Question Regarding Development with Simulation

[biosero-simon]

Hi,

I'm currently working on a driver for the device and do not have access to the physical machine.
Is there documentation around using a simulated device? I'm having issues with the method call.

Best,
Simon

[0x55555555]

Hi @biosero-simon , can you be more specific around what method you are calling and what is happening?

What version of the software are you using?
What OS are you using, and what device are you trying to simulate?

• George

[biosero-simon]

Hi George,

I'm trying to simulate a MinION using version 5.2.13

Using Windows 10, C#, .NET 6.

        channel = GrpcChannel.ForAddress(ipAddress + ':' + port);
        manager = new MinknowApi.Manager.ManagerService.ManagerServiceClient(channel);

        var request = new AddSimulatedDeviceRequest();
        request.Name = "MS12345";
        request.Type = SimulatedDeviceType.SimulatedAuto;
        manager.add_simulated_device(request);

--> Status(StatusCode="Internal", Detail="Error starting gRPC call. HttpRequestException: The SSL connection could not be established, see inner exception. AuthenticationException: The remote certificate is invalid because of errors in the certificate chain: PartialChain", DebugException="System.Net.Http.HttpRequestException: The SSL connection could not be established, see inner exception.
---> System.Security.Authentication.AuthenticationException: The remote certificate is invalid because of errors in the certificate chain: PartialChain
at System.Net.Security.SslStream.SendAuthResetSignal(ProtocolToken message, ExceptionDispatchInfo exception)
at System.Net.Security.SslStream.CompleteHandshake(SslAuthenticationOptions sslAuthenticationOptions)
at System.Net.Security.SslStream.ForceAuthenticationAsync[TIOAdapter](TIOAdapter adapter, Boolean receiveFirst, Byte[] reAuthenticationData, Boolean isApm)
at System.Net.Http.ConnectHelper.EstablishSslConnectionAsync(SslClientAuthenticationOptions sslOptions, HttpRequestMessage request, Boolean async, Stream stream, CancellationToken cancellationToken)
--- End of inner exception stack trace ---
at System.Net.Http.ConnectHelper.EstablishSslConnectionAsync(SslClientAuthenticationOptions sslOptions, HttpRequestMessage request, Boolean async, Stream stream, CancellationToken cancellationToken)
at System.Net.Http.HttpConnectionPool.ConnectAsync(HttpRequestMessage request, Boolean async, CancellationToken cancellationToken)
at System.Net.Http.HttpConnectionPool.AddHttp2ConnectionAsync(HttpRequestMessage request)
at System.Threading.Tasks.TaskCompletionSourceWithCancellation1.WaitWithCancellationAsync(CancellationToken cancellationToken) at System.Net.Http.HttpConnectionPool.GetHttp2ConnectionAsync(HttpRequestMessage request, Boolean async, CancellationToken cancellationToken) at System.Net.Http.HttpConnectionPool.SendWithVersionDetectionAndRetryAsync(HttpRequestMessage request, Boolean async, Boolean doRequestAuth, CancellationToken cancellationToken) at System.Net.Http.RedirectHandler.SendAsync(HttpRequestMessage request, Boolean async, CancellationToken cancellationToken) at Grpc.Net.Client.Balancer.Internal.BalancerHttpHandler.SendAsync(HttpRequestMessage request, CancellationToken cancellationToken) at Grpc.Net.Client.Internal.GrpcCall2.RunCall(HttpRequestMessage request, Nullable`1 timeout)

[biosero-simon]

End goal is to integrate into an existing project using .NET Framework 4.8, seeing that .NET Framework 4.8 does not support gRPC over HTTP/2, a second question would be whether this is even possible using .NET Framework

[0x55555555]

Hi @biosero-simon ,

a second question would be whether this is even possible using .NET Framework

I cant really comment here - I am not a .NET expert.

It looks like you are having issues connecting to minknow even before you get a simulated device setup.

Where is minknow running? on the local device, or a remote device?

When you dont use our python support library, you must handle the gRPC SSL setup yourself, this is your current issue.

See https://github.com/nanoporetech/minknow_api/blob/master/python/minknow_api/__init__.py#L344 for how we handle this.

Once you have a connection I can assist you setting up simulation, if required.

• George

[biosero-simon]

Minknow is running locally.

