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Merge remote-tracking branch 'upstream/dev' into es6

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This commit is contained in:
Dannon Baker
2017-10-12 15:57:35 -04:00
parent 731a9a6d3e 16843cee9a
commit 1486ee3730
14 changed files with 53 additions and 23 deletions
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client/galaxy/scripts/layout/router.js
+1 -1
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@@ -19,7 +19,7 @@ var Router = Backbone.Router.extend({
url += url.indexOf( '?' ) == -1 ? '?' : '&';
url += $.param( data , true );
}
Galaxy.params = {};
Galaxy.params = data;
this.navigate( url, { 'trigger': true } );
},
client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
+20 -5
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@@ -49,20 +49,26 @@ var DatasetListItemEdit = _super.extend(
/** Render icon-button to edit the attributes (format, permissions, etc.) this dataset. */
_renderEditButton : function(){
var self = this;
// don't show edit while uploading, in-accessible
// DO show if in error (ala previous history panel)
if( ( this.model.get( 'state' ) === STATES.DISCARDED )
|| ( !this.model.get( 'accessible' ) ) ){
return null;
}
var purged = this.model.get( 'purged' ),
deleted = this.model.get( 'deleted' ),
editBtnData = {
title : _l( 'Edit attributes' ),
href : Galaxy.root + 'datasets/edit?dataset_id=' + this.model.attributes.id,
faIcon : 'fa-pencil',
classes : 'edit-btn'
classes : 'edit-btn',
onclick : function( ev ) {
if ( Galaxy.router ) {
ev.preventDefault();
Galaxy.router.push( 'datasets/edit', { dataset_id : self.model.attributes.id } );
}
}
};
// disable if purged or deleted and explain why in the tooltip
if( deleted || purged ){
@@ -195,11 +201,18 @@ var DatasetListItemEdit = _super.extend(
/** Render icon-button to report an error on this dataset to the galaxy admin. */
_renderErrButton : function(){
var self = this;
return faIconButton({
title : _l( 'View or report this error' ),
href : Galaxy.root + 'datasets/error?dataset_id=' + this.model.attributes.id,
classes : 'report-error-btn',
faIcon : 'fa-bug'
faIcon : 'fa-bug',
onclick : function( ev ) {
if ( Galaxy.router ) {
ev.preventDefault();
Galaxy.router.push( 'datasets/error', { dataset_id : self.model.attributes.id } );
}
}
});
},
@@ -214,8 +227,10 @@ var DatasetListItemEdit = _super.extend(
target : this.linkTarget,
faIcon : 'fa-refresh',
onclick : function( ev ) {
ev.preventDefault();
Galaxy.router.push( '/', { job_id : creating_job } );
if ( Galaxy.router ) {
ev.preventDefault();
Galaxy.router.push( '/', { job_id : creating_job } );
}
}
});
}
lib/galaxy/tools/parser/xml.py
+2 -2
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@@ -201,7 +201,7 @@ class XmlToolSource(ToolSource):
def parse_provided_metadata_style(self):
style = None
out_elem = self.root.find("outputs")
if out_elem and "provided_metadata_style" in out_elem.attrib:
if out_elem is not None and "provided_metadata_style" in out_elem.attrib:
style = out_elem.attrib["provided_metadata_style"]
if style is None:
@@ -213,7 +213,7 @@ class XmlToolSource(ToolSource):
def parse_provided_metadata_file(self):
provided_metadata_file = "galaxy.json"
out_elem = self.root.find("outputs")
if out_elem and "provided_metadata_file" in out_elem.attrib:
if out_elem is not None and "provided_metadata_file" in out_elem.attrib:
provided_metadata_file = out_elem.attrib["provided_metadata_file"]
return provided_metadata_file
lib/galaxy/webapps/galaxy/controllers/admin.py
+18 -4
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@@ -121,6 +121,10 @@ class UserListGrid(grids.Grid):
grids.GridAction("Create new user", url_args=dict(webapp="galaxy", action="create_new_user"))
]
operations = [
grids.GridOperation("Manage Information",
condition=(lambda item: not item.deleted),
allow_multiple=False,
url_args=dict(controller="user", action="information", webapp="galaxy")),
grids.GridOperation("Manage Roles and Groups",
condition=(lambda item: not item.deleted),
allow_multiple=False,
@@ -208,7 +212,8 @@ class RoleListGrid(grids.Grid):
