From 017e181063f419d61d5055b8fa2d19bb71453bf8 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <ghv2@psu.edu>
Date: Fri, 12 Jun 2015 15:41:10 -0400
Subject: [PATCH 01/20] Add a GreaterThanZeroValidator for numeric tool
 parameters.

---
 lib/galaxy/tools/parameters/validation.py | 35 +++++++++++++++++++++--
 1 file changed, 33 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/tools/parameters/validation.py b/lib/galaxy/tools/parameters/validation.py
index 588949d63eb..132d439410d 100644
--- a/lib/galaxy/tools/parameters/validation.py
+++ b/lib/galaxy/tools/parameters/validation.py
@@ -324,6 +324,37 @@ class MetadataInDataTableColumnValidator( Validator ):
         raise ValueError( self.message )
 
 
+class GreaterThanZeroValidator( Validator ):
+    """
+    Validator that ensures a number is greater than zero.
+
+    >>> from galaxy.tools.parameters import ToolParameter
+    >>> p = ToolParameter.build( None, XML( '''
+    ... <param name="blah" type="integer" size="10" value="10">
+    ...     <validator type="greater_than_zero" />
+    ... </param>
+    ... ''' ) )
+    >>> t = p.validate( 1 )
+    >>> t = p.validate( 0.5 )
+    >>> t = p.validate( 0.0 )
+    Traceback (most recent call last):
+        ...
+    ValueError: Value must be greater than zero
+    """
+
+    def __init__( self, message=None ):
+        self.message = message
+
+    @classmethod
+    def from_element( cls, param, elem ):
+        return cls( elem.get( 'message', None ) )
+
+    def validate( self, value, history=None ):
+        if value <= 0:
+            if self.message is None:
+                self.message = "Value must be greater than zero"
+            raise ValueError( self.message )
+
 validator_types = dict( expression=ExpressionValidator,
                         regex=RegexValidator,
                         in_range=InRangeValidator,
@@ -334,10 +365,10 @@ validator_types = dict( expression=ExpressionValidator,
                         empty_field=EmptyTextfieldValidator,
                         dataset_metadata_in_file=MetadataInFileColumnValidator,
                         dataset_metadata_in_data_table=MetadataInDataTableColumnValidator,
-                        dataset_ok_validator=DatasetOkValidator )
+                        dataset_ok_validator=DatasetOkValidator,
+                        greater_than_zero=GreaterThanZeroValidator )
 
 def get_suite():
     """Get unittest suite for this module"""
     import doctest, sys
     return doctest.DocTestSuite( sys.modules[__name__] )
-

From 2a7f1f741e466223cf3d1e7c414ede5ee7ac4c5a Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <ghv2@psu.edu>
Date: Mon, 15 Jun 2015 12:16:37 -0400
Subject: [PATCH 02/20] Enhance the InRangeValidator to enalbe the use of new
 strict_min and strict_max attributes which, if set to true, will exclude the
 range end points.  For example, if strict_min is true, min < value, whereas
 if strict_min is false (the default), then min <= value.  Combinations of
 strict_min and strict_max are allowed.

---
 lib/galaxy/tools/parameters/validation.py | 128 +++++++++++++++-------
 1 file changed, 88 insertions(+), 40 deletions(-)

diff --git a/lib/galaxy/tools/parameters/validation.py b/lib/galaxy/tools/parameters/validation.py
index 132d439410d..0bab4837be8 100644
--- a/lib/galaxy/tools/parameters/validation.py
+++ b/lib/galaxy/tools/parameters/validation.py
@@ -5,25 +5,32 @@ Classes related to parameter validation.
 import os, re, logging
 from xml.etree.ElementTree import XML
 from galaxy import model
+from galaxy import util
 
 log = logging.getLogger( __name__ )
 
+
 class LateValidationError( Exception ):
+
     def __init__( self, message ):
         self.message = message
 
+
 class Validator( object ):
     """
     A validator checks that a value meets some conditions OR raises ValueError
     """
+
     @classmethod
     def from_element( cls, param, elem ):
         type = elem.get( 'type', None )
         assert type is not None, "Required 'type' attribute missing from validator"
         return validator_types[type].from_element( param, elem )
+
     def validate( self, value, history=None ):
         raise TypeError( "Abstract Method" )
 
+
 class RegexValidator( Validator ):
     """
     Validator that evaluates a regular expression
@@ -41,18 +48,22 @@ class RegexValidator( Validator ):
         ...
     ValueError: Not gonna happen
     """
+
     @classmethod
     def from_element( cls, param, elem ):
         return cls( elem.get( 'message' ), elem.text )
+
     def __init__( self, message, expression ):
         self.message = message
         # Compile later. RE objects used to not be thread safe. Not sure about
         # the sre module.
         self.expression = expression
+
     def validate( self, value, history=None ):
         if re.match( self.expression, value ) is None:
             raise ValueError( self.message )
 
+
 class ExpressionValidator( Validator ):
     """
     Validator that evaluates a python expression using the value
@@ -70,14 +81,17 @@ class ExpressionValidator( Validator ):
         ...
     ValueError: Not gonna happen
     """
+
     @classmethod
     def from_element( cls, param, elem ):
         return cls( elem.get( 'message' ), elem.text, elem.get( 'substitute_value_in_message' ) )
+
     def __init__( self, message, expression, substitute_value_in_message ):
         self.message = message
         self.substitute_value_in_message = substitute_value_in_message
         # Save compiled expression, code objects are thread safe (right?)
         self.expression = compile( expression, '<string>', 'eval' )
+
     def validate( self, value, history=None ):
         if not( eval( self.expression, dict( value=value ) ) ):
             message = self.message
@@ -85,6 +99,7 @@ class ExpressionValidator( Validator ):
                 message = message % value
             raise ValueError( message )
 
+
 class InRangeValidator( Validator ):
     """
     Validator that ensures a number is in a specific range
@@ -92,10 +107,13 @@ class InRangeValidator( Validator ):
     >>> from galaxy.tools.parameters import ToolParameter
     >>> p = ToolParameter.build( None, XML( '''
     ... <param name="blah" type="integer" size="10" value="10">
-    ...     <validator type="in_range" message="Not gonna happen" min="10" max="20"/>
+    ...     <validator type="in_range" message="Not gonna happen" min="10" strict_min="true" max="20"/>
     ... </param>
     ... ''' ) )
     >>> t = p.validate( 10 )
+    Traceback (most recent call last):
+        ...
+    ValueError: Not gonna happen
     >>> t = p.validate( 15 )
     >>> t = p.validate( 20 )
     >>> t = p.validate( 21 )
@@ -103,20 +121,54 @@ class InRangeValidator( Validator ):
         ...
     ValueError: Not gonna happen
     """
+
     @classmethod
     def from_element( cls, param, elem ):
-        return cls( elem.get( 'message', None ), elem.get( 'min' ), elem.get( 'max' ) )
-    def __init__( self, message, range_min, range_max ):
+        return cls( elem.get( 'message', None ), elem.get( 'min' ),
+                    elem.get( 'max' ), elem.get( 'strict_min', 'false' ), 
+                    elem.get( 'strict_max', 'false' ) )
+
+    def __init__( self, message, range_min, range_max, strict_min=False, strict_max=False ):
+        """
+        When the optional strict_min and strict_max attributes are set
+        to true, the range excludes the end points (i.e., min < value < max),
+        while if set to False ( the default), then range includes the end points
+        (1.e., min <= value <= max).  Combinations of strict_min and strict_max
+        values are allowed.
+        """
         self.min = float( range_min if range_min is not None else '-inf' )
+        self.strict_min = util.asbool( strict_min )
         self.max = float( range_max if range_max is not None else 'inf' )
+        self.strict_max = util.asbool( strict_max )
         assert self.min <= self.max, 'min must be less than or equal to max'
         # Remove unneeded 0s and decimal from floats to make message pretty.
         self_min_str = str( self.min ).rstrip( '0' ).rstrip( '.' )
         self_max_str = str( self.max ).rstrip( '0' ).rstrip( '.' )
-        self.message = message or "Value must be between %s and %s" % ( self_min_str, self_max_str )
+        op1 = '>='
+        op2 = '<='
+        if self.strict_min and self.strict_max:
+            op1 = '>'
+            op2 = '<'
+        if self.strict_min and not self.strict_max:
+            op1 = '>'
+        elif not self.strict_min and self.strict_max:
+            op2 = '<'
+        self.message = message or "Value must be %s %s and %s %s" % ( op1, self_min_str, op2, self_max_str )
+
     def validate( self, value, history=None ):
-        if not( self.min <= float( value ) <= self.max ):
-            raise ValueError( self.message )
+        if self.strict_min and self.strict_max:
+            if not( self.min < float( value ) < self.max ):
+                raise ValueError( self.message )
+        elif self.strict_min and not self.strict_max:
+            if not( self.min < float( value ) <= self.max ):
+                raise ValueError( self.message )
+        elif not self.strict_min and self.strict_max:
+            if not( self.min <= float( value ) < self.max ):
+                raise ValueError( self.message )
+        elif not self.strict_min and not self.strict_max:
+            if not( self.min <= float( value ) <= self.max ):
+                raise ValueError( self.message )
+
 
 class LengthValidator( Validator ):
     """
@@ -139,9 +191,11 @@ class LengthValidator( Validator ):
         ...
     ValueError: Must have length no more than 8
     """
+
     @classmethod
     def from_element( cls, param, elem ):
         return cls( elem.get( 'message', None ), elem.get( 'min', None ), elem.get( 'max', None ) )
+
     def __init__( self, message, length_min, length_max ):
         self.message = message
         if length_min is not None:
@@ -150,38 +204,47 @@ class LengthValidator( Validator ):
             length_max = int( length_max )
         self.min = length_min
         self.max = length_max
+
     def validate( self, value, history=None ):
         if self.min is not None and len( value ) < self.min:
             raise ValueError( self.message or ( "Must have length of at least %d" % self.min ) )
         if self.max is not None and len( value ) > self.max:
             raise ValueError( self.message or ( "Must have length no more than %d" % self.max ) )
 
+
 class DatasetOkValidator( Validator ):
     """
     Validator that checks if a dataset is in an 'ok' state
     """
+
     def __init__( self, message=None ):
         self.message = message
+
     @classmethod
     def from_element( cls, param, elem ):
         return cls( elem.get( 'message', None ) )
+
     def validate( self, value, history=None ):
         if value and value.state != model.Dataset.states.OK:
             if self.message is None:
                 self.message = "The selected dataset is still being generated, select another dataset or wait until it is completed"
             raise ValueError( self.message )
 
+
 class MetadataValidator( Validator ):
     """
     Validator that checks for missing metadata
     """
+
     def __init__( self, message = None, check = "", skip = "" ):
         self.message = message
         self.check = check.split( "," )
         self.skip = skip.split( "," )
+
     @classmethod
     def from_element( cls, param, elem ):
         return cls( message=elem.get( 'message', None ), check=elem.get( 'check', "" ), skip=elem.get( 'skip', "" ) )
+
     def validate( self, value, history=None ):
         if value:
             if not isinstance( value, model.DatasetInstance ):
@@ -191,18 +254,22 @@ class MetadataValidator( Validator ):
                     self.message = "Metadata missing, click the pencil icon in the history item to edit / save the metadata attributes"
                 raise ValueError( self.message )
 
+
 class UnspecifiedBuildValidator( Validator ):
     """
     Validator that checks for dbkey not equal to '?'
     """
+
     def __init__( self, message=None ):
         if message is None:
             self.message = "Unspecified genome build, click the pencil icon in the history item to set the genome build"
         else:
             self.message = message
+
     @classmethod
     def from_element( cls, param, elem ):
         return cls( elem.get( 'message', None ) )
+
     def validate( self, value, history=None ):
         #if value is None, we cannot validate
         if value:
@@ -212,36 +279,46 @@ class UnspecifiedBuildValidator( Validator ):
             if dbkey == '?':
                 raise ValueError( self.message )
 
+
 class NoOptionsValidator( Validator ):
     """Validator that checks for empty select list"""
+
     def __init__( self, message=None ):
         self.message = message
+
     @classmethod
     def from_element( cls, param, elem ):
         return cls( elem.get( 'message', None ) )
+
     def validate( self, value, history=None ):
         if value is None:
             if self.message is None:
                 self.message = "No options available for selection"
             raise ValueError( self.message )
 
+
 class EmptyTextfieldValidator( Validator ):
     """Validator that checks for empty text field"""
+
     def __init__( self, message=None ):
         self.message = message
+
     @classmethod
     def from_element( cls, param, elem ):
         return cls( elem.get( 'message', None ) )
+
     def validate( self, value, history=None ):
         if value == '':
             if self.message is None:
                 self.message = "Field requires a value"
             raise ValueError( self.message )
 
+
 class MetadataInFileColumnValidator( Validator ):
     """
     Validator that checks if the value for a dataset's metadata item exists in a file.
     """
+
     @classmethod
     def from_element( cls, param, elem ):
         filename = elem.get( "filename", None )
@@ -256,6 +333,7 @@ class MetadataInFileColumnValidator( Validator ):
         if line_startswith:
             line_startswith = line_startswith.strip()
         return cls( filename, metadata_name, metadata_column, message, line_startswith )
+
     def __init__( self, filename, metadata_name, metadata_column, message="Value for metadata not found.", line_startswith=None ):
         self.metadata_name = metadata_name
         self.message = message
@@ -265,6 +343,7 @@ class MetadataInFileColumnValidator( Validator ):
                 fields = line.split( '\t' )
                 if metadata_column < len( fields ):
                     self.valid_values.append( fields[metadata_column].strip() )
+
     def validate( self, value, history = None ):
         if not value: return
         if hasattr( value, "metadata" ):
@@ -272,10 +351,12 @@ class MetadataInFileColumnValidator( Validator ):
                 return
         raise ValueError( self.message )
 
+
 class MetadataInDataTableColumnValidator( Validator ):
     """
     Validator that checks if the value for a dataset's metadata item exists in a file.
     """
+
     @classmethod
     def from_element( cls, param, elem ):
         table_name = elem.get( "table_name", None )
@@ -323,38 +404,6 @@ class MetadataInDataTableColumnValidator( Validator ):
                 return
         raise ValueError( self.message )
 
-
-class GreaterThanZeroValidator( Validator ):
-    """
-    Validator that ensures a number is greater than zero.
-
-    >>> from galaxy.tools.parameters import ToolParameter
-    >>> p = ToolParameter.build( None, XML( '''
-    ... <param name="blah" type="integer" size="10" value="10">
-    ...     <validator type="greater_than_zero" />
-    ... </param>
-    ... ''' ) )
-    >>> t = p.validate( 1 )
-    >>> t = p.validate( 0.5 )
-    >>> t = p.validate( 0.0 )
-    Traceback (most recent call last):
-        ...
-    ValueError: Value must be greater than zero
-    """
-
-    def __init__( self, message=None ):
-        self.message = message
-
-    @classmethod
-    def from_element( cls, param, elem ):
-        return cls( elem.get( 'message', None ) )
-
-    def validate( self, value, history=None ):
-        if value <= 0:
-            if self.message is None:
-                self.message = "Value must be greater than zero"
-            raise ValueError( self.message )
-
 validator_types = dict( expression=ExpressionValidator,
                         regex=RegexValidator,
                         in_range=InRangeValidator,
@@ -365,8 +414,7 @@ validator_types = dict( expression=ExpressionValidator,
                         empty_field=EmptyTextfieldValidator,
                         dataset_metadata_in_file=MetadataInFileColumnValidator,
                         dataset_metadata_in_data_table=MetadataInDataTableColumnValidator,
-                        dataset_ok_validator=DatasetOkValidator,
-                        greater_than_zero=GreaterThanZeroValidator )
+                        dataset_ok_validator=DatasetOkValidator )
 
 def get_suite():
     """Get unittest suite for this module"""

From 2a3ad8148b95dc964620e8c6f0caff43c2c1d561 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <ghv2@psu.edu>
Date: Mon, 15 Jun 2015 13:21:24 -0400
Subject: [PATCH 03/20] Simplify the checks for setting strict_min and
 strict_max operators.

