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From: Morris S. <m.a...@ru...> - 2010-03-11 12:03:46
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Dear all, We have updated MOLGENIS with a draft of an RestApi as well as a nifty javascript that remembers scroll positions between page views. This is great if you have a big user interface and find yourself scrolling all the time :-) You can get it from SVN. Because we changed the libraries you may encounter some issues. This blog entry gives some help on issues you may encounter http://www.molgenis.org/blog/2010/03/11 Cheers, Morris |
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From: Morris S. <m.a...@ru...> - 2009-06-22 09:02:23
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Hi molgenis friends, It seems MOLGENIS is in need of a slogan [which I realised when preparing for ISMB saturday to demo, flyer and present MOLGENIS at the Netherlands BioInformatics Center booth I was even thinking on getting some pens if I can get them printed in time...] So I send this email to put our collective subconcious to work to come up with one. Please let me know if it produces anything ;-) Some examples we have come up with up 'til now, please let me know if your (dis)like any. MOLGENIS: * Generates life science databases quickly * Your database at the push of a button * Flexible software for your life science data Cheers, Morris |
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From: Morris S. <m.a...@ru...> - 2009-06-16 21:01:02
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Hi Henrikki, I suppose that by now we have checked the obvious: - downloaded and installed the latest version from sourceforge - regenerated the app, cleaned and updated the server - checked if there actually is a UI (because the getSelected error refers to the default screen to show) So I propose to do a skype to resolve this. Can you send me your details (or Juha knows mine) and propose a date/time? Alternatively you can send me the XMLs to try and reproduce your problems.... Cheers, Morris Henrikki Almusa wrote: > Hi, > > I'm using using the 3.2-testing to try to load an older molgenis xmls > (which was one of the first I did and then let go as there was too > many rows in the database for it work fast). However when running the > server from eclipse it fails to start to an attached error. The > MolgenisGenerate.java does run without any errors. > > Any help to this would be most welcome. Thanks, > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------------ > Crystal Reports - New Free Runtime and 30 Day Trial > Check out the new simplified licensing option that enables unlimited > royalty-free distribution of the report engine for externally facing > server and web deployment. > http://p.sf.net/sfu/businessobjects > ------------------------------------------------------------------------ > > _______________________________________________ > Molgenis-users mailing list > Mol...@li... > https://lists.sourceforge.net/lists/listinfo/molgenis-users |
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From: Henrikki A. <hen...@he...> - 2009-06-11 09:03:59
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Hi, I'm using using the 3.2-testing to try to load an older molgenis xmls (which was one of the first I did and then let go as there was too many rows in the database for it work fast). However when running the server from eclipse it fails to start to an attached error. The MolgenisGenerate.java does run without any errors. Any help to this would be most welcome. Thanks, -- Henrikki Almusa |
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From: Morris S. <m.a...@ru...> - 2009-04-02 09:05:38
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Hi Tjeerd,
Thank you for this error message. It is actually a bug in the 'testing'
release, that is why we call it testing :-)
The issue has to do with uppercase/lowercase on the entity/class names
Immediate fix:
You need to edit the generator template responsible for this bug:
-> In the 'testing' distro, in project 'molgenis3.2'
-> in file org.molgenis.generate.assets.html.HtmlFormGen.java.ftl
-> line 63:
change
input.setXrefEntity("${name(model)}.data.types.${field.XRefEntity}");
input.setXrefEntity("${name(model)}.data.types.${Name(field.XRefEntity)}");
Of course this will be fixed in the next testing release, scheduled
somewhere this month.
Cheers,
Morris
Abma, T.W. wrote:
> When trying to select a dropdown box in a form, sometimes a dialog appears saying:
>
> "There was a problem retrieving the XML data: Internal Server Error"
>
> Currently no idea how to reproduce it, it just happens sometimes. I am running on SARA using Tomcat 5.5.26.
>
> Just to let you know.
>
> Tjeerd
>
> Scientific programmer/Bioinformatician
> UMCU Metabolomics Centre
> Dept. Metabolic and Endocrine Diseases
> Wilhelmina Childrens Hospital, UMC Utrecht
> T: 088-7554330
> E: t.w...@um...
>
> http://www.metabolomics-utrecht.nl
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> Molgenis-users mailing list
> Mol...@li...
> https://lists.sourceforge.net/lists/listinfo/molgenis-users
>
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From: Abma, T.W. <T.W...@um...> - 2009-04-02 08:38:21
|
When trying to select a dropdown box in a form, sometimes a dialog appears saying: "There was a problem retrieving the XML data: Internal Server Error" Currently no idea how to reproduce it, it just happens sometimes. I am running on SARA using Tomcat 5.5.26. Just to let you know. Tjeerd Scientific programmer/Bioinformatician UMCU Metabolomics Centre Dept. Metabolic and Endocrine Diseases Wilhelmina Childrens Hospital, UMC Utrecht T: 088-7554330 E: t.w...@um... http://www.metabolomics-utrecht.nl |
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From: Abma, T.W. <T.W...@um...> - 2009-03-02 10:03:35
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Hello,
I am writing plugins for Molgenis and want to use generated forms in it to add new records. This is possible with the following code:
---------------------------------------------------------------------------------------------------
ExperimentForm ef = (ExperimentForm)this.get("molgenis_main_Experiment_Experiment");
this.getDatabase().cacheXrefOptions(Experiment.class);
return ef.getNewInputs();
---------------------------------------------------------------------------------------------------
In my template I can show the form by saying {screen.getForm("formname")} which works perfectly. The cacheXrefOptions()-method
is required to initialize the crossreference fields.
But, how to edit existing records in Molgenis in my own plugin and using generated forms? At the moment I've got the following:
------------- -----------------------------------------------------------------------------------
ProjectForm pfedit = (ProjectForm)this.get("molgenis_main_Project_Project");
Vector<HtmlInput> inputs = pfedit.getNewInputs();
for(HtmlInput i: inputs)
{
if(i.getName().equals("project_id"))
{
i.setValue(p.getProject_id());
}
}
this.getDatabase().cacheXrefOptions(Project.class);
return inputs;
}
--------------------------------------------------------------------------------------------------------
The above code shows a generated form for a Project. I can initialize individual fields, but is there a way to retrieve a record
and put all values in a form? Something in pseudo-code like: this.getDatabase().cacheFields(Project.class) ?
No idea how to do it at the moment, but I hope my problem is clear. Any solution out there?
With kind regards,
Tjeerd
Scientific programmer/Bioinformatician
UMCU Metabolomics Centre
Dept. Metabolic and Endocrine Diseases
Wilhelmina Childrens Hospital, UMC Utrecht
T: 088-7554330
E: t.w...@um...
http://www.metabolomics-utrecht.nl
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From: Morris S. <m.a...@ru...> - 2009-02-24 09:11:26
|
Dear MOLGENIS friends, We have prepared a MOLGENIS 3.2 "testing" release today, 2008-02-24. It should be fully functional but we are interested in your experiences :-) Like always you can download it from http://dl.sourceforge.net/sourceforge/molgenis/molgenis_workspace-3.2-testing.zip This MOLGENIS update provides a number of enhancements: - Added AJAX based lookup boxes to the GUI so genome scale data sets should work now. - Added support to parse/download many-to-many relationships in the tab/csv import/export - Included the MOLGENIS source code as part of the distro to ease enhancements/bugfixing - Enhanced the standard plugin to show error/success messages using "this.setMessages(new ScreenMessage("my message", true or false));" - Cleanup of the CSS which should help you to customize the layout - Many small improvements following your feedback on the previous release. If you don't need these features, you can happily keep using 3.03 :-) We hope you'll enjoy the release. As always, please report any bugs, issues and questions and join our mailing list at mol...@li... https://lists.sourceforge.net/lists/listinfo/molgenis-users Cheers, Morris On behalve of the MOLGENIS team |
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From: Frank v. Z. <fra...@ho...> - 2009-02-20 13:18:01
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Hello all, Molgenis worked for a while, but now I am getting the BasicDataSource classcast error again. I have commons-dbcp-1.2.1.jar removed from Web-Content/WEB-INF/lib. All I changed was molgens_db.xml and molgenis_ui.xml. Any help would be much appreciated. Best, Frank From: fra...@ho... To: mol...@li... Date: Fri, 12 Dec 2008 13:56:27 +0000 Subject: Re: [Molgenis-users] Where should I put molgenis-3.0.3.jar ? Great!! That worked!!! Molgenis is now up and running!!! Thank you Morris and Ate for your help!! Best, Frank > Date: Wed, 10 Dec 2008 17:12:50 +0100 > From: m.a...@ru... > To: fra...@ho... > CC: mol...@li... > Subject: Re: [Molgenis-users] Where should I put molgenis-3.0.3.jar ? > > Hmm, this get stranger and stranger. > > It seems there are multiple jars lying around. Your best bet is to have > only one jar in the common/lib, and remove it from MOLGENIS. > (so kind of the opposite of what you tried). Because the reason it now > fails is because Tomcat doesn't know the BasicDataSource anymore. > > If this doesn't work, I propose that we do a skype chat to get to the > bottom of this. > My skype name is "mswertz" > > Good luck, > Morris. > > P.S. we usually use 6.0 or 5.5 but the mechanism should not be different > between them. > > Frank van Zimmeren wrote: > > Hello again, > > > > I have finally managed to get a Tomcat version to work with Eclipse. I > > could not get version 6.0 nor 5.5 to work, but 5.0 will. I can now > > successfully use the "Run on server" option. However > > http://localhost:8080/molgenis/molgenis.do gives the following error > > report: > > > > > > HTTP Status 500 - > > > > ------------------------------------------------------------------------ > > *type* Exception report > > *message* > > *description* _The server encountered an internal error () that > > prevented it from fulfilling this request._ > > *exception* > > java.lang.RuntimeException: java.lang.ClassCastException: org.apache.commons.dbcp.BasicDataSource cannot be cast to org.apache.commons.dbcp.BasicDataSource > > org.molgenis.assets.server.AbstractMolgenisServlet.handleGUIrequest(AbstractMolgenisServlet.java:215) > > org.molgenis.assets.server.AbstractMolgenisServlet.service(AbstractMolgenisServlet.java:184) > > javax.servlet.http.HttpServlet.service(HttpServlet.java:802) > > > > *note* _The full stack trace of the root cause is available in the > > Apache Tomcat/5.0.30 logs._ > > > > Googling did not help with this problem. Strange, I see no reason why > > the cast of org.apache.commons.dbcp.BasicDataSource to itself > > (org.apache.commons.dbcp.BasicDataSource) should not work. I have > > tried removing commons-dbcp-1.2.1.jar from $TOMCAT _HOME/common/lib > > but then I get the following: > > > > *description* _The server encountered an internal error () that > > prevented it from fulfilling this request._ > > *exception* > > java.lang.RuntimeException: javax.naming.NamingException: Cannot create resource instance > > org.molgenis.assets.server.AbstractMolgenisServlet.handleGUIrequest(AbstractMolgenisServlet.java:215) > > org.molgenis.assets.server.AbstractMolgenisServlet.service(AbstractMolgenisServlet.java:184) > > javax.servlet.http.HttpServlet.service(HttpServlet.java:802) > > > > *note* _The full stack trace of the root cause is available in the > > Apache Tomcat/5.0.30 logs._ > > > > Any ideas? > > > > Best, > > Frank > > > > > > > From: A.S...@ru... > > > Subject: Re: [Molgenis-users] Where should I put molgenis-3.0.3.jar ? > > > To: fra...@ho...; mol...@li... > > > Date: Sat, 29 Nov 2008 12:39:32 +0100 > > > > > > Hi Frank, > > > > > > I'm not really an eclipse guru, but it sounds as if your eclipse > > > environment is not aware of the tomcat server. > > > > > > I think you should add your Tomcat instance under under the server --> > > > runtime environment --> add option in eclipse preferences. > > > > > > I think you can run the project on that server afterwards. > > > good luck. > > > > > > Ate > > > > > > think you do not haveOn Fri, 28 Nov 2008 15:33:02 +0000 > > > Frank van Zimmeren <fra...@ho...> wrote: > > > > > > > > Great! MolgenisGenerate now runs without any problems. So does > > > >MolgenisUpdateDatabase. > > > > > > > > I am now at step 5 of chapter 1.2 of the manual: > > > > "Run the MOLGENIS and see if you like it already.Right-click the > > > >'molgenis' project folder and choose 'run > > > > as' and ' run on server"I do not have the option 'run on > > > >server'...Frank > > > > > > > >> Subject: Re: [Molgenis-users] Where should I put molgenis-3.0.3.jar > > > >>? > > > >> From: A.S...@ru... > > > >> To: fra...@ho... > > > >> CC: mol...@li... > > > >> Date: Fri, 28 Nov 2008 15:38:38 +0100 > > > >> > > > >> I think you need to add: > > > >> > > > >> output_web = WebContent > > > >> > > > >> (or the correct path to your webfolder) to the output section of > > > >>your > > > >> molgenis.properties file. > > > >> > > > >> Ate > > > >> > > > >> On Fri, 2008-11-28 at 14:21 +0000, Frank van Zimmeren wrote: > > > >> > Hello Ate, > > > >> > > > > >> > Thank you! That did the trick. The program gets further but now > > > >>ends > > > >> > with: > > > >> > > > > >> > Exception in thread "main" > > > >> > java.io.FileNotFoundException: /META-INF/context.xml (No such file > > > >>or > > > >> > directory) > > > >> > at java.io.FileOutputStream.open(Native Method) > > > >> > at java.io.FileOutputStream.<init>(FileOutputStream.java:179) > > > >> > at java.io.FileOutputStream.