Fix validated-statistics run summaries 500 (invalid GROUP BY aggregation) by hyperpolymath · Pull Request #218 · hyperpolymath/MetaManifold-WebUI

hyperpolymath · 2026-10-23T01:07:58Z

Follow-up to #214: main CI still fails at 'Run validated-statistics tests first'.

Root cause (reproduced against DuckDB locally): _validated_duckdb_counts selected bare count columns beside GROUP BY <feature>:

Binder Error: column "s1" must appear in the GROUP BY clause or must be part of an aggregate function

so POST /api/v1/studies/{study}/runs/{run}/statistics/summaries returned 500 and test_validated_statistics.jl:180 failed on every branch.

Fix: fetch rows ORDER BY feature and sum rows sharing a feature in Julia BigInt. Aggregating in SQL is not an option: SUM over HUGEINT counts overflows exactly the values this path exists to keep exact (the test sums 2^126 + 2^126). Per-cell missing/negative/non-integer validation is unchanged; the cell budget is now checked on aggregated features.

Julia evidence is CI on this PR (no Julia runtime in the authoring sandbox; the SQL failure itself was reproduced with Python duckdb 2.0.0).

#193) Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

…nifold-webui # Conflicts: # README.md # config/defaults/pipeline.yml # frontend/src/api/types.ts # frontend/src/components/PipelineStages.tsx # frontend/src/components/differentialTable.ts # src/analysis/differential.jl Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

The squash merges of #196-#207 left main unable to build: PR-branch conflict resolutions overwrote each other's differential method registry, dropped the compositional include and cladistics routes, duplicated the clade-cumulus include and frontend panel import, and corrupted _differential_settings_error. - MetaManifold.jl: restore analysis/compositional.jl, include clade_cumulus.jl once; server.jl includes routes/cladistics.jl and routes/clade_cumulus.jl. - differential.jl: rebuild the 9-method registry and DifferentialConfig union (mn/dm optimiser + mc_samples), restore ancom_bc/aldex2/ songbird and multinomial dispatch branches alongside the two-part models; routes build the union config; config validation regains the mn/dm cross-key rules. - Frontend: union DifferentialMethod/config/diagnostics types, restore cladistics client imports, alias the cladistics panel so it no longer collides with the clade-cumulus panel, restore per-method CSV config lines and PipelineStages entries for all nine methods. - Tests that pinned pre-union method lists and the 11-column CSV are updated to the union reality. Frontend: tsc clean, bun test 87/87, production build passes. Julia: exercised by CI (no Julia runtime in the authoring sandbox). Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

…nifold-webui # Conflicts: # config/defaults/pipeline.yml # frontend/src/api/types.ts # frontend/src/components/PipelineStages.test.ts # frontend/src/components/PipelineStages.tsx # frontend/src/components/differentialTable.ts # frontend/src/views/StudyView.tsx # src/analysis/differential.jl # src/server/routes/analysis.jl # test/unit/test_differential.jl Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

…nifold-webui # Conflicts: # README.md Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

…nifold-webui Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

…d GROUP BY SQL _validated_duckdb_counts selected bare count columns beside GROUP BY <feature>, which DuckDB rejects with a BinderError, so POST /studies/{study}/runs/{run}/statistics/summaries returned 500 and step 'Run validated-statistics tests first' failed on every branch. Fetch rows ordered by feature and sum rows sharing a feature in Julia BigInt instead: SQL SUM over HUGEINT counts would overflow exactly the values this path exists to keep exact (the test sums 2^126 + 2^126). Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

chatgpt-codex-connector · 2026-10-23T01:08:06Z

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src/analysis/exact_summaries.jl
src/server/routes/validated_statistics.jl
src/server/server.jl
test/unit/test_exact_summaries.jl
test/unit/test_validated_statistics.jl

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github-actions · 2026-10-23T01:09:03Z

Fork governance

Lane	Status	Run
DEED syntax (repo deed)	🟢 conformant	run 39914815267
Hypatia verdict grid	purple (job: success)	same run

🟣 critical · commit 4833974baaf7 · run 39914815267

Reporter	Status	Critical	High	Medium	Since previous revision
Hypatia scan	🟣 critical	43	59	31	↑ improved (8 fewer blocking)
panic-attack assail	🔴 high	0	6	13	↔ unchanged
pons asinorum	🟡 medium	0	0	10	↔ unchanged
rhodibot (RSR compliance)	🟠 indeterminate	0	0	0	— indeterminate
panicbot (panic recovery, error handling)	🟠 indeterminate	0	0	0	— indeterminate
echidnabot (formal verification: proofs/)	🟠 indeterminate	0	0	0	— indeterminate
seambot (integration health: API routes)	🟠 indeterminate	0	0	0	— indeterminate
finishingbot (release readiness)	🟠 indeterminate	0	0	0	— indeterminate
accessibilitybot (WCAG on the React UI)	🟠 indeterminate	0	0	0	— indeterminate
glambot (presentation quality)	🟠 indeterminate	0	0	0	— indeterminate
cipherbot	⚪ not applicable	0	0	0	↔ unchanged
sustainabot	⚪ not applicable	0	0	0	↔ unchanged

