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Rationalises the SearchObjectRequest semantics. #253

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May 28, 2015
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Rationalises the SearchObjectRequest semantics. #253

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23 changes: 12 additions & 11 deletions src/main/resources/avro/metadatamethods.avdl
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Original file line number Diff line number Diff line change
Expand Up @@ -8,10 +8,9 @@ import idl "metadata.avdl";
/** This request maps to the body of `POST /individuals/search` as JSON. */
record SearchIndividualsRequest {
/**
If specified, restrict this query to individuals within the given
individual groups.
The Group to search.
*/
array<string> groupIds = [];
string groupId;

/**
Only return individuals with this name (case-sensitive, exact match).
Expand Down Expand Up @@ -52,8 +51,8 @@ record SearchIndividualsResponse {
/**
Gets a list of `Individual` matching the search criteria.

`POST /individuals/search` must accept a JSON version of
`SearchIndividualsRequest` as the post body and will return a JSON version of
`POST /individuals/search` must accept a JSON version of
`SearchIndividualsRequest` as the post body and will return a JSON version of
`SearchIndividualsResponse`.
*/
SearchIndividualsResponse searchIndividuals(
Expand All @@ -65,8 +64,10 @@ SearchIndividualsResponse searchIndividuals(
/** This request maps to the body of `POST /samples/search` as JSON. */

record SearchSamplesRequest {
/** If specified, restrict this query to samples for the given individuals. */
array<string> individualIds = [];
/**
The Individual to search.
*/
string individualId;

/**
Only return samples with this name (case-sensitive, exact match).
Expand Down Expand Up @@ -107,8 +108,8 @@ record SearchSamplesResponse {
/**
Gets a list of `Sample` matching the search criteria.

`POST /samples/search` must accept a JSON version of
`SearchSamplesRequest` as the post body and will return a JSON version of
`POST /samples/search` must accept a JSON version of
`SearchSamplesRequest` as the post body and will return a JSON version of
`SearchSamplesResponse`.
*/
SearchSamplesResponse searchSamples(
Expand Down Expand Up @@ -158,8 +159,8 @@ record SearchExperimentsResponse {
/**
Gets a list of `Experiment` matching the search criteria.

`POST /experiments/search` must accept a JSON version of
`SearchExperimentsRequest` as the post body and will return a JSON version of
`POST /experiments/search` must accept a JSON version of
`SearchExperimentsRequest` as the post body and will return a JSON version of
`SearchExperimentsResponse`.
*/
SearchExperimentsResponse searchExperiments(
Expand Down
12 changes: 8 additions & 4 deletions src/main/resources/avro/readmethods.avdl
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Expand Up @@ -14,8 +14,10 @@ to `ReferenceSet`s containing that same `Reference`. If no reference is
specified, all `ReadGroup`s must be aligned to the same `ReferenceSet`.
*/
record SearchReadsRequest {
/** If nonempty, restrict this query to reads within the given readgroups. */
array<string> readGroupIds = [];
/**
The ReadGroups to search. At least one readGroupId must be specified.
*/
array<string> readGroupIds;

/**
The reference to query. Leaving blank returns results from all
Expand Down Expand Up @@ -82,8 +84,10 @@ SearchReadsResponse searchReads(
/****************** /readgroupsets/search *********************/
/** This request maps to the body of `POST /readgroupsets/search` as JSON. */
record SearchReadGroupSetsRequest {
/** The list of datasets to search. */
array<string> datasetIds = [];
/**
The dataset to search.
*/
string datasetId;

/**
Only return read group sets with this name (case-sensitive, exact match).
Expand Down
12 changes: 6 additions & 6 deletions src/main/resources/avro/sequenceAnnotationmethods.avdl
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Expand Up @@ -7,24 +7,24 @@ protocol SequenceAnnotationMethods {
import idl "sequenceAnnotations.avdl";

// FIXME: wiggle methods not defined.

