mstritt/orbit-image-analysis

cannot connect to omero

Closed this issue · 17 comments

CFGrote commented

hi,
trying to run orbit v363 on debian10.

installed to /opt/orbit

$> /opt/orbit/orbit.sh

launches the orbit gui but i get this message:

image

The complete startup log:

$> /opt/orbit/orbit.sh                                    
17:39:48,657 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.groovy]
17:39:48,657 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
17:39:48,658 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [jar:file:/opt/orbit/lib/image-provider-omero-1.7.2.jar!/logback.xml]
17:39:48,658 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs multiple times on the classpath.
17:39:48,658 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:/opt/orbit/lib/orbit-image-analysis.jar!/logback.xml]
17:39:48,658 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:/opt/orbit/lib/image-provider-omero-1.7.2.jar!/logback.xml]
17:39:48,675 |-INFO in ch.qos.logback.core.joran.spi.ConfigurationWatchList@6236eb5f - URL [jar:file:/opt/orbit/lib/image-provider-omero-1.7.2.jar!/logback.xml] is not of type file
17:39:48,745 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - debug attribute not set
17:39:48,754 |-INFO in ch.qos.logback.classic.joran.action.LoggerAction - Setting level of logger [org.apache] to WARN
17:39:48,754 |-INFO in ch.qos.logback.classic.joran.action.LoggerAction - Setting level of logger [httpclient] to WARN
17:39:48,754 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - End of configuration.
17:39:48,755 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@7c1e2a9e - Registering current configuration as safe fallback point

java.lang.IllegalArgumentException: wrong number of arguments
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
	at java.base/java.lang.reflect.Constructor.newInstance(Unknown Source)
	at com.actelion.research.orbit.imageAnalysis.dal.DALConfig.<clinit>(DALConfig.java:79)
	at com.actelion.research.orbit.imageAnalysis.components.OrbitImageAnalysis.getInfoString(OrbitImageAnalysis.java:794)
	at com.actelion.research.orbit.imageAnalysis.components.OrbitImageAnalysis.<init>(OrbitImageAnalysis.java:281)
	at com.actelion.research.orbit.imageAnalysis.components.OrbitImageAnalysis.getInstance(OrbitImageAnalysis.java:2782)
	at com.actelion.research.orbit.imageAnalysis.components.OrbitImageAnalysis.lambda$initSingleApplication$7(OrbitImageAnalysis.java:2864)
	at java.desktop/java.awt.event.InvocationEvent.dispatch(Unknown Source)
	at java.desktop/java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.desktop/java.awt.EventQueue$4.run(Unknown Source)
	at java.desktop/java.awt.EventQueue$4.run(Unknown Source)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.desktop/java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.desktop/java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.desktop/java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.desktop/java.awt.EventDispatchThread.run(Unknown Source)
Orbit Image Analysis Version  3.63
Copyright (c) 2009-2020, Idorsia Pharmaceuticals Ltd. under GPLv3 license.
Developed by Manuel Stritt and Jonathan Fuller.

Login User: guest
Available temporary disk space: 8698 MB.
Tile memory size (Read): 0 tiles
Tile memory capacity (Write): 788 MB
Tile temp directory: /tmp
JVM Memory used/total: 248 / 3940 MB
Available Cores: 8
JVM version: 11.0.7+10
Lib directory: /opt/orbit/lib
Loaded model: none

Optional parameters: [.orbit|image file(.jpg,.tif,.bmp,.png,.gif,.svs)|url|rdf id  ]
use -noErrorPopups to get rid of error popups (can be useful if you have no network connection)

use --hideQuickSearch to hide the left search bar (can be useful if you have no network connection)

And my ~/OrbitOmero.properties:

#Orbit Omero Config
OmeroHost=undisclosed.server.domain
SearchLimit=1000
UseSSL=false
OmeroPort=4064
OmeroWebPort=80

Any help would be appreciated.

CFGrote commented

And of course I checked that the omero server is online and I can login to the web interface and omero.insight

mstritt commented

Hi @CFGrote ,
I can have a closer look on it tomorrow, but Omero Port 4064 is for ssl, so either set usessl to true or set port to 4063 (no encryption). Can you please try?
Regards,
Manuel

CFGrote commented

hi @mstritt ,
thanks for the quick reply. i tested all combinations of ssl=true/false and port 4064/4063 and always got the same message posted above.

when i log in to omero-web, the connection is not encrypted (for reasons beyond this scope) and omero runs on port 4064 on the same host as omero-web.

mstritt commented

Dear @CFGrote ,
I'm trying to reproduce...
So when you see the popup window and click on "Continue" - what happens then? Does Orbit start in standalone mode (without Omero connection) or does it crash?
Regards,
Manuel

CFGrote commented
mstritt commented

can you please try to create an OrbitOmero.properties.template file in your usse home?
e.g.
touch ~/OrbitOmero.properties.template
and retry?

CFGrote commented
mstritt commented

Dear @CFGrote ,
we really tested a lot but always came to the same conclusion that your error appears if the OMERO connection parameters are not correct.
Can you please try to set
OmeroWebPort=4080
for the OME demo server?

Regards,
Manuel

mstritt commented

@CFGrote , Orbit first checks in the current (installation) directory and then in your user home directory and searches for the OrbitOmero.properties file.
Maybe you edit the one in you user-home but have an existing (non-valid) file in the install directory?
Regards,
Manuel

CFGrote commented
CFGrote commented
mstritt commented

I think it should be

#Orbit Omero Config
OmeroHost=demo.openmicroscopy.org
SearchLimit=10000
UseSSL=true
OmeroPort=4064
OmeroWebPort=4080

Regards,
Manuel

CFGrote commented
  • 👍1
mstritt commented

thanks a lot @CFGrote for digging into this. We're currently having a loot into it - seems to something really wired.
Can you please test what happens if you simply call start-orbit.sh within the temp dir (extracted tar.gz folder). ?

Regards,
Manuel

CFGrote commented
mstritt commented

Orbit version 3.64 is out which hopefully fixes this bug. Can you please give it a try?
Manuel

CFGrote commented