Page 2 of 3

Re: Migrating from old (5.1.2) to latest version: the safest

PostPosted: Thu Jan 31, 2019 9:28 pm
by foisys
Hi again,

I used omero admin diagnostics to see if anything was wrong; I came upon the Blitz log showing multiple errors. Looking at the log, I see multiple instances of this type of error:

Code: Select all
omero.InternalException: null
   at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:1.8.0_201]
   at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) ~[na:1.8.0_201]
   at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[na:1.8.0_201]
   at java.lang.reflect.Constructor.newInstance(Constructor.java:423) ~[na:1.8.0_201]
   at java.lang.Class.newInstance(Class.java:442) ~[na:1.8.0_201]
   at IceInternal.BasicStream.createUserException(BasicStream.java:2779) ~[ice.jar:na]
   at IceInternal.BasicStream.access$300(BasicStream.java:14) ~[ice.jar:na]
   at IceInternal.BasicStream$EncapsDecoder11.throwException(BasicStream.java:3614) ~[ice.jar:na]
   at IceInternal.BasicStream.throwException(BasicStream.java:2291) ~[ice.jar:na]
   at IceInternal.OutgoingAsync.throwUserException(OutgoingAsync.java:399) ~[ice.jar:na]
   at omero.grid.InteractiveProcessorPrxHelper.end_params(InteractiveProcessorPrxHelper.java:874) ~[blitz.jar:na]
   at omero.grid.InteractiveProcessorPrxHelper.params(InteractiveProcessorPrxHelper.java:761) ~[blitz.jar:na]
   at omero.grid.InteractiveProcessorPrxHelper.params(InteractiveProcessorPrxHelper.java:754) ~[blitz.jar:na]
   at omero.grid.ParamsHelper.generateScriptParams(ParamsHelper.java:153) ~[blitz.jar:na]
   at ome.services.blitz.util.ParamsCache$Loader.createParams(ParamsCache.java:304) ~[blitz.jar:na]
   at ome.services.blitz.util.ParamsCache._load(ParamsCache.java:217) [blitz.jar:na]
   at ome.services.blitz.util.ParamsCache.lookupAll(ParamsCache.java:181) [blitz.jar:na]
   at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.0_201]
   at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:1.8.0_201]
   at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_201]
   at java.lang.reflect.Method.invoke(Method.java:498) ~[na:1.8.0_201]
   at org.springframework.util.MethodInvoker.invoke(MethodInvoker.java:273) [spring-core.jar:3.0.1.RELEASE]
   at org.springframework.scheduling.quartz.MethodInvokingJobDetailFactoryBean$MethodInvokingJob.executeInternal(MethodInvokingJobDetailFactoryBean.java:264) [spring-context-support.jar:3.0.1.RELEASE]
   at org.springframework.scheduling.quartz.QuartzJobBean.execute(QuartzJobBean.java:86) [spring-context-support.jar:3.0.1.RELEASE]
   at org.quartz.core.JobRunShell.run(JobRunShell.java:203) [quartz.jar:1.5.2]
   at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [na:1.8.0_201]
   at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [na:1.8.0_201]
   at java.lang.Thread.run(Thread.java:748) [na:1.8.0_201]


Would that be the problem?

Best regards

S

Re: Migrating from old (5.1.2) to latest version: the safest

PostPosted: Fri Feb 01, 2019 10:01 am
by mtbc
It could be: the errors do postdate your Ice library fix? Maybe paste your current diagnostics output. Also, what error do you get if you try to log in from OMERO.cli? Did you fix the SSL version issue from the previous troubleshooting link? Also, do you have anything interesting in an omeroinsight.log or similar?

Cheers,
Mark

Re: Migrating from old (5.1.2) to latest version: the safest

PostPosted: Mon Feb 04, 2019 7:49 pm
by foisys
Hi,

> It could be: the errors do postdate your Ice library fix?
Don't think so: before the fix, omero just refused to work; I see the error showing from the timepoint of 5.3.5 install and no trace of it in the 5.2.8 log. Possibly a result of the Debian 8 to 9 transition?

> Maybe paste your current diagnostics output.

