[ome-devel] Server build questions.
Will Moore
will at lifesci.dundee.ac.uk
Fri Feb 26 11:57:28 GMT 2010
Hi All,
I am forwarding this question to the list since I am not too hot at
trouble-shooting server builds.
Cheers,
Will.
Begin forwarded message:
> From: "Ingvar Lagerstedt" <Ingvar at ebi.ac.uk>
> Date: 26 February 2010 11:33:40 GMT
> To: "Will Moore" <will at lifesci.dundee.ac.uk>
> Subject: Re: EMAN2-OMERO scripts
> Reply-To: Ingvar at ebi.ac.uk
>
> Hi Will,
>
> I have started to look at your EMAN2 scripts. My previous checkout
> was
> for the tagged 4.1.0 release, so "svn up" did not do what I
> thought. So I
> did a fresh checkout of the trunk, which by the way do not have a
> "home"
> in the path, at least not when accessing remotely. I am now at
> revision
> 6149.
>
> The build does not finish. I had the same warnings in the 4.1.0
> build,
> but as they have now turned in to errors - see the cc1plus line
> below. So
> the questions are, is it is safe to ignore this warning, and
> secondly if
> so, what is the easiest way to revert back to the old behaviour of
> ignoring the warnings.
>
> Below is the end of the build log file.
> Cheers,
> Ingvar
>
> Compiling target/omero/model/XmlAnnotation.os
> Compiling target/omero/model/XmlAnnotationI.os
> Compiling target/omero/API.os
> cc1plus: warnings being treated as errors
> target/omero/API.cpp: In member function ‘virtual Ice::DispatchStatus
> IceDelegateD::omero::api::ServiceFactory::sharedResources(const
> Ice::Context*)::_DirectI::run(Ice::Object*)’:
> target/omero/API.cpp:83475:60: error: ‘virtual
> omero::grid::SharedResourcesPrx
> omero::api::ServiceFactory::sharedResources(const Ice::Current&)’ is
> deprecated (declared at target/omero/API.h:32780)
> target/omero/API.cpp: In member function ‘virtual Ice::DispatchStatus
> IceDelegateD::omero::api::ServiceFactory::close(const
> Ice::Context*)::_DirectI::run(Ice::Object*)’:
> target/omero/API.cpp:83852:36: error: ‘virtual void
> omero::api::ServiceFactory::close(const Ice::Current&)’ is deprecated
> (declared at target/omero/API.h:32795)
> target/omero/API.cpp: In member function ‘Ice::DispatchStatus
> omero::api::ServiceFactory::___sharedResources(IceInternal::Incoming&,
> const Ice::Current&)’:
> target/omero/API.cpp:100717:76: error: ‘virtual
> omero::grid::SharedResourcesPrx
> omero::api::ServiceFactory::sharedResources(const Ice::Current&)’ is
> deprecated (declared at target/omero/API.h:32780)
> target/omero/API.cpp: In member function ‘Ice::DispatchStatus
> omero::api::ServiceFactory::___close(IceInternal::Incoming&, const
> Ice::Current&)’:
> target/omero/API.cpp:100816:20: error: ‘virtual void
> omero::api::ServiceFactory::close(const Ice::Current&)’ is deprecated
> (declared at target/omero/API.h:32795)
> scons: *** [target/omero/API.os] Error 1
>
>> Hi Ingvar,
>>
>> I remember that you wanted to try running the latest server and test
>> my EMAN2 scripts?
>> I realise there are a few steps you'll need to do...
>>
>> Are you currently running the latest server on your laptop?
>>
>> svn.openmicroscopy.org.uk/home/svn/omero/trunk
>> If you check out this code, then build by running ant in the root
>> directory, it should put the code in a folder called dist.
>>
>> You'll need to have the latest database (for storing ROIs on the
>> server). We don't have upgrade scripts to upgrade to this DB from the
>> previous one yet, since we haven't released this version. The easiest
>> thing to do is to dropdb and make a new one using the
>> $ bin/omero db script
>> command as described here
>> https://www.openmicroscopy.org.uk/site/support/omero4/server/installation
>>
>>
>> For EMAN2 install....
>> http://blake.bcm.edu/emanwiki/EMAN2/Install/BinaryInstall
>> I downloaded the latest EMAN2 dmg here
>> http://ncmi.bcm.edu/ncmi/software/counter_222/software_86
>>
>> I think the EMAN2 install includes numpy.
