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Diffstat (limited to 'third_party/googleapis/google/genomics/v1/annotations.proto')
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diff --git a/third_party/googleapis/google/genomics/v1/annotations.proto b/third_party/googleapis/google/genomics/v1/annotations.proto deleted file mode 100644 index dea5406..0000000 --- a/third_party/googleapis/google/genomics/v1/annotations.proto +++ /dev/null @@ -1,705 +0,0 @@ -// Copyright 2016 Google Inc. -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. - -syntax = "proto3"; - -package google.genomics.v1; - -import "google/api/annotations.proto"; -import "google/protobuf/empty.proto"; -import "google/protobuf/field_mask.proto"; -import "google/protobuf/struct.proto"; -import "google/protobuf/wrappers.proto"; -import "google/rpc/status.proto"; - -option cc_enable_arenas = true; -option go_package = "google.golang.org/genproto/googleapis/genomics/v1;genomics"; -option java_multiple_files = true; -option java_outer_classname = "AnnotationsProto"; -option java_package = "com.google.genomics.v1"; - -// This service provides storage and positional retrieval of genomic -// reference annotations, including variant annotations. -service AnnotationServiceV1 { - // Creates a new annotation set. Caller must have WRITE permission for the - // associated dataset. - // - // The following fields are required: - // - // * [datasetId][google.genomics.v1.AnnotationSet.dataset_id] - // * [referenceSetId][google.genomics.v1.AnnotationSet.reference_set_id] - // - // All other fields may be optionally specified, unless documented as being - // server-generated (for example, the `id` field). - rpc CreateAnnotationSet(CreateAnnotationSetRequest) returns (AnnotationSet) { - option (google.api.http) = { - post: "/v1/annotationsets" - body: "annotation_set" - }; - } - - // Gets an annotation set. Caller must have READ permission for - // the associated dataset. - rpc GetAnnotationSet(GetAnnotationSetRequest) returns (AnnotationSet) { - option (google.api.http) = { - get: "/v1/annotationsets/{annotation_set_id}" - }; - } - - // 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. - rpc UpdateAnnotationSet(UpdateAnnotationSetRequest) returns (AnnotationSet) { - option (google.api.http) = { - put: "/v1/annotationsets/{annotation_set_id}" - body: "annotation_set" - }; - } - - // Deletes an annotation set. Caller must have WRITE permission - // for the associated annotation set. - rpc DeleteAnnotationSet(DeleteAnnotationSetRequest) - returns (google.protobuf.Empty) { - option (google.api.http) = { - delete: "/v1/annotationsets/{annotation_set_id}" - }; - } - - // Searches for annotation sets that match the given criteria. Annotation sets - // are returned in an unspecified order. This order is consistent, such that - // two queries for the same content (regardless of page size) yield annotation - // sets in the same order across their respective streams of paginated - // responses. Caller must have READ permission for the queried datasets. - rpc SearchAnnotationSets(SearchAnnotationSetsRequest) - returns (SearchAnnotationSetsResponse) { - option (google.api.http) = { - post: "/v1/annotationsets/search" - body: "*" - }; - } - - // Creates a new annotation. Caller must have WRITE permission - // for the associated annotation set. - // - // The following fields are required: - // - // * [annotationSetId][google.genomics.v1.Annotation.annotation_set_id] - // * [referenceName][google.genomics.v1.Annotation.reference_name] or - // [referenceId][google.genomics.v1.Annotation.reference_id] - // - // ### Transcripts - // - // For annotations of type TRANSCRIPT, the following fields of - // [transcript][google.genomics.v1.Annotation.transcript] must be provided: - // - // * [exons.start][google.genomics.v1.Transcript.Exon.start] - // * [exons.end][google.genomics.v1.Transcript.Exon.end] - // - // All other fields may be optionally specified, unless documented as being - // server-generated (for example, the `id` field). The annotated - // range must be no longer than 100Mbp (mega base pairs). See the - // [Annotation resource][google.genomics.v1.Annotation] - // for additional restrictions on each field. - rpc CreateAnnotation(CreateAnnotationRequest) returns (Annotation) { - option (google.api.http) = { - post: "/v1/annotations" - body: "annotation" - }; - } - - // 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. - // - // For details on the requirements for each individual annotation resource, - // see - // [CreateAnnotation][google.genomics.v1.AnnotationServiceV1.CreateAnnotation]. - rpc BatchCreateAnnotations(BatchCreateAnnotationsRequest) - returns (BatchCreateAnnotationsResponse) { - option (google.api.http) = { - post: "/v1/annotations:batchCreate" - body: "*" - }; - } - - // Gets an annotation. Caller must have READ permission - // for the associated annotation set. - rpc GetAnnotation(GetAnnotationRequest) returns (Annotation) { - option (google.api.http) = { - get: "/v1/annotations/{annotation_id}" - }; - } - - // Updates an annotation. Caller must have - // WRITE permission for the associated dataset. - rpc UpdateAnnotation(UpdateAnnotationRequest) returns (Annotation) { - option (google.api.http) = { - put: "/v1/annotations/{annotation_id}" - body: "annotation" - }; - } - - // Deletes an annotation. Caller must have WRITE permission for - // the associated annotation set. - rpc DeleteAnnotation(DeleteAnnotationRequest) - returns (google.protobuf.Empty) { - option (google.api.http) = { - delete: "/v1/annotations/{annotation_id}" - }; - } - - // Searches for annotations that match the given criteria. Results are - // ordered by genomic coordinate (by reference sequence, then position). - // Annotations with equivalent genomic coordinates are returned in an - // unspecified order. This order is consistent, such that two queries for the - // same content (regardless of page size) yield annotations in the same order - // across their respective streams of paginated responses. Caller must have - // READ permission for the queried annotation sets. - rpc SearchAnnotations(SearchAnnotationsRequest) - returns (SearchAnnotationsResponse) { - option (google.api.http) = { - post: "/v1/annotations/search" - body: "*" - }; - } -} - -// 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'. -message AnnotationSet { - // The server-generated annotation set ID, unique across all annotation sets. - string id = 1; - - // The dataset to which this annotation set belongs. - string dataset_id = 2; - - // The ID of the reference set that defines the coordinate space for this - // set's annotations. - string reference_set_id = 3; - - // The display name for this annotation set. - string name = 4; - - // The source URI describing the file from which this annotation set was - // generated, if any. - string source_uri = 5; - - // The type of annotations contained within this set. - AnnotationType type = 6; - - // A map of additional read alignment information. This must be of the form - // map<string, string[]> (string key mapping to a list of string values). - map<string, google.protobuf.ListValue> info = 17; -} - -// 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. 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`. -message Annotation { - // The server-generated annotation ID, unique across all annotations. - string id = 1; - - // The annotation set to which this annotation belongs. - string annotation_set_id = 2; - - // The display name of this annotation. - string name = 3; - - // The ID of the Google Genomics reference associated with this range. - string reference_id = 4; - - // The display name corresponding to the reference specified by - // `referenceId`, for example `chr1`, `1`, or `chrX`. - string reference_name = 5; - - // The start position of the range on the reference, 0-based inclusive. - int64 start = 6; - - // The end position of the range on the reference, 0-based exclusive. - int64 end = 7; - - // 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. - bool reverse_strand = 8; - - // The data type for this annotation. Must match the containing annotation - // set's type. - AnnotationType type = 9; - - oneof value { - // 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 = 10; - - // 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 = 11; - } - - // A map of additional read alignment information. This must be of the form - // map<string, string[]> (string key mapping to a list of string values). - map<string, google.protobuf.ListValue> info = 12; -} - -message VariantAnnotation { - message ClinicalCondition { - // A set of names for the condition. - repeated string names = 1; - - // The set of external IDs for this condition. - repeated ExternalId external_ids = 2; - - // The MedGen concept id associated with this gene. - // Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/ - string concept_id = 3; - - // The OMIM id for this condition. - // Search for these IDs at http://omim.org/ - string omim_id = 4; - } - - enum Type { - TYPE_UNSPECIFIED = 0; - - // `TYPE_OTHER` should be used when no other Type will suffice. - // Further explanation of the variant type may be included in the - // [info][google.genomics.v1.Annotation.info] field. - TYPE_OTHER = 1; - - // `INSERTION` indicates an insertion. - INSERTION = 2; - - // `DELETION` indicates a deletion. - DELETION = 3; - - // `SUBSTITUTION` indicates a block substitution of - // two or more nucleotides. - SUBSTITUTION = 4; - - // `SNP` indicates a single nucleotide polymorphism. - SNP = 5; - - // `STRUCTURAL` indicates a large structural variant, - // including chromosomal fusions, inversions, etc. - STRUCTURAL = 6; - - // `CNV` indicates a variation in copy number. - CNV = 7; - } - - enum Effect { - EFFECT_UNSPECIFIED = 0; - - // `EFFECT_OTHER` should be used when no other Effect - // will suffice. - EFFECT_OTHER = 1; - - // `FRAMESHIFT` indicates a mutation in which the insertion or - // deletion of nucleotides resulted in a frameshift change. - FRAMESHIFT = 2; - - // `FRAME_PRESERVING_INDEL` indicates a mutation in which a - // multiple of three nucleotides has been inserted or deleted, resulting - // in no change to the reading frame of the coding sequence. - FRAME_PRESERVING_INDEL = 3; - - // `SYNONYMOUS_SNP` indicates a single nucleotide polymorphism - // mutation that results in no amino acid change. - SYNONYMOUS_SNP = 4; - - // `NONSYNONYMOUS_SNP` indicates a single nucleotide - // polymorphism mutation that results in an amino acid change. - NONSYNONYMOUS_SNP = 5; - - // `STOP_GAIN` indicates