Incorporate generation of OMEX metadata files

[jonrkarr]

@jhgennari @CiaranWelsh

We've basically set up a list of tasks that are run for each BioModel's entry to clean it up, or in the case of OMEX meta enhance the entry. We can add generation of OMEX meta files to this. I think this should be the last step so that libOmexMeta sees valid model and simulation files (eventually they will be valid, right now some are still invalid).

We can incorporate generation of OMEX meta files by adding a function like below. Your function can then work with any of the files for the entry and save an OMEX meta file to the directory for the entry.

The function can be saved to a new file at the root of this repository, ./build_omex_meta_file.py

def run(id, working_dir):
   dirname = os.path.join(working_dir, id)
   pass

[jonrkarr]

@jhgennari @CiaranWelsh @nickerso I'll do my best to use pyomexmeta to generate RDF files for BioModels, collect a list of the failed models, and send that to you.

At the BioModels meeting on Friday, @jhgennari suggested that OMEX metadata recommends a particular filename for these files. What is this? {name of model file}.rdf (e.g., for a model BIOMD0001.xml, use BIOMD0001.rdf)?

[jonrkarr]

@luciansmith, FYI I won't be able to make pyomexmeta work well with Windows. The only way to collect errors from pyomexmeta is to collect C-level stdout and parse it. To my knowledge, there's no way to do this with Windows; the only way it can be done relies on a feature only available in Mac OS/Linux.

[luciansmith]

OK, I'll keep that in mind. For the pyomexmeta team, that would obviously be something to work on in the future, but it sounds like it'll work for now on the other OSes.

-Lucian

On Sun, Jul 18, 2021 at 12:48 PM Jonathan Karr @.***> wrote:

@luciansmith https://github.com/luciansmith, FYI I won't be able to make pyomexmeta work well with Windows. The only way to collect errors from pyomexmeta is to collect C-level stdout and parse it. To my knowledge, there's no way to do this with Windows; the only way it can be done relies on a feature only available in Mac OS/Linux.

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[jonrkarr]

I've created a few GitHub issues about this. This issue really affects all OSes, but its particularly tough for Windows.

[CiaranWelsh]

Just to let you know that the issues in libOmexMeta are my priority for as soon as the sensitivity stuff is done in RoadRunner. I'm making good progress - just swigging the last few bits and bobs, then make sure the tests still work and I should be ready to merge.