._tooltip(this.text_enable,this.cls_enable),this.field.value&&this.field.value(this.default_value)):(this.$field.fadeIn("fast"),this._tooltip(this.text_disable,this.cls_disable))},_tooltip:function(a,b){this.$optional.length&&this.$optional_icon.addClass(b).tooltip({placement:"bottom"}).attr("data-original-title",a).tooltip("fixTitle").tooltip("hide")},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title">';return b+=a.optional?'<div class="ui-table-form-optional"><i class="icon"/>'+a.label+"</div>":a.label,b+='</div><div class="ui-table-form-field">',b+='<div class="ui-table-form-info">',a.help&&(b+=a.help),b+="</div>",b+="</div></div>"}})});
+define([],function(){return Backbone.View.extend({initialize:function(a,b){this.app=a,this.text_enable=a.options.text_enable||"Enable",this.text_disable=a.options.text_disable||"Disable",this.cls_enable=a.options.cls_enable||"fa fa-plus-square",this.cls_disable=a.options.cls_disable||"fa fa-minus-square",this.field=b.field,this.default_value=b.default_value,this.setElement(this._template(b)),this.$field=this.$el.find(".ui-table-form-field"),this.$optional=this.$el.find(".ui-table-form-optional"),this.$optional_icon=this.$el.find(".ui-table-form-optional").find(".icon"),this.$error_text=this.$el.find(".ui-table-form-error-text"),this.$error=this.$el.find(".ui-table-form-error"),this.$field.prepend(this.field.$el),this.field.skip=!1;var c=this.field.value&&this.field.value();this.field.skip=Boolean(b.optional&&(c===this.default_value||String(c)===String(this.default_value)||Number(c)===Number(this.default_value)||JSON.stringify(c)===JSON.stringify(this.default_value))),this._refresh();var d=this;this.$optional.on("click",function(){d.field.skip=!d.field.skip,d._refresh(),d.app.trigger("change")})},error:function(a){this.$error_text.html(a),this.$error.show(),this.$el.addClass("ui-error")},reset:function(){this.$error.hide(),this.$el.removeClass("ui-error")},_refresh:function(){this.$optional_icon.removeClass().addClass("icon"),this.field.skip?(this.$field.hide(),this._tooltip(this.text_enable,this.cls_enable),this.field.value&&this.field.value(this.default_value)):(this.$field.fadeIn("fast"),this._tooltip(this.text_disable,this.cls_disable))},_tooltip:function(a,b){this.$optional.length&&this.$optional_icon.addClass(b).tooltip({placement:"bottom"}).attr("data-original-title",a).tooltip("fixTitle").tooltip("hide")},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title">';return b+=a.optional?'<div class="ui-table-form-optional"><i class="icon"/>'+a.label+"</div>":a.label,b+='</div><div class="ui-table-form-field">',b+='<div class="ui-table-form-info">',a.help&&(b+=a.help),b+="</div>",b+="</div></div>"}})});
 //# sourceMappingURL=../../../maps/mvc/form/form-input.js.map
\ No newline at end of file

From 182fac5ad658ed73bf37b01469353da66bd4e8bd Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 10 Apr 2015 01:07:36 -0400
Subject: [PATCH 77/88] Re-insert classic tool form

---
 client/galaxy/scripts/mvc/form/form-view.js |   7 +
 static/maps/mvc/form/form-view.js.map       |   2 +-
 static/scripts/mvc/form/form-view.js        |   2 +-
 templates/webapps/galaxy/tool_form.mako     | 469 +++++++++++++++++++-
 4 files changed, 460 insertions(+), 20 deletions(-)

diff --git a/client/galaxy/scripts/mvc/form/form-view.js b/client/galaxy/scripts/mvc/form/form-view.js
index 2f9b2ae36f5..0ad6f12093b 100644
--- a/client/galaxy/scripts/mvc/form/form-view.js
+++ b/client/galaxy/scripts/mvc/form/form-view.js
@@ -200,6 +200,13 @@ define(['utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc',
                 inputs : this.options.inputs
             });
 
