syntax = "proto3";

option java_multiple_files = true;
option java_package = "dev.ikm.tinkar.schema";
option java_outer_classname = "TinkarSchema";

option csharp_namespace = "Dev.IKM.Tinkar.Schema";

package dev.ikm.tinkar.schema;

// Vertex UUID message.
message VertexUUID {
    // Unique vertex UUID.
    string uuid = 1;
}

// Public id message.
// A public id is the base unique id for Tinkar concepts, semantics, and other publicly
// identifiable Tinkar items.
message PublicId {
    // Unique Public id.
    repeated string uuids = 1 ;
}

// Public id list message.
// A list of public ids.
message PublicIdList {
  repeated PublicId public_ids = 1 ;
}

// Field message.
// Fields are used in Vertex and SemanticVersion objects to store
// that can have varying types.
// Each message contains one field item and the data type of that field item.
message Field {
    // Field value. This is one of the types defined in the protobuf message.

    oneof Value {
        // String value.
        string string_value = 1;

        // Boolean value.
        bool boolean_value = 2;

        // Int32 value.
        sint32 int_value = 3;

        // Single precision floating point value.
        float float_value = 4;

        // Byte string value.
        bytes bytes_value = 5;

        // Time value.
        int64 time_value = 6;

        // Tinkar Public id value.
        PublicId public_id = 21;

        // Tinkar Vertex uuid value.
        VertexUUID vertex_uuid = 22;

        // Tinkar Public id list value.
        PublicIdList public_ids = 23;

        // Tinkar Directed graph value.
        DiGraph di_graph = 30;

        // Tinkar Directed tree value.
        DiTree di_tree = 31;

        // Tinkar Graph value.
        Graph graph = 32;

        // Tinkar Vertex value.
        Vertex vertex = 33;

        // Tinkar Planar Point value
        PlanarPoint planar_point = 40;

        // Tinkar Spatial Point value
        SpatialPoint spatial_point = 41;

        // Tinkar Int to Int Map
        IntToIntMap int_to_int_map = 50;

        // Tinkar Int to Multiple Int Map
        IntToMultipleIntMap int_to_multiple_int_map = 51;

        // TODO: Consider future use of a Tinkar Object array.
    };
}

// Planar point value.
// Float point on a 2 dimensional plane.
message PlanarPoint {
    // X position of point.
    float x = 1;
    // Y position of point.
    float y = 2;
}

// Spatial point value.
// Float point in a 3 dimensional space.
message SpatialPoint {
    // X position of point.
    float x = 1;
    // Y position of point.
    float y = 2;
    // Z position of point.
    float z = 3;
}

// Integer to Integer Map.
// Maps one integer value to another integer value.
message IntToIntMap {
    // Source value.
    int32 source = 1;
    // Target value.
    int32 target = 2;
}

// Integer to Multiple Integer Map.
// Maps one integer value to multiple other integer values.
message IntToMultipleIntMap {
    // Source value.
    int32 source = 1;

    // Target values.
    repeated int32 targets = 2;
}

// Directed Tree message.
// A directed tree is a tree with a single root. Each vertex in the Tree
// except the root contains a single predecessor, and may contain zero to many
// successors.
message DiTree {
    // List of all vertices in this DiTree. Each vertex contains a
    // VertexIndex which must match that vertex's index in this map.
    repeated Vertex vertices = 1;

    // Root vertex.
    int32 root = 2;

    // Maps each vertex with a predecessor to its predecessor.
    repeated IntToIntMap predecessor_map = 3;

    // Maps each vertex with successors to its successors.
    repeated IntToMultipleIntMap successor_map = 4;
}

// Directed Graph message.
// A directed graph is a graph with a multiple roots. Each vertex in the graph
// may contain zero to many successors and predecessors.
message DiGraph {
    // List of all vertices in this DiTree. Each vertex contains a
    // VertexIndex which must match that vertex's index in this map.
    repeated Vertex vertices = 1;

    // List of all root vertices.
    repeated int32 roots = 2;

    // Maps each vertex to its predecessors.
    repeated IntToMultipleIntMap successor_map = 3;

    // Maps each vertex to its successors.
    repeated IntToMultipleIntMap predecessor_map = 4;
}

// Graph message.
message Graph {
    // List of all vertices in this graph. Each vertex contains a
    // VertexIndex which must match that vertex's index in this map
    repeated Vertex vertices = 1;

    // Maps each vertex to its successors.
    repeated IntToMultipleIntMap successor_map = 2;

    // List of all root vertices.
    repeated int32 roots = 3;
}

// Vertex message.
message Vertex {
    // Vertex property message
    message Property {
        // Concept identifying this property.
        PublicId public_id = 1;

