Merge branch 'release_24.0' into release_24.1

galaxyproject · Aug 13, 2024 · 0bc1a46 · 0bc1a46
2 parents 8d13d70 + cd2f1f8
commit 0bc1a46
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Showing 4 changed files with 17 additions and 12 deletions.
diff --git a/client/src/components/Libraries/LibraryFolder/TopToolbar/FolderTopBar.vue b/client/src/components/Libraries/LibraryFolder/TopToolbar/FolderTopBar.vue
@@ -210,6 +210,9 @@ export default {
             // logic from legacy code
             return !!(this.contains_file_or_folder && Galaxy.user);
         },
+        totalRows: function () {
+            return this.metadata?.total_rows ?? 0;
+        },
     },
     created() {
         const Galaxy = getGalaxyInstance();
@@ -241,7 +244,8 @@ export default {
                 const selected = await this.services.getFilteredFolderContents(
                     this.folder_id,
                     this.unselected,
-                    this.$parent.searchText
+                    this.$parent.searchText,
+                    this.totalRows
                 );
                 this.$emit("setBusy", false);
                 return selected;

diff --git a/client/src/components/Libraries/LibraryFolder/services.js b/client/src/components/Libraries/LibraryFolder/services.js
@@ -30,12 +30,13 @@ export class Services {
         }
     }
 
-    async getFilteredFolderContents(id, excluded, searchText) {
+    async getFilteredFolderContents(id, excluded, searchText, limit) {
         // The intent of this method is to get folder contents applying
-        // seachText filters only; we explicitly set limit to 0
+        // seachText filters only; limit should match the total number of
+        // items in the folder, so that all items are returned.
         const config = {
             params: {
-                limit: 0,
+                limit,
             },
         };
         searchText = searchText?.trim();

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
@@ -2005,13 +2005,13 @@ def fail(message=job.info, exception=None):
         # Once datasets are collected, set the total dataset size (includes extra files)
         for dataset_assoc in job.output_datasets:
             dataset = dataset_assoc.dataset.dataset
-            if not dataset.purged:
-                # assume all datasets in a job get written to the same objectstore
-                quota_source_info = dataset.quota_source_info
-                collected_bytes += dataset.set_total_size()
-            else:
+            # assume all datasets in a job get written to the same objectstore
+            quota_source_info = dataset.quota_source_info
+            collected_bytes += dataset.set_total_size()
+            if dataset.purged:
                 # Purge, in case job wrote directly to object store
                 dataset.full_delete()
+                collected_bytes = 0
 
         user = job.user
         if user and collected_bytes > 0 and quota_source_info is not None and quota_source_info.use:

diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
@@ -668,9 +668,9 @@ def handle_dataset_object_edit(dataset_instance, dataset_attrs):
                                 assert file_source_root
                                 dataset_extra_files_path = os.path.join(file_source_root, dataset_extra_files_path)
                                 persist_extra_files(self.object_store, dataset_extra_files_path, dataset_instance)
-                            # Don't trust serialized file size
-                        dataset_instance.dataset.file_size = None
-                        dataset_instance.dataset.set_total_size()  # update the filesize record in the database
+                            # Only trust file size if the dataset is purged. If we keep the data we should check the file size.
+                            dataset_instance.dataset.file_size = None
+                            dataset_instance.dataset.set_total_size()  # update the filesize record in the database
 
                     if dataset_instance.deleted:
                         dataset_instance.dataset.deleted = True