| Index: generated/googleapis/lib/genomics/v1.dart
|
| diff --git a/generated/googleapis_beta/lib/genomics/v1beta2.dart b/generated/googleapis/lib/genomics/v1.dart
|
| similarity index 56%
|
| copy from generated/googleapis_beta/lib/genomics/v1beta2.dart
|
| copy to generated/googleapis/lib/genomics/v1.dart
|
| index 52d92a112c906bd1cec5924db12ea44b488b96fb..de702f908e6e2130a0bf293b206c9591f301f09c 100644
|
| --- a/generated/googleapis_beta/lib/genomics/v1beta2.dart
|
| +++ b/generated/googleapis/lib/genomics/v1.dart
|
| @@ -1,6 +1,6 @@
|
| // This is a generated file (see the discoveryapis_generator project).
|
|
|
| -library googleapis_beta.genomics.v1beta2;
|
| +library googleapis.genomics.v1;
|
|
|
| import 'dart:core' as core;
|
| import 'dart:async' as async;
|
| @@ -12,9 +12,12 @@ import 'package:http/http.dart' as http;
|
| export 'package:_discoveryapis_commons/_discoveryapis_commons.dart' show
|
| ApiRequestError, DetailedApiRequestError;
|
|
|
| -const core.String USER_AGENT = 'dart-api-client genomics/v1beta2';
|
| +const core.String USER_AGENT = 'dart-api-client genomics/v1';
|
|
|
| -/** Provides access to Genomics data. */
|
| +/**
|
| + * An API to store, process, explore, and share DNA sequence reads,
|
| + * reference-based alignments, and variant calls.
|
| + */
|
| class GenomicsApi {
|
| /** View and manage your data in Google BigQuery */
|
| static const BigqueryScope = "https://www.googleapis.com/auth/bigquery";
|
| @@ -34,12 +37,9 @@ class GenomicsApi {
|
|
|
| final commons.ApiRequester _requester;
|
|
|
| - AnnotationSetsResourceApi get annotationSets => new AnnotationSetsResourceApi(_requester);
|
| - AnnotationsResourceApi get annotations => new AnnotationsResourceApi(_requester);
|
| CallsetsResourceApi get callsets => new CallsetsResourceApi(_requester);
|
| DatasetsResourceApi get datasets => new DatasetsResourceApi(_requester);
|
| - ExperimentalResourceApi get experimental => new ExperimentalResourceApi(_requester);
|
| - JobsResourceApi get jobs => new JobsResourceApi(_requester);
|
| + OperationsResourceApi get operations => new OperationsResourceApi(_requester);
|
| ReadgroupsetsResourceApi get readgroupsets => new ReadgroupsetsResourceApi(_requester);
|
| ReadsResourceApi get reads => new ReadsResourceApi(_requester);
|
| ReferencesResourceApi get references => new ReferencesResourceApi(_requester);
|
| @@ -47,26 +47,25 @@ class GenomicsApi {
|
| VariantsResourceApi get variants => new VariantsResourceApi(_requester);
|
| VariantsetsResourceApi get variantsets => new VariantsetsResourceApi(_requester);
|
|
|
| - GenomicsApi(http.Client client, {core.String rootUrl: "https://www.googleapis.com/", core.String servicePath: "genomics/v1beta2/"}) :
|
| + GenomicsApi(http.Client client, {core.String rootUrl: "https://genomics.googleapis.com/", core.String servicePath: ""}) :
|
| _requester = new commons.ApiRequester(client, rootUrl, servicePath, USER_AGENT);
|
| }
|
|
|
|
|
| -class AnnotationSetsResourceApi {
|
| +class CallsetsResourceApi {
|
| final commons.ApiRequester _requester;
|
|
|
| - AnnotationSetsResourceApi(commons.ApiRequester client) :
|
| + CallsetsResourceApi(commons.ApiRequester client) :
|
| _requester = client;
|
|
|
| /**
|
| - * Creates a new annotation set. Caller must have WRITE permission for the
|
| - * associated dataset.
|
| + * Creates a new call set.
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| * Request parameters:
|
| *
|
| - * Completes with a [AnnotationSet].
|
| + * Completes with a [CallSet].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -74,7 +73,7 @@ class AnnotationSetsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<AnnotationSet> create(AnnotationSet request) {
|
| + async.Future<CallSet> create(CallSet request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -86,7 +85,7 @@ class AnnotationSetsResourceApi {
|
| _body = convert.JSON.encode((request).toJson());
|
| }
|
|
|
| - _url = 'annotationSets';
|
| + _url = 'v1/callsets';
|
|
|
| var _response = _requester.request(_url,
|
| "POST",
|
| @@ -95,16 +94,17 @@ class AnnotationSetsResourceApi {
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new AnnotationSet.fromJson(data));
|
| + return _response.then((data) => new CallSet.fromJson(data));
|
| }
|
|
|
| /**
|
| - * Deletes an annotation set. Caller must have WRITE permission for the
|
| - * associated annotation set.
|
| + * Deletes a call set.
|
| *
|
| * Request parameters:
|
| *
|
| - * [annotationSetId] - The ID of the annotation set to be deleted.
|
| + * [callSetId] - The ID of the call set to be deleted.
|
| + *
|
| + * Completes with a [Empty].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -112,7 +112,7 @@ class AnnotationSetsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future delete(core.String annotationSetId) {
|
| + async.Future<Empty> delete(core.String callSetId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -120,13 +120,11 @@ class AnnotationSetsResourceApi {
|
| var _downloadOptions = commons.DownloadOptions.Metadata;
|
| var _body = null;
|
|
|
| - if (annotationSetId == null) {
|
| - throw new core.ArgumentError("Parameter annotationSetId is required.");
|
| + if (callSetId == null) {
|
| + throw new core.ArgumentError("Parameter callSetId is required.");
|
| }
|
|
|
| - _downloadOptions = null;
|
| -
|
| - _url = 'annotationSets/' + commons.Escaper.ecapeVariable('$annotationSetId');
|
| + _url = 'v1/callsets/' + commons.Escaper.ecapeVariable('$callSetId');
|
|
|
| var _response = _requester.request(_url,
|
| "DELETE",
|
| @@ -135,18 +133,17 @@ class AnnotationSetsResourceApi {
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => null);
|
| + return _response.then((data) => new Empty.fromJson(data));
|
| }
|
|
|
| /**
|
| - * Gets an annotation set. Caller must have READ permission for the associated
|
| - * dataset.
|
| + * Gets a call set by ID.
|
| *
|
| * Request parameters:
|
| *
|
| - * [annotationSetId] - The ID of the annotation set to be retrieved.
|
| + * [callSetId] - The ID of the call set.
|
| *
|
| - * Completes with a [AnnotationSet].
|
| + * Completes with a [CallSet].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -154,7 +151,7 @@ class AnnotationSetsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<AnnotationSet> get(core.String annotationSetId) {
|
| + async.Future<CallSet> get(core.String callSetId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -162,11 +159,11 @@ class AnnotationSetsResourceApi {
|
| var _downloadOptions = commons.DownloadOptions.Metadata;
|
| var _body = null;
|
|
|
| - if (annotationSetId == null) {
|
| - throw new core.ArgumentError("Parameter annotationSetId is required.");
|
| + if (callSetId == null) {
|
| + throw new core.ArgumentError("Parameter callSetId is required.");
|
| }
|
|
|
| - _url = 'annotationSets/' + commons.Escaper.ecapeVariable('$annotationSetId');
|
| + _url = 'v1/callsets/' + commons.Escaper.ecapeVariable('$callSetId');
|
|
|
| var _response = _requester.request(_url,
|
| "GET",
|
| @@ -175,22 +172,24 @@ class AnnotationSetsResourceApi {
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new AnnotationSet.fromJson(data));
|
| + return _response.then((data) => new CallSet.fromJson(data));
|
| }
|
|
|
| /**
|
| - * Updates an annotation set. The update must respect all mutability
|
| - * restrictions and other invariants described on the annotation set resource.
|
| - * Caller must have WRITE permission for the associated dataset. This method
|
| - * supports patch semantics.
|
| + * Updates a call set. This method supports patch semantics.
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| * Request parameters:
|
| *
|
| - * [annotationSetId] - The ID of the annotation set to be updated.
|
| + * [callSetId] - The ID of the call set to be updated.
|
| + *
|
| + * [updateMask] - An optional mask specifying which fields to update. At this
|
| + * time, the only mutable field is [name][google.genomics.v1.CallSet.name].
|
| + * The only acceptable value is "name". If unspecified, all mutable fields
|
| + * will be updated.
|
| *
|
| - * Completes with a [AnnotationSet].
|
| + * Completes with a [CallSet].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -198,7 +197,7 @@ class AnnotationSetsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<AnnotationSet> patch(AnnotationSet request, core.String annotationSetId) {
|
| + async.Future<CallSet> patch(CallSet request, core.String callSetId, {core.String updateMask}) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -209,11 +208,14 @@ class AnnotationSetsResourceApi {
|
| if (request != null) {
|
| _body = convert.JSON.encode((request).toJson());
|
| }
|
| - if (annotationSetId == null) {
|
| - throw new core.ArgumentError("Parameter annotationSetId is required.");
|
| + if (callSetId == null) {
|
| + throw new core.ArgumentError("Parameter callSetId is required.");
|
| + }
|
| + if (updateMask != null) {
|
| + _queryParams["updateMask"] = [updateMask];
|
| }
|
|
|
| - _url = 'annotationSets/' + commons.Escaper.ecapeVariable('$annotationSetId');
|
| + _url = 'v1/callsets/' + commons.Escaper.ecapeVariable('$callSetId');
|
|
|
| var _response = _requester.request(_url,
|
| "PATCH",
|
| @@ -222,19 +224,18 @@ class AnnotationSetsResourceApi {
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new AnnotationSet.fromJson(data));
|
| + return _response.then((data) => new CallSet.fromJson(data));
|
| }
|
|
|
| /**
|
| - * Searches for annotation sets that match the given criteria. Results are
|
| - * returned in a deterministic order. Caller must have READ permission for the
|
| - * queried datasets.
|
| + * Gets a list of call sets matching the criteria. Implements
|
| + * [GlobalAllianceApi.searchCallSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L178).
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| * Request parameters:
|
| *
|
| - * Completes with a [SearchAnnotationSetsResponse].
|
| + * Completes with a [SearchCallSetsResponse].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -242,7 +243,7 @@ class AnnotationSetsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<SearchAnnotationSetsResponse> search(SearchAnnotationSetsRequest request) {
|
| + async.Future<SearchCallSetsResponse> search(SearchCallSetsRequest request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -254,7 +255,7 @@ class AnnotationSetsResourceApi {
|
| _body = convert.JSON.encode((request).toJson());
|
| }
|
|
|
| - _url = 'annotationSets/search';
|
| + _url = 'v1/callsets/search';
|
|
|
| var _response = _requester.request(_url,
|
| "POST",
|
| @@ -263,82 +264,26 @@ class AnnotationSetsResourceApi {
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new SearchAnnotationSetsResponse.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Updates an annotation set. The update must respect all mutability
|
| - * restrictions and other invariants described on the annotation set resource.
|
| - * Caller must have WRITE permission for the associated dataset.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [annotationSetId] - The ID of the annotation set to be updated.
|
| - *
|
| - * Completes with a [AnnotationSet].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<AnnotationSet> update(AnnotationSet request, core.String annotationSetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| - if (annotationSetId == null) {
|
| - throw new core.ArgumentError("Parameter annotationSetId is required.");
|
| - }
|
| -
|
| - _url = 'annotationSets/' + commons.Escaper.ecapeVariable('$annotationSetId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "PUT",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new AnnotationSet.fromJson(data));
|
| + return _response.then((data) => new SearchCallSetsResponse.fromJson(data));
|
| }
|
|
|
| }
|
|
|
|
|
| -class AnnotationsResourceApi {
|
| +class DatasetsResourceApi {
|
| final commons.ApiRequester _requester;
|
|
|
| - AnnotationsResourceApi(commons.ApiRequester client) :
|
| + DatasetsResourceApi(commons.ApiRequester client) :
|
| _requester = client;
|
|
|
| /**
|
| - * Creates one or more new annotations atomically. All annotations must belong
|
| - * to the same annotation set. Caller must have WRITE permission for this
|
| - * annotation set. For optimal performance, batch positionally adjacent
|
| - * annotations together.
|
| - *
|
| - *
|
| - * If the request has a systemic issue, such as an attempt to write to an
|
| - * inaccessible annotation set, the entire RPC will fail accordingly. For
|
| - * lesser data issues, when possible an error will be isolated to the
|
| - * corresponding batch entry in the response; the remaining well formed
|
| - * annotations will be created normally.
|
| + * Creates a new dataset.
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| * Request parameters:
|
| *
|
| - * Completes with a [BatchAnnotationsResponse].
|
| + * Completes with a [Dataset].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -346,7 +291,7 @@ class AnnotationsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<BatchAnnotationsResponse> batchCreate(BatchCreateAnnotationsRequest request) {
|
| + async.Future<Dataset> create(Dataset request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -358,7 +303,7 @@ class AnnotationsResourceApi {
|
| _body = convert.JSON.encode((request).toJson());
|
| }
|
|
|
| - _url = 'annotations:batchCreate';
|
| + _url = 'v1/datasets';
|
|
|
| var _response = _requester.request(_url,
|
| "POST",
|
| @@ -367,18 +312,17 @@ class AnnotationsResourceApi {
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new BatchAnnotationsResponse.fromJson(data));
|
| + return _response.then((data) => new Dataset.fromJson(data));
|
| }
|
|
|
| /**
|
| - * Creates a new annotation. Caller must have WRITE permission for the
|
| - * associated annotation set.
|
| - *
|
| - * [request] - The metadata request object.
|
| + * Deletes a dataset.
|
| *
|
| * Request parameters:
|
| *
|
| - * Completes with a [Annotation].
|
| + * [datasetId] - The ID of the dataset to be deleted.
|
| + *
|
| + * Completes with a [Empty].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -386,7 +330,7 @@ class AnnotationsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<Annotation> create(Annotation request) {
|
| + async.Future<Empty> delete(core.String datasetId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -394,29 +338,30 @@ class AnnotationsResourceApi {
|
| var _downloadOptions = commons.DownloadOptions.Metadata;
|
| var _body = null;
|
|
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| + if (datasetId == null) {
|
| + throw new core.ArgumentError("Parameter datasetId is required.");
|
| }
|
|
|
| - _url = 'annotations';
|
| + _url = 'v1/datasets/' + commons.Escaper.ecapeVariable('$datasetId');
|
|
|
| var _response = _requester.request(_url,
|
| - "POST",
|
| + "DELETE",
|
| body: _body,
|
| queryParams: _queryParams,
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new Annotation.fromJson(data));
|
| + return _response.then((data) => new Empty.fromJson(data));
|
| }
|
|
|
| /**
|
| - * Deletes an annotation. Caller must have WRITE permission for the associated
|
| - * annotation set.
|
| + * Gets a dataset by ID.
|
| *
|
| * Request parameters:
|
| *
|
| - * [annotationId] - The ID of the annotation set to be deleted.
|
| + * [datasetId] - The ID of the dataset.
|
| + *
|
| + * Completes with a [Dataset].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -424,7 +369,7 @@ class AnnotationsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future delete(core.String annotationId) {
|
| + async.Future<Dataset> get(core.String datasetId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -432,33 +377,37 @@ class AnnotationsResourceApi {
|
| var _downloadOptions = commons.DownloadOptions.Metadata;
|
| var _body = null;
|
|
|
| - if (annotationId == null) {
|
| - throw new core.ArgumentError("Parameter annotationId is required.");
|
| + if (datasetId == null) {
|
| + throw new core.ArgumentError("Parameter datasetId is required.");
|
| }
|
|
|
| - _downloadOptions = null;
|
| -
|
| - _url = 'annotations/' + commons.Escaper.ecapeVariable('$annotationId');
|
| + _url = 'v1/datasets/' + commons.Escaper.ecapeVariable('$datasetId');
|
|
|
| var _response = _requester.request(_url,
|
| - "DELETE",
|
| + "GET",
|
| body: _body,
|
| queryParams: _queryParams,
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => null);
|
| + return _response.then((data) => new Dataset.fromJson(data));
|
| }
|
|
|
| /**
|
| - * Gets an annotation. Caller must have READ permission for the associated
|
| - * annotation set.
|
| + * Lists datasets within a project.
|
| *
|
| * Request parameters:
|
| *
|
| - * [annotationId] - The ID of the annotation set to be retrieved.
|
| + * [projectId] - Required. The project to list datasets for.
|
| + *
|
| + * [pageSize] - The maximum number of results returned by this request. If
|
| + * unspecified, defaults to 50. The maximum value is 1024.
|
| + *
|
| + * [pageToken] - The continuation token, which is used to page through large
|
| + * result sets. To get the next page of results, set this parameter to the
|
| + * value of `nextPageToken` from the previous response.
|
| *
|
| - * Completes with a [Annotation].
|
| + * Completes with a [ListDatasetsResponse].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -466,7 +415,7 @@ class AnnotationsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<Annotation> get(core.String annotationId) {
|
| + async.Future<ListDatasetsResponse> list({core.String projectId, core.int pageSize, core.String pageToken}) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -474,11 +423,17 @@ class AnnotationsResourceApi {
|
| var _downloadOptions = commons.DownloadOptions.Metadata;
|
| var _body = null;
|
|
|
| - if (annotationId == null) {
|
| - throw new core.ArgumentError("Parameter annotationId is required.");
|
| + if (projectId != null) {
|
| + _queryParams["projectId"] = [projectId];
|
| + }
|
| + if (pageSize != null) {
|
| + _queryParams["pageSize"] = ["${pageSize}"];
|
| + }
|
| + if (pageToken != null) {
|
| + _queryParams["pageToken"] = [pageToken];
|
| }
|
|
|
| - _url = 'annotations/' + commons.Escaper.ecapeVariable('$annotationId');
|
| + _url = 'v1/datasets';
|
|
|
| var _response = _requester.request(_url,
|
| "GET",
|
| @@ -487,22 +442,24 @@ class AnnotationsResourceApi {
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new Annotation.fromJson(data));
|
| + return _response.then((data) => new ListDatasetsResponse.fromJson(data));
|
| }
|
|
|
| /**
|
| - * Updates an annotation. The update must respect all mutability restrictions
|
| - * and other invariants described on the annotation resource. Caller must have
|
| - * WRITE permission for the associated dataset. This method supports patch
|
| - * semantics.
|
| + * Updates a dataset. This method supports patch semantics.
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| * Request parameters:
|
| *
|
| - * [annotationId] - The ID of the annotation set to be updated.
|
| + * [datasetId] - The ID of the dataset to be updated.
|
| + *
|
| + * [updateMask] - An optional mask specifying which fields to update. At this
|
| + * time, the only mutable field is [name][google.genomics.v1.Dataset.name].
|
| + * The only acceptable value is "name". If unspecified, all mutable fields
|
| + * will be updated.
|
| *
|
| - * Completes with a [Annotation].
|
| + * Completes with a [Dataset].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -510,7 +467,7 @@ class AnnotationsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<Annotation> patch(Annotation request, core.String annotationId) {
|
| + async.Future<Dataset> patch(Dataset request, core.String datasetId, {core.String updateMask}) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -521,11 +478,14 @@ class AnnotationsResourceApi {
|
| if (request != null) {
|
| _body = convert.JSON.encode((request).toJson());
|
| }
|
| - if (annotationId == null) {
|
| - throw new core.ArgumentError("Parameter annotationId is required.");
|
| + if (datasetId == null) {
|
| + throw new core.ArgumentError("Parameter datasetId is required.");
|
| + }
|
| + if (updateMask != null) {
|
| + _queryParams["updateMask"] = [updateMask];
|
| }
|
|
|
| - _url = 'annotations/' + commons.Escaper.ecapeVariable('$annotationId');
|
| + _url = 'v1/datasets/' + commons.Escaper.ecapeVariable('$datasetId');
|
|
|
| var _response = _requester.request(_url,
|
| "PATCH",
|
| @@ -534,20 +494,20 @@ class AnnotationsResourceApi {
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new Annotation.fromJson(data));
|
| + return _response.then((data) => new Dataset.fromJson(data));
|
| }
|
|
|
| /**
|
| - * Searches for annotations that match the given criteria. Results are
|
| - * returned ordered by start position. Annotations that have matching start
|
| - * positions are ordered deterministically. Caller must have READ permission
|
| - * for the queried annotation sets.
|
| + * Undeletes a dataset by restoring a dataset which was deleted via this API.
|
| + * This operation is only possible for a week after the deletion occurred.
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| * Request parameters:
|
| *
|
| - * Completes with a [SearchAnnotationsResponse].
|
| + * [datasetId] - The ID of the dataset to be undeleted.
|
| + *
|
| + * Completes with a [Dataset].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -555,7 +515,7 @@ class AnnotationsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<SearchAnnotationsResponse> search(SearchAnnotationsRequest request) {
|
| + async.Future<Dataset> undelete(UndeleteDatasetRequest request, core.String datasetId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -566,8 +526,11 @@ class AnnotationsResourceApi {
|
| if (request != null) {
|
| _body = convert.JSON.encode((request).toJson());
|
| }
|
| + if (datasetId == null) {
|
| + throw new core.ArgumentError("Parameter datasetId is required.");
|
| + }
|
|
|
| - _url = 'annotations/search';
|
| + _url = 'v1/datasets/' + commons.Escaper.ecapeVariable('$datasetId') + ':undelete';
|
|
|
| var _response = _requester.request(_url,
|
| "POST",
|
| @@ -576,21 +539,35 @@ class AnnotationsResourceApi {
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new SearchAnnotationsResponse.fromJson(data));
|
| + return _response.then((data) => new Dataset.fromJson(data));
|
| }
|
|
|
| +}
|
| +
|
| +
|
| +class OperationsResourceApi {
|
| + final commons.ApiRequester _requester;
|
| +
|
| + OperationsResourceApi(commons.ApiRequester client) :
|
| + _requester = client;
|
| +
|
| /**
|
| - * Updates an annotation. The update must respect all mutability restrictions
|
| - * and other invariants described on the annotation resource. Caller must have
|
| - * WRITE permission for the associated dataset.
|
| + * Starts asynchronous cancellation on a long-running operation. The server
|
| + * makes a best effort to cancel the operation, but success is not guaranteed.
|
| + * Clients may use
|
| + * [Operations.GetOperation][google.longrunning.Operations.GetOperation] or
|
| + * [Operations.ListOperations][google.longrunning.Operations.ListOperations]
|
| + * to check whether the cancellation succeeded or the operation completed
|
| + * despite cancellation.
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| * Request parameters:
|
| *
|
| - * [annotationId] - The ID of the annotation set to be updated.
|
| + * [name] - The name of the operation resource to be cancelled.
|
| + * Value must have pattern "^operations/.*$".
|
| *
|
| - * Completes with a [Annotation].
|
| + * Completes with a [Empty].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -598,7 +575,7 @@ class AnnotationsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<Annotation> update(Annotation request, core.String annotationId) {
|
| + async.Future<Empty> cancel(CancelOperationRequest request, core.String name) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -609,39 +586,32 @@ class AnnotationsResourceApi {
|
| if (request != null) {
|
| _body = convert.JSON.encode((request).toJson());
|
| }
|
| - if (annotationId == null) {
|
| - throw new core.ArgumentError("Parameter annotationId is required.");
|
| + if (name == null) {
|
| + throw new core.ArgumentError("Parameter name is required.");
|
| }
|
|
|
| - _url = 'annotations/' + commons.Escaper.ecapeVariable('$annotationId');
|
| + _url = 'v1/' + commons.Escaper.ecapeVariableReserved('$name') + ':cancel';
|
|
|
| var _response = _requester.request(_url,
|
| - "PUT",
|
| + "POST",
|
| body: _body,
|
| queryParams: _queryParams,
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new Annotation.fromJson(data));
|
| + return _response.then((data) => new Empty.fromJson(data));
|
| }
|
|
|
| -}
|
| -
|
| -
|
| -class CallsetsResourceApi {
|
| - final commons.ApiRequester _requester;
|
| -
|
| - CallsetsResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| /**
|
| - * Creates a new call set.
|
| - *
|
| - * [request] - The metadata request object.
|
| + * This method is not implemented. To cancel an operation, please use
|
| + * [Operations.CancelOperation][google.longrunning.Operations.CancelOperation].
|
| *
|
| * Request parameters:
|
| *
|
| - * Completes with a [CallSet].
|
| + * [name] - The name of the operation resource to be deleted.
|
| + * Value must have pattern "^operations/.*$".
|
| + *
|
| + * Completes with a [Empty].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -649,7 +619,7 @@ class CallsetsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<CallSet> create(CallSet request) {
|
| + async.Future<Empty> delete(core.String name) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -657,28 +627,33 @@ class CallsetsResourceApi {
|
| var _downloadOptions = commons.DownloadOptions.Metadata;
|
| var _body = null;
|
|
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| + if (name == null) {
|
| + throw new core.ArgumentError("Parameter name is required.");
|
| }
|
|
|
| - _url = 'callsets';
|
| + _url = 'v1/' + commons.Escaper.ecapeVariableReserved('$name');
|
|
|
| var _response = _requester.request(_url,
|
| - "POST",
|
| + "DELETE",
|
| body: _body,
|
| queryParams: _queryParams,
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new CallSet.fromJson(data));
|
| + return _response.then((data) => new Empty.fromJson(data));
|
| }
|
|
|
| /**
|
| - * Deletes a call set.
|
| + * Gets the latest state of a long-running operation. Clients can use this
|
| + * method to poll the operation result at intervals as recommended by the API
|
| + * service.
|
| *
|
| * Request parameters:
|
| *
|
| - * [callSetId] - The ID of the call set to be deleted.
|
| + * [name] - The name of the operation resource.
|
| + * Value must have pattern "^operations/.*$".
|
| + *
|
| + * Completes with a [Operation].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -686,7 +661,7 @@ class CallsetsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future delete(core.String callSetId) {
|
| + async.Future<Operation> get(core.String name) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -694,32 +669,45 @@ class CallsetsResourceApi {
|
| var _downloadOptions = commons.DownloadOptions.Metadata;
|
| var _body = null;
|
|
|
| - if (callSetId == null) {
|
| - throw new core.ArgumentError("Parameter callSetId is required.");
|
| + if (name == null) {
|
| + throw new core.ArgumentError("Parameter name is required.");
|
| }
|
|
|
| - _downloadOptions = null;
|
| -
|
| - _url = 'callsets/' + commons.Escaper.ecapeVariable('$callSetId');
|
| + _url = 'v1/' + commons.Escaper.ecapeVariableReserved('$name');
|
|
|
| var _response = _requester.request(_url,
|
| - "DELETE",
|
| + "GET",
|
| body: _body,
|
| queryParams: _queryParams,
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => null);
|
| + return _response.then((data) => new Operation.fromJson(data));
|
| }
|
|
|
| /**
|
| - * Gets a call set by ID.
|
| + * Lists operations that match the specified filter in the request.
|
| *
|
| * Request parameters:
|
| *
|
| - * [callSetId] - The ID of the call set.
|
| + * [name] - The name of the operation collection.
|
| + * Value must have pattern "^operations$".
|
| *
|
| - * Completes with a [CallSet].
|
| + * [filter] - A string for filtering
|
| + * [Operations][google.longrunning.Operation]. The following filter fields are
|
| + * supported: * projectId: Required. Corresponds to
|
| + * [OperationMetadata.projectId][google.genomics.v1.OperationMetadata.project_id].
|
| + * * createTime: The time this job was created, in seconds from the
|
| + * [epoch](http://en.wikipedia.org/wiki/Unix_time). Can use `>=` and/or `=
|
| + * 1432140000` * `projectId = my-project AND createTime >= 1432140000 AND
|
| + * createTime <= 1432150000 AND status = RUNNING`
|
| + *
|
| + * [pageSize] - The maximum number of results to return. If unspecified,
|
| + * defaults to 256. The maximum value is 2048.
|
| + *
|
| + * [pageToken] - The standard list page token.
|
| + *
|
| + * Completes with a [ListOperationsResponse].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -727,7 +715,7 @@ class CallsetsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<CallSet> get(core.String callSetId) {
|
| + async.Future<ListOperationsResponse> list(core.String name, {core.String filter, core.int pageSize, core.String pageToken}) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -735,11 +723,20 @@ class CallsetsResourceApi {
|
| var _downloadOptions = commons.DownloadOptions.Metadata;
|
| var _body = null;
|
|
|
| - if (callSetId == null) {
|
| - throw new core.ArgumentError("Parameter callSetId is required.");
|
| + if (name == null) {
|
| + throw new core.ArgumentError("Parameter name is required.");
|
| + }
|
| + if (filter != null) {
|
| + _queryParams["filter"] = [filter];
|
| + }
|
| + if (pageSize != null) {
|
| + _queryParams["pageSize"] = ["${pageSize}"];
|
| + }
|
| + if (pageToken != null) {
|
| + _queryParams["pageToken"] = [pageToken];
|
| }
|
|
|
| - _url = 'callsets/' + commons.Escaper.ecapeVariable('$callSetId');
|
| + _url = 'v1/' + commons.Escaper.ecapeVariableReserved('$name');
|
|
|
| var _response = _requester.request(_url,
|
| "GET",
|
| @@ -748,19 +745,30 @@ class CallsetsResourceApi {
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new CallSet.fromJson(data));
|
| + return _response.then((data) => new ListOperationsResponse.fromJson(data));
|
| }
|
|
|
| +}
|
| +
|
| +
|
| +class ReadgroupsetsResourceApi {
|
| + final commons.ApiRequester _requester;
|
| +
|
| + ReadgroupsetsCoveragebucketsResourceApi get coveragebuckets => new ReadgroupsetsCoveragebucketsResourceApi(_requester);
|
| +
|
| + ReadgroupsetsResourceApi(commons.ApiRequester client) :
|
| + _requester = client;
|
| +
|
| /**
|
| - * Updates a call set. This method supports patch semantics.
|
| - *
|
| - * [request] - The metadata request object.
|
| + * Deletes a read group set.
|
| *
|
| * Request parameters:
|
| *
|
| - * [callSetId] - The ID of the call set to be updated.
|
| + * [readGroupSetId] - The ID of the read group set to be deleted. The caller
|
| + * must have WRITE permissions to the dataset associated with this read group
|
| + * set.
|
| *
|
| - * Completes with a [CallSet].
|
| + * Completes with a [Empty].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -768,7 +776,7 @@ class CallsetsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<CallSet> patch(CallSet request, core.String callSetId) {
|
| + async.Future<Empty> delete(core.String readGroupSetId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -776,35 +784,37 @@ class CallsetsResourceApi {
|
| var _downloadOptions = commons.DownloadOptions.Metadata;
|
| var _body = null;
|
|
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| - if (callSetId == null) {
|
| - throw new core.ArgumentError("Parameter callSetId is required.");
|
| + if (readGroupSetId == null) {
|
| + throw new core.ArgumentError("Parameter readGroupSetId is required.");
|
| }
|
|
|
| - _url = 'callsets/' + commons.Escaper.ecapeVariable('$callSetId');
|
| + _url = 'v1/readgroupsets/' + commons.Escaper.ecapeVariable('$readGroupSetId');
|
|
|
| var _response = _requester.request(_url,
|
| - "PATCH",
|
| + "DELETE",
|
| body: _body,
|
| queryParams: _queryParams,
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new CallSet.fromJson(data));
|
| + return _response.then((data) => new Empty.fromJson(data));
|
| }
|
|
|
| /**
|
| - * Gets a list of call sets matching the criteria.
|
| - *
|
| - * Implements GlobalAllianceApi.searchCallSets.
|
| + * Exports a read group set to a BAM file in Google Cloud Storage. Note that
|
| + * currently there may be some differences between exported BAM files and the
|
| + * original BAM file at the time of import. In particular, comments in the
|
| + * input file header will not be preserved, some custom tags will be converted
|
| + * to strings, and original reference sequence order is not necessarily
|
| + * preserved.
