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IDR
Replace existing Fileset with NGFF Fileset
To avoid re-importing Images when updating data to NGFF, we want to create a new Fileset for the NGFF data, and replace old Filesets.
Testing workflow:
Imported png: https://merge-ci.openmicroscopy.org/web/webclient/?show=image-257915
Converted same png to NGFF:
$ bioformats2raw OME_screenshot.png OME_screenshot.zarr --tile_width 256
To be able to tell an NGFF image, removed chunk of alpha channel:
$ rm OME_screenshot.zarr/0/0/0/3/0/0/0
Edited import.py to upload ALL files in directory:
def get_files_for_fileset(fs_path):
filepaths = []
for path, subdirs, files in os.walk(fs_path):
for name in files:
print(os.path.join(path, name))
filepaths.append(os.path.join(path, name))
return filepaths
Import the Zarr to create a Fileset AND import the Fileset
$ python import.py OME_screenshot.zarr --dataset 67919
Re-import this... NGFF_missing_chunk - as expected
https://merge-ci.openmicroscopy.org/web/webclient/?show=image-257917
Fileset ID: 138110
We want to update the Image:257915 (png) above to use Fileset:138110
$ omero obj update Image:257915 fileset=Fileset:138110
The 'png' image now lists NGFF files in it's Fileset, but looks the same.
Now try deleting the png Fileset...
$ omero delete Fileset:138108 --report
omero.cmd.Delete2 Fileset:138108 ok
Steps: 6
Elapsed time: 0.674 secs.
Flags: []
Deleted objects
OriginalFile:1767759,1767760
Fileset:138108
FilesetEntry:1058458
FilesetJobLink:429236-429240
IndexingJob:498962
JobOriginalFileLink:216552
MetadataImportJob:498959
PixelDataJob:498960
ThumbnailGenerationJob:498961
UploadJob:498958
Now, trying to view the 'png' image gives:
File "/home/omero/workspace/OMERO-web/.venv3/lib64/python3.6/site-packages/omero_api_RenderingEngine_ice.py", line 1192, in load
return _M_omero.api.RenderingEngine._op_load.invoke(self, ((), _ctx))
...
serverExceptionClass = ome.conditions.ResourceError
message = Error instantiating pixel buffer: /home/omero/omero-server-data/ManagedRepository/user-3_454/Blitz-0-Ice.ThreadPool.Server-10/2023-02/23/09-01-23.654/OME_screenshot.png
}
To cut a long story short...
@jburel found that you need to update Pixels to point at the new NGFF data:
psql -U postgres -d OMERO-server -c "UPDATE pixels SET name = '.zattrs', path = 'user-3_454/Blitz-0-Ice.ThreadPool.Server-5/2023-02/23/09-26-58.983/OME_screenshot.zarr' where id = 256813" UPDATE 1
This allows you to view the original `png` using the underlying NGFF Fileset!
Strategy in place in omero-blitz/src/main/java/omero/cmd/graphs/DuplicateI.java could be re-used
and we can introduce a "swapFileSet"
Created a script at https://gist.github.com/will-moore/56f03cd126dcac9981bceeb8e7cdb393
This uploads a directory of files (all files uploaded) to create a new Fileset.
Then it finds the images linked to the replacefileset specified and re-links those Images
to the new Fileset.
The old Fileset is deleted.
The only step that is needed after this is a psql command that is printed by the script.
$ python replace_fileset.py OME_screenshot.zarr/ --replacefileset=138127
Importing: OME_screenshot.zarr/
Uploading: OME_screenshot.zarr/.zattrs
Uploading: OME_screenshot.zarr/.zgroup
Uploading: OME_screenshot.zarr/0/.zattrs
Uploading: OME_screenshot.zarr/0/.zgroup
Uploading: OME_screenshot.zarr/0/0/.zarray
Uploading: OME_screenshot.zarr/0/0/0/0/0/0/1
Uploading: OME_screenshot.zarr/0/0/0/1/0/0/0
Uploading: OME_screenshot.zarr/0/0/0/1/0/0/1
Uploading: OME_screenshot.zarr/0/0/0/3/0/0/1
Uploading: OME_screenshot.zarr/0/0/0/2/0/0/0
Uploading: OME_screenshot.zarr/0/0/0/2/0/0/1
Uploading: OME_screenshot.zarr/0/1/.zarray
Uploading: OME_screenshot.zarr/0/1/0/1/0/0/0
Uploading: OME_screenshot.zarr/0/1/0/3/0/0/0
Uploading: OME_screenshot.zarr/0/1/0/2/0/0/0
Uploading: OME_screenshot.zarr/OME/METADATA.ome.xml
orig_file 1768428
orig_file user-3_454/Blitz-0-Ice.ThreadPool.Server-53/2023-02/23/17-52-58.270/OME_screenshot.zarr/
orig_file .zattrs
Updating image OME_screenshot.png 257920
psql -U postgres -d OMERO-server -c "UPDATE pixels SET name = '.zattrs', path = 'user-3_454/Blitz-0-Ice.ThreadPool.Server-53/2023-02/23/17-52-58.270/OME_screenshot.zarr/' where id = 256818
Deleting Fileset 138127
In order to avoid the direct psql command
We will need to do something like https://github.com/ome/omero-blitz/blob/master/src/main/java/omero/cmd/graphs/DuplicateI.java#L1019
via a new command e.g. swapFileset
The script above uses regular "upload" to create a Fileset. But for IDR we will really want an "in-place" Fileset creation. However, I don't know how to adapt the script to achieve that?? cc @joshmoore
Discussed today: https://github.com/ome/omero-upload/blob/master/src/omero_upload/library.py#L36 looks like a good place to start looking at in-place import
Test on training server 3 or 4
The library above creates file with conn.createOriginalFileFromFileObj() and creates a file at managed-repo/Files/ID which is then replaced with a sym-link to the actual in-place file.
Is that what happens with a standard in-place import @sbesson? It seems not, because in general on IDR, when you check the paths to files in a Fileset, these are not of that form with Files but are like demo_2/2015-11/23/16-25-15.579/Meas_03(2012-07-31_13-12-10)/005010001.flex
Perhaps I can create the symlinks in the ManagedRepository, similar to https://github.com/IDR/idr0125-way-cellpainting/blob/main/scripts/symlinks.bash and then create an OriginalFile object, simply passing it the path...?
To test creation of a Fileset, can try to create symlinks as above, then create the Fileset from there.
First, try to import a test image into a test server. Use idr0125-pilot, since I have been using this as a test server and creating symlinks there etc...
Try to connect locally...
$ ssh pilot-idr0125 -L 40064:localhost:4064
then
$ omero import -d 15301 OME_screenshot.png
# login to localhost:40064
Fileset:5286801
$ omero import -d 15301 --depth=20 OME_screenshot.zarr/
Fileset:5286802
I assume that if a File doesn't exist for an Original File based on it's ID: e.g. 4879195 is in:
$ ls /data/OMERO/Files/Dir-004/Dir-879
then OMERO uses the path and name to find the file directly?
E.g. from import above: Original File: 48780012, path: demo_2/Blitz-0-Ice.ThreadPool.Server-25/2023-03/06/15-59-36.479/OME_screenshot.zarr/ name: .zattrs.
Test on idr0054 Tonsil 2 image: https://idr.openmicroscopy.org/webclient/?show=image-5025552
NGFF data is at...
$ ssh pilot-idrtesting
$ ls /ngff/idr0054
Tonsil 2.ome.zarr
So we want to try an in-place import to the server there. Unfortunately that server doesn't have the original pattern file imported image, but we can use the NGFF image instead...
e.g. use this to access via web...
ssh -A -o 'ProxyCommand ssh idr-pilot.openmicroscopy.org -W %h:%p' pilot-idrtesting-omeroreadwrite -L 1080:localhost:80
NGFF Image has been imported previously (regular ZarrReader import) at:
demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/Tonsil 2.ome.zarr/
So we want to create symlinks:
$ ssh pilot-idrtesting
sudo -u omero-server -s
cd /data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557
mkdir ngff
cd ngff
ln -s "/ngff/idr0054/Tonsil 2.ome.zarr" "Tonsil 2.ome.zarr"
Using script at https://gist.github.com/will-moore/671a9f971f49661d097aa1655476878e
$ sudo -u omero-server -s
$ cd
$ pwd
/opt/omero/server
$ vi inplace_fileset.py
# paste in script above and save...
$ source /opt/omero/server/venv3/bin/activate
$ omero login demo@localhost
$ python inplace_fileset.py 9353 9353
...
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr .zattrs 33 1a45bdb742869f84fd71ae0fd67f79f1b26923fe
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr .zgroup 23 63de336a45370c236af207996ffd1bca2d7ae2f4
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr/0 .zattrs 9024 d1081971a9fa36eab85dfc677c8d41fdbcd71ef8
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr/0 .zgroup 23 63de336a45370c236af207996ffd1bca2d7ae2f4
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr/0/0 .zarray 328 a902050bf764318cdb65511209294d576723e7d2
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr/0/1 .zarray 328 5acab8b416b346283b6fe770c205aa40f92d784e
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr/0/2 .zarray 324 0be6b77260346499af5633a763571753660ee9ab
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr/0/3 .zarray 324 daad3d12d69b2c5e1daa6499a2ac9d15027444fc
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr/0/4 .zarray 324 5d9f748f84e3e21f8e77d8b47e8742cacde376db
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr/OME .zattrs 24 156e48269827cb4611d5a3899d862c60c8f483f4
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr/OME .zgroup 23 63de336a45370c236af207996ffd1bca2d7ae2f4
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr/OME METADATA.ome.xml 2391 8f01227852e065e2bd8ac6d82be8644654089898
Created new_fileset 9363
Updating image METADATA.ome.xml 46035
psql -U postgres -d OMERO-server -c "UPDATE pixels SET name = '.zattrs', path = '/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr' where id = 46035
Delete Fileset:
$ omero delete Fileset:9353 --report
Using session for demo@localhost:4064. Idle timeout: 10 min. Current group: demo
omero.cmd.Delete2 Fileset:9353 ok
Steps: 6
Elapsed time: 3.818 secs.
