From andreas at sdsc.edu Tue Sep 1 00:03:14 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Mon, 31 Aug 2009 21:03:14 -0700 Subject: [Biojava-dev] maven progress In-Reply-To: References: <59a41c430908301823s6e2e3d7fi6caffc47e1a8c0ff@mail.gmail.com> Message-ID: <59a41c430908312103w7ba30a83s12d48884957be371@mail.gmail.com> >> The new SVN location is emerging here: >> >> http://dev.open-bio.org/home/svn-repositories/biojava/biojava-live/biojava > > That seems like an odd place for it, at the same level as branches, tags, > and trunk? > > If you've branched for 1.7 and called for the freeze on trunk, I don't see > any reason not to do this work on trunk. ok. makes sense. It is easy to flip locations around in svn.. I can move the old trunk e.g. to a tag folder for archive purposes and make what is called biojava right now the future trunk. (in svn this moves or copy operations are cheap) For the moment things are not stabilized yet and I will do this once things are there... At the moment I am chasing an "interesting" problem. When I run the junit tests on the new core module in eclipse, they run fine. When I do the same via a mvn test I get several issues like the one below. Anybody got an idea? ------------------------------------------------------------------------------- Test set: org.biojava.bio.seq.project.ProjectedFeatureHolderTest ------------------------------------------------------------------------------- Tests run: 6, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.036 sec <<< FAILURE! testFeatureChangeEvent(org.biojava.bio.seq.project.ProjectedFeatureHolderTest) Time elapsed: 0.011 sec <<< ERROR! java.lang.AssertionError: firePreChangeEvent must be called in a synchronized block locking the ChangeSupport at org.biojava.utils.ChangeSupport.firePreChangeEvent(ChangeSupport.java:281) at org.biojava.bio.seq.projection.ReparentContext$PFChangeForwarder.preChange(ReparentContext.java:299) at org.biojava.utils.ChangeSupport.firePreChangeEvent(ChangeSupport.java:297) at org.biojava.bio.seq.impl.SimpleFeature.setLocation(SimpleFeature.java:173) at org.biojava.bio.seq.project.ProjectedFeatureHolderTest.testFeatureChangeEvent(ProjectedFeatureHolderTest.java:297) Andreas From heuermh at acm.org Tue Sep 1 00:12:38 2009 From: heuermh at acm.org (Michael Heuer) Date: Tue, 1 Sep 2009 00:12:38 -0400 (EDT) Subject: [Biojava-dev] maven progress In-Reply-To: <59a41c430908312103w7ba30a83s12d48884957be371@mail.gmail.com> Message-ID: Andreas Prlic wrote: > >> The new SVN location is emerging here: > >> > >> http://dev.open-bio.org/home/svn-repositories/biojava/biojava-live/biojava > > > > That seems like an odd place for it, at the same level as branches, tags, > > and trunk? > > > > If you've branched for 1.7 and called for the freeze on trunk, I don't see > > any reason not to do this work on trunk. > > ok. makes sense. It is easy to flip locations around in svn.. I can > move the old trunk e.g. to a tag folder for archive purposes and make > what is called biojava right now the future trunk. (in svn this moves > or copy operations are cheap) For the moment things are not > stabilized yet and I will do this once things are there... That's cool. I wanted to check in some preliminary fastq stuff and wasn't sure where it should go. I'm in the biojava3 branch for now, and will move to the right place once things settle. > At the moment I am chasing an "interesting" problem. When I run the > junit tests on the new core module in eclipse, they run fine. When I > do the same via a mvn test I get several issues like the one below. > Anybody got an idea? > > ------------------------------------------------------------------------------- > Test set: org.biojava.bio.seq.project.ProjectedFeatureHolderTest > ------------------------------------------------------------------------------- > Tests run: 6, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.036 > sec <<< FAILURE! > testFeatureChangeEvent(org.biojava.bio.seq.project.ProjectedFeatureHolderTest) > Time elapsed: 0.011 sec <<< ERROR! > java.lang.AssertionError: firePreChangeEvent must be called in a > synchronized block locking the ChangeSupport > at org.biojava.utils.ChangeSupport.firePreChangeEvent(ChangeSupport.java:281) > at org.biojava.bio.seq.projection.ReparentContext$PFChangeForwarder.preChange(ReparentContext.java:299) > at org.biojava.utils.ChangeSupport.firePreChangeEvent(ChangeSupport.java:297) > at org.biojava.bio.seq.impl.SimpleFeature.setLocation(SimpleFeature.java:173) > at org.biojava.bio.seq.project.ProjectedFeatureHolderTest.testFeatureChangeEvent(ProjectedFeatureHolderTest.java:297) I've always disliked the change stuff, how about get rid of it all and make everything immutable? ;) michael From andreas at sdsc.edu Tue Sep 1 00:17:47 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Mon, 31 Aug 2009 21:17:47 -0700 Subject: [Biojava-dev] maven progress In-Reply-To: References: <59a41c430908312103w7ba30a83s12d48884957be371@mail.gmail.com> Message-ID: <59a41c430908312117x641453c0yc26be5cb669b4396@mail.gmail.com> Can you start using the biojava-live/biojava/sequencing module for the fastq stuff? that way we can already be in sync. I will do svn updates every time before I start working on something and commits when I stop.... Andreas On Mon, Aug 31, 2009 at 9:12 PM, Michael Heuer wrote: > Andreas Prlic wrote: > >> >> The new SVN location is emerging here: >> >> >> >> http://dev.open-bio.org/home/svn-repositories/biojava/biojava-live/biojava >> > >> > That seems like an odd place for it, at the same level as branches, tags, >> > and trunk? >> > >> > If you've branched for 1.7 and called for the freeze on trunk, I don't see >> > any reason not to do this work on trunk. >> >> ok. makes sense. ?It is easy to flip locations around in svn.. ?I can >> move the old trunk ?e.g. to a tag folder for archive purposes and make >> what is called biojava right now the future trunk. (in svn this moves >> or copy operations are cheap) ?For the moment things are not >> stabilized yet and I will do this once things are there... > > That's cool. ?I wanted to check in some preliminary fastq stuff and wasn't > sure where it should go. ?I'm in the biojava3 branch for now, and will > move to the right place once things settle. > > >> At the moment I am chasing an "interesting" problem. When I run the >> junit tests on the new core module in eclipse, they run fine. ? When I >> do the same via a mvn test I get several issues like the one below. >> Anybody got an idea? >> >> ------------------------------------------------------------------------------- >> Test set: org.biojava.bio.seq.project.ProjectedFeatureHolderTest >> ------------------------------------------------------------------------------- >> Tests run: 6, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.036 >> sec <<< FAILURE! >> testFeatureChangeEvent(org.biojava.bio.seq.project.ProjectedFeatureHolderTest) >> ?Time elapsed: 0.011 sec ?<<< ERROR! >> java.lang.AssertionError: firePreChangeEvent must be called in a >> synchronized block locking the ChangeSupport >> ? ? ? at org.biojava.utils.ChangeSupport.firePreChangeEvent(ChangeSupport.java:281) >> ? ? ? at org.biojava.bio.seq.projection.ReparentContext$PFChangeForwarder.preChange(ReparentContext.java:299) >> ? ? ? at org.biojava.utils.ChangeSupport.firePreChangeEvent(ChangeSupport.java:297) >> ? ? ? at org.biojava.bio.seq.impl.SimpleFeature.setLocation(SimpleFeature.java:173) >> ? ? ? at org.biojava.bio.seq.project.ProjectedFeatureHolderTest.testFeatureChangeEvent(ProjectedFeatureHolderTest.java:297) > > I've always disliked the change stuff, how about get rid of it all and > make everything immutable? ?;) > > ? michael > > From heuermh at acm.org Tue Sep 1 00:27:19 2009 From: heuermh at acm.org (Michael Heuer) Date: Tue, 1 Sep 2009 00:27:19 -0400 (EDT) Subject: [Biojava-dev] maven progress In-Reply-To: <59a41c430908312117x641453c0yc26be5cb669b4396@mail.gmail.com> Message-ID: Andreas Prlic wrote: > Can you start using the biojava-live/biojava/sequencing module for the > fastq stuff? that way we can already be in sync. I will do svn updates > every time before I start working on something and commits when I > stop.... The build for the fastq stuff is currently fully self-contained, since I've been away from biojava development for some time and prefer to do things "my way" . . . it will take me a while to merge it back into the biojava way of doing things, and that is after the funtionality is complete. michael From andreas at sdsc.edu Tue Sep 1 10:37:57 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Tue, 1 Sep 2009 07:37:57 -0700 Subject: [Biojava-dev] maven progress In-Reply-To: References: <59a41c430908301823s6e2e3d7fi6caffc47e1a8c0ff@mail.gmail.com> <59a41c430908312103w7ba30a83s12d48884957be371@mail.gmail.com> Message-ID: <59a41c430909010737r731f9b58p2a96bf8558822de3@mail.gmail.com> Hi Andy, this repository location is ssh protected. Anonymous checkouts are possible via svn://code.open-bio.org/biojava/biojava-live/biojava viewing in your web browser is possible at http://code.open-bio.org/svnweb/index.cgi/biojava/browse/biojava-live/biojava Andreas >>>> The new SVN location is emerging here: >>>> >>>> >>>> http://dev.open-bio.org/home/svn-repositories/biojava/biojava-live/biojava > > > I can't see that from where I'm sitting. Is the server down or are there > firewalls or other corporateness blocking me out? > > >> >> At the moment I am chasing an "interesting" problem. When I run the >> junit tests on the new core module in eclipse, they run fine. ? When I >> do the same via a mvn test I get several issues like the one below. >> Anybody got an idea? >> >> >> ------------------------------------------------------------------------------- >> Test set: org.biojava.bio.seq.project.ProjectedFeatureHolderTest >> >> ------------------------------------------------------------------------------- >> Tests run: 6, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.036 >> sec <<< FAILURE! >> >> testFeatureChangeEvent(org.biojava.bio.seq.project.ProjectedFeatureHolderTest) >> Time elapsed: 0.011 sec ?