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| * Request parameters:
|
| *
|
| - * Completes with a [SearchCallSetsResponse].
|
| + * [readGroupSetId] - Required. The ID of the read group set to export.
|
| + *
|
| + * Completes with a [Operation].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -812,7 +822,7 @@ class CallsetsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<SearchCallSetsResponse> search(SearchCallSetsRequest request) {
|
| + async.Future<Operation> export(ExportReadGroupSetRequest request, core.String readGroupSetId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -823,8 +833,11 @@ class CallsetsResourceApi {
|
| if (request != null) {
|
| _body = convert.JSON.encode((request).toJson());
|
| }
|
| + if (readGroupSetId == null) {
|
| + throw new core.ArgumentError("Parameter readGroupSetId is required.");
|
| + }
|
|
|
| - _url = 'callsets/search';
|
| + _url = 'v1/readgroupsets/' + commons.Escaper.ecapeVariable('$readGroupSetId') + ':export';
|
|
|
| var _response = _requester.request(_url,
|
| "POST",
|
| @@ -833,19 +846,17 @@ class CallsetsResourceApi {
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new SearchCallSetsResponse.fromJson(data));
|
| + return _response.then((data) => new Operation.fromJson(data));
|
| }
|
|
|
| /**
|
| - * Updates a call set.
|
| - *
|
| - * [request] - The metadata request object.
|
| + * Gets a read group set by ID.
|
| *
|
| * Request parameters:
|
| *
|
| - * [callSetId] - The ID of the call set to be updated.
|
| + * [readGroupSetId] - The ID of the read group set.
|
| *
|
| - * Completes with a [CallSet].
|
| + * Completes with a [ReadGroupSet].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -853,7 +864,7 @@ class CallsetsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<CallSet> update(CallSet request, core.String callSetId) {
|
| + async.Future<ReadGroupSet> get(core.String readGroupSetId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -861,42 +872,34 @@ class CallsetsResourceApi {
|
| var _downloadOptions = commons.DownloadOptions.Metadata;
|
| var _body = null;
|
|
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| - if (callSetId == null) {
|
| - throw new core.ArgumentError("Parameter callSetId is required.");
|
| + if (readGroupSetId == null) {
|
| + throw new core.ArgumentError("Parameter readGroupSetId is required.");
|
| }
|
|
|
| - _url = 'callsets/' + commons.Escaper.ecapeVariable('$callSetId');
|
| + _url = 'v1/readgroupsets/' + commons.Escaper.ecapeVariable('$readGroupSetId');
|
|
|
| var _response = _requester.request(_url,
|
| - "PUT",
|
| + "GET",
|
| body: _body,
|
| queryParams: _queryParams,
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new CallSet.fromJson(data));
|
| + return _response.then((data) => new ReadGroupSet.fromJson(data));
|
| }
|
|
|
| -}
|
| -
|
| -
|
| -class DatasetsResourceApi {
|
| - final commons.ApiRequester _requester;
|
| -
|
| - DatasetsResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| /**
|
| - * Creates a new dataset.
|
| + * Creates read group sets by asynchronously importing the provided
|
| + * information. Note that currently comments in the input file header are
|
| + * **not** imported and some custom tags will be converted to strings, rather
|
| + * than preserving tag types. The caller must have WRITE permissions to the
|
| + * dataset.
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| * Request parameters:
|
| *
|
| - * Completes with a [Dataset].
|
| + * Completes with a [Operation].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -904,7 +907,7 @@ class DatasetsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<Dataset> create(Dataset request) {
|
| + async.Future<Operation> import(ImportReadGroupSetsRequest request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -916,7 +919,7 @@ class DatasetsResourceApi {
|
| _body = convert.JSON.encode((request).toJson());
|
| }
|
|
|
| - _url = 'datasets';
|
| + _url = 'v1/readgroupsets:import';
|
|
|
| var _response = _requester.request(_url,
|
| "POST",
|
| @@ -925,15 +928,28 @@ class DatasetsResourceApi {
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new Dataset.fromJson(data));
|
| + return _response.then((data) => new Operation.fromJson(data));
|
| }
|
|
|
| /**
|
| - * Deletes a dataset.
|
| + * Updates a read group set. This method supports patch semantics.
|
| + *
|
| + * [request] - The metadata request object.
|
| *
|
| * Request parameters:
|
| *
|
| - * [datasetId] - The ID of the dataset to be deleted.
|
| + * [readGroupSetId] - The ID of the read group set to be updated. The caller
|
| + * must have WRITE permissions to the dataset associated with this read group
|
| + * set.
|
| + *
|
| + * [updateMask] - An optional mask specifying which fields to update. At this
|
| + * time, mutable fields are
|
| + * [referenceSetId][google.genomics.v1.ReadGroupSet.reference_set_id] and
|
| + * [name][google.genomics.v1.ReadGroupSet.name]. Acceptable values are
|
| + * "referenceSetId" and "name". If unspecified, all mutable fields will be
|
| + * updated.
|
| + *
|
| + * Completes with a [ReadGroupSet].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -941,7 +957,7 @@ class DatasetsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future delete(core.String datasetId) {
|
| + async.Future<ReadGroupSet> patch(ReadGroupSet request, core.String readGroupSetId, {core.String updateMask}) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -949,32 +965,37 @@ class DatasetsResourceApi {
|
| var _downloadOptions = commons.DownloadOptions.Metadata;
|
| var _body = null;
|
|
|
| - if (datasetId == null) {
|
| - throw new core.ArgumentError("Parameter datasetId is required.");
|
| + if (request != null) {
|
| + _body = convert.JSON.encode((request).toJson());
|
| + }
|
| + if (readGroupSetId == null) {
|
| + throw new core.ArgumentError("Parameter readGroupSetId is required.");
|
| + }
|
| + if (updateMask != null) {
|
| + _queryParams["updateMask"] = [updateMask];
|
| }
|
|
|
| - _downloadOptions = null;
|
| -
|
| - _url = 'datasets/' + commons.Escaper.ecapeVariable('$datasetId');
|
| + _url = 'v1/readgroupsets/' + commons.Escaper.ecapeVariable('$readGroupSetId');
|
|
|
| var _response = _requester.request(_url,
|
| - "DELETE",
|
| + "PATCH",
|
| body: _body,
|
| queryParams: _queryParams,
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => null);
|
| + return _response.then((data) => new ReadGroupSet.fromJson(data));
|
| }
|
|
|
| /**
|
| - * Gets a dataset by ID.
|
| + * Searches for read group sets matching the criteria. Implements
|
| + * [GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L135).
|
| *
|
| - * Request parameters:
|
| + * [request] - The metadata request object.
|
| *
|
| - * [datasetId] - The ID of the dataset.
|
| + * Request parameters:
|
| *
|
| - * Completes with a [Dataset].
|
| + * Completes with a [SearchReadGroupSetsResponse].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -982,7 +1003,7 @@ class DatasetsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<Dataset> get(core.String datasetId) {
|
| + async.Future<SearchReadGroupSetsResponse> search(SearchReadGroupSetsRequest request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -990,37 +1011,71 @@ class DatasetsResourceApi {
|
| var _downloadOptions = commons.DownloadOptions.Metadata;
|
| var _body = null;
|
|
|
| - if (datasetId == null) {
|
| - throw new core.ArgumentError("Parameter datasetId is required.");
|
| + if (request != null) {
|
| + _body = convert.JSON.encode((request).toJson());
|
| }
|
|
|
| - _url = 'datasets/' + commons.Escaper.ecapeVariable('$datasetId');
|
| + _url = 'v1/readgroupsets/search';
|
|
|
| var _response = _requester.request(_url,
|
| - "GET",
|
| + "POST",
|
| body: _body,
|
| queryParams: _queryParams,
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new Dataset.fromJson(data));
|
| + return _response.then((data) => new SearchReadGroupSetsResponse.fromJson(data));
|
| }
|
|
|
| +}
|
| +
|
| +
|
| +class ReadgroupsetsCoveragebucketsResourceApi {
|
| + final commons.ApiRequester _requester;
|
| +
|
| + ReadgroupsetsCoveragebucketsResourceApi(commons.ApiRequester client) :
|
| + _requester = client;
|
| +
|
| /**
|
| - * Lists datasets within a project.
|
| + * Lists fixed width coverage buckets for a read group set, each of which
|
| + * correspond to a range of a reference sequence. Each bucket summarizes
|
| + * coverage information across its corresponding genomic range. Coverage is
|
| + * defined as the number of reads which are aligned to a given base in the
|
| + * reference sequence. Coverage buckets are available at several precomputed
|
| + * bucket widths, enabling retrieval of various coverage 'zoom levels'. The
|
| + * caller must have READ permissions for the target read group set.
|
| *
|
| * Request parameters:
|
| *
|
| - * [pageSize] - The maximum number of results returned by this request. If
|
| - * unspecified, defaults to 50.
|
| + * [readGroupSetId] - Required. The ID of the read group set over which
|
| + * coverage is requested.
|
| + *
|
| + * [referenceName] - The name of the reference to query, within the reference
|
| + * set associated with this query. Optional.
|
| + *
|
| + * [start] - The start position of the range on the reference, 0-based
|
| + * inclusive. If specified, `referenceName` must also be specified. Defaults
|
| + * to 0.
|
| + *
|
| + * [end] - The end position of the range on the reference, 0-based exclusive.
|
| + * If specified, `referenceName` must also be specified. If unset or 0,
|
| + * defaults to the length of the reference.
|
| + *
|
| + * [targetBucketWidth] - The desired width of each reported coverage bucket in
|
| + * base pairs. This will be rounded down to the nearest precomputed bucket
|
| + * width; the value of which is returned as `bucketWidth` in the response.
|
| + * Defaults to infinity (each bucket spans an entire reference sequence) or
|
| + * the length of the target range, if specified. The smallest precomputed
|
| + * `bucketWidth` is currently 2048 base pairs; this is subject to change.
|
| *
|
| * [pageToken] - The continuation token, which is used to page through large
|
| * result sets. To get the next page of results, set this parameter to the
|
| - * value of nextPageToken from the previous response.
|
| + * value of `nextPageToken` from the previous response.
|
| *
|
| - * [projectNumber] - Required. The project to list datasets for.
|
| + * [pageSize] - The maximum number of results to return in a single page. If
|
| + * unspecified, defaults to 1024. The maximum value is 2048.
|
| *
|
| - * Completes with a [ListDatasetsResponse].
|
| + * Completes with a [ListCoverageBucketsResponse].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1028,7 +1083,7 @@ class DatasetsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<ListDatasetsResponse> list({core.int pageSize, core.String pageToken, core.String projectNumber}) {
|
| + async.Future<ListCoverageBucketsResponse> list(core.String readGroupSetId, {core.String referenceName, core.String start, core.String end, core.String targetBucketWidth, core.String pageToken, core.int pageSize}) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1036,17 +1091,29 @@ class DatasetsResourceApi {
|
| var _downloadOptions = commons.DownloadOptions.Metadata;
|
| var _body = null;
|
|
|
| - if (pageSize != null) {
|
| - _queryParams["pageSize"] = ["${pageSize}"];
|
| + if (readGroupSetId == null) {
|
| + throw new core.ArgumentError("Parameter readGroupSetId is required.");
|
| + }
|
| + if (referenceName != null) {
|
| + _queryParams["referenceName"] = [referenceName];
|
| + }
|
| + if (start != null) {
|
| + _queryParams["start"] = [start];
|
| + }
|
| + if (end != null) {
|
| + _queryParams["end"] = [end];
|
| + }
|
| + if (targetBucketWidth != null) {
|
| + _queryParams["targetBucketWidth"] = [targetBucketWidth];
|
| }
|
| if (pageToken != null) {
|
| _queryParams["pageToken"] = [pageToken];
|
| }
|
| - if (projectNumber != null) {
|
| - _queryParams["projectNumber"] = [projectNumber];
|
| + if (pageSize != null) {
|
| + _queryParams["pageSize"] = ["${pageSize}"];
|
| }
|
|
|
| - _url = 'datasets';
|
| + _url = 'v1/readgroupsets/' + commons.Escaper.ecapeVariable('$readGroupSetId') + '/coveragebuckets';
|
|
|
| var _response = _requester.request(_url,
|
| "GET",
|
| @@ -1055,19 +1122,36 @@ class DatasetsResourceApi {
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new ListDatasetsResponse.fromJson(data));
|
| + return _response.then((data) => new ListCoverageBucketsResponse.fromJson(data));
|
| }
|
|
|
| +}
|
| +
|
| +
|
| +class ReadsResourceApi {
|
| + final commons.ApiRequester _requester;
|
| +
|
| + ReadsResourceApi(commons.ApiRequester client) :
|
| + _requester = client;
|
| +
|
| /**
|
| - * Updates a dataset. This method supports patch semantics.
|
| + * Gets a list of reads for one or more read group sets. Reads search operates
|
| + * over a genomic coordinate space of reference sequence & position defined
|
| + * over the reference sequences to which the requested read group sets are
|
| + * aligned. If a target positional range is specified, search returns all
|
| + * reads whose alignment to the reference genome overlap the range. A query
|
| + * which specifies only read group set IDs yields all reads in those read
|
| + * group sets, including unmapped reads. All reads returned (including reads
|
| + * on subsequent pages) are ordered by genomic coordinate (reference sequence
|
| + * & position). Reads with equivalent genomic coordinates are returned in a
|
| + * deterministic order. Implements
|
| + * [GlobalAllianceApi.searchReads](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L85).
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| * Request parameters:
|
| *
|
| - * [datasetId] - The ID of the dataset to be updated.
|
| - *
|
| - * Completes with a [Dataset].
|
| + * Completes with a [SearchReadsResponse].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1075,7 +1159,7 @@ class DatasetsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<Dataset> patch(Dataset request, core.String datasetId) {
|
| + async.Future<SearchReadsResponse> search(SearchReadsRequest request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1086,31 +1170,39 @@ class DatasetsResourceApi {
|
| if (request != null) {
|
| _body = convert.JSON.encode((request).toJson());
|
| }
|
| - if (datasetId == null) {
|
| - throw new core.ArgumentError("Parameter datasetId is required.");
|
| - }
|
|
|
| - _url = 'datasets/' + commons.Escaper.ecapeVariable('$datasetId');
|
| + _url = 'v1/reads/search';
|
|
|
| var _response = _requester.request(_url,
|
| - "PATCH",
|
| + "POST",
|
| body: _body,
|
| queryParams: _queryParams,
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new Dataset.fromJson(data));
|
| + return _response.then((data) => new SearchReadsResponse.fromJson(data));
|
| }
|
|
|
| +}
|
| +
|
| +
|
| +class ReferencesResourceApi {
|
| + final commons.ApiRequester _requester;
|
| +
|
| + ReferencesBasesResourceApi get bases => new ReferencesBasesResourceApi(_requester);
|
| +
|
| + ReferencesResourceApi(commons.ApiRequester client) :
|
| + _requester = client;
|
| +
|
| /**
|
| - * Undeletes a dataset by restoring a dataset which was deleted via this API.
|
| - * This operation is only possible for a week after the deletion occurred.
|
| + * Gets a reference. Implements
|
| + * [GlobalAllianceApi.getReference](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L158).
|
| *
|
| * Request parameters:
|
| *
|
| - * [datasetId] - The ID of the dataset to be undeleted.
|
| + * [referenceId] - The ID of the reference.
|
| *
|
| - * Completes with a [Dataset].
|
| + * Completes with a [Reference].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1118,7 +1210,7 @@ class DatasetsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<Dataset> undelete(core.String datasetId) {
|
| + async.Future<Reference> get(core.String referenceId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1126,32 +1218,31 @@ class DatasetsResourceApi {
|
| var _downloadOptions = commons.DownloadOptions.Metadata;
|
| var _body = null;
|
|
|
| - if (datasetId == null) {
|
| - throw new core.ArgumentError("Parameter datasetId is required.");
|
| + if (referenceId == null) {
|
| + throw new core.ArgumentError("Parameter referenceId is required.");
|
| }
|
|
|
| - _url = 'datasets/' + commons.Escaper.ecapeVariable('$datasetId') + '/undelete';
|
| + _url = 'v1/references/' + commons.Escaper.ecapeVariable('$referenceId');
|
|
|
| var _response = _requester.request(_url,
|
| - "POST",
|
| + "GET",
|
| body: _body,
|
| queryParams: _queryParams,
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new Dataset.fromJson(data));
|
| + return _response.then((data) => new Reference.fromJson(data));
|
| }
|
|
|
| /**
|
| - * Updates a dataset.
|
| + * Searches for references which match the given criteria. Implements
|
| + * [GlobalAllianceApi.searchReferences](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L146).
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| * Request parameters:
|
| *
|
| - * [datasetId] - The ID of the dataset to be updated.
|
| - *
|
| - * Completes with a [Dataset].
|
| + * Completes with a [SearchReferencesResponse].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1159,7 +1250,7 @@ class DatasetsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<Dataset> update(Dataset request, core.String datasetId) {
|
| + async.Future<SearchReferencesResponse> search(SearchReferencesRequest request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1170,50 +1261,50 @@ class DatasetsResourceApi {
|
| if (request != null) {
|
| _body = convert.JSON.encode((request).toJson());
|
| }
|
| - if (datasetId == null) {
|
| - throw new core.ArgumentError("Parameter datasetId is required.");
|
| - }
|
|
|
| - _url = 'datasets/' + commons.Escaper.ecapeVariable('$datasetId');
|
| + _url = 'v1/references/search';
|
|
|
| var _response = _requester.request(_url,
|
| - "PUT",
|
| + "POST",
|
| body: _body,
|
| queryParams: _queryParams,
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new Dataset.fromJson(data));
|
| + return _response.then((data) => new SearchReferencesResponse.fromJson(data));
|
| }
|
|
|
| }
|
|
|
|
|
| -class ExperimentalResourceApi {
|
| - final commons.ApiRequester _requester;
|
| -
|
| - ExperimentalJobsResourceApi get jobs => new ExperimentalJobsResourceApi(_requester);
|
| -
|
| - ExperimentalResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
| -}
|
| -
|
| -
|
| -class ExperimentalJobsResourceApi {
|
| +class ReferencesBasesResourceApi {
|
| final commons.ApiRequester _requester;
|
|
|
| - ExperimentalJobsResourceApi(commons.ApiRequester client) :
|
| + ReferencesBasesResourceApi(commons.ApiRequester client) :
|
| _requester = client;
|
|
|
| /**
|
| - * Creates and asynchronously runs an ad-hoc job. This is an experimental call
|
| - * and may be removed or changed at any time.
|
| - *
|
| - * [request] - The metadata request object.
|
| + * Lists the bases in a reference, optionally restricted to a range.
|
| + * Implements
|
| + * [GlobalAllianceApi.getReferenceBases](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L221).
|
| *
|
| * Request parameters:
|
| *
|
| - * Completes with a [ExperimentalCreateJobResponse].
|
| + * [referenceId] - The ID of the reference.
|
| + *
|
| + * [start] - The start position (0-based) of this query. Defaults to 0.
|
| + *
|
| + * [end] - The end position (0-based, exclusive) of this query. Defaults to
|
| + * the length of this reference.
|
| + *
|
| + * [pageToken] - The continuation token, which is used to page through large
|
| + * result sets. To get the next page of results, set this parameter to the
|
| + * value of `nextPageToken` from the previous response.
|
| + *
|
| + * [pageSize] - Specifies the maximum number of bases to return in a single
|
| + * page.
|
| + *
|
| + * Completes with a [ListBasesResponse].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1221,7 +1312,7 @@ class ExperimentalJobsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<ExperimentalCreateJobResponse> create(ExperimentalCreateJobRequest request) {
|
| + async.Future<ListBasesResponse> list(core.String referenceId, {core.String start, core.String end, core.String pageToken, core.int pageSize}) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1229,79 +1320,52 @@ class ExperimentalJobsResourceApi {
|
| var _downloadOptions = commons.DownloadOptions.Metadata;
|
| var _body = null;
|
|
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| + if (referenceId == null) {
|
| + throw new core.ArgumentError("Parameter referenceId is required.");
|
| + }
|
| + if (start != null) {
|
| + _queryParams["start"] = [start];
|
| + }
|
| + if (end != null) {
|
| + _queryParams["end"] = [end];
|
| + }
|
| + if (pageToken != null) {
|
| + _queryParams["pageToken"] = [pageToken];
|
| + }
|
| + if (pageSize != null) {
|
| + _queryParams["pageSize"] = ["${pageSize}"];
|
| }
|
|
|
| - _url = 'experimental/jobs/create';
|
| + _url = 'v1/references/' + commons.Escaper.ecapeVariable('$referenceId') + '/bases';
|
|
|
| var _response = _requester.request(_url,
|
| - "POST",
|
| + "GET",
|
| body: _body,
|
| queryParams: _queryParams,
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new ExperimentalCreateJobResponse.fromJson(data));
|
| + return _response.then((data) => new ListBasesResponse.fromJson(data));
|
| }
|
|
|
| }
|
|
|
|
|
| -class JobsResourceApi {
|
| +class ReferencesetsResourceApi {
|
| final commons.ApiRequester _requester;
|
|
|
| - JobsResourceApi(commons.ApiRequester client) :
|
| + ReferencesetsResourceApi(commons.ApiRequester client) :
|
| _requester = client;
|
|
|
| /**
|
| - * Cancels a job by ID. Note that it is possible for partial results to be
|
| - * generated and stored for cancelled jobs.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [jobId] - Required. The ID of the job.
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future cancel(core.String jobId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (jobId == null) {
|
| - throw new core.ArgumentError("Parameter jobId is required.");
|
| - }
|
| -
|
| - _downloadOptions = null;
|
| -
|
| - _url = 'jobs/' + commons.Escaper.ecapeVariable('$jobId') + '/cancel';
|
| -
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => null);
|
| - }
|
| -
|
| - /**
|
| - * Gets a job by ID.
|
| + * Gets a reference set. Implements
|
| + * [GlobalAllianceApi.getReferenceSet](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L83).
|
| *
|
| * Request parameters:
|
| *
|
| - * [jobId] - Required. The ID of the job.
|
| + * [referenceSetId] - The ID of the reference set.
|
| *
|
| - * Completes with a [Job].
|
| + * Completes with a [ReferenceSet].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1309,7 +1373,7 @@ class JobsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<Job> get(core.String jobId) {
|
| + async.Future<ReferenceSet> get(core.String referenceSetId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1317,11 +1381,11 @@ class JobsResourceApi {
|
| var _downloadOptions = commons.DownloadOptions.Metadata;
|
| var _body = null;
|
|
|
| - if (jobId == null) {
|
| - throw new core.ArgumentError("Parameter jobId is required.");
|
| + if (referenceSetId == null) {
|
| + throw new core.ArgumentError("Parameter referenceSetId is required.");
|
| }
|
|
|
| - _url = 'jobs/' + commons.Escaper.ecapeVariable('$jobId');
|
| + _url = 'v1/referencesets/' + commons.Escaper.ecapeVariable('$referenceSetId');
|
|
|
| var _response = _requester.request(_url,
|
| "GET",
|
| @@ -1330,17 +1394,18 @@ class JobsResourceApi {
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new Job.fromJson(data));
|
| + return _response.then((data) => new ReferenceSet.fromJson(data));
|
| }
|
|
|
| /**
|
| - * Gets a list of jobs matching the criteria.
|
| + * Searches for reference sets which match the given criteria. Implements
|
| + * [GlobalAllianceApi.searchReferenceSets](http://ga4gh.org/documentation/api/v0.5.1/ga4gh_api.html#/schema/org.ga4gh.searchReferenceSets).
