Open Microscopy Environment

I'm installing OMERO server on Windows and am having some problems.

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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)

When I use 'omero admin start', the icegridnode server does not start, but after using 'omero admin startasync' it does.

During the first few mins, Blitz-0 & DropBox both report the following:

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Server:     icegridnode                    running
Server:     Blitz-0                        activating (enabled)
Server:     DropBox                        activating (enabled)
Server:     FileServer                     active (pid = 2540, enabled)
Server:     Indexer-0                      activating (enabled)
Server:     MonitorServer                  active (pid = 2956, enabled)
Server:     OMERO.Glacier2                 active (pid = 3196, enabled)
Server:     OMERO.IceStorm                 active (pid = 2588, enabled)
Server:     PixelData-0                    activating (enabled)
Server:     Processor-0                    activating (enabled)
Server:     Tables-0                       inactive (disabled)
Server:     TestDropBox                    inactive (enabled)
Server:     OMERO.master                   active (running as LocalSystem)


...but shortly afterwards report this:

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Server:     icegridnode                    running
Server:     Blitz-0                        inactive (disabled)
Server:     DropBox                        inactive (disabled)
Server:     FileServer                     active (pid = 2540, enabled)
Server:     Indexer-0                      inactive (disabled)
Server:     MonitorServer                  active (pid = 2956, enabled)
Server:     OMERO.Glacier2                 active (pid = 3196, enabled)
Server:     OMERO.IceStorm                 active (pid = 2588, enabled)
Server:     PixelData-0                    inactive (disabled)
Server:     Processor-0                    activating (enabled)
Server:     Tables-0                       inactive (disabled)
Server:     TestDropBox                    inactive (enabled)
Server:     OMERO.master                   active (running as LocalSystem)

I also get this:

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C:\OMERO.server-5.2.2-ice35-b17\var\log>.\..\..\bin\omero login
Server: [localhost:4064]
Username: [Administrator]
Password:
internal server error

Where should I look please?

Kevin

Was a var\log\Blitz-0.log file produced? Could you paste the entire diagnostics output and optimally attach a zip of the logs files if available?

Cheers,
~Josh

P.S. so that there are no surprises for you down the road, please also read http://blog.openmicroscopy.org/tech-issues/future-plans/deployment/2016/03/22/windows-support/.

The Blitz log shows activiry at startup, but then stops. Here's an extract of the Blitz log. I don't have a database table dbpatch...not sure why I'd need one...but perhaps that fact that nothing is written to the log after startup is more telling:

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********************************************************************************
*******
Error connecting to database table dbpatch. You may need to bootstrap.
See http://www.openmicroscopy.org/site/support/omero5.2/sysadmins/server-upgrade
.html
********************************************************************************
*******

        at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:1
41) ~[spring-beans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.SimpleInstantiationStrategy
.instantiate(SimpleInstantiationStrategy.java:107) ~[spring-beans.jar:3.0.1.RELE
ASE]
        at org.springframework.beans.factory.support.ConstructorResolver.autowir
eConstructor(ConstructorResolver.java:273) ~[spring-beans.jar:3.0.1.RELEASE]
        ... 25 common frames omitted
Caused by: org.springframework.beans.factory.BeanCreationException: Error creati
ng bean with name 'currentDetails' defined in class path resource [ome/services/
sec-primitives.xml]: Cannot resolve reference to bean 'roles' while setting cons
tructor argument; nested exception is org.springframework.beans.factory.BeanCrea
tionException: Error creating bean with name 'dbPatchCheck' defined in class pat
h resource [ome/services/startup.xml]: Invocation of init method failed; nested
exception is ome.conditions.InternalException:
********************************************************************************
*******
Error connecting to database table dbpatch. You may need to bootstrap.
See http://www.openmicroscopy.org/site/support/omero5.2/sysadmins/server-upgrade
.html
********************************************************************************
*******

