Merge branch 'dev' into ui_pref_routing

client/galaxy/scripts/onload.js

@@ -18,7 +18,6 @@ window.async_save_text = require( 'utils/async-save-text' );
 var POPUPMENU = require( 'ui/popupmenu' );
 window.make_popupmenu = POPUPMENU.make_popupmenu;
 window.make_popup_menus = POPUPMENU.make_popup_menus;
-window.toolform = require( 'mvc/tool/tool-form' );
 window.init_tag_click_function = require( 'ui/autocom_tagging' );
 var TOURS = require( 'mvc/tours' );
 var QUERY_STRING = require( 'utils/query-string-parsing' );

lib/galaxy/model/__init__.py

@@ -28,6 +28,7 @@ import galaxy.model.orm.now
 import galaxy.security.passwords
 import galaxy.util
 from galaxy.model.item_attrs import UsesAnnotations
+from galaxy.model.util import pgcalc
 from galaxy.security import get_permitted_actions
 from galaxy.util import (directory_hash_id, Params, ready_name_for_url,
                          restore_text, send_mail, unicodify, unique_id)
@@ -275,6 +276,31 @@ class User( object, Dictifiable ):
                     total += hda.dataset.get_total_size()
         return total
 
+    def calculate_and_set_disk_usage( self ):
+        """
+        Calculates and sets user disk usage.
+        """
+        new = None
+        db_session = object_session(self)
+        current = self.get_disk_usage()
+        if db_session.get_bind().dialect.name not in ( 'postgres', 'postgresql' ):
+            done = False
+            while not done:
+                new = self.calculate_disk_usage()
+                db_session.refresh( self )
+                # make sure usage didn't change while calculating
+                # set done if it has not, otherwise reset current and iterate again.
+                if self.get_disk_usage() == current:
+                    done = True
+                else:
+                    current = self.get_disk_usage()
+        else:
+            new = pgcalc(db_session, self.id)
+        if new not in (current, None):
+            self.set_disk_usage( new )
+            db_session.add( self )
+            db_session.flush()
+
     @staticmethod
     def user_template_environment( user ):
         """

lib/galaxy/queue_worker.py

@@ -9,7 +9,6 @@ import time
 
 import galaxy.queues
 from galaxy import util
-from galaxy.model.util import pgcalc
 
 from kombu import Connection
 from kombu.mixins import ConsumerMixin
@@ -143,13 +142,11 @@ def recalculate_user_disk_usage(app, **kwargs):
     if user_id:
         user = sa_session.query( app.model.User ).get( app.security.decode_id( user_id ) )
         if user:
-            if sa_session.get_bind().dialect.name not in ( 'postgres', 'postgresql' ):
-                new = user.calculate_disk_usage()
-            else:
-                new = pgcalc(sa_session, user.id)
-            user.set_disk_usage(new)
-            sa_session.add(user)
-            sa_session.flush()
+            user.calculate_and_set_disk_usage()
+        else:
+            log.error("Recalculate user disk usage task failed, user %s not found" % user_id)
+    else:
+        log.error("Recalculate user disk usage task received without user_id.")
 
 
 def reload_tool_data_tables(app, **kwargs):

lib/galaxy/webapps/galaxy/controllers/admin.py

@@ -10,7 +10,6 @@ from galaxy import web
 from galaxy.actions.admin import AdminActions
 from galaxy.exceptions import MessageException
 from galaxy.model import tool_shed_install as install_model
-from galaxy.model.util import pgcalc
 from galaxy.util import nice_size, sanitize_text, url_get
 from galaxy.util.odict import odict
 from galaxy.web import url_for
@@ -875,27 +874,9 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuotaMixin, QuotaP
         user = trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( user_id ) )
         if not user:
             return trans.show_error_message( "User not found for id (%s)" % sanitize_text( str( user_id ) ) )
-        engine = None
-        if trans.app.config.database_connection:
-            engine = trans.app.config.database_connection.split(':')[0]
-        if engine not in ( 'postgres', 'postgresql' ):
-            done = False
-            while not done:
-                current = user.get_disk_usage()
-                new = user.calculate_disk_usage()
-                trans.sa_session.refresh( user )
-                # make sure usage didn't change while calculating, set done
-                if user.get_disk_usage() == current:
-                    done = True
-                if new not in (current, None):
-                    user.set_disk_usage( new )
-                    trans.sa_session.add( user )
-                    trans.sa_session.flush()
-        else:
-            # We can use the lightning fast pgcalc!
-            current = user.get_disk_usage()
-            new = pgcalc( self.sa_session, user.id )
-        # yes, still a small race condition between here and the flush
+        current = user.get_disk_usage()
+        user.calculate_and_set_disk_usage()
+        new = user.get_disk_usage()
         if new in ( current, None ):
             message = 'Usage is unchanged at %s.' % nice_size( current )
         else:

static/maps/onload.js.map

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static/scripts/bundled/login.bundled.js

@@ -1,2 +1,2 @@
-webpackJsonp([4],[function(e,r,n){(function(e){var r=n(1),a=r,i=n(36).GalaxyApp,o=n(9),t=n(4),l=n(38);window.app=function(n,c){window.Galaxy=new i(n,c),Galaxy.debug("login app");var d=encodeURI(n.redirect);if(!n.show_welcome_with_login){var w=r.param({use_panels:"True",redirect:d});return void(window.location.href=Galaxy.root+"user/login?"+w)}var p=new l.PageLayoutView(e.extend(n,{el:"body",center:new o.CenterPanel({el:"#center"}),right:new o.RightPanel({title:t("Login required"),el:"#right"})}));a(function(){var e=r.param({redirect:d}),a=Galaxy.root+"user/login?"+e;p.render(),p.center.$("#galaxy_main").prop("src",n.welcome_url),p.right.$(".unified-panel-body").css("overflow","hidden").html('<iframe src="'+a+'" frameborder="0" style="width: 100%; height: 100%;"/>')})}}).call(r,n(2))}]);
+webpackJsonp([4],[function(e,r,n){(function(e){var r=n(1),a=r,i=n(57).GalaxyApp,o=n(10),t=n(5),l=n(59);window.app=function(n,c){window.Galaxy=new i(n,c),Galaxy.debug("login app");var d=encodeURI(n.redirect);if(!n.show_welcome_with_login){var w=r.param({use_panels:"True",redirect:d});return void(window.location.href=Galaxy.root+"user/login?"+w)}var p=new l.PageLayoutView(e.extend(n,{el:"body",center:new o.CenterPanel({el:"#center"}),right:new o.RightPanel({title:t("Login required"),el:"#right"})}));a(function(){var e=r.param({redirect:d}),a=Galaxy.root+"user/login?"+e;p.render(),p.center.$("#galaxy_main").prop("src",n.welcome_url),p.right.$(".unified-panel-body").css("overflow","hidden").html('<iframe src="'+a+'" frameborder="0" style="width: 100%; height: 100%;"/>')})}}).call(r,n(2))}]);
 //# sourceMappingURL=login.bundled.js.map