---
 lib/galaxy/tools/parameters/validation.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/tools/parameters/validation.py b/lib/galaxy/tools/parameters/validation.py
index 0bab4837be8..13647e3db22 100644
--- a/lib/galaxy/tools/parameters/validation.py
+++ b/lib/galaxy/tools/parameters/validation.py
@@ -149,9 +149,9 @@ class InRangeValidator( Validator ):
         if self.strict_min and self.strict_max:
             op1 = '>'
             op2 = '<'
-        if self.strict_min and not self.strict_max:
+        if self.strict_min:
             op1 = '>'
-        elif not self.strict_min and self.strict_max:
+        elif self.strict_max:
             op2 = '<'
         self.message = message or "Value must be %s %s and %s %s" % ( op1, self_min_str, op2, self_max_str )
 

From e8087f7b12d76aceeff38f0a2c70706e3ee676b7 Mon Sep 17 00:00:00 2001
From: Martin Cech <cech.marten@gmail.com>
Date: Mon, 15 Jun 2015 13:31:16 -0400
Subject: [PATCH 04/20] refactor TS javascript files to be separated from
 Galaxy JS thanks to Carl for helping me with this

---
 .../scripts/mvc/groups/group-detail-view.js               | 2 +-
 .../scripts/mvc/groups/group-list-view.js                 | 8 ++++----
 .../scripts/mvc/groups/group-listrow-view.js              | 0
 .../scripts/mvc/groups/group-model.js                     | 0
 client/toolshed/scripts/test-file.js                      | 3 ---
 client/{galaxy => toolshed}/scripts/toolshed.groups.js    | 6 +++---
 lib/galaxy/webapps/tool_shed/controllers/groups.py        | 2 +-
 static/scripts/mvc/groups/group-detail-view.js            | 2 --
 static/scripts/mvc/groups/group-groupdetail-view.js       | 2 --
 static/scripts/mvc/groups/group-grouprow-view.js          | 2 --
 static/scripts/mvc/groups/group-list-view.js              | 2 --
 static/scripts/mvc/groups/group.model.js                  | 2 --
 static/scripts/toolshed.groups.js                         | 2 --
 static/toolshed/maps/mvc/groups/group-detail-view.js.map  | 1 +
 static/toolshed/maps/mvc/groups/group-list-view.js.map    | 1 +
 static/toolshed/maps/mvc/groups/group-listrow-view.js.map | 1 +
 static/toolshed/maps/mvc/groups/group-model.js.map        | 1 +
 static/toolshed/maps/test-file.js.map                     | 1 +
 static/toolshed/maps/toolshed.groups.js.map               | 1 +
 static/toolshed/scripts/mvc/groups/group-detail-view.js   | 2 ++
 static/toolshed/scripts/mvc/groups/group-list-view.js     | 2 ++
 .../scripts/mvc/groups/group-listrow-view.js              | 0
 static/{ => toolshed}/scripts/mvc/groups/group-model.js   | 0
 static/toolshed/scripts/test-file.js                      | 2 ++
 static/toolshed/scripts/toolshed.groups.js                | 2 ++
 templates/webapps/tool_shed/group/index.mako              | 8 ++++++++
 26 files changed, 31 insertions(+), 24 deletions(-)
 rename client/{galaxy => toolshed}/scripts/mvc/groups/group-detail-view.js (99%)
 rename client/{galaxy => toolshed}/scripts/mvc/groups/group-list-view.js (96%)
 rename client/{galaxy => toolshed}/scripts/mvc/groups/group-listrow-view.js (100%)
 rename client/{galaxy => toolshed}/scripts/mvc/groups/group-model.js (100%)
 delete mode 100644 client/toolshed/scripts/test-file.js
 rename client/{galaxy => toolshed}/scripts/toolshed.groups.js (91%)
 delete mode 100644 static/scripts/mvc/groups/group-detail-view.js
 delete mode 100644 static/scripts/mvc/groups/group-groupdetail-view.js
 delete mode 100644 static/scripts/mvc/groups/group-grouprow-view.js
 delete mode 100644 static/scripts/mvc/groups/group-list-view.js
 delete mode 100644 static/scripts/mvc/groups/group.model.js
 delete mode 100644 static/scripts/toolshed.groups.js
 create mode 100644 static/toolshed/maps/mvc/groups/group-detail-view.js.map
 create mode 100644 static/toolshed/maps/mvc/groups/group-list-view.js.map
 create mode 100644 static/toolshed/maps/mvc/groups/group-listrow-view.js.map
 create mode 100644 static/toolshed/maps/mvc/groups/group-model.js.map
 create mode 100644 static/toolshed/maps/test-file.js.map
 create mode 100644 static/toolshed/maps/toolshed.groups.js.map
 create mode 100644 static/toolshed/scripts/mvc/groups/group-detail-view.js
 create mode 100644 static/toolshed/scripts/mvc/groups/group-list-view.js
 rename static/{ => toolshed}/scripts/mvc/groups/group-listrow-view.js (100%)
 rename static/{ => toolshed}/scripts/mvc/groups/group-model.js (100%)
 create mode 100644 static/toolshed/scripts/test-file.js
 create mode 100644 static/toolshed/scripts/toolshed.groups.js

diff --git a/client/galaxy/scripts/mvc/groups/group-detail-view.js b/client/toolshed/scripts/mvc/groups/group-detail-view.js
similarity index 99%
rename from client/galaxy/scripts/mvc/groups/group-detail-view.js
rename to client/toolshed/scripts/mvc/groups/group-detail-view.js
index 062ae79274e..f00454ac6fa 100644
--- a/client/galaxy/scripts/mvc/groups/group-detail-view.js
+++ b/client/toolshed/scripts/mvc/groups/group-detail-view.js
@@ -1,6 +1,6 @@
 define([
     "libs/toastr",
-    "mvc/groups/group-model"
+    "group_model"
     ],
 function(
     mod_toastr,
diff --git a/client/galaxy/scripts/mvc/groups/group-list-view.js b/client/toolshed/scripts/mvc/groups/group-list-view.js
similarity index 96%
rename from client/galaxy/scripts/mvc/groups/group-list-view.js
rename to client/toolshed/scripts/mvc/groups/group-list-view.js
index 3adeb0feefb..82b912c8b13 100644
--- a/client/galaxy/scripts/mvc/groups/group-list-view.js
+++ b/client/toolshed/scripts/mvc/groups/group-list-view.js
@@ -1,12 +1,12 @@
 define([
     "libs/toastr",
-    "mvc/groups/group-model",
-    "mvc/groups/group-listrow-view"
+    "group_model",
+    "group_row"
 
 ], function(
     mod_toastr,
     mod_group_model,
-    mod_group_listrow_view
+    mod_group_row
 ){
 
 var GroupListView = Backbone.View.extend({
@@ -71,7 +71,7 @@ var GroupListView = Backbone.View.extend({
      * @param {Group} model of the view that will be rendered
      */
     renderOne: function( options ){
-        var rowView = new mod_group_listrow_view.GroupListRowView( options );
+        var rowView = new mod_group_row.GroupListRowView( options );
         this.$el.find( '#group_list_body' ).append( rowView.el );
     },
 
diff --git a/client/galaxy/scripts/mvc/groups/group-listrow-view.js b/client/toolshed/scripts/mvc/groups/group-listrow-view.js
similarity index 100%
rename from client/galaxy/scripts/mvc/groups/group-listrow-view.js
rename to client/toolshed/scripts/mvc/groups/group-listrow-view.js
diff --git a/client/galaxy/scripts/mvc/groups/group-model.js b/client/toolshed/scripts/mvc/groups/group-model.js
similarity index 100%
rename from client/galaxy/scripts/mvc/groups/group-model.js
rename to client/toolshed/scripts/mvc/groups/group-model.js
diff --git a/client/toolshed/scripts/test-file.js b/client/toolshed/scripts/test-file.js
deleted file mode 100644
index 093dfad294e..00000000000
--- a/client/toolshed/scripts/test-file.js
+++ /dev/null
@@ -1,3 +0,0 @@
-define( [], function() {
-	return 'Remove this file';
-});
\ No newline at end of file
diff --git a/client/galaxy/scripts/toolshed.groups.js b/client/toolshed/scripts/toolshed.groups.js
similarity index 91%
rename from client/galaxy/scripts/toolshed.groups.js
rename to client/toolshed/scripts/toolshed.groups.js
index 1785878ed51..4e02146a2fb 100644
--- a/client/galaxy/scripts/toolshed.groups.js
+++ b/client/toolshed/scripts/toolshed.groups.js
@@ -3,9 +3,9 @@
 // MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM
 