        // Value of this property.
        Field field = 2;
    }

    // Unique uuid for this vertex.
    VertexUUID vertex_uuid = 1;

    // Vertex index if containers vertex map.
    int32 index = 2;

    // Meaning of this vertex.
    PublicId meaning_public_id = 3;

    // Properties for this vertex.
    repeated Property properties = 4;
}

// Stamp Chronology message
// This contains a list of stamp versions (a chronology)
message StampChronology {
    // Unique public id for this STAMP.
    PublicId public_id = 1;

    // The stamp version.
    StampVersion first_stamp_version = 2;

    // Second stamp version.
    optional StampVersion second_stamp_version = 3;
}

// Stamp Version message
// This contains the info for a single version of a STAMP, sans the STAMP public id.
message StampVersion {
    // Status of the item this STAMP references.
    PublicId status_public_id = 1;

    // Status of the item this STAMP references.
    PublicId author_public_id = 2;

    // Module of the item this STAMP references.
    PublicId module_public_id = 3;

    // Path of the item this STAMP references.
    PublicId path_public_id = 4;

    // Creation time of the item this STAMP references.
    int64 time = 5;
}

// Concept Chronology message.
// This contains a chronology (multiple versions) of a single concept.
message ConceptChronology {
    // Unique Public id of this concept.
    PublicId public_id = 1;

    // List of concept versions.
    repeated ConceptVersion concept_versions = 2;
}

// Concept Version message.
// This contains a version of a single concept.
message ConceptVersion {
    // STAMP chronology public ID for this version.
    PublicId stamp_chronology_public_id = 1;
}


// Field definition message.
// Defines the information for a field in a pattern.
message FieldDefinition {
    // Meaning of the field.    
    PublicId meaning_public_id = 1;

    // Data type of the field.
    PublicId data_type_public_id = 2;

    // Purpose of the field.
    PublicId purpose_public_id = 3;

    //Index of a given pattern.
    int32 index = 4;
}

// Pattern chronology
// Contains multiple versions of pattern item.
message PatternChronology {
    // Unique Public id of this pattern chronology.
    PublicId public_id = 1;

    // Versions of pattern.
    repeated PatternVersion pattern_versions = 2;
}


// Pattern Version
// Single version of pattern item.
message PatternVersion {

    // STAMP chronology public ID for this version.
    PublicId stamp_chronology_public_id = 1;

    // Purpose of the Semantic that this pattern references.
    PublicId referenced_component_purpose_public_id = 2;

    // Meaning of the Semantic that this pattern references.
    PublicId referenced_component_meaning_public_id = 3;

    // Definitions for each field in the Semantic that this pattern references.
    repeated FieldDefinition field_definitions = 4;
}

// Semantic Chronology.
// Contains list of Semantic versions.
message SemanticChronology {
    // Unique Public id of this semantic chronology.
    PublicId public_id = 1;

    // ID of Concept that this semantic references.
    PublicId referenced_component_public_id = 2;

    // ID of Pattern that defines the allowable fields in this semantic.
    PublicId pattern_for_semantic_public_id = 3;

    // List of versions of this semantic.
    repeated SemanticVersion semantic_versions = 4;
}

// Semantic Version.
// Single Semantic versions.
message SemanticVersion {
    // STAMP chronology public ID for this version.
    PublicId stamp_chronology_public_id = 1;

    // Fields for this semantic. Each field defined is defined by
    // a matching entry in the pattern field definition list.
    repeated Field fields = 2;
}

// Tinkar Message. This is a wrapper around the Tinkar messages that may be serialized out to a persistent
// storage. This wrapper allows any of the indicated message types to be stored and when deserialized the type
// of the message can be determined.
message TinkarMsg {
    // Value of the message. This can be one and only one 
    // of the indicated types as defined in the protobuf description.
    oneof Value {
        // Re-evaluate to see if one-of value can be changed, to help with change-sets and represent more of a "commit-style"
        // One STAMP_chronology, One or more of the other types of chronologies (concept, pattern, or semantic)

        // Message contains a Concept Chronology.
        ConceptChronology concept_chronology = 10;

        // Message contains a Semantic Chronology.
        SemanticChronology semantic_chronology = 20;

        // Message contains a Pattern Chronology.
        PatternChronology pattern_chronology = 30;

        // Message contains a Stamp Chronology.
        StampChronology stamp_chronology = 40;
    };
}
      
    

      
message TinkarMsg { 
  StampChronology { 
    PublicId public_id = "NEW STAMP CHRONOLOGY Public ID"; 

    // The stamp version. 
    StampVersion first_stamp_version =  StampVersion { 
      // Status of the item this STAMP references.
      PublicId status_public_id = "Active Status Public ID"; 