UsersColumn("Users", attach_popup=False),
StatusColumn("Status", attach_popup=False),
# Columns that are valid for filtering but are not visible.
grids.DeletedColumn("Deleted", key="deleted", visible=False, filterable="advanced")
grids.DeletedColumn("Deleted", key="deleted", visible=False, filterable="advanced"),
grids.GridColumn("Last Updated", key="update_time", format=time_ago)
]
columns.append(grids.MulticolFilterColumn("Search",
cols_to_filter=[columns[0], columns[1], columns[2]],
@@ -218,10 +223,14 @@ class RoleListGrid(grids.Grid):
global_actions = [
grids.GridAction("Add new role", url_args=dict(action="form/create_role"))
]
operations = [grids.GridOperation("Edit",
operations = [grids.GridOperation("Edit Name/Description",
condition=(lambda item: not item.deleted),
allow_multiple=False,
url_args=dict(action="form/rename_role")),
grids.GridOperation("Edit Permissions",
condition=(lambda item: not item.deleted),
allow_multiple=False,
url_args=dict(action="form/manage_users_and_groups_for_role", webapp="galaxy")),
grids.GridOperation("Delete",
condition=(lambda item: not item.deleted),
allow_multiple=True),
@@ -283,7 +292,8 @@ class GroupListGrid(grids.Grid):
RolesColumn("Roles", attach_popup=False),
StatusColumn("Status", attach_popup=False),
# Columns that are valid for filtering but are not visible.
grids.DeletedColumn("Deleted", key="deleted", visible=False, filterable="advanced")
grids.DeletedColumn("Deleted", key="deleted", visible=False, filterable="advanced"),
grids.GridColumn("Last Updated", key="update_time", format=time_ago)
]
columns.append(grids.MulticolFilterColumn("Search",
cols_to_filter=[columns[0]],
@@ -293,10 +303,14 @@ class GroupListGrid(grids.Grid):
global_actions = [
grids.GridAction("Add new group", url_args=dict(action="form/create_group"))
]
operations = [grids.GridOperation("Rename",
operations = [grids.GridOperation("Edit Name",
condition=(lambda item: not item.deleted),
allow_multiple=False,
url_args=dict(action="form/rename_group")),
grids.GridOperation("Edit Permissions",
condition=(lambda item: not item.deleted),
allow_multiple=False,
url_args=dict(action="form/manage_users_and_roles_for_group", webapp="galaxy")),
grids.GridOperation("Delete",
condition=(lambda item: not item.deleted),
allow_multiple=True),
static/maps/layout/router.js.map
+1 -1
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@@ -1 +1 @@
{"version":3,"sources":["layout/router.js"],"names":["jQuery","require","$","Ui","Router","extend","initialize","page","options","this","push","url","data","__identifer","Math","toString","substr","random","isEmptyObject","navigate","trigger","execute","callback","args","name","Galaxy","debug","QUERY_STRING","queryObj","apply","authenticate","access_denied","display","Message","status","message","persistent","module","exports"],"mappings":"aAAA,IAAIA,OAASC,QAAS,UAClBC,EAAIF,OADJA,aAASC,QAAS,8BAClBC,GAAIF,QADR,kBAGIG,OAAKF,SAASG,OAAAC,QAGdC,WAAA,SAAAC,EAAAC,GACAC,KAAAF,KAAAA,EACAD,KAAAA,QAAaE,GAMbE,KAAM,SAAUC,EAAKC,IADrBA,EAAAA,OACMC,YAAAC,KAAeF,SAAOG,SAAA,IAAAC,OAAA,GACxBJ,EAAOA,cAAPA,KACAA,IAAiCG,GAA5BF,EAAAA,QAAmBI,KAASF,IAAd,IACdJ,GAAGO,EAAAA,MAAFN,GAAN,IAEID,OAAAA,UACHF,KAAAU,SAAAR,GAAAS,SAAA,KAMLC,QAAS,SAAUC,EAAUC,EAAMC,GADnCC,OAAAC,MAAA,kBAAAJ,EAAAC,EAAAC,GACAH,IAAAA,EAASM,aAAUL,MAAUC,EAAMC,OAC/BC,EAAAA,KAAOC,GACHE,IACJnB,KAAWmB,aAAXL,EAAAC,GACIF,EAAUO,MAAApB,KAAAc,GAEND,KAAAA,kBAKXQ,aAhC+B,SAAAP,EAAAC,GAmC5B,OAAO,GACVO,cApC+B,WAuC5BtB,KAAKF,KAAKyB,QAAS,IAAI7B,GAAG8B,SAAWC,OAAQ,SAAUC,QAAS,sEAAuEC,YAAY,QAvCvHC,OAApCC,QAAAlC","file":"../../scripts/layout/router.js","sourcesContent":["var jQuery = require( 'jquery' ),\n $ = jQuery,\n QUERY_STRING = require( 'utils/query-string-parsing' ),\n Ui = require( 'mvc/ui/ui-misc' );\n\nvar Router = Backbone.Router.extend({\n // TODO: not many client routes at this point - fill and remove from server.