From jithesh at ibioinformatics.org Sat Aug 7 07:47:59 2004 From: jithesh at ibioinformatics.org (Jithesh M K) Date: Sat Aug 7 07:52:39 2004 Subject: [DAS] Setting up DAS with ensembl plugin Message-ID: <20040807114759.27478.qmail@ibioinformatics.org> Hi all, I am a newbie in this field. I would like to set up a DAS server with the ensembl plugin. I have tried configuring it but in vain. This is what I have tried. I downloaded the dazzle-1.00 source from the site and compiled it using the ant utility. It gave me errors in the file AbstractDataSource.java telling about the MatchType. So I used the DazzleDataSource.MatchType to remove this error. I got the jar file using the ant compile then. I got only one datasource ID test and the tss was giving errors. 2004-08-03 15:57:51 Couldn't initialize datasource tss org.biojava.servlets.dazzle.datasource.DataSourceException: java.lang.IllegalAccessError: tried to access field org.biojava.servlets.dazzle.datasource.GFFAnnotationSource.REGION_PATTERN from class org.biojava.servlets.dazzle.datasource.GFFAnnotationSource$Handler ...... 2004-08-03 15:57:51 DazzleServerMain: *** WARNING *** Lost a data source tss When I tried it with the test file provided with a client it also didn't give a proper output. I had followed the manual provided at the site. If anyone can assist me in setting up the server, I would definitely appreciate. Thanks in Advance From td2 at sanger.ac.uk Sat Aug 7 08:26:12 2004 From: td2 at sanger.ac.uk (Thomas Down) Date: Sat Aug 7 08:27:26 2004 Subject: [DAS] Setting up DAS with ensembl plugin In-Reply-To: <20040807114759.27478.qmail@ibioinformatics.org> References: <20040807114759.27478.qmail@ibioinformatics.org> Message-ID: Hi Jithesh, On 7 Aug 2004, at 12:47, Jithesh M K wrote: > Hi all, > I am a newbie in this field. I would like to set up a DAS server with > the ensembl plugin. I have tried configuring it but in vain. This is > what I have tried. > I downloaded the dazzle-1.00 source from the site and compiled it > using the ant utility. It gave me errors in the file > AbstractDataSource.java telling about the MatchType. So I used the > DazzleDataSource.MatchType to remove this error. I got the jar file > using the ant compile then. Where did you download the source from? Official place to get it is: http://www.biojava.org/download/dazzle/ (I'd also recommend that you use version 1.01 instead, although off the top of my head I can't think of any 1.00 -> 1.01 changes which are likely to be significant in this case). What errors did you see when compiling? And what changes did you make to get it to compile? It would also be helpful to know some details about your system configuration. What operating system are you using? Which release of Java (if you're not sure, try "java -version"). > I got only one datasource ID test and the tss was giving errors. > 2004-08-03 15:57:51 Couldn't initialize datasource tss > org.biojava.servlets.dazzle.datasource.DataSourceException: > java.lang.IllegalAccessError: tried to access field > org.biojava.servlets.dazzle.datasource.GFFAnnotationSource.REGION_PATTE > RN from class > org.biojava.servlets.dazzle.datasource.GFFAnnotationSource$Handler That's an extremely strange error to see, since if there *were* an illegal access of that field, it should be caught at compile time, not runtime. If I had to guess, I'd say that this was the result of using a Java compiler which doesn't handle nested classes (sometimes called inner classes) quite right. Which compiler are you using? Thomas. From jithesh at ibioinformatics.org Tue Aug 3 06:54:45 2004 From: jithesh at ibioinformatics.org (Jithesh) Date: Thu Aug 12 11:42:35 2004 Subject: [DAS] Setting up DAS with ensembl plugin Message-ID: <1091530484.9324.46.camel@nemesis> Hi all, I am a newbie in this field. I would like to set up a DAS server with the ensembl plugin. I have tried configuring it but in vain. This is what I have tried. I downloaded the dazzle-1.00 source from the site and compiled it using the ant utility. It gave me errors in the file AbstractDataSource.java telling about the MatchType. So I used the DazzleDataSource.MatchType to remove this error. I got the jar file using the ant compile then. I got only one datasource ID test and the tss was giving errors. 2004-08-03 15:57:51 Couldn't initialize datasource tss org.biojava.servlets.dazzle.datasource.DataSourceException: java.lang.IllegalAccessError: tried to access field org.biojava.servlets.dazzle.datasource.GFFAnnotationSource.REGION_PATTERN from class org.biojava.servlets.dazzle.datasource.GFFAnnotationSource$Handler ...... 2004-08-03 15:57:51 DazzleServerMain: *** WARNING *** Lost a data source tss When I tried it with the test file provided with a client it also didn't give a proper output. I had followed the manual provided at the site. If anyone can assist me in setting up the server, I would definitely appreciate. Thanks in Advance -- Jithesh From lstein at cshl.edu Thu Aug 26 09:35:34 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Fri Sep 3 13:46:18 2004 Subject: [DAS] Fwd: Returned mail: see transcript for details Message-ID: <200408260935.34420.lstein@cshl.edu> Hi Folks, This mail from two weeks ago bounced. It contains an update to the DAS/2 URL specification. I am about 75% through another revision which is mostly cleaning up and HTML-izing. Lincoln ---------- Forwarded Message ---------- Subject: Returned mail: see transcript for details Date: Friday 13 August 2004 12:15 pm From: Mail Delivery Subsystem To: The original message was received at Fri, 13 Aug 2004 12:13:26 -0400 from IDENT:1001@localhost [127.0.0.1] ----- The following addresses had permanent fatal errors ----- ----- Transcript of session follows ----- 550 5.1.2 ,,,,,... Host unknown (Name server: mail.lsjs.org: no data known) ------------------------------------------------------- -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 -------------- next part -------------- The original message was received at Fri, 13 Aug 2004 12:13:26 -0400 from IDENT:1001@localhost [127.0.0.1] ----- The following addresses had permanent fatal errors ----- ----- Transcript of session follows ----- 550 5.1.2 ,,,,,... Host unknown (Name server: mail.lsjs.org: no data known) -------------- next part -------------- Skipped content of type message/delivery-status-------------- next part -------------- An embedded message was scrubbed... From: Lincoln Stein Subject: Current das/2 notes Date: Fri, 13 Aug 2004 12:12:45 -0400 Size: 50504 Url: http://portal.open-bio.org/pipermail/das/attachments/20040826/30387f37/attachment-0001.eml