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WiP Blosc#88

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pwalczysko wants to merge 3 commits intoome:masterfrom
pwalczysko:blosc
Open

WiP Blosc#88
pwalczysko wants to merge 3 commits intoome:masterfrom
pwalczysko:blosc

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@pwalczysko pwalczysko commented Jan 23, 2024

This is based on #87 (comment) -

Rationale:

The import of ome.zarr files into OMERO based on #87 (comment) is not successful, as blosc is not installed and found.
See also ome/ZarrReader#76 (comment)

Adding blosc install as per this PR is fixing the issue of stacktrace=java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll at com.bc.zarr.CompressorFactory$BloscCompressor.cbufferSizes(CompressorFactory.java:371 but a new issue emerges:

New issue (specific to Docker (possibly) and Rockylinux-9 image (?):

2024-01-23 16:18:15,889 6364       [l.Client-0] ERROR     ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /Users/pwalczysko/Work/18188.zarr/0/0/0
java.lang.RuntimeException: Failure response on import!
Category: ::omero::grid::ImportRequest
Name: import-request-failure
Parameters: {stacktrace=java.lang.IndexOutOfBoundsException
	at java.base/java.io.DataInputStream.readFully(DataInputStream.java:197)
	at com.bc.zarr.CompressorFactory$BloscCompressor.uncompress(CompressorFactory.java:342)
	at com.bc.zarr.chunk.ChunkReaderWriterImpl_Byte.read(ChunkReaderWriterImpl_Byte.java:50)
	at com.bc.zarr.ZarrArray.read(ZarrArray.java:278)
	at com.bc.zarr.ZarrArray.read(ZarrArray.java:255)
...

Several points to discuss:

  1. should we maybe rather install blosc by default in the ansible-role-omero-server ?
  2. Is the IndexOOBounds error above connected with my Rockylinux-9 docker on M1 Mac setup ? Note that this problem is not encountered on RHEL 9 VM setup, where the install of sudo dnf install blosc fixes the ome.zarr import fully. How to fix the IndexOOB error on Docker ?

cc @khaledk2 @jburel

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2 participants