<init>(FileOutputStream.java:131) > > > >> > at > > > >> > > > > > > >>org.molgenis.generate.servlet.MolgenisServletContextGen.generate(MolgenisServletContextGen.java:44) > > > >> > at > > > >> > > > > > > >>org.molgenis.generate.MolgenisFactory.generate(MolgenisFactory.java:244) > > > >> > at > > > >> > > > > >>org.molgenis.generate.MolgenisFactory.run(MolgenisFactory.java:325) > > > >> > at > > > >> > > > > >>org.molgenis.generate.MolgenisFactory.main(MolgenisFactory.java:342) > > > >> > at MolgenisGenerate.main(MolgenisGenerate.java:7) > > > >> > > > > >> > This file is present and has read permission for all users. Do I > > > >>need > > > >> > to set a path somewhere? > > > >> > > > > >> > Best, > > > >> > Frank > > > >> > > > > >> > > From: A.S...@ru... > > > >> > > To: mol...@li... > > > >> > > Date: Wed, 26 Nov 2008 15:40:50 +0100 > > > >> > > Subject: Re: [Molgenis-users] Where should I put > > > >> > molgenis-3.0.3.jar ? > > > >> > > > > > >> > > Hello Frank, > > > >> > > > > > >> > > I'm not sure whether this is related to your error, but I just > > > >> > notice > > > >> > > the libgcj.so.90 in your error, suggesting that you use gnu > > > >>java. > > > >> > > > > > >> > > I vaguely remember that I had to install the ia32-java6-sun > > > >>packages > > > >> > and > > > >> > > use sun java as default workspace jre before things worked in > > > >> > ubuntu. > > > >> > > > > > >> > > Ate > > > >> > > > > > >> > > > > > >> > > > > > >> > > > > > >> > > On Wed, 2008-11-26 at 13:50 +0000, Frank van Zimmeren wrote: > > > >> > > > Dear Morris, > > > >> > > > > > > >> > > > Thank you for your help. > > > >> > > > > > > >> > > > That library is in my Java Build Path. The library is named > > > >> > "Persisted > > > >> > > > container [org.eclipse.jst.j2ee.internal.web.container for > > > >>project > > > >> > > > [molgenis3_distro]] > > > >> > > > > > > >> > > > However, after adding the library again I do not get the error > > > >> > message > > > >> > > > about MolgenisFactory anymore. But now I get the following: > > > >> > > > > > > >> > > > Exception in thread "main" java.lang.IllegalAccessError: > > > >> > > > org.molgenis.language.MolgenisLanguage can't access class > > > >> > > > org.molgenis.language.syntax.UISchema$Type > > > >> > > > at java.lang.Class.isAnonymousClass(libgcj.so.90) > > > >> > > > at java.lang.Class.getSimpleName(libgcj.so.90) > > > >> > > > at > > > >> > > > > > > >> > > > > > > >>org.molgenis.language.MolgenisLanguage.<clinit>(MolgenisLanguage.java:23) > > > >> > > > at java.lang.Class.initializeClass(libgcj.so.90) > > > >> > > > at > > > >> > > > > > > >> > > > > >>org.molgenis.generate.MolgenisFactory.run(MolgenisFactory.java:315) > > > >> > > > at > > > >> > > > > > > >> > > > > >>org.molgenis.generate.MolgenisFactory.main(MolgenisFactory.java:342) > > > >> > > > at MolgenisGenerate.main(MolgenisGenerate.java:7) > > > >> > > > > > > >> > > > I see UISchema$Type.class in molgenis-3.0.3.jar but I do not > > > >>see > > > >> > it in > > > >> > > > my library in Eclipse. I'm at a loss. > > > >> > > > > > > >> > > > Best, > > > >> > > > Frank > > > >> > > > > > > >> > > > > Date: Wed, 26 Nov 2008 10:05:21 +0100 > > > >> > > > > From: m.a...@ru... > > > >> > > > > To: fra...@ho...; > > > >> > > > mol...@li... > > > >> > > > > Subject: Re: [Molgenis-users] Where should I put > > > >> > > > molgenis-3.0.3.jar ? > > > >> > > > > > > > >> > > > > Dear Frank, > > > >> > > > > > > > >> > > > > Normally one downloads the Eclipse workspace, and that > > > >>should > > > >> > work. > > > >> > > > > It seems there is a path issue; all the jars are in > > > >> > > > WebContent/WEB-INF/lib > > > >> > > > > Check your Java Build Path (right-click project -> > > > >>properties) > > > >> > to > > > >> > > > see of > > > >> > > > > they are loaded. > > > >> > > > > Also a clean built may help. > > > >> > > > > > > > >> > > > > (The seperate jar is only for people who already downloaded > > > >>a > > > >> > > > previous > > > >> > > > > version; the you can paste that into your > > > >>WebContent/WEB-INF/lib > > > >> > to > > > >> > > > be > > > >> > > > > updated. > > > >> > > > > So that shouldn't help in your situation) > > > >> > > > > > > > >> > > > > I hope this helps, > > > >> > > > > Morris > > > >> > > > > > > > >> > > > > Frank van Zimmeren wrote: > > > >> > > > > > Hello, > > > >> > > > > > > > > >> > > > > > I am trying to install and use Molgenis. I have unzipped > > > >>the > > > >> > > > molgenis > > > >> > > > > > workspace as described in the manual. I am, however, stuck > > > >>at > > > >> > > > chapter > > > >> > > > > > 1.2 step 3: "Go to the folder 'handwritten/java' and > > > >> > right-click > > > >> > > > > > 'MolgenisGenerate' Choose 'run as' and then 'run as java > > > >> > > > > > application'". I get the following error: > > > >> > > > > > > > > >> > > > > > Exception in thread "main" java.lang.NoClassDefFoundError: > > > >> > > > > > org.molgenis.generate.MolgenisFactory > > > >> > > > > > at MolgenisGenerate.main(MolgenisGenerate.java:7) > > > >> > > > > > > > > >> > > > > > I found the MolgenisFactory.java and .class in > > > >> > molgenis-3.0.3.jar > > > >> > > > > > which is also on the SourceForge page. But I did not find > > > >>any > > > >> > > > > > documentation about this .jar. I have tried putting it in > > > >> > > > > > /usr/lib/java but this does not help. Where should I put > > > >> > > > this .jar? > > > >> > > > > > > > > >> > > > > > Best, > > > >> > > > > > Frank van Zimmeren > > > >> > > > > > > > > >> > > > > > > > > >> > > > > > > >> > > > > > > >>------------------------------------------------------------------------ > > > >> > > > > > Windows Live Hotmail now works up to 70% faster. Sign up > > > >> > today. > > > >> > > > > > > > > >> > > > > > > >> > > > > > > >><http://windowslive.com/Explore/Hotmail?ocid=TXT_TAGLM_WL_hotmail_acq_faster_112008> > > > > > >> > > > > > > > > >> > > > > > > > > >> > > > > > > >> > > > > > > >>------------------------------------------------------------------------ > > > >> > > > > > > > > >> > > > > > > > > >> > > > > > > >> > > > > > > >>------------------------------------------------------------------------- > > > >> > > > > > This SF.Net email is sponsored by the Moblin Your Move > > > >> > Developer's > > > >> > > > challenge > > > >> > > > > > Build the coolest Linux based applications with Moblin SDK > > > >>& > > > >> > win > > > >> > > > great prizes > > > >> > > > > > Grand prize is a trip for two to an Open Source event > > > >>anywhere > > > >> > in > > > >> > > > the world > > > >> > > > > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > > >> > > > > > > > > >> > > > > > > >> > > > > > > >>------------------------------------------------------------------------ > > > >> > > > > > > > > >> > > > > > _______________________________________________ > > > >> > > > > > Molgenis-users mailing list > > > >> > > > > > Mol...@li... > > > >> > > > > > > > > >>https://lists.sourceforge.net/lists/listinfo/molgenis-users > > > >> > > > > > > > > >> > > > > > > > >> > > > > > > >> > > > > > > >> > > > > > > >> > > > > >>______________________________________________________________________ > > > >> > > > Access your email online and on the go with Windows Live > > > >>Hotmail. > > > >> > Sign > > > >> > > > up today. > > > >> > > > > > > >> > > > > > > >>------------------------------------------------------------------------- > > > >> > > > This SF.Net email is sponsored by the Moblin Your Move > > > >>Developer's > > > >> > challenge > > > >> > > > Build the coolest Linux based applications with Moblin SDK & > > > >>win > > > >> > great prizes > > > >> > > > Grand prize is a trip for two to an Open Source event anywhere > > > >>in > > > >> > the world > > > >> > > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > > >> > > > _______________________________________________ Molgenis-users > > > >> > mailing list Mol...@li... > > > >> > https://lists.sourceforge.net/lists/listinfo/molgenis-users > > > >> > > > > > >> > > > > > >> > > > > > >> > > > > > > >>------------------------------------------------------------------------- > > > >> > > This SF.Net email is sponsored by the Moblin Your Move > > > >>Developer's > > > >> > challenge > > > >> > > Build the coolest Linux based applications with Moblin SDK & win > > > >> > great prizes > > > >> > > Grand prize is a trip for two to an Open Source event anywhere > > > >>in > > > >> > the world > > > >> > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > > >> > > _______________________________________________ > > > >> > > Molgenis-users mailing list > > > >> > > Mol...@li... > > > >> > > https://lists.sourceforge.net/lists/listinfo/molgenis-users > > > >> > > > > >> > > > > >> > > > > >>______________________________________________________________________ > > > >> > Access your email online and on the go with Windows Live Hotmail. > > > >>Sign > > > >> > up today. > > > >> > > > > > > >>------------------------------------------------------------------------- > > > >> > This SF.Net email is sponsored by the Moblin Your Move Developer's > > > >>challenge > > > >> > Build the coolest Linux based applications with Moblin SDK & win > > > >>great prizes > > > >> > Grand prize is a trip for two to an Open Source event anywhere in > > > >>the world > > > >> > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > > >> > _______________________________________________ Molgenis-users > > > >>mailing list Mol...@li... > > > >>https://lists.sourceforge.net/lists/listinfo/molgenis-users > > > >> > > > > > > > > _________________________________________________________________ > > > > Proud to be a PC? Show the world. Download the “I’m a PC” Messenger > > > >themepack now. > > > > hthttp://clk.atdmt.com/MRT/go/119642558/direct/01/ > > > > > > > ------------------------------------------------------------------------ > > Send e-mail faster without improving your typing skills. Get your > > Hotmail® account. > > <http://windowslive.com/Explore/hotmail?ocid=TXT_TAGLM_WL_hotmail_acq_speed_122008> > > > > ------------------------------------------------------------------------ > > > > ------------------------------------------------------------------------------ > > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. > > The future of the web can't happen without you. Join us at MIX09 to help > > pave the way to the Next Web now. Learn more and register at > > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Molgenis-users mailing list > > Mol...@li... > > https://lists.sourceforge.net/lists/listinfo/molgenis-users > > > Send e-mail faster without improving your typing skills. Get your Hotmail® account. _________________________________________________________________ Windows Live™: E-mail. Chat. Share. Get more ways to connect. http://windowslive.com/explore?ocid=TXT_TAGLM_WL_t2_allup_explore_022009 |
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From: Henrikki A. <hen...@he...> - 2009-02-05 10:29:35
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Hi all, I've been trying to modify colours on molgenis generated site. It seems that all is being done in css files in 'WebContent/res/css' directory. Now it's easy to change most colours there. However I've hit problem with changing the colour of the bars in right area. As far as I've understood it's in 'data.css', but changing the background of those doesn't seem to do anything. So where should this be done? Second thing is that is there a place for logo anywhere there? Third thing is that I hit an error when I put a dot in the _db.xml in name. Eg: <molgenis name="foo.org"> errors out when trying to run the molgenis in the eclipse. Thanks, -- Henrikki Almusa |
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From: Henrikki A. <hen...@he...> - 2009-01-08 10:05:00
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Hi, I have another question with regards to csv import. There type mref which allows creating many to many relations between tables. So I have table like <entity name="Publication"> <field name="id" type="autoid"/> <field name="Pubmed_id" label="Pubmed_id" unique="true" type="int" nillable="false"/> </entity> Then I have another table with many to many relation to that <field name="Publication_id" label="Publication" type="mref" xref_field="Publication.id" xref_label="Pubmed_id" /> Now the header would be "publication_id_pubmed_id", but how do I add two (or more) records to that one field? What's the separator in records within csv (in my case tab delimited) format? For example (using '|' as separator): publication_id_pubmed_id 100|200 Regards, -- Henrikki Almusa |
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From: Henrikki A. <hen...@he...> - 2009-01-08 07:50:52
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Morris Swertz wrote: > For the csv loading of a foreign key field (type="xref") 'x' the > following columns can be used for csv loading: > <name> > <name>_<xref_label> > In the second case the field used as xref_label will also be used to > retrieve the primary key of the xref_field. So the system uses underscore between the two and can use only the xref_label field for this. That's good to know when making the _db.xml file in future. > In your case: > name = Gene_id > xref_label = Name > > So I suppose your column should be named (case insensitive): > gene_id_name Great, that works. Thanks. > (if you really want to know, the code is in > generated/java/yourproject/data/types/yourclass.java and then the > function called 'set') Right. Regards, -- Henrikki Almusa |
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From: Morris S. <m.a...@ru...> - 2009-01-07 14:54:47
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Hi Henrikki, For the csv loading of a foreign key field (type="xref") 'x' the following columns can be used for csv loading: <name> <name>_<xref_label> In the second case the field used as xref_label will also be used to retrieve the primary key of the xref_field. In your case: name = Gene_id xref_label = Name So I suppose your column should be named (case insensitive): gene_id_name (if you really want to know, the code is in generated/java/yourproject/data/types/yourclass.java and then the function called 'set') Cheers, Morris Henrikki Almusa wrote: > Hi, > > I'm trying to insert data into molgenis 3.0.3 installation using the csv > import function. I have a table with columns like below > > <entity name="Gene"> > <field name="id" type="autoid"> > <field name="Name" unique="true"> > </entity> > > Then I have a second table with a foreign key reference to that > > <field name="Gene_id" label="Gene" type="xref" xref_field="Gene.id" > xref_label="Name" /> > > Now I would like to import multiple records to both tables. Since the > gene id's are autogenerated, I don't know the values in advance. I do > however know the name of the gene and would like to use that to tell the > molgenis which gene is used in the second table row. However my attempts > like (in the import csv table dialogs csv section) > > gene_id.gene.name > <genename> > > haven't worked. It just complains that gene_id is null. > > I'm not subscribed to list so please cc in any replies, thanks. > > Regards, > |
