sequence_annotation_service

************* /featuresets **************** ************* /features ************ ************* /continuoussets **************** ************* /continuous ************

GetFeature(request)
Parameters:requestGetFeatureRequest
Return type:Feature
Throws:GAException

Gets a Feature by ID.

GET /features/{id} will return a JSON version of Feature.

SearchContinuousSets(request)
Parameters:requestSearchContinuousSetsRequest
Return type:SearchContinuousSetsResponse
Throws:GAException

Gets a list of ContinuousSet matching the search criteria.

POST /continuoussets/search must accept a JSON version of SearchContinuousSetsRequest as the post body and will return a JSON version of SearchContinuousSetsResponse.

SearchContinuous(request)
Parameters:requestSearchContinuousRequest
Return type:SearchContinuousResponse
Throws:GAException

Gets continuous values matching the search criteria.

POST /continuous/search must accept a JSON version of SearchContinuousRequest as the post body and will return a JSON version of SearchContinuousResponse.

GetFeatureSet(request)
Parameters:requestGetFeatureSetRequest
Return type:FeatureSet
Throws:GAException

Gets a FeatureSet by ID.

GET /featuresets/{id} will return a JSON version of FeatureSet.

SearchFeatures(request)
Parameters:requestSearchFeaturesRequest
Return type:SearchFeaturesResponse
Throws:GAException

Gets a list of Feature matching the search criteria.

POST /features/search must accept a JSON version of SearchFeaturesRequest as the post body and will return a JSON version of SearchFeaturesResponse.

SearchFeatureSets(request)
Parameters:requestSearchFeatureSetsRequest
Return type:SearchFeatureSetsResponse
Throws:GAException

Gets a list of FeatureSet matching the search criteria.

POST /featuresets/search must accept a JSON version of SearchFeatureSetsRequest as the post body and will return a JSON version of SearchFeatureSetsResponse.

GetContinuousSet(request)
Parameters:requestGetContinuousSetRequest
Return type:ContinuousSet
Throws:GAException

Gets a ContinuousSet by ID.

GET /continuoussets/{id} will return a JSON version of ContinuousSet.

message SearchFeatureSetsRequest
Fields:
  • dataset_id (string) – The Dataset to search.
  • page_size (integer) – Specifies the maximum number of results to return in a single page. If unspecified, a system default will be used.
  • page_token (string) – 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 next_page_token from the previous response.
  • This request maps to the body of POST /featuresets/search as JSON.
message SearchFeatureSetsResponse
Fields:
  • feature_sets (list of FeatureSet) – The list of matching feature sets.
  • next_page_token (string) – 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.

This is the response from POST /featuresets/search expressed as JSON.

message GetFeatureSetRequest
Fields:
  • feature_set_id (string) – The ID of the FeatureSet to be retrieved.

This request maps to the URL GET /featuresets/{id}.

message SearchFeaturesRequest
Fields:
  • feature_set_id (string) – The annotation set to search within. Either feature_set_id or parent_id must be non-empty.
  • name (string) – Only returns features with this name (case-sensitive, exact match).
  • gene_symbol (string) – Only return features with matching the provided gene symbol (case-sensitive, exact match). This field may be replaced with a more generic representation in a future version.
  • parent_id (string) – Restricts the search to direct children of the given parent feature ID. Either feature_set_id or parent_id must be non-empty.
  • reference_name (string) – Only return features on the reference with this name (matched to literal reference name as imported from the GFF3).
  • start (long) – Required, if name or symbol not provided. The beginning of the window (0-based, inclusive) for which overlapping features should be returned. Genomic positions are non-negative integers less than reference length. Requests spanning the join of circular genomes are represented as two requests one on each side of the join (position 0).
  • end (long) – Required, if name or symbol not provided. The end of the window (0-based, exclusive) for which overlapping features should be returned.
  • feature_types (string) – TODO: To be replaced with a fully featured ontology search once the Metadata definitions are rounded out. If specified, this query matches only annotations whose feature_type matches one of the provided ontology terms.
  • page_size (integer) – Specifies the maximum number of results to return in a single page. If unspecified, a system default will be used.
  • page_token (string) – 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 next_page_token from the previous response.

This request maps to the body of POST /features/search as JSON.

message SearchFeaturesResponse
Fields:
  • features (list of Feature) – The list of matching annotations, sorted by start position. Annotations which share a start position are returned in a deterministic order.
  • next_page_token (string) – 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.

This is the response from POST /features/search expressed as JSON.

message GetFeatureRequest
Fields:
  • feature_id (string) – The ID of the Feature to be retrieved.

This request maps to the URL GET /features/{id}.

message SearchContinuousSetsRequest
Fields:
  • dataset_id (string) – The Dataset to search.
  • page_size (integer) – Specifies the maximum number of results to return in a single page. If unspecified, a system default will be used.
  • page_token (string) – 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 next_page_token from the previous response.
  • This request maps to the body of POST /continuoussets/search as JSON.
message SearchContinuousSetsResponse
Fields:
  • continuous_sets (list of ContinuousSet) – The list of matching feature sets.
  • next_page_token (string) – 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.

This is the response from POST /continuoussets/search expressed as JSON.

message GetContinuousSetRequest
Fields:
  • continuous_set_id (string) – The ID of the ContinuousSet to be retrieved.

This request maps to the URL GET /continuoussets/{id}.

message SearchContinuousRequest
Fields:
  • continuous_set_id (string) – The annotation set to search within. Required value.
  • reference_name (string) – Get continuous values on this reference. Required value.
  • start (long) – The beginning of the window (0-based, inclusive) for which continuous values should be returned. Required value.
  • end (long) – The end of the window (0-based, exclusive) for which continuous values should be returned. Required value.
  • page_size (integer) – Specifies the maximum number of results to return in a single page. If unspecified, a system default will be used.
  • page_token (string) – 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 next_page_token from the previous response.

This request maps to the body of POST /continuous/search as JSON.

message SearchContinuousResponse
Fields:
  • continuous (list of Continuous) – The list of matching continuous values, sorted by start position. All sampled values within the query range are returned. Unsampled values are assigned ‘NaN’ value. The values returned do not necessarily cover the same range as the query as all unsampled values might not be returned or if the query range extends beyond the reference range.
  • next_page_token (string) – 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.

This is the response from POST /continuous/search expressed as JSON.