diff --git a/doc/release-notes.md b/doc/release-notes.md index c7f116c1..4732a4cd 100644 --- a/doc/release-notes.md +++ b/doc/release-notes.md @@ -1,65 +1,50 @@ # Changes to `ga4gh/schemas` `master` branch since version `v0.5.1` (Oct 2, 2014) -### Pervasive changes +## Pervasive changes Renamed all protocols and records to remove the "`GA`" prefix from their names. (Hence `GASearchVariantSetsRequest` is now -`SearchVariantSetsRequest`, etc.) The exception is `GAException`, -which is unchanged. +`SearchVariantSetsRequest`, etc.) +The exception is `GAException`, which is unchanged. There is no longer one unitary namespace. Objects now reside in "`org.ga4gh.models`", methods in "`org.ga4gh.methods`". -Updated the version number to `0.6.0-SNAPSHOT`. +Updated the version number to `0.6.0a1`. -### Added -Datasets are now used throughout the API. +## Changes visible to API clients -#### Methods: +### Additions -* `getDataset` -* `searchDatasets` -* `getReadGroupSet` -* `getReadGroup` -* `getVariant` -* `getVariantSet` -* `getCallSet` +`Dataset` is now utilized throughout the API. -#### Records: +#### New methods, HTTP endpoints: -* `ExternalIdentifier` -* `Experiment` -* `Dataset` -* `ReadStats` -* `Fragment` _(apparently unused)_ +* `getDataset` via GET `datasets/` +* `searchDatasets` via POST `/datasets/search` +* `getReadGroupSet` via GET `/readgroupsets/` +* `getReadGroup` via GET `/readgroups/` +* `getVariant` via GET `/variants/` +* `getVariantSet` via GET `/variantsets/` +* `getCallSet` via GET `/callsets/` -#### Enum: +#### New and modified entities: -* `Strand` - -### Removed - -* `src/main/resources/avro/beacon.avdl` -* Files designated "Work In Progress" ("`wip`"): - * `src/main/resources/avro/wip/metadata.avdl` - * `src/main/resources/avro/wip/metadatamethods.avdl` - * `src/main/resources/avro/wip/variationReference.avdl` - -### Changed - -Moved `GAException` to `methods.avdl`. +* New record type `ExternalIdentifier` introduced. +* New record type `ReadStats` now optionally part of a returned `ReadGroup` or `ReadGroupSet` object. +* `Position` record type now specifies strand via new enum `Strand` (in place of `boolean reverseStrand`). #### Field default values: -* `SearchReadsRequest.start` is optional and no longer defaults to 0. -* Boolean fields in `ReadAlignment` now default to `null` instead of `false`. +* `SearchReadsRequest.start` as passed into `/reads/search` is optional and no longer defaults to 0. +* Boolean fields in `ReadAlignment` as returned from `/reads/search` now default to `null` instead of `false`. #### Field types: -* `SearchVariantSetsRequest` now takes a single dataset ID, not an array. -* `SearchCallSetsRequest` now takes a single variant set ID, not an array. -* `SearchReferenceSetsRequest` changed two parameters from arrays to +* `SearchVariantSetsRequest` as passed into `/variantsets/search` now takes a single dataset ID, not an array. +* `SearchCallSetsRequest` as passed into `/callsets/search` now takes a single variant set ID, not an array. +* `SearchReferenceSetsRequest` as passed into `/referencesets/search` changed two parameters from arrays to singletons: * `md5checksum` @@ -67,13 +52,28 @@ singletons: #### New fields: -* `SearchReferencesRequest` now accepts a `referenceSetId` parameter. -* `SearchVariantsRequest` now takes a `variantSetId` parameter. -* `SearchReadsRequest` now includes `readGroupIds`. -* `SearchReadGroupSetsRequest` takes a `datasetId`. -* `ReferenceSet` now includes a name. -* `VariantSet` adds name and reference set ID fields. -* `ReadGroup` adds `stats`. +* `SearchReferencesRequest` passed into `/references/search` now accepts a `referenceSetId` parameter. +* `SearchVariantsRequest` passed into `/variants/search` now takes a `variantSetId` parameter. +* `SearchReadsRequest` passed into `/reads/search` now includes `readGroupIds`. +* `SearchReadGroupSetsRequest` passed into `/readgroupsets/search` takes a `datasetId`. +* `ReferenceSet` returned from `/references/search` now includes a name. +* `VariantSet` returned from `/variants/search` adds name and reference set ID fields. +* `ReadGroup` returned from `/readgroups/` adds `stats`. + + +## Changes internal to Schemas, documentation and organization + +### Removed + +* `src/main/resources/avro/beacon.avdl` +* Files designated "Work In Progress" ("`wip`"): + * `src/main/resources/avro/wip/metadata.avdl` + * `src/main/resources/avro/wip/metadatamethods.avdl` + * `src/main/resources/avro/wip/variationReference.avdl` + +### Changed + +Moved `GAException` to `methods.avdl`. ## Documentation