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From: Henrikki A. <hen...@he...> - 2009-01-07 14:00:54
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Hi, I'm trying to insert data into molgenis 3.0.3 installation using the csv import function. I have a table with columns like below <entity name="Gene"> <field name="id" type="autoid"> <field name="Name" unique="true"> </entity> Then I have a second table with a foreign key reference to that <field name="Gene_id" label="Gene" type="xref" xref_field="Gene.id" xref_label="Name" /> Now I would like to import multiple records to both tables. Since the gene id's are autogenerated, I don't know the values in advance. I do however know the name of the gene and would like to use that to tell the molgenis which gene is used in the second table row. However my attempts like (in the import csv table dialogs csv section) gene_id.gene.name <genename> haven't worked. It just complains that gene_id is null. I'm not subscribed to list so please cc in any replies, thanks. Regards, -- Henrikki Almusa |
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From: Frank v. Z. <fra...@ho...> - 2008-12-12 13:56:38
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Great!! That worked!!! Molgenis is now up and running!!! Thank you Morris and Ate for your help!! Best, Frank > Date: Wed, 10 Dec 2008 17:12:50 +0100 > From: m.a...@ru... > To: fra...@ho... > CC: mol...@li... > Subject: Re: [Molgenis-users] Where should I put molgenis-3.0.3.jar ? > > Hmm, this get stranger and stranger. > > It seems there are multiple jars lying around. Your best bet is to have > only one jar in the common/lib, and remove it from MOLGENIS. > (so kind of the opposite of what you tried). Because the reason it now > fails is because Tomcat doesn't know the BasicDataSource anymore. > > If this doesn't work, I propose that we do a skype chat to get to the > bottom of this. > My skype name is "mswertz" > > Good luck, > Morris. > > P.S. we usually use 6.0 or 5.5 but the mechanism should not be different > between them. > > Frank van Zimmeren wrote: > > Hello again, > > > > I have finally managed to get a Tomcat version to work with Eclipse. I > > could not get version 6.0 nor 5.5 to work, but 5.0 will. I can now > > successfully use the "Run on server" option. However > > http://localhost:8080/molgenis/molgenis.do gives the following error > > report: > > > > > > HTTP Status 500 - > > > > ------------------------------------------------------------------------ > > *type* Exception report > > *message* > > *description* _The server encountered an internal error () that > > prevented it from fulfilling this request._ > > *exception* > > java.lang.RuntimeException: java.lang.ClassCastException: org.apache.commons.dbcp.BasicDataSource cannot be cast to org.apache.commons.dbcp.BasicDataSource > > org.molgenis.assets.server.AbstractMolgenisServlet.handleGUIrequest(AbstractMolgenisServlet.java:215) > > org.molgenis.assets.server.AbstractMolgenisServlet.service(AbstractMolgenisServlet.java:184) > > javax.servlet.http.HttpServlet.service(HttpServlet.java:802) > > > > *note* _The full stack trace of the root cause is available in the > > Apache Tomcat/5.0.30 logs._ > > > > Googling did not help with this problem. Strange, I see no reason why > > the cast of org.apache.commons.dbcp.BasicDataSource to itself > > (org.apache.commons.dbcp.BasicDataSource) should not work. I have > > tried removing commons-dbcp-1.2.1.jar from $TOMCAT _HOME/common/lib > > but then I get the following: > > > > *description* _The server encountered an internal error () that > > prevented it from fulfilling this request._ > > *exception* > > java.lang.RuntimeException: javax.naming.NamingException: Cannot create resource instance > > org.molgenis.assets.server.AbstractMolgenisServlet.handleGUIrequest(AbstractMolgenisServlet.java:215) > > org.molgenis.assets.server.AbstractMolgenisServlet.service(AbstractMolgenisServlet.java:184) > > javax.servlet.http.HttpServlet.service(HttpServlet.java:802) > > > > *note* _The full stack trace of the root cause is available in the > > Apache Tomcat/5.0.30 logs._ > > > > Any ideas? > > > > Best, > > Frank > > > > > > > From: A.S...@ru... > > > Subject: Re: [Molgenis-users] Where should I put molgenis-3.0.3.jar ? > > > To: fra...@ho...; mol...@li... > > > Date: Sat, 29 Nov 2008 12:39:32 +0100 > > > > > > Hi Frank, > > > > > > I'm not really an eclipse guru, but it sounds as if your eclipse > > > environment is not aware of the tomcat server. > > > > > > I think you should add your Tomcat instance under under the server --> > > > runtime environment --> add option in eclipse preferences. > > > > > > I think you can run the project on that server afterwards. > > > good luck. > > > > > > Ate > > > > > > think you do not haveOn Fri, 28 Nov 2008 15:33:02 +0000 > > > Frank van Zimmeren <fra...@ho...> wrote: > > > > > > > > Great! MolgenisGenerate now runs without any problems. So does > > > >MolgenisUpdateDatabase. > > > > > > > > I am now at step 5 of chapter 1.2 of the manual: > > > > "Run the MOLGENIS and see if you like it already.Right-click the > > > >'molgenis' project folder and choose 'run > > > > as' and ' run on server"I do not have the option 'run on > > > >server'...Frank > > > > > > > >> Subject: Re: [Molgenis-users] Where should I put molgenis-3.0.3.jar > > > >>? > > > >> From: A.S...@ru... > > > >> To: fra...@ho... > > > >> CC: mol...@li... > > > >> Date: Fri, 28 Nov 2008 15:38:38 +0100 > > > >> > > > >> I think you need to add: > > > >> > > > >> output_web = WebContent > > > >> > > > >> (or the correct path to your webfolder) to the output section of > > > >>your > > > >> molgenis.properties file. > > > >> > > > >> Ate > > > >> > > > >> On Fri, 2008-11-28 at 14:21 +0000, Frank van Zimmeren wrote: > > > >> > Hello Ate, > > > >> > > > > >> > Thank you! That did the trick. The program gets further but now > > > >>ends > > > >> > with: > > > >> > > > > >> > Exception in thread "main" > > > >> > java.io.FileNotFoundException: /META-INF/context.xml (No such file > > > >>or > > > >> > directory) > > > >> > at java.io.FileOutputStream.open(Native Method) > > > >> > at java.io.FileOutputStream.<init>(FileOutputStream.java:179) > > > >> > at java.io.FileOutputStream.<init>(FileOutputStream.java:131) > > > >> > at > > > >> > > > > > > >>org.molgenis.generate.servlet.MolgenisServletContextGen.generate(MolgenisServletContextGen.java:44) > > > >> > at > > > >> > > > > > > >>org.molgenis.generate.MolgenisFactory.generate(MolgenisFactory.java:244) > > > >> > at > > > >> > > > > >>org.molgenis.generate.MolgenisFactory.run(MolgenisFactory.java:325) > > > >> > at > > > >> > > > > >>org.molgenis.generate.MolgenisFactory.main(MolgenisFactory.java:342) > > > >> > at MolgenisGenerate.main(MolgenisGenerate.java:7) > > > >> > > > > >> > This file is present and has read permission for all users. Do I > > > >>need > > > >> > to set a path somewhere? > > > >> > > > > >> > Best, > > > >> > Frank > > > >> > > > > >> > > From: A.S...@ru... > > > >> > > To: mol...@li... > > > >> > > Date: Wed, 26 Nov 2008 15:40:50 +0100 > > > >> > > Subject: Re: [Molgenis-users] Where should I put > > > >> > molgenis-3.0.3.jar ? > > > >> > > > > > >> > > Hello Frank, > > > >> > > > > > >> > > I'm not sure whether this is related to your error, but I just > > > >> > notice > > > >> > > the libgcj.so.90 in your error, suggesting that you use gnu > > > >>java. > > > >> > > > > > >> > > I vaguely remember that I had to install the ia32-java6-sun > > > >>packages > > > >> > and > > > >> > > use sun java as default workspace jre before things worked in > > > >> > ubuntu. > > > >> > > > > > >> > > Ate > > > >> > > > > > >> > > > > > >> > > > > > >> > > > > > >> > > On Wed, 2008-11-26 at 13:50 +0000, Frank van Zimmeren wrote: > > > >> > > > Dear Morris, > > > >> > > > > > > >> > > > Thank you for your help. > > > >> > > > > > > >> > > > That library is in my Java Build Path. The library is named > > > >> > "Persisted > > > >> > > > container [org.eclipse.jst.j2ee.internal.web.container for > > > >>project > > > >> > > > [molgenis3_distro]] > > > >> > > > > > > >> > > > However, after adding the library again I do not get the error > > > >> > message > > > >> > > > about MolgenisFactory anymore. But now I get the following: > > > >> > > > > > > >> > > > Exception in thread "main" java.lang.IllegalAccessError: > > > >> > > > org.molgenis.language.MolgenisLanguage can't access class > > > >> > > > org.molgenis.language.syntax.UISchema$Type > > > >> > > > at java.lang.Class.isAnonymousClass(libgcj.so.90) > > > >> > > > at java.lang.Class.getSimpleName(libgcj.so.90) > > > >> > > > at > > > >> > > > > > > >> > > > > > > >>org.molgenis.language.MolgenisLanguage.<clinit>(MolgenisLanguage.java:23) > > > >> > > > at java.lang.Class.initializeClass(libgcj.so.90) > > > >> > > > at > > > >> > > > > > > >> > > > > >>org.molgenis.generate.MolgenisFactory.run(MolgenisFactory.java:315) > > > >> > > > at > > > >> > > > > > > >> > > > > >>org.molgenis.generate.MolgenisFactory.main(MolgenisFactory.java:342) > > > >> > > > at MolgenisGenerate.main(MolgenisGenerate.java:7) > > > >> > > > > > > >> > > > I see UISchema$Type.class in molgenis-3.0.3.jar but I do not > > > >>see > > > >> > it in > > > >> > > > my library in Eclipse. I'm at a loss. > > > >> > > > > > > >> > > > Best, > > > >> > > > Frank > > > >> > > > > > > >> > > > > Date: Wed, 26 Nov 2008 10:05:21 +0100 > > > >> > > > > From: m.a...@ru... > > > >> > > > > To: fra...@ho...; > > > >> > > > mol...@li... > > > >> > > > > Subject: Re: [Molgenis-users] Where should I put > > > >> > > > molgenis-3.0.3.jar ? > > > >> > > > > > > > >> > > > > Dear Frank, > > > >> > > > > > > > >> > > > > Normally one downloads the Eclipse workspace, and that > > > >>should > > > >> > work. > > > >> > > > > It seems there is a path issue; all the jars are in > > > >> > > > WebContent/WEB-INF/lib > > > >> > > > > Check your Java Build Path (right-click project -> > > > >>properties) > > > >> > to > > > >> > > > see of > > > >> > > > > they are loaded. > > > >> > > > > Also a clean built may help. > > > >> > > > > > > > >> > > > > (The seperate jar is only for people who already downloaded > > > >>a > > > >> > > > previous > > > >> > > > > version; the you can paste that into your > > > >>WebContent/WEB-INF/lib > > > >> > to > > > >> > > > be > > > >> > > > > updated. > > > >> > > > > So that shouldn't help in your situation) > > > >> > > > > > > > >> > > > > I hope this helps, > > > >> > > > > Morris > > > >> > > > > > > > >> > > > > Frank van Zimmeren wrote: > > > >> > > > > > Hello, > > > >> > > > > > > > > >> > > > > > I am trying to install and use Molgenis. I have unzipped > > > >>the > > > >> > > > molgenis > > > >> > > > > > workspace as described in the manual. I am, however, stuck > > > >>at > > > >> > > > chapter > > > >> > > > > > 1.2 step 3: "Go to the folder 'handwritten/java' and > > > >> > right-click > > > >> > > > > > 'MolgenisGenerate' Choose 'run as' and then 'run as java > > > >> > > > > > application'". I get the following error: > > > >> > > > > > > > > >> > > > > > Exception in thread "main" java.lang.NoClassDefFoundError: > > > >> > > > > > org.molgenis.generate.MolgenisFactory > > > >> > > > > > at MolgenisGenerate.main(MolgenisGenerate.java:7) > > > >> > > > > > > > > >> > > > > > I found the MolgenisFactory.java and .class in > > > >> > molgenis-3.0.3.jar > > > >> > > > > > which is also on the SourceForge page. But I did not find > > > >>any > > > >> > > > > > documentation about this .jar. I have tried putting it in > > > >> > > > > > /usr/lib/java but this does not help. Where should I put > > > >> > > > this .jar? > > > >> > > > > > > > > >> > > > > > Best, > > > >> > > > > > Frank van Zimmeren > > > >> > > > > > > > > >> > > > > > > > > >> > > > > > > >> > > > > > > >>------------------------------------------------------------------------ > > > >> > > > > > Windows Live Hotmail now works up to 70% faster. Sign up > > > >> > today. > > > >> > > > > > > > > >> > > > > > > >> > > > > > > >><http://windowslive.com/Explore/Hotmail?ocid=TXT_TAGLM_WL_hotmail_acq_faster_112008> > > > > > >> > > > > > > > > >> > > > > > > > > >> > > > > > > >> > > > > > > >>------------------------------------------------------------------------ > > > >> > > > > > > > > >> > > > > > > > > >> > > > > > > >> > > > > > > >>------------------------------------------------------------------------- > > > >> > > > > > This SF.Net email is sponsored by the Moblin Your Move > > > >> > Developer's > > > >> > > > challenge > > > >> > > > > > Build the coolest Linux based applications with Moblin SDK > > > >>& > > > >> > win > > > >> > > > great prizes > > > >> > > > > > Grand prize is a trip for two to an Open Source event > > > >>anywhere > > > >> > in > > > >> > > > the world > > > >> > > > > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > > >> > > > > > > > > >> > > > > > > >> > > > > > > >>------------------------------------------------------------------------ > > > >> > > > > > > > > >> > > > > > _______________________________________________ > > > >> > > > > > Molgenis-users mailing list > > > >> > > > > > Mol...@li... > > > >> > > > > > > > > >>https://lists.sourceforge.net/lists/listinfo/molgenis-users > > > >> > > > > > > > > >> > > > > > > > >> > > > > > > >> > > > > > > >> > > > > > > >> > > > > >>______________________________________________________________________ > > > >> > > > Access your email online and on the go with Windows Live > > > >>Hotmail. > > > >> > Sign > > > >> > > > up today. > > > >> > > > > > > >> > > > > > > >>------------------------------------------------------------------------- > > > >> > > > This SF.Net email is sponsored by the Moblin Your Move > > > >>Developer's > > > >> > challenge > > > >> > > > Build the coolest Linux based applications with Moblin SDK & > > > >>win > > > >> > great prizes > > > >> > > > Grand prize is a trip for two to an Open Source event anywhere > > > >>in > > > >> > the world > > > >> > > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > > >> > > > _______________________________________________ Molgenis-users > > > >> > mailing list Mol...@li... > > > >> > https://lists.sourceforge.net/lists/listinfo/molgenis-users > > > >> > > > > > >> > > > > > >> > > > > > >> > > > > > > >>------------------------------------------------------------------------- > > > >> > > This SF.Net email is sponsored by the Moblin Your Move > > > >>Developer's > > > >> > challenge > > > >> > > Build the coolest Linux based applications with Moblin SDK & win > > > >> > great prizes > > > >> > > Grand prize is a trip for two to an Open Source event anywhere > > > >>in > > > >> > the world > > > >> > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > > >> > > _______________________________________________ > > > >> > > Molgenis-users mailing list > > > >> > > Mol...