+            // switch to classic tool form mako if the form definition is incompatible
+            if (this.incompatible) {
+                this.$el.hide();
+                $('#tool-form-classic').show();
+                return;
+            }
+
             // create portlet
             this.portlet = new Portlet.View({
                 icon        : 'fa-wrench',
diff --git a/static/maps/mvc/form/form-view.js.map b/static/maps/mvc/form/form-view.js.map
index 36735cbe682..10d6646b3c8 100644
--- a/static/maps/mvc/form/form-view.js.map
+++ b/static/maps/mvc/form/form-view.js.map
@@ -1 +1 @@
-{"version":3,"file":"form-view.js","sources":["../../../src/mvc/form/form-view.js"],"names":["define","Utils","Portlet","Ui","FormSection","FormData","Backbone","View","extend","initialize","options","this","optionsDefault","is_dynamic","narrow","initial_errors","cls","merge","console","debug","galaxy","parent","Galaxy","modal","Modal","setElement","_build","update","new_model","self","data","matchModel","input_id","node","input","input_list","_","isEqual","field","field_list","new_options","indexOf","type","i","opt","length","push","label","value","trigger","wait","active","unwait","reciept","$el","empty","append","highlight","message","silent","input_element","element_list","error","$","animate","scrollTop","offset","top","errors","error_messages","matchResponse","off","_renderForm","create","current_check","checksum","on","new_check","onchange","reset","Message","section","inputs","portlet","icon","title","operations","buttons","addClass","persistent","status"],"mappings":"AAGAA,QAAQ,cAAe,oBAAqB,iBACpC,wBAAyB,sBAC7B,SAASC,EAAOC,EAASC,EAAIC,EAAaC,GAG1C,MAAOC,UAASC,KAAKC,QAEjBC,WAAY,SAASC,GAEjBC,KAAKC,gBAEDC,YAAkB,EAElBC,QAAkB,EAElBC,gBAAkB,EAElBC,IAAkB,sBAItBL,KAAKD,QAAUT,EAAMgB,MAAMP,EAASC,KAAKC,gBAGzCM,QAAQC,MAAMR,KAAKD,QAGnB,IAAIU,GAASC,OAAOC,MAEhBX,MAAKY,MADLH,GAAUA,EAAOG,MACJH,EAAOG,MAEP,GAAIpB,GAAGqB,MAAMjB,KAI9BI,KAAKc,WAAW,UAGhBd,KAAKe,UAITC,OAAQ,SAASC,GACb,GAAIC,GAAOlB,IACXA,MAAKmB,KAAKC,WAAWH,EAAW,SAASI,EAAUC,GAC/C,GAAIC,GAAQL,EAAKM,WAAWH,EAC5B,IAAIE,GAASA,EAAMxB,UACV0B,EAAEC,QAAQH,EAAMxB,QAASuB,EAAKvB,SAAU,CAEzCwB,EAAMxB,QAAUuB,EAAKvB,OAGrB,IAAI4B,GAAQT,EAAKU,WAAWP,EAC5B,IAAIM,EAAMX,OAAQ,CACd,GAAIa,KACJ,IAAuE,KAAjE,OAAQ,kBAAmB,cAAeC,QAAQP,EAAMQ,MAC1DF,EAAcN,EAAMxB,YAEpB,KAAK,GAAIiC,KAAKV,GAAKvB,QAAS,CACxB,GAAIkC,GAAMX,EAAKvB,QAAQiC,EACnBC,GAAIC,OAAS,GACbL,EAAYM,MACRC,MAASH,EAAI,GACbI,MAASJ,EAAI,KAK7BN,EAAMX,OAAOa,GACbF,EAAMW,QAAQ,UACd/B,QAAQC,MAAM,wBAA0Ba,QAQ5DkB,KAAM,SAASC,GACX,IAAK,GAAIR,KAAKhC,MAAKwB,WAAY,CAC3B,GAAIG,GAAQ3B,KAAK4B,WAAWI,GACxBT,EAAQvB,KAAKwB,WAAWQ,EACxBT,GAAMrB,YAAcyB,EAAMY,MAAQZ,EAAMc,SACpCD,EACAb,EAAMY,OAENZ,EAAMc,YAQtBC,QAAS,SAASC,GACd3C,KAAK2C,IAAIC,QACT5C,KAAK2C,IAAIE,OAAOF,IAKpBG,UAAW,SAAUzB,EAAU0B,EAASC,GAEpC,GAAIC,GAAgBjD,KAAKkD,aAAa7B,EAGlC4B,KAEAA,EAAcE,MAAMJ,GAAW,iCAG1BC,GACDI,EAAE,cAAcC,SACZC,UAAWL,EAAcN,IAAIY,SAASC,IAAM,IAC7C,OAOfC,OAAQ,SAAS1D,GAKb,GAHAC,KAAKsC,QAAQ,SAGTvC,GAAWA,EAAQ0D,OAAQ,CAC3B,GAAIC,GAAiB1D,KAAKmB,KAAKwC,cAAc5D,EAAQ0D,OACrD,KAAK,GAAIpC,KAAYrB,MAAKkD,aAAc,CACpC,CAAYlD,KAAKkD,aAAa7B,GAC1BqC,EAAerC,IACfrB,KAAK8C,UAAUzB,EAAUqC,EAAerC,IAAW,MAQnEN,OAAQ,WAEJ,GAAIG,GAAOlB,IAGXA,MAAK4D,IAAI,UACT5D,KAAK4D,IAAI,SAGT5D,KAAK4B,cAGL5B,KAAKwB,cAGLxB,KAAKkD,gBAGLlD,KAAKmB,KAAO,GAAIzB,GAASM,MAGzBA,KAAK6D,cAGL7D,KAAKmB,KAAK2C,SAGN9D,KAAKD,QAAQK,gBACbJ,KAAKyD,OAAOzD,KAAKD,QAIrB,IAAIgE,GAAgB/D,KAAKmB,KAAK6C,UAC9BhE,MAAKiE,GAAG,SAAU,WACd,GAAIC,GAAYhD,EAAKC,KAAK6C,UACtBE,IAAaH,IACbA,EAAgBG,EAChBhD,EAAKnB,QAAQoE,UAAYjD,EAAKnB,QAAQoE,cAK9CnE,KAAKiE,GAAG,QAAS,WACb,IAAK,GAAIjC,KAAKhC,MAAKkD,aACflD,KAAKkD,aAAalB,GAAGoC,WAOjCP,YAAa,WAET7D,KAAK+C,QAAU,GAAIvD,GAAG6E,QAGtBrE,KAAKsE,QAAU,GAAI7E,GAAYG,KAAKI,MAChCuE,OAASvE,KAAKD,QAAQwE,SAI1BvE,KAAKwE,QAAU,GAAIjF,GAAQK,MACvB6E,KAAc,YACdC,MAAc1E,KAAKD,QAAQ2E,MAC3BrE,IAAcL,KAAKD,QAAQM,IAC3BsE,WAAc3E,KAAKD,QAAQ4E,WAC3BC,QAAc5E,KAAKD,QAAQ6E,UAI/B5E,KAAKwE,QAAQ3B,OAAO7C,KAAK+C,QAAQJ,IAAIkC,SAAS,kBAG9C7E,KAAKwE,QAAQ3B,OAAO7C,KAAKsE,QAAQ3B,KAGjC3C,KAAK2C,IAAIC,QACT5C,KAAK2C,IAAIE,OAAO7C,KAAKwE,QAAQ7B,KAGzB3C,KAAKD,QAAQgD,SACb/C,KAAK+C,QAAQ/B,QACT8D,YAAc,EACdC,OAAc,UACdhC,QAAc/C,KAAKD,QAAQgD,UAKnCxC,QAAQC,MAAM"}
\ No newline at end of file
+{"version":3,"file":"form-view.js","sources":["../../../src/mvc/form/form-view.js"],"names":["define","Utils","Portlet","Ui","FormSection","FormData","Backbone","View","extend","initialize","options","this","optionsDefault","is_dynamic","narrow","initial_errors","cls","merge","console","debug","galaxy","parent","Galaxy","modal","Modal","setElement","_build","update","new_model","self","data","matchModel","input_id","node","input","input_list","_","isEqual","field","field_list","new_options","indexOf","type","i","opt","length","push","label","value","trigger","wait","active","unwait","reciept","$el","empty","append","highlight","message","silent","input_element","element_list","error","$","animate","scrollTop","offset","top","errors","error_messages","matchResponse","off","_renderForm","create","current_check","checksum","on","new_check","onchange","reset","Message","section","inputs","incompatible","hide","show","portlet","icon","title","operations","buttons","addClass","persistent","status"],"mappings":"AAGAA,QAAQ,cAAe,oBAAqB,iBACpC,wBAAyB,sBAC7B,SAASC,EAAOC,EAASC,EAAIC,EAAaC,GAG1C,MAAOC,UAASC,KAAKC,QAEjBC,WAAY,SAASC,GAEjBC,KAAKC,gBAEDC,YAAkB,EAElBC,QAAkB,EAElBC,gBAAkB,EAElBC,IAAkB,sBAItBL,KAAKD,QAAUT,EAAMgB,MAAMP,EAASC,KAAKC,gBAGzCM,QAAQC,MAAMR,KAAKD,QAGnB,IAAIU,GAASC,OAAOC,MAEhBX,MAAKY,MADLH,GAAUA,EAAOG,MACJH,EAAOG,MAEP,GAAIpB,GAAGqB,MAAMjB,KAI9BI,KAAKc,WAAW,UAGhBd,KAAKe,UAITC,OAAQ,SAASC,GACb,GAAIC,GAAOlB,IACXA,MAAKmB,KAAKC,WAAWH,EAAW,SAASI,EAAUC,GAC/C,GAAIC,GAAQL,EAAKM,WAAWH,EAC5B,IAAIE,GAASA,EAAMxB,UACV0B,EAAEC,QAAQH,EAAMxB,QAASuB,EAAKvB,SAAU,CAEzCwB,EAAMxB,QAAUuB,EAAKvB,OAGrB,IAAI4B,GAAQT,EAAKU,WAAWP,EAC5B,IAAIM,EAAMX,OAAQ,CACd,GAAIa,KACJ,IAAuE,KAAjE,OAAQ,kBAAmB,cAAeC,QAAQP,EAAMQ,MAC1DF,EAAcN,EAAMxB,YAEpB,KAAK,GAAIiC,KAAKV,GAAKvB,QAAS,CACxB,GAAIkC,GAAMX,EAAKvB,QAAQiC,EACnBC,GAAIC,OAAS,GACbL,EAAYM,MACRC,MAASH,EAAI,GACbI,MAASJ,EAAI,KAK7BN,EAAMX,OAAOa,GACbF,EAAMW,QAAQ,UACd/B,QAAQC,MAAM,wBAA0Ba,QAQ5DkB,KAAM,SAASC,GACX,IAAK,GAAIR,KAAKhC,MAAKwB,WAAY,CAC3B,GAAIG,GAAQ3B,KAAK4B,WAAWI,GACxBT,EAAQvB,KAAKwB,WAAWQ,EACxBT,GAAMrB,YAAcyB,EAAMY,MAAQZ,EAAMc,SACpCD,EACAb,EAAMY,OAENZ,EAAMc,YAQtBC,QAAS,SAASC,GACd3C,KAAK2C,IAAIC,QACT5C,KAAK2C,IAAIE,OAAOF,IAKpBG,UAAW,SAAUzB,EAAU0B,EAASC,GAEpC,GAAIC,GAAgBjD,KAAKkD,aAAa7B,EAGlC4B,KAEAA,EAAcE,MAAMJ,GAAW,iCAG1BC,GACDI,EAAE,cAAcC,SACZC,UAAWL,EAAcN,IAAIY,SAASC,IAAM,IAC7C,OAOfC,OAAQ,SAAS1D,GAKb,GAHAC,KAAKsC,QAAQ,SAGTvC,GAAWA,EAAQ0D,OAAQ,CAC3B,GAAIC,GAAiB1D,KAAKmB,KAAKwC,cAAc5D,EAAQ0D,OACrD,KAAK,GAAIpC,KAAYrB,MAAKkD,aAAc,CACpC,CAAYlD,KAAKkD,aAAa7B,GAC1BqC,EAAerC,IACfrB,KAAK8C,UAAUzB,EAAUqC,EAAerC,IAAW,MAQnEN,OAAQ,WAEJ,GAAIG,GAAOlB,IAGXA,MAAK4D,IAAI,UACT5D,KAAK4D,IAAI,SAGT5D,KAAK4B,cAGL5B,KAAKwB,cAGLxB,KAAKkD,gBAGLlD,KAAKmB,KAAO,GAAIzB,GAASM,MAGzBA,KAAK6D,cAGL7D,KAAKmB,KAAK2C,SAGN9D,KAAKD,QAAQK,gBACbJ,KAAKyD,OAAOzD,KAAKD,QAIrB,IAAIgE,GAAgB/D,KAAKmB,KAAK6C,UAC9BhE,MAAKiE,GAAG,SAAU,WACd,GAAIC,GAAYhD,EAAKC,KAAK6C,UACtBE,IAAaH,IACbA,EAAgBG,EAChBhD,EAAKnB,QAAQoE,UAAYjD,EAAKnB,QAAQoE,cAK9CnE,KAAKiE,GAAG,QAAS,WACb,IAAK,GAAIjC,KAAKhC,MAAKkD,aACflD,KAAKkD,aAAalB,GAAGoC,WAOjCP,YAAa,WAUT,MARA7D,MAAK+C,QAAU,GAAIvD,GAAG6E,QAGtBrE,KAAKsE,QAAU,GAAI7E,GAAYG,KAAKI,MAChCuE,OAASvE,KAAKD,QAAQwE,SAItBvE,KAAKwE,cACLxE,KAAK2C,IAAI8B,WACTrB,GAAE,sBAAsBsB,SAK5B1E,KAAK2E,QAAU,GAAIpF,GAAQK,MACvBgF,KAAc,YACdC,MAAc7E,KAAKD,QAAQ8E,MAC3BxE,IAAcL,KAAKD,QAAQM,IAC3ByE,WAAc9E,KAAKD,QAAQ+E,WAC3BC,QAAc/E,KAAKD,QAAQgF,UAI/B/E,KAAK2E,QAAQ9B,OAAO7C,KAAK+C,QAAQJ,IAAIqC,SAAS,kBAG9ChF,KAAK2E,QAAQ9B,OAAO7C,KAAKsE,QAAQ3B,KAGjC3C,KAAK2C,IAAIC,QACT5C,KAAK2C,IAAIE,OAAO7C,KAAK2E,QAAQhC,KAGzB3C,KAAKD,QAAQgD,SACb/C,KAAK+C,QAAQ/B,QACTiE,YAAc,EACdC,OAAc,UACdnC,QAAc/C,KAAKD,QAAQgD,cAKnCxC,SAAQC,MAAM"}
\ No newline at end of file
diff --git a/static/scripts/mvc/form/form-view.js b/static/scripts/mvc/form/form-view.js
index 44340dd8e60..5f2312fd115 100644
--- a/static/scripts/mvc/form/form-view.js
+++ b/static/scripts/mvc/form/form-view.js
@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/form/form-section","mvc/form/form-data"],function(a,b,c,d,e){return Backbone.View.extend({initialize:function(b){this.optionsDefault={is_dynamic:!0,narrow:!1,initial_errors:!1,cls:"ui-portlet-limited"},this.options=a.merge(b,this.optionsDefault),console.debug(this.options);var d=parent.Galaxy;this.modal=d&&d.modal?d.modal:new c.Modal.View,this.setElement("<div/>"),this._build()},update:function(a){var b=this;this.data.matchModel(a,function(a,c){var d=b.input_list[a];if(d&&d.options&&!_.isEqual(d.options,c.options)){d.options=c.options;var e=b.field_list[a];if(e.update){var f=[];if(-1!=["data","data_collection","drill_down"].indexOf(d.type))f=d.options;else for(var g in c.options){var h=c.options[g];h.length>2&&f.push({label:h[0],value:h[1]})}e.update(f),e.trigger("change"),console.debug("Updating options for "+a)}}})},wait:function(a){for(var b in this.input_list){var c=this.field_list[b],d=this.input_list[b];d.is_dynamic&&c.wait&&c.unwait&&(a?c.wait():c.unwait())}},reciept:function(a){this.$el.empty(),this.$el.append(a)},highlight:function(a,b,c){var d=this.element_list[a];d&&(d.error(b||"Please verify this parameter."),c||$("html, body").animate({scrollTop:d.$el.offset().top-20},500))},errors:function(a){if(this.trigger("reset"),a&&a.errors){var b=this.data.matchResponse(a.errors);for(var c in this.element_list){{this.element_list[c]}b[c]&&this.highlight(c,b[c],!0)}}},_build:function(){var a=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new e(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var b=this.data.checksum();this.on("change",function(){var c=a.data.checksum();c!=b&&(b=c,a.options.onchange&&a.options.onchange())}),this.on("reset",function(){for(var a in this.element_list)this.element_list[a].reset()})},_renderForm:function(){this.message=new c.Message,this.section=new d.View(this,{inputs:this.options.inputs}),this.portlet=new b.View({icon:"fa-wrench",title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.section.$el),this.$el.empty(),this.$el.append(this.portlet.$el),this.options.message&&this.message.update({persistent:!0,status:"warning",message:this.options.message}),console.debug("tools-form-base::initialize() - Completed.")}})});
+define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/form/form-section","mvc/form/form-data"],function(a,b,c,d,e){return Backbone.View.extend({initialize:function(b){this.optionsDefault={is_dynamic:!0,narrow:!1,initial_errors:!1,cls:"ui-portlet-limited"},this.options=a.merge(b,this.optionsDefault),console.debug(this.options);var d=parent.Galaxy;this.modal=d&&d.modal?d.modal:new c.Modal.View,this.setElement("<div/>"),this._build()},update:function(a){var b=this;this.data.matchModel(a,function(a,c){var d=b.input_list[a];if(d&&d.options&&!_.isEqual(d.options,c.options)){d.options=c.options;var e=b.field_list[a];if(e.update){var f=[];if(-1!=["data","data_collection","drill_down"].indexOf(d.type))f=d.options;else for(var g in c.options){var h=c.options[g];h.length>2&&f.push({label:h[0],value:h[1]})}e.update(f),e.trigger("change"),console.debug("Updating options for "+a)}}})},wait:function(a){for(var b in this.input_list){var c=this.field_list[b],d=this.input_list[b];d.is_dynamic&&c.wait&&c.unwait&&(a?c.wait():c.unwait())}},reciept:function(a){this.$el.empty(),this.$el.append(a)},highlight:function(a,b,c){var d=this.element_list[a];d&&(d.error(b||"Please verify this parameter."),c||$("html, body").animate({scrollTop:d.$el.offset().top-20},500))},errors:function(a){if(this.trigger("reset"),a&&a.errors){var b=this.data.matchResponse(a.errors);for(var c in this.element_list){{this.element_list[c]}b[c]&&this.highlight(c,b[c],!0)}}},_build:function(){var a=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new e(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var b=this.data.checksum();this.on("change",function(){var c=a.data.checksum();c!=b&&(b=c,a.options.onchange&&a.options.onchange())}),this.on("reset",function(){for(var a in this.element_list)this.element_list[a].reset()})},_renderForm:function(){return this.message=new c.Message,this.section=new d.View(this,{inputs:this.options.inputs}),this.incompatible?(this.$el.hide(),void $("#tool-form-classic").show()):(this.portlet=new b.View({icon:"fa-wrench",title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.section.$el),this.$el.empty(),this.$el.append(this.portlet.$el),this.options.message&&this.message.update({persistent:!0,status:"warning",message:this.options.message}),void console.debug("tools-form-base::initialize() - Completed."))}})});
 //# sourceMappingURL=../../../maps/mvc/form/form-view.js.map
\ No newline at end of file
diff --git a/templates/webapps/galaxy/tool_form.mako b/templates/webapps/galaxy/tool_form.mako
index 69e173f9acf..f271f99fa07 100644
--- a/templates/webapps/galaxy/tool_form.mako
+++ b/templates/webapps/galaxy/tool_form.mako
@@ -3,22 +3,455 @@
 ${h.js("libs/bibtex", "libs/jquery/jquery-ui")}
 ${h.css('base', 'jquery-ui/smoothness/jquery-ui')}
 
