Epic: fix remaining issues in biosimulators_vcell for nonspatial simulations

[jcschaff]

Motivation

VCell solvers are made available for third party usage through the biosimulators_vcell container. This container is used when running vcell simulations on the run.biosimulations.org service. On some occasions, external investigators have used biosimulators_vcell container to run vcell solvers standalone. Our biosimulators_vcell container must conform to the common requirements for all biosimulators containers in order to be interoperable.

Completion Criteria

• the biosimulators_vcell container must pass the BSTS acceptance tests (Biosimulators Test Suite)
• the biosimulators_vcell container must run those vcell published biomodels which are to be deployed as biosimulations.org projects, and similarly have them pass when run through run.biosimulations.org.

Tasks

• VCell CLI can not handle nested sed-documents #291
• VCell Can no longer run published model "Elowitz-Nature-2000-Repressilator" #293
• VCell CLI does not output correctly #294
• CLI Throws exception trying to run URI Fragment defined ModelSources #321
• Running VCell CLI in Debug Mode causes model simulations to fail (!) #256
• Certain tests run by BioSimulators Test Suite should not be skipped. #375
• VCell does not read nor process BSTS algorithm substitution environment variable #418
• Jlibsedml is throwing a null pointer exception when VCell is validated by local BSTS #496
• Biosimulators GitHub-Hosted Test Suite does not properly validate (VCell) #647
• VCell HDF5 File not properly formatted for BSTS specifications #769
• Sedml HDF5 is missing some data sets with repeated tasks. #863
• VCell can accidentally delete input file when output is not "encapsulated" #871
• VCell CLI does not produce a data-filled HDF5 file for spatial simulations #875
• VCell Spatial HDF5 does not meet BioSimulators Standards #876
• List of multiple models / multiple publications. #921
• VCell Biosimulations Container no longer validates (singularity) #1007
• Bean Utills has too much disparate functionally with many side effects; Need to separate into different utility classes #1044
• VCell CLI uses GUI components preventing it being used in BioSimulators' Biosimulators microservice through Singularity. #1045
• refine biosimulations_pipeline and vcell_pipeline python tools #1059
• Upload All Nonspatial VCell Projects to BioSimulations #1074

Future Work

• Jhdf5 may have newer major (and minor) version under different "hdfjni" name #987