Open Microscopy Environment

Hey OMERO

We've been using ( https://github.com/joshmoore/openmicros ... components ) the chgrp branch of OMERO now for a month or two and its been going really well, so a major thank you for that! Now we are looking to migrate it from Centos to Redhat and our sysadmin is having trouble getting Ice 3.3 installed onto the server we are working on, so has tried to get it working using ice 3.4. Its mentioned in the documentation that you can use either ice 3.3 or ice 3.4, but we are getting the following errors on startup.


bin/omero admin start
********************************************************************************

ERROR: Could not import omero.cli! (No module named Ice)

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

https://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=/opt/OmeroServerChgrp
VERSION=2.4.6 (#1, Feb 24 2012, 11:27:12) [GCC 4.4.6 20110731
(Red Hat 4.4.6-3)]
OMERO_HOME=/opt/OmeroServerChgrp
PYTHONPATH=['/opt/OmeroServerChgrp/lib/python',
'/opt/OmeroServerChgrp/var/lib', '/opt/OmeroServerChgrp/bin',
'/usr/local/lib/python24.zip', '/usr/local/lib/python2.4',
'/usr/local/lib/python2.4/plat-linux2',
'/usr/local/lib/python2.4/lib-tk',
'/usr/local/lib/python2.4/lib-dynload',
'/usr/local/lib/python2.4/site-packages',
'/opt/OmeroServerChgrp/lib/fallback']

Hi Manda,

before we get too deep into debugging the Ice issue, would it be possible for you to switch to the official "develop" branch? We've integrated my chgrp branch into this primary development line along with the rest of the work that is slated for 4.4.

A few things to keep in mind, though:

• The web infrastructure has changed as well. Since you are extending the web templates, you will need to look into upgrading what you've done for 4.4.
• Both in my 3532-chgrp branch as well as in "develop" there is a rather serious bug: https://trac.openmicroscopy.org.uk/ome/ticket/8037 Primarily, this makes it possible to see other users' data. If this is not a large concern while you test, you should be alright. I'll be fixing this within the next week or so.
• Eventually, database changes will start making their way into develop, at which point it will become more difficult for you to track our development. In general, we will need to discuss an upgrade strategy for you.

Best wishes,
~Josh

Is there a version I can use that has Chrgrp in it where the bug has been fixed? And should I be pulling down 'develop' or 'dev_4_3' ?

Those fixes have happened on develop and you'll want that branch however you should be aware over the next 6-8 weeks these branches will be in huge flux and many features may not have been updated yet or may be missing in one or both primary clients.

Hey, we've downloaded version joshmoore-openmicroscopy-998dfd9 and are getting the following errors. Any ideas? You mentioned there was a lot of work going on in this branch so is it worth just downloading the newer version and going from there instead? Is this the best branch to download , with both the security vunerability fixed and chgrp working ?

Code: Select all

$ python build.py
Buildfile: /opt/OmeroServerDevel/build.xml

check-ivy:
:: Ivy 2.1.0 - 20090925235825 :: http://ant.apache.org/ivy/ ::
:: loading settings :: file = /opt/OmeroServerDevel/etc/ivysettings.xml

BUILD FAILED
/opt/OmeroServerDevel/build.xml:51: impossible to parse ivy file for /opt/OmeroServerDevel/components/blitz/build.xml: ivyfile=/opt/OmeroServerDevel/components/blitz/ivy.xml exception=java.text.ParseException: http://java.sun.com/xml/jaxp/properties/schemaLanguage in file:/opt/OmeroServerDevel/components/blitz/ivy.xml
   at org.apache.ivy.plugins.parser.xml.XmlModuleDescriptorParser$Parser.parse(XmlModuleDescriptorParser.java:263)
   at org.apache.ivy.plugins.parser.xml.XmlModuleDescriptorParser.parseDescriptor(XmlModuleDescriptorParser.java:102)
   at org.apache.ivy.plugins.parser.ModuleDescriptorParserRegistry.parseDescriptor(ModuleDescriptorParserRegistry.java:86)
   at org.apache.ivy.plugins.parser.AbstractModuleDescriptorParser.parseDescriptor(AbstractModuleDescriptorParser.java:48)
   at org.apache.ivy.ant.IvyBuildList.doExecute(IvyBuildList.java:207)
   at org.apache.ivy.ant.IvyTask.execute(IvyTask.java:277)
   at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
   at java.lang.reflect.Method.invoke(libgcj.so.10)
   at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
   at org.apache.tools.ant.Task.perform(Task.java:348)
   at org.apache.tools.ant.Target.execute(Target.java:390)
   at org.apache.tools.ant.Target.performTasks(Target.java:411)
   at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1360)
   at org.apache.tools.ant.Project.executeTarget(Project.java:1329)
   at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
   at org.apache.tools.ant.Project.executeTargets(Project.java:1212)
   at org.apache.tools.ant.Main.runBuild(Main.java:801)
   at org.apache.tools.ant.Main.startAnt(Main.java:218)
   at java.lang.reflect.Method.invoke(libgcj.so.10)
   at omero.startAnt(omero.java:285)
   at omero.main(omero.java:313)
Caused by: org.xml.sax.SAXNotSupportedException: http://java.sun.com/xml/jaxp/properties/schemaLanguage
   at gnu.xml.stream.SAXParser.setProperty(libgcj.so.10)
   at org.apache.ivy.util.XMLHelper.newSAXParser(XMLHelper.java:67)
   at org.apache.ivy.util.XMLHelper.parse(XMLHelper.java:120)
   at org.apache.ivy.util.XMLHelper.parse(XMLHelper.java:96)
   at org.apache.ivy.util.XMLHelper.parse(XMLHelper.java:86)
   at org.apache.ivy.plugins.parser.xml.XmlModuleDescriptorParser$Parser.parse(XmlModuleDescriptorParser.java:238)
   ...20 more

Total time: 4 seconds
[omero@ettin OmeroServerDevel]$




Would it be possible to line up a skype or another version of chat with you guys in regard to the what changes are coming to OMERO in the future and how best to set up our functions for future versions of OMERO? I can come in any time, so office time in your country is fine for me.

Manz wrote:Hey, we've downloaded version joshmoore-openmicroscopy-998dfd9 and are getting the following errors. Any ideas? You mentioned there was a lot of work going on in this branch so is it worth just downloading the newer version and going from there instead? Is this the best branch to download , with both the security vunerability fixed and chgrp working ?

The best branch is now the mainline: https://github.com/openmicroscopy/openmicroscopy/tree/develop If you don't want to track the development but want a more or less stable point to build from, we can suggest a particular commit and/or tag.

That beind said, I don't know why the ivy file would be causing problems. Can you perhaps paste it to me?

Would it be possible to line up a skype or another version of chat with you guys in regard to the what changes are coming to OMERO in the future and how best to set up our functions for future versions of OMERO? I can come in any time, so office time in your country is fine for me.

At this week's meeting, we discussed your email re: giiaf-micro-lib (many thanks for the feedback) and discussed that it's important that we get an email out to ome-devel soon with the upcoming features for 4.4. Let us get our ducks in a row, and then you can let us know what you might need to move forward.

Best wishes,
~Josh.