@li... > > > >> > > https://lists.sourceforge.net/lists/listinfo/molgenis-users > > > >> > > > > >> > > > > >> > > > > >>______________________________________________________________________ > > > >> > Access your email online and on the go with Windows Live Hotmail. > > > >>Sign > > > >> > up today. > > > >> > > > > > > >>------------------------------------------------------------------------- > > > >> > This SF.Net email is sponsored by the Moblin Your Move Developer's > > > >>challenge > > > >> > Build the coolest Linux based applications with Moblin SDK & win > > > >>great prizes > > > >> > Grand prize is a trip for two to an Open Source event anywhere in > > > >>the world > > > >> > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > > >> > _______________________________________________ Molgenis-users > > > >>mailing list Mol...@li... > > > >>https://lists.sourceforge.net/lists/listinfo/molgenis-users > > > >> > > > > > > > > _________________________________________________________________ > > > > Proud to be a PC? Show the world. Download the “I’m a PC” Messenger > > > >themepack now. > > > > hthttp://clk.atdmt.com/MRT/go/119642558/direct/01/ > > > > > > > ------------------------------------------------------------------------ > > Send e-mail faster without improving your typing skills. Get your > > Hotmail® account. > > <http://windowslive.com/Explore/hotmail?ocid=TXT_TAGLM_WL_hotmail_acq_speed_122008> > > > > ------------------------------------------------------------------------ > > > > ------------------------------------------------------------------------------ > > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. > > The future of the web can't happen without you. Join us at MIX09 to help > > pave the way to the Next Web now. Learn more and register at > > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Molgenis-users mailing list > > Mol...@li... > > https://lists.sourceforge.net/lists/listinfo/molgenis-users > > > _________________________________________________________________ Send e-mail faster without improving your typing skills. http://windowslive.com/Explore/hotmail?ocid=TXT_TAGLM_WL_hotmail_acq_speed_122008 |
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From: Morris S. <m.a...@ru...> - 2008-12-10 16:12:40
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Hmm, this get stranger and stranger. It seems there are multiple jars lying around. Your best bet is to have only one jar in the common/lib, and remove it from MOLGENIS. (so kind of the opposite of what you tried). Because the reason it now fails is because Tomcat doesn't know the BasicDataSource anymore. If this doesn't work, I propose that we do a skype chat to get to the bottom of this. My skype name is "mswertz" Good luck, Morris. P.S. we usually use 6.0 or 5.5 but the mechanism should not be different between them. Frank van Zimmeren wrote: > Hello again, > > I have finally managed to get a Tomcat version to work with Eclipse. I > could not get version 6.0 nor 5.5 to work, but 5.0 will. I can now > successfully use the "Run on server" option. However > http://localhost:8080/molgenis/molgenis.do gives the following error > report: > > > HTTP Status 500 - > > ------------------------------------------------------------------------ > *type* Exception report > *message* > *description* _The server encountered an internal error () that > prevented it from fulfilling this request._ > *exception* > java.lang.RuntimeException: java.lang.ClassCastException: org.apache.commons.dbcp.BasicDataSource cannot be cast to org.apache.commons.dbcp.BasicDataSource > org.molgenis.assets.server.AbstractMolgenisServlet.handleGUIrequest(AbstractMolgenisServlet.java:215) > org.molgenis.assets.server.AbstractMolgenisServlet.service(AbstractMolgenisServlet.java:184) > javax.servlet.http.HttpServlet.service(HttpServlet.java:802) > > *note* _The full stack trace of the root cause is available in the > Apache Tomcat/5.0.30 logs._ > > Googling did not help with this problem. Strange, I see no reason why > the cast of org.apache.commons.dbcp.BasicDataSource to itself > (org.apache.commons.dbcp.BasicDataSource) should not work. I have > tried removing commons-dbcp-1.2.1.jar from $TOMCAT _HOME/common/lib > but then I get the following: > > *description* _The server encountered an internal error () that > prevented it from fulfilling this request._ > *exception* > java.lang.RuntimeException: javax.naming.NamingException: Cannot create resource instance > org.molgenis.assets.server.AbstractMolgenisServlet.handleGUIrequest(AbstractMolgenisServlet.java:215) > org.molgenis.assets.server.AbstractMolgenisServlet.service(AbstractMolgenisServlet.java:184) > javax.servlet.http.HttpServlet.service(HttpServlet.java:802) > > *note* _The full stack trace of the root cause is available in the > Apache Tomcat/5.0.30 logs._ > > Any ideas? > > Best, > Frank > > > > From: A.S...@ru... > > Subject: Re: [Molgenis-users] Where should I put molgenis-3.0.3.jar ? > > To: fra...@ho...; mol...@li... > > Date: Sat, 29 Nov 2008 12:39:32 +0100 > > > > Hi Frank, > > > > I'm not really an eclipse guru, but it sounds as if your eclipse > > environment is not aware of the tomcat server. > > > > I think you should add your Tomcat instance under under the server --> > > runtime environment --> add option in eclipse preferences. > > > > I think you can run the project on that server afterwards. > > good luck. > > > > Ate > > > > think you do not haveOn Fri, 28 Nov 2008 15:33:02 +0000 > > Frank van Zimmeren <fra...@ho...> wrote: > > > > > > Great! MolgenisGenerate now runs without any problems. So does > > >MolgenisUpdateDatabase. > > > > > > I am now at step 5 of chapter 1.2 of the manual: > > > "Run the MOLGENIS and see if you like it already.Right-click the > > >'molgenis' project folder and choose 'run > > > as' and ' run on server"I do not have the option 'run on > > >server'...Frank > > > > > >> Subject: Re: [Molgenis-users] Where should I put molgenis-3.0.3.jar > > >>? > > >> From: A.S...@ru... > > >> To: fra...@ho... > > >> CC: mol...@li... > > >> Date: Fri, 28 Nov 2008 15:38:38 +0100 > > >> > > >> I think you need to add: > > >> > > >> output_web = WebContent > > >> > > >> (or the correct path to your webfolder) to the output section of > > >>your > > >> molgenis.properties file. > > >> > > >> Ate > > >> > > >> On Fri, 2008-11-28 at 14:21 +0000, Frank van Zimmeren wrote: > > >> > Hello Ate, > > >> > > > >> > Thank you! That did the trick. The program gets further but now > > >>ends > > >> > with: > > >> > > > >> > Exception in thread "main" > > >> > java.io.FileNotFoundException: /META-INF/context.xml (No such file > > >>or > > >> > directory) > > >> > at java.io.FileOutputStream.open(Native Method) > > >> > at java.io.FileOutputStream.<init>(FileOutputStream.java:179) > > >> > at java.io.FileOutputStream.<init>(FileOutputStream.java:131) > > >> > at > > >> > > > > >>org.molgenis.generate.servlet.MolgenisServletContextGen.generate(MolgenisServletContextGen.java:44) > > >> > at > > >> > > > > >>org.molgenis.generate.MolgenisFactory.generate(MolgenisFactory.java:244) > > >> > at > > >> > > > >>org.molgenis.generate.MolgenisFactory.run(MolgenisFactory.java:325) > > >> > at > > >> > > > >>org.molgenis.generate.MolgenisFactory.main(MolgenisFactory.java:342) > > >> > at MolgenisGenerate.main(MolgenisGenerate.java:7) > > >> > > > >> > This file is present and has read permission for all users. Do I > > >>need > > >> > to set a path somewhere? > > >> > > > >> > Best, > > >> > Frank > > >> > > > >> > > From: A.S...@ru... > > >> > > To: mol...@li... > > >> > > Date: Wed, 26 Nov 2008 15:40:50 +0100 > > >> > > Subject: Re: [Molgenis-users] Where should I put > > >> > molgenis-3.0.3.jar ? > > >> > > > > >> > > Hello Frank, > > >> > > > > >> > > I'm not sure whether this is related to your error, but I just > > >> > notice > > >> > > the libgcj.so.90 in your error, suggesting that you use gnu > > >>java. > > >> > > > > >> > > I vaguely remember that I had to install the ia32-java6-sun > > >>packages > > >> > and > > >> > > use sun java as default workspace jre before things worked in > > >> > ubuntu. > > >> > > > > >> > > Ate > > >> > > > > >> > > > > >> > > > > >> > > > > >> > > On Wed, 2008-11-26 at 13:50 +0000, Frank van Zimmeren wrote: > > >> > > > Dear Morris, > > >> > > > > > >> > > > Thank you for your help. > > >> > > > > > >> > > > That library is in my Java Build Path. The library is named > > >> > "Persisted > > >> > > > container [org.eclipse.jst.j2ee.internal.web.container for > > >>project > > >> > > > [molgenis3_distro]] > > >> > > > > > >> > > > However, after adding the library again I do not get the error > > >> > message > > >> > > > about MolgenisFactory anymore. But now I get the following: > > >> > > > > > >> > > > Exception in thread "main" java.lang.IllegalAccessError: > > >> > > > org.molgenis.language.MolgenisLanguage can't access class > > >> > > > org.molgenis.language.syntax.UISchema$Type > > >> > > > at java.lang.Class.isAnonymousClass(libgcj.so.90) > > >> > > > at java.lang.Class.getSimpleName(libgcj.so.90) > > >> > > > at > > >> > > > > > >> > > > > >>org.molgenis.language.MolgenisLanguage.<clinit>(MolgenisLanguage.java:23) > > >> > > > at java.lang.Class.initializeClass(libgcj.so.90) > > >> > > > at > > >> > > > > > >> > > > >>org.molgenis.generate.MolgenisFactory.run(MolgenisFactory.java:315) > > >> > > > at > > >> > > > > > >> > > > >>org.molgenis.generate.MolgenisFactory.main(MolgenisFactory.java:342) > > >> > > > at MolgenisGenerate.main(MolgenisGenerate.java:7) > > >> > > > > > >> > > > I see UISchema$Type.class in molgenis-3.0.3.jar but I do not > > >>see > > >> > it in > > >> > > > my library in Eclipse. I'm at a loss. > > >> > > > > > >> > > > Best, > > >> > > > Frank > > >> > > > > > >> > > > > Date: Wed, 26 Nov 2008 10:05:21 +0100 > > >> > > > > From: m.a...@ru... > > >> > > > > To: fra...@ho...; > > >> > > > mol...@li... > > >> > > > > Subject: Re: [Molgenis-users] Where should I put > > >> > > > molgenis-3.0.3.jar ? > > >> > > > > > > >> > > > > Dear Frank, > > >> > > > > > > >> > > > > Normally one downloads the Eclipse workspace, and that > > >>should > > >> > work. > > >> > > > > It seems there is a path issue; all the jars are in > > >> > > > WebContent/WEB-INF/lib > > >> > > > > Check your Java Build Path (right-click project -> > > >>properties) > > >> > to > > >> > > > see of > > >> > > > > they are loaded. > > >> > > > > Also a clean built may help. > > >> > > > > > > >> > > > > (The seperate jar is only for people who already downloaded > > >>a > > >> > > > previous > > >> > > > > version; the you can paste that into your > > >>WebContent/WEB-INF/lib > > >> > to > > >> > > > be > > >> > > > > updated. > > >> > > > > So that shouldn't help in your situation) > > >> > > > > > > >> > > > > I hope this helps, > > >> > > > > Morris > > >> > > > > > > >> > > > > Frank van Zimmeren wrote: > > >> > > > > > Hello, > > >> > > > > > > > >> > > > > > I am trying to install and use Molgenis. I have unzipped > > >>the > > >> > > > molgenis > > >> > > > > > workspace as described in the manual. I am, however, stuck > > >>at > > >> > > > chapter > > >> > > > > > 1.2 step 3: "Go to the folder 'handwritten/java' and > > >> > right-click > > >> > > > > > 'MolgenisGenerate' Choose 'run as' and then 'run as java > > >> > > > > > application'". I get the following error: > > >> > > > > > > > >> > > > > > Exception in thread "main" java.lang.NoClassDefFoundError: > > >> > > > > > org.molgenis.generate.MolgenisFactory > > >> > > > > > at MolgenisGenerate.main(MolgenisGenerate.java:7) > > >> > > > > > > > >> > > > > > I found the MolgenisFactory.java and .class in > > >> > molgenis-3.0.3.jar > > >> > > > > > which is also on the SourceForge page. But I did not find > > >>any > > >> > > > > > documentation about this .jar. I have tried putting it in > > >> > > > > > /usr/lib/java but this does not help. Where should I put > > >> > > > this .jar? > > >> > > > > > > > >> > > > > > Best, > > >> > > > > > Frank van Zimmeren > > >> > > > > > > > >> > > > > > > > >> > > > > > >> > > > > >>------------------------------------------------------------------------ > > >> > > > > > Windows Live Hotmail now works up to 70% faster. Sign up > > >> > today. > > >> > > > > > > > >> > > > > > >> > > > > >><http://windowslive.com/Explore/Hotmail?ocid=TXT_TAGLM_WL_hotmail_acq_faster_112008> > > > >> > > > > > > > >> > > > > > > > >> > > > > > >> > > > > >>------------------------------------------------------------------------ > > >> > > > > > > > >> > > > > > > > >> > > > > > >> > > > > >>------------------------------------------------------------------------- > > >> > > > > > This SF.Net email is sponsored by the Moblin Your Move > > >> > Developer's > > >> > > > challenge > > >> > > > > > Build the coolest Linux based applications with Moblin SDK > > >>& > > >> > win > > >> > > > great prizes > > >> > > > > > Grand prize is a trip for two to an Open Source event > > >>anywhere > > >> > in > > >> > > > the world > > >> > > > > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > >> > > > > > > > >> > > > > > >> > > > > >>------------------------------------------------------------------------ > > >> > > > > > > > >> > > > > > _______________________________________________ > > >> > > > > > Molgenis-users mailing list > > >> > > > > > Mol...@li... > > >> > > > > > > > >>https://lists.sourceforge.net/lists/listinfo/molgenis-users > > >> > > > > > > > >> > > > > > > >> > > > > > >> > > > > > >> > > > > > >> > > > >>______________________________________________________________________ > > >> > > > Access your email online and on the go with Windows Live > > >>Hotmail. > > >> > Sign > > >> > > > up today. > > >> > > > > > >> > > > > >>------------------------------------------------------------------------- > > >> > > > This SF.Net email is sponsored by the Moblin Your Move > > >>Developer's > > >> > challenge > > >> > > > Build the coolest Linux based applications with Moblin SDK & > > >>win > > >> > great prizes > > >> > > > Grand prize is a trip for two to an Open Source event anywhere > > >>in > > >> > the world > > >> > > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > >> > > > _______________________________________________ Molgenis-users > > >> > mailing list Mol...