Ported over scripts from Transform to work as SDK modules and deconstructed to allow SDK Data <-> File methods for SDK developers. Previously those scripts called the FBA service, but now call a local FBA service code implementation directly.
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Not sure how biomass is passed into the file- the script takes a single string, the Narrative method takes a list- probably we need to convert the list to a comma or semicolon separated string? For now, it looks like somewhere in the code it is split by semicolon, so we pass in a single string with elements delimited by semicolons. Related- in some places this seems to be required (method spec), but others (like printing and running the actual script) it is optional. For now, this was made optional in the method spec too.
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SBML validator cannot run, because it looks for a specific executable in the base image that does not exist and it is unclear how to get it. For now, the sbml validator does not run.
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It seems most formats that are available to download produce files which cannot be directly uploaded back to the system. This seems to be the case at least for models in excel (worksheet names don't match) and sbml (duplicate id in file error), media in excel (worksheet names don't match).
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Workspace client in implementation of KBaseFBAModeling somehow tries to save objects before being instantiated. Thus, the user token isn't properly set. This is fixed with a patched workspace client (in lib directory) that always sends the right token read in from the environment of the SDK job, but this should be fixed in the implementation.
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Provenance should be updated so that it is fetched from the context object. Right now, the FBA modeling implementation sets the provenance internally, so not all modules used are recorded.
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3 transform scripts do not work because of bugs in parsing the workspace and fba service URL. Patched scripts are in the lib directory.
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Tests run through basic cases (so any errors will fail tests), but checks for test output don't exist. This would require someone with some knowledge on what to expect when downloading/uploading data under different circumstances.