 define([
-        "mvc/groups/group-list-view",
-        "mvc/groups/group-detail-view",
-        "mvc/groups/group-model"
+        'group_list',
+        'group_detail',
+        'group_model'
     ],
     function(
         mod_group_list,
diff --git a/lib/galaxy/webapps/tool_shed/controllers/groups.py b/lib/galaxy/webapps/tool_shed/controllers/groups.py
index 1e1e80f1351..3fac05dee17 100644
--- a/lib/galaxy/webapps/tool_shed/controllers/groups.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/groups.py
@@ -14,7 +14,7 @@ class Group( BaseUIController ):
     def index( self, trans, **kwd ):
         # define app configuration for generic mako template
         app = {
-            'jscript'       : "toolshed.groups"
+            'jscript'       : "../toolshed/scripts/toolshed.groups"
         }
         return trans.fill_template( '/webapps/tool_shed/group/index.mako',
                                     config = { 
diff --git a/static/scripts/mvc/groups/group-detail-view.js b/static/scripts/mvc/groups/group-detail-view.js
deleted file mode 100644
index fcee488d131..00000000000
--- a/static/scripts/mvc/groups/group-detail-view.js
+++ /dev/null
@@ -1,2 +0,0 @@
-define(["libs/toastr","mvc/groups/group-model"],function(a,b){var c=Backbone.View.extend({el:"#groups_element",options:{},app:null,initialize:function(a){this.options=_.extend(this.options,a),this.app=window.globalTS.groups,null!==this.app.collection?(this.model=this.app.collection.get(this.options.group_id),this.render()):this.fetchGroup()},fetchGroup:function(c){var d=this;this.options=_.extend(this.options,c),this.model=new b.Group({id:this.options.group_id}),this.model.fetch({success:function(a){console.log("received data: "),console.log(a),d.render()},error:function(b,c){a.error("undefined"!=typeof c.responseJSON?c.responseJSON.err_msg:"An error ocurred.")}})},render:function(){var a=this.templateRow();this.$el.html(a({group:this.model})),$("#center [data-toggle]").tooltip()},templateRow:function(){return _.template(["<div>",'<h3><%= group.get("name") %></h3>','<p class="" style="color:gray;">','A group of <%= group.get("members").length %> members with <%= group.get("repositories").length %> repositories and a total of <%= group.get("total_downloads") %> combined tool downloads.</p>',"<h3>Members</h3>",'<table class="grid table table-condensed">',"<thead>","<th>Name</th>","<th>Repositories</th>","<th>Registered</th>","</thead>","<tbody>",'<% _.each(group.get("members"), function(member) { %>',"<tr>","<td>","<%= member.username %>","</td>","<td>",'<a data-toggle="tooltip" data-placement="top" title="Repositories of <%= member.username %>" href="/repository/browse_repositories_by_user?user_id=<%= member.id %>&use_panels=true" id="<%= member.id %>"><%= member.user_repos_count %></a>',"</td>","<td>","<%= member.time_created %>","</td>","</tr>","<% }); %>","</tbody>","</table>","<h3>Repositories</h3>",'<table class="grid table table-condensed">',"<thead>","<th>Name</th>","<th>Description</th>","<th>Downloads</th>","<th>Owner</th>","<th>Created</th>","<th>Rating</th>","<th>Verified</th>","</thead>","<tbody>",'<% _.each(group.get("repositories"), function(repo) { %>',"<tr>","<td>",'<a data-toggle="tooltip" data-placement="top" title="Details of <%= repo.name %>" href="/view/<%= repo.owner %>/<%= repo.name %>" id="<%= repo.id %>"><%= repo.name %></a>',"</td>","<td>","<%= repo.description %>","</td>","<td>","<%= repo.times_downloaded %>","</td>","<td>","<%= repo.owner %>","</td>","<td>","<%= repo.time_created %>","</td>","<td>","<%= repo.ratings_mean %>","</td>","<td>","<%= repo.approved %>","</td>","</tr>","<% }); %>","</tbody>","</table>","</div>"].join(""))}});return{GroupDetailView:c}});
-//# sourceMappingURL=../../../maps/mvc/groups/group-detail-view.js.map
\ No newline at end of file
diff --git a/static/scripts/mvc/groups/group-groupdetail-view.js b/static/scripts/mvc/groups/group-groupdetail-view.js
deleted file mode 100644
index ac9d5f5c776..00000000000
--- a/static/scripts/mvc/groups/group-groupdetail-view.js
+++ /dev/null
@@ -1,2 +0,0 @@
-define([],function(){var a=Backbone.View.extend({events:{},initialize:function(a){this.render(a)},render:function(a){var b=this.templateRow();return this.setElement(b({group:a})),this.$el.show(),this},templateRow:function(){return _.template(["<div>TEST GROUP PAGE</div>"].join(""))}});return{GroupDetailView:a}});
-//# sourceMappingURL=../../../maps/mvc/groups/group-groupdetail-view.js.map
\ No newline at end of file
diff --git a/static/scripts/mvc/groups/group-grouprow-view.js b/static/scripts/mvc/groups/group-grouprow-view.js
deleted file mode 100644
index 49178b680f1..00000000000
--- a/static/scripts/mvc/groups/group-grouprow-view.js
+++ /dev/null
@@ -1,2 +0,0 @@
-define([],function(){var a=Backbone.View.extend({events:{},initialize:function(a){this.render(a)},render:function(a){var b=this.templateRow();return this.setElement(b({group:a})),this.$el.show(),this},templateRow:function(){return _.template(['<tr class="" data-id="<%- group.get("id") %>">','<td><a href="/groups/<%= group.get("id") %>"><%= group.get("name") %></a></td>',"<td>description</td>",'<td><%= group.get("total_members") %></td>','<td><%= group.get("total_repos") %></td>',"</tr>"].join(""))}});return{GroupRowView:a}});
-//# sourceMappingURL=../../../maps/mvc/groups/group-grouprow-view.js.map
\ No newline at end of file
diff --git a/static/scripts/mvc/groups/group-list-view.js b/static/scripts/mvc/groups/group-list-view.js
deleted file mode 100644
index d14a196bd3f..00000000000
--- a/static/scripts/mvc/groups/group-list-view.js
+++ /dev/null
@@ -1,2 +0,0 @@
-define(["libs/toastr","mvc/groups/group-model","mvc/groups/group-listrow-view"],function(a,b,c){var d=Backbone.View.extend({el:"#groups_element",defaults:{},initialize:function(c){this.options=_.defaults(this.options||{},this.defaults,c);var d=this;window.globalTS.groups.collection=new b.Groups,window.globalTS.groups.collection.fetch({success:function(a){console.log("received data: "),console.log(a),d.render()},error:function(b,c){a.error("undefined"!=typeof c.responseJSON?c.responseJSON.err_msg:"An error ocurred.")}})},fetch:function(){},render:function(a){this.options=_.extend(this.options,a),$(".tooltip").hide();var b=this.templateGroupsList();this.$el.html(b({length:10,order:"asc"})),this.renderRows(window.globalTS.groups.collection.models),$("#center [data-toggle]").tooltip(),$("#center").css("overflow","auto")},renderRows:function(a){for(var b=0;b<a.length;b++){var c=a[b];this.renderOne({group:c})}},renderOne:function(a){var b=new c.GroupListRowView(a);this.$el.find("#group_list_body").append(b.el)},templateGroupsList:function(){return tmpl_array=[],tmpl_array.push('<div id="groups">'),tmpl_array.push("</div>"),tmpl_array.push('<div class="groups_container table-responsive">'),tmpl_array.push("<% if(length === 0) { %>"),tmpl_array.push("<div>There are no groups yet.</div>"),tmpl_array.push("<% } else{ %>"),tmpl_array.push('<table class="grid table table-condensed">'),tmpl_array.push("   <thead>"),tmpl_array.push('     <th style="width:30%;"><a class="sort-groups-link" title="Click to reverse order" href="#">name</a> <span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>'),tmpl_array.push('     <th style="width:22%;">description</th>'),tmpl_array.push('     <th style="width:22%;">members</th> '),tmpl_array.push('     <th style="width:26%;">repositories</th>'),tmpl_array.push("   </thead>"),tmpl_array.push('   <tbody id="group_list_body">'),tmpl_array.push("   </tbody>"),tmpl_array.push("</table>"),tmpl_array.push("<% }%>"),tmpl_array.push("</div>"),_.template(tmpl_array.join(""))}});return{GroupListView:d}});
-//# sourceMappingURL=../../../maps/mvc/groups/group-list-view.js.map
\ No newline at end of file
diff --git a/static/scripts/mvc/groups/group.model.js b/static/scripts/mvc/groups/group.model.js
deleted file mode 100644
index b050bdad096..00000000000
--- a/static/scripts/mvc/groups/group.model.js
+++ /dev/null
@@ -1,2 +0,0 @@
-define([],function(){var a=Backbone.Model.extend({urlRoot:"/api/groups/"}),b=Backbone.Collection.extend({url:"/api/groups",model:a});return{Group:a,Groups:b}});
-//# sourceMappingURL=../../../maps/mvc/groups/group.model.js.map
\ No newline at end of file
diff --git a/static/scripts/toolshed.groups.js b/static/scripts/toolshed.groups.js
deleted file mode 100644
index 4c0663b9afb..00000000000
--- a/static/scripts/toolshed.groups.js
+++ /dev/null
@@ -1,2 +0,0 @@
-define(["mvc/groups/group-list-view","mvc/groups/group-detail-view","mvc/groups/group-model"],function(a,b){var c=Backbone.Router.extend({routes:{"":"groups",":group_id":"group_page"}}),d=Backbone.View.extend({groupListView:null,groupDetailView:null,collection:null,initialize:function(){window.globalTS.groups=this,this.ts_router=new c,this.ts_router.on("route:groups",function(){window.globalTS.groups.groupListView=new a.GroupListView}),this.ts_router.on("route:group_page",function(a){window.globalTS.groups.groupDetailView=new b.GroupDetailView({group_id:a})}),Backbone.history.start({pushState:!1})}});return{ToolshedGroups:d}});
-//# sourceMappingURL=../maps/toolshed.groups.js.map
\ No newline at end of file
diff --git a/static/toolshed/maps/mvc/groups/group-detail-view.js.map b/static/toolshed/maps/mvc/groups/group-detail-view.js.map
new file mode 100644
index 00000000000..9324e9d2023
--- /dev/null
+++ b/static/toolshed/maps/mvc/groups/group-detail-view.js.map
@@ -0,0 +1 @@
+{"version":3,"file":"group-detail-view.js","sources":["../../../src/mvc/groups/group-detail-view.js"],"names":["define","mod_toastr","mod_group_model","GroupDetailView","Backbone","View","extend","el","options","app","initialize","this","_","window","globalTS","groups","collection","model","get","group_id","render","fetchGroup","that","Group","id","fetch","success","console","log","error","response","responseJSON","err_msg","template","templateRow","$el","html","group","$","tooltip","join"],"mappings":"AAAAA,QACI,cACA,eAEJ,SACIC,EACAC,GAIJ,GAAIC,GAAkBC,SAASC,KAAKC,QAChCC,GAAI,kBACJC,WACAC,IAAK,KAELC,WAAa,SAAUF,GACnBG,KAAKH,QAAUI,EAAEN,OAAQK,KAAKH,QAASA,GACvCG,KAAKF,IAAMI,OAAOC,SAASC,OAEE,OAAxBJ,KAAKF,IAAIO,YACVL,KAAKM,MAAQN,KAAKF,IAAIO,WAAWE,IAAKP,KAAKH,QAAQW,UACnDR,KAAKS,UAELT,KAAKU,cAKbA,WAAY,SAAUb,GAClB,GAAIc,GAAOX,IACXA,MAAKH,QAAUI,EAAEN,OAAQK,KAAKH,QAASA,GACvCG,KAAKM,MAAQ,GAAIf,GAAgBqB,OAASC,GAAIb,KAAKH,QAAQW,WAC3DR,KAAKM,MAAMQ,OACTC,QAAS,SAAUT,GACjBU,QAAQC,IAAK,mBACbD,QAAQC,IAAKX,GACbK,EAAKF,UAEPS,MAAO,SAAUZ,EAAOa,GAElB7B,EAAW4B,MADyB,mBAA1BC,GAASC,aACDD,EAASC,aAAaC,QAEtB,yBAM9BZ,OAAQ,WACJ,GAAIa,GAAWtB,KAAKuB,aACpBvB,MAAKwB,IAAIC,KAAMH,GAAYI,MAAO1B,KAAKM,SACvCqB,EAAE,yBAAyBC,WAG/BL,YAAa,WACT,MAAOtB,GAAEqB,UACD,QACI,oCACA,mCACA,kMAEA,mBACA,6CACI,UACI,gBACA,wBACA,sBACJ,WACA,UACI,wDACA,OACI,OACI,yBACJ,QACA,OACI,gPACJ,QACA,OACI,6BACJ,QACJ,QACA,YACJ,WACJ,WAEA,wBACA,6CACI,UACI,gBACA,uBACA,qBACA,iBACA,mBACA,kBACA,oBACJ,WACA,UACI,2DACA,OACI,OACI,6KACJ,QACA,OACI,0BACJ,QACA,OACI,+BACJ,QACA,OACI,oBACJ,QACA,OACI,2BACJ,QACA,OACI,2BACJ,QACA,OACI,uBACJ,QACJ,QACA,YACJ,WACJ,WACJ,UACNO,KAAK,OAGf,QACIrC,gBAAiBA"}
\ No newline at end of file
diff --git a/static/toolshed/maps/mvc/groups/group-list-view.js.map b/static/toolshed/maps/mvc/groups/group-list-view.js.map
new file mode 100644
index 00000000000..f440744e057
--- /dev/null
+++ b/static/toolshed/maps/mvc/groups/group-list-view.js.map
@@ -0,0 +1 @@
+{"version":3,"file":"group-list-view.js","sources":["../../../src/mvc/groups/group-list-view.js"],"names":["define","mod_toastr","mod_group_model","mod_group_row","GroupListView","Backbone","View","extend","el","defaults","initialize","options","this","_","that","window","globalTS","groups","collection","Groups","fetch","success","model","console","log","render","error","response","responseJSON","err_msg","$","hide","template","templateGroupsList","$el","html","length","order","renderRows","models","tooltip","css","groups_to_render","i","group","renderOne","rowView","GroupListRowView","find","append","tmpl_array","push","join"],"mappings":"AAAAA,QACI,cACA,cACA,aAED,SACCC,EACAC,EACAC,GAGJ,GAAIC,GAAgBC,SAASC,KAAKC,QAC9BC,GAAI,kBACJC,YAOAC,WAAa,SAAUC,GACnBC,KAAKD,QAAUE,EAAEJ,SAAUG,KAAKD,YAAeC,KAAKH,SAAUE,EAC9D,IAAIG,GAAOF,IACXG,QAAOC,SAASC,OAAOC,WAAa,GAAIhB,GAAgBiB,OACxDJ,OAAOC,SAASC,OAAOC,WAAWE,OAChCC,QAAS,SAAUC,GACjBC,QAAQC,IAAK,mBACbD,QAAQC,IAAKF,GACbR,EAAKW,UAEPC,MAAO,SAAUJ,EAAOK,GAElB1B,EAAWyB,MADyB,mBAA1BC,GAASC,aACDD,EAASC,aAAaC,QAEtB,yBAO9BT,MAAO,aAMPK,OAAQ,SAAWd,GACfC,KAAKD,QAAUE,EAAEN,OAAQK,KAAKD,QAASA,GACvCmB,EAAG,YAAaC,MAChB,IAAIC,GAAWpB,KAAKqB,oBACpBrB,MAAKsB,IAAIC,KAAMH,GAAYI,OAAQ,GAAIC,MAAO,SAC9CzB,KAAK0B,WAAYvB,OAAOC,SAASC,OAAOC,WAAWqB,QACnDT,EAAG,yBAA0BU,UAC7BV,EAAG,WAAYW,IAAK,WAAW,SAOnCH,WAAY,SAAUI,GAClB,IAAM,GAAIC,GAAI,EAAGA,EAAID,EAAiBN,OAAQO,IAAM,CAChD,GAAIC,GAAQF,EAAiBC,EAC7B/B,MAAKiC,WAAaD,MAAOA,MAQjCC,UAAW,SAAUlC,GACjB,GAAImC,GAAU,GAAI3C,GAAc4C,iBAAkBpC,EAClDC,MAAKsB,IAAIc,KAAM,oBAAqBC,OAAQH,EAAQtC,KAyCxDyB,mBAAoB,WAuBhB,MAtBAiB,eAEAA,WAAWC,KAAK,qBAChBD,WAAWC,KAAK,UAChBD,WAAWC,KAAK,mDAChBD,WAAWC,KAAK,4BAChBD,WAAWC,KAAK,uCAChBD,WAAWC,KAAK,iBAChBD,WAAWC,KAAK,8CAChBD,WAAWC,KAAK,cAChBD,WAAWC,KAAK,mMAChBD,WAAWC,KAAK,gDAChBD,WAAWC,KAAK,6CAChBD,WAAWC,KAAK,iDAChBD,WAAWC,KAAK,eAChBD,WAAWC,KAAK,mCAEhBD,WAAWC,KAAK,eAChBD,WAAWC,KAAK,YAChBD,WAAWC,KAAK,UAChBD,WAAWC,KAAK,UAETtC,EAAEmB,SAASkB,WAAWE,KAAK,OAK1C,QACIhD,cAAeA"}
\ No newline at end of file
diff --git a/static/toolshed/maps/mvc/groups/group-listrow-view.js.map b/static/toolshed/maps/mvc/groups/group-listrow-view.js.map
new file mode 100644
index 00000000000..a3a50073eab
--- /dev/null
+++ b/static/toolshed/maps/mvc/groups/group-listrow-view.js.map
@@ -0,0 +1 @@
+{"version":3,"file":"group-listrow-view.js","sources":["../../../src/mvc/groups/group-listrow-view.js"],"names":["define","GroupListRowView","Backbone","View","extend","events","initialize","options","this","render","group","tmpl","templateRow","setElement","$el","show","_","template","join"],"mappings":"AAAAA,UACA,WAGA,GAAIC,GAAmBC,SAASC,KAAKC,QACjCC,UAEAC,WAAa,SAAUC,GACnBC,KAAKC,OAAQF,EAAQG,QAGzBD,OAAQ,SAAUC,GACd,GAAIC,GAAOH,KAAKI,aAGhB,OAFAJ,MAAKK,WAAWF,GAAQD,MAAMA,KAC9BF,KAAKM,IAAIC,OACFP,MAGXI,YAAa,WACT,MAAOI,GAAEC,UACD,iDACA,iFACA,uBACA,6CACA,2CACA,SACNC,KAAK,OAKf,QACIjB,iBAAkBA"}
\ No newline at end of file
diff --git a/static/toolshed/maps/mvc/groups/group-model.js.map b/static/toolshed/maps/mvc/groups/group-model.js.map
new file mode 100644
index 00000000000..7cf16222049
--- /dev/null
+++ b/static/toolshed/maps/mvc/groups/group-model.js.map
@@ -0,0 +1 @@
+{"version":3,"file":"group-model.js","sources":["../../../src/mvc/groups/group-model.js"],"names":["define","Group","Backbone","Model","extend","urlRoot","Groups","Collection","url","model"],"mappings":"AAAAA,UAAW,WAKP,GAAIC,GAAQC,SAASC,MAAMC,QACzBC,QAAS,gBAGPC,EAASJ,SAASK,WAAWH,QAC/BI,IAAK,cAELC,MAAOR,GAIb,QACIA,MAAOA,EACPK,OAAQA"}
\ No newline at end of file
diff --git a/static/toolshed/maps/test-file.js.map b/static/toolshed/maps/test-file.js.map
new file mode 100644
index 00000000000..60e635db925
--- /dev/null
+++ b/static/toolshed/maps/test-file.js.map
@@ -0,0 +1 @@
+{"version":3,"file":"test-file.js","sources":["../src/test-file.js"],"names":["define"],"mappings":"AAAAA,UAAY,WACX,MAAO"}
\ No newline at end of file
diff --git a/static/toolshed/maps/toolshed.groups.js.map b/static/toolshed/maps/toolshed.groups.js.map
new file mode 100644
index 00000000000..f8ba4759d22
--- /dev/null
+++ b/static/toolshed/maps/toolshed.groups.js.map
@@ -0,0 +1 @@
+{"version":3,"file":"toolshed.groups.js","sources":["../src/toolshed.groups.js"],"names":["define","mod_group_list","mod_group_detail","ToolshedRouter","Backbone","Router","extend","routes",":group_id","ToolshedGroups","View","groupListView","groupDetailView","collection","initialize","window","globalTS","groups","this","ts_router","on","GroupListView","group_id","GroupDetailView","history","start","pushState"],"mappings":"AAIAA,QACQ,aACA,eACA,eAEJ,SACIC,EACAC,GAMR,GAAIC,GAAiBC,SAASC,OAAOC,QACjCC,QACI,GAA4B,SAC5BC,YAA4B,gBAKhCC,EAAiBL,SAASM,KAAKJ,QAC/BK,cAAe,KACfC,gBAAiB,KACjBC,WAAY,KAEZC,WAAa,WACTC,OAAOC,SAASC,OAASC,KAEzBA,KAAKC,UAAY,GAAIhB,GACrBe,KAAKC,UAAUC,GAAI,eAAgB,WAC/BL,OAAOC,SAASC,OAAON,cAAgB,GAAIV,GAAeoB,gBAG9DH,KAAKC,UAAUC,GAAI,mBAAoB,SAAUE,GAC7CP,OAAOC,SAASC,OAAOL,gBAAkB,GAAIV,GAAiBqB,iBAAmBD,SAAUA,MAG/FlB,SAASoB,QAAQC,OAAOC,WAAW,MAI3C,QACIjB,eAAgBA"}
\ No newline at end of file
diff --git a/static/toolshed/scripts/mvc/groups/group-detail-view.js b/static/toolshed/scripts/mvc/groups/group-detail-view.js
new file mode 100644
index 00000000000..a4ecf8189a1
--- /dev/null
+++ b/static/toolshed/scripts/mvc/groups/group-detail-view.js
@@ -0,0 +1,2 @@
+define(["libs/toastr","group_model"],function(a,b){var c=Backbone.View.extend({el:"#groups_element",options:{},app:null,initialize:function(a){this.options=_.extend(this.options,a),this.app=window.globalTS.groups,null!==this.app.collection?(this.model=this.app.collection.get(this.options.group_id),this.render()):this.fetchGroup()},fetchGroup:function(c){var d=this;this.options=_.extend(this.options,c),this.model=new b.Group({id:this.options.group_id}),this.model.fetch({success:function(a){console.log("received data: "),console.log(a),d.render()},error:function(b,c){a.error("undefined"!=typeof c.responseJSON?c.responseJSON.err_msg:"An error ocurred.")}})},render:function(){var a=this.templateRow();this.$el.html(a({group:this.model})),$("#center [data-toggle]").tooltip()},templateRow:function(){return _.template(["<div>",'<h3><%= group.get("name") %></h3>','<p class="" style="color:gray;">','A group of <%= group.get("members").length %> members with <%= group.get("repositories").length %> repositories and a total of <%= group.get("total_downloads") %> combined tool downloads.</p>',"<h3>Members</h3>",'<table class="grid table table-condensed">',"<thead>","<th>Name</th>","<th>Repositories</th>","<th>Registered</th>","</thead>","<tbody>",'<% _.each(group.get("members"), function(member) { %>',"<tr>","<td>","<%= member.username %>","</td>","<td>",'<a data-toggle="tooltip" data-placement="top" title="Repositories of <%= member.username %>" href="/repository/browse_repositories_by_user?user_id=<%= member.id %>&use_panels=true" id="<%= member.id %>"><%= member.user_repos_count %></a>',"</td>","<td>","<%= member.time_created %>","</td>","</tr>","<% }); %>","</tbody>","</table>","<h3>Repositories</h3>",'<table class="grid table table-condensed">',"<thead>","<th>Name</th>","<th>Description</th>","<th>Downloads</th>","<th>Owner</th>","<th>Created</th>","<th>Rating</th>","<th>Verified</th>","</thead>","<tbody>",'<% _.each(group.get("repositories"), function(repo) { %>',"<tr>","<td>",'<a data-toggle="tooltip" data-placement="top" title="Details of <%= repo.name %>" href="/view/<%= repo.owner %>/<%= repo.name %>" id="<%= repo.id %>"><%= repo.name %></a>',"</td>","<td>","<%= repo.description %>","</td>","<td>","<%= repo.times_downloaded %>","</td>","<td>","<%= repo.owner %>","</td>","<td>","<%= repo.time_created %>","</td>","<td>","<%= repo.ratings_mean %>","</td>","<td>","<%= repo.approved %>","</td>","</tr>","<% }); %>","</tbody>","</table>","</div>"].join(""))}});return{GroupDetailView:c}});
+//# sourceMappingURL=../../../maps/mvc/groups/group-detail-view.js.map
\ No newline at end of file
diff --git a/static/toolshed/scripts/mvc/groups/group-list-view.js b/static/toolshed/scripts/mvc/groups/group-list-view.js
new file mode 100644
index 00000000000..2d6b5f0b477
--- /dev/null
+++ b/static/toolshed/scripts/mvc/groups/group-list-view.js
@@ -0,0 +1,2 @@
+define(["libs/toastr","group_model","group_row"],function(a,b,c){var d=Backbone.View.extend({el:"#groups_element",defaults:{},initialize:function(c){this.options=_.defaults(this.options||{},this.defaults,c);var d=this;window.globalTS.groups.collection=new b.Groups,window.globalTS.groups.collection.fetch({success:function(a){console.log("received data: "),console.log(a),d.render()},error:function(b,c){a.error("undefined"!=typeof c.responseJSON?c.responseJSON.err_msg:"An error ocurred.")}})},fetch:function(){},render:function(a){this.options=_.extend(this.options,a),$(".tooltip").hide();var b=this.templateGroupsList();this.$el.html(b({length:10,order:"asc"})),this.renderRows(window.globalTS.groups.collection.models),$("#center [data-toggle]").tooltip(),$("#center").css("overflow","auto")},renderRows:function(a){for(var b=0;b<a.length;b++){var c=a[b];this.renderOne({group:c})}},renderOne:function(a){var b=new c.GroupListRowView(a);this.$el.find("#group_list_body").append(b.el)},templateGroupsList:function(){return tmpl_array=[],tmpl_array.push('<div id="groups">'),tmpl_array.push("</div>"),tmpl_array.push('<div class="groups_container table-responsive">'),tmpl_array.push("<% if(length === 0) { %>"),tmpl_array.push("<div>There are no groups yet.</div>"),tmpl_array.push("<% } else{ %>"),tmpl_array.push('<table class="grid table table-condensed">'),tmpl_array.push("   <thead>"),tmpl_array.push('     <th style="width:30%;"><a class="sort-groups-link" title="Click to reverse order" href="#">name</a> <span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>'),tmpl_array.push('     <th style="width:22%;">description</th>'),tmpl_array.push('     <th style="width:22%;">members</th> '),tmpl_array.push('     <th style="width:26%;">repositories</th>'),tmpl_array.push("   </thead>"),tmpl_array.push('   <tbody id="group_list_body">'),tmpl_array.push("   </tbody>"),tmpl_array.push("</table>"),tmpl_array.push("<% }%>"),tmpl_array.push("</div>"),_.template(tmpl_array.join(""))}});return{GroupListView:d}});
+//# sourceMappingURL=../../../maps/mvc/groups/group-list-view.js.map
\ No newline at end of file
diff --git a/static/scripts/mvc/groups/group-listrow-view.js b/static/toolshed/scripts/mvc/groups/group-listrow-view.js
similarity index 100%
rename from static/scripts/mvc/groups/group-listrow-view.js
rename to static/toolshed/scripts/mvc/groups/group-listrow-view.js
diff --git a/static/scripts/mvc/groups/group-model.js b/static/toolshed/scripts/mvc/groups/group-model.js
similarity index 100%
rename from static/scripts/mvc/groups/group-model.js
rename to static/toolshed/scripts/mvc/groups/group-model.js
diff --git a/static/toolshed/scripts/test-file.js b/static/toolshed/scripts/test-file.js
new file mode 100644
index 00000000000..57532f0ce9d
--- /dev/null
+++ b/static/toolshed/scripts/test-file.js
@@ -0,0 +1,2 @@
+define([],function(){return"Remove this file"});
+//# sourceMappingURL=../maps/test-file.js.map
\ No newline at end of file
diff --git a/static/toolshed/scripts/toolshed.groups.js b/static/toolshed/scripts/toolshed.groups.js
new file mode 100644
index 00000000000..92f9e3f2f28
--- /dev/null
+++ b/static/toolshed/scripts/toolshed.groups.js
@@ -0,0 +1,2 @@
+define(["group_list","group_detail","group_model"],function(a,b){var c=Backbone.Router.extend({routes:{"":"groups",":group_id":"group_page"}}),d=Backbone.View.extend({groupListView:null,groupDetailView:null,collection:null,initialize:function(){window.globalTS.groups=this,this.ts_router=new c,this.ts_router.on("route:groups",function(){window.globalTS.groups.groupListView=new a.GroupListView}),this.ts_router.on("route:group_page",function(a){window.globalTS.groups.groupDetailView=new b.GroupDetailView({group_id:a})}),Backbone.history.start({pushState:!1})}});return{ToolshedGroups:d}});
+//# sourceMappingURL=../maps/toolshed.groups.js.map
\ No newline at end of file
diff --git a/templates/webapps/tool_shed/group/index.mako b/templates/webapps/tool_shed/group/index.mako
index e070faec5ee..f72eedb6e72 100644
--- a/templates/webapps/tool_shed/group/index.mako
+++ b/templates/webapps/tool_shed/group/index.mako
@@ -41,6 +41,14 @@
     <script type="text/javascript">
         window.globalTS = new Object();
         $( function(){
+            require.config({
+                paths: {
+                group_model: '../toolshed/scripts/mvc/groups/group-model',
+                group_row: '../toolshed/scripts/mvc/groups/group-listrow-view',
+                group_detail: '../toolshed/scripts/mvc/groups/group-detail-view',
+                group_list: '../toolshed/scripts/mvc/groups/group-list-view'
+            }
+            });
             require([ '${config.get( "app" ).get( "jscript" )}' ], function( groups ){
                 app = new groups.ToolshedGroups();
             });