Code: Select all
================================================================================
OMERO Diagnostics 5.3.5-ice36-b73
================================================================================
       
WARNING:omero.util.UpgradeCheck:UPGRADE AVAILABLE:Please upgrade to 5.4.9. See http://downloads.openmicroscopy.org/latest/omero for the latest version.

Commands:   java -version                  1.8.0     (/usr/bin/java -- 2 others)
Commands:   python -V                      2.7.13    (/usr/bin/python)
Commands:   icegridnode --version          3.6.3     (/usr/bin/icegridnode)
Commands:   icegridadmin --version         3.6.3     (/usr/bin/icegridadmin)
Commands:   psql --version                 11.1      (/usr/bin/psql)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 6893, enabled)
Server:     DropBox                        active (pid = 6913, enabled)
Server:     FileServer                     active (pid = 6917, enabled)
Server:     Indexer-0                      active (pid = 6919, enabled)
Server:     MonitorServer                  active (pid = 6922, enabled)
Server:     OMERO.Glacier2                 active (pid = 6924, enabled)
Server:     OMERO.IceStorm                 active (pid = 6925, enabled)
Server:     PixelData-0                    active (pid = 6934, enabled)
Server:     Processor-0                    active (pid = 6939, enabled)
Server:     Tables-0                       active (pid = 6947, enabled)
Server:     TestDropBox                    inactive (enabled)

Log dir:    /home/OMS/apps/OMERO/OMERO.server-5.3.5-ice36-b73/var/log exists
Log files:  Blitz-0.log                    11.0 MB       errors=154  warnings=13 
Log files:  DropBox.log                    11.0 KB       errors=0    warnings=4   
Log files:  FileServer.log                 1.0 KB       
Log files:  Indexer-0.log                  111.0 KB     
Log files:  MonitorServer.log              6.0 KB       
Log files:  OMEROweb.log                   n/a
Log files:  PixelData-0.log                48.0 KB     
Log files:  Processor-0.log                166.0 KB      errors=0    warnings=154
Log files:  Tables-0.log                   7.0 KB        errors=0    warnings=1   
Log files:  TestDropBox.log                n/a
Log files:  master.err                     6.0 KB        errors=3    warnings=2   
Log files:  master.out                     0.0 KB       
Log files:  Total size                     12.09 MB


Environment:OMERO_HOME=(unset)             
Environment:OMERO_NODE=(unset)             
Environment:OMERO_MASTER=(unset)           
Environment:OMERO_USERDIR=(unset)         
Environment:OMERO_TMPDIR=(unset)           
Environment:PATH=/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/usr/lib/jvm/java-8-oracle/bin:/usr/share/Ice-3.6.3:/etc/postgresql/9.4/bin:/home/OMS/apps/OMERO/OMERO.server/bin
Environment:PYTHONPATH=/usr/lib/pymodules/python2.7
Environment:ICE_HOME=/usr/share/Ice-3.6.3 
Environment:LD_LIBRARY_PATH=/usr/share/java:/usr/lib:
Environment:DYLD_LIBRARY_PATH=(unset)     

OMERO SSL port:4064                           
OMERO TCP port:4063                           
OMERO data dir:'/home/OMS/OMERO.data'         Exists? True   Is writable? True
OMERO temp dir:'/home/omero/omero/tmp'        Exists? True   Is writable? True   (Size: 0)

JVM settings: Blitz-${index}                -Xmx3790m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index}              -Xmx2527m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index}            -Xmx3790m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index}           -Xmx2527m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions

OMERO.web status... [NOT STARTED]
Django version: 1.8.19


> Also, what error do you get if you try to log in from OMERO.cli? Did you fix the SSL version issue from the previous troubleshooting link? Also, do you have anything interesting in an omeroinsight.log or similar?

omero.cli fails like this:

Code: Select all
Server:
Username: foisys
Password:
InternalException: Failed to connect: exception ::Ice::ProtocolException
{
    reason = SSL error occurred for new outgoing connection:
remote address = 127.0.0.1:4064
no ciphers available
}
!! 02/04/19 14:46:20.362 error: 2 communicators not destroyed during global destruction.


