[BBPBGLIB-1030] Reject *.sonata nodes and edges file

neurodamus/core/configuration.py

@@ -510,6 +510,7 @@ def _projection_params(config: _SimConfig, run_conf):
     non_negatives = ("PopulationID",)
     for name, proj in config.projections.items():
         _check_params("Projection " + name, compat.Map(proj), required_fields, (), non_negatives)
+        _validate_file_extension(compat.Map(proj).get("Path"))
 
 
 @SimConfig.validator
@@ -553,6 +554,8 @@ def _make_circuit_config(config_dict, req_morphology=True):
     elif config_dict.get("nrnPath") == "<NONE>":
         config_dict["nrnPath"] = False
     _validate_circuit_morphology(config_dict, req_morphology)
+    _validate_file_extension(config_dict.get("CellLibraryFile"))
+    _validate_file_extension(config_dict.get("nrnPath"))
     return CircuitConfig(config_dict)
 
 
@@ -575,6 +578,15 @@ def _validate_circuit_morphology(config_dict, required=True):
     log_verbose(" > MorphologyType = %s, src: %s", morph_type, morph_path)
 
 
+def _validate_file_extension(path):
+    if not path:
+        return
+    filepath = path.split(":")[0]  # for sonata, remove the edge_pop name appended to the file path
+    if filepath.endswith(".sonata"):
+        raise ConfigurationError("*.sonata files are no longer supported, "
+                                 "please rename them to *.h5")
+
+
 @SimConfig.validator
 def _base_circuit(config: _SimConfig, run_conf):
     log_verbose("CIRCUIT (default): %s", run_conf.get("CircuitPath", "<DISABLED>"))

neurodamus/io/synapse_reader.py

@@ -172,13 +172,7 @@ def has_property(self, field_name):
     def _get_sonata_circuit(path):
         """Returns a SONATA edge file in path if present
         """
-        if os.path.isdir(path):
-            filename = os.path.join(path, "edges.sonata")
-            if os.path.exists(filename):
-                return filename
-        elif path.endswith(".sonata"):
-            return path
-        elif path.endswith(".h5"):
+        if path.endswith(".h5"):
             import h5py
             f = h5py.File(path, 'r')
             if "edges" in f:

neurodamus/node.py

@@ -125,7 +125,7 @@ def get_edge_managers(self, source, destination):
 
     def get_edge_manager(self, source, destination, conn_type=SynapseRuleManager):
         managers = [manager for manager in self.get_edge_managers(source, destination)
-                    if type(manager) == conn_type]
+                    if isinstance(manager, conn_type)]
         return managers[0] if managers else None
 
     def get_create_edge_manager(self, conn_type, source, destination, src_target,

neurodamus/target_manager.py

@@ -118,7 +118,7 @@ def load_targets(self, circuit):
         instantiated, and potentially split.
         """
         def _is_sonata_file(file_name):
-            if file_name.endswith(".h5") or file_name.endswith(".sonata"):
+            if file_name.endswith(".h5"):
                 return True
             return False
         if circuit.CircuitPath:

tests/simulations/neuromodulation/BlueConfig

@@ -1,7 +1,7 @@
 Run Default
 {
     CircuitPath ./minimal_circuit
-    nrnPath ./minimal_circuit/edges.sonata
+    nrnPath ./minimal_circuit/edges.h5
     CellLibraryFile circuit.mvd3
     MorphologyPath ./minimal_circuit/morph-release-2020-08-10
     MorphologyType asc
@@ -23,7 +23,7 @@ Run Default
 
 Projection proj
 {
-    Path ./minimal_circuit/projections.sonata
+    Path ./minimal_circuit/projections.h5
     PopulationID 1
     Source virtual_neurons
     Type NeuroModulation
@@ -35,7 +35,7 @@ Report soma
     Type compartment
     ReportOn v
     Unit mV
-    Format Bin
+    Format SONATA
     Dt 0.1
     StartTime 0
     EndTime 5000

tests/test_patched_delays.py

@@ -97,7 +97,7 @@ def test_eager_caching():
 
     # set nrnPath (w/plasticity)
     SimConfig.base_circuit['nrnPath'] = \
-        "/gpfs/bbp.cscs.ch/project/proj83/circuits/sscx-v7-plasticity/edges.sonata"
+        "/gpfs/bbp.cscs.ch/project/proj83/circuits/sscx-v7-plasticity/edges.h5"
 
     # append Connection blocks programmatically
     # plasticity

tests/test_synapses.py

@@ -11,7 +11,7 @@
 Run Default
 {{
     CellLibraryFile /gpfs/bbp.cscs.ch/project/proj83/circuits/Bio_M/20200805/circuit.mvd3
-    nrnPath /gpfs/bbp.cscs.ch/project/proj83/circuits/sscx-v7-plasticity/edges.sonata
+    nrnPath /gpfs/bbp.cscs.ch/project/proj83/circuits/sscx-v7-plasticity/edges.h5
 
     # Use a fake circuit path to avoid loading the HUGE start.target of the real circuit
     CircuitPath /gpfs/bbp.cscs.ch/project/proj12/jenkins/cellular/circuit-1k
@@ -49,7 +49,7 @@
 Projection Thalamocortical_input_VPM
 {{
     Path /gpfs/bbp.cscs.ch/project/proj83/circuits/Bio_M/20200805/projections/\
-2023_01_16/vpm/edges.sonata
+2023_01_16/vpm/edges.h5
     Source pre_VPM
     PopulationID 1
 }}
@@ -149,7 +149,7 @@ def test_synapses_params(blueconfig1):
     SimConfig.connections.hoc_map.put("init_I_E", CONN_i2e.hoc_map)
     # init_VPM
     CONN_vpm = compat.Map(Nd.Map())
-    CONN_vpm["Source"] = "pre_VPM"
+    CONN_vpm["Source"] = "projections:pre_VPM"
     CONN_vpm["Destination"] = "post_L5_PC"
     CONN_vpm["Weight"] = conn_weight
     SimConfig.connections.hoc_map.put("init_VPM", CONN_vpm.hoc_map)