<<< ERROR! >> java.lang.AssertionError: firePreChangeEvent must be called in a >> synchronized block locking the ChangeSupport >> ? ? ? ?at >> org.biojava.utils.ChangeSupport.firePreChangeEvent(ChangeSupport.java:281) >> ? ? ? ?at >> org.biojava.bio.seq.projection.ReparentContext$PFChangeForwarder.preChange(ReparentContext.java:299) >> ? ? ? ?at >> org.biojava.utils.ChangeSupport.firePreChangeEvent(ChangeSupport.java:297) >> ? ? ? ?at >> org.biojava.bio.seq.impl.SimpleFeature.setLocation(SimpleFeature.java:173) >> ? ? ? ?at >> org.biojava.bio.seq.project.ProjectedFeatureHolderTest.testFeatureChangeEvent(ProjectedFeatureHolderTest.java:297) >> > > > That's certainly not one that I've ever seen, but then I probably don't > write code that is as complicated as BioJava :o} > > If I could get a checkout (see above) then I would try it out in NetBeans to > see if it is something that Eclipse is doing to "protect" against the > synchronisation problem. But I can't get the code so I can't test it :o{ > > > > > Later, > > Andy > -------- > Yada, yada, yada... > The University of Edinburgh is a charitable body, registered in Scotland, > with registration number SC005336 > Disclaimer: This e-mail and any attachments are confidential and intended > solely for the use of the recipient(s) to whom they are addressed. If you > have received it in error, please destroy all copies and inform the sender. > > > > From andy.law at roslin.ed.ac.uk Tue Sep 1 12:30:32 2009 From: andy.law at roslin.ed.ac.uk (Andy Law (RI)) Date: Tue, 1 Sep 2009 17:30:32 +0100 Subject: [Biojava-dev] maven progress In-Reply-To: <59a41c430909010737r731f9b58p2a96bf8558822de3@mail.gmail.com> References: <59a41c430908301823s6e2e3d7fi6caffc47e1a8c0ff@mail.gmail.com> <59a41c430908312103w7ba30a83s12d48884957be371@mail.gmail.com> <59a41c430909010737r731f9b58p2a96bf8558822de3@mail.gmail.com> Message-ID: <32C14A50-465E-423B-9816-F1B995CBDC16@roslin.ed.ac.uk> On 1 Sep 2009, at 15:37, Andreas Prlic wrote: > Hi Andy, > > this repository location is ssh protected. Anonymous checkouts are > possible via > > svn://code.open-bio.org/biojava/biojava-live/biojava OK. I've got a checkout from there thanks. I trip up over a dependency on bytecode version 3.0. That will need to either be incorporated into the tree or published to maven central before the system works as it should (version 1.5 is on the maven central repo but I couldn't find a later version) >>> >>> At the moment I am chasing an "interesting" problem. When I run the >>> junit tests on the new core module in eclipse, they run fine. >>> When I >>> do the same via a mvn test I get several issues like the one below. >>> Anybody got an idea? >>> >>> >>> ------------------------------------------------------------------------------- >>> Test set: org.biojava.bio.seq.project.ProjectedFeatureHolderTest >>> >>> ------------------------------------------------------------------------------- >>> Tests run: 6, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: >>> 0.036 >>> sec <<< FAILURE! >>> >>> testFeatureChangeEvent >>> (org.biojava.bio.seq.project.ProjectedFeatureHolderTest) >>> Time elapsed: 0.011 sec <<< ERROR! >>> java.lang.AssertionError: firePreChangeEvent must be called in a >>> synchronized block locking the ChangeSupport >>> at >>> org >>> .biojava.utils.ChangeSupport.firePreChangeEvent(ChangeSupport.java: >>> 281) >>> at >>> org.biojava.bio.seq.projection.ReparentContext >>> $PFChangeForwarder.preChange(ReparentContext.java:299) >>> at >>> org >>> .biojava.utils.ChangeSupport.firePreChangeEvent(ChangeSupport.java: >>> 297) >>> at >>> org >>> .biojava.bio.seq.impl.SimpleFeature.setLocation(SimpleFeature.java: >>> 173) >>> at >>> org >>> .biojava >>> .bio >>> .seq >>> .project >>> .ProjectedFeatureHolderTest >>> .testFeatureChangeEvent(ProjectedFeatureHolderTest.java:297) >>> >> >> >> That's certainly not one that I've ever seen, but then I probably >> don't >> write code that is as complicated as BioJava :o} >> >> If I could get a checkout (see above) then I would try it out in >> NetBeans to >> see if it is something that Eclipse is doing to "protect" against the >> synchronisation problem. But I can't get the code so I can't test >> it :o{ >> Thos error messages *do* appear when running the tests from inside Netbeans, so clearly something that Eclipse is doing must be hiding the errors from you :o} From what I can tell, there are instances in the code that fire off preChange()/postChange() in ChangeListeners without first locking down the ChangeSupport object (whatever that is - this is the first real delve that I've had in the BioJava guts). For example, SimpleSequence.java contains a private class called FeatureForwarder that implements ChangeListener (lines 322:332) This currently reads: private class FeatureForwarder implements ChangeListener { public void preChange(ChangeEvent cev) throws ChangeVetoException { getChangeSupport(cev.getType()).firePreChangeEvent(cev); } public void postChange(ChangeEvent cev) { getChangeSupport(cev.getType()).firePostChangeEvent(cev); } } I think that it *should* read something like private class FeatureForwarder implements ChangeListener { public void preChange(ChangeEvent cev) throws ChangeVetoException { ChangeSupport cs = getChangeSupport(cev.getType()); synchronized(cs) { cs.firePreChangeEvent(cev); } } public void postChange(ChangeEvent cev) { ChangeSupport cs = getChangeSupport(cev.getType()); synchronized(cs) { cs.firePostChangeEvent(cev); } } } and when I change my local copy to this, the problems go away (for at least one section of the tests). I still get the same error cropping up in other parts (where the code funnels through different ChangeListener implementations which all have the same style as the first version above but that, I guess, is to be expected. There are test problems relating to file paths too - but I presume that you knew that stuff already. Later, Andy -------- Yada, yada, yada... The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336 Disclaimer: This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. From andreas at sdsc.edu Tue Sep 1 13:12:16 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Tue, 1 Sep 2009 10:12:16 -0700 Subject: [Biojava-dev] maven progress In-Reply-To: <32C14A50-465E-423B-9816-F1B995CBDC16@roslin.ed.ac.uk> References: <59a41c430908301823s6e2e3d7fi6caffc47e1a8c0ff@mail.gmail.com> <59a41c430908312103w7ba30a83s12d48884957be371@mail.gmail.com> <59a41c430909010737r731f9b58p2a96bf8558822de3@mail.gmail.com> <32C14A50-465E-423B-9816-F1B995CBDC16@roslin.ed.ac.uk> Message-ID: <59a41c430909011012t69fa1837sc92bb654434dd9a7@mail.gmail.com> Thanks, Andy I will try to chase up the calls and make sure they get properly synchronized. Not sure why those issues did not get detected already earlier! The broken file paths I am aware of. That has to do with me moving the files around to make the organization of the directories maven standard compliant. probably will get fixed by tonight (west coast) ... Andreas On Tue, Sep 1, 2009 at 9:30 AM, Andy Law (RI) wrote: > > On 1 Sep 2009, at 15:37, Andreas Prlic wrote: > >> Hi Andy, >> >> this repository location is ssh protected. ?Anonymous checkouts are >> possible via >> >> svn://code.open-bio.org/biojava/biojava-live/biojava > > > OK. I've got a checkout from there thanks. > > I trip up over a dependency on bytecode version 3.0. That will need to > either be incorporated into the tree or published to maven central before > the system works as it should (version 1.5 is on the maven central repo but > I couldn't find a later version) > > > >>>> >>>> At the moment I am chasing an "interesting" problem. When I run the >>>> junit tests on the new core module in eclipse, they run fine. ? When I >>>> do the same via a mvn test I get several issues like the one below. >>>> Anybody got an idea? >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------- >>>> Test set: org.biojava.bio.seq.project.ProjectedFeatureHolderTest >>>> >>>> >>>> ------------------------------------------------------------------------------- >>>> Tests run: 6, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.036 >>>> sec <<< FAILURE! >>>> >>>> >>>> testFeatureChangeEvent(org.biojava.bio.seq.project.ProjectedFeatureHolderTest) >>>> Time elapsed: 0.011 sec ?<<< ERROR! >>>> java.lang.AssertionError: firePreChangeEvent must be called in a >>>> synchronized block locking the ChangeSupport >>>> ? ? ? at >>>> >>>> org.biojava.utils.ChangeSupport.firePreChangeEvent(ChangeSupport.java:281) >>>> ? ? ? at >>>> >>>> org.biojava.bio.seq.projection.ReparentContext$PFChangeForwarder.preChange(ReparentContext.java:299) >>>> ? ? ? at >>>> >>>> org.biojava.utils.ChangeSupport.firePreChangeEvent(ChangeSupport.java:297) >>>> ? ? ? at >>>> >>>> org.biojava.bio.seq.impl.SimpleFeature.setLocation(SimpleFeature.java:173) >>>> ? ? ? at >>>> >>>> org.biojava.bio.seq.project.ProjectedFeatureHolderTest.testFeatureChangeEvent(ProjectedFeatureHolderTest.java:297) >>>> >>> >>> >>> That's certainly not one that I've ever seen, but then I probably don't >>> write code that is as complicated as BioJava :o} >>> >>> If I could get a checkout (see above) then I would try it out in NetBeans >>> to >>> see if it is something that Eclipse is doing to "protect" against the >>> synchronisation problem. But I can't get the code so I can't test it :o{ >>> > > > > Thos error messages *do* appear when running the tests from inside Netbeans, > so clearly something that Eclipse is doing must be hiding the errors from > you :o} > > From what I can tell, there are instances in the code that fire off > preChange()/postChange() in ChangeListeners without first locking down the > ChangeSupport object (whatever that is - this is the first real delve that > I've had in the BioJava guts). > > For example, SimpleSequence.java contains a private class called > FeatureForwarder that implements ChangeListener (lines 322:332) > This currently reads: > > ? ?private class FeatureForwarder implements ChangeListener { > ? ? ?public void preChange(ChangeEvent cev) > ? ? ?throws ChangeVetoException > ? ? ?{ > ? ? ? ?getChangeSupport(cev.getType()).firePreChangeEvent(cev); > ? ? ? ? ?} > > ? ? ?public void postChange(ChangeEvent cev) { > ? ? ? ?getChangeSupport(cev.getType()).firePostChangeEvent(cev); > ? ? ? ? ?} > ? ?} > > > > I think that it *should* read something like > > ? ?private class FeatureForwarder implements ChangeListener { > ? ? ?public void preChange(ChangeEvent cev) > ? ? ?throws ChangeVetoException > ? ? ?{ > ? ? ? ? ?ChangeSupport cs = getChangeSupport(cev.getType()); > ? ? ? ? ?synchronized(cs) { > ? ? ? ?cs.firePreChangeEvent(cev); > ? ? ? ? ?} > ? ? ?} > > ? ? ?public void postChange(ChangeEvent cev) { > ? ? ? ?ChangeSupport cs = getChangeSupport(cev.getType()); > ? ? ? ? ?synchronized(cs) { > ? ? ? ?cs.firePostChangeEvent(cev); > ? ? ? ? ?} > ? ? ?} > ? ?