Open Microscopy Environment

I have been having an issue logging into the OMERO.web. The directions posted at https://www.openmicroscopy.org/site/sup ... ice36.html were used for the installation.

When a login is attempted it results in the following error.

Error: Server is not responding, please contact administrator.

Results of:
bin/omero admin diagnostics

================================================================================
OMERO Diagnostics 5.2.6-ice36-b35
================================================================================

Commands: java -version 1.8.0 (/usr/bin/java)
Commands: python -V 2.7.5 (/usr/bin/python)
Commands: icegridnode --version 3.6.3 (/usr/bin/icegridnode)
Commands: icegridadmin --version 3.6.3 (/usr/bin/icegridadmin)
Commands: psql --version 9.4.9 (/usr/bin/psql)

Server: icegridnode running
Server: Blitz-0 inactive (disabled)
Server: DropBox inactive (disabled)
Server: FileServer active (pid = 4915, enabled)
Server: Indexer-0 inactive (disabled)
Server: MonitorServer active (pid = 4891, enabled)
Server: OMERO.Glacier2 active (pid = 4918, enabled)
Server: OMERO.IceStorm active (pid = 4893, enabled)
Server: PixelData-0 inactive (disabled)
Server: Processor-0 activating (enabled)
Server: Tables-0 inactive (disabled)
Server: TestDropBox inactive (enabled)

Log dir: /home/omero/OMERO.server-5.2.6-ice36-b35/var/log exists
Log files: Blitz-0.log 102.0 KB errors=52 warnings=0
Log files: DropBox.log 3.0 KB errors=4 warnings=2
Log files: FileServer.log 0.0 KB
Log files: Indexer-0.log 103.0 KB errors=70 warnings=0
Log files: MonitorServer.log 0.0 KB
Log files: OMEROweb.lock 0.0 KB
Log files: OMEROweb.log 63.0 KB errors=60 warnings=42
Log files: OMEROweb_brokenrequest.lock 0.0 KB
Log files: OMEROweb_brokenrequest.log 0.0 KB
Log files: PixelData-0.log 103.0 KB errors=70 warnings=0
Log files: Processor-0.log 3.0 MB errors=2096 warnings=1048
Log files: Tables-0.log n/a
Log files: TestDropBox.log n/a
Log files: master.err 1.0 KB errors=4 warnings=4
Log files: master.out 0.0 KB
Log files: Total size 3.97 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:/usr/local/sbin:/usr/sbin:/home/omero/.local/bin:/home/omero/bin
Environment:PYTHONPATH=(unset)
Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)

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

JVM settings: Blitz-${index} -Xmx580m -XX:MaxPermSize=256m -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index} -Xmx387m -XX:MaxPermSize=256m -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index} -Xmx580m -XX:MaxPermSize=256m -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index} -Xmx387m -XX:MaxPermSize=256m -XX:+IgnoreUnrecognizedVMOptions

OMERO.web status... [RUNNING] (PID 2516)
Django version: 1.8.15

Hi,

could you send us all the logs from /home/omero/OMERO.server-5.2.6-ice36-b35/var/log
and output of bin/omero config get --hide-password


Ola

Thank you for the response.

$ bin/omero config get --hide-password
omero.data.dir=/omero
omero.db.name=omero
omero.db.pass=********
omero.db.user=omero-db
omero.web.application_server=wsgi-tcp

Hi,

From your Blitz-0 log, it appears that OMERO can't find a table it expects in the database.

If you could please verify that the database-creation script was run. The link you pasted has a step "Configure", and it's the last two lines of that section.

If you'd like to, you can always connect to the database with the psql tool, manually, to double check:

Code: Select all

psql -h localhost -U "$OMERO_DB_USER" "$OMERO_DB_NAME" -c "\dt"

This would list all the tables in the database.

Best,

Kenny

Hi looks like OMERO.server cannot establish connection to the postgres DB

Code: Select all

java.sql.SQLException: unable to get a connection from pool of a PoolingDataSource containing an XAPool of resource

Could you double check if you can connect via:

Code: Select all

psql -h localhost -U omero-db omero

?

didn't you swap db username and db name in config?

Code: Select all

omero.db.name=omero
omero.db.user=omero-db

Ola

There was an issue with the DB when I looked at it more closely the <Omero Database User> was not created correctly. I ran back through that portion of the installation. The end result is very similar.