\n // since we're at root here, this may be the last to be routed entirely on the client.\n initialize : function( page, options ){\n this.page = page;\n this.options = options;\n },\n\n /** helper to push a new navigation state */\n push: function( url, data ) {\n data = data || {};\n data.__identifer = Math.random().toString( 36 ).substr( 2 );\n if ( !$.isEmptyObject( data ) ) {\n url += url.indexOf( '?' ) == -1 ? '?' : '&';\n url += $.param( data , true );\n }\n Galaxy.params = {};\n this.navigate( url, { 'trigger': true } );\n },\n\n /** override to parse query string into obj and send to each route */\n execute: function( callback, args, name ){\n Galaxy.debug( 'router execute:', callback, args, name );\n var queryObj = QUERY_STRING.parse( args.pop() );\n args.push( queryObj );\n if( callback ){\n if ( this.authenticate( args, name ) ) {\n callback.apply( this, args );\n } else {\n this.access_denied();\n }\n }\n },\n\n authenticate: function( args, name ) {\n return true;\n },\n\n access_denied: function() {\n this.page.display( new Ui.Message( { status: 'danger', message: 'You must be logged in with proper credentials to make this request.', persistent: true } ) );\n }\n});\n\nmodule.exports = Router"]}
{"version":3,"sources":["layout/router.js"],"names":["jQuery","require","$","Ui","Router","extend","initialize","page","options","this","push","url","data","__identifer","Math","toString","substr","random","isEmptyObject","param","navigate","trigger","execute","callback","args","name","Galaxy","debug","QUERY_STRING","queryObj","apply","authenticate","access_denied","display","Message","status","message","persistent","module","exports"],"mappings":"aAAA,IAAIA,OAASC,QAAS,UAClBC,EAAIF,OADJA,aAASC,QAAS,8BAClBC,GAAIF,QADR,kBAGIG,OAAKF,SAASG,OAAAC,QAGdC,WAAA,SAAAC,EAAAC,GACAC,KAAAF,KAAAA,EACAD,KAAAA,QAAaE,GAMbE,KAAM,SAAUC,EAAKC,IADrBA,EAAAA,OACMC,YAAAC,KAAeF,SAAOG,SAAA,IAAAC,OAAA,GACxBJ,EAAOA,cAAPA,KACAA,IAAiCG,GAA5BF,EAAAA,QAAmBI,KAASF,IAAd,IACdJ,GAAGO,EAAAA,MAAFN,GAAN,IAEID,OAAAA,OAASQ,EACZV,KAAAW,SAAAT,GAAAU,SAAA,KAMLC,QAAS,SAAUC,EAAUC,EAAMC,GADnCC,OAAAC,MAAA,kBAAAJ,EAAAC,EAAAC,GACAH,IAAAA,EAASM,aAAUL,MAAUC,EAAMC,OAC/BC,EAAAA,KAAOC,GACHE,IACJpB,KAAWoB,aAAXL,EAAAC,GACIF,EAAUO,MAAArB,KAAAe,GAEND,KAAAA,kBAKXQ,aAhC+B,SAAAP,EAAAC,GAmC5B,OAAO,GACVO,cApC+B,WAuC5BvB,KAAKF,KAAK0B,QAAS,IAAI9B,GAAG+B,SAAWC,OAAQ,SAAUC,QAAS,sEAAuEC,YAAY,QAvCvHC,OAApCC,QAAAnC","file":"../../scripts/layout/router.js","sourcesContent":["var jQuery = require( 'jquery' ),\n $ = jQuery,\n QUERY_STRING = require( 'utils/query-string-parsing' ),\n Ui = require( 'mvc/ui/ui-misc' );\n\nvar Router = Backbone.Router.extend({\n // TODO: not many client routes at this point - fill and remove from server.\n // since we're at root here, this may be the last to be routed entirely on the client.\n initialize : function( page, options ){\n this.page = page;\n this.options = options;\n },\n\n /** helper to push a new navigation state */\n push: function( url, data ) {\n data = data || {};\n data.__identifer = Math.random().toString( 36 ).substr( 2 );\n if ( !