From 6eddbf524b023115568cfbda7c396c9f54c1b798 Mon Sep 17 00:00:00 2001
From: Martin Cech <cech.marten@gmail.com>
Date: Mon, 15 Jun 2015 13:57:20 -0400
Subject: [PATCH 05/20] allow the js dependencies to use generalized path using
 requirejs paths to provide the relative prefix

---
 client/toolshed/scripts/mvc/groups/group-detail-view.js  | 2 +-
 client/toolshed/scripts/mvc/groups/group-list-view.js    | 4 ++--
 client/toolshed/scripts/toolshed.groups.js               | 6 +++---
 static/toolshed/maps/mvc/groups/group-detail-view.js.map | 2 +-
 static/toolshed/maps/mvc/groups/group-list-view.js.map   | 2 +-
 static/toolshed/maps/toolshed.groups.js.map              | 2 +-
 static/toolshed/scripts/mvc/groups/group-detail-view.js  | 2 +-
 static/toolshed/scripts/mvc/groups/group-list-view.js    | 2 +-
 static/toolshed/scripts/toolshed.groups.js               | 2 +-
 templates/webapps/tool_shed/group/index.mako             | 5 +----
 10 files changed, 13 insertions(+), 16 deletions(-)

diff --git a/client/toolshed/scripts/mvc/groups/group-detail-view.js b/client/toolshed/scripts/mvc/groups/group-detail-view.js
index f00454ac6fa..aa42e4bcaa5 100644
--- a/client/toolshed/scripts/mvc/groups/group-detail-view.js
+++ b/client/toolshed/scripts/mvc/groups/group-detail-view.js
@@ -1,6 +1,6 @@
 define([
     "libs/toastr",
-    "group_model"
+    "toolshed/scripts/mvc/groups/group-model"
     ],
 function(
     mod_toastr,
diff --git a/client/toolshed/scripts/mvc/groups/group-list-view.js b/client/toolshed/scripts/mvc/groups/group-list-view.js
index 82b912c8b13..a34f332f78a 100644
--- a/client/toolshed/scripts/mvc/groups/group-list-view.js
+++ b/client/toolshed/scripts/mvc/groups/group-list-view.js
@@ -1,7 +1,7 @@
 define([
     "libs/toastr",
-    "group_model",
-    "group_row"
+    "toolshed/scripts/mvc/groups/group-model",
+    "toolshed/scripts/mvc/groups/group-listrow-view"
 
 ], function(
     mod_toastr,
diff --git a/client/toolshed/scripts/toolshed.groups.js b/client/toolshed/scripts/toolshed.groups.js
index 4e02146a2fb..d4843e4979a 100644
--- a/client/toolshed/scripts/toolshed.groups.js
+++ b/client/toolshed/scripts/toolshed.groups.js
@@ -3,9 +3,9 @@
 // MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM
 
