Add source/target to the available properties for edges (#69)

BlueBrain · Jul 3, 2020 · f90fc4f · f90fc4f
1 parent a81f40a
commit f90fc4f
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Showing 3 changed files with 35 additions and 9 deletions.
diff --git a/bluepysnap/edges.py b/bluepysnap/edges.py
@@ -24,7 +24,7 @@
 import libsonata
 import numpy as np
 import pandas as pd
-
+import six
 from cached_property import cached_property
 
 from bluepysnap.exceptions import BluepySnapError
@@ -137,17 +137,26 @@ def target(self):
         return self._nodes(self._population.target)
 
     @cached_property
-    def _property_names(self):
+    def _attribute_names(self):
         return set(self._population.attribute_names)
 
     @cached_property
     def _dynamics_params_names(self):
         return set(utils.add_dynamic_prefix(self._population.dynamics_attribute_names))
 
+    @property
+    def _topology_property_names(self):
+        return {six.text_type(Edge.SOURCE_NODE_ID), six.text_type(Edge.TARGET_NODE_ID)}
+
     @property
     def property_names(self):
-        """Set of available edge properties."""
-        return self._property_names | self._dynamics_params_names
+        """Set of available edge properties.
+
+        Notes:
+            Properties are a combination of the group attributes, the dynamics_params and the
+            topology properties.
+        """
+        return self._attribute_names | self._dynamics_params_names | self._topology_property_names
 
     @cached_property
     def property_dtypes(self):
@@ -185,7 +194,7 @@ def _get_property(self, prop, selection):
             result = self._population.source_nodes(selection)
         elif prop == Edge.TARGET_NODE_ID:
             result = self._population.target_nodes(selection)
-        elif prop in self._property_names:
+        elif prop in self._attribute_names:
             result = self._population.get_attribute(prop, selection)
         elif prop in self._dynamics_params_names:
             result = self._population.get_dynamics_attribute(
@@ -231,6 +240,10 @@ def properties(self, edge_ids, properties):
             pandas.Series/pandas.DataFrame:
                 A pandas Series indexed by edge IDs if ``properties`` is scalar.
                 A pandas DataFrame indexed by edge IDs if ``properties`` is list.
+
+        Notes:
+            The EdgePopulation.property_names function will give you all the usable properties
+            for the `properties` argument.
         """
         selection = libsonata.Selection(edge_ids)
         return self._get(selection, properties)

diff --git a/bluepysnap/nodes.py b/bluepysnap/nodes.py
@@ -157,7 +157,11 @@ def _dynamics_params_names(self):
 
     @property
     def property_names(self):
-        """Set of available node properties."""
+        """Set of available node properties.
+
+        Notes:
+            Properties are a combination of the group attributes and the dynamics_params.
+        """
         return self._property_names | self._dynamics_params_names
 
     def container_property_names(self, container):
@@ -420,6 +424,10 @@ def get(self, group=None, properties=None):
             pandas.Series/pandas.DataFrame:
                 If single node ID is passed as ``group`` returns a pandas Series.
                 Otherwise return a pandas DataFrame indexed by node IDs.
+
+        Notes:
+            The NodePopulation.property_names function will give you all the usable properties
+            for the `properties` argument.
         """
         result = self._data
         if properties is not None:

diff --git a/tests/test_edges.py b/tests/test_edges.py
@@ -106,6 +106,8 @@ def test_basic(self):
         assert (
                 sorted(self.test_obj.property_names) ==
                 sorted([
+                    Synapse.SOURCE_NODE_ID,
+                    Synapse.TARGET_NODE_ID,
                     Synapse.AXONAL_DELAY,
                     Synapse.G_SYNX,
                     Synapse.POST_X_CENTER,
@@ -134,7 +136,8 @@ def test_container_properties(self):
             ['PRE_Y_SURFACE', 'PRE_Z_SURFACE', 'PRE_X_CENTER', 'POST_Y_CENTER', 'AXONAL_DELAY',
              'POST_X_CENTER', 'POST_Y_SURFACE', 'POST_Z_SURFACE', 'PRE_Y_CENTER', 'POST_Z_CENTER',
              'PRE_Z_CENTER', 'PRE_X_SURFACE', 'POST_X_SURFACE', 'POST_SECTION_ID', 'PRE_SECTION_ID',
-             'POST_SECTION_POS', 'PRE_SECTION_POS', 'SYN_WEIGHT'])
+             'POST_SECTION_POS', 'PRE_SECTION_POS', 'SYN_WEIGHT',
+             'SOURCE_NODE_ID', 'TARGET_NODE_ID'])
         assert sorted(self.test_obj.container_property_names(Edge)) == expected
         with pytest.raises(BluepySnapError):
             mapping = {"X": "x"}
@@ -164,7 +167,8 @@ def test_property_dtypes(self):
                 'float32'), dtype('float64'), dtype('float32'), dtype('float64'), dtype(
                 'int64'), dtype('int64'), dtype('float64'), dtype('float64'), dtype(
                 'float64'), dtype('float64'), dtype('float64'), dtype('float64'), dtype(
-                'float32'), dtype('float32'), dtype('float64'), dtype('float64')]
+                'float32'), dtype('float32'), dtype('float64'), dtype('float64'),
+                dtype('uint64'), dtype('uint64')]
             , index=['syn_weight', '@dynamics:param1', 'afferent_surface_y',
                      'afferent_surface_z', 'conductance', 'efferent_center_x',
                      'delay', 'afferent_center_z', 'efferent_section_id',
@@ -173,7 +177,8 @@ def test_property_dtypes(self):
                      'afferent_center_y', 'afferent_surface_x',
                      'efferent_surface_x', 'afferent_section_pos',
                      'efferent_section_pos', 'efferent_surface_y',
-                     'efferent_center_z']).sort_index()
+                     'efferent_center_z',
+                     '@source_node', '@target_node']).sort_index()
 
         pdt.assert_series_equal(expected, self.test_obj.property_dtypes)