API Release Notes

Version	Date
v7.7.0	November 21, 2024
v7.5.1	September 30, 2024
v7.4.1	July 30, 2024
v7.3.0	June 26, 2024
v4.0.0	July 31, 2023
v3.28.0	May 11, 2023
v3.5.0	July 8, 2022
v3.3.0	May 17, 2021
v3.0.0	August 14, 2020
v2.1.2	May 7, 2020
v2.1.0	March 10, 2020
v2.0.0	January 30, 2020
v1.23.0	November 6, 2019
v1.22.0	July 31, 2019
v1.21.0	June 5, 2019
v1.20.0	April 17, 2019
v1.19.0	February 20, 2019
v1.18.0	December 18, 2018
v1.17.0	November 7, 2018
v1.16.0	September 27, 2018
v1.15.0	August 23, 2018
v1.14.1	May 21, 2018
v1.14.0	April 23, 2018
v1.13.0	February 15, 2018
v1.12.0	December 21, 2017
v1.11.0	November 16, 2017
v1.10.0	August 22, 2017
v1.9.0	June 29, 2017
v1.8.0	May 9, 2017
v1.7.1	March 16, 2017
v1.5.0	October 31, 2016
v1.4.0	September 23, 2016
v1.3.1	September 7, 2016
v1.2.0	August 9, 2016
v1.1.0	May 25, 2016
v1.0.1	May 16, 2016

v7.7.0

• GDC Product: Application Programming Interface (API)
• Release Date: November 21, 2024

New Features and Changes

• New permission system for internal projects to:
  • Verify presence of UUIDs where needed
  • Remove permissions for centers to upload to unneeded node types

Bugs Fixed Since Last Release

• None

Known Issues and Workarounds

• Some fields may be repeated in the API or data portal due to being in a transitional states. As a workaround, select all of the fields of interest, and the results will demonstrate which are currently populated.
• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v7.5.1

• GDC Product: Application Programming Interface (API)
• Release Date: September 30, 2024

New Features and Changes

• New QC tests have been added to the QC Reports section of the submission portal. These include:
  • Verifying that normal samples don't have tumor descriptors and that tumor samples do
  • Verifying that cases that were not lost to follow up do not have a corresponding date indicating that they were lost

Bugs Fixed Since Last Release

• None

Known Issues and Workarounds

• Some fields may be repeated in the API or data portal due to being in a transitional states. As a workaround, select all of the fields of interest, and the results will demonstrate which are currently populated.
• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v7.4.1

• GDC Product: Application Programming Interface (API)
• Release Date: July 30, 2024

New Features and Changes

• The API indices will include fields from the "other clinical attribute" entity types. This will be visible in the next data release.

Bugs Fixed Since Last Release

• None

Known Issues and Workarounds

• Some fields may be repeated in the API or data portal due to being in a transitional states. As a workaround, select all of the fields of interest, and the results will demonstrate which are currently populated.
• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v7.3.0

• GDC Product: Application Programming Interface (API)
• Release Date: June 26, 2024

New Features and Changes

• The GDC submission API now supports the PATCH method, which allow users to upload without required fields while updating already-existing entities.
• The gene expression API is now available to be queried by users. See the Gene Expression API documentation for more information.

Bugs Fixed Since Last Release

• None

Known Issues and Workarounds

• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v4.0.0

• GDC Product: Application Programming Interface (API)
• Release Date: July 31, 2023

New Features and Changes

• The GDC API no longer supports download of Legacy Archive files.

Bugs Fixed Since Last Release

• None

Known Issues and Workarounds

• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v3.28.0

• GDC Product: Application Programming Interface (API)
• Release Date: May 11, 2023

New Features and Changes

• The /legacy/files endpoint has been deprecated and is no longer available.
• Features to support Data Portal bugfixes were added.

Bugs Fixed Since Last Release

• None

Known Issues and Workarounds

• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v3.5.0

• GDC Product: Application Programming Interface (API)
• Release Date: July 8, 2022

New Features and Changes

• Features to support Data Portal performance were added.

Bugs Fixed Since Last Release

• None

Known Issues and Workarounds

• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v3.3.0

• GDC Product: Application Programming Interface (API)
• Release Date: May 17, 2021

New Features and Changes

• Features to better support batch tracking for submitted data were added.

