fix #40

bluepysnap/circuit.py

@@ -49,6 +49,7 @@ def __init__(self, config):
             Circuit: A Circuit object.
         """
         self._config = Config(config).resolve()
+        self.is_open = True
 
     @property
     def config(self):
@@ -58,15 +59,42 @@ def config(self):
     @cached_property
     def nodes(self):
         """Access to node population(s). See :py:class:`~bluepysnap.nodes.NodePopulation`."""
-        return _collect_populations(
-            self._config['networks']['nodes'],
-            lambda cfg: NodeStorage(cfg, self)
-        )
+        if self.is_open:
+            return _collect_populations(
+                self._config['networks']['nodes'],
+                lambda cfg: NodeStorage(cfg, self)
+            )
+        raise BluepySnapError("I/O error. Cannot access the h5 files with closed context.")
 
     @cached_property
     def edges(self):
         """Access to edge population(s). See :py:class:`~bluepysnap.edges.EdgePopulation`."""
-        return _collect_populations(
-            self._config['networks']['edges'],
-            lambda cfg: EdgeStorage(cfg, self)
-        )
+        if self.is_open:
+            return _collect_populations(
+                self._config['networks']['edges'],
+                lambda cfg: EdgeStorage(cfg, self)
+            )
+        raise BluepySnapError("I/O error. Cannot access the h5 files with closed context.")
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        """Close the context for all populations."""
+
+        def _close_context(pop):
+            """Close the h5 context for population."""
+            if "_population" in pop.__dict__:
+                del pop.__dict__["_population"]
+
+        if self.nodes:
+            for population in self.nodes.values():
+                _close_context(population)
+        if self.edges:
+            for population in self.edges.values():
+                _close_context(population)
+
+        del self.__dict__["nodes"]
+        del self.__dict__["edges"]
+        self.is_open = False
+
+    def __enter__(self):
+        """Enter the context manager for circuit."""
+        return self

bluepysnap/edges.py

@@ -50,7 +50,7 @@ def __init__(self, config, circuit):
         self._circuit = circuit
         self._populations = {}
 
-    @cached_property
+    @property
     def storage(self):
         """Access to the libsonata edge storage."""
         return libsonata.EdgeStorage(self._h5_filepath)
@@ -111,9 +111,11 @@ def __init__(self, edge_storage, population_name):
 
     @cached_property
     def _population(self):
-        return self._edge_storage.storage.open_population(self.name)
+        if self._edge_storage.circuit.is_open:
+            return self._edge_storage.storage.open_population(self.name)
+        raise BluepySnapError("I/O error. Cannot access the h5 files with closed context.")
 
-    @property
+    @cached_property
     def size(self):
         """Population size."""
         return self._population.size
@@ -396,7 +398,6 @@ def _optimal_direction():
             secondary_node_ids = np.unique(secondary_node_ids)
 
         secondary_node_ids_used = set()
-
         for key_node_id in primary_node_ids:
             connected_node_ids = get_connected_node_ids(key_node_id, unique=False)
             connected_node_ids_with_count = np.stack(

bluepysnap/nodes.py

@@ -54,7 +54,7 @@ def __init__(self, config, circuit):
         self._circuit = circuit
         self._populations = {}
 
-    @cached_property
+    @property
     def storage(self):
         """Access to the libsonata node storage."""
         return libsonata.NodeStorage(self._h5_filepath)
@@ -174,7 +174,9 @@ def _data(self):
 
     @cached_property
     def _population(self):
-        return self._node_storage.storage.open_population(self.name)
+        if self._node_storage.circuit.is_open:
+            return self._node_storage.storage.open_population(self.name)
+        raise BluepySnapError("I/O error. Cannot access the h5 files with closed context.")
 
     @cached_property
     def size(self):

tests/test_circuit.py

@@ -1,4 +1,5 @@
 import pytest
+import h5py
 
 from bluepysnap.nodes import NodePopulation
 from bluepysnap.edges import EdgePopulation
@@ -11,12 +12,12 @@
 def test_all():
     circuit = test_module.Circuit(
         str(TEST_DATA_DIR / 'circuit_config.json'))
-    assert(
-        circuit.config['networks']['nodes'][0] ==
-        {
-            'nodes_file': str(TEST_DATA_DIR / 'nodes.h5'),
-            'node_types_file': None,
-        }
+    assert (
+            circuit.config['networks']['nodes'][0] ==
+            {
+                'nodes_file': str(TEST_DATA_DIR / 'nodes.h5'),
+                'node_types_file': None,
+            }
     )
     assert isinstance(circuit.nodes, dict)
     assert isinstance(circuit.edges, dict)
@@ -34,3 +35,37 @@ def test_duplicate_population():
     with pytest.raises(BluepySnapError):
         circuit.nodes
 
+
+def test_close_contexts():
+    with test_module.Circuit(str(TEST_DATA_DIR / 'circuit_config.json')) as circuit:
+        edge = circuit.edges['default']
+        edge.size
+        node = circuit.nodes['default']
+        node.size
+        node_file = circuit.config['networks']['nodes'][0]['nodes_file']
+        edge_file = circuit.config['networks']['edges'][0]['edges_file']
+
+    with h5py.File(node_file, "r+") as h5:
+        list(h5)
+
+    with h5py.File(edge_file, "r+") as h5:
+        list(h5)
+
+def test_close_contexts_errors_extracted_obj():
+    with test_module.Circuit(str(TEST_DATA_DIR / 'circuit_config.json')) as circuit:
+        edges = circuit.edges['default']
+        edges.size
+        nodes = circuit.nodes['default']
+        nodes.size
+
+    with pytest.raises(BluepySnapError):
+        circuit.nodes
+
+    with pytest.raises(BluepySnapError):
+        circuit.edges
+
+    with pytest.raises(BluepySnapError):
+        nodes.property_names
+
+    with pytest.raises(BluepySnapError):
+        edges.property_names

tests/test_edges.py

@@ -4,6 +4,7 @@
 import pandas as pd
 import pandas.testing as pdt
 import pytest
+import h5py
 
 import libsonata
 from mock import Mock

tests/test_nodes.py

@@ -1,8 +1,9 @@
 import numpy as np
 import numpy.testing as npt
 import pandas as pd
-import pandas.util.testing as pdt
+import pandas.testing as pdt
 import pytest
+import h5py
 
 import libsonata
 from mock import Mock