[Biojava-l] BioJava, Dazzle and Google App Engine (Java version)
Andreas Prlic
andreas at sdsc.edu
Tue Aug 11 21:04:11 UTC 2009
Hi Vincent,
interesting approach... Want to add your notes to the wiki pages as well?
Thanks,
Andreas
On Tue, Aug 11, 2009 at 2:16 AM, Rouilly, Vincent <
vincent.rouilly03 at imperial.ac.uk> wrote:
> Hi,
>
> thanks a lot for those who provided me advices.
> I finally got 'dazzle' to work on the Google App Engine.
>
> In short, it means that you can get a free/scalable DAS server on the
> Google Cloud.
>
> check:
> http://dazzle-das.appspot.com/das/dsn
> http://dazzle-das.appspot.com/das/test/entry_points
>
> If you are interested, you can find below the process I followed.
> My next target is to get 'dazzle' to fetch annotation directly from the
> Google Data Store provided in the Google App Engine (as opposed to from a
> flat file).
>
> best,
>
> Vincent.
> ----------------------
>
> Prerequisites:
> - Java 1.5
> - Eclipse 3.4.1 + Google App Engine plug-in from
> http://code.google.com/appengine/docs/java/tools/eclipse.html
> - Dazzle code into /tmp/dazzle from: svn checkout
> http://www.derkholm.net/svn/repos/dazzle/trunk /tmp/dazzle
>
>
> 1- Create new Google App Engine project from Eclipse (after Google Engine
> plug-in installation):
> Project name: dazzle
> Package: org.biojava.servlets.dazzle
> Uncheck 'Use Google Web Toolkit'
> Finish
>
> 2- Import 'dazzle' Jar files into 'dazzle google engine' project
> In Eclipse, 'dazzle' project Properties -> Java Build Path -> Add
> External Jars
> Import from /tmp/dazzle/jars: bioJava.jar, bytecode.jar,
> dasmi-model.jar, servlet-api-2.3.jar
>
> 3- Import 'dazzle' ressources folder into 'dazzle google engine' project
> drag-and-drop /tmp/dazzle/resources folder into 'Eclipse:/dazzle'
> folder
>
> 4- Import 'dazzle' src files into 'dazzle google engine' project
> drag-and-drop /tmp/dazzle/src/org folder into 'Eclipse:/ dazzle/src'
> folder
> Comment: you should have 3 errors due to the use of Context in
> 'MysqlFeatureCache'. For now, I just commented the 2 lines involved.
>
> 5- Import /tmp/dazzle/dazzle-webapp files into 'dazzle google engine'
> project
> drag-and-drop files from /tmp/dazzle/dazzle-webapp into
> Eclipse:/dazzle/war/. (do not select WEB-INF folder)
>
> 6- Import Jars to WEB-INF/lib
> drag and drop jar files from /tmp/dazzle/jars into 'dazzle google
> engine' Eclipse:/dazzle/war/WEB-INF/lib
> biojava.jar, bytecode.jar, dasmi-model.jar, servelt-api-2.3.jar,
> dazzle.jar
>
> 6- Update web.xml file in Eclipse:/dazzle/war/WEB-INF/
>
> [....]
> <servlet>
> <servlet-name>Dazzle</servlet-name>
>
> <servlet-class>org.biojava.servlets.dazzle.DazzleServlet</servlet-class>
> </servlet>
>
> <servlet-mapping>
> <servlet-name>Dazzle</servlet-name>
> <url-pattern>/das/*</url-pattern>
> </servlet-mapping>
>
> <welcome-file-list>
> <welcome-file>das_welcome.html</welcome-file>
> </welcome-file-list>
> [...]
>
> 6- Run application in Eclipse as web Application (standalone test)
> check with your web browser: http://localhost:8080/das/dsn
>
> 7- If it works, you can create a Google App Engine Application ID and
> deploy your dazzle server on the cloud.
> http://code.google.com/appengine/docs/java/tools/uploadinganapp.html
>
> ________________________________________
> From: Jonathan Warren [jw12 at sanger.ac.uk]
> Sent: Monday, August 10, 2009 5:28 PM
> To: Rouilly, Vincent
> Cc: Andreas Prlic; Richard Holland
> Subject: Re: [Biojava-l] BioJava, Dazzle and Google App Engine (Java
> version)
>
> I had a look at this and it seems the container works differently from
> tomcat and resin. I think you may have to change the way dazzle gets it's
> datasource information?
> The problem is that the google servlet adds dazzle to this nameComponents
> list whereas tomcat and resin don't when reading the xml config:
>
> public Set getDataSourceIDs(List nameComponents, HttpServletRequest req)
> throws DataSourceException
> {
> System.err.println("Address: " + req.getRemoteAddr());
> System.err.println("Host: " + req.getRemoteHost());
>
>
> if (nameComponents.size() != 0) {
> System.out.println(nameComponents.toString());
> throw new DataSourceException("Basic installation only covers flat
> namespace of data-sources");
> }
>
>
>
> I got some requests to work by adding
> /dazzle/* in the web.xml like this:
> <servlet-mapping>
> <servlet-name>DazzleServerMain</servlet-name>
> <url-pattern>/dazzle/*</url-pattern>
> </servlet-mapping>
>
> however some requests then work and others don't.
