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Always use write_table in tasks (rather than directly calling anndata) #580

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tcompa opened this issue Oct 19, 2023 · 0 comments · Fixed by #581
Closed

Always use write_table in tasks (rather than directly calling anndata) #580

tcompa opened this issue Oct 19, 2023 · 0 comments · Fixed by #581
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Tables AnnData and ROI/feature tables

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@tcompa
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tcompa commented Oct 19, 2023

We need to update three tasks

$ git grep write_elem fractal_tasks_core/ | grep -v lib_write

fractal_tasks_core/tasks/apply_registration_to_ROI_tables.py:from anndata._io.specs import write_elem
fractal_tasks_core/tasks/apply_registration_to_ROI_tables.py:        write_elem(group_tables, new_roi_table, shifted_rois[acq])
fractal_tasks_core/tasks/apply_registration_to_image.py:from anndata._io.specs import write_elem
fractal_tasks_core/tasks/apply_registration_to_image.py:            write_elem(new_tables_group, table, curr_table)

fractal_tasks_core/tasks/calculate_registration_image_based.py:from anndata._io.specs import write_elem
fractal_tasks_core/tasks/calculate_registration_image_based.py:    write_elem(group_tables, roi_table, new_ROI_table)

fractal_tasks_core/tasks/copy_ome_zarr.py:from anndata._io.specs import write_elem
fractal_tasks_core/tasks/copy_ome_zarr.py:                        write_elem(

so that we'll write tables complying with our own V1 (ref #529)
@tcompa tcompa added the Tables AnnData and ROI/feature tables label Oct 19, 2023
tcompa added a commit that referenced this issue Oct 19, 2023
@tcompa
Use write_table in copy_ome_zarr task (ref #580)
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@tcompa tcompa mentioned this issue Oct 19, 2023
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@tcompa tcompa linked a pull request Oct 19, 2023 that will close this issue
Always use write_table wrapper in tasks #581
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tcompa added a commit that referenced this issue Oct 20, 2023
@tcompa
Use write_table in calculate_registration_image_based (ref #580)
5adc63c
tcompa added a commit that referenced this issue Oct 20, 2023
@tcompa
Use write_table in apply_registration_to_ROI_tables (ref #580)
576ae2e
tcompa added a commit that referenced this issue Oct 20, 2023
@tcompa
Use write_table in apply_registration_to_image (ref #580)
9b9807a
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Always use write_table wrapper in tasks fractal-analytics-platform/fractal-tasks-core
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@tcompa