-<%
-    ## TEMPORARY: create tool dictionary in mako while both tool forms are in use.
-    ## This avoids making two separate requests since the classic form requires the mako anyway.
-    params = dict(trans.request.params)
-    params['__dataset_id__'] = params.get('id', None)
-    self.form_config = tool.to_json(trans, params)
-    self.form_config.update({
-        'id'                : tool.id,
-        'job_id'            : trans.security.encode_id( job.id ) if job else None,
-        'history_id'        : trans.security.encode_id( trans.history.id )
-    })
-%>
-<script>
-    require(['mvc/tools/tools-form'], function(ToolsForm){
-        $(function(){
-            var form = new ToolsForm.View(${ h.dumps(self.form_config) });
+## skip new tool form code if disabled
+%if util.string_as_bool(trans.app.config.get('toolform_upgrade',  True)):
+    <%
+        ## TEMPORARY: create tool dictionary in mako while both tool forms are in use.
+        ## This avoids making two separate requests since the classic form requires the mako anyway.
+        params = dict(trans.request.params)
+        params['__dataset_id__'] = params.get('id', None)
+        self.form_config = tool.to_json(trans, params)
+        self.form_config.update({
+            'id'                : tool.id,
+            'job_id'            : trans.security.encode_id( job.id ) if job else None,
+            'history_id'        : trans.security.encode_id( trans.history.id )
+        })
+    %>
+    <script>
+        require(['mvc/tools/tools-form'], function(ToolsForm){
+            $(function(){
+                var form = new ToolsForm.View(${ h.dumps(self.form_config) });
+            });
         });
-    });
-</script>
\ No newline at end of file
+    </script>
+    <div id="tool-form-classic" style="display: none;">
+%else:
+    <div id="tool-form-classic">
+%endif
+
+    <%namespace file="/message.mako" import="render_msg" />
+    <%namespace file="/base_panels.mako" import="overlay" />
+
+    <% import galaxy.util %>
+
+    <%def name="stylesheets()">
+        ${h.css( "autocomplete_tagging", "base", "library" )}
+        <style type="text/css">
+            html, body {
+                background-color: #fff;
+            }
+        </style>
+    </%def>
+
+    <%def name="javascripts()">
+        ${parent.javascripts()}
+        ${h.js( "galaxy.panels", "libs/jquery/jstorage" )}
+        ${h.js( "libs/bibtex" )}
+        <script type="text/javascript">
+            require( [ "galaxy.tools" ] );
+            window.enhanced_galaxy_tools = true;
+        </script>
+        <script type="text/javascript">
+        $(function() {
+            $(window).bind("refresh_on_change", function() {
+                $(':file').each( function() {
+                    var file = $(this);
+                    var file_value = file.val();
+                    if (file_value) {
+                        // disable file input, since we don't want to upload the file on refresh
+                        var file_name = $(this).attr("name");
+                        file.attr( { name: 'replaced_file_input_' + file_name, disabled: true } );
+                        // create a new hidden field which stores the filename and has the original name of the file input
+                        var new_file_input = $(document.createElement('input'));
+                        new_file_input.attr( { "type": "hidden", "value": file_value, "name": file_name } );
+                        file.after(new_file_input);
+                    }
+                });
+            });
+
+            // For drilldown parameters: add expand/collapse buttons and collapse initially-collapsed elements
+            $( 'div.drilldown-container' ).each( function() {
+                $(this).find('span.form-toggle' ).each( function() {
+                    var show_hide_click_elt = $(this);
+                    var group_id = show_hide_click_elt.attr('id').substring( 0, show_hide_click_elt.attr('id').lastIndexOf( '-click' ) );
+                    $('#' + group_id + '-container').each( function() {
+                        var show_hide_elt = $(this);
+                        if (  show_hide_click_elt.hasClass( 'toggle-expand' ) ) {
+                            show_hide_elt.hide();
+                        }
+                        show_hide_click_elt.click( function() {
+                            if ( show_hide_click_elt.hasClass("toggle") ){
+                                show_hide_click_elt.addClass("toggle-expand");
+                                show_hide_click_elt.removeClass("toggle");
+                                show_hide_elt.slideUp( 'fast' );
+                            }
+                            else {
+                                show_hide_click_elt.addClass("toggle");
+                                show_hide_click_elt.removeClass("toggle-expand");
+                                show_hide_elt.slideDown( 'fast' );
+                            }
+                        });
+                    });
+                });
+            });
+
+            $(".add-librarydataset").click(function() {
+                var link = $(this);
+                $.ajax({
+                    url: "/visualization/list_libraries",
+                    error: function(xhr, ajaxOptions, thrownError) { alert( "Grid failed" ); console.log(xhr, ajaxOptions, thrownError); },
+                    success: function(table_html) {
+                        show_modal(
+                            "Select Library Dataset",
+                            table_html, {
+                                "Cancel": function() {
+                                    hide_modal();
+                                },
+                                "Select": function() {
+                                    var names = [];
+                                    var ids = [];
+                                    counter = 1;
+                                    $('input[name=ldda_ids]:checked').each(function() {
+                                        var name = $.trim( $(this).siblings("label").text() );
+                                        var id = $(this).val();
+                                        names.push( counter + ". " + name );
+                                        counter += 1;
+                                        ids.push(id);
+                                    });
+                                    link.html( names.join("<br/>") );
+                                    link.siblings("input[type=hidden]").val( ids.join("||") );
+                                    hide_modal();
+                                }
+                            }
+                        );
+                    }
+                });
+            });
+        });
+
+        %if not add_frame.debug:
+            if( window.name != "galaxy_main" ) {
+                location.replace( '${h.url_for( controller='root', action='index', tool_id=tool.id )}' );
+            }
+        %endif
+
+        </script>
+
+    </%def>
+
+    <%def name="do_inputs( inputs, tool_state, errors, prefix, other_values=None )">
+        <%
+        from galaxy.util.expressions import ExpressionContext
+        other_values = ExpressionContext( tool_state, other_values )
+        %>
+        %for input_index, input in enumerate( inputs.itervalues() ):
+            %if not input.visible:
+                <% pass %>
+            %elif input.type == "repeat":
+              <div class="repeat-group">
+                  <div class="form-title-row"><strong>${input.title_plural}</strong>
+                  %if input.help:
+                      <div class="toolParamHelp" style="clear: both;">
+                          ${input.help}
+                      </div>
+                  %endif
+                  </div>
+                  <%
+                  repeat_state = tool_state[input.name]
+                  num_repeats = len( repeat_state )
+                  %>
+                  %for i in range( num_repeats ):
+                    <div class="repeat-group-item">
+                        <%
+                        if input.name in errors:
+                            rep_errors = errors[input.name][i]
+                        else:
+                            rep_errors = dict()
+                        index = repeat_state[i]['__index__']
+                        %>
+                        <div class="form-title-row"><strong>${input.title} ${i + 1}</strong></div>
+                        ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )}
+                        %if input.min < num_repeats:
+                            <div class="form-row"><input type="submit" class="btn" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div>
+                        %endif
+                    </div>
+                    %if rep_errors.has_key( '__index__' ):
+                        <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}">&nbsp;<span style="vertical-align: middle;">${rep_errors['__index__']}</span></div>
+                    %endif
+                  %endfor
+                  %if input.max > num_repeats:
+                      <div class="form-row"><input type="submit" class="btn" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div>
+                  %endif
+              </div>
+            %elif input.type == "conditional":
+                <%
+                group_state = tool_state[input.name]
+                group_errors = errors.get( input.name, {} )
+                current_case = group_state['__current_case__']
+                group_prefix = prefix + input.name + "|"
+                %>
+                %if input.value_ref_in_group:
+                    ${row_for_param( group_prefix, input.test_param, group_state, group_errors, other_values )}
+                %endif
+                ${do_inputs( input.cases[current_case].inputs, group_state, group_errors, group_prefix, other_values )}
+            %elif input.type == "upload_dataset":
+                %if input.get_datatype( trans, other_values ).composite_type is None: #have non-composite upload appear as before
+                    <%
+                    if input.name in errors:
+                        rep_errors = errors[input.name][0]
+                    else:
+                        rep_errors = dict()
+                    %>
+                  ${do_inputs( input.inputs, tool_state[input.name][0], rep_errors, prefix + input.name + "_" + str( 0 ) + "|", other_values )}
+                %else:
+                    <div class="repeat-group">
+                        <div class="form-title-row"><strong>${input.group_title( other_values )}</strong></div>
+                        <%
+                        repeat_state = tool_state[input.name]
+                        %>
+                        %for i in range( len( repeat_state ) ):
+                          <div class="repeat-group-item">
+                          <%
+                          if input.name in errors:
+                              rep_errors = errors[input.name][i]
+                          else:
+                              rep_errors = dict()
+                          index = repeat_state[i]['__index__']
+                          %>
+                          <div class="form-title-row"><strong>File Contents for ${input.title_by_index( trans, i, other_values )}</strong></div>
