Add support for OME-Zarr hosted on AWS S3 #25
Merged
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This makes a few functional changes on top of #23 allowing the pixel-buffer micro-service to use the
ZarrPixelBuffer
and access raw data of Zarr and non-Zarr images.The following changes have been made:
/OMERO/Pixels
bean pointing to the removedcom.glencoesoftware.omero.ms.image.region.PixelsService
implementation and replace by an alias pointing atZarrPixelsService
by defaultTileRequestHandler.getPixels
is updated to retrieve the additional columns required for theZarrPixelsService
checks i.e. the image externalInfo as well as its formatinternal-ome.api.IQuery
is set to theNoopQueryImpl
implemented inomero-ms-core 0.9.0
org.apache.httpcomponent
libraries includinghttpclient
are unexcluded. Without this change, when accessing OME-Zarr on S3, theAmazonS3Client
constructor would throw anjava.lang.NoClassDefFoundError: org/apache/http/conn/routing/HttpRoutePlanner
Testing-wise, a good functional workflow is to deploy an OMERO deployment including this version micro-service with QuPath and our QuPath OMERO.web extension which uses this micro-service for retrieving raw data, in particular for fluorescence data.
s3://gs-public-zarr-archive
/cc @erindiel @melissalinkert