// Copyright 2026 Google LLC.
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
//     http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.

syntax = "proto3";

package google.gdm.gdmscience.alphagenome.atlas.v1main;

import "alphagenome/protos/dna_model.proto";

option go_package = "cloud.google.com/go/gdm/gdmscience/alphagenome/atlas/apiv1main/atlaspb;atlaspb";
option java_multiple_files = true;
option java_outer_classname = "AtlasServiceProto";
option java_package = "com.google.gdm.gdmscience.alphagenome.atlas.v1main";

// Atlas service for querying genomic data from AlphaGenome Atlas.
service AtlasService {
  // Lists variant scores for a given interval and organism as a dense array.
  rpc ListDenseVariantScores(ListDenseVariantScoresRequest)
      returns (ListDenseVariantScoresResponse) {}

  // Gets variant scores for a given variant and organism as a dense array.
  rpc GetDenseVariantScores(GetDenseVariantScoresRequest)
      returns (DenseVariantScores) {}

  // List the variant score metadata for a given organism.
  rpc ListVariantScoresMetadata(ListVariantScoresMetadataRequest)
      returns (ListVariantScoresMetadataResponse) {}
}

// Metadata for a single variant scorer.
message VariantScorerInfo {
  // Name for the variant scorer.
  string name = 1;

  // Whether the variant scorer is signed.
  bool is_signed = 2;
}

message GeneScorersMetadata {
  repeated google.gdm.gdmscience.alphagenome.v1main.GeneScorerMetadata
      metadata = 1;
}

// Container for all atlas metadata.
message Metadata {
  oneof payload {
    google.gdm.gdmscience.alphagenome.v1main.TracksMetadata tracks = 1;

    GeneScorersMetadata gene_scorers = 2;
  }
}

// Scores for a single variant and scorer.
message DenseVariantScore {
  // The variant scorer used to compute the score.
  VariantScorerInfo variant_scorer = 1;

  // Optional metadata for each dimension of the values array.
  repeated Metadata metadata = 2;

  // Shape of the scores array. The product of the shape dimensions must equal
  // the number of values.
  repeated int32 shape = 3;

  // N-d array of scores, in row-major order. Values are stored as single
  // precision floats.
  bytes scores = 4;

  // Optional calibrated scores for the variant. This may not be set for scores
  // that have not been calibrated (e.g. mouse scores).
  optional bytes calibrated_scores = 5;
}

// Dense variant scores for a single variant.
message DenseVariantScores {
  // The variant for which the score is computed.
  google.gdm.gdmscience.alphagenome.v1main.Variant variant = 1;

  // The interval used to calculate the variant scores.
  google.gdm.gdmscience.alphagenome.v1main.Interval interval = 3;

  repeated DenseVariantScore scores = 2;
}

// Metadata for a single variant scorer.
message VariantScorerMetadata {
  // The variant scorer used to compute the score.
  VariantScorerInfo variant_scorer = 1;

  // Fixed metadata for each variant score that is returned for this scorer.
  repeated Metadata metadata = 2;
}

// Request message for AtlasService.ListDenseVariantScores.
message ListDenseVariantScoresRequest {
  // Required. The genomic interval to list variant scores for.
  google.gdm.gdmscience.alphagenome.v1main.Interval interval = 1;

  // Required. The organism to list variant scores for.
  google.gdm.gdmscience.alphagenome.v1main.Organism organism = 2;

  // Optional. Requested page size. Server may return fewer variant scores than
  // requested. If unspecified, server will pick an appropriate default.
  int32 page_size = 3;

  // Optional. A page token, received from a previous `ListDenseVariantScores`
  // call. Provide this to retrieve the subsequent page. Please refer to
  // https://google.aip.dev/158 for more details.
  string page_token = 4;

  // Optional. The filter to apply to the list of variant scores.
  //
  // Please refer to https://google.aip.dev/160 for the filter syntax.
  //
  // The filter is applied to the DenseVariantScores proto.
  string filter = 5;
}

// Response message for AtlasService.ListDenseVariantScores.
message ListDenseVariantScoresResponse {
  // The list of dense variant scores.
  repeated DenseVariantScores variant_scores = 1;

  // A token that can be sent as `page_token` to retrieve the next page.
  // If this field is omitted, there are no subsequent pages.
  // Please refer to https://google.aip.dev/158 for more details.
  string next_page_token = 2;

  // The interval used to query the scores that are being returned.
  // If the requested interval extends beyond chromosome boundaries, this
  // reflects the valid range.
  google.gdm.gdmscience.alphagenome.v1main.Interval interval = 3;
}

// Request message for AtlasService.GetDenseVariantScores.
message GetDenseVariantScoresRequest {
  // Required. The variant to get variant scores for.
  google.gdm.gdmscience.alphagenome.v1main.Variant variant = 1;

  // Required. The organism to get variant scores for.
  google.gdm.gdmscience.alphagenome.v1main.Organism organism = 2;

  // Optional. The filter to apply to the variant scores.
  //
  // Please refer to https://google.aip.dev/160 for the filter syntax.
  string filter = 3;
}

// Request message for AtlasService.GetVariantScoresMetadata.
message ListVariantScoresMetadataRequest {
  // Required. The organism to get variant score filters for.
  google.gdm.gdmscience.alphagenome.v1main.Organism organism = 1;
}

// Response message for AtlasService.GetVariantScoresMetadata.
message ListVariantScoresMetadataResponse {
  // The metadata for each variant scorer.
  repeated VariantScorerMetadata variant_scorer_metadata = 1;
}