+                          ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )}
+                          ##<div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div>
+                          </div>
+                        %endfor
+                        ##<div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div>
+                    </div>
+                %endif
+            %elif input.type != "section":
+                ${row_for_param( prefix, input, tool_state, errors, other_values )}
+            %endif
+        %endfor
+    </%def>
+
+    <%def name="row_for_param( prefix, param, parent_state, parent_errors, other_values )">
+        <%
+        if parent_errors.has_key( param.name ):
+            cls = "form-row form-row-error"
+        else:
+            cls = "form-row"
+
+        field = param.get_html_field( trans, parent_state[ param.name ], other_values )
+        field.refresh_on_change = param.refresh_on_change
+
+        # Field may contain characters submitted by user and these characters may
+        # be unicode; handle non-ascii characters gracefully.
+        field_html = field.get_html( prefix )
+        if type( field_html ) is not unicode:
+            field_html = unicode( field_html, 'utf-8', 'replace' )
+
+        if param.type == "hidden":
+            return field_html
+        %>
+        <div class="${cls}">
+            ${label_for_param( param )}
+            ${input_for_param( param, field_html )}
+            ${errors_for_param( param, parent_errors )}
+            ${help_for_param( param )}
+            <div style="clear: both;"></div>
+        </div>
+    </%def>
+
+    <%def name="input_for_param( param, field_html )">
+        <div class="form-row-input">${field_html}</div>
+    </%def>
+
+    <%def name="label_for_param( param )">
+        <% label = param.get_label()%>
+        %if label:
+            <label for="${param.name}">${label}:</label>
+        %endif
+    </%def>
+
+    <%def name="errors_for_param( param, parent_errors )">
+        %if parent_errors.has_key( param.name ):
+            <div class="form-row-error-message">
+                <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}">&nbsp;<span style="vertical-align: middle;">${parent_errors[param.name]}</span></div>
+            </div>
+        %endif
+    </%def>
+
+    <%def name="help_for_param( param )">
+        %if param.help:
+            <div class="toolParamHelp" style="clear: both;">
+                ${param.help}
+            </div>
+        %endif
+    </%def>
+
+    <%def name="row_for_rerun()">
+        %if trans.app.config.track_jobs_in_database and tool_state.rerun_remap_job_id is not None:
+            <div id="remap-row" class="form-row">
+                <input type="checkbox" name="rerun_remap_job_id" value="${tool_state.rerun_remap_job_id}"> Resume dependencies from this job
+                <div class="toolParamHelp" style="clear: both;">
+                    The previous run of this tool failed and other tools were waiting for it to finish successfully, use this option to resume those tools using the outputs of this tool run.
+                </div>
+            </div>
+            <div style="clear: both;"></div>
+        %endif
+    </%def>
+
+    <% overlay(visible=False) %>
+
+    %if add_frame.from_noframe:
+        <div class="warningmessage">
+            <strong>Welcome to Galaxy</strong>
+            <hr/>
+            It appears that you found this tool from a link outside of Galaxy.
+            If you're not familiar with Galaxy, please consider visiting the
+            <a href="${h.url_for( controller='root' )}" target="_top">welcome page</a>.
+            To learn more about what Galaxy is and what it can do for you, please visit
+            the <a href="${add_frame.wiki_url}" target="_top">Galaxy wiki</a>.
+        </div>
+        <br/>
+    %endif
+
+    <%
+        # Render an error message if a dynamically generated select list is missing a required
+        # index file or entry in the tool_data_table_conf.xml file.
+        message = ""
+        params_with_missing_data_table_entry = tool.params_with_missing_data_table_entry
+        params_with_missing_index_file = tool.params_with_missing_index_file
+        if params_with_missing_data_table_entry:
+            param = params_with_missing_data_table_entry[0]
+            message += "Data table named '%s' is required by tool but not configured.  " % param.options.missing_tool_data_table_name
+        if tool.params_with_missing_index_file:
+            param = params_with_missing_index_file[0]
+            message += "Index file named '%s' is required by tool but not available.  " % param.options.missing_index_file
+
+        # Handle calculating the redirect url for the special case where we have nginx proxy
+        # upload and need to do url_for on the redirect portion of the tool action.
+        try:
+            tool_url = h.url_for(tool.action)
+        except AttributeError:
+            assert len(tool.action) == 2
+            tool_url = tool.action[0] + h.url_for(tool.action[1])
+    %>
+
+    <%
+        # Name of the tool in lower case
+        low_tool_name = tool.name.lower()
+    %>
+
+    %if tool_id_version_message:
+        ${render_msg( tool_id_version_message, 'warning' )}
+    %endif
+
+    <div class="toolForm" id="${tool.id}">
+        <form id="tool_form" name="tool_form" action="${tool_url}" enctype="${tool.enctype}" target="${tool.target}" method="${tool.method}">
+            %if tool.has_multiple_pages:
+                <div class="toolFormTitle">${tool.name} (step ${tool_state.page+1} of ${tool.npages})
+            %elif not tool_version_select_field:
+                <div class="toolFormTitle">${tool.name} (Galaxy tool version ${tool.version})
+            %else:
+                <div class="toolFormTitle">${tool.name} ${tool_version_select_field.get_html()}
+            %endif
+            ## Show information button with underlying requirements and their versions
+            %if tool.requirements:
+                <a href="#" class="icon-btn" title="Underlying versions" tabindex="0" data-toggle="popover" data-placement="bottom" data-content=
+                "
+                %for i, requirement in enumerate( tool.requirements ):
+                    ${ requirement.name } ${ ('v ' + requirement.version ) if requirement.version else ' ' } ${ '' if i + 1 == len( tool.requirements ) else ' | ' } 
+                %endfor
+                "
+                 onclick="$(function () {
+                              $( '[ data-toggle=\'popover\' ]' ).popover();
+                              $( this ).popover( 'show' );
+                          })">
+                    <span class="fa fa-info-circle"></span>
+                </a>
+            %endif
+
+            <span class="pull-right">
+            %if trans.app.config.biostar_url:
+                    ## BioStar links
+                    Help from Biostar
+                    <div class="icon-btn-group">
+                        <a href="${h.url_for( controller='biostar', action='biostar_tool_tag_redirect', tool_id=tool.id )}"
+                            target="_blank" class="icon-btn" title="Search for this tool" data-toggle="tooltip" data-placement="bottom"><span class="fa fa-search"></span></a>
+                        <a href="${h.url_for( controller='biostar', action='biostar_tool_question_redirect', tool_id=tool.id )}"
+                            target="_blank" class="icon-btn" title="Ask a question about this tool" data-toggle="tooltip" data-placement="bottom"><span class="fa fa-question-circle"></a>
+                    </div>
+            %endif
+                <div class="icon-btn-group">
+                    <a href="#" data-link="${h.url_for( controller='root', action='index', tool_id=tool.id, qualified=True )}"
+                        class="icon-btn tool-share-link" title="Share this tool" data-toggle="tooltip" data-placement="bottom"><span class="fa fa-share"></span></a>
+                </div>
+            </span>
+            </div>
+            <div class="toolFormBody">
+                <input type="hidden" name="refresh" value="refresh">
+                <input type="hidden" name="tool_id" value="${tool.id}">
+                <input type="hidden" name="tool_state" value="${util.object_to_string( tool_state.encode( tool, app ) )}">
+                %if tool.display_by_page[tool_state.page]:
+                    ${trans.fill_template_string( tool.display_by_page[tool_state.page], context=tool.get_param_html_map( trans, tool_state.page, tool_state.inputs ) )}
+                    ${row_for_rerun()}
+                    <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute">
+                %else:
+                    ${do_inputs( tool.inputs_by_page[ tool_state.page ], tool_state.inputs, errors, "" )}
+                    %if tool_state.page == tool.last_page:
+                        ${row_for_rerun()}
+                    %endif
+                    <div class="form-row form-actions">
+                        %if tool_state.page == tool.last_page:
+                            <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute">
+                        %else:
+                            <input type="submit" class="btn btn-primary" name="runtool_btn" value="Next step">
+                        %endif
+                    </div>
+                %endif
+            </div>
+        </form>
+    </div>
+    %if tool.help:
+        <div class="toolHelp">
+            <div class="toolHelpBody">
+                <%
+                    if tool.has_multiple_pages:
+                        tool_help = tool.help_by_page[tool_state.page]
+                    else:
+                        tool_help = tool.help
+
+                    # Help is Mako template, so render using current static path.
+                    tool_help = tool_help.render( static_path=h.url_for( '/static' ), host_url=h.url_for('/', qualified=True) )
+
+                    # Convert to unicode to display non-ascii characters.
+                    if type( tool_help ) is not unicode:
+                        tool_help = unicode( tool_help, 'utf-8')
+                %>
+                ${tool_help}
+            </div>
+        </div>
+    %endif
+    %if tool.tool_shed_repository:
+        <% tool_url = tool.tool_shed_repository.get_sharable_url( tool.app ) %>
+        %if tool_url:
+            <br/>
+            ${ render_msg( 'This tool was installed from a ToolShed, you may be able to find additional information by following this link: <a href="%s" target="_blank">%s</a>' % ( tool_url, tool_url ), 'info' ) }
+        %endif
+    %endif
+    %if tool.citations:
+        <script>
+        require(["mvc/citation/citation-model", "mvc/citation/citation-view"
+        ], function( citationModel, citationView ){
+            $(function() {
+                var citations = new citationModel.ToolCitationCollection();
+                citations.tool_id = "${tool.id}";
+                var citation_list_view = new citationView.CitationListView({ collection: citations } );
+                citation_list_view.render();
+                citations.fetch();
+            } );
+        } );
+        </script>
+        <div id="citations">
+        </div>
+    %endif
+</div>
\ No newline at end of file