} > > and when I change my local copy to this, the problems go away (for at least > one section of the tests). I still get the same error cropping up in other > parts (where the code funnels through different ChangeListener > implementations which all have the same style as the first version above but > that, I guess, is to be expected. > > There are test problems relating to file paths too - but I presume that you > knew that stuff already. > > Later, > > Andy > -------- > Yada, yada, yada... > The University of Edinburgh is a charitable body, registered in Scotland, > with registration number SC005336 > Disclaimer: This e-mail and any attachments are confidential and intended > solely for the use of the recipient(s) to whom they are addressed. If you > have received it in error, please destroy all copies and inform the sender. > > > > From andreas at sdsc.edu Tue Sep 1 22:39:37 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Tue, 1 Sep 2009 19:39:37 -0700 Subject: [Biojava-dev] today's update Message-ID: <59a41c430909011939q13caf8e1p5487ba8ae4d33ccf@mail.gmail.com> * fixed the synchronisation problems with the JUnit tests. * started to work on the das module * general refactoring. The whole feels much more stable now. Still missing: * demos and apps subdirectories. Shall I move them to a biojava-demos module? * Can we drop the docs dir? if this is relevant it should be moved to the wiki. * refactor the biosql code to its module * signing - need to re-enable the digital signature * need to update cruisecontrol to use maven instead of ant Done: The following modules have been refactored and mavenized so far: * alignment, blast, structure, phylo, sequence, sequencing Did I miss anything? Andreas From markjschreiber at gmail.com Tue Sep 1 22:51:32 2009 From: markjschreiber at gmail.com (Mark Schreiber) Date: Wed, 2 Sep 2009 10:51:32 +0800 Subject: [Biojava-dev] today's update In-Reply-To: <59a41c430909011939q13caf8e1p5487ba8ae4d33ccf@mail.gmail.com> References: <59a41c430909011939q13caf8e1p5487ba8ae4d33ccf@mail.gmail.com> Message-ID: <93b45ca50909011951t74440edaye427625d6986acec@mail.gmail.com> I think the demos apps and docs dirs are all badly out of date and should be dropped. Going forward material like this should go to the wiki. On Sep 2, 2009 10:44 AM, "Andreas Prlic" wrote: * fixed the synchronisation problems with the JUnit tests. * started to work on the das module * general refactoring. The whole feels much more stable now. Still missing: * demos and apps subdirectories. Shall I move them to a biojava-demos module? * Can we drop the docs dir? if this is relevant it should be moved to the wiki. * refactor the biosql code to its module * signing - need to re-enable the digital signature * need to update cruisecontrol to use maven instead of ant Done: The following modules have been refactored and mavenized so far: * alignment, blast, structure, phylo, sequence, sequencing Did I miss anything? Andreas _______________________________________________ biojava-dev mailing list biojava-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-dev From andy.law at roslin.ed.ac.uk Wed Sep 2 04:45:03 2009 From: andy.law at roslin.ed.ac.uk (Andy Law (RI)) Date: Wed, 2 Sep 2009 09:45:03 +0100 Subject: [Biojava-dev] today's update In-Reply-To: <93b45ca50909011951t74440edaye427625d6986acec@mail.gmail.com> References: <59a41c430909011939q13caf8e1p5487ba8ae4d33ccf@mail.gmail.com> <93b45ca50909011951t74440edaye427625d6986acec@mail.gmail.com> Message-ID: <0BCEDF5F-6857-43D3-8025-329E4F50A37E@roslin.ed.ac.uk> On 2 Sep 2009, at 03:51, Mark Schreiber wrote: > I think the demos apps and docs dirs are all badly out of date and > should be > dropped. Going forward material like this should go to the wiki. Docs should get autogenerated from the javadoc. Maven will do this for you (maven-javadoc-plugin, goal site:site). I would argue that the demos are (will be) useful to newcomers. There is nothing like code to get you to understand how the bits fit together. Wiki pages just don't cut it for me. Plus, with maven and a decent set of test routines you can be certain that your demos are up- to-date going forward. But then I'm *not* volunteering to make sure that the demos actually work from the off so my opinion counts for nothing :o} Later, Andy -------- Yada, yada, yada... The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336 Disclaimer: This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. From HWillis at scripps.edu Wed Sep 2 10:45:57 2009 From: HWillis at scripps.edu (Scooter Willis) Date: Wed, 2 Sep 2009 10:45:57 -0400 Subject: [Biojava-dev] today's update In-Reply-To: <59a41c430909011939q13caf8e1p5487ba8ae4d33ccf@mail.gmail.com> Message-ID: Andreas Looks like you are getting close! One advantage of hosting the BioJava demo code with detailed tutorial on the web site is the ability to gather information about what modules or source code is of the most interest to developers. The download could include jars for the module with java doc and demo code to test. The tutorial related content would remain hosted as a way of measuring usage/interest. Scooter On 9/1/09 10:39 PM, "Andreas Prlic" wrote: * fixed the synchronisation problems with the JUnit tests. * started to work on the das module * general refactoring. The whole feels much more stable now. Still missing: * demos and apps subdirectories. Shall I move them to a biojava-demos module? * Can we drop the docs dir? if this is relevant it should be moved to the wiki. * refactor the biosql code to its module * signing - need to re-enable the digital signature * need to update cruisecontrol to use maven instead of ant Done: The following modules have been refactored and mavenized so far: * alignment, blast, structure, phylo, sequence, sequencing Did I miss anything? Andreas _______________________________________________ biojava-dev mailing list biojava-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-dev From andreas at sdsc.edu Thu Sep 3 02:25:58 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Wed, 2 Sep 2009 23:25:58 -0700 Subject: [Biojava-dev] today's update In-Reply-To: References: <59a41c430909011939q13caf8e1p5487ba8ae4d33ccf@mail.gmail.com> Message-ID: <59a41c430909022325n753d8c5dvcc4643ba2acbdc6b@mail.gmail.com> > One advantage of hosting the BioJava demo code with detailed tutorial on the > web site is the ability to gather information about what modules or source > code is of the most interest to developers. The download could include jars > for the module with java doc and demo code to test. The tutorial related > content would remain hosted as a way of measuring usage/interest. interesting point. I see it is easy to create javadoc via maven. Any suggestions for a plugin to create doc jars? Andreas From andreas at sdsc.edu Fri Sep 4 02:53:11 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Thu, 3 Sep 2009 23:53:11 -0700 Subject: [Biojava-dev] more updates... Message-ID: <59a41c430909032353m1a4cc116o62a98e1673da0243@mail.gmail.com> Hi, quick update: new modules: biojava-biosql and biojava-gui biojava-das compiles, still talking off list with Jonathan about details. mvn install works fine for me on the current svn. With this the most critical part of the reorganization should be done and it is time for more eyes to take a look and perhaps do some more refinement. It would be good if the module maintainers would start to take a look at their modules and see if they work for them like that. I also started to use some of the modules in a real project and looks good so far. Andreas From andy.law at roslin.ed.ac.uk Fri Sep 4 06:03:12 2009 From: andy.law at roslin.ed.ac.uk (Andy Law (RI)) Date: Fri, 4 Sep 2009 11:03:12 +0100 Subject: [Biojava-dev] more updates... In-Reply-To: <59a41c430909032353m1a4cc116o62a98e1673da0243@mail.gmail.com> References: <59a41c430909032353m1a4cc116o62a98e1673da0243@mail.gmail.com> Message-ID: <7DF95F57-F3EF-4ACB-B1FE-13CD82595341@roslin.ed.ac.uk> Andreas, On 4 Sep 2009, at 07:53, Andreas Prlic wrote: > Hi, > > quick update: new modules: > biojava-biosql and > biojava-gui > biojava-das compiles, still talking off list with Jonathan about > details. > > mvn install works fine for me on the current svn. We can't get a clean check-out to build on our systems at Roslin. I have Trevor Paterson (my local maven maven) working on detailing why not - he'll be joining us later on the list to give us a rundown. First issue is the bytecode jar. I recognise that you have stuck it into a folder with a README file, but that is not a good solution. The folder that you have put it in is not displayed in the Project view of the Netbeans IDE because it is not a standard maven location. Obviously the best solution would be to include the bytecode source as a subproject and have it build or alternatively to publish the bytecode jar into a publicly accessible (central) maven repository. Having got that in place, we then descend into jaxb hell. At that point I gave up and handed the baton to Trevor. Later, Andy -------- Yada, yada, yada... The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336 Disclaimer: This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. From trevor.paterson at roslin.ed.ac.uk Fri Sep 4 06:28:48 2009 From: trevor.paterson at roslin.ed.ac.uk (trevor paterson (RI)) Date: Fri, 4 Sep 2009 11:28:48 +0100 Subject: [Biojava-dev] JAXB plugin dependencies in sequence-blastxml module Message-ID: <050C9A545DC1D84BAC7A678B76A56C3C15CE0B48FD@ebrcexch1.ebrc.bbsrc.ac.uk> Hi Andreas I have been looking at compiling the maven project with Andy and am getting stuck at the maven-jaxb2-plugin specified for the sequence-balstxml module This is lacking a required version identifier - ( I seem to recall that only core maven plugins can skip the version) I tried a couple of the available plugins (see http://download.java.net/maven/2/org/jvnet/jaxb2/maven2/maven-jaxb2-plugin/ ) But these were failing for other non standard artifact dependencies.. e.g version 0.6.0 Path to dependency: 1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.6.0 2) org.jvnet.jaxb2_commons:jaxb-xjc:jar:2.1.6 3) org.kohsuke.rngom:rngom:jar:20061207 Path to dependency: 1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.6.0 2) org.jfrog.maven.annomojo:maven-plugin-anno:jar:1.2.4 e.g version 0.7.1 Path to dependency: 1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.7.1 2) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin-raw:jar:0.7.1 3) org.jfrog.maven.annomojo:maven-plugin-anno:jar:1.3.1 Path to dependency: 1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.7.1 2) org.jvnet.jaxb2_commons:jaxb-xjc:jar:2.1.10 3) org.kohsuke.rngom:rngom:jar:20061207 Which version of the maven-jaxb2-plugin should the build be using? And am I missing a required repository for the dependencies for the maven-jaxb2-plugin Or is it necessary to find these dependencies manually and install them locally? We are currently configured system wide to use the following repos ( and whatever plugin repos etc you add in project POMs) Central Repository http://repo1.maven.org/maven2 Java.net Repository http://download.java.net/maven/2/ Netbeans Repository http://deadlock.netbeans.org/maven2/ Trevor Paterson PhD new email trevor.paterson at roslin.ed.ac.uk Bioinformatics The Roslin Institute Edinburgh University Scotland EH25 9PS phone +44 (0)131 5274402 http://www.roslin.ed.ac.uk http://www.comparagrid.org http://www.thearkdb.org Please consider the environment before printing this e-mail The University of Edinburgh is a charitable body, registered in Scotland with registration number SC005336 Disclaimer:This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. From trevor.paterson at roslin.ed.ac.uk Fri Sep 4 06:59:58 2009 From: trevor.paterson at roslin.ed.ac.uk (trevor paterson (RI)) Date: Fri, 4 Sep 2009 11:59:58 +0100 Subject: [Biojava-dev] JAXB plugin dependencies in sequence-blastxml module In-Reply-To: <050C9A545DC1D84BAC7A678B76A56C3C15CE0B48FD@ebrcexch1.ebrc.bbsrc.ac.uk> Message-ID: <050C9A545DC1D84BAC7A678B76A56C3C15CE0B48FE@ebrcexch1.ebrc.bbsrc.ac.uk> Apologies It looks like we are failing to get these dependencies because we use a local Archiva repository to mirror the external world.... and for some reason it is failing to pull down these dependencies which have checksum failures ( even though Archiva is set to Ignore checksum failures ) When we don't use archiva as a mirror we can get the dependencies... Trevor Paterson PhD new email trevor.paterson at roslin.ed.ac.uk Bioinformatics The Roslin Institute Edinburgh University Scotland EH25 9PS phone +44 (0)131 5274402 http://www.roslin.ed.ac.uk http://www.comparagrid.org http://www.thearkdb.org Please consider the environment before printing this e-mail The University of Edinburgh is a charitable body, registered in Scotland with registration number SC005336 Disclaimer:This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. -----Original