Version v3.6.0 bump

LIMS_README.md

@@ -5,7 +5,7 @@ MinKNOW LIMS Interface
 
 MinKNOW is Oxford Nanopore Technologies Device Control software embedded in MinIT, GridION, PromethION and provided for installation on user PCs to run MinION.
 MinKNOW carries out several core tasks: data acquisition; real-time analysis and feedback; basecalling; data streaming; device control including selecting the run parameters; sample identification and tracking and ensuring that the platform chemistry is performing correctly to run the samples. 
-With the deployment of Oxford Nanopore devices into production sequencing environements, the ability to interface with MinKNOW and pull useful metadata such as Run IDs, Flow Cell IDs, run statistics becomes more important.
+With the deployment of Oxford Nanopore devices into production sequencing environments, the ability to interface with MinKNOW and pull useful metadata such as Run IDs, Flow Cell IDs, run statistics becomes more important.
 
 Getting Started
 ===============

bream/mux_scan_results.proto

@@ -31,6 +31,9 @@ message Result {
     //
     // eg. 'sequencing': 1500
     map<string, uint32> counts = 1;
+
+    // When this mux scan result was added (Seconds since the start of the acquisition)
+    uint64 mux_scan_timestamp = 2;
 }
 
 message Style {
@@ -41,7 +44,7 @@ message Style {
     //
     // This can be used as a tooltip, for example.
     string description = 2;
-    
+
     // The colour to use when rendering this mux category or group.
     //
     // This is a six-digit hex string describing an RGB colour (eg: "ff00ff" for purple).

bream/protocol_communication.proto

@@ -33,18 +33,30 @@ message ProtocolData {
   int32 bias_voltage_offset = 4;
 
 
+  // Reserved values: 2, 4
   enum ProtocolInternalState {
     RUNNING_MUX_SCAN = 0;
     RUNNING_SEQUENCING = 1;
-    PAUSE_REQUEST = 2;
     PAUSED = 3;
-    RESUME_REQUEST = 4;
+    PAUSING = 5;
+    RESUMING = 6;
+    PREPARING_FOR_MUX_SCAN = 7;
   }
 
   // State of the experiment
-  // UI will set to PAUSE_REQUEST and bream will change to PAUSED
-  // UI will set to RESUME_REQUEST and bream will change back to RUNNING_SEQUENCING
-  // UI will ideally not ask to pause during a mux scan as it won't be actioned immediately
   ProtocolInternalState state = 5;
 
-}
+  message MuxScan {}
+  message Pause {}
+  message Resume {}
+
+  // UI will send MUX_SCAN and bream will set ProtocolInternalState to PREPARING_FOR_MUX_SCAN => RUNNING_MUX_SCAN
+  // UI will send PAUSE and bream will set ProtocolInternalState to PAUSING => PAUSED
+  // UI will send RESUME and bream will set ProtocolInternalState to RESUMING => RUNNING_SEQUENCING
+  // UI will ideally not ask to pause during a mux scan as it won't be actioned immediately
+  oneof protocol_event_trigger {
+    MuxScan mux_scan = 6;
+    Pause pause = 7;
+    Resume resume = 8;
+  };
+}

minknow/rpc/acquisition.proto

@@ -1,5 +1,6 @@
 syntax="proto3";
 
+import "minknow/rpc/rpc_options.proto";
 import "google/protobuf/timestamp.proto";
 
 package ont.rpc.acquisition;
@@ -42,7 +43,7 @@ service AcquisitionService {
 
     // Returns current acquisition run info and streams any changes to the current acquisition
     //
-    // This call can be made even if there is no current protocol running. In this case, the next streamed
+    // This call can be made even if acquisition is not running. In this case, the next streamed
     // response will be the start of a new acquisition and you will receive updates for that acquisition
     // until it finishes.
     //
@@ -67,7 +68,7 @@ service AcquisitionService {
     // Since 1.11
     rpc get_acquisition_info (GetAcquisitionRunInfoRequest) returns (AcquisitionRunInfo) {}
 