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| * Request parameters:
|
| *
|
| - * Completes with a [SearchJobsResponse].
|
| + * Completes with a [SearchReferenceSetsResponse].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1348,7 +1413,7 @@ class JobsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<SearchJobsResponse> search(SearchJobsRequest request) {
|
| + async.Future<SearchReferenceSetsResponse> search(SearchReferenceSetsRequest request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1360,7 +1425,7 @@ class JobsResourceApi {
|
| _body = convert.JSON.encode((request).toJson());
|
| }
|
|
|
| - _url = 'jobs/search';
|
| + _url = 'v1/referencesets/search';
|
|
|
| var _response = _requester.request(_url,
|
| "POST",
|
| @@ -1369,30 +1434,26 @@ class JobsResourceApi {
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new SearchJobsResponse.fromJson(data));
|
| + return _response.then((data) => new SearchReferenceSetsResponse.fromJson(data));
|
| }
|
|
|
| }
|
|
|
|
|
| -class ReadgroupsetsResourceApi {
|
| +class VariantsResourceApi {
|
| final commons.ApiRequester _requester;
|
|
|
| - ReadgroupsetsCoveragebucketsResourceApi get coveragebuckets => new ReadgroupsetsCoveragebucketsResourceApi(_requester);
|
| -
|
| - ReadgroupsetsResourceApi(commons.ApiRequester client) :
|
| + VariantsResourceApi(commons.ApiRequester client) :
|
| _requester = client;
|
|
|
| /**
|
| - * Aligns read data from existing read group sets or files from Google Cloud
|
| - * Storage. See the alignment and variant calling documentation for more
|
| - * details.
|
| + * Creates a new variant.
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| * Request parameters:
|
| *
|
| - * Completes with a [AlignReadGroupSetsResponse].
|
| + * Completes with a [Variant].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1400,7 +1461,7 @@ class ReadgroupsetsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<AlignReadGroupSetsResponse> align(AlignReadGroupSetsRequest request) {
|
| + async.Future<Variant> create(Variant request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1412,7 +1473,7 @@ class ReadgroupsetsResourceApi {
|
| _body = convert.JSON.encode((request).toJson());
|
| }
|
|
|
| - _url = 'readgroupsets/align';
|
| + _url = 'v1/variants';
|
|
|
| var _response = _requester.request(_url,
|
| "POST",
|
| @@ -1421,19 +1482,17 @@ class ReadgroupsetsResourceApi {
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new AlignReadGroupSetsResponse.fromJson(data));
|
| + return _response.then((data) => new Variant.fromJson(data));
|
| }
|
|
|
| /**
|
| - * Calls variants on read data from existing read group sets or files from
|
| - * Google Cloud Storage. See the alignment and variant calling documentation
|
| - * for more details.
|
| - *
|
| - * [request] - The metadata request object.
|
| + * Deletes a variant.
|
| *
|
| * Request parameters:
|
| *
|
| - * Completes with a [CallReadGroupSetsResponse].
|
| + * [variantId] - The ID of the variant to be deleted.
|
| + *
|
| + * Completes with a [Empty].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1441,7 +1500,7 @@ class ReadgroupsetsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<CallReadGroupSetsResponse> call(CallReadGroupSetsRequest request) {
|
| + async.Future<Empty> delete(core.String variantId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1449,30 +1508,30 @@ class ReadgroupsetsResourceApi {
|
| var _downloadOptions = commons.DownloadOptions.Metadata;
|
| var _body = null;
|
|
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| + if (variantId == null) {
|
| + throw new core.ArgumentError("Parameter variantId is required.");
|
| }
|
|
|
| - _url = 'readgroupsets/call';
|
| + _url = 'v1/variants/' + commons.Escaper.ecapeVariable('$variantId');
|
|
|
| var _response = _requester.request(_url,
|
| - "POST",
|
| + "DELETE",
|
| body: _body,
|
| queryParams: _queryParams,
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new CallReadGroupSetsResponse.fromJson(data));
|
| + return _response.then((data) => new Empty.fromJson(data));
|
| }
|
|
|
| /**
|
| - * Deletes a read group set.
|
| + * Gets a variant by ID.
|
| *
|
| * Request parameters:
|
| *
|
| - * [readGroupSetId] - The ID of the read group set to be deleted. The caller
|
| - * must have WRITE permissions to the dataset associated with this read group
|
| - * set.
|
| + * [variantId] - The ID of the variant.
|
| + *
|
| + * Completes with a [Variant].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1480,7 +1539,7 @@ class ReadgroupsetsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future delete(core.String readGroupSetId) {
|
| + async.Future<Variant> get(core.String variantId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1488,38 +1547,37 @@ class ReadgroupsetsResourceApi {
|
| var _downloadOptions = commons.DownloadOptions.Metadata;
|
| var _body = null;
|
|
|
| - if (readGroupSetId == null) {
|
| - throw new core.ArgumentError("Parameter readGroupSetId is required.");
|
| + if (variantId == null) {
|
| + throw new core.ArgumentError("Parameter variantId is required.");
|
| }
|
|
|
| - _downloadOptions = null;
|
| -
|
| - _url = 'readgroupsets/' + commons.Escaper.ecapeVariable('$readGroupSetId');
|
| + _url = 'v1/variants/' + commons.Escaper.ecapeVariable('$variantId');
|
|
|
| var _response = _requester.request(_url,
|
| - "DELETE",
|
| + "GET",
|
| body: _body,
|
| queryParams: _queryParams,
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => null);
|
| + return _response.then((data) => new Variant.fromJson(data));
|
| }
|
|
|
| /**
|
| - * Exports read group sets to a BAM file in Google Cloud Storage.
|
| - *
|
| - * Note that currently there may be some differences between exported BAM
|
| - * files and the original BAM file at the time of import. In particular,
|
| - * comments in the input file header will not be preserved, some custom tags
|
| - * will be converted to strings, and original reference sequence order is not
|
| - * necessarily preserved.
|
| + * Creates variant data by asynchronously importing the provided information.
|
| + * The variants for import will be merged with any existing data and each
|
| + * other according to the behavior of mergeVariants. In particular, this means
|
| + * for merged VCF variants that have conflicting INFO fields, some data will
|
| + * be arbitrarily discarded. As a special case, for single-sample VCF files,
|
| + * QUAL and FILTER fields will be moved to the call level; these are sometimes
|
| + * interpreted in a call-specific context. Imported VCF headers are appended
|
| + * to the metadata already in a variant set.
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| * Request parameters:
|
| *
|
| - * Completes with a [ExportReadGroupSetsResponse].
|
| + * Completes with a [Operation].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1527,7 +1585,7 @@ class ReadgroupsetsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<ExportReadGroupSetsResponse> export(ExportReadGroupSetsRequest request) {
|
| + async.Future<Operation> import(ImportVariantsRequest request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1539,7 +1597,7 @@ class ReadgroupsetsResourceApi {
|
| _body = convert.JSON.encode((request).toJson());
|
| }
|
|
|
| - _url = 'readgroupsets/export';
|
| + _url = 'v1/variants:import';
|
|
|
| var _response = _requester.request(_url,
|
| "POST",
|
| @@ -1548,17 +1606,25 @@ class ReadgroupsetsResourceApi {
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new ExportReadGroupSetsResponse.fromJson(data));
|
| + return _response.then((data) => new Operation.fromJson(data));
|
| }
|
|
|
| /**
|
| - * Gets a read group set by ID.
|
| + * Updates a variant. This method supports patch semantics. Returns the
|
| + * modified variant without its calls.
|
| + *
|
| + * [request] - The metadata request object.
|
| *
|
| * Request parameters:
|
| *
|
| - * [readGroupSetId] - The ID of the read group set.
|
| + * [variantId] - The ID of the variant to be updated.
|
| *
|
| - * Completes with a [ReadGroupSet].
|
| + * [updateMask] - An optional mask specifying which fields to update. At this
|
| + * time, mutable fields are [names][google.genomics.v1.Variant.names] and
|
| + * [info][google.genomics.v1.Variant.info]. Acceptable values are "names" and
|
| + * "info". If unspecified, all mutable fields will be updated.
|
| + *
|
| + * Completes with a [Variant].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1566,7 +1632,7 @@ class ReadgroupsetsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<ReadGroupSet> get(core.String readGroupSetId) {
|
| + async.Future<Variant> patch(Variant request, core.String variantId, {core.String updateMask}) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1574,35 +1640,37 @@ class ReadgroupsetsResourceApi {
|
| var _downloadOptions = commons.DownloadOptions.Metadata;
|
| var _body = null;
|
|
|
| - if (readGroupSetId == null) {
|
| - throw new core.ArgumentError("Parameter readGroupSetId is required.");
|
| + if (request != null) {
|
| + _body = convert.JSON.encode((request).toJson());
|
| + }
|
| + if (variantId == null) {
|
| + throw new core.ArgumentError("Parameter variantId is required.");
|
| + }
|
| + if (updateMask != null) {
|
| + _queryParams["updateMask"] = [updateMask];
|
| }
|
|
|
| - _url = 'readgroupsets/' + commons.Escaper.ecapeVariable('$readGroupSetId');
|
| + _url = 'v1/variants/' + commons.Escaper.ecapeVariable('$variantId');
|
|
|
| var _response = _requester.request(_url,
|
| - "GET",
|
| + "PATCH",
|
| body: _body,
|
| queryParams: _queryParams,
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new ReadGroupSet.fromJson(data));
|
| + return _response.then((data) => new Variant.fromJson(data));
|
| }
|
|
|
| /**
|
| - * Creates read group sets by asynchronously importing the provided
|
| - * information.
|
| - *
|
| - * Note that currently comments in the input file header are not imported and
|
| - * some custom tags will be converted to strings, rather than preserving tag
|
| - * types. The caller must have WRITE permissions to the dataset.
|
| + * Gets a list of variants matching the criteria. Implements
|
| + * [GlobalAllianceApi.searchVariants](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L126).
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| * Request parameters:
|
| *
|
| - * Completes with a [ImportReadGroupSetsResponse].
|
| + * Completes with a [SearchVariantsResponse].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1610,7 +1678,7 @@ class ReadgroupsetsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<ImportReadGroupSetsResponse> import(ImportReadGroupSetsRequest request) {
|
| + async.Future<SearchVariantsResponse> search(SearchVariantsRequest request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1622,7 +1690,7 @@ class ReadgroupsetsResourceApi {
|
| _body = convert.JSON.encode((request).toJson());
|
| }
|
|
|
| - _url = 'readgroupsets/import';
|
| + _url = 'v1/variants/search';
|
|
|
| var _response = _requester.request(_url,
|
| "POST",
|
| @@ -1631,21 +1699,26 @@ class ReadgroupsetsResourceApi {
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new ImportReadGroupSetsResponse.fromJson(data));
|
| + return _response.then((data) => new SearchVariantsResponse.fromJson(data));
|
| }
|
|
|
| +}
|
| +
|
| +
|
| +class VariantsetsResourceApi {
|
| + final commons.ApiRequester _requester;
|
| +
|
| + VariantsetsResourceApi(commons.ApiRequester client) :
|
| + _requester = client;
|
| +
|
| /**
|
| - * Updates a read group set. This method supports patch semantics.
|
| + * Creates a new variant set.
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| * Request parameters:
|
| *
|
| - * [readGroupSetId] - The ID of the read group set to be updated. The caller
|
| - * must have WRITE permissions to the dataset associated with this read group
|
| - * set.
|
| - *
|
| - * Completes with a [ReadGroupSet].
|
| + * Completes with a [VariantSet].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1653,7 +1726,7 @@ class ReadgroupsetsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<ReadGroupSet> patch(ReadGroupSet request, core.String readGroupSetId) {
|
| + async.Future<VariantSet> create(VariantSet request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1664,32 +1737,28 @@ class ReadgroupsetsResourceApi {
|
| if (request != null) {
|
| _body = convert.JSON.encode((request).toJson());
|
| }
|
| - if (readGroupSetId == null) {
|
| - throw new core.ArgumentError("Parameter readGroupSetId is required.");
|
| - }
|
|
|
| - _url = 'readgroupsets/' + commons.Escaper.ecapeVariable('$readGroupSetId');
|
| + _url = 'v1/variantsets';
|
|
|
| var _response = _requester.request(_url,
|
| - "PATCH",
|
| + "POST",
|
| body: _body,
|
| queryParams: _queryParams,
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new ReadGroupSet.fromJson(data));
|
| + return _response.then((data) => new VariantSet.fromJson(data));
|
| }
|
|
|
| /**
|
| - * Searches for read group sets matching the criteria.
|
| - *
|
| - * Implements GlobalAllianceApi.searchReadGroupSets.
|
| - *
|
| - * [request] - The metadata request object.
|
| + * Deletes the contents of a variant set. The variant set object is not
|
| + * deleted.
|
| *
|
| * Request parameters:
|
| *
|
| - * Completes with a [SearchReadGroupSetsResponse].
|
| + * [variantSetId] - The ID of the variant set to be deleted.
|
| + *
|
| + * Completes with a [Empty].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1697,7 +1766,7 @@ class ReadgroupsetsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<SearchReadGroupSetsResponse> search(SearchReadGroupSetsRequest request) {
|
| + async.Future<Empty> delete(core.String variantSetId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1705,34 +1774,34 @@ class ReadgroupsetsResourceApi {
|
| var _downloadOptions = commons.DownloadOptions.Metadata;
|
| var _body = null;
|
|
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| + if (variantSetId == null) {
|
| + throw new core.ArgumentError("Parameter variantSetId is required.");
|
| }
|
|
|
| - _url = 'readgroupsets/search';
|
| + _url = 'v1/variantsets/' + commons.Escaper.ecapeVariable('$variantSetId');
|
|
|
| var _response = _requester.request(_url,
|
| - "POST",
|
| + "DELETE",
|
| body: _body,
|
| queryParams: _queryParams,
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new SearchReadGroupSetsResponse.fromJson(data));
|
| + return _response.then((data) => new Empty.fromJson(data));
|
| }
|
|
|
| /**
|
| - * Updates a read group set.
|
| + * Exports variant set data to an external destination.
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| * Request parameters:
|
| *
|
| - * [readGroupSetId] - The ID of the read group set to be updated. The caller
|
| - * must have WRITE permissions to the dataset associated with this read group
|
| - * set.
|
| + * [variantSetId] - Required. The ID of the variant set that contains variant
|
| + * data which should be exported. The caller must have READ access to this
|
| + * variant set.
|
| *
|
| - * Completes with a [ReadGroupSet].
|
| + * Completes with a [Operation].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1740,7 +1809,7 @@ class ReadgroupsetsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<ReadGroupSet> update(ReadGroupSet request, core.String readGroupSetId) {
|
| + async.Future<Operation> export(ExportVariantSetRequest request, core.String variantSetId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1751,71 +1820,30 @@ class ReadgroupsetsResourceApi {
|
| if (request != null) {
|
| _body = convert.JSON.encode((request).toJson());
|
| }
|
| - if (readGroupSetId == null) {
|
| - throw new core.ArgumentError("Parameter readGroupSetId is required.");
|
| + if (variantSetId == null) {
|
| + throw new core.ArgumentError("Parameter variantSetId is required.");
|
| }
|
|
|
| - _url = 'readgroupsets/' + commons.Escaper.ecapeVariable('$readGroupSetId');
|
| + _url = 'v1/variantsets/' + commons.Escaper.ecapeVariable('$variantSetId') + ':export';
|
|
|
| var _response = _requester.request(_url,
|
| - "PUT",
|
| + "POST",
|
| body: _body,
|
| queryParams: _queryParams,
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new ReadGroupSet.fromJson(data));
|
| + return _response.then((data) => new Operation.fromJson(data));
|
| }
|
|
|
| -}
|
| -
|
| -
|
| -class ReadgroupsetsCoveragebucketsResourceApi {
|
| - final commons.ApiRequester _requester;
|
| -
|
| - ReadgroupsetsCoveragebucketsResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| /**
|
| - * Lists fixed width coverage buckets for a read group set, each of which
|
| - * correspond to a range of a reference sequence. Each bucket summarizes
|
| - * coverage information across its corresponding genomic range.
|
| - *
|
| - * Coverage is defined as the number of reads which are aligned to a given
|
| - * base in the reference sequence. Coverage buckets are available at several
|
| - * precomputed bucket widths, enabling retrieval of various coverage 'zoom
|
| - * levels'. The caller must have READ permissions for the target read group
|
| - * set.
|
| + * Gets a variant set by ID.
|
| *
|
| * Request parameters:
|
| *
|
| - * [readGroupSetId] - Required. The ID of the read group set over which
|
| - * coverage is requested.
|
| - *
|
| - * [pageSize] - The maximum number of results to return in a single page. If
|
| - * unspecified, defaults to 1024. The maximum value is 2048.
|
| - *
|
| - * [pageToken] - The continuation token, which is used to page through large
|
| - * result sets. To get the next page of results, set this parameter to the
|
| - * value of nextPageToken from the previous response.
|
| - *
|
| - * [range_end] - The end position of the range on the reference, 0-based
|
| - * exclusive. If specified, referenceName must also be specified.
|
| - *
|
| - * [range_referenceName] - The reference sequence name, for example chr1, 1,
|
| - * or chrX.
|
| - *
|
| - * [range_start] - The start position of the range on the reference, 0-based
|
| - * inclusive. If specified, referenceName must also be specified.
|
| - *
|
| - * [targetBucketWidth] - The desired width of each reported coverage bucket in
|
| - * base pairs. This will be rounded down to the nearest precomputed bucket
|
| - * width; the value of which is returned as bucketWidth in the response.
|
| - * Defaults to infinity (each bucket spans an entire reference sequence) or
|
| - * the length of the target range, if specified. The smallest precomputed
|
| - * bucketWidth is currently 2048 base pairs; this is subject to change.
|
| + * [variantSetId] - Required. The ID of the variant set.
|
| *
|
| - * Completes with a [ListCoverageBucketsResponse].
|
| + * Completes with a [VariantSet].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1823,7 +1851,7 @@ class ReadgroupsetsCoveragebucketsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<ListCoverageBucketsResponse> list(core.String readGroupSetId, {core.int pageSize, core.String pageToken, core.String range_end, core.String range_referenceName, core.String range_start, core.String targetBucketWidth}) {
|
| + async.Future<VariantSet> get(core.String variantSetId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1831,29 +1859,11 @@ class ReadgroupsetsCoveragebucketsResourceApi {
|
| var _downloadOptions = commons.DownloadOptions.Metadata;
|
| var _body = null;
|
|
|
| - if (readGroupSetId == null) {
|
| - throw new core.ArgumentError("Parameter readGroupSetId is required.");
|
| - }
|
| - if (pageSize != null) {
|
| - _queryParams["pageSize"] = ["${pageSize}"];
|
| - }
|
| - if (pageToken != null) {
|
| - _queryParams["pageToken"] = [pageToken];
|
| - }
|
| - if (range_end != null) {
|
| - _queryParams["range.end"] = [range_end];
|
| - }
|
| - if (range_referenceName != null) {
|
| - _queryParams["range.referenceName"] = [range_referenceName];
|
| - }
|
| - if (range_start != null) {
|
| - _queryParams["range.start"] = [range_start];
|
| - }
|
| - if (targetBucketWidth != null) {
|
| - _queryParams["targetBucketWidth"] = [targetBucketWidth];
|
| + if (variantSetId == null) {
|
| + throw new core.ArgumentError("Parameter variantSetId is required.");
|
| }
|
|
|
| - _url = 'readgroupsets/' + commons.Escaper.ecapeVariable('$readGroupSetId') + '/coveragebuckets';
|
| + _url = 'v1/variantsets/' + commons.Escaper.ecapeVariable('$variantSetId');
|
|
|
| var _response = _requester.request(_url,
|
| "GET",
|
| @@ -1862,40 +1872,24 @@ class ReadgroupsetsCoveragebucketsResourceApi {
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new ListCoverageBucketsResponse.fromJson(data));
|
| + return _response.then((data) => new VariantSet.fromJson(data));
|
| }
|
|
|
| -}
|
| -
|
| -
|
| -class ReadsResourceApi {
|
| - final commons.ApiRequester _requester;
|
| -
|
| - ReadsResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| /**
|
| - * Gets a list of reads for one or more read group sets. Reads search operates
|
| - * over a genomic coordinate space of reference sequence & position defined
|
| - * over the reference sequences to which the requested read group sets are
|
| - * aligned.
|
| - *
|
| - * If a target positional range is specified, search returns all reads whose
|
| - * alignment to the reference genome overlap the range. A query which
|
| - * specifies only read group set IDs yields all reads in those read group
|
| - * sets, including unmapped reads.
|
| - *
|
| - * All reads returned (including reads on subsequent pages) are ordered by
|
| - * genomic coordinate (reference sequence & position). Reads with equivalent
|
| - * genomic coordinates are returned in a deterministic order.
|
| - *
|
| - * Implements GlobalAllianceApi.searchReads.
|
| + * Updates a variant set. This method supports patch semantics.
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| * Request parameters:
|
| *
|
| - * Completes with a [SearchReadsResponse].
|
| + * [variantSetId] - The ID of the variant to be updated (must already exist).
|
| + *
|
| + * [updateMask] - An optional mask specifying which fields to update. At this
|
| + * time, the only mutable field is
|
| + * [metadata][google.genomics.v1.VariantSet.metadata]. The only acceptable
|
| + * value is "metadata". If unspecified, all mutable fields will be updated.
|
| + *
|
| + * Completes with a [VariantSet].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1903,7 +1897,7 @@ class ReadsResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<SearchReadsResponse> search(SearchReadsRequest request) {
|
| + async.Future<VariantSet> patch(VariantSet request, core.String variantSetId, {core.String updateMask}) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1914,81 +1908,34 @@ class ReadsResourceApi {
|
| if (request != null) {
|
| _body = convert.JSON.encode((request).toJson());
|
| }
|
| -
|
| - _url = 'reads/search';
|
| -
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new SearchReadsResponse.fromJson(data));
|
| - }
|
| -
|
| -}
|
| -
|
| -
|
| -class ReferencesResourceApi {
|
| - final commons.ApiRequester _requester;
|
| -
|
| - ReferencesBasesResourceApi get bases => new ReferencesBasesResourceApi(_requester);
|
| -
|
| - ReferencesResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Gets a reference.
|
| - *
|
| - * Implements GlobalAllianceApi.getReference.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [referenceId] - The ID of the reference.
|
| - *
|
| - * Completes with a [Reference].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<Reference> get(core.String referenceId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (referenceId == null) {
|
| - throw new core.ArgumentError("Parameter referenceId is required.");
|
| + if (variantSetId == null) {
|
| + throw new core.ArgumentError("Parameter variantSetId is required.");
|
| + }
|
| + if (updateMask != null) {
|
| + _queryParams["updateMask"] = [updateMask];
|
| }
|
|
|
| - _url = 'references/' + commons.Escaper.ecapeVariable('$referenceId');
|
| + _url = 'v1/variantsets/' + commons.Escaper.ecapeVariable('$variantSetId');
|
|
|
| var _response = _requester.request(_url,
|
| - "GET",
|
| + "PATCH",
|
| body: _body,
|
| queryParams: _queryParams,
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new Reference.fromJson(data));
|
| + return _response.then((data) => new VariantSet.fromJson(data));
|
| }
|
|
|
| /**
|
| - * Searches for references which match the given criteria.
|
| - *
|
| - * Implements GlobalAllianceApi.searchReferences.
|
| + * Returns a list of all variant sets matching search criteria. Implements
|
| + * [GlobalAllianceApi.searchVariantSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L49).
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| * Request parameters:
|
| *
|
| - * Completes with a [SearchReferencesResponse].
|
| + * Completes with a [SearchVariantSetsResponse].
|
| *
|
| * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1996,7 +1943,7 @@ class ReferencesResourceApi {
|
| * If the used [http.Client] completes with an error when making a REST call,
|
| * this method will complete with the same error.
|
| */
|
| - async.Future<SearchReferencesResponse> search(SearchReferencesRequest request) {
|
| + async.Future<SearchVariantSetsResponse> search(SearchVariantSetsRequest request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -2008,7 +1955,7 @@ class ReferencesResourceApi {
|
| _body = convert.JSON.encode((request).toJson());
|
| }
|
|
|
| - _url = 'references/search';
|
| + _url = 'v1/variantsets/search';
|
|
|
| var _response = _requester.request(_url,
|
| "POST",
|
| @@ -2017,1330 +1964,40 @@ class ReferencesResourceApi {
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new SearchReferencesResponse.fromJson(data));
|
| + return _response.then((data) => new SearchVariantSetsResponse.fromJson(data));
|
| }
|
|
|
| }
|
|
|
|
|
| -class ReferencesBasesResourceApi {
|
| - final commons.ApiRequester _requester;
|
| -
|
| - ReferencesBasesResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
|
|
| +/**
|
| + * A call set is a collection of variant calls, typically for one sample. It
|
| + * belongs to a variant set.
|
| + */
|
| +class CallSet {
|
| + /** The date this call set was created in milliseconds from the epoch. */
|
| + core.String created;
|
| + /** The server-generated call set ID, unique across all call sets. */
|
| + core.String id;
|
| /**
|
| - * Lists the bases in a reference, optionally restricted to a range.
|
| + * A map of additional call set information. This must be of the form map
|
| + * (string key mapping to a list of string values).
|
| *
|
| - * Implements GlobalAllianceApi.getReferenceBases.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [referenceId] - The ID of the reference.
|
| - *
|
| - * [end] - The end position (0-based, exclusive) of this query. Defaults to
|
| - * the length of this reference.
|
| - *
|
| - * [pageSize] - Specifies the maximum number of bases to return in a single
|
| - * page.
|
| - *
|
| - * [pageToken] - The continuation token, which is used to page through large
|
| - * result sets. To get the next page of results, set this parameter to the
|
| - * value of nextPageToken from the previous response.
|
| - *
|
| - * [start] - The start position (0-based) of this query. Defaults to 0.
|
| - *
|
| - * Completes with a [ListBasesResponse].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<ListBasesResponse> list(core.String referenceId, {core.String end, core.int pageSize, core.String pageToken, core.String start}) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (referenceId == null) {
|
| - throw new core.ArgumentError("Parameter referenceId is required.");
|
| - }
|
| - if (end != null) {
|
| - _queryParams["end"] = [end];
|
| - }
|
| - if (pageSize != null) {
|
| - _queryParams["pageSize"] = ["${pageSize}"];
|
| - }
|
| - if (pageToken != null) {
|
| - _queryParams["pageToken"] = [pageToken];
|
| - }
|
| - if (start != null) {
|
| - _queryParams["start"] = [start];
|
| - }
|
| -
|
| - _url = 'references/' + commons.Escaper.ecapeVariable('$referenceId') + '/bases';
|
| -
|
| - var _response = _requester.request(_url,
|
| - "GET",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new ListBasesResponse.fromJson(data));
|
| - }
|
| -
|
| -}
|
| -
|
| -
|
| -class ReferencesetsResourceApi {
|
| - final commons.ApiRequester _requester;
|
| -
|
| - ReferencesetsResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Gets a reference set.
|
| - *
|
| - * Implements GlobalAllianceApi.getReferenceSet.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [referenceSetId] - The ID of the reference set.
|
| - *
|
| - * Completes with a [ReferenceSet].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<ReferenceSet> get(core.String referenceSetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (referenceSetId == null) {
|
| - throw new core.ArgumentError("Parameter referenceSetId is required.");
|
| - }
|
| -
|
| - _url = 'referencesets/' + commons.Escaper.ecapeVariable('$referenceSetId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "GET",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new ReferenceSet.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Searches for reference sets which match the given criteria.
|
| - *
|
| - * Implements GlobalAllianceApi.searchReferenceSets.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [SearchReferenceSetsResponse].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<SearchReferenceSetsResponse> search(SearchReferenceSetsRequest request) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| -
|
| - _url = 'referencesets/search';
|
| -
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new SearchReferenceSetsResponse.fromJson(data));
|
| - }
|
| -
|
| -}
|
| -
|
| -
|
| -class VariantsResourceApi {
|
| - final commons.ApiRequester _requester;
|
| -
|
| - VariantsResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Creates a new variant.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [Variant].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<Variant> create(Variant request) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| -
|
| - _url = 'variants';
|
| -
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new Variant.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Deletes a variant.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [variantId] - The ID of the variant to be deleted.
