Web API extensions for querying AnalysisResultSet and additional filters for DE and EE #134
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| @@ -40,4 +44,5 @@ | |||
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| ExpressionAnalysisResultSet thawWithoutContrasts( ExpressionAnalysisResultSet resultSet ); | |||
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| ExpressionAnalysisResultSetValueObject loadValueObjectsLimit( int i ); | |||
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This is the main way repository layers are extended with Spring Data to support defining queries via method name. Although load...By is not really a support prefix, find...By is already used for another purpose in BaseDao.
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| @@ -168,7 +170,7 @@ public void addTestAnalyses( ExpressionExperiment ee ) { | |||
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| pca.setExperimentAnalyzed( ee ); | |||
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| persisterHelper.persist( pca ); | |||
| analyses.add( ( Analysis ) persisterHelper.persist( pca ) ); | |||
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Maybe we could make persist routine generic to avoid casting at this stage.
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Jersey has been updated to 2.25.1. It's the latest version that still has Spring 3 support, so we need to consider #116 if we want to use a newer version. |
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I got the filtering by dataset and database entry done. I had to move the accession (a.k.a. database entry) of an EE up into the BioAssaySet because the experimentAnalyzed by a given expression analysis is not necessarily an EE, but can also be an EE subset. It makes much more sense though because BioAssay have an accession field as well, and having gene expression data is not a prerequisite for GEO series. I moved on to implement the other generic filtering, offset, limit and sort features. |
Add persister for DifferentialExpressionAnalysis
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The main idea is to add generic services that expose result sets form co-expression and expression analysis to fulfill the requirements from #127. For other issues, we need to take a similar approach by extending the service and DAO routines to accept more parameters to filter.
I've updated Jersey in the process which allow us to register and use parameter converters (yay!), which is much nicer than doing the conversion ourselves every time we pass parameters in the controller layer. I think we could take advantage of Jersy test framework to really test out the API via actual requests, but that will require some setup.
I'm not exactly looking for review, but I would really like to leave some notes here and there because there are some concepts that I really liked from using Spring Boot on another project that would be highly beneficial to our codebase. I took quite a big dive in the codebase to understand these changes.
Relates to #123, #126, #127 and #132