Develop updated the archiving in dispatcher

hed/tools/remodeling/cli/run_remodel.py

@@ -39,7 +39,7 @@ def get_parser():
                         help="Format for saving any summaries, if any. If empty, then no summaries are saved.")
     parser.add_argument("-b", "--bids-format", action='store_true', dest="use_bids",
                         help="If present, the dataset is in BIDS format with sidecars. HED analysis is available.")
-    parser.add_argument("-n", "--backup_name", default=BackupManager.DEFAULT_BACKUP_NAME, dest="backup_name",
+    parser.add_argument("-n", "--backup-name", default=BackupManager.DEFAULT_BACKUP_NAME, dest="backup_name",
                         help="Name of the default backup for remodeling")
     parser.add_argument("-v", "--verbose", action='store_true',
                         help="If present, output informative messages as computation progresses.")

hed/tools/remodeling/dispatcher.py

@@ -52,7 +52,7 @@ def archive_context(self, archive=None, file_formats=['.txt', '.json'], verbose=
             archive = io.BytesIO()
         for context_name, context_item in self.context_dict.items():
             file_base = generate_filename(context_item.context_filename, append_datetime=True)
-            with zipfile.ZipFile(archive, mode="w", compression=zipfile.ZIP_DEFLATED) as zf:
+            with zipfile.ZipFile(archive, mode="a", compression=zipfile.ZIP_DEFLATED) as zf:
                 for file_format in file_formats:
                     if file_format == '.txt':
                         summary = context_item.get_text_summary(verbose=True)

tests/tools/remodeling/test_dispatcher.py

@@ -100,6 +100,8 @@ def test_archive_context(self):
         with open(self.archive_zip, "wb") as f:  # use `wb` mode
             f.write(archive_io.getvalue())
         self.assertTrue(os.path.exists(self.archive_zip))
+        the_zip = zipfile.ZipFile(self.archive_zip)
+        self.assertFalse(the_zip.testzip())
 
     def test_archive_data_file(self):
         file_list = get_file_list(self.test_root_back1, name_suffix='events', extensions=['.tsv'],
@@ -108,21 +110,27 @@ def test_archive_data_file(self):
         for file in file_list:
             df = pd.read_csv(file, sep='\t', header=0)
             self.assertIsInstance(df, pd.DataFrame)
-            Dispatcher.archive_data_file(df, file, archive=archive_one)
+            archive_one = Dispatcher.archive_data_file(df, file, archive=archive_one)
         self.assertFalse(os.path.exists(self.archive_zip))
         Dispatcher.save_archive(archive_one, self.archive_zip)
         self.assertTrue(os.path.exists(self.archive_zip))
+        the_zip = zipfile.ZipFile(self.archive_zip)
+        self.assertFalse(the_zip.testzip())
 
     def test_archive_data_file_with_context(self):
         with open(self.summarize_model) as fp:
             model1 = json.load(fp)
         dispatch1 = Dispatcher(model1, data_root=self.test_root_back1, backup_name='back1')
         file_list = get_file_list(self.test_root_back1, name_suffix='events', extensions=['.tsv'],
                                   exclude_dirs=['derivatives'])
-        for file in file_list:
-            dispatch1.run_operations(file)
-
-        archive_io = dispatch1.archive_context()
+        df = dispatch1.run_operations(file_list[0])
+        archive_one = io.BytesIO()
+        archive_one = Dispatcher.archive_data_file(df, file_list[0], archive=archive_one)
+        archive_one = dispatch1.archive_context(archive=archive_one)
+        Dispatcher.save_archive(archive_one, self.archive_zip)
+        self.assertTrue(os.path.exists(self.archive_zip))
+        the_zip = zipfile.ZipFile(self.archive_zip)
+        self.assertFalse(the_zip.testzip())
 
     def test_get_context_save_dir(self):
         model_path1 = os.path.join(self.data_path, 'simple_reorder_remdl.json')