Merge branch 'dev' into remove_toolshed_grids

client/galaxy/scripts/mvc/library/library-folderlist-view.js

@@ -357,7 +357,7 @@ var FolderListView = Backbone.View.extend({
       '</ol>',
 
       // FOLDER CONTENT
-      '<table data-library-id="<%- parent_library_id  %>" id="folder_table" class="grid table table-condensed">',
+      '<table data-library-id="<%- parent_library_id  %>" class="grid table table-condensed">',
         '<thead>',
           '<th class="button_heading"></th>',
           '<th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>',

client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js

@@ -207,8 +207,8 @@ var FolderToolbarView = Backbone.View.extend({
 
   // show bulk import modal
   modalBulkImport : function(){
-      var checkedValues = $('#folder_table').find(':checked');
-      if(checkedValues.length === 0){
+      var $checkedValues = this.findCheckedRows();
+      if($checkedValues.length === 0){
           mod_toastr.info('You must select some datasets first.');
       } else {
         var that = this;
@@ -268,7 +268,7 @@ var FolderToolbarView = Backbone.View.extend({
   processImportToHistory: function( history_id, history_name ){
     var dataset_ids = [];
     var folder_ids = [];
-    $('#folder_table').find(':checked').each(function(){
+    this.findCheckedRows().each(function(){
         var row_id = $(this).closest('tr').data('id');
         if (row_id.substring(0,1) == 'F'){
             folder_ids.push(row_id);
@@ -323,7 +323,7 @@ var FolderToolbarView = Backbone.View.extend({
   download : function( folder_id, format ){
     var dataset_ids = [];
     var folder_ids = [];
-        $( '#folder_table' ).find( ':checked' ).each( function(){
+        this.findCheckedRows().each( function(){
             var row_id = $(this).closest('tr').data('id');
             if (row_id.substring(0,1) == 'F'){
                 folder_ids.push(row_id);
@@ -997,7 +997,7 @@ var FolderToolbarView = Backbone.View.extend({
   deleteSelectedItems: function(){
     var dataset_ids = [];
     var folder_ids = [];
-    var $checkedValues = $('#folder_table').find(':checked');
+    var $checkedValues = this.findCheckedRows();
     if($checkedValues.length === 0){
         mod_toastr.info('You must select at least one item for deletion.');
     } else {
@@ -1116,6 +1116,10 @@ var FolderToolbarView = Backbone.View.extend({
     }
   },
 
+  findCheckedRows: function(){
+    return $('#folder_list_body').find(':checked');
+  },
+
   templateToolBar: function(){
     return _.template([
     // container start

client/galaxy/scripts/onload.js

@@ -184,13 +184,21 @@ $(document).ready( function() {
         }
     }
 
-    // Load all webhooks with the type 'onload'
-    $.getJSON( Galaxy.root + 'api/webhooks/onload/all', function(webhooks) {
-        _.each(webhooks, function(webhook) {
-            if (webhook.activate && webhook.script) {
-                $('<script/>', {type: 'text/javascript'}).text(webhook.script).appendTo('head');
-                $('<style/>', {type: 'text/css'}).text(webhook.styles).appendTo('head');
-            }
-        });
-    });
+    function onloadWebhooks() {
+        if (Galaxy.root !== undefined){
+            // Load all webhooks with the type 'onload'
+            $.getJSON( Galaxy.root + 'api/webhooks/onload/all', function(webhooks) {
+                _.each(webhooks, function(webhook) {
+                    if (webhook.activate && webhook.script) {
+                        $('<script/>', {type: 'text/javascript'}).text(webhook.script).appendTo('head');
+                        $('<style/>', {type: 'text/css'}).text(webhook.styles).appendTo('head');
+                    }
+                });
+            });
+        }
+        else {
+            setTimeout(onloadWebhooks, 100);
+        }
+    }
+    onloadWebhooks();
 });

config/galaxy.ini.sample

@@ -979,7 +979,7 @@ use_interactive = True
 # Galaxy encodes various internal values when these values will be output in
 # some format (for example, in a URL or cookie).  You should set a key to be
 # used by the algorithm that encodes and decodes these values.  It can be any
-# string.
+# string up to 448 bits long.
 # One simple way to generate a value for this is with the shell command:
 #   python -c 'import time; print time.time()' | md5sum | cut -f 1 -d ' '
 #id_secret = USING THE DEFAULT IS NOT SECURE!

lib/galaxy/dependencies/conditional-requirements.txt

@@ -12,7 +12,7 @@ statsd
 graphitesend
 azure-storage==0.32.0
 # PyRods not in PyPI
-python-ldap==2.4.27
+python-ldap==2.4.44
 
 # Chronos client
 chronos-python==0.38.0

lib/galaxy/web/security/__init__.py

@@ -3,14 +3,21 @@
 import os.path
 import logging
 
-import galaxy.exceptions
-
 from Crypto.Cipher import Blowfish
 from Crypto.Util.randpool import RandomPool
 from Crypto.Util import number
 
+import galaxy.exceptions
+
+from galaxy.util import smart_str
+
 log = logging.getLogger(__name__)
 
+MAXIMUM_ID_SECRET_BITS = 448
+MAXIMUM_ID_SECRET_LENGTH = MAXIMUM_ID_SECRET_BITS / 8
+KIND_TOO_LONG_MESSAGE = "Galaxy coding error, keep encryption 'kinds' smaller to utilize more bites of randomness from id_secret values."
+
+
 if os.path.exists("/dev/urandom"):
     # We have urandom, use it as the source of random data
     random_fd = os.open("/dev/urandom", os.O_RDONLY)
@@ -37,7 +44,8 @@ def get_random_bytes(nbytes):
 class SecurityHelper(object):
 
     def __init__(self, **config):
-        self.id_secret = config['id_secret']
+        id_secret = config['id_secret']
+        self.id_secret = id_secret
         self.id_cipher = Blowfish.new(self.id_secret)
 
         per_kind_id_secret_base = config.get('per_kind_id_secret_base', self.id_secret)
@@ -127,4 +135,15 @@ def __init__(self, secret_base):
         self.secret_base = secret_base
 
     def __missing__(self, key):
-        return Blowfish.new(self.secret_base + "__" + key)
+        assert len(key) < 15, KIND_TOO_LONG_MESSAGE
+        secret = self.secret_base + "__" + key
+        return Blowfish.new(_last_bits(secret))
+
+
+def _last_bits(secret):
+    """We append the kind at the end, so just use the bits at the end.
+    """
+    last_bits = smart_str(secret)
+    if len(last_bits) > MAXIMUM_ID_SECRET_LENGTH:
+        last_bits = last_bits[-MAXIMUM_ID_SECRET_LENGTH:]
+    return last_bits