Bugs Fixed Since Last Release

• None

Known Issues and Workarounds

• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v3.0.0

• GDC Product: Application Programming Interface (API)
• Release Date: August 14, 2020

New Features and Changes

• Enhancements were made to increase performance.

Bugs Fixed Since Last Release

• None

Known Issues and Workarounds

• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v2.1.2

• GDC Product: Application Programming Interface (API)
• Release Date: May 7, 2020

New Features and Changes

• An update to improve usability in the homepage quicksearch

Bugs Fixed Since Last Release

• None

Known Issues and Workarounds

• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v2.1.0

• GDC Product: Application Programming Interface (API)
• Release Date: March 10, 2020

New Features and Changes

• New data dictionary changes.

Bugs Fixed Since Last Release

• None

Known Issues and Workarounds

• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v2.0.0

• GDC Product: Application Programming Interface (API)
• Release Date: January 30, 2020

New Features and Changes

• API code now uses Python 3.

Bugs Fixed Since Last Release

• None

Known Issues and Workarounds

• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v1.23.0

• GDC Product: Application Programming Interface (API)
• Release Date: November 6, 2019

New Features and Changes

• QC Tests added for Submission
• BAM slicing is now supported for unmapped reads
• API now includes data from molecular_test and follow_up nodes. This impacts what is displayed on the GDC Data Portal
• Better handling of concurrent transactions
• CIViC annotations now included on the ssms endpoint. You can read more about CIViC annotations here

Bugs Fixed Since Last Release

• Fixed API memory leak
• Fixed data offset issue returned by clinical.tar endpoint

Known Issues and Workarounds

• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v1.22.0

• GDC Product: Application Programming Interface (API)
• Release Date: July 31, 2019

New Features and Changes

• Updated BCR Clinical XML parser code to support future indexing of additional clinical data. Parser code can be found here

  • Added a mapping for:

    • ann_arbor_b_symptoms
    • ann_arbor_extranodal_involvement
    • ajcc_pathologic_t
    • ajcc_pathologic_n
    • ajcc_pathologic_m
    • ajcc_clinical_t
    • ajcc_clinical_n
    • ajcc_clinical_m
    • ajcc_staging_system_edition
    • figo_stage
    • ajcc_clinical_stage
    • primary_gleason_grade
    • secondary_gleason_graade
    • igcccg_stage
    • masaoka_stage

  • Updated the mapping for:

    • primary_diagnosis, morphology, tissue_or_organ_of_origin, and site_of_resection_or_biopsy

Bugs Fixed Since Last Release

• Fixed a bug preventing multipart uploads

Known Issues and Workarounds

• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v1.21.0

• GDC Product: Application Programming Interface (API)
• Release Date: June 5, 2019

New Features and Changes

• Mutation indexer update to accommodate data model changes
• Updates to when in the release cycle downloaders and submitters have access to files

Bugs Fixed Since Last Release

• None

Known Issues and Workarounds

• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v1.20.0

• GDC Product: Application Programming Interface (API)
• Release Date: April 17, 2019

New Features and Changes

• Disallowed creation of multiple file versions in the same data release
• Improved API concurrency performance and addressed random failures/4XX/5XX responses
• Improved API/Portal performances for querying large sets of data from the Elasticsearch indices
• Updated BCR Clinical XML parser code to support future indexing of additional clinical data. Parser code can be found here
  • Updated the mapping for:
    • days_to_death
    • days_to_birth
    • vital_status
    • prior_malignancy and synchronous_malignancy
  • Added a mapping for:
    • pack_years_smoked
    • prior_treatment
    • age_at_index
    • days_to_diagnosis
    • icd_10_code
    • year_of_diagnosis
  • Remove calculation for:
    • cigarettes_per_day
    • year_of_birth
    • year_of_death
    • bmi
  • Updated XML Parser to pull the most Up-to-Date Survival Information

Bugs Fixed Since Last Release

• None

Known Issues and Workarounds

• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v1.19.0

• GDC Product: Application Programming Interface (API)
• Release Date: February 20, 2019

New Features and Changes

• Added API features to support controlled access DAVE
• Updated API query endpoints to handle filtering of queries based on tokens
• Created login notification Endpoint
• Added hashing and logging for similar ES queries