>> Try
>> $ python
>>>>> import numpy
>>
>> Also you'll need to configure your Python path as described on the
>> install pages, if you haven't done it already so that you can do
>>>>> import omero
>>
>> You will also need Python Imaging Library if you don't already have
>> it
>> Some tips here:
>> http://www.openmicroscopy.org.uk/site/support/omero4/server/install-omero-4.1-on-mac-os-x-10.5
>>
>> The sample images I have been using are from
>> http://ami.scripps.edu/experiment/index.php
>> Go to GroEL, view 06jul12a>>
>> I downloaded image: 00027gr_00065sq_00009hl_00003en.mrc
>> Click to view the image, then click the little save icon to download.
>>
>> Unfortunately, this image is too big to import with our current
>> importer.
>> I had to open in ImageJ, change to 8 bit and save as tiff, which you
>> can import OK.
>>
>> You can draw ROIs
>> http://cvs.openmicroscopy.org.uk/snapshots/movies/omero-4-0/mov/MeasurementTool-DrawingROI.mov
>> and then go to the bottom of the "Inspector" tab to set the width and
>> height to be a square (I use 330 pixels).
>>
>>
>> I have written the Python scripts to be run by the scripting service
>> on the server.
>> They need to be "uploaded" to the server, so that the scripting
>> service database is aware of them.
>>
>> You need to have the server running.
>> Then, if you start in the Omero src folder, you can do:
>> $ cd components/tools/OmeroPy/scripts
>> $ python uploadscript.py -h <host> -u <username> -p <password> -s
>> EMAN2/boxer.py
>>
>> If you don't want to check out and build from source, you can get the
>> latest OMERO.server build from hudson
>> http://hudson.openmicroscopy.org.uk/job/OMERO/
>>
>> and you can find the scripts here
>> http://trac.openmicroscopy.org.uk/omero/browser/trunk/components/tools/OmeroPy/scripts/
>>
>>
>> To run the boxer script, you'll need the ID that is printed out when
>> you upload the script above.
>> I use this script to run the boxer script, passing it a list of the
>> image IDs for it to process, in this case 101.
>> You can see the image ID when you view your imported image in
>> Insight.
>>
>>
>> import omero
>> import getopt, sys, os, subprocess
>> import omero_api_IScript_ice
>> from omero.rtypes import *
>>
>> def run():
>>
>> # edit these manually, then run the script!
>> host = "localhost"
>> user = "root"
>> password = "omero"
>> scriptId = 152
>>
>> client = omero.client(host)
>> session = client.createSession(user, password)
>> scriptService = session.getScriptService()
>>
>> # edit the IDs of the images you want to process...
>> ids = [omero.rtypes.rint(101), ]
>> imageIds = omero.rtypes.rlist(ids)
>>
>> map = {
>> "imageIds": imageIds,
>> }
>>
>> argMap = omero.rtypes.rmap(map)
>> scriptService.runScript(scriptId, map)
>>
>>
>> if __name__ == "__main__":
>> run()
>>
>>
>> You can find output of the script (standard output and errors) in the
>> last 2 files under
>> /OMERO/Files
>>
>> Good luck, and let me know if/when you need some help!
>>
>> Cheers,
>>
>> Will.
>>
>>
>>
>> On 22 Feb 2010, at 13:25, Ingvar Lagerstedt wrote:
>>
>>> Hi Will,
>>>
>>> It could be that I failed to clear out some class file from the
>>> previous
>>> build.
>>> Took a couple of rounds to exclude enough files to get down to a
>>> file that
>>> our mailer is happy with.
>>> I wrote my own ant-file. Something like:
>>> ant compile-renderer
>>> ant dist
>>>
>>> should build it.
>>>
>>> Cheers,
>>> Ingvar
>>>
>>>
>>>> Hi Ingvar,
>>>>
>>>> I'm getting exactly the same error with this new jar, although I
>>>> have
>>>> java 1.5.
>>>> I wonder if something in your system is still using 1.6?
>>>> I don't really want to upgrade to 1.6 since everything we release
>>>> is
>>>> built for java 1.5.
>>>>
>>>> You could just send me your code. Zip up the whole OpenAstexViewer
>>>> folder, just like they do on the web-site.
>>>> Then I can Open it as a new project and build it.
>>>> Obviously this is not a good long-term solution, but should work
>>>> for
>>>> now.