        at org.springframework.beans.factory.support.BeanDefinitionValueResolver
.resolveReference(BeanDefinitionValueResolver.java:328) ~[spring-beans.jar:3.0.1
.RELEASE]
        at org.springframework.beans.factory.support.BeanDefinitionValueResolver
.resolveValueIfNecessary(BeanDefinitionValueResolver.java:106) ~[spring-beans.ja
r:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.ConstructorResolver.resolve
ConstructorArguments(ConstructorResolver.java:600) ~[spring-beans.jar:3.0.1.RELE
ASE]
        at org.springframework.beans.factory.support.ConstructorResolver.autowir
eConstructor(ConstructorResolver.java:140) ~[spring-beans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBean
Factory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:984) ~[sprin
g-beans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBean
Factory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:888) ~[spring
-beans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBean
Factory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479) ~[spring-beans
.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBean
Factory.createBean(AbstractAutowireCapableBeanFactory.java:450) ~[spring-beans.j
ar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getOb
ject(AbstractBeanFactory.java:290) ~[spring-beans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistr
y.getSingleton(DefaultSingletonBeanRegistry.java:222) ~[spring-beans.jar:3.0.1.R
ELEASE]
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBe
an(AbstractBeanFactory.java:287) ~[spring-beans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean
(AbstractBeanFactory.java:189) ~[spring-beans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.
preInstantiateSingletons(DefaultListableBeanFactory.java:562) ~[spring-beans.jar
:3.0.1.RELEASE]
        at org.springframework.context.support.AbstractApplicationContext.finish
BeanFactoryInitialization(AbstractApplicationContext.java:871) ~[spring-context.
jar:3.0.1.RELEASE]
        at org.springframework.context.support.AbstractApplicationContext.refres
h(AbstractApplicationContext.java:423) ~[spring-context.jar:3.0.1.RELEASE]
        at org.springframework.context.support.ClassPathXmlApplicationContext.<i
nit>(ClassPathXmlApplicationContext.java:139) ~[spring-context.jar:3.0.1.RELEASE
]
        at org.springframework.context.support.ClassPathXmlApplicationContext.<i
nit>(ClassPathXmlApplicationContext.java:105) ~[spring-context.jar:3.0.1.RELEASE
]
        at ome.system.OmeroContext.<init>(OmeroContext.java:97) ~[common.jar:na]
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
~[na:1.8.0_77]
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
~[na:1.8.0_77]
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Sou
rce) ~[na:1.8.0_77]
        at java.lang.reflect.Constructor.newInstance(Unknown Source) ~[na:1.8.0_
77]
        at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:1
26) ~[spring-beans.jar:3.0.1.RELEASE]
        ... 27 common frames omitted
Caused by: org.springframework.beans.factory.BeanCreationException: Error creati
ng bean with name 'dbPatchCheck' defined in class path resource [ome/services/st
artup.xml]: Invocation of init method failed; nested exception is ome.conditions
.InternalException:
********************************************************************************
*******
Error connecting to database table dbpatch. You may need to bootstrap.
See http://www.openmicroscopy.org/site/support/omero5.2/sysadmins/server-upgrade
.html
********************************************************************************
*******

