Merge branch 'dev' into remove_samples_000

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

@@ -248,10 +248,6 @@ var LibraryDatasetView = Backbone.View.extend({
       });
   },
 
-  goBack: function(){
-    Galaxy.libraries.library_router.back();
-  },
-
   showPermissions: function(options){
     this.options = _.extend(this.options, options);
     $(".tooltip").remove();
@@ -270,11 +266,13 @@ var LibraryDatasetView = Backbone.View.extend({
     var template = this.templateDatasetPermissions();
     this.$el.html(template({item: this.model, is_admin: is_admin}));
     var self = this;
-    $.get( Galaxy.root + "api/libraries/datasets/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) {
-      self.prepareSelectBoxes({fetched_permissions: fetched_permissions, is_admin: is_admin});
-    }).fail(function(){
-        mod_toastr.error('An error occurred while attempting to fetch dataset permissions.');
-    });
+    $.get(Galaxy.root + "api/libraries/datasets/" + self.id + "/permissions?scope=current")
+        .done(function(fetched_permissions) {
+            self.prepareSelectBoxes({fetched_permissions: fetched_permissions, is_admin: is_admin});
+        })
+        .fail(function(){
+            mod_toastr.error('An error occurred while attempting to fetch dataset permissions.');
+        });
     $("#center [data-toggle]").tooltip();
     $("#center").css('overflow','auto');
   },

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

@@ -49,10 +49,6 @@ var FolderView = Backbone.View.extend({
     });
   },
 
-  goBack: function(){
-    Galaxy.libraries.library_router.back();
-  },
-
   showPermissions: function(options){
     this.options = _.extend(this.options, options);
     $(".tooltip").remove();

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

@@ -942,8 +942,8 @@ var FolderToolbarView = Backbone.View.extend({
   chainCallDeletingItems: function( items_to_delete ){
   var self = this;
   this.deleted_items = new mod_library_model.Folder();
-  var popped_item = items_to_delete.pop();
-  if ( typeof popped_item === "undefined" ) {
+  var item_to_delete = items_to_delete.pop();
+  if ( typeof item_to_delete === "undefined" ) {
     if ( this.options.chain_call_control.failed_number === 0 ){
       mod_toastr.success( 'Selected items were deleted.' );
     } else if ( this.options.chain_call_control.failed_number === this.options.chain_call_control.total_number ){
@@ -954,10 +954,9 @@ var FolderToolbarView = Backbone.View.extend({
     Galaxy.modal.hide();
     return this.deleted_items;
   }
-  var promise = $.when( popped_item.destroy() );
-
-  promise.done( function( item ){
-            Galaxy.libraries.folderListView.collection.remove( popped_item.id );
+  item_to_delete.destroy()
+      .done( function( item ){
+            Galaxy.libraries.folderListView.collection.remove( item_to_delete.id );
             self.updateProgress();
             // add the deleted item to collection, triggers rendering
             if ( Galaxy.libraries.folderListView.options.include_deleted ){
@@ -974,11 +973,11 @@ var FolderToolbarView = Backbone.View.extend({
             }
             self.chainCallDeletingItems( items_to_delete );
           })
-          .fail( function(){
-            self.options.chain_call_control.failed_number += 1;
-            self.updateProgress();
-            self.chainCallDeletingItems( items_to_delete );
-          });
+      .fail( function(){
+        self.options.chain_call_control.failed_number += 1;
+        self.updateProgress();
+        self.chainCallDeletingItems( items_to_delete );
+      });
   },
 