And omeroinsight.log tells me the following:
Code: Select all
2019-01-31 16:02:36,312 DEBUG [   o.o.s.env.data.login.LoginServiceImpl] (nitializer) Failed to log onto OMERO.
Reason: javax.net.ssl.SSLHandshakeException: No appropriate protocol (protocol is disabled or cipher suites are inappropriate)
OMERO address: omero.inflammgen.local
User Name: foisys -- Password: ********
Ice.SecurityException
    reason = "IceSSL: handshake error"
   at IceInternal.AsyncResultI.__wait(AsyncResultI.java:270)
   at Ice.ObjectPrxHelperBase.end_ice_isA(ObjectPrxHelperBase.java:310)
   at Ice.ObjectPrxHelperBase.ice_isA(ObjectPrxHelperBase.java:92)
   at Ice.ObjectPrxHelperBase.ice_isA(ObjectPrxHelperBase.java:69)
   at Ice.ObjectPrxHelperBase.checkedCastImpl(ObjectPrxHelperBase.java:2810)
   at Ice.ObjectPrxHelperBase.checkedCastImpl(ObjectPrxHelperBase.java:2770)
   at Glacier2.RouterPrxHelper.checkedCast(RouterPrxHelper.java:1787)
   at omero.client.getRouter(client.java:802)
   at omero.client.createSession(client.java:723)
   at omero.gateway.Gateway.createSession(Gateway.java:1055)
   at omero.gateway.Gateway.connect(Gateway.java:257)
   at org.openmicroscopy.shoola.env.data.OMEROGateway.connect(OMEROGateway.java:1432)
   at org.openmicroscopy.shoola.env.data.DataServicesFactory.connect(DataServicesFactory.java:560)
   at org.openmicroscopy.shoola.env.data.login.LoginServiceImpl.attempt(LoginServiceImpl.java:141)
   at org.openmicroscopy.shoola.env.data.login.LoginServiceImpl.login(LoginServiceImpl.java:268)
   at org.openmicroscopy.shoola.env.data.login.LoginManager.login(LoginManager.java:98)
   at org.openmicroscopy.shoola.env.init.SplashScreenInit.onEnd(SplashScreenInit.java:163)
   at org.openmicroscopy.shoola.env.init.Initializer.notifyEnd(Initializer.java:189)
   at org.openmicroscopy.shoola.env.Container.runStartupProcedure(Container.java:125)
   at org.openmicroscopy.shoola.env.Container.access$000(Container.java:74)
   at org.openmicroscopy.shoola.env.Container$1.run(Container.java:170)
   at java.lang.Thread.run(Thread.java:748)
Caused by: javax.net.ssl.SSLHandshakeException: No appropriate protocol (protocol is disabled or cipher suites are inappropriate)
   at sun.security.ssl.Handshaker.activate(Handshaker.java:509)
   at sun.security.ssl.SSLEngineImpl.kickstartHandshake(SSLEngineImpl.java:714)
   at sun.security.ssl.SSLEngineImpl.beginHandshake(SSLEngineImpl.java:741)
   at IceSSL.SSLEngine.createSSLEngine(SSLEngine.java:856)
   at IceSSL.Instance.createSSLEngine(Instance.java:42)
   at IceSSL.ConnectorI.connect(ConnectorI.java:30)
   at IceInternal.OutgoingConnectionFactory$ConnectCallback.nextConnector(OutgoingConnectionFactory.java:1074)
   at IceInternal.OutgoingConnectionFactory$ConnectCallback.access$100(OutgoingConnectionFactory.java:841)
   at IceInternal.OutgoingConnectionFactory.getConnection(OutgoingConnectionFactory.java:542)
   at IceInternal.OutgoingConnectionFactory.access$800(OutgoingConnectionFactory.java:12)
   at IceInternal.OutgoingConnectionFactory$ConnectCallback.getConnection(OutgoingConnectionFactory.java:1021)
   at IceInternal.OutgoingConnectionFactory$ConnectCallback.connectors(OutgoingConnectionFactory.java:905)
   at IceInternal.EndpointHostResolver$1.run(EndpointHostResolver.java:103)
   at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
   at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
   ... 1 more


So the SSL thing? I feel stupid: which troubleshooting link?

