internal server error

[hippogriff]

Hi Josh, I'm assuming this is what you mean:

Code: Select all

C:\PostgreSQL\9.5\bin>psql -h localhost -U postgres -d omero -l
Password for user postgres:
                                                 List of databases
   Name    |  Owner   | Encoding |          Collate           |           Ctype
           |   Access privileges
-----------+----------+----------+----------------------------+-----------------
-----------+-----------------------
omero     | postgres | UTF8     | English_United States.1252 | English_United S
tates.1252 |
postgres  | postgres | UTF8     | English_United States.1252 | English_United S
tates.1252 |
template0 | postgres | UTF8     | English_United States.1252 | English_United S
tates.1252 | =c/postgres          +
           |          |          |                            |
           | postgres=CTc/postgres
template1 | postgres | UTF8     | English_United States.1252 | English_United S
tates.1252 | =c/postgres          +
           |          |          |                            |
           | postgres=CTc/postgres
(4 rows)

Here's a config settings check...

Code: Select all

C:\PostgreSQL\9.5\bin>\OMERO.server-5.2.2-ice35-b17\bin\omero config get
omero.db.name=omero
omero.db.pass=*************************
omero.db.user=postgres
omero.web.application_server=development
omero.web.debug=True

C:\PostgreSQL\9.5\bin>

[jmoore]

And what does this return?

Code: Select all

C:\PostgreSQL\9.5\bin>psql -h localhost -U postgres -d omero -c "\d"


Cheers,
~Josh

[hippogriff]

Code: Select all

C:\PostgreSQL\9.5\bin>psql -h localhost -U postgres -d omero -c "\d"
Password for user postgres:
No relations found.


[kennethgillen]

Code: Select all

No relations found.


This tells us that the OMERO database is empty, so the database boostrapping stage of your installation somehow failed.

Presuming this is a completely new OMERO install, please re-run the Database related section of the Windows server install instructions, starting from "Create the OMERO database initialization script".

https://www.openmicroscopy.org/site/sup ... stallation

Please let us know how you get on!

All the best,

Kenny

[hippogriff]

That fixed something, thanks - icegridnode & other processes now running!

Code: Select all

C:\OMERO.server-5.2.2-ice35-b17\bin>omero admin diagnostics

================================================================================

OMERO Diagnostics 5.2.2-ice35-b17
================================================================================


Commands:   java -version                  1.8.0     (C:\ProgramData\Oracle\Java
\javapath\java.EXE)
Commands:   python -V                      2.7.9     (C:\Python27\python.EXE)
Commands:   icegridnode --version          3.5.1     (C:\Ice-3.5.1-b4-win-x64-Re
lease\bin\icegridnode.EXE)
Commands:   icegridadmin --version         3.5.1     (C:\Ice-3.5.1-b4-win-x64-Re
lease\bin\icegridadmin.EXE)
Commands:   psql --version                 9.5.1     (C:\PostgreSQL\9.5\bin\psql
.EXE)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 3816, enabled)
Server:     DropBox                        active (pid = 3980, enabled)
Server:     FileServer                     active (pid = 3324, enabled)
Server:     Indexer-0                      active (pid = 3176, enabled)
Server:     MonitorServer                  active (pid = 1064, enabled)
Server:     OMERO.Glacier2                 active (pid = 1892, enabled)
Server:     OMERO.IceStorm                 active (pid = 2324, enabled)
Server:     PixelData-0                    active (pid = 3268, enabled)
Server:     Processor-0                    active (pid = 2780, enabled)
Server:     Tables-0                       inactive (disabled)
Server:     TestDropBox                    inactive (enabled)
Server:     OMERO.master                   active (running as LocalSystem)

Log dir:    C:\OMERO.server-5.2.2-ice35-b17\var\log exists
Log files:  Blitz-0.log                    1.0 MB        errors=409  warnings=17

Log files:  DropBox.log                    26.0 KB       errors=32   warnings=16

Log files:  FileServer.log                 5.0 KB
Log files:  Indexer-0.log                  710.0 KB      errors=460  warnings=0

Log files:  MonitorServer.log              6.0 KB
Log files:  OMEROweb.log                   405.0 KB      errors=108  warnings=37

Log files:  OMEROweb_brokenrequest.log     0.0 KB
Log files:  PixelData-0.log                710.0 KB      errors=460  warnings=0

Log files:  Processor-0.log                1.0 MB        errors=913  warnings=45
2
Log files:  Processor-0.log.1              4.0 MB        errors=2829 warnings=14
14
Log files:  Processor-0.log.2              4.0 MB        errors=2824 warnings=14
12
Log files:  Tables-0.log                   n/a
Log files:  TestDropBox.log                n/a
Log files:  master.err                     0.0 KB
Log files:  master.out                     0.0 KB
Log files:  Total size                     15.03 MB


Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_USERDIR=(unset)
Environment:OMERO_TMPDIR=(unset)
Environment:PATH=C:\Python27;C:\ProgramData\Oracle\Java\javapath;C:\Windows\syst
em32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v
1.0\;C:\PostgreSQL\9.5\bin;C:\Ice-3.5.1-b4-win-x64-Release\bin;
Environment:PYTHONPATH=C:\Ice-3.5.1-b4-win-x64-Release\python
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? Tru
e
OMERO temp dir:'C:\Users\Administrator\AppData\Roaming\omero\tmp' Exists? True
Is writable? True   (Size: 0)

JVM settings: Blitz-${index}                -Xmx2657m -XX:MaxPermSize=1g -XX:+Ig
noreUnrecognizedVMOptions
JVM settings: Indexer-${index}              -Xmx1771m -XX:MaxPermSize=1g -XX:+Ig
noreUnrecognizedVMOptions
JVM settings: PixelData-${index}            -Xmx2657m -XX:MaxPermSize=1g -XX:+Ig
noreUnrecognizedVMOptions
JVM settings: Repository-${index}           -Xmx1771m -XX:MaxPermSize=1g -XX:+Ig
noreUnrecognizedVMOptions

OMERO.web status... DEVELOPMENT: You will have to kill processes by hand!
Django version: 1.8.11

However, logins not working...I can't login with the user credentials (they are correct)...Is my db screwed...or is it time for me to go home and try again tomorrow?

[kennethgillen]

That fixed something, thanks

You're welcome. It created the database, which OMERO needs to run.

However, logins not working...I can't login with the user credentials (they are correct)...Is my db screwed...or is it time for me to go home and try again tomorrow?

So just to be clear, the OMERO credentials are *different* to the username/password you're logging into the server operating system with. The OMERO accounts are -not- the same as the system accounts, unless you've set up ldap authentication.

So the database script you just ran created the OMERO administrative user. Can you please tell us the username you're trying to connect to OMERO with?

The password for the OMERO 'root' account, is one you just set when you ran the DB initialisation:

e.g. in the example in the documentation:

Code: Select all

C:\OMERO.server> bin\omero db script --password root_password

The OMERO admin user `root` has password `root_password`.

[hippogriff]

You're welcome. It created the database, which OMERO needs to run.

Well, I had done that once already and I'd made notes along the way, so not sure what happened to the first attempt.

I've not yet re-run the 'omero db script --password' command - I did switch user earlier in this thread though, so I will do so.

[kennethgillen]

I've not yet re-run the 'omero db script --password' command - I did switch user earlier in this thread though, so I will do so.

That command sets the password you'll need to log into OMERO.

Once you've created the script, and ran it against your OMERO database, the user account you'll need to log in will be the OMERO user 'root' and the password you set with that command.

[hippogriff]

I've re-run the script command.

I've then run the script against my db and got an error for every line - here are the last few lines:

Code: Select all

psql:C:/OMERO.server-5.2.2-ice35-b17/bin/OMERO5.2__0.sql:9119: ERROR:  current t
ransaction is aborted, commands ignored until end of transaction block
psql:C:/OMERO.server-5.2.2-ice35-b17/bin/OMERO5.2__0.sql:9120: ERROR:  current t
ransaction is aborted, commands ignored until end of transaction block
psql:C:/OMERO.server-5.2.2-ice35-b17/bin/OMERO5.2__0.sql:9121: ERROR:  current t
ransaction is aborted, commands ignored until end of transaction block
psql:C:/OMERO.server-5.2.2-ice35-b17/bin/OMERO5.2__0.sql:9122: ERROR:  current t
ransaction is aborted, commands ignored until end of transaction block
psql:C:/OMERO.server-5.2.2-ice35-b17/bin/OMERO5.2__0.sql:9129: ERROR:  current t
ransaction is aborted, commands ignored until end of transaction block
ROLLBACK


I've then tried logging in again with the same password in the '--password' command:

Code: Select all

C:\OMERO.server-5.2.2-ice35-b17\bin>omero login
Server: [localhost:4064]
Username: [Administrator]root
Password:
Password check failed for 'root': [id=0]
Password:
Password check failed for 'root': [id=0]
Password:
3 incorrect password attempts


...and for good measure...

Code: Select all

C:\OMERO.server-5.2.2-ice35-b17\bin>omero login
Server: [localhost:4064]
Username: [Administrator]
Password:
Password check failed for 'Administrator': []
Password:
Password check failed for 'Administrator': []
Password:
3 incorrect password attempts



I'm starting to think I'd be best leaving Windows behind and trying CentOS.

Kevin

[kennethgillen]

Hi Kevin,

I'm starting to think I'd be best leaving Windows behind and trying CentOS.

I'd seriously recommend it, if it's possible. We mentioned before, Windows support for OMERO server is about to be dropped.

That being said, if you do want to continue to work through your troubles here, we'd need more details, such as the full output of your psql script run, not just the last few lines, to try and work out why it failed.

As well as some details about the ownership of the databases, and the content again.

Similar SQL to the following thread: viewtopic.php?f=5&t=8030 to show database ownership etc.

Please reply if you would like more specifics about the SQL to run to show database ownership etc if you do want to continue trying to debug this installation.

All the best,

Kenny