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API Release Notes Archive

v0.3.24.3

  • GDC Product: Application Programming Interface (API)
  • Release Date: May 2, 2016

New Features and Changes

  • BAM slicing: regions can be specified using a GENCODE v22 (HGNC) gene names
  • BAM slicing: disabled for files in GDC legacy archive
  • New YAML format of upload manifests
  • Annotations no longer include creator information
  • legacy endpoint added; provides access to data in legacy archive
  • Certain API responses now include MD5 checksums, using Content-MD5 HTTP header

Bugs Fixed Since Last Release

  • Authentication system fixed to allow download of harmonized files
  • BCR clinical XML follow_up element is not required
  • Index files can be downloaded
  • Downloaded data files are named correctly

Known Issues and Workarounds

  • None to report

Release details are maintained in the GDC API change log

v0.3.24-spr5

  • GDC Product: Application Programming Interface (API)
  • Release Date: April 19, 2016

New Features and Changes

  • None to report

Bugs Fixed Since Last Release

  • API responds with an error when multiple submitter_id properties are submitted for the same entity in a transaction.
  • API download functionality now provides indication when when no related files (e.g. SRA XML) exist.

Known Issues and Workarounds

  • None to report

Release details are maintained in the GDC API change log

v0.3.24.2

  • GDC Product: Application Programming Interface (API)
  • Release Date: April 5, 2016

New Features and Changes

  • Updates to GDC data model
  • File metadata can be submitted before file upload
  • GQL improvements
  • /download/metadata endpoint allows download of MAGE-TAB and SRA XML
  • /submission/<Program.name>/<Project.code>/entities/<uuid> endpoint allows retrieval of Submission Portal entities by UUID

Bugs Fixed Since Last Release

  • Submission: files in validated, submitted, processing, and processed states can no longer be updated. To change these files the user must delete or redact them.
  • _mapping endpoint now available for annotations endpoint
  • Order of files submitted in same transaction does not matter
  • Fixed incorrect response for bulk transactions

Known Issues and Workarounds

  • None to report

Release details are maintained in the GDC API change log

v0.3.24.1

  • GDC Product: Application Programming Interface (API)
  • Release Date: March 1, 2016

New Features and Changes

  • New entities: Slide Data Bundle and Pathology Data Bundle
  • New _dictionary/_all endpoint displays the entire GDC dictionary for the submission endpoint, and project-specific dictionaries for project endpoints; e.g. https://api.gdc.cancer.gov/v0/submission/_dictionary/_all and https://api.gdc.cancer.gov/v0/submission/TCGA/SKCM/_dictionary/_all.
  • Support for releases
  • Project state property definition has been updated. The property can now have one of six values: open (default), review, submitted, processing, closed, and legacy.
  • days_to_index property has been removed from Case
  • template endpoint for submissions returns archive of all templates, e.g. https://api.gdc.cancer.gov/v0/submission/TCGA/SKCM/template
  • template endpoint can generate JSON using /template?format=json
  • export endpoint now supports POST requests
  • GraphQL: lists are accepted as top level property filters
  • GraphQL: not filter was added

Bugs Fixed Since Last Release

  • Portion is now linked to Center

Known Issues and Workarounds

  • None to report

Release details are maintained in the GDC API change log

v0.3.20.1

  • GDC Product: Application Programming Interface (API)
  • Release Date: January 28, 2016

New Features and Changes

  • Metadata export support for TSV, CSV and JSON formats, including:
  • Clinical metadata
  • Biospecimen metadata
  • Project and case entities
  • Annotations
  • Export of metadata can be filtered by category
  • Support for generating a TSV template
  • Additional details are provided in JSON parsing error messages

Bugs Fixed Since Last Release

  • Biospecimen XML submissions with shipment_portion nodes now parsed correctly
  • Correct HTTP code returned upon authentication failure
  • API URLs work with and without trailing slash
  • Miscellaneous bug fixes

Known Issues and Workarounds

  • None to report

Release details are maintained in the GDC API change log

v0.2.18

  • GDC Product: Application Programming Interface (API)
  • Release Date: November 18, 2015

New Features and Changes

  • Added support for molecular data upload.
  • Users can submit data bundle entities to specify the molecular data and relations to be uploaded.
  • Users can update existing data by submitting update data bundles.
  • Manifest files can be downloaded to allow for molecular data upload via the API or Data Transfer Tool.
  • Users can delete previously submitted entities.