      // Author of the item this STAMP references. 
      PublicId author_public_id = "SNOMED CT Author Public ID"; 

      // Module of the item this STAMP references. 
      PublicId module_public_id = "SNOMED CT US EDITION Public ID"; 

      // Path of the item this STAMP references. 
      PublicId path_public_id = "Development Path Public ID"; 

      // Creation time of the item this STAMP references. 
      google.protobuf.Timestamp time = "Current Date/Time";// Or if we wanted to simulate the update this would be the 2021-03-01 Timestamp 
    };         
  } 
} 
      
    

      
message TinkarMsg { 
  SemanticChronology { 
    // Unique Public id of this semantic chronology. 
    PublicId public_id = "New Axiom Definition Semantic Chronology Public ID"; 

    // ID of Concept that this semantic references. 
    PublicId referenced_component_public_id = "Chronic Lung Disease Public ID"; 

    // ID of Pattern that defines the allowable fields in this semantic. 
    PublicId pattern_for_semantic_public_id = "Axiom Definition Pattern Public ID"; 

    // List of versions of this semantic. 
    repeated SemanticVersion semantic_versions = [ 
      // Thew New Semantic version 
      SemanticVersion { 
        // STAMP chronology public ID for this version. (Message 1) 
        PublicId stamp_chronology_public_id = "NEW STAMP CHRONOLOGY Public ID"; 

        // Fields for this semantic. Each field defined is defined by 
        // a matching entry in the pattern field definition list. 
        repeated Field fields = [ 
          Field { 
            string string_value = " EquivalentClasses( 
              :413839001 |Chronic lung disease (disorder)| 
              ObjectIntersectionOf( 
                :64572001 |Disease (disorder)| 
                ObjectSomeValuesFrom( 
                  :609096000 |Role group (attribute)| 
                  ObjectSomeValuesFrom( 
                    :263502005 |Clinical course (attribute)| 
                    :90734009 |Chronic (qualifier value)| 
                  ) 
                ) 
                ObjectSomeValuesFrom( 
                  :609096000 |Role group (attribute)| 
                  ObjectSomeValuesFrom( 
                    :363698007 |Finding site (attribute)| 
                    :39607008 |Lung structure (body structure)| 
                  ) 
                ) 
              ) 
            ) "; 
          } 
        ]; 
      }, 

      // Then you can re-use all previously assigned version values since the version is repeatable 
      SemanticVersion { 
        // STAMP chronology public ID for this OLDER version. 
        PublicId stamp_chronology_public_id = "OLDER STAMP CHRONOLOGY Public ID"; 

        // Fields for this semantic. Each field defined is defined by
        // a matching entry in the pattern field definition list. 
        repeated Field fields = [ 
          Field { 
            string string_value = " SubClassOf( 
              :413839001 |Chronic lung disease (disorder)| 
              ObjectIntersectionOf( 
                :17097001 |Chronic disease of respiratory system (disorder)| 
                ObjectSomeValuesFrom( 
                  :609096000 |Role group (attribute)| 
                  ObjectSomeValuesFrom( 
                    :363698007 |Finding site (attribute)| 
                    :39607008 |Lung structure (body structure)| 
                  ) 
                ) 
              ) 
            ) "; 
          } 
        ] 
      }; 
    ]; 
  } 
} 
      
    

      
message TinkarMsg { 
  StampChronology { 
    PublicId public_id = "NEW STAMP CHRONOLOGY Public ID"; 

    // The stamp version. 
    StampVersion first_stamp_version =  StampVersion { 
        // Status of the item this STAMP references. 
        PublicId status_public_id = "Active Status Public ID"; 

        // Author of the item this STAMP references. 
        PublicId author_public_id = "ABC-Labs Public ID"; 

        // Module of the item this STAMP references. 
        PublicId module_public_id = "LOINC Module Public ID"; 

        // Path of the item this STAMP references. 
        PublicId path_public_id = "Development Path Public ID"; 

        // Creation time of the item this STAMP references. 
        google.protobuf.Timestamp time = "Current Date/Time"; 
    };         
  }
} 
      
    

      
message TinkarMsg {
  ConceptChronology {
    PublicId public_id = "New Concept Chronology Public ID";

    repeated ConceptVersion concept_versions = [
      ConceptVersion {
        // STAMP chronology public ID for this version. ID from Message 1
        PublicId stamp_chronology_public_id = "NEW STAMP CHRONOLOGY Public ID";
      }
    ];
  }
}
      
    

      
message TinkarMsg { 
  SemanticChronology { 
    // Unique Public id of this semantic chronology. 
    PublicId public_id = "New Identifier Semantic Chronology Public ID"; 

    // ID of Concept that this semantic references. (Message 2) 
    PublicId referenced_component_public_id = "New Concept Chronology Public ID"; 

