|
BioJava, Dazzle and Google App Engine (Java version)
|
View:
New views
6 Messages
—
Rating Filter:
Alert me
|
 |
BioJava, Dazzle and Google App Engine (Java version)
by Rouilly, Vincent
::
Rate this Message:
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@... http://lists.open-bio.org/mailman/listinfo/biojava-l |
|
|
Re: BioJava, Dazzle and Google App Engine (Java version)
by Richard Holland-6
::
Rate this Message:
Hello. Dazzle/DAS is not BioJava, but I happen to know that Jon Warren
at the Sanger Centre is an expert in all things DAS, so he might be able to help you. I've copied him on this. cheers, Richard On 8 Aug 2009, at 18:33, Rouilly, Vincent 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@... > http://lists.open-bio.org/mailman/listinfo/biojava-l -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland@... http://www.eaglegenomics.com/ _______________________________________________ Biojava-l mailing list - Biojava-l@... http://lists.open-bio.org/mailman/listinfo/biojava-l |
|
|
|
|
|
|
|
|
|
|
|
Re: BioJava, Dazzle and Google App Engine (Java version)
by Andreas Prlic-3
::
Rate this Message:
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@...> 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@...] > 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@...<mailto:andreas.prlic@...> [ > andreas.prlic@...<mailto:andreas.prlic@...>] On Behalf Of > Andreas Prlic [andreas@...<mailto:andreas@...>] > 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@...<mailto:vincent.rouilly03@...>> > 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@...<mailto: > Biojava-l@...> > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > Jonathan Warren > Senior Developer and DAS coordinator > jw12@...<mailto:jw12@...> > 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 - Biojava-l@... http://lists.open-bio.org/mailman/listinfo/biojava-l |
| Free embeddable forum powered by Nabble | Forum Help |
