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VCell HDF5 File not properly formatted for BSTS specifications #769

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Tracked by #1046
CodeByDrescher opened this issue Jan 31, 2023 · 2 comments · May be fixed by #779
Closed
Tracked by #1046

VCell HDF5 File not properly formatted for BSTS specifications #769

CodeByDrescher opened this issue Jan 31, 2023 · 2 comments · May be fixed by #779
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BioSimulators java Pull requests that update Java code Standards Type: Bug bug report validation VCell-7.5.1 VCell-7.6.0

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Problem

For the past many weeks, BSTS has been reporting we are not meeting their standards, and not executing correctly.
After much investigation, it was determined that BSTS was not in the wrong (see #647), and the problem lied within VCell.

Specifically, VCell is not producing the expected HDF5 results file with the proper format. With recent changes to how our HDF5 results file is generated (previously "outsourced" to a python library, currently done "in house" within VCell), this is very plausible.
@CodeByDrescher CodeByDrescher added this to the Adherance to Biosimulators CLI Standard milestone Jan 31, 2023
@CodeByDrescher CodeByDrescher self-assigned this Jan 31, 2023
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Updates: The HDF5 file VCell produces is now nearly identical in fields to previously generated versions. However, BSTS still complains...Turns out, Biosimulations has incorrect documentation regarding how their HDF5 should be formatted. The source code of BSTS asks for (at least some) different information that what the document claims is needed. Fixed the obvious issue, but there may be more problems hidden by faulty online documentation and lightly documented source code.

@CodeByDrescher CodeByDrescher mentioned this issue Jan 31, 2023
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@CodeByDrescher CodeByDrescher added validation java Pull requests that update Java code labels Jan 31, 2023
@CodeByDrescher CodeByDrescher linked a pull request Feb 7, 2023 that will close this issue
VCell CLI HDF5 rewrite #779
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@CodeByDrescher CodeByDrescher added VCell-7.5.1 and removed High Priority VCell-7.5.0 Needed for Release 7.5 labels Mar 15, 2023
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closed by PR #844

@jcschaff jcschaff mentioned this issue Nov 15, 2023
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BioSimulators java Pull requests that update Java code Standards Type: Bug bug report validation VCell-7.5.1 VCell-7.6.0
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vcell development
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VCell CLI HDF5 rewrite virtualcell/vcell
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@ACowan0105 @CodeByDrescher