Merge branch 'release_23.2' into dev

client/src/components/Collections/ListCollectionCreatorModal.js

@@ -29,7 +29,6 @@ function listCollectionCreatorModal(elements, options) {
  */
 function createListCollection(contents, defaultHideSourceItems = true) {
     const elements = contents.toJSON();
-    let copyElements;
     const promise = listCollectionCreatorModal(elements, {
         defaultHideSourceItems: defaultHideSourceItems,
         creationFn: function (elements, name, hideSourceItems) {
@@ -39,8 +38,7 @@ function createListCollection(contents, defaultHideSourceItems = true) {
                 //TODO: this allows for list:list even if the filter above does not - reconcile
                 src: element.src || (element.history_content_type == "dataset" ? "hda" : "hdca"),
             }));
-            copyElements = !hideSourceItems;
-            return contents.createHDCA(elements, "list", name, hideSourceItems, copyElements);
+            return contents.createHDCA(elements, "list", name, hideSourceItems);
         },
     });
     return promise;

client/src/components/Collections/PairCollectionCreatorModal.js

@@ -25,16 +25,14 @@ function pairCollectionCreatorModal(elements, options) {
 }
 function createPairCollection(contents, defaultHideSourceItems = true) {
     var elements = contents.toJSON();
-    var copyElements;
     var promise = pairCollectionCreatorModal(elements, {
         defaultHideSourceItems: defaultHideSourceItems,
         creationFn: function (elements, name, hideSourceItems) {
             elements = [
                 { name: "forward", src: elements[0].src || "hda", id: elements[0].id },
                 { name: "reverse", src: elements[1].src || "hda", id: elements[1].id },
             ];
-            copyElements = !hideSourceItems;
-            return contents.createHDCA(elements, "paired", name, hideSourceItems, copyElements);
+            return contents.createHDCA(elements, "paired", name, hideSourceItems);
         },
     });
     return promise;

client/src/components/Collections/PairedListCollectionCreatorModal.js

@@ -29,7 +29,6 @@ function pairedListCollectionCreatorModal(elements, options) {
  */
 function createPairedListCollection(contents, defaultHideSourceItems) {
     const elements = contents.toJSON();
-    var copyElements;
     const promise = pairedListCollectionCreatorModal(elements, {
         defaultHideSourceItems: defaultHideSourceItems,
         creationFn: function (elements, name, hideSourceItems) {
@@ -50,8 +49,7 @@ function createPairedListCollection(contents, defaultHideSourceItems) {
                     },
                 ],
             }));
-            copyElements = !hideSourceItems;
-            return contents.createHDCA(elements, "list:paired", name, hideSourceItems, copyElements);
+            return contents.createHDCA(elements, "list:paired", name, hideSourceItems);
         },
     });
     return promise;

client/src/components/Collections/RuleBasedCollectionCreatorModal.js

@@ -48,7 +48,6 @@ function createCollectionViaRules(selection, defaultHideSourceItems = true) {
     let elementsType;
     let importType;
     const selectionType = selection.selectionType;
-    const copyElements = !defaultHideSourceItems;
     if (!selectionType) {
         // Have HDAs from the history panel.
         elements = selection.toJSON();
@@ -82,7 +81,7 @@ function createCollectionViaRules(selection, defaultHideSourceItems = true) {
         ftpUploadSite: selection.ftpUploadSite,
         defaultHideSourceItems: defaultHideSourceItems,
         creationFn: function (elements, collectionType, name, hideSourceItems) {
-            return selection.createHDCA(elements, collectionType, name, hideSourceItems, copyElements);
+            return selection.createHDCA(elements, collectionType, name, hideSourceItems);
         },
     });
     return promise;

client/src/components/History/adapters/buildCollectionModal.js

@@ -45,12 +45,11 @@ const createBackboneContent = (historyId, selection) => {
         toJSON: () => selectionJson,
         // result must be a $.Deferred object instead of a promise because
         // that's the kind of deprecated data format that backbone likes to use.
-        createHDCA(element_identifiers, collection_type, name, hide_source_items, copy_elements, options = {}) {
+        createHDCA(element_identifiers, collection_type, name, hide_source_items, options = {}) {
             const def = jQuery.Deferred();
             return def.resolve(null, {
                 collection_type,
                 name,
-                copy_elements,
                 hide_source_items,
                 element_identifiers,
                 options,

lib/galaxy_test/selenium/test_collection_builders.py

@@ -17,7 +17,7 @@ def test_build_list_simple_hidden(self):
         self.collection_builder_set_name("my cool list")
         self.screenshot("collection_builder_list")
         self.collection_builder_create()
-        self._wait_for_hid_visible(2)
+        self._wait_for_hid_visible(3)
 
     @selenium_test
     @managed_history
@@ -30,7 +30,6 @@ def test_build_list_and_show_items(self):
         self.collection_builder_hide_originals()
         self.collection_builder_set_name("my cool list")
         self.collection_builder_create()
-        self.home()  # this shouldn't be necessary, and it isn't with a real browser.
         self._wait_for_hid_visible(3)
 
     @selenium_test
@@ -43,7 +42,7 @@ def test_build_pair_simple_hidden(self):
         self.collection_builder_set_name("my awesome pair")
         self.screenshot("collection_builder_pair")
         self.collection_builder_create()
-        self._wait_for_hid_visible(3)
+        self._wait_for_hid_visible(5)
 