 define([
-        'group_list',
-        'group_detail',
-        'group_model'
+        'toolshed/scripts/mvc/groups/group-list-view',
+        'toolshed/scripts/mvc/groups/group-detail-view',
+        'toolshed/scripts/mvc/groups/group-model'
     ],
     function(
         mod_group_list,
diff --git a/static/toolshed/maps/mvc/groups/group-detail-view.js.map b/static/toolshed/maps/mvc/groups/group-detail-view.js.map
index 9324e9d2023..516498bde80 100644
--- a/static/toolshed/maps/mvc/groups/group-detail-view.js.map
+++ b/static/toolshed/maps/mvc/groups/group-detail-view.js.map
@@ -1 +1 @@
-{"version":3,"file":"group-detail-view.js","sources":["../../../src/mvc/groups/group-detail-view.js"],"names":["define","mod_toastr","mod_group_model","GroupDetailView","Backbone","View","extend","el","options","app","initialize","this","_","window","globalTS","groups","collection","model","get","group_id","render","fetchGroup","that","Group","id","fetch","success","console","log","error","response","responseJSON","err_msg","template","templateRow","$el","html","group","$","tooltip","join"],"mappings":"AAAAA,QACI,cACA,eAEJ,SACIC,EACAC,GAIJ,GAAIC,GAAkBC,SAASC,KAAKC,QAChCC,GAAI,kBACJC,WACAC,IAAK,KAELC,WAAa,SAAUF,GACnBG,KAAKH,QAAUI,EAAEN,OAAQK,KAAKH,QAASA,GACvCG,KAAKF,IAAMI,OAAOC,SAASC,OAEE,OAAxBJ,KAAKF,IAAIO,YACVL,KAAKM,MAAQN,KAAKF,IAAIO,WAAWE,IAAKP,KAAKH,QAAQW,UACnDR,KAAKS,UAELT,KAAKU,cAKbA,WAAY,SAAUb,GAClB,GAAIc,GAAOX,IACXA,MAAKH,QAAUI,EAAEN,OAAQK,KAAKH,QAASA,GACvCG,KAAKM,MAAQ,GAAIf,GAAgBqB,OAASC,GAAIb,KAAKH,QAAQW,WAC3DR,KAAKM,MAAMQ,OACTC,QAAS,SAAUT,GACjBU,QAAQC,IAAK,mBACbD,QAAQC,IAAKX,GACbK,EAAKF,UAEPS,MAAO,SAAUZ,EAAOa,GAElB7B,EAAW4B,MADyB,mBAA1BC,GAASC,aACDD,EAASC,aAAaC,QAEtB,yBAM9BZ,OAAQ,WACJ,GAAIa,GAAWtB,KAAKuB,aACpBvB,MAAKwB,IAAIC,KAAMH,GAAYI,MAAO1B,KAAKM,SACvCqB,EAAE,yBAAyBC,WAG/BL,YAAa,WACT,MAAOtB,GAAEqB,UACD,QACI,oCACA,mCACA,kMAEA,mBACA,6CACI,UACI,gBACA,wBACA,sBACJ,WACA,UACI,wDACA,OACI,OACI,yBACJ,QACA,OACI,gPACJ,QACA,OACI,6BACJ,QACJ,QACA,YACJ,WACJ,WAEA,wBACA,6CACI,UACI,gBACA,uBACA,qBACA,iBACA,mBACA,kBACA,oBACJ,WACA,UACI,2DACA,OACI,OACI,6KACJ,QACA,OACI,0BACJ,QACA,OACI,+BACJ,QACA,OACI,oBACJ,QACA,OACI,2BACJ,QACA,OACI,2BACJ,QACA,OACI,uBACJ,QACJ,QACA,YACJ,WACJ,WACJ,UACNO,KAAK,OAGf,QACIrC,gBAAiBA"}
\ No newline at end of file
+{"version":3,"file":"group-detail-view.js","sources":["../../../src/mvc/groups/group-detail-view.js"],"names":["define","mod_toastr","mod_group_model","GroupDetailView","Backbone","View","extend","el","options","app","initialize","this","_","window","globalTS","groups","collection","model","get","group_id","render","fetchGroup","that","Group","id","fetch","success","console","log","error","response","responseJSON","err_msg","template","templateRow","$el","html","group","$","tooltip","join"],"mappings":"AAAAA,QACI,cACA,2CAEJ,SACIC,EACAC,GAIJ,GAAIC,GAAkBC,SAASC,KAAKC,QAChCC,GAAI,kBACJC,WACAC,IAAK,KAELC,WAAa,SAAUF,GACnBG,KAAKH,QAAUI,EAAEN,OAAQK,KAAKH,QAASA,GACvCG,KAAKF,IAAMI,OAAOC,SAASC,OAEE,OAAxBJ,KAAKF,IAAIO,YACVL,KAAKM,MAAQN,KAAKF,IAAIO,WAAWE,IAAKP,KAAKH,QAAQW,UACnDR,KAAKS,UAELT,KAAKU,cAKbA,WAAY,SAAUb,GAClB,GAAIc,GAAOX,IACXA,MAAKH,QAAUI,EAAEN,OAAQK,KAAKH,QAASA,GACvCG,KAAKM,MAAQ,GAAIf,GAAgBqB,OAASC,GAAIb,KAAKH,QAAQW,WAC3DR,KAAKM,MAAMQ,OACTC,QAAS,SAAUT,GACjBU,QAAQC,IAAK,mBACbD,QAAQC,IAAKX,GACbK,EAAKF,UAEPS,MAAO,SAAUZ,EAAOa,GAElB7B,EAAW4B,MADyB,mBAA1BC,GAASC,aACDD,EAASC,aAAaC,QAEtB,yBAM9BZ,OAAQ,WACJ,GAAIa,GAAWtB,KAAKuB,aACpBvB,MAAKwB,IAAIC,KAAMH,GAAYI,MAAO1B,KAAKM,SACvCqB,EAAE,yBAAyBC,WAG/BL,YAAa,WACT,MAAOtB,GAAEqB,UACD,QACI,oCACA,mCACA,kMAEA,mBACA,6CACI,UACI,gBACA,wBACA,sBACJ,WACA,UACI,wDACA,OACI,OACI,yBACJ,QACA,OACI,gPACJ,QACA,OACI,6BACJ,QACJ,QACA,YACJ,WACJ,WAEA,wBACA,6CACI,UACI,gBACA,uBACA,qBACA,iBACA,mBACA,kBACA,oBACJ,WACA,UACI,2DACA,OACI,OACI,6KACJ,QACA,OACI,0BACJ,QACA,OACI,+BACJ,QACA,OACI,oBACJ,QACA,OACI,2BACJ,QACA,OACI,2BACJ,QACA,OACI,uBACJ,QACJ,QACA,YACJ,WACJ,WACJ,UACNO,KAAK,OAGf,QACIrC,gBAAiBA"}
\ No newline at end of file
diff --git a/static/toolshed/maps/mvc/groups/group-list-view.js.map b/static/toolshed/maps/mvc/groups/group-list-view.js.map
index f440744e057..2214b0b5952 100644
--- a/static/toolshed/maps/mvc/groups/group-list-view.js.map
+++ b/static/toolshed/maps/mvc/groups/group-list-view.js.map
@@ -1 +1 @@
-{"version":3,"file":"group-list-view.js","sources":["../../../src/mvc/groups/group-list-view.js"],"names":["define","mod_toastr","mod_group_model","mod_group_row","GroupListView","Backbone","View","extend","el","defaults","initialize","options","this","_","that","window","globalTS","groups","collection","Groups","fetch","success","model","console","log","render","error","response","responseJSON","err_msg","$","hide","template","templateGroupsList","$el","html","length","order","renderRows","models","tooltip","css","groups_to_render","i","group","renderOne","rowView","GroupListRowView","find","append","tmpl_array","push","join"],"mappings":"AAAAA,QACI,cACA,cACA,aAED,SACCC,EACAC,EACAC,GAGJ,GAAIC,GAAgBC,SAASC,KAAKC,QAC9BC,GAAI,kBACJC,YAOAC,WAAa,SAAUC,GACnBC,KAAKD,QAAUE,EAAEJ,SAAUG,KAAKD,YAAeC,KAAKH,SAAUE,EAC9D,IAAIG,GAAOF,IACXG,QAAOC,SAASC,OAAOC,WAAa,GAAIhB,GAAgBiB,OACxDJ,OAAOC,SAASC,OAAOC,WAAWE,OAChCC,QAAS,SAAUC,GACjBC,QAAQC,IAAK,mBACbD,QAAQC,IAAKF,GACbR,EAAKW,UAEPC,MAAO,SAAUJ,EAAOK,GAElB1B,EAAWyB,MADyB,mBAA1BC,GAASC,aACDD,EAASC,aAAaC,QAEtB,yBAO9BT,MAAO,aAMPK,OAAQ,SAAWd,GACfC,KAAKD,QAAUE,EAAEN,OAAQK,KAAKD,QAASA,GACvCmB,EAAG,YAAaC,MAChB,IAAIC,GAAWpB,KAAKqB,oBACpBrB,MAAKsB,IAAIC,KAAMH,GAAYI,OAAQ,GAAIC,MAAO,SAC9CzB,KAAK0B,WAAYvB,OAAOC,SAASC,OAAOC,WAAWqB,QACnDT,EAAG,yBAA0BU,UAC7BV,EAAG,WAAYW,IAAK,WAAW,SAOnCH,WAAY,SAAUI,GAClB,IAAM,GAAIC,GAAI,EAAGA,EAAID,EAAiBN,OAAQO,IAAM,CAChD,GAAIC,GAAQF,EAAiBC,EAC7B/B,MAAKiC,WAAaD,MAAOA,MAQjCC,UAAW,SAAUlC,GACjB,GAAImC,GAAU,GAAI3C,GAAc4C,iBAAkBpC,EAClDC,MAAKsB,IAAIc,KAAM,oBAAqBC,OAAQH,EAAQtC,KAyCxDyB,mBAAoB,WAuBhB,MAtBAiB,eAEAA,WAAWC,KAAK,qBAChBD,WAAWC,KAAK,UAChBD,WAAWC,KAAK,mDAChBD,WAAWC,KAAK,4BAChBD,WAAWC,KAAK,uCAChBD,WAAWC,KAAK,iBAChBD,WAAWC,KAAK,8CAChBD,WAAWC,KAAK,cAChBD,WAAWC,KAAK,mMAChBD,WAAWC,KAAK,gDAChBD,WAAWC,KAAK,6CAChBD,WAAWC,KAAK,iDAChBD,WAAWC,KAAK,eAChBD,WAAWC,KAAK,mCAEhBD,WAAWC,KAAK,eAChBD,WAAWC,KAAK,YAChBD,WAAWC,KAAK,UAChBD,WAAWC,KAAK,UAETtC,EAAEmB,SAASkB,WAAWE,KAAK,OAK1C,QACIhD,cAAeA"}
\ No newline at end of file
+{"version":3,"file":"group-list-view.js","sources":["../../../src/mvc/groups/group-list-view.js"],"names":["define","mod_toastr","mod_group_model","mod_group_row","GroupListView","Backbone","View","extend","el","defaults","initialize","options","this","_","that","window","globalTS","groups","collection","Groups","fetch","success","model","console","log","render","error","response","responseJSON","err_msg","$","hide","template","templateGroupsList","$el","html","length","order","renderRows","models","tooltip","css","groups_to_render","i","group","renderOne","rowView","GroupListRowView","find","append","tmpl_array","push","join"],"mappings":"AAAAA,QACI,cACA,0CACA,kDAED,SACCC,EACAC,EACAC,GAGJ,GAAIC,GAAgBC,SAASC,KAAKC,QAC9BC,GAAI,kBACJC,YAOAC,WAAa,SAAUC,GACnBC,KAAKD,QAAUE,EAAEJ,SAAUG,KAAKD,YAAeC,KAAKH,SAAUE,EAC9D,IAAIG,GAAOF,IACXG,QAAOC,SAASC,OAAOC,WAAa,GAAIhB,GAAgBiB,OACxDJ,OAAOC,SAASC,OAAOC,WAAWE,OAChCC,QAAS,SAAUC,GACjBC,QAAQC,IAAK,mBACbD,QAAQC,IAAKF,GACbR,EAAKW,UAEPC,MAAO,SAAUJ,EAAOK,GAElB1B,EAAWyB,MADyB,mBAA1BC,GAASC,aACDD,EAASC,aAAaC,QAEtB,yBAO9BT,MAAO,aAMPK,OAAQ,SAAWd,GACfC,KAAKD,QAAUE,EAAEN,OAAQK,KAAKD,QAASA,GACvCmB,EAAG,YAAaC,MAChB,IAAIC,GAAWpB,KAAKqB,oBACpBrB,MAAKsB,IAAIC,KAAMH,GAAYI,OAAQ,GAAIC,MAAO,SAC9CzB,KAAK0B,WAAYvB,OAAOC,SAASC,OAAOC,WAAWqB,QACnDT,EAAG,yBAA0BU,UAC7BV,EAAG,WAAYW,IAAK,WAAW,SAOnCH,WAAY,SAAUI,GAClB,IAAM,GAAIC,GAAI,EAAGA,EAAID,EAAiBN,OAAQO,IAAM,CAChD,GAAIC,GAAQF,EAAiBC,EAC7B/B,MAAKiC,WAAaD,MAAOA,MAQjCC,UAAW,SAAUlC,GACjB,GAAImC,GAAU,GAAI3C,GAAc4C,iBAAkBpC,EAClDC,MAAKsB,IAAIc,KAAM,oBAAqBC,OAAQH,EAAQtC,KAyCxDyB,mBAAoB,WAuBhB,MAtBAiB,eAEAA,WAAWC,KAAK,qBAChBD,WAAWC,KAAK,UAChBD,WAAWC,KAAK,mDAChBD,WAAWC,KAAK,4BAChBD,WAAWC,KAAK,uCAChBD,WAAWC,KAAK,iBAChBD,WAAWC,KAAK,8CAChBD,WAAWC,KAAK,cAChBD,WAAWC,KAAK,mMAChBD,WAAWC,KAAK,gDAChBD,WAAWC,KAAK,6CAChBD,WAAWC,KAAK,iDAChBD,WAAWC,KAAK,eAChBD,WAAWC,KAAK,mCAEhBD,WAAWC,KAAK,eAChBD,WAAWC,KAAK,YAChBD,WAAWC,KAAK,UAChBD,WAAWC,KAAK,UAETtC,EAAEmB,SAASkB,WAAWE,KAAK,OAK1C,QACIhD,cAAeA"}
\ No newline at end of file
diff --git a/static/toolshed/maps/toolshed.groups.js.map b/static/toolshed/maps/toolshed.groups.js.map
index f8ba4759d22..654c967d2c1 100644
--- a/static/toolshed/maps/toolshed.groups.js.map
+++ b/static/toolshed/maps/toolshed.groups.js.map
@@ -1 +1 @@
-{"version":3,"file":"toolshed.groups.js","sources":["../src/toolshed.groups.js"],"names":["define","mod_group_list","mod_group_detail","ToolshedRouter","Backbone","Router","extend","routes",":group_id","ToolshedGroups","View","groupListView","groupDetailView","collection","initialize","window","globalTS","groups","this","ts_router","on","GroupListView","group_id","GroupDetailView","history","start","pushState"],"mappings":"AAIAA,QACQ,aACA,eACA,eAEJ,SACIC,EACAC,GAMR,GAAIC,GAAiBC,SAASC,OAAOC,QACjCC,QACI,GAA4B,SAC5BC,YAA4B,gBAKhCC,EAAiBL,SAASM,KAAKJ,QAC/BK,cAAe,KACfC,gBAAiB,KACjBC,WAAY,KAEZC,WAAa,WACTC,OAAOC,SAASC,OAASC,KAEzBA,KAAKC,UAAY,GAAIhB,GACrBe,KAAKC,UAAUC,GAAI,eAAgB,WAC/BL,OAAOC,SAASC,OAAON,cAAgB,GAAIV,GAAeoB,gBAG9DH,KAAKC,UAAUC,GAAI,mBAAoB,SAAUE,GAC7CP,OAAOC,SAASC,OAAOL,gBAAkB,GAAIV,GAAiBqB,iBAAmBD,SAAUA,MAG/FlB,SAASoB,QAAQC,OAAOC,WAAW,MAI3C,QACIjB,eAAgBA"}
\ No newline at end of file
+{"version":3,"file":"toolshed.groups.js","sources":["../src/toolshed.groups.js"],"names":["define","mod_group_list","mod_group_detail","ToolshedRouter","Backbone","Router","extend","routes",":group_id","ToolshedGroups","View","groupListView","groupDetailView","collection","initialize","window","globalTS","groups","this","ts_router","on","GroupListView","group_id","GroupDetailView","history","start","pushState"],"mappings":"AAIAA,QACQ,8CACA,gDACA,2CAEJ,SACIC,EACAC,GAMR,GAAIC,GAAiBC,SAASC,OAAOC,QACjCC,QACI,GAA4B,SAC5BC,YAA4B,gBAKhCC,EAAiBL,SAASM,KAAKJ,QAC/BK,cAAe,KACfC,gBAAiB,KACjBC,WAAY,KAEZC,WAAa,WACTC,OAAOC,SAASC,OAASC,KAEzBA,KAAKC,UAAY,GAAIhB,GACrBe,KAAKC,UAAUC,GAAI,eAAgB,WAC/BL,OAAOC,SAASC,OAAON,cAAgB,GAAIV,GAAeoB,gBAG9DH,KAAKC,UAAUC,GAAI,mBAAoB,SAAUE,GAC7CP,OAAOC,SAASC,OAAOL,gBAAkB,GAAIV,GAAiBqB,iBAAmBD,SAAUA,MAG/FlB,SAASoB,QAAQC,OAAOC,WAAW,MAI3C,QACIjB,eAAgBA"}
\ No newline at end of file
diff --git a/static/toolshed/scripts/mvc/groups/group-detail-view.js b/static/toolshed/scripts/mvc/groups/group-detail-view.js
index a4ecf8189a1..92a188269c3 100644
--- a/static/toolshed/scripts/mvc/groups/group-detail-view.js
+++ b/static/toolshed/scripts/mvc/groups/group-detail-view.js
@@ -1,2 +1,2 @@
-define(["libs/toastr","group_model"],function(a,b){var c=Backbone.View.extend({el:"#groups_element",options:{},app:null,initialize:function(a){this.options=_.extend(this.options,a),this.app=window.globalTS.groups,null!==this.app.collection?(this.model=this.app.collection.get(this.options.group_id),this.render()):this.fetchGroup()},fetchGroup:function(c){var d=this;this.options=_.extend(this.options,c),this.model=new b.Group({id:this.options.group_id}),this.model.fetch({success:function(a){console.log("received data: "),console.log(a),d.render()},error:function(b,c){a.error("undefined"!=typeof c.responseJSON?c.responseJSON.err_msg:"An error ocurred.")}})},render:function(){var a=this.templateRow();this.$el.html(a({group:this.model})),$("#center [data-toggle]").tooltip()},templateRow:function(){return _.template(["<div>",'<h3><%= group.get("name") %></h3>','<p class="" style="color:gray;">','A group of <%= group.get("members").length %> members with <%= group.get("repositories").length %> repositories and a total of <%= group.get("total_downloads") %> combined tool downloads.</p>',"<h3>Members</h3>",'<table class="grid table table-condensed">',"<thead>","<th>Name</th>","<th>Repositories</th>","<th>Registered</th>","</thead>","<tbody>",'<% _.each(group.get("members"), function(member) { %>',"<tr>","<td>","<%= member.username %>","</td>","<td>",'<a data-toggle="tooltip" data-placement="top" title="Repositories of <%= member.username %>" href="/repository/browse_repositories_by_user?user_id=<%= member.id %>&use_panels=true" id="<%= member.id %>"><%= member.user_repos_count %></a>',"</td>","<td>","<%= member.time_created %>","</td>","</tr>","<% }); %>","</tbody>","</table>","<h3>Repositories</h3>",'<table class="grid table table-condensed">',"<thead>","<th>Name</th>","<th>Description</th>","<th>Downloads</th>","<th>Owner</th>","<th>Created</th>","<th>Rating</th>","<th>Verified</th>","</thead>","<tbody>",'<% _.each(group.get("repositories"), function(repo) { %>',"<tr>","<td>",'<a data-toggle="tooltip" data-placement="top" title="Details of <%= repo.name %>" href="/view/<%= repo.owner %>/<%= repo.name %>" id="<%= repo.id %>"><%= repo.name %></a>',"</td>","<td>","<%= repo.description %>","</td>","<td>","<%= repo.times_downloaded %>","</td>","<td>","<%= repo.owner %>","</td>","<td>","<%= repo.time_created %>","</td>","<td>","<%= repo.ratings_mean %>","</td>","<td>","<%= repo.approved %>","</td>","</tr>","<% }); %>","</tbody>","</table>","</div>"].join(""))}});return{GroupDetailView:c}});
+define(["libs/toastr","toolshed/scripts/mvc/groups/group-model"],function(a,b){var c=Backbone.View.extend({el:"#groups_element",options:{},app:null,initialize:function(a){this.options=_.extend(this.options,a),this.app=window.globalTS.groups,null!==this.app.collection?(this.model=this.app.collection.get(this.options.group_id),this.render()):this.fetchGroup()},fetchGroup:function(c){var d=this;this.options=_.extend(this.options,c),this.model=new b.Group({id:this.options.group_id}),this.model.fetch({success:function(a){console.log("received data: "),console.log(a),d.render()},error:function(b,c){a.error("undefined"!=typeof c.responseJSON?c.responseJSON.err_msg:"An error ocurred.")}})},render:function(){var a=this.templateRow();this.$el.html(a({group:this.model})),$("#center [data-toggle]").tooltip()},templateRow:function(){return _.template(["<div>",'<h3><%= group.get("name") %></h3>','<p class="" style="color:gray;">','A group of <%= group.get("members").length %> members with <%= group.get("repositories").length %> repositories and a total of <%= group.get("total_downloads") %> combined tool downloads.</p>',"<h3>Members</h3>",'<table class="grid table table-condensed">',"<thead>","<th>Name</th>","<th>Repositories</th>","<th>Registered</th>","</thead>","<tbody>",'<% _.each(group.get("members"), function(member) { %>',"<tr>","<td>","<%= member.username %>","</td>","<td>",'<a data-toggle="tooltip" data-placement="top" title="Repositories of <%= member.username %>" href="/repository/browse_repositories_by_user?user_id=<%= member.id %>&use_panels=true" id="<%= member.id %>"><%= member.user_repos_count %></a>',"</td>","<td>","<%= member.time_created %>","</td>","</tr>","<% }); %>","</tbody>","</table>","<h3>Repositories</h3>",'<table class="grid table table-condensed">',"<thead>","<th>Name</th>","<th>Description</th>","<th>Downloads</th>","<th>Owner</th>","<th>Created</th>","<th>Rating</th>","<th>Verified</th>","</thead>","<tbody>",'<% _.each(group.get("repositories"), function(repo) { %>',"<tr>","<td>",'<a data-toggle="tooltip" data-placement="top" title="Details of <%= repo.name %>" href="/view/<%= repo.owner %>/<%= repo.name %>" id="<%= repo.id %>"><%= repo.name %></a>',"</td>","<td>","<%= repo.description %>","</td>","<td>","<%= repo.times_downloaded %>","</td>","<td>","<%= repo.owner %>","</td>","<td>","<%= repo.time_created %>","</td>","<td>","<%= repo.ratings_mean %>","</td>","<td>","<%= repo.approved %>","</td>","</tr>","<% }); %>","</tbody>","</table>","</div>"].join(""))}});return{GroupDetailView:c}});
 //# sourceMappingURL=../../../maps/mvc/groups/group-detail-view.js.map
\ No newline at end of file
diff --git a/static/toolshed/scripts/mvc/groups/group-list-view.js b/static/toolshed/scripts/mvc/groups/group-list-view.js
index 2d6b5f0b477..f956c996d92 100644
--- a/static/toolshed/scripts/mvc/groups/group-list-view.js
+++ b/static/toolshed/scripts/mvc/groups/group-list-view.js
@@ -1,2 +1,2 @@
-define(["libs/toastr","group_model","group_row"],function(a,b,c){var d=Backbone.View.extend({el:"#groups_element",defaults:{},initialize:function(c){this.options=_.defaults(this.options||{},this.defaults,c);var d=this;window.globalTS.groups.collection=new b.Groups,window.globalTS.groups.collection.fetch({success:function(a){console.log("received data: "),console.log(a),d.render()},error:function(b,c){a.error("undefined"!=typeof c.responseJSON?c.responseJSON.err_msg:"An error ocurred.")}})},fetch:function(){},render:function(a){this.options=_.extend(this.options,a),$(".tooltip").hide();var b=this.templateGroupsList();this.$el.html(b({length:10,order:"asc"})),this.renderRows(window.globalTS.groups.collection.models),$("#center [data-toggle]").tooltip(),$("#center").css("overflow","auto")},renderRows:function(a){for(var b=0;b<a.length;b++){var c=a[b];this.renderOne({group:c})}},renderOne:function(a){var b=new c.GroupListRowView(a);this.$el.find("#group_list_body").append(b.el)},templateGroupsList:function(){return tmpl_array=[],tmpl_array.push('<div id="groups">'),tmpl_array.push("</div>"),tmpl_array.push('<div class="groups_container table-responsive">'),tmpl_array.push("<% if(length === 0) { %>"),tmpl_array.push("<div>There are no groups yet.</div>"),tmpl_array.push("<% } else{ %>"),tmpl_array.push('<table class="grid table table-condensed">'),tmpl_array.push("   <thead>"),tmpl_array.push('     <th style="width:30%;"><a class="sort-groups-link" title="Click to reverse order" href="#">name</a> <span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>'),tmpl_array.push('     <th style="width:22%;">description</th>'),tmpl_array.push('     <th style="width:22%;">members</th> '),tmpl_array.push('     <th style="width:26%;">repositories</th>'),tmpl_array.push("   </thead>"),tmpl_array.push('   <tbody id="group_list_body">'),tmpl_array.push("   </tbody>"),tmpl_array.push("</table>"),tmpl_array.push("<% }%>"),tmpl_array.push("</div>"),_.template(tmpl_array.join(""))}});return{GroupListView:d}});
+define(["libs/toastr","toolshed/scripts/mvc/groups/group-model","toolshed/scripts/mvc/groups/group-listrow-view"],function(a,b,c){var d=Backbone.View.extend({el:"#groups_element",defaults:{},initialize:function(c){this.options=_.defaults(this.options||{},this.defaults,c);var d=this;window.globalTS.groups.collection=new b.Groups,window.globalTS.groups.collection.fetch({success:function(a){console.log("received data: "),console.log(a),d.render()},error:function(b,c){a.error("undefined"!=typeof c.responseJSON?c.responseJSON.err_msg:"An error ocurred.")}})},fetch:function(){},render:function(a){this.options=_.extend(this.options,a),$(".tooltip").hide();var b=this.templateGroupsList();this.$el.html(b({length:10,order:"asc"})),this.renderRows(window.globalTS.groups.collection.models),$("#center [data-toggle]").tooltip(),$("#center").css("overflow","auto")},renderRows:function(a){for(var b=0;b<a.length;b++){var c=a[b];this.renderOne({group:c})}},renderOne:function(a){var b=new c.GroupListRowView(a);this.$el.find("#group_list_body").append(b.el)},templateGroupsList:function(){return tmpl_array=[],tmpl_array.push('<div id="groups">'),tmpl_array.push("</div>"),tmpl_array.push('<div class="groups_container table-responsive">'),tmpl_array.push("<% if(length === 0) { %>"),tmpl_array.push("<div>There are no groups yet.</div>"),tmpl_array.push("<% } else{ %>"),tmpl_array.push('<table class="grid table table-condensed">'),tmpl_array.push("   <thead>"),tmpl_array.push('     <th style="width:30%;"><a class="sort-groups-link" title="Click to reverse order" href="#">name</a> <span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>'),tmpl_array.push('     <th style="width:22%;">description</th>'),tmpl_array.push('     <th style="width:22%;">members</th> '),tmpl_array.push('     <th style="width:26%;">repositories</th>'),tmpl_array.push("   </thead>"),tmpl_array.push('   <tbody id="group_list_body">'),tmpl_array.push("   </tbody>"),tmpl_array.push("</table>"),tmpl_array.push("<% }%>"),tmpl_array.push("</div>"),_.template(tmpl_array.join(""))}});return{GroupListView:d}});
 //# sourceMappingURL=../../../maps/mvc/groups/group-list-view.js.map
\ No newline at end of file
diff --git a/static/toolshed/scripts/toolshed.groups.js b/static/toolshed/scripts/toolshed.groups.js
index 92f9e3f2f28..87de050425f 100644
--- a/static/toolshed/scripts/toolshed.groups.js
+++ b/static/toolshed/scripts/toolshed.groups.js
@@ -1,2 +1,2 @@
-define(["group_list","group_detail","group_model"],function(a,b){var c=Backbone.Router.extend({routes:{"":"groups",":group_id":"group_page"}}),d=Backbone.View.extend({groupListView:null,groupDetailView:null,collection:null,initialize:function(){window.globalTS.groups=this,this.ts_router=new c,this.ts_router.on("route:groups",function(){window.globalTS.groups.groupListView=new a.GroupListView}),this.ts_router.on("route:group_page",function(a){window.globalTS.groups.groupDetailView=new b.GroupDetailView({group_id:a})}),Backbone.history.start({pushState:!1})}});return{ToolshedGroups:d}});
+define(["toolshed/scripts/mvc/groups/group-list-view","toolshed/scripts/mvc/groups/group-detail-view","toolshed/scripts/mvc/groups/group-model"],function(a,b){var c=Backbone.Router.extend({routes:{"":"groups",":group_id":"group_page"}}),d=Backbone.View.extend({groupListView:null,groupDetailView:null,collection:null,initialize:function(){window.globalTS.groups=this,this.ts_router=new c,this.ts_router.on("route:groups",function(){window.globalTS.groups.groupListView=new a.GroupListView}),this.ts_router.on("route:group_page",function(a){window.globalTS.groups.groupDetailView=new b.GroupDetailView({group_id:a})}),Backbone.history.start({pushState:!1})}});return{ToolshedGroups:d}});
 //# sourceMappingURL=../maps/toolshed.groups.js.map
\ No newline at end of file
diff --git a/templates/webapps/tool_shed/group/index.mako b/templates/webapps/tool_shed/group/index.mako
index f72eedb6e72..297c16fda8d 100644
--- a/templates/webapps/tool_shed/group/index.mako
+++ b/templates/webapps/tool_shed/group/index.mako
@@ -43,10 +43,7 @@
         $( function(){
             require.config({
                 paths: {
-                group_model: '../toolshed/scripts/mvc/groups/group-model',
-                group_row: '../toolshed/scripts/mvc/groups/group-listrow-view',
-                group_detail: '../toolshed/scripts/mvc/groups/group-detail-view',
-                group_list: '../toolshed/scripts/mvc/groups/group-list-view'
+                    'toolshed': '../toolshed'
             }
             });
             require([ '${config.get( "app" ).get( "jscript" )}' ], function( groups ){

