'set' object has no attribute 'get_by_id'

[Harry-Pollitt]

Hi

I've been following along with your test case scenario found here https://cobramod.readthedocs.io/en/latest/homoserine_cycle.html however when I try to visualise the "Homoserine-PWY" group with escher using the code provided I get an AttributeError. I have double checked that I have all the required packages I may be mistaken however.

Using the following code in my jupyter notebook

solution01 = model.optimize()
print(solution01)
model.groups.get_by_id("Homoserine-PWY").color_negative = "red"
model.groups.get_by_id("Homoserine-PWY").color_positive = "green"
model.groups.get_by_id("Homoserine-PWY").visualize(solution_fluxes=solution01)

produces the error:

<Solution 12.330 at 0x7f7858795d60>

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Input In [45], in <cell line: 5>()
      3 model.groups.get_by_id("Homoserine-PWY").color_negative = "red"
      4 model.groups.get_by_id("Homoserine-PWY").color_positive = "green"
----> 5 model.groups.get_by_id("Homoserine-PWY").visualize(solution_fluxes=solution01)

File ~/anaconda3/lib/python3.9/site-packages/cobramod/core/pathway.py:276, in Pathway.visualize(self, solution_fluxes, filename)
    274 # Get graph and add to json_dict
    275 json_dict.graph = self.graph.copy()
--> 276 json_dict.reaction_strings = {
    277     reaction: self.members.get_by_id(reaction).reaction
    278     for reaction in json_dict.graph.keys()
    279 }
    281 return json_dict.visualize(
    282     filepath=filename,
    283     vertical=self.vertical,
   (...)
    288     n_steps=self.color_n_steps,
    289 )

File ~/anaconda3/lib/python3.9/site-packages/cobramod/core/pathway.py:277, in <dictcomp>(.0)
    274 # Get graph and add to json_dict
    275 json_dict.graph = self.graph.copy()
    276 json_dict.reaction_strings = {
--> 277     reaction: self.members.get_by_id(reaction).reaction
    278     for reaction in json_dict.graph.keys()
    279 }
    281 return json_dict.visualize(
    282     filepath=filename,
    283     vertical=self.vertical,
   (...)
    288     n_steps=self.color_n_steps,
    289 )

AttributeError: 'set' object has no attribute 'get_by_id'

The group itself exists as model.groups.get_by_id("Homoserine-PWY") produces the expected result.
Any help would be appreciated.

Regards,
Harry

[cambordas]

Hi @Harry-Pollitt , thank you very much for opening the issue. Indeed, there is a problem with the actual version of COBRApy. In their previous versions, Groups.members was a DictList but they changed it in opencobra/cobrapy#1221
We will update CobraMod soon to be compatible with the latest version of COBRApy. I will notify you soon

[cambordas]

We are sorry for the very late response!
Nonetheless, the new version of CobraMod #53 should have fix that error