// This file defines common types used in other parts of the schema.
// There are no directly associated methods.

syntax = "proto3";

import "google/protobuf/struct.proto";

package ga4ghmetadata;

// When returning an HTTP error response, a server may also return a JSON formatted GAException
// to better describe the error.
message GAException {
  // Numerical error code
  int32 error_code = 1;

  // The error message.
  string message = 2;
}

// Identifier from a public database, describing a representation of
// the record, and the relation between record and external reference
// TODO: relation as OntologyTerm object (e.g. as IAO property).
// Example:
//  {
//    "relation" : "reported_in",
//    "identifier" : "pubmed:25752754"
//  }
//
message ExternalIdentifier {
  // The CURIE of the identifier.
  string identifier = 1;

  // The relation between identifier and the object ist was reported from.
  string relation = 2;
}

// An ontology term describing an attribute. (e.g. the phenotype attribute
// 'polydactyly' from HPO)
message OntologyTerm {
  // Ontology term identifier - the CURIE for an ontology term. It
  // differs from the standard GA4GH schema's :ref:`id <apidesign_object_ids>`
  // in that it is a CURIE pointing to an information resource outside of the
  // scope of the schema or its resource implementation.
  string term_id = 1;

  // Ontology term - the label of the ontology term the termId is pointing to.
  string term_label = 2;
}

// A GeoLocation object provides information about a geographic position
// related to a record. Examples could be:
//  - an address, e.g. of a lab performing an analysis
//  - provenance of an individual, obfuscated to a larger order administrative
//    entity (Suffolk, U.K.)
//  - a lat/long/alt position where an environmental sample was collected
//   The geographic point object uses the default units from the DCMI point scheme
//  http://dublincore.org/documents/dcmi-point/
//  and avoids optional representation in non-standard units.

message GeoLocation {
  // a text representation, preferably using standard geographic identification
  // elements, of the corresponding latitude,longitude(,altitude)
  // This representation serves the purposes to
  //  - capture standard data entry parameters
  //  - provide a sanity check for latitude,longitude values
  // Example:
  //  - 34 Washington Blvd, Marina del Rey, CA  90292, United States
  //  - Str Marasesti 5, 300077 Timisoara, Romania
  //  - Heidelberg, Deutschland
  string label = 1;

  // an optional indication of the maximum precision to be derived from the
  // latitude,longitude values
  // Example:
  // Given a street address "Winterthurerstrasse 190, 8057 Zürich, Switzerland",
  // a privacy driven (destructive) obfuscation approach could recode this
  // to
  //  "latitude": 47.37, "longitude": 8.54
  //  while providing
  //  "precision":"city", "label": "Zürich, Switzerland"
  // ... indicating that the original location could correspond to any
  // latitude,longitude point value inside the administrative boundaries of
  // the city of Zürich, Switzerland
  string precision = 2;

  // signed decimal degrees (North, relative to Equator)
  double latitude = 3;

  // signed decimal degrees (East, relative to IERS Reference Meridian)
  double longitude = 4;

  // optional, e.g. for environmental samples
  double altitude = 5;
}

enum NullValue {
  // Null value.
  NULL_VALUE = 0;
}

// Type defining a collection of attributes associated with various protocol
// records. Each attribute is a name that maps to an array of one or more
// values. Values are chosen from both internal protobuf types and GA4GH.
//  Values should be split into array elements instead of using a separator
// syntax that needs to parsed.
message AttributeValue {
  oneof value {
    string string_value = 1;
    int64 int64_value = 2;
    int32 int32_value = 3;
    bool bool_value = 4;
    double double_value = 5;
    ExternalIdentifier external_identifier = 6;
    OntologyTerm ontology_term = 7;
    Experiment experiment = 8;
    Program program = 9;
    Analysis analysis = 10;
    NullValue null_value = 11;
    Attributes attributes = 12;
    AttributeValueList attribute_list = 13;
  }
}

message AttributeValueList {
  repeated AttributeValue values = 1;
}

message Attributes {
  map<string, AttributeValueList> attr = 1;
}