Feature/msk ucsf ingestion#9
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…r-upload-areas-morphic-redesign-util Feature/submission envelop UUID for upload areas morphic redesign util
…list md5 sums computation while listing files
…ocessing for UCSF datasets
… on the context argument
…type, --derived-from
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Description:
This pull request improves our dataset ingestion workflow by refactoring the linking logic for different dataset contexts (MSK, UCSF, and legacy JAX). The key changes include:
MSK-Specific Enhancements
Supports many-to-one relationships between differentiated cell lines and a shared library preparation.
New Context Support:
A new
--contextcommand‑line argument is introduced (e.g.,--context unperturbed_multiple) so that the ingestion process can use a different linking strategy for UCSF datasets while preserving legacy behaviour for MSK and JAX when the context is not specified.Refactored Linking:
The previously monolithic
establish_linksfunction is split into smaller helper methods (_link_cell_lines_to_children, _process_library_preparations, and _link_sequencing_files) to improve maintainability.Enhanced Robustness:
A new helper,
request_with_retries, has been added to implement exponential backoff for HTTP requests, improving resilience against transient connection errors.Related tickets #126, #61