   /**
@@ -996,8 +995,10 @@ var FolderToolbarView = Backbone.View.extend({
    * Delete the selected items. Atomic. One by one.
    */
   deleteSelectedItems: function(){
-    var checkedValues = $('#folder_table').find(':checked');
-    if(checkedValues.length === 0){
+    var dataset_ids = [];
+    var folder_ids = [];
+    var $checkedValues = $('#folder_table').find(':checked');
+    if($checkedValues.length === 0){
         mod_toastr.info('You must select at least one item for deletion.');
     } else {
       var template = this.templateDeletingItemsProgressBar();
@@ -1013,10 +1014,7 @@ var FolderToolbarView = Backbone.View.extend({
       // init the control counters
       this.options.chain_call_control.total_number = 0;
       this.options.chain_call_control.failed_number = 0;
-
-      var dataset_ids = [];
-      var folder_ids = [];
-      checkedValues.each(function(){
+      $checkedValues.each(function(){
           var row_id = $(this).closest('tr').data('id');
           if (row_id !== undefined) {
               if (row_id.substring(0,1) == 'F'){
@@ -1042,7 +1040,7 @@ var FolderToolbarView = Backbone.View.extend({
           items_to_delete.push(folder);
       }
 
-      this.options.chain_call_control.total_number = items_total.length;
+      this.options.chain_call_control.total_number = items_total;
       // call the recursive function to call ajax one after each other (request FIFO queue)
       this.chainCallDeletingItems(items_to_delete);
     }

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

@@ -49,10 +49,6 @@ var LibraryView = Backbone.View.extend({
     });
   },
 
-  goBack: function(){
-    Galaxy.libraries.library_router.back();
-  },
-
   showPermissions: function(options){
     this.options = _.extend(this.options, options);
     $(".tooltip").remove();

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

@@ -1,15 +1,9 @@
 define([
-    "layout/masthead",
-    "mvc/base-mvc",
-    "utils/utils",
     "libs/toastr",
     "mvc/library/library-model",
     "mvc/library/library-libraryrow-view",
     "libs/underscore"
 ], function(
-    mod_masthead,
-    mod_baseMVC,
-    mod_utils,
     mod_toastr,
     mod_library_model,
     mod_library_libraryrow_view,
@@ -199,13 +193,6 @@ var LibraryListView = Backbone.View.extend({
         }
     },
 
-    redirectToHome: function(){
-        window.location = '../';
-    },
-    redirectToLogin: function(){
-        window.location = '/user/login';
-    },
-
     /**
      * In case the search_term is not empty perform the search and render
      * the result. Render all visible libraries otherwise.
@@ -217,7 +204,7 @@ var LibraryListView = Backbone.View.extend({
         var results = null
         results = this.collection.search( search_term );
         this.options.searching = true;
-        this.render({'models': results});
+        this.render({models: results, show_page: 1});
       } else {
         this.options.searching = false;
         this.render();

client/toolshed/scripts/mvc/groups/group-list-view.js

@@ -14,7 +14,7 @@ var GroupListView = Backbone.View.extend({
     defaults: {},
 
     /**
-     * Initialize and fetch the groups from server. 
+     * Initialize and fetch the groups from server.
      * Async render afterwards.
      * @param  {object} options an object with options
      */
@@ -36,14 +36,14 @@ var GroupListView = Backbone.View.extend({
               }
           }
         });
-        
+
     },
 
     fetch: function(){
     },
 
-    /** 
-     * Render the groups table from the object's own collection. 
+    /**
+     * Render the groups table from the object's own collection.
      */
     render: function ( options ) {
         this.options = _.extend( this.options, options );
@@ -55,7 +55,7 @@ var GroupListView = Backbone.View.extend({
         $( "#center" ).css( 'overflow','auto' );
     },
 
-    /** 
+    /**
      * Render all given models as rows in the groups list
      * @param  {array} groups_to_render array of group models to render
      */
@@ -90,7 +90,7 @@ var GroupListView = Backbone.View.extend({
 
     /**
      * Sort the underlying collection according to the parameters received.
-     * Currently supports only sorting by name. 
+     * Currently supports only sorting by name.
      */
     // sortLibraries: function(){
     //     if (Galaxy.libraries.preferences.get('sort_by') === 'name'){
@@ -102,13 +102,6 @@ var GroupListView = Backbone.View.extend({
     //     }
     // },
 
