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ersilia-os / ersilia

The Ersilia Model Hub, a repository of AI/ML models for infectious and neglected disease research.
https://ersilia.io
GNU General Public License v3.0
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🐛 Bug: calculate api exits without any output #332

Closed mamabear25 closed 2 years ago

mamabear25 commented 2 years ago

Describe the bug.

calculate api exits without any output

running the calculate api doesn’t output anything, it just exits.

Describe the steps to reproduce the behavior

  1. ersilia fetch -v eos8a4x
  2. ersilia -v serve eos8a4x
  3. ersilia -v calculate -i "eml_canonical.csv" -o "eos8a4x" > my.log 2>&1

Expected behavior.

calculated outputs should be saved or printed to the screen

Screenshots.

Screenshot 2022-10-13 at 12 09 44

Operating environment

macOs Monterey Version 12.5.1

Additional context

No response

Zainab-ik commented 2 years ago

Hi @mamabear25, I think you didn't add .csv at the end of your output doc. should be ersilia -v calculate -i "eml_canonical.csv" -o "eos8a4x.csv" > my.log 2>&1. You should probably try this

Zainab-ik commented 2 years ago

Describe the bug.

calculate api exits without any output

running the calculate api doesn’t output anything, it just exits.

Describe the steps to reproduce the behavior

  1. ersilia fetch -v eos8a4x
  2. ersilia -v serve eos8a4x
  3. ersilia -v calculate -i "eml_canonical.csv" -o "eos8a4x" > my.log 2>&1

Expected behavior.

calculated outputs should be saved or printed to the screen

Screenshots.

Screenshot 2022-10-13 at 12 09 44

Operating environment

macOs Monterey Version 12.5.1

Additional context

No response

also include your error file

mamabear25 commented 2 years ago

Hi @mamabear25, I think you didn't add .csv at the end of your output doc. should be ersilia -v calculate -i "eml_canonical.csv" -o "eos8a4x.csv" > my.log 2>&1. You should probably try this

okay, let me try that out thanks

mamabear25 commented 2 years ago

it's not working @Zainab-ik

GemmaTuron commented 2 years ago

Hi @mamabear25 I think you are missing the api command?

ersilia -v api calculate ...

mamabear25 commented 2 years ago

@GemmaTuron I ran it correctly this time, still no output ersilia -v api calculate -i "eml_canonical.csv" -o "eos8a4x" > my.log 2>&1

GemmaTuron commented 2 years ago

can you attach the log of this last run?

GemmaTuron commented 2 years ago

and @mamabear25 I still miss the .csv on the output file.. so you are not creating any file actually. Hope this helps!

mamabear25 commented 2 years ago

@GemmaTuron I've fixed the issue... I removed the quotes around the csv file, and ran it this way

ersilia -v api calculate -i eml_canonical.csv -o "eos8a4x.csv"