Best regards

S

Re: Migrating from old (5.1.2) to latest version: the safest

PostPosted: Tue Feb 05, 2019 12:01 pm
by mtbc
I think that error in your Blitz logs is okay, let's come back to that. I had been thinking of viewtopic.php?f=5&t=8638#p20477 -- specifically, "SSLHandshakeException: No appropriate protocol" makes me wonder if you need to try the OpenSSL tweak at https://docs.openmicroscopy.org/omero/5 ... sl-version. Let us know how that goes! You might also have to do the PyTables thing listed there.

Cheers,
Mark

Re: Migrating from old (5.1.2) to latest version: the safest

PostPosted: Tue Feb 05, 2019 2:12 pm
by foisys
Hi,

I actually had found this link (https://docs.openmicroscopy.org/omero/5 ... oting.html) with some steps to solve the SSL issue as well as the one-liner that is suggested in the link you wrote about and it fixed half of my problem:

- I can log onto the omero server using omero cli and I can import a file w/o problem:
Code: Select all
./omero import /home/foisys/Z3COLOC0.TIF
Using session 161c070d-f121-434a-b270-375d3e38bfec (foisys@localhost:4064). Idle timeout: 10 min. Current group: IG_OMERO_USRs
2019-02-05 09:09:09,865 497        [      main] INFO          ome.formats.importer.ImportConfig - OMERO Version: 5.3.5-ice36-b73
2019-02-05 09:09:09,924 556        [      main] INFO          ome.formats.importer.ImportConfig - Bioformats version: 5.5.3 revision: 7bed1b04d071667d7b8a2e8c5d42f05fbfc07ecc date: 5 July 2017
2019-02-05 09:09:10,003 635        [      main] INFO   formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2019-02-05 09:09:10,887 1519       [      main] INFO      ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM
2019-02-05 09:09:11,261 1893       [      main] INFO      ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 367ms. (374ms total) [0 unknowns]
2019-02-05 09:09:12,064 2696       [      main] WARN                    ome.system.UpgradeCheck - UPGRADE AVAILABLE:Please upgrade to 5.4.9. See http://downloads.openmicroscopy.org/latest/omero for the latest version.
2019-02-05 09:09:12,307 2939       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:4064
2019-02-05 09:09:13,328 3960       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back
2019-02-05 09:09:14,391 5023       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Server: 5.3.5
2019-02-05 09:09:14,391 5023       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Client: 5.3.5-ice36-b73
2019-02-05 09:09:14,396 5028       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Java Version: 1.8.0_201
2019-02-05 09:09:14,397 5029       [      main] INFO       ome.formats.OMEROMetadataStoreClient - OS Name: Linux
2019-02-05 09:09:14,397 5029       [      main] INFO       ome.formats.OMEROMetadataStoreClient - OS Arch: amd64
2019-02-05 09:09:14,397 5029       [      main] INFO       ome.formats.OMEROMetadataStoreClient - OS Version: 4.9.0-8-amd64
2019-02-05 09:09:14,624 5256       [      main] INFO   ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION
2019-02-05 09:09:16,469 7101       [      main] INFO   ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START
2019-02-05 09:09:16,510 7142       [      main] INFO   ts.importer.transfers.UploadFileTransfer - Transferring /home/foisys/Z3COLOC0.TIF...
2019-02-05 09:09:16,607 7239       [      main] INFO   ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/foisys/Z3COLOC0.TIF
2019-02-05 09:09:16,733 7365       [      main] INFO   ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/foisys/Z3COLOC0.TIF
2019-02-05 09:09:17,690 8322       [      main] INFO   ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END
2019-02-05 09:09:18,141 8773       [      main] INFO   ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 38871
2019-02-05 09:09:19,578 10210      [l.Client-0] INFO   ormats.importer.cli.LoggingImportMonitor - METADATA_IMPORTED Step: 1 of 5  Logfile: 38871
2019-02-05 09:09:20,233 10865      [l.Client-1] INFO   ormats.importer.cli.LoggingImportMonitor - PIXELDATA_PROCESSED Step: 2 of 5  Logfile: 38871
2019-02-05 09:09:22,426 13058      [l.Client-0] INFO   ormats.importer.cli.LoggingImportMonitor - THUMBNAILS_GENERATED Step: 3 of 5  Logfile: 38871
2019-02-05 09:09:22,467 13099      [l.Client-1] INFO   ormats.importer.cli.LoggingImportMonitor - METADATA_PROCESSED Step: 4 of 5  Logfile: 38871
2019-02-05 09:09:22,501 13133      [l.Client-0] INFO   ormats.importer.cli.LoggingImportMonitor - OBJECTS_RETURNED Step: 5 of 5  Logfile: 38871
2019-02-05 09:09:22,822 13454      [l.Client-1] INFO   ormats.importer.cli.LoggingImportMonitor - IMPORT_DONE Imported file: /home/foisys/Z3COLOC0.TIF
Image:13401
Other imported objects:
Fileset:12751
2019-02-05 09:09:22,839 13471      [l.Client-1] INFO      ome.formats.importer.cli.ErrorHandler - Number of errors: 0

