CLI reports.h5: sedmlDataSetShapes per job, and Y curves labelled ::X

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Evaluación

Dificultad
3/5
Tiempo estimado
1-2 días
Aptitud para principiantes
55/100
Tipo de issue
Error
Claridad
Bastante claro
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 line 170, where one shapes list is shared across data sets and each job's flat size is appended. Then check the label format strings in ResultsConverter.java at lines 84 and 93, and the comment above add2DPlotsAsReports in prepareNonSpatialDataForHdf5. Done means one comma-joined shape per data set, curve data sets labelled without the ::X suffix, and the comment matching the BioSimulators-mode condition. Confirm the output still matches the legacy writer's expected reports.h5 on the UnifiedDataModel branch, since the issue asks for both changes to be deliberate.

Escrito por el modelo de indexación a partir del texto del issue.

Descripción

Summary

Two places where the CLI's reports.h5 deviates from the BioSimulators conventions. Both are intentionally reproduced, for now, by the new data system on the UnifiedDataModel branch so its output can be checked byte-for-byte against the legacy writer. Fix them deliberately, in both places.

1. sedmlDataSetShapes has one entry per data set per job. NonSpatialResultsConverter.java:170 shares one shapes list across all data sets and appends each job's flat size to it. A 3-data-set report over a 3-value scan gets 9 entries such as "21", where the convention is one comma-joined shape per data set.

2. Plots reported as reports label every curve data set <plot>.<curve>::X. That includes the Y data generators: ResultsConverter.java:84 and line 93 use the same format string.

Related, minor: the comment above add2DPlotsAsReports in prepareNonSpatialDataForHdf5 says plots are added when not in BioSimulators mode, but the code adds them only in BioSimulators mode.

Lenguaje dominante
Java
Estrellas
140
Forks
35
Merge medio
11 h 28 min
PR fusionados (30 d)
19

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