        at org.springframework.beans.factory.support.AbstractAutowireCapableBean
Factory.initializeBean(AbstractAutowireCapableBeanFactory.java:1403) ~[spring-be
ans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBean
Factory.doCreateBean(AbstractAutowireCapableBeanFactory.java:513) ~[spring-beans
.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBean
Factory.createBean(AbstractAutowireCapableBeanFactory.java:450) ~[spring-beans.j
ar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getOb
ject(AbstractBeanFactory.java:290) ~[spring-beans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistr
y.getSingleton(DefaultSingletonBeanRegistry.java:222) ~[spring-beans.jar:3.0.1.R
ELEASE]
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBe
an(AbstractBeanFactory.java:287) ~[spring-beans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean
(AbstractBeanFactory.java:189) ~[spring-beans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBe
an(AbstractBeanFactory.java:280) ~[spring-beans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean
(AbstractBeanFactory.java:189) ~[spring-beans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.ConstructorResolver.instant
iateUsingFactoryMethod(ConstructorResolver.java:344) ~[spring-beans.jar:3.0.1.RE
LEASE]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBean
Factory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:96
4) ~[spring-beans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBean
Factory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:870) ~[spring
-beans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBean
Factory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479) ~[spring-beans
.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBean
Factory.createBean(AbstractAutowireCapableBeanFactory.java:450) ~[spring-beans.j
ar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getOb
ject(AbstractBeanFactory.java:290) ~[spring-beans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistr
y.getSingleton(DefaultSingletonBeanRegistry.java:222) ~[spring-beans.jar:3.0.1.R
ELEASE]
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBe
an(AbstractBeanFactory.java:287) ~[spring-beans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean
(AbstractBeanFactory.java:189) ~[spring-beans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.BeanDefinitionValueResolver
.resolveReference(BeanDefinitionValueResolver.java:322) ~[spring-beans.jar:3.0.1
.RELEASE]
        ... 49 common frames omitted
Caused by: ome.conditions.InternalException:
********************************************************************************
*******
Error connecting to database table dbpatch. You may need to bootstrap.
See http://www.openmicroscopy.org/site/support/omero5.2/sysadmins/server-upgrade
.html
********************************************************************************
*******

        at ome.services.util.DBPatchCheck.start(DBPatchCheck.java:60) ~[server.j
ar:na]
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.
0_77]
        at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) ~[na:1.8.
0_77]
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) ~[na:
1.8.0_77]
        at java.lang.reflect.Method.invoke(Unknown Source) ~[na:1.8.0_77]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBean
Factory.invokeCustomInitMethod(AbstractAutowireCapableBeanFactory.java:1527) ~[s
pring-beans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBean
Factory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1468) ~[spring
-beans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBean
Factory.initializeBean(AbstractAutowireCapableBeanFactory.java:1400) ~[spring-be
ans.jar:3.0.1.RELEASE]
        ... 67 common frames omitted

Here's the diag:

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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                        inactive (disabled)
Server:     DropBox                        inactive (disabled)
Server:     FileServer                     active (pid = 1996, enabled)
Server:     Indexer-0                      inactive (disabled)
Server:     MonitorServer                  active (pid = 2028, enabled)
Server:     OMERO.Glacier2                 active (pid = 1204, enabled)
Server:     OMERO.IceStorm                 active (pid = 1296, enabled)
Server:     PixelData-0                    inactive (disabled)
Server:     Processor-0                    activating (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                    659.0 KB      errors=332  warnings=0

Log files:  DropBox.log                    20.0 KB       errors=26   warnings=13

Log files:  FileServer.log                 4.0 KB
Log files:  Indexer-0.log                  661.0 KB      errors=430  warnings=0

Log files:  MonitorServer.log              4.0 KB
Log files:  OMEROweb.log                   226.0 KB      errors=96   warnings=29

Log files:  OMEROweb_brokenrequest.log     0.0 KB
Log files:  PixelData-0.log                661.0 KB      errors=430  warnings=0

Log files:  Processor-0.log                3.0 MB        errors=2081 warnings=10
39
Log files:  Processor-0.log.1              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                     10.92 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


If this doesn't give enough clues I'll gladly upload the rest of the logs (the only active one is Processor). I'm concerned there isn't much in the way of log activity and commands such as 'pg_ctl status' and 'omero admin status' don't do much:

Code: Select all

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

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

Code: Select all

C:\PostgreSQL\9.5\bin>pg_ctl status

C:\PostgreSQL\9.5\bin>

Here's the list of log files showing where the activity is - service startup here was at 14:02:

Code: Select all

C:\OMERO.server-5.2.2-ice35-b17\var\log>dir /o:d
Volume in drive C has no label.
Volume Serial Number is 8A3C-03D6