-    // redirectToHome: function(){
-    //     window.location = '../';
-    // },
-    // redirectToLogin: function(){
-    //     window.location = '/user/login';
-    // },
-
 // MMMMMMMMMMMMMMMMMM
 // === TEMPLATES ====
 // MMMMMMMMMMMMMMMMMM

lib/galaxy/app.py

@@ -3,7 +3,6 @@
 import signal
 import sys
 import time
-import os
 
 from galaxy import config, jobs
 import galaxy.model
@@ -224,13 +223,6 @@ def shutdown(self):
         except AttributeError:
             # There is no control_worker
             pass
-        try:
-            # If the datatypes registry was persisted, attempt to
-            # remove the temporary file in which it was written.
-            if self.datatypes_registry.integrated_datatypes_configs is not None:
-                os.unlink(self.datatypes_registry.integrated_datatypes_configs)
-        except:
-            pass
 
     def configure_fluent_log(self):
         if self.config.fluent_log:

lib/galaxy/datatypes/registry.py

@@ -6,8 +6,8 @@
 import imp
 import logging
 import os
-import tempfile
 from collections import OrderedDict as odict
+from string import Template
 from xml.etree.ElementTree import Element
 
 import yaml
@@ -72,7 +72,7 @@ def __init__(self, config=None):
         self.imported_modules = []
         self.datatype_elems = []
         self.sniffer_elems = []
-        self.xml_filename = None
+        self._registry_xml_string = None
         self._edam_formats_mapping = None
         self._edam_data_mapping = None
         self._converters_by_datatype = {}
@@ -672,7 +672,6 @@ def load_external_metadata_tool(self, toolbox):
         # We need to be able to add a job to the queue to set metadata. The queue will currently only accept jobs with an associated
         # tool.  We'll load a special tool to be used for Auto-Detecting metadata; this is less than ideal, but effective
         # Properly building a tool without relying on parsing an XML file is near difficult...so we bundle with Galaxy.
-        self.to_xml_file()
         set_meta_tool = toolbox.load_hidden_lib_tool("galaxy/datatypes/set_metadata_tool.xml")
         self.set_external_metadata_tool = set_meta_tool
         self.log.debug("Loaded external metadata tool: %s", self.set_external_metadata_tool.id)
@@ -870,43 +869,29 @@ def edam_data(self):
             self._edam_data_mapping = dict((k, v.edam_data) for k, v in self.datatypes_by_extension.items())
         return self._edam_data_mapping
 
-    @property
-    def integrated_datatypes_configs(self):
-        if self.xml_filename and os.path.isfile(self.xml_filename):
-            return self.xml_filename
-        return self.xml_filename
-
-    def to_xml_file(self):
-        if self.xml_filename is not None:
-            # If persisted previously, attempt to remove the temporary file in which we were written.
-            try:
-                os.unlink(self.xml_filename)
-            except:
-                pass
-            self.xml_filename = None
-        fd, filename = tempfile.mkstemp()
-        self.xml_filename = os.path.abspath(filename)
-        if self.converters_path_attr:
-            converters_path_str = ' converters_path="%s"' % self.converters_path_attr
-        else:
-            converters_path_str = ''
-        if self.display_path_attr:
-            display_path_str = ' display_path="%s"' % self.display_path_attr
-        else:
-            display_path_str = ''
-        os.write(fd, '<?xml version="1.0"?>\n')
-        os.write(fd, '<datatypes>\n')
-        os.write(fd, '<registration%s%s>\n' % (converters_path_str, display_path_str))
-        for elem in self.datatype_elems:
-            os.write(fd, '%s' % galaxy.util.xml_to_string(elem))
-        os.write(fd, '</registration>\n')
-        os.write(fd, '<sniffers>\n')
-        for elem in self.sniffer_elems:
-            os.write(fd, '%s' % galaxy.util.xml_to_string(elem))
-        os.write(fd, '</sniffers>\n')
-        os.write(fd, '</datatypes>\n')
-        os.close(fd)
-        os.chmod(self.xml_filename, 0o644)
+    def to_xml_file(self, path):
+        if not self._registry_xml_string:
+            registry_string_template = Template("""<?xml version="1.0"?>
+            <datatypes>
+              <registration converters_path="$converters_path" display_path="$display_path">
+                $datatype_elems
+              </registration>
+              <sniffers>
+                $sniffer_elems
+              </sniffers>
+            </datatypes>
+            """)
+            converters_path = self.converters_path_attr or ''
+            display_path = self.display_path_attr or ''
+            datatype_elems = "".join((galaxy.util.xml_to_string(elem) for elem in self.datatype_elems))
+            sniffer_elems = "".join((galaxy.util.xml_to_string(elem) for elem in self.sniffer_elems))
+            self._registry_xml_string = registry_string_template.substitute(converters_path=converters_path,
+                                                                            display_path=display_path,
+                                                                            datatype_elems=datatype_elems,
+                                                                            sniffer_elems=sniffer_elems)
+        with open(os.path.abspath(path), 'w') as registry_xml:
+            os.chmod(path, 0o644)
+            registry_xml.write(self._registry_xml_string)
 
