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 < [email protected]> 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 [[email protected]] > 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: [email protected]<mailto:[email protected]> [ > [email protected]<mailto:[email protected]>] On Behalf Of > Andreas Prlic [[email protected]<mailto:[email protected]>] > 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 < > [email protected]<mailto:[email protected]>> > 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 - [email protected]<mailto: > [email protected]> > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > Jonathan Warren > Senior Developer and DAS coordinator > [email protected]<mailto:[email protected]> > 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. > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
