Do not use colon-separated string yaml keys

Author: acrellin

cesium_app/handlers/dataset.py

@@ -37,7 +37,7 @@ def post(self):
 
         zipfile_name = (str(uuid.uuid4()) + "_" +
                         util.secure_filename(zipfile['name']))
-        zipfile_path = pjoin(self.cfg['paths:upload_folder'], zipfile_name)
+        zipfile_path = pjoin(self.cfg['paths']['upload_folder'], zipfile_name)
 
         for prefix in tarball_content_types:
             zipfile['body'] = zipfile['body'].replace(prefix, '')
@@ -55,7 +55,7 @@ def post(self):
             headerfile = data['headerFile']
             headerfile_name = (str(uuid.uuid4()) + "_" +
                                util.secure_filename(headerfile['name']))
-            headerfile_path = pjoin(self.cfg['paths:upload_folder'], headerfile_name)
+            headerfile_path = pjoin(self.cfg['paths']['upload_folder'], headerfile_name)
 
             with open(headerfile_path, 'w') as f:
                 f.write(headerfile['body'])
@@ -66,7 +66,7 @@ def post(self):
         p = Project.query.filter(Project.id == project_id).one()
         ts_paths = data_management.parse_and_store_ts_data(
             zipfile_path,
-            self.cfg['paths:ts_data_folder'],
+            self.cfg['paths']['ts_data_folder'],
             headerfile_path)
         meta_features = list(time_series.load(ts_paths[0]).meta_features.keys())
         unique_ts_paths = [os.path.join(os.path.dirname(ts_path),

cesium_app/handlers/feature.py

@@ -94,7 +94,7 @@ async def post(self):
         if not dataset.is_owned_by(self.current_user):
             raise AccessError('No such data set')
 
-        fset_path = pjoin(self.cfg['paths:features_folder'],
+        fset_path = pjoin(self.cfg['paths']['features_folder'],
                           '{}_featureset.npz'.format(uuid.uuid4()))
 
         fset = Featureset(name=featureset_name,
@@ -161,7 +161,7 @@ def post(self):
         else:
             labels = [None]
         fset_path = pjoin(
-            self.cfg['paths:features_folder'],
+            self.cfg['paths']['features_folder'],
             '{}_{}.npz'.format(uuid.uuid4(), data['dataFile']['name']))
 
         featurize.save_featureset(fset, fset_path, labels=labels)

cesium_app/handlers/model.py

@@ -148,7 +148,7 @@ async def post(self):
         model_params, params_to_optimize = check_model_param_types(model_type,
                                                                    model_params)
         model_type = model_type.split()[0]
-        model_path = pjoin(self.cfg['paths:models_folder'],
+        model_path = pjoin(self.cfg['paths']['models_folder'],
                            '{}_model.pkl'.format(uuid.uuid4()))
 
         model = Model(name=model_name, file_uri=model_path,

cesium_app/handlers/prediction.py

@@ -68,7 +68,7 @@ async def post(self):
         if (model.finished is None) or (fset.finished is None):
             return self.error('Computation of model or feature set still in progress')
 
-        pred_path = os.path.abspath(pjoin(self.cfg['paths:predictions_folder'],
+        pred_path = os.path.abspath(pjoin(self.cfg['paths']['predictions_folder'],
                                           '{}_prediction.npz'.format(uuid.uuid4())))
         prediction = Prediction(file_uri=pred_path, dataset=dataset,
                                 project=dataset.project, model=model)

cesium_app/tests/conftest.py

@@ -17,7 +17,7 @@
 print('Loading test configuration from test_config.yaml')
 basedir = pathlib.Path(os.path.dirname(__file__))/'../..'
 cfg = load_config([basedir/'test_config.yaml'])
-set_server_url(f'http://localhost:{cfg["ports:app"]}')
+set_server_url(f'http://localhost:{cfg["ports"]["app"]}')
 print('Setting test database to:', cfg['database'])
 models.init_db(**cfg['database'])
 

cesium_app/tests/frontend/test_predict.py

@@ -159,7 +159,7 @@ def test_download_prediction_csv_class(driver, project, dataset, featureset,
                                        model, prediction):
     driver.get('/')
     _click_download(project.id, driver)
-    matching_downloads_paths = glob.glob(f'{cfg["paths:downloads_folder"]}/'
+    matching_downloads_paths = glob.glob(f'{cfg["paths"]["downloads_folder"]}/'
                                          'cesium_prediction_results*')
     assert len(matching_downloads_paths) == 1
     try:
@@ -179,7 +179,7 @@ def test_download_prediction_csv_class(driver, project, dataset, featureset,
 def test_download_prediction_csv_class_unlabeled(driver, project, unlabeled_prediction):
     driver.get('/')
     _click_download(project.id, driver)
-    matching_downloads_paths = glob.glob(f'{cfg["paths:downloads_folder"]}/'
+    matching_downloads_paths = glob.glob(f'{cfg["paths"]["downloads_folder"]}/'
                                          'cesium_prediction_results*')
     assert len(matching_downloads_paths) == 1
     try:
@@ -195,7 +195,7 @@ def test_download_prediction_csv_class_prob(driver, project, dataset,
                                             featureset, model, prediction):
     driver.get('/')
     _click_download(project.id, driver)
-    matching_downloads_paths = glob.glob(f'{cfg["paths:downloads_folder"]}/'
+    matching_downloads_paths = glob.glob(f'{cfg["paths"]["downloads_folder"]}/'
                                          'cesium_prediction_results*')
     assert len(matching_downloads_paths) == 1
     try:
@@ -217,7 +217,7 @@ def test_download_prediction_csv_regr(driver, project, dataset, featureset,
                                       model, prediction):
     driver.get('/')
     _click_download(project.id, driver)
-    matching_downloads_paths = glob.glob(f'{cfg["paths:downloads_folder"]}/'
+    matching_downloads_paths = glob.glob(f'{cfg["paths"]["downloads_folder"]}/'
                                          'cesium_prediction_results*')
     assert len(matching_downloads_paths) == 1
     try:

config.yaml

@@ -15,7 +15,6 @@ paths:
     features_folder: './data/extracted_features'
     predictions_folder: './data/predictions'
     ts_data_folder: './data/ts_data'
-
     upload_folder: './data/uploads'
     custom_feature_script_folder: './data/uploads/custom_feature_scripts'