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Power model service with ILoop data

License: Apache License 2.0

Python 85.89% Shell 5.76% Makefile 7.19% Dockerfile 1.17%

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iloop-to-model's Issues

Unconventional message format

The response from this endpoint resembles the one we receive from model service, but it is a bit different:
growthRate should be growth-rate (the best would be to update it in model service, use camelCase if possible)
added and removed reactions are missing although they are included in the messages.

Is it possible to add them?

add https/http proxy for bigg api

make simple workaround to the problem of not being able to call bigg's http

Fix the model taking up glucose when the medium actually doesn't contain glucose

Fix genotype changes not being correct

For example, for C25 B3 in the iloop, the reaction ARGSS is removed although the responsible gene argG is not deleted?

As user I want to see information about organisms

done: organisms names come with 3-letter ids

Minimize Manhattan distance to fluxomics data to avoid infeasible solutions

Potion-client dependency outdated

The iloop-to-model service is failing with the latest version of iloop due to an issue fixed in potion-client v2.5.1.

[iloop-to-model-1]2017-05-05T09:09:17.725263194Z [2017-05-05 09:09:17 +0000] [15] [ERROR] Error handling request
[iloop-to-model-1]2017-05-05T09:09:17.725318530Z Traceback (most recent call last):
[iloop-to-model-1]2017-05-05T09:09:17.725328484Z   File "/usr/local/lib/python3.5/site-packages/aiohttp/web_server.py", line 62, in handle_request
[iloop-to-model-1]2017-05-05T09:09:17.725336720Z     resp = yield from self._handler(request)
[iloop-to-model-1]2017-05-05T09:09:17.725349157Z   File "/usr/local/lib/python3.5/site-packages/aiohttp/web.py", line 270, in _handle
[iloop-to-model-1]2017-05-05T09:09:17.725356950Z     resp = yield from handler(request)
[iloop-to-model-1]2017-05-05T09:09:17.725364297Z   File "/iloop-to-model/iloop_to_model/app.py", line 21, in wrapper
[iloop-to-model-1]2017-05-05T09:09:17.725372010Z     iloop = iloop_client(api, token)
[iloop-to-model-1]2017-05-05T09:09:17.725379224Z   File "/iloop-to-model/iloop_to_model/__init__.py", line 19, in iloop_client
[iloop-to-model-1]2017-05-05T09:09:17.725387020Z     verify=False
[iloop-to-model-1]2017-05-05T09:09:17.725394054Z   File "/usr/local/lib/python3.5/site-packages/potion_client/__init__.py", line 32, in __init__
[iloop-to-model-1]2017-05-05T09:09:17.725401717Z     self._fetch_schema()
[iloop-to-model-1]2017-05-05T09:09:17.725408894Z   File "/usr/local/lib/python3.5/site-packages/potion_client/__init__.py", line 43, in _fetch_schema
[iloop-to-model-1]2017-05-05T09:09:17.725422104Z     resource = self.resource_factory(name, resource_schema)
[iloop-to-model-1]2017-05-05T09:09:17.725429420Z   File "/usr/local/lib/python3.5/site-packages/potion_client/__init__.py", line 114, in resource_factory
[iloop-to-model-1]2017-05-05T09:09:17.725452870Z     for property_name, property_schema in schema['properties'].items():
[iloop-to-model-1]2017-05-05T09:09:17.725460014Z   File "/usr/local/lib/python3.5/site-packages/potion_client/resource.py", line 56, in __getitem__
[iloop-to-model-1]2017-05-05T09:09:17.725466887Z     return self._properties[item]
[iloop-to-model-1]2017-05-05T09:09:17.725473234Z KeyError: 'properties'

Add more nodes

Fix glucose plot in theoretical yield app when using GECKO model

From @phantomas1234 on August 30, 2017 10:30

null

Copied from original issue: DD-DeCaF/metabolica-ui-yields#8

make model service handle multiple samples

From @hredestig on April 4, 2017 8:52

done: model service can adjust bounds based on multiple samples

Copied from original issue: DD-DeCaF/simulations#6

As a user I want to filter the experiments with the particular organism

done: after selecting an organism it is possible to get only the experiments with this organism

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