From 8e3bb7029c4e0aa2f21e08064f87a8ea9efad67f Mon Sep 17 00:00:00 2001
From: James Taylor <james@jamestaylor.org>
Date: Mon, 15 Jun 2015 14:24:12 -0400
Subject: [PATCH 06/20] Add list of contributors

---
 CONTRIBUTORS.md | 128 ++++++++++++++++++++++++++++++++++++++++++++++++
 LICENSE.txt     |   2 +-
 2 files changed, 129 insertions(+), 1 deletion(-)
 create mode 100644 CONTRIBUTORS.md

diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md
new file mode 100644
index 00000000000..47d02386267
--- /dev/null
+++ b/CONTRIBUTORS.md
@@ -0,0 +1,128 @@
+# Contributors
+
+The following individuals have contributed code to Galaxy:
+
+* Enis Afgan <afgane@gmail.com>
+* Istvan Albert <istvan.albert@gmail.com>
+* Renato Alves <alves.rjc@gmail.com> <rjalves@igc.gulbenkian.pt>
+* Guruprasad Anada <gua110@bx.psu.edu>
+* Florent Angly <florent.angly@gmail.com>
+* Raj Ayyampalayam <raj76@uga.edu>
+* Finn Bacall <finn.bacall@cs.man.ac.uk>
+* Dannon Baker <dannon.baker@gmail.com>
+* Christopher Bare <christopherbare@gmail.com>
+* Dan Blanchard <dan.blanchard@gmail.com>
+* Daniel Blankenberg <dan.blankenberg@gmail.com> <dan@bx.psu.edu>
+* James Boocock <sfk2001@gmail.com>
+* Carlos Borroto <carlos.borroto@gmail.com>
+* Daniel Bouchard <dbouchard@corefacility.ca> <daniel.bouchard@phac-aspc.gc.ca>
+* Dave Bouvier <dave@bx.psu.edu>
+* Adam Brenner <aebrenne@uci.edu>
+* Anthony Bretaudeau <anthony.bretaudeau@rennes.inra.fr> <abretaud@irisa.fr>
+* Richard Burhans <burhans@bx.psu.edu>
+* Jennifer Cabral <jencabral@gmail.com>
+* Martin Cech <cech.marten@gmail.com> <emulatorer@gmail.com>
+* Ramkrishna Chakrabarty <rc@bx.psu.edu>
+* Brad Chapman <chapmanb@50mail.com>
+* John Chilton <jmchilton@gmail.com>
+* Saket Choudhary <saketkc@gmail.com>
+* Wen-Yu Chung <wychung@bx.psu.edu>
+* Dave Clements <clements@galaxyproject.org>
+* Peter Cock <p.j.a.cock@googlemail.com>
+* Ira Cooke <iracooke@gmail.com>
+* Nate Coraor <nate@bx.psu.edu>
+* Michael Cotterell <mepcotterell@gmail.com>
+* Gianmauro Cuccuru <gmauro@crs4.it>
+* Frederik Delaere <frederik.delaere@gmail.com>
+* Olivia Doppelt <olivia.doppelt@pasteur.fr>
+* John Duddy <jduddy@illumina.com>
+* Carl Eberhard <carlfeberhard@gmail.com>
+* Kyle Ellrott <kellrott@gmail.com> <kellrott@soe.ucsc.edu>
+* Eric Enns <eric.enns@gmail.com>
+* Dorine Francheteau <dorine@bx.psu.edu>
+* Jaime Frey <jfrey@cs.wisc.edu>
+* Carie Genote <cganote@iu.edu>
+* Jeremy Goecks <jeremy.goecks@emory.edu> <jgoecks@gwu.edu>
+* Nuwan Goonasekera <nuwan.goonasekera@gmail.com>
+* Björn Grüning <bjoern.gruening@gmail.com> <bjoern@gruenings.eu>
+* Aysam Guerler <aysam.guerler@gmail.com>
+* Simon Guest <simon.guest@agresearch.co.nz>
+* Jianbin He <jbhe@bx.psu.edu>
+* Morita Hideyuki <h-morita@esm.co.jp>
+* Rob Hooft <rob.hooft@nbic.nl>
+* Y. Hoogstrate <y.hoogstrate@erasmusmc.nl>
+* Jian-Long Huang <jlh@pyhub.org>
+* Gert Hulselmans <gert.hulselmans@med.kuleuven.be>
+* Jennifer Jackson <jen@bx.psu.edu>
+* Joachim Jacob <joachim.jacob@gmail.com>
+* Jim Johnson <jj@umn.edu> <jj@msi.umn.edu>
+* Radhesh Kamath <radhesh@bx.psu.edu>
+* Jan Kanis <jan.code@jankanis.nl>
+* David King <dcking@bx.psu.edu>
+* Rory Kirchner <roryk@mit.edu>
+* Brad Langhorst <langhorst@neb.com>
+* Ross Lazarus <ross.lazarus@gmail.com> <rossl@bx.psu.edu>
+* Simone Leo <simone.leo@gmail.com>
+* Kanwei Li <kanwei@gmail.com>
+* Michael Li <michael.li@uwaterloo.ca>
+* Philip Mabon <philipmabon@gmail.com>
+* Remi Marenco <remi.marenco@gmail.com> <remimarenco@gmail.com>
+* Thomas McGowan <mcgo0092@msi.umn.edu>
+* Scott McManus <scottmcmanus@emory.edu> <scottmcmanus@gatech.edu>
+* Hunter Moseley <hunter.moseley@louisville.edu>
+* Arjun Nath <arjun@bx.psu.edu>
+* Anton Nekrutenko <anton@bx.psu.edu> <anton@nekrut.org>
+* Eric Paniagua <paniagua.cshl@gmail.com>
+* Richard Park <rpark@bu.edu>
+* Lance Parsons <lparsons@princeton.edu>
+* Chinmay Rao <chinmay@bx.psu.edu>
+* Eric Rasche <esr@tamu.edu> <rasche.eric@gmail.com> <rasche.eric@yandex.ru>
+* Andrew Robinson <Andrew.Robinson@latrobe.edu.au>
+* Andrea Sbardellati <andrea.sbardellati@crs4.it>
+* Ian Schenck <ian@bx.psu.edu>
+* Nick Semenkovich <semenko@alum.mit.edu>
+* Matthew Shirley <mdshw5@gmail.com>
+* Clare Sloggett <sloc@unimelb.edu.au>
+* Nicola Soranzo <nicola.soranzo@tgac.ac.uk> <nsoranzo@tiscali.it> <soranzo@crs4.it>
+* Roy Storey <kiwiroy@gmail.com>
+* Hanfei Sun <ad9075@gmail.com>
+* Ilya Sytchev <hackdna@gmail.com>
+* James Taylor <james@jamestaylor.org>
+* Tomithy Too <tomithy.too@gmail.com>
+* David Trudgian <dave@trudgian.net> <david.trudgian@utsouthwestern.edu>
+* Nitesh Turaga <nitesh.turaga@gmail.com>
+* Clayton Turner <clayclay911@gmail.com>
+* Marek Vavruša <marek@vavrusa.com>
+* Martijn Vermaat <m.vermaat.hg@lumc.nl>
+* Kelly Vincent <kpvincent@bx.psu.edu>
+* Greg Von Kuster <greg@bx.psu.edu>
+* Hiral Vora <hvora1@uncc.edu>
+* Andrew Warren <anwarren@vbi.vt.edu>
+* Trevor Wennblom <trevor@well.com>
+* Yi Zhang <yizhang@bx.psu.edu>
+* Freek de Bruijn <freek.de.bruijn@nbic.nl>
+* Peter van Heusden <pvh@sanbi.ac.za>
+* Marius van den Beek <m.vandenbeek@gmail.com>
+
+# Institutional sponsors
+
+Galaxy development began at The Pennsylvania State University in 2006.
+In 2009 all contributions to that point were licensed by Penn State
+under the terms of the Academic Free License 3.0 (see LICENSE.txt). This
+license applies to all subsequent contributions as well.  Significant
+portions of Galaxy development have continued at Penn State, Emory
+University, Johns Hopkins University, and George Washington University
+with support from the following NIH and NSF grants:
+
+* NSF DBI 0543285, “Tailoring genomic data to the needs of experimental
+  biologists and educators”
+* NIH R21 HG005133, “A turnkey solution for next generation sequence
+  data analysis”
+* NIH R01 HG004909, “An efficient lightweight environment for biomedical
+  computation”
+* NSF DBI 0850103, “Cyberinfrastructure for accessible and reproducible
+  research in life sciences”
+* NIH RC2 HG005542, “Dynamically scalable accessible analysis for next
+  generation sequence data”
+* NIH U41 HG006620, “Democratization of data analysis in life sciences
+  through Galaxy”
diff --git a/LICENSE.txt b/LICENSE.txt
index ee1e8c0c716..b9664cb17c2 100644
--- a/LICENSE.txt
+++ b/LICENSE.txt
@@ -1,4 +1,4 @@
-Copyright (c) 2005-2013 Pennsylvania State University
+Copyright (c) 2005-2015 Galaxy Contributors (see CONTRIBUTORS.md)
 
 Licensed under the Academic Free License version 3.0
 

From 14ae88251eb20d26759f4d7a9b51e2c439f8e76b Mon Sep 17 00:00:00 2001
From: Martin Cech <cech.marten@gmail.com>
Date: Mon, 15 Jun 2015 14:41:08 -0400
Subject: [PATCH 07/20] update my contact

---
 CONTRIBUTORS.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md
index 47d02386267..11f78465081 100644
--- a/CONTRIBUTORS.md
+++ b/CONTRIBUTORS.md
@@ -21,7 +21,7 @@ The following individuals have contributed code to Galaxy:
 * Anthony Bretaudeau <anthony.bretaudeau@rennes.inra.fr> <abretaud@irisa.fr>
 * Richard Burhans <burhans@bx.psu.edu>
 * Jennifer Cabral <jencabral@gmail.com>
-* Martin Cech <cech.marten@gmail.com> <emulatorer@gmail.com>
+* Martin Čech <marten@bx.psu.edu>
 * Ramkrishna Chakrabarty <rc@bx.psu.edu>
 * Brad Chapman <chapmanb@50mail.com>
 * John Chilton <jmchilton@gmail.com>

From aa2a7c9fb3e5a4830720b6f13f1fe705ff5c93e0 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <ghv2@psu.edu>
Date: Mon, 15 Jun 2015 14:46:36 -0400
Subject: [PATCH 08/20] Added @nsoranzo's simplified validation logic.

