v3.0.0: MoH data model 3, performance improvements

MoH data model 3, performance improvements

What's Changed

• v2.0.0: Katsu UUIDs, completeness stats by @daisieh in #16
• v2.1.0: Clinical discovery and bugfixes by @OrdiNeu in #23
• v2.3.0: Discovery queries by @daisieh in #34
• DIG-1630: Match chromosomes with single digits/letters by @mshadbolt in #35
• DIG-1664: Silence logging for service-info calls (to prevent health check flooding) by @OrdiNeu in #38
• Don't pass in OPA_SECRET by @daisieh in #41
• DIG-1533: cancer_type->primary_site & DIG-1583: Implement censoring on aggregate count threshold by @OrdiNeu in #40
• Replace 'single quote' in PR titles by @mshadbolt in #43
• Bump flask-cors from 3.0.10 to 4.0.1 by @dependabot in #39
• Feature/whoami by @OrdiNeu in #42
• Bugfix: sidebar cohort style pipeDeliminated by @CourtneyGosselin in #44
• DIG-1686: Update query to work with updated katsu endpoints by @OrdiNeu in #45
• Use generic drug names when querying by @OrdiNeu in #46
• DIG-1719: switch to candigv2-logging module by @daisieh in #47
• Fixup the counts of the primary sites in the main query call by @OrdiNeu in #48
• Merge model_3 into develop by @mshadbolt in #49
• Bump flask-cors from 4.0.1 to 5.0.0 by @dependabot in #50
• DIG-1761: switch to gunicorn by @daisieh in #51
• DIG-1778: Improve timing of query calls by @OrdiNeu in #52
• v3.0.0: MoH data model 3, performance improvements by @daisieh in #53
• Add link to API in readme by @kcranston in #54
• DIG-1803, DIG-1810: query fixes by @daisieh in #55
• Query should handle 401 unauthorized exceptions from Katsu gracefully by @OrdiNeu in #56
• Hotfix: handle 401 unauthorized exceptions by @daisieh in #57
• DIG-1833: Query returns all donors to the clinical data table when no donors match a genomic query by @OrdiNeu in #58
• Stable: Missing response hotfix by @OrdiNeu in #59

New Contributors

• @dependabot made their first contribution in #39
• @CourtneyGosselin made their first contribution in #44
• @kcranston made their first contribution in #54

Full Changelog: v2.3.0...v3.0.0

v2.3.0: Discovery queries

Highlights

• Query can assemble discovery queries
• Speedups

What's Changed

• Protect against a few null cases by @OrdiNeu in #26
• Extend timeout for queries to be 60s by @OrdiNeu in #27
• DIG-1597: primary site query fix by @mshadbolt in #29
• DIG-1372: Query can assemble discovery queries by @OrdiNeu in #28
• Use Opa Secret and update authx by @daisieh in #30
• Allow parameters with commas by switching the internal splitter to pipe-delimiters by @OrdiNeu in #32
• DIG-1616: Stop using donor-with-clinical-data endpoint for clinical data table by @OrdiNeu in #31
• Switch to using the new endpoint for genomic_completeness by @OrdiNeu in #33

Full Changelog: v2.2.0...v2.3.0

v2.2.0: Bugfixes

What's Changed

• DIG-1527: Catch error when treatment_type is null by @mshadbolt in #24
• Add summary_cases to summary_stats by @mshadbolt in #25

Full Changelog: v2.1.0...v2.2.0

v2.1.0: Clinical discovery and bugfixes

Summary of Changes

• Update versions of Alpine and Python and other dependencies
• Several fixes to make it work with the new frontend, including genomic search fixes, etc.
• Fix a miscount on donors contributing to age summary stats once per treatment

What's Changed

• Add fixes for things that changed with the Katsu UUID fix by @OrdiNeu in #6
• DIG-1149: Update Alpine to 3.18 by @daisieh in #8
• DIG-1377: Be consistent in our use of candig user inside containers by @OrdiNeu in #7
• DIG-1144: update to python 3.12 by @daisieh in #9
• Fix for the search page on query by @OrdiNeu in #12
• DIG-1382, DIG-1384: query uses a service token with htsget by @daisieh in #11
• add libffi-dev dependency by @mshadbolt in #13
• DIG-1447: Fix the miscount on donors contributing to age summary stats once per treatment by @OrdiNeu in #14
• Genomic search fix by @OrdiNeu in #15
• Add workflow file (copied from HTSGet) by @OrdiNeu in #10
• DIG-1416: Add intervals support by @OrdiNeu in #17
• Add clinical discovery queries by @OrdiNeu in #18
• DIG-1376 :Update GH Action to improve PR title and description by @mshadbolt in #19
• Bugfix: Missing data and completeness data by @OrdiNeu in #20
• Bump versions to fix Snyk vulnerabilities by @OrdiNeu in #21
• Bugfix/htsget pruning by @OrdiNeu in #22

New Contributors

• @mshadbolt made their first contribution in #13

Full Changelog: v2.0.0...v2.1.0

v2.0.0: Katsu UUIDs, completeness stats

What's Changed

• DIG-1240: API middleware service to handle queries across federated instances by @OrdiNeu in #1
• Fix to the age at diagnosis summary stat not working by @OrdiNeu in #4
• Completeness stats query by @OrdiNeu in #2
• Fix an issue where an unknown date of birth or diagnosis would fail by @OrdiNeu in #5

Full Changelog: v1.0.0...v2.0.0

v1.0.0: Initial Release

Initial release of the query microservice.