CLI reports.h5: repeated task without changes loses its iteration dimension

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
35/100
Issue type
Bug
Clarity
Mostly clear
Activity status
Active
Tech stack
java
Domain
backend

Research direction

Start with the synthetic archive SimulatorSupportsRepeatedTasksWithLinearUniformRanges/1.execution-should-succeed.omex under vcell-cli/src/test/resources/bsts-omex/synths/sedml/ and with BSTSBasedOmexExecTest, which currently checks only success. Then trace how the SED-ML importer turns a repeatedTask with no setValue changes into MathOverrides, and why the run collapses to one job. Done means the __repeated_task_report shape matches the expected [4, 2, 1, 11] and the test asserts report shapes.

Written by the indexing model from the issue text.

Description

Summary

A SED-ML repeatedTask that iterates without changing anything is reported without its iteration dimension.

The BioSimulators synthetic archive SimulatorSupportsRepeatedTasksWithLinearUniformRanges/1.execution-should-succeed.omex (in vcell-cli/src/test/resources/bsts-omex/synths/sedml/) has a repeated task over a 2-point uniformRange with no setValue changes. VCell writes __repeated_task_report with shape [4, 11]. BioSimulators expects [4, 2, 1, 11]: data sets × iterations × sub-tasks × time points.

The same happens for the other synthetic repeated-task archives I checked: Logarithmic, Vector, Functional, Nested and MultipleSubTasks ranges.

BSTSBasedOmexExecTest doesn't catch this because it only checks that execution succeeds, not the report shapes.

Likely cause

Repeated tasks become VCell parameter scans through MathOverrides. With no change targeting a parameter there is nothing to scan, so the run collapses to one job and the iteration axis disappears. This needs confirming in the SED-ML importer.

Dominant language
Java
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Forks
35
Avg merge
11h 28m
Merged PRs (30d)
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