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Re-include xalan as a dependency of the image-region micro-service #147
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This library is required for upgrading older version of the OME-XML schema (currently at 2016-06) using the XSLT transformation sheets in the memo regeneration utility. Without it, the XML transformation will fail and the reader stack will typically fallback to the generic TIFF reader causing metadata mismatch when reading planes/series greater than zero.
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👍 We might want to evaluate other places where this dependency is excluded too (e.g. https://github.com/search?q=org%3Aglencoesoftware+%22exclude+group%3A+%27xalan%27%22&type=code)
As discussed separately with @sbesson, a potential follow-up is to warn in the memo regenerator if the regenerated memo's reader does not match the DB reader (and/or the previous memo's reader), as that could have helped to catch this issue sooner.
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Throw a quick unit test in to make sure that the requisite classes are on the classpath?
Do we need to initialize everything and run what is essentially an integration test to check if Xalan is on the classpath? |
576cfdc should include a first unit test for the Running the tests on top of the current HEAD of the micro-service should fail with an |
Definitely not necessary. In the spirit of keeping the changes minimal, I force pushed the TIFFs and added a test which should throw a |
👍 Let's loose the TIFFs from 576cfdc then? Maybe just force push it away? |
This library is required for upgrading older version of the OME-XML schema (currently at 2016-06) using the XSLT transformation sheets in the memo regeneration utility.
Without it, the XML transformation will fail and the reader stack will typically fallback to the generic TIFF reader causing metadata mismatch when reading planes/series greater than zero.
This can be tested by importing a multidimensional multi-file OME-TIFF created with an old version of the OME data model e.g. https://downloads.openmicroscopy.org/images/OME-TIFF/2013-06/tubhiswt-4D/ and regenerating the memo file using the utility shipped with the micro-service. With the current version of the micro-service, the memo file will be generated using the standard TIFF reader and any rendering call on a plane other than the first one should result in an
Error instantiating pixel buffer
due to an underlyingjava.lang.IllegalArgumentException
.With this PR included, the rendering calls should work as expected for all planes