Open Microscopy Environment

This looks like a version mismatch with the other Bio-Formats jars, you will have to keep the core Bio-Formats jars to at least the same minor version. In this case if you have a 5.9 version of formats-gpl then upgrading formats-api and formats-bsd to a 5.9 version to match should prevent these errors.

Hi David,

The link you sent previously are for bio-formats 5.10 jars today. I don't think you keep previous build online on Jenkins. Do you have them somewhere else?

Sure, you can retrieve the 5.9 components at https://web-proxy.openmicroscopy.org/we ... omponents/

Notably the 3 core components are the ones you will need:
formats-api
formats-bsd
formats-gpl

Hi David,

I am currently working with Etienne and Oren (from the previous posts in this thread). I have tried swapping the library versions to the newer 5.9.2 and 6.0.0 but still can't seem to have the PlaneID of the Columbus data imported. The imports are still single z-plane. I noticed similarity between the Columbus data and the PE Operetta format. After some modification to the xml file, I was able to make the Operetta reader ingest the columbus data and correctly import the filesets. Unfortunately, depending on the version of Bio Formats (5.9.2 or 6.0.0), I get some funky errors in from the ImportLibrary saying that there is a "checksum mismatch".

What would you suggest I try to get the z-plane imported from a columbus dataset?

Thanks,
Frank Gu

Hi Frank,

Do you have the stack trace for the error you are seeing with Bio-Formats 6.0.0?

Hi David,

With the 5.9.3 library:

Code: Select all

2019-02-28 02:52:43,704 1707658    [2-thread-1] ERROR        ome.formats.importer.ImportLibrary - Error on import: A checksum mismatch has occurred.
omero.ChecksumValidationException: null
   at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:1.8.0_191]
   at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) ~[na:1.8.0_191]
   at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[na:1.8.0_191]
   at java.lang.reflect.Constructor.newInstance(Constructor.java:423) ~[na:1.8.0_191]
   at java.lang.Class.newInstance(Class.java:442) ~[na:1.8.0_191]
   at IceInternal.BasicStream.createUserException(BasicStream.java:2779) ~[ice.jar:na]
   at IceInternal.BasicStream.access$300(BasicStream.java:14) ~[ice.jar:na]
   at IceInternal.BasicStream$EncapsDecoder10.throwException(BasicStream.java:3298) ~[ice.jar:na]
   at IceInternal.BasicStream.throwException(BasicStream.java:2291) ~[ice.jar:na]
   at IceInternal.OutgoingAsync.throwUserException(OutgoingAsync.java:399) ~[ice.jar:na]
   at omero.grid.ImportProcessPrxHelper.end_verifyUpload(ImportProcessPrxHelper.java:1616) ~[blitz.jar:na]
   at omero.grid.ImportProcessPrxHelper.verifyUpload(ImportProcessPrxHelper.java:1495) ~[blitz.jar:na]
   at omero.grid.ImportProcessPrxHelper.verifyUpload(ImportProcessPrxHelper.java:1482) ~[blitz.jar:na]
   at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:607) ~[blitz.jar:na]
   at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:306) [blitz.jar:na]
   at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:286) [blitz.jar:na]
   at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_191]
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) [na:1.8.0_191]
   at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_191]
   at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [na:1.8.0_191]
   at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [na:1.8.0_191]
   at java.lang.Thread.run(Thread.java:748) [na:1.8.0_191]
2019-02-28 02:52:43,704 1707658    [2-thread-1] INFO         ome.formats.importer.ImportLibrary - Exiting on error

With the 6.0.0 library:

Code: Select all

2019-02-28 16:27:50,596 168803     [2-thread-1] INFO   ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION
2019-02-28 16:27:50,612 168819     [2-thread-1] DEBUG   ome.services.blitz.util.CurrentPlatform - recognized current operating system as being Linux
2019-02-28 16:27:56,743 174950     [2-thread-1] ERROR        ome.formats.importer.ImportLibrary - Error on import: could not insert: [ome.model.core.OriginalFile]; SQL [insert into originalfile (atime, ctime, creation_id, external_id, group_id, owner_id, permissions, update_id, hash, hasher, mimetype, mtime, name, path, repo, "size", version, id) values (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)]; constraint [originalfile_repo_path_index]; nested exception is org.hibernate.exception.ConstraintViolationException: could not insert: [ome.model.core.OriginalFile]
omero.ValidationException: null
   at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:1.8.0_191]
   at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) ~[na:1.8.0_191]
   at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[na:1.8.0_191]
   at java.lang.reflect.Constructor.newInstance(Constructor.java:423) ~[na:1.8.0_191]
   at java.lang.Class.newInstance(Class.java:442) ~[na:1.8.0_191]
   at IceInternal.BasicStream.createUserException(BasicStream.java:2779) ~[ice.jar:na]
   at IceInternal.BasicStream.access$300(BasicStream.java:14) ~[ice.jar:na]
   at IceInternal.BasicStream$EncapsDecoder10.throwException(BasicStream.java:3298) ~[ice.jar:na]
   at IceInternal.BasicStream.throwException(BasicStream.java:2291) ~[ice.jar:na]
   at IceInternal.OutgoingAsync.throwUserException(OutgoingAsync.java:399) ~[ice.jar:na]
   at omero.grid.ManagedRepositoryPrxHelper.end_importFileset(ManagedRepositoryPrxHelper.java:175) ~[blitz.jar:na]
   at omero.grid.ManagedRepositoryPrxHelper.importFileset(ManagedRepositoryPrxHelper.java:46) ~[blitz.jar:na]
   at omero.grid.ManagedRepositoryPrxHelper.importFileset(ManagedRepositoryPrxHelper.java:33) ~[blitz.jar:na]
   at ome.formats.importer.ImportLibrary.createImport(ImportLibrary.java:420) ~[blitz.jar:na]
   at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:563) ~[blitz.jar:na]
   at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:306) [blitz.jar:na]
   at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:286) [blitz.jar:na]
   at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_191]
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) [na:1.8.0_191]
   at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_191]
   at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [na:1.8.0_191]
   at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [na:1.8.0_191]
   at java.lang.Thread.run(Thread.java:748) [na:1.8.0_191]
2019-02-28 16:27:56,743 174950     [2-thread-1] INFO         ome.formats.importer.ImportLibrary - Exiting on error

Hope this helps!

Thanks,
Frank Gu

Thanks Frank,

Would it also be possible to upload the original unmodified Columbus dataset to https://www.openmicroscopy.org/qa2/qa/upload/

We received a partial dataset last time but having the full set would allow us to hopefully put in place a long term fix.

Hi David,

The dataset is 115G. Can the upload portal support this?

Frank

Hi Frank,

Datasets that large cannot be uploaded to the QA page, but we have an FTP server that can be used instead. I have sent instructions for uploading via FTP in a private message.

-Melissa