Message----- From: biojava-dev-bounces at lists.open-bio.org [mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of trevor paterson (RI) Sent: 04 September 2009 11:29 To: 'biojava-dev at biojava.org' Subject: [Biojava-dev] JAXB plugin dependencies in sequence-blastxml module Hi Andreas I have been looking at compiling the maven project with Andy and am getting stuck at the maven-jaxb2-plugin specified for the sequence-balstxml module This is lacking a required version identifier - ( I seem to recall that only core maven plugins can skip the version) I tried a couple of the available plugins (see http://download.java.net/maven/2/org/jvnet/jaxb2/maven2/maven-jaxb2-plugin/ ) But these were failing for other non standard artifact dependencies.. e.g version 0.6.0 Path to dependency: 1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.6.0 2) org.jvnet.jaxb2_commons:jaxb-xjc:jar:2.1.6 3) org.kohsuke.rngom:rngom:jar:20061207 Path to dependency: 1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.6.0 2) org.jfrog.maven.annomojo:maven-plugin-anno:jar:1.2.4 e.g version 0.7.1 Path to dependency: 1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.7.1 2) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin-raw:jar:0.7.1 3) org.jfrog.maven.annomojo:maven-plugin-anno:jar:1.3.1 Path to dependency: 1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.7.1 2) org.jvnet.jaxb2_commons:jaxb-xjc:jar:2.1.10 3) org.kohsuke.rngom:rngom:jar:20061207 Which version of the maven-jaxb2-plugin should the build be using? And am I missing a required repository for the dependencies for the maven-jaxb2-plugin Or is it necessary to find these dependencies manually and install them locally? We are currently configured system wide to use the following repos ( and whatever plugin repos etc you add in project POMs) Central Repository http://repo1.maven.org/maven2 Java.net Repository http://download.java.net/maven/2/ Netbeans Repository http://deadlock.netbeans.org/maven2/ Trevor Paterson PhD new email trevor.paterson at roslin.ed.ac.uk Bioinformatics The Roslin Institute Edinburgh University Scotland EH25 9PS phone +44 (0)131 5274402 http://www.roslin.ed.ac.uk http://www.comparagrid.org http://www.thearkdb.org Please consider the environment before printing this e-mail The University of Edinburgh is a charitable body, registered in Scotland with registration number SC005336 Disclaimer:This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. _______________________________________________ biojava-dev mailing list biojava-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-dev From andy.law at roslin.ed.ac.uk Fri Sep 4 07:57:10 2009 From: andy.law at roslin.ed.ac.uk (Andy Law (RI)) Date: Fri, 4 Sep 2009 12:57:10 +0100 Subject: [Biojava-dev] more updates... In-Reply-To: <59a41c430909032353m1a4cc116o62a98e1673da0243@mail.gmail.com> References: <59a41c430909032353m1a4cc116o62a98e1673da0243@mail.gmail.com> Message-ID: Andreas, The pom.xml file under the sequence module says that its name is 'biojava'. I think this should be 'sequence' (line 8). This causes bad things to happen in NetBeans. Can you add 'svn:ignore target' properties to all the module top-level folders please? I still do not believe that there is a DEPENDENCY on the maven- dependency-plugin (in top-level pom.xml and sequence/pom.xml). I can remove those and still have everything compile cleanly either on the command line or in netbeans. The plugin may be being used as a plugin, but it is NOT a dependency. What are other people seeing? ...and our archiva system is *still* not behaving and making us look silly (but you can't do anything about that from where you are sat) :o} On 4 Sep 2009, at 07:53, Andreas Prlic wrote: > Hi, > > quick update: new modules: > biojava-biosql and > biojava-gui > biojava-das compiles, still talking off list with Jonathan about > details. > > mvn install works fine for me on the current svn. > > With this the most critical part of the reorganization should be done > and it is time for more eyes to take a look and perhaps do some more > refinement. > It would be good if the module maintainers would start to take a look > at their modules and see if they work for them like that. > > I also started to use some of the modules in a real project and looks > good so far. Later, Andy -------- Yada, yada, yada... The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336 Disclaimer: This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. From trevor.paterson at roslin.ed.ac.uk Fri Sep 4 10:13:56 2009 From: trevor.paterson at roslin.ed.ac.uk (trevor paterson (RI)) Date: Fri, 4 Sep 2009 15:13:56 +0100 Subject: [Biojava-dev] JAXB plugin dependencies in sequence-blastxml module In-Reply-To: <050C9A545DC1D84BAC7A678B76A56C3C15CE0B48FE@ebrcexch1.ebrc.bbsrc.ac.uk> Message-ID: <050C9A545DC1D84BAC7A678B76A56C3C15CE0B4900@ebrcexch1.ebrc.bbsrc.ac.uk> I managed to fix the Archiva configuration by adding '**/*' to the whitelist for http://download.java.net/maven/2/ Somehow available artifacts had been added to the whitelist (in my world you would expect unavailable artifacts to be added to the blacklist...;) So I can almost get the whole project to compile on linux/netbeans The remaining bug is with the jaxb-api, the pom includes v2.2 as a dependency, but netbeans seems to have an internal version of v2.0 which it bootstraps with - so wont use 2.2 ( as far as I can tell java1.6 includes v2.2 - but as an internal ??runtime only?? Library) I am trying to kill this somehow - or put the correct version in lib/endorsed Trevor Paterson PhD new email trevor.paterson at roslin.ed.ac.uk Bioinformatics The Roslin Institute Edinburgh University Scotland EH25 9PS phone +44 (0)131 5274402 http://www.roslin.ed.ac.uk http://www.comparagrid.org http://www.thearkdb.org Please consider the environment before printing this e-mail The University of Edinburgh is a charitable body, registered in Scotland with registration number SC005336 Disclaimer:This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. -----Original Message----- From: biojava-dev-bounces at lists.open-bio.org [mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of trevor paterson (RI) Sent: 04 September 2009 12:00 To: 'biojava-dev at biojava.org' Subject: Re: [Biojava-dev] JAXB plugin dependencies in sequence-blastxml module Apologies It looks like we are failing to get these dependencies because we use a local Archiva repository to mirror the external world.... and for some reason it is failing to pull down these dependencies which have checksum failures ( even though Archiva is set to Ignore checksum failures ) When we don't use archiva as a mirror we can get the dependencies... Trevor Paterson PhD new email trevor.paterson at roslin.ed.ac.uk Bioinformatics The Roslin Institute Edinburgh University Scotland EH25 9PS phone +44 (0)131 5274402 http://www.roslin.ed.ac.uk http://www.comparagrid.org http://www.thearkdb.org Please consider the environment before printing this e-mail The University of Edinburgh is a charitable body, registered in Scotland with registration number SC005336 Disclaimer:This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. -----Original Message----- From: biojava-dev-bounces at lists.open-bio.org [mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of trevor paterson (RI) Sent: 04 September 2009 11:29 To: 'biojava-dev at biojava.org' Subject: [Biojava-dev] JAXB plugin dependencies in sequence-blastxml module Hi Andreas I have been looking at compiling the maven project with Andy and am getting stuck at the maven-jaxb2-plugin specified for the sequence-balstxml module This is lacking a required version identifier - ( I seem to recall that only core maven plugins can skip the version) I tried a couple of the available plugins (see http://download.java.net/maven/2/org/jvnet/jaxb2/maven2/maven-jaxb2-plugin/ ) But these were failing for other non standard artifact dependencies.. e.g version 0.6.0 Path to dependency: 1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.6.0 2) org.jvnet.jaxb2_commons:jaxb-xjc:jar:2.1.6 3) org.kohsuke.rngom:rngom:jar:20061207 Path to dependency: 1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.6.0 2) org.jfrog.maven.annomojo:maven-plugin-anno:jar:1.2.4 e.g version 0.7.1 Path to dependency: 1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.7.1 2) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin-raw:jar:0.7.1 3) org.jfrog.maven.annomojo:maven-plugin-anno:jar:1.3.1 Path to dependency: 1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.7.1 2) org.jvnet.jaxb2_commons:jaxb-xjc:jar:2.1.10 3) org.kohsuke.rngom:rngom:jar:20061207 Which version of the maven-jaxb2-plugin should the build be using? And am I missing a required repository for the dependencies for the maven-jaxb2-plugin Or is it necessary to find these dependencies manually and install them locally? We are currently configured system wide to use the following repos ( and whatever plugin repos etc you add in project POMs) Central Repository http://repo1.maven.org/maven2 Java.net Repository http://download.java.net/maven/2/ Netbeans Repository http://deadlock.netbeans.org/maven2/ Trevor Paterson PhD new email trevor.paterson at roslin.ed.ac.uk Bioinformatics The Roslin Institute Edinburgh University Scotland EH25 9PS phone +44 (0)131 5274402 http://www.roslin.ed.ac.uk http://www.comparagrid.org http://www.thearkdb.org Please consider the environment before printing this e-mail The University of Edinburgh is a charitable body, registered in Scotland with registration number SC005336 Disclaimer:This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. _______________________________________________ biojava-dev mailing list biojava-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-dev _______________________________________________ biojava-dev mailing list biojava-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-dev From trevor.paterson at roslin.ed.ac.uk Fri Sep 4 12:12:47 2009 From: trevor.paterson at roslin.ed.ac.uk (trevor paterson (RI)) Date: Fri, 4 Sep 2009 17:12:47 +0100 Subject: [Biojava-dev] JAXB plugin dependencies in sequence-blastxml module In-Reply-To: <050C9A545DC1D84BAC7A678B76A56C3C15CE0B4900@ebrcexch1.ebrc.bbsrc.ac.uk> Message-ID: <050C9A545DC1D84BAC7A678B76A56C3C15CE0B4901@ebrcexch1.ebrc.bbsrc.ac.uk> [ONLY OF INTEREST TO NETBEANS USERS] I can't find a way to configure Netbeans6.5 to not use its bundled jaxb-api, so am having to use the endorsed libraries route.... Until netbeans 6.7 (which is allegedly still flakey) you can't alter the jdk for maven to use by default, it just uses whatever JAVA_HOME is. You can however add a -D property flag to any global or custom maven action. So you can either set to build with a different jdk (containing your endorsed libraries) Or you can just point at the ensdorsed libraries location itself i.e. -DEnv.JAVA_HOME=/nfs_netapp/paterson/MyJava6/jdk1.6.0_04/ -Djava.endorsed.dirs= /nfs_netapp/paterson/MyJava6/jdk1.6.0_04/jre/lib/endorsed You don't seem to be able to add these as as maven properties in a POM or settings.xml And I am not sure why andy is not getting this happenning in his OSX.5/MACJava worl - probably he has not installed some netbeans plugin module that wired in this jaxb version Trevor -----Original Message----- From: biojava-dev-bounces at lists.open-bio.org [mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of trevor paterson (RI) Sent: 04 September 2009 15:14 To: 'biojava-dev at biojava.org' Subject: Re: [Biojava-dev] JAXB plugin dependencies in sequence-blastxml module I managed to fix the Archiva configuration by adding '**/*' to the whitelist for http://download.java.net/maven/2/ Somehow available artifacts had been added to the whitelist (in my world you would expect unavailable artifacts to be added to the blacklist...;) So I can almost get the whole project to compile on linux/netbeans The remaining bug is with the jaxb-api, the pom includes v2.2 as a dependency, but netbeans seems to have an internal version of v2.0 which it bootstraps with - so wont use 2.2 ( as far as I can tell java1.6 includes v2.2 - but as an internal ??runtime only?? Library) I am trying to kill this somehow - or put the correct version in lib/endorsed Trevor Paterson -----Original Message----- From: biojava-dev-bounces at lists.open-bio.org [mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of trevor paterson (RI) Sent: 04 September 2009 12:00 To: 'biojava-dev at biojava.org' Subject: Re: [Biojava-dev] JAXB plugin dependencies in sequence-blastxml module Apologies It looks like we are failing to get these dependencies because we use a local Archiva repository to mirror the external world.... and for some reason it is failing to pull down these dependencies which have checksum failures ( even though Archiva is set to Ignore checksum failures ) When we don't use archiva as a mirror we can get the dependencies... Trevor Paterson -----Original Message----- From: biojava-dev-bounces at lists.open-bio.org [mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of trevor paterson (RI) Sent: 04 September 2009 11:29 To: 'biojava-dev at biojava.org' Subject: [Biojava-dev] JAXB plugin dependencies in sequence-blastxml module Hi Andreas I have been looking at compiling the maven project with Andy and am getting stuck at the maven-jaxb2-plugin specified for the sequence-balstxml module This is lacking a required version identifier - ( I seem to recall that only core maven plugins can skip the version) I tried a couple of the available plugins (see http://download.java.net/maven/2/org/jvnet/jaxb2/maven2/maven-jaxb2-plugin/ ) But these were failing for other non standard artifact dependencies.. e.g version 0.6.0 Path to dependency: 1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.6.0 2) org.jvnet.jaxb2_commons:jaxb-xjc:jar:2.1.6 3) org.kohsuke.rngom:rngom:jar:20061207 Path to dependency: 1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.6.0 2) org.jfrog.maven.annomojo:maven-plugin-anno:jar:1.2.4 e.g version 0.7.1 Path to dependency: 1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.7.1 2) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin-raw:jar:0.7.1 3) org.jfrog.maven.annomojo:maven-plugin-anno:jar:1.3.1 Path to dependency: 1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.7.1 2) org.jvnet.jaxb2_commons:jaxb-xjc:jar:2.1.10 3) org.kohsuke.rngom:rngom:jar:20061207 Which version of the maven-jaxb2-plugin should the build be using? And am I missing a required repository for the dependencies for the maven-jaxb2-plugin Or is it necessary to find these dependencies manually and install them locally? We are currently configured system wide to use the following repos ( and whatever plugin repos etc you add in project POMs) Central Repository http://repo1.maven.org/maven2 Java.net Repository http://download.java.net/maven/2/ Netbeans Repository http://deadlock.netbeans.org/maven2/ Trevor Paterson PhD new email trevor.paterson at roslin.ed.ac.uk Bioinformatics The Roslin Institute Edinburgh University Scotland EH25 9PS phone +44 (0)131 5274402 http://www.roslin.ed.ac.uk http://www.comparagrid.org http://www.thearkdb.org Please consider the environment before printing this e-mail The University of Edinburgh is a charitable body, registered in Scotland with registration number SC005336 Disclaimer:This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. _______________________________________________ biojava-dev mailing list biojava-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-dev _______________________________________________ biojava-dev mailing list biojava-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-dev _______________________________________________ biojava-dev mailing list biojava-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-dev From andreas at sdsc.edu Fri Sep 4 17:49:32 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Fri, 4 Sep 2009 14:49:32 -0700 Subject: [Biojava-dev] JAXB plugin dependencies in sequence-blastxml module In-Reply-To: <050C9A545DC1D84BAC7A678B76A56C3C15CE0B4900@ebrcexch1.ebrc.bbsrc.ac.uk> References: <050C9A545DC1D84BAC7A678B76A56C3C15CE0B48FE@ebrcexch1.ebrc.bbsrc.ac.uk> <050C9A545DC1D84BAC7A678B76A56C3C15CE0B4900@ebrcexch1.ebrc.bbsrc.ac.uk> Message-ID: <59a41c430909041449p24e90756l97aec6cd9fcbe6e6@mail.gmail.com> Hi Trevor and Andy, Thanks for the detailed feedback. To make sure nothing gets lost I added a todo list to the wiki. Feel free to add other action items... http://biojava.org/wiki/BioJava:MavenMigration * I understand the jaxb problem is mainly related to netbeans. I think we should support easy setup on all popular IDEs. Would it be of advantage to change the dependency to a different jaxb package? Seems there are many available... Richard, do you as the module lead have an opinion which version of jaxb to depend on? - I suppose you will say the latest... :-) Andreas From heuermh at acm.org Fri Sep 4 22:40:48 2009 From: heuermh at acm.org (Michael Heuer) Date: Fri, 4 Sep 2009 22:40:48 -0400 (EDT) Subject: [Biojava-dev] more updates... In-Reply-To: <7DF95F57-F3EF-4ACB-B1FE-13CD82595341@roslin.ed.ac.uk> Message-ID: Andy Law (RI) wrote: > Andreas, > > On 4 Sep 2009, at 07:53, Andreas Prlic wrote: > > > Hi, > > > > quick update: new modules: > > biojava-biosql and > > biojava-gui > > biojava-das compiles, still talking off list with Jonathan about > > details. > > > > mvn install works fine for me on the current svn. > > > We can't get a clean check-out to build on our systems at Roslin. > > I have Trevor Paterson (my local maven maven) working on detailing why > not - he'll be joining us later on the list to give us a rundown. > > First issue is the bytecode jar. I recognise that you have stuck it > into a folder with a README file, but that is not a good solution. The > folder that you have put it in is not displayed in the Project view of > the Netbeans IDE because it is not a standard maven location. > Obviously the best solution would be to include the bytecode source as > a subproject and have it build or alternatively to publish the > bytecode jar into a publicly accessible (central) maven repository. Perhaps the biojava code that depends on bytecode.jar should be refactored to use BCEL or some other third party bytecode generation library. michael From holland at eaglegenomics.com Sat Sep 5 05:12:32 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Sat, 5 Sep 2009 11:12:32 +0200 Subject: [Biojava-dev] JAXB plugin dependencies in sequence-blastxml module In-Reply-To: <59a41c430909041449p24e90756l97aec6cd9fcbe6e6@mail.gmail.com> References: <050C9A545DC1D84BAC7A678B76A56C3C15CE0B48FE@ebrcexch1.ebrc.bbsrc.ac.uk> <050C9A545DC1D84BAC7A678B76A56C3C15CE0B4900@ebrcexch1.ebrc.bbsrc.ac.uk> <59a41c430909041449p24e90756l97aec6cd9fcbe6e6@mail.gmail.com> Message-ID: <600E7D2C-179E-4BAE-B554-AA3E44A3C043@eaglegenomics.com> Yup I would say the latest but as I can see no specific feature in it which is required as a dependency, then any version will probably do. On 4 Sep 2009, at 23:49, Andreas Prlic wrote: > Hi Trevor and Andy, > > Thanks for the detailed feedback. To make sure nothing gets lost I > added a todo list to the wiki. Feel free to add other action items... > http://biojava.org/wiki/BioJava:MavenMigration > > * I understand the jaxb problem is mainly related to netbeans. I think > we should support easy setup on all popular IDEs. Would it be of > advantage to change the dependency to a different jaxb package? Seems > there are many available... > > Richard, do you as the module lead have an opinion which version of > jaxb to depend on? - I suppose you will say the latest... :-) > > Andreas > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From holland at eaglegenomics.com Sat Sep 5 05:13:49 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Sat, 5 Sep 2009 11:13:49 +0200 Subject: [Biojava-dev] more updates... In-Reply-To: References: Message-ID: <883EF3DE-E522-4121-A978-C13377CA2475@eaglegenomics.com> What bit of the code is it actually used for? Do we still need to do that? Either way, the easiest solution is to make bytecode.jar into its own separate maven/svn project. It's not really bio-specific and so could live quite happily as its own project. On 5 Sep 2009, at 04:40, Michael Heuer wrote: > Andy Law (RI) wrote: > >> Andreas, >> >> On 4 Sep 2009, at 07:53, Andreas Prlic wrote: >> >>> Hi, >>> >>> quick update: new modules: >>> biojava-biosql and >>> biojava-gui >>> biojava-das compiles, still talking off list with Jonathan about >>> details. >>> >>> mvn install works fine for me on the current svn. >> >> >> We can't get a clean check-out to build on our systems at Roslin. >> >> I have Trevor Paterson (my local maven maven) working on detailing >> why >> not - he'll be joining us later on the list to give us a rundown. >> >> First issue is the bytecode jar. I recognise that you have stuck it >> into a folder with a README file, but that is not a good solution. >> The >> folder that you have put it in is not displayed in the Project view >> of >> the Netbeans IDE because it is not a standard maven location. >> Obviously the best solution would be to include the bytecode source >> as >> a subproject and have it build or alternatively to publish the >> bytecode jar into a publicly accessible (central) maven repository. > > Perhaps the biojava code that depends on bytecode.jar should be > refactored > to use BCEL or some other third party bytecode generation library. > > michael > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From trevor.paterson at roslin.ed.ac.uk Mon Sep 7 04:13:34 2009 From: trevor.paterson at roslin.ed.ac.uk (trevor paterson (RI)) Date: Mon, 7 Sep 2009 09:13:34 +0100 Subject: [Biojava-dev] JAXB plugin dependencies in sequence-blastxml module In-Reply-To: <59a41c430909041449p24e90756l97aec6cd9fcbe6e6@mail.gmail.com> Message-ID: <050C9A545DC1D84BAC7A678B76A56C3C15CE0B4902@ebrcexch1.ebrc.bbsrc.ac.uk> Personally I think that the code should be independent of any IDE quirks - not tailored to work with every possible IDE. As we know what the issue is and how to avoid it I think the dependency should be left as it is. It looks like netbeans is supplying something equivalent to jaxb 2.0 which lacks the Marshaller.marshall(Object, File) method signature - found since version 2.1. - the sequence-blastxml BlastXMLTYools object uses this convenience method. Trevor Paterson PhD new email trevor.paterson at roslin.ed.ac.uk Bioinformatics The Roslin Institute Edinburgh University Scotland EH25 9PS phone +44 (0)131 5274402 