>
> Maybe the other guys have some ideas, but I couldn't see a particular
> reason or quick hack to overcome the difference.
>
> On 9 Aug 2009, at 11:50, Rouilly, Vincent wrote:
>
>
> Hi,
>
> thanks for your quick replies.
>
> Sorry, I forgot to mention that I am also using the stand-alone Google
> Engine for now, with the Eclipse plug-in.
> And, my development platform is a Mac OS 10.4.11, with JRE 1.6 from
> Soylatte, and Eclipse v3.4.2.
>
> I have read through the dazzle documentation, but I still can't get it to
> work within the Google App Engine / Eclipse environment.
> I am not very familiar with Eclipse, so it is very likely that I am not
> doing things right.
>
> Here is the process I have followed to give Dazzle a try to on the Google
> Engine. But remember, this process doesn't work for me.
> I hope it makes sense, and that someone can point me to the right
> direction.
>
> many thanks,
> Vincent.
>
> 1- Download 'dazzle' in /tmp/ using subversion (
> http://biojava.org/wiki/Dazzle):
> svn checkout http://www.derkholm.net/svn/repos/dazzle/trunk /tmp/dazzle
>
> 2- Create new Google App Engine project from Eclipse (after Google Engine
> plugin installation):
> Project name: dazzle
> Package: org.biojava.servlets.dazzle
> Uncheck 'Use Google Web Toolkit'
> Finish
>
> 3- Import 'dazzle' Jar files into 'dazzle google engine' project
> import from /tmp/dazzle/jars: bioJava.jar, bytecode.jar, dasmi-model.jar,
> servlet-api-2.3.jar
> In Eclipse, 'dazzle' project Properties -> Java Build Path -> Add External
> Jars
>
> 4- Import 'dazzle' src files into 'dazzle google engine' project
> drag-and-drop /tmp/dazzle/src/org folder into 'Eclipse:/ dazzle/src' folder
>
> 5- Import 'dazzle' ressources folder into 'dazzle google engine' project
> drag-and-drop /tmp/dazzle/resources folder into 'Eclipse:/dazzle' folder
>
> 5- Import WEB-INF files into 'dazzle google engine' project
> drag-and-drop files from /tmp/dazzle/dazzle-webapp into
> Eclipse:/dazzle/war/.
>
> 6- Update web.xml file in Eclipse:/dazzle/war/WEB-INF/
> <servlet>
> <servlet-name>DazzleServerMain</servlet-name>
>
> <servlet-class>org.biojava.servlets.dazzle.DazzleServlet</servlet-class>
> </servlet>
>
> <servlet-mapping>
> <servlet-name>DazzleServerMain</servlet-name>
> <url-pattern>/*</url-pattern>
> </servlet-mapping>
>
> welcome-file-list: dazzle-welcome.html
>
> 6- Run application as web Application in Eclipse
> check with web browser: http://localhost:8080/das/dsn
>
>
>
> ________________________________________
> From: andreas.prlic at gmail.com<mailto:andreas.prlic at gmail.com> [
> andreas.prlic at gmail.com<mailto:andreas.prlic at gmail.com>] On Behalf Of
> Andreas Prlic [andreas at sdsc.edu<mailto:andreas at sdsc.edu>]
> Sent: Saturday, August 08, 2009 9:50 PM
> To: Rouilly, Vincent
> Subject: Re: [Biojava-l] BioJava, Dazzle and Google App Engine (Java
> version)
>
> Hi Vincent,
>
> did you try following the instructions at
> http://biojava.org/wiki/Dazzle ?
>
> I have never tried to run it using the google app engine, but it works fine
> for me using Eclipse or standalone... Also have a look at
> http://biojava.org/wiki/Dazzle:deployment
>
> Hope that helps,
> Andreas
>
>
>
> On Sat, Aug 8, 2009 at 10:33 AM, Rouilly, Vincent <
> vincent.rouilly03 at imperial.ac.uk<mailto:vincent.rouilly03 at imperial.ac.uk>>
> wrote:
> Hi,
>
> first of all, congratulations and thanks to all BioJava contributors for
> providing such a great library.
>
> Over the last few days, I have been trying to use BioJava on the Google App
> Engine (with its latest Java support).
> http://code.google.com/appengine/docs/java/gettingstarted/
>
> Has anyone got experience with that ?
>
> I am especially interested in setting up a Dazzle DAS server on the google
> app engine (basic configuration).
> It would be a great way for people to easily share their data through DAS.
>
> However, whatever DAS request, I always get the exceptions:
> DataSourceException("Basic installation only covers flat namespace of
> data-sources");
>
> Any suggestions ?
>
> many thanks,
>
> Vincent.
>
> _______________________________________________
> Biojava-l mailing list - Biojava-l at lists.open-bio.org<mailto:
> Biojava-l at lists.open-bio.org>
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>
> Jonathan Warren
> Senior Developer and DAS coordinator
> jw12 at sanger.ac.uk<mailto:jw12 at sanger.ac.uk>
> Ext: 2314
> Telephone: 01223 492314
>
>
>
>
>
>
> -- The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a compa ny
> registered in England with number 2742969, whose registered office is 2 15
> Euston Road, London, NW1 2BE.
>
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