Cell-level measurements #1375
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Cell-level measurements #1375
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Apr 19, 2025
arteymix
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Apr 19, 2025
...n/java/ubic/gemma/persistence/service/expression/experiment/ExpressionExperimentDaoImpl.java
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...c/gemma/persistence/service/expression/experiment/SingleCellExpressionExperimentService.java
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Always write the ExternalDatabase update first so that it will not be ignored if the write to disk or admin email fails. Do not rethrow an exception when writing the update status to disk fails.
In tests, this ensures that the database is always initialized before any test that uses the SessionFactory runs.
filter categories based on their presence in the BioMaterial factorValues
…yPowerToolsProbesetSummarize Improve usages of the Process API: - use waitFor() with a timeout instead of Thread.sleep() - replace GenericStreamConsumer and GenericParsingConsumer with ProcessBuider and appropriate stream redirections - always specify arguments as an array of strings. - always pipe the standard error and include it in the exception message Replace File with Path. Eliminate native BLAT. It is unused and if we ever want to add it back, it will have to be updated anyway.
Do no allow custom MEX to be written to the dataFiles directory. Do not create lock files when writing MEX to a custom directory. Honor the EE last updated when force-writing MEX and tabular single-cell data to the standard location.
Fix autoFlush not being passed in some cases. Fix CELL_IDS format not being written to file. Add more destination options for writing single-cell metadata file.
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Add an experimental BITSET primitive type for storing bit vectors.
…hing the one being added Indicate which CLC/CTA in the dimension is conflicting with the new one.
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…utput Make CellLevelMeasurements describable.
Handle bitsets as a special case because they cannot be sliced in the database.
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CellLevelMeasurements.category)