regenerate tests...add semmeddb tests

[sierra-moxon]

the old process used to change test numbers, but I don't see that old python script ... I did change some testcases (adding testassets).

can you remind me of the process here? I am drafting the PR for now.

[Copilot]

Pull request overview

This PR refreshes a large portion of the acceptance test corpus by swapping out older “NeverShow”/legacy cases for new SemMedDB replacement cases, and by adding/updating the corresponding standalone test_assets/* JSON files used to construct test cases and suites.

Changes:

• Replaced a set of test_cases/TestCase_*.json entries with SemMedDB replacement “treats” and “affects” assertions (and updated metadata/tags accordingly).
• Added many new test_assets/Asset_*.json files (and updated a few existing ones) to match the new/updated test cases.
• Standardized test metadata for the new assets (e.g., test_source: "TranslatorTeam" and semmeddb_replacement tagging).

Reviewed changes

Copilot reviewed 85 out of 85 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
test_cases/TestCase_1.json	Replaces legacy treats case with SemMedDB replacement Parkinson disease treatments
test_cases/TestCase_3.json	Replaces legacy treats case with SemMedDB replacement rheumatoid arthritis treatments
test_cases/TestCase_6.json	Replaces legacy treats case with SemMedDB replacement schizophrenia treatments
test_cases/TestCase_7.json	Replaces legacy treats case with SemMedDB replacement migraine treatments
test_cases/TestCase_8.json	Replaces legacy treats case with SemMedDB replacement epilepsy treatments
test_cases/TestCase_9.json	Replaces legacy treats case with SemMedDB replacement BPH treatment
test_cases/TestCase_10.json	Replaces legacy treats case with SemMedDB replacement malaria treatment
test_cases/TestCase_11.json	Replaces legacy treats case with SemMedDB replacement diarrhea treatment
test_cases/TestCase_12.json	Replaces legacy treats case with SemMedDB replacement ulcerative colitis treatment
test_cases/TestCase_13.json	Replaces legacy treats case with SemMedDB replacement ALS treatment
test_cases/TestCase_14.json	Replaces legacy treats case with SemMedDB replacement Alzheimer disease treatment
test_cases/TestCase_15.json	Replaces legacy treats case with SemMedDB replacement plasma cell myeloma treatment
test_cases/TestCase_16.json	Replaces legacy treats case with SemMedDB replacement ovarian cancer treatment
test_cases/TestCase_17.json	Replaces legacy treats case with SemMedDB replacement COPD treatment
test_cases/TestCase_18.json	Replaces legacy treats case with SemMedDB replacement “affects gene” case (ADORA2B)
test_cases/TestCase_19.json	Replaces legacy treats case with SemMedDB replacement “affects gene” cases (PTGS2)
test_cases/TestCase_20.json	Replaces legacy treats case with SemMedDB replacement “affects gene” case (HTR1A)
test_cases/TestCase_22.json	Replaces legacy treats case with SemMedDB replacement “affects gene” cases (HMGCR)
test_cases/TestCase_23.json	Replaces legacy treats case with SemMedDB replacement “affects gene” case (ACE)
test_cases/TestCase_24.json	Replaces legacy “affects gene” case with SemMedDB replacement “affects gene” case (COMT)
test_cases/TestCase_26.json	Replaces legacy treats case with SemMedDB replacement “affects gene” case (SLC5A2)
test_cases/TestCase_29.json	Replaces legacy treats case with SemMedDB replacement “affects gene” case (SMO)
test_cases/TestCase_30.json	Replaces legacy treats case with SemMedDB replacement “affects gene” case (BCL2)
test_cases/TestCase_31.json	Replaces legacy treats case with SemMedDB replacement “affects gene” case (ADORA2A)
test_cases/TestCase_32.json	Replaces legacy treats case with SemMedDB replacement “affects gene” case (SLC12A1)
test_assets/Asset_670.json	Adds SemMedDB replacement standalone asset (multiple sclerosis)
test_assets/Asset_671.json	Adds SemMedDB replacement standalone asset (Apomorphine → Parkinson disease)
test_assets/Asset_672.json	Adds SemMedDB replacement standalone asset (Clonidine → hypertension)
test_assets/Asset_673.json	Adds SemMedDB replacement standalone asset (Levodopa → Parkinson disease)
test_assets/Asset_674.json	Adds SemMedDB replacement standalone asset (Methylprednisolone → RA)
test_assets/Asset_675.json	Adds SemMedDB replacement standalone asset (Fenofibrate → Hypercholesterolemia)
test_assets/Asset_676.json	Adds SemMedDB replacement standalone asset (Pyridostigmine → myasthenia gravis)
test_assets/Asset_677.json	Adds SemMedDB replacement standalone asset (Selegiline → Parkinson disease)
