v3.0.0-rc.1

What's Changed

• feat: typed extra properties by @v-rocheleau in #387

• feat: explorer biosample experiment search by @noctillion in #399

• feat: add 'max_query_params' to public_overview response by @brouillette in #394

• feat: beacon search endpoint by @gsfk in #402

• feat: add data type counts & queryable flag to data types by @davidlougheed in #403

• chore: codecov github actions by @v-rocheleau in #393

• chore: change exp_type elisa to neutralizing antibody by @noctillion in #404

• chore(deps): bump sqlparse from 0.4.3 to 0.4.4 in /docs by @dependabot in #397

• chore(deps): bump django from 4.1.7 to 4.1.9 by @dependabot in #400

• chore(deps): bump django from 4.1.7 to 4.1.9 in /docs by @dependabot in #401

• chore(deps): bump requests from 2.28.2 to 2.31.0 by @dependabot in #405

• chore(deps): bump requests from 2.28.2 to 2.31.0 in /docs by @dependabot in #406

• chore: bump version to 3.0.0 by @davidlougheed in #407

• docs: Add logo and one-sentence description to README by @davidlougheed in #395

Version 2.18.2

• fix: properly log failed DRS response content/status code
• fix: properly obtain file path for DRS record (bento_lib 6.0.1)
• fix: security issue in Redis version

Version 2.18.1

• chore: update base image versions
• chore: add devcontainer metadata to dev image
• chore: don't use virtualenv in dev containers
• docs: update docs dependencies and Python version
• docs: read project metadata from pyproject.toml
• docs: add README note on debugging / container dev

Version 2.18.0

• feat: add bento.dataService and bento.gitCommit properties to /service-info
• feat: update bento_lib to 6 and add starts/ends-with and wildcard operators for Bento string search
• refact: move views in CHORD app into corresponding modules
• refact: move export-related code into chord.export module
• refact: improve cBioPortal-related code
• fix: don't spam Git config with safe path lines
• fix: separate allowed hosts and container name; allow both
• fix: only auto-generate migrations for auth and admin apps in runner script
• chore: non-root image user
• chore: use Poetry for dependency management
• chore: use base image Git config implementation
• chore: update WDLs to v1.0
• chore: annotate workflows with purpose property
• chore: update dependencies
• ci: remove Travis config file
• ci: update Bento build action to 0.11.0

Version 2.17.3

• feat: configurable log level
• fix: set individual id in biosamples if not specified and a subject is present in the phenopacket
• chore: log more about public endpoint requests
• chore: update some dependency patch versions
• test: make sure biosamples and individuals are properly associated

Version 2.17.2

• chore: update Django patch version

Version 2.17.1

• fix: leaking 0-count categories if using derived-from-DB category labels

Version 2.17.0

• feat: more robust validation of data prior to ingestion
  • actually validates the objects against the schema & returns errors
  • validates all objects prior to starting ingest
• feat: garbage collection - objects unused by table objects are deleted upon table deletion
• feat: support bento_wes 0.8 (Cromwell-based) with new workflows
• feat: delete phenotypic features when parent objects are deleted
• feat: configurable port in Docker image entrypoint
• chore: /service-info updates
• chore: improve logging
• chore: dependency updates

Version 2.16.1

• quick labels-related patch

Version 2.16.0

• feat: allow extra_properties overwriting for individuals during re-ingestion
• feat: add ASGI support
• feat: add 'self-hosted' Dockerfiles + CI image building
• feat: add data type labels
• feat: add custom label environment variable for phenopacket data type
• chore: disable mcode for now
• chore: update dependencies
• refact: split apart ingest module into multiple files