Flags: []
Deleted objects
CommentAnnotation:33553
FilesetAnnotationLink:9303
OriginalFile:1067474-1067918
Fileset:9353
FilesetEntry:975569-976012
FilesetJobLink:45909-45913
IndexingJob:45913
JobOriginalFileLink:9353
MetadataImportJob:45910
PixelDataJob:45911
ThumbnailGenerationJob:45912
UploadJob:45909
Use omero config get --show-password to get psql credentials etc.. then
PGPASSWORD=password psql -U omero -d idr -h 192.168.10.117
idr=> UPDATE pixels SET name = '.zattrs', path = 'demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr' where id = 46035;
UPDATE 1
But we get this error when trying to view the image:
ResourceError
Traceback (most recent call last):
File "/opt/omero/web/venv3/lib64/python3.6/site-packages/django/core/handlers/exception.py", line 41, in inner
response = get_response(request)
File "/opt/omero/web/venv3/lib64/python3.6/site-packages/django/core/handlers/base.py", line 187, in _get_response
response = self.process_exception_by_middleware(e, request)
File "/opt/omero/web/venv3/lib64/python3.6/site-packages/django/core/handlers/base.py", line 185, in _get_response
response = wrapped_callback(request, *callback_args, **callback_kwargs)
File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omeroweb/decorators.py", line 538, in wrapped
retval = f(request, *args, **kwargs)
File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omeroweb/decorators.py", line 597, in wrapper
context = f(request, *args, **kwargs)
File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omeroweb/webclient/views.py", line 1754, in load_metadata_preview
rdefId = manager.image.getRenderingDefId()
File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omero/gateway/__init__.py", line 7881, in wrapped
if not self._prepareRenderingEngine() \
File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omero/gateway/__init__.py", line 8157, in _prepareRenderingEngine
self._re = self._prepareRE(rdid=rdid)
File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omero/gateway/__init__.py", line 8136, in _prepareRE
re.load(ctx)
File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omero/gateway/__init__.py", line 4796, in __call__
return self.handle_exception(e, *args, **kwargs)
File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omeroweb/webclient/webclient_gateway.py", line 2222, in handle_exception
super(OmeroWebSafeCallWrapper, self).handle_exception(e, *args, **kwargs)
File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omero/gateway/__init__.py", line 4793, in __call__
return self.f(*args, **kwargs)
File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omero_api_RenderingEngine_ice.py", line 1192, in load
return _M_omero.api.RenderingEngine._op_load.invoke(self, ((), _ctx))
omero.ResourceError: exception ::omero::ResourceError
{
serverStackTrace = ome.conditions.ResourceError: Error instantiating pixel buffer: /data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr/.zattrs
at ome.io.nio.PixelsService.createBfPixelBuffer(PixelsService.java:907)
at ome.io.nio.PixelsService._getPixelBuffer(PixelsService.java:653)
at ome.io.nio.PixelsService.getPixelBuffer(PixelsService.java:571)
at ome.services.RenderingBean$12.doWork(RenderingBean.java:2205)
at jdk.internal.reflect.GeneratedMethodAccessor302.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:282)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy100.doWork(Unknown Source)
at ome.services.util.Executor$Impl.execute(Executor.java:447)
at ome.services.util.Executor$Impl.execute(Executor.java:392)
at ome.services.RenderingBean.getPixelBuffer(RenderingBean.java:2202)
at ome.services.RenderingBean.load(RenderingBean.java:417)
at jdk.internal.reflect.GeneratedMethodAccessor1950.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy122.load(Unknown Source)
at jdk.internal.reflect.GeneratedMethodAccessor1950.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy122.load(Unknown Source)
at jdk.internal.reflect.GeneratedMethodAccessor1978.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:172)
at ome.services.throttling.Callback.run(Callback.java:56)
at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140)
at ome.services.blitz.impl.RenderingEngineI.load_async(RenderingEngineI.java:316)
at jdk.internal.reflect.GeneratedMethodAccessor1977.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at omero.cmd.CallContext.invoke(CallContext.java:85)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy124.load_async(Unknown Source)
at omero.api._RenderingEngineTie.load_async(_RenderingEngineTie.java:248)
at omero.api._RenderingEngineDisp.___load(_RenderingEngineDisp.java:1223)
at omero.api._RenderingEngineDisp.__dispatch(_RenderingEngineDisp.java:2405)
at IceInternal.Incoming.invoke(Incoming.java:221)
at Ice.ConnectionI.invokeAll(ConnectionI.java:2536)
at Ice.ConnectionI.dispatch(ConnectionI.java:1145)
at Ice.ConnectionI.message(ConnectionI.java:1056)
at IceInternal.ThreadPool.run(ThreadPool.java:395)
at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)
at java.base/java.lang.Thread.run(Thread.java:829)
serverExceptionClass = ome.conditions.ResourceError
message = Error instantiating pixel buffer: /data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr/.zattrs
}
<WSGIRequest: GET '/webclient/metadata_preview/image/46035/?_=1678226804231'>
cc @joshmoore @jburel That's the current state of where I'm at with creating a Fileset in-place... I don't know why I'm getting that exception. The path in the exception certainly points at correct files (via the symlink):
$ ls -alh "/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr/"
total 8.0K
drwxrwxr-x. 4 dlindner dlindner 56 Feb 17 13:27 .
drwxrwxr-x. 3 dlindner dlindner 31 Feb 17 13:27 ..
drwxrwxr-x. 7 dlindner dlindner 81 Feb 17 13:27 0
drwxrwxr-x. 2 dlindner dlindner 60 Feb 17 13:27 OME
-rw-rw-r--. 1 dlindner dlindner 33 Feb 17 13:27 .zattrs
-rw-rw-r--. 1 dlindner dlindner 23 Feb 17 13:27 .zgroup
The server master.err log shows:
java.io.IOException: '.zarray' expected but is not readable or missing in store.
at com.bc.zarr.ZarrArray.open(ZarrArray.java:106)
"escaped in anyway" - you mean the file path escaping of white-space? Is that needed when I use quotes in:
UPDATE pixels SET name = '.zattrs', path = 'demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr' where id = 46035;
Looking for the ".zarray" files, they seem to be there...
$ cd "/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr/"
$ find ./ -name ".zarray"
./0/0/.zarray
./0/1/.zarray
./0/2/.zarray
./0/3/.zarray
./0/4/.zarray
Ah, I wonder if the ".zattrs" that I'm pointing to in this case is the wrong file? I pointed at the image.zarr/.zattrs in our previous tests on this, but that was the image itself, not a bioformats2raw.layout, so maybe I should point to the /Tonsil 2.ome.zarr/OME/METADATA.xml?...
UPDATE pixels SET name = 'METADATA.ome.xml', path = 'demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr/OME' where id = 46035;
UPDATE 1
Hmm - now I just get...
serverExceptionClass = ome.conditions.ResourceError
message = Error instantiating pixel buffer: /data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr/OME/METADATA.ome.xml
}
Full stack track is:
ome.conditions.ResourceError
2023-03-13 10:52:34,794 ERROR [ ome.io.nio.PixelsService] (l.Server-0) Error instantiating pixel buffer: /data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr/OME/METADATA.ome.xml
java.lang.RuntimeException: java.lang.IllegalArgumentException: Invalid index: -1
at ome.io.bioformats.BfPixelBuffer.reader(BfPixelBuffer.java:79)
at ome.io.bioformats.BfPixelBuffer.setSeries(BfPixelBuffer.java:124)
at ome.io.nio.PixelsService.createBfPixelBuffer(PixelsService.java:898)
at ome.io.nio.PixelsService._getPixelBuffer(PixelsService.java:653)
at ome.io.nio.PixelsService.getPixelBuffer(PixelsService.java:571)
at ome.services.RenderingBean$12.doWork(RenderingBean.java:2205)
at jdk.internal.reflect.GeneratedMethodAccessor302.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:282)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy100.doWork(Unknown Source)
at ome.services.util.Executor$Impl.execute(Executor.java:447)
at ome.services.util.Executor$Impl.execute(Executor.java:392)
at ome.services.RenderingBean.getPixelBuffer(RenderingBean.java:2202)
at ome.services.RenderingBean.load(RenderingBean.java:417)
at jdk.internal.reflect.GeneratedMethodAccessor1950.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy122.load(Unknown Source)
at jdk.internal.reflect.GeneratedMethodAccessor1950.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy122.load(Unknown Source)
at jdk.internal.reflect.GeneratedMethodAccessor1978.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:172)
at ome.services.throttling.Callback.run(Callback.java:56)
at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140)
at ome.services.blitz.impl.RenderingEngineI.load_async(RenderingEngineI.java:316)
at jdk.internal.reflect.GeneratedMethodAccessor1977.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at omero.cmd.CallContext.invoke(CallContext.java:85)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy124.load_async(Unknown Source)
at omero.api._RenderingEngineTie.load_async(_RenderingEngineTie.java:248)
at omero.api._RenderingEngineDisp.___load(_RenderingEngineDisp.java:1223)
at omero.api._RenderingEngineDisp.__dispatch(_RenderingEngineDisp.java:2405)
at IceInternal.Incoming.invoke(Incoming.java:221)
at Ice.ConnectionI.invokeAll(ConnectionI.java:2536)
at Ice.ConnectionI.dispatch(ConnectionI.java:1145)
at Ice.ConnectionI.message(ConnectionI.java:1056)
at IceInternal.ThreadPool.run(ThreadPool.java:395)
at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)
at java.base/java.lang.Thread.run(Thread.java:829)
Caused by: java.lang.IllegalArgumentException: Invalid index: -1
at loci.formats.FormatReader.coreIndexToSeries(FormatReader.java:1328)
at loci.formats.FormatReader.getSeriesCount(FormatReader.java:963)
at loci.formats.MetadataTools.populatePixels(MetadataTools.java:137)
at loci.formats.MetadataTools.populatePixels(MetadataTools.java:116)
at loci.formats.in.ZarrReader.initFile(ZarrReader.java:282)
at loci.formats.FormatReader.setId(FormatReader.java:1443)
at loci.formats.ImageReader.setId(ImageReader.java:849)
at ome.io.nio.PixelsService$3.setId(PixelsService.java:869)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
at loci.formats.ChannelFiller.setId(ChannelFiller.java:234)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
at loci.formats.Memoizer.setId(Memoizer.java:690)
at ome.io.bioformats.BfPixelsWrapper.<init>(BfPixelsWrapper.java:52)
at ome.io.bioformats.BfPixelBuffer.reader(BfPixelBuffer.java:73)
... 82 common frames omitted
But I don't see any new errors added to the master.err log.
