Merge branch 'develop'

Author: whitews

examples/data/8_color_data_set/reused_quad_gate_with_child.wsp

@@ -75,6 +75,16 @@ def _process_results(self):
 
         self.report = df.sort_values(['sample', 'level', 'gate_name'])
 
+    def _filter_gate_report(self, gate_name, gate_path=None):
+        results = self.report[(self.report['sample'] == self.sample_id) & (self.report['gate_name'] == gate_name)]
+
+        if gate_path is not None:
+            results = results[results.gate_path == gate_path]
+        elif len(results) > 1:
+            raise ValueError("Gate name %s is ambiguous, specify the full gate path")
+
+        return results
+
     def get_gate_membership(self, gate_name, gate_path=None):
         """
         Retrieve a boolean array indicating gate membership for the events in the GatingResults sample.
@@ -108,45 +118,39 @@ def get_gate_membership(self, gate_name, gate_path=None):
         else:
             raise ValueError("Report as bug: The gate %s appears to have multiple quadrant parents." % gate_name)
 
-    def get_gate_count(self, gate_name):
+    def get_gate_count(self, gate_name, gate_path=None):
         """
         Retrieve event count for the specified gate ID for the gating results sample
 
         :param gate_name: text string of a gate name
+        :param gate_path: tuple of ancestor gate names
         :return: integer count of events in gate ID
         """
-        results = self.report[(self.report['sample'] == self.sample_id) & (self.report['gate_name'] == gate_name)]
-
-        if len(results) > 1:
-            raise NotImplementedError("Gate ID %s is ambiguous and gate_path is not yet implemented for this method")
+        results = self._filter_gate_report(gate_name, gate_path=gate_path)
 
         return results['count'].values[0]
 
-    def get_gate_absolute_percent(self, gate_name):
+    def get_gate_absolute_percent(self, gate_name, gate_path=None):
         """
         Retrieve percent of events, relative to the total sample events, of the specified gate ID for the
         gating results sample
 
         :param gate_name: text string of a gate name
+        :param gate_path: tuple of ancestor gate names
         :return: floating point number of the absolute percent
         """
-        results = self.report[(self.report['sample'] == self.sample_id) & (self.report['gate_name'] == gate_name)]
-
-        if len(results) > 1:
-            raise NotImplementedError("Gate ID %s is ambiguous and gate_path is not yet implemented for this method")
+        results = self._filter_gate_report(gate_name, gate_path=gate_path)
 
         return results['absolute_percent'].values[0]
 
-    def get_gate_relative_percent(self, gate_name):
+    def get_gate_relative_percent(self, gate_name, gate_path=None):
         """
         Retrieve percent of events, relative to parent gate, of the specified gate ID for the gating results sample
 
         :param gate_name: text string of a gate name
+        :param gate_path: tuple of ancestor gate names
         :return: floating point number of the relative percent
         """
-        results = self.report[(self.report['sample'] == self.sample_id) & (self.report['gate_name'] == gate_name)]
-
-        if len(results) > 1:
-            raise NotImplementedError("Gate ID %s is ambiguous and gate_path is not yet implemented for this method")
+        results = self._filter_gate_report(gate_name, gate_path=gate_path)
 
         return results['relative_percent'].values[0]

examples/flowkit-session-replicate-flowjo-wsp.ipynb

@@ -426,12 +426,10 @@ def _get_orig_events(self, subsample=False):
         :return: NumPy array of original events
         """
         if self._orig_events is None:
-            warnings.warn(
+            raise ValueError(
                 "Original events were not cached, to retrieve them create a "
-                "Sample instance with cache_original_events=True",
-                UserWarning
+                "Sample instance with cache_original_events=True"
             )
-            return None
 
         if subsample:
             return self._orig_events[self.subsample_indices]

flowkit/_models/gating_results.py

@@ -84,7 +84,7 @@ def _gate_samples(gating_strategies, samples, cache_events, verbose, use_mp=Fals
             proc_count = sample_count
 
         with mp.get_context(mp_context).Pool(processes=proc_count, maxtasksperchild=1) as pool:
-            if True:
+            if verbose:
                 print(
                     '#### Processing gates for %d samples (multiprocessing is enabled - %d cpus) ####'
                     % (sample_count, proc_count)

flowkit/_models/sample.py

@@ -282,7 +282,9 @@ def _recurse_wsp_sub_populations(sub_pop_el, gate_path, gating_ns, data_type_ns)
     ns_map = sub_pop_el.nsmap
 
     if gate_path is None:
-        gate_path = []
+        # here we'll create the gate path as a list b/c we will append to it for recursion
+        # however, when it is finally stored in the list of gate dicts we will convert to tuple
+        gate_path = ['root']
         parent_id = None
     else:
         parent_id = gate_path[-1]
@@ -324,7 +326,7 @@ def _recurse_wsp_sub_populations(sub_pop_el, gate_path, gating_ns, data_type_ns)
             {
                 'owning_group': owning_group,
                 'gate': g,
-                'gate_path': gate_path
+                'gate_path': tuple(gate_path)  # converting to tuple!
             }
         )
 

flowkit/_models/session.py

@@ -1 +1 @@
-__version__ = "0.8.0"
+__version__ = "0.8.1"

flowkit/_utils/wsp_utils.py

@@ -11,6 +11,7 @@
 from .gating_strategy_tests import GatingStrategyTestCase, GatingStrategyReusedGatesTestCase
 from .session_tests import SessionTestCase
 from .flowjo_wsp_tests import FlowJoWSPTestCase
+from .gating_results_tests import GatingResultsTestCase
 from .matrix_tests import MatrixTestCase
 from .transform_tests import TransformsTestCase
 from .gate_tests import GateTestCase

flowkit/_version.py

@@ -196,6 +196,22 @@ def test_get_ambiguous_gate_objects(self):
         self.assertIsInstance(gate_indices, np.ndarray)
         self.assertEqual(np.sum(gate_indices), 21)
 
+    def test_parse_wsp_reused_gate_with_child(self):
+        wsp_path = "examples/data/8_color_data_set/reused_quad_gate_with_child.wsp"
+
+        fks = Session(copy.deepcopy(test_samples_8c_full_set))
+        fks.import_flowjo_workspace(wsp_path, ignore_missing_files=True)
+        group_name = 'All Samples'
+        gate_name = 'some_child_gate'
+
+        gate_ids = fks.get_gate_ids(group_name)
+
+        gate_id_1 = (gate_name, ('root', 'good cells', 'cd4+', 'Q2: CD107a+, IL2+'))
+        gate_id_2 = (gate_name, ('root', 'good cells', 'cd8+', 'Q2: CD107a+, IL2+'))
+
+        self.assertIn(gate_id_1, gate_ids)
+        self.assertIn(gate_id_2, gate_ids)
+
     def test_analyze_single_sample(self):
         wsp_path = "examples/data/8_color_data_set/8_color_ICS_simple.wsp"
         sample_id = '101_DEN084Y5_15_E01_008_clean.fcs'

flowkit/tests/__init__.py

@@ -4,7 +4,7 @@
 import unittest
 import numpy as np
 
-from flowkit import gates, Dimension
+from flowkit import Dimension
 from .gating_strategy_tests import poly1_gate
 
 test_data_range1 = np.linspace(0.0, 10.0, 101)