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Update minknow api (#58)
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* implement minimal API to support readfish

* create cDNA squiggle array

* update read_detection field in analysis config

---------

Co-authored-by: satriobio <[email protected]>
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@Adoni5 @satriobio
Adoni5 and satriobio authored Oct 24, 2023
1 parent ceee837 commit 47bacf0
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Showing 13 changed files with 1,569 additions and 51 deletions.
17 changes: 17 additions & 0 deletions Profile_tomls/config-short.toml
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@@ -0,0 +1,17 @@
output_path = "/tmp/"
target_yield = 100000000000
working_pore_percent = 85

[parameters]
sample_name = "test-cdna"
experiment_name = "titin"
flowcell_name = "FAQ1234"
experiment_duration_set = 4800
device_id = "Bantersaurus"
position = "FenceSitter"

[[sample]]
name = "Bacteria 1"
input_genome = "squiggle_arrs/ENST00000589042.5.squiggle.npy"
mean_read_length = 20000
weight = 1
1 change: 1 addition & 0 deletions build.rs
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Expand Up @@ -21,6 +21,7 @@ fn main() -> Result<(), Box<dyn std::error::Error>> {
"proto/minknow_api/instance.proto",
"proto/minknow_api/log.proto",
"proto/minknow_api/keystore.proto",
"proto/minknow_api/run_until.proto",
"proto/minknow_api/rpc_options.proto",
"proto/minknow_api/device.proto",
],
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4 changes: 2 additions & 2 deletions config.ini
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Expand Up @@ -2,8 +2,8 @@
cert-dir = /opt/ont/minknow/conf/rpc-certs/

[PORTS]
manager = 10000
manager = 9502
position = 10001

[SEQUENCER]
channels = 3000
channels = 3000
104 changes: 102 additions & 2 deletions proto/minknow_api/acquisition.proto
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Expand Up @@ -5,10 +5,50 @@ package minknow_api.acquisition;
option java_package = "com.nanoporetech.minknow_api";
option objc_class_prefix = "MKAPI";

import "minknow_api/run_until.proto";
import "minknow_api/rpc_options.proto";
import "google/protobuf/timestamp.proto";

service AcquisitionService {
// Starts reading data from the device
//
// Some setup calls will need to be made before starting data acquisition: particularly setting the analysis configuration,
// calibration, read writer and bulk writer config and some device calls such as setting the sampling frequency
//
// If acquisition is already running (even in the FINISHING state), this call will fail.
//
// On MinIONs and GridIONs, this will enable the ASIC power supply if it is not already enabled.
// See StopRequest.keep_power_on for more details about the implications of this.
//
// The rpc will return once `current_status` is "PROCESSING" or an error occurs and acquisition fails to start.
// rpc start (StartRequest) returns (StartResponse) {}

// Stops data acquisition.
//
// Can specify a stop mode that handles what is done with the data when data acquisition is stopped. Refer to the enum
// description for documentation on what each mode does.
//
// Be aware that this command will return as soon as Minknow enters the FINISHING state and not the READY state.
// So if starting a new experiment then you will have to wait for the READY state separately
// rpc stop (StopRequest) returns (StopResponse) {}

// Watches for status changes within MinKNOW. Status states are defined from MinknowStatus enum.
// This is a bi-directional stream where the incoming response stream will return every time the status has changed
// and the request stream is used to stop the watcher. Refer to http://www.grpc.io/docs/tutorials/basic/python.html
// to see how bi-directional streaming works in grpc, but essentially when calling this function the user will have
// to pass in a generator that will eventually yield a WatchForStatusChangeRequest(stop=True) to the cpp side.
// A wrapper class for this is provided in the Python code.
//
// The function will first return with the current status that MinKNOW is in. Every response thereafter will be a
// change from one status to another.
//
// The ERROR_STATUS state includes errors during transition between states. If that happens, MinKNOW will
// try to revert to the READY state. It is up to the user to determine if they wish to try to wait for MinKNOW to
// correct itself or to try some other course of action
// rpc watch_for_status_change (stream WatchForStatusChangeRequest) returns (stream WatchForStatusChangeResponse) {
// option idempotency_level = NO_SIDE_EFFECTS;
// }

// Returns current acquisition run info and streams any changes to the current acquisition
//
// This call can be made even if acquisition is not running. In this case, the next streamed
Expand All @@ -33,7 +73,25 @@ service AcquisitionService {
rpc get_progress (GetProgressRequest) returns (GetProgressResponse) {
option idempotency_level = NO_SIDE_EFFECTS;
}
// Returns the name and run id of the currently running acquisition.

// Gets information about an acquisition run, run within this instance on MinKNOW.
//
// If no run ID is provided, information about the most recently started acquisition run is
// provided.
//
// Since 1.11
rpc get_acquisition_info (GetAcquisitionRunInfoRequest) returns (AcquisitionRunInfo) {
option idempotency_level = NO_SIDE_EFFECTS;
}

// Gets information about all previous acquisitions.
//
// Since 1.11
// rpc list_acquisition_runs (ListAcquisitionRunsRequest) returns (ListAcquisitionRunsResponse) {
// option idempotency_level = NO_SIDE_EFFECTS;
// }

// Returns the name and run id of the currently running acquisition.
//
// Will fail with FAILED_PRECONDITION if there is no acquisition running
//
Expand All @@ -42,6 +100,38 @@ service AcquisitionService {
option idempotency_level = NO_SIDE_EFFECTS;
}

// Specify the signal reader to use
//
// Since 3.6
// rpc set_signal_reader (SetSignalReaderRequest) returns (SetSignalReaderResponse) {
// option idempotency_level = IDEMPOTENT;
// }

// Set the bream information for the current acquisition.
//
// This should only be called by the protocol. It will only affect the last acquisition that was
// started in the current protocol.
//
// If no protocol is running, or no acquisition has been started during the current protocol, a
// FAILED_PRECONDITION error will be returned.
//
// Since 5.0
// rpc set_bream_info (SetBreamInfoRequest) returns (SetBreamInfoResponse) {
// option idempotency_level = IDEMPOTENT;
// }

// Add a mux scan result to the bream information for the current acquisition.
//
// This should only be called by the protocol. It will only affect the last acquisition that was
// started in the current protocol.
//
// If no protocol is running, or no acquisition has been started during the current protocol, a
// FAILED_PRECONDITION error will be returned.
//
// Since 5.0
// rpc append_mux_scan_result (MuxScanResult) returns (AppendMuxScanResultResponse) {
// option idempotency_level = IDEMPOTENT;
// }
}

//
Expand Down Expand Up @@ -98,7 +188,6 @@ enum Purpose {
//
// Protobuf messages for input/output of RPC calls
//

message StartRequest {
// Prevent waiting until the device is ready before starting acquisition.
//
Expand Down Expand Up @@ -730,6 +819,11 @@ message BreamInfo {
Range target_temperature = 5;
}

message TargetRunUntilCriteria {
run_until.CriteriaValues pause_criteria = 1;
run_until.CriteriaValues stop_criteria = 2;
}

message AcquisitionRunInfo {
// The unique identifier assigned to this acquisition run.
//
Expand Down Expand Up @@ -796,6 +890,12 @@ message AcquisitionRunInfo {

// Set information provided by the Bream toolkit.
BreamInfo bream_info = 15;

// Target Run-Until Critiera, used to determine when the acquisition should be paused
// or stopped.
//
// Since 5.3
TargetRunUntilCriteria target_run_until_criteria = 16;
}

message ListAcquisitionRunsRequest {
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