Version 5.9.1 bump

proto/minknow_api/acquisition.proto

@@ -405,6 +405,7 @@ enum AcquisitionState {
 
 enum AcquisitionStopReason {
     // The acquisition has not yet stopped.
+    // Or the stop reason is unknown
     STOPPED_NOT_SET = 0;
 
     // The user called the stop rpc.

proto/minknow_api/analysis_configuration.proto

@@ -6,6 +6,7 @@ option java_package = "com.nanoporetech.minknow_api";
 option objc_class_prefix = "MKAPI";
 
 import "google/protobuf/duration.proto";
+import "google/protobuf/empty.proto";
 import "google/protobuf/wrappers.proto";
 import "minknow_api/rpc_options.proto";
 
@@ -171,7 +172,6 @@ service AnalysisConfigurationService {
         option idempotency_level = NO_SIDE_EFFECTS;
     }
 
-
     // Get the dynamic analysis configuration - this configuration can be changed during acquisition periods,
     // and is reset at the start of acquisition.
     rpc get_dynamic_analysis_configuration (GetDynamicAnalysisConfigurationRequest) returns (DynamicAnalysisConfiguration) {
@@ -187,6 +187,13 @@ service AnalysisConfigurationService {
 }
 
 message EventDetection {
+    enum DetectionType {
+        MULTITTEST = 0; // Default and older style detector.
+        DMEAN = 1; // New, faster detector.
+    }
+
+    DetectionType type = 19;
+
     // The window size that the tstats are calculated from
     uint32 window_size = 3;
 
@@ -200,6 +207,8 @@ message EventDetection {
     // And what goes up must come down.
     // Once it has detected a peak going up, it will also have to go down by 'peak_height'
     // in order for the peak to be classified as a found event
+    //
+    // Note: only used for MULTITTEST detector.
     double peak_height = 9;
 
     // Conversion factor used to convert from events to bases.
@@ -212,6 +221,8 @@ message EventDetection {
     // This will eliminate "mux_uncertain" events and reads. Note that this will cause starting or
     // stopping unblocking to break events as well (even though the mux does not normally change in
     // this case).
+    //
+    // Note: no longer used.
     bool break_on_mux_changes = 17;
 
     // Control the number of samples MinKNOW will shift mux changes back by in order to align mux changes
@@ -224,6 +235,8 @@ message EventDetection {
     // recorded the change as active. Mux changes are never shifted forwards.
     //
     // A value of 0 will disable shifting of mux changes.
+    //
+    // Note: no longer used.
     uint32 max_mux_change_back_shift = 18;
 }
 
@@ -840,12 +853,16 @@ message BasecallerConfiguration
     // Enable read splitting in guppy.
     //
     // Since 4.5
+    //
+    // Note: Since 5.9 this option has no effect, the basecaller is responsible for deciding when read splitting should be enabled.
     bool enable_read_splitting = 8;
 
     // Override score to use for guppy read splitting. If not specified a default value
     // is used from guppy.
     //
     // Since 4.5
+    //
+    // Note: Since 5.9 this option has no effect, the basecaller is responsible for deciding read splitting score.
     google.protobuf.FloatValue min_score_read_splitting = 9;
 }
 
@@ -1054,6 +1071,10 @@ message WriterConfiguration {
 
             // Number of estimated bases within a batch before it rotates to a new batch
             uint64 bases_per_batch = 15;
+
+            // Do not perform batching based on output
+            // (time-based batching is still performed, if specified)
+            google.protobuf.Empty no_output_based_batching = 17;
         }
 
         // The batch duration, for time-based batching
@@ -1099,6 +1120,10 @@ message WriterConfiguration {
 
             // Number of estimated bases within a batch before it rotates to a new batch
             uint64 bases_per_batch = 6;
+
+            // Do not perform batching based on output
+            // (time-based batching is still performed, if specified)
+            google.protobuf.Empty no_output_based_batching = 11;
         }
 
         // Compress fastq files with gzip compression.
@@ -1149,6 +1174,10 @@ message WriterConfiguration {
 
             // Number of estimated bases within a batch before it rotates to a new batch
             uint64 bases_per_batch = 5;
+
+            // Do not perform batching based on output
+            // (time-based batching is still performed, if specified)
+            google.protobuf.Empty no_output_based_batching = 10;
         }
 
         // If true minknow will only write the primary alignment for each read.
@@ -1198,6 +1227,10 @@ message WriterConfiguration {
 
