GA4GH API v0.6.0a10

Changes to ga4gh/schemas master branch since version 0.6.0a9 (Jan
23, 2016)

Features:

• Remove feature_id from ExpressionLevel and added ability to search by Name field. #818 Impacts

  • POST /expressionlevels/search
  • GET /expressionlevels/{id}

• Added support for BigWig files in a new Continuous Data object #802 Adds the following new endpoints:

  • Continuous Data: POST /continuoussets/search
  • Continuous Data: GET /continuoussets/{id}
  • Continuous Data: POST /continuous/search

• Add deep set/get attr to protocol module #816

• Changed ontology term “id” to “term_id” #805 Impacts the
  message type OntologyTerm

• Replaced info fields with rich type Attributes fields #700 Impacts the following message types:

  • TranscriptEffect
  • VariantAnnotation
  • Individual
  • Biosample
  • Experiment (new)
  • Analysis (new)
  • Dataset
  • ReadGroup
  • ReadGroupSet
  • ReadAlignment
  • Reference
  • ReferenceSet
  • RnaQuantificationSet
  • RnaQuantification
  • ExpressionLevel
  • Feature
  • VariantSetMetadata
  • CallSet
  • Call
  • Variant

• Add ability to list and join peer server networks #760 Adds the following new endpoints:

  • Peer: POST /peers/list
  • Peer: POST /peers/announce
  • Peer: GET /info

* Replace NCBI taxon ID integer with ontology term #699 Impacts the following message types:

• Reference
  - ReferenceSet

Documentation:

• Add instructions for viewing the UML diagram #835
• Expand on schema usage instructions #786
• Expand on release process documentation #753

Infrastructure:

• Automatically deploy tagged releases to PyPi from Travis #825
• Add tests to verify constraints files #817
• Continued effort to separate out common methods

GA4GH API v0.6.0a9

This is the first release that supports the separately pip-installable ga4gh-schemas module. It also includes some bug fixes, schema changes and some documentation updates.

Changes to ga4gh/schemas master branch since version 0.6.0a8 (Oct 26, 2016)

• Fixed bugs:
  • Fixed typo in get: /v0.6.0a8/variantannotationset/{variant_annotation_set_id}
  • Fix to be able to handle VCFs with genotype == ./.
• Upgrade to use protobuf release 3.1
• Introduced a pip installable schemas package called ga4gh-schemas. We have also
  created pip installable packages for a support library called ga4gh-common
  and a client library module called ga4gh-client.
• Introduced a schemas package release to Maven Central. We will be posting regular
  ga4gh packages for each official schema release to Maven going forward.
• Changed the name of the biosample terms to track be consistent with the use
  of camel-case and the underscore character.
• Added a new schema visualization tool to create UML diagrams from the schemas.
  The new diagrams can be viewed on the Schemas page in the Read The Docs documents.

GA4GH API v0.6.0a8

• Introduced G2P API endpoints including the following:
  • POST /phenotypeassociationsets/search
  • POST /phenotypes/search
  • POST /featurephenotypeassociations/search
• Add biometadata to RNA quantifications
• Add protobuf based HTTP annotations

GA4GH API v0.6.0a7

Alpha pre-release supporting major feature update.

• RNA functionality added to support the following API endpoints
• POST /rnaquantificationsets/search
• GET /rnaquantificationsets/{id}
• POST /rnaquantifications/search
• GET /rnaquantifications/{id}
• POST /expressionlevels/search
• GET /expressionlevels/{id}

GA4GH API v0.6.0a6

• Metadata section added
• Now support searching features by 'name' and 'gene_symbol'

GA4GH API v0.6.0a5

First Protocol Buffers (protobuf v3.0.0) version of the GA4GH API. Same set of features (messages, endpoints) as previous alpha release.

IMPORTANT: The switch from AVRO to protobuf in this pre-release will break compatibility with all client applications written against the previous AVRO schema version.

GA4GH API v0.6.0a4

Introduced Sequence Annotations API record types (FeatureSet and Feature) and associated endpoints (POST featuresets/search, GET featuresets/<id>, POST features/search, GET features/<id>).

GA4GH API v0.6.0a3

Changed properPlacement in Reads API to improperPlacement (defaults to False), corrected documentation on variation annotation and dateTime format.

GA4GH API v0.6.0a2

Added Variant Annotations draft API

GA4GH API v0.6.0a1

Changes to ga4gh/schemas master branch since version v0.5.1 (Oct 2, 2014)

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.

There is no longer one unitary namespace. Objects now reside in
"org.ga4gh.models", methods in "org.ga4gh.methods".

Updated the version number to 0.6.0a1.

Changes visible to API clients

Additions

Dataset is now utilized throughout the API.

New methods, HTTP endpoints:

• getDataset via GET datasets/<id>
• searchDatasets via POST /datasets/search
• getReadGroupSet via GET /readgroupsets/<id>
• getReadGroup via GET /readgroups/<id>
• getVariant via GET /variants/<id>
• getVariantSet via GET /variantsets/<id>
• getCallSet via GET /callsets/<id>

New and modified entities:

• 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 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 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
  • accession

New fields:

• 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/<id> 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

Using Doxygen to generate HTML documentation from schema (*.avdl) files.

Clarifications:

• How the SearchReadGroupSetsRequest.name field is interpreted.
• The meaning of SearchCallSetsRequest.name.
• Reference, ReferenceSet docs.

Updated CONTRIBUTING.md to describe the latest contribution rules.

Moved GeneratingDocumentation.md to doc/.

README.md now includes information about the Metadata Task Team.

Tests

Added tests to ensure Maven processes the schemas into a jar file
successfully, and that we can compile the schemas into Python.