Feedback on CLI

[davidsebfischer]

• create-dataloader: does not ask for gene_id_symbol_var_key. check if this is desired
• "Year" is a string after create-datalaoder but this throws errorr in verify-dataloader
• create-dataloader creates empty yaml key gene_id_symbols_var_key but verify-dataloader tests if gene_id_symbol_var_key is present (no "s")

Thanks @lauradmartens!

[lauradmartens]

Currently addressing it.

Just to make sure: should year rather be an integer or string for your downstream tasks?

[davidsebfischer]

Just to make sure: should year rather be an integer or string for your downstream tasks?

Let's use integer because it is more constrained!

[lauradmartens]

sfaira annotate_dataloader does not work properly but as far as I can see only two lines need to be changed:

sfaira/sfaira/data/dataloaders/base/dataset_group.py

Line 362 in 68c7531

v.adata.obs[v.cell_type_original_obs_key].values

changed to cell_type_obs_key

and

sfaira/sfaira/data/dataloaders/base/dataset_group.py

Line 369 in 68c7531

omit_list=v._unknown_celltype_identifiers,

but I am not sure if we have a new argument for _unknown_celltype_identifiers (if any)

[davidsebfischer]

sfaira annotate_dataloader does not work properly but as far as I can see only two lines need to be changed:

sfaira/sfaira/data/dataloaders/base/dataset_group.py

Line 362 in 68c7531

v.adata.obs[v.cell_type_original_obs_key].values

changed to cell_type_obs_key

Correct!

sfaira/sfaira/data/dataloaders/base/dataset_group.py

Line 369 in 68c7531

omit_list=v._unknown_celltype_identifiers,

but I am not sure if we have a new argument for _unknown_celltype_identifiers (if any)

• we can depreceate

  sfaira/sfaira/data/dataloaders/base/dataset_group.py

  Line 110 in 68c7531

  @property

• this line needs to be changed to use the global field access object:

omit_list=[v._adata_ids.not_a_cell_celltype_identifier, v._adata_ids.unknown_metadata_identifier],

[Zethson]

Been on holiday for a long time. Feel free to ping me if you run into any issue @lauradmartens