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future delete(core.String variantId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (variantId == null) {
|
| - throw new core.ArgumentError("Parameter variantId is required.");
|
| - }
|
| -
|
| - _downloadOptions = null;
|
| -
|
| - _url = 'variants/' + commons.Escaper.ecapeVariable('$variantId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "DELETE",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => null);
|
| - }
|
| -
|
| - /**
|
| - * Gets a variant by ID.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [variantId] - The ID of the variant.
|
| - *
|
| - * Completes with a [Variant].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<Variant> get(core.String variantId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (variantId == null) {
|
| - throw new core.ArgumentError("Parameter variantId is required.");
|
| - }
|
| -
|
| - _url = 'variants/' + commons.Escaper.ecapeVariable('$variantId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "GET",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new Variant.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Gets a list of variants matching the criteria.
|
| - *
|
| - * Implements GlobalAllianceApi.searchVariants.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [SearchVariantsResponse].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<SearchVariantsResponse> search(SearchVariantsRequest request) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| -
|
| - _url = 'variants/search';
|
| -
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new SearchVariantsResponse.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Updates a variant's names and info fields. All other modifications are
|
| - * silently ignored. Returns the modified variant without its calls.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [variantId] - The ID of the variant to be updated.
|
| - *
|
| - * Completes with a [Variant].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<Variant> update(Variant request, core.String variantId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| - if (variantId == null) {
|
| - throw new core.ArgumentError("Parameter variantId is required.");
|
| - }
|
| -
|
| - _url = 'variants/' + commons.Escaper.ecapeVariable('$variantId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "PUT",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new Variant.fromJson(data));
|
| - }
|
| -
|
| -}
|
| -
|
| -
|
| -class VariantsetsResourceApi {
|
| - final commons.ApiRequester _requester;
|
| -
|
| - VariantsetsResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Deletes the contents of a variant set. The variant set object is not
|
| - * deleted.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [variantSetId] - The ID of the variant set to be deleted.
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future delete(core.String variantSetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (variantSetId == null) {
|
| - throw new core.ArgumentError("Parameter variantSetId is required.");
|
| - }
|
| -
|
| - _downloadOptions = null;
|
| -
|
| - _url = 'variantsets/' + commons.Escaper.ecapeVariable('$variantSetId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "DELETE",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => null);
|
| - }
|
| -
|
| - /**
|
| - * Exports variant set data to an external destination.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [variantSetId] - Required. The ID of the variant set that contains variant
|
| - * data which should be exported. The caller must have READ access to this
|
| - * variant set.
|
| - *
|
| - * Completes with a [ExportVariantSetResponse].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<ExportVariantSetResponse> export(ExportVariantSetRequest request, core.String variantSetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| - if (variantSetId == null) {
|
| - throw new core.ArgumentError("Parameter variantSetId is required.");
|
| - }
|
| -
|
| - _url = 'variantsets/' + commons.Escaper.ecapeVariable('$variantSetId') + '/export';
|
| -
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new ExportVariantSetResponse.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Gets a variant set by ID.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [variantSetId] - Required. The ID of the variant set.
|
| - *
|
| - * Completes with a [VariantSet].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<VariantSet> get(core.String variantSetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (variantSetId == null) {
|
| - throw new core.ArgumentError("Parameter variantSetId is required.");
|
| - }
|
| -
|
| - _url = 'variantsets/' + commons.Escaper.ecapeVariable('$variantSetId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "GET",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new VariantSet.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Creates variant data by asynchronously importing the provided information.
|
| - *
|
| - * The variants for import will be merged with any existing data and each
|
| - * other according to the behavior of mergeVariants. In particular, this means
|
| - * for merged VCF variants that have conflicting INFO fields, some data will
|
| - * be arbitrarily discarded. As a special case, for single-sample VCF files,
|
| - * QUAL and FILTER fields will be moved to the call level; these are sometimes
|
| - * interpreted in a call-specific context. Imported VCF headers are appended
|
| - * to the metadata already in a variant set.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [variantSetId] - Required. The variant set to which variant data should be
|
| - * imported.
|
| - *
|
| - * Completes with a [ImportVariantsResponse].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<ImportVariantsResponse> importVariants(ImportVariantsRequest request, core.String variantSetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| - if (variantSetId == null) {
|
| - throw new core.ArgumentError("Parameter variantSetId is required.");
|
| - }
|
| -
|
| - _url = 'variantsets/' + commons.Escaper.ecapeVariable('$variantSetId') + '/importVariants';
|
| -
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new ImportVariantsResponse.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Merges the given variants with existing variants. Each variant will be
|
| - * merged with an existing variant that matches its reference sequence, start,
|
| - * end, reference bases, and alternative bases. If no such variant exists, a
|
| - * new one will be created.
|
| - *
|
| - * When variants are merged, the call information from the new variant is
|
| - * added to the existing variant, and other fields (such as key/value pairs)
|
| - * are discarded.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [variantSetId] - The destination variant set.
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future mergeVariants(MergeVariantsRequest request, core.String variantSetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| - if (variantSetId == null) {
|
| - throw new core.ArgumentError("Parameter variantSetId is required.");
|
| - }
|
| -
|
| - _downloadOptions = null;
|
| -
|
| - _url = 'variantsets/' + commons.Escaper.ecapeVariable('$variantSetId') + '/mergeVariants';
|
| -
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => null);
|
| - }
|
| -
|
| - /**
|
| - * Updates a variant set's metadata. All other modifications are silently
|
| - * ignored. This method supports patch semantics.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [variantSetId] - The ID of the variant to be updated (must already exist).
|
| - *
|
| - * Completes with a [VariantSet].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<VariantSet> patch(VariantSet request, core.String variantSetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| - if (variantSetId == null) {
|
| - throw new core.ArgumentError("Parameter variantSetId is required.");
|
| - }
|
| -
|
| - _url = 'variantsets/' + commons.Escaper.ecapeVariable('$variantSetId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "PATCH",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new VariantSet.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Returns a list of all variant sets matching search criteria.
|
| - *
|
| - * Implements GlobalAllianceApi.searchVariantSets.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [SearchVariantSetsResponse].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<SearchVariantSetsResponse> search(SearchVariantSetsRequest request) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| -
|
| - _url = 'variantsets/search';
|
| -
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new SearchVariantSetsResponse.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Updates a variant set's metadata. All other modifications are silently
|
| - * ignored.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [variantSetId] - The ID of the variant to be updated (must already exist).
|
| - *
|
| - * Completes with a [VariantSet].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<VariantSet> update(VariantSet request, core.String variantSetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| - if (variantSetId == null) {
|
| - throw new core.ArgumentError("Parameter variantSetId is required.");
|
| - }
|
| -
|
| - _url = 'variantsets/' + commons.Escaper.ecapeVariable('$variantSetId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "PUT",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new VariantSet.fromJson(data));
|
| - }
|
| -
|
| -}
|
| -
|
| -
|
| -
|
| -/** The read group set align request. */
|
| -class AlignReadGroupSetsRequest {
|
| - /**
|
| - * The BAM source files for alignment. Exactly one of readGroupSetId,
|
| - * bamSourceUris, interleavedFastqSource or pairedFastqSource must be
|
| - * provided. The caller must have READ permissions for these files.
|
| - */
|
| - core.List<core.String> bamSourceUris;
|
| - /**
|
| - * Required. The ID of the dataset the newly aligned read group sets will
|
| - * belong to. The caller must have WRITE permissions to this dataset.
|
| - */
|
| - core.String datasetId;
|
| - /**
|
| - * The interleaved FASTQ source files for alignment, where both members of
|
| - * each pair of reads are found on consecutive records within the same FASTQ
|
| - * file. Exactly one of readGroupSetId, bamSourceUris, interleavedFastqSource
|
| - * or pairedFastqSource must be provided.
|
| - */
|
| - InterleavedFastqSource interleavedFastqSource;
|
| - /**
|
| - * The paired end FASTQ source files for alignment, where each member of a
|
| - * pair of reads are found in separate files. Exactly one of readGroupSetId,
|
| - * bamSourceUris, interleavedFastqSource or pairedFastqSource must be
|
| - * provided.
|
| - */
|
| - PairedFastqSource pairedFastqSource;
|
| - /**
|
| - * The ID of the read group set which will be aligned. A new read group set
|
| - * will be generated to hold the aligned data, the originals will not be
|
| - * modified. The caller must have READ permissions for this read group set.
|
| - * Exactly one of readGroupSetId, bamSourceUris, interleavedFastqSource or
|
| - * pairedFastqSource must be provided.
|
| - */
|
| - core.String readGroupSetId;
|
| -
|
| - AlignReadGroupSetsRequest();
|
| -
|
| - AlignReadGroupSetsRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("bamSourceUris")) {
|
| - bamSourceUris = _json["bamSourceUris"];
|
| - }
|
| - if (_json.containsKey("datasetId")) {
|
| - datasetId = _json["datasetId"];
|
| - }
|
| - if (_json.containsKey("interleavedFastqSource")) {
|
| - interleavedFastqSource = new InterleavedFastqSource.fromJson(_json["interleavedFastqSource"]);
|
| - }
|
| - if (_json.containsKey("pairedFastqSource")) {
|
| - pairedFastqSource = new PairedFastqSource.fromJson(_json["pairedFastqSource"]);
|
| - }
|
| - if (_json.containsKey("readGroupSetId")) {
|
| - readGroupSetId = _json["readGroupSetId"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (bamSourceUris != null) {
|
| - _json["bamSourceUris"] = bamSourceUris;
|
| - }
|
| - if (datasetId != null) {
|
| - _json["datasetId"] = datasetId;
|
| - }
|
| - if (interleavedFastqSource != null) {
|
| - _json["interleavedFastqSource"] = (interleavedFastqSource).toJson();
|
| - }
|
| - if (pairedFastqSource != null) {
|
| - _json["pairedFastqSource"] = (pairedFastqSource).toJson();
|
| - }
|
| - if (readGroupSetId != null) {
|
| - _json["readGroupSetId"] = readGroupSetId;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** The read group set align response. */
|
| -class AlignReadGroupSetsResponse {
|
| - /** A job ID that can be used to get status information. */
|
| - core.String jobId;
|
| -
|
| - AlignReadGroupSetsResponse();
|
| -
|
| - AlignReadGroupSetsResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("jobId")) {
|
| - jobId = _json["jobId"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (jobId != null) {
|
| - _json["jobId"] = jobId;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/**
|
| - * An annotation describes a region of reference genome. The value of an
|
| - * annotation may be one of several canonical types, supplemented by arbitrary
|
| - * info tags. A variant annotation is represented by one or more of these
|
| - * canonical types. An annotation is not inherently associated with a specific
|
| - * sample or individual (though a client could choose to use annotations in this
|
| - * way). Example canonical annotation types are 'Gene' and 'Variant'.
|
| - */
|
| -class Annotation {
|
| - /** The ID of the containing annotation set. */
|
| - core.String annotationSetId;
|
| - /** The generated unique ID for this annotation. */
|
| - core.String id;
|
| - /** A string which maps to an array of values. */
|
| - core.Map<core.String, core.List<core.String>> info;
|
| - /** The display name of this annotation. */
|
| - core.String name;
|
| - /** The position of this annotation on the reference sequence. */
|
| - RangePosition position;
|
| - /**
|
| - * A transcript value represents the assertion that a particular region of the
|
| - * reference genome may be transcribed as RNA. An alternative splicing pattern
|
| - * would be represented as a separate transcript object. This field is only
|
| - * set for annotations of type TRANSCRIPT.
|
| - */
|
| - Transcript transcript;
|
| - /**
|
| - * The data type for this annotation. Must match the containing annotation
|
| - * set's type.
|
| - * Possible string values are:
|
| - * - "GENE"
|
| - * - "GENERIC"
|
| - * - "TRANSCRIPT"
|
| - * - "VARIANT"
|
| - */
|
| - core.String type;
|
| - /**
|
| - * A variant annotation, which describes the effect of a variant on the
|
| - * genome, the coding sequence, and/or higher level consequences at the
|
| - * organism level e.g. pathogenicity. This field is only set for annotations
|
| - * of type VARIANT.
|
| - */
|
| - VariantAnnotation variant;
|
| -
|
| - Annotation();
|
| -
|
| - Annotation.fromJson(core.Map _json) {
|
| - if (_json.containsKey("annotationSetId")) {
|
| - annotationSetId = _json["annotationSetId"];
|
| - }
|
| - if (_json.containsKey("id")) {
|
| - id = _json["id"];
|
| - }
|
| - if (_json.containsKey("info")) {
|
| - info = _json["info"];
|
| - }
|
| - if (_json.containsKey("name")) {
|
| - name = _json["name"];
|
| - }
|
| - if (_json.containsKey("position")) {
|
| - position = new RangePosition.fromJson(_json["position"]);
|
| - }
|
| - if (_json.containsKey("transcript")) {
|
| - transcript = new Transcript.fromJson(_json["transcript"]);
|
| - }
|
| - if (_json.containsKey("type")) {
|
| - type = _json["type"];
|
| - }
|
| - if (_json.containsKey("variant")) {
|
| - variant = new VariantAnnotation.fromJson(_json["variant"]);
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (annotationSetId != null) {
|
| - _json["annotationSetId"] = annotationSetId;
|
| - }
|
| - if (id != null) {
|
| - _json["id"] = id;
|
| - }
|
| - if (info != null) {
|
| - _json["info"] = info;
|
| - }
|
| - if (name != null) {
|
| - _json["name"] = name;
|
| - }
|
| - if (position != null) {
|
| - _json["position"] = (position).toJson();
|
| - }
|
| - if (transcript != null) {
|
| - _json["transcript"] = (transcript).toJson();
|
| - }
|
| - if (type != null) {
|
| - _json["type"] = type;
|
| - }
|
| - if (variant != null) {
|
| - _json["variant"] = (variant).toJson();
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/**
|
| - * An annotation set is a logical grouping of annotations that share consistent
|
| - * type information and provenance. Examples of annotation sets include 'all
|
| - * genes from refseq', and 'all variant annotations from ClinVar'.
|
| - */
|
| -class AnnotationSet {
|
| - /** The ID of the containing dataset. */
|
| - core.String datasetId;
|
| - /** The generated unique ID for this annotation set. */
|
| - core.String id;
|
| - /** A string which maps to an array of values. */
|
| - core.Map<core.String, core.List<core.String>> info;
|
| - /** The display name for this annotation set. */
|
| - core.String name;
|
| - /**
|
| - * The ID of the reference set that defines the coordinate space for this
|
| - * set's annotations.
|
| - */
|
| - core.String referenceSetId;
|
| - /**
|
| - * The source URI describing the file from which this annotation set was
|
| - * generated, if any.
|
| - */
|
| - core.String sourceUri;
|
| - /**
|
| - * The type of annotations contained within this set.
|
| - * Possible string values are:
|
| - * - "GENE"
|
| - * - "GENERIC"
|
| - * - "TRANSCRIPT"
|
| - * - "VARIANT"
|
| - */
|
| - core.String type;
|
| -
|
| - AnnotationSet();
|
| -
|
| - AnnotationSet.fromJson(core.Map _json) {
|
| - if (_json.containsKey("datasetId")) {
|
| - datasetId = _json["datasetId"];
|
| - }
|
| - if (_json.containsKey("id")) {
|
| - id = _json["id"];
|
| - }
|
| - if (_json.containsKey("info")) {
|
| - info = _json["info"];
|
| - }
|
| - if (_json.containsKey("name")) {
|
| - name = _json["name"];
|
| - }
|
| - if (_json.containsKey("referenceSetId")) {
|
| - referenceSetId = _json["referenceSetId"];
|
| - }
|
| - if (_json.containsKey("sourceUri")) {
|
| - sourceUri = _json["sourceUri"];
|
| - }
|
| - if (_json.containsKey("type")) {
|
| - type = _json["type"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (datasetId != null) {
|
| - _json["datasetId"] = datasetId;
|
| - }
|
| - if (id != null) {
|
| - _json["id"] = id;
|
| - }
|
| - if (info != null) {
|
| - _json["info"] = info;
|
| - }
|
| - if (name != null) {
|
| - _json["name"] = name;
|
| - }
|
| - if (referenceSetId != null) {
|
| - _json["referenceSetId"] = referenceSetId;
|
| - }
|
| - if (sourceUri != null) {
|
| - _json["sourceUri"] = sourceUri;
|
| - }
|
| - if (type != null) {
|
| - _json["type"] = type;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class BatchAnnotationsResponse {
|
| - /**
|
| - * The resulting per-annotation entries, ordered consistently with the
|
| - * original request.
|
| - */
|
| - core.List<BatchAnnotationsResponseEntry> entries;
|
| -
|
| - BatchAnnotationsResponse();
|
| -
|
| - BatchAnnotationsResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("entries")) {
|
| - entries = _json["entries"].map((value) => new BatchAnnotationsResponseEntry.fromJson(value)).toList();
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (entries != null) {
|
| - _json["entries"] = entries.map((value) => (value).toJson()).toList();
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class BatchAnnotationsResponseEntry {
|
| - /** The annotation, if any. */
|
| - Annotation annotation;
|
| - /** The resulting status for this annotation operation. */
|
| - BatchAnnotationsResponseEntryStatus status;
|
| -
|
| - BatchAnnotationsResponseEntry();
|
| -
|
| - BatchAnnotationsResponseEntry.fromJson(core.Map _json) {
|
| - if (_json.containsKey("annotation")) {
|
| - annotation = new Annotation.fromJson(_json["annotation"]);
|
| - }
|
| - if (_json.containsKey("status")) {
|
| - status = new BatchAnnotationsResponseEntryStatus.fromJson(_json["status"]);
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (annotation != null) {
|
| - _json["annotation"] = (annotation).toJson();
|
| - }
|
| - if (status != null) {
|
| - _json["status"] = (status).toJson();
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class BatchAnnotationsResponseEntryStatus {
|
| - /** The HTTP status code for this operation. */
|
| - core.int code;
|
| - /** Error message for this status, if any. */
|
| - core.String message;
|
| -
|
| - BatchAnnotationsResponseEntryStatus();
|
| -
|
| - BatchAnnotationsResponseEntryStatus.fromJson(core.Map _json) {
|
| - if (_json.containsKey("code")) {
|
| - code = _json["code"];
|
| - }
|
| - if (_json.containsKey("message")) {
|
| - message = _json["message"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (code != null) {
|
| - _json["code"] = code;
|
| - }
|
| - if (message != null) {
|
| - _json["message"] = message;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class BatchCreateAnnotationsRequest {
|
| - /**
|
| - * The annotations to be created. At most 4096 can be specified in a single
|
| - * request.
|
| - */
|
| - core.List<Annotation> annotations;
|
| -
|
| - BatchCreateAnnotationsRequest();
|
| -
|
| - BatchCreateAnnotationsRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("annotations")) {
|
| - annotations = _json["annotations"].map((value) => new Annotation.fromJson(value)).toList();
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (annotations != null) {
|
| - _json["annotations"] = annotations.map((value) => (value).toJson()).toList();
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/**
|
| - * A call represents the determination of genotype with respect to a particular
|
| - * variant. It may include associated information such as quality and phasing.
|
| - * For example, a call might assign a probability of 0.32 to the occurrence of a
|
| - * SNP named rs1234 in a call set with the name NA12345.
|
| - */
|
| -class Call {
|
| - /** The ID of the call set this variant call belongs to. */
|
| - core.String callSetId;
|
| - /** The name of the call set this variant call belongs to. */
|
| - core.String callSetName;
|
| - /**
|
| - * The genotype of this variant call. Each value represents either the value
|
| - * of the referenceBases field or a 1-based index into alternateBases. If a
|
| - * variant had a referenceBases value of T and an alternateBases value of
|
| - * ["A", "C"], and the genotype was [2, 1], that would mean the call
|
| - * represented the heterozygous value CA for this variant. If the genotype was
|
| - * instead [0, 1], the represented value would be TA. Ordering of the genotype
|
| - * values is important if the phaseset is present. If a genotype is not called
|
| - * (that is, a . is present in the GT string) -1 is returned.
|
| - */
|
| - core.List<core.int> genotype;
|
| - /**
|
| - * The genotype likelihoods for this variant call. Each array entry represents
|
| - * how likely a specific genotype is for this call. The value ordering is
|
| - * defined by the GL tag in the VCF spec. If Phred-scaled genotype likelihood
|
| - * scores (PL) are available and log10(P) genotype likelihood scores (GL) are
|
| - * not, PL scores are converted to GL scores. If both are available, PL scores
|
| - * are stored in info.
|
| - */
|
| - core.List<core.double> genotypeLikelihood;
|
| - /** A string which maps to an array of values. */
|
| - core.Map<core.String, core.List<core.String>> info;
|
| - /**
|
| - * If this field is present, this variant call's genotype ordering implies the
|
| - * phase of the bases and is consistent with any other variant calls in the
|
| - * same reference sequence which have the same phaseset value. When importing
|
| - * data from VCF, if the genotype data was phased but no phase set was
|
| - * specified this field will be set to *.
|
| - */
|
| - core.String phaseset;
|
| -
|
| - Call();
|
| -
|
| - Call.fromJson(core.Map _json) {
|
| - if (_json.containsKey("callSetId")) {
|
| - callSetId = _json["callSetId"];
|
| - }
|
| - if (_json.containsKey("callSetName")) {
|
| - callSetName = _json["callSetName"];
|
| - }
|
| - if (_json.containsKey("genotype")) {
|
| - genotype = _json["genotype"];
|
| - }
|
| - if (_json.containsKey("genotypeLikelihood")) {
|
| - genotypeLikelihood = _json["genotypeLikelihood"];
|
| - }
|
| - if (_json.containsKey("info")) {
|
| - info = _json["info"];
|
| - }
|
| - if (_json.containsKey("phaseset")) {
|
| - phaseset = _json["phaseset"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (callSetId != null) {
|
| - _json["callSetId"] = callSetId;
|
| - }
|
| - if (callSetName != null) {
|
| - _json["callSetName"] = callSetName;
|
| - }
|
| - if (genotype != null) {
|
| - _json["genotype"] = genotype;
|
| - }
|
| - if (genotypeLikelihood != null) {
|
| - _json["genotypeLikelihood"] = genotypeLikelihood;
|
| - }
|
| - if (info != null) {
|
| - _json["info"] = info;
|
| - }
|
| - if (phaseset != null) {
|
| - _json["phaseset"] = phaseset;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** The read group set call request. */
|
| -class CallReadGroupSetsRequest {
|
| - /**
|
| - * Required. The ID of the dataset the called variants will belong to. The
|
| - * caller must have WRITE permissions to this dataset.
|
| + * The values for Object must be JSON objects. It can consist of `num`,
|
| + * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| */
|
| - core.String datasetId;
|
| - /**
|
| - * The IDs of the read group sets which will be called. The caller must have
|
| - * READ permissions for these read group sets. One of readGroupSetId or
|
| - * sourceUris must be provided.
|
| - */
|
| - core.String readGroupSetId;
|
| - /**
|
| - * A list of URIs pointing at BAM files in Google Cloud Storage which will be
|
| - * called. FASTQ files are not allowed. The caller must have READ permissions
|
| - * for these files. One of readGroupSetId or sourceUris must be provided.
|
| - */
|
| - core.List<core.String> sourceUris;
|
| -
|
| - CallReadGroupSetsRequest();
|
| -
|
| - CallReadGroupSetsRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("datasetId")) {
|
| - datasetId = _json["datasetId"];
|
| - }
|
| - if (_json.containsKey("readGroupSetId")) {
|
| - readGroupSetId = _json["readGroupSetId"];
|
| - }
|
| - if (_json.containsKey("sourceUris")) {
|
| - sourceUris = _json["sourceUris"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (datasetId != null) {
|
| - _json["datasetId"] = datasetId;
|
| - }
|
| - if (readGroupSetId != null) {
|
| - _json["readGroupSetId"] = readGroupSetId;
|
| - }
|
| - if (sourceUris != null) {
|
| - _json["sourceUris"] = sourceUris;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** The read group set call response. */
|
| -class CallReadGroupSetsResponse {
|
| - /** A job ID that can be used to get status information. */
|
| - core.String jobId;
|
| -
|
| - CallReadGroupSetsResponse();
|
| -
|
| - CallReadGroupSetsResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("jobId")) {
|
| - jobId = _json["jobId"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (jobId != null) {
|
| - _json["jobId"] = jobId;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/**
|
| - * A call set is a collection of variant calls, typically for one sample. It
|
| - * belongs to a variant set.
|
| - */
|
| -class CallSet {
|
| - /** The date this call set was created in milliseconds from the epoch. */
|
| - core.String created;
|
| - /** The Google generated ID of the call set, immutable. */
|
| - core.String id;
|
| - /** A string which maps to an array of values. */
|
| - core.Map<core.String, core.List<core.String>> info;
|
| + core.Map<core.String, core.List<core.Object>> info;
|
| /** The call set name. */
|
| core.String name;
|
| /** The sample ID this call set corresponds to. */
|
| core.String sampleId;
|
| - /** The IDs of the variant sets this call set belongs to. */
|
| + /**
|
| + * The IDs of the variant sets this call set belongs to. This field must have
|
| + * exactly length one, as a call set belongs to a single variant set. This
|
| + * field is repeated for compatibility with the [GA4GH 0.5.1
|
| + * API](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variants.avdl#L76).
|
| + */
|
| core.List<core.String> variantSetIds;
|
|
|
| CallSet();
|
| @@ -3390,28 +2047,45 @@ class CallSet {
|
| }
|
| }
|
|
|
| +/**
|
| + * The request message for
|
| + * [Operations.CancelOperation][google.longrunning.Operations.CancelOperation].
|
| + */
|
| +class CancelOperationRequest {
|
| +
|
| + CancelOperationRequest();
|
| +
|
| + CancelOperationRequest.fromJson(core.Map _json) {
|
| + }
|
| +
|
| + core.Map toJson() {
|
| + var _json = new core.Map();
|
| + return _json;
|
| + }
|
| +}
|
| +
|
| /** A single CIGAR operation. */
|
| class CigarUnit {
|
| /**
|
| *
|
| * Possible string values are:
|
| - * - "ALIGNMENT_MATCH"
|
| - * - "CLIP_HARD"
|
| - * - "CLIP_SOFT"
|
| - * - "DELETE"
|
| - * - "INSERT"
|
| - * - "OPERATION_UNSPECIFIED"
|
| - * - "PAD"
|
| - * - "SEQUENCE_MATCH"
|
| - * - "SEQUENCE_MISMATCH"
|
| - * - "SKIP"
|
| + * - "OPERATION_UNSPECIFIED" : A OPERATION_UNSPECIFIED.
|
| + * - "ALIGNMENT_MATCH" : A ALIGNMENT_MATCH.
|
| + * - "INSERT" : A INSERT.
|
| + * - "DELETE" : A DELETE.
|
| + * - "SKIP" : A SKIP.
|
| + * - "CLIP_SOFT" : A CLIP_SOFT.
|
| + * - "CLIP_HARD" : A CLIP_HARD.
|
| + * - "PAD" : A PAD.
|
| + * - "SEQUENCE_MATCH" : A SEQUENCE_MATCH.
|
| + * - "SEQUENCE_MISMATCH" : A SEQUENCE_MISMATCH.
|
| */
|
| core.String operation;
|
| - /** The number of bases that the operation runs for. Required. */
|
| + /** The number of genomic bases that the operation runs for. Required. */
|
| core.String operationLength;
|
| /**
|
| - * referenceSequence is only used at mismatches (SEQUENCE_MISMATCH) and
|
| - * deletions (DELETE). Filling this field replaces SAM's MD tag. If the
|
| + * `referenceSequence` is only used at mismatches (`SEQUENCE_MISMATCH`) and
|
| + * deletions (`DELETE`). Filling this field replaces SAM's MD tag. If the
|
| * relevant information is not available, this field is unset.
