Ga4gh-server

=====

This an alpha pre-release that contains some major updates. The most
important changes are highlighted in **bold** below. We have also made
some updates to the documentation.

Features:

- **Rename package from “ga4gh” to “ga4gh-server”** [\1582], [\1583]
- Added **support for BigWig files** in a new Continuous Data object
[\1573] New endpoints and message types include:

> - `POST /continuoussets/search`
> - `GET /continuoussets/{id}`
> - `POST /continuous/search`
> - Continuous (new)
> - ContinuousSet (new)

- Add **ability to list and join peer server networks** [\1507] New
endpoints and message types include:

> - `POST /peers/list`
> - `POST /peers/announce`
> - `GET /info`
> - ListPeersResponse (new)
> - Peer (new)
> - AnnouncePeerResponse (new)
> - GetInfoResponse (new)

- Remove feature\_id from ExpressionLevel and add ability to search by
the Name field [\1580] Impacts

> - `POST /expressionlevels/search`
> - `GET /expressionlevels/{id}`

- Replaced info fields with rich type Attributes fields [\1521]
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

- Replace NCBI taxon ID integer with ontology term [\1551] Impacts
the following message types:

> - Reference
> - ReferenceSet

- Changed ontology term “id” to “term\_id” [\1513] Impacts the
following message types:

> - OntologyTerm

Documentation:

- Document auto-releases, constraint instructions [\1578]
- Improved development document for virtualenv command [\1550]

Infrastructure:

- Automatically deploy tagged releases to Pypi from Travis [\1576]
- Refactor transcript annotation [\1334]
- Speedups to rna quantification ingest [\1564]

[\1582]: https://github.com/ga4gh/ga4gh-server/issues/1582
[\1583]: https://github.com/ga4gh/ga4gh-server/issues/1583
[\1573]: https://github.com/ga4gh/ga4gh-server/issues/1573
[\1507]: https://github.com/ga4gh/ga4gh-server/issues/1507
[\1580]: https://github.com/ga4gh/ga4gh-server/issues/1580
[\1521]: https://github.com/ga4gh/ga4gh-server/issues/1521
[\1551]: https://github.com/ga4gh/ga4gh-server/issues/1551
[\1513]: https://github.com/ga4gh/ga4gh-server/issues/1513
[\1578]: https://github.com/ga4gh/ga4gh-server/issues/1578
[\1550]: https://github.com/ga4gh/ga4gh-server/issues/1550
[\1576]: https://github.com/ga4gh/ga4gh-server/issues/1576
[\1334]: https://github.com/ga4gh/ga4gh-server/issues/1334
[\1564]: https://github.com/ga4gh/ga4gh-server/issues/1564

The main focus of this release is to break out reusable components into separately installable modules. These include:
- ga4gh: Main PyPi module that contains all the server code. This module depends on all of the following modules.
- ga4gh-schemas: PyPi module that provides access to the compiled schema code
- ga4gh-client: PyPi module that includes the full client API library
- ga4gh-common: PyPi module that has common code needed by the server, client and schemas. This module will be installed automatically as a dependency.

There are a number of bugfixes and documentation changes also included in this release. Details can be found in the release notes.

Alpha pre-release supporting major feature update.
- G2P functionality added to support the following API endpoints:
- POST `/phenotypeassociationsets/search`
- POST `/phenotypes/search`
- POST `/featurephenotypeassociations/search`
- Biometadata tags for RNA quantifications.
- Improvements to the RNA quantification ingestion pipeline.
- Migrated CLI related code to `cli` module.
- Add demonstration RNA quantification data.
- Minor doc fixes

Known Issues
- When searching using a wildcard, *, an Internal Server Error
occurs. 1379
- When listing many Read Group Sets, responses can be quite slow
causing timeouts. 1316

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}

Fixed bug where transcript effects would be repeated within a search result.

Alpha pre-release supporting major feature update.
- Metadata functionality added to support biosample and individual metadata capabilities.
- Now support searching features by 'name' and 'gene_symbol'. These fields have been promoted to facilitate the future integration of the RNA and G2P modules.

Alpha pre-release supporting major feature update. This release is not
backwards compatible with previous releases due to several changes to
the schemas that were required to move to protocol buffers.
- This release includes the code changes necessary for the migration
to protocol buffers from Avro.
- Client applications will need to be rebuilt to the new schemas and
use the protobuf json serialization libraries to be compatible
with this version of the server.