Fix extended_download function to allow download of multiple experiment

elab_bridge/server_interface.py

@@ -4,7 +4,24 @@
 import pandas as pd
 
 
-def extended_download(server_config_json, experiment_tags):
+def extended_download(save_to, server_config_json, experiment_tags):
+    """
+    Download an individual experiment.
+
+    Parameters
+    ----------
+    save_to: str
+        Path where to save the retrieved experiment data
+    server_config_json: str
+        Path to the json file containing the api_url and the api_token
+    experiment_tags: list
+        List of tags of your experiments
+
+    Returns
+    -------
+        (list) List of the experiment downloaded
+    """
+
     api_client = get_elab_config(server_config_json)
     experiment_api = elabapi_python.ExperimentsApi(api_client)
 
@@ -17,7 +34,14 @@ def extended_download(server_config_json, experiment_tags):
     for experiment in experiments:
         experiment_ids.append(experiment.id)
 
-    return experiment_ids
+    downloaded_experiments = []
+
+    for experiment_id in experiment_ids:
+        metadata = download_experiment(save_to, server_config_json, experiment_id, format='json',
+                                       experiment_axis='columns')
+        downloaded_experiments.append(metadata)
+
+    return downloaded_experiments
 
 
 def download_experiment(save_to, server_config_json, experiment_id, format='json', experiment_axis='columns'):
@@ -64,10 +88,10 @@ 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, index=False)
+            df.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, index=True)
+            df.to_csv(save_to, mode='a', index=True)
         else:
             raise ValueError(f'Unknown experiment axis: {experiment_axis}. Valid arguments are '
                              f'"columns" and "rows".')

elab_bridge/tests/test_server_interface.py

@@ -57,17 +57,12 @@ def test_download_experiment(initialize_test_dir):
 def test_extended_download(initialize_test_dir):
     json_file = test_directory / 'testfiles_elab' / 'downloaded_experiment.json'
 
-    experiments_ids = extended_download(server_config_json=SERVER_CONFIG_YAML,
+    experiment = extended_download(save_to=json_file, server_config_json=SERVER_CONFIG_YAML,
                                         experiment_tags=['BIDS'])
-    print(experiments_ids)
-
-    for experiment_id in experiments_ids:
-        experiment = download_experiment(save_to=json_file,
-                                         server_config_json=SERVER_CONFIG_YAML,
-                                         experiment_id=experiment_id,
-                                         format='json')
-        assert json_file.exists()
-        assert 'extra_fields' in experiment
+
+    assert json_file.exists()
+    for exp in experiment:
+        assert 'extra_fields' in exp
 
     # cleanup
     json_file.unlink()

redcap_bridge/tests/testfiles_redcap/TestProject/project.json

@@ -9,7 +9,7 @@
   "external_modules": {
     "auto_populate_fields": {
       "link": "https://github.com/ctsit/auto_populate_fields",
-      "version": "v2.5.2"
+      "version": "v2.6.0"
     }
   },
   "api_token": "REDCAP_API_TOKEN",