Skip to content

WIP: ISARIC data schema integration - #16

Draft
sr-murthy wants to merge 20 commits into
mainfrom
integrate-isaric-schema
Draft

WIP: ISARIC data schema integration#16
sr-murthy wants to merge 20 commits into
mainfrom
integrate-isaric-schema

Conversation

@sr-murthy

@sr-murthy sr-murthy commented Jun 17, 2026

Copy link
Copy Markdown
Member
  • New ISARIC data schema lib. supporting transformations of raw custom clinical datasets into ISARIC data schema form via ADTL.
  • Transformations of ISARIC data schema-compliant data to "analysis data" format expected by VERTEX for the dashboard (insight panels).

Plus some other unrelated but useful improvements including:

PR RTD site.

@codecov

codecov Bot commented Jun 17, 2026

Copy link
Copy Markdown

Codecov Report

❌ Patch coverage is 76.36364% with 13 lines in your changes missing coverage. Please review.

Files with missing lines Patch % Lines
src/isaricanalytics/isaric_data_schema.py 63.63% 12 Missing ⚠️
src/isaricanalytics/isaric_transformations.py 95.45% 1 Missing ⚠️
Files with missing lines Coverage Δ
src/isaricanalytics/__init__.py 100.00% <ø> (ø)
src/isaricanalytics/analytics.py 11.33% <ø> (ø)
src/isaricanalytics/logging/logger.py 89.47% <ø> (ø)
src/isaricanalytics/redcap_data.py 11.72% <ø> (ø)
src/isaricanalytics/utils.py 93.75% <ø> (ø)
src/isaricanalytics/visualisation.py 60.00% <ø> (ø)
src/isaricanalytics/isaric_transformations.py 95.45% <95.45%> (ø)
src/isaricanalytics/isaric_data_schema.py 63.63% <63.63%> (ø)
🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

@sr-murthy sr-murthy linked an issue Jun 17, 2026 that may be closed by this pull request
@sr-murthy
sr-murthy marked this pull request as draft June 19, 2026 14:35
@sr-murthy sr-murthy self-assigned this Jun 19, 2026
@sr-murthy
sr-murthy force-pushed the integrate-isaric-schema branch from 0c32d80 to adecb32 Compare August 3, 2026 13:40
@sr-murthy
sr-murthy force-pushed the integrate-isaric-schema branch 2 times, most recently from 237f894 to 223245e Compare August 4, 2026 08:40
@sr-murthy sr-murthy added the enhancement New feature or request label Aug 4, 2026
Comment thread src/isaricanalytics/isaric_transformations.py Fixed
Comment thread src/isaricanalytics/isaric_transformations.py Fixed
@sr-murthy
sr-murthy force-pushed the integrate-isaric-schema branch from 681b4cb to b7a571c Compare August 6, 2026 10:21
@sr-murthy sr-murthy linked an issue Aug 6, 2026 that may be closed by this pull request
@sr-murthy
sr-murthy force-pushed the integrate-isaric-schema branch 10 times, most recently from 0f5425a to b5fb493 Compare August 7, 2026 08:11
@sr-murthy
sr-murthy marked this pull request as ready for review August 7, 2026 10:19
@sr-murthy sr-murthy changed the title WIP: Integrate ISARIC Schema Integrate ISARIC Data Schema Aug 7, 2026
@sr-murthy sr-murthy changed the title Integrate ISARIC Data Schema ISARIC data schema integration Aug 7, 2026
@sr-murthy sr-murthy added the documentation Improvements or additions to documentation label Aug 7, 2026
@sr-murthy

sr-murthy commented Aug 7, 2026

Copy link
Copy Markdown
Member Author

@alasdairwilson Please review, if you have time.

This is back in development again because of additional requirements, and will be resubmitted when it is ready.

@sr-murthy
sr-murthy force-pushed the integrate-isaric-schema branch 2 times, most recently from 7b5e7f3 to 125a3b5 Compare August 12, 2026 12:55
@sr-murthy
sr-murthy force-pushed the integrate-isaric-schema branch from 125a3b5 to e2a448a Compare August 13, 2026 13:11
@sr-murthy
sr-murthy removed the request for review from alasdairwilson August 17, 2026 10:05
@sr-murthy sr-murthy changed the title ISARIC data schema integration WIP: ISARIC data schema integration Aug 17, 2026
@sr-murthy
sr-murthy marked this pull request as draft August 17, 2026 10:06
This was linked to issues Aug 17, 2026
…, and switching to an `src`-style package layout
Comment thread src/isaricanalytics/isaric_transformations.py Dismissed
Comment thread src/isaricanalytics/isaric_transformations.py Dismissed
@sr-murthy sr-murthy added ci Continuous integration packaging Packaging including management of project metadata and dependencies in the TOML. refactor Refactoring changes tests All test-related changes labels Aug 17, 2026
@sr-murthy
sr-murthy force-pushed the integrate-isaric-schema branch from b0b85ec to ea5c141 Compare August 18, 2026 09:38
@sr-murthy sr-murthy linked an issue Aug 18, 2026 that may be closed by this pull request
@sr-murthy
sr-murthy force-pushed the integrate-isaric-schema branch from 6867375 to 7a6722d Compare August 18, 2026 09:53
@sr-murthy
sr-murthy force-pushed the integrate-isaric-schema branch from 7a6722d to 1c04ce8 Compare August 18, 2026 09:55
Comment thread src/isaricanalytics/isaric_data_schema.py Fixed
Comment thread src/isaricanalytics/isaric_data_schema.py Fixed
Comment thread src/isaricanalytics/isaric_data_schema.py Fixed
Comment thread src/isaricanalytics/isaric_data_schema.py Fixed
Comment thread src/isaricanalytics/isaric_data_schema.py Fixed
@sr-murthy
sr-murthy force-pushed the integrate-isaric-schema branch from 25dc778 to a7e4434 Compare August 18, 2026 11:30
Comment thread src/isaricanalytics/isaric_data_schema.py Fixed
Comment thread src/isaricanalytics/isaric_data_schema.py Fixed
Comment thread src/isaricanalytics/isaric_data_schema.py Fixed
Comment thread src/isaricanalytics/isaric_data_schema.py Fixed
Comment thread src/isaricanalytics/isaric_data_schema.py Dismissed
Comment thread tests/unit/test_isaric_data_schema.py Dismissed
@sr-murthy
sr-murthy force-pushed the integrate-isaric-schema branch from 56a02d8 to e43d1b6 Compare August 27, 2026 10:08
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

ci Continuous integration documentation Improvements or additions to documentation enhancement New feature or request packaging Packaging including management of project metadata and dependencies in the TOML. refactor Refactoring changes tests All test-related changes

Projects

None yet

Development

Successfully merging this pull request may close these issues.

Bump min. Python version to 3.12 pytest fixtures Switch to src-style package layout Doctests Integrate ISARIC schema

1 participant