From a5c75d2f954f697497747412fd2a998fa61019b0 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Fri, 20 Apr 2018 17:10:28 +0200 Subject: [PATCH 1/2] Correct access for FTP files in composite datatype --- lib/galaxy/tools/parameters/grouping.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/lib/galaxy/tools/parameters/grouping.py b/lib/galaxy/tools/parameters/grouping.py index ed050edc971..f5cc0b34eab 100644 --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -214,7 +214,10 @@ class UploadDataset(Group): if dataset_name is None: filenames = list() for composite_file in context.get('files', []): - filenames.append(composite_file.get('file_data', {}).get('filename', '')) + if not composite_file.get('ftp_files', ''): + filenames.append(composite_file.get('file_data', {}).get('filename', '')) + else: + filenames.append(composite_file.get('ftp_files', [])[0]) dataset_name = os.path.commonprefix(filenames).rstrip('.') or None if dataset_name is None: dataset_name = 'Uploaded Composite Dataset (%s)' % self.get_file_type(context) From 3ab2afb5e5bd82b3aa89500b9c2f80913a054316 Mon Sep 17 00:00:00 2001 From: Anthony Bretaudeau Date: Mon, 23 Apr 2018 17:19:17 +0200 Subject: [PATCH 2/2] backport move_merge fix from #5922 --- lib/galaxy/tools/data_manager/manager.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/tools/data_manager/manager.py b/lib/galaxy/tools/data_manager/manager.py index 0d6e8ea157d..03befb2eb4b 100644 --- a/lib/galaxy/tools/data_manager/manager.py +++ b/lib/galaxy/tools/data_manager/manager.py @@ -326,7 +326,8 @@ class DataManager(object): # moving a directory and the target already exists, we move the contents instead log.debug('Attempting to add entries for undeclared tables: %s.', ', '.join(data_tables_dict.keys())) for ref_file in out_data.values(): - util.move_merge(ref_file.extra_files_path, self.data_managers.app.config.galaxy_data_manager_data_path) + if os.path.exists(ref_file.extra_files_path): + util.move_merge(ref_file.extra_files_path, self.data_managers.app.config.galaxy_data_manager_data_path) path_column_names = ['path'] for data_table_name, data_table_values in data_tables_dict.items(): data_table = self.data_managers.app.tool_data_tables.get(data_table_name, None) @@ -373,7 +374,8 @@ class DataManager(object): if e.errno != errno.EEXIST: raise e # moving a directory and the target already exists, we move the contents instead - util.move_merge(source, target) + if os.path.exists(source): + util.move_merge(source, target) if move_dict.get('relativize_symlinks', False): util.relativize_symlinks(target)