a mutation that leads to the creation - // of a stop codon at the variant site. Frameshift mutations creating - // downstream stop codons do not count as `STOP_GAIN`. - STOP_GAIN = 6; - - // `STOP_LOSS` indicates a mutation that eliminates a - // stop codon at the variant site. - STOP_LOSS = 7; - - // `SPLICE_SITE_DISRUPTION` indicates that this variant is - // found in a splice site for the associated transcript, and alters the - // normal splicing pattern. - SPLICE_SITE_DISRUPTION = 8; - } - - enum ClinicalSignificance { - CLINICAL_SIGNIFICANCE_UNSPECIFIED = 0; - - // `OTHER` should be used when no other clinical significance - // value will suffice. - CLINICAL_SIGNIFICANCE_OTHER = 1; - - UNCERTAIN = 2; - - BENIGN = 3; - - LIKELY_BENIGN = 4; - - LIKELY_PATHOGENIC = 5; - - PATHOGENIC = 6; - - DRUG_RESPONSE = 7; - - HISTOCOMPATIBILITY = 8; - - CONFERS_SENSITIVITY = 9; - - RISK_FACTOR = 10; - - ASSOCIATION = 11; - - PROTECTIVE = 12; - - // `MULTIPLE_REPORTED` should be used when multiple clinical - // signficances are reported for a variant. The original clinical - // significance values may be provided in the `info` field. - MULTIPLE_REPORTED = 13; - } - - // Type has been adapted from ClinVar's list of variant types. - Type type = 1; - - // Effect of the variant on the coding sequence. - Effect effect = 2; - - // 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. - string alternate_bases = 3; - - // Google annotation ID of the gene affected by this variant. This should - // be provided when the variant is created. - string gene_id = 4; - - // Google annotation IDs of the transcripts affected by this variant. These - // should be provided when the variant is created. - repeated string transcript_ids = 5; - - // The set of conditions associated with this variant. - // A condition describes the way a variant influences human health. - repeated ClinicalCondition conditions = 6; - - // 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/ - ClinicalSignificance clinical_significance = 7; -} - -// A transcript represents the assertion that a particular region of the -// reference genome may be transcribed as RNA. -message Transcript { - message Exon { - // 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. - int64 start = 1; - - // 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. - int64 end = 2; - - // 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.reverse_strand][google.genomics.v1.Annotation.reverse_strand]). - // For forward stranded annotations, this offset is relative to the - // [exon.start][google.genomics.v1.Transcript.Exon.start]. For reverse - // strand annotations, this offset is relative to the - // [exon.end][google.genomics.v1.Transcript.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. - google.protobuf.Int32Value frame = 3; - } - - message CodingSequence { - // 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. - int64 start = 1; - - // 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. - int64 end = 2; - } - - // The annotation ID of the gene from which this transcript is transcribed. - string gene_id = 1; - - // The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> 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. - // - // Exonic sequences do not necessarily code for a translational product - // (amino acids). Only the regions of exons bounded by the - // [codingSequence][google.genomics.v1.Transcript.coding_sequence] correspond - // to coding DNA sequence. - // - // Exons are ordered by start position and may not overlap. - repeated Exon exons = 2; - - // 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][google.genomics.v1.Transcript.exons], if any. If there are any - // [exons][google.genomics.v1.Transcript.exons], the - // [codingSequence][google.genomics.v1.Transcript.coding_sequence] 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][google.genomics.v1.Transcript.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. - CodingSequence coding_sequence = 3; -} - -message ExternalId { - // The name of the source of this data. - string source_name = 1; - - // The id used by the source of this data. - string id = 2; -} - -message CreateAnnotationSetRequest { - // The annotation set to create. - AnnotationSet annotation_set = 1; -} - -message GetAnnotationSetRequest { - // The ID of the annotation set to be retrieved. - string annotation_set_id = 1; -} - -message UpdateAnnotationSetRequest { - // The ID of the annotation set to be updated. - string annotation_set_id = 1; - - // The new annotation set. - AnnotationSet annotation_set = 2; - - // An optional mask specifying which fields to update. Mutable fields are - // [name][google.genomics.v1.AnnotationSet.name], - // [source_uri][google.genomics.v1.AnnotationSet.source_uri], and - // [info][google.genomics.v1.AnnotationSet.info]. If unspecified, all - // mutable fields will be updated. - google.protobuf.FieldMask update_mask = 3; -} - -message DeleteAnnotationSetRequest { - // The ID of the annotation set to be deleted. - string annotation_set_id = 1; -} - -message SearchAnnotationSetsRequest { - // Required. The dataset IDs to search within. Caller must have `READ` access - // to these datasets. - repeated string dataset_ids = 1; - - // If specified, only annotation sets associated with