Bugs Fixed Since Last Release

  • None to report

Known Issues and Workarounds

  • None to report

Release details are maintained in the GDC API change log

v0.2.18-spr1

  • GDC Product: Application Programming Interface (API)
  • Release Date: November 2, 2015

New Features and Changes

  • Entity Metadata submission added with support for JSON, CSV, TSV, and XML formats and the following data entities:
    • Clinical metadata
    • Biospecimen metadata
    • Project and case entities
    • Annotations
  • Dry run option available for metadata submission to validate metadata files prior to submission
  • Submission integrated with authorization to ensure read, create, update, and admin roles can be controlled at the project level

Bugs Fixed Since Last Release

  • None to report

Known Issues and Workarounds

  • None to report

Release details are maintained in the GDC API change log

v0.2.15-oicr1

  • GDC Product: Application Programming Interface (API)
  • Release Date: August 7, 2015

New Features and Changes

  • None to report

Bugs Fixed Since Last Release

  • Addressed an issue in the range aggregation feature (used by facets)

Known Issues and Workarounds

  • Query and Download Service
    • Universal Resource Locator (URL) length is limited. As such, download requests with many files have to be divided into multiple requests. A feature that allows a payload to specify the file identifiers to download to overcome this limitation is planned for a future release.
    • All TARGET, CGCI, and CCLE data is currently not available via the GDC API but will be made available as data is continously imported into the GDC
  • Authentication and Authorization Service
    • Obtaining a token requires browser access. This is a limitation of eRA Commons and not the GDC authorization service. The Security Assertion Markup Language (SAML) based protocol eRA Commons uses does not support ECP (or similar)

Release details are maintained in the GDC API change log

v0.2.13

  • GDC Product: Application Programming Interface (API)
  • Release Date: July 23, 2015

New Features and Changes

  • Query and Download Service
    • Implemented server-side related files
    • Created a quick search endpoint
  • Misc
    • Added POST support
    • Added range support (used by range facet)
    • Hooked-up reports to new reports index

Bugs Fixed Since Last Release

  • Query and Download Service
    • Fixed error (500) on annotations without notes
    • Correct structure for related files
    • Fixed error (404) with annotation download
    • Fixed issue with support for IS NOT operator

Known Issues and Workarounds

  • Query and Download Service
    • Universal Resource Locator (URL) length is limited. As such, download requests with many files have to be ivided into multiple requests. A feature that allows a payload to specify the file identifiers to download to zovercome this limitation is planned for a future release.
    • All TARGET, CGCI, and CCLE data is currently not available via the GDC API but will be made available as data is continously imported into the GDC
  • Authentication and Authorization Service
    • Obtaining a token requires browser access. This is a limitation of eRA Commons and not the GDC authorization service. The Security Assertion Markup Language (SAML) based protocol eRA Commons uses does not support ECP (or similar)

Release details are maintained in the GDC API change log

v0.1.10

  • GDC Product: Application Programming Interface (API)
  • Release Date: March 18, 2015

New Features and Changes

  • Query and Download Service
    • Supports query for files, participants, annotations, and projects by metadata. Interfaces with ElasticSearch for efficient queries.
    • Provides a RESTful interface to support the download of data, metadata, and annotations
    • Supports the download of multiple files, manifests, or annotations in compressed (gzip) format by default
  • Authentication and Authorization Service
    • Authenticates users using the GDC authorization service which authorizes against dbGaP
    • Manages tokens and token-based authorization using OpenStack Keystone
    • Implements federated authentication with eRA Commons to generate a Keystone token
    • Downloads Comma Separated Values (CSVs) from dbGaP at regular intervals and verifies authorization using eRA Commons credentials

Bugs Fixed Since Last Release

  • Query and Download Service
    • Initial Release - Not Applicable
  • Authentication and Authorization Service
    • Further developed the prototype into a production ready service

Known Issues and Workarounds

  • Query and Download Service
    • Universal Resource Locator (URL) length is limited. As such, download requests with many files have to be divided into multiple requests. A feature that allows a payload to specify the file identifiers to download to overcome this limitation is planned for a future release.
    • All TARGET, CGCI, and CCLE data is currently not available via the GDC API but will be made available as data is continously imported into the GDC
  • Authentication and Authorization Service
    • Obtaining a token requires browser access. This is a limitation of eRA Commons and not the GDC authorization service. The Security Assertion Markup Language (SAML) based protocol eRA Commons uses does not support ECP (or similar)

Release details are maintained in the GDC API change log

v0.1.8

  • GDC Product: Application Programming Interface (API)
  • Release Date: January 22, 2015

New Features and Changes

  • Identity Service (Signpost)
    • Provides an internal identity service used for assigning Digital IDs to all GDC data
    • Tracks the location of data in GDC object stores
  • Authentication and Authorization Service
    • Provides a prototype service for authenticating using eRA Commons as the identity provider and dbGaP for authorization

Bugs Fixed Since Last Release

  • None to report

Known Issues and Workarounds

  • Identify Service (Signpost)
    • The internal identity service does not support authentication for create, read, update, and delete operations as this is an internal service
  • Authentication and Authorization Service
  • Obtaining a token requires browser access. This is a limitation of eRA Commons, not the GDC authorization service. The SAML based protocol eRA Commons uses does not support ECP (or similar)

Release details are maintained in the GDC API change log.