The last error on that log is the one Josh reported above:
master.err
java.io.IOException: '.zarray' expected but is not readable or missing in store.
at com.bc.zarr.ZarrArray.open(ZarrArray.java:106)
at com.bc.zarr.ZarrArray.open(ZarrArray.java:99)
at com.bc.zarr.ZarrArray.open(ZarrArray.java:95)
at com.bc.zarr.ZarrArray.open(ZarrArray.java:91)
at loci.formats.services.JZarrServiceImpl.open(JZarrServiceImpl.java:89)
at loci.formats.in.ZarrReader.openZarr(ZarrReader.java:434)
at loci.formats.in.ZarrReader.setSeries(ZarrReader.java:414)
at loci.formats.ImageReader.setSeries(ImageReader.java:491)
at loci.formats.ReaderWrapper.setSeries(ReaderWrapper.java:375)
at loci.formats.ReaderWrapper.setSeries(ReaderWrapper.java:375)
at loci.formats.ReaderWrapper.setSeries(ReaderWrapper.java:375)
at ome.io.bioformats.BfPixelBuffer.setSeries(BfPixelBuffer.java:125)
at ome.io.nio.PixelsService.createBfPixelBuffer(PixelsService.java:898)
at ome.io.nio.PixelsService._getPixelBuffer(PixelsService.java:653)
at ome.io.nio.PixelsService.getPixelBuffer(PixelsService.java:571)
at ome.services.RenderingBean$12.doWork(RenderingBean.java:2205)
at jdk.internal.reflect.GeneratedMethodAccessor302.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:282)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy100.doWork(Unknown Source)
at ome.services.util.Executor$Impl.execute(Executor.java:447)
at ome.services.util.Executor$Impl.execute(Executor.java:392)
at ome.services.RenderingBean.getPixelBuffer(RenderingBean.java:2202)
at ome.services.RenderingBean.load(RenderingBean.java:417)
at jdk.internal.reflect.GeneratedMethodAccessor1950.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy122.load(Unknown Source)
at jdk.internal.reflect.GeneratedMethodAccessor1950.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy122.load(Unknown Source)
at jdk.internal.reflect.GeneratedMethodAccessor1978.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:172)
at ome.services.throttling.Callback.run(Callback.java:56)
at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140)
at ome.services.blitz.impl.RenderingEngineI.load_async(RenderingEngineI.java:316)
at jdk.internal.reflect.GeneratedMethodAccessor1977.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at omero.cmd.CallContext.invoke(CallContext.java:85)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy124.load_async(Unknown Source)
at omero.api._RenderingEngineTie.load_async(_RenderingEngineTie.java:248)
at omero.api._RenderingEngineDisp.___load(_RenderingEngineDisp.java:1223)
at omero.api._RenderingEngineDisp.__dispatch(_RenderingEngineDisp.java:2405)
at IceInternal.Incoming.invoke(Incoming.java:221)
at Ice.ConnectionI.invokeAll(ConnectionI.java:2536)
at Ice.ConnectionI.dispatch(ConnectionI.java:1145)
at Ice.ConnectionI.message(ConnectionI.java:1056)
at IceInternal.ThreadPool.run(ThreadPool.java:395)
at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)
at java.base/java.lang.Thread.run(Thread.java:829)
Checking image again...
ssh -A -o 'ProxyCommand ssh idr-pilot.openmicroscopy.org -W %h:%p' idrtesting-omeroreadwrite -L 1080:localhost:80
http://localhost:1080/webclient/?show=image-46035
This uses Fileset: 9363 with paths on server (from web UI):
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr/OMEMETADATA.ome.xml
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr/OME.zgroup
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr/OME.zattrs
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr/0/4.zarray
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr/0/3.zarray
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr/0/2.zarray
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr/0/1.zarray
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr/0/0.zarray
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr/0.zgroup
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr/0.zattrs
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr.zgroup
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr.zattrs
NB: These paths are missing the trailing / compared to other images in IDR. Also, the whitespace might be causing problems...
Use $ omero delete Fileset:9363 --report --dry-run to get a handle on OriginalFile IDs for this Fileset:
OriginalFile:1999565-1999576
then:
$ omero hql -q --limit=10 "select name, path from OriginalFile where id=1999576"
# | Col1 | Col2
---+------------------+--------------------------------------------------------------------------------------------------------------------------
0 | METADATA.ome.xml | /data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil 2.ome.zarr/OME
Try to fix...
For 1999574, 1999575, 1999576:
$ omero obj update OriginalFile:1999574 path=/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil2.ome.zarr/OME/
For 1999565 - 1999574:
$ omero obj update OriginalFile:1999573 path=/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil2.ome.zarr/
Update symlink, replacing link from "Tonsil 2.ome.zarr" with link from "Tonsil2.ome.zarr"
$ ssh pilot-idrtesting
$ sudo -u omero-server -s
$ cd /data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff
$ ln -s "/ngff/idr0054/Tonsil 2.ome.zarr" "Tonsil2.ome.zarr"
$ ls -alh
total 0
drwxr-sr-x. 2 omero-server idr-data 55 Mar 21 10:23 .
drwxrwsr-x. 4 omero-server idr-data 43 Mar 7 16:23 ..
lrwxrwxrwx. 1 omero-server idr-data 31 Mar 7 16:23 Tonsil 2.ome.zarr -> /ngff/idr0054/Tonsil 2.ome.zarr
lrwxrwxrwx. 1 omero-server idr-data 31 Mar 21 10:23 Tonsil2.ome.zarr -> /ngff/idr0054/Tonsil 2.ome.zarr
$ rm "Tonsil 2.ome.zarr"
idr=> UPDATE pixels SET name = '.zattrs', path = 'demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil2.ome.zarr' where id = 46035;
UPDATE 1
Then tried to view image again - still fails:
Exception
Traceback (most recent call last):
File "/opt/omero/web/venv3/lib64/python3.6/site-packages/django/core/handlers/exception.py", line 41, in inner
response = get_response(request)
File "/opt/omero/web/venv3/lib64/python3.6/site-packages/django/core/handlers/base.py", line 187, in _get_response
response = self.process_exception_by_middleware(e, request)
File "/opt/omero/web/venv3/lib64/python3.6/site-packages/django/core/handlers/base.py", line 185, in _get_response
response = wrapped_callback(request, *callback_args, **callback_kwargs)
File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omeroweb/decorators.py", line 538, in wrapped
retval = f(request, *args, **kwargs)
File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omeroweb/decorators.py", line 597, in wrapper
context = f(request, *args, **kwargs)
File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omeroweb/webclient/views.py", line 1754, in load_metadata_preview
rdefId = manager.image.getRenderingDefId()
File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omero/gateway/__init__.py", line 7881, in wrapped
if not self._prepareRenderingEngine() \
File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omero/gateway/__init__.py", line 8157, in _prepareRenderingEngine
self._re = self._prepareRE(rdid=rdid)
File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omero/gateway/__init__.py", line 8136, in _prepareRE
re.load(ctx)
File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omero/gateway/__init__.py", line 4796, in __call__
return self.handle_exception(e, *args, **kwargs)
File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omeroweb/webclient/webclient_gateway.py", line 2222, in handle_exception
super(OmeroWebSafeCallWrapper, self).handle_exception(e, *args, **kwargs)
File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omero/gateway/__init__.py", line 4793, in __call__
return self.f(*args, **kwargs)
File "/opt/omero/web/venv3/lib64/python3.6/site-packages/omero_api_RenderingEngine_ice.py", line 1192, in load
return _M_omero.api.RenderingEngine._op_load.invoke(self, ((), _ctx))
omero.ResourceError: exception ::omero::ResourceError
{
serverStackTrace = ome.conditions.ResourceError: Error instantiating pixel buffer: /data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil2.ome.zarr/.zattrs
at ome.io.nio.PixelsService.createBfPixelBuffer(PixelsService.java:907)
at ome.io.nio.PixelsService._getPixelBuffer(PixelsService.java:653)
at ome.io.nio.PixelsService.getPixelBuffer(PixelsService.java:571)
at ome.services.RenderingBean$12.doWork(RenderingBean.java:2205)
at jdk.internal.reflect.GeneratedMethodAccessor302.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:282)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy100.doWork(Unknown Source)
at ome.services.util.Executor$Impl.execute(Executor.java:447)
at ome.services.util.Executor$Impl.execute(Executor.java:392)
at ome.services.RenderingBean.getPixelBuffer(RenderingBean.java:2202)
at ome.services.RenderingBean.load(RenderingBean.java:417)
at jdk.internal.reflect.GeneratedMethodAccessor1950.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy122.load(Unknown Source)
at jdk.internal.reflect.GeneratedMethodAccessor1950.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy122.load(Unknown Source)
at jdk.internal.reflect.GeneratedMethodAccessor1978.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:172)
at ome.services.throttling.Callback.run(Callback.java:56)
at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140)
at ome.services.blitz.impl.RenderingEngineI.load_async(RenderingEngineI.java:316)
at jdk.internal.reflect.GeneratedMethodAccessor1977.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at omero.cmd.CallContext.invoke(CallContext.java:85)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy124.load_async(Unknown Source)
at omero.api._RenderingEngineTie.load_async(_RenderingEngineTie.java:248)
at omero.api._RenderingEngineDisp.___load(_RenderingEngineDisp.java:1223)
at omero.api._RenderingEngineDisp.__dispatch(_RenderingEngineDisp.java:2405)
at IceInternal.Incoming.invoke(Incoming.java:221)
at Ice.ConnectionI.invokeAll(ConnectionI.java:2536)
at Ice.ConnectionI.dispatch(ConnectionI.java:1145)
at Ice.ConnectionI.message(ConnectionI.java:1056)
at IceInternal.ThreadPool.run(ThreadPool.java:395)
at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)
at java.base/java.lang.Thread.run(Thread.java:829)
serverExceptionClass = ome.conditions.ResourceError
message = Error instantiating pixel buffer: /data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil2.ome.zarr/.zattrs
}
<WSGIRequest: GET '/webclient/metadata_preview/image/46035/?_=1679392109084'>
Tried pointing at a few different locations, but each gave the same error
idr=> UPDATE pixels SET name = '.zattrs', path = 'demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil2.ome.zarr' where id = 46035;
UPDATE 1
idr=> UPDATE pixels SET name = '.zattrs', path = 'demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil2.ome.zarr/0/' where id = 46035;
UPDATE 1
idr=> UPDATE pixels SET name = 'METADATA.ome.xml', path = 'demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil2.ome.zarr/OME/' where id = 46035;
UPDATE 1
idr=> UPDATE pixels SET name = '.zattrs', path = 'demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil2.ome.zarr/' where id = 46035;
UPDATE 1
cc @joshmoore @sbesson @jburel - I'm still stuck at the same point here, and this is currently a blocker for NGFF Fileset replacement.
I have created a new Fileset, with links to new OriginalFiles (except for chunks), based on path/name of NGFF files, where the path contains a symlink to files at /ngff/idr0054/Tonsil 2.ome.zarr. Also updated the pixels to point at symlinked files.
Discussed in IDR meeting today: Need Blitz log...
$ ssh -A -o 'ProxyCommand ssh idr-pilot.openmicroscopy.org -W %h:%p' idrtesting-omeroreadwrite -L 1080:localhost:80
$ cd /opt/omero/server/OMERO.server
$ $ tail -f var/log/Blitz-0.log
Then go to http://localhost:1080/webclient/?show=image-46035 and open Preview Tab...
NB: lots of other activity adding to the Blitz log just now, so not limited to the action above...
Blitz log
2023-03-27 10:00:00,914 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911200914] time[0] tag[omero.repo.internal_register.find_repo_files]
2023-03-27 10:00:02,979 INFO [ ome.services.blitz.fire.SessionManagerI] (.Server-11) Found session locally: e5218453-c253-4b07-b3dd-3d7c0ffd2cfc
2023-03-27 10:00:02,980 INFO [ ome.services.blitz.fire.SessionManagerI] (.Server-11) Rejoining session ServiceFactoryI(session-878a0e38-c7f9-4558-b354-987a7c1be757/e5218453-c253-4b07-b3dd-3d7c0ffd2cfc) (agent=OMERO.web)
2023-03-27 10:00:02,985 INFO [ omero.cmd.SessionI] (.Server-13) Added servant to adapter: e5218453-c253-4b07-b3dd-3d7c0ffd2cfc/878a0e38-c7f9-4558-b354-987a7c1be757omero.api.IConfig(omero.api._IConfigTie@5a03ddb1)
2023-03-27 10:00:02,986 INFO [ ome.services.util.ServiceHandler] (.Server-14) Meth: interface ome.api.IConfig.getConfigValues
2023-03-27 10:00:02,986 INFO [ ome.services.util.ServiceHandler] (.Server-14) Args: [^omero\.cluster\.read_only\.runtime\.]
