How to reference gap junctions in the configuration file

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Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
30/100
Issue type
Bug
Clarity
Needs clarification
Activity status
Stale
Tech stack
python
Domain
backend

Research direction

Start with simulator_network.py at load_gap_junc_files, called by PointNetwork.from_config, and inspect the configured gap_juncs files alongside the HDF5 error for the missing source_ids object. Confirm the expected gap-junction file structure and configuration entry points, then verify that loading the supplied files completes without the KeyError.

Written by the indexing model from the issue text.

Description

Hello,

I want to create a network of gap junctions and simulate it using the PointNet simulator, but I'm not sure how to reference the gap junctions in the configuration file.

I have created gap junction connections as follows:

net_pre.import_nodes(nodes_file_name=path_pre_h5,node_types_file_name=path_pre_csv)
net_post.import_nodes(nodes_file_name=path_post_h5,node_types_file_name=path_post_csv)


net_pre.add_gap_junctions(source=net_pre.nodes(pop_name='PV'), target=net_post.nodes(pop_name='SST'), connection_rule=connection_rule,resistance=1250)

net_pre.build()
net_pre.save_edge('network')

Then I referenced these gap junctions in the configuration file as follows:

    "networks": {
        "nodes": [
            {
                "nodes_file": "$NETWORK_DIR/test_net_nodes.h5",
                "node_types_file": "$NETWORK_DIR/test_net_node_types.csv"
            }
        ],
        "edges": [],
        "gap_juncs": [
        	{
        	"gap_juncs_file":"$NETWORK_DIR/test_net_test_net_edges.h5",
        	"gap_juncs_types_file":"$NETWORK_DIR/test_net_test_net_edge_types.csv"
            }
            
        ]

However, I am getting this error:


Traceback (most recent call last):
  File "/home/margaux/miniconda3/envs/ENV_NEST/config_command_run_pointnet.py", line 20, in <module>
    main(sys.argv)
  File "/home/margaux/miniconda3/envs/ENV_NEST/config_command_run_pointnet.py", line 15, in main
    network = pointnet.PointNetwork.from_config(configure)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/margaux/miniconda3/envs/ENV_NEST/lib/python3.11/site-packages/bmtk/simulator/core/simulator_network.py", line 260, in from_config
    network.load_gap_junc_files(config.gap_juncs)
  File "/home/margaux/miniconda3/envs/ENV_NEST/lib/python3.11/site-packages/bmtk/simulator/core/simulator_network.py", line 192, in load_gap_junc_files
    self._gap_juncs[network][key] = f[key][()]
                                    ~^^^^^
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "/home/margaux/miniconda3/envs/ENV_NEST/lib/python3.11/site-packages/h5py/_hl/group.py", line 357, in __getitem__
    oid = h5o.open(self.id, self._e(name), lapl=self._lapl)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py/h5o.pyx", line 190, in h5py.h5o.open
KeyError: "Unable to open object (object 'source_ids' doesn't exist)"

Thank you for your help!
Margaux

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