From ec0fa276fa45feaf8a2a80424ccf43307f5902ab Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 10 Apr 2015 01:12:44 -0400
Subject: [PATCH 78/88] Add new-line to end of file

---
 templates/webapps/galaxy/tool_form.mako | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/templates/webapps/galaxy/tool_form.mako b/templates/webapps/galaxy/tool_form.mako
index f271f99fa07..2fd94873903 100644
--- a/templates/webapps/galaxy/tool_form.mako
+++ b/templates/webapps/galaxy/tool_form.mako
@@ -454,4 +454,4 @@ ${h.css('base', 'jquery-ui/smoothness/jquery-ui')}
         <div id="citations">
         </div>
     %endif
-</div>
\ No newline at end of file
+</div>

From 30c004bd8c18124b5195b8535b415c6b075bd153 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 10 Apr 2015 11:23:46 -0400
Subject: [PATCH 79/88] Check to see if toolshed install is actually bound
 prior to disposing (exact same functionality here, but it's less chatty this
 way, since it might not be bound)

---
 lib/galaxy/webapps/galaxy/buildapp.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index b124d8b1f7f..f6148079644 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -107,7 +107,9 @@ def app_factory( global_conf, **kwargs ):
     except:
         log.exception("Unable to dispose of pooled galaxy model database connections.")
     try:
-        galaxy.model.tool_shed_install.mapping.metadata.bind.dispose()
+        # This model may not actually be bound.
+        if galaxy.model.tool_shed_install.mapping.metadata.bind:
+            galaxy.model.tool_shed_install.mapping.metadata.bind.dispose()
     except:
         log.exception("Unable to dispose of pooled toolshed install model database connections.")
 

From aad36d0776a5b7bb55068476dc4a6317aa586e1b Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Fri, 10 Apr 2015 12:16:48 -0400
Subject: [PATCH 80/88] Rev pulsar client code.

Updates Pulsar client through https://github.com/galaxyproject/pulsar/commit/f1a9e83674dd98affbed476ba36b3ad07fa5e88b. The most important and substantial change here is a fix for galaxyproject/pulsar#63 provided by @dctrud.
---
 lib/pulsar/client/amqp_exchange.py | 2 +-
 lib/pulsar/client/client.py        | 8 ++++++--
 lib/pulsar/client/staging/up.py    | 2 +-
 3 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/lib/pulsar/client/amqp_exchange.py b/lib/pulsar/client/amqp_exchange.py
index 896efd19f96..ae22c82f5af 100644
--- a/lib/pulsar/client/amqp_exchange.py
+++ b/lib/pulsar/client/amqp_exchange.py
@@ -83,7 +83,7 @@ class PulsarExchange(object):
                                 connection.drain_events(timeout=self.__timeout)
                             except socket.timeout:
                                 pass
-            except (IOError, socket.error), exc:
+            except (IOError, socket.error) as exc:
                 self.__handle_io_error(exc, heartbeat_thread)
             except BaseException:
                 log.exception("Problem consuming queue, consumer quitting in problematic fashion!")
diff --git a/lib/pulsar/client/client.py b/lib/pulsar/client/client.py
index cbd755e0aed..27bb22ab37b 100644
--- a/lib/pulsar/client/client.py
+++ b/lib/pulsar/client/client.py
@@ -1,5 +1,6 @@
 import os
 from json import dumps
+from json import loads
 
 from .destination import submit_params
 from .setup_handler import build as build_setup_handler
@@ -170,10 +171,13 @@ class JobClient(BaseJobClient):
         input_path = path
         if contents:
             input_path = None
-        if action_type == 'transfer':
+        # action type == 'message' should either copy or transfer
+        # depending on default not just fallback to transfer.
+        if action_type in ['transfer', 'message']:
             return self._upload_file(args, contents, input_path)
         elif action_type == 'copy':
-            pulsar_path = self._raw_execute('path', args)
+            path_response = self._raw_execute('path', args)
+            pulsar_path = loads(path_response)['path']
             copy(path, pulsar_path)
             return {'path': pulsar_path}
 
diff --git a/lib/pulsar/client/staging/up.py b/lib/pulsar/client/staging/up.py
index 3daf124085e..6fd01136aca 100644
--- a/lib/pulsar/client/staging/up.py
+++ b/lib/pulsar/client/staging/up.py
@@ -348,7 +348,7 @@ class TransferTracker(object):
         if action.staging_needed:
             local_action = action.staging_action_local
             if local_action:
-                response = self.client.put_file(path, type, name=name, contents=contents)
+                response = self.client.put_file(path, type, name=name, contents=contents, action_type=action.action_type)
 
                 def get_path():
                     return response['path']

From 34d2564a27bb29c56c70b4dd91e5a96f41bf1384 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan.blankenberg@gmail.com>
Date: Fri, 10 Apr 2015 13:17:08 -0400
Subject: [PATCH 81/88] Enhance BAM metadata to include bam_version,
 sort_order, read_groups, reference_names, reference_lengths, and a dictionary
 of bam_header.

---
 lib/galaxy/datatypes/binary.py | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index 42f80cacc84..16e2a87f797 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -24,6 +24,9 @@ from galaxy.datatypes.metadata import MetadataElement, MetadataParameter, ListPa
 from galaxy.datatypes import metadata
 import dataproviders
 
+eggs.require( "pysam" )
+from pysam import csamtools
+
 log = logging.getLogger(__name__)
 
 # Currently these supported binary data types must be manually set on upload
@@ -146,6 +149,12 @@ class Bam( Binary ):
     data_sources = { "data": "bai", "index": "bigwig" }
 
     MetadataElement( name="bam_index", desc="BAM Index File", param=metadata.FileParameter, file_ext="bai", readonly=True, no_value=None, visible=False, optional=True )
+    MetadataElement( name="bam_version", default=None, desc="BAM Version", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value=None )
+    MetadataElement( name="sort_order", default=None, desc="Sort Order", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value=None )
+    MetadataElement( name="read_groups", default=[], desc="Read Groups", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value=[] )
+    MetadataElement( name="reference_names", default=[], desc="Chromosome Names", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value=[] )
+    MetadataElement( name="reference_lengths", default=[], desc="Chromosome Lengths", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value=[] )
+    MetadataElement( name="bam_header", default={}, desc="Dictionary of BAM Headers", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value={} )
 
     def _get_samtools_version( self ):
         # Determine the version of samtools being used.  Wouldn't it be nice if
@@ -291,6 +300,14 @@ class Bam( Binary ):
         dataset.metadata.bam_index = index_file
         # Remove temp file
         os.unlink( stderr_name )
+        # Now use pysam with BAI index to determine additional metadata
+        bam_file = csamtools.Samfile( filename=dataset.file_name, mode='rb', index_filename=index_file.file_name )
+        dataset.metadata.bam_header = bam_file.header
+        dataset.metadata.read_groups = [ read_group['ID'] for read_group in dataset.metadata.bam_header.get( 'RG', [] ) if 'ID' in read_group ]
+        dataset.metadata.reference_names = list( bam_file.references )
+        dataset.metadata.reference_lengths = list( bam_file.lengths )
+        dataset.metadata.sort_order = dataset.metadata.bam_header.get( 'HD', {} ).get( 'SO', None )
+        dataset.metadata.bam_version = dataset.metadata.bam_header.get( 'HD', {} ).get( 'VN', None )
 
     def sniff( self, filename ):
         # BAM is compressed in the BGZF format, and must not be uncompressed in Galaxy.