http://www.roslin.ed.ac.uk http://www.comparagrid.org http://www.thearkdb.org Please consider the environment before printing this e-mail The University of Edinburgh is a charitable body, registered in Scotland with registration number SC005336 Disclaimer:This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. -----Original Message----- From: andreas.prlic at gmail.com [mailto:andreas.prlic at gmail.com] On Behalf Of Andreas Prlic Sent: 04 September 2009 22:50 To: trevor paterson (RI) Cc: biojava-dev at biojava.org; andy law (RI) Subject: Re: [Biojava-dev] JAXB plugin dependencies in sequence-blastxml module Hi Trevor and Andy, Thanks for the detailed feedback. To make sure nothing gets lost I added a todo list to the wiki. Feel free to add other action items... http://biojava.org/wiki/BioJava:MavenMigration * I understand the jaxb problem is mainly related to netbeans. I think we should support easy setup on all popular IDEs. Would it be of advantage to change the dependency to a different jaxb package? Seems there are many available... Richard, do you as the module lead have an opinion which version of jaxb to depend on? - I suppose you will say the latest... :-) Andreas From andy.law at roslin.ed.ac.uk Mon Sep 7 11:35:56 2009 From: andy.law at roslin.ed.ac.uk (Andy Law (RI)) Date: Mon, 7 Sep 2009 16:35:56 +0100 Subject: [Biojava-dev] File path problem Message-ID: All, Clean checkout of the code gives me multiple test failures (FileNotFoundException) if the path to the code includes spaces. Seems that calls to open test files are failing. The path to the file has been encoded with %20 instead of the spaces but the open file is failing - apparently inside of the Sun code in java.io.RandomAccessFile.open(Native Method). Anyone else seeing this on any other platform (I'm on a Mac) Later, Andy -------- Yada, yada, yada... The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336 Disclaimer: This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. From andreas at sdsc.edu Mon Sep 7 16:01:45 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Mon, 7 Sep 2009 13:01:45 -0700 Subject: [Biojava-dev] replacing trunk with new modules Message-ID: <59a41c430909071301x21885fb9m6b8d6af32ad43df6@mail.gmail.com> Hi, unless I hear any objections, I would like to replace the ("old") biojava-trunk with the new modularized svn location tomorrow evening (San Diego time). I will move the current trunk location to a tag directory in svn, so it is still possible to refer to it and compare with it. This is to avoid any confusion about where any new development should happen. Any objections? Andreas From andreas.prlic at gmail.com Mon Sep 7 16:03:35 2009 From: andreas.prlic at gmail.com (Andreas Prlic) Date: Mon, 7 Sep 2009 13:03:35 -0700 Subject: [Biojava-dev] File path problem In-Reply-To: References: Message-ID: <59a41c430909071303o347ef9au1b9a056ea2d606e9@mail.gmail.com> Hi Andy, Can you send me a few stacktraces / file locations that you are having problems with? works fine for me on OSX using eclipse and command line mvn... Andreas On Mon, Sep 7, 2009 at 8:35 AM, Andy Law (RI) wrote: > All, > > Clean checkout of the code gives me multiple test failures > (FileNotFoundException) if the path to the code includes spaces. Seems that > calls to open test files are failing. The path to the file has been encoded > with %20 instead of the spaces but the open file is failing - apparently > inside of the Sun code in java.io.RandomAccessFile.open(Native Method). > > Anyone else seeing this on any other platform (I'm on a Mac) > > Later, > > Andy > -------- > Yada, yada, yada... > The University of Edinburgh is a charitable body, registered in Scotland, > with registration number SC005336 > Disclaimer: This e-mail and any attachments are confidential and intended > solely for the use of the recipient(s) to whom they are addressed. If you > have received it in error, please destroy all copies and inform the sender. > > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From heuermh at acm.org Mon Sep 7 22:01:01 2009 From: heuermh at acm.org (Michael Heuer) Date: Mon, 7 Sep 2009 22:01:01 -0400 (EDT) Subject: [Biojava-dev] replacing trunk with new modules In-Reply-To: <59a41c430909071301x21885fb9m6b8d6af32ad43df6@mail.gmail.com> Message-ID: Andreas Prlic wrote: > unless I hear any objections, I would like to replace the ("old") > biojava-trunk with the new modularized svn location tomorrow evening > (San Diego time). I will move the current trunk location to a tag > directory in svn, so it is still possible to refer to it and compare > with it. This is to avoid any confusion about where any new > development should happen. I will need to get a 1.7.1 release out quickly for this FASTQ paper submission. Do you feel that we'd be able to get a 1.7.1 release built off the new structure without any problems, or is the modularized tree slated for a version 1.8? In that case, I can do a release from the 1.7 release branch no problem. michael From andreas at sdsc.edu Mon Sep 7 22:57:06 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Mon, 7 Sep 2009 19:57:06 -0700 Subject: [Biojava-dev] replacing trunk with new modules In-Reply-To: References: <59a41c430909071301x21885fb9m6b8d6af32ad43df6@mail.gmail.com> Message-ID: <59a41c430909071957kf7699cah7635f07efd1386af@mail.gmail.com> better do a 1.7.1 build from the current code in the trunk. the modularized new thingy probably should be called v. 3.0 and will only be ready at some point after the hackaton... do you need a full release or just some kind of jar file available for download? Andreas On Mon, Sep 7, 2009 at 7:01 PM, Michael Heuer wrote: > Andreas Prlic wrote: > >> unless I hear any objections, I would like to replace the ("old") >> biojava-trunk with the new modularized svn location tomorrow evening >> (San Diego time). I will move the current trunk location to a tag >> directory in svn, so it is still possible to refer to it and compare >> with it. This is to avoid any confusion about where any new >> development should happen. > > I will need to get a 1.7.1 release out quickly for this FASTQ paper > submission. ?Do you feel that we'd be able to get a 1.7.1 release built > off the new structure without any problems, or is the modularized tree > slated for a version 1.8? ?In that case, I can do a release from the 1.7 > release branch no problem. > > ? michael > > From andy.law at roslin.ed.ac.uk Tue Sep 8 05:26:25 2009 From: andy.law at roslin.ed.ac.uk (Andy Law (RI)) Date: Tue, 8 Sep 2009 10:26:25 +0100 Subject: [Biojava-dev] more updates... In-Reply-To: References: Message-ID: On 5 Sep 2009, at 03:40, Michael Heuer wrote: > Perhaps the biojava code that depends on bytecode.jar should be > refactored > to use BCEL or some other third party bytecode generation library. Where *is* the code that underpins this library? It's all org.biojava.util package so presumably it's lying around somewhere in the biojava vaults? Later, Andy -------- Yada, yada, yada... The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336 Disclaimer: This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. From andy.law at roslin.ed.ac.uk Tue Sep 8 05:43:48 2009 From: andy.law at roslin.ed.ac.uk (Andy Law (RI)) Date: Tue, 8 Sep 2009 10:43:48 +0100 Subject: [Biojava-dev] File path problem In-Reply-To: <59a41c430909071303o347ef9au1b9a056ea2d606e9@mail.gmail.com> References: <59a41c430909071303o347ef9au1b9a056ea2d606e9@mail.gmail.com> Message-ID: <2256B94E-ADF8-4781-9E60-DE5935C62973@roslin.ed.ac.uk> On 7 Sep 2009, at 21:03, Andreas Prlic wrote: > Hi Andy, > > Can you send me a few stacktraces / file locations that you are having > problems with? works fine for me on OSX using eclipse and command line > mvn... > http://tr.im/y8YT I have lots like this (generated from the command line). If I move the biojava folder to the Desktop (i.e. at "~/Desktop/ biojava/" rather than "~/Desktop/No Time Machine Backup/biojava/") then the problem goes away. Later, Andy -------- Yada, yada, yada... The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336 Disclaimer: This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. From phidias51 at gmail.com Tue Sep 8 12:08:40 2009 From: phidias51 at gmail.com (Mark Fortner) Date: Tue, 8 Sep 2009 09:08:40 -0700 Subject: [Biojava-dev] File path problem In-Reply-To: <2256B94E-ADF8-4781-9E60-DE5935C62973@roslin.ed.ac.uk> References: <59a41c430909071303o347ef9au1b9a056ea2d606e9@mail.gmail.com> <2256B94E-ADF8-4781-9E60-DE5935C62973@roslin.ed.ac.uk> Message-ID: <6e1d61f50909080908t7d982cb3oa844e902ad75a7aa@mail.gmail.com> Andreas & Andy, AFAIK this is a long-standing JVM/OS dependent issue. The only workaround I know of is to escape the spaces by preceding them with a backslash. You may be able to create a relative root directory from which all other subdirectories can be resolved. Andy, do you encounter a problem if you do something like this: File biojavaHome = new File("."); in the ~/Desktop/No Time Machine Backup/biojava directory? Does biojavaHome.exists() return true? If you don't, then it may be able to resolve subdirectories of the biojavaHome file object. You might also try to declare a biojava home env variable and use it throughout the unit tests. The other thing that you might try is the new File(new URI("blah")) constructor. According to the URI javadoc it apparently can deal with %20 spaces in file names. Hope this helps, Mark On Tue, Sep 8, 2009 at 2:43 AM, Andy Law (RI) wrote: > > On 7 Sep 2009, at 21:03, Andreas Prlic wrote: > > Hi Andy, >> >> Can you send me a few stacktraces / file locations that you are having >> problems with? works fine for me on OSX using eclipse and command line >> mvn... >> >> > > > http://tr.im/y8YT > > > I have lots like this (generated from the command line). > > If I move the biojava folder to the Desktop (i.e. at "~/Desktop/biojava/" > rather than "~/Desktop/No Time Machine Backup/biojava/") then the problem > goes away. > > > > > Later, > > Andy > -------- > Yada, yada, yada... > The University of Edinburgh is a charitable body, registered in Scotland, > with registration number SC005336 > Disclaimer: This e-mail and any attachments are confidential and intended > solely for the use of the recipient(s) to whom they are addressed. If you > have received it in error, please destroy all copies and inform the sender. > > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > -- Mark Fortner blog: http://feeds.feedburner.com/jroller/ideafactory From andreas.prlic at gmail.com Tue Sep 8 12:47:37 2009 From: andreas.prlic at gmail.com (Andreas Prlic) Date: Tue, 8 Sep 2009 09:47:37 -0700 Subject: [Biojava-dev] File path problem In-Reply-To: <6e1d61f50909080908t7d982cb3oa844e902ad75a7aa@mail.gmail.com> References: <59a41c430909071303o347ef9au1b9a056ea2d606e9@mail.gmail.com> <2256B94E-ADF8-4781-9E60-DE5935C62973@roslin.ed.ac.uk> <6e1d61f50909080908t7d982cb3oa844e902ad75a7aa@mail.gmail.com> Message-ID: <59a41c430909080947q7661b604j76d0f0e2c774aff3@mail.gmail.com> Another work around is to use symbolic links... The standard way to request files form the file system in biojava is like this: String resName = "org/biojava/bio/program/sax/blastxml/input.xml"; InputStream resStream = getClass().getClassLoader().getResourceAsStream(resName); Not sure if this will work with