2023-03-27 10:00:02,990 INFO [ ome.security.basic.EventHandler] (.Server-14) Auth: user=2,group=3,event=null(User),sess=e5218453-c253-4b07-b3dd-3d7c0ffd2cfc
2023-03-27 10:00:02,993 INFO [ org.perf4j.TimingLogger] (.Server-14) start[1679911202986] time[6] tag[omero.call.success.ome.logic.ConfigImpl.getConfigValues]
2023-03-27 10:00:02,993 INFO [ ome.services.util.ServiceHandler] (.Server-14) Rslt: {omero.cluster.read_only.runtime.db=false, omero.cluster.read_only.runtime.repo=false}
2023-03-27 10:00:02,994 INFO [ ome.services.util.ServiceHandler] (l.Server-5) Meth: interface ome.api.IConfig.getClientConfigValues
2023-03-27 10:00:02,994 INFO [ ome.services.util.ServiceHandler] (l.Server-5) Args: ()
2023-03-27 10:00:02,997 INFO [ ome.security.basic.EventHandler] (l.Server-5) Auth: user=2,group=3,event=null(User),sess=e5218453-c253-4b07-b3dd-3d7c0ffd2cfc
2023-03-27 10:00:03,016 INFO [ org.perf4j.TimingLogger] (l.Server-5) start[1679911202994] time[22] tag[omero.call.success.ome.logic.ConfigImpl.getClientConfigValues]
2023-03-27 10:00:03,017 INFO [ ome.services.util.ServiceHandler] (l.Server-5) Rslt: {omero.client.ui.tree.orphans.name=Orphaned Images, omero.client.browser.thumb_default_size=96, omero.client.viewer.initial_zoom_level=0, ... 14 more}
2023-03-27 10:00:03,018 INFO [ ome.services.util.ServiceHandler] (l.Server-2) Meth: interface ome.api.IConfig.getConfigValue
2023-03-27 10:00:03,018 INFO [ ome.services.util.ServiceHandler] (l.Server-2) Args: [omero.mail.config]
2023-03-27 10:00:03,020 INFO [ ome.security.basic.EventHandler] (l.Server-2) Auth: user=2,group=3,event=null(User),sess=e5218453-c253-4b07-b3dd-3d7c0ffd2cfc
2023-03-27 10:00:03,022 INFO [ org.perf4j.TimingLogger] (l.Server-2) start[1679911203018] time[3] tag[omero.call.success.ome.logic.ConfigImpl.getConfigValue]
2023-03-27 10:00:03,022 INFO [ ome.services.util.ServiceHandler] (l.Server-2) Rslt: false
2023-03-27 10:00:03,023 INFO [ ome.services.util.ServiceHandler] (.Server-15) Executor.doWork -- ome.services.blitz.impl.ServiceFactoryI.isGuest[]
2023-03-27 10:00:03,023 INFO [ ome.services.util.ServiceHandler] (.Server-15) Args: [null, InternalSF@38784987]
2023-03-27 10:00:03,024 INFO [ ome.security.basic.EventHandler] (.Server-15) Auth: user=2,group=3,event=null(User),sess=e5218453-c253-4b07-b3dd-3d7c0ffd2cfc
2023-03-27 10:00:03,025 INFO [ org.perf4j.TimingLogger] (.Server-15) start[1679911203023] time[1] tag[omero.call.success.ome.services.blitz.impl.ServiceFactoryI$3.doWork]
2023-03-27 10:00:03,025 INFO [ ome.services.util.ServiceHandler] (.Server-15) Rslt: false
2023-03-27 10:00:03,025 INFO [ omero.cmd.SessionI] (.Server-15) Added servant to adapter: e5218453-c253-4b07-b3dd-3d7c0ffd2cfc/878a0e38-c7f9-4558-b354-987a7c1be757omero.api.IQuery(omero.api._IQueryTie@40b97a27)
2023-03-27 10:00:03,026 INFO [ ome.services.util.ServiceHandler] (l.Server-0) Meth: interface ome.api.IQuery.findAllByQuery
2023-03-27 10:00:03,026 INFO [ ome.services.util.ServiceHandler] (l.Server-0) Args: [select obj from Screen obj join fetch obj.details.owner as owner join fetch obj.details.creationEven, PARAMS:ids=ArrayList(1) ]
2023-03-27 10:00:03,027 INFO [ ome.security.basic.BasicEventContext] (l.Server-0) cctx: group=-1
2023-03-27 10:00:03,029 INFO [ ome.security.basic.EventHandler] (l.Server-0) Auth: user=2,group=-1,event=null(User),sess=e5218453-c253-4b07-b3dd-3d7c0ffd2cfc
2023-03-27 10:00:03,030 INFO [ org.perf4j.TimingLogger] (l.Server-0) start[1679911203026] time[3] tag[omero.call.success.ome.logic.QueryImpl.findAllByQuery]
2023-03-27 10:00:03,030 INFO [ ome.services.util.ServiceHandler] (l.Server-0) Rslt: ()
2023-03-27 10:00:03,031 INFO [ ome.services.util.ServiceHandler] (l.Server-7) Meth: interface ome.api.IQuery.findByQuery
2023-03-27 10:00:03,031 INFO [ ome.services.util.ServiceHandler] (l.Server-7) Args: [select obj from Screen obj join fetch obj.details.owner as owner join fetch obj.details.creationEven, PARAMS:ids=ArrayList(1) ]
2023-03-27 10:00:03,031 INFO [ ome.security.basic.BasicEventContext] (l.Server-7) cctx: group=-1
2023-03-27 10:00:03,033 INFO [ ome.security.basic.EventHandler] (l.Server-7) Auth: user=2,group=-1,event=null(User),sess=e5218453-c253-4b07-b3dd-3d7c0ffd2cfc
2023-03-27 10:00:03,034 INFO [ org.perf4j.TimingLogger] (l.Server-7) start[1679911203031] time[2] tag[omero.call.success.ome.logic.QueryImpl.findByQuery]
2023-03-27 10:00:03,034 INFO [ ome.services.util.ServiceHandler] (l.Server-7) Rslt: null
2023-03-27 10:00:03,036 INFO [o.services.sessions.SessionContext$Count] (l.Server-3) -Reference count: e5218453-c253-4b07-b3dd-3d7c0ffd2cfc=0
2023-03-27 10:00:03,036 INFO [ omero.cmd.SessionI] (l.Server-3) cleanupSelf(ServiceFactoryI(session-878a0e38-c7f9-4558-b354-987a7c1be757/e5218453-c253-4b07-b3dd-3d7c0ffd2cfc)).
2023-03-27 10:00:03,036 INFO [ omero.cmd.SessionI] (l.Server-3) Unregistered servant:e5218453-c253-4b07-b3dd-3d7c0ffd2cfc/878a0e38-c7f9-4558-b354-987a7c1be757omero.api.IQuery(omero.api._IQueryTie@40b97a27)
2023-03-27 10:00:03,036 INFO [ omero.cmd.SessionI] (l.Server-3) Removed servant from adapter: 878a0e38-c7f9-4558-b354-987a7c1be757omero.api.IQuery
2023-03-27 10:00:03,036 INFO [ omero.cmd.SessionI] (l.Server-3) Unregistered servant:e5218453-c253-4b07-b3dd-3d7c0ffd2cfc/878a0e38-c7f9-4558-b354-987a7c1be757omero.api.IConfig(omero.api._IConfigTie@5a03ddb1)
2023-03-27 10:00:03,036 INFO [ omero.cmd.SessionI] (l.Server-3) Removed servant from adapter: 878a0e38-c7f9-4558-b354-987a7c1be757omero.api.IConfig
2023-03-27 10:00:03,862 INFO [ ome.security.basic.CurrentDetails] (l.Server-8) Adding log:INSERT,class ome.model.core.OriginalFile,2943659
2023-03-27 10:00:04,112 INFO [ ome.services.util.ServiceHandler] (read-11649) Executor.doWork -- ome.services.sessions.SessionManagerImpl.reload[9da4d1e1-1d05-4e19-9ea7-0cf90e0a1c0f]
2023-03-27 10:00:04,112 INFO [ ome.services.util.ServiceHandler] (read-11649) Args: [null, InternalSF@38784987]
2023-03-27 10:00:04,116 INFO [ ome.security.basic.EventHandler] (read-11649) Auth: user=0,group=0,event=null(Sessions),sess=3cd415eb-d1f7-4d4e-970f-2c59b8ff4b9d
2023-03-27 10:00:04,121 INFO [ org.perf4j.TimingLogger] (read-11649) start[1679911204112] time[8] tag[omero.call.success.ome.services.sessions.SessionManagerImpl$6.doWork]
2023-03-27 10:00:04,121 INFO [ ome.services.util.ServiceHandler] (read-11649) Rslt: (ome.model.meta.Experimenter:Id_52, ome.model.meta.ExperimenterGroup:Id_3, (), ... 5 more)
2023-03-27 10:00:04,316 INFO [ ome.security.basic.CurrentDetails] (.Server-12) Adding log:INSERT,class ome.model.core.OriginalFile,2943660
2023-03-27 10:00:04,316 INFO [ ome.security.basic.CurrentDetails] (.Server-12) Adding log:INSERT,class ome.model.core.OriginalFile,2943661
2023-03-27 10:00:04,333 INFO [ ome.services.blitz.fire.SessionManagerI] (l.Server-3) Found session locally: 54f159c4-dfe3-4f43-8de4-60b0a9a9fb84
2023-03-27 10:00:04,334 INFO [ ome.services.blitz.fire.SessionManagerI] (l.Server-3) Rejoining session ServiceFactoryI(session-0bdc9399-a412-4b0f-bdb6-59c54d84602b/54f159c4-dfe3-4f43-8de4-60b0a9a9fb84) (agent=OMERO.web)
2023-03-27 10:00:04,339 INFO [ ome.services.util.ServiceHandler] (l.Server-4) Executor.doWork -- ome.services.blitz.impl.ServiceFactoryI.isGuest[]
2023-03-27 10:00:04,339 INFO [ ome.services.util.ServiceHandler] (l.Server-4) Args: [null, InternalSF@38784987]
2023-03-27 10:00:04,343 INFO [ ome.security.basic.EventHandler] (l.Server-4) Auth: user=2,group=3,event=null(User),sess=54f159c4-dfe3-4f43-8de4-60b0a9a9fb84
2023-03-27 10:00:04,344 INFO [ org.perf4j.TimingLogger] (l.Server-4) start[1679911204339] time[4] tag[omero.call.success.ome.services.blitz.impl.ServiceFactoryI$3.doWork]
2023-03-27 10:00:04,344 INFO [ ome.services.util.ServiceHandler] (l.Server-4) Rslt: false
2023-03-27 10:00:04,344 INFO [ omero.cmd.SessionI] (l.Server-4) Added servant to adapter: 54f159c4-dfe3-4f43-8de4-60b0a9a9fb84/0bdc9399-a412-4b0f-bdb6-59c54d84602bomero.api.IQuery(omero.api._IQueryTie@5b3bd1c5)
2023-03-27 10:00:04,346 INFO [ ome.services.util.ServiceHandler] (l.Server-6) Meth: interface ome.api.IQuery.findByQuery
2023-03-27 10:00:04,346 INFO [ ome.services.util.ServiceHandler] (l.Server-6) Args: [select obj from Image obj join fetch obj.details.owner as owner join fetch obj.details.creationEvent, PARAMS:ids=ArrayList(1) ]
2023-03-27 10:00:04,347 INFO [ ome.security.basic.BasicEventContext] (l.Server-6) cctx: group=-1