From 91f424a55ab493572a8e34e9e327621fa3e84166 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan.blankenberg@gmail.com>
Date: Fri, 10 Apr 2015 13:50:11 -0400
Subject: [PATCH 82/88] Add try/except around BAM metadata pysam actions.

---
 lib/galaxy/datatypes/binary.py | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index 16e2a87f797..3b9f2f6e166 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -301,13 +301,16 @@ class Bam( Binary ):
         # Remove temp file
         os.unlink( stderr_name )
         # Now use pysam with BAI index to determine additional metadata
-        bam_file = csamtools.Samfile( filename=dataset.file_name, mode='rb', index_filename=index_file.file_name )
-        dataset.metadata.bam_header = bam_file.header
-        dataset.metadata.read_groups = [ read_group['ID'] for read_group in dataset.metadata.bam_header.get( 'RG', [] ) if 'ID' in read_group ]
-        dataset.metadata.reference_names = list( bam_file.references )
-        dataset.metadata.reference_lengths = list( bam_file.lengths )
-        dataset.metadata.sort_order = dataset.metadata.bam_header.get( 'HD', {} ).get( 'SO', None )
-        dataset.metadata.bam_version = dataset.metadata.bam_header.get( 'HD', {} ).get( 'VN', None )
+        try:
+            bam_file = csamtools.Samfile( filename=dataset.file_name, mode='rb', index_filename=index_file.file_name )
+            dataset.metadata.bam_header = bam_file.header
+            dataset.metadata.read_groups = [ read_group['ID'] for read_group in dataset.metadata.bam_header.get( 'RG', [] ) if 'ID' in read_group ]
+            dataset.metadata.reference_names = list( bam_file.references )
+            dataset.metadata.reference_lengths = list( bam_file.lengths )
+            dataset.metadata.sort_order = dataset.metadata.bam_header.get( 'HD', {} ).get( 'SO', None )
+            dataset.metadata.bam_version = dataset.metadata.bam_header.get( 'HD', {} ).get( 'VN', None )
+        except:
+            pass
 
     def sniff( self, filename ):
         # BAM is compressed in the BGZF format, and must not be uncompressed in Galaxy.

From 56dc50d4fc1e79e5a1715c724eaf92043499f0d0 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan.blankenberg@gmail.com>
Date: Fri, 10 Apr 2015 15:00:27 -0400
Subject: [PATCH 83/88] Reorder BAM metadata to set reference names and lengths
 before attempting to parse header. pysam will die on parsing headers from
 e.g. 3unsorted.bam (sorted).

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

diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index 3b9f2f6e166..3d6f6e0e1e4 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -303,10 +303,10 @@ class Bam( Binary ):
         # Now use pysam with BAI index to determine additional metadata
         try:
             bam_file = csamtools.Samfile( filename=dataset.file_name, mode='rb', index_filename=index_file.file_name )
-            dataset.metadata.bam_header = bam_file.header
-            dataset.metadata.read_groups = [ read_group['ID'] for read_group in dataset.metadata.bam_header.get( 'RG', [] ) if 'ID' in read_group ]
             dataset.metadata.reference_names = list( bam_file.references )
             dataset.metadata.reference_lengths = list( bam_file.lengths )
+            dataset.metadata.bam_header = bam_file.header
+            dataset.metadata.read_groups = [ read_group['ID'] for read_group in dataset.metadata.bam_header.get( 'RG', [] ) if 'ID' in read_group ]
             dataset.metadata.sort_order = dataset.metadata.bam_header.get( 'HD', {} ).get( 'SO', None )
             dataset.metadata.bam_version = dataset.metadata.bam_header.get( 'HD', {} ).get( 'VN', None )
         except:

From 1167c7d7242ae8a6353a7273695b1bb77da7896b Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Fri, 10 Apr 2015 15:29:18 -0400
Subject: [PATCH 84/88] Enable use of nginx_upload_module for the job files
 api.

---
 config/galaxy.ini.sample                   |  7 +++++++
 lib/galaxy/config.py                       |  2 ++
 lib/galaxy/jobs/runners/pulsar.py          |  7 ++++++-
 lib/galaxy/webapps/galaxy/api/job_files.py | 14 +++++++++++++-
 4 files changed, 28 insertions(+), 2 deletions(-)

diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample
index fcd4d6e73f3..cba7dbe4c5b 100644
--- a/config/galaxy.ini.sample
+++ b/config/galaxy.ini.sample
@@ -580,6 +580,13 @@ nglims_config_file = tool-data/nglims.yaml
 # requests.
 #nginx_upload_path = False
 
+# Galaxy can also use nginx_upload_module to receive files staged out upon job
+# completion by remote job runners (i.e. Pulsar) that initiate staging
+# operations on the remote end.  See the Galaxy nginx documentation for the
+# corresponding nginx configuration.
+#nginx_upload_job_files_store = False
+#nginx_upload_job_files_path = False
+
 # Have Galaxy manage dynamic proxy component for routing requests to other
 # services based on Galaxy's session cookie.  It will attempt to do this by
 # default though you do need to install node+npm and do an npm install from
diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py
index 4ba5e7d8547..34472c7bdaf 100644
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -293,6 +293,8 @@ class Configuration( object ):
         self.nginx_x_archive_files_base = kwargs.get( 'nginx_x_archive_files_base', False )
         self.nginx_upload_store = kwargs.get( 'nginx_upload_store', False )
         self.nginx_upload_path = kwargs.get( 'nginx_upload_path', False )
+        self.nginx_upload_job_files_store = kwargs.get( 'nginx_upload_job_files_store', False )
+        self.nginx_upload_job_files_path = kwargs.get( 'nginx_upload_job_files_path', False )
         if self.nginx_upload_store:
             self.nginx_upload_store = os.path.abspath( self.nginx_upload_store )
         self.object_store = kwargs.get( 'object_store', 'disk' )
diff --git a/lib/galaxy/jobs/runners/pulsar.py b/lib/galaxy/jobs/runners/pulsar.py
index f1da51ff963..763e41c9a21 100644
--- a/lib/galaxy/jobs/runners/pulsar.py
+++ b/lib/galaxy/jobs/runners/pulsar.py
@@ -342,7 +342,12 @@ class PulsarJobRunner( AsynchronousJobRunner ):
 
         encoded_job_id = self.app.security.encode_id(job_id)
         job_key = self.app.security.encode_id( job_id, kind="jobs_files" )
-        files_endpoint = "%s/api/jobs/%s/files?job_key=%s" % (
+        endpoint_base = "%s/api/jobs/%s?job_key=%s"
+        if self.app.config.nginx_upload_job_files_path:
+            endpoint_base = "%s" + \
+                            self.app.config.nginx_upload_job_files_path + \
+                            "?job_id=%s&job_key=%s"
+        files_endpoint = endpoint_base % (
             self.galaxy_url,
             encoded_job_id,
             job_key
diff --git a/lib/galaxy/webapps/galaxy/api/job_files.py b/lib/galaxy/webapps/galaxy/api/job_files.py
index 27445beac38..a6e2fbae870 100644
--- a/lib/galaxy/webapps/galaxy/api/job_files.py
+++ b/lib/galaxy/webapps/galaxy/api/job_files.py
@@ -83,7 +83,19 @@ class JobFilesAPIController( BaseAPIController ):
         self.__check_job_can_write_to_path( trans, job, path )
 
         # Is this writing an unneeded file? Should this just copy in Python?
-        input_file = payload.get( "file", payload.get( "__file", None ) ).file
+        if '__file_path' in payload:
+            file_path = payload.get( '__file_path' )
+            upload_store = trans.app.config.nginx_upload_job_files_store
+            assert upload_store, ( "Request appears to have been processed by"
+                                   " nginx_upload_module but Galaxy is not"
+                                   " configured to recognize it" )
+            assert file_path.startswith( upload_store ), \
+                    ( "Filename provided by nginx (%s) is not in correct"
+                      " directory (%s)" % ( file_path, upload_store ) )
+            input_file = open( file_path )
+        else:
+            input_file = payload.get( "file",
+                                      payload.get( "__file", None ) ).file
         try:
             shutil.copyfile( input_file.name, path )
         finally:

From 7210e5d46ebd2bb6509daf80d4fa3ff228164d26 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Fri, 10 Apr 2015 15:30:31 -0400
Subject: [PATCH 85/88] Move, rather than copy files staged back to Galaxy via
 the job files api. Moving is a rename when the source and destination are on
 the same filesystem, which is nearly instantaneous and greatly reduces the
 possibility for failure due to mid-copy restarts.

