Open Microscopy Environment

I am using Windows 2008 server (64-bit), Java 1.7.0_21, Python 2.6 and Ice 3.4.2. I have successfully installed Omero.server (4.4.8). I access the server via http://10.100.52.14:4080/webstart/ or http://ustor:4080/webstart. But on clicking OMERO.insight, following error appears:

Unable to launch the application.
Name: OMERO.insight
Publisher: The Openmicroscopy Environment
From: http://10.100.52.14:4080/webstart/jars/insight.jnlp

Following information is displayed on clicking details:
Error: Unable to load resource: http://10.100.52.14:4080/static/webstar ... nsight.jar

Launch File

<jnlp codebase="http://10.100.52.14:4080/static/webstart/jars/" href="http://10.100.52.14:4080/webstart/jars/insight.jnlp">
<information>
<title>OMERO.insight</title>
<vendor>The Open Microscopy Environment</vendor>
<homepage href="http://www.openmicroscopy.org"/>
<icon href="/static/webstart/img/icon-omero-insight.png"/>
<shortcut online="false">
<desktop/>
</shortcut>
<offline-allowed/>
</information>
<security>
<all-permissions/>
</security>
<resources>
<j2se version="1.5+" max-heap-size="1024m"/>
<jar href="omero.insight.jar"/>
<jar href="ai_path.jar"/>
<jar href="axis.jar"/>
<jar href="backport-util-concurrent.jar"/>
<jar href="bio-formats.jar"/>
<jar href="blitz.jar"/>
<jar href="bufr.jar"/>
<jar href="common.jar"/>
<jar href="commons-codec.jar"/>
<jar href="commons-collections.jar"/>
<jar href="commons-digester.jar"/>
<jar href="commons-discovery.jar"/>
<jar href="commons-httpclient.jar"/>
<jar href="commons-io.jar"/>
<jar href="commons-lang.jar"/>
<jar href="commons-logging.jar"/>
<jar href="commons-validator.jar"/>
<jar href="ehcache.jar"/>
<jar href="gicentreUtils.jar"/>
<jar href="gluegen-rt.jar"/>
<jar href="grib.jar"/>
<jar href="guava-jdk5.jar"/>
<jar href="hibernate-jpa-2.0-api.jar"/>
<jar href="ice.jar"/>
<jar href="ij.jar"/>
<jar href="ini4j.jar"/>
<jar href="jai_imageio.jar"/>
<jar href="java-getopt.jar"/>
<jar href="java-image-scaling.jar"/>
<jar href="jaxrpc.jar"/>
<jar href="jcommon.jar"/>
<jar href="jfreechart.jar"/>
<jar href="JHotDraw.jar"/>
<jar href="jna.jar"/>
<jar href="jogl.jar"/>
<jar href="loci-common.jar"/>
<jar href="log4j.jar"/>
<jar href="mdbtools-java.jar"/>
<jar href="metakit.jar"/>
<jar href="model-psql.jar"/>
<jar href="netcdf.jar"/>
<jar href="ols-client.jar"/>
<jar href="ome-io.jar"/>
<jar href="ome-java.jar"/>
<jar href="ome-xml.jar"/>
<jar href="physics.jar"/>
<jar href="platform.jar"/>
<jar href="poi-loci.jar"/>
<jar href="poi.jar"/>
<jar href="processing-controlP5.jar"/>
<jar href="processing-core.jar"/>
<jar href="saaj.jar"/>
<jar href="scifio.jar"/>
<jar href="serializer.jar"/>
<jar href="slf4j-api.jar"/>
<jar href="slf4j-log4j12.jar"/>
<jar href="specification.jar"/>
<jar href="swingx.jar"/>
<jar href="TableLayout.jar"/>
<jar href="wsdl4j.jar"/>
<jar href="nanoxml.jar"/>
<jar href="xalan.jar"/>
<property name="jnlp.omero.host" value="localhost"/>
<property name="jnlp.omero.port" value="4064"/>
</resources>
<application-desc main-class="org.openmicroscopy.shoola.Main"/>
</jnlp>


