nanoporetech / nanoporetech/minknow_api
restart position without the MiKNOW UI
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- Dominant language
- Python
- Stars
- 73
- Forks
- 16
- PR merge metrics
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Description
Hello ONT,
We are trying to run our minion directly from the command line. For this we are using the start_protocol.py.
We initially had an authentication issue (Issues #34), however we set "--no-tls True" as a workaround.
Now when running we receive the following error:
`No flow cell present in position MN39033 (running)`
However, the flow cell is definitely inserted in the minion. I can see that "position_connection.device.get_flow_cell_info()" is used to obtain the flow cell information which is defined in minknow_api.device_service.DeviceService.
Notably, using "position_connection = spec.position.connect()" I can see that the device is running:
[FlowCellPosition('localhost', {name: "MN39033"
state: STATE_RUNNING
rpc_ports {
secure: 8001
insecure: 8000
secure_grpc_web: 8002
}
})]
Also, using "position_connection.device.get_device_info()" I can return information on the device;
device_info device_id: "MN39033"
max_channel_count: 512
max_wells_per_channel: 4
digitisation: 8192
So cool, I can see the device, just not the flow cell. If restart the position using the MiKNOW UI the start_protocol.py script progresses (alas to another issue);
Failed to find protocol for position MN39033 (running)
Requested protocol:
product-code: None
kit: SQK-LSK109
basecalling: False
basecall_config: None
barcode-kits: None
barcoding: False
However, I can now retrieve the flow cell info using "position_connection.device.get_flow_cell_info()" after restarting the position with MiKNOW UI
has_flow_cell: true
channel_count: 126
wells_per_channel: 1
has_adapter: true
adapter_id: "FA-05846"
temperature_offset: 327.6700134277344
asic_version: "IA02D"
asic_id_str: "7735955"
So this leads to my question, how do we restart the position without the MiKNOW UI? I am probably missing something obvious and I apologize in advance. Thank you for any help.
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reading start_protocol.py and the minknow_api.device_service.DeviceService usage described in the report, then inspect the available position connection and restart-related API entry points. Compare the command-line flow with the state observed after restarting through the MiKNOW UI. Done means a command-line workflow can restart the position and retrieve flow-cell information without the UI.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- grpc, python
- Domain
- api
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100