Continuous Features (Wiggles) and Peer Service

0.3.6

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

GA4GH Modularization

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.

Genotype to Phenotype API

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

Initial release supporting RNA

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.

Initial release supporting Metadata

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.

Initial release based on Protobuf

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.

Initial release based on SQLite registry

Alpha pre-release supporting major feature update. This release is not backwards compatible with previous releases, and requires the data files be re-imported.

• File locations are now tracked in a repo.db registry such that the files can be located anywhere. The information from the json sidecar files are also included in the database.
• Ontology terms are now imported via an OBO file instead of the old pre-packaged sequence_ontology.txt file. A sample OBO file has been added to the sample data set for the reference server.
• Added a custom landing page option for the main page of the server.
• Performance improvement for variant search when calls are set to an empty string.
• Improved server configuration including Apache configuration and robots.txt file.

Feature release

Alpha pre-release supporting major feature update. This release is backwards
incompatible with previous releases, and requires a revised data directory
layout.

• Added sequence and variant annotations (which introduces a sqlite
  database component)
• Added repo manager, a command line tool to manage data files and
  import them into the server's data repository
• Supported searching over multiple ReadGroups, so long as they are
  all in the same ReadGroupSet and all of the ReadGroups in the
  ReadGroupSet are specified

Example data

This release contains example data that can be used with the GA4GH server for demonstration purposes. More documentation can be found here.

Bugfix release

This bugfix release fixes a problem introduced by upstream package changes.