Uploading Files and Tests of Metabolic Data by VicTorres23 · Pull Request #6 · PNNL-Predictive-Phenomics/concerto

VicTorres23 · 2024-07-05T23:29:43Z

Uploading 6 files related to the creation of the Exchange Metabolomics Data File used at AgileBioCyc to create a SmartTable and omics Dashboard analysis for each 5 organisms of the CarbStor project.

mcnaughtonadm · 2024-09-04T18:58:47Z

@djinnome can this be merged?

djinnome · 2024-09-06T21:09:21Z

@djinnome can this be merged?

I would like @tiekneeshrimp to go through it and clean up the code first. I don't think it will run as is.

djinnome · 2024-09-06T21:10:16Z

CarbStor_Community_Models/Community_Model_Information.py

+from micom import load_pickle
+from micom.viz import plot_tradeoff, plot_exchanges_per_sample, plot_growth
+
+com1 = load_pickle("/Users/rodr579/Library/CloudStorage/OneDrive-PNNL/venv/CarbStor_Community/One.pickle")


Convert absolute path names to relative pathnames

djinnome · 2024-09-06T21:10:32Z

CarbStor_Community_Models/Community_Model_Information.py

+# In[4]:
+
+
+com2 = load_pickle("/Users/rodr579/Library/CloudStorage/OneDrive-PNNL/venv/CarbStor_Community_NoCurtobacterium/One.pickle")


Convert absolute pathnames to relative pathnames

tiekneeshrimp · 2024-09-09T20:07:51Z

@djinnome can this be merged?

I would like @tiekneeshrimp to go through it and clean up the code first. I don't think it will run as is.

Thought this would be solved withhh issue 15? Maybe it can be merged?

Changed to relative (github) filepath

mcnaughtonadm · 2024-09-09T22:48:16Z

CarbStor_Community_Models/Community_Model_Information.py

These paths are close, but could benefit from slight tweaking. The way they are written, it could break if run on different systems. Let's add in a pathlib Path to make sure that everyone who runs this will be able to get the data.

First we should add:

from pathlib import Path

with the top imports.

Then we can set a few variables:

HERE = Path(__file__).parent.resolve() ROOT = HERE.parent.resolve() COM_MODEL = HERE.joinpath("One.pickle") NO_CURTO = ROOT.joinpath("CarbStor_Community_NoCurtobacterium/One.pickle")

These will resolve to PosixPaths that we can leverage for the load_pickle methods.

com1 = load_pickle(COM_MODEL) com2 = load_pickle(NO_CURTO)

this will make it so we don't have to guess at the folder structure of people using the code, it will just get there for us.

…nd com2

djinnome

Very nice!

djinnome · 2024-09-09T20:21:38Z

CarbStor_Community_Models/Community_Model_Information.py

 from micom.viz import plot_tradeoff, plot_exchanges_per_sample, plot_growth

-com1 = load_pickle("/Users/rodr579/Library/CloudStorage/OneDrive-PNNL/venv/CarbStor_Community/One.pickle")
+com1 = load_pickle("/CarbStor_Community_Models/One.pickle")


When you put a / in front of the path, it makes it absolute. I think since the code is already in the CarbStor_Community_Models directory. you can just load_pickle("CarbStor_Community/One.pickle")

djinnome · 2024-09-09T20:26:46Z

CarbStor_Community_Models/Community_Model_Information.py

+# In[4]:
+
+
+com2 = load_pickle("CarbStor_Community_NoCurtobacterium/One.pickle")


I think this should work.

mcnaughtonadm · 2024-09-13T20:48:15Z

The last thing this needs @tiekneeshrimp is to remove a few things that are normally captured in a .gitignore file (for some reason that is missing in our repo, whoops)

There are 2 things that are typically not committed to the repo.

.DS_Store :: an annoying file management hidden file created by Mac's Finder.
__pycache__ :: a cache directory created when running python that has some of the cached compiled code.

Let's remove those for this PR. If you look in the Files Changed tab on this PR you can see where those things are located. I think the __pycache__ directory is located under the utils folder.

CarbStor_Community_Models/.DS_Store

mcnaughtonadm · 2024-09-13T20:49:17Z

concerto/utils/__pycache__/__init__.cpython-312.pyc

This entire directory should be removed. Just a rm -rf __pycache__ while in the utils directory

tiekneeshrimp · 2024-09-13T22:28:37Z

@mcnaughtonadm resolved!

mcnaughtonadm · 2024-09-13T23:10:33Z

Alright great, I pulled the branch and tried to run the code, there are a few things I noticed that are throwing errors and some formatting things that can be fixed to make this a full script!

I'll try to comment on each part of the file that needs some modification.

mcnaughtonadm · 2024-09-13T23:11:42Z

CarbStor_Community_Models/Community_Model_Information.py

+#!/usr/bin/env python
+# coding: utf-8
+
+# In[ ]:


This # In[ ]: should be removed throughout the script, they are artifacts from saving a jupyter notebook to python script and are just unnecessary clutter now.

mcnaughtonadm · 2024-09-13T23:13:57Z

CarbStor_Community_Models/Community_Model_Information.py

+import pandas as pd
+from cobra.io import read_sbml_model
+from pathlib import Path
+
+from micom import Community
+from micom.workflows import build, grow, tradeoff, fix_medium,build_database
+from micom import load_pickle
+from micom.viz import plot_tradeoff, plot_exchanges_per_sample, plot_growth


We actually only need 2 of these import statements:

from pathlib import Path from micom import load_pickle

the rest are unused in this script.