Is it possible to set up an insecure connection with the server?

[0x55555555]

Is it possible to set up an insecure connection with the server?

It is not, the minknow service requires a secure connection - gRPC does natively support these.

[biosero-simon]

Hi George, I have a connection and am attempting to use a simulated device. The device however is reporting back no port on which I can connect the protocol channel to. Can you guide me on fixing this?

[0x55555555]

Can you describe more what youve done to get a simulated device, and what specific responses from API's you are seeing please?

Thanks,

• George

[biosero-simon]

I have attached an image of the position below.

Manager is set up, simulated device is added successfully, but the RPC ports are null on the device connection.

[0x55555555]

Can you share your mk_manager log file, and a script youve run to trigger this?

Are you providing time for the sequencer to initialise after adding the sequencer?

Thanks,

• George

[biosero-simon]

mk_manager_svc_log-2022-09-21_17-45-45.txt

[biosero-simon]

Would be happy to hop on a call and share my screen to walk you through the code. The project consists of multiple different classes to manage the calls, similar to the python client within the repo.

[biosero-simon]

Can push meetings this morning

[0x55555555]

From your log:

2022-09-22 04:48:48.951329    INFO: hardware_state_changed (host)
    name: MS99999
    os_identifier: 
    state: ready
2022-09-22 04:48:49.667186    INFO: instance_started (host)
    grpc_secure_port: 8000
    grpcweb_tls_port: 8001
    instance: MS99999
2022-09-22 04:51:50.020448    INFO: hardware_state_changed (host)
    name: MS99999
    os_identifier: <unchanged>
    state: absent
2022-09-22 04:51:55.188033    INFO: instance_stopped (host)
    instance: MS99999
    std_ec: (0:std::system): [0x00007FF7F5D5B910]: The operation completed successfully
2022-09-22 04:53:12.363774    INFO: attempt_to_remove_simulated_device_that_does_not_exist (host)
    name: MS99999

You can see the device is added, then 1s later ports are assigned, then its eventually stopped (I assume your code stops the device).

How are you monitoring for device connections? do you watch a stream, or query the flow cell info once?

What happens if you add the device, then poll flow_cell_positions() once a second for a minute?

I suspect your code is not waiting long enough for the device to initialise - but cant say more without a clear reproducible segment of code.

Thanks,

• George

[0x55555555]

I've got no idea how to escape github and setup a call - I'm around in 1h to talk through your code - if we can work out a call!

• George

[biosero-simon]

Great, I can send you an invite if there is a good email I can use?

[biosero-simon]

My email is simoncoelho@biosero.com if it's easier for you to email me too

[0x55555555]

I've emailed a zoom link

[ChristopherAdelmann]

Hello @0x55555555,
I had a similar issue while using the minknow API. After creating a simulated device, it appears in the minknow UI. The problem is that it returns false when I check if the device is running. If I try to connect anyway, an "Invalid port for connection to [...]" error is thrown. Some assistance with this issue would be great. Here is the according code:

    def connect_to_positions(
        self, run_config: RunConfig, retries: int = 3
    ) -> List[mk.Connection]:
        positions = self.get_sequencing_positions(run_config)

        connections: List[mk.Connection] = []

        for position in positions:
            for _ in range(retries):
                try:
                    if not position.running:
                        raise Exception(f"Position {position.name} is not running.")

                    connections.append(position.connect())
                    break
                except Exception as e:
                    print(
                        f"Failed to connect to position {position.name}. Retrying... Info: {e}"
                    )
                    time.sleep(5)

        if len(connections) != run_config.replicate_count:
            raise Exception(
                f"Could not connect to all positions. Expected {run_config.replicate_count}, got {len(connections)}"
            )
        return connections

    def __create_simulated_position(self, name: Optional[str] = None) -> str:
        def generate_random_string(length=8) -> str:
            characters = string.ascii_letters + string.digits
            random_string = "".join(secrets.choice(characters) for _ in range(length))
            return random_string

        if name is None:
            name = generate_random_string()

        if self.__get_sequencing_position_by_position_id(name) is not None:
            return name

        self.manager.add_simulated_device(
            name,
            mk.manager_pb2.SimulatedDeviceType.SIMULATED_P2,  # type: ignore
        )

        return name

[Other code that returns the simulated devices if requested]