==> Summary
1 file uploaded, 1 fileset created, 1 image imported, 0 errors in 0:00:08.248


However, OMERO.Insight 5.3.5 does not work:
Code: Select all
2019-02-05 09:07:00,452 DEBUG [   o.o.s.env.data.login.LoginServiceImpl] (nitializer) Failed to log onto OMERO.
Reason: javax.net.ssl.SSLHandshakeException: No appropriate protocol (protocol is disabled or cipher suites are inappropriate)
OMERO address: omero.inflammgen.local
User Name: foisys -- Password: ********
Ice.SecurityException
    reason = "IceSSL: handshake error"
   at IceInternal.AsyncResultI.__wait(AsyncResultI.java:270)
   at Ice.ObjectPrxHelperBase.end_ice_isA(ObjectPrxHelperBase.java:310)
   at Ice.ObjectPrxHelperBase.ice_isA(ObjectPrxHelperBase.java:92)
   at Ice.ObjectPrxHelperBase.ice_isA(ObjectPrxHelperBase.java:69)
   at Ice.ObjectPrxHelperBase.checkedCastImpl(ObjectPrxHelperBase.java:2810)
   at Ice.ObjectPrxHelperBase.checkedCastImpl(ObjectPrxHelperBase.java:2770)
   at Glacier2.RouterPrxHelper.checkedCast(RouterPrxHelper.java:1787)
   at omero.client.getRouter(client.java:802)
   at omero.client.createSession(client.java:723)
   at omero.gateway.Gateway.createSession(Gateway.java:1055)
   at omero.gateway.Gateway.connect(Gateway.java:257)
   at org.openmicroscopy.shoola.env.data.OMEROGateway.connect(OMEROGateway.java:1432)
   at org.openmicroscopy.shoola.env.data.DataServicesFactory.connect(DataServicesFactory.java:560)
   at org.openmicroscopy.shoola.env.data.login.LoginServiceImpl.attempt(LoginServiceImpl.java:141)
   at org.openmicroscopy.shoola.env.data.login.LoginServiceImpl.login(LoginServiceImpl.java:268)
   at org.openmicroscopy.shoola.env.data.login.LoginManager.login(LoginManager.java:98)
   at org.openmicroscopy.shoola.env.init.SplashScreenInit.onEnd(SplashScreenInit.java:163)
   at org.openmicroscopy.shoola.env.init.Initializer.notifyEnd(Initializer.java:189)
   at org.openmicroscopy.shoola.env.Container.runStartupProcedure(Container.java:125)
   at org.openmicroscopy.shoola.env.Container.access$000(Container.java:74)
   at org.openmicroscopy.shoola.env.Container$1.run(Container.java:170)
   at java.lang.Thread.run(Thread.java:748)
Caused by: javax.net.ssl.SSLHandshakeException: No appropriate protocol (protocol is disabled or cipher suites are inappropriate)
   at sun.security.ssl.Handshaker.activate(Handshaker.java:509)
   at sun.security.ssl.SSLEngineImpl.kickstartHandshake(SSLEngineImpl.java:714)
   at sun.security.ssl.SSLEngineImpl.beginHandshake(SSLEngineImpl.java:741)
   at IceSSL.SSLEngine.createSSLEngine(SSLEngine.java:856)
   at IceSSL.Instance.createSSLEngine(Instance.java:42)
   at IceSSL.ConnectorI.connect(ConnectorI.java:30)
   at IceInternal.OutgoingConnectionFactory$ConnectCallback.nextConnector(OutgoingConnectionFactory.java:1074)
   at IceInternal.OutgoingConnectionFactory$ConnectCallback.access$100(OutgoingConnectionFactory.java:841)
   at IceInternal.OutgoingConnectionFactory.getConnection(OutgoingConnectionFactory.java:542)
   at IceInternal.OutgoingConnectionFactory.access$800(OutgoingConnectionFactory.java:12)
   at IceInternal.OutgoingConnectionFactory$ConnectCallback.getConnection(OutgoingConnectionFactory.java:1021)
   at IceInternal.OutgoingConnectionFactory$ConnectCallback.connectors(OutgoingConnectionFactory.java:905)
   at IceInternal.EndpointHostResolver$1.run(EndpointHostResolver.java:103)
   at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
