CLI reports.h5: wrong repeated-task values and parameter names for multi-parameter scans

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Evaluación

Dificultad
4/5
Tiempo estimado
3-5 días
Aptitud para principiantes
50/100
Tipo de issue
Error
Claridad
Bien especificado
Estado de actividad
Activo
Stack tecnológico
java
Área
cli, data

Línea de trabajo

Start in vcell-cli/src/main/java/org/vcell/cli/run/results/NonSpatialResultsConverter.java around lines 144-150, where the repeated-task names and values are built, then compare with getScanBounds() and getConstantArraySpec(name) in vcell-core's MathOverrides.java to see how jobs are numbered. Done means each constant's values are listed in the same sorted order as the HDF5 dimensions, and names, values and dimensions agree for a scan of two or more parameters. No existing test covers a two-parameter scan, so a new one is needed.

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Descripción

Summary

For a simulation with two or more scanned constants, the CLI writes wrong repeated-task metadata into the BioSimulators reports.h5. The data itself is laid out correctly. Single-parameter scans are unaffected.

Two defects

1. Wrong values in sedmlRepeatedTaskValues. NonSpatialResultsConverter.java:150 fills each constant's value list with getActualExpression(name, new ScanIndex(i)). ScanIndex is a job index, not a position within that constant's own values. MathOverrides numbers jobs row-major over the sorted constant names, first one outermost (MathOverrides.java:186), so job i only lines up with value i when one constant is scanned.

Example: scanning Ka = [0.5, 5] and kOn = [10, 20, 30] gives jobs 0 and 1 at coordinates (0,0) and (0,1). Ka is reported as [0.5, 0.5] instead of [0.5, 5].

2. Parameter names in hash order. sedmlRepeatedTaskParameterNames comes from getScannedConstantNames() (line 144), which reads from a HashMap (MathOverrides.java:47). The scan bounds, and therefore the HDF5 dimensions and data, use sorted order (getScanBounds()). When the two orders differ, names, value lists and dimensions refer to different parameters.

Fix

Take each constant's own values, getConstantArraySpec(name).getConstants(), and list constants in sorted order. The new data system (org.vcell.data, on the UnifiedDataModel branch) does this in SedmlReportDatasets.scanDimensions, with a test against MathOverrides' job numbering. No test archive scans two parameters, so neither system is exercised on this end to end.

Lenguaje dominante
Java
Estrellas
140
Forks
35
Merge medio
22 h 6 min
PR fusionados (30 d)
14

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