|
| */
|
| core.String referenceSequence;
|
| @@ -3485,19 +2159,12 @@ class CoverageBucket {
|
| class Dataset {
|
| /** The time this dataset was created, in seconds from the epoch. */
|
| core.String createTime;
|
| - /** The Google generated ID of the dataset, immutable. */
|
| + /** The server-generated dataset ID, unique across all datasets. */
|
| core.String id;
|
| - /**
|
| - * Flag indicating whether or not a dataset is publicly viewable. If a dataset
|
| - * is not public, it inherits viewing permissions from its project.
|
| - */
|
| - core.bool isPublic;
|
| /** The dataset name. */
|
| core.String name;
|
| - /**
|
| - * The Google Developers Console project number that this dataset belongs to.
|
| - */
|
| - core.String projectNumber;
|
| + /** The Google Developers Console project ID that this dataset belongs to. */
|
| + core.String projectId;
|
|
|
| Dataset();
|
|
|
| @@ -3508,14 +2175,11 @@ class Dataset {
|
| if (_json.containsKey("id")) {
|
| id = _json["id"];
|
| }
|
| - if (_json.containsKey("isPublic")) {
|
| - isPublic = _json["isPublic"];
|
| - }
|
| if (_json.containsKey("name")) {
|
| name = _json["name"];
|
| }
|
| - if (_json.containsKey("projectNumber")) {
|
| - projectNumber = _json["projectNumber"];
|
| + if (_json.containsKey("projectId")) {
|
| + projectId = _json["projectId"];
|
| }
|
| }
|
|
|
| @@ -3527,125 +2191,94 @@ class Dataset {
|
| if (id != null) {
|
| _json["id"] = id;
|
| }
|
| - if (isPublic != null) {
|
| - _json["isPublic"] = isPublic;
|
| - }
|
| if (name != null) {
|
| _json["name"] = name;
|
| }
|
| - if (projectNumber != null) {
|
| - _json["projectNumber"] = projectNumber;
|
| + if (projectId != null) {
|
| + _json["projectId"] = projectId;
|
| }
|
| return _json;
|
| }
|
| }
|
|
|
| -/** The job creation request. */
|
| -class ExperimentalCreateJobRequest {
|
| - /**
|
| - * Specifies whether or not to run the alignment pipeline. Either align or
|
| - * callVariants must be set.
|
| - */
|
| - core.bool align;
|
| - /**
|
| - * Specifies whether or not to run the variant calling pipeline. Either align
|
| - * or callVariants must be set.
|
| - */
|
| - core.bool callVariants;
|
| - /**
|
| - * Specifies where to copy the results of certain pipelines. This should be in
|
| - * the form of gs://bucket/path.
|
| - */
|
| - core.String gcsOutputPath;
|
| +/**
|
| + * A generic empty message that you can re-use to avoid defining duplicated
|
| + * empty messages in your APIs. A typical example is to use it as the request or
|
| + * the response type of an API method. For instance: service Foo { rpc
|
| + * Bar(google.protobuf.Empty) returns (google.protobuf.Empty); } The JSON
|
| + * representation for `Empty` is empty JSON object `{}`.
|
| + */
|
| +class Empty {
|
| +
|
| + Empty();
|
| +
|
| + Empty.fromJson(core.Map _json) {
|
| + }
|
| +
|
| + core.Map toJson() {
|
| + var _json = new core.Map();
|
| + return _json;
|
| + }
|
| +}
|
| +
|
| +class Experiment {
|
| /**
|
| - * A list of Google Cloud Storage URIs of paired end .fastq files to operate
|
| - * upon. If specified, this represents the second file of each paired .fastq
|
| - * file. The first file of each pair should be specified in sourceUris.
|
| + * The instrument model used as part of this experiment. This maps to
|
| + * sequencing technology in BAM.
|
| */
|
| - core.List<core.String> pairedSourceUris;
|
| + core.String instrumentModel;
|
| /**
|
| - * Required. The Google Cloud Project ID with which to associate the request.
|
| + * The library used as part of this experiment. Note: This is not an actual ID
|
| + * within this repository, but rather an identifier for a library which may be
|
| + * meaningful to some external system.
|
| */
|
| - core.String projectNumber;
|
| + core.String libraryId;
|
| /**
|
| - * A list of Google Cloud Storage URIs of data files to operate upon. These
|
| - * can be .bam, interleaved .fastq, or paired .fastq. If specifying paired
|
| - * .fastq files, the first of each pair of files should be listed here, and
|
| - * the second of each pair should be listed in pairedSourceUris.
|
| + * The platform unit used as part of this experiment e.g.
|
| + * flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
|
| + * @RG PU field in the SAM spec.
|
| */
|
| - core.List<core.String> sourceUris;
|
| + core.String platformUnit;
|
| + /** The sequencing center used as part of this experiment. */
|
| + core.String sequencingCenter;
|
|
|
| - ExperimentalCreateJobRequest();
|
| + Experiment();
|
|
|
| - ExperimentalCreateJobRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("align")) {
|
| - align = _json["align"];
|
| - }
|
| - if (_json.containsKey("callVariants")) {
|
| - callVariants = _json["callVariants"];
|
| - }
|
| - if (_json.containsKey("gcsOutputPath")) {
|
| - gcsOutputPath = _json["gcsOutputPath"];
|
| + Experiment.fromJson(core.Map _json) {
|
| + if (_json.containsKey("instrumentModel")) {
|
| + instrumentModel = _json["instrumentModel"];
|
| }
|
| - if (_json.containsKey("pairedSourceUris")) {
|
| - pairedSourceUris = _json["pairedSourceUris"];
|
| + if (_json.containsKey("libraryId")) {
|
| + libraryId = _json["libraryId"];
|
| }
|
| - if (_json.containsKey("projectNumber")) {
|
| - projectNumber = _json["projectNumber"];
|
| + if (_json.containsKey("platformUnit")) {
|
| + platformUnit = _json["platformUnit"];
|
| }
|
| - if (_json.containsKey("sourceUris")) {
|
| - sourceUris = _json["sourceUris"];
|
| + if (_json.containsKey("sequencingCenter")) {
|
| + sequencingCenter = _json["sequencingCenter"];
|
| }
|
| }
|
|
|
| core.Map toJson() {
|
| var _json = new core.Map();
|
| - if (align != null) {
|
| - _json["align"] = align;
|
| - }
|
| - if (callVariants != null) {
|
| - _json["callVariants"] = callVariants;
|
| - }
|
| - if (gcsOutputPath != null) {
|
| - _json["gcsOutputPath"] = gcsOutputPath;
|
| - }
|
| - if (pairedSourceUris != null) {
|
| - _json["pairedSourceUris"] = pairedSourceUris;
|
| - }
|
| - if (projectNumber != null) {
|
| - _json["projectNumber"] = projectNumber;
|
| + if (instrumentModel != null) {
|
| + _json["instrumentModel"] = instrumentModel;
|
| }
|
| - if (sourceUris != null) {
|
| - _json["sourceUris"] = sourceUris;
|
| + if (libraryId != null) {
|
| + _json["libraryId"] = libraryId;
|
| }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** The job creation response. */
|
| -class ExperimentalCreateJobResponse {
|
| - /** A job ID that can be used to get status information. */
|
| - core.String jobId;
|
| -
|
| - ExperimentalCreateJobResponse();
|
| -
|
| - ExperimentalCreateJobResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("jobId")) {
|
| - jobId = _json["jobId"];
|
| + if (platformUnit != null) {
|
| + _json["platformUnit"] = platformUnit;
|
| }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (jobId != null) {
|
| - _json["jobId"] = jobId;
|
| + if (sequencingCenter != null) {
|
| + _json["sequencingCenter"] = sequencingCenter;
|
| }
|
| return _json;
|
| }
|
| }
|
|
|
| /** The read group set export request. */
|
| -class ExportReadGroupSetsRequest {
|
| +class ExportReadGroupSetRequest {
|
| /**
|
| * Required. A Google Cloud Storage URI for the exported BAM file. The
|
| * currently authenticated user must have write access to the new file. An
|
| @@ -3653,30 +2286,24 @@ class ExportReadGroupSetsRequest {
|
| */
|
| core.String exportUri;
|
| /**
|
| - * Required. The Google Developers Console project number that owns this
|
| - * export.
|
| + * Required. The Google Developers Console project ID that owns this export.
|
| */
|
| - core.String projectNumber;
|
| - /** Required. The IDs of the read group sets to export. */
|
| - core.List<core.String> readGroupSetIds;
|
| + core.String projectId;
|
| /**
|
| * The reference names to export. If this is not specified, all reference
|
| - * sequences, including unmapped reads, are exported. Use * to export only
|
| + * sequences, including unmapped reads, are exported. Use `*` to export only
|
| * unmapped reads.
|
| */
|
| core.List<core.String> referenceNames;
|
|
|
| - ExportReadGroupSetsRequest();
|
| + ExportReadGroupSetRequest();
|
|
|
| - ExportReadGroupSetsRequest.fromJson(core.Map _json) {
|
| + ExportReadGroupSetRequest.fromJson(core.Map _json) {
|
| if (_json.containsKey("exportUri")) {
|
| exportUri = _json["exportUri"];
|
| }
|
| - if (_json.containsKey("projectNumber")) {
|
| - projectNumber = _json["projectNumber"];
|
| - }
|
| - if (_json.containsKey("readGroupSetIds")) {
|
| - readGroupSetIds = _json["readGroupSetIds"];
|
| + if (_json.containsKey("projectId")) {
|
| + projectId = _json["projectId"];
|
| }
|
| if (_json.containsKey("referenceNames")) {
|
| referenceNames = _json["referenceNames"];
|
| @@ -3688,11 +2315,8 @@ class ExportReadGroupSetsRequest {
|
| if (exportUri != null) {
|
| _json["exportUri"] = exportUri;
|
| }
|
| - if (projectNumber != null) {
|
| - _json["projectNumber"] = projectNumber;
|
| - }
|
| - if (readGroupSetIds != null) {
|
| - _json["readGroupSetIds"] = readGroupSetIds;
|
| + if (projectId != null) {
|
| + _json["projectId"] = projectId;
|
| }
|
| if (referenceNames != null) {
|
| _json["referenceNames"] = referenceNames;
|
| @@ -3701,28 +2325,6 @@ class ExportReadGroupSetsRequest {
|
| }
|
| }
|
|
|
| -/** The read group set export response. */
|
| -class ExportReadGroupSetsResponse {
|
| - /** A job ID that can be used to get status information. */
|
| - core.String jobId;
|
| -
|
| - ExportReadGroupSetsResponse();
|
| -
|
| - ExportReadGroupSetsResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("jobId")) {
|
| - jobId = _json["jobId"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (jobId != null) {
|
| - _json["jobId"] = jobId;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| /** The variant data export request. */
|
| class ExportVariantSetRequest {
|
| /**
|
| @@ -3743,15 +2345,16 @@ class ExportVariantSetRequest {
|
| /**
|
| * The format for the exported data.
|
| * Possible string values are:
|
| - * - "BIGQUERY"
|
| + * - "FORMAT_UNSPECIFIED" : A FORMAT_UNSPECIFIED.
|
| + * - "FORMAT_BIGQUERY" : A FORMAT_BIGQUERY.
|
| */
|
| core.String format;
|
| /**
|
| - * Required. The Google Cloud project number that owns the destination
|
| - * BigQuery dataset. The caller must have WRITE access to this project. This
|
| - * project will also own the resulting export job.
|
| + * Required. The Google Cloud project ID that owns the destination BigQuery
|
| + * dataset. The caller must have WRITE access to this project. This project
|
| + * will also own the resulting export job.
|
| */
|
| - core.String projectNumber;
|
| + core.String projectId;
|
|
|
| ExportVariantSetRequest();
|
|
|
| @@ -3759,146 +2362,36 @@ class ExportVariantSetRequest {
|
| if (_json.containsKey("bigqueryDataset")) {
|
| bigqueryDataset = _json["bigqueryDataset"];
|
| }
|
| - if (_json.containsKey("bigqueryTable")) {
|
| - bigqueryTable = _json["bigqueryTable"];
|
| - }
|
| - if (_json.containsKey("callSetIds")) {
|
| - callSetIds = _json["callSetIds"];
|
| - }
|
| - if (_json.containsKey("format")) {
|
| - format = _json["format"];
|
| - }
|
| - if (_json.containsKey("projectNumber")) {
|
| - projectNumber = _json["projectNumber"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (bigqueryDataset != null) {
|
| - _json["bigqueryDataset"] = bigqueryDataset;
|
| - }
|
| - if (bigqueryTable != null) {
|
| - _json["bigqueryTable"] = bigqueryTable;
|
| - }
|
| - if (callSetIds != null) {
|
| - _json["callSetIds"] = callSetIds;
|
| - }
|
| - if (format != null) {
|
| - _json["format"] = format;
|
| - }
|
| - if (projectNumber != null) {
|
| - _json["projectNumber"] = projectNumber;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** The variant data export response. */
|
| -class ExportVariantSetResponse {
|
| - /** A job ID that can be used to get status information. */
|
| - core.String jobId;
|
| -
|
| - ExportVariantSetResponse();
|
| -
|
| - ExportVariantSetResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("jobId")) {
|
| - jobId = _json["jobId"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (jobId != null) {
|
| - _json["jobId"] = jobId;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class ExternalId {
|
| - /** The id used by the source of this data. */
|
| - core.String id;
|
| - /** The name of the source of this data. */
|
| - core.String sourceName;
|
| -
|
| - ExternalId();
|
| -
|
| - ExternalId.fromJson(core.Map _json) {
|
| - if (_json.containsKey("id")) {
|
| - id = _json["id"];
|
| - }
|
| - if (_json.containsKey("sourceName")) {
|
| - sourceName = _json["sourceName"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (id != null) {
|
| - _json["id"] = id;
|
| - }
|
| - if (sourceName != null) {
|
| - _json["sourceName"] = sourceName;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class FastqMetadata {
|
| - /** Optionally specifies the library name for alignment from FASTQ. */
|
| - core.String libraryName;
|
| - /**
|
| - * Optionally specifies the platform name for alignment from FASTQ. For
|
| - * example: CAPILLARY, LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT, PACBIO.
|
| - */
|
| - core.String platformName;
|
| - /**
|
| - * Optionally specifies the platform unit for alignment from FASTQ. For
|
| - * example: flowcell-barcode.lane for Illumina or slide for SOLID.
|
| - */
|
| - core.String platformUnit;
|
| - /** Optionally specifies the read group name for alignment from FASTQ. */
|
| - core.String readGroupName;
|
| - /** Optionally specifies the sample name for alignment from FASTQ. */
|
| - core.String sampleName;
|
| -
|
| - FastqMetadata();
|
| -
|
| - FastqMetadata.fromJson(core.Map _json) {
|
| - if (_json.containsKey("libraryName")) {
|
| - libraryName = _json["libraryName"];
|
| - }
|
| - if (_json.containsKey("platformName")) {
|
| - platformName = _json["platformName"];
|
| + if (_json.containsKey("bigqueryTable")) {
|
| + bigqueryTable = _json["bigqueryTable"];
|
| }
|
| - if (_json.containsKey("platformUnit")) {
|
| - platformUnit = _json["platformUnit"];
|
| + if (_json.containsKey("callSetIds")) {
|
| + callSetIds = _json["callSetIds"];
|
| }
|
| - if (_json.containsKey("readGroupName")) {
|
| - readGroupName = _json["readGroupName"];
|
| + if (_json.containsKey("format")) {
|
| + format = _json["format"];
|
| }
|
| - if (_json.containsKey("sampleName")) {
|
| - sampleName = _json["sampleName"];
|
| + if (_json.containsKey("projectId")) {
|
| + projectId = _json["projectId"];
|
| }
|
| }
|
|
|
| core.Map toJson() {
|
| var _json = new core.Map();
|
| - if (libraryName != null) {
|
| - _json["libraryName"] = libraryName;
|
| + if (bigqueryDataset != null) {
|
| + _json["bigqueryDataset"] = bigqueryDataset;
|
| }
|
| - if (platformName != null) {
|
| - _json["platformName"] = platformName;
|
| + if (bigqueryTable != null) {
|
| + _json["bigqueryTable"] = bigqueryTable;
|
| }
|
| - if (platformUnit != null) {
|
| - _json["platformUnit"] = platformUnit;
|
| + if (callSetIds != null) {
|
| + _json["callSetIds"] = callSetIds;
|
| }
|
| - if (readGroupName != null) {
|
| - _json["readGroupName"] = readGroupName;
|
| + if (format != null) {
|
| + _json["format"] = format;
|
| }
|
| - if (sampleName != null) {
|
| - _json["sampleName"] = sampleName;
|
| + if (projectId != null) {
|
| + _json["projectId"] = projectId;
|
| }
|
| return _json;
|
| }
|
| @@ -3915,8 +2408,9 @@ class ImportReadGroupSetsRequest {
|
| * The partition strategy describes how read groups are partitioned into read
|
| * group sets.
|
| * Possible string values are:
|
| - * - "MERGE_ALL"
|
| - * - "PER_FILE_PER_SAMPLE"
|
| + * - "PARTITION_STRATEGY_UNSPECIFIED" : A PARTITION_STRATEGY_UNSPECIFIED.
|
| + * - "PER_FILE_PER_SAMPLE" : A PER_FILE_PER_SAMPLE.
|
| + * - "MERGE_ALL" : A MERGE_ALL.
|
| */
|
| core.String partitionStrategy;
|
| /**
|
| @@ -3966,21 +2460,21 @@ class ImportReadGroupSetsRequest {
|
|
|
| /** The read group set import response. */
|
| class ImportReadGroupSetsResponse {
|
| - /** A job ID that can be used to get status information. */
|
| - core.String jobId;
|
| + /** IDs of the read group sets that were created. */
|
| + core.List<core.String> readGroupSetIds;
|
|
|
| ImportReadGroupSetsResponse();
|
|
|
| ImportReadGroupSetsResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("jobId")) {
|
| - jobId = _json["jobId"];
|
| + if (_json.containsKey("readGroupSetIds")) {
|
| + readGroupSetIds = _json["readGroupSetIds"];
|
| }
|
| }
|
|
|
| core.Map toJson() {
|
| var _json = new core.Map();
|
| - if (jobId != null) {
|
| - _json["jobId"] = jobId;
|
| + if (readGroupSetIds != null) {
|
| + _json["readGroupSetIds"] = readGroupSetIds;
|
| }
|
| return _json;
|
| }
|
| @@ -3990,10 +2484,11 @@ class ImportReadGroupSetsResponse {
|
| class ImportVariantsRequest {
|
| /**
|
| * The format of the variant data being imported. If unspecified, defaults to
|
| - * to "VCF".
|
| + * to `VCF`.
|
| * Possible string values are:
|
| - * - "COMPLETE_GENOMICS"
|
| - * - "VCF"
|
| + * - "FORMAT_UNSPECIFIED" : A FORMAT_UNSPECIFIED.
|
| + * - "FORMAT_VCF" : A FORMAT_VCF.
|
| + * - "FORMAT_COMPLETE_GENOMICS" : A FORMAT_COMPLETE_GENOMICS.
|
| */
|
| core.String format;
|
| /**
|
| @@ -4008,10 +2503,13 @@ class ImportVariantsRequest {
|
| core.bool normalizeReferenceNames;
|
| /**
|
| * A list of URIs referencing variant files in Google Cloud Storage. URIs can
|
| - * include wildcards as described here. Note that recursive wildcards ('**')
|
| - * are not supported.
|
| + * include wildcards [as described
|
| + * here](https://cloud.google.com/storage/docs/gsutil/addlhelp/WildcardNames).
|
| + * Note that recursive wildcards ('**') are not supported.
|
| */
|
| core.List<core.String> sourceUris;
|
| + /** Required. The variant set to which variant data should be imported. */
|
| + core.String variantSetId;
|
|
|
| ImportVariantsRequest();
|
|
|
| @@ -4025,6 +2523,9 @@ class ImportVariantsRequest {
|
| if (_json.containsKey("sourceUris")) {
|
| sourceUris = _json["sourceUris"];
|
| }
|
| + if (_json.containsKey("variantSetId")) {
|
| + variantSetId = _json["variantSetId"];
|
| + }
|
| }
|
|
|
| core.Map toJson() {
|
| @@ -4038,279 +2539,30 @@ class ImportVariantsRequest {
|
| if (sourceUris != null) {
|
| _json["sourceUris"] = sourceUris;
|
| }
|
| + if (variantSetId != null) {
|
| + _json["variantSetId"] = variantSetId;
|
| + }
|
| return _json;
|
| }
|
| }
|
|
|
| /** The variant data import response. */
|
| class ImportVariantsResponse {
|
| - /** A job ID that can be used to get status information. */
|
| - core.String jobId;
|
| + /** IDs of the call sets that were created. */
|
| + core.List<core.String> callSetIds;
|
|
|
| ImportVariantsResponse();
|
|
|
| ImportVariantsResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("jobId")) {
|
| - jobId = _json["jobId"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (jobId != null) {
|
| - _json["jobId"] = jobId;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/**
|
| - * Wrapper message for `int32`.
|
| - *
|
| - * The JSON representation for `Int32Value` is JSON number.
|
| - */
|
| -class Int32Value {
|
| - /** The int32 value. */
|
| - core.int value;
|
| -
|
| - Int32Value();
|
| -
|
| - Int32Value.fromJson(core.Map _json) {
|
| - if (_json.containsKey("value")) {
|
| - value = _json["value"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (value != null) {
|
| - _json["value"] = value;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** Describes an interleaved FASTQ file source for alignment. */
|
| -class InterleavedFastqSource {
|
| - /**
|
| - * Optionally specifies the metadata to be associated with the final aligned
|
| - * read group set.
|
| - */
|
| - FastqMetadata metadata;
|
| - /**
|
| - * A list of URIs pointing at interleaved FASTQ files in Google Cloud Storage
|
| - * which will be aligned. The caller must have READ permissions for these
|
| - * files.
|
| - */
|
| - core.List<core.String> sourceUris;
|
| -
|
| - InterleavedFastqSource();
|
| -
|
| - InterleavedFastqSource.fromJson(core.Map _json) {
|
| - if (_json.containsKey("metadata")) {
|
| - metadata = new FastqMetadata.fromJson(_json["metadata"]);
|
| - }
|
| - if (_json.containsKey("sourceUris")) {
|
| - sourceUris = _json["sourceUris"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (metadata != null) {
|
| - _json["metadata"] = (metadata).toJson();
|
| - }
|
| - if (sourceUris != null) {
|
| - _json["sourceUris"] = sourceUris;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/**
|
| - * A Job represents an ongoing process that can be monitored for status
|
| - * information.
|
| - */
|
| -class Job {
|
| - /** The date this job was created, in milliseconds from the epoch. */
|
| - core.String created;
|
| - /** A more detailed description of this job's current status. */
|
| - core.String detailedStatus;
|
| - /** Any errors that occurred during processing. */
|
| - core.List<core.String> errors;
|
| - /** The job ID. */
|
| - core.String id;
|
| - /**
|
| - * If this Job represents an import, this field will contain the IDs of the
|
| - * objects that were successfully imported.
|
| - */
|
| - core.List<core.String> importedIds;
|
| - /**
|
| - * The Google Developers Console project number to which this job belongs.
|
| - */
|
| - core.String projectNumber;
|
| - /** A summarized representation of the original service request. */
|
| - JobRequest request;
|
| - /**
|
| - * The status of this job.
|
| - * Possible string values are:
|
| - * - "CANCELED"
|
| - * - "FAILURE"
|
| - * - "NEW"
|
| - * - "PENDING"
|
| - * - "RUNNING"
|
| - * - "SUCCESS"
|
| - * - "UNKNOWN_STATUS"
|
| - */
|
| - core.String status;
|
| - /** Any warnings that occurred during processing. */
|
| - core.List<core.String> warnings;
|
| -
|
| - Job();
|
| -
|
| - Job.fromJson(core.Map _json) {
|
| - if (_json.containsKey("created")) {
|
| - created = _json["created"];
|
| - }
|
| - if (_json.containsKey("detailedStatus")) {
|
| - detailedStatus = _json["detailedStatus"];
|
| - }
|
| - if (_json.containsKey("errors")) {
|
| - errors = _json["errors"];
|
| - }
|
| - if (_json.containsKey("id")) {
|
| - id = _json["id"];
|
| - }
|
| - if (_json.containsKey("importedIds")) {
|
| - importedIds = _json["importedIds"];
|
| - }
|
| - if (_json.containsKey("projectNumber")) {
|
| - projectNumber = _json["projectNumber"];
|
| - }
|
| - if (_json.containsKey("request")) {
|
| - request = new JobRequest.fromJson(_json["request"]);
|
| - }
|
| - if (_json.containsKey("status")) {
|
| - status = _json["status"];
|
| - }
|
| - if (_json.containsKey("warnings")) {
|
| - warnings = _json["warnings"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (created != null) {
|
| - _json["created"] = created;
|
| - }
|
| - if (detailedStatus != null) {
|
| - _json["detailedStatus"] = detailedStatus;
|
| - }
|
| - if (errors != null) {
|
| - _json["errors"] = errors;
|
| - }
|
| - if (id != null) {
|
| - _json["id"] = id;
|
| - }
|
| - if (importedIds != null) {
|
| - _json["importedIds"] = importedIds;
|
| - }
|
| - if (projectNumber != null) {
|
| - _json["projectNumber"] = projectNumber;
|
| - }
|
| - if (request != null) {
|
| - _json["request"] = (request).toJson();
|
| - }
|
| - if (status != null) {
|
| - _json["status"] = status;
|
| - }
|
| - if (warnings != null) {
|
| - _json["warnings"] = warnings;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** A summary representation of the service request that spawned the job. */
|
| -class JobRequest {
|
| - /**
|
| - * The data destination of the request, for example, a Google BigQuery Table
|
| - * or Dataset ID.
|
| - */
|
| - core.List<core.String> destination;
|
| - /**
|
| - * The data source of the request, for example, a Google Cloud Storage object
|
| - * path or Readset ID.
|
| - */
|
| - core.List<core.String> source;
|
| - /**
|
| - * The original request type.
|
| - * Possible string values are:
|
| - * - "ALIGN_READSETS"
|
| - * - "CALL_READSETS"
|
| - * - "EXPERIMENTAL_CREATE_JOB"
|
| - * - "EXPORT_READSETS"
|
| - * - "EXPORT_VARIANTS"
|
| - * - "IMPORT_READSETS"
|
| - * - "IMPORT_VARIANTS"
|
| - * - "UNKNOWN_TYPE"
|
| - */
|
| - core.String type;
|
| -
|
| - JobRequest();
|
| -
|
| - JobRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("destination")) {
|
| - destination = _json["destination"];
|
| - }
|
| - if (_json.containsKey("source")) {
|
| - source = _json["source"];
|
| - }
|
| - if (_json.containsKey("type")) {
|
| - type = _json["type"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (destination != null) {
|
| - _json["destination"] = destination;
|
| - }
|
| - if (source != null) {
|
| - _json["source"] = source;
|
| - }
|
| - if (type != null) {
|
| - _json["type"] = type;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** Used to hold basic key value information. */
|
| -class KeyValue {
|
| - /** A string which maps to an array of values. */
|
| - core.String key;
|
| - /** The string values. */
|
| - core.List<core.String> value;
|
| -
|
| - KeyValue();
|
| -
|
| - KeyValue.fromJson(core.Map _json) {
|
| - if (_json.containsKey("key")) {
|
| - key = _json["key"];
|
| - }
|
| - if (_json.containsKey("value")) {
|
| - value = _json["value"];
|
| + if (_json.containsKey("callSetIds")) {
|
| + callSetIds = _json["callSetIds"];
|
| }
|
| }
|
|
|
| core.Map toJson() {
|
| var _json = new core.Map();
|
| - if (key != null) {
|
| - _json["key"] = key;
|
| - }
|
| - if (value != null) {
|
| - _json["value"] = value;
|
| + if (callSetIds != null) {
|
| + _json["callSetIds"] = callSetIds;
|
| }
|
| return _json;
|
| }
|
| @@ -4371,8 +2623,9 @@ class ListBasesResponse {
|
| */
|
| core.String nextPageToken;
|
| /**
|
| - * The offset position (0-based) of the given sequence from the start of this
|
| - * Reference. This value will differ for each page in a paginated request.