Hypatia scan: 133 finding(s)

critical cicd_rules/banned_language_file — frontend/src/views/run/parseFilterYaml.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/figure/encode.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/figure/charts.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/figure/export.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/figure/figure.test.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/figure/legend.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/figure/types.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/utils/download.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/utils/text.test.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/utils/timeago.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/utils/text.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/hooks/useUnsavedGuard.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/hooks/useApi.test.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/hooks/useApi.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/hooks/useAnalysis.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/hooks/useSSE.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/hooks/useTabParam.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/hooks/useNavRefresh.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/hooks/useJobEvents.ts — TypeScript file detected -- banned language
critical cicd_rules/banned_language_file — frontend/src/about.ts — TypeScript file detected -- banned language
113 more; see the structured report in the artifact.

panic-attack assail: 19 finding(s)

high DynamicCodeExecution — src/pipeline/dada2/context.jl — eval/Meta.parse in src/pipeline/dada2/context.jl
high DynamicCodeExecution — src/analysis/analysis.jl — eval/Meta.parse in src/analysis/analysis.jl
high DynamicCodeExecution — src/analysis/differential.jl — eval/Meta.parse in src/analysis/differential.jl
high DynamicCodeExecution — src/core/provenance.jl — eval/Meta.parse in src/core/provenance.jl
high DynamicCodeExecution — scripts/check-julia-syntax.jl — eval/Meta.parse in scripts/check-julia-syntax.jl
high DynamicCodeExecution — test/unit/test_permanova.jl — eval/Meta.parse in test/unit/test_permanova.jl
medium UnsafeFFI — src/core/memory_probe.jl — 3 ccall/FFI calls in src/core/memory_probe.jl
medium InputBoundary — src/server/routes/runs.jl — 2 JSON3.read/JSON.parse call(s) with 0 try block(s) in src/server/routes/runs.jl — these throw on malformed input; wrap in try/catch
medium InputBoundary — src/server/routes/composition.jl — 6 JSON3.read/JSON.parse call(s) with 2 try block(s) in src/server/routes/composition.jl — these throw on malformed input; wrap in try/catch
medium InputBoundary — src/server/routes/studies.jl — 4 JSON3.read/JSON.parse call(s) with 2 try block(s) in src/server/routes/studies.jl — these throw on malformed input; wrap in try/catch
medium InputBoundary — src/server/routes/analysis.jl — 9 JSON3.read/JSON.parse call(s) with 3 try block(s) in src/server/routes/analysis.jl — these throw on malformed input; wrap in try/catch
medium UnsafeFFI — install.jl — 1 ccall/FFI calls in install.jl
medium ProofDrift — test/unit/test_occupancy_grade.jl — 2 `@test x isa Y` assertion(s) with no value check — type-only tests may substitute for an unwritten formal theorem in test/unit/test_occupancy_grade.jl
medium ProofDrift — test/unit/test_evidence.jl — 1 `@test x isa Y` assertion(s) with no value check — type-only tests may substitute for an unwritten formal theorem in test/unit/test_evidence.jl
medium InputBoundary — bench/advanced_zero_handling/benchmark.jl — 1 JSON3.read/JSON.parse call(s) with 0 try block(s) in bench/advanced_zero_handling/benchmark.jl — these throw on malformed input; wrap in try/catch
medium InputBoundary — frontend/src/figure/charts.ts — 1 JSON.parse call(s) with 0 try block(s) in frontend/src/figure/charts.ts — JSON.parse throws SyntaxError on malformed input; wrap in try-catch
medium InputBoundary — frontend/src/tree/model.ts — 1 JSON.parse call(s) with 0 try block(s) in frontend/src/tree/model.ts — JSON.parse throws SyntaxError on malformed input; wrap in try-catch
medium InputBoundary — frontend/src/api/events.ts — 2 JSON.parse call(s) with 0 try block(s) in frontend/src/api/events.ts — JSON.parse throws SyntaxError on malformed input; wrap in try-catch
medium InputBoundary — frontend/src/components/alphaMetrics.tsx — 1 JSON.parse call(s) with 0 try block(s) in frontend/src/components/alphaMetrics.tsx — JSON.parse throws SyntaxError on malformed input; wrap in try-catch

pons asinorum: 10 finding(s)

