Make multiplexing converter work with arbitrarily named acquisitions

We've generalized the handling of acquisition names with the 1.0.0 release of fractal-tasks-core. But some tasks still assume acquisitions are named "0", "1", "2". Let's generalize that.

First issue Nicole found:

TASK ERROR: Task name: Convert Cellvoyager Multiplexing to OME-Zarr, position in Workflow: 0
TRACEBACK:
Traceback (most recent call last):
  File "/path/to/python/lib64/python3.9/site-packages/fractal_server/app/runner/v2/runner_functions_low_level.py", line 116, in run_single_task
    raise e
  File "/path/to/python/lib64/python3.9/site-packages/fractal_server/app/runner/v2/runner_functions_low_level.py", line 105, in run_single_task
    _call_command_wrapper(
  File "/path/to/python/lib64/python3.9/site-packages/fractal_server/app/runner/v2/runner_functions_low_level.py", line 52, in _call_command_wrapper
    raise TaskExecutionError(err)
fractal_server.app.runner.exceptions.TaskExecutionError: 2024-07-08 13:07:15,771; INFO; START cellvoyager_to_ome_zarr_init_multiplex task
2024-07-08 13:07:15,772; INFO; [glob_with_multiple_patterns] patterns=['*.tif']
2024-07-08 13:07:15,800; INFO; [glob_with_multiple_patterns] Found 3512 items
2024-07-08 13:07:15,803; WARNING; Skipping "DC_DCAM#2_CAM4_BIN2.tif". Original error: Something wrong with filename='DC_DCAM#2_CAM4_BIN2', TFLAZC='BIN2'
2024-07-08 13:07:15,812; WARNING; Skipping "SC_BP676-29_60xW_M01_CH04.tif". Original error: Something wrong with filename='SC_BP676-29_60xW_M01_CH04', TFLAZC='CH04'
2024-07-08 13:07:15,823; WARNING; Skipping "SC_BP600-37_60xW_M01_CH03.tif". Original error: Something wrong with filename='SC_BP600-37_60xW_M01_CH03', TFLAZC='CH03'
2024-07-08 13:07:15,824; WARNING; Skipping "DC_DCAM#2_CAM4.tif". Original error: Something wrong with filename='DC_DCAM#2_CAM4', TFLAZC='CAM4'
2024-07-08 13:07:15,836; WARNING; Skipping "DC_DCAM#1_CAM3_BIN2.tif". Original error: Something wrong with filename='DC_DCAM#1_CAM3_BIN2', TFLAZC='BIN2'
2024-07-08 13:07:15,853; WARNING; Skipping "SC_BP445-45_60xW_M01_CH01.tif". Original error: Something wrong with filename='SC_BP445-45_60xW_M01_CH01', TFLAZC='CH01'
2024-07-08 13:07:15,856; WARNING; Skipping "SC_BP525-50_60xW_M01_CH02.tif". Original error: Something wrong with filename='SC_BP525-50_60xW_M01_CH02', TFLAZC='CH02'
2024-07-08 13:07:15,858; WARNING; Skipping "DC_DCAM#1_CAM3.tif". Original error: Something wrong with filename='DC_DCAM#1_CAM3', TFLAZC='CAM3'
Traceback (most recent call last):
  File "/path/to/FRACTAL_TASK_DIR/.fractal/fractal-tasks-core1.1.0/venv/lib/python3.9/site-packages/fractal_tasks_core/tasks/cellvoyager_to_ome_zarr_init_multiplex.py", line 521, in <module>
    run_fractal_task(
  File "/path/to/FRACTAL_TASK_DIR/.fractal/fractal-tasks-core1.1.0/venv/lib64/python3.9/site-packages/fractal_tasks_core/tasks/_utils.py", line 79, in run_fractal_task
    metadata_update = task_function(**pars)
  File "/path/to/FRACTAL_TASK_DIR/.fractal/fractal-tasks-core1.1.0/venv/lib64/python3.9/site-packages/pydantic/v1/decorator.py", line 40, in wrapper_function
    return vd.call(*args, **kwargs)
  File "/path/to/FRACTAL_TASK_DIR/.fractal/fractal-tasks-core1.1.0/venv/lib64/python3.9/site-packages/pydantic/v1/decorator.py", line 134, in call
    return self.execute(m)
  File "/path/to/FRACTAL_TASK_DIR/.fractal/fractal-tasks-core1.1.0/venv/lib64/python3.9/site-packages/pydantic/v1/decorator.py", line 206, in execute
    return self.raw_function(**d, **var_kwargs)
  File "/path/to/FRACTAL_TASK_DIR/.fractal/fractal-tasks-core1.1.0/venv/lib/python3.9/site-packages/fractal_tasks_core/tasks/cellvoyager_to_ome_zarr_init_multiplex.py", line 198, in cellvoyager_to_ome_zarr_init_multiplex
    plate = dict_acquisitions["0"]["plate"]
KeyError: '0'

fractal-analytics-platform / fractal-tasks-core

Make multiplexing converter work with arbitrarily named acquisitions #782