@li... > > >> > https://lists.sourceforge.net/lists/listinfo/molgenis-users > > >> > > > > >> > > > > >> > > > > >> > > > > >>------------------------------------------------------------------------- > > >> > > This SF.Net email is sponsored by the Moblin Your Move > > >>Developer's > > >> > challenge > > >> > > Build the coolest Linux based applications with Moblin SDK & win > > >> > great prizes > > >> > > Grand prize is a trip for two to an Open Source event anywhere > > >>in > > >> > the world > > >> > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > >> > > _______________________________________________ > > >> > > Molgenis-users mailing list > > >> > > Mol...@li... > > >> > > https://lists.sourceforge.net/lists/listinfo/molgenis-users > > >> > > > >> > > > >> > > > >>______________________________________________________________________ > > >> > Access your email online and on the go with Windows Live Hotmail. > > >>Sign > > >> > up today. > > >> > > > > >>------------------------------------------------------------------------- > > >> > This SF.Net email is sponsored by the Moblin Your Move Developer's > > >>challenge > > >> > Build the coolest Linux based applications with Moblin SDK & win > > >>great prizes > > >> > Grand prize is a trip for two to an Open Source event anywhere in > > >>the world > > >> > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > >> > _______________________________________________ Molgenis-users > > >>mailing list Mol...@li... > > >>https://lists.sourceforge.net/lists/listinfo/molgenis-users > > >> > > > > > > _________________________________________________________________ > > > Proud to be a PC? Show the world. Download the “I’m a PC” Messenger > > >themepack now. > > > hthttp://clk.atdmt.com/MRT/go/119642558/direct/01/ > > > > ------------------------------------------------------------------------ > Send e-mail faster without improving your typing skills. Get your > Hotmail® account. > <http://windowslive.com/Explore/hotmail?ocid=TXT_TAGLM_WL_hotmail_acq_speed_122008> > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------------ > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. > The future of the web can't happen without you. Join us at MIX09 to help > pave the way to the Next Web now. Learn more and register at > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ > ------------------------------------------------------------------------ > > _______________________________________________ > Molgenis-users mailing list > Mol...@li... > https://lists.sourceforge.net/lists/listinfo/molgenis-users > |
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From: Morris S. <m.a...@ru...> - 2008-12-10 08:26:44
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Dear Miguel, I think your problem has to do with the path to META-INF/context.xml The default setting doesn't work for you. Solution: Edit molgenis.properties file In the section "# Output options" add the output_web option as follows (assuming your META-INF folder in WebContent) # the directory where the documentation is generated into output_web = WebContent Hope this helps, (I will make this default in the next release). Morris Miguel Rojas Cherto wrote: > Dear! > > I am Miguel from Universiteit Leiden by the group of Thomas Hankemeier. > I was playing with the new version of molgenis3 downloaded from > sourceforge. All work fine, synchronization with mysql, web-services > over wsdl. But afterwards I wanted to create a new model with the > MolgenisGenerator class following the README instructions. It is not > possible in my case because I receive a strange error. > > 6165 WARN [PluginScreenJavaTemplateGen] Skipped because exists: > handwritten/java/plugins/dbquery/ExperimentQueryPlugin.java > Exception in thread "main" > java.io.FileNotFoundException: /META-INF/context.xml (No such file or > directory) > at java.io.FileOutputStream.open(Native Method) > at java.io.FileOutputStream.<init>(FileOutputStream.java:209) > at java.io.FileOutputStream.<init>(FileOutputStream.java:160) > at > org.molgenis.generate.servlet.MolgenisServletContextGen.generate(MolgenisServletContextGen.java:44) > at > org.molgenis.generate.MolgenisFactory.generate(MolgenisFactory.java:244) > at org.molgenis.generate.MolgenisFactory.run(MolgenisFactory.java:325) > at org.molgenis.generate.MolgenisFactory.main(MolgenisFactory.java:342) > at MolgenisGenerate.main(MolgenisGenerate.java:7) > > It is saying it can not found the file /META-INF/context.xml when it is > there. I tried again to compile with new extraction of the zip. But the > same. > > I have a Ubuntu SO. I don't know if this problem is a particular case of > linux. When I was using molgenis2 with ant the compilation worked > perfectly. > > Do you know what I am doing wrong? I would thank you if you could solve > my doubt. > > > > Thanks in advance, > > Best regards, > Miquel > > > |
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From: Miguel R. C. <m....@la...> - 2008-12-09 19:11:55
|
Dear! I am Miguel from Universiteit Leiden by the group of Thomas Hankemeier. I was playing with the new version of molgenis3 downloaded from sourceforge. All work fine, synchronization with mysql, web-services over wsdl. But afterwards I wanted to create a new model with the MolgenisGenerator class following the README instructions. It is not possible in my case because I receive a strange error. 6165 WARN [PluginScreenJavaTemplateGen] Skipped because exists: handwritten/java/plugins/dbquery/ExperimentQueryPlugin.java Exception in thread "main" java.io.FileNotFoundException: /META-INF/context.xml (No such file or directory) at java.io.FileOutputStream.open(Native Method) at java.io.FileOutputStream.<init>(FileOutputStream.java:209) at java.io.FileOutputStream.<init>(FileOutputStream.java:160) at org.molgenis.generate.servlet.MolgenisServletContextGen.generate(MolgenisServletContextGen.java:44) at org.molgenis.generate.MolgenisFactory.generate(MolgenisFactory.java:244) at org.molgenis.generate.MolgenisFactory.run(MolgenisFactory.java:325) at org.molgenis.generate.MolgenisFactory.main(MolgenisFactory.java:342) at MolgenisGenerate.main(MolgenisGenerate.java:7) It is saying it can not found the file /META-INF/context.xml when it is there. I tried again to compile with new extraction of the zip. But the same. I have a Ubuntu SO. I don't know if this problem is a particular case of linux. When I was using molgenis2 with ant the compilation worked perfectly. Do you know what I am doing wrong? I would thank you if you could solve my doubt. Thanks in advance, Best regards, Miquel -- Miguel Rojas Cherto Netherlands Metabolomics Centre Analytical Biosciences Leiden University Einsteinweg 55 NL-2333 CC Leiden tel : +31 715276326 fax: +31 715274277 |
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From: Frank v. Z. <fra...@ho...> - 2008-12-09 16:31:58
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Hello again, I have finally managed to get a Tomcat version to work with Eclipse. I could not get version 6.0 nor 5.5 to work, but 5.0 will. I can now successfully use the "Run on server" option. However http://localhost:8080/molgenis/molgenis.do gives the following error report: HTTP Status 500 - type Exception reportmessage description The server encountered an internal error () that prevented it from fulfilling this request.exception java.lang.RuntimeException: java.lang.ClassCastException: org.apache.commons.dbcp.BasicDataSource cannot be cast to org.apache.commons.dbcp.BasicDataSource org.molgenis.assets.server.AbstractMolgenisServlet.handleGUIrequest(AbstractMolgenisServlet.java:215) org.molgenis.assets.server.AbstractMolgenisServlet.service(AbstractMolgenisServlet.java:184) javax.servlet.http.HttpServlet.service(HttpServlet.java:802) note The full stack trace of the root cause is available in the Apache Tomcat/5.0.30 logs. Googling did not help with this problem. Strange, I see no reason why the cast of org.apache.commons.dbcp.BasicDataSource to itself (org.apache.commons.dbcp.BasicDataSource) should not work. I have tried removing commons-dbcp-1.2.1.jar from $TOMCAT _HOME/common/lib but then I get the following: description The server encountered an internal error () that prevented it from fulfilling this request.exception java.lang.RuntimeException: javax.naming.NamingException: Cannot create resource instance org.molgenis.assets.server.AbstractMolgenisServlet.handleGUIrequest(AbstractMolgenisServlet.java:215) org.molgenis.assets.server.AbstractMolgenisServlet.service(AbstractMolgenisServlet.java:184) javax.servlet.http.HttpServlet.service(HttpServlet.java:802) note The full stack trace of the root cause is available in the Apache Tomcat/5.0.30 logs. Any ideas? Best, Frank > From: A.S...@ru... > Subject: Re: [Molgenis-users] Where should I put molgenis-3.0.3.jar ? > To: fra...@ho...; mol...@li... > Date: Sat, 29 Nov 2008 12:39:32 +0100 > > Hi Frank, > > I'm not really an eclipse guru, but it sounds as if your eclipse > environment is not aware of the tomcat server. > > I think you should add your Tomcat instance under under the server --> > runtime environment --> add option in eclipse preferences. > > I think you can run the project on that server afterwards. > good luck. > > Ate > > think you do not haveOn Fri, 28 Nov 2008 15:33:02 +0000 > Frank van Zimmeren <fra...@ho...> wrote: > > > > Great! MolgenisGenerate now runs without any problems. So does > >MolgenisUpdateDatabase. > > > > I am now at step 5 of chapter 1.2 of the manual: > > "Run the MOLGENIS and see if you like it already.Right-click the > >'molgenis' project folder and choose 'run > > as' and ' run on server"I do not have the option 'run on > >server'...Frank > > > >> Subject: Re: [Molgenis-users] Where should I put molgenis-3.0.3.jar > >>? > >> From: A.S...@ru... > >> To: fra...@ho... > >> CC: mol...@li... > >> Date: Fri, 28 Nov 2008 15:38:38 +0100 > >> > >> I think you need to add: > >> > >> output_web = WebContent > >> > >> (or the correct path to your webfolder) to the output section of > >>your > >> molgenis.properties file. > >> > >> Ate > >> > >> On Fri, 2008-11-28 at 14:21 +0000, Frank van Zimmeren wrote: > >> > Hello Ate, > >> > > >> > Thank you! That did the trick. The program gets further but now > >>ends > >> > with: > >> > > >> > Exception in thread "main" > >> > java.io.FileNotFoundException: /META-INF/context.xml (No such file > >>or > >> > directory) > >> > at java.io.FileOutputStream.open(Native Method) > >> > at java.io.FileOutputStream.<init>(FileOutputStream.java:179) > >> > at java.io.FileOutputStream.<init>(FileOutputStream.java:131) > >> > at > >> > > >>org.molgenis.generate.servlet.MolgenisServletContextGen.generate(MolgenisServletContextGen.java:44) > >> > at > >> > > >>org.molgenis.generate.MolgenisFactory.generate(MolgenisFactory.java:244) > >> > at > >> > > >>org.molgenis.generate.MolgenisFactory.run(MolgenisFactory.java:325) > >> > at > >> > > >>org.molgenis.generate.MolgenisFactory.main(MolgenisFactory.java:342) > >> > at MolgenisGenerate.main(MolgenisGenerate.java:7) > >> > > >> > This file is present and has read permission for all users. Do I > >>need > >> > to set a path somewhere? > >> > > >> > Best, > >> > Frank > >> > > >> > > From: A.S...@ru... > >> > > To: mol...@li... > >> > > Date: Wed, 26 Nov 2008 15:40:50 +0100 > >> > > Subject: Re: [Molgenis-users] Where should I put > >> > molgenis-3.0.3.jar ? > >> > > > >> > > Hello Frank, > >> > > > >> > > I'm not sure whether this is related to your error, but I just > >> > notice > >> > > the libgcj.so.90 in your error, suggesting that you use gnu > >>java. > >> > > > >> > > I vaguely remember that I had to install the ia32-java6-sun > >>packages > >> > and > >> > > use sun java as default workspace jre before things worked in > >> > ubuntu. > >> > > > >> > > Ate > >> > > > >> > > > >> > > > >> > > > >> > > On Wed, 2008-11-26 at 13:50 +0000, Frank van Zimmeren wrote: > >> > > > Dear Morris, > >> > > > > >> > > > Thank you for your help. > >> > > > > >> > > > That library is in my Java Build Path. The library is named > >> > "Persisted > >> > > > container [org.eclipse.jst.j2ee.internal.web.container for > >>project > >> > > > [molgenis3_distro]] > >> > > > > >> > > > However, after adding the library again I do not get the error > >> > message > >> > > > about MolgenisFactory anymore. But now I get the following: > >> > > > > >> > > > Exception in thread "main" java.lang.IllegalAccessError: > >> > > > org.molgenis.language.MolgenisLanguage can't access class > >> > > > org.molgenis.language.syntax.UISchema$Type > >> > > > at java.lang.Class.isAnonymousClass(libgcj.so.90) > >> > > > at java.lang.Class.getSimpleName(libgcj.so.90) > >> > > > at > >> > > > > >> > > >>org.molgenis.language.MolgenisLanguage.<clinit>(MolgenisLanguage.java:23) > >> > > > at java.lang.Class.initializeClass(libgcj.so.90) > >> > > > at > >> > > > > >> > > >>org.molgenis.generate.MolgenisFactory.run(MolgenisFactory.java:315) > >> > > > at > >> > > > > >> > > >>org.molgenis.generate.MolgenisFactory.main(MolgenisFactory.java:342) > >> > > > at MolgenisGenerate.main(MolgenisGenerate.java:7) > >> > > > > >> > > > I see UISchema$Type.class in molgenis-3.0.3.jar but I do not > >>see > >> > it in > >> > > > my library in Eclipse. I'm at a loss. > >> > > > > >> > > > Best, > >> > > > Frank > >> > > > > >> > > > > Date: Wed, 26 Nov 2008 10:05:21 +0100 > >> > > > > From: m.a...@ru... > >> > > > > To: fra...@ho...; > >> > > > mol...@li... > >> > > > > Subject: Re: [Molgenis-users] Where should I put > >> > > > molgenis-3.0.3.jar ? > >> > > > > > >> > > > > Dear Frank, > >> > > > > > >> > > > > Normally one downloads the Eclipse workspace, and that > >>should > >> > work. > >> > > > > It seems there is a path issue; all the jars are in > >> > > > WebContent/WEB-INF/lib > >> > > > > Check your Java Build Path (right-click project -> > >>properties) > >> > to > >> > > > see of > >> > > > > they are loaded. > >> > > > > Also a clean built may help. > >> > > > > > >> > > > > (The seperate jar is only for people who already downloaded > >>a > >> > > > previous > >> > > > > version; the you can paste that into your > >>WebContent/WEB-INF/lib > >> > to > >> > > > be > >> > > > > updated. > >> > > > > So that shouldn't help in your situation) > >> > > > > > >> > > > > I hope this helps, > >> > > > > Morris > >> > > > > > >> > > > > Frank van Zimmeren wrote: > >> > > > > > Hello, > >> > > > > > > >> > > > > > I am trying to install and use Molgenis. I have unzipped > >>the > >> > > > molgenis > >> > > > > > workspace as described in the manual. I am, however, stuck > >>at > >> > > > chapter > >> > > > > > 1.2 step 3: "Go to the folder 'handwritten/java' and > >> > right-click > >> > > > > > 'MolgenisGenerate' Choose 'run as' and then 'run as java > >> > > > > > application'". I get the following error: > >> > > > > > > >> > > > > > Exception in thread "main" java.lang.NoClassDefFoundError: > >> > > > > > org.molgenis.generate.MolgenisFactory > >> > > > > > at MolgenisGenerate.main(MolgenisGenerate.java:7) > >> > > > > > > >> > > > > > I found the MolgenisFactory.java and .class in > >> > molgenis-3.0.3.jar > >> > > > > > which is also on the SourceForge page. But I did not find > >>any > >> > > > > > documentation about this .jar. I have tried putting it in > >> > > > > > /usr/lib/java but this does not help. Where should I put > >> > > > this .jar? > >> > > > > > > >> > > > > > Best, > >> > > > > > Frank van Zimmeren > >> > > > > > > >> > > > > > > >> > > > > >> > > >>------------------------------------------------------------------------ > >> > > > > > Windows Live Hotmail now works up to 70% faster. Sign up > >> > today. > >> > > > > > > >> > > > > >> > > >><http://windowslive.com/Explore/Hotmail?ocid=TXT_TAGLM_WL_hotmail_acq_faster_112008> > >> > > > > > > >> > > > > > > >> > > > > >> > > >>------------------------------------------------------------------------ > >> > > > > > > >> > > > > > > >> > > > > >> > > >>------------------------------------------------------------------------- > >> > > > > > This SF.Net email is sponsored by the Moblin Your Move > >> > Developer's > >> > > > challenge > >> > > > > > Build the coolest Linux based applications with Moblin SDK > >>& > >> > win > >> > > > great prizes > >> > > > > > Grand prize is a trip for two to an Open Source event > >>anywhere > >> > in > >> > > > the world > >> > > > > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > >> > > > > > > >> > > > > >> > > >>------------------------------------------------------------------------ > >> > > > > > > >> > > > > > _______________________________________________ > >> > > > > > Molgenis-users mailing list > >> > > > > > Mol...