Hotfix 1.32.5 #1580
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Hotfix 1.32.5 #1580
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…ggregated single-cell data
Mention that in the CLI option.
Add basic support for downloading data from CELLxGENE for datasets that are also available in GEO.
When the option is set, no symlink is created.
Feature cellxgene
Filter taxa and assays when scraping CELLxGENE. Add an option to select specific allowed taxa. Add more supported single-cell assays. Detect unsecure http:// links to GEO.
Increase reporting frequency to every 100 vectors for agggregation.
Reduce the number of times we compute start/end positions by caching the value. Unfortunately, because we keep cell types contiguous, there's no suitable workaround. Report aggregation throughput and indicate that we are loading single-cell vectors. Indicate progress when loading vectors for aggregation and add support for streaming single-cell vectors when aggregating.
Make sure that we do not report progress to the console when writing single-cell data to the standard output.
Remove the edit button, there is no editBioMaterial.html page anymore.
Refactor CompletionGenerator subclasses to reuse some of thet logic in an abstract class. Add a sample output for reviewing (will be removed before merging!)
Generate wiki markup for updating curator documentation
…ls-in-bulk-data-vectors Store number of cells in raw/processed bulk vectors
display cell counts on diff exp tree
remove gene search and redirect to gembrow
Make ExpressionDataDoubleMatrix immutable. Use a raw double[][] matrix for ExpressionDataDoubleMatrix and other multi-assay matrices to minimize bookeeping. Pefer DoubleMatrix2D from Colt over DoubleMatrix when modifying a matrix without altering the columns/rows labels. Add asDoubleMatrix2D() to conveniently obtain a Colt matrix. Rename getMatrix() to asDoubleMatrix() to make it clear that the matrix is being copied to a new data format. Rename getRawMatrix() to getMatrix(). Fix ExpressionDataDoubleMatrix not being able to hold negative infinities since those were converted to NaNs. Fix LowVarianceTest, two zeroes were sampled and converted to negative infinities.
This reverts commit 8924c04.
…uction The TwoChannelMissingValues implementation was accessing the dimension of the preferred matrix with a design element from the base channel. This fails if the design element was filtered out.
…ject Use data vector slicing utilities to re-arrange the preferred raw data and mask to match the target dimension that will be used for the processed data. Fix #1572 since we no-longer need to initialize the assays/samples from the vectors.
Add some basic type safety to the Persister interface.
The contiguous trick cannot be used if there are no assays to slice.
Rewriting the ProcessedExpressionDataVectorCreationHelperService to not use DoubleVectorValueObject resulted in a regression in outlier masking. Those were actually performing the masking when being converted back to processed data vectors. Instead, explicitly mask outlier assays in the service.
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Make sure that URLs generated by the REST API are to other resources provided by the API. Add missing beans in tests.
Remove plexus-io workaround, it's been updated in the affected Maven plugins. Update baseCode to 1.1.33. Update gsec to 0.0.22.
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