Thanks in advance for the assistance.


$ bin/omero config get --hide-password
omero.data.dir=/omero
omero.db.name=omero_db
omero.db.pass=********
omero.db.user=omero
omero.web.application_server=wsgi-tcp


$ bin/omero admin diagnostics

================================================================================
OMERO Diagnostics 5.2.6-ice36-b35
================================================================================

Commands: java -version 1.8.0 (/usr/bin/java)
Commands: python -V 2.7.5 (/usr/bin/python)
Commands: icegridnode --version 3.6.3 (/usr/bin/icegridnode)
Commands: icegridadmin --version 3.6.3 (/usr/bin/icegridadmin)
Commands: psql --version 9.4.9 (/usr/bin/psql)

Server: icegridnode running
Server: Blitz-0 inactive (disabled)
Server: DropBox inactive (disabled)
Server: FileServer active (pid = 2799, enabled)
Server: Indexer-0 inactive (disabled)
Server: MonitorServer active (pid = 2773, enabled)
Server: OMERO.Glacier2 active (pid = 2756, enabled)
Server: OMERO.IceStorm active (pid = 2777, enabled)
Server: PixelData-0 inactive (disabled)
Server: Processor-0 activating (enabled)
Server: Tables-0 inactive (disabled)
Server: TestDropBox inactive (enabled)

Log dir: /home/omero/OMERO.server-5.2.6-ice36-b35/var/log exists
Log files: Blitz-0.log 51.0 KB errors=26 warnings=0
Log files: Blitz-0_01.log 153.0 KB errors=78 warnings=0
Log files: DropBox.log 6.0 KB errors=8 warnings=4
Log files: FileServer.log 1.0 KB
Log files: Indexer-0.log 205.0 KB errors=140 warnings=0
Log files: MonitorServer.log 1.0 KB
Log files: OMEROweb.lock 0.0 KB
Log files: OMEROweb.log 79.0 KB errors=74 warnings=58
Log files: OMEROweb_brokenrequest.lock 0.0 KB
Log files: OMEROweb_brokenrequest.log 0.0 KB
Log files: PixelData-0.log 206.0 KB errors=140 warnings=0
Log files: Processor-0.log 2.0 MB errors=1506 warnings=751
Log files: Processor-0.log.1 4.0 MB errors=2916 warnings=1459
Log files: Tables-0.log n/a
Log files: TestDropBox.log n/a
Log files: master.err 4.0 KB errors=8 warnings=12
Log files: master.out 0.0 KB
Log files: Total size 8.29 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:/usr/local/sbin:/usr/sbin:/home/omero/.local/bin:/home/omero/bin
Environment:PYTHONPATH=(unset)
Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)

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

JVM settings: Blitz-${index} -Xmx580m -XX:MaxPermSize=256m -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index} -Xmx387m -XX:MaxPermSize=256m -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index} -Xmx580m -XX:MaxPermSize=256m -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index} -Xmx387m -XX:MaxPermSize=256m -XX:+IgnoreUnrecognizedVMOptions