@li... > >> > > > > > > >>https://lists.sourceforge.net/lists/listinfo/molgenis-users > >> > > > > > > >> > > > > > >> > > > > >> > > > > >> > > > > >> > > >>______________________________________________________________________ > >> > > > Access your email online and on the go with Windows Live > >>Hotmail. > >> > Sign > >> > > > up today. > >> > > > > >> > > >>------------------------------------------------------------------------- > >> > > > This SF.Net email is sponsored by the Moblin Your Move > >>Developer's > >> > challenge > >> > > > Build the coolest Linux based applications with Moblin SDK & > >>win > >> > great prizes > >> > > > Grand prize is a trip for two to an Open Source event anywhere > >>in > >> > the world > >> > > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > >> > > > _______________________________________________ Molgenis-users > >> > mailing list Mol...@li... > >> > https://lists.sourceforge.net/lists/listinfo/molgenis-users > >> > > > >> > > > >> > > > >> > > >>------------------------------------------------------------------------- > >> > > This SF.Net email is sponsored by the Moblin Your Move > >>Developer's > >> > challenge > >> > > Build the coolest Linux based applications with Moblin SDK & win > >> > great prizes > >> > > Grand prize is a trip for two to an Open Source event anywhere > >>in > >> > the world > >> > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > >> > > _______________________________________________ > >> > > Molgenis-users mailing list > >> > > Mol...@li... > >> > > https://lists.sourceforge.net/lists/listinfo/molgenis-users > >> > > >> > > >> > > >>______________________________________________________________________ > >> > Access your email online and on the go with Windows Live Hotmail. > >>Sign > >> > up today. > >> > > >>------------------------------------------------------------------------- > >> > This SF.Net email is sponsored by the Moblin Your Move Developer's > >>challenge > >> > Build the coolest Linux based applications with Moblin SDK & win > >>great prizes > >> > Grand prize is a trip for two to an Open Source event anywhere in > >>the world > >> > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > >> > _______________________________________________ Molgenis-users > >>mailing list Mol...@li... > >>https://lists.sourceforge.net/lists/listinfo/molgenis-users > >> > > > > _________________________________________________________________ > > Proud to be a PC? Show the world. Download the “I’m a PC” Messenger > >themepack now. > > hthttp://clk.atdmt.com/MRT/go/119642558/direct/01/ > _________________________________________________________________ Send e-mail faster without improving your typing skills. http://windowslive.com/Explore/hotmail?ocid=TXT_TAGLM_WL_hotmail_acq_speed_122008 |
|
From: A.S.Boerema <A.S...@ru...> - 2008-11-29 12:57:00
|
Hi Frank, I'm not really an eclipse guru, but it sounds as if your eclipse environment is not aware of the tomcat server. I think you should add your Tomcat instance under under the server --> runtime environment --> add option in eclipse preferences. I think you can run the project on that server afterwards. good luck. Ate think you do not haveOn Fri, 28 Nov 2008 15:33:02 +0000 Frank van Zimmeren <fra...@ho...> wrote: > > Great! MolgenisGenerate now runs without any problems. So does >MolgenisUpdateDatabase. > > I am now at step 5 of chapter 1.2 of the manual: > "Run the MOLGENIS and see if you like it already.Right-click the >'molgenis' project folder and choose 'run > as' and ' run on server"I do not have the option 'run on >server'...Frank > >> Subject: Re: [Molgenis-users] Where should I put molgenis-3.0.3.jar >>? >> From: A.S...@ru... >> To: fra...@ho... >> CC: mol...@li... >> Date: Fri, 28 Nov 2008 15:38:38 +0100 >> >> I think you need to add: >> >> output_web = WebContent >> >> (or the correct path to your webfolder) to the output section of >>your >> molgenis.properties file. >> >> Ate >> >> On Fri, 2008-11-28 at 14:21 +0000, Frank van Zimmeren wrote: >> > Hello Ate, >> > >> > Thank you! That did the trick. The program gets further but now >>ends >> > with: >> > >> > Exception in thread "main" >> > java.io.FileNotFoundException: /META-INF/context.xml (No such file >>or >> > directory) >> > at java.io.FileOutputStream.open(Native Method) >> > at java.io.FileOutputStream.<init>(FileOutputStream.java:179) >> > at java.io.FileOutputStream.<init>(FileOutputStream.java:131) >> > at >> > >>org.molgenis.generate.servlet.MolgenisServletContextGen.generate(MolgenisServletContextGen.java:44) >> > at >> > >>org.molgenis.generate.MolgenisFactory.generate(MolgenisFactory.java:244) >> > at >> > >>org.molgenis.generate.MolgenisFactory.run(MolgenisFactory.java:325) >> > at >> > >>org.molgenis.generate.MolgenisFactory.main(MolgenisFactory.java:342) >> > at MolgenisGenerate.main(MolgenisGenerate.java:7) >> > >> > This file is present and has read permission for all users. Do I >>need >> > to set a path somewhere? >> > >> > Best, >> > Frank >> > >> > > From: A.S...@ru... >> > > To: mol...@li... >> > > Date: Wed, 26 Nov 2008 15:40:50 +0100 >> > > Subject: Re: [Molgenis-users] Where should I put >> > molgenis-3.0.3.jar ? >> > > >> > > Hello Frank, >> > > >> > > I'm not sure whether this is related to your error, but I just >> > notice >> > > the libgcj.so.90 in your error, suggesting that you use gnu >>java. >> > > >> > > I vaguely remember that I had to install the ia32-java6-sun >>packages >> > and >> > > use sun java as default workspace jre before things worked in >> > ubuntu. >> > > >> > > Ate >> > > >> > > >> > > >> > > >> > > On Wed, 2008-11-26 at 13:50 +0000, Frank van Zimmeren wrote: >> > > > Dear Morris, >> > > > >> > > > Thank you for your help. >> > > > >> > > > That library is in my Java Build Path. The library is named >> > "Persisted >> > > > container [org.eclipse.jst.j2ee.internal.web.container for >>project >> > > > [molgenis3_distro]] >> > > > >> > > > However, after adding the library again I do not get the error >> > message >> > > > about MolgenisFactory anymore. But now I get the following: >> > > > >> > > > Exception in thread "main" java.lang.IllegalAccessError: >> > > > org.molgenis.language.MolgenisLanguage can't access class >> > > > org.molgenis.language.syntax.UISchema$Type >> > > > at java.lang.Class.isAnonymousClass(libgcj.so.90) >> > > > at java.lang.Class.getSimpleName(libgcj.so.90) >> > > > at >> > > > >> > >>org.molgenis.language.MolgenisLanguage.<clinit>(MolgenisLanguage.java:23) >> > > > at java.lang.Class.initializeClass(libgcj.so.90) >> > > > at >> > > > >> > >>org.molgenis.generate.MolgenisFactory.run(MolgenisFactory.java:315) >> > > > at >> > > > >> > >>org.molgenis.generate.MolgenisFactory.main(MolgenisFactory.java:342) >> > > > at MolgenisGenerate.main(MolgenisGenerate.java:7) >> > > > >> > > > I see UISchema$Type.class in molgenis-3.0.3.jar but I do not >>see >> > it in >> > > > my library in Eclipse. I'm at a loss. >> > > > >> > > > Best, >> > > > Frank >> > > > >> > > > > Date: Wed, 26 Nov 2008 10:05:21 +0100 >> > > > > From: m.a...@ru... >> > > > > To: fra...@ho...; >> > > > mol...@li... >> > > > > Subject: Re: [Molgenis-users] Where should I put >> > > > molgenis-3.0.3.jar ? >> > > > > >> > > > > Dear Frank, >> > > > > >> > > > > Normally one downloads the Eclipse workspace, and that >>should >> > work. >> > > > > It seems there is a path issue; all the jars are in >> > > > WebContent/WEB-INF/lib >> > > > > Check your Java Build Path (right-click project -> >>properties) >> > to >> > > > see of >> > > > > they are loaded. >> > > > > Also a clean built may help. >> > > > > >> > > > > (The seperate jar is only for people who already downloaded >>a >> > > > previous >> > > > > version; the you can paste that into your >>WebContent/WEB-INF/lib >> > to >> > > > be >> > > > > updated. >> > > > > So that shouldn't help in your situation) >> > > > > >> > > > > I hope this helps, >> > > > > Morris >> > > > > >> > > > > Frank van Zimmeren wrote: >> > > > > > Hello, >> > > > > > >> > > > > > I am trying to install and use Molgenis. I have unzipped >>the >> > > > molgenis >> > > > > > workspace as described in the manual. I am, however, stuck >>at >> > > > chapter >> > > > > > 1.2 step 3: "Go to the folder 'handwritten/java' and >> > right-click >> > > > > > 'MolgenisGenerate' Choose 'run as' and then 'run as java >> > > > > > application'". I get the following error: >> > > > > > >> > > > > > Exception in thread "main" java.lang.NoClassDefFoundError: >> > > > > > org.molgenis.generate.MolgenisFactory >> > > > > > at MolgenisGenerate.main(MolgenisGenerate.java:7) >> > > > > > >> > > > > > I found the MolgenisFactory.java and .class in >> > molgenis-3.0.3.jar >> > > > > > which is also on the SourceForge page. But I did not find >>any >> > > > > > documentation about this .jar. I have tried putting it in >> > > > > > /usr/lib/java but this does not help. Where should I put >> > > > this .jar? >> > > > > > >> > > > > > Best, >> > > > > > Frank van Zimmeren >> > > > > > >> > > > > > >> > > > >> > >>------------------------------------------------------------------------ >> > > > > > Windows Live Hotmail now works up to 70% faster. Sign up >> > today. >> > > > > > >> > > > >> > >><http://windowslive.com/Explore/Hotmail?ocid=TXT_TAGLM_WL_hotmail_acq_faster_112008> >> > > > > > >> > > > > > >> > > > >> > >>------------------------------------------------------------------------ >> > > > > > >> > > > > > >> > > > >> > >>------------------------------------------------------------------------- >> > > > > > This SF.Net email is sponsored by the Moblin Your Move >> > Developer's >> > > > challenge >> > > > > > Build the coolest Linux based applications with Moblin SDK >>& >> > win >> > > > great prizes >> > > > > > Grand prize is a trip for two to an Open Source event >>anywhere >> > in >> > > > the world >> > > > > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> > > > > > >> > > > >> > >>------------------------------------------------------------------------ >> > > > > > >> > > > > > _______________________________________________ >> > > > > > Molgenis-users mailing list >> > > > > > Mol...@li... >> > > > > > >>https://lists.sourceforge.net/lists/listinfo/molgenis-users >> > > > > > >> > > > > >> > > > >> > > > >> > > > >> > >>______________________________________________________________________ >> > > > Access your email online and on the go with Windows Live >>Hotmail. >> > Sign >> > > > up today. >> > > > >> > >>------------------------------------------------------------------------- >> > > > This SF.Net email is sponsored by the Moblin Your Move >>Developer's >> > challenge >> > > > Build the coolest Linux based applications with Moblin SDK & >>win >> > great prizes >> > > > Grand prize is a trip for two to an Open Source event anywhere >>in >> > the world >> > > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> > > > _______________________________________________ Molgenis-users >> > mailing list Mol...@li... >> > https://lists.sourceforge.net/lists/listinfo/molgenis-users >> > > >> > > >> > > >> > >>------------------------------------------------------------------------- >> > > This SF.Net email is sponsored by the Moblin Your Move >>Developer's >> > challenge >> > > Build the coolest Linux based applications with Moblin SDK & win >> > great prizes >> > > Grand prize is a trip for two to an Open Source event anywhere >>in >> > the world >> > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> > > _______________________________________________ >> > > Molgenis-users mailing list >> > > Mol...@li... >> > > https://lists.sourceforge.net/lists/listinfo/molgenis-users >> > >> > >> > >>______________________________________________________________________ >> > Access your email online and on the go with Windows Live Hotmail. >>Sign >> > up today. >> > >>------------------------------------------------------------------------- >> > This SF.Net email is sponsored by the Moblin Your Move Developer's >>challenge >> > Build the coolest Linux based applications with Moblin SDK & win >>great prizes >> > Grand prize is a trip for two to an Open Source event anywhere in >>the world >> > http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> > _______________________________________________ Molgenis-users >>mailing list Mol...@li... >>https://lists.sourceforge.net/lists/listinfo/molgenis-users >> > > _________________________________________________________________ > Proud to be a PC? Show the world. Download the “I’m a PC” Messenger >themepack now. > hthttp://clk.atdmt.com/MRT/go/119642558/direct/01/ |
|
From: Frank v. Z. <fra...@ho...> - 2008-11-28 15:33:07
|
Great! MolgenisGenerate now runs without any problems. So does MolgenisUpdateDatabase.
I am now at step 5 of chapter 1.2 of the manual:
"Run the MOLGENIS and see if you like it already.Right-click the 'molgenis' project folder and choose 'run
as' and ' run on server"I do not have the option 'run on server'...Frank
> Subject: Re: [Molgenis-users] Where should I put molgenis-3.0.3.jar ?
> From: A.S...@ru...
> To: fra...@ho...
> CC: mol...@li...
> Date: Fri, 28 Nov 2008 15:38:38 +0100
>
> I think you need to add:
>
> output_web = WebContent
>
> (or the correct path to your webfolder) to the output section of your
> molgenis.properties file.