/****************** /features/search *********************/

/**
This request maps to the body of `POST /features/search` as JSON.
*/
record SearchFeaturesRequest {
/**
The annotation sets to search within. Either `featureSetIds` or
`parentIds` must be non-empty.
The annotation set to search within. Either `featureSetId` or
`parentId` must be non-empty.
*/
array<string> featureSetIds = [];
union { null, string } featureSetId;

/**
Restricts the search to direct children of the given parent `feature`
IDs. Either `featureSetIds` or `parentIds` must be non-empty.
ID. Either `featureSetId` or `parentId` must be non-empty.
*/
array<string> parentIds = [];
union { null, string } parentId;

/**
If specified, this query matches only annotations which overlap this path.
Expand Down
227 changes: 94 additions & 133 deletions src/main/resources/avro/variantmethods.avdl
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Expand Up @@ -8,10 +8,9 @@ import idl "variants.avdl";
/** This request maps to the body of `POST /variantsets/search` as JSON. */
record SearchVariantSetsRequest {
/**
If nonempty, will restrict the query to variant sets within the
given datasets.
The Dataset to search.
*/
array<string> datasetIds = [];
string datasetId;

/**
Specifies the maximum number of results to return in a single page.
Expand Down Expand Up @@ -62,11 +61,95 @@ org.ga4gh.models.VariantSet getVariantSet(
*/
string id) throws GAException;

/****************** /variantsets/{id}/sequences/search *********************/
/**
This request maps to the body of `POST /variantsets/{id}/sequences/search` as
JSON.
*/
record SearchVariantSetSequencesRequest {
/**
Return `Segment`s describing novel sequences in the `VariantSet`
that are joined onto the sequence with the specified ID.
*/
string parentId;

/**
Specifies the maximum number of results to return in a single page.
If unspecified, a system default will be used.
*/
union { null, int } pageSize = null;

/**
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.
*/
union { null, string } pageToken = null;
}

/**
This is the response from `POST /variantsets/{id}/sequences/search` expressed as
JSON.
*/
record SearchVariantSetSequencesResponse {
/**
The list of `Segment`s for matching sequences from the novel sequence graph
for the `VariantSet`.
*/
array<org.ga4gh.models.Segment> segments = [];

/**
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.
*/
union { null, string } nextPageToken = null;
}

/**
Gets `Segment`s covering the sequences that match the search criteria.

`POST /variantsets/{id}/sequences/search` must accept a JSON version of
`SearchVariantSetSequencesRequest` as the post body and will return a JSON
version of `SearchVariantSetSequencesResponse`.
*/
SearchVariantSetSequencesResponse searchVariantSetSequences(
/**
The ID of the `VariantSet` which provides the novel sequences.
*/
string variantSetId,
/**
This request maps to the body of `POST variantsets/{id}/sequences/search` as
JSON.
*/
SearchVariantSetSequencesRequest request) throws GAException;

/***************** /variantsets/{id}/sequences/{id} *******************/
/**
Gets a `Segment` describing a novel sequence in a `VariantSet`, by sequence
ID.

`GET /variantsets/{id}/sequences/{id}` will return a JSON version of a `Segment`
covering the novel sequence with the given ID, and describing where it is
joined onto its parent sequences.
*/
org.ga4gh.models.Segment getVariantSetSequence(
/**
The ID of the `VariantSet` which provides the novel sequence.
*/
string variantSetId,
/**
The ID of the novel sequence to get a covering `Segment` for.
*/
string sequenceId) throws GAException;

/****************** /variants/search *********************/
/** This request maps to the body of `POST /variants/search` as JSON. */
record SearchVariantsRequest {
/** Required. The IDs of the variant sets to search over. */
array<string> variantSetIds = [];
/**
The VariantSet to search.
*/
string variantSetId;

