Error when creating the data universe (10.1164/rccm.201712-2410OC)

Describe the bug I am getting an error message when I try to create the data universe:

Error in checkForRemoteErrors(lapply(cl, recvResult)) : 
 one node produced an error: ValueError: '53-year-old human stage' is not a valid entry for development_stage in data set ['10.1164/rccm.201712-2410OC'].

Detailed traceback:
 File "/home/.cache/R/basilisk/1.4.0/SimBu/0.99.0/sfaira_env2/lib/python3.9/site-packages/sfaira/data/dataloaders/super_group.py", line 31, in __init__
   DatasetSuperGroupLoaders(
 File "/home/.cache/R/basilisk/1.4.0/SimBu/0.99.0/sfaira_env2/lib/python3.9/site-packages/sfaira/data/dataloaders/loaders/super_group.py", line 39, in __init__
   dsg = DatasetGroupDirectoryOriented(
 File "/home/.cache/R/basilisk/1.4.0/SimBu/0.99.0/sfaira_env2/lib/python3.9/site-packages/sfaira/data/dataloaders/base/dataset_group.py", line 773, in __init__
   DatasetBase(
 File "/home/.cache/R/basilisk/1.4.0/SimBu/0.99.0/sfaira_env2/lib/python3.9/site-packages/sfaira/data/dataloaders/base/dataset.py", line 310, in __init__
   set

To Reproduce I am using sfaira in R via reticulate and a conda environment where only sfaira and its dependencies are installed. This is how I am calling sfaira in R (though this error message does not seem to be R related I feel like…):

sfaira <- reticulate::import("sfaira")  
ds <- sfaira$data$Universe(data_path = paste0(tempdir(), "/raw"),
                             meta_path = paste0(tempdir(), "/meta"),
                             cache_path = paste0(tempdir(), "/cache"))

I had sfaira working previously with this setup when I was using the development version 0.3.9+4.gdd849d5 and wanted to upgrade to 0.3.12.

System [please complete the following information]:

• OS: Ubuntu 20.04.4
• Language Version: Python 3.9
• Virtual environment: Conda
• Sfaira version: 0.3.12

Cheers, Alex

[alex-d13]

Yep, thats what I tried and it just finished without any errors 😃 I used tables==3.7.0.

Thank your for the fast responses!

[davidsebfischer]

• We ll add tables to the requirements, for now try installing that package into your environment manually?