test_assets/Asset_678.json	Adds SemMedDB replacement standalone asset (Haloperidol → schizophrenia)
test_assets/Asset_679.json	Adds SemMedDB replacement standalone asset (Quinapril → hypertension)
test_assets/Asset_680.json	Adds SemMedDB replacement standalone asset (Simvastatin → Hypercholesterolemia)
test_assets/Asset_681.json	Updates existing asset to SemMedDB replacement standalone asset (Sumatriptan → migraine)
test_assets/Asset_682.json	Updates existing asset to SemMedDB replacement standalone asset (Phenytoin → epilepsy)
test_assets/Asset_683.json	Adds SemMedDB replacement standalone asset (Iloperidone → schizophrenia)
test_assets/Asset_684.json	Adds SemMedDB replacement standalone asset (Telmisartan → hypertension)
test_assets/Asset_685.json	Adds SemMedDB replacement standalone asset (Tamsulosin → BPH)
test_assets/Asset_686.json	Adds SemMedDB replacement standalone asset (Quetiapine → schizophrenia)
test_assets/Asset_687.json	Adds SemMedDB replacement standalone asset (Zolmitriptan → migraine)
test_assets/Asset_688.json	Adds SemMedDB replacement standalone asset (Celecoxib → RA)
test_assets/Asset_689.json	Adds SemMedDB replacement standalone asset (Pyrimethamine → malaria)
test_assets/Asset_690.json	Updates existing asset to SemMedDB replacement standalone asset (Loperamide → diarrhea)
test_assets/Asset_691.json	Adds SemMedDB replacement standalone asset (Mesalazine → ulcerative colitis)
test_assets/Asset_692.json	Adds SemMedDB replacement standalone asset (Riluzole → ALS)
test_assets/Asset_693.json	Updates existing asset to SemMedDB replacement standalone asset (Lamotrigine → epilepsy)
test_assets/Asset_694.json	Adds SemMedDB replacement standalone asset (Rizatriptan → migraine)
test_assets/Asset_695.json	Adds SemMedDB replacement standalone asset (Rivastigmine → Alzheimer disease)
test_assets/Asset_696.json	Adds SemMedDB replacement standalone asset (Rosuvastatin → Hypercholesterolemia)
test_assets/Asset_697.json	Adds SemMedDB replacement standalone asset (Bortezomib → plasma cell myeloma)
test_assets/Asset_698.json	Adds SemMedDB replacement standalone asset (Olaparib → ovarian cancer)
test_assets/Asset_699.json	Adds SemMedDB replacement standalone asset (Aclidinium → COPD)
test_assets/Asset_700.json	Adds SemMedDB replacement standalone asset (Adenosine affects ADORA2B)
test_assets/Asset_701.json	Adds SemMedDB replacement standalone asset (Aspirin affects PTGS2)
test_assets/Asset_702.json	Adds SemMedDB replacement standalone asset (Buspirone affects HTR1A)
test_assets/Asset_703.json	Adds SemMedDB replacement standalone asset (Fluoxetine affects SLC6A4)
test_assets/Asset_704.json	Adds SemMedDB replacement standalone asset (Indomethacin affects PTGS2)
test_assets/Asset_705.json	Adds SemMedDB replacement standalone asset (Lovastatin affects HMGCR)
test_assets/Asset_706.json	Adds SemMedDB replacement standalone asset (Ramipril affects ACE)
test_assets/Asset_707.json	Adds SemMedDB replacement standalone asset (Simvastatin affects HMGCR)
test_assets/Asset_708.json	Adds SemMedDB replacement standalone asset (Tolcapone affects COMT)
test_assets/Asset_709.json	Adds SemMedDB replacement standalone asset (Erlotinib affects EGFR)
test_assets/Asset_710.json	Adds SemMedDB replacement standalone asset (Canagliflozin affects SLC5A2)
test_assets/Asset_711.json	Adds SemMedDB replacement standalone asset (Dabrafenib affects BRAF)
test_assets/Asset_712.json	Adds SemMedDB replacement standalone asset (Ibrutinib affects BTK)
test_assets/Asset_713.json	Adds SemMedDB replacement standalone asset (Sonidegib affects SMO)
test_assets/Asset_714.json	Adds SemMedDB replacement standalone asset (Venetoclax affects BCL2)
test_assets/Asset_715.json	Adds SemMedDB replacement standalone asset (Adenosine affects ADORA2A)
test_assets/Asset_716.json	Adds SemMedDB replacement standalone asset (Bumetanide affects SLC12A1)
test_assets/Asset_717.json	Adds SemMedDB replacement standalone asset (Citalopram affects SLC6A4)
test_assets/Asset_718.json	Adds SemMedDB replacement standalone asset (Clozapine affects HTR2A)
test_assets/Asset_719.json	Adds SemMedDB replacement standalone asset (Dinoprostone affects PTGER2)

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[maximusunc]

I think the test cases being overwritten and getting all mangled has been an issue without a fix for a while.

[maximusunc]

Lots of changes here, a little too much to look through. The summary is nice. I think my only question is why are some test assets looking like they're being overwritten? For example, it looks like test asset 69 is being overwritten by test asset 681, which seems weird.