>>>>
>>>> Do you commit your code to a repository anywhere that I could
>>>> access
>>>> it from?
>>>>
>>>> Cheers,
>>>>
>>>> Will.
>>>>
>>>>
>>>> On 22 Feb 2010, at 12:13, Ingvar Lagerstedt wrote:
>>>>
>>>>> Hi Will,
>>>>>
>>>>> Could be that I compiled with java 1.6, and your java runtime is
>>>>> slightly
>>>>> out of date. I am rather new to java, but that seems like a
>>>>> reasonable
>>>>> first guess.
>>>>>
>>>>> I recompiled using java 1.4, attached, unless you want to upgrade.
>>>>>
>>>>> You are likely to run out of memory with the default jvm memory
>>>>> settings.
>>>>> The Astex viewer is a bit of a memory black hole. Use something
>>>>> like:
>>>>> java -Xmx1G -jar OpenAstexViewer.jar
>>>>>
>>>>> Hope this helps,
>>>>> Ingvar
>>>>>
>>>>>>
>>>>>> Hi Ingvar,
>>>>>>
>>>>>> I just tried to run the jar, but got this error....
>>>>>>
>>>>>> will$ java -jar OpenAstexViewer.jar
>>>>>> Exception in thread "main"
>>>>>> java.lang.UnsupportedClassVersionError:
>>>>>> Bad
>>>>>> version number in .class file
>>>>>> at java.lang.ClassLoader.defineClass1(Native Method)
>>>>>> at java.lang.ClassLoader.defineClass(ClassLoader.java:676)
>>>>>> at
>>>>>> java
>>>>>> .security.SecureClassLoader.defineClass(SecureClassLoader.java:
>>>>>> 124)
>>>>>> at java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
>>>>>> at java.net.URLClassLoader.access$100(URLClassLoader.java:56)
>>>>>> at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
>>>>>> at java.security.AccessController.doPrivileged(Native Method)
>>>>>> at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
>>>>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:317)
>>>>>> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:280)
>>>>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:252)
>>>>>> at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:375)
>>>>>>
>>>>>> Hope you can see what is going on here?
>>>>>> Does this jar work for you?
>>>>>> Do I need to do something different?
>>>>>>
>>>>>> Many thanks,
>>>>>>
>>>>>> Will.
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 22 Feb 2010, at 11:38, Ingvar Lagerstedt wrote:
>>>>>>
>>>>>>> Hi Will,
>>>>>>>
>>>>>>> As discussed last Friday I send you my current version of the
>>>>>>> Astex
>>>>>>> Viewer.
>>>>>>> We are trying to do a merge of three EBI branches of the viewer,
>>>>>>> so
>>>>>>> here
>>>>>>> is likely to be changes in the near future...
>>>>>>>
>>>>>>> My current favourite test case is EMD_5036 available from:
>>>>>>> http://www.ebi.ac.uk/pdbe-srv/emsearch/atlas/5036_summary.html
>>>>>>> http://www.ebi.ac.uk/pdbe-srv/emsearch/atlas/5036_downloads.html
>>>>>>>
>>>>>>> The first link for the PDB ids, the second for the EM map.
>>>>>>>
>>>>>>> All the best,
>>>>>>> Ingvar
>>>>>>>
>>>>>>>> Hi Christoph, Ingvar, Jason,
>>>>>>>>
>>>>>>>> Just wanted to note a few points for discussion this afternoon.
>>>>>>>>
>>>>>>>> Here's a short presentation I did recently for our group
>>>>>>>> discussion:
>>>>>>>>
>>>>>>>>
>>>>>>>> To summarise:
>>>>>>>> - There are several different directions I could work on at
>>>>>>>> this
>>>>>>>> point
>>>>>>>> Eg: Publication Web client?
>>>>>>>> EM submission client? (needs web import)
>>>>>>>> 3D viewer? (Client-side or server-side?)
>>>>>>>> EMAN2 – OMERO interaction?
>>>>>>>> Server stuff? Big Images, arbitrary planes/proj
>>>>>>>> OMERO.editor?
>>>>>>>> - What I do depends on:
>>>>>>>> The other members of OME team
>>>>>>>> EM project goals - needs some discussion
>>>>>>>>
>>>>>>>> - I included some slides from the EMEN2 WebEx demo the other
>>>>>>>> day,
>>>>>>>> since there seems to be a lot of overlap with what they are
>>>>>>>> doing
>>>>>>>> and
>>>>>>>> what we are thinking of.