|
| + * The offset position (0-based) of the given `sequence` from the start of
|
| + * this `Reference`. This value will differ for each page in a paginated
|
| + * request.
|
| */
|
| core.String offset;
|
| /** A substring of the bases that make up this reference. */
|
| @@ -4412,13 +2665,13 @@ class ListCoverageBucketsResponse {
|
| * The length of each coverage bucket in base pairs. Note that buckets at the
|
| * end of a reference sequence may be shorter. This value is omitted if the
|
| * bucket width is infinity (the default behaviour, with no range or
|
| - * targetBucketWidth).
|
| + * `targetBucketWidth`).
|
| */
|
| core.String bucketWidth;
|
| /**
|
| * The coverage buckets. The list of buckets is sparse; a bucket with 0
|
| * overlapping reads is not returned. A bucket never crosses more than one
|
| - * reference sequence. Each bucket has width bucketWidth, unless its end is
|
| + * reference sequence. Each bucket has width `bucketWidth`, unless its end is
|
| * the end of the reference sequence.
|
| */
|
| core.List<CoverageBucket> coverageBuckets;
|
| @@ -4492,168 +2745,194 @@ class ListDatasetsResponse {
|
| }
|
| }
|
|
|
| -class MergeVariantsRequest {
|
| - /** The variants to be merged with existing variants. */
|
| - core.List<Variant> variants;
|
| +/**
|
| + * The response message for
|
| + * [Operations.ListOperations][google.longrunning.Operations.ListOperations].
|
| + */
|
| +class ListOperationsResponse {
|
| + /** The standard List next-page token. */
|
| + core.String nextPageToken;
|
| + /** A list of operations that matches the specified filter in the request. */
|
| + core.List<Operation> operations;
|
|
|
| - MergeVariantsRequest();
|
| + ListOperationsResponse();
|
|
|
| - MergeVariantsRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("variants")) {
|
| - variants = _json["variants"].map((value) => new Variant.fromJson(value)).toList();
|
| + ListOperationsResponse.fromJson(core.Map _json) {
|
| + if (_json.containsKey("nextPageToken")) {
|
| + nextPageToken = _json["nextPageToken"];
|
| + }
|
| + if (_json.containsKey("operations")) {
|
| + operations = _json["operations"].map((value) => new Operation.fromJson(value)).toList();
|
| }
|
| }
|
|
|
| core.Map toJson() {
|
| var _json = new core.Map();
|
| - if (variants != null) {
|
| - _json["variants"] = variants.map((value) => (value).toJson()).toList();
|
| + if (nextPageToken != null) {
|
| + _json["nextPageToken"] = nextPageToken;
|
| + }
|
| + if (operations != null) {
|
| + _json["operations"] = operations.map((value) => (value).toJson()).toList();
|
| }
|
| return _json;
|
| }
|
| }
|
|
|
| /**
|
| - * Metadata describes a single piece of variant call metadata. These data
|
| - * include a top level key and either a single value string (value) or a list of
|
| - * key-value pairs (info.) Value and info are mutually exclusive.
|
| + * This resource represents a long-running operation that is the result of a
|
| + * network API call.
|
| */
|
| -class Metadata {
|
| - /** A textual description of this metadata. */
|
| - core.String description;
|
| +class Operation {
|
| /**
|
| - * User-provided ID field, not enforced by this API. Two or more pieces of
|
| - * structured metadata with identical id and key fields are considered
|
| - * equivalent.
|
| + * If the value is `false`, it means the operation is still in progress. If
|
| + * true, the operation is completed and the `result` is available.
|
| */
|
| - core.String id;
|
| - /** A string which maps to an array of values. */
|
| - core.Map<core.String, core.List<core.String>> info;
|
| - /** The top-level key. */
|
| - core.String key;
|
| + core.bool done;
|
| + /** The error result of the operation in case of failure. */
|
| + Status error;
|
| /**
|
| - * The number of values that can be included in a field described by this
|
| - * metadata.
|
| + * An [OperationMetadata][google.genomics.v1.OperationMetadata] object. This
|
| + * will always be returned with the [Operation][google.longrunning.Operation].
|
| + *
|
| + * The values for Object must be JSON objects. It can consist of `num`,
|
| + * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| */
|
| - core.String number;
|
| + core.Map<core.String, core.Object> metadata;
|
| /**
|
| - * The type of data. Possible types include: Integer, Float, Flag, Character,
|
| - * and String.
|
| - * Possible string values are:
|
| - * - "CHARACTER"
|
| - * - "FLAG"
|
| - * - "FLOAT"
|
| - * - "INTEGER"
|
| - * - "STRING"
|
| - * - "UNKNOWN_TYPE"
|
| + * The server-assigned name, which is only unique within the same service that
|
| + * originally returns it. For example:
|
| + * `operations/CJHU7Oi_ChDrveSpBRjfuL-qzoWAgEw`
|
| */
|
| - core.String type;
|
| - /** The value field for simple metadata */
|
| - core.String value;
|
| + core.String name;
|
| + /**
|
| + * If importing [ReadGroupSets][google.genomics.v1.ReadGroupSet], an
|
| + * [ImportReadGroupSetsResponse][google.genomics.v1.ImportReadGroupSetsResponse]
|
| + * is returned. If importing [Variants][google.genomics.v1.Variant], an
|
| + * [ImportVariantsResponse][google.genomics.v1.ImportVariantsResponse] is
|
| + * returned. For exports, an empty response is returned.
|
| + *
|
| + * The values for Object must be JSON objects. It can consist of `num`,
|
| + * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| + */
|
| + core.Map<core.String, core.Object> response;
|
|
|
| - Metadata();
|
| + Operation();
|
|
|
| - Metadata.fromJson(core.Map _json) {
|
| - if (_json.containsKey("description")) {
|
| - description = _json["description"];
|
| - }
|
| - if (_json.containsKey("id")) {
|
| - id = _json["id"];
|
| - }
|
| - if (_json.containsKey("info")) {
|
| - info = _json["info"];
|
| + Operation.fromJson(core.Map _json) {
|
| + if (_json.containsKey("done")) {
|
| + done = _json["done"];
|
| }
|
| - if (_json.containsKey("key")) {
|
| - key = _json["key"];
|
| + if (_json.containsKey("error")) {
|
| + error = new Status.fromJson(_json["error"]);
|
| }
|
| - if (_json.containsKey("number")) {
|
| - number = _json["number"];
|
| + if (_json.containsKey("metadata")) {
|
| + metadata = _json["metadata"];
|
| }
|
| - if (_json.containsKey("type")) {
|
| - type = _json["type"];
|
| + if (_json.containsKey("name")) {
|
| + name = _json["name"];
|
| }
|
| - if (_json.containsKey("value")) {
|
| - value = _json["value"];
|
| + if (_json.containsKey("response")) {
|
| + response = _json["response"];
|
| }
|
| }
|
|
|
| core.Map toJson() {
|
| var _json = new core.Map();
|
| - if (description != null) {
|
| - _json["description"] = description;
|
| + if (done != null) {
|
| + _json["done"] = done;
|
| }
|
| - if (id != null) {
|
| - _json["id"] = id;
|
| + if (error != null) {
|
| + _json["error"] = (error).toJson();
|
| }
|
| - if (info != null) {
|
| - _json["info"] = info;
|
| + if (metadata != null) {
|
| + _json["metadata"] = metadata;
|
| }
|
| - if (key != null) {
|
| - _json["key"] = key;
|
| + if (name != null) {
|
| + _json["name"] = name;
|
| }
|
| - if (number != null) {
|
| - _json["number"] = number;
|
| + if (response != null) {
|
| + _json["response"] = response;
|
| }
|
| - if (type != null) {
|
| - _json["type"] = type;
|
| + return _json;
|
| + }
|
| +}
|
| +
|
| +/**
|
| + * An event that occurred during an [Operation][google.longrunning.Operation].
|
| + */
|
| +class OperationEvent {
|
| + /** Required description of event. */
|
| + core.String description;
|
| +
|
| + OperationEvent();
|
| +
|
| + OperationEvent.fromJson(core.Map _json) {
|
| + if (_json.containsKey("description")) {
|
| + description = _json["description"];
|
| }
|
| - if (value != null) {
|
| - _json["value"] = value;
|
| + }
|
| +
|
| + core.Map toJson() {
|
| + var _json = new core.Map();
|
| + if (description != null) {
|
| + _json["description"] = description;
|
| }
|
| return _json;
|
| }
|
| }
|
|
|
| -/** Describes a paired-end FASTQ file source for alignment. */
|
| -class PairedFastqSource {
|
| - /**
|
| - * A list of URIs pointing at paired end FASTQ files in Google Cloud Storage
|
| - * which will be aligned. The first of each paired file should be specified
|
| - * here, in an order that matches the second of each paired file specified in
|
| - * secondSourceUris. For example: firstSourceUris: [file1_1.fq, file2_1.fq],
|
| - * secondSourceUris: [file1_2.fq, file2_2.fq]. The caller must have READ
|
| - * permissions for these files.
|
| - */
|
| - core.List<core.String> firstSourceUris;
|
| +/** Metadata describing an [Operation][google.longrunning.Operation]. */
|
| +class OperationMetadata {
|
| + /** The time at which the job was submitted to the Genomics service. */
|
| + core.String createTime;
|
| /**
|
| - * Optionally specifies the metadata to be associated with the final aligned
|
| - * read group set.
|
| + * Optional event messages that were generated during the job's execution.
|
| + * This also contains any warnings that were generated during import or
|
| + * export.
|
| */
|
| - FastqMetadata metadata;
|
| + core.List<OperationEvent> events;
|
| + /** The Google Cloud Project in which the job is scoped. */
|
| + core.String projectId;
|
| /**
|
| - * A list of URIs pointing at paired end FASTQ files in Google Cloud Storage
|
| - * which will be aligned. The second of each paired file should be specified
|
| - * here, in an order that matches the first of each paired file specified in
|
| - * firstSourceUris. For example: firstSourceUris: [file1_1.fq, file2_1.fq],
|
| - * secondSourceUris: [file1_2.fq, file2_2.fq]. The caller must have READ
|
| - * permissions for these files.
|
| + * The original request that started the operation. Note that this will be in
|
| + * current version of the API. If the operation was started with v1beta2 API
|
| + * and a GetOperation is performed on v1 API, a v1 request will be returned.
|
| + *
|
| + * The values for Object must be JSON objects. It can consist of `num`,
|
| + * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| */
|
| - core.List<core.String> secondSourceUris;
|
| + core.Map<core.String, core.Object> request;
|
|
|
| - PairedFastqSource();
|
| + OperationMetadata();
|
|
|
| - PairedFastqSource.fromJson(core.Map _json) {
|
| - if (_json.containsKey("firstSourceUris")) {
|
| - firstSourceUris = _json["firstSourceUris"];
|
| + OperationMetadata.fromJson(core.Map _json) {
|
| + if (_json.containsKey("createTime")) {
|
| + createTime = _json["createTime"];
|
| }
|
| - if (_json.containsKey("metadata")) {
|
| - metadata = new FastqMetadata.fromJson(_json["metadata"]);
|
| + if (_json.containsKey("events")) {
|
| + events = _json["events"].map((value) => new OperationEvent.fromJson(value)).toList();
|
| + }
|
| + if (_json.containsKey("projectId")) {
|
| + projectId = _json["projectId"];
|
| }
|
| - if (_json.containsKey("secondSourceUris")) {
|
| - secondSourceUris = _json["secondSourceUris"];
|
| + if (_json.containsKey("request")) {
|
| + request = _json["request"];
|
| }
|
| }
|
|
|
| core.Map toJson() {
|
| var _json = new core.Map();
|
| - if (firstSourceUris != null) {
|
| - _json["firstSourceUris"] = firstSourceUris;
|
| + if (createTime != null) {
|
| + _json["createTime"] = createTime;
|
| }
|
| - if (metadata != null) {
|
| - _json["metadata"] = (metadata).toJson();
|
| + if (events != null) {
|
| + _json["events"] = events.map((value) => (value).toJson()).toList();
|
| }
|
| - if (secondSourceUris != null) {
|
| - _json["secondSourceUris"] = secondSourceUris;
|
| + if (projectId != null) {
|
| + _json["projectId"] = projectId;
|
| + }
|
| + if (request != null) {
|
| + _json["request"] = request;
|
| }
|
| return _json;
|
| }
|
| @@ -4707,149 +2986,80 @@ class Position {
|
| }
|
| }
|
|
|
| -/** A 0-based half-open genomic coordinate range for search requests. */
|
| -class QueryRange {
|
| - /**
|
| - * The end position of the range on the reference, 0-based exclusive. If
|
| - * specified, referenceId or referenceName must also be specified. If unset or
|
| - * 0, defaults to the length of the reference.
|
| - */
|
| - core.String end;
|
| - /**
|
| - * The ID of the reference to query. At most one of referenceId and
|
| - * referenceName should be specified.
|
| - */
|
| - core.String referenceId;
|
| - /**
|
| - * The name of the reference to query, within the reference set associated
|
| - * with this query. At most one of referenceId and referenceName pshould be
|
| - * specified.
|
| - */
|
| - core.String referenceName;
|
| +class Program {
|
| + /** The command line used to run this program. */
|
| + core.String commandLine;
|
| /**
|
| - * The start position of the range on the reference, 0-based inclusive. If
|
| - * specified, referenceId or referenceName must also be specified. Defaults to
|
| - * 0.
|
| + * The user specified locally unique ID of the program. Used along with
|
| + * `prevProgramId` to define an ordering between programs.
|
| */
|
| - core.String start;
|
| + core.String id;
|
| + /** The name of the program. */
|
| + core.String name;
|
| + /** The ID of the program run before this one. */
|
| + core.String prevProgramId;
|
| + /** The version of the program run. */
|
| + core.String version;
|
|
|
| - QueryRange();
|
| + Program();
|
|
|
| - QueryRange.fromJson(core.Map _json) {
|
| - if (_json.containsKey("end")) {
|
| - end = _json["end"];
|
| + Program.fromJson(core.Map _json) {
|
| + if (_json.containsKey("commandLine")) {
|
| + commandLine = _json["commandLine"];
|
| }
|
| - if (_json.containsKey("referenceId")) {
|
| - referenceId = _json["referenceId"];
|
| + if (_json.containsKey("id")) {
|
| + id = _json["id"];
|
| }
|
| - if (_json.containsKey("referenceName")) {
|
| - referenceName = _json["referenceName"];
|
| + if (_json.containsKey("name")) {
|
| + name = _json["name"];
|
| }
|
| - if (_json.containsKey("start")) {
|
| - start = _json["start"];
|
| + if (_json.containsKey("prevProgramId")) {
|
| + prevProgramId = _json["prevProgramId"];
|
| + }
|
| + if (_json.containsKey("version")) {
|
| + version = _json["version"];
|
| }
|
| }
|
|
|
| core.Map toJson() {
|
| var _json = new core.Map();
|
| - if (end != null) {
|
| - _json["end"] = end;
|
| - }
|
| - if (referenceId != null) {
|
| - _json["referenceId"] = referenceId;
|
| - }
|
| - if (referenceName != null) {
|
| - _json["referenceName"] = referenceName;
|
| - }
|
| - if (start != null) {
|
| - _json["start"] = start;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** A 0-based half-open genomic coordinate range over a reference sequence. */
|
| -class Range {
|
| - /**
|
| - * The end position of the range on the reference, 0-based exclusive. If
|
| - * specified, referenceName must also be specified.
|
| - */
|
| - core.String end;
|
| - /** The reference sequence name, for example chr1, 1, or chrX. */
|
| - core.String referenceName;
|
| - /**
|
| - * The start position of the range on the reference, 0-based inclusive. If
|
| - * specified, referenceName must also be specified.
|
| - */
|
| - core.String start;
|
| -
|
| - Range();
|
| -
|
| - Range.fromJson(core.Map _json) {
|
| - if (_json.containsKey("end")) {
|
| - end = _json["end"];
|
| - }
|
| - if (_json.containsKey("referenceName")) {
|
| - referenceName = _json["referenceName"];
|
| + if (commandLine != null) {
|
| + _json["commandLine"] = commandLine;
|
| }
|
| - if (_json.containsKey("start")) {
|
| - start = _json["start"];
|
| + if (id != null) {
|
| + _json["id"] = id;
|
| }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (end != null) {
|
| - _json["end"] = end;
|
| + if (name != null) {
|
| + _json["name"] = name;
|
| }
|
| - if (referenceName != null) {
|
| - _json["referenceName"] = referenceName;
|
| + if (prevProgramId != null) {
|
| + _json["prevProgramId"] = prevProgramId;
|
| }
|
| - if (start != null) {
|
| - _json["start"] = start;
|
| + if (version != null) {
|
| + _json["version"] = version;
|
| }
|
| return _json;
|
| }
|
| }
|
|
|
| -/**
|
| - * A 0-based half-open genomic coordinate range over a reference sequence, for
|
| - * representing the position of a genomic resource.
|
| - */
|
| -class RangePosition {
|
| +/** A 0-based half-open genomic coordinate range for search requests. */
|
| +class Range {
|
| /** The end position of the range on the reference, 0-based exclusive. */
|
| core.String end;
|
| - /** The ID of the Google Genomics reference associated with this range. */
|
| - core.String referenceId;
|
| - /**
|
| - * The display name corresponding to the reference specified by referenceId,
|
| - * for example chr1, 1, or chrX.
|
| - */
|
| + /** The reference sequence name, for example `chr1`, `1`, or `chrX`. */
|
| core.String referenceName;
|
| - /**
|
| - * Whether this range refers to the reverse strand, as opposed to the forward
|
| - * strand. Note that regardless of this field, the start/end position of the
|
| - * range always refer to the forward strand.
|
| - */
|
| - core.bool reverseStrand;
|
| /** The start position of the range on the reference, 0-based inclusive. */
|
| core.String start;
|
|
|
| - RangePosition();
|
| + Range();
|
|
|
| - RangePosition.fromJson(core.Map _json) {
|
| + Range.fromJson(core.Map _json) {
|
| if (_json.containsKey("end")) {
|
| end = _json["end"];
|
| }
|
| - if (_json.containsKey("referenceId")) {
|
| - referenceId = _json["referenceId"];
|
| - }
|
| if (_json.containsKey("referenceName")) {
|
| referenceName = _json["referenceName"];
|
| }
|
| - if (_json.containsKey("reverseStrand")) {
|
| - reverseStrand = _json["reverseStrand"];
|
| - }
|
| if (_json.containsKey("start")) {
|
| start = _json["start"];
|
| }
|
| @@ -4860,15 +3070,9 @@ class RangePosition {
|
| if (end != null) {
|
| _json["end"] = end;
|
| }
|
| - if (referenceId != null) {
|
| - _json["referenceId"] = referenceId;
|
| - }
|
| if (referenceName != null) {
|
| _json["referenceName"] = referenceName;
|
| }
|
| - if (reverseStrand != null) {
|
| - _json["reverseStrand"] = reverseStrand;
|
| - }
|
| if (start != null) {
|
| _json["start"] = start;
|
| }
|
| @@ -4878,33 +3082,33 @@ class RangePosition {
|
|
|
| /**
|
| * A read alignment describes a linear alignment of a string of DNA to a
|
| - * reference sequence, in addition to metadata about the fragment (the molecule
|
| - * of DNA sequenced) and the read (the bases which were read by the sequencer).
|
| - * A read is equivalent to a line in a SAM file. A read belongs to exactly one
|
| - * read group and exactly one read group set. Generating a reference-aligned
|
| + * [reference sequence][google.genomics.v1.Reference], in addition to metadata
|
| + * about the fragment (the molecule of DNA sequenced) and the read (the bases
|
| + * which were read by the sequencer). A read is equivalent to a line in a SAM
|
| + * file. A read belongs to exactly one read group and exactly one [read group
|
| + * set][google.genomics.v1.ReadGroupSet]. ### Generating a reference-aligned
|
| * sequence string When interacting with mapped reads, it's often useful to
|
| * produce a string representing the local alignment of the read to reference.
|
| - * The following pseudocode demonstrates one way of doing this:
|
| - * out = "" offset = 0 for c in read.alignment.cigar { switch c.operation { case
|
| + * The following pseudocode demonstrates one way of doing this: out = "" offset
|
| + * = 0 for c in read.alignment.cigar { switch c.operation { case
|
| * "ALIGNMENT_MATCH", "SEQUENCE_MATCH", "SEQUENCE_MISMATCH": out +=
|
| * read.alignedSequence[offset:offset+c.operationLength] offset +=
|
| * c.operationLength break case "CLIP_SOFT", "INSERT": offset +=
|
| * c.operationLength break case "PAD": out += repeat("*", c.operationLength)
|
| * break case "DELETE": out += repeat("-", c.operationLength) break case "SKIP":
|
| * out += repeat(" ", c.operationLength) break case "CLIP_HARD": break } }
|
| - * return out
|
| - * Converting to SAM's CIGAR string The following pseudocode generates a SAM
|
| - * CIGAR string from the cigar field. Note that this is a lossy conversion
|
| - * (cigar.referenceSequence is lost).
|
| - * cigarMap = { "ALIGNMENT_MATCH": "M", "INSERT": "I", "DELETE": "D", "SKIP":
|
| - * "N", "CLIP_SOFT": "S", "CLIP_HARD": "H", "PAD": "P", "SEQUENCE_MATCH": "=",
|
| + * return out ### Converting to SAM's CIGAR string The following pseudocode
|
| + * generates a SAM CIGAR string from the `cigar` field. Note that this is a
|
| + * lossy conversion (`cigar.referenceSequence` is lost). cigarMap = {
|
| + * "ALIGNMENT_MATCH": "M", "INSERT": "I", "DELETE": "D", "SKIP": "N",
|
| + * "CLIP_SOFT": "S", "CLIP_HARD": "H", "PAD": "P", "SEQUENCE_MATCH": "=",
|
| * "SEQUENCE_MISMATCH": "X", } cigarStr = "" for c in read.alignment.cigar {
|
| * cigarStr += c.operationLength + cigarMap[c.operation] } return cigarStr
|
| */
|
| class Read {
|
| /**
|
| * The quality of the read sequence contained in this alignment record.
|
| - * alignedSequence and alignedQuality may be shorter than the full read
|
| + * `alignedSequence` and `alignedQuality` may be shorter than the full read
|
| * sequence and quality. This will occur if the alignment is part of a
|
| * chimeric alignment, or if the read was trimmed. When this occurs, the CIGAR
|
| * for this read will begin/end with a hard clip operator that will indicate
|
| @@ -4912,16 +3116,16 @@ class Read {
|
| */
|
| core.List<core.int> alignedQuality;
|
| /**
|
| - * The bases of the read sequence contained in this alignment record, without
|
| - * CIGAR operations applied. alignedSequence and alignedQuality may be shorter
|
| - * than the full read sequence and quality. This will occur if the alignment
|
| - * is part of a chimeric alignment, or if the read was trimmed. When this
|
| - * occurs, the CIGAR for this read will begin/end with a hard clip operator
|
| - * that will indicate the length of the excised sequence.
|
| + * The bases of the read sequence contained in this alignment record, *without
|
| + * CIGAR operations applied*. `alignedSequence` and `alignedQuality` may be
|
| + * shorter than the full read sequence and quality. This will occur if the
|
| + * alignment is part of a chimeric alignment, or if the read was trimmed. When
|
| + * this occurs, the CIGAR for this read will begin/end with a hard clip
|
| + * operator that will indicate the length of the excised sequence.
|
| */
|
| core.String alignedSequence;
|
| /**
|
| - * The linear alignment for this alignment record. This field will be unset if
|
| + * The linear alignment for this alignment record. This field will be null if
|
| * the read is unmapped.
|
| */
|
| LinearAlignment alignment;
|
| @@ -4934,17 +3138,21 @@ class Read {
|
| /** The fragment name. Equivalent to QNAME (query template name) in SAM. */
|
| core.String fragmentName;
|
| /**
|
| - * The unique ID for this read. This is a generated unique ID, not to be
|
| - * confused with fragmentName.
|
| + * The server-generated read ID, unique across all reads. This is different
|
| + * from the `fragmentName`.
|
| */
|
| core.String id;
|
| - /** A string which maps to an array of values. */
|
| - core.Map<core.String, core.List<core.String>> info;
|
| /**
|
| - * The position of the primary alignment of the (readNumber+1)%numberReads
|
| + * A map of additional read alignment information. This must be of the form
|
| + * map (string key mapping to a list of string values).
|
| + *
|
| + * The values for Object must be JSON objects. It can consist of `num`,
|
| + * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| + */
|
| + core.Map<core.String, core.List<core.Object>> info;
|
| + /**
|
| + * The mapping of the primary alignment of the `(readNumber+1)%numberReads`
|
| * read in the fragment. It replaces mate position and mate strand in SAM.
|
| - * This field will be unset if that read is unmapped or if the fragment only
|
| - * has a single read.
|
| */
|
| Position nextMatePosition;
|
| /** The number of reads in the fragment (extension to SAM flag 0x1). */
|
| @@ -4974,8 +3182,8 @@ class Read {
|
| * secondary alignment represents an alternative to the primary alignment for
|
| * this read. Aligners may return secondary alignments if a read can map
|
| * ambiguously to multiple coordinates in the genome. By convention, each read
|
| - * has one and only one alignment where both secondaryAlignment and
|
| - * supplementaryAlignment are false.
|
| + * has one and only one alignment where both `secondaryAlignment` and
|
| + * `supplementaryAlignment` are false.
|
| */
|
| core.bool secondaryAlignment;
|
| /**
|
| @@ -4987,7 +3195,7 @@ class Read {
|
| * the remaining linear alignments will be designated as supplementary
|
| * alignments. These alignments may have different mapping quality scores. In
|
| * each linear alignment in a chimeric alignment, the read will be hard
|
| - * clipped. The alignedSequence and alignedQuality fields in the alignment
|
| + * clipped. The `alignedSequence` and `alignedQuality` fields in the alignment
|
| * record will only represent the bases for its respective linear alignment.
|
| */
|
| core.bool supplementaryAlignment;
|
| @@ -5114,14 +3322,21 @@ class ReadGroup {
|
| /** A free-form text description of this read group. */
|
| core.String description;
|
| /** The experiment used to generate this read group. */
|
| - ReadGroupExperiment experiment;
|
| + Experiment experiment;
|
| /**
|
| - * The generated unique read group ID. Note: This is different than the @RG ID
|
| - * field in the SAM spec. For that value, see the name field.
|
| + * The server-generated read group ID, unique for all read groups. Note: This
|
| + * is different than the `@RG ID` field in the SAM spec. For that value, see
|
| + * the `name` field.
|
| */
|
| core.String id;
|
| - /** A string which maps to an array of values. */
|
| - core.Map<core.String, core.List<core.String>> info;
|
| + /**
|
| + * A map of additional read group information. This must be of the form map
|
| + * (string key mapping to a list of string values).
|
| + *
|
| + * The values for Object must be JSON objects. It can consist of `num`,
|
| + * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| + */
|
| + core.Map<core.String, core.List<core.Object>> info;
|
| /**
|
| * The read group name. This corresponds to the @RG ID field in the SAM spec.