   at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
   ... 1 more
Failed to log onto OMERO.
Reason: javax.net.ssl.SSLHandshakeException: No appropriate protocol (protocol is disabled or cipher suites are inappropriate)
OMERO address: omero.inflammgen.local
User Name: foisys -- Password: ********
Ice.SecurityException
    reason = "IceSSL: handshake error"
   at IceInternal.AsyncResultI.__wait(AsyncResultI.java:270)
   at Ice.ObjectPrxHelperBase.end_ice_isA(ObjectPrxHelperBase.java:310)
   at Ice.ObjectPrxHelperBase.ice_isA(ObjectPrxHelperBase.java:92)
   at Ice.ObjectPrxHelperBase.ice_isA(ObjectPrxHelperBase.java:69)
   at Ice.ObjectPrxHelperBase.checkedCastImpl(ObjectPrxHelperBase.java:2810)
   at Ice.ObjectPrxHelperBase.checkedCastImpl(ObjectPrxHelperBase.java:2770)
   at Glacier2.RouterPrxHelper.checkedCast(RouterPrxHelper.java:1787)
   at omero.client.getRouter(client.java:802)
   at omero.client.createSession(client.java:723)
   at omero.gateway.Gateway.createSession(Gateway.java:1055)
   at omero.gateway.Gateway.connect(Gateway.java:257)
   at org.openmicroscopy.shoola.env.data.OMEROGateway.connect(OMEROGateway.java:1432)
   at org.openmicroscopy.shoola.env.data.DataServicesFactory.connect(DataServicesFactory.java:560)
   at org.openmicroscopy.shoola.env.data.login.LoginServiceImpl.attempt(LoginServiceImpl.java:141)
   at org.openmicroscopy.shoola.env.data.login.LoginServiceImpl.login(LoginServiceImpl.java:268)
   at org.openmicroscopy.shoola.env.data.login.LoginManager.login(LoginManager.java:98)
   at org.openmicroscopy.shoola.env.init.SplashScreenInit.onEnd(SplashScreenInit.java:163)
   at org.openmicroscopy.shoola.env.init.Initializer.notifyEnd(Initializer.java:189)
   at org.openmicroscopy.shoola.env.Container.runStartupProcedure(Container.java:125)
   at org.openmicroscopy.shoola.env.Container.access$000(Container.java:74)
   at org.openmicroscopy.shoola.env.Container$1.run(Container.java:170)
   at java.lang.Thread.run(Thread.java:748)
Caused by: javax.net.ssl.SSLHandshakeException: No appropriate protocol (protocol is disabled or cipher suites are inappropriate)
   at sun.security.ssl.Handshaker.activate(Handshaker.java:509)
   at sun.security.ssl.SSLEngineImpl.kickstartHandshake(SSLEngineImpl.java:714)
   at sun.security.ssl.SSLEngineImpl.beginHandshake(SSLEngineImpl.java:741)
   at IceSSL.SSLEngine.createSSLEngine(SSLEngine.java:856)
   at IceSSL.Instance.createSSLEngine(Instance.java:42)
   at IceSSL.ConnectorI.connect(ConnectorI.java:30)
   at IceInternal.OutgoingConnectionFactory$ConnectCallback.nextConnector(OutgoingConnectionFactory.java:1074)
   at IceInternal.OutgoingConnectionFactory$ConnectCallback.access$100(OutgoingConnectionFactory.java:841)
   at IceInternal.OutgoingConnectionFactory.getConnection(OutgoingConnectionFactory.java:542)
   at IceInternal.OutgoingConnectionFactory.access$800(OutgoingConnectionFactory.java:12)
   at IceInternal.OutgoingConnectionFactory$ConnectCallback.getConnection(OutgoingConnectionFactory.java:1021)
   at IceInternal.OutgoingConnectionFactory$ConnectCallback.connectors(OutgoingConnectionFactory.java:905)
   at IceInternal.EndpointHostResolver$1.run(EndpointHostResolver.java:103)
   at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
   at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
   ... 1 more
Exception in thread "Initializer"