mcnaughtonadm · 2024-09-13T23:15:00Z

CarbStor_Community_Models/Community_Model_Information.py

+#set variables for importing data
+HERE = Path(__file__).parent.resolve()
+ROOT = HERE.parent.resolve()
+COM_MODEL = HERE.joinpath("One.pickle")


I think this needs an additional folder:

COM_MODEL = HERE.joinpath("CarbStor_Community/One.pickle"

Also I think I messed you up with giving the ROOT, I wasn't sure where that file was being run from. Try something like this:

# set variables for importing data HERE = Path(__file__).parent.resolve() COM_MODEL = HERE.joinpath("Carbstor_Community/One.pickle") NO_CURTO = HERE.joinpath("CarbStor_Community_NoCurtobacterium/One.pickle")

mcnaughtonadm · 2024-09-13T23:25:01Z

CarbStor_Community_Models/Community_Model_Information.py

+#load communities and define parameters
+com1 = load_pickle(COM_MODEL)
+result1 = com1.optimize(fluxes=True, pfba=True)
+#result1
+result1.summary()
+
+
+# In[4]:
+
+com2 = load_pickle(NO_CURTO)
+result2 = com2.optimize(fluxes=True, pfba=True)
+#result2
+result2.summary()
+
+
+# In[ ]:


2 things here. First let's wrap this code into a main() method:

def main(): com1 = load_pickle(COM_MODEL) ... the rest of the code on same indentation level ... result2.summary()

then adding at the bottom of the file:

if __name__ == "__main__": main()

Second thing is that result1.summary() and result2.summary() don't actually work outside of a jupyter notebook with micom for some weird cobrapy integration reason. Therefore we need to do something else here as an output to this script.

One thing I think we can do is return the community members. This can be done by replacing those summary() lines with print(result1.members) and the same for result2.

…a imports, redefined variables

mcnaughtonadm · 2024-09-16T21:32:03Z

Metabolic_Data_Files/ProgramToTestMetaboliteData_HILPosAndHILNeg.py

Can we do the same pathlib treatment for the paths present in this file?

djinnome

looks good to me. Tests pass according to @tiekneeshrimp

djinnome · 2024-09-17T20:20:18Z

@tiekneeshrimp will move directories:

move source code in concerto to src/concerto
Move test code to the tests directory and confirm the tests still pass
Modify the test code if they don't pass

… Metabolites_Data_Files to ./testing

… in Test_ and changed name of Program_to_Test (now Metabolite_Data)

VicTorres23 added 2 commits July 5, 2024 16:22

Uploading Files and Tests of Metabolic Data

4a806b2

Uploading Community Model Files for CarbStor

13a73c8

mcnaughtonadm requested a review from djinnome September 4, 2024 18:58

djinnome reviewed Sep 6, 2024

View reviewed changes

Update Community_Model_Information.py

c687cde

Changed to relative (github) filepath

mcnaughtonadm reviewed Sep 9, 2024

View reviewed changes

tiekneeshrimp self-assigned this Sep 13, 2024

Addition of pathlib to Community_Model_Information and updated com1 a…

92335b0

…nd com2

djinnome approved these changes Sep 13, 2024

View reviewed changes

mcnaughtonadm reviewed Sep 13, 2024

View reviewed changes

CarbStor_Community_Models/.DS_Store Outdated Show resolved Hide resolved

mcnaughtonadm reviewed Sep 13, 2024

View reviewed changes

tiekneeshrimp added 2 commits September 13, 2024 15:25

Delete DS_Store

9003b3e

removed utils pycache

cee4aab

mcnaughtonadm reviewed Sep 13, 2024

View reviewed changes

tiekneeshrimp and others added 2 commits September 16, 2024 13:06

removed jupyter notebook cells, defined function main(), removed extr…

f3e8020

…a imports, redefined variables

Slight fixes to Community_Model_Information.py

b280377

mcnaughtonadm reviewed Sep 16, 2024

View reviewed changes

tiekneeshrimp added 2 commits September 17, 2024 11:07

Defined some filepaths, imported path, ran test

edc2c61

Updated with filepaths, updated file names to match those in directory

1f42ad1

djinnome approved these changes Sep 17, 2024

View reviewed changes

move two folders out to concerto source folders, move test files from…

78a2cef

… Metabolites_Data_Files to ./testing

tiekneeshrimp mentioned this pull request Sep 18, 2024

Ref Issue #6: moved files to test directory, tests do not pass #23

Open

3 tasks

tiekneeshrimp added 9 commits September 19, 2024 12:55

tried to resolve filepath issues, no pass

28b06df

pytest ran

f5f2669

added init_py file to Metabolic_Data_Files folder, updated file paths…

e325426

… in Test_ and changed name of Program_to_Test (now Metabolite_Data)

tried pytest on Test_Metabolic

31dfd8e

removed pycache files

0628738

failed pytest on \testing folder

398fea3

test errors

c7499c2

moved Test_Metabolic file into root concerto directory

99decee

some resolution in Metabolite_Files and test_Metabolite

9024859

		# In[4]:


		com2 = load_pickle("/Users/rodr579/Library/CloudStorage/OneDrive-PNNL/venv/CarbStor_Community_NoCurtobacterium/One.pickle")

		# In[4]:


		com2 = load_pickle("CarbStor_Community_NoCurtobacterium/One.pickle")

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VicTorres23 commented Jul 5, 2024

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mcnaughtonadm commented Sep 13, 2024

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tiekneeshrimp commented Sep 13, 2024

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