medium string-concat-in-loop — ./frontend/src/tree/model.ts:122 — string built by repeated concatenation in a loop (T0, HEURISTIC)
medium string-concat-in-loop — ./frontend/src/tree/model.ts:118 — string built by repeated concatenation in a loop (T0, HEURISTIC)
medium string-concat-in-loop — ./frontend/src/tree/TreeShapes.tsx:69 — string built by repeated concatenation in a loop (T0, HEURISTIC)
medium string-concat-in-loop — ./frontend/src/tree/TreeShapes.tsx:66 — string built by repeated concatenation in a loop (T0, HEURISTIC)
medium string-concat-in-loop — ./frontend/src/tree/TreeShapes.tsx:61 — string built by repeated concatenation in a loop (T0, HEURISTIC)
medium string-concat-in-loop — ./frontend/src/tree/TreeShapes.tsx:53 — string built by repeated concatenation in a loop (T0, HEURISTIC)
medium string-concat-in-loop — ./frontend/src/tree/TreeShapes.tsx:43 — string built by repeated concatenation in a loop (T0, HEURISTIC)
medium string-concat-in-loop — ./frontend/src/tree/TreeShapes.tsx:42 — string built by repeated concatenation in a loop (T0, HEURISTIC)
medium unreachable-after-jump — ./frontend/src/figure/PaneEditor.tsx:45 — statement is unreachable after an unconditional jump (T0, HEURISTIC)
medium unreachable-after-jump — ./frontend/src/components/PublicationTablesPanel.tsx:208 — statement is unreachable after an unconditional jump (T0, HEURISTIC)

rhodibot (RSR compliance): not_run — enrolled, but no report-back was received

🟠 indeterminate: enrolled, but no report-back was received

panicbot (panic recovery, error handling): not_run — enrolled, but no report-back was received

🟠 indeterminate: enrolled, but no report-back was received

echidnabot (formal verification: proofs/): not_run — enrolled, but no report-back was received

🟠 indeterminate: enrolled, but no report-back was received

seambot (integration health: API routes): not_run — enrolled, but no report-back was received

🟠 indeterminate: enrolled, but no report-back was received

finishingbot (release readiness): not_run — enrolled, but no report-back was received

🟠 indeterminate: enrolled, but no report-back was received

accessibilitybot (WCAG on the React UI): not_run — enrolled, but no report-back was received

🟠 indeterminate: enrolled, but no report-back was received

glambot (presentation quality): not_run — enrolled, but no report-back was received

🟠 indeterminate: enrolled, but no report-back was received

cipherbot: not_applicable — no cryptography is implemented in this repository

⚪ not applicable: no cryptography is implemented in this repository

sustainabot: not_applicable — fleet adapter slot reserved; no adapter exists yet (gitbot-fleet README)

⚪ not applicable: fleet adapter slot reserved; no adapter exists yet (gitbot-fleet README)

Scope: static findings reported by each row's tool at the named commit. Purple, red, yellow and blue grade the worst finding present; orange is evidence missing, malformed or a scanner that did not run; grey is an explicit scope exclusion with its reason. No row is a security certification. report.json, badge.json and the raw findings are in the verdict-grid artifact on the linked run.

…res; dedupe cladistics routes - exact_summaries _summarise returned an exact 0 for a zero-count feature; the storage contract (and both test assertions) define an unobserved feature's proportion as undefined (nothing), never a substituted zero. summary_to_display renders it as such instead of calling exact_value(nothing). - server.jl included routes/cladistics.jl twice (parallel repair residue), re-registering every cladistics route. - test_validated_statistics: the integral-float token case cannot be expressed through a Dict round-trip (JSON3.write(1.0) emits an integer token), so 1.0 joins 1e0 as raw-body cases; the server-side rejection they exercise is unchanged. Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

…ependent reference computes The handwritten assertions expected nothing for a zero-count feature in a positive-total sample, contradicting both the implementation (since #199) and the independent Python fractions verifier, which computes Fraction(0, total) = 0/1. Only a zero total leaves proportions undefined. Aligns the two assertions; implementation reverted to the plain exact_relative_abundance call. Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

…equest text JSON3 collapses integral float tokens (1.0, 1e0) to integers when parsing, so the parsed-body check in _json_exact_count can never see them and the endpoint accepted them with 200. _reject_float_count_tokens scans the raw body to the top-level counts member and refuses any numeric token that is not a plain integer token (strings skipped and validated separately after parsing), restoring the fail-closed contract the tests assert. Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

sonarqubecloud · 2026-10-23T06:59:14Z

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

hyperpolymath and others added 7 commits October 23, 2026 00:13

bench(differential): null-calibration bench + small-sample caveat (refs

ad7f5f2

#193) Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

Merge remote-tracking branch 'origin/main' into arena/dc1d6938-metama…

b7539f9

…nifold-webui # Conflicts: # README.md Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

Merge remote-tracking branch 'origin/main' into arena/dc1d6938-metama…

6b81ba5

…nifold-webui Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>

hyperpolymath and others added 4 commits October 23, 2026 01:18

Merge branch 'main' into arena/dc1d6938-metamanifold-webui

4833974

hyperpolymath merged commit a9b82e2 into main Oct 23, 2026
9 of 10 checks passed

hyperpolymath deleted the arena/dc1d6938-metamanifold-webui branch October 23, 2026 06:58

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Fix validated-statistics run summaries 500 (invalid GROUP BY aggregation) - #218

Fix validated-statistics run summaries 500 (invalid GROUP BY aggregation)#218
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