>>>>>>>> How does their work affect what we do?
>>>>>>>>
>>>>>>>> - I have been working on EMAN2 - OMERO integration (adding
>>>>>>>> EMAN2
>>>>>>>> functionality to the server via Python). Not sure if this is
>>>>>>>> something
>>>>>>>> we want to pursue?
>>>>>>>> Do we want users to eventually use OMERO as their image
>>>>>>>> repository
>>>>>>>> for
>>>>>>>> single-particle workflow?
>>>>>>>> - What are the benefits of this that we can offer them?
>>>>>>>> - If so, do we need to target more than 1 application (EMAN2)?
>>>>>>>> Spider?
>>>>>>>> IMOD? BSoft? etc
>>>>>>>>
>>>>>>>> Speak later (3pm)?
>>>>>>>>
>>>>>>>> Cheers,
>>>>>>>>
>>>>>>>> Will .
>>>>>>>>
>>>>>>>>
>>>>>>>> On 18 Feb 2010, at 08:28, Christoph Best wrote:
>>>>>>>>
>>>>>>>>> Hi Will and Jason,
>>>>>>>>>
>>>>>>>>> I am back at EBI tomorrow (Friday) afternoon, or we can talk
>>>>>>>>> next
>>>>>>>>> week
>>>>>>>>> (except Wednesday and Friday since we are conducting all-day
>>>>>>>>> interviews...).
>>>>>>>>>
>>>>>>>>> Best
>>>>>>>>> -Christoph
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Christoph Best
>>>>>>>>> cb at tigertiger.de
>>>>>>>>> +49-177-492 2916 / +44-7525-208650
>>>>>>>>> http://tigertiger.de/cb
>>>>>>>>
>>>>>>>> William Moore
>>>>>>>> Wellcome Trust Centre for Gene Regulation & Expression
>>>>>>>> College of Life Sciences
>>>>>>>> MSI/WTB/JBC Complex
>>>>>>>> University of Dundee
>>>>>>>> Dow Street
>>>>>>>> Dundee DD1 5EH
>>>>>>>> United Kingdom
>>>>>>>>
>>>>>>>> Phone 01382 386364
>>>>>>>> http://openmicroscopy.org.uk
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Ingvar Lagerstedt, PDBe, EMBL-EBI, Hinxton, UK
>>>>>>> Ingvar at ebi.ac.uk<OpenAstexViewer.jar>
>>>>>>
>>>>>> William Moore
>>>>>> Wellcome Trust Centre for Gene Regulation & Expression
>>>>>> College of Life Sciences
>>>>>> MSI/WTB/JBC Complex
>>>>>> University of Dundee
>>>>>> Dow Street
>>>>>> Dundee DD1 5EH
>>>>>> United Kingdom
>>>>>>
>>>>>> Phone 01382 386364
>>>>>> http://openmicroscopy.org.uk
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Ingvar Lagerstedt, PDBe, EMBL-EBI, Hinxton, UK
>>>>> Ingvar at ebi.ac.uk<OpenAstexViewer.jar>
>>>>
>>>> William Moore
>>>> Wellcome Trust Centre for Gene Regulation & Expression
>>>> College of Life Sciences
>>>> MSI/WTB/JBC Complex
>>>> University of Dundee
>>>> Dow Street
>>>> Dundee DD1 5EH
>>>> United Kingdom
>>>>
>>>> Phone 01382 386364
>>>> http://openmicroscopy.org.uk
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Ingvar Lagerstedt, PDBe, EMBL-EBI, Hinxton, UK
>>> Ingvar at ebi.ac.uk<OpenAstexViewer.tgz>
>>
>> William Moore
>> Wellcome Trust Centre for Gene Regulation & Expression
>> College of Life Sciences
>> MSI/WTB/JBC Complex
>> University of Dundee
>> Dow Street
>> Dundee DD1 5EH
>> United Kingdom
>>
>> Phone 01382 386364
>> http://openmicroscopy.org.uk
>>
>>
>>
>>
>>
>
>
> --
> Ingvar Lagerstedt, PDBe, EMBL-EBI, Hinxton, UK
> Ingvar at ebi.ac.uk
>
William Moore
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee DD1 5EH
United Kingdom
Phone 01382 386364
http://openmicroscopy.org.uk
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