             // Number of estimated bases within a batch before it rotates to a new batch
             uint64 bases_per_batch = 7;
+
+            // Do not perform batching based on output
+            // (time-based batching is still performed, if specified)
+            google.protobuf.Empty no_output_based_batching = 9;
         }
 
         // Prevent reads which have successfully basecalled being written to pod5.

proto/minknow_api/basecaller.proto

@@ -63,6 +63,25 @@ service Basecaller {
         option idempotency_level = NO_SIDE_EFFECTS;
     }
 
+
+    // Clears run info data for each analysis specified
+    //
+    // Run info data is the data returned by `get_info()`.
+    //
+    // Also clears any persistence data that has been written to disk for those analyses -- this
+    // data will not be available after a restart.
+    //
+    // Run info will not be cleared for analyses which are still in-progress. If an invalid or
+    // in-progress analysis id is specified, that analysis id is ignored.
+    //
+    // Does NOT clear results from analyses (e.g. bam files, reports, etc.)
+    //
+    // Since 5.9
+    //
+    rpc clear_info(ClearInfoRequest) returns (ClearInfoResponse) {
+        option idempotency_level = IDEMPOTENT;
+    }
+
     // Monitors basecalls, returning messages when basecalls are started, stopped or receive
     // progress updates.
     //
@@ -183,10 +202,14 @@ message StartBasecallingRequest {
     analysis_configuration.AlignmentConfiguration alignment_configuration = 11;
 
     // Enable read splitting in guppy
+    //
+    // Note: Since 5.9 this option has no effect, the basecaller is responsible for deciding when read splitting should be enabled.
     bool enable_read_splitting = 13;
 
     // Override score to use for guppy read splitting. If not specified a default value
     // is used from guppy.
+    //
+    // Note: Since 5.9 this option has no effect, the basecaller is responsible for deciding when read splitting should be enabled.
     google.protobuf.FloatValue min_score_read_splitting = 14;
 }
 
@@ -421,6 +444,14 @@ message GetInfoResponse {
     repeated RunInfo runs = 1;
 }
 
+message ClearInfoRequest {
+    repeated string ids = 1;
+}
+
+message ClearInfoResponse {
+
+}
+
 message WatchRequest {
     // By default, no information will be sent about runs that were already finished when this call
     // was made. Setting this to true will cause the state of already-finished runs to be returned.

proto/minknow_api/device.proto

@@ -383,6 +383,7 @@ message GetDeviceInfoResponse {
         MINION_MK1C = 4;
         TRAXION = 5;
         P2_SOLO = 6;
+        MINION_MK1D = 7;
     }
 
     // A unique identifier for the device.

proto/minknow_api/manager.proto

@@ -20,6 +20,13 @@ service ManagerService {
     rpc describe_host (DescribeHostRequest) returns (DescribeHostResponse) {
         option idempotency_level = NO_SIDE_EFFECTS;
     }
+
+    // Get features from the basecaller, for whether the server can support live basecalling with adaptive sampling
+    //
+    // Since 5.9
+    rpc get_basecaller_features (GetBasecallerFeaturesRequest) returns (GetBasecallerFeaturesResponse) {
+        option idempotency_level = NO_SIDE_EFFECTS;
+    }
 
     // List all known positions where flow cells can be inserted.
     //
@@ -453,6 +460,17 @@ message DescribeHostResponse {
      BasecallingAvailability can_basecall = 6;
 }
 
+message GetBasecallerFeaturesRequest {}
+
+message GetBasecallerFeaturesResponse {
+    // Is live basecalling with adaptive sampling
+    // recommended on this hardware
+    // Currently not recommended for Apple or Mk1C
+    //
+    // Since 5.9
+    bool is_live_basecalling_with_adaptive_sampling_recommended = 1;
+}
+
 enum SimpleProtocolState {
     // No protocol has been started on this position (since MinKNOW was started, or the position
     // was reset). It may also indicate that the protocol state has been manually cleared by the

proto/minknow_api/protocol.proto

@@ -277,6 +277,9 @@ message BarcodeUserData {
 
     // Sample type grouping for the barcode.
     SampleType type = 4;
+
+    // Extra context per barcode
+    map<string, string> passenger_info  = 6;
 }
 
 message KitInfo {
@@ -287,17 +290,6 @@ message KitInfo {
     repeated string barcode_expansion_kits = 2;
 }
 