Directory of C:\OMERO.server-5.2.2-ice35-b17\var\log

22/03/2016  17:59                 0 master.err
22/03/2016  17:59                 0 master.out
24/03/2016  12:46                 0 OMEROweb_brokenrequest.log
13/04/2016  20:43         4,999,862 Processor-0.log.1
13/04/2016  20:44    <DIR>          ..
13/04/2016  20:44    <DIR>          .
14/04/2016  14:02             4,243 FileServer.log
14/04/2016  14:02             4,318 MonitorServer.log
14/04/2016  14:02           659,561 Blitz-0.log
14/04/2016  14:02           661,816 PixelData-0.log
14/04/2016  14:02           661,660 Indexer-0.log
14/04/2016  14:02            20,176 DropBox.log
14/04/2016  17:05           226,881 OMEROweb.log
14/04/2016  17:24         3,682,772 Processor-0.log
              12 File(s)     10,921,289 bytes
               2 Dir(s)  69,836,877,824 bytes free

hippogriff wrote:...Here's an extract of the Blitz log. I don't have a database table dbpatch...not sure why I'd need one...

You'll definitely need to have all the database tables present and accessible for the OMERO server to start correctly.

...

If this doesn't give enough clues I'll gladly upload the rest of the logs (the only active one is Processor). I'm concerned there isn't much in the way of log activity and commands such as 'pg_ctl status' and 'omero admin status' don't do much

Shouldn't be necessary to upload anything else yet. Until OMERO has access to a full DB, we're stuck.

Interpolating in your configuration parameters from `bin\omero config get`, does the following work for you?

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psql -h ${omero.db.host} -U ${omero.db.user} ${omero.db.name} -l


from the machine that the OMERO server is running on?

Cheers,
~Josh.

Thanks Josh...Here's the result:

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


Hi Hippogriff,

the owner of the DB is "postgres". This is likely the root of your problem if you are connecting to the DB as the user "omero".

Cheers,
~Josh.

Thanks for spotting that...I've set omero to use the postgres user which owns the 'omero' db, and shut things down and rebooted server.

Here's the db connection output:

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C:\OMERO.server-5.2.2-ice35-b17\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)


I've got a different error...icegridnode fails to start:

Code: Select all

C:\OMERO.server-5.2.2-ice35-b17\bin>omero admin start
Found default value: c:\omero_dist\var\master
Attempting to correct...
Converting from c:\omero_dist to C:\OMERO.server-5.2.2-ice35-b17
Changes made: 6
No descriptor given. Using etc\grid\windefault.xml
Installing OMERO.master Windows service.
Successfully installed OMERO.master Windows service.
Starting OMERO.master Windows service.
Waiting on startup. Use CTRL-C to exit
.............................
Failed to startup some components after 300 seconds
Calling "stop" on remaining components
OMERO.master service deleted.
Waiting on shutdown. Use CTRL-C to exit
......
C:\OMERO.server-5.2.2-ice35-b17\bin>


Here are the diags:

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                    not started

Log dir:    C:\OMERO.server-5.2.2-ice35-b17\var\log exists
Log files:  Blitz-0.log                    730.0 KB      errors=372  warnings=0

Log files:  DropBox.log                    23.0 KB       errors=30   warnings=15

Log files:  FileServer.log                 5.0 KB
Log files:  Indexer-0.log                  692.0 KB      errors=450  warnings=0

Log files:  MonitorServer.log              5.0 KB
Log files:  OMEROweb.log                   333.0 KB      errors=106  warnings=35

Log files:  OMEROweb_brokenrequest.log     0.0 KB
Log files:  PixelData-0.log                692.0 KB      errors=450  warnings=0

Log files:  Processor-0.log                1.0 MB        errors=888  warnings=44
3
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                     14.05 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)

Cannot list deployed applications.
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


If you have any suggestions, I'd be very grateful.

