Add a command line tool for linting ACLs #997
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arteymix
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We don't assign ACEs on entities that inherit permissions from their parent, so we can add that check to the linter. |
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Update commons-lang3 to 3.18.0.
Detect single-cell datasets based on assay tags.
Add a warning if the number of cells with expression data in Gemma is less than 90% of that number.
Use async factories for the OpenAPI and UserAgentAnalyzer beans so that they can use background threads. Add support for destroying singleton instances in AbstractAsyncFactoryBean. Remove AsyncFactoryBeanUtils in favour of FutureUtils.
Use a qualifier for HomologeneService to prevent type conflict with the OpenAPI as they both appear as Future to the context.
Relocate low-variance filter in ubic.gemma.core.analysis.preprocess.filter
Cleanup expression data filters Rename LowVarianceFilter to RepetitiveValuesFilter to avoid confusion with other filters that actually filter based on variance. Add FilteringException to the signature of Filter.filter(). Add more tests for individual filters.
Add support for parsing and list datasets available in the UCSC Cell Browser
This has the main advantage of not altering the JAR (from Maven's perspective) when re-building, packaging is much faster when gemma-core is not modified. It's also a better place to put version information in general.
Remove EHDAA2
Treat suppress missing documentation entries (return value, method descriptions). This will eventually be addressed, but there are simply too many warnings for it to be useful.
This field can actually be of use if we need to override the URI/URL of a particular database entry.
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Move build information into the manifest
Retrieve the subsets from the processed vectors' dimension instead of potentially running the batch confound algorithm on irrelevant subsets. Move batch confound/effect update logic from the ExpressionExperimentController into the ExpressionExperimentReportService. This will provide us audit events when it is triggered from the frontend. Make subset name creation consistent for DEA and single-cell pseudo-bulk subsetting. Fix #1588 by shortening the subset names to only the relevant part and thus making it very unlikely to exceed size of a TEXT column. Recalculate batch info as an agent with elevated privilege instead of using the "no update" trick.
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TODO
GROUP_ADMINThis is useful for identifying issues such as those reported in #994.