-message PassengerInfo {
-    enum Extension {
-        TXT = 0;
-        CSV = 1;
-        JSON = 2;
-    }
-
-    bytes passenger_info = 1;
-    Extension file_extension = 2;
-}
-
 message ProtocolRunUserInfo {
     // The group which the experiment should be held in.
     //
@@ -374,15 +366,6 @@ message StartProtocolRequest {
     //
     // Since 5.3
     acquisition.TargetRunUntilCriteria target_run_until_criteria = 5;
-
-    // Extra info taken as bytes, that will be output to a file in the output location
-    //
-    // The filename in the output location will be in the format:
-    // passenger_info_{run_id}.{extension}
-    //
-    // If the size of this argument exceeds 2MB in size, then the call will fail
-    // with INVALID_ARGUMENT
-    PassengerInfo passenger_info = 6;
 }
 
 message StartProtocolResponse {
@@ -537,7 +520,7 @@ enum ProtocolState {
 
     // Enums 20-120 are "reserved" for any new script exit codes we may want to forward
 
-    // The protocol has reported and error during calibration
+    // The protocol has reported an error during calibration
     PROTOCOL_FINISHED_WITH_ERROR_CALIBRATION = 20;              // Exit with code 20
 
     // Setting basecall settings failed (Bad config etc)
@@ -548,6 +531,15 @@ enum ProtocolState {
 
     // The protocol was terminated due to insufficient disk space
     PROTOCOL_FINISHED_WITH_ERROR_NO_DISK_SPACE = 23;            // Exit with code 23
+
+    // The protocol was terminated due to a high temperature issue
+    // Since 5.9
+    PROTOCOL_FINISHED_WITH_ERROR_TEMPERATURE_HIGH = 25;         // Exit with code 25
+
+    // The protocol was terminated due to an issue with
+    // communications with the basecaller
+    // Since 5.9
+    PROTOCOL_FINISHED_WITH_ERROR_BASECALLER_COMMUNICATION = 26; // Exit with code 26
 }
 
 enum ProtocolPhase {
@@ -759,9 +751,25 @@ message ProtocolRunInfo {
 
     // Output location for protocol data (eg. reads).
     //
+    // If data offload is being used, this is the offload source directory.  Any files written to
+    // this location will be output alongside the rest of the experiment data
+    //
     // Since 1.16.
     string output_path = 11;
 
+    // Output location to report to the user
+    //
+    // This is the location at which files will eventually be written.
+    //
+    // This path will be present, but empty, when writing to user-specified offload locations, as
+    // there isn't a "local output path" when offload is used.
+    //
+    // For backwards compatibility, if this this field is not present, then `output_path` can be
+    // reported to the user instead.
+    //
+    // Since 5.9
+    optional string reported_output_path = 24;
+
     // Indicates the current state of the protocol run.
     ProtocolState state = 4;
 
@@ -1046,15 +1054,6 @@ message BeginProtocolRequest {
 
     // Any settings changed from the defaults specified in the protocol's .toml file.
     map<string, protocol_settings.ProtocolSetting.ProtocolSettingValue> settings = 4;
-
-    // Extra info taken as bytes, that will be output to a file in the output location
-    //
-    // The filename in the output location will be in the format:
-    // passenger_info_{run_id}.{extension}
-    //
-    // If the size of this argument exceeds 2MB in size, then the call will fail
-    // with INVALID_ARGUMENT
-    PassengerInfo passenger_info = 7;
 }
 
 message BeginProtocolResponse {

proto/minknow_api/report_data.proto

@@ -3,6 +3,7 @@ syntax="proto3";
 package minknow_api.report_data;
 
 import "minknow_api/acquisition.proto";
+import "minknow_api/analysis_configuration.proto";
 import "minknow_api/log.proto";
 import "minknow_api/protocol.proto";
 import "minknow_api/run_until.proto";
@@ -62,6 +63,16 @@ message AcquistionReportData {
     repeated BasecallBoxplot basecall_boxplot = 9;
 
     run_until.Update run_until_update = 10;
+
+    // Information about the writer configuration
+    //
+    // Since 5.9
+    analysis_configuration.WriterConfiguration writer_config = 12;
+
+    // Information about the basecaller configuration
+    //
+    // Since 5.9
+    analysis_configuration.BasecallerConfiguration basecaller_config = 13;
 }
 
 // This is a subset of the information available from the describe_host() call