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

diff --git a/lib/galaxy/tools/parameters/validation.py b/lib/galaxy/tools/parameters/validation.py
index 13647e3db22..4f685e42a60 100644
--- a/lib/galaxy/tools/parameters/validation.py
+++ b/lib/galaxy/tools/parameters/validation.py
@@ -156,17 +156,17 @@ class InRangeValidator( Validator ):
         self.message = message or "Value must be %s %s and %s %s" % ( op1, self_min_str, op2, self_max_str )
 
     def validate( self, value, history=None ):
-        if self.strict_min and self.strict_max:
-            if not( self.min < float( value ) < self.max ):
+        if self.strict_min:
+            if not self.min < float( value ):
                 raise ValueError( self.message )
-        elif self.strict_min and not self.strict_max:
-            if not( self.min < float( value ) <= self.max ):
+        else:
+            if not self.min <= float( value ):
                 raise ValueError( self.message )
-        elif not self.strict_min and self.strict_max:
-            if not( self.min <= float( value ) < self.max ):
+        if self.strict_max:
+            if not float( value ) < self.max:
                 raise ValueError( self.message )
-        elif not self.strict_min and not self.strict_max:
-            if not( self.min <= float( value ) <= self.max ):
+        else:
+            if not float( value ) <= self.max:
                 raise ValueError( self.message )
 
 

From 0c69c5b92f3461559133b57637006d9614752eec Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 15 Jun 2015 14:58:20 -0400
Subject: [PATCH 09/20] Add parenthesis to argument name search

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

diff --git a/client/galaxy/scripts/mvc/form/form-input.js b/client/galaxy/scripts/mvc/form/form-input.js
index 7cbf3f91c45..fd51ceaae10 100644
--- a/client/galaxy/scripts/mvc/form/form-input.js
+++ b/client/galaxy/scripts/mvc/form/form-input.js
@@ -124,7 +124,7 @@ define([], function() {
             tmp +=              '<div class="ui-table-form-info">';
             if (options.help) {
                 tmp +=              options.help;
-                if (options.argument && options.help.indexOf(options.argument) == -1) {
+                if (options.argument && options.help.indexOf('(' + options.argument + ')') == -1) {
                     tmp += ' (' + options.argument + ')';
                 }
             }
diff --git a/static/maps/mvc/form/form-input.js.map b/static/maps/mvc/form/form-input.js.map
index bb5a13f8723..a7c7c96b5f6 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","collapsed","collapsible","value","JSON","stringify","collapsible_value","_refresh","self","on","trigger","error","text","html","show","addClass","reset","hide","removeClass","_tooltip","fadeIn","title","cls","length","tooltip","placement","attr","tmp","label","help","argument","indexOf"],"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,4BAChDH,KAAKI,YAAiBN,EAAIC,QAAQK,aAAe,0BAGjDJ,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,UAAalB,EAAQmB,aAAenB,EAAQoB,OAC/BC,KAAKC,UAAUtB,EAAQoB,QAAUC,KAAKC,UAAUtB,EAAQuB,mBAGhFtB,KAAKuB,UAGL,IAAIC,GAAOxB,IACXA,MAAKY,UAAUa,GAAG,QAAS,WAEvBD,EAAKnB,MAAMY,WAAaO,EAAKnB,MAAMY,UAGnCO,EAAKD,WAGLC,EAAK1B,IAAI4B,QAAQ,aAMzBC,MAAO,SAASC,GACZ5B,KAAKc,YAAYe,KAAKD,GACtB5B,KAAKe,OAAOe,OACZ9B,KAAKU,IAAIqB,SAAS,aAKtBC,MAAO,WACHhC,KAAKe,OAAOkB,OACZjC,KAAKU,IAAIwB,YAAY,aAKzBX,SAAU,WAENvB,KAAKa,eAAeqB,cAAcH,SAAS,QAGtC/B,KAAKK,MAAMY,WAOZjB,KAAKS,OAAOwB,OACZjC,KAAKmC,SAASnC,KAAKC,YAAaD,KAAKG,YACrCH,KAAKK,MAAMc,OAASnB,KAAKK,MAAMc,MAAMnB,KAAKM,iBAP1CN,KAAKS,OAAO2B,OAAO,QACnBpC,KAAKmC,SAASnC,KAAKE,aAAcF,KAAKI,aACtCJ,KAAKF,IAAI4B,QAAQ,YAWzBS,SAAU,SAASE,EAAOC,GAClBtC,KAAKY,UAAU2B,QACfvC,KAAKa,eAAekB,SAASO,GACTE,SAAUC,UAAW,WACrBC,KAAK,sBAAuBL,GAC5BG,QAAQ,YAAYA,QAAQ,SAMxDhC,UAAW,SAAST,GAEhB,GAAI4C,GAAQ,8LAkCZ,OA1BIA,IADA5C,EAAQmB,YACQ,wDAC0BnB,EAAQ6C,MAClC,SAET7C,EAAQ6C,MAInBD,GAAgB,0CAIhBA,GAAoB,mCAChB5C,EAAQ8C,OACRF,GAAoB5C,EAAQ8C,KACxB9C,EAAQ+C,UAAsD,IAA1C/C,EAAQ8C,KAAKE,QAAQhD,EAAQ+C,YACjDH,GAAO,KAAO5C,EAAQ+C,SAAW,MAGzCH,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","collapsed","collapsible","value","JSON","stringify","collapsible_value","_refresh","self","on","trigger","error","text","html","show","addClass","reset","hide","removeClass","_tooltip","fadeIn","title","cls","length","tooltip","placement","attr","tmp","label","help","argument","indexOf"],"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,4BAChDH,KAAKI,YAAiBN,EAAIC,QAAQK,aAAe,0BAGjDJ,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,UAAalB,EAAQmB,aAAenB,EAAQoB,OAC/BC,KAAKC,UAAUtB,EAAQoB,QAAUC,KAAKC,UAAUtB,EAAQuB,mBAGhFtB,KAAKuB,UAGL,IAAIC,GAAOxB,IACXA,MAAKY,UAAUa,GAAG,QAAS,WAEvBD,EAAKnB,MAAMY,WAAaO,EAAKnB,MAAMY,UAGnCO,EAAKD,WAGLC,EAAK1B,IAAI4B,QAAQ,aAMzBC,MAAO,SAASC,GACZ5B,KAAKc,YAAYe,KAAKD,GACtB5B,KAAKe,OAAOe,OACZ9B,KAAKU,IAAIqB,SAAS,aAKtBC,MAAO,WACHhC,KAAKe,OAAOkB,OACZjC,KAAKU,IAAIwB,YAAY,aAKzBX,SAAU,WAENvB,KAAKa,eAAeqB,cAAcH,SAAS,QAGtC/B,KAAKK,MAAMY,WAOZjB,KAAKS,OAAOwB,OACZjC,KAAKmC,SAASnC,KAAKC,YAAaD,KAAKG,YACrCH,KAAKK,MAAMc,OAASnB,KAAKK,MAAMc,MAAMnB,KAAKM,iBAP1CN,KAAKS,OAAO2B,OAAO,QACnBpC,KAAKmC,SAASnC,KAAKE,aAAcF,KAAKI,aACtCJ,KAAKF,IAAI4B,QAAQ,YAWzBS,SAAU,SAASE,EAAOC,GAClBtC,KAAKY,UAAU2B,QACfvC,KAAKa,eAAekB,SAASO,GACTE,SAAUC,UAAW,WACrBC,KAAK,sBAAuBL,GAC5BG,QAAQ,YAAYA,QAAQ,SAMxDhC,UAAW,SAAST,GAEhB,GAAI4C,GAAQ,8LAkCZ,OA1BIA,IADA5C,EAAQmB,YACQ,wDAC0BnB,EAAQ6C,MAClC,SAET7C,EAAQ6C,MAInBD,GAAgB,0CAIhBA,GAAoB,mCAChB5C,EAAQ8C,OACRF,GAAoB5C,EAAQ8C,KACxB9C,EAAQ+C,UAAkE,IAAtD/C,EAAQ8C,KAAKE,QAAQ,IAAMhD,EAAQ+C,SAAW,OAClEH,GAAO,KAAO5C,EAAQ+C,SAAW,MAGzCH,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 72b89e1821c..076cd0680fe 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-caret-square-o-down",this.cls_disable=a.options.cls_disable||"fa fa-caret-square-o-up",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.collapsed=b.collapsible&&b.value&&JSON.stringify(b.value)==JSON.stringify(b.collapsible_value),this._refresh();var c=this;this.$optional.on("click",function(){c.field.collapsed=!c.field.collapsed,c._refresh(),c.app.trigger("change")})},error:function(a){this.$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.$optional_icon.removeClass().addClass("icon"),this.field.collapsed?(this.$field.hide(),this._tooltip(this.text_enable,this.cls_enable),this.field.value&&this.field.value(this.default_value)):(this.$field.fadeIn("fast"),this._tooltip(this.text_disable,this.cls_disable),this.app.trigger("change"))},_tooltip:function(a,b){this.$optional.length&&this.$optional_icon.addClass(b).tooltip({placement:"bottom"}).attr("data-original-title",a).tooltip("fixTitle").tooltip("hide")},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title">';return b+=a.collapsible?'<div class="ui-table-form-optional"><i class="icon"/>'+a.label+"</div>":a.label,b+='</div><div class="ui-table-form-field">',b+='<div class="ui-table-form-info">',a.help&&(b+=a.help,a.argument&&-1==a.help.indexOf(a.argument)&&(b+=" ("+a.argument+")")),b+="</div>",b+="</div></div>"}})});
+define([],function(){return Backbone.View.extend({initialize:function(a,b){this.app=a,this.text_enable=a.options.text_enable||"Enable",this.text_disable=a.options.text_disable||"Disable",this.cls_enable=a.options.cls_enable||"fa fa-caret-square-o-down",this.cls_disable=a.options.cls_disable||"fa fa-caret-square-o-up",this.field=b.field,this.default_value=b.default_value,this.setElement(this._template(b)),this.$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.$el),this.field.collapsed=b.collapsible&&b.value&&JSON.stringify(b.value)==JSON.stringify(b.collapsible_value),this._refresh();var c=this;this.$optional.on("click",function(){c.field.collapsed=!c.field.collapsed,c._refresh(),c.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.collapsed?(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),this.app.trigger("change"))},_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.collapsible?'<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,a.argument&&-1==a.help.indexOf("("+a.argument+")")&&(b+=" ("+a.argument+")")),b+="</div>",b+="</div></div>"}})});
 //# sourceMappingURL=../../../maps/mvc/form/form-input.js.map
\ No newline at end of file

From db5c81acd78728dee37173aaf034024af2e5f302 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@tgac.ac.uk>
Date: Mon, 15 Jun 2015 20:04:06 +0100
Subject: [PATCH 10/20] Simplify strict_min strict_max logic.

---
 lib/galaxy/tools/parameters/validation.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/lib/galaxy/tools/parameters/validation.py b/lib/galaxy/tools/parameters/validation.py
index 4f685e42a60..360b8e1970d 100644
--- a/lib/galaxy/tools/parameters/validation.py
+++ b/lib/galaxy/tools/parameters/validation.py
@@ -146,12 +146,9 @@ class InRangeValidator( Validator ):
         self_max_str = str( self.max ).rstrip( '0' ).rstrip( '.' )
         op1 = '>='
         op2 = '<='
-        if self.strict_min and self.strict_max:
-            op1 = '>'
-            op2 = '<'
         if self.strict_min:
             op1 = '>'
-        elif self.strict_max:
+        if self.strict_max:
             op2 = '<'
         self.message = message or "Value must be %s %s and %s %s" % ( op1, self_min_str, op2, self_max_str )
 

From 7742e6d23c5a859ed53b531bb5fc02236a7f2cb6 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Mon, 15 Jun 2015 15:10:21 -0400
Subject: [PATCH 11/20] Fix Guru's name in CONTRIBUTORS.md

Apparently I messed it up during the hg->git conversion, I'll have to see if I can fix that. =(
---
 CONTRIBUTORS.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md
index 11f78465081..86e24d1f355 100644
--- a/CONTRIBUTORS.md
+++ b/CONTRIBUTORS.md
@@ -5,7 +5,7 @@ The following individuals have contributed code to Galaxy:
 * Enis Afgan <afgane@gmail.com>
 * Istvan Albert <istvan.albert@gmail.com>
 * Renato Alves <alves.rjc@gmail.com> <rjalves@igc.gulbenkian.pt>
-* Guruprasad Anada <gua110@bx.psu.edu>
+* Guruprasad Ananda <gua110@bx.psu.edu>
 * Florent Angly <florent.angly@gmail.com>
 * Raj Ayyampalayam <raj76@uga.edu>
 * Finn Bacall <finn.bacall@cs.man.ac.uk>

From 508b685c70f648f100dc3230d3105bd1ca95977d Mon Sep 17 00:00:00 2001
From: Martin Cech <cech.marten@gmail.com>
Date: Mon, 15 Jun 2015 16:12:21 -0400
Subject: [PATCH 12/20] fix common API scripts so they dont fail when response
 has no url param

---
 lib/tool_shed/scripts/api/common.py | 6 ++++--
 scripts/api/common.py               | 6 ++++--
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/lib/tool_shed/scripts/api/common.py b/lib/tool_shed/scripts/api/common.py
index 13ea5847599..ef8651bcc06 100644
--- a/lib/tool_shed/scripts/api/common.py
+++ b/lib/tool_shed/scripts/api/common.py
@@ -94,8 +94,10 @@ def display( url, api_key=None, return_formatted=True ):
         print 'Collection Members'
         print '------------------'
         for n, i in enumerate(r):
-            # All collection members should have a name and url in the response.
-            print '#%d: %s' % (n+1, i.pop( 'url' ) )
+            # All collection members should have a name in the response.
+            # url is optional
+            if 'url' in i:
+                print '#%d: %s' % (n+1, i.pop( 'url' ) )
             if 'name' in i:
                 print '  name: %s' % i.pop( 'name' )
             for k, v in i.items():
diff --git a/scripts/api/common.py b/scripts/api/common.py
index d81c351a5c2..d1a58b50d77 100644
--- a/scripts/api/common.py
+++ b/scripts/api/common.py
@@ -89,8 +89,10 @@ def display( api_key, url, return_formatted=True ):
         print 'Collection Members'
         print '------------------'
         for n, i in enumerate(r):
-            # All collection members should have a name and url in the response.
-            print '#%d: %s' % (n+1, i.pop( 'url' ) )
+            # All collection members should have a name in the response.
+            # url is optional
+            if 'url' in i:
+                print '#%d: %s' % (n+1, i.pop( 'url' ) )
             if 'name' in i:
                 print '  name: %s' % i.pop( 'name' )
             for k, v in i.items():

From c68fc22171144fd44fc153641c6a3180ed70082f Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 15 Jun 2015 12:04:14 -0400
Subject: [PATCH 13/20] Initial restriction of metadata size to ~5MB in-memory
 size per element