-    // Gets information about all previous protocol runs.
+    // Gets information about all previous acquisitions.
     //
     // Since 1.11
     rpc list_acquisition_runs (ListAcquisitionRunsRequest) returns (ListAcquisitionRunsResponse) {}
@@ -78,6 +79,11 @@ service AcquisitionService {
     //
     // Since 1.11
     rpc get_current_acquisition_run (GetCurrentAcquisitionRunRequest) returns (AcquisitionRunInfo) {}
+
+    // Specify the signal reader to use
+    //
+    // Since 3.6
+    rpc set_signal_reader (SetSignalReaderRequest) returns (SetSignalReaderResponse) {}
 }
 
 //
@@ -229,10 +235,24 @@ message StartRequest {
     //
     // Since 3.2
     Option file_output = 8;
+
+    // Write a final_summary.txt file.
+    //
+    // If file_output is disabled, the final_summary.txt file will not be written regardless of
+    // this setting.
+    //
+    // The default setting (AUTO) will only enable writing a final_summary.txt file if the purpose
+    // is set to SEQUENCING.
+    //
+    // Since 3.5 (NB: in 3.3 and 3.4, final_summary.txt was always written out if file_output was
+    // enabled).
+    Option generate_final_summary = 9;
 }
 
 message StartResponse {
-    // UUID generated when the protocol is started, to uniquely represent this protocol instance
+    // Globally-unique identifier generated when the acquisition is started.
+    //
+    // This is guaranteed to unique, including aross sequencing devices.
     string run_id = 1;
 }
 
@@ -313,7 +333,7 @@ message GetProgressResponse {
 }
 
 message GetAcquisitionRunInfoRequest {
-    // The protocol run to get information about.
+    // The acquisition period to get information about.
     string run_id = 1;
 }
 
@@ -488,6 +508,8 @@ message ChannelStateInfo {
 message AcquisitionConfigSummary {
     // Was basecalling enabled for the run.
     bool basecalling_enabled = 1;
+    // Is barcoding enabled for the run
+    bool barcoding_enabled = 13;
 
     // Root directory reads were written to for the run.
     //
@@ -535,10 +557,10 @@ message AcquisitionRunInfo {
     //
     // This is guaranteed to be made of ASCII characters, and at
     // most 40 characters. It is globally unique across all
-    // protocols runs on all MinKNOW instances.
+    // acquisitions on all MinKNOW instances.
     string run_id = 1;
 
-    // Indicates the current state of the protocol run.
+    // Indicates the current state of the acquisition.
     AcquisitionState state = 2;
 
     // If the experiment is finishing, an extra piece of state
@@ -563,7 +585,7 @@ message AcquisitionRunInfo {
 
     // When the acquisition terminated (UTC).
     //
-    // Unset if the protocol is still running.
+    // Unset if the acquisition period is still running.
     google.protobuf.Timestamp end_time = 7;
 
     // Summary of acquisition yields.
@@ -590,3 +612,30 @@ message GetCurrentAcquisitionRunRequest {
 
 message WatchCurrentAcquisitionRunRequest {
 }
+
+message SetSignalReaderRequest {
+
+    // Available signal reader types
+    enum SignalReaderType {
+        HDF5 = 0; // Default value
+        DEVICE = 1;
+    }
+
+    // The type of signal reader to use
+    SignalReaderType reader = 1 [(rpc_required) = true];
+
+    // The following settings are optional, and only used when setting the reader to hdf5
+    string hdf_source = 2;
+
+    enum SourceFileMode {
+        UNSPECIFIED = 0; // Default value
+        SINGLE_RUN = 1;
+        LOOP = 2;
+    }
+
+    SourceFileMode hdf_mode = 3; // Defaults to UNSPECIFIED, since this setting is optional
+
+    float sample_rate_scale_factor = 4;
+}
+
+message SetSignalReaderResponse {}