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nadeemlab / SPT

Spatial profiling toolbox for spatial characterization of tumor immune microenvironment in multiplex images
https://oncopathtk.org
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Deprecate resource-intensive views #222

Closed jimmymathews closed 12 months ago

jimmymathews commented 1 year ago

The database views marker_positive_cell_count_by_study_specimen and its associates are expensive to create/refresh (often crashing pg_restore and similar db management operations) and don't offer much functionality. They are only used to support the precomputed t-tests between predefined phenotype fractions. But these fractions can be computed much more quickly now that we have the dedicated counts service.

For this issue, deprecate marker_positive_cell_count_by_study_specimen and related views, replacing fraction_stats with a table that is created at initialization using the more optimized counts service functions.

jimmymathews commented 1 year ago

This also includes deprecation of the create-schema command, since its main functionality is absorbed into the tabular import workflow setup.