Exception

com.sun.deploy.net.FailedDownloadException: Unable to load resource: http://10.100.52.14:4080/static/webstar ... nsight.jar
at com.sun.deploy.net.DownloadEngine.actionDownload(Unknown Source)
at com.sun.deploy.net.DownloadEngine.downloadResource(Unknown Source)
at com.sun.deploy.cache.ResourceProviderImpl.getResource(Unknown Source)
at com.sun.deploy.cache.ResourceProviderImpl.getResource(Unknown Source)
at com.sun.javaws.LaunchDownload$DownloadTask.call(Unknown Source)
at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)


Wrapped Exception

java.io.FileNotFoundException: http://10.100.52.14:4080/static/webstar ... nsight.jar
at sun.reflect.GeneratedConstructorAccessor1.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
at java.lang.reflect.Constructor.newInstance(Unknown Source)
at sun.net.www.protocol.http.HttpURLConnection$6.run(Unknown Source)
at sun.net.www.protocol.http.HttpURLConnection$6.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at sun.net.www.protocol.http.HttpURLConnection.getChainedException(Unknown Source)
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
at com.sun.deploy.net.BasicHttpRequest.doRequest(Unknown Source)
at com.sun.deploy.net.BasicHttpRequest.doGetRequestEX(Unknown Source)
at com.sun.deploy.net.DownloadEngine.actionDownload(Unknown Source)
at com.sun.deploy.net.DownloadEngine.downloadResource(Unknown Source)
at com.sun.deploy.cache.ResourceProviderImpl.getResource(Unknown Source)
at com.sun.deploy.cache.ResourceProviderImpl.getResource(Unknown Source)
at com.sun.javaws.LaunchDownload$DownloadTask.call(Unknown Source)
at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
Caused by: java.io.FileNotFoundException: http://10.100.52.14:4080/static/webstar ... nsight.jar
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
at java.net.HttpURLConnection.getResponseCode(Unknown Source)
... 12 more

The contents of jnlp file are as follows:
<?xml version="1.0" encoding="utf-8"?>
<jnlp codebase="http://10.100.52.14:4080/static/webstart/jars/" href="http://10.100.52.14:4080/webstart/jars/insight.jnlp">
<information>
<title>OMERO.insight</title>
<vendor>The Open Microscopy Environment</vendor>
<homepage href="http://www.openmicroscopy.org"/>
<icon href="/static/webstart/img/icon-omero-insight.png"/>
<shortcut online="false">
<desktop/>
</shortcut>
<offline-allowed/>
</information>
<security>
<all-permissions/>
</security>
<resources>
<j2se version="1.5+" max-heap-size="1024m"/>
<jar href="omero.insight.jar"/>
<jar href="ai_path.jar"/>
<jar href="axis.jar"/>
<jar href="backport-util-concurrent.jar"/>
<jar href="bio-formats.jar"/>
<jar href="blitz.jar"/>
<jar href="bufr.jar"/>
<jar href="common.jar"/>
<jar href="commons-codec.jar"/>
<jar href="commons-collections.jar"/>
<jar href="commons-digester.jar"/>
<jar href="commons-discovery.jar"/>
<jar href="commons-httpclient.jar"/>
<jar href="commons-io.jar"/>
<jar href="commons-lang.jar"/>
<jar href="commons-logging.jar"/>
<jar href="commons-validator.jar"/>
<jar href="ehcache.jar"/>
<jar href="gicentreUtils.jar"/>
<jar href="gluegen-rt.jar"/>
<jar href="grib.jar"/>
<jar href="guava-jdk5.jar"/>
<jar href="hibernate-jpa-2.0-api.jar"/>
<jar href="ice.jar"/>
<jar href="ij.jar"/>
<jar href="ini4j.jar"/>
<jar href="jai_imageio.jar"/>
<jar href="java-getopt.jar"/>
<jar href="java-image-scaling.jar"/>
<jar href="jaxrpc.jar"/>
<jar href="jcommon.jar"/>
<jar href="jfreechart.jar"/>
<jar href="JHotDraw.jar"/>
<jar href="jna.jar"/>
<jar href="jogl.jar"/>
<jar href="loci-common.jar"/>
<jar href="log4j.jar"/>
<jar href="mdbtools-java.jar"/>
<jar href="metakit.jar"/>
<jar href="model-psql.jar"/>
<jar href="netcdf.jar"/>
<jar href="ols-client.jar"/>
<jar href="ome-io.jar"/>
<jar href="ome-java.jar"/>
<jar href="ome-xml.jar"/>
<jar href="physics.jar"/>
<jar href="platform.jar"/>
<jar href="poi-loci.jar"/>
<jar href="poi.jar"/>
<jar href="processing-controlP5.jar"/>
<jar href="processing-core.jar"/>
<jar href="saaj.jar"/>
<jar href="scifio.jar"/>
<jar href="serializer.jar"/>
<jar href="slf4j-api.jar"/>
<jar href="slf4j-log4j12.jar"/>
<jar href="specification.jar"/>
<jar href="swingx.jar"/>
<jar href="TableLayout.jar"/>
<jar href="wsdl4j.jar"/>
<jar href="nanoxml.jar"/>
<jar href="xalan.jar"/>
<property name="jnlp.omero.host" value="localhost"/>
<property name="jnlp.omero.port" value="4064"/>
</resources>
<application-desc main-class="org.openmicroscopy.shoola.Main"/>
</jnlp>