|
| */
|
| @@ -5136,7 +3351,7 @@ class ReadGroup {
|
| * identical for all read groups within a read group set. For this reason,
|
| * only the first read group in a returned set will have this field populated.
|
| */
|
| - core.List<ReadGroupProgram> programs;
|
| + core.List<Program> programs;
|
| /**
|
| * The reference set the reads in this read group are aligned to. Required if
|
| * there are any read alignments.
|
| @@ -5159,7 +3374,7 @@ class ReadGroup {
|
| description = _json["description"];
|
| }
|
| if (_json.containsKey("experiment")) {
|
| - experiment = new ReadGroupExperiment.fromJson(_json["experiment"]);
|
| + experiment = new Experiment.fromJson(_json["experiment"]);
|
| }
|
| if (_json.containsKey("id")) {
|
| id = _json["id"];
|
| @@ -5174,7 +3389,7 @@ class ReadGroup {
|
| predictedInsertSize = _json["predictedInsertSize"];
|
| }
|
| if (_json.containsKey("programs")) {
|
| - programs = _json["programs"].map((value) => new ReadGroupProgram.fromJson(value)).toList();
|
| + programs = _json["programs"].map((value) => new Program.fromJson(value)).toList();
|
| }
|
| if (_json.containsKey("referenceSetId")) {
|
| referenceSetId = _json["referenceSetId"];
|
| @@ -5207,125 +3422,14 @@ class ReadGroup {
|
| if (predictedInsertSize != null) {
|
| _json["predictedInsertSize"] = predictedInsertSize;
|
| }
|
| - if (programs != null) {
|
| - _json["programs"] = programs.map((value) => (value).toJson()).toList();
|
| - }
|
| - if (referenceSetId != null) {
|
| - _json["referenceSetId"] = referenceSetId;
|
| - }
|
| - if (sampleId != null) {
|
| - _json["sampleId"] = sampleId;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class ReadGroupExperiment {
|
| - /**
|
| - * The instrument model used as part of this experiment. This maps to
|
| - * sequencing technology in BAM.
|
| - */
|
| - core.String instrumentModel;
|
| - /**
|
| - * The library used as part of this experiment. Note: This is not an actual ID
|
| - * within this repository, but rather an identifier for a library which may be
|
| - * meaningful to some external system.
|
| - */
|
| - core.String libraryId;
|
| - /**
|
| - * The platform unit used as part of this experiment e.g.
|
| - * flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
|
| - */
|
| - core.String platformUnit;
|
| - /** The sequencing center used as part of this experiment. */
|
| - core.String sequencingCenter;
|
| -
|
| - ReadGroupExperiment();
|
| -
|
| - ReadGroupExperiment.fromJson(core.Map _json) {
|
| - if (_json.containsKey("instrumentModel")) {
|
| - instrumentModel = _json["instrumentModel"];
|
| - }
|
| - if (_json.containsKey("libraryId")) {
|
| - libraryId = _json["libraryId"];
|
| - }
|
| - if (_json.containsKey("platformUnit")) {
|
| - platformUnit = _json["platformUnit"];
|
| - }
|
| - if (_json.containsKey("sequencingCenter")) {
|
| - sequencingCenter = _json["sequencingCenter"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (instrumentModel != null) {
|
| - _json["instrumentModel"] = instrumentModel;
|
| - }
|
| - if (libraryId != null) {
|
| - _json["libraryId"] = libraryId;
|
| - }
|
| - if (platformUnit != null) {
|
| - _json["platformUnit"] = platformUnit;
|
| - }
|
| - if (sequencingCenter != null) {
|
| - _json["sequencingCenter"] = sequencingCenter;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class ReadGroupProgram {
|
| - /** The command line used to run this program. */
|
| - core.String commandLine;
|
| - /**
|
| - * The user specified locally unique ID of the program. Used along with
|
| - * prevProgramId to define an ordering between programs.
|
| - */
|
| - core.String id;
|
| - /** The name of the program. */
|
| - core.String name;
|
| - /** The ID of the program run before this one. */
|
| - core.String prevProgramId;
|
| - /** The version of the program run. */
|
| - core.String version;
|
| -
|
| - ReadGroupProgram();
|
| -
|
| - ReadGroupProgram.fromJson(core.Map _json) {
|
| - if (_json.containsKey("commandLine")) {
|
| - commandLine = _json["commandLine"];
|
| - }
|
| - if (_json.containsKey("id")) {
|
| - id = _json["id"];
|
| - }
|
| - if (_json.containsKey("name")) {
|
| - name = _json["name"];
|
| - }
|
| - if (_json.containsKey("prevProgramId")) {
|
| - prevProgramId = _json["prevProgramId"];
|
| - }
|
| - if (_json.containsKey("version")) {
|
| - version = _json["version"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (commandLine != null) {
|
| - _json["commandLine"] = commandLine;
|
| - }
|
| - if (id != null) {
|
| - _json["id"] = id;
|
| - }
|
| - if (name != null) {
|
| - _json["name"] = name;
|
| - }
|
| - if (prevProgramId != null) {
|
| - _json["prevProgramId"] = prevProgramId;
|
| + if (programs != null) {
|
| + _json["programs"] = programs.map((value) => (value).toJson()).toList();
|
| }
|
| - if (version != null) {
|
| - _json["version"] = version;
|
| + if (referenceSetId != null) {
|
| + _json["referenceSetId"] = referenceSetId;
|
| + }
|
| + if (sampleId != null) {
|
| + _json["sampleId"] = sampleId;
|
| }
|
| return _json;
|
| }
|
| @@ -5335,10 +3439,8 @@ class ReadGroupProgram {
|
| * A read group set is a logical collection of read groups, which are
|
| * collections of reads produced by a sequencer. A read group set typically
|
| * models reads corresponding to one sample, sequenced one way, and aligned one
|
| - * way.
|
| - * - A read group set belongs to one dataset.
|
| - * - A read group belongs to one read group set.
|
| - * - A read belongs to one read group.
|
| + * way. * A read group set belongs to one dataset. * A read group belongs to one
|
| + * read group set. * A read belongs to one read group.
|
| */
|
| class ReadGroupSet {
|
| /** The dataset ID. */
|
| @@ -5347,10 +3449,17 @@ class ReadGroupSet {
|
| * The filename of the original source file for this read group set, if any.
|
| */
|
| core.String filename;
|
| - /** The read group set ID. */
|
| + /**
|
| + * The server-generated read group set ID, unique for all read group sets.
|
| + */
|
| core.String id;
|
| - /** A string which maps to an array of values. */
|
| - core.Map<core.String, core.List<core.String>> info;
|
| + /**
|
| + * A map of additional read group set information.
|
| + *
|
| + * The values for Object must be JSON objects. It can consist of `num`,
|
| + * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| + */
|
| + core.Map<core.String, core.List<core.Object>> info;
|
| /**
|
| * The read group set name. By default this will be initialized to the sample
|
| * name of the sequenced data contained in this set.
|
| @@ -5424,7 +3533,7 @@ class ReadGroupSet {
|
| * reference belongs to one or more reference sets.
|
| */
|
| class Reference {
|
| - /** The Google generated immutable ID of the reference. */
|
| + /** The server-generated reference ID, unique across all references. */
|
| core.String id;
|
| /** The length of this reference's sequence. */
|
| core.String length;
|
| @@ -5434,7 +3543,7 @@ class Reference {
|
| * hexadecimal format.
|
| */
|
| core.String md5checksum;
|
| - /** The name of this reference, for example 22. */
|
| + /** The name of this reference, for example `22`. */
|
| core.String name;
|
| /**
|
| * ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g. 9606->human) if not
|
| @@ -5443,14 +3552,14 @@ class Reference {
|
| core.int ncbiTaxonId;
|
| /**
|
| * All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
|
| - * with a version number, for example GCF_000001405.26.
|
| + * with a version number, for example `GCF_000001405.26`.
|
| */
|
| core.List<core.String> sourceAccessions;
|
| /**
|
| * The URI from which the sequence was obtained. Specifies a FASTA format
|
| * file/string with one name, sequence pair.
|
| */
|
| - core.String sourceURI;
|
| + core.String sourceUri;
|
|
|
| Reference();
|
|
|
| @@ -5473,8 +3582,8 @@ class Reference {
|
| if (_json.containsKey("sourceAccessions")) {
|
| sourceAccessions = _json["sourceAccessions"];
|
| }
|
| - if (_json.containsKey("sourceURI")) {
|
| - sourceURI = _json["sourceURI"];
|
| + if (_json.containsKey("sourceUri")) {
|
| + sourceUri = _json["sourceUri"];
|
| }
|
| }
|
|
|
| @@ -5498,8 +3607,8 @@ class Reference {
|
| if (sourceAccessions != null) {
|
| _json["sourceAccessions"] = sourceAccessions;
|
| }
|
| - if (sourceURI != null) {
|
| - _json["sourceURI"] = sourceURI;
|
| + if (sourceUri != null) {
|
| + _json["sourceUri"] = sourceUri;
|
| }
|
| return _json;
|
| }
|
| @@ -5543,22 +3652,24 @@ class ReferenceBound {
|
|
|
| /**
|
| * A reference set is a set of references which typically comprise a reference
|
| - * assembly for a species, such as GRCh38 which is representative of the human
|
| + * assembly for a species, such as `GRCh38` which is representative of the human
|
| * genome. A reference set defines a common coordinate space for comparing
|
| * reference-aligned experimental data. A reference set contains 1 or more
|
| * references.
|
| */
|
| class ReferenceSet {
|
| - /** Public id of this reference set, such as GRCh37. */
|
| + /** Public id of this reference set, such as `GRCh37`. */
|
| core.String assemblyId;
|
| /** Free text description of this reference set. */
|
| core.String description;
|
| - /** The Google generated immutable ID of the reference set. */
|
| + /**
|
| + * The server-generated reference set ID, unique across all reference sets.
|
| + */
|
| core.String id;
|
| /**
|
| * Order-independent MD5 checksum which identifies this reference set. The
|
| * checksum is computed by sorting all lower case hexidecimal string
|
| - * reference.md5checksum (for all reference in this set) in ascending
|
| + * `reference.md5checksum` (for all reference in this set) in ascending
|
| * lexicographic order, concatenating, and taking the MD5 of that value. The
|
| * resulting value is represented in lower case hexadecimal format.
|
| */
|
| @@ -5566,23 +3677,23 @@ class ReferenceSet {
|
| /**
|
| * ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g. 9606->human) indicating
|
| * the species which this assembly is intended to model. Note that contained
|
| - * references may specify a different ncbiTaxonId, as assemblies may contain
|
| + * references may specify a different `ncbiTaxonId`, as assemblies may contain
|
| * reference sequences which do not belong to the modeled species, e.g. EBV in
|
| * a human reference genome.
|
| */
|
| core.int ncbiTaxonId;
|
| /**
|
| * The IDs of the reference objects that are part of this set.
|
| - * Reference.md5checksum must be unique within this set.
|
| + * `Reference.md5checksum` must be unique within this set.
|
| */
|
| core.List<core.String> referenceIds;
|
| /**
|
| * All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
|
| - * with a version number, for example NC_000001.11.
|
| + * with a version number, for example `NC_000001.11`.
|
| */
|
| core.List<core.String> sourceAccessions;
|
| /** The URI from which the references were obtained. */
|
| - core.String sourceURI;
|
| + core.String sourceUri;
|
|
|
| ReferenceSet();
|
|
|
| @@ -5608,8 +3719,8 @@ class ReferenceSet {
|
| if (_json.containsKey("sourceAccessions")) {
|
| sourceAccessions = _json["sourceAccessions"];
|
| }
|
| - if (_json.containsKey("sourceURI")) {
|
| - sourceURI = _json["sourceURI"];
|
| + if (_json.containsKey("sourceUri")) {
|
| + sourceUri = _json["sourceUri"];
|
| }
|
| }
|
|
|
| @@ -5636,212 +3747,8 @@ class ReferenceSet {
|
| if (sourceAccessions != null) {
|
| _json["sourceAccessions"] = sourceAccessions;
|
| }
|
| - if (sourceURI != null) {
|
| - _json["sourceURI"] = sourceURI;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class SearchAnnotationSetsRequest {
|
| - /**
|
| - * The dataset IDs to search within. Caller must have READ access to these
|
| - * datasets.
|
| - */
|
| - core.List<core.String> datasetIds;
|
| - /**
|
| - * Only return annotations sets for which a substring of the name matches this
|
| - * string (case insensitive).
|
| - */
|
| - core.String name;
|
| - /**
|
| - * Specifies number of results to return in a single page. If unspecified, it
|
| - * will default to 128. The maximum value is 1024.
|
| - */
|
| - core.int pageSize;
|
| - /**
|
| - * The continuation token, which is used to page through large result sets. To
|
| - * get the next page of results, set this parameter to the value of
|
| - * nextPageToken from the previous response.
|
| - */
|
| - core.String pageToken;
|
| - /**
|
| - * If specified, only annotation sets associated with the given reference set
|
| - * are returned.
|
| - */
|
| - core.String referenceSetId;
|
| - /**
|
| - * If specified, only annotation sets that have any of these types are
|
| - * returned.
|
| - */
|
| - core.List<core.String> types;
|
| -
|
| - SearchAnnotationSetsRequest();
|
| -
|
| - SearchAnnotationSetsRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("datasetIds")) {
|
| - datasetIds = _json["datasetIds"];
|
| - }
|
| - if (_json.containsKey("name")) {
|
| - name = _json["name"];
|
| - }
|
| - if (_json.containsKey("pageSize")) {
|
| - pageSize = _json["pageSize"];
|
| - }
|
| - if (_json.containsKey("pageToken")) {
|
| - pageToken = _json["pageToken"];
|
| - }
|
| - if (_json.containsKey("referenceSetId")) {
|
| - referenceSetId = _json["referenceSetId"];
|
| - }
|
| - if (_json.containsKey("types")) {
|
| - types = _json["types"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (datasetIds != null) {
|
| - _json["datasetIds"] = datasetIds;
|
| - }
|
| - if (name != null) {
|
| - _json["name"] = name;
|
| - }
|
| - if (pageSize != null) {
|
| - _json["pageSize"] = pageSize;
|
| - }
|
| - if (pageToken != null) {
|
| - _json["pageToken"] = pageToken;
|
| - }
|
| - if (referenceSetId != null) {
|
| - _json["referenceSetId"] = referenceSetId;
|
| - }
|
| - if (types != null) {
|
| - _json["types"] = types;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class SearchAnnotationSetsResponse {
|
| - /** The matching annotation sets. */
|
| - core.List<AnnotationSet> annotationSets;
|
| - /**
|
| - * The continuation token, which is used to page through large result sets.
|
| - * Provide this value in a subsequent request to return the next page of
|
| - * results. This field will be empty if there aren't any additional results.
|
| - */
|
| - core.String nextPageToken;
|
| -
|
| - SearchAnnotationSetsResponse();
|
| -
|
| - SearchAnnotationSetsResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("annotationSets")) {
|
| - annotationSets = _json["annotationSets"].map((value) => new AnnotationSet.fromJson(value)).toList();
|
| - }
|
| - if (_json.containsKey("nextPageToken")) {
|
| - nextPageToken = _json["nextPageToken"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (annotationSets != null) {
|
| - _json["annotationSets"] = annotationSets.map((value) => (value).toJson()).toList();
|
| - }
|
| - if (nextPageToken != null) {
|
| - _json["nextPageToken"] = nextPageToken;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class SearchAnnotationsRequest {
|
| - /**
|
| - * The annotation sets to search within. The caller must have READ access to
|
| - * these annotation sets. Required. All queried annotation sets must have the
|
| - * same type.
|
| - */
|
| - core.List<core.String> annotationSetIds;
|
| - /**
|
| - * Specifies number of results to return in a single page. If unspecified, it
|
| - * will default to 256. The maximum value is 2048.
|
| - */
|
| - core.int pageSize;
|
| - /**
|
| - * The continuation token, which is used to page through large result sets. To
|
| - * get the next page of results, set this parameter to the value of
|
| - * nextPageToken from the previous response.
|
| - */
|
| - core.String pageToken;
|
| - /**
|
| - * If specified, this query matches only annotations that overlap this range.
|
| - */
|
| - QueryRange range;
|
| -
|
| - SearchAnnotationsRequest();
|
| -
|
| - SearchAnnotationsRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("annotationSetIds")) {
|
| - annotationSetIds = _json["annotationSetIds"];
|
| - }
|
| - if (_json.containsKey("pageSize")) {
|
| - pageSize = _json["pageSize"];
|
| - }
|
| - if (_json.containsKey("pageToken")) {
|
| - pageToken = _json["pageToken"];
|
| - }
|
| - if (_json.containsKey("range")) {
|
| - range = new QueryRange.fromJson(_json["range"]);
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (annotationSetIds != null) {
|
| - _json["annotationSetIds"] = annotationSetIds;
|
| - }
|
| - if (pageSize != null) {
|
| - _json["pageSize"] = pageSize;
|
| - }
|
| - if (pageToken != null) {
|
| - _json["pageToken"] = pageToken;
|
| - }
|
| - if (range != null) {
|
| - _json["range"] = (range).toJson();
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class SearchAnnotationsResponse {
|
| - /** The matching annotations. */
|
| - core.List<Annotation> annotations;
|
| - /**
|
| - * The continuation token, which is used to page through large result sets.
|
| - * Provide this value in a subsequent request to return the next page of
|
| - * results. This field will be empty if there aren't any additional results.
|
| - */
|
| - core.String nextPageToken;
|
| -
|
| - SearchAnnotationsResponse();
|
| -
|
| - SearchAnnotationsResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("annotations")) {
|
| - annotations = _json["annotations"].map((value) => new Annotation.fromJson(value)).toList();
|
| - }
|
| - if (_json.containsKey("nextPageToken")) {
|
| - nextPageToken = _json["nextPageToken"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (annotations != null) {
|
| - _json["annotations"] = annotations.map((value) => (value).toJson()).toList();
|
| - }
|
| - if (nextPageToken != null) {
|
| - _json["nextPageToken"] = nextPageToken;
|
| + if (sourceUri != null) {
|
| + _json["sourceUri"] = sourceUri;
|
| }
|
| return _json;
|
| }
|
| @@ -5862,7 +3769,7 @@ class SearchCallSetsRequest {
|
| /**
|
| * The continuation token, which is used to page through large result sets. To
|
| * get the next page of results, set this parameter to the value of
|
| - * nextPageToken from the previous response.
|
| + * `nextPageToken` from the previous response.
|
| */
|
| core.String pageToken;
|
| /**
|
| @@ -5907,133 +3814,21 @@ class SearchCallSetsRequest {
|
| }
|
|
|
| /** The call set search response. */
|
| -class SearchCallSetsResponse {
|
| - /** The list of matching call sets. */
|
| - core.List<CallSet> callSets;
|
| - /**
|
| - * The continuation token, which is used to page through large result sets.
|
| - * Provide this value in a subsequent request to return the next page of
|
| - * results. This field will be empty if there aren't any additional results.
|
| - */
|
| - core.String nextPageToken;
|
| -
|
| - SearchCallSetsResponse();
|
| -
|
| - SearchCallSetsResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("callSets")) {
|
| - callSets = _json["callSets"].map((value) => new CallSet.fromJson(value)).toList();
|
| - }
|
| - if (_json.containsKey("nextPageToken")) {
|
| - nextPageToken = _json["nextPageToken"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (callSets != null) {
|
| - _json["callSets"] = callSets.map((value) => (value).toJson()).toList();
|
| - }
|
| - if (nextPageToken != null) {
|
| - _json["nextPageToken"] = nextPageToken;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** The jobs search request. */
|
| -class SearchJobsRequest {
|
| - /**
|
| - * If specified, only jobs created on or after this date, given in
|
| - * milliseconds since Unix epoch, will be returned.
|
| - */
|
| - core.String createdAfter;
|
| - /**
|
| - * If specified, only jobs created prior to this date, given in milliseconds
|
| - * since Unix epoch, will be returned.
|
| - */
|
| - core.String createdBefore;
|
| - /**
|
| - * Specifies the number of results to return in a single page. Defaults to
|
| - * 128. The maximum value is 256.
|
| - */
|
| - core.int pageSize;
|
| - /**
|
| - * The continuation token which is used to page through large result sets. To
|
| - * get the next page of results, set this parameter to the value of the
|
| - * nextPageToken from the previous response.
|
| - */
|
| - core.String pageToken;
|
| - /**
|
| - * Required. Only return jobs which belong to this Google Developers Console
|
| - * project.
|
| - */
|
| - core.String projectNumber;
|
| - /** Only return jobs which have a matching status. */
|
| - core.List<core.String> status;
|
| -
|
| - SearchJobsRequest();
|
| -
|
| - SearchJobsRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("createdAfter")) {
|
| - createdAfter = _json["createdAfter"];
|
| - }
|
| - if (_json.containsKey("createdBefore")) {
|
| - createdBefore = _json["createdBefore"];
|
| - }
|
| - if (_json.containsKey("pageSize")) {
|
| - pageSize = _json["pageSize"];
|
| - }
|
| - if (_json.containsKey("pageToken")) {
|
| - pageToken = _json["pageToken"];
|
| - }
|
| - if (_json.containsKey("projectNumber")) {
|
| - projectNumber = _json["projectNumber"];
|
| - }
|
| - if (_json.containsKey("status")) {
|
| - status = _json["status"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (createdAfter != null) {
|
| - _json["createdAfter"] = createdAfter;
|
| - }
|
| - if (createdBefore != null) {
|
| - _json["createdBefore"] = createdBefore;
|
| - }
|
| - if (pageSize != null) {
|
| - _json["pageSize"] = pageSize;
|
| - }
|
| - if (pageToken != null) {
|
| - _json["pageToken"] = pageToken;
|
| - }
|
| - if (projectNumber != null) {
|
| - _json["projectNumber"] = projectNumber;
|
| - }
|
| - if (status != null) {
|
| - _json["status"] = status;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** The job search response. */
|
| -class SearchJobsResponse {
|
| - /** The list of jobs results, ordered newest to oldest. */
|
| - core.List<Job> jobs;
|
| +class SearchCallSetsResponse {
|
| + /** The list of matching call sets. */
|
| + core.List<CallSet> callSets;
|
| /**
|
| - * The continuation token which is used to page through large result sets.
|
| - * Provide this value is a subsequent request to return the next page of
|
| - * results. This field will be empty if there are no more results.
|
| + * The continuation token, which is used to page through large result sets.
|
| + * Provide this value in a subsequent request to return the next page of
|
| + * results. This field will be empty if there aren't any additional results.
|
| */
|
| core.String nextPageToken;
|
|
|
| - SearchJobsResponse();
|
| + SearchCallSetsResponse();
|
|
|
| - SearchJobsResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("jobs")) {
|
| - jobs = _json["jobs"].map((value) => new Job.fromJson(value)).toList();
|
| + SearchCallSetsResponse.fromJson(core.Map _json) {
|
| + if (_json.containsKey("callSets")) {
|
| + callSets = _json["callSets"].map((value) => new CallSet.fromJson(value)).toList();
|
| }
|
| if (_json.containsKey("nextPageToken")) {
|
| nextPageToken = _json["nextPageToken"];
|
| @@ -6042,8 +3837,8 @@ class SearchJobsResponse {
|
|
|
| core.Map toJson() {
|
| var _json = new core.Map();
|
| - if (jobs != null) {
|
| - _json["jobs"] = jobs.map((value) => (value).toJson()).toList();
|
| + if (callSets != null) {
|
| + _json["callSets"] = callSets.map((value) => (value).toJson()).toList();
|
| }
|
| if (nextPageToken != null) {
|
| _json["nextPageToken"] = nextPageToken;
|
| @@ -6072,7 +3867,7 @@ class SearchReadGroupSetsRequest {
|
| /**
|
| * The continuation token, which is used to page through large result sets. To
|
| * get the next page of results, set this parameter to the value of
|
| - * nextPageToken from the previous response.
|
| + * `nextPageToken` from the previous response.
|
| */
|
| core.String pageToken;
|
|
|
| @@ -6149,7 +3944,7 @@ class SearchReadGroupSetsResponse {
|
| class SearchReadsRequest {
|
| /**
|
| * The end position of the range on the reference, 0-based exclusive. If
|
| - * specified, referenceName must also be specified.
|
| + * specified, `referenceName` must also be specified.
|
| */
|
| core.String end;
|
| /**
|
| @@ -6160,30 +3955,30 @@ class SearchReadsRequest {
|
| /**
|
| * The continuation token, which is used to page through large result sets. To
|
| * get the next page of results, set this parameter to the value of
|
| - * nextPageToken from the previous response.
|
| + * `nextPageToken` from the previous response.
|
| */
|
| core.String pageToken;
|
| /**
|
| * The IDs of the read groups within which to search for reads. All specified
|
| * read groups must belong to the same read group sets. Must specify one of
|
| - * readGroupSetIds or readGroupIds.
|
| + * `readGroupSetIds` or `readGroupIds`.
|
| */
|
| core.List<core.String> readGroupIds;
|
| /**
|
| * The IDs of the read groups sets within which to search for reads. All
|
| * specified read group sets must be aligned against a common set of reference
|
| * sequences; this defines the genomic coordinates for the query. Must specify
|
| - * one of readGroupSetIds or readGroupIds.
|
| + * one of `readGroupSetIds` or `readGroupIds`.
|
| */
|
| core.List<core.String> readGroupSetIds;
|
| /**
|
| - * The reference sequence name, for example chr1, 1, or chrX. If set to *,
|
| - * only unmapped reads are returned.
|
| + * The reference sequence name, for example `chr1`, `1`, or `chrX`. If set to
|
| + * *, only unmapped reads are returned.
|
| */
|
| core.String referenceName;
|
| /**
|
| * The start position of the range on the reference, 0-based inclusive. If
|
| - * specified, referenceName must also be specified.
|
| + * specified, `referenceName` must also be specified.
|
| */
|
| core.String start;
|
|
|
| @@ -6245,7 +4040,7 @@ class SearchReadsResponse {
|
| /**
|
| * The list of matching alignments sorted by mapped genomic coordinate, if
|
| * any, ascending in position within the same reference. Unmapped reads, which
|
| - * have no position, are returned last and are further sorted in ascending
|
| + * have no position, are returned contiguously and are sorted in ascending
|
| * lexicographic order by fragment name.
|
| */
|
| core.List<Read> alignments;
|
| @@ -6282,20 +4077,20 @@ class SearchReadsResponse {
|
| class SearchReferenceSetsRequest {
|
| /**
|
| * If present, return references for which the accession matches any of these
|
| - * strings. Best to give a version number, for example GCF_000001405.26. If
|
| + * strings. Best to give a version number, for example `GCF_000001405.26`. If
|
| * only the main accession number is given then all records with that main
|
| * accession will be returned, whichever version. Note that different versions
|
| * will have different sequences.
|
| */
|
| core.List<core.String> accessions;
|
| /**
|
| - * If present, return reference sets for which a substring of their assemblyId
|
| - * matches this string (case insensitive).
|
| + * If present, return reference sets for which a substring of their
|
| + * `assemblyId` matches this string (case insensitive).
|
| */
|
| core.String assemblyId;
|
| /**
|
| - * If present, return references for which the md5checksum matches. See
|
| - * ReferenceSet.md5checksum for details.
|
| + * If present, return references for which the `md5checksum` matches. See
|
| + * `ReferenceSet.md5checksum` for details.
|
| */
|
| core.List<core.String> md5checksums;
|
| /** Specifies the maximum number of results to return in a single page. */
|
| @@ -6303,7 +4098,7 @@ class SearchReferenceSetsRequest {
|
| /**
|
| * The continuation token, which is used to page through large result sets. To
|
| * get the next page of results, set this parameter to the value of
|
| - * nextPageToken from the previous response.
