better error for invalid gate names '.' & '..' (closes #220)

src/flowkit/_models/gating_strategy.py

@@ -71,11 +71,21 @@ def add_gate(self, gate, gate_path, sample_id=None):
         if not isinstance(gate_path, tuple):
             raise TypeError("gate_path must be a tuple not %s" % str(type(gate_path)))
 
+        # make string representation of parent path, used for anytree Resolver later
+        parent_abs_gate_path = "/" + "/".join(gate_path)
+
+        # Verify gate name is not "." or ".." as these are incompatible w/ the
+        # current version of anytree (see open issue https://github.com/c0fec0de/anytree/issues/269)
+        if gate.gate_name in ['.', '..']:
+            raise GateTreeError(
+                "Gate name '%s' is incompatible with FlowKit. Gate was found in path: %s" %
+                (gate.gate_name, parent_abs_gate_path)
+            )
+
         # We need the parent gate (via its node) for 2 reasons:
         #   1) To verify the parent exists when creating a new node
         #   2) Verify the parent is NOT a QuadrantGate, as only
         #      Quadrants of a QuadrantGate can be a parent.
-        parent_abs_gate_path = "/" + "/".join(gate_path)
         try:
             parent_node = self.resolver.get(self._gate_tree, parent_abs_gate_path)
         except anytree.ResolverError:

tests/workspace_tests.py

@@ -11,7 +11,7 @@
 # noinspection PyProtectedMember
 from flowkit._models.transforms._base_transform import Transform
 from flowkit._models.gating_results import GatingResults
-from flowkit.exceptions import GateReferenceError
+from flowkit.exceptions import GateReferenceError, GateTreeError
 
 from tests.test_config import test_samples_8c_full_set
 
@@ -426,6 +426,18 @@ def test_parse_wsp_with_ellipse(self):
         self.assertIsInstance(gate_indices, np.ndarray)
         self.assertEqual(np.sum(gate_indices), 7023)
 
+    def test_parse_wsp_with_invalid_gate_name(self):
+        wsp_path = "data/8_color_data_set/8_color_ICS_dot_gate_name.wsp"
+
+        self.assertRaisesRegex(
+            GateTreeError,
+            r"Gate name '\.' is incompatible with FlowKit\. " 
+            r"Gate was found in path: \/root\/Time\/Singlets\/aAmine-\/CD3\+\/CD4\+",
+            Workspace,
+            wsp_path,
+            ignore_missing_files=True
+        )
+
     def test_parse_wsp_with_boolean_gates(self):
         wsp_path = "data/8_color_data_set/8_color_ICS_boolean_gate_testing.wsp"
         fcs_path = "data/8_color_data_set/fcs_files/101_DEN084Y5_15_E01_008_clean.fcs"