Four BMDB models fail at a second point, revealed once the COPASI annotation cast was fixed

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Valutazione

Difficoltà
4/5
Tempo stimato
3-5 giorni
Idoneità per principianti
52/100
Tipo di issue
Bug
Chiarezza
Abbastanza chiara
Stato di attività
Tranquilla
Stack tecnologico
java
Ambito
backend

Direzione di ricerca

Start at the SBML importer code that binds global parameters — the wording 'Error binding global parameter … is either not found in your model' should be searchable in the vcell-core import path. Load the BIOMD0000000872 (UNRESOLVED.initConc) and BIOMD0000000961 (rateOf_re15) archives to trace where UNRESOLVED. placeholders and SBML L3 rateOf terms are produced versus resolved. Done when both bindings succeed or fail with an actionable message, verified against the other ten SYSBIO_BIOMD archives from nightly run 32005421226.

Scritto dal modello di indicizzazione a partire dal testo della issue.

Descrizione

Split out from the baseline accept (PR to follow) so these do not disappear into test_cases.ndjson as permanent known-bad.

The COPASI annotation ClassCastException fix (#1974, issue #1461) let twelve SYSBIO_BIOMD archives get past SBML import for the first time. Eight now run clean. These four fail at a later stage — the cast had been masking a second fault in each, and nightly run 32005421226 is the first diagnosis we have of what that fault actually is.

model new failure_type message
BIOMD0000000849 DIVIDE_BY_ZERO Solver (CVodeSolverStandalone) status: Aborted (CVODE solver could not generate input file: …)
BIOMD0000000872 SBML_IMPORT_FAILURE Error binding global parameter 'beta' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used…
BIOMD0000000925 SOLVER_FAILURE Solver (CVodeSolverStandalone) status: Aborted (Could not e…)
BIOMD0000000961 SBML_IMPORT_FAILURE Error binding global parameter 'rateOf_re15' to model: 're15' is either not found in your model or is not allowed to be used…

These are not regressions

Every one of them was failing before, at an earlier point, for a reason that told us nothing. Nothing got worse; we can just see further now. The baseline accept is therefore correct — they genuinely do fail, and documenting that is honest.

But recording them as known-bad also makes them silent again, which is the exact failure mode the nightly gate exists to prevent. Hence this issue.

Worth noting: two look like distinct, tractable bugs

  • 872 and 961 are the same shape — a global parameter bound to something the model does not define (UNRESOLVED.initConc, rateOf_re15). rateOf is an SBML L3 construct; UNRESOLVED. looks like a VCell-side placeholder that escaped into a binding. Both are in our SBML importer, not the solver, and both may be one fix.
  • 849 and 925 are CVODE aborting before it starts — "could not generate input file" is a solver-input generation failure, not a numerical one. DIVIDE_BY_ZERO and SOLVER_FAILURE may be misclassifications of the same underlying problem.

Not urgent — these are curated BioModels that have never worked in VCell, and no user is waiting on them. But four archives moving from "unknown import error" to two identifiable pairs is the most tractable this has ever been.

Suggested next step

Take 872 or 961 first. A rateOf / unresolved-parameter binding bug in the SBML importer is likely to affect more than these two models — the other ten just failed earlier for a different reason, so we have no idea how many otherwise-importable models hit it.

Lingua principale
Java
Stelle
140
Fork
35
Merge medio
17h 39m
PR unite (30g)
19

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