2023-03-27 10:00:04,352 INFO [ ome.security.basic.EventHandler] (l.Server-6) Auth: user=2,group=-1,event=null(User),sess=54f159c4-dfe3-4f43-8de4-60b0a9a9fb84
2023-03-27 10:00:04,356 INFO [ org.perf4j.TimingLogger] (l.Server-6) start[1679911204346] time[10] tag[omero.call.success.ome.logic.QueryImpl.findByQuery]
2023-03-27 10:00:04,356 INFO [ ome.services.util.ServiceHandler] (l.Server-6) Rslt: ome.model.core.Image:Id_46035
2023-03-27 10:00:04,362 INFO [ ome.services.util.ServiceHandler] (.Server-13) Executor.doWork -- ome.services.blitz.impl.ServiceFactoryI.isGuest[]
2023-03-27 10:00:04,362 INFO [ ome.services.util.ServiceHandler] (.Server-13) Args: [null, InternalSF@38784987]
2023-03-27 10:00:04,364 INFO [ ome.security.basic.EventHandler] (.Server-13) Auth: user=2,group=3,event=null(User),sess=54f159c4-dfe3-4f43-8de4-60b0a9a9fb84
2023-03-27 10:00:04,364 INFO [ org.perf4j.TimingLogger] (.Server-13) start[1679911204362] time[2] tag[omero.call.success.ome.services.blitz.impl.ServiceFactoryI$3.doWork]
2023-03-27 10:00:04,364 INFO [ ome.services.util.ServiceHandler] (.Server-13) Rslt: false
2023-03-27 10:00:04,364 INFO [ omero.cmd.SessionI] (.Server-13) Added servant to adapter: 54f159c4-dfe3-4f43-8de4-60b0a9a9fb84/0bdc9399-a412-4b0f-bdb6-59c54d84602bomero.api.IContainer(omero.api._IContainerTie@55c38123)
2023-03-27 10:00:04,366 INFO [ ome.services.util.ServiceHandler] (.Server-14) Meth: interface ome.api.IContainer.getImages
2023-03-27 10:00:04,366 INFO [ ome.services.util.ServiceHandler] (.Server-14) Args: [class ome.model.core.Image, (46035), null]
2023-03-27 10:00:04,367 INFO [ ome.security.basic.BasicEventContext] (.Server-14) cctx: group=3
2023-03-27 10:00:04,368 INFO [ ome.security.basic.EventHandler] (.Server-14) Auth: user=2,group=3,event=null(User),sess=54f159c4-dfe3-4f43-8de4-60b0a9a9fb84
2023-03-27 10:00:04,374 INFO [ org.perf4j.TimingLogger] (.Server-14) start[1679911204366] time[7] tag[omero.call.success.ome.logic.PojosImpl.getImages]
2023-03-27 10:00:04,374 INFO [ ome.services.util.ServiceHandler] (.Server-14) Rslt: (ome.model.core.Image:Id_46035)
2023-03-27 10:00:04,380 INFO [ ome.services.util.ServiceHandler] (l.Server-5) Executor.doWork -- ome.services.blitz.impl.ServiceFactoryI.isGuest[]
2023-03-27 10:00:04,380 INFO [ ome.services.util.ServiceHandler] (l.Server-5) Args: [null, InternalSF@38784987]
2023-03-27 10:00:04,381 INFO [ ome.security.basic.EventHandler] (l.Server-5) Auth: user=2,group=3,event=null(User),sess=54f159c4-dfe3-4f43-8de4-60b0a9a9fb84
2023-03-27 10:00:04,382 INFO [ org.perf4j.TimingLogger] (l.Server-5) start[1679911204380] time[1] tag[omero.call.success.ome.services.blitz.impl.ServiceFactoryI$3.doWork]
2023-03-27 10:00:04,382 INFO [ ome.services.util.ServiceHandler] (l.Server-5) Rslt: false
2023-03-27 10:00:04,382 INFO [ omero.cmd.SessionI] (l.Server-5) Added servant to adapter: 54f159c4-dfe3-4f43-8de4-60b0a9a9fb84/0bdc9399-a412-4b0f-bdb6-59c54d84602bomero.api.IPixels(omero.api._IPixelsTie@4e092dcb)
2023-03-27 10:00:04,384 INFO [ ome.services.util.ServiceHandler] (l.Server-2) Meth: interface ome.api.IPixels.retrieveAllRndSettings
2023-03-27 10:00:04,384 INFO [ ome.services.util.ServiceHandler] (l.Server-2) Args: [46035, -1]
2023-03-27 10:00:04,384 INFO [ ome.security.basic.BasicEventContext] (l.Server-2) cctx: group=-1
2023-03-27 10:00:04,386 INFO [ ome.security.basic.EventHandler] (l.Server-2) Auth: user=2,group=-1,event=null(User),sess=54f159c4-dfe3-4f43-8de4-60b0a9a9fb84
2023-03-27 10:00:04,399 INFO [ org.perf4j.TimingLogger] (l.Server-2) start[1679911204384] time[15] tag[omero.call.success.ome.logic.PixelsImpl.retrieveAllRndSettings]
2023-03-27 10:00:04,399 INFO [ ome.services.util.ServiceHandler] (l.Server-2) Rslt: (ome.model.display.RenderingDef:Id_42502)
2023-03-27 10:00:04,414 INFO [ ome.services.util.ServiceHandler] (.Server-15) Executor.doWork -- ome.services.blitz.impl.ServiceFactoryI.isGuest[]
2023-03-27 10:00:04,414 INFO [ ome.services.util.ServiceHandler] (.Server-15) Args: [null, InternalSF@38784987]
2023-03-27 10:00:04,418 INFO [ ome.security.basic.EventHandler] (.Server-15) Auth: user=2,group=3,event=null(User),sess=54f159c4-dfe3-4f43-8de4-60b0a9a9fb84
2023-03-27 10:00:04,419 INFO [ org.perf4j.TimingLogger] (.Server-15) start[1679911204414] time[4] tag[omero.call.success.ome.services.blitz.impl.ServiceFactoryI$3.doWork]
2023-03-27 10:00:04,419 INFO [ ome.services.util.ServiceHandler] (.Server-15) Rslt: false
2023-03-27 10:00:04,420 INFO [ ome.services.util.ServiceHandler] (.Server-15) Executor.doWork -- ome.services.blitz.impl.ServiceFactoryI.isGuest[]
2023-03-27 10:00:04,420 INFO [ ome.services.util.ServiceHandler] (.Server-15) Args: [null, InternalSF@38784987]
2023-03-27 10:00:04,422 INFO [ ome.security.basic.EventHandler] (.Server-15) Auth: user=2,group=3,event=null(User),sess=54f159c4-dfe3-4f43-8de4-60b0a9a9fb84
2023-03-27 10:00:04,422 INFO [ org.perf4j.TimingLogger] (.Server-15) start[1679911204420] time[2] tag[omero.call.success.ome.services.blitz.impl.ServiceFactoryI$3.doWork]
2023-03-27 10:00:04,422 INFO [ ome.services.util.ServiceHandler] (.Server-15) Rslt: false
2023-03-27 10:00:04,423 INFO [ omero.cmd.SessionI] (.Server-15) Added servant to adapter: 54f159c4-dfe3-4f43-8de4-60b0a9a9fb84/0bdc9399-a412-4b0f-bdb6-59c54d84602bomero.api.IRoi(omero.api._IRoiTie@2e1aa143)
2023-03-27 10:00:04,423 INFO [ omero.cmd.SessionI] (.Server-15) Added servant to adapter: 54f159c4-dfe3-4f43-8de4-60b0a9a9fb84/acdfc40d-858d-4254-96ac-9e5c8dca2f5bomero.api.RenderingEngine(omero.api._RenderingEngineTie@2917797f)
2023-03-27 10:00:04,426 INFO [ ome.services.util.ServiceHandler] (l.Server-0) Meth: interface omeis.providers.re.RenderingEngine.lookupPixels
2023-03-27 10:00:04,426 INFO [ ome.services.util.ServiceHandler] (l.Server-0) Args: [46035]
2023-03-27 10:00:04,427 INFO [ ome.services.util.ServiceHandler] (l.Server-0) Executor.doWork -- ome.services.RenderingBean.retrievePixels[]
2023-03-27 10:00:04,427 INFO [ ome.services.util.ServiceHandler] (l.Server-0) Args: [null, InternalSF@38784987]
2023-03-27 10:00:04,428 INFO [ ome.security.basic.BasicEventContext] (l.Server-0) cctx: group=3
2023-03-27 10:00:04,429 INFO [ ome.security.basic.EventHandler] (l.Server-0) Auth: user=2,group=3,event=null(User),sess=54f159c4-dfe3-4f43-8de4-60b0a9a9fb84
2023-03-27 10:00:04,440 INFO [ org.perf4j.TimingLogger] (l.Server-0) start[1679911204427] time[13] tag[omero.call.success.ome.services.RenderingBean$4.doWork]
2023-03-27 10:00:04,440 INFO [ ome.services.util.ServiceHandler] (l.Server-0) Rslt: ome.model.core.Pixels:Id_46035
2023-03-27 10:00:04,440 INFO [ org.perf4j.TimingLogger] (l.Server-0) start[1679911204426] time[13] tag[omero.call.success.ome.services.RenderingBean.lookupPixels]
2023-03-27 10:00:04,441 INFO [ ome.services.util.ServiceHandler] (l.Server-0) Rslt: null
2023-03-27 10:00:04,442 INFO [ ome.services.util.ServiceHandler] (l.Server-7) Meth: interface omeis.providers.re.RenderingEngine.lookupRenderingDef
2023-03-27 10:00:04,442 INFO [ ome.services.util.ServiceHandler] (l.Server-7) Args: [46035]
2023-03-27 10:00:04,442 INFO [ ome.services.util.ServiceHandler] (l.Server-7) Executor.doWork -- ome.services.RenderingBean.retrieveRndDef[]
2023-03-27 10:00:04,442 INFO [ ome.services.util.ServiceHandler] (l.Server-7) Args: [null, InternalSF@38784987]
2023-03-27 10:00:04,443 INFO [ ome.security.basic.BasicEventContext] (l.Server-7) cctx: group=3
2023-03-27 10:00:04,444 INFO [ ome.security.basic.EventHandler] (l.Server-7) Auth: user=2,group=3,event=null(User),sess=54f159c4-dfe3-4f43-8de4-60b0a9a9fb84
2023-03-27 10:00:04,458 INFO [ org.perf4j.TimingLogger] (l.Server-7) start[1679911204442] time[15] tag[omero.call.success.ome.services.RenderingBean$5.doWork]
2023-03-27 10:00:04,458 INFO [ ome.services.util.ServiceHandler] (l.Server-7) Rslt: ome.model.display.RenderingDef:Id_42502
2023-03-27 10:00:04,458 INFO [ org.perf4j.TimingLogger] (l.Server-7) start[1679911204442] time[15] tag[omero.call.success.ome.services.RenderingBean.lookupRenderingDef]
2023-03-27 10:00:04,458 INFO [ ome.services.util.ServiceHandler] (l.Server-7) Rslt: true
2023-03-27 10:00:04,459 INFO [ ome.services.util.ServiceHandler] (.Server-16) Meth: interface omeis.providers.re.RenderingEngine.getRenderingDefId
2023-03-27 10:00:04,459 INFO [ ome.services.util.ServiceHandler] (.Server-16) Args: ()
2023-03-27 10:00:04,459 INFO [ org.perf4j.TimingLogger] (.Server-16) start[1679911204459] time[0] tag[omero.call.success.ome.services.RenderingBean.getRenderingDefId]