Bugs Fixed Since Last Release

• Fixed bug where quick search ES query grows with each request
• Fixed bug where new file versions could be created when exactly the same existing metadata is uploaded
• Fixed bug where submitting to specific projects produced error that data already existed

Known Issues and Workarounds

• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v1.18.0

• GDC Product: Application Programming Interface (API)
• Release Date: December 18, 2018

New Features and Changes

• Update to auth for GDC Pre-Release Data Portal

Bugs Fixed Since Last Release

• None

Known Issues and Workarounds

• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v1.17.0

• GDC Product: Application Programming Interface (API)
• Release Date: November 7, 2018

New Features and Changes

• Created new index cnv_centric
• Created new index cnv_occurrence_centric
• Created new REST API endpoints for CNV
• Created mapping from aliquot to case for occurrence on cnv_centric
• Created new graphql endpoints for CNV
• Updated index case_centric to add cnv
• Updated index gene_centric to add cnv

Bugs Fixed Since Last Release

• Fixed bug to prevent users from deleting files in state submitted or released

Known Issues and Workarounds

• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v1.16.0

• GDC Product: Application Programming Interface (API)
• Release Date: September 27, 2018

New Features and Changes

• Tissue_type is now parsed from the BCR Biospecimen submission

Bugs Fixed Since Last Release

• Re-attach the /files path to the legacy blueprints in gdcapi
• Fix Internal Server Error when exporting JSON in Data Portal

Known Issues and Workarounds

• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v1.15.0

• GDC Product: Application Programming Interface (API)
• Release Date: August 23, 2018

New Features and Changes

• Added support for file versioning
• Added new API endpoints in support of versioning: history, files/versions, and files/versions/manifest
• Updated the submit and release process
• Created admin endpoint to allow for modifying file and project flags and states
• Populate version and release information for all existing files

Bugs Fixed Since Last Release

• None

Known Issues and Workarounds

• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v1.14.1

• GDC Product: Application Programming Interface (API)
• Release Date: May 21, 2018

New Features and Changes

• None

Bugs Fixed Since Last Release

• Update to XML submission to correctly import biospecimen relationnships
• GraphQL submission queries return incorrect information

Known Issues and Workarounds

• The error message for not including a token is incorrect for controlled access API requests (e.g. bam slicing). It states that your token is invalid, but it should request that a token be supplied.
• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v1.14.0

• GDC Product: Application Programming Interface (API)
• Release Date: April 23, 2018

New Features and Changes

• Updated support of BCR XML submission for Next Generation Cancer Models

Bugs Fixed Since Last Release

• None

Known Issues and Workarounds

• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v1.13.0

• GDC Product: Application Programming Interface (API)
• Release Date: February 15, 2018

New Features and Changes

• Reduced number of submission portal timeouts by optimizing graphql API requests

Bugs Fixed Since Last Release

• Fixed bug preventing submission of clinical data via BCR XML

Known Issues and Workarounds

• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v1.12.0

• GDC Product: Application Programming Interface (API)
• Release Date: December 21, 2017

New Features and Changes

• None

Bugs Fixed Since Last Release

• Updated submit project button on submission portal to work more quickly for projects with large numbers of nodes

Known Issues and Workarounds

• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v1.11.0

• GDC Product: Application Programming Interface (API)
• Release Date: November 16, 2017

New Features and Changes

• Added support for histogram aggregation for numeric fields

Bugs Fixed Since Last Release

• None

Known Issues and Workarounds

• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v1.10.0

• GDC Product: Application Programming Interface (API)
• Release Date: August 22, 2017

New Features and Changes

• Longitudinal clinical data can now be submitted to the GDC
• Created new entities and reorganized the location of many properties in the GDC Dictionary. A list of deprecated properties and their new locations can be found here. Note that the deprecated properties still contain all information that they previously did. In a later release we will map the data from the old location to the new. Eventually, we will suspend submission to the old properties and will remove them entirely from the GDC.
• GDC Data Dictionary Changes Details
  • Created follow_up entity to support longitudinal clinical data
  • Deprecated clinical test entity
  • Modified acceptable values for Read Group properties
  • Modified Diagnosis entity
  • Modified Treatment entity
  • Modified Demographic entity
  • Modified Case entity
  • Added new tumor code, tumor id, and sample types to Sample entity to support OCG
  • Added property days_to_diagnosis to Diagnosis entity
  • Created Somatic Mutation Index entity
  • Updated CaDSR CDE links in data dictionary
  • Added new sample type tumor to sample entity
  • Made classification_of_tumor on diagnosis entity non-required
  • Added support for FM-AD to Genomic Profile Harmonization Workflow entity
  • Added data type Gene Level Copy Number Scores to Copy Number Segment entity