>
> Ate
>
> On Fri, 2008-11-28 at 14:21 +0000, Frank van Zimmeren wrote:
> > Hello Ate,
> >
> > Thank you! That did the trick. The program gets further but now ends
> > with:
> >
> > Exception in thread "main"
> > java.io.FileNotFoundException: /META-INF/context.xml (No such file or
> > directory)
> > at java.io.FileOutputStream.open(Native Method)
> > at java.io.FileOutputStream.<init>(FileOutputStream.java:179)
> > at java.io.FileOutputStream.<init>(FileOutputStream.java:131)
> > at
> > org.molgenis.generate.servlet.MolgenisServletContextGen.generate(MolgenisServletContextGen.java:44)
> > at
> > org.molgenis.generate.MolgenisFactory.generate(MolgenisFactory.java:244)
> > at
> > org.molgenis.generate.MolgenisFactory.run(MolgenisFactory.java:325)
> > at
> > org.molgenis.generate.MolgenisFactory.main(MolgenisFactory.java:342)
> > at MolgenisGenerate.main(MolgenisGenerate.java:7)
> >
> > This file is present and has read permission for all users. Do I need
> > to set a path somewhere?
> >
> > Best,
> > Frank
> >
> > > From: A.S...@ru...
> > > To: mol...@li...
> > > Date: Wed, 26 Nov 2008 15:40:50 +0100
> > > Subject: Re: [Molgenis-users] Where should I put
> > molgenis-3.0.3.jar ?
> > >
> > > Hello Frank,
> > >
> > > I'm not sure whether this is related to your error, but I just
> > notice
> > > the libgcj.so.90 in your error, suggesting that you use gnu java.
> > >
> > > I vaguely remember that I had to install the ia32-java6-sun packages
> > and
> > > use sun java as default workspace jre before things worked in
> > ubuntu.
> > >
> > > Ate
> > >
> > >
> > >
> > >
> > > On Wed, 2008-11-26 at 13:50 +0000, Frank van Zimmeren wrote:
> > > > Dear Morris,
> > > >
> > > > Thank you for your help.
> > > >
> > > > That library is in my Java Build Path. The library is named
> > "Persisted
> > > > container [org.eclipse.jst.j2ee.internal.web.container for project
> > > > [molgenis3_distro]]
> > > >
> > > > However, after adding the library again I do not get the error
> > message
> > > > about MolgenisFactory anymore. But now I get the following:
> > > >
> > > > Exception in thread "main" java.lang.IllegalAccessError:
> > > > org.molgenis.language.MolgenisLanguage can't access class
> > > > org.molgenis.language.syntax.UISchema$Type
> > > > at java.lang.Class.isAnonymousClass(libgcj.so.90)
> > > > at java.lang.Class.getSimpleName(libgcj.so.90)
> > > > at
> > > >
> > org.molgenis.language.MolgenisLanguage.<clinit>(MolgenisLanguage.java:23)
> > > > at java.lang.Class.initializeClass(libgcj.so.90)
> > > > at
> > > >
> > org.molgenis.generate.MolgenisFactory.run(MolgenisFactory.java:315)
> > > > at
> > > >
> > org.molgenis.generate.MolgenisFactory.main(MolgenisFactory.java:342)
> > > > at MolgenisGenerate.main(MolgenisGenerate.java:7)
> > > >
> > > > I see UISchema$Type.class in molgenis-3.0.3.jar but I do not see
> > it in
> > > > my library in Eclipse. I'm at a loss.
> > > >
> > > > Best,
> > > > Frank
> > > >
> > > > > Date: Wed, 26 Nov 2008 10:05:21 +0100
> > > > > From: m.a...@ru...
> > > > > To: fra...@ho...;
> > > > mol...@li...
> > > > > Subject: Re: [Molgenis-users] Where should I put
> > > > molgenis-3.0.3.jar ?
> > > > >
> > > > > Dear Frank,
> > > > >
> > > > > Normally one downloads the Eclipse workspace, and that should
> > work.
> > > > > It seems there is a path issue; all the jars are in
> > > > WebContent/WEB-INF/lib
> > > > > Check your Java Build Path (right-click project -> properties)
> > to
> > > > see of
> > > > > they are loaded.
> > > > > Also a clean built may help.
> > > > >
> > > > > (The seperate jar is only for people who already downloaded a
> > > > previous
> > > > > version; the you can paste that into your WebContent/WEB-INF/lib
> > to
> > > > be
> > > > > updated.
> > > > > So that shouldn't help in your situation)
> > > > >
> > > > > I hope this helps,
> > > > > Morris
> > > > >
> > > > > Frank van Zimmeren wrote:
> > > > > > Hello,
> > > > > >
> > > > > > I am trying to install and use Molgenis. I have unzipped the
> > > > molgenis
> > > > > > workspace as described in the manual. I am, however, stuck at
> > > > chapter
> > > > > > 1.2 step 3: "Go to the folder 'handwritten/java' and
> > right-click
> > > > > > 'MolgenisGenerate' Choose 'run as' and then 'run as java
> > > > > > application'". I get the following error:
> > > > > >
> > > > > > Exception in thread "main" java.lang.NoClassDefFoundError:
> > > > > > org.molgenis.generate.MolgenisFactory
> > > > > > at MolgenisGenerate.main(MolgenisGenerate.java:7)
> > > > > >
> > > > > > I found the MolgenisFactory.java and .class in
> > molgenis-3.0.3.jar
> > > > > > which is also on the SourceForge page. But I did not find any
> > > > > > documentation about this .jar. I have tried putting it in
> > > > > > /usr/lib/java but this does not help. Where should I put
> > > > this .jar?
> > > > > >
> > > > > > Best,
> > > > > > Frank van Zimmeren
> > > > > >
> > > > > >
> > > >
> > ------------------------------------------------------------------------
> > > > > > Windows Live Hotmail now works up to 70% faster. Sign up
> > today.
> > > > > >
> > > >
> > <http://windowslive.com/Explore/Hotmail?ocid=TXT_TAGLM_WL_hotmail_acq_faster_112008>
> > > > > >
> > > > > >
> > > >
> > ------------------------------------------------------------------------
> > > > > >
> > > > > >
> > > >
> > -------------------------------------------------------------------------
> > > > > > This SF.Net email is sponsored by the Moblin Your Move
> > Developer's
> > > > challenge
> > > > > > Build the coolest Linux based applications with Moblin SDK &
> > win
> > > > great prizes
> > > > > > Grand prize is a trip for two to an Open Source event anywhere
> > in
> > > > the world
> > > > > > http://moblin-contest.org/redirect.php?banner_id=100&url=/
> > > > > >
> > > >
> > ------------------------------------------------------------------------
> > > > > >
> > > > > > _______________________________________________
> > > > > > Molgenis-users mailing list
> > > > > > Mol...@li...
> > > > > > https://lists.sourceforge.net/lists/listinfo/molgenis-users
> > > > > >
> > > > >
> > > >
> > > >
> > > >
> > ______________________________________________________________________
> > > > Access your email online and on the go with Windows Live Hotmail.
> > Sign
> > > > up today.
> > > >
> > -------------------------------------------------------------------------
> > > > This SF.Net email is sponsored by the Moblin Your Move Developer's
> > challenge
> > > > Build the coolest Linux based applications with Moblin SDK & win
> > great prizes
> > > > Grand prize is a trip for two to an Open Source event anywhere in
> > the world
> > > > http://moblin-contest.org/redirect.php?banner_id=100&url=/
> > > > _______________________________________________ Molgenis-users
> > mailing list Mol...@li...
> > https://lists.sourceforge.net/lists/listinfo/molgenis-users
> > >
> > >
> > >
> > -------------------------------------------------------------------------
> > > This SF.Net email is sponsored by the Moblin Your Move Developer's
> > challenge
> > > Build the coolest Linux based applications with Moblin SDK & win
> > great prizes
> > > Grand prize is a trip for two to an Open Source event anywhere in
> > the world
> > > http://moblin-contest.org/redirect.php?banner_id=100&url=/
> > > _______________________________________________
> > > Molgenis-users mailing list
> > > Mol...@li...
> > > https://lists.sourceforge.net/lists/listinfo/molgenis-users
> >
> >
> > ______________________________________________________________________
> > Access your email online and on the go with Windows Live Hotmail. Sign
> > up today.
> > -------------------------------------------------------------------------
> > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> > Build the coolest Linux based applications with Moblin SDK & win great prizes
> > Grand prize is a trip for two to an Open Source event anywhere in the world
> > http://moblin-contest.org/redirect.php?banner_id=100&url=/
> > _______________________________________________ Molgenis-users mailing list Mol...@li... https://lists.sourceforge.net/lists/listinfo/molgenis-users
>
_________________________________________________________________
Proud to be a PC? Show the world. Download the “I’m a PC” Messenger themepack now.
hthttp://clk.atdmt.com/MRT/go/119642558/direct/01/ |
|
From: A.S. B. <A.S...@ru...> - 2008-11-28 14:38:46
|
I think you need to add: output_web = WebContent (or the correct path to your webfolder) to the output section of your molgenis.properties file. Ate On Fri, 2008-11-28 at 14:21 +0000, Frank van Zimmeren wrote: > Hello Ate, > > Thank you! That did the trick. The program gets further but now ends > with: > > Exception in thread "main" > java.io.FileNotFoundException: /META-INF/context.xml (No such file or > directory) > at java.io.FileOutputStream.open(Native Method) > at java.io.FileOutputStream.<init>(FileOutputStream.java:179) > at java.io.FileOutputStream.<init>(FileOutputStream.java:131) > at > org.molgenis.generate.servlet.MolgenisServletContextGen.generate(MolgenisServletContextGen.java:44) > at > org.molgenis.generate.MolgenisFactory.generate(MolgenisFactory.java:244) > at > org.molgenis.generate.MolgenisFactory.run(MolgenisFactory.java:325) > at > org.molgenis.generate.MolgenisFactory.main(MolgenisFactory.java:342) > at MolgenisGenerate.main(MolgenisGenerate.java:7) > > This file is present and has read permission for all users. Do I need > to set a path somewhere? > > Best, > Frank > > > From: A.S...@ru... > > To: mol...@li... > > Date: Wed, 26 Nov 2008 15:40:50 +0100 > > Subject: Re: [Molgenis-users] Where should I put > molgenis-3.0.3.jar ? > > > > Hello Frank, > > > > I'm not sure whether this is related to your error, but I just > notice > > the libgcj.so.90 in your error, suggesting that you use gnu java. > > > > I vaguely remember that I had to install the ia32-java6-sun packages > and > > use sun java as default workspace jre before things worked in > ubuntu. > > > > Ate > > > > > > > > > > On Wed, 2008-11-26 at 13:50 +0000, Frank van Zimmeren wrote: > > > Dear Morris, > > > > > > Thank you for your help. > > > > > > That library is in my Java Build Path. The library is named > "Persisted > > > container [org.eclipse.jst.j2ee.internal.web.container for project > > > [molgenis3_distro]] > > > > > > However, after adding the library again I do not get the error > message > > > about MolgenisFactory anymore. But now I get the following: > > > > > > Exception in thread "main" java.lang.IllegalAccessError: > > > org.molgenis.language.MolgenisLanguage can't access class > > > org.molgenis.language.syntax.UISchema$Type > > > at java.lang.Class.isAnonymousClass(libgcj.so.90) > > > at java.lang.Class.getSimpleName(libgcj.so.90) > > > at > > > > org.molgenis.language.MolgenisLanguage.<clinit>(MolgenisLanguage.java:23) > > > at java.lang.Class.initializeClass(libgcj.so.90) > > > at > > > > org.molgenis.generate.MolgenisFactory.run(MolgenisFactory.java:315) > > > at > > > > org.molgenis.generate.MolgenisFactory.main(MolgenisFactory.java:342) > > > at MolgenisGenerate.main(MolgenisGenerate.java:7) > > > > > > I see UISchema$Type.class in molgenis-3.0.3.jar but I do not see > it in > > > my library in Eclipse. I'm at a loss. > > > > > > Best, > > > Frank > > > > > > > Date: Wed, 26 Nov 2008 10:05:21 +0100 > > > > From: m.a...@ru... > > > > To: fra...@ho...; > > > mol...@li... > > > > Subject: Re: [Molgenis-users] Where should I put > > > molgenis-3.0.3.jar ? > > > > > > > > Dear Frank, > > > > > > > > Normally one downloads the Eclipse workspace, and that should > work. > > > > It seems there is a path issue; all the jars are in > > > WebContent/WEB-INF/lib > > > > Check your Java Build Path (right-click project -> properties) > to > > > see of > > > > they are loaded. > > > > Also a clean built may help. > > > > > > > > (The seperate jar is only for people who already downloaded a > > > previous > > > > version; the you can paste that into your WebContent/WEB-INF/lib > to > > > be > > > > updated. > > > > So that shouldn't help in your situation) > > > > > > > > I hope this helps, > > > > Morris > > > > > > > > Frank van Zimmeren wrote: > > > > > Hello, > > > > > > > > > > I am trying to install and use Molgenis. I have unzipped the > > > molgenis > > > > > workspace as described in the manual. I am, however, stuck at > > > chapter > > > > > 1.2 step 3: "Go to the folder 'handwritten/java' and > right-click > > > > > 'MolgenisGenerate' Choose 'run as' and then 'run as java > > > > > application'". I get the following error: > > > > > > > > > > Exception in thread "main" java.lang.NoClassDefFoundError: > > > > > org.molgenis.generate.MolgenisFactory > > > > > at MolgenisGenerate.main(MolgenisGenerate.java:7) > > > > > > > > > > I found the MolgenisFactory.java and .class in > molgenis-3.0.3.jar > > > > > which is also on the SourceForge page. But I did not find any > > > > > documentation about this .jar. I have tried putting it in > > > > > /usr/lib/java but this does not help. Where should I put > > > this .jar? > > > > > > > > > > Best, > > > > > Frank van Zimmeren > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > Windows Live Hotmail now works up to 70% faster. Sign up > today. > > > > > > > > > <http://windowslive.com/Explore/Hotmail?ocid=TXT_TAGLM_WL_hotmail_acq_faster_112008> > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > > > > > > > > ------------------------------------------------------------------------- > > > > > This SF.Net email is sponsored by the Moblin Your Move > Developer's > > > challenge > > > > > Build the coolest Linux based applications with Moblin SDK & > win > > > great prizes > > > > > Grand prize is a trip for two to an Open Source event anywhere > in > > > the world > > > > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > > > > _______________________________________________ > > > > > Molgenis-users mailing list > > > > > Mol...@li... > > > > > https://lists.sourceforge.net/lists/listinfo/molgenis-users > > > > > > > > > > > > > > > > > > > ______________________________________________________________________ > > > Access your email online and on the go with Windows Live Hotmail. > Sign > > > up today. > > > > ------------------------------------------------------------------------- > > > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > > > Build the coolest Linux based applications with Moblin SDK & win > great prizes > > > Grand prize is a trip for two to an Open Source event anywhere in > the world > > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > > _______________________________________________ Molgenis-users > mailing list Mol...@li... > https://lists.sourceforge.net/lists/listinfo/molgenis-users > > > > > > > ------------------------------------------------------------------------- > > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > > Build the coolest Linux based applications with Moblin SDK & win > great prizes > > Grand prize is a trip for two to an Open Source event anywhere in > the world > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > _______________________________________________ > > Molgenis-users mailing list > > Mol...@li... > > https://lists.sourceforge.net/lists/listinfo/molgenis-users > > > ______________________________________________________________________ > Access your email online and on the go with Windows Live Hotmail. Sign > up today. > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ Molgenis-users mailing list Mol...@li... https://lists.sourceforge.net/lists/listinfo/molgenis-users |
|
From: Frank v. Z. <fra...@ho...> - 2008-11-28 14:21:49
|
Hello Ate,
Thank you! That did the trick. The program gets further but now ends with:
Exception in thread "main" java.io.FileNotFoundException: /META-INF/context.xml (No such file or directory)
at java.io.FileOutputStream.open(Native Method)
at java.io.FileOutputStream.<init>(FileOutputStream.java:179)
at java.io.FileOutputStream.<init>(FileOutputStream.java:131)
at org.molgenis.generate.servlet.MolgenisServletContextGen.generate(MolgenisServletContextGen.java:44)
at org.molgenis.generate.MolgenisFactory.generate(MolgenisFactory.java:244)
at org.molgenis.generate.MolgenisFactory.run(MolgenisFactory.java:325)
at org.molgenis.generate.MolgenisFactory.main(MolgenisFactory.java:342)
at MolgenisGenerate.main(MolgenisGenerate.java:7)
This file is present and has read permission for all users. Do I need to set a path somewhere?