     @selenium_test
     @managed_history
@@ -58,11 +57,13 @@ def test_build_paired_list_simple(self):
         self.collection_builder_set_name("my awesome paired list")
         self.screenshot("collection_builder_paired_list")
         self.collection_builder_create()
-        self._wait_for_hid_visible(3)
+        self._wait_for_hid_visible(5)
         # switch to hidden filters to see the hidden datasets appear
         self._show_hidden_content()
         self._wait_for_hid_visible(1)
         self._wait_for_hid_visible(2)
+        self._wait_for_hid_visible(3)
+        self._wait_for_hid_visible(4)
 
     @selenium_test
     @managed_history
@@ -98,9 +99,10 @@ def test_build_simple_list_via_rules_hidden(self):
         self.collection_builder_set_name("my cool list")
         self.screenshot("collection_builder_rules_list")
         self.collection_builder_create()
-        self._wait_for_hid_visible(2)
+        self._wait_for_hid_visible(3)
         self._show_hidden_content()
         self._wait_for_hid_visible(1)
+        self._wait_for_hid_visible(2)
 
     def _wait_for_hid_visible(self, hid, state="ok"):
         # takes a little while for these things to upload and end up in the history

lib/galaxy_test/selenium/test_collection_edit.py

@@ -20,7 +20,7 @@ def test_change_dbkey_simple_list(self):
         self.check_current_data_value(dataValue)
         dataNew = "hg17"
         self.change_dbkey_value_and_click_submit(dataValue, dataNew)
-        self.history_panel_wait_for_hid_ok(4)
+        self.history_panel_wait_for_hid_ok(5)
         self.open_collection_edit_view()
         self.navigate_to_database_tab()
         self.check_current_data_value(dataNew)
@@ -42,7 +42,7 @@ def test_change_datatype_simple_list(self):
         self.change_datatype_value_and_click_submit(dataValue, dataNew)
         self.check_current_data_value(dataNew)
         self.wait_for_history()
-        self.history_panel_expand_collection(2)
+        self.history_panel_expand_collection(3)
         self.history_panel_ensure_showing_item_details(1)
         item = self.history_panel_item_component(hid=1)
         item.datatype.wait_for_visible()
@@ -56,7 +56,7 @@ def _create_simple_list_collection(self, filename, ext):
 
         self.collection_builder_set_name("my cool list")
         self.collection_builder_create()
-        self._wait_for_hid_visible(2)
+        self._wait_for_hid_visible(3)
 
     def open_collection_edit_view(self):
         self.components.history_panel.collection_menu_edit_attributes.wait_for_and_click()

lib/galaxy_test/selenium/test_uploads.py

@@ -118,27 +118,29 @@ def test_upload_deferred(self):
     @selenium_test
     def test_upload_list(self):
         self.upload_list([self.get_filename("1.tabular")], name="Test List")
-        self.history_panel_wait_for_hid_ok(2)
+        self.history_panel_wait_for_hid_ok(3)
         # Make sure modals disappeared - both List creator (TODO: upload).
         self.wait_for_selector_absent_or_hidden(".collection-creator")
 
-        self.assert_item_name(2, "Test List")
+        self.assert_item_name(3, "Test List")
 
         # Make sure source item is hidden when the collection is created.
         self.history_panel_wait_for_hid_hidden(1)
 
     @selenium_test
     def test_upload_pair(self):
         self.upload_list([self.get_filename("1.tabular"), self.get_filename("2.tabular")], name="Test Pair")
-        self.history_panel_wait_for_hid_ok(3)
+        self.history_panel_wait_for_hid_ok(5)
         # Make sure modals disappeared - both collection creator (TODO: upload).
         self.wait_for_selector_absent_or_hidden(".collection-creator")
 
-        self.assert_item_name(3, "Test Pair")
+        self.assert_item_name(5, "Test Pair")
 
         # Make sure source items are hidden when the collection is created.
         self.history_panel_wait_for_hid_hidden(1)
         self.history_panel_wait_for_hid_hidden(2)
+        self.history_panel_wait_for_hid_hidden(3)
+        self.history_panel_wait_for_hid_hidden(4)
 
     @selenium_test
     def test_upload_pair_specify_extension(self):
@@ -161,14 +163,16 @@ def test_upload_paired_list(self):
         self.upload_paired_list(
             [self.get_filename("1.tabular"), self.get_filename("2.tabular")], name="Test Paired List"
         )
-        self.history_panel_wait_for_hid_ok(3)
+        self.history_panel_wait_for_hid_ok(5)
         # Make sure modals disappeared - both collection creator (TODO: upload).
         self.wait_for_selector_absent_or_hidden(".collection-creator")
-        self.assert_item_name(3, "Test Paired List")
+        self.assert_item_name(5, "Test Paired List")
 
         # Make sure source items are hidden when the collection is created.
         self.history_panel_wait_for_hid_hidden(1)
         self.history_panel_wait_for_hid_hidden(2)
+        self.history_panel_wait_for_hid_hidden(3)
+        self.history_panel_wait_for_hid_hidden(4)
 
     @selenium_test
     @pytest.mark.gtn_screenshot