$.isEmptyObject( data ) ) {\n url += url.indexOf( '?' ) == -1 ? '?' : '&';\n url += $.param( data , true );\n }\n Galaxy.params = data;\n this.navigate( url, { 'trigger': true } );\n },\n\n /** override to parse query string into obj and send to each route */\n execute: function( callback, args, name ){\n Galaxy.debug( 'router execute:', callback, args, name );\n var queryObj = QUERY_STRING.parse( args.pop() );\n args.push( queryObj );\n if( callback ){\n if ( this.authenticate( args, name ) ) {\n callback.apply( this, args );\n } else {\n this.access_denied();\n }\n }\n },\n\n authenticate: function( args, name ) {\n return true;\n },\n\n access_denied: function() {\n this.page.display( new Ui.Message( { status: 'danger', message: 'You must be logged in with proper credentials to make this request.', persistent: true } ) );\n }\n});\n\nmodule.exports = Router"]}
static/maps/mvc/dataset/dataset-li-edit.js.map
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static/scripts/bundled/admin.bundled.js
+1 -1
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static/scripts/bundled/admin.bundled.js.map
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static/scripts/bundled/analysis.bundled.js
+2 -2
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static/scripts/bundled/analysis.bundled.js.map
+1 -1
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static/scripts/bundled/libs.bundled.js.map
+1 -1
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static/scripts/layout/router.js
+1 -1
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@@ -1,2 +1,2 @@
"use strict";var jQuery=require("jquery"),$=jQuery,QUERY_STRING=require("utils/query-string-parsing"),Ui=require("mvc/ui/ui-misc"),Router=Backbone.Router.extend({initialize:function(e,t){this.page=e,this.options=t},push:function(e,t){(t=t||{}).__identifer=Math.random().toString(36).substr(2),$.isEmptyObject(t)||(e+=-1==e.indexOf("?")?"?":"&",e+=$.param(t,!0)),Galaxy.params={},this.navigate(e,{trigger:!0})},execute:function(e,t,i){Galaxy.debug("router execute:",e,t,i);var s=QUERY_STRING.parse(t.pop());t.push(s),e&&(this.authenticate(t,i)?e.apply(this,t):this.access_denied())},authenticate:function(e,t){return!0},access_denied:function(){this.page.display(new Ui.Message({status:"danger",message:"You must be logged in with proper credentials to make this request.",persistent:!0}))}});module.exports=Router;
"use strict";var jQuery=require("jquery"),$=jQuery,QUERY_STRING=require("utils/query-string-parsing"),Ui=require("mvc/ui/ui-misc"),Router=Backbone.Router.extend({initialize:function(e,t){this.page=e,this.options=t},push:function(e,t){(t=t||{}).__identifer=Math.random().toString(36).substr(2),$.isEmptyObject(t)||(e+=-1==e.indexOf("?")?"?":"&",e+=$.param(t,!0)),Galaxy.params=t,this.navigate(e,{trigger:!0})},execute:function(e,t,i){Galaxy.debug("router execute:",e,t,i);var s=QUERY_STRING.parse(t.pop());t.push(s),e&&(this.authenticate(t,i)?e.apply(this,t):this.access_denied())},authenticate:function(e,t){return!0},access_denied:function(){this.page.display(new Ui.Message({status:"danger",message:"You must be logged in with proper credentials to make this request.",persistent:!0}))}});module.exports=Router;
//# sourceMappingURL=../../maps/layout/router.js.map
static/scripts/mvc/dataset/dataset-li-edit.js
+1 -1
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templates/show_params.mako
+2 -1
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@@ -1,6 +1,6 @@
<%inherit file="/base.mako"/>
<%namespace file="/message.mako" import="render_msg" />
<% from galaxy.util import listify, nice_size, unicodify %>
<% from galaxy.util import nice_size, unicodify %>
<style>
.inherit {
@@ -22,6 +22,7 @@
<%def name="inputs_recursive( input_params, param_values, depth=1, upgrade_messages=None )">
<%
from galaxy.util import listify
if upgrade_messages is None:
upgrade_messages = {}
%>