Problem with importing ndpi to OMERO

Hello,

I have one ndpi file I had difficulty to import data into OMERO. Could anyone from @OMETeam have a look at why import is hanging on metadata? They are on ftp

$ /opt/omero/server/OMERO.server/bin/omero import -d 202 --transfer=ln_s --skip checksum /path/to/the/file
Using session for user@localhost:4064. Idle timeout: 10 min. Current group: default
2019-09-05 09:56:06,338 227        [      main] INFO          ome.formats.importer.ImportConfig - OMERO Version: 5.5.0-m9
2019-09-05 09:56:06,351 240        [      main] INFO          ome.formats.importer.ImportConfig - Bioformats version: 6.1.0-m1 revision: b1fb61f7a0c6f506d23239b96bdc8929953738cb date: 22 April 2019
2019-09-05 09:56:06,388 277        [      main] INFO   formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64
2019-09-05 09:56:06,389 278        [      main] INFO   formats.importer.cli.CommandLineImporter - Setting transfer to ln_s
2019-09-05 09:56:06,392 281        [      main] INFO   formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2019-09-05 09:56:06,695 584        [      main] INFO      ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM
and hangs
2019-09-05 09:56:05,786 INFO  [ ome.services.blitz.fire.SessionManagerI] (Server-419) Found session locally: e3a11f36-2e09-4765-8b96-865fe4efc7e9
2019-09-05 09:56:05,787 INFO  [ ome.services.blitz.fire.SessionManagerI] (Server-419) Rejoining session ServiceFactoryI(session-6ad1bc17-074b-44d2-af7a-88fb2896ff94/e3a11f36-2e09-4765-8b96-865fe4efc7e9) (agent=OMERO.sessions)
2019-09-05 09:56:05,789 INFO  [                      omero.cmd.SessionI] (Server-417) Added servant to adapter: e3a11f36-2e09-4765-8b96-865fe4efc7e9/6ad1bc17-074b-44d2-af7a-88fb2896ff94omero.api.IAdmin(omero.api._IAdminTie@c72bcbf0)
2019-09-05 09:56:05,790 INFO  [        ome.services.util.ServiceHandler] (Server-417)  Meth:	interface ome.api.IAdmin.getEventContext
2019-09-05 09:56:05,790 INFO  [        ome.services.util.ServiceHandler] (Server-417)  Args:	()
2019-09-05 09:56:05,791 WARN  [    ome.security.basic.BasicEventContext] (Server-417) Ignoring invalid requested group: omero.group=default
2019-09-05 09:56:05,792 INFO  [         ome.security.basic.EventHandler] (Server-417)  Auth:	user=154,group=103,event=null(User),sess=e3a11f36-2e09-4765-8b96-865fe4efc7e9
2019-09-05 09:56:05,792 INFO  [        ome.services.util.ServiceHandler] (thread-115)  Executor.doWork -- ome.services.sessions.SessionManagerImpl.reload[e3a11f36-2e09-4765-8b96-865fe4efc7e9]
2019-09-05 09:56:05,792 INFO  [        ome.services.util.ServiceHandler] (thread-115)  Args:	[null, InternalSF@454096398]
2019-09-05 09:56:05,794 INFO  [         ome.security.basic.EventHandler] (thread-115)  Auth:	user=0,group=0,event=null(Sessions),sess=26db200e-233d-480b-b9cf-ad81a418481c
2019-09-05 09:56:05,807 INFO  [                 org.perf4j.TimingLogger] (thread-115) start[1567677365792] time[15] tag[omero.call.success.ome.services.sessions.SessionManagerImpl$6.doWork]
2019-09-05 09:56:05,807 INFO  [        ome.services.util.ServiceHandler] (thread-115)  Rslt:	(ome.model.meta.Experimenter:Id_154, ome.model.meta.ExperimenterGroup:Id_103, (), ... 5 more)