2023-03-27 10:00:04,459 INFO [ ome.services.util.ServiceHandler] (.Server-16) Rslt: 42502
2023-03-27 10:00:04,460 INFO [ ome.services.util.ServiceHandler] (.Server-16) Meth: interface omeis.providers.re.RenderingEngine.load
2023-03-27 10:00:04,460 INFO [ ome.services.util.ServiceHandler] (.Server-16) Args: ()
2023-03-27 10:00:04,460 INFO [ ome.services.util.ServiceHandler] (.Server-16) Executor.doWork -- ome.services.RenderingBean.getAllEnumerations[]
2023-03-27 10:00:04,460 INFO [ ome.services.util.ServiceHandler] (.Server-16) Args: [null, InternalSF@38784987]
2023-03-27 10:00:04,461 INFO [ ome.security.basic.BasicEventContext] (.Server-16) cctx: group=3
2023-03-27 10:00:04,462 INFO [ ome.security.basic.EventHandler] (.Server-16) Auth: user=2,group=3,event=null(User),sess=54f159c4-dfe3-4f43-8de4-60b0a9a9fb84
2023-03-27 10:00:04,463 INFO [ org.perf4j.TimingLogger] (.Server-16) start[1679911204460] time[2] tag[omero.call.success.ome.services.RenderingBean$7.doWork]
2023-03-27 10:00:04,463 INFO [ ome.services.util.ServiceHandler] (.Server-16) Rslt: (ome.model.enums.Family:linear:Id_1, ome.model.enums.Family:polynomial:Id_2, ome.model.enums.Family:exponential:Id_3, ... 1 more)
2023-03-27 10:00:04,463 INFO [ ome.services.util.ServiceHandler] (.Server-16) Executor.doWork -- ome.services.RenderingBean.getAllEnumerations[]
2023-03-27 10:00:04,463 INFO [ ome.services.util.ServiceHandler] (.Server-16) Args: [null, InternalSF@38784987]
2023-03-27 10:00:04,464 INFO [ ome.security.basic.BasicEventContext] (.Server-16) cctx: group=3
2023-03-27 10:00:04,465 INFO [ ome.security.basic.EventHandler] (.Server-16) Auth: user=2,group=3,event=null(User),sess=54f159c4-dfe3-4f43-8de4-60b0a9a9fb84
2023-03-27 10:00:04,465 INFO [ org.perf4j.TimingLogger] (.Server-16) start[1679911204463] time[2] tag[omero.call.success.ome.services.RenderingBean$7.doWork]
2023-03-27 10:00:04,465 INFO [ ome.services.util.ServiceHandler] (.Server-16) Rslt: (ome.model.enums.RenderingModel:rgb:Id_1, ome.model.enums.RenderingModel:greyscale:Id_2)
2023-03-27 10:00:04,466 INFO [ ome.services.util.ServiceHandler] (.Server-16) Executor.doWork -- ome.services.RenderingBean.getPixelBuffer[]
2023-03-27 10:00:04,466 INFO [ ome.services.util.ServiceHandler] (.Server-16) Args: [null, InternalSF@38784987]
2023-03-27 10:00:04,466 INFO [ ome.security.basic.BasicEventContext] (.Server-16) cctx: group=3
2023-03-27 10:00:04,467 INFO [ ome.security.basic.EventHandler] (.Server-16) Auth: user=2,group=3,event=null(User),sess=54f159c4-dfe3-4f43-8de4-60b0a9a9fb84
2023-03-27 10:00:04,468 INFO [ ome.services.OmeroFilePathResolver] (.Server-16) Metadata only file, resulting path: /data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil2.ome.zarr/.zattrs
2023-03-27 10:00:04,474 INFO [ loci.formats.ImageReader] (.Server-16) ZarrReader initializing /data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil2.ome.zarr/.zattrs
2023-03-27 10:00:04,484 DEBUG [ loci.formats.Memoizer] (.Server-16) start[1679911204471] time[12] tag[loci.formats.Memoizer.setId]
2023-03-27 10:00:04,485 ERROR [ ome.io.bioformats.BfPixelBuffer] (.Server-16) Failed to instantiate BfPixelsWrapper with /data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil2.ome.zarr/.zattrs
2023-03-27 10:00:04,485 ERROR [ ome.io.nio.PixelsService] (.Server-16) Error instantiating pixel buffer: /data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil2.ome.zarr/.zattrs
java.lang.RuntimeException: java.lang.IllegalArgumentException: Invalid index: -1
at ome.io.bioformats.BfPixelBuffer.reader(BfPixelBuffer.java:79)
at ome.io.bioformats.BfPixelBuffer.setSeries(BfPixelBuffer.java:124)
at ome.io.nio.PixelsService.createBfPixelBuffer(PixelsService.java:898)
at ome.io.nio.PixelsService._getPixelBuffer(PixelsService.java:653)
at ome.io.nio.PixelsService.getPixelBuffer(PixelsService.java:571)
at ome.services.RenderingBean$12.doWork(RenderingBean.java:2205)
at jdk.internal.reflect.GeneratedMethodAccessor302.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:282)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy100.doWork(Unknown Source)
at ome.services.util.Executor$Impl.execute(Executor.java:447)
at ome.services.util.Executor$Impl.execute(Executor.java:392)
at ome.services.RenderingBean.getPixelBuffer(RenderingBean.java:2202)
at ome.services.RenderingBean.load(RenderingBean.java:417)
at jdk.internal.reflect.GeneratedMethodAccessor1950.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy122.load(Unknown Source)
at jdk.internal.reflect.GeneratedMethodAccessor1950.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy122.load(Unknown Source)
at jdk.internal.reflect.GeneratedMethodAccessor1978.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:172)
at ome.services.throttling.Callback.run(Callback.java:56)
at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140)
at ome.services.blitz.impl.RenderingEngineI.load_async(RenderingEngineI.java:316)
at jdk.internal.reflect.GeneratedMethodAccessor1977.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at omero.cmd.CallContext.invoke(CallContext.java:85)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy124.load_async(Unknown Source)
at omero.api._RenderingEngineTie.load_async(_RenderingEngineTie.java:248)
at omero.api._RenderingEngineDisp.___load(_RenderingEngineDisp.java:1223)
at omero.api._RenderingEngineDisp.__dispatch(_RenderingEngineDisp.java:2405)
at IceInternal.Incoming.invoke(Incoming.java:221)
at Ice.ConnectionI.invokeAll(ConnectionI.java:2536)
at Ice.ConnectionI.dispatch(ConnectionI.java:1145)
at Ice.ConnectionI.message(ConnectionI.java:1056)
at IceInternal.ThreadPool.run(ThreadPool.java:395)
at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)
at java.base/java.lang.Thread.run(Thread.java:829)
Caused by: java.lang.IllegalArgumentException: Invalid index: -1
at loci.formats.FormatReader.coreIndexToSeries(FormatReader.java:1328)
at loci.formats.FormatReader.getSeriesCount(FormatReader.java:963)
at loci.formats.MetadataTools.populatePixels(MetadataTools.java:137)
at loci.formats.MetadataTools.populatePixels(MetadataTools.java:116)
at loci.formats.in.ZarrReader.initFile(ZarrReader.java:282)
at loci.formats.FormatReader.setId(FormatReader.java:1443)
at loci.formats.ImageReader.setId(ImageReader.java:849)
at ome.io.nio.PixelsService$3.setId(PixelsService.java:869)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
at loci.formats.ChannelFiller.setId(ChannelFiller.java:234)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
at loci.formats.Memoizer.setId(Memoizer.java:690)
at ome.io.bioformats.BfPixelsWrapper.<init>(BfPixelsWrapper.java:52)
at ome.io.bioformats.BfPixelBuffer.reader(BfPixelBuffer.java:73)
... 82 common frames omitted
2023-03-27 10:00:04,486 INFO [ org.perf4j.TimingLogger] (.Server-16) start[1679911204466] time[20] tag[omero.call.exception]
2023-03-27 10:00:04,487 INFO [ ome.services.util.ServiceHandler] (.Server-16) Excp: ome.conditions.ResourceError: Error instantiating pixel buffer: /data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil2.ome.zarr/.zattrs
2023-03-27 10:00:04,487 INFO [ org.perf4j.TimingLogger] (.Server-16) start[1679911204460] time[26] tag[omero.call.exception]
2023-03-27 10:00:04,487 INFO [ ome.services.util.ServiceHandler] (.Server-16) Excp: ome.conditions.ResourceError: Error instantiating pixel buffer: /data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil2.ome.zarr/.zattrs
2023-03-27 10:00:04,491 INFO [ ome.services.util.ServiceHandler] (l.Server-3) Meth: interface ome.api.StatefulServiceInterface.close
2023-03-27 10:00:04,491 INFO [ ome.services.util.ServiceHandler] (l.Server-3) Args: ()
2023-03-27 10:00:04,491 INFO [ org.perf4j.TimingLogger] (l.Server-3) start[1679911204491] time[0] tag[omero.call.success.ome.services.RenderingBean.close]
2023-03-27 10:00:04,491 INFO [ ome.services.util.ServiceHandler] (l.Server-3) Rslt: null
2023-03-27 10:00:04,491 INFO [ omero.cmd.SessionI] (l.Server-3) Unregistered servant:54f159c4-dfe3-4f43-8de4-60b0a9a9fb84/acdfc40d-858d-4254-96ac-9e5c8dca2f5bomero.api.RenderingEngine(omero.api._RenderingEngineTie@2917797f)
2023-03-27 10:00:04,492 INFO [o.services.sessions.SessionContext$Count] (.Server-11) -Reference count: 54f159c4-dfe3-4f43-8de4-60b0a9a9fb84=0
2023-03-27 10:00:04,492 INFO [ omero.cmd.SessionI] (.Server-11) cleanupSelf(ServiceFactoryI(session-0bdc9399-a412-4b0f-bdb6-59c54d84602b/54f159c4-dfe3-4f43-8de4-60b0a9a9fb84)).