    // ID of Pattern that defines the allowable fields in this semantic. 
    PublicId pattern_for_semantic_public_id = "Identifier Pattern Public ID"; 

    // List of versions of this semantic. 
    repeated SemanticVersion semantic_versions = [ 
      SemanticVersion { 
        // STAMP chronology public ID for this version. (Message 1) 
        PublicId stamp_chronology_public_id = "NEW STAMP CHRONOLOGY Public ID"; 

        // Fields for this semantic. Each field defined is defined by 
        // a matching entry in the pattern field definition list. 
        repeated Field fields = [
          Field { 
            PublicId public_id = "LOINC ID Concept Public ID"; 
          }, 
          Field { 
            string string_value = "e.g. 12345-6"; 
          } 
        ]; 
      } 
    ]; 
  } 
} 
      
    

      
message TinkarMsg { 
  SemanticChronology { 
    // Unique Public id of this semantic chronology. 
    PublicId public_id = "New Description Semantic Chronology Public ID"; 

    // ID of Concept that this semantic references. (Message 2) 
    PublicId referenced_component_public_id = "New Concept Chronology Public ID"; 

    // ID of Pattern that defines the allowable fields in this semantic. 
    PublicId pattern_for_semantic_public_id = "Description Pattern Public ID"; 

    // List of versions of this semantic. 
    repeated SemanticVersion semantic_versions = [ 
      SemanticVersion { 
        // STAMP chronology public ID for this version. (Message 1) 
        PublicId stamp_chronology_public_id = "NEW STAMP CHRONOLOGY Public ID"; 

        // Fields for this semantic. Each field defined is defined by 
        // a matching entry in the pattern field definition list. 
        repeated Field fields = [ 
          Field { 
            PublicId public_id = "English Language Concept Public ID"; 
          }, 
          Field { 
            string string_value = "XYZ [presence] in Serum"; 
          }, 
          Field { 
            PublicId public_id = "Case Insensitive Concept Public ID"; 
          }, 
          Field { 
            PublicId public_id = "LOINC Long Name Concept Public ID"; 
          } 
        ]; 
      } 
    ]; 
  } 
} 
      
    

      
message TinkarMsg { 
  SemanticChronology { 
    // Unique Public id of this semantic chronology. 
    PublicId public_id = "New Axiom Definition Semantic Chronology Public ID"; 

    // ID of Concept that this semantic references. (Message 2) 
    PublicId referenced_component_public_id = "New Concept Chronology Public ID"; 

    // ID of Pattern that defines the allowable fields in this semantic. 
    PublicId pattern_for_semantic_public_id = "Axiom Definition Pattern Public ID"; 

    // List of versions of this semantic. 
    repeated SemanticVersion semantic_versions = [ 
      // Thew New Semantic version 
      SemanticVersion { 
        // STAMP chronology public ID for this version. (Message 1) 
        PublicId stamp_chronology_public_id = "NEW STAMP CHRONOLOGY Public ID"; 

        // Fields for this semantic. Each field defined is defined by 
        // a matching entry in the pattern field definition list. 
        repeated Field fields = [ 
          Field { 
            string string_value = " EquivalentClasses( 
              ObjectIntersectionOf( 
                :363787002 |Observable entity (observable entity)| 
                ObjectSomeValuesFrom( 
                  :609096000 |Role group (attribute)| 
                  ObjectSomeValuesFrom( 
                    :246093002 |Component (attribute)| 
                    :######## |XYZ (substance)| 
                  ) 
                ) 
                ObjectSomeValuesFrom( 
                  :609096000 |Role group (attribute)| 
                  ObjectSomeValuesFrom( 
                    :370130000 |Property (attribute)| 
                    :705057003 |Presence (property) (qualifier value)|			) 
                ) 
                ObjectSomeValuesFrom( 
                  :609096000 |Role group (attribute)| 
                  ObjectSomeValuesFrom( 
                    :370132008 |Scale type (attribute)| 
                    :117363000 |Ordinal value (qualifier value)|			) 
                ) 
                ObjectSomeValuesFrom( 
                  :609096000 |Role group (attribute)| 
                  ObjectSomeValuesFrom( 
                    :370134009 |Time aspect (attribute)| 
                    :123029007 |Single point in time (qualifier value)| 
                  ) 
                ) 
                ObjectSomeValuesFrom( 
                  :609096000 |Role group (attribute)| 
                  ObjectSomeValuesFrom( 
                    :704327008 |Direct site (attribute)| 
                    :119297000 |Blood specimen (specimen)| 
                  ) 
                ) 
              ) 
            )"; 
          } 
        ]; 
      } 
    ]; 
  } 
}