🐛 Bug: Incorrect API call in AutomatedTests.ipynb

[pavithranair]

Describe the bug.

The API call in AutomatedTests.ipynb is passing a python variable to a terminal command. Hence, the variable name is being treated as a string and the following error is encountered:

The command causing the error: !ersilia api -i smi

Describe the steps to reproduce the behavior

1. Open AutomatedTests.ipynb in Colab
2. Run the cells

Expected behavior.

No response

Screenshots.

Operating environment

Ubuntu 18.04.2 lts

Additional context

No response

[pavithranair]

Hi! Is this the required output of the API call?

[GemmaTuron]

Hi @pavithranair !

Thanks, this notebook for automated testing of models in Google Colab is still work in progress so many of the inputs still need work, we are working with @miquelduranfrigola and @megamanics. The input needs to be modified because many models do not require a single smiles, but two smiles or other combinations. This needs to automatically be taken from the internal tests that happen at fetch time (see #488 )

[GemmaTuron]

Hi,

Just to comment on this for clarification. Sorry I rushed through the comments and did not check properly. We have now edited the different notebooks we will be using:

• ersilia-on-colab (for general users, a simple form-based colab notebook without code exposed)
• test-ersilia ...: automated tests that will be run everytime we make changes to ersilia's code

The change that @pavithranair was suggesting is actually not ideal, since we want to pass smiles as strings, if you pass any smiles with a () it will fail with the following error: !ersilia api -i $smi /bin/bash: -c: line 0: syntax error near unexpected token(' /bin/bash: -c: line 0: ersilia api -i CC(C)CC1=CC=C(C=C1)C(C)C(=O)O'

The solution is: !ersilia api -i "$smi"

[pavithranair]

Hi!

My bad, I didn't account for smiles with parenthesis. Your solution seems to be doing the trick!