workflow.proto

// --------------------------------------------------------------------------
//   SmartPeak -- Fast and Accurate CE-, GC- and LC-MS(/MS) Data Processing
// --------------------------------------------------------------------------
// Copyright The SmartPeak Team -- Novo Nordisk Foundation
// Center for Biosustainability, Technical University of Denmark 2018-2022.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Ahmed Khalil $
// $Authors: Ahmed Khalil $
// --------------------------------------------------------------------------
// To generate :
// protoc -I . --grpc_out=. --plugin=protoc-gen-grpc=grpc_cpp_plugin \
// workflow.proto
// protoc -I . --cpp_out=. workflow.proto

syntax = "proto3";
package SmartPeakServer;

service Workflow {
  rpc runWorkflow (WorkflowParameters) returns (WorkflowResult) {}
  rpc getLogStream (InquireLogs) returns (stream LogStream) {}
  rpc getProgressInfo (WorkflowParameters) returns (ProgressInfo) {}
  rpc getWorkflowEvent (WorkflowParameters) returns (WorkflowEvent) {}
  rpc stopRunningWorkflow (Interrupter) returns (Interrupter) {}
}

message WorkflowParameters {
  enum ExportReport {
    ALL = 0;
    FEATUREDB = 1;
    PIVOTTABLE = 2;
  }
  string dataset_path = 1;
  ExportReport export = 2;
  string report_metadata = 3;
  string report_sample_types = 4;
  string integrity = 5; 
}

message Interrupter {
  bool to_interrupt = 1;
  bool is_interrupted = 2;
}

// message SingleAxisData {
//   repeated float axis_data = 1;
// }

// message GraphData {
//   repeated string series_names_area = 1;
//   repeated SingleAxisData x_data = 2;
//   repeated SingleAxisData y_data = 3;
//   repeated SingleAxisData z_data = 4;
//   repeated string series_names_scatter = 5;
//   repeated SingleAxisData x_data_scatter = 6;
//   repeated SingleAxisData y_data_scatter = 7;
//   string x_axis_title = 8;
//   string y_axis_title = 9;
//   string z_axis_title = 10;
//   float x_min = 11;
//   float x_max = 12;
//   float y_min = 13;
//   float y_max = 14;
//   int32 nb_points = 15;
//   int32 max_nb_points = 16;
// }

// message HeatmapData {
//   repeated string selected_sample_names = 1;
//   repeated string selected_transitions = 2;
//   repeated string selected_transition_groups = 3;
//   repeated string header_row = 4;
//   repeated string header_column = 5;
//   repeated SingleAxisData column_data = 6;
//   string x_axis_title = 7;
//   string y_axis_title = 8;
//   string selected_feature = 9;
//   float feat_value_min = 10;
//   float feat_value_max = 11;
// }

message WorkflowResult {
  string status_code = 1;
  string session_id = 2;
  string path_to_results = 3;
  // GraphData graph_data = 4;
  // HeatmapData heatmap_data = 5;
}

message InquireLogs {
  int32 nr_lines = 1;
}

message LogStream {
  enum LogSeverity {
    NONE = 0;
    FATAL = 1;
    ERROR = 2;
    WARNING = 3;
    INFO = 4;
    DEBUG = 5;
    VERBOSE = 6;
  }
  string log_line = 1;
  LogSeverity log_severity = 2;
}

message ProgressInfo {
  string status_code = 1;
}

message WorkflowEvent {
  string event_name = 1;
  int64 event_index = 2;
  string item_name = 3;
  repeated string command_list = 4;
}