OMERO.web status... [RUNNING] (PID 2330)
Django version: 1.8.15



psql -h localhost -U omero omero-db -c "\dt"
Password for user omero:
List of relations
Schema | Name | Type | Owner
--------+---------------------------------+-------+-------
public | _fs_deletelog | table | omero
public | _lock_ids | table | omero
public | _updated_annotations | table | omero
public | acquisitionmode | table | omero
public | annotation | table | omero
public | annotation_mapvalue | table | omero
public | annotationannotationlink | table | omero
public | arc | table | omero
public | arctype | table | omero
public | binning | table | omero
public | channel | table | omero
public | channelannotationlink | table | omero
public | channelbinding | table | omero
public | checksumalgorithm | table | omero
public | codomainmapcontext | table | omero
public | configuration | table | omero
public | contrastmethod | table | omero
public | contraststretchingcontext | table | omero
public | correction | table | omero
public | dataset | table | omero
public | datasetannotationlink | table | omero
public | datasetimagelink | table | omero
public | dbpatch | table | omero
public | detector | table | omero
public | detectorannotationlink | table | omero
public | detectorsettings | table | omero
public | detectortype | table | omero
public | dichroic | table | omero
public | dichroicannotationlink | table | omero
public | dimensionorder | table | omero
public | event | table | omero
public | eventlog | table | omero
public | eventtype | table | omero
public | experiment | table | omero
public | experimenter | table | omero
public | experimenterannotationlink | table | omero
public | experimentergroup | table | omero
public | experimentergroup_config | table | omero
public | experimentergroupannotationlink | table | omero
public | experimenttype | table | omero
public | externalinfo | table | omero
public | family | table | omero
public | filament | table | omero
public | filamenttype | table | omero
public | fileset | table | omero
public | filesetannotationlink | table | omero
public | filesetentry | table | omero
public | filesetjoblink | table | omero
public | filter | table | omero
public | filterannotationlink | table | omero
public | filterset | table | omero
public | filtersetemissionfilterlink | table | omero
public | filtersetexcitationfilterlink | table | omero
public | filtertype | table | omero
public | format | table | omero
public | genericexcitationsource | table | omero
public | genericexcitationsource_map | table | omero
public | groupexperimentermap | table | omero
public | illumination | table | omero
public | image | table | omero
public | imageannotationlink | table | omero
public | imagingenvironment | table | omero
public | imagingenvironment_map | table | omero
public | immersion | table | omero
public | importjob | table | omero
public | indexingjob | table | omero
public | instrument | table | omero
public | instrumentannotationlink | table | omero
public | integritycheckjob | table | omero
public | job | table | omero
public | joboriginalfilelink | table | omero
public | jobstatus | table | omero
public | laser | table | omero
public | lasermedium | table | omero
public | lasertype | table | omero
public | lightemittingdiode | table | omero
public | lightpath | table | omero
public | lightpathannotationlink | table | omero
public | lightpathemissionfilterlink | table | omero
public | lightpathexcitationfilterlink | table | omero
public | lightsettings | table | omero
public | lightsource | table | omero
public | lightsourceannotationlink | table | omero
public | link | table | omero
public | logicalchannel | table | omero
public | medium | table | omero
public | metadataimportjob | table | omero
public | metadataimportjob_versioninfo | table | omero
public | microbeammanipulation | table | omero
public | microbeammanipulationtype | table | omero
public | microscope | table | omero
public | microscopetype | table | omero
public | namespace | table | omero
public | namespaceannotationlink | table | omero
public | node | table | omero
public | nodeannotationlink | table | omero
public | objective | table | omero
public | objectiveannotationlink | table | omero
public | objectivesettings | table | omero
public | originalfile | table | omero
public | originalfileannotationlink | table | omero
public | otf | table | omero
public | parsejob | table | omero
public | password | table | omero
public | photometricinterpretation | table | omero
public | pixeldatajob | table | omero
public | pixels | table | omero
public | pixelsoriginalfilemap | table | omero
public | pixelstype | table | omero
public | planeinfo | table | omero
public | planeinfoannotationlink | table | omero
public | planeslicingcontext | table | omero
public | plate | table | omero
public | plateacquisition | table | omero
public | plateacquisitionannotationlink | table | omero
public | plateannotationlink | table | omero
public | project | table | omero
public | projectannotationlink | table | omero
public | projectdatasetlink | table | omero
public | pulse | table | omero
public | quantumdef | table | omero
public | reagent | table | omero
public | reagentannotationlink | table | omero
public | renderingdef | table | omero
public | renderingmodel | table | omero
public | reverseintensitycontext | table | omero
public | roi | table | omero
public | roiannotationlink | table | omero
public | screen | table | omero
public | screenannotationlink | table | omero
public | screenplatelink | table | omero
public | scriptjob | table | omero
public | session | table | omero
public | sessionannotationlink | table | omero
public | shape | table | omero
public | shapeannotationlink | table | omero
public | share | table | omero
public | sharemember | table | omero
public | stagelabel | table | omero
public | statsinfo | table | omero
public | thumbnail | table | omero
public | thumbnailgenerationjob | table | omero
public | transmittancerange | table | omero
public | uploadjob | table | omero
public | uploadjob_versioninfo | table | omero
public | well | table | omero
public | wellannotationlink | table | omero
public | wellreagentlink | table | omero
public | wellsample | table | omero
(149 rows)

Hi,

I can see the problem here:

omero config has "omero.db.name=omero_db", with an underscore.