|
| + * `nextPageToken` from the previous response.
|
| */
|
| core.String pageToken;
|
|
|
| @@ -6384,15 +4179,15 @@ class SearchReferenceSetsResponse {
|
| class SearchReferencesRequest {
|
| /**
|
| * If present, return references for which the accession matches this string.
|
| - * Best to give a version number, for example GCF_000001405.26. If only the
|
| + * Best to give a version number, for example `GCF_000001405.26`. If only the
|
| * main accession number is given then all records with that main accession
|
| * will be returned, whichever version. Note that different versions will have
|
| * different sequences.
|
| */
|
| core.List<core.String> accessions;
|
| /**
|
| - * If present, return references for which the md5checksum matches. See
|
| - * Reference.md5checksum for construction details.
|
| + * If present, return references for which the `md5checksum` matches. See
|
| + * `Reference.md5checksum` for construction details.
|
| */
|
| core.List<core.String> md5checksums;
|
| /** Specifies the maximum number of results to return in a single page. */
|
| @@ -6400,7 +4195,7 @@ class SearchReferencesRequest {
|
| /**
|
| * The continuation token, which is used to page through large result sets. To
|
| * get the next page of results, set this parameter to the value of
|
| - * nextPageToken from the previous response.
|
| + * `nextPageToken` from the previous response.
|
| */
|
| core.String pageToken;
|
| /** If present, return only references which belong to this reference set. */
|
| @@ -6492,7 +4287,7 @@ class SearchVariantSetsRequest {
|
| /**
|
| * The continuation token, which is used to page through large result sets. To
|
| * get the next page of results, set this parameter to the value of
|
| - * nextPageToken from the previous response.
|
| + * `nextPageToken` from the previous response.
|
| */
|
| core.String pageToken;
|
|
|
| @@ -6586,7 +4381,7 @@ class SearchVariantsRequest {
|
| /**
|
| * The continuation token, which is used to page through large result sets. To
|
| * get the next page of results, set this parameter to the value of
|
| - * nextPageToken from the previous response.
|
| + * `nextPageToken` from the previous response.
|
| */
|
| core.String pageToken;
|
| /** Required. Only return variants in this reference sequence. */
|
| @@ -6705,164 +4500,100 @@ class SearchVariantsResponse {
|
| }
|
|
|
| /**
|
| - * A transcript represents the assertion that a particular region of the
|
| - * reference genome may be transcribed as RNA.
|
| + * The `Status` type defines a logical error model that is suitable for
|
| + * different programming environments, including REST APIs and RPC APIs. It is
|
| + * used by [gRPC](https://github.com/grpc). The error model is designed to be: -
|
| + * Simple to use and understand for most users - Flexible enough to meet
|
| + * unexpected needs # Overview The `Status` message contains three pieces of
|
| + * data: error code, error message, and error details. The error code should be
|
| + * an enum value of [google.rpc.Code][google.rpc.Code], but it may accept
|
| + * additional error codes if needed. The error message should be a
|
| + * developer-facing English message that helps developers *understand* and
|
| + * *resolve* the error. If a localized user-facing error message is needed, put
|
| + * the localized message in the error details or localize it in the client. The
|
| + * optional error details may contain arbitrary information about the error.
|
| + * There is a predefined set of error detail types in the package `google.rpc`
|
| + * which can be used for common error conditions. # Language mapping The
|
| + * `Status` message is the logical representation of the error model, but it is
|
| + * not necessarily the actual wire format. When the `Status` message is exposed
|
| + * in different client libraries and different wire protocols, it can be mapped
|
| + * differently. For example, it will likely be mapped to some exceptions in
|
| + * Java, but more likely mapped to some error codes in C. # Other uses The error
|
| + * model and the `Status` message can be used in a variety of environments,
|
| + * either with or without APIs, to provide a consistent developer experience
|
| + * across different environments. Example uses of this error model include: -
|
| + * Partial errors. If a service needs to return partial errors to the client, it
|
| + * may embed the `Status` in the normal response to indicate the partial errors.
|
| + * - Workflow errors. A typical workflow has multiple steps. Each step may have
|
| + * a `Status` message for error reporting purpose. - Batch operations. If a
|
| + * client uses batch request and batch response, the `Status` message should be
|
| + * used directly inside batch response, one for each error sub-response. -
|
| + * Asynchronous operations. If an API call embeds asynchronous operation results
|
| + * in its response, the status of those operations should be represented
|
| + * directly using the `Status` message. - Logging. If some API errors are stored
|
| + * in logs, the message `Status` could be used directly after any stripping
|
| + * needed for security/privacy reasons.
|
| */
|
| -class Transcript {
|
| +class Status {
|
| /**
|
| - * The range of the coding sequence for this transcript, if any. To determine
|
| - * the exact ranges of coding sequence, intersect this range with those of the
|
| - * exons, if any. If there are any exons, the codingSequence must start and
|
| - * end within them.
|
| - *
|
| - * Note that in some cases, the reference genome will not exactly match the
|
| - * observed mRNA transcript e.g. due to variance in the source genome from
|
| - * reference. In these cases, exon.frame will not necessarily match the
|
| - * expected reference reading frame and coding exon reference bases cannot
|
| - * necessarily be concatenated to produce the original transcript mRNA.
|
| + * The status code, which should be an enum value of
|
| + * [google.rpc.Code][google.rpc.Code].
|
| */
|
| - TranscriptCodingSequence codingSequence;
|
| + core.int code;
|
| /**
|
| - * The exons that compose this transcript. This field should be unset for
|
| - * genomes where transcript splicing does not occur, for example prokaryotes.
|
| - *
|
| - *
|
| - * Introns are regions of the transcript that are not included in the spliced
|
| - * RNA product. Though not explicitly modeled here, intron ranges can be
|
| - * deduced; all regions of this transcript that are not exons are introns.
|
| + * A list of messages that carry the error details. There will be a common set
|
| + * of message types for APIs to use.
|
| *
|
| - *
|
| - * Exonic sequences do not necessarily code for a translational product (amino
|
| - * acids). Only the regions of exons bounded by the codingSequence correspond
|
| - * to coding DNA sequence.
|
| - *
|
| - *
|
| - * Exons are ordered by start position and may not overlap.
|
| + * The values for Object must be JSON objects. It can consist of `num`,
|
| + * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| */
|
| - core.List<TranscriptExon> exons;
|
| + core.List<core.Map<core.String, core.Object>> details;
|
| /**
|
| - * The annotation ID of the gene from which this transcript is transcribed.
|
| + * A developer-facing error message, which should be in English. Any
|
| + * user-facing error message should be localized and sent in the
|
| + * [google.rpc.Status.details][google.rpc.Status.details] field, or localized
|
| + * by the client.
|
| */
|
| - core.String geneId;
|
| + core.String message;
|
|
|
| - Transcript();
|
| + Status();
|
|
|
| - Transcript.fromJson(core.Map _json) {
|
| - if (_json.containsKey("codingSequence")) {
|
| - codingSequence = new TranscriptCodingSequence.fromJson(_json["codingSequence"]);
|
| + Status.fromJson(core.Map _json) {
|
| + if (_json.containsKey("code")) {
|
| + code = _json["code"];
|
| }
|
| - if (_json.containsKey("exons")) {
|
| - exons = _json["exons"].map((value) => new TranscriptExon.fromJson(value)).toList();
|
| + if (_json.containsKey("details")) {
|
| + details = _json["details"];
|
| }
|
| - if (_json.containsKey("geneId")) {
|
| - geneId = _json["geneId"];
|
| + if (_json.containsKey("message")) {
|
| + message = _json["message"];
|
| }
|
| }
|
|
|
| core.Map toJson() {
|
| var _json = new core.Map();
|
| - if (codingSequence != null) {
|
| - _json["codingSequence"] = (codingSequence).toJson();
|
| - }
|
| - if (exons != null) {
|
| - _json["exons"] = exons.map((value) => (value).toJson()).toList();
|
| - }
|
| - if (geneId != null) {
|
| - _json["geneId"] = geneId;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class TranscriptCodingSequence {
|
| - /**
|
| - * The end of the coding sequence on this annotation's reference sequence,
|
| - * 0-based exclusive. Note that this position is relative to the reference
|
| - * start, and not the containing annotation start.
|
| - */
|
| - core.String end;
|
| - /**
|
| - * The start of the coding sequence on this annotation's reference sequence,
|
| - * 0-based inclusive. Note that this position is relative to the reference
|
| - * start, and not the containing annotation start.
|
| - */
|
| - core.String start;
|
| -
|
| - TranscriptCodingSequence();
|
| -
|
| - TranscriptCodingSequence.fromJson(core.Map _json) {
|
| - if (_json.containsKey("end")) {
|
| - end = _json["end"];
|
| - }
|
| - if (_json.containsKey("start")) {
|
| - start = _json["start"];
|
| + if (code != null) {
|
| + _json["code"] = code;
|
| }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (end != null) {
|
| - _json["end"] = end;
|
| + if (details != null) {
|
| + _json["details"] = details;
|
| }
|
| - if (start != null) {
|
| - _json["start"] = start;
|
| + if (message != null) {
|
| + _json["message"] = message;
|
| }
|
| return _json;
|
| }
|
| }
|
|
|
| -class TranscriptExon {
|
| - /**
|
| - * The end position of the exon on this annotation's reference sequence,
|
| - * 0-based exclusive. Note that this is relative to the reference start, and
|
| - * not the containing annotation start.
|
| - */
|
| - core.String end;
|
| - /**
|
| - * The frame of this exon. Contains a value of 0, 1, or 2, which indicates the
|
| - * offset of the first coding base of the exon within the reading frame of the
|
| - * coding DNA sequence, if any. This field is dependent on the strandedness of
|
| - * this annotation (see Annotation.position.reverseStrand). For forward
|
| - * stranded annotations, this offset is relative to the exon.start. For
|
| - * reverse strand annotations, this offset is relative to the exon.end-1.
|
| - *
|
| - * Unset if this exon does not intersect the coding sequence. Upon creation of
|
| - * a transcript, the frame must be populated for all or none of the coding
|
| - * exons.
|
| - */
|
| - Int32Value frame;
|
| - /**
|
| - * The start position of the exon on this annotation's reference sequence,
|
| - * 0-based inclusive. Note that this is relative to the reference start, and
|
| - * not the containing annotation start.
|
| - */
|
| - core.String start;
|
| +class UndeleteDatasetRequest {
|
|
|
| - TranscriptExon();
|
| + UndeleteDatasetRequest();
|
|
|
| - TranscriptExon.fromJson(core.Map _json) {
|
| - if (_json.containsKey("end")) {
|
| - end = _json["end"];
|
| - }
|
| - if (_json.containsKey("frame")) {
|
| - frame = new Int32Value.fromJson(_json["frame"]);
|
| - }
|
| - if (_json.containsKey("start")) {
|
| - start = _json["start"];
|
| - }
|
| + UndeleteDatasetRequest.fromJson(core.Map _json) {
|
| }
|
|
|
| core.Map toJson() {
|
| var _json = new core.Map();
|
| - if (end != null) {
|
| - _json["end"] = end;
|
| - }
|
| - if (frame != null) {
|
| - _json["frame"] = (frame).toJson();
|
| - }
|
| - if (start != null) {
|
| - _json["start"] = start;
|
| - }
|
| return _json;
|
| }
|
| }
|
| @@ -6883,7 +4614,7 @@ class Variant {
|
| * The variant calls for this particular variant. Each one represents the
|
| * determination of genotype with respect to this variant.
|
| */
|
| - core.List<Call> calls;
|
| + core.List<VariantCall> calls;
|
| /** The date this variant was created, in milliseconds from the epoch. */
|
| core.String created;
|
| /**
|
| @@ -6894,14 +4625,20 @@ class Variant {
|
| */
|
| core.String end;
|
| /**
|
| - * A list of filters (normally quality filters) this variant has failed. PASS
|
| - * indicates this variant has passed all filters.
|
| + * A list of filters (normally quality filters) this variant has failed.
|
| + * `PASS` indicates this variant has passed all filters.
|
| */
|
| core.List<core.String> filter;
|
| - /** The Google generated ID of the variant, immutable. */
|
| + /** The server-generated variant ID, unique across all variants. */
|
| core.String id;
|
| - /** A string which maps to an array of values. */
|
| - core.Map<core.String, core.List<core.String>> info;
|
| + /**
|
| + * A map of additional variant information. This must be of the form map
|
| + * (string key mapping to a list of string values).
|
| + *
|
| + * The values for Object must be JSON objects. It can consist of `num`,
|
| + * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| + */
|
| + core.Map<core.String, core.List<core.Object>> info;
|
| /** Names for the variant, for example a RefSNP ID. */
|
| core.List<core.String> names;
|
| /**
|
| @@ -6913,7 +4650,7 @@ class Variant {
|
| * The reference bases for this variant. They start at the given position.
|
| */
|
| core.String referenceBases;
|
| - /** The reference on which this variant occurs. (such as chr20 or X) */
|
| + /** The reference on which this variant occurs. (such as `chr20` or `X`) */
|
| core.String referenceName;
|
| /**
|
| * The position at which this variant occurs (0-based). This corresponds to
|
| @@ -6930,7 +4667,7 @@ class Variant {
|
| alternateBases = _json["alternateBases"];
|
| }
|
| if (_json.containsKey("calls")) {
|
| - calls = _json["calls"].map((value) => new Call.fromJson(value)).toList();
|
| + calls = _json["calls"].map((value) => new VariantCall.fromJson(value)).toList();
|
| }
|
| if (_json.containsKey("created")) {
|
| created = _json["created"];
|
| @@ -7012,176 +4749,96 @@ class Variant {
|
| }
|
| }
|
|
|
| -/** A Variant annotation. */
|
| -class VariantAnnotation {
|
| - /**
|
| - * The alternate allele for this variant. If multiple alternate alleles exist
|
| - * at this location, create a separate variant for each one, as they may
|
| - * represent distinct conditions.
|
| - */
|
| - core.String alternateBases;
|
| +/**
|
| + * A call represents the determination of genotype with respect to a particular
|
| + * variant. It may include associated information such as quality and phasing.
|
| + * For example, a call might assign a probability of 0.32 to the occurrence of a
|
| + * SNP named rs1234 in a call set with the name NA12345.
|
| + */
|
| +class VariantCall {
|
| + /** The ID of the call set this variant call belongs to. */
|
| + core.String callSetId;
|
| + /** The name of the call set this variant call belongs to. */
|
| + core.String callSetName;
|
| /**
|
| - * Describes the clinical significance of a variant. It is adapted from the
|
| - * ClinVar controlled vocabulary for clinical significance described at:
|
| - * http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
|
| - * Possible string values are:
|
| - * - "ASSOCIATION"
|
| - * - "BENIGN"
|
| - * - "CLINICAL_SIGNIFICANCE_UNSPECIFIED"
|
| - * - "CONFERS_SENSITIVITY"
|
| - * - "DRUG_RESPONSE"
|
| - * - "HISTOCOMPATIBILITY"
|
| - * - "LIKELY_BENIGN"
|
| - * - "LIKELY_PATHOGENIC"
|
| - * - "MULTIPLE_REPORTED"
|
| - * - "OTHER"
|
| - * - "PATHOGENIC"
|
| - * - "PROTECTIVE"
|
| - * - "RISK_FACTOR"
|
| - * - "UNCERTAIN"
|
| - */
|
| - core.String clinicalSignificance;
|
| - /**
|
| - * The set of conditions associated with this variant. A condition describes
|
| - * the way a variant influences human health.
|
| - */
|
| - core.List<VariantAnnotationCondition> conditions;
|
| - /**
|
| - * Effect of the variant on the coding sequence.
|
| - * Possible string values are:
|
| - * - "EFFECT_UNSPECIFIED"
|
| - * - "FRAMESHIFT"
|
| - * - "FRAME_PRESERVING_INDEL"
|
| - * - "NONSYNONYMOUS_SNP"
|
| - * - "OTHER"
|
| - * - "SPLICE_SITE_DISRUPTION"
|
| - * - "STOP_GAIN"
|
| - * - "STOP_LOSS"
|
| - * - "SYNONYMOUS_SNP"
|
| + * The genotype of this variant call. Each value represents either the value
|
| + * of the `referenceBases` field or a 1-based index into `alternateBases`. If
|
| + * a variant had a `referenceBases` value of `T` and an `alternateBases` value
|
| + * of `["A", "C"]`, and the `genotype` was `[2, 1]`, that would mean the call
|
| + * represented the heterozygous value `CA` for this variant. If the `genotype`
|
| + * was instead `[0, 1]`, the represented value would be `TA`. Ordering of the
|
| + * genotype values is important if the `phaseset` is present. If a genotype is
|
| + * not called (that is, a `.` is present in the GT string) -1 is returned.
|
| */
|
| - core.String effect;
|
| + core.List<core.int> genotype;
|
| /**
|
| - * Google annotation ID of the gene affected by this variant. This should be
|
| - * provided when the variant is created.
|
| + * The genotype likelihoods for this variant call. Each array entry represents
|
| + * how likely a specific genotype is for this call. The value ordering is
|
| + * defined by the GL tag in the VCF spec. If Phred-scaled genotype likelihood
|
| + * scores (PL) are available and log10(P) genotype likelihood scores (GL) are
|
| + * not, PL scores are converted to GL scores. If both are available, PL scores
|
| + * are stored in `info`.
|
| */
|
| - core.String geneId;
|
| + core.List<core.double> genotypeLikelihood;
|
| /**
|
| - * Google annotation IDs of the transcripts affected by this variant. These
|
| - * should be provided when the variant is created.
|
| + * A map of additional variant call information. This must be of the form map
|
| + * (string key mapping to a list of string values).
|
| + *
|
| + * The values for Object must be JSON objects. It can consist of `num`,
|
| + * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| */
|
| - core.List<core.String> transcriptIds;
|
| + core.Map<core.String, core.List<core.Object>> info;
|
| /**
|
| - * Type has been adapted from ClinVar's list of variant types.
|
| - * Possible string values are:
|
| - * - "CNV"
|
| - * - "DELETION"
|
| - * - "INSERTION"
|
| - * - "OTHER"
|
| - * - "SNP"
|
| - * - "STRUCTURAL"
|
| - * - "SUBSTITUTION"
|
| - * - "TYPE_UNSPECIFIED"
|
| + * If this field is present, this variant call's genotype ordering implies the
|
| + * phase of the bases and is consistent with any other variant calls in the
|
| + * same reference sequence which have the same phaseset value. When importing
|
| + * data from VCF, if the genotype data was phased but no phase set was
|
| + * specified this field will be set to `*`.
|
| */
|
| - core.String type;
|
| + core.String phaseset;
|
|
|
| - VariantAnnotation();
|
| + VariantCall();
|
|
|
| - VariantAnnotation.fromJson(core.Map _json) {
|
| - if (_json.containsKey("alternateBases")) {
|
| - alternateBases = _json["alternateBases"];
|
| - }
|
| - if (_json.containsKey("clinicalSignificance")) {
|
| - clinicalSignificance = _json["clinicalSignificance"];
|
| + VariantCall.fromJson(core.Map _json) {
|
| + if (_json.containsKey("callSetId")) {
|
| + callSetId = _json["callSetId"];
|
| }
|
| - if (_json.containsKey("conditions")) {
|
| - conditions = _json["conditions"].map((value) => new VariantAnnotationCondition.fromJson(value)).toList();
|
| + if (_json.containsKey("callSetName")) {
|
| + callSetName = _json["callSetName"];
|
| }
|
| - if (_json.containsKey("effect")) {
|
| - effect = _json["effect"];
|
| + if (_json.containsKey("genotype")) {
|
| + genotype = _json["genotype"];
|
| }
|
| - if (_json.containsKey("geneId")) {
|
| - geneId = _json["geneId"];
|
| + if (_json.containsKey("genotypeLikelihood")) {
|
| + genotypeLikelihood = _json["genotypeLikelihood"];
|
| }
|
| - if (_json.containsKey("transcriptIds")) {
|
| - transcriptIds = _json["transcriptIds"];
|
| + if (_json.containsKey("info")) {
|
| + info = _json["info"];
|
| }
|
| - if (_json.containsKey("type")) {
|
| - type = _json["type"];
|
| + if (_json.containsKey("phaseset")) {
|
| + phaseset = _json["phaseset"];
|
| }
|
| }
|
|
|
| core.Map toJson() {
|
| var _json = new core.Map();
|
| - if (alternateBases != null) {
|
| - _json["alternateBases"] = alternateBases;
|
| - }
|
| - if (clinicalSignificance != null) {
|
| - _json["clinicalSignificance"] = clinicalSignificance;
|
| - }
|
| - if (conditions != null) {
|
| - _json["conditions"] = conditions.map((value) => (value).toJson()).toList();
|
| - }
|
| - if (effect != null) {
|
| - _json["effect"] = effect;
|
| - }
|
| - if (geneId != null) {
|
| - _json["geneId"] = geneId;
|
| - }
|
| - if (transcriptIds != null) {
|
| - _json["transcriptIds"] = transcriptIds;
|
| - }
|
| - if (type != null) {
|
| - _json["type"] = type;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class VariantAnnotationCondition {
|
| - /**
|
| - * The MedGen concept id associated with this gene. Search for these IDs at
|
| - * http://www.ncbi.nlm.nih.gov/medgen/
|
| - */
|
| - core.String conceptId;
|
| - /** The set of external IDs for this condition. */
|
| - core.List<ExternalId> externalIds;
|
| - /** A set of names for the condition. */
|
| - core.List<core.String> names;
|
| - /**
|
| - * The OMIM id for this condition. Search for these IDs at http://omim.org/
|
| - */
|
| - core.String omimId;
|
| -
|
| - VariantAnnotationCondition();
|
| -
|
| - VariantAnnotationCondition.fromJson(core.Map _json) {
|
| - if (_json.containsKey("conceptId")) {
|
| - conceptId = _json["conceptId"];
|
| - }
|
| - if (_json.containsKey("externalIds")) {
|
| - externalIds = _json["externalIds"].map((value) => new ExternalId.fromJson(value)).toList();
|
| - }
|
| - if (_json.containsKey("names")) {
|
| - names = _json["names"];
|
| + if (callSetId != null) {
|
| + _json["callSetId"] = callSetId;
|
| }
|
| - if (_json.containsKey("omimId")) {
|
| - omimId = _json["omimId"];
|
| + if (callSetName != null) {
|
| + _json["callSetName"] = callSetName;
|
| }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (conceptId != null) {
|
| - _json["conceptId"] = conceptId;
|
| + if (genotype != null) {
|
| + _json["genotype"] = genotype;
|
| }
|
| - if (externalIds != null) {
|
| - _json["externalIds"] = externalIds.map((value) => (value).toJson()).toList();
|
| + if (genotypeLikelihood != null) {
|
| + _json["genotypeLikelihood"] = genotypeLikelihood;
|
| }
|
| - if (names != null) {
|
| - _json["names"] = names;
|
| + if (info != null) {
|
| + _json["info"] = info;
|
| }
|
| - if (omimId != null) {
|
| - _json["omimId"] = omimId;
|
| + if (phaseset != null) {
|
| + _json["phaseset"] = phaseset;
|
| }
|
| return _json;
|
| }
|
| @@ -7192,12 +4849,12 @@ class VariantAnnotationCondition {
|
| * statistics of those contents. A variant set belongs to a dataset.
|
| */
|
| class VariantSet {
|
| - /** The dataset to which this variant set belongs. Immutable. */
|
| + /** The dataset to which this variant set belongs. */
|
| core.String datasetId;
|
| - /** The Google-generated ID of the variant set. Immutable. */
|
| + /** The server-generated variant set ID, unique across all variant sets. */
|
| core.String id;
|
| /** The metadata associated with this variant set. */
|
| - core.List<Metadata> metadata;
|
| + core.List<VariantSetMetadata> metadata;
|
| /**
|
| * A list of all references used by the variants in a variant set with
|
| * associated coordinate upper bounds for each one.
|
| @@ -7214,7 +4871,7 @@ class VariantSet {
|
| id = _json["id"];
|
| }
|
| if (_json.containsKey("metadata")) {
|
| - metadata = _json["metadata"].map((value) => new Metadata.fromJson(value)).toList();
|
| + metadata = _json["metadata"].map((value) => new VariantSetMetadata.fromJson(value)).toList();
|
| }
|
| if (_json.containsKey("referenceBounds")) {
|
| referenceBounds = _json["referenceBounds"].map((value) => new ReferenceBound.fromJson(value)).toList();
|
| @@ -7238,3 +4895,100 @@ class VariantSet {
|
| return _json;
|
| }
|
| }
|
| +
|
| +/**
|
| + * Metadata describes a single piece of variant call metadata. These data
|
| + * include a top level key and either a single value string (value) or a list of
|
| + * key-value pairs (info.) Value and info are mutually exclusive.
|
| + */
|
| +class VariantSetMetadata {
|
| + /** A textual description of this metadata. */
|
| + core.String description;
|
| + /**
|
| + * User-provided ID field, not enforced by this API. Two or more pieces of
|
| + * structured metadata with identical id and key fields are considered
|
| + * equivalent.
|
| + */
|
| + core.String id;
|
| + /**
|
| + * Remaining structured metadata key-value pairs. This must be of the form map
|
| + * (string key mapping to a list of string values).
|
| + *
|
| + * The values for Object must be JSON objects. It can consist of `num`,
|
| + * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| + */
|
| + core.Map<core.String, core.List<core.Object>> info;
|
| + /** The top-level key. */
|
| + core.String key;
|
| + /**
|
| + * The number of values that can be included in a field described by this
|
| + * metadata.
|
| + */
|
| + core.String number;
|
| + /**
|
| + * The type of data. Possible types include: Integer, Float, Flag, Character,
|
| + * and String.
|
| + * Possible string values are:
|
| + * - "TYPE_UNSPECIFIED" : A TYPE_UNSPECIFIED.
|
| + * - "INTEGER" : A INTEGER.
|
| + * - "FLOAT" : A FLOAT.
|
| + * - "FLAG" : A FLAG.
|
| + * - "CHARACTER" : A CHARACTER.
|
| + * - "STRING" : A STRING.
|
| + */
|
| + core.String type;
|
| + /** The value field for simple metadata */
|
| + core.String value;
|
| +
|
| + VariantSetMetadata();
|
| +
|
| + VariantSetMetadata.fromJson(core.Map _json) {
|
| + if (_json.containsKey("description")) {
|
| + description = _json["description"];
|
| + }
|
| + if (_json.containsKey("id")) {
|
| + id = _json["id"];
|
| + }
|
| + if (_json.containsKey("info")) {
|
| + info = _json["info"];
|
| + }
|
| + if (_json.containsKey("key")) {
|
| + key = _json["key"];
|
| + }
|
| + if (_json.containsKey("number")) {
|
| + number = _json["number"];
|
| + }
|
| + if (_json.containsKey("type")) {
|
| + type = _json["type"];
|
| + }
|
| + if (_json.containsKey("value")) {
|
| + value = _json["value"];
|
| + }
|
| + }
|
| +
|
| + core.Map toJson() {
|
| + var _json = new core.Map();
|
| + if (description != null) {
|
| + _json["description"] = description;
|
| + }
|
| + if (id != null) {
|
| + _json["id"] = id;
|
| + }
|
| + if (info != null) {
|
| + _json["info"] = info;
|
| + }
|
| + if (key != null) {
|
| + _json["key"] = key;
|
| + }
|
| + if (number != null) {
|
| + _json["number"] = number;
|
| + }
|
| + if (type != null) {
|
| + _json["type"] = type;
|
| + }
|
| + if (value != null) {
|
| + _json["value"] = value;
|
| + }
|
| + return _json;
|
| + }
|
| +}
|
|
|
Chromium Code Reviews
Issue 1268013003:
Api-roll 21: 2015-08-04 (Closed)
Base URL: git@github.com:dart-lang/googleapis.git@master