Opened 6 years ago

Closed 6 years ago

#331 closed task (fixed)

Updates required for BASE 3

Reported by: nicklas Owned by: nicklas
Priority: major Milestone: Normalization package v1.1
Component: net.sf.basedb.normalizers Keywords:


Need to make some packaging changes. Eg. Plugin definitions should be moved into extensions.xml. Plugin configurations file should be renamed to plugin-configurations.xml. Build script changes needed since BASE jar file have different names. See the net.sf.basedb.examples build script for ideas.

Verify that the code works with BASE 3.

Change History (3)

comment:1 Changed 6 years ago by nicklas

  • Owner changed from martin to nicklas
  • Status changed from new to assigned

comment:2 Changed 6 years ago by nicklas

(In [1410]) References #331: Updates required for BASE 3 support

The code compiles and installs. The only exception is the qQuantileNormalizer which uses the BioAssaySetExporter. This exporter has been removed in BASE 3 so this export needs to be re-implemented.

comment:3 Changed 6 years ago by nicklas

  • Resolution set to fixed
  • Status changed from assigned to closed

Since there are other tickets (#267 and #268) for getting rid of BioAssaySetExporter in the qQuantileNormalizer plug-in, I'll close this ticket as fixed.

I have tested the AverageNormalization, QuantileNormalization and RankInvariantNormalization and they run to completion and produces a result, so I'll assume that if there are any issues with them, they are not part of the BASE 2->BASE 3 upgrade and should be added as new tickets.

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