the given reference set - // are returned. - string reference_set_id = 2; - - // Only return annotations sets for which a substring of the name matches this - // string (case insensitive). - string name = 3; - - // If specified, only annotation sets that have any of these types are - // returned. - repeated AnnotationType types = 4; - - // 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. - string page_token = 5; - - // The maximum number of results to return in a single page. If unspecified, - // defaults to 128. The maximum value is 1024. - int32 page_size = 6; -} - -message SearchAnnotationSetsResponse { - // The matching annotation sets. - repeated AnnotationSet annotation_sets = 1; - - // 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. - string next_page_token = 2; -} - -message CreateAnnotationRequest { - // The annotation to be created. - Annotation annotation = 1; -} - -message BatchCreateAnnotationsRequest { - // The annotations to be created. At most 4096 can be specified in a single - // request. - repeated Annotation annotations = 1; - - // A unique request ID which enables the server to detect duplicated requests. - // If provided, duplicated requests will result in the same response; if not - // provided, duplicated requests may result in duplicated data. For a given - // annotation set, callers should not reuse `request_id`s when writing - // different batches of annotations - behavior in this case is undefined. - // A common approach is to use a UUID. For batch jobs where worker crashes are - // a possibility, consider using some unique variant of a worker or run ID. - string request_id = 2; -} - -message BatchCreateAnnotationsResponse { - message Entry { - // The creation status. - google.rpc.Status status = 1; - - // The created annotation, if creation was successful. - Annotation annotation = 2; - } - - // The resulting per-annotation entries, ordered consistently with the - // original request. - repeated Entry entries = 1; -} - -message GetAnnotationRequest { - // The ID of the annotation to be retrieved. - string annotation_id = 1; -} - -message UpdateAnnotationRequest { - // The ID of the annotation to be updated. - string annotation_id = 1; - - // The new annotation. - Annotation annotation = 2; - - // An optional mask specifying which fields to update. Mutable fields are - // [name][google.genomics.v1.Annotation.name], - // [variant][google.genomics.v1.Annotation.variant], - // [transcript][google.genomics.v1.Annotation.transcript], and - // [info][google.genomics.v1.Annotation.info]. If unspecified, all mutable - // fields will be updated. - google.protobuf.FieldMask update_mask = 3; -} - -message DeleteAnnotationRequest { - // The ID of the annotation to be deleted. - string annotation_id = 1; -} - -message SearchAnnotationsRequest { - // Required. The annotation sets to search within. The caller must have - // `READ` access to these annotation sets. - // All queried annotation sets must have the same type. - repeated string annotation_set_ids = 1; - - // Required. `reference_id` or `reference_name` must be set. - oneof reference { - // The ID of the reference to query. - string reference_id = 2; - - // The name of the reference to query, within the reference set associated - // with this query. - string reference_name = 3; - } - - // The start position of the range on the reference, 0-based inclusive. If - // specified, - // [referenceId][google.genomics.v1.SearchAnnotationsRequest.reference_id] or - // [referenceName][google.genomics.v1.SearchAnnotationsRequest.reference_name] - // must be specified. Defaults to 0. - int64 start = 4; - - // The end position of the range on the reference, 0-based exclusive. If - // [referenceId][google.genomics.v1.SearchAnnotationsRequest.reference_id] or - // [referenceName][google.genomics.v1.SearchAnnotationsRequest.reference_name] - // must be specified, Defaults to the length of the reference. - int64 end = 5; - - // 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. - string page_token = 6; - - // The maximum number of results to return in a single page. If unspecified, - // defaults to 256. The maximum value is 2048. - int32 page_size = 7; -} - -message SearchAnnotationsResponse { - // The matching annotations. - repeated Annotation annotations = 1; - - // 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. - string next_page_token = 2; -} - -// When an [Annotation][google.genomics.v1.Annotation] or -// [AnnotationSet][google.genomics.v1.AnnotationSet] is created, if `type` is -// not specified it will be set to `GENERIC`. -enum AnnotationType { - ANNOTATION_TYPE_UNSPECIFIED = 0; - - // A `GENERIC` annotation type should be used when no other annotation - // type will suffice. This represents an untyped annotation of the reference - // genome. - GENERIC = 1; - - // A `VARIANT` annotation type. - VARIANT = 2; - - // A `GENE` annotation type represents the existence of a gene at the - // associated reference coordinates. The start coordinate is typically the - // gene's transcription start site and the end is typically the end of the - // gene's last exon. - GENE = 3; - - // A `TRANSCRIPT` annotation type represents the assertion that a - // particular region of the reference genome may be transcribed as RNA. - TRANSCRIPT = 4; -} |