Please help me.

Hi,

I am trying to reproduce the issue you have. In the meantime could you send us log files from C:\OMERO.server\var\log as well as output of bin\omero admin diagnostics please?

Ola

Thanks for the reply. I am unable to attach the log file. How do I send it over to you? Meanwhile I am appending the diagnostics for your reference.


C:\OMERO.server\bin>omero admin diagnostics

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

OMERO Diagnostics 4.4.8-ice34-b256
================================================================================


Commands: java -version 1.7.0 (C:\Program Files\Java\jdk1
.7.0_21\bin\java.EXE)
Commands: python -V 2.6.6 (c:\Python26\python.EXE)
Commands: icegridnode --version 3.4.2 (c:\ZeroC\Ice-3.4.2\bin\x64
\icegridnode.EXE -- 2 others)
Commands: icegridadmin --version 3.4.2 (c:\ZeroC\Ice-3.4.2\bin\x64
\icegridadmin.EXE -- 2 others)
Commands: psql --version not found

Server: icegridnode running
Server: Blitz-0 active (pid = 5636, enabled)
Server: DropBox inactive (disabled)
Server: FileServer active (pid = 2004, enabled)
Server: Indexer-0 active (pid = 6088, enabled)
Server: MonitorServer inactive (disabled)
Server: OMERO.Glacier2 active (pid = 2552, enabled)
Server: OMERO.IceStorm active (pid = 4808, enabled)
Server: PixelData-0 active (pid = 5504, enabled)
Server: Processor-0 active (pid = 5060, enabled)
Server: Tables-0 inactive (disabled)
Server: TestDropBox inactive (enabled)
Server: OMERO.master active (running as LocalSystem)

OMERO: SSL port 4064
OMERO: TCP port 4063

Log dir: C:\OMERO.server\var\log exists

Log files: Blitz-0.log 53.0 MB errors=1 warnings=16

Log files: DropBox.log 0.0 KB errors=2 warnings=0

Log files: FileServer.log 0.0 KB
Log files: Indexer-0.log 4.0 MB errors=1 warnings=49

Log files: MonitorServer.log 0.0 KB errors=1 warnings=0

Log files: OMEROweb.log 2.0 MB
Log files: OMEROweb_request.log 0.0 KB errors=0 warnings=2

Log files: PixelData-0.log 1.0 KB
Log files: Processor-0.log 32.0 KB
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 60.19 MB

Parsing Blitz-0.log:[line:30] => Server restarted <=

Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:PATH=C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;c:\php;
C:\Windows\System32\WindowsPowerShell\v1.0\;c:\Python26;c:\ZeroC\Ice-3.4.2\bin\x
64;c:\zeroc\ice-3.4.2\bin;C:\Program Files (x86)\Microsoft SQL Server\100\Tools\
Binn\;C:\Program Files (x86)\Microsoft SQL Server\100\DTS\Binn\;C:\Program Files
\Java\jdk1.7.0_21\bin
Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)

OMERO data dir: '/OMERO' Exists? True Is writable? True
OMERO.web status... DEVELOPMENT: You will have to check status by hand!