You're connecting to the database on the command line, with a dash: omero-db.

Hope that gets you going!

That have been corrected by rerunning the OMERO.server/bin/omero config set commands.

Now there seems to be a Django issue


2016-10-27 11:39:52,675 INFO [ omeroweb.webclient.views] (proc.02551) <module>():105 INIT '2551'
2016-10-27 11:39:52,687 WARNI [ django.request] (proc.02551) _reject():98 Forbidden (CSRF token missing or incorrect.): /webclient/login/
2016-10-27 11:39:52,687 WARNI [ omeroweb.feedback.views] (proc.02551) csrf_failure():136 csrf_failure: Forbidden
2016-10-27 11:40:00,059 INFO [ omeroweb.webclient.views] (proc.02549) <module>():105 INIT '2549'
2016-10-27 11:40:00,200 INFO [ omeroweb.webclient.views] (proc.02545) <module>():105 INIT '2545'
2016-10-27 11:40:23,328 INFO [ omero.gateway] (proc.02551) connect():2066 created connection (uuid=352e9002-9123-4e89-aff0-b7cc629a8832)
2016-10-27 11:40:23,360 INFO [ omeroweb.connector] (proc.02551) check_version():229 Client version: '['5', '2', '6']'; Server version: '['5', '2', '6']'
2016-10-27 11:40:23,377 INFO [ omero.gateway] (proc.02551) connect():2055 Failed to create session.
2016-10-27 11:40:23,526 INFO [ omero.gateway] (proc.02551) connect():2066 created connection (uuid=4a37a617-3afe-423b-8393-ac4b542797e4)
2016-10-27 11:40:33,275 INFO [ omero.gateway] (proc.02549) connect():2066 created connection (uuid=3fb86d92-85f5-4680-a301-155a8ef5ee06)
2016-10-27 11:40:33,304 INFO [ omeroweb.connector] (proc.02549) check_version():229 Client version: '['5', '2', '6']'; Server version: '['5', '2', '6']'
2016-10-27 11:40:33,325 INFO [ omero.gateway] (proc.02549) connect():2055 Failed to create session.
2016-10-27 11:40:36,486 INFO [ omero.gateway] (proc.02549) connect():2066 created connection (uuid=f3df6c5a-2d91-4a88-a727-5960904061b6)

I see the CSRF warning at 11:39:52 followed about 30 seconds later by a login failures at 11:40:23 and 11:40:33 (the "created connection" lines refer to a guest connection that is used to check the version check right before login).

The CSRF failure means that the login form didn't contain a valid csrf token for your Django session. Did you restart web between loading the login page and submitting the form?
Do you still see this error if you refresh the login page and then try to login?

You may be able to get more details on the failed login from the server's main Blitz-0.log
E.g. look for ome.security.auth.LoginAttemptListener.

Have you tried logging in with the other clients yet?
You can check with Insight or the command line, E.g.

// this will prompt you for server, username, password

Code: Select all

$ bin/omero login

OR if you set omero.web.debug to True you might see more info in the web log, E.g.
NB: Don't do this in production!
$ bin/omero config omero.web.debug True // then restart web

Code: Select all

2016-10-28 11:16:33,318 DEBUG [                           omero.gateway] (proc.48272) connect():2099 connect(): Traceback (most recent call last):
...
PermissionDeniedException: exception ::Glacier2::PermissionDeniedException
{
    reason = Password check failed for 'will': [id=3]
}


Hope that helps,
Let us know what you find,
Regards,

Will.

Did you restart web between loading the login page and submitting the form?
No

Do you still see this error if you refresh the login page and then try to login?
Yes

You may be able to get more details on the failed login from the server's main Blitz-0.log?
I am getting this error: 907 WARN [ ome.security.auth.LoginAttemptListener] (l.Server-4) 2 failed logins for root. Throttling for 3000
The latest logs have been attached.

Have you tried logging in with the other clients yet?
The CLI login does not work. The result is "Password check failed for 'omero': []"
The password has bee verified and reverified.

The configuration has been updated to enable debug mode.
bin/omero config set omero.web.debug True

The logs attached are after debug was set and login was attempted. It is still giving me password errors.