2023-03-27 10:00:04,492 INFO [ omero.cmd.SessionI] (.Server-11) Unregistered servant:54f159c4-dfe3-4f43-8de4-60b0a9a9fb84/0bdc9399-a412-4b0f-bdb6-59c54d84602bomero.api.IRoi(omero.api._IRoiTie@2e1aa143)
2023-03-27 10:00:04,492 INFO [ omero.cmd.SessionI] (.Server-11) Removed servant from adapter: 0bdc9399-a412-4b0f-bdb6-59c54d84602bomero.api.IRoi
2023-03-27 10:00:04,492 INFO [ omero.cmd.SessionI] (.Server-11) Unregistered servant:54f159c4-dfe3-4f43-8de4-60b0a9a9fb84/0bdc9399-a412-4b0f-bdb6-59c54d84602bomero.api.IContainer(omero.api._IContainerTie@55c38123)
2023-03-27 10:00:04,492 INFO [ omero.cmd.SessionI] (.Server-11) Removed servant from adapter: 0bdc9399-a412-4b0f-bdb6-59c54d84602bomero.api.IContainer
2023-03-27 10:00:04,492 INFO [ omero.cmd.SessionI] (.Server-11) Unregistered servant:54f159c4-dfe3-4f43-8de4-60b0a9a9fb84/0bdc9399-a412-4b0f-bdb6-59c54d84602bomero.api.IQuery(omero.api._IQueryTie@5b3bd1c5)
2023-03-27 10:00:04,492 INFO [ omero.cmd.SessionI] (.Server-11) Removed servant from adapter: 0bdc9399-a412-4b0f-bdb6-59c54d84602bomero.api.IQuery
2023-03-27 10:00:04,492 INFO [ omero.cmd.SessionI] (.Server-11) Unregistered servant:54f159c4-dfe3-4f43-8de4-60b0a9a9fb84/0bdc9399-a412-4b0f-bdb6-59c54d84602bomero.api.IPixels(omero.api._IPixelsTie@4e092dcb)
2023-03-27 10:00:04,493 INFO [ omero.cmd.SessionI] (.Server-11) Removed servant from adapter: 0bdc9399-a412-4b0f-bdb6-59c54d84602bomero.api.IPixels
2023-03-27 10:00:04,721 INFO [ org.perf4j.TimingLogger] (l.Server-8) start[1679911200273] time[4448] tag[omero.repo.create_original_file.save]
2023-03-27 10:00:04,721 INFO [ org.perf4j.TimingLogger] (l.Server-8) start[1679911204721] time[0] tag[omero.repo.create_original_file.internal_mkdir]
2023-03-27 10:00:04,721 INFO [ org.perf4j.TimingLogger] (l.Server-8) start[1679911204721] time[0] tag[omero.repo.internal_register.load]
2023-03-27 10:00:04,722 INFO [ org.perf4j.TimingLogger] (l.Server-8) start[1679911204721] time[0] tag[omero.repo.internal_register.find_repo_files]
2023-03-27 10:00:05,173 INFO [ org.perf4j.TimingLogger] (.Server-12) start[1679911198425] time[6748] tag[omero.repo.create_original_file.save]
2023-03-27 10:00:05,173 INFO [ org.perf4j.TimingLogger] (.Server-12) start[1679911205173] time[0] tag[omero.repo.create_original_file.internal_mkdir]
2023-03-27 10:00:05,173 INFO [ org.perf4j.TimingLogger] (.Server-12) start[1679911205173] time[0] tag[omero.repo.internal_register.load]
2023-03-27 10:00:05,174 INFO [ org.perf4j.TimingLogger] (.Server-12) start[1679911205174] time[0] tag[omero.repo.internal_register.find_repo_files]
2023-03-27 10:00:07,290 INFO [ ome.security.basic.CurrentDetails] (l.Server-9) Adding log:INSERT,class ome.model.core.OriginalFile,2943662
2023-03-27 10:00:07,979 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911204121] time[3857] tag[omero.repo.create_original_file.save]
2023-03-27 10:00:07,979 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911207979] time[0] tag[omero.repo.create_original_file.internal_mkdir]
2023-03-27 10:00:07,979 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911207979] time[0] tag[omero.repo.internal_register.load]
2023-03-27 10:00:07,979 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911207979] time[0] tag[omero.repo.file.find]
2023-03-27 10:00:07,979 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911207979] time[0] tag[omero.repo.file.check_group]
2023-03-27 10:00:07,980 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911207979] time[0] tag[omero.repo.file.find]
2023-03-27 10:00:07,980 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911207980] time[0] tag[omero.repo.file.check_group]
2023-03-27 10:00:07,980 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911207980] time[0] tag[omero.repo.file.find]
2023-03-27 10:00:07,980 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911207980] time[0] tag[omero.repo.file.check_group]
2023-03-27 10:00:07,980 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911207980] time[0] tag[omero.repo.file.find]
2023-03-27 10:00:07,980 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911207980] time[0] tag[omero.repo.file.check_group]
2023-03-27 10:00:07,981 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911207980] time[0] tag[omero.repo.file.find]
2023-03-27 10:00:07,981 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911207981] time[0] tag[omero.repo.file.check_group]
2023-03-27 10:00:07,981 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911207981] time[0] tag[omero.repo.file.find]
2023-03-27 10:00:07,981 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911207981] time[0] tag[omero.repo.file.check_group]
2023-03-27 10:00:07,981 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911207981] time[0] tag[omero.repo.file.find]
2023-03-27 10:00:07,981 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911207981] time[0] tag[omero.repo.file.check_group]
2023-03-27 10:00:07,982 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911207982] time[0] tag[omero.repo.file.find]
2023-03-27 10:00:07,982 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911207982] time[0] tag[omero.repo.file.check_group]
2023-03-27 10:00:07,982 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911207982] time[0] tag[omero.repo.file.find]
2023-03-27 10:00:07,982 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911207982] time[0] tag[omero.repo.file.check_group]
2023-03-27 10:00:07,983 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911207982] time[0] tag[omero.repo.file.find]
2023-03-27 10:00:07,983 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911207983] time[0] tag[omero.repo.file.check_group]
2023-03-27 10:00:07,983 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911207983] time[0] tag[omero.repo.file.find]
2023-03-27 10:00:07,983 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911207983] time[0] tag[omero.repo.file.check_group]
2023-03-27 10:00:07,983 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911207983] time[0] tag[omero.repo.file.find]
2023-03-27 10:00:07,983 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911207983] time[0] tag[omero.repo.file.check_group]
2023-03-27 10:00:07,984 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911207983] time[0] tag[omero.repo.file.find]
2023-03-27 10:00:07,984 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911207984] time[0] tag[omero.repo.file.check_group]
2023-03-27 10:00:08,111 INFO [ ome.services.util.ServiceHandler] (read-11649) Executor.doWork -- ome.services.sessions.SessionManagerImpl.reload[9da4d1e1-1d05-4e19-9ea7-0cf90e0a1c0f]
2023-03-27 10:00:08,111 INFO [ ome.services.util.ServiceHandler] (read-11649) Args: [null, InternalSF@38784987]
2023-03-27 10:00:08,116 INFO [ ome.security.basic.EventHandler] (read-11649) Auth: user=0,group=0,event=null(Sessions),sess=3cd415eb-d1f7-4d4e-970f-2c59b8ff4b9d
2023-03-27 10:00:08,120 INFO [ ome.services.util.ServiceHandler] (read-11650) Executor.doWork -- ome.services.sessions.SessionManagerImpl.reload[8eb39a2f-b26d-446c-9d2e-13feb6c68ebf]
2023-03-27 10:00:08,120 INFO [ ome.services.util.ServiceHandler] (read-11650) Args: [null, InternalSF@38784987]
2023-03-27 10:00:08,124 INFO [ org.perf4j.TimingLogger] (read-11649) start[1679911208112] time[12] tag[omero.call.success.ome.services.sessions.SessionManagerImpl$6.doWork]
2023-03-27 10:00:08,125 INFO [ ome.services.util.ServiceHandler] (read-11649) Rslt: (ome.model.meta.Experimenter:Id_52, ome.model.meta.ExperimenterGroup:Id_3, (), ... 5 more)
2023-03-27 10:00:08,132 INFO [ ome.security.basic.EventHandler] (read-11650) Auth: user=0,group=0,event=null(Sessions),sess=3cd415eb-d1f7-4d4e-970f-2c59b8ff4b9d
2023-03-27 10:00:08,139 INFO [ org.perf4j.TimingLogger] (read-11650) start[1679911208120] time[18] tag[omero.call.success.ome.services.sessions.SessionManagerImpl$6.doWork]
2023-03-27 10:00:08,139 INFO [ ome.services.util.ServiceHandler] (read-11650) Rslt: (ome.model.meta.Experimenter:Id_52, ome.model.meta.ExperimenterGroup:Id_3, (), ... 5 more)
2023-03-27 10:00:10,839 INFO [ ome.services.blitz.fire.SessionManagerI] (l.Server-4) Found session locally: 54f159c4-dfe3-4f43-8de4-60b0a9a9fb84
2023-03-27 10:00:10,840 INFO [ ome.services.blitz.fire.SessionManagerI] (l.Server-4) Rejoining session ServiceFactoryI(session-36ba35e0-3a0f-4d9d-8708-0ad3991b6e7b/54f159c4-dfe3-4f43-8de4-60b0a9a9fb84) (agent=OMERO.web)
2023-03-27 10:00:10,846 INFO [o.services.sessions.SessionContext$Count] (.Server-13) -Reference count: 54f159c4-dfe3-4f43-8de4-60b0a9a9fb84=0
2023-03-27 10:00:10,846 INFO [ omero.cmd.SessionI] (.Server-13) cleanupSelf(ServiceFactoryI(session-36ba35e0-3a0f-4d9d-8708-0ad3991b6e7b/54f159c4-dfe3-4f43-8de4-60b0a9a9fb84)).