C:\OMERO.server\bin>

Thank you for a quick response. Right, I think the problem is related to the fact that you are running OMERO.web on the build-in development web server that is not set up to server static content as production server (IIS). Jars are not a part of the static file management path. It is true that limitation is not a part of our documentation.

However, if you still want to continue testing with development server you can copy those jars by hand.
Jars are stored now in

Code: Select all

C:\OMERO.server\lib\python\omeroweb\static\webstart\jars\*.*

and they need to go to

Code: Select all

C:\OMERO.server\lib\python\omeroweb\webstart\static\webstart\jars\*.*

But in general you have no choice but to set up your Django/OMERO.web environment properly with IIS, please check Omero.web deployment documentation.

Ola

Thanks for the prompt response. By copying the files, the application works. I am using Apache web server with FastCGI enabled. Do I necessarily have to use IIS? The server has been configured using Apache a couple of applications are running on it. Will there be any issue if IIS is also configured on it?

Thanks a lot once again.

Hi,

Right, we have never tested the following documentation as compiling mod_fastcgi with Visual Studio wasn't really trivial. OMERO.web requires Flup that doesn't work on Windows, see Windows support of FastCGI feature.

Ola

I am again installing OMERO 4.4.8 but this time on IIS7. I am using 32-bit version of Python, Java, PostgreSQL on Windows Server 2008 (64-bit). The moment I issue the command
C:\OMERO.server\bin>omero admin diagnostics
the following error is displayed:
++++++++++++++++++++++++++++++++++++++++++++++++
C:\OMERO.server\bin>omero admin diagnostics
********************************************************************************

ERROR: Could not import omero.cli! (DLL load failed: %1 is not a valid W
in32 application.)

This means that your installation is incomplete. Contact
the OME mailing lists for more information:

http://www.openmicroscopy.org/site/community

If you are building from source, please supply the build log
as well as which version you are building from. If you
downloaded a distribution, please provide which link you
used.

********************************************************************************


Debugging Info:
--------------
CWD=C:\OMERO.server\bin
VERSION=2.6 (r26:66721, Oct 2 2008, 11:35:03) [MSC v.1500 32 bit (Intel
)]
OMERO_HOME=None
PYTHONPATH=['C:\\OMERO.server\\lib\\python', 'C:\\OMERO.server\\var\\lib
', 'C:\\OMERO.server\\bin', 'C:\\OMERO.server\\lib\\python', 'C:\\ZeroC\\Ice-3.4
.2\\python\\x64', 'C:\\ZeroC\\Ice-3.4.2\\python', 'C:\\Python26\\python26.zip',
'C:\\Python26\\DLLs', 'C:\\Python26\\lib', 'C:\\Python26\\lib\\plat-win', 'C:\\P
ython26\\lib\\lib-tk', 'C:\\Python26', 'C:\\Python26\\lib\\site-packages', 'C:\\
Python26\\lib\\site-packages\\PIL', 'C:\\Python26\\lib\\site-packages\\win32', '
C:\\Python26\\lib\\site-packages\\win32\\lib', 'C:\\Python26\\lib\\site-packages
\\Pythonwin', 'C:\\OMERO.server\\lib\\fallback']

++++++++++++++++++++++++++++++++++++++++++++++++

I have even preferred the x64 directories over the other directories. The output of path and pythonpath are as follows:

C:\OMERO.server\bin>echo %path%
C:\Python26;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;c:\php;C:\Wi
ndows\System32\WindowsPowerShell\v1.0\;C:\Program Files (x86)\Microsoft SQL Serv
er\100\Tools\Binn\;C:\Program Files (x86)\Microsoft SQL Server\100\DTS\Binn\;C:\
Program Files (x86)\Java\jdk1.7.0_21\bin;C:\ZeroC\Ice-3.4.2\bin\x64;C:\ZeroC\Ice
-3.4.2\bin

C:\OMERO.server\bin>echo %pythonpath%
C:\OMERO.server\lib\python;C:\ZeroC\Ice-3.4.2\python\x64;C:\ZeroC\Ice-3.4.2\pyth
on

Please suggest where had I gone wrong.

