Duplicate MUSICA name keys are not detected

[K20shores]

@SancyW reported a configuration to use which was failing in music box interactive. The configuration is listed below. The issue is that there were 6 reactions which were actually 3 reactions, each duplicated. Their musica names are

• LOSS_FORM_depo
• LOSS_NO2_depo
• LOSS_FORM_washout

configuration.zip

Reproduce

To see the incorrect behavior, download and unzip the configuraiton and run music_box -c configuration/my_config.json -o output.csv

Observe that there is a key index error.

Then, open up configuration/camp_data/reactions.json and find the duplicated reactions above. Delete one of each pair and rerun the configuration. You'll see that it passes.

We should alert when we find duplicate keys and let the user know and then exit

Acceptance criteria

• All reactions with duplicate musica names are detected
• Duplicate reactions are printed to the terminal and the error is explicitly listed with instructions on how to fix them
• A unit test is added that successfully detects duplicate keys

Ideas

[SancyW]

Oh, yes, sorry, that was my mistake. It’s a good idea to add an alert to remind users. Thanks for that!

[carl-drews]

The run-time error looks like this:

2024-09-12 13:28:52 - DEBUG - main.main - Working directory = /home/drews/MusicBox/music-box-duplicate-keys-235/temp
2024-09-12 13:28:52 - DEBUG - main.main - Configuration file = configuration/my_config.json
Traceback (most recent call last):
File "/home/drews/.conda/envs/musicbox/bin/music_box", line 8, in
sys.exit(main())
^^^^^^
File "/home/drews/.conda/envs/musicbox/lib/python3.12/site-packages/acom_music_box/main.py", line 161, in main
result = myBox.solve(musicBoxOutputPath)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/drews/.conda/envs/musicbox/lib/python3.12/site-packages/acom_music_box/music_box.py", line 154, in solve
ordered_rate_constants = self.order_reaction_rates(
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/drews/.conda/envs/musicbox/lib/python3.12/site-packages/acom_music_box/music_box.py", line 325, in order_reaction_rates
ordered_rate_constants[rate_constant_ordering[key]] = float(value)
~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
IndexError: list assignment index out of range

[carl-drews]

The branch is here:
main...duplicate-keys-235

Not completed yet - still need to add the unit test.

[carl-drews]

Pull request is:
#241