2023-03-27 10:00:11,057 INFO [ ome.security.basic.CurrentDetails] (l.Server-9) Adding log:UPDATE,class ome.model.core.OriginalFile,2943658
2023-03-27 10:00:11,399 INFO [ ome.security.basic.CurrentDetails] (l.Server-8) Adding log:INSERT,class ome.model.core.OriginalFile,2943663
2023-03-27 10:00:11,858 INFO [ ome.logic.AdminImpl] (l.Server-9) Moved object to common space: ome.model.core.OriginalFile:Id_2943658
2023-03-27 10:00:11,858 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911207984] time[3874] tag[omero.repo.file.move_to_common]
2023-03-27 10:00:11,859 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911211858] time[0] tag[omero.repo.file.find]
2023-03-27 10:00:11,859 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911211859] time[0] tag[omero.repo.file.check_group]
2023-03-27 10:00:12,387 INFO [ org.perf4j.TimingLogger] (l.Server-8) start[1679911208125] time[4262] tag[omero.repo.create_original_file.save]
2023-03-27 10:00:12,388 INFO [ org.perf4j.TimingLogger] (l.Server-8) start[1679911212388] time[0] tag[omero.repo.create_original_file.internal_mkdir]
2023-03-27 10:00:12,388 INFO [ org.perf4j.TimingLogger] (l.Server-8) start[1679911212388] time[0] tag[omero.repo.internal_register.load]
2023-03-27 10:00:12,388 INFO [ org.perf4j.TimingLogger] (l.Server-8) start[1679911212388] time[0] tag[omero.repo.internal_register.find_repo_files]
2023-03-27 10:00:13,001 INFO [ ome.services.blitz.fire.Ring] (2-thread-2) Checking cluster
2023-03-27 10:00:13,003 INFO [ ome.services.blitz.fire.Registry] (2-thread-2) Found 1 cluster node(s) : [ClusterNode/3cd415eb-d1f7-4d4e-970f-2c59b8ff4b9d -t -e 1.1:tcp -h 127.0.0.1 -p 40023 -t 60000]
2023-03-27 10:00:13,003 INFO [ ome.services.blitz.fire.Ring] (2-thread-2) Got 1 cluster uuids : [3cd415eb-d1f7-4d4e-970f-2c59b8ff4b9d]
2023-03-27 10:00:13,003 INFO [ ome.services.util.ServiceHandler] (2-thread-2) Executor.doWork -- ome.security.basic.NodeProviderInDb.getManagerList[]
2023-03-27 10:00:13,004 INFO [ ome.services.util.ServiceHandler] (2-thread-2) Args: [null, InternalSF@38784987]
2023-03-27 10:00:13,013 INFO [ ome.security.basic.EventHandler] (2-thread-2) Auth: user=0,group=0,event=null(Internal),sess=3cd415eb-d1f7-4d4e-970f-2c59b8ff4b9d
2023-03-27 10:00:13,016 INFO [ org.perf4j.TimingLogger] (2-thread-2) start[1679911213004] time[12] tag[omero.call.success.ome.security.basic.NodeProviderInDb$1.doWork]
2023-03-27 10:00:13,016 INFO [ ome.services.util.ServiceHandler] (2-thread-2) Rslt: (3cd415eb-d1f7-4d4e-970f-2c59b8ff4b9d)
2023-03-27 10:00:14,032 INFO [ ome.security.basic.CurrentDetails] (.Server-12) Adding log:INSERT,class ome.model.core.OriginalFile,2943664
2023-03-27 10:00:14,825 INFO [ org.perf4j.TimingLogger] (.Server-12) start[1679911208140] time[6684] tag[omero.repo.create_original_file.save]
2023-03-27 10:00:14,825 INFO [ org.perf4j.TimingLogger] (.Server-12) start[1679911214825] time[0] tag[omero.repo.create_original_file.internal_mkdir]
2023-03-27 10:00:14,825 INFO [ org.perf4j.TimingLogger] (.Server-12) start[1679911214825] time[0] tag[omero.repo.internal_register.load]
2023-03-27 10:00:14,826 INFO [ org.perf4j.TimingLogger] (.Server-12) start[1679911214825] time[0] tag[omero.repo.internal_register.find_repo_files]
2023-03-27 10:00:14,998 INFO [ ome.security.basic.CurrentDetails] (l.Server-9) Adding log:UPDATE,class ome.model.core.OriginalFile,2943662
2023-03-27 10:00:15,777 INFO [ ome.logic.AdminImpl] (l.Server-9) Moved object to common space: ome.model.core.OriginalFile:Id_2943662
2023-03-27 10:00:15,777 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911211859] time[3918] tag[omero.repo.file.move_to_common]
2023-03-27 10:00:15,777 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1679911207979] time[7798] tag[omero.repo.user_dir]
2023-03-27 10:00:15,778 INFO [ ome.services.util.ServiceHandler] (read-11650) Executor.doWork -- ome.services.sessions.SessionManagerImpl.reload[9da4d1e1-1d05-4e19-9ea7-0cf90e0a1c0f]
cc @jburel @joshmoore @sbesson
Relevant part
Caused by: java.lang.IllegalArgumentException: Invalid index: -1
at loci.formats.FormatReader.coreIndexToSeries(FormatReader.java:1328)
at loci.formats.FormatReader.getSeriesCount(FormatReader.java:963)
at loci.formats.MetadataTools.populatePixels(MetadataTools.java:137)
at loci.formats.MetadataTools.populatePixels(MetadataTools.java:116)
at loci.formats.in.ZarrReader.initFile(ZarrReader.java:282)
cc @dgault
@dgault Any ideas what's failing here? Am I missing a File in the Fileset, or pointing to the wrong one from the Pixels?
The exception here looks as though the reader has failed to create any series metadata at all.
The reader logic for that part of the code is as below:
- find the root .zarr folder from the initial supplied id
- from the top level group file find the array keys (locating the .zarray files)
- for each key the reader will create metadata
So it seems to have failed quite early on just locating the .zgroup and .zarray files
Looking at the pathset you listed, the top level folder had 2 sets of zgroup and zattrs, do you know where the first 2 OME.zgroup and OME.zattrs come from?
OME.zgroup
OME.zattrs
.zattrs
.zgroup
@dgault I "fixed" those paths above, so now in the web UI I see:
EDIT (31.3.2021 13:53 - after call with David): I see that a bunch of these are identical and WRONG! /data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil2.ome.zarr/.zarray
Paths on server:
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil2.ome.zarr/OME/METADATA.ome.xml
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil2.ome.zarr/OME/.zgroup
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil2.ome.zarr/OME/.zattrs
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil2.ome.zarr/.zarray
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil2.ome.zarr/.zarray
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil2.ome.zarr/.zarray
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil2.ome.zarr/.zarray
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil2.ome.zarr/.zarray
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil2.ome.zarr/.zgroup
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil2.ome.zarr/.zattrs
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil2.ome.zarr/.zgroup
/data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil2.ome.zarr/.zattrs
If I check they exist and look at the contents...
$ ssh -A -o 'ProxyCommand ssh idr-pilot.openmicroscopy.org -W %h:%p' idrtesting-omeroreadwrite -L 1080:localhost:80
$ cd /data/OMERO/ManagedRepository/demo_52/Blitz-0-Ice.ThreadPool.Server-6/2023-02/27/13-19-26.557/ngff/Tonsil2.ome.zarr/
[wmoore@pilot-idrtesting-omeroreadwrite Tonsil2.ome.zarr]$ ls -al OME/
total 12
drwxrwxr-x. 2 dlindner dlindner 60 Feb 17 13:27 .
drwxrwxr-x. 4 dlindner dlindner 56 Feb 17 13:27 ..
-rw-rw-r--. 1 dlindner dlindner 2391 Feb 17 13:27 METADATA.ome.xml
-rw-rw-r--. 1 dlindner dlindner 24 Feb 17 13:27 .zattrs
-rw-rw-r--. 1 dlindner dlindner 23 Feb 17 13:27 .zgroup
$ cat OME/.zattrs
{
"series" : [ "0" ]
}
$ cat OME/.zgroup
{
"zarr_format" : 2
}
So far I have been able to reproduce the same error using showinf when reading the dataset from pilot-idrtesting. If I copy the dataset locally using the exact same file structure then it reads just fine without the same issue. I will try to dig a bit further, seems something odd is going on.
The issue seems to be coming from within jzarr, it is able to find the attributes for the top level group but can't find any additional .group or .array files. The problem seems to be that the below code is not returning any matches, the internalRoot should be the top level folder and the suffix will be zgroup and zarray:
https://github.com/bcdev/jzarr/blob/master/src/main/java/com/bc/zarr/storage/FileSystemStore.java#L120-L123
I'm having a hard time reproducing the same issue, but having the OME/.zgroup file does cause some issues on occasion (though that failure looks different from the original stack trace).
OK, I'm going to start from scratch....
ssh -A -o 'ProxyCommand ssh idr-pilot.openmicroscopy.org -W %h:%p' idrtesting-omeroreadwrite -L 1080:localhost:80
$ cd /ngff/idr0054
# in order to avoid path escaping issues, created a copy under `Tonsil_2.ome.zarr`
$ sudo cp -r Tonsil\ 2.ome.zarr/ Tonsil_2.ome.zarr/
$ ls -alh Tonsil_2.ome.zarr/OME/
total 12K
drwxr-xr-x. 2 root root 60 Mar 30 14:53 .
drwxr-xr-x. 4 root root 56 Mar 30 14:53 ..
-rw-r--r--. 1 root root 2.4K Mar 30 14:53 METADATA.ome.xml
-rw-r--r--. 1 root root 24 Mar 30 14:53 .zattrs
-rw-r--r--. 1 root root 23 Mar 30 14:53 .zgroup
$ source /opt/omero/server/venv3/bin/activate
$ export OMERODIR=/opt/omero/server/OMERO.server
$ omero login demo@localhost
$ omero import --transfer=ln_s --depth=10 -d 151 Tonsil_2.ome.zarr/OME/METADATA.ome.xml
...
2023-03-30 15:03:36,679 186064 [l.Client-0] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_DONE Imported file: /data/ngff/idr0054/Tonsil_2.ome.zarr/OME/METADATA.ome.xml
Image:49072
Other imported objects:
Fileset:9403
==> Summary
444 files uploaded, 1 fileset created, 1 image imported, 0 errors in 0:03:03.448
I ran the import twice to give 2 images to compare...
Image:49073
Other imported objects:
Fileset:9404
==> Summary
444 files uploaded, 1 fileset created, 1 image imported, 0 errors in 0:02:02.928
Test import without chunks...
$ cd Tonsil_2.ome.zarr
$ sudo find -type f -name '0' -delete
$ sudo find -type f -name '1' -delete
$ sudo find -type f -name '2' -delete
$ cd ../
$ omero import --transfer=ln_s --depth=10 -d 151 Tonsil_2.ome.zarr/OME/METADATA.ome.xml
...
2023-03-30 15:34:38,151 13100 [l.Client-0] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_DONE Imported file: /data/ngff/idr0054/Tonsil_2.ome.zarr/OME/METADATA.ome.xml
Image:49074
Other imported objects:
Fileset:9405
==> Summary
12 files uploaded, 1 fileset created, 1 image imported, 0 errors in 0:00:10.810
Then replace the chunks by copying over as above...
sudo rm -rf Tonsil_2.ome.zarr/
sudo cp -r Tonsil\ 2.ome.zarr/ Tonsil_2.ome.zarr/
The previously-imported images (49072 and 49073) are showing OK - can render in viewer etc. But 49074, imported without chunks is NOT showing any pixel data, even though the chunks were added back later: http://localhost:1080/webclient/?show=image-49074
Ooops - I was going to reproduce, but accidentally ran the delete chunk commands above from the parent /ngff/idr0054 directory instead of in Tonsil_2.ome.zarr, so this deleted original chunks!