New model ready for testing!

[github-actions[bot]]

This model is ready for testing. If you are assigned to this issue, please try it out using the CLI, Google Colab and DockerHub and let us know if it works!

[emmakodes]

@samuelmaina @GemmaTuron

CLI

The predict api is still effective instead of run api cause I'm getting the following error when I try to make predictions:

Traceback (most recent call last):
  File "/home/emma/miniconda3/envs/ersilia/bin/ersilia", line 33, in <module>
    sys.exit(load_entry_point('ersilia', 'console_scripts', 'ersilia')())
  File "/home/emma/miniconda3/envs/ersilia/lib/python3.7/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/home/emma/miniconda3/envs/ersilia/lib/python3.7/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/home/emma/miniconda3/envs/ersilia/lib/python3.7/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/emma/miniconda3/envs/ersilia/lib/python3.7/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/emma/miniconda3/envs/ersilia/lib/python3.7/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/home/emma/miniconda3/envs/ersilia/lib/python3.7/site-packages/bentoml/cli/click_utils.py", line 138, in wrapper
    return func(*args, **kwargs)
  File "/home/emma/miniconda3/envs/ersilia/lib/python3.7/site-packages/bentoml/cli/click_utils.py", line 115, in wrapper
    return_value = func(*args, **kwargs)
  File "/home/emma/miniconda3/envs/ersilia/lib/python3.7/site-packages/bentoml/cli/click_utils.py", line 99, in wrapper
    return func(*args, **kwargs)
  File "/home/emma/ersilia/ersilia/cli/commands/api.py", line 42, in api
    api_name=api_name, input=input, output=output, batch_size=batch_size
  File "/home/emma/ersilia/ersilia/core/model.py", line 194, in _api_runner_iter
    for result in api.post(input=input, output=output, batch_size=batch_size):
  File "/home/emma/ersilia/ersilia/serve/api.py", line 320, in post
    input=unique_input, output=None, batch_size=batch_size
  File "/home/emma/ersilia/ersilia/serve/api.py", line 290, in post_unique_input
    or not schema.is_h5_serializable(api_name=self.api_name)
  File "/home/emma/ersilia/ersilia/serve/schema.py", line 89, in is_h5_serializable
    schema = self.get_output_by_api(api_name)
  File "/home/emma/ersilia/ersilia/serve/schema.py", line 86, in get_output_by_api
    return self.schema[api_name]["output"]
KeyError: 'run'

[samuelmaina]

@emmakodes , I know where the problem is let me correct it.

[samuelmaina]

Hi @GemmaTuron , I have raised a PR https://github.com/ersilia-os/eos93h2/pull/8 to correct this issue.

[GemmaTuron]

Hi @emmakodes

Can you confirm the changes work and then we can close this issue?

[emmakodes]

I guess I need to fetch via github since Upload model to DockerHub workflow failed at the Install Ersilia step

[emmakodes]

Hello @samuelmaina @GemmaTuron

CLI

I fetched the model via github on cli and I got the following error: ImportError: libXrender.so.1: cannot open shared object file: No such file or directory eos93h2_cli_fetch.log The model requires libXrender dependency.

Colab

I got this: ModuleNotFoundError: No module named 'click' This should be as a result of ersilia currently failing.

[samuelmaina]

Hello @emmakodes , I don't know why this is the case, on my my machine its not asking libXrender module but I will look into it.

[GemmaTuron]

Hi @samuelmaina

This is the same as for eos526j. Could you add this dependency and submit a PR?

[GemmaTuron]

@emmakodes

The model has been updated, can you confirm it works? Thanks!

[emmakodes]

Hello @samuelmaina @GemmaTuron

The model fetch and makes prediction successfully on CLI, Colab, and Docker. However, the prediction values I get on CLI and Docker somewhat vary from the prediction values I get on Colab. You can check the prediction CSV files below to see

input file: 5_input_smile.csv

CLI

eos93h2_cli_pred.csv

DockerHub

eos93h2_docker_pred.csv

colab

eos93h2_output.csv

[GemmaTuron]

Fantastic, I'll close this issue