---
 lib/galaxy/model/custom_types.py | 53 ++++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)

diff --git a/lib/galaxy/model/custom_types.py b/lib/galaxy/model/custom_types.py
index 96a8ea084cd..39aef1b3e0c 100644
--- a/lib/galaxy/model/custom_types.py
+++ b/lib/galaxy/model/custom_types.py
@@ -4,6 +4,10 @@ import json
 import logging
 import uuid
 
+from sys import getsizeof
+from itertools import chain
+from collections import deque
+
 from galaxy import eggs
 eggs.require("SQLAlchemy")
 import sqlalchemy
@@ -18,6 +22,8 @@ log = logging.getLogger( __name__ )
 json_encoder = json.JSONEncoder( sort_keys=True )
 json_decoder = json.JSONDecoder( )
 
+MAX_METADATA_SIZE = 5000000  # 5MB in memory max.  No required metadata should be larger than this.
+
 
 def _sniffnfix_pg9_hex(value):
     """
@@ -217,11 +223,58 @@ metadata_pickler = AliasPickleModule( {
 } )
 
 
+def total_size(o, handlers={}, verbose=False):
+    """ Returns the approximate memory footprint an object and all of its contents.
+
+    Automatically finds the contents of the following builtin containers and
+    their subclasses:  tuple, list, deque, dict, set and frozenset.
+    To search other containers, add handlers to iterate over their contents:
+
+        handlers = {SomeContainerClass: iter,
+                    OtherContainerClass: OtherContainerClass.get_elements}
+
+    Recipe from:  https://code.activestate.com/recipes/577504-compute-memory-footprint-of-an-object-and-its-cont/
+    """
+    dict_handler = lambda d: chain.from_iterable(d.items())
+    all_handlers = { tuple: iter,
+                     list: iter,
+                     deque: iter,
+                     dict: dict_handler,
+                     set: iter,
+                     frozenset: iter }
+    all_handlers.update(handlers)     # user handlers take precedence
+    seen = set()                      # track which object id's have already been seen
+    default_size = getsizeof(0)       # estimate sizeof object without __sizeof__
+
+    def sizeof(o):
+        if id(o) in seen:       # do not double count the same object
+            return 0
+        seen.add(id(o))
+        s = getsizeof(o, default_size)
+
+        for typ, handler in all_handlers.items():
+            if isinstance(o, typ):
+                s += sum(map(sizeof, handler(o)))
+                break
+        return s
+
+    return sizeof(o)
+
+
 class MetadataType( JSONType ):
     """
     Backward compatible metadata type. Can read pickles or JSON, but always
     writes in JSON.
     """
+
+    def process_bind_param(self, value, dialect):
+        if value is not None:
+            for k, v in value.items():
+                if total_size(v) > MAX_METADATA_SIZE:
+                    del value[k]
+            value = json_encoder.encode(value)
+        return value
+
     def process_result_value( self, value, dialect ):
         if value is None:
             return None

From 1d5d322a15d34c5c8f8f9a509d6532ef7f06909d Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 15 Jun 2015 13:11:18 -0400
Subject: [PATCH 14/20] Make metadata limit configurable, off by default.

---
 config/galaxy.ini.sample         |  5 +++++
 lib/galaxy/config.py             |  1 +
 lib/galaxy/model/custom_types.py | 10 +++++-----
 3 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample
index 10c3f633a7e..aa319b22ba1 100644
--- a/config/galaxy.ini.sample
+++ b/config/galaxy.ini.sample
@@ -973,6 +973,11 @@ use_interactive = True
 # option to retry externally, or set metadata manually (when possible).
 #retry_metadata_internally = True
 
+# Very large metadata values can cause Galaxy crashes.  This will allow
+# limiting the maximum metadata size Galaxy will attempt to save with a
+# dataset.  0 to disable this feature.  5000000 is a reasonable size.
+#max_metadata_value_size = 0
+
 # If (for example) you run on a cluster and your datasets (by default,
 # database/files/) are mounted read-only, this option will override tool output
 # paths to write outputs to the working directory instead, and the job manager
diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py
index 006167a5303..dcf0d1c6a64 100644
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -148,6 +148,7 @@ class Configuration( object ):
         self.tool_secret = kwargs.get( "tool_secret", "" )
         self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" )
         self.retry_metadata_internally = string_as_bool( kwargs.get( "retry_metadata_internally", "True" ) )
+        self.max_metadata_value_size = int( kwargs.get( "max_metadata_value_size", 0 ) )
         self.use_remote_user = string_as_bool( kwargs.get( "use_remote_user", "False" ) )
         self.normalize_remote_user_email = string_as_bool( kwargs.get( "normalize_remote_user_email", "False" ) )
         self.remote_user_maildomain = kwargs.get( "remote_user_maildomain", None )
diff --git a/lib/galaxy/model/custom_types.py b/lib/galaxy/model/custom_types.py
index 39aef1b3e0c..308b40201ad 100644
--- a/lib/galaxy/model/custom_types.py
+++ b/lib/galaxy/model/custom_types.py
@@ -12,6 +12,7 @@ from galaxy import eggs
 eggs.require("SQLAlchemy")
 import sqlalchemy
 
+from galaxy import app
 from galaxy.util.aliaspickler import AliasPickleModule
 from sqlalchemy.types import CHAR, LargeBinary, String, TypeDecorator
 from sqlalchemy.ext.mutable import Mutable
@@ -22,8 +23,6 @@ log = logging.getLogger( __name__ )
 json_encoder = json.JSONEncoder( sort_keys=True )
 json_decoder = json.JSONDecoder( )
 
-MAX_METADATA_SIZE = 5000000  # 5MB in memory max.  No required metadata should be larger than this.
-
 
 def _sniffnfix_pg9_hex(value):
     """
@@ -269,9 +268,10 @@ class MetadataType( JSONType ):
 
     def process_bind_param(self, value, dialect):
         if value is not None:
-            for k, v in value.items():
-                if total_size(v) > MAX_METADATA_SIZE:
-                    del value[k]
+            if app.app and app.app.config.max_metadata_value_size:
+                for k, v in value.items():
+                    if total_size(v) > app.app.config.max_metadata_value_size:
+                        del value[k]
             value = json_encoder.encode(value)
         return value
 

From 4f975da4b6a2343e3b5e1c75f5388e5a51ed71b3 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 15 Jun 2015 15:22:49 -0400
Subject: [PATCH 15/20] Add log indicating when metadata setting is being
 aborted

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

diff --git a/lib/galaxy/model/custom_types.py b/lib/galaxy/model/custom_types.py
index 308b40201ad..5387a582d90 100644
--- a/lib/galaxy/model/custom_types.py
+++ b/lib/galaxy/model/custom_types.py
@@ -270,8 +270,10 @@ class MetadataType( JSONType ):
         if value is not None:
             if app.app and app.app.config.max_metadata_value_size:
                 for k, v in value.items():
-                    if total_size(v) > app.app.config.max_metadata_value_size:
+                    sz = total_size(v)
+                    if sz > app.app.config.max_metadata_value_size:
                         del value[k]
+                        log.error('Refusing to bind metadata key %s due to size (%s)' % (k, sz))
             value = json_encoder.encode(value)
         return value
 

From 6423454857bbc4b958ec1966b184cc4133edeb94 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 16 Jun 2015 10:23:46 -0400
Subject: [PATCH 16/20] Update sample text.

---
 config/galaxy.ini.sample | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample
index aa319b22ba1..a9276c73f74 100644
--- a/config/galaxy.ini.sample
+++ b/config/galaxy.ini.sample
@@ -974,8 +974,9 @@ use_interactive = True
 #retry_metadata_internally = True
 
 # Very large metadata values can cause Galaxy crashes.  This will allow
-# limiting the maximum metadata size Galaxy will attempt to save with a
-# dataset.  0 to disable this feature.  5000000 is a reasonable size.
+# limiting the maximum metadata key size (in bytes used in memory, not the end
+# result database value size) Galaxy will attempt to save with a dataset.  0 to
+# disable this feature.  5000000 seems to be a reasonable size.
 #max_metadata_value_size = 0
 
 # If (for example) you run on a cluster and your datasets (by default,

From 373c98098c884f85ef24a795334d4e49c10d4f58 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <ghv2@psu.edu>
Date: Tue, 16 Jun 2015 13:55:06 -0400
Subject: [PATCH 17/20] Change strict_mXX to exclude_mXX for InRangeValidator
 enhancement.

---
 lib/galaxy/tools/parameters/validation.py | 24 +++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/lib/galaxy/tools/parameters/validation.py b/lib/galaxy/tools/parameters/validation.py
index 360b8e1970d..5641b86e9cf 100644
--- a/lib/galaxy/tools/parameters/validation.py
+++ b/lib/galaxy/tools/parameters/validation.py
@@ -107,7 +107,7 @@ class InRangeValidator( Validator ):
     >>> from galaxy.tools.parameters import ToolParameter
     >>> p = ToolParameter.build( None, XML( '''
     ... <param name="blah" type="integer" size="10" value="10">
-    ...     <validator type="in_range" message="Not gonna happen" min="10" strict_min="true" max="20"/>
+    ...     <validator type="in_range" message="Not gonna happen" min="10" exclude_min="true" max="20"/>
     ... </param>
     ... ''' ) )
     >>> t = p.validate( 10 )
@@ -125,41 +125,41 @@ class InRangeValidator( Validator ):
     @classmethod
     def from_element( cls, param, elem ):
         return cls( elem.get( 'message', None ), elem.get( 'min' ),
-                    elem.get( 'max' ), elem.get( 'strict_min', 'false' ), 
-                    elem.get( 'strict_max', 'false' ) )
+                    elem.get( 'max' ), elem.get( 'exclude_min', 'false' ), 
+                    elem.get( 'exclude_max', 'false' ) )
 
-    def __init__( self, message, range_min, range_max, strict_min=False, strict_max=False ):
+    def __init__( self, message, range_min, range_max, exclude_min=False, exclude_max=False ):
         """
-        When the optional strict_min and strict_max attributes are set
+        When the optional exclude_min and exclude_max attributes are set
         to true, the range excludes the end points (i.e., min < value < max),
         while if set to False ( the default), then range includes the end points
-        (1.e., min <= value <= max).  Combinations of strict_min and strict_max
+        (1.e., min <= value <= max).  Combinations of exclude_min and exclude_max
         values are allowed.
         """
         self.min = float( range_min if range_min is not None else '-inf' )
-        self.strict_min = util.asbool( strict_min )
+        self.exclude_min = util.asbool( exclude_min )
         self.max = float( range_max if range_max is not None else 'inf' )
-        self.strict_max = util.asbool( strict_max )
+        self.exclude_max = util.asbool( exclude_max )
         assert self.min <= self.max, 'min must be less than or equal to max'
         # Remove unneeded 0s and decimal from floats to make message pretty.
         self_min_str = str( self.min ).rstrip( '0' ).rstrip( '.' )
         self_max_str = str( self.max ).rstrip( '0' ).rstrip( '.' )
         op1 = '>='
         op2 = '<='
-        if self.strict_min:
+        if self.exclude_min:
             op1 = '>'
-        if self.strict_max:
+        if self.exclude_max:
             op2 = '<'
         self.message = message or "Value must be %s %s and %s %s" % ( op1, self_min_str, op2, self_max_str )
 
     def validate( self, value, history=None ):
-        if self.strict_min:
+        if self.exclude_min:
             if not self.min < float( value ):
                 raise ValueError( self.message )
         else:
             if not self.min <= float( value ):
                 raise ValueError( self.message )
-        if self.strict_max:
+        if self.exclude_max:
             if not float( value ) < self.max:
                 raise ValueError( self.message )
         else:

From ea0d5a9c8605903cf9a658f11ea6bfd61e44bddc Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 16 Jun 2015 14:18:11 -0400
Subject: [PATCH 18/20] Fix bug with runtime post job actions.

Runtime post job actions are post job actions inserted when the workflow is invoked instead of being part of the workflow object in the database. The bug noticed by @kellrott was that these actions were being appended to the original workflow post job actions instead of being transient things just attached to the jobs themselves.

This fixes that problem and adds a test to try to prevent regressions.
---
 lib/galaxy/workflow/modules.py | 9 ++++++---
 test/api/test_workflows.py     | 7 +++++++
 2 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index 1c9bb8c49ae..91c201e81b4 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -863,10 +863,13 @@ class ToolModule( WorkflowModule ):
         # Create new PJA associations with the created job, to be run on completion.
         # PJA Parameter Replacement (only applies to immediate actions-- rename specifically, for now)
         # Pass along replacement dict with the execution of the PJA so we don't have to modify the object.
-        post_job_actions = step.post_job_actions
+
+        # Combine workflow and runtime post job actions into the effective post
+        # job actions for this execution.
+        effective_post_job_actions = step.post_job_actions[:]
         for key, value in self.runtime_post_job_actions.iteritems():
-            post_job_actions.append( self.__to_pja( key, value, step ) )
-        for pja in post_job_actions:
+            effective_post_job_actions.append( self.__to_pja( key, value, None ) )
+        for pja in effective_post_job_actions:
             if pja.action_type in ActionBox.immediate_actions:
                 ActionBox.execute( self.trans.app, self.trans.sa_session, pja, job, replacement_dict )
             else:
diff --git a/test/api/test_workflows.py b/test/api/test_workflows.py
index 2e057545ec7..ac5a8c43c63 100644
--- a/test/api/test_workflows.py
+++ b/test/api/test_workflows.py
@@ -867,6 +867,13 @@ test_data:
         content = self.dataset_populator.get_history_dataset_details( history_id, wait=True, assert_ok=True )
         assert content[ "name" ] == "foo was replaced", content[ "name" ]
 
+        # Test for regression of previous behavior where runtime post job actions
+        # would be added to the original workflow post job actions.
+        workflow_id = workflow_request["workflow_id"]
+        downloaded_workflow = self._download_workflow( workflow_id )
+        pjas = downloaded_workflow[ "steps" ][ "2" ][ "post_job_actions" ].values()
+        assert len( pjas ) == 0, len( pjas )
+
     @skip_without_tool( "cat1" )
     def test_run_with_delayed_runtime_pja( self ):
         workflow_id = self._upload_yaml_workflow("""

From 188f90e8f17278f9ece7b825584e0479c60e7c97 Mon Sep 17 00:00:00 2001
From: Martin Cech <cech.marten@gmail.com>
Date: Tue, 16 Jun 2015 14:22:36 -0400
Subject: [PATCH 19/20] remove the test file

---
 static/toolshed/scripts/test-file.js | 2 --
 1 file changed, 2 deletions(-)
 delete mode 100644 static/toolshed/scripts/test-file.js

diff --git a/static/toolshed/scripts/test-file.js b/static/toolshed/scripts/test-file.js
deleted file mode 100644
index 57532f0ce9d..00000000000
--- a/static/toolshed/scripts/test-file.js
+++ /dev/null
@@ -1,2 +0,0 @@
-define([],function(){return"Remove this file"});
-//# sourceMappingURL=../maps/test-file.js.map
\ No newline at end of file

From 4e7dad284a04dd1f4f83af64fa32e339ccf3bcfb Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 16 Jun 2015 15:29:51 -0400
Subject: [PATCH 20/20] Tweak institutional support language in
 CONTRIBUTORS.md.

---
 CONTRIBUTORS.md | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md
index 86e24d1f355..cfa5f147908 100644
--- a/CONTRIBUTORS.md
+++ b/CONTRIBUTORS.md
@@ -107,12 +107,13 @@ The following individuals have contributed code to Galaxy:
 # Institutional sponsors
 
 Galaxy development began at The Pennsylvania State University in 2006.
-In 2009 all contributions to that point were licensed by Penn State
-under the terms of the Academic Free License 3.0 (see LICENSE.txt). This
-license applies to all subsequent contributions as well.  Significant
-portions of Galaxy development have continued at Penn State, Emory
-University, Johns Hopkins University, and George Washington University
-with support from the following NIH and NSF grants:
+In 2009 all contributions to that point were licensed by The
+Pennsylvania State University under the terms of the Academic Free
+License 3.0 (see LICENSE.txt). This license applies to all subsequent
+contributions - including but not limited to development at The
+Pennsylvania State University, Emory University, Johns Hopkins
+University, and George Washington University as part of the following
+NIH and NSF grants:
 
 * NSF DBI 0543285, “Tailoring genomic data to the needs of experimental
   biologists and educators”