From 628ea1579f516f8561a33038c0bd1762e2a6ad69 Mon Sep 17 00:00:00 2001 From: Chris Bizon Date: Thu, 25 Jul 2024 10:15:50 -0400 Subject: [PATCH 1/3] Updated Priorities --- PrioritiesSprint5.md | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/PrioritiesSprint5.md b/PrioritiesSprint5.md index ed97aca..8398a0f 100644 --- a/PrioritiesSprint5.md +++ b/PrioritiesSprint5.md @@ -21,10 +21,9 @@ Note that ARAs will be required to implement at least one of MCQ, Pathfinder, or - Continue to improve results # MultiCURIE Query (MCQ) -## Fugu (TEST) work: +## Guppy (CI) work: +- Complete inferred mode MCQ of - Develop UI. UI must be developed in a way that the build could be pushed to PROD with or without MCQ enabled -- Manual MCQ testing once the UI is developed -- Go / No-go decision on releasing MCQ to PROD # LLM Summarization ## Pre-development work: @@ -40,10 +39,16 @@ Note that ARAs will be required to implement at least one of MCQ, Pathfinder, or ## Fugu (TEST): - Initial UI implmentation +# Treats Refactor +## Guppy (CI): +- Teams remove Chembl Clinical Trials ingests +- Clinical Trial KP deploys TRAPI endpoint; SmartAPI registration + # Develop Automated Tests ## Pre-Development - Run Benchmarking Suite -- Run MCQ Suite +- Develop MCQ Suite +- Develop Pathfinder Suite # Fix Failing Automated Tests ## Guppy (CI): @@ -52,7 +57,7 @@ Note that ARAs will be required to implement at least one of MCQ, Pathfinder, or # Collect Feedback Issues ## Fugu (TEST): - Each team must perform manual testing of the Fugu release in TEST and report issues to the Feedback repo -between July 2 and July 9, 2024 +between August 2 and August 9, 2024 - TAQA will review and prioritize the discovered issues # Fix Feedback issues @@ -67,4 +72,4 @@ between July 2 and July 9, 2024 ## Pre-development # Publications -## Pre-development \ No newline at end of file +## Pre-development From 9733b5b6dde56709073fe37cf855ae53dc079a55 Mon Sep 17 00:00:00 2001 From: Chris Bizon Date: Thu, 25 Jul 2024 11:58:02 -0400 Subject: [PATCH 2/3] TACT Meeting updates --- PrioritiesSprint5.md | 34 ++++++++++++++++++++++++++-------- 1 file changed, 26 insertions(+), 8 deletions(-) diff --git a/PrioritiesSprint5.md b/PrioritiesSprint5.md index 8398a0f..484b74e 100644 --- a/PrioritiesSprint5.md +++ b/PrioritiesSprint5.md @@ -16,14 +16,20 @@ Note that ARAs will be required to implement at least one of MCQ, Pathfinder, or # Develop Pathfinder Query ## Pre-development work: - Implement automated tests -- Establish performance goals ## Guppy (CI) work: -- Continue to improve results +- ARAs Pass TRAPI validation +- Non-responding ARAs return 501(or 405 - double check) +- ARS to test merging of Pathfinder responses +- ARAs implement Constraints # MultiCURIE Query (MCQ) ## Guppy (CI) work: -- Complete inferred mode MCQ of -- Develop UI. UI must be developed in a way that the build could be pushed to PROD with or without MCQ enabled +- Genetics KP to deploy GeneSet Enrichment +- Complete inferred mode MCQ in ARA +- Non responding ARAs return 501(or 405 - double check) +- Test results on example queries +- ARS to test merging of MCQ responses +- UI inspects inferred results; begins development # LLM Summarization ## Pre-development work: @@ -35,24 +41,33 @@ Note that ARAs will be required to implement at least one of MCQ, Pathfinder, or # Display Full KL/AT in the UI ## Guppy (CI): +- KPs complete implementation; reduce level of "unknown/not provided" - Complete QA of KP implementation ## Fugu (TEST): -- Initial UI implmentation +- Initial UI implmentation; dependent on KP completion # Treats Refactor ## Guppy (CI): -- Teams remove Chembl Clinical Trials ingests - Clinical Trial KP deploys TRAPI endpoint; SmartAPI registration +- KPs (SPOKE, KG2, MolePro, SP) to start removing Chembl Clinical Trial ingests + +Move to Sprint 6: +- KP remove Chembl Clinical Trials ingests # Develop Automated Tests ## Pre-Development -- Run Benchmarking Suite +- Develop Benchmarking Suite - Develop MCQ Suite - Develop Pathfinder Suite +- Work on TRAPI Validation Runner +- Address issues in the Test repo to improve the test cases +- Programmatically address test case names and identifiers +- Update Evaluation of Top Answer to move towards an absolute cutoff of 30 # Fix Failing Automated Tests ## Guppy (CI): -- Each ARA is expected to pass X tests from the Sprint 5 test suite +- Each ARA is expected to pass 55 tests from the Top Answer Sprint 5 test suite +- Each ARA is expected to pass 360 tests from the Never Show Sprint 5 test suite # Collect Feedback Issues ## Fugu (TEST): @@ -70,6 +85,9 @@ between August 2 and August 9, 2024 # CLEAN-UP EFFORT: Documentation ## Pre-development +- Each team closes Guppy documentation issues # Publications ## Pre-development +- Circulate Outline of proposed pub +- Collect feedback and updates of outline From f9a6cfdd1be44769df7aea49e47e371c61827894 Mon Sep 17 00:00:00 2001 From: cbizon Date: Mon, 5 Aug 2024 20:13:56 -0400 Subject: [PATCH 3/3] Update PrioritiesSprint5.md Cleaned up 501/405 and Publications --- PrioritiesSprint5.md | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/PrioritiesSprint5.md b/PrioritiesSprint5.md index 484b74e..24c4cc7 100644 --- a/PrioritiesSprint5.md +++ b/PrioritiesSprint5.md @@ -18,7 +18,7 @@ Note that ARAs will be required to implement at least one of MCQ, Pathfinder, or - Implement automated tests ## Guppy (CI) work: - ARAs Pass TRAPI validation -- Non-responding ARAs return 501(or 405 - double check) +- Non-responding ARAs return 501 - ARS to test merging of Pathfinder responses - ARAs implement Constraints @@ -26,7 +26,7 @@ Note that ARAs will be required to implement at least one of MCQ, Pathfinder, or ## Guppy (CI) work: - Genetics KP to deploy GeneSet Enrichment - Complete inferred mode MCQ in ARA -- Non responding ARAs return 501(or 405 - double check) +- Non responding ARAs return 501 - Test results on example queries - ARS to test merging of MCQ responses - UI inspects inferred results; begins development @@ -89,5 +89,4 @@ between August 2 and August 9, 2024 # Publications ## Pre-development -- Circulate Outline of proposed pub -- Collect feedback and updates of outline +- Collect feedback and use cases