Weird? I did check PyTables via pip and it was already installed.

Best regards

S

Re: Migrating from old (5.1.2) to latest version: the safest

PostPosted: Tue Feb 05, 2019 5:24 pm
by mtbc
What does java -version report on your current system? I'm wondering if it's recent enough that your JRE's java.security file includes "anon" among the jdk.tls.disabledAlgorithms. (Insight needs to use an "anon" algorithm.) https://bugs.java.com/bugdatabase/view_ ... DK-8211883 has some background.

Cheers,
Mark

Re: Migrating from old (5.1.2) to latest version: the safest

PostPosted: Wed Feb 06, 2019 1:34 pm
by foisys
HI,

I get this info:
Code: Select all
$ java -version
java version "1.8.0_201"
Java(TM) SE Runtime Environment (build 1.8.0_201-b09)
Java HotSpot(TM) 64-Bit Server VM (build 25.201-b09, mixed mode)


Oracle Java was installed on this system at the very beginning of OMERO operation.

Best regards

S

Re: Migrating from old (5.1.2) to latest version: the safest

PostPosted: Wed Feb 06, 2019 2:03 pm
by mtbc
Ah yes, this Java has that linked fix that stops Insight connecting: the issue is fixed in 5.4.10 so when you get that far you should find that Insight connects fine. Interesting CLI import still worked though, I assume it's using the same Java.

To test on 5.3, your easiest route might be to find whichever java.security file applies (I guess somewhere in /etc/ or /usr/) and remove "anon" from among the jdk.tls.disabledAlgorithms it sets. Does Insight start working fine then? If so, when you get to 5.4.10 remember to put any java.security files that you changed back to how they were.

If that doesn't get Insight working for you we'll have to dig deeper.

Cheers,
Mark

Re: Migrating from old (5.1.2) to latest version: the safest

PostPosted: Wed Feb 06, 2019 2:27 pm
by foisys
Hi,

Interesting: anon is not found among the jdk.tls.disabledAlgorithms choices in /etc/java-8-oracle/java.security:
Code: Select all
jdk.tls.disabledAlgorithms=SSLv3, RC4, DES, MD5withRSA, DH keySize < 1024, \
    EC keySize < 224, 3DES_EDE_CBC


In any case, I'll move forward toward v.5.4 and not lose to much time with this.

Best regards

S

Re: Migrating from old (5.1.2) to latest version: the safest

PostPosted: Thu Feb 07, 2019 8:19 am
by mtbc
For your interest, I tried installing a current Oracle Java on Debian 9 using make-jpkg (turned out to be 1.8.0_202-b08 so not quite yours) and ended up with "anon" being included among /usr/lib/jvm/oracle-java8-jdk-amd64/jre/lib/security/java.security but, yes, we can spend more time on the issue if you still see it with 5.4.10. Good luck!

Mark