Version 2.15.1

• chore: log which biosample not being found triggers a failure in experiments ingestion

Version 2.15.0

• feat: support cBioPortal-formatting analysis workflow
• fix: issues with Bento Public result values

Version 2.15.0 alpha 1

• feat: support cBioPortal-formatting analysis workflow
• fix: issues with Bento Public result values

Version 2.14.1

Patches three issues:

• correct overcount of biosamples in Bento search results
• remove "containing" option from search of fields with controlled vocabularies (use = only)
• remove controlled vocabulary from usage field in experiment results schema

Version 2.14.0

New features

• Search statistics endpoint: /api/search_overview this endpoint receives a query with the id parameter corresponding to a list of individual ids and returns a JSON response with various statistics. This is used for displaying a search overview in Bento after a search has returned with some results.
• Statistics added to the public search endpoint
• Features from CANDig fork merged

Libraries upgrade

• Django 4.1.1
• Python requirements 3.8, 3.9 and 3.10

Fixes

• swagger UI and Django Rest Framework API run in contenairized environment
• improved public config features
• improved speed for fulltext search (skipping serializer)

Version 2.14.0 Release Candidate 4

New features

• Search statistics endpoint: /api/search_overview this endpoint receives a query with the id parameter corresponding to a list of individual ids and returns a JSON response with various statistics. This is used for displaying a search overview in Bento after a search has returned with some results.
• Statistics added to the public search endpoint
• Features from CANDig fork merged

Libraries upgrade

• Django 4.1.1
• Python requirements 3.8, 3.9 and 3.10

Fixes

• swagger UI and Django Rest Framework API run in contenairized environment

Version 2.13.0

New Features

• Added batch/ endpoint to query individuals and get csv as a response
• Bento Query searches: added two response formast, values list and bento_search_results for smaller payload (and faster serialization)
• Added Public datasets endpoint. Also serve DATS file for provenance data.
• augment controlled vocabulary for experiments (for BQC19 experiments)

Fixes

• overview: months before october have no reported values

Full Changelog: v2.12.0...v2.13.0

Version 2.12.0

Public endpoints revision, Improvements in overview generation and developer experience

Public configuration

The format of the public configuration file (config.json) has been modified. Please see the documentation for a detailed explanation of the latest specifications.

Public enpoints

The three public endpoints have been modified to apply privacy rules to the computation of their responses and restrict the queries accordingly.

Overview

The statistics generated for the overview response are now computed using distinct queries to the database. This reduces the computations on the backend side and the overall response time

Developper experience

• swagger documentation is available in the repository directly
• debugpy is invoked in DEBUG mode. This allows attaching the VS-code debugger to a running instance of Katsu within a container. Amongst other features, it is possible to step through the code execution, add breakpoints, inspect variables as the code is running in a complete microservice architecture.

Version v2.11.0

This version:

• Adds Experiments controlled vocabularies to schemas and removes them from models.py;
• Adds filters for Experiment results API;
• Adds datasets metadata to the api/public_overview response so that it can be used as provenance metadata in the public portal;
• Updates and adds more documentation;
• Sets Python 3.6 for readthedocs documentation build;
• Updates PyJWT library to 2.4.0 version;
• Updates rdflib to 5.0.0 and rdflib-jsonld to 0.5.0 versions.

Version v2.10.0

This version:

• Adds the ability to export a dataset as a series of text files suitable for ingestion by cBioPortal at /private/export;
• Adds type exception for public overview count;
• Updates django from 2.2.27 to 2.2.28