---
 lib/galaxy/webapps/galaxy/api/job_files.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/api/job_files.py b/lib/galaxy/webapps/galaxy/api/job_files.py
index a6e2fbae870..4b21c1ceb5b 100644
--- a/lib/galaxy/webapps/galaxy/api/job_files.py
+++ b/lib/galaxy/webapps/galaxy/api/job_files.py
@@ -97,7 +97,7 @@ class JobFilesAPIController( BaseAPIController ):
             input_file = payload.get( "file",
                                       payload.get( "__file", None ) ).file
         try:
-            shutil.copyfile( input_file.name, path )
+            shutil.move( input_file.name, path )
         finally:
             input_file.close()
         return {"message": "ok"}

From 647cf55a11a71e1fc7743b685ded0b6dd1b0fffd Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Fri, 10 Apr 2015 15:39:36 -0400
Subject: [PATCH 86/88] Tweaks to the Pulsar job runners handling of async
 messags.

 - Report a more appropriate message for responding to "failed" status.
 - Respond to the new "lost" message (https://github.com/galaxyproject/pulsar/commit/61ed774ae6c67e7f0d891999def7233d1572013c).
 - Do not fail "lost" or "failed" jobs that may Galaxy may think have already completed (roughly).
---
 lib/galaxy/jobs/runners/pulsar.py | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/jobs/runners/pulsar.py b/lib/galaxy/jobs/runners/pulsar.py
index f1da51ff963..0463f26ec22 100644
--- a/lib/galaxy/jobs/runners/pulsar.py
+++ b/lib/galaxy/jobs/runners/pulsar.py
@@ -32,6 +32,8 @@ __all__ = [ 'PulsarLegacyJobRunner', 'PulsarRESTJobRunner', 'PulsarMQJobRunner'
 NO_REMOTE_GALAXY_FOR_METADATA_MESSAGE = "Pulsar misconfiguration - Pulsar client configured to set metadata remotely, but remote Pulsar isn't properly configured with a galaxy_home directory."
 NO_REMOTE_DATATYPES_CONFIG = "Pulsar client is configured to use remote datatypes configuration when setting metadata externally, but Pulsar is not configured with this information. Defaulting to datatypes_conf.xml."
 GENERIC_REMOTE_ERROR = "Failed to communicate with remote job server."
+FAILED_REMOTE_ERROR = "Remote job server indicated a problem running or monitoring this job."
+LOST_REMOTE_ERROR = "Remote job server could not determine this job's state."
 
 # Is there a good way to infer some default for this? Can only use
 # url_for from web threads. https://gist.github.com/jmchilton/9098762
@@ -170,8 +172,13 @@ class PulsarJobRunner( AsynchronousJobRunner ):
         if pulsar_status == "complete":
             self.mark_as_finished(job_state)
             return None
-        if pulsar_status == "failed":
-            self.fail_job(job_state)
+        if pulsar_status in ["failed", "lost"]:
+            if pulsar_status == "failed":
+                message = FAILED_REMOTE_ERROR
+            else:
+                message = LOST_REMOTE_ERROR
+            if not job_state.job_wrapper.get_job().finished:
+                self.fail_job(job_state, message)
             return None
         if pulsar_status == "running" and not job_state.running:
             job_state.running = True
@@ -398,12 +405,12 @@ class PulsarJobRunner( AsynchronousJobRunner ):
             log.exception("Job wrapper finish method failed")
             job_wrapper.fail("Unable to finish job", exception=True)
 
-    def fail_job( self, job_state ):
+    def fail_job( self, job_state, message=GENERIC_REMOTE_ERROR ):
         """
         Seperated out so we can use the worker threads for it.
         """
         self.stop_job( self.sa_session.query( self.app.model.Job ).get( job_state.job_wrapper.job_id ) )
-        job_state.job_wrapper.fail( getattr( job_state, "fail_message", GENERIC_REMOTE_ERROR ) )
+        job_state.job_wrapper.fail( getattr( job_state, "fail_message", message ) )
 
     def check_pid( self, pid ):
         try:

From 53258816a7eca8749ecfeb326c60d37bb7a2ad36 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan.blankenberg@gmail.com>
Date: Fri, 10 Apr 2015 15:46:52 -0400
Subject: [PATCH 87/88] Add test for BAM metadata reference name selector in
 tool to test/functional/tools.

---
 test/functional/tools/metadata_bam.xml      | 25 +++++++++++++++++++++
 test/functional/tools/samples_tool_conf.xml |  1 +
 2 files changed, 26 insertions(+)
 create mode 100644 test/functional/tools/metadata_bam.xml

diff --git a/test/functional/tools/metadata_bam.xml b/test/functional/tools/metadata_bam.xml
new file mode 100644
index 00000000000..aa8a52b43d8
--- /dev/null
+++ b/test/functional/tools/metadata_bam.xml
@@ -0,0 +1,25 @@
+<tool id="metadata_bam" name="metadata BAM" version="1.0.0">
+  <command>echo "${ref_names}" &gt; "${output_of_input_metadata}"</command>
+  <inputs>
+    <param name="input_bam" type="data" format="bam" label="BAM File"/>
+    <param name="ref_names" type="select" optional="False" label="Select references you would like to restrict bam to" multiple="True">
+        <options>
+            <filter type="data_meta" ref="input_bam" key="reference_names" />
+        </options>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="txt" name="output_of_input_metadata" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input_bam" value="3unsorted.bam" ftype="bam" />
+      <!-- This output tests setting using bam reference name metadata above -->
+      <param name="ref_names" value="chr10_random,chr11,chrM,chrX,chr16" />
+      <output name="output_of_input_metadata" ftype="txt">
+        <assert_contents>
+          <has_line line="chr10_random,chr11,chrM,chrX,chr16" />
+        </assert_contents>
+      </output>
+    </test>
+  </tests></tool>
diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
index c4fd339afeb..2c3961dd21e 100644
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -15,6 +15,7 @@
   <tool file="multi_output_assign_primary.xml" />
   <tool file="composite_output.xml" />
   <tool file="metadata.xml" />
+  <tool file="metadata_bam.xml" />
   <tool file="job_properties.xml" />
   <tool file="gzipped_inputs.xml" />
   <tool file="output_order.xml" />

From 4716d30b6915672d0526ad4ce5f81aff5beea622 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan.blankenberg@gmail.com>
Date: Fri, 10 Apr 2015 16:38:34 -0400
Subject: [PATCH 88/88] Minor typos fixed in test/functional/tools/README.txt

---
 test/functional/tools/README.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/functional/tools/README.txt b/test/functional/tools/README.txt
index 39bb6e748be..f4d08778269 100644
--- a/test/functional/tools/README.txt
+++ b/test/functional/tools/README.txt
@@ -5,11 +5,11 @@ these tests. Pass in an '-id' along with one of these tool ids to test
 a single tool.
 
 Some API tests use these tools to test various features of the API,
-tool, and workflow subsystems. Pass the arugment
+tool, and workflow subsystems. Pass the argument
 '-with_framework_test_tools' to 'run_tests.sh' in addition to '-api'
 to ensure these tools get loaded during the testing process.
 
-Finally, to play around witht these tools interactively - simply
+Finally, to play around with these tools interactively - simply
 replace the 'galaxy.ini' option 'tool_config_file' with:
 
 tool_config_file = test/functional/tools/samples_tool_conf.xml