kbaseapps/cobrapybasedfba

Wrapper of COBRApy FBA functions in KBase replacing some functionality in the fba_tools module

COBRApyBasedFBA

This is a KBase module generated by the KBase Software Development Kit (SDK).

You will need to have the SDK installed to use this module. Learn more about the SDK and how to use it.

You can also learn more about the apps implemented in this module from its catalog page or its spec file.

Setup and test

Add your KBase developer token to test_local/test.cfg and run the following:

$ make
$ kb-sdk test

After making any additional changes to this repo, run kb-sdk test again to verify that everything still works.

Installation from another module

To use this code in another SDK module, call kb-sdk install COBRApyBasedFBA in the other module's root directory.

Help

You may find the answers to your questions in our FAQ or Troubleshooting Guide.

cobrapybasedfba's Issues

Error from COBRApyBasedFBA_server_test.py

Error output

======================================================================
ERROR: Failure: KeyError ('getpwuid(): uid not found: 1000')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/miniconda/lib/python3.6/site-packages/nose/failure.py", line 39, in runTest
    raise self.exc_val.with_traceback(self.tb)
  File "/miniconda/lib/python3.6/site-packages/nose/loader.py", line 418, in loadTestsFromName
    addr.filename, addr.module)
  File "/miniconda/lib/python3.6/site-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/miniconda/lib/python3.6/site-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/miniconda/lib/python3.6/imp.py", line 235, in load_module
    return load_source(name, filename, file)
  File "/miniconda/lib/python3.6/imp.py", line 172, in load_source
    module = _load(spec)
  File "<frozen importlib._bootstrap>", line 684, in _load
  File "<frozen importlib._bootstrap>", line 665, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 678, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "/kb/module/test/COBRApyBasedFBA_server_test.py", line 18, in <module>
    from COBRApyBasedFBA.COBRApyBasedFBAServer import MethodContext
  File "/kb/module/lib/COBRApyBasedFBA/COBRApyBasedFBAServer.py", line 490, in <module>
    application = Application()
  File "/kb/module/lib/COBRApyBasedFBA/COBRApyBasedFBAServer.py", line 334, in __init__
    config=get_config_file())
  File "/kb/deployment/lib/biokbase/log.py", line 137, in __init__
    self.user = _getpass.getuser()
  File "/miniconda/lib/python3.6/getpass.py", line 169, in getuser
    return pwd.getpwuid(os.getuid())[0]
KeyError: 'getpwuid(): uid not found: 1000'

@Fxe Let me know what you think of this

Add Custom bounds list to UI

Add option for cplex solver.

Currently supported solvers are GLPK and COINOR-CBC. This can be handled with a dropdown UI menu.
This is easy to do because these are both open source solvers.

Adding a cplex option may be more complicated because it requires the user confirming a cplex license on kbase.

Custom cobrapy/optlang dependency

We need to add the forked versions of cobrapy and optlang that contain the COINOR-CBC and OSQP solvers.

This was the way that I installed them for testing. We can probably run the installs for optlang and cobrapy without the -e flag.
@Fxe what is the best way to add this to the docker image?

git clone https://github.com/braceal/MFApy.git
cd MFApy
python3 -m venv env
source env/bin/activate
pip install --upgrade pip setuptools wheel
mkdir deps && cd deps
git clone https://github.com/braceal/optlang.git
cd optlang && git checkout test/coinor-cbc_osqp && cd ..
git clone https://github.com/braceal/cobrapy.git
cd cobrapy && git ceckout feature/coinor-cbc_osqp && cd ..
pip install -e optlang/
pip install -e cobrapy/
cd .. && pip install -e .