     def get_extension(self, elem):
         """

lib/galaxy/jobs/__init__.py

@@ -1645,8 +1645,7 @@ def invalidate_external_metadata(self):
 
     def setup_external_metadata(self, exec_dir=None, tmp_dir=None,
                                 dataset_files_path=None, config_root=None,
-                                config_file=None, datatypes_config=None,
-                                resolve_metadata_dependencies=False,
+                                config_file=None, resolve_metadata_dependencies=False,
                                 set_extension=True, **kwds):
         # extension could still be 'auto' if this is the upload tool.
         job = self.get_job()
@@ -1665,8 +1664,8 @@ def setup_external_metadata(self, exec_dir=None, tmp_dir=None,
             config_root = self.app.config.root
         if config_file is None:
             config_file = self.app.config.config_file
-        if datatypes_config is None:
-            datatypes_config = self.app.datatypes_registry.integrated_datatypes_configs
+        datatypes_config = os.path.join(self.working_directory, 'registry.xml')
+        self.app.datatypes_registry.to_xml_file(path=datatypes_config)
         command = self.external_output_metadata.setup_external_metadata([output_dataset_assoc.dataset for
                                                                          output_dataset_assoc in
                                                                          job.output_datasets + job.output_library_datasets],
@@ -1677,7 +1676,7 @@ def setup_external_metadata(self, exec_dir=None, tmp_dir=None,
                                                                         config_root=config_root,
                                                                         config_file=config_file,
                                                                         datatypes_config=datatypes_config,
-                                                                        job_metadata=os.path.join(self.tool_working_directory, self.tool.provided_metadata_file),
+                                                                        job_metadata=os.path.join(self.tool_working_directory, TOOL_PROVIDED_JOB_METADATA_FILE),
                                                                         max_metadata_value_size=self.app.config.max_metadata_value_size,
                                                                         **kwds)
         if resolve_metadata_dependencies:
@@ -1975,7 +1974,7 @@ def get_dataset_finish_context(self, job_context, dataset):
         pass
 
     def setup_external_metadata(self, exec_dir=None, tmp_dir=None, dataset_files_path=None,
-                                config_root=None, config_file=None, datatypes_config=None,
+                                config_root=None, config_file=None,
                                 set_extension=True, **kwds):
         # There is no metadata setting for tasks.  This is handled after the merge, at the job level.
         return ""

lib/galaxy/jobs/command_factory.py

@@ -198,7 +198,6 @@ def __handle_metadata(commands_builder, job_wrapper, runner, remote_command_para
     output_fnames = metadata_kwds.get('output_fnames', job_wrapper.get_output_fnames())
     config_root = metadata_kwds.get('config_root', None)
     config_file = metadata_kwds.get('config_file', None)
-    datatypes_config = metadata_kwds.get('datatypes_config', None)
     compute_tmp_dir = metadata_kwds.get('compute_tmp_dir', None)
     resolve_metadata_dependencies = job_wrapper.commands_in_new_shell
     metadata_command = job_wrapper.setup_external_metadata(
@@ -209,7 +208,6 @@ def __handle_metadata(commands_builder, job_wrapper, runner, remote_command_para
         set_extension=False,
         config_root=config_root,
         config_file=config_file,
-        datatypes_config=datatypes_config,
         compute_tmp_dir=compute_tmp_dir,
         resolve_metadata_dependencies=resolve_metadata_dependencies,
         kwds={'overwrite': False}