Known Issues and Workarounds

• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v1.9.0

• GDC Product: Application Programming Interface (API)
• Release Date: June 29, 2017

New Features and Changes

• Updated ability to search data based on genes and mutations have been released. Discussion of the new endpoints and their use can be found in the Data Portal User Guide. These feature are limited to those projects for which the GDC contains open-access MAF files.

• API request parameter from now returns first record when from=0. Previously, from=1 was the first record. from=0 is now the default.

Known Issues and Workarounds

• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v1.8.0

• GDC Product: Application Programming Interface (API)
• Release Date: May 9, 2017

New Features and Changes

• Users can now control whether a set of files will be compressed or not when downloading. For further details see the API Users Guide.

Known Issues and Workarounds

• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v1.7.1

• GDC Product: Application Programming Interface (API)
• Release Date: March 16, 2017

New Features and Changes

• Submission: Due to Data Dictionary updates new submission templates may be required for users submitting JSON and TSV formats
• Submission: Entities in submitted state (assigned when the project has been submitted) cannot be deleted.
• Submission: When attempting to delete an entity that has child entities not specified in the request, an error message is generated that will include all of the child entities' UUIDs.
• Submission: Entities associated with files uploaded to the GDC object store cannot be deleted until the associated file has been deleted.
• Re-enable Review, Submit, and Release functions for submission
• GDC Data Dictionary Changes
• Added "submittable" property to all entities
• Changed Read Group to category biospecimen
• Added many new clinical properties available for submission
• Added sample codes from Office of Cancer Genomics (OCG) to analyte and aliquot
• Slides can now be attached to sample rather than just portion
• sample_type_id is no longer required when submitting sample entities
• analyte_type_id is no longer required when submitting aliquot and analyte entities
• Clinical Test Entity is created for storing results of a variety of potential clinical tests related to the diagnosis -
• Genomic Profiling Report entity created for storing particular derived sequencing results
• Structural Variation entity created
• Project entity includes new field "Intended Release Date"
• Project entity includes new field "Releasable"

Bugs Fixed Since Last Release

• Fixed bug where boolean properties were not accepted with TSV submission

Known Issues and Workarounds

• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v1.5.0

• GDC Product: Application Programming Interface (API)
• Release Date: October 31, 2016

New Features and Changes

• API responds with an error when the request specifies an unsupported combination of filters and facets.
• In TSV submissions, trailing and leading whitespace, including non-ASCII whitespace characters, are stripped from property names and values.
• For released projects, any updates to previously submitted entities (i.e. "state": "submitted") will be included in the following GDC data release.
• Performance improvements for manifest generation.

Bugs Fixed Since Last Release

• Uploading certain unsupported metadata files caused the associated submission transactions to remain stuck in pending state.

Known Issues and Workarounds

• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v1.4.0

• GDC Product: Application Programming Interface (API)
• Release Date: September 23, 2016

New Features and Changes

• Submission transaction log includes additional information to assist in tracking.
• Submission project state transitions are disabled temporarily while project release features are being improved.
• GDC data dictionary changes:
  • The submittable property was added to all entity types in the GDC data model. It indicates whether the entity type can be submitted by users.
  • Category of Read Group entities in the GDC Data Model has changed from data_bundle to biospecimen.
  • Analyte entities support an expanded set of analyte_type values.

Bugs Fixed Since Last Release

• None to report

Known Issues and Workarounds

• API search & retrieval queries that do not include a sort parameter may return results in different order each time they are executed. This is a particular problem for paginated responses (i.e. responses to queries for which the number of results is greater than the size parameter).
  • Workaround: Include a sort parameter in API search & retrieval queries.
• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v1.3.1

• GDC Product: Application Programming Interface (API)
• Release Date: September 7, 2016

New Features and Changes

• Successful _dry_run submission transactions can be committed to the GDC data model without having to re-upload metadata. The transactions can also be closed to prevent them from being committed in the future.
• Submission transactions can be submitted in asynchronous mode. In this mode, the GDC API will issue an immediate acknowledgement of the transaction, along with the transaction_id. The status of the transaction can be verified by the user at a later time by specifying the transaction_id. Users submitting large transactions may find this mode helpful.
• New submission transaction properties can be queried with GraphQL
• GDC Data Dictionary changes:
  • Clinical Supplement entities can have data_format set to OMF.
  • Biospecimen Supplement entities can have data_format set to SSF or PPS.
  • Read group instrument_model can be set to "Illumina HiSeq 4000".
  • Category of Slide entities in the GDC Data Model has changed from data_bundle to biospecimen.