/** Only return variants which have exactly this name (case-sensitive, exact match). */
union { null, string } name = null;
Expand Down Expand Up @@ -163,8 +246,10 @@ org.ga4gh.models.Variant getVariant(
/****************** /alleles/search *********************/
/** This request maps to the body of `POST /alleles/search` as JSON. */
record SearchAllelesRequest {
/** Required. The IDs of the variant sets to search over. */
array<string> variantSetIds = [];
/**
The VariantSet to search.
*/
string variantSetId;

/**
Required. Only return `Allele`s on the sequence with this ID.
Expand Down Expand Up @@ -243,10 +328,9 @@ org.ga4gh.models.Allele getAllele(
/** This request maps to the body of `POST /callsets/search` as JSON. */
record SearchCallSetsRequest {
/**
If nonempty, will restrict the query to call sets within the
given variant sets.
The VariantSet to search.
*/
array<string> variantSetIds = [];
string variantSetId;

/**
Only return call sets with this name (case-sensitive, exact match).
Expand Down Expand Up @@ -300,127 +384,4 @@ org.ga4gh.models.CallSet getCallSet(
The ID of the `CallSet`.
*/
string id) throws GAException;

/****************** /calls/search *********************/
/** This request maps to the body of `POST /calls/search` as JSON. */
record SearchCallsRequest {

/**
If nonempty, only return the `Call`s in these `CallSet`s.
*/
array<string> callSetIds = [];

/**
If nonempty, return only `Call`s in these `VariantSet`s.
*/
array<string> variantSetIds = [];

/**
If nonempty, return only `Call`s associated with one of these `Variant`s.
*/
array<string> variantIds = [];

/**
Specifies the maximum number of results to return in a single page.
If unspecified, a system default will be used.
*/
union { null, int } pageSize = null;

/**
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.
*/
union { null, string } pageToken = null;
}

/**
This is the response from `POST /calls/search` expressed as JSON.
*/
record SearchCallsResponse {
/** The list of matching calls. */
array<org.ga4gh.models.Call> calls = [];

/**
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.
*/
union { null, string } nextPageToken = null;
}

/**
Gets a list of `Call` matching the search criteria.
`POST /calls/search` must accept a JSON version of
`SearchCallsRequest` as the post body and will return a JSON version of
`SearchCallsResponse`.
*/
SearchCallsResponse searchCalls(
/** This request maps to the body of `POST /calls/search` as JSON. */
SearchCallsRequest request) throws GAException;

/****************** /allelecalls/search *********************/
/** This request maps to the body of `POST /allelecalls/search` as JSON. */
record SearchAlleleCallsRequest {

/**
If nonempty, only return the `AlleleCall`s in these `CallSet`s.
*/
array<string> callSetIds = [];

/**
If nonempty, return only `AlleleCall`s in these `VariantSet`s.
*/
array<string> variantSetIds = [];

/**
If nonempty, return only `AlleleCall`s associated with one of these `Allele`s.
*/
array<string> alleleIds = [];

/**
If nonempty, return only `AlleleCall`s associated with one of these
`Variant`s.
*/
array<string> variantIds = [];

/**
Specifies the maximum number of results to return in a single page.
If unspecified, a system default will be used.
*/
union { null, int } pageSize = null;

/**
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.
*/
union { null, string } pageToken = null;
}

/**
This is the response from `POST /allelecalls/search` expressed as JSON.
*/
record SearchAlleleCallsResponse {
/** The list of matching calls. */
array<org.ga4gh.models.AlleleCall> alleleCalls = [];

/**
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.
*/
union { null, string } nextPageToken = null;
}

/**
Gets a list of `AlleleCall` matching the search criteria.
`POST /allelecalls/search` must accept a JSON version of
`SearchAlleleCallsRequest` as the post body and will return a JSON version of
`SearchAlleleCallsResponse`.
*/
SearchAlleleCallsResponse searchAlleleCalls(
/** This request maps to the body of `POST /allelecalls/search` as JSON. */
SearchAlleleCallsRequest request) throws GAException;

}