fixing leftover datasets when post_dataset fails to link it to a pr…

…oject (#87)

* deleting created dataset if it cannot be linked to project

* removed naked except and bad type tests

* flake8

* removing print

ezomero/_posts.py

@@ -16,6 +16,7 @@
 from omero.gateway import MapAnnotationWrapper, OriginalFileWrapper
 from omero.gateway import CommentAnnotationWrapper
 from omero.rtypes import rstring, rint, rdouble
+from omero import SecurityViolation
 from .rois import Point, Line, Rectangle, Ellipse
 from .rois import Polygon, Polyline, Label
 import importlib.util
@@ -96,8 +97,16 @@ def post_dataset(conn: BlitzGateway, dataset_name: str,
     dataset.save()
 
     if project_id is not None:
-        link_datasets_to_project(conn, [dataset.getId()], project_id)
-    return dataset.getId()
+        try:
+            link_datasets_to_project(conn, [dataset.getId()], project_id)
+            return dataset.getId()
+        except SecurityViolation:
+            logging.warning('You do not have permission to create new '
+                            f'datasets in project {project_id}.')
+            conn.deleteObject("Dataset", dataset.getId())
+            return None
+    else:
+        return dataset.getId()
 
 
 def post_image(conn: BlitzGateway, image: np.ndarray, image_name: str,
@@ -689,7 +698,7 @@ def create_columns(table: Any,
                    headers: bool) -> List[Column]:
     """Helper function to create the correct column types from a table"""
     cols = []
-    if type(table) == list:
+    if isinstance(table, list):
         if headers:
             titles = table[0]
             data = table[1:]
@@ -712,7 +721,7 @@ def create_columns(table: Any,
                 max_size = len(max(data[i], key=len))
                 cols.append(StringColumn(titles[i], '',
                             max_size, data[i]))
-    elif type(table) == pd.core.frame.DataFrame:
+    elif isinstance(table, pd.core.frame.DataFrame):
         df = table.convert_dtypes()
         ints = df.select_dtypes(include='int')
         for col in ints:

tests/conftest.py

@@ -92,7 +92,7 @@ def omero_params(request):
     web_host = request.config.getoption("--omero-web-host")
     port = request.config.getoption("--omero-port")
     secure = request.config.getoption("--omero-secure")
-    return(user, password, host, web_host, port, secure)
+    return (user, password, host, web_host, port, secure)
 
 
 @pytest.fixture(scope='session')

tests/test_gets.py

@@ -538,7 +538,7 @@ def test_get_shape_and_get_shape_ids(conn, project_structure,
         shape = ezomero.get_shape(conn, shape_ids[i])
         assert hasattr(shape, 'label')
         for pre_shape in shapes:
-            if type(shape) == type(pre_shape):
+            if type(shape) is type(pre_shape):
                 assert shape.fill_color == pre_shape.fill_color
                 assert shape.stroke_color == pre_shape.stroke_color
                 assert shape.stroke_width == pre_shape.stroke_width

tests/test_posts.py

@@ -38,7 +38,9 @@ def test_post_dataset(conn, project_structure, users_groups, timestamp):
     ds_test_name3 = 'test_post_dataset3_' + timestamp
     pid = 99999999
     did3 = ezomero.post_dataset(conn, ds_test_name3, project_id=pid)
+    ds_ids = ezomero.get_dataset_ids(conn)
     assert did3 is None
+    assert len(ds_ids) == 2
 
     # Dataset in cross-group project, valid permissions
     username = users_groups[1][0][0]  # test_user1
@@ -62,6 +64,8 @@ def test_post_dataset(conn, project_structure, users_groups, timestamp):
     project_info = project_structure[0]
     pid = project_info[1][1]  # proj1 (in test_group_1)
     did5 = ezomero.post_dataset(current_conn, ds_test_name5, project_id=pid)
+    ds_ids = ezomero.get_dataset_ids(current_conn)
+    assert len(ds_ids) == 1
     current_conn.close()
     assert did5 is None