static/scripts/onload.js

@@ -1,2 +1,2 @@
-function replace_big_select_inputs(a,b,c){function d(a){var b=$(a),c={placeholder:"Click to select",closeOnSelect:!b.is("[MULTIPLE]"),dropdownAutoWidth:!0,containerCssClass:"select2-minwidth"};return a.select2(c)}jQuery.fn.select2&&(void 0===a&&(a=20),void 0===b&&(b=3e3),c=c||$("select"),c.each(function(){var c=$(this).not("[multiple]"),e=c.find("option").length;a>e||e>b||c.hasClass("no-autocomplete")||d(c)}))}function init_refresh_on_change(){$("select[refresh_on_change='true']").off("change").change(function(){var a=$(this),b=a.val(),c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var d=a.attr("last_selected_value");if(-1===$.inArray(b,c)&&-1===$.inArray(d,c))return}$(window).trigger("refresh_on_change"),$(document).trigger("convert_to_values"),a.get(0).form.submit()}),$(":checkbox[refresh_on_change='true']").off("click").click(function(){var a=$(this),b=a.val(),c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var d=a.attr("last_selected_value");if(-1===$.inArray(b,c)&&-1===$.inArray(d,c))return}$(window).trigger("refresh_on_change"),a.get(0).form.submit()}),$("a[confirm]").off("click").click(function(){return confirm($(this).attr("confirm"))})}window.jQuery=jQuery,window.$=jQuery,window._=_,window.Backbone=Backbone,window.panels=require("layout/panel"),_.extend(window,require("layout/modal")),window.async_save_text=require("utils/async-save-text");var POPUPMENU=require("ui/popupmenu");window.make_popupmenu=POPUPMENU.make_popupmenu,window.make_popup_menus=POPUPMENU.make_popup_menus,window.toolform=require("mvc/tool/tool-form"),window.init_tag_click_function=require("ui/autocom_tagging");var TOURS=require("mvc/tours"),QUERY_STRING=require("utils/query-string-parsing");window.init_refresh_on_change=init_refresh_on_change,$(document).ready(function(){init_refresh_on_change(),$.fn.tooltip&&($(".unified-panel-header [title]").tooltip({placement:"bottom"}),$("[title]").tooltip()),make_popup_menus(),replace_big_select_inputs(20,1500),$("a").click(function(){var a=$(this),b=parent.frames&&parent.frames.galaxy_main;if("galaxy_main"==a.attr("target")&&!b){var c=a.attr("href");c+=-1==c.indexOf("?")?"?":"&",c+="use_panels=True",a.attr("href",c),a.attr("target","_self")}return a});var a=JSON.parse(sessionStorage.getItem("activeGalaxyTour"));if(a&&(a=TOURS.hooked_tour_from_data(a),a&&a.steps&&window&&window.self===window.top)){var b=new Tour(_.extend({steps:a.steps},TOURS.tour_opts));b.init(),b.restart()}});
+function replace_big_select_inputs(a,b,c){function d(a){var b=$(a),c={placeholder:"Click to select",closeOnSelect:!b.is("[MULTIPLE]"),dropdownAutoWidth:!0,containerCssClass:"select2-minwidth"};return a.select2(c)}jQuery.fn.select2&&(void 0===a&&(a=20),void 0===b&&(b=3e3),c=c||$("select"),c.each(function(){var c=$(this).not("[multiple]"),e=c.find("option").length;a>e||e>b||c.hasClass("no-autocomplete")||d(c)}))}function init_refresh_on_change(){$("select[refresh_on_change='true']").off("change").change(function(){var a=$(this),b=a.val(),c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var d=a.attr("last_selected_value");if(-1===$.inArray(b,c)&&-1===$.inArray(d,c))return}$(window).trigger("refresh_on_change"),$(document).trigger("convert_to_values"),a.get(0).form.submit()}),$(":checkbox[refresh_on_change='true']").off("click").click(function(){var a=$(this),b=a.val(),c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var d=a.attr("last_selected_value");if(-1===$.inArray(b,c)&&-1===$.inArray(d,c))return}$(window).trigger("refresh_on_change"),a.get(0).form.submit()}),$("a[confirm]").off("click").click(function(){return confirm($(this).attr("confirm"))})}window.jQuery=jQuery,window.$=jQuery,window._=_,window.Backbone=Backbone,window.panels=require("layout/panel"),_.extend(window,require("layout/modal")),window.async_save_text=require("utils/async-save-text");var POPUPMENU=require("ui/popupmenu");window.make_popupmenu=POPUPMENU.make_popupmenu,window.make_popup_menus=POPUPMENU.make_popup_menus,window.init_tag_click_function=require("ui/autocom_tagging");var TOURS=require("mvc/tours"),QUERY_STRING=require("utils/query-string-parsing");window.init_refresh_on_change=init_refresh_on_change,$(document).ready(function(){init_refresh_on_change(),$.fn.tooltip&&($(".unified-panel-header [title]").tooltip({placement:"bottom"}),$("[title]").tooltip()),make_popup_menus(),replace_big_select_inputs(20,1500),$("a").click(function(){var a=$(this),b=parent.frames&&parent.frames.galaxy_main;if("galaxy_main"==a.attr("target")&&!b){var c=a.attr("href");c+=-1==c.indexOf("?")?"?":"&",c+="use_panels=True",a.attr("href",c),a.attr("target","_self")}return a});var a=JSON.parse(sessionStorage.getItem("activeGalaxyTour"));if(a&&(a=TOURS.hooked_tour_from_data(a),a&&a.steps&&window&&window.self===window.top)){var b=new Tour(_.extend({steps:a.steps},TOURS.tour_opts));b.init(),b.restart()}});
 //# sourceMappingURL=../maps/onload.js.map