Removed the GUI

To reduce the amount of deprecated/unsecure dependencies, we've removed most of the GUI.

v1.5.0 Alpha Release

This pre-release introduces

• The Variants Discovery APIs, which includes /variants/beacon/range/search, which returns variants above reporting threshold, and /variants/beacon/allele/freq/search, which returns variants with their AF info.
• The related API definition.

And fixes

• The /info endpoint
• A bug when variants search may error out due to some incorrect annotation parsing.

v1.4.0

This is the v1.4.0 release of the candig-server.

This release introduces:

• Database Snapshot Report: A new functionality that creates reports either in HTML or Markup containing information about Clinical; Pipeline; Genomic; Dataset; and Id of Patients stored in the database.

For more information about Database Snapshot Report. please check the documentation.

Improvements:

• Some improvements on the documentation
• Upgrade of some third-party libraries, improving security

Component	Changes were made	Backward compatibility
API	No	N/A
Server Side Configs	No	N/A

v1.3.0

This is the v1.3.0 release of the candig-server.

This release introduces:

• The updated candig-server data schema to incorporate the needs of RedCap data.
• A re-organized static directory.
• Updated dependencies.

In order to help you smoothly transition to the new data schema, we have provided a schema migration script that helps you convert existing databases. If you are installing the server for the first time with no existing databases, you may ignore the following part.

To upgrade your existing database, please follow the upgrade guideline here: https://candig-server.readthedocs.io/en/v1.3.0/status.html.

Component	Changes were made	Backward compatibility
API	No	N/A
Server Side Configs	No	N/A
Database Schema	Yes	No (migration script provided)

v1.2.3

This is the v1.2.3 release of the candig-server.

This release introduces:

• A mobile-responsive dashboard.
• Updated dependencies.

Fixes:

• A timeout limit on peer server request. It's supposed to be included in a previous release, but was not.

---

Component	Changes were made	Backward compatibility
API	No	N/A
Server Side Configs	No	N/A

v1.2.2

This is the v1.2.2 release of the candig-server.

This release introduces:

• A now-backward-compatible access_list handling method that correctly supports specifying X, (empty space), or null (not specifying anything) to indicate no access.

Fixes:

• Some typos on the documentation.

---

Component	Changes were made	Backward compatibility
API	No	N/A
Server Side Configs	Yes	Yes

v1.2.1

This is the v1.2.1 of the candig-server.

This release introduces:

• The updated access_list mechanism that now uses X to indicate a user having no access to a particular dataset.
• The updated acceptable list of DUO ids, as DUO:0000002 and DUO:0000003 have now been removed in the most recent release of DUO.

Fixes:

• A bug that incorrectly throws BadRequestException at valid queries for users with partial data access (0 <= level < 4).
• A bug where session_id was not removed from some client side functions that make requests.

We now recommend against

• The usage of empty space to indicate the user having no access to a particular dataset. It is recommended to use X instead.

---

For system administrators:
From this release onwards, we will now include an Upgrade Guideline for every new release, which will include our recommendations on any updates to the server-side configurations, it will be under the Status at https://candig-server.readthedocs.org

---

Component	Changes were made	Backward compatibility
API	No	N/A
Server Side Configs	Yes	Yes

v1.2.0

This is the v1.2.0 of the candig-server.

This release introduces:

• the removal of authentication-related code to work with the virtual endpoints
• the timeout limit of federation-related calls, in case the peer server is timing out
• the updated docs

Please note that from this release onwards, candig-server will not work with the old Tyk setup, as the authentication code has been moved up to Tyk virtual endpoints, with updated middleware. If you are running this candig-server in standalone mode, this should not affect you. Otherwise, make sure you update your Tyk configs while updating to this version of candig-server.

---

Component	Changes were made	Backward compatibility
API	No	N/A
Server Side Configs	Yes	Yes (See note below)

• If you deploy candig-server with Tyk, then you will need to make configuration changes. Using this package standalone does not require any changes.

v1.1.0

This is the v1.1.0 of the candig-server.

This release introduces:

• the ability to add and retrieve DUO info of a dataset.
• the addition of variants/gene/search endpoint.
• the updated variants component for /search and /count, which now accepts a gene.
• the initial release of a public-facing doc available at https://candig-server.readthedocs.io.
• two updated API specs, one for regular endpoints, one for /search and /count endpoints.
• additional unit tests to the new variants components.

Fixes:

• the bug where the nextPageToken may not work correctly for variants/search endpoint.
• the bug where the nextPageToken may not work correctly for /search endpoint when you specify fields.
• the bug where the /variantsbygenesearch endpoint sometimes returns variantsByGene as the key under /search endpoint, while it should have been variants.
• the flaky firefox selenium test.

Deprecates:

• the endpoint, /variantsbygenesearch, you should use variants/gene/search instead. Everything else stays the same.
• the component key variantsByGene, you should now specify variants instead. Everything else stays the same.

---

Component	Changes were made	Backward compatibility
API	Yes	Yes
Server Side Configs	No	N/A

v1.0.3

This release mainly focuses on performance improvement, with minor improvement on error message handling.

This release introduces:

• Ingest commands add-variantset, add-readgroupset and add-featureset can now be completed faster.
• A larger default cache size for pysam file handles caching. We recommend users who set up the server in production environment manually overwrite this value should they feel the need, and adjust the file handles cache limit of their OS correspondingly.
• Improved error handling for ingesting duplicated pysam-related datasets.
• Use <form> element so users can click 'Enter' to initiate a search.

This is an intermediate release before the release v1.1.0, whose progress is available from https://github.com/CanDIG/candig-server/projects/2