Code: Select all

Log files:  Blitz-0.log                    730.0 KB      errors=372  warnings=0


Knowing the latest error from the Blitz-0.log file would be helpful. You can also zip the file and upload it if you'd rather.

All the best,
~Josh

Here is the last x lines of the Blitz log - there are repeating messages. If this isn't sufficient info, let me know and I'll zip upload the whole thing:

Code: Select all

Caused by: org.springframework.beans.factory.BeanCreationException: Error creati
ng bean with name 'dbPatchCheck' defined in class path resource [ome/services/st
artup.xml]: Invocation of init method failed; nested exception is ome.conditions
.InternalException:
********************************************************************************
*******
Error connecting to database table dbpatch. You may need to bootstrap.
See http://www.openmicroscopy.org/site/support/omero5.2/sysadmins/server-upgrade
.html
********************************************************************************
*******

        at org.springframework.beans.factory.support.AbstractAutowireCapableBean
Factory.initializeBean(AbstractAutowireCapableBeanFactory.java:1403) ~[spring-be
ans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBean
Factory.doCreateBean(AbstractAutowireCapableBeanFactory.java:513) ~[spring-beans
.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBean
Factory.createBean(AbstractAutowireCapableBeanFactory.java:450) ~[spring-beans.j
ar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getOb
ject(AbstractBeanFactory.java:290) ~[spring-beans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistr
y.getSingleton(DefaultSingletonBeanRegistry.java:222) ~[spring-beans.jar:3.0.1.R
ELEASE]
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBe
an(AbstractBeanFactory.java:287) ~[spring-beans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean
(AbstractBeanFactory.java:189) ~[spring-beans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBe
an(AbstractBeanFactory.java:280) ~[spring-beans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean
(AbstractBeanFactory.java:189) ~[spring-beans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.ConstructorResolver.instant
iateUsingFactoryMethod(ConstructorResolver.java:344) ~[spring-beans.jar:3.0.1.RE
LEASE]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBean
Factory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:96
4) ~[spring-beans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBean
Factory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:870) ~[spring
-beans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBean
Factory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479) ~[spring-beans
.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBean
Factory.createBean(AbstractAutowireCapableBeanFactory.java:450) ~[spring-beans.j
ar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getOb
ject(AbstractBeanFactory.java:290) ~[spring-beans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistr
y.getSingleton(DefaultSingletonBeanRegistry.java:222) ~[spring-beans.jar:3.0.1.R
ELEASE]
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBe
an(AbstractBeanFactory.java:287) ~[spring-beans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean
(AbstractBeanFactory.java:189) ~[spring-beans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.BeanDefinitionValueResolver
.resolveReference(BeanDefinitionValueResolver.java:322) ~[spring-beans.jar:3.0.1
.RELEASE]
        ... 49 common frames omitted
Caused by: ome.conditions.InternalException:
********************************************************************************
*******
Error connecting to database table dbpatch. You may need to bootstrap.
See http://www.openmicroscopy.org/site/support/omero5.2/sysadmins/server-upgrade
.html
********************************************************************************
*******

        at ome.services.util.DBPatchCheck.start(DBPatchCheck.java:60) ~[server.j
ar:na]
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.
0_77]
        at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) ~[na:1.8.
0_77]
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) ~[na:
1.8.0_77]
        at java.lang.reflect.Method.invoke(Unknown Source) ~[na:1.8.0_77]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBean
Factory.invokeCustomInitMethod(AbstractAutowireCapableBeanFactory.java:1527) ~[s
pring-beans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBean
Factory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1468) ~[spring
-beans.jar:3.0.1.RELEASE]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBean
Factory.initializeBean(AbstractAutowireCapableBeanFactory.java:1400) ~[spring-be
ans.jar:3.0.1.RELEASE]
        ... 67 common frames omitted

This still seems to say that the database initialization has gone amiss. Could you give us the output of running "\d" in the psql console?

Cheers,
~Josh.