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ALCF fixes: tiff_to_zarr.py dynamic pixelsize, init_tiff_to_zarr_globus_flow.py, fix for issue #27 #29

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merged 4 commits into from
Oct 7, 2024

Commits on Oct 2, 2024

  1. Updated tiff_to_zarr.py to read pixelsize from the raw h5 file and co…

    …nvert to micrometer for the multiscales step. Updated init_tiff_to_zarr_globus_flow.py to account for the new change (passing in the h5 path to the flow) as well as automatically updating the Prefect Secret Block on the server with the new flow_id and func_id. Updated instructions for running check_globus_compute.py in the docstring.
    davramov committed Oct 2, 2024
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  2. Removed comments

    davramov committed Oct 2, 2024
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  3. Addressed issue with test_globus_flow.py, where MockGlobusComputeClie…

    …nt was inheriting from globus_sdk.Client: als-computing#27
    davramov committed Oct 2, 2024
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Commits on Oct 4, 2024

  1. Updated config.yml so all endpoints have a name field. Update orchest…

    …ration/_tests/test_globus_flow.py to include a test for process_new_832_file_flow() in orchestration/flows/bl832/move.py (note that this still needs work to properly validate the data pruning task). Updated move.py to accept a config as input (similar to what we did in the ALCF script) so we can inject Config832 from the test script. Fixed a typo in orchestration/flows/bl832/prune.py where there was missing parantheses causing an issue on the flow-prd agent. Updated scripts/init_tiff_to_zarr_globus_flow.py, tiff_to_zarr.py, and alcf.py to address hardcoded path concerns.
    davramov committed Oct 4, 2024
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