Best,
Frank
> From: A.S...@ru...
> To: mol...@li...
> Date: Wed, 26 Nov 2008 15:40:50 +0100
> Subject: Re: [Molgenis-users] Where should I put molgenis-3.0.3.jar ?
>
> Hello Frank,
>
> I'm not sure whether this is related to your error, but I just notice
> the libgcj.so.90 in your error, suggesting that you use gnu java.
>
> I vaguely remember that I had to install the ia32-java6-sun packages and
> use sun java as default workspace jre before things worked in ubuntu.
>
> Ate
>
>
>
>
> On Wed, 2008-11-26 at 13:50 +0000, Frank van Zimmeren wrote:
> > Dear Morris,
> >
> > Thank you for your help.
> >
> > That library is in my Java Build Path. The library is named "Persisted
> > container [org.eclipse.jst.j2ee.internal.web.container for project
> > [molgenis3_distro]]
> >
> > However, after adding the library again I do not get the error message
> > about MolgenisFactory anymore. But now I get the following:
> >
> > Exception in thread "main" java.lang.IllegalAccessError:
> > org.molgenis.language.MolgenisLanguage can't access class
> > org.molgenis.language.syntax.UISchema$Type
> > at java.lang.Class.isAnonymousClass(libgcj.so.90)
> > at java.lang.Class.getSimpleName(libgcj.so.90)
> > at
> > org.molgenis.language.MolgenisLanguage.<clinit>(MolgenisLanguage.java:23)
> > at java.lang.Class.initializeClass(libgcj.so.90)
> > at
> > org.molgenis.generate.MolgenisFactory.run(MolgenisFactory.java:315)
> > at
> > org.molgenis.generate.MolgenisFactory.main(MolgenisFactory.java:342)
> > at MolgenisGenerate.main(MolgenisGenerate.java:7)
> >
> > I see UISchema$Type.class in molgenis-3.0.3.jar but I do not see it in
> > my library in Eclipse. I'm at a loss.
> >
> > Best,
> > Frank
> >
> > > Date: Wed, 26 Nov 2008 10:05:21 +0100
> > > From: m.a...@ru...
> > > To: fra...@ho...;
> > mol...@li...
> > > Subject: Re: [Molgenis-users] Where should I put
> > molgenis-3.0.3.jar ?
> > >
> > > Dear Frank,
> > >
> > > Normally one downloads the Eclipse workspace, and that should work.
> > > It seems there is a path issue; all the jars are in
> > WebContent/WEB-INF/lib
> > > Check your Java Build Path (right-click project -> properties) to
> > see of
> > > they are loaded.
> > > Also a clean built may help.
> > >
> > > (The seperate jar is only for people who already downloaded a
> > previous
> > > version; the you can paste that into your WebContent/WEB-INF/lib to
> > be
> > > updated.
> > > So that shouldn't help in your situation)
> > >
> > > I hope this helps,
> > > Morris
> > >
> > > Frank van Zimmeren wrote:
> > > > Hello,
> > > >
> > > > I am trying to install and use Molgenis. I have unzipped the
> > molgenis
> > > > workspace as described in the manual. I am, however, stuck at
> > chapter
> > > > 1.2 step 3: "Go to the folder 'handwritten/java' and right-click
> > > > 'MolgenisGenerate' Choose 'run as' and then 'run as java
> > > > application'". I get the following error:
> > > >
> > > > Exception in thread "main" java.lang.NoClassDefFoundError:
> > > > org.molgenis.generate.MolgenisFactory
> > > > at MolgenisGenerate.main(MolgenisGenerate.java:7)
> > > >
> > > > I found the MolgenisFactory.java and .class in molgenis-3.0.3.jar
> > > > which is also on the SourceForge page. But I did not find any
> > > > documentation about this .jar. I have tried putting it in
> > > > /usr/lib/java but this does not help. Where should I put
> > this .jar?
> > > >
> > > > Best,
> > > > Frank van Zimmeren
> > > >
> > > >
> > ------------------------------------------------------------------------
> > > > Windows Live Hotmail now works up to 70% faster. Sign up today.
> > > >
> > <http://windowslive.com/Explore/Hotmail?ocid=TXT_TAGLM_WL_hotmail_acq_faster_112008>
> > > >
> > > >
> > ------------------------------------------------------------------------
> > > >
> > > >
> > -------------------------------------------------------------------------
> > > > This SF.Net email is sponsored by the Moblin Your Move Developer's
> > challenge
> > > > Build the coolest Linux based applications with Moblin SDK & win
> > great prizes
> > > > Grand prize is a trip for two to an Open Source event anywhere in
> > the world
> > > > http://moblin-contest.org/redirect.php?banner_id=100&url=/
> > > >
> > ------------------------------------------------------------------------
> > > >
> > > > _______________________________________________
> > > > Molgenis-users mailing list
> > > > Mol...@li...
> > > > https://lists.sourceforge.net/lists/listinfo/molgenis-users
> > > >
> > >
> >
> >
> > ______________________________________________________________________
> > Access your email online and on the go with Windows Live Hotmail. Sign
> > up today.
> > -------------------------------------------------------------------------
> > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> > Build the coolest Linux based applications with Moblin SDK & win great prizes
> > Grand prize is a trip for two to an Open Source event anywhere in the world
> > http://moblin-contest.org/redirect.php?banner_id=100&url=/
> > _______________________________________________ Molgenis-users mailing list Mol...@li... https://lists.sourceforge.net/lists/listinfo/molgenis-users
>
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Molgenis-users mailing list
> Mol...@li...
> https://lists.sourceforge.net/lists/listinfo/molgenis-users
_________________________________________________________________
Access your email online and on the go with Windows Live Hotmail.
http://windowslive.com/Explore/Hotmail?ocid=TXT_TAGLM_WL_hotmail_acq_access_112008 |
|
From: A.S. B. <A.S...@ru...> - 2008-11-26 15:13:38
|
Hello Frank, I'm not sure whether this is related to your error, but I just notice the libgcj.so.90 in your error, suggesting that you use gnu java. I vaguely remember that I had to install the ia32-java6-sun packages and use sun java as default workspace jre before things worked in ubuntu. Ate On Wed, 2008-11-26 at 13:50 +0000, Frank van Zimmeren wrote: > Dear Morris, > > Thank you for your help. > > That library is in my Java Build Path. The library is named "Persisted > container [org.eclipse.jst.j2ee.internal.web.container for project > [molgenis3_distro]] > > However, after adding the library again I do not get the error message > about MolgenisFactory anymore. But now I get the following: > > Exception in thread "main" java.lang.IllegalAccessError: > org.molgenis.language.MolgenisLanguage can't access class > org.molgenis.language.syntax.UISchema$Type > at java.lang.Class.isAnonymousClass(libgcj.so.90) > at java.lang.Class.getSimpleName(libgcj.so.90) > at > org.molgenis.language.MolgenisLanguage.<clinit>(MolgenisLanguage.java:23) > at java.lang.Class.initializeClass(libgcj.so.90) > at > org.molgenis.generate.MolgenisFactory.run(MolgenisFactory.java:315) > at > org.molgenis.generate.MolgenisFactory.main(MolgenisFactory.java:342) > at MolgenisGenerate.main(MolgenisGenerate.java:7) > > I see UISchema$Type.class in molgenis-3.0.3.jar but I do not see it in > my library in Eclipse. I'm at a loss. > > Best, > Frank > > > Date: Wed, 26 Nov 2008 10:05:21 +0100 > > From: m.a...@ru... > > To: fra...@ho...; > mol...@li... > > Subject: Re: [Molgenis-users] Where should I put > molgenis-3.0.3.jar ? > > > > Dear Frank, > > > > Normally one downloads the Eclipse workspace, and that should work. > > It seems there is a path issue; all the jars are in > WebContent/WEB-INF/lib > > Check your Java Build Path (right-click project -> properties) to > see of > > they are loaded. > > Also a clean built may help. > > > > (The seperate jar is only for people who already downloaded a > previous > > version; the you can paste that into your WebContent/WEB-INF/lib to > be > > updated. > > So that shouldn't help in your situation) > > > > I hope this helps, > > Morris > > > > Frank van Zimmeren wrote: > > > Hello, > > > > > > I am trying to install and use Molgenis. I have unzipped the > molgenis > > > workspace as described in the manual. I am, however, stuck at > chapter > > > 1.2 step 3: "Go to the folder 'handwritten/java' and right-click > > > 'MolgenisGenerate' Choose 'run as' and then 'run as java > > > application'". I get the following error: > > > > > > Exception in thread "main" java.lang.NoClassDefFoundError: > > > org.molgenis.generate.MolgenisFactory > > > at MolgenisGenerate.main(MolgenisGenerate.java:7) > > > > > > I found the MolgenisFactory.java and .class in molgenis-3.0.3.jar > > > which is also on the SourceForge page. But I did not find any > > > documentation about this .jar. I have tried putting it in > > > /usr/lib/java but this does not help. Where should I put > this .jar? > > > > > > Best, > > > Frank van Zimmeren > > > > > > > ------------------------------------------------------------------------ > > > Windows Live Hotmail now works up to 70% faster. Sign up today. > > > > <http://windowslive.com/Explore/Hotmail?ocid=TXT_TAGLM_WL_hotmail_acq_faster_112008> > > > > > > > ------------------------------------------------------------------------ > > > > > > > ------------------------------------------------------------------------- > > > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > > > Build the coolest Linux based applications with Moblin SDK & win > great prizes > > > Grand prize is a trip for two to an Open Source event anywhere in > the world > > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > Molgenis-users mailing list > > > Mol...@li... > > > https://lists.sourceforge.net/lists/listinfo/molgenis-users > > > > > > > > ______________________________________________________________________ > Access your email online and on the go with Windows Live Hotmail. Sign > up today. > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ Molgenis-users mailing list Mol...@li... https://lists.sourceforge.net/lists/listinfo/molgenis-users |
|
From: Frank v. Z. <fra...@ho...> - 2008-11-26 13:50:19
|
Dear Morris, Thank you for your help. That library is in my Java Build Path. The library is named "Persisted container [org.eclipse.jst.j2ee.internal.web.container for project [molgenis3_distro]] However, after adding the library again I do not get the error message about MolgenisFactory anymore. But now I get the following: Exception in thread "main" java.lang.IllegalAccessError: org.molgenis.language.MolgenisLanguage can't access class org.molgenis.language.syntax.UISchema$Type at java.lang.Class.isAnonymousClass(libgcj.so.90) at java.lang.Class.getSimpleName(libgcj.so.90) at org.molgenis.language.MolgenisLanguage.<clinit>(MolgenisLanguage.java:23) at java.lang.Class.initializeClass(libgcj.so.90) at org.molgenis.generate.MolgenisFactory.run(MolgenisFactory.java:315) at org.molgenis.generate.MolgenisFactory.main(MolgenisFactory.java:342) at MolgenisGenerate.main(MolgenisGenerate.java:7) I see UISchema$Type.class in molgenis-3.0.3.jar but I do not see it in my library in Eclipse. I'm at a loss. Best, Frank > Date: Wed, 26 Nov 2008 10:05:21 +0100 > From: m.a...@ru... > To: fra...@ho...; mol...@li... > Subject: Re: [Molgenis-users] Where should I put molgenis-3.0.3.jar ? > > Dear Frank, > > Normally one downloads the Eclipse workspace, and that should work. > It seems there is a path issue; all the jars are in WebContent/WEB-INF/lib > Check your Java Build Path (right-click project -> properties) to see of > they are loaded. > Also a clean built may help. > > (The seperate jar is only for people who already downloaded a previous > version; the you can paste that into your WebContent/WEB-INF/lib to be > updated. > So that shouldn't help in your situation) > > I hope this helps, > Morris > > Frank van Zimmeren wrote: > > Hello, > > > > I am trying to install and use Molgenis. I have unzipped the molgenis > > workspace as described in the manual. I am, however, stuck at chapter > > 1.2 step 3: "Go to the folder 'handwritten/java' and right-click > > 'MolgenisGenerate' Choose 'run as' and then 'run as java > > application'". I get the following error: > > > > Exception in thread "main" java.lang.NoClassDefFoundError: > > org.molgenis.generate.MolgenisFactory > > at MolgenisGenerate.main(MolgenisGenerate.java:7) > > > > I found the MolgenisFactory.java and .class in molgenis-3.0.3.jar > > which is also on the SourceForge page. But I did not find any > > documentation about this .jar. I have tried putting it in > > /usr/lib/java but this does not help. Where should I put this .jar? > > > > Best, > > Frank van Zimmeren > > > > ------------------------------------------------------------------------ > > Windows Live Hotmail now works up to 70% faster. Sign up today. > > <http://windowslive.com/Explore/Hotmail?ocid=TXT_TAGLM_WL_hotmail_acq_faster_112008> > > > > ------------------------------------------------------------------------ > > > > ------------------------------------------------------------------------- > > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > > Build the coolest Linux based applications with Moblin SDK & win great prizes > > Grand prize is a trip for two to an Open Source event anywhere in the world > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Molgenis-users mailing list > > Mol...@li... > > https://lists.sourceforge.net/lists/listinfo/molgenis-users > > > _________________________________________________________________ Access your email online and on the go with Windows Live Hotmail. http://windowslive.com/Explore/Hotmail?ocid=TXT_TAGLM_WL_hotmail_acq_access_112008 |
