Renku update error

Renku (CLI)
1

Hi all,

I have created a renku workflow in a private repo on renkulab:
https://renkulab.io/projects/hluetcke/calcium-movie-analysis

The workflow consists of Jupyter notebooks run through papermill. I can run it through renku successfully:

renku run papermill --kernel Python3 PreprocessMovies.ipynb PreprocessMovies.ran.ipynb -p input_path ../data/test_dataset/rawMovie.h5 -p output_path ../data/test_dataset/preprocessedMovie.h5 -p n_jobs 1
renku run papermill --kernel Python3 ExtractSignals.ipynb ExtractSignals.ran.ipynb -p input_path ../data/test_dataset/preprocessedMovie.h5 -p output_path ../data/test_dataset/resultsPCAICA_python.h5
renku run papermill --kernel Python3 AnnotateSignals.ipynb AnnotateSignals.ran.ipynb -p input_path ../data/test_dataset/resultsPCAICA_python.h5 -p output_path ../data/test_dataset/PCAICAsorted.h5 -p update_existing False

This also creates a nice graph of the workflow in the renkulab UI. Now, I want to change some code in the first notebook, commit the changes and run renku update but I get the following error:
https://pastebin.pl/view/c113d85f

Do you have any idea what could be the problem?

Thanks, Henry

1 Like
2

Hi,

The same kind of error occured in renkulab environment too when i was running renku update on a several-steps knowledge graph.

If you have for example A–>B–>C–>D, I found out that running :

renku update B
renku update C
renku update D

was working fine for me.

I hope that can help you or help to find a solution to this issue.

Have a good day,

Adrien

1 Like
3

Thanks for the hint. I found that there was still an old unused dataset dangling around in .renku/refs/datasets. After removing it, the error disappeared.

Best, Henry

1 Like