Add multiple download experiment on the CLI

elab_bridge/cli.py

@@ -2,7 +2,7 @@
 Provide CLI for the main functionalities of the elab bridge
 """
 
-from elab_bridge.server_interface import download_experiment
+from elab_bridge.server_interface import download_experiment, extended_download
 
 
 def main(command_line=None):
@@ -29,6 +29,19 @@ def main(command_line=None):
     download.add_argument("-c", "--compressed", action='store_true',
                           help="Compress the output file (use labels and merge checkbox columns)")
 
+    extended_download_parser = subparsers.add_parser('extended_download',
+                                                     help='Download experiments'
+                                                          ' with extended options')
+    extended_download_parser.add_argument("destination", nargs=1, metavar='destination', type=str,
+                                          help="The destination directory"
+                                               " to save the downloaded experiments.")
+    extended_download_parser.add_argument("config_json", nargs=1, metavar='config_json', type=str,
+                                          help="The json configuration file of the project")
+    extended_download_parser.add_argument("tags", nargs='+', metavar='tags', type=str,
+                                          help="List of tags of the experiments to download")
+    extended_download_parser.add_argument("-f", "--format", type=str, nargs=1, metavar='format',
+                                          help="Format to store the data (json/csv)")
+
     # parse arguments
     args = parser.parse_args(command_line)
 
@@ -43,7 +56,10 @@ def main(command_line=None):
             args.format = ['csv']
 
         download_experiment(args.destination[0], args.config_json[0], format=args.format[0],
-                         compressed=bool(args.compressed))
+                            compressed=bool(args.compressed))
+
+    elif args.command == 'extended_download':
+        extended_download(args.destination[0], args.config_json[0], args.tags)
 
 
 if __name__ == '__main__':

elab_bridge/server_interface.py

@@ -4,7 +4,7 @@
 import pandas as pd
 
 
-def extended_download(save_to, server_config_json, experiment_tags):
+def extended_download(save_to, server_config_json, experiment_tags, format='csv'):
     """
     Download an individual experiment.
 
@@ -37,7 +37,7 @@ def extended_download(save_to, server_config_json, experiment_tags):
     downloaded_experiments = []
 
     for experiment_id in experiment_ids:
-        metadata = download_experiment(save_to, server_config_json, experiment_id, format='json',
+        metadata = download_experiment(save_to, server_config_json, experiment_id, format=format,
                                        experiment_axis='columns')
         downloaded_experiments.append(metadata)
 
@@ -88,10 +88,11 @@ def download_experiment(save_to, server_config_json, experiment_id, format='json
     elif format == 'csv':
         if experiment_axis == 'columns':
             df = pd.DataFrame.from_dict(extra_fields, orient='columns')
-            df.to_csv(save_to, mode='a', index=False)
+            df.iloc[[1]].to_csv(save_to, mode='a', index=False)
         elif experiment_axis == 'rows':
             df = pd.DataFrame.from_dict(extra_fields, orient='index')
-            df.to_csv(save_to, mode='a', index=True)
+            df = df[['value']]
+            df.to_csv(save_to, mode='a', index=True, header=False)
         else:
             raise ValueError(f'Unknown experiment axis: {experiment_axis}. Valid arguments are '
                              f'"columns" and "rows".')

elab_bridge/tests/test_cli.py

@@ -7,6 +7,7 @@
 
 project_dir = test_directory / 'testfiles_elab' / 'TestProject'
 
+
 @pytest.mark.skip('Requires `upload_experiment` to be implemented')
 def test_installed(initialize_test_dir):
     """
@@ -15,6 +16,7 @@ def test_installed(initialize_test_dir):
     result = subprocess.run(['ElabBridge', '--help'], stdout=subprocess.PIPE)
     assert 'usage:' in str(result.stdout)
 
+
 @pytest.mark.skip('Requires `upload_experiment` to be implemented')
 def test_download(initialize_test_dir):
     """
@@ -50,3 +52,19 @@ def test_download(initialize_test_dir):
     #                         stdout=subprocess.PIPE)
     # assert 'error' not in str(result.stdout)
     # assert pathlib.Path(output_file).exists()
+
+
+def test_extended_download(initialize_test_dir):
+    """
+    Check extended_download
+    """
+
+    tags = ['BIDS']
+    output_file = test_directory / 'cli_download_test.csv'
+
+    result = subprocess.run(['ElabBridge', 'extended_download', output_file,
+                             SERVER_CONFIG_YAML] + tags, stdout=subprocess.PIPE)
+
+    assert 'error' not in str(result.stdout)
+    assert output_file.exists()
+    output_file.unlink()

elab_bridge/tests/test_server_interface.py

@@ -58,7 +58,7 @@ def test_extended_download(initialize_test_dir):
     json_file = test_directory / 'testfiles_elab' / 'downloaded_multiple_experiment.json'
 
     experiment = extended_download(save_to=json_file, server_config_json=SERVER_CONFIG_YAML,
-                                   experiment_tags=['BIDS'])
+                                   experiment_tags=['BIDS'], format='csv')
 
     assert json_file.exists()
     for exp in experiment:

redcap_bridge/tests/test_server_interface.py

@@ -132,6 +132,7 @@ def test_download_datadict(clean_server, initialize_test_dir):
         assert oline == dline
 
 
+@pytest.mark.skip('RedCap not use')
 def test_check_external_modules(clean_server, initialize_test_dir):
     """
     Download project info from server and compare to required external modules
@@ -151,6 +152,7 @@ def test_download_project_settings(clean_server):
         assert key in res
 
 
+@pytest.mark.skip('RedCap not use')
 def test_configure_project_settings(clean_server, initialize_test_dir):
     """
     Test configure server project based on default values and project.json