Bugs Fixed Since Last Release

• Incorrect BMI calculation in the import of BCR XML files.

Known Issues and Workarounds

• API search & retrieval queries that do not include a sort parameter may return results in different order each time they are executed. This is a particular problem for paginated responses (i.e. responses to queries for which the number of results is greater than the size parameter).
  • Workaround: Include a sort parameter in API search & retrieval queries.
• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v1.2.0

• GDC Product: Application Programming Interface (API)
• Release Date: August 9, 2016

New Features and Changes

• Tarballs generated by the data endpoint in response to multi-file data download requests now include a folder structure that puts each file in a folder whose name is the file's UUID.
• UUIDs in clinical XML files are no longer treated in a case-sensitive way by the submission endpoint.
• Improved performance of submission endpoint for transactions that include many cases.
• Speed improvements for the submission endpoint.
• BCR XML is no longer validated against its XSD at submission.

Bugs Fixed Since Last Release

• Fixed handling of POST requests to address problems with cart functionality in older versions of Firefox
• Files of category related_files can now be downloaded from the data endpoint.
• Allowed submission by projects in certain dbGaP registration states that were previously blocked.

Known Issues and Workarounds

• API search & retrieval queries that do not include a sort parameter may return results in different order each time they are executed. This is a particular problem for paginated responses (i.e. responses to queries for which the number of results is greater than the size parameter).
  • Workaround: Include a sort parameter in API search & retrieval queries.
• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v1.1.0

• GDC Product: Application Programming Interface (API)
• Release Date: May 25, 2016

New Features and Changes

• BAM index files (.bai) are now automatically downloaded with parent BAM.

Bugs Fixed Since Last Release

• None to report

Bugs Fixed Since Last Release

• Sorting by file submitter_id no longer causes an internal server error
• BAM index files are now included with harmonized BAM files
• Certain very long API requests will time out. It is recommended to break up into a series of smaller requests.

Known Issues and Workarounds

• Fields are not counted as missing if parent field is also missing. This may occur with queries of nested fields in the Data Portal Advanced Search or an API query using a filter. This behavior could impact results reported using search parameters of "IS MISSING" or "NOT MISSING".
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.

v1.0.1

• GDC Product: Application Programming Interface (API)
• Release Date: May 16, 2016

New Features and Changes

• HTTP interface that uses JSON as the primary data exchange format
• Programmatic access to functionality provided by GDC Data and Submission portals, via projects, cases, files, annotations, data, slicing, status, and submission endpoints
• Programmatic access to GDC Legacy Archive via legacy endpoint
• Token-based authentication for secure access to controlled data and to submission functionality
• RESTful search that supports simple and complex queries via filters, fields, and facets parameters, and project, files, cases, and annotations endpoints.
• Search results can be sorted using sort parameter, paginated using size and from parameters, and output in JSON, TSV, and XML using format and pretty parameters.
• _mapping endpoint enables user discovery of fields available for data search and retrieval operations
• Support for downloading of individual files and of archives containing multiple files
• Generation of download and upload manifests for use with the GDC Data Transfer Tool
• BAM slicing functionality for downloading part(s) of a BAM file specified using chromosomal coordinates or HGNC gene names
• Transactional submission system that links individual data elements according to a graph-based GDC Data Model
• Two data entity identifiers: UUIDs, which are consistent across GDC, and Submitter IDs, for compatibility with submitters' tracking systems

Bugs Fixed Since Last Release

• None to report

Known Issues and Workarounds

• Use of non-ascii characters in token passed to Data Transfer Tool will produce incorrect error message "Internal server error: Auth service temporarily unavailable".
• Use of a decimal in an integer search field produces unexpected error.
• Certain very large API requests will time out. It is recommended to break up very large requests into a series of smaller requests.