Anand wrote:I am again installing OMERO 4.4.8 but this time on IIS7. I am using 32-bit version of Python, Java, PostgreSQL on Windows Server 2008 (64-bit).
...
ERROR: Could not import omero.cli! (DLL load failed: %1 is not a valid W
in32 application.)
...
PYTHONPATH=[... 'C:\\ZeroC\\Ice-3.4
.2\\python\\x64', 'C:\\ZeroC\\Ice-3.4.2\\python',
...

All of the various libraries on your PATH will need to match in their versions. Could you try removing `python\\x64` from your PATH system environment? After a reboot, I would think that the diagnostics command you succeed.

Cheers,
~Josh.

Josh,

Thanks for the reply. After removing python\x64, unfortunately it did not work. The error is as follows:
* * * * * * * * *
C:\OMERO.server\bin>omero admin diagnostics
Error loading: C:\OMERO.server\lib\python\omero\plugins\admin.py
Traceback (most recent call last):
File "C:\OMERO.server\lib\python\omero\cli.py", line 1139, in loadpath
execfile( str(pathobj), loc )
File "C:\OMERO.server\lib\python\omero\plugins\admin.py", line 22, in <module>

import portalocker
File "C:\OMERO.server\lib\python\portalocker.py", line 72, in <module>
import win32file
ImportError: DLL load failed: The specified module could not be found.
Error loading: C:\OMERO.server\lib\python\omero\plugins\node.py
Traceback (most recent call last):
File "C:\OMERO.server\lib\python\omero\cli.py", line 1139, in loadpath
execfile( str(pathobj), loc )
File "C:\OMERO.server\lib\python\omero\plugins\node.py", line 18, in <module>
from omero.plugins.admin import AdminControl
File "C:\OMERO.server\lib\python\omero\plugins\admin.py", line 22, in <module>

import portalocker
File "C:\OMERO.server\lib\python\portalocker.py", line 72, in <module>
import win32file
ImportError: DLL load failed: The specified module could not be found.
Error loading: C:\OMERO.server\lib\python\omero\plugins\perf.py
Traceback (most recent call last):
File "C:\OMERO.server\lib\python\omero\cli.py", line 1139, in loadpath
execfile( str(pathobj), loc )
File "C:\OMERO.server\lib\python\omero\plugins\perf.py", line 18, in <module>
import omero.install.perf_test as perf_test
File "C:\OMERO.server\lib\python\omero\install\perf_test.py", line 23, in <mod
ule>
import omero.util.temp_files
File "C:\OMERO.server\lib\python\omero\util\temp_files.py", line 19, in <modul
e>
import portalocker
File "C:\OMERO.server\lib\python\portalocker.py", line 72, in <module>
import win32file
ImportError: DLL load failed: The specified module could not be found.
Error loading: C:\OMERO.server\lib\python\omero\plugins\prefs.py
Traceback (most recent call last):
File "C:\OMERO.server\lib\python\omero\cli.py", line 1139, in loadpath
execfile( str(pathobj), loc )
File "C:\OMERO.server\lib\python\omero\plugins\prefs.py", line 17, in <module>

import portalocker
File "C:\OMERO.server\lib\python\portalocker.py", line 72, in <module>
import win32file
ImportError: DLL load failed: The specified module could not be found.
usage: C:\OMERO.server\bin\\omero [-h] [-v] [-d DEBUG] [--path PATH] [-C]
[-s SERVER] [-p PORT] [-g GROUP] [-u USER]
[-w PASSWORD] [-k KEY]
<subcommand> ...
C:\OMERO.server\bin\\omero: error: argument <subcommand>: invalid choice: 'admin
'

choose from:
cecog, chgrp, db, delete, download, export, group, help, hql,
import, ldap, load, login, logout, quit, script, search, server,
sessions, shell, testengine, upload, user, version, web

C:\OMERO.server\bin>
* * * * * * * *
I had tried it before but did not work out.

Hi Anand,

I'm sorry to hear that you're having troubles running the server. We have often tested a Windows deployment of OMERO.server using Python 2.6 (32 bit) and the required prerequisites.

The error I can see from your post implies that the PyWin32 library isn't being picked up by Python. Could you please try uninstalling the one you currently have and using http://sourceforge.net/projects/pywin32 ... e/download. Please let me know if the error goes away.

Regards,
Błażej