2019-09-05 09:56:05,809 INFO  [                 org.perf4j.TimingLogger] (Server-417) start[1567677365790] time[18] tag[omero.call.success.ome.logic.AdminImpl.getEventContext]
2019-09-05 09:56:05,809 INFO  [        ome.services.util.ServiceHandler] (Server-417)  Rslt:	ome.system.SimpleEventContext@1d163ea7
2019-09-05 09:56:05,810 INFO  [                      omero.cmd.SessionI] (Server-420) Added servant to adapter: e3a11f36-2e09-4765-8b96-865fe4efc7e9/6ad1bc17-074b-44d2-af7a-88fb2896ff94omero.api.ISession(omero.api._ISessionTie@eddd958c)
2019-09-05 09:56:05,811 INFO  [        ome.services.util.ServiceHandler] (Server-419)  Meth:	interface ome.api.ISession.getSession
2019-09-05 09:56:05,811 INFO  [        ome.services.util.ServiceHandler] (Server-419)  Args:	[e3a11f36-2e09-4765-8b96-865fe4efc7e9]
2019-09-05 09:56:05,811 INFO  [                 org.perf4j.TimingLogger] (Server-419) start[1567677365811] time[0] tag[omero.call.success.ome.services.sessions.SessionBean.getSession]
2019-09-05 09:56:05,811 INFO  [        ome.services.util.ServiceHandler] (Server-419)  Rslt:	ome.model.meta.Session:Id_4500
2019-09-05 09:56:05,814 INFO  [        ome.services.util.ServiceHandler] (Server-418)  Meth:	interface ome.api.IAdmin.getEventContext
2019-09-05 09:56:05,814 INFO  [        ome.services.util.ServiceHandler] (Server-418)  Args:	()
2019-09-05 09:56:05,815 WARN  [    ome.security.basic.BasicEventContext] (Server-418) Ignoring invalid requested group: omero.group=default
2019-09-05 09:56:05,816 INFO  [         ome.security.basic.EventHandler] (Server-418)  Auth:	user=154,group=103,event=null(User),sess=e3a11f36-2e09-4765-8b96-865fe4efc7e9
2019-09-05 09:56:05,816 INFO  [        ome.services.util.ServiceHandler] (thread-115)  Executor.doWork -- ome.services.sessions.SessionManagerImpl.reload[e3a11f36-2e09-4765-8b96-865fe4efc7e9]
2019-09-05 09:56:05,816 INFO  [        ome.services.util.ServiceHandler] (thread-115)  Args:	[null, InternalSF@454096398]
2019-09-05 09:56:05,817 INFO  [         ome.security.basic.EventHandler] (thread-115)  Auth:	user=0,group=0,event=null(Sessions),sess=26db200e-233d-480b-b9cf-ad81a418481c
2019-09-05 09:56:05,828 INFO  [                 org.perf4j.TimingLogger] (thread-115) start[1567677365816] time[12] tag[omero.call.success.ome.services.sessions.SessionManagerImpl$6.doWork]
2019-09-05 09:56:05,828 INFO  [        ome.services.util.ServiceHandler] (thread-115)  Rslt:	(ome.model.meta.Experimenter:Id_154, ome.model.meta.ExperimenterGroup:Id_103, (), ... 5 more)
2019-09-05 09:56:05,829 INFO  [                 org.perf4j.TimingLogger] (Server-418) start[1567677365814] time[15] tag[omero.call.success.ome.logic.AdminImpl.getEventContext]
2019-09-05 09:56:05,829 INFO  [        ome.services.util.ServiceHandler] (Server-418)  Rslt:	ome.system.SimpleEventContext@3a1daa1a

I’ve managed to open that file in QuPath and load the annotations, not sure why I cannot import it to Omero

Thanks
Ola

That does look like a bug, it’s not apparent to me that the NDPI reader is making any progress in setId so I’ve opened https://github.com/ome/bioformats/issues/3432. It’s a pity that Bio-Formats runs in the same JVM as OMERO.server as it might be keeping server threads tied up. Thank you for providing the sample image, that’s a great help.