spaces in directory names.... Andreas On Tue, Sep 8, 2009 at 9:08 AM, Mark Fortner wrote: > Andreas & Andy, > AFAIK this is a long-standing JVM/OS dependent issue.? The only workaround I > know of is to escape the spaces by preceding them with a backslash. > > You may be able to create a relative root directory from which all other > subdirectories can be resolved.? Andy, do you encounter a problem if you do > something like this: > > File biojavaHome = new File("."); > > in the ~/Desktop/No Time Machine Backup/biojava directory?? Does > biojavaHome.exists() return true? > > If you don't, then it may be able to resolve subdirectories of the > biojavaHome file object.? You might also try to declare a biojava home env > variable and use it throughout the unit tests. > > The other thing that you might try is the new File(new URI("blah")) > constructor.? According to the URI javadoc? it apparently can deal with %20 > spaces in file names. > > Hope this helps, > > Mark > > On Tue, Sep 8, 2009 at 2:43 AM, Andy Law (RI) > wrote: >> >> On 7 Sep 2009, at 21:03, Andreas Prlic wrote: >> >>> Hi Andy, >>> >>> Can you send me a few stacktraces / file locations that you are having >>> problems with? works fine for me on OSX using eclipse and command line >>> mvn... >>> >> >> >> >> http://tr.im/y8YT >> >> >> I have lots like this (generated from the command line). >> >> If I move the biojava folder to the Desktop (i.e. at "~/Desktop/biojava/" >> rather than "~/Desktop/No Time Machine Backup/biojava/") then the problem >> goes away. >> >> >> >> Later, >> >> Andy >> -------- >> Yada, yada, yada... >> The University of Edinburgh is a charitable body, registered in Scotland, >> with registration number SC005336 >> Disclaimer: This e-mail and any attachments are confidential and intended >> solely for the use of the recipient(s) to whom they are addressed. If you >> have received it in error, please destroy all copies and inform the sender. >> >> >> >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev > > > > -- > Mark Fortner > > blog: http://feeds.feedburner.com/jroller/ideafactory > From andreas at sdsc.edu Tue Sep 8 13:03:11 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Tue, 8 Sep 2009 10:03:11 -0700 Subject: [Biojava-dev] more updates... In-Reply-To: References: Message-ID: <59a41c430909081003v267cd167ofb3d4f9adaa26e9b@mail.gmail.com> The bytecode.jar source is in a different location in SVN: http://code.open-bio.org/svnweb/index.cgi/biojava/browse/bytecode/trunk Not sure how this one will go, since it seems to be a bit special, but I will try to make this another maven module, so things are consistent. Andreas On Tue, Sep 8, 2009 at 2:26 AM, Andy Law (RI) wrote: > > On 5 Sep 2009, at 03:40, Michael Heuer wrote: > >> Perhaps the biojava code that depends on bytecode.jar should be refactored >> to use BCEL or some other third party bytecode generation library. > > Where *is* the code that underpins this library? It's all org.biojava.util > package so presumably it's lying around somewhere in the biojava vaults? > > Later, > > Andy > -------- > Yada, yada, yada... > The University of Edinburgh is a charitable body, registered in Scotland, > with registration number SC005336 > Disclaimer: This e-mail and any attachments are confidential and intended > solely for the use of the recipient(s) to whom they are addressed. If you > have received it in error, please destroy all copies and inform the sender. > > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From andreas at sdsc.edu Wed Sep 9 00:05:07 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Tue, 8 Sep 2009 21:05:07 -0700 Subject: [Biojava-dev] bytecode module (was: more updates...) Message-ID: <59a41c430909082105v4ee83c0bmeb29b7f80bd5ad16@mail.gmail.com> To follow up on the bytecode module: Turned out it was easy to move the code into its own module. The core module is now set up correctly and does not require any local installations of bytecode.jar any longer. Andreas On Tue, Sep 8, 2009 at 10:03 AM, Andreas Prlic wrote: > The bytecode.jar source is in a different location in SVN: > > http://code.open-bio.org/svnweb/index.cgi/biojava/browse/bytecode/trunk > > Not sure how this one will go, since it seems to be a bit special, but > I will try to ?make this another maven module, so things are > consistent. > > Andreas > > > > On Tue, Sep 8, 2009 at 2:26 AM, Andy Law (RI) wrote: >> >> On 5 Sep 2009, at 03:40, Michael Heuer wrote: >> >>> Perhaps the biojava code that depends on bytecode.jar should be refactored >>> to use BCEL or some other third party bytecode generation library. >> >> Where *is* the code that underpins this library? It's all org.biojava.util >> package so presumably it's lying around somewhere in the biojava vaults? >> >> Later, >> >> Andy >> -------- >> Yada, yada, yada... >> The University of Edinburgh is a charitable body, registered in Scotland, >> with registration number SC005336 >> Disclaimer: This e-mail and any attachments are confidential and intended >> solely for the use of the recipient(s) to whom they are addressed. If you >> have received it in error, please destroy all copies and inform the sender. >> >> >> >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev >> > From andy.law at roslin.ed.ac.uk Wed Sep 9 06:30:40 2009 From: andy.law at roslin.ed.ac.uk (Andy Law (RI)) Date: Wed, 9 Sep 2009 11:30:40 +0100 Subject: [Biojava-dev] File path problem In-Reply-To: <6e1d61f50909080908t7d982cb3oa844e902ad75a7aa@mail.gmail.com> References: <59a41c430909071303o347ef9au1b9a056ea2d606e9@mail.gmail.com> <2256B94E-ADF8-4781-9E60-DE5935C62973@roslin.ed.ac.uk> <6e1d61f50909080908t7d982cb3oa844e902ad75a7aa@mail.gmail.com> Message-ID: <58E00A8B-DAD7-46D2-AAF8-424C9F896C40@roslin.ed.ac.uk> The problem appears not to be in accessing the file - the test code generates File objects correctly with the paths escaped to contain %20 instead of spaces. If I modify the source code of the test so that the names of the files are incorrect then the failure is that the File object is returned as null. I am confident that this part of the code is working. The problem arises when the biojava code asks for a biojava RAF object to be constructed from the File object. RAF is a wrapper around java.io.RandomAccessFile, seemingly simply to allow access to the File object although java.io.RandomAccessFile does provide access to a FileDescriptor. The RAF constructor calls the RandomAccessFile constructor passing it the (perfectly valid) File object it was itself handed. The failure occurs inside the RandomAccessFile constructor. I suspect that this occurs in the call to 'open' in the constructor which is - obviously - a platform-specific piece of code. Thus we seem to have tripped over a bug in the Apple implementation of the JVM. I will look into this further if/when time permits. It may be possible to workaround it by manipulating the path in the RAF constructor on a platform-by-platform basis but that kind of hacking should only be a short-term solution. On 8 Sep 2009, at 17:08, Mark Fortner wrote: > Andreas & Andy, > AFAIK this is a long-standing JVM/OS dependent issue. The only > workaround I know of is to escape the spaces by preceding them with > a backslash. > > You may be able to create a relative root directory from which all > other subdirectories can be resolved. Andy, do you encounter a > problem if you do something like this: > > File biojavaHome = new File("."); > > in the ~/Desktop/No Time Machine Backup/biojava directory? Does > biojavaHome.exists() return true? > > If you don't, then it may be able to resolve subdirectories of the > biojavaHome file object. You might also try to declare a biojava > home env variable and use it throughout the unit tests. > > The other thing that you might try is the new File(new URI("blah")) > constructor. According to the URI javadoc it apparently can deal > with %20 spaces in file names. > > Hope this helps, > > Mark > > On Tue, Sep 8, 2009 at 2:43 AM, Andy Law (RI) > wrote: > > On 7 Sep 2009, at 21:03, Andreas Prlic wrote: > > Hi Andy, > > Can you send me a few stacktraces / file locations that you are having > problems with? works fine for me on OSX using eclipse and command line > mvn... > > > > > http://tr.im/y8YT > > > I have lots like this (generated from the command line). > > If I move the biojava folder to the Desktop (i.e. at "~/Desktop/ > biojava/" rather than "~/Desktop/No Time Machine Backup/biojava/") > then the problem goes away. > > > > > Later, > > Andy > -------- > Yada, yada, yada... > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336 > Disclaimer: This e-mail and any attachments are confidential and > intended solely for the use of the recipient(s) to whom they are > addressed. If you have received it in error, please destroy all > copies and inform the sender. > > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > > > > -- > Mark Fortner > > blog: http://feeds.feedburner.com/jroller/ideafactory Later, Andy -------- Yada, yada, yada... The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336 Disclaimer: This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. From andy.law at roslin.ed.ac.uk Thu Sep 10 11:00:53 2009 From: andy.law at roslin.ed.ac.uk (Andy Law (RI)) Date: Thu, 10 Sep 2009 16:00:53 +0100 Subject: [Biojava-dev] Spaces in file paths - resolved Message-ID: All, I've been digging about in the bowels of the java.io libraries and the biojava core tests and I have a fix. From what I can tell, the problem with spaces in file paths is NOT a Mac-specific thing. I threw together some tests (attached as a tgz version of the maven project) that demonstrate the problem on the Mac but then when I ran them on the linux box, the same tests failed so I think it is a general issue. However, in doing so I was able to get to grips with why it is failing and how to work around it. The problem stems from the RandomAccessFile constructor being given a File whose path contains encoded spaces. The File objects in question are constructed (in the tests) using the file path extracted from a URL object i.e. the MO of the tests is: (1) create URL pointing at the file (2) create a File from that (using the *path* extracted from the URL [via getFile()! go figure]) (3) create a RandomAccessFile from the File There are similar problems creating Streams from the File object but points (1) and (2) are the same in that situation. However, it is possible to construct a File from a URI (note UR*I* not UR*L*) and it is possible to extract a URI from a URL. The File generated this way seems to have the path escaped or handled properly. Thus if we replace step (2) with "create a File from a URI extracted from the URL" then all seems to be well. Changes required: Change .getFile() to .getURI() at: Line 196: biojava/core/src/test/java/org/biojava/bio/program/indexdb/ IndexToolsTest.java Line 53: biojava/core/src/test/java/org/biojava/bio/seq/db/emblcd/ DivisionLkpReaderTest.java Line 58: biojava/core/src/test/java/org/biojava/bio/seq/db/emblcd/ EntryNamIdxReaderTest.java Line 54: biojava/core/src/test/java/org/biojava/bio/seq/db/emblcd/ EntryNamRandomAccessTest.java Line 70: biojava/core/src/test/java/org/biojava/bio/seq/db/ EmblCDROMIndexStoreTest.java Line 71: biojava/core/src/test/java/org/biojava/bio/seq/db/ EmblCDROMIndexStoreTest.java Hope that helps. Later, Andy -------- Yada, yada, yada... The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336 Disclaimer: This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. -------------- next part -------------- A non-text attachment was scrubbed... Name: testfiles.tgz Type: application/octet-stream Size: 1749 bytes Desc: not available URL: From andreas at sdsc.edu Thu Sep 10 17:38:22 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Thu, 10 Sep 2009 14:38:22 -0700 Subject: [Biojava-dev] Spaces in file paths - resolved In-Reply-To: References: Message-ID: <59a41c430909101438r3b3a572au6efa15fcba1af63b@mail.gmail.com> Hi Andy, thanks for figuring this out. I committed the patches to SVN. what used to read URL url = EntryNamRandomAccessTest.class.getResource("entrynam.idx"); File f = new File(url.getFile()); now reads: URL url = EntryNamRandomAccessTest.class.getResource("entrynam.idx"); File f = new File(new URI("file://"+url.getFile())); Andreas On Thu, Sep 10, 2009 at 8:00 AM, Andy Law (RI) wrote: > All, > > I've been digging about in the bowels of the java.io libraries and the > biojava core tests and I have a fix. > > From what I can tell, the problem with spaces in file paths is NOT a > Mac-specific thing. I threw together some tests (attached as a tgz version > of the maven project) that demonstrate the problem on the Mac but then when > I ran them on the linux box, the same tests failed so I think it is a > general issue. However, in doing so I was able to get to grips with why it > is failing and how to work around it. > > The problem stems from the RandomAccessFile constructor being given a File > whose path contains encoded spaces. The File objects in question are > constructed (in the tests) using the file path extracted from a URL object > i.e. the MO of the tests is: > > (1) create URL pointing at the file > (2) create a File from that (using the *path* extracted from the URL [via > getFile()! go figure]) > (3) create a RandomAccessFile from the File > > There are similar problems creating Streams from the File object but points > (1) and (2) are the same in that situation. > > However, it is possible to construct a File from a URI (note UR*I* not > UR*L*) and it is possible to extract a URI from a URL. The File generated > this way seems to have the path escaped or handled properly. Thus if we > replace step (2) with "create a File from a URI extracted from the URL" then > all seems to be well. > > > > Changes required: > > Change .getFile() to .getURI() at: > > Line 196: > biojava/core/src/test/java/org/biojava/bio/program/indexdb/IndexToolsTest.java > Line ?53: > biojava/core/src/test/java/org/biojava/bio/seq/db/emblcd/DivisionLkpReaderTest.java > Line ?58: > biojava/core/src/test/java/org/biojava/bio/seq/db/emblcd/EntryNamIdxReaderTest.java > Line ?54: > biojava/core/src/test/java/org/biojava/bio/seq/db/emblcd/EntryNamRandomAccessTest.java > Line ?70: > biojava/core/src/test/java/org/biojava/bio/seq/db/EmblCDROMIndexStoreTest.java > Line ?71: > biojava/core/src/test/java/org/biojava/bio/seq/db/EmblCDROMIndexStoreTest.java > > > > Hope that helps. > > > Later, > > Andy > -------- > Yada, yada, yada... > The University of Edinburgh is a charitable body, registered in Scotland, > with registration number SC005336 > Disclaimer: This e-mail and any attachments are confidential and intended > solely for the use of the recipient(s) to whom they are addressed. If you > have received it in error, please destroy all copies and inform the sender. > > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > > From holland at eaglegenomics.com Mon Sep 14 04:44:57 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Mon, 14 Sep 2009 09:44:57 +0100 Subject: [Biojava-dev] BioJava Hackathon in January Message-ID: <844D84C0-3363-4A3E-84B5-472C1E296B0E@eaglegenomics.com> Hi all, The January hackathon is now confirmed. It will take place from January 18th-22nd 2010, at the Wellcome Trust Genome Campus (at Hinxton, near Cambridge). Exact location on the campus will be determined nearer the time as it will depend on final numbers attending. If you will definitely be attending, _please email me_ to let me know as soon as possible so that I can ensure we get a big enough room. This is also important because unless I know you're coming, I won't be able to arrange you a security pass to get onto the campus. No funding is available at present so attendance will be at your own cost (or your employer's if you can persuade them!). If this changes I will let you know but don't hold your hopes too high! There is no accommodation near the campus itself but there is a free bus shuttle linking it to central Cambridge where you can find hotels and hostels of all kinds and for all budgets. The purpose of the hackathon is to make progress towards achieving the goals listed on this wiki page, which Andreas Prlic is maintaining: http://biojava.org/wiki/BioJava:Modules cheers, Richard -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From HWillis at scripps.edu Mon Sep 14 09:33:43 2009 From: HWillis at scripps.edu (Scooter Willis) Date: Mon, 14 Sep 2009 09:33:43 -0400 Subject: [Biojava-dev] BioJava Hackathon in January In-Reply-To: <844D84C0-3363-4A3E-84B5-472C1E296B0E@eaglegenomics.com> Message-ID: Richard Count me in! Thanks Scooter On 9/14/09 4:44 AM, "Richard Holland" wrote: Hi all, The January hackathon is now confirmed. It will take place from January 18th-22nd 2010, at the Wellcome Trust Genome Campus (at Hinxton, near Cambridge). Exact location on the campus will be determined nearer the time as it will depend on final numbers attending. If you will definitely be attending, _please email me_ to let me know as soon as possible so that I can ensure we get a big enough room. This is also important because unless I know you're coming, I won't be able to arrange you a security pass to get onto the campus. No funding is available at present so attendance will be at your own cost (or your employer's if you can persuade them!). If this changes I will let you know but don't hold your hopes too high! There is no accommodation near the campus itself but there is a free bus shuttle linking it to central Cambridge where you can find hotels and hostels of all kinds and for all budgets. The purpose of the hackathon is to make progress towards achieving the goals listed on this wiki page, which Andreas Prlic is maintaining: http://biojava.org/wiki/BioJava:Modules cheers, Richard -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ _______________________________________________ biojava-dev mailing list biojava-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-dev From andreas at sdsc.edu Mon Sep 14 11:33:27 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Mon, 14 Sep 2009 08:33:27 -0700 Subject: [Biojava-dev] BioJava Hackathon in January In-Reply-To: <844D84C0-3363-4A3E-84B5-472C1E296B0E@eaglegenomics.com> References: <844D84C0-3363-4A3E-84B5-472C1E296B0E@eaglegenomics.com> Message-ID: <59a41c430909140833i2827cd30g5ac83f134a1b5f21@mail.gmail.com> Excellent, thanks for organizing this, Richard! Looking forward to meeting you all in Cambridge! Andreas On Mon, Sep 14, 2009 at 1:44 AM, Richard Holland wrote: > Hi all, > > The January hackathon is now confirmed. It will take place from January > 18th-22nd 2010, at the Wellcome Trust Genome Campus (at Hinxton, near > Cambridge). Exact location on the campus will be determined nearer the time > as it will depend on final numbers attending. > > If you will definitely be attending, _please email me_ to let me know as > soon as possible so that I can ensure we get a big enough room. This is also > important because unless I know you're coming, I won't be able to arrange > you a security pass to get onto the campus. > > No funding is available at present so attendance will be at your own cost > (or your employer's if you can persuade them!). If this changes I will let > you know but don't hold your hopes too high! > > There is no accommodation near the campus itself but there is a free bus > shuttle linking it to central Cambridge where you can find hotels and > hostels of all kinds and for all budgets. > > The purpose of the hackathon is to make progress towards achieving the goals > listed on this wiki page, which Andreas Prlic is maintaining: > > ?http://biojava.org/wiki/BioJava:Modules > > cheers, > Richard > > -- > Richard Holland, BSc MBCS > Operations and Delivery Director, Eagle Genomics Ltd > T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com > http://www.eaglegenomics.com/ > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From andreas at sdsc.edu Tue Sep 15 12:22:36 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Tue, 15 Sep 2009 09:22:36 -0700 Subject: [Biojava-dev] trunk now mavenized Message-ID: <59a41c430909150922l1b19a597g12f0b893930194f7@mail.gmail.com> Hi, The Biojava - trunk is now pointing to the new mavenized and modularized code. The old ant-based trunk has been moved to a branch ( biojava-live/branches/trunk_1_7_ant ) so it is still easy to find. Seems we have only found minor issues with the new modules so far and they are ready for more people to try the checkouts. More feedback is welcome. Andreas From jacobsen at ebi.ac.uk Wed Sep 16 12:43:44 2009 From: jacobsen at ebi.ac.uk (Jules Jacobsen) Date: Wed, 16 Sep 2009 17:43:44 +0100 Subject: [Biojava-dev] BioJava Hackathon in January In-Reply-To: <844D84C0-3363-4A3E-84B5-472C1E296B0E@eaglegenomics.com> References: <844D84C0-3363-4A3E-84B5-472C1E296B0E@eaglegenomics.com> Message-ID: <12c279870909160943x15d5ff76q488f6696f597d121@mail.gmail.com> Hi Richard, Sounds cool - count me in. Jules On Mon, Sep 14, 2009 at 9:44 AM, Richard Holland wrote: > Hi all, > > The January hackathon is now confirmed. It will take place from January > 18th-22nd 2010, at the Wellcome Trust Genome Campus (at Hinxton, near > Cambridge). Exact location on the campus will be determined nearer the time > as it will depend on final numbers attending. > > If you will definitely be attending, _please email me_ to let me know as > soon as possible so that I can ensure we get a big enough room. This is also > important because unless I know you're coming, I won't be able to arrange > you a security pass to get onto the campus. > > No funding is available at present so attendance will be at your own cost > (or your employer's if you can persuade them!). If this changes I will let > you know but don't hold your hopes too high! > > There is no accommodation near the campus itself but there is a free bus > shuttle linking it to central Cambridge where you can find hotels and > hostels of all kinds and for all budgets. > > The purpose of the hackathon is to make progress towards achieving the goals > listed on this wiki page, which Andreas Prlic is maintaining: > > ?http://biojava.org/wiki/BioJava:Modules > > cheers, > Richard > > -- > Richard Holland, BSc MBCS > Operations and Delivery Director, Eagle Genomics Ltd > T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com > http://www.eaglegenomics.com/ > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From andy.law at roslin.ed.ac.uk Mon Sep 21 09:36:39 2009 From: andy.law at roslin.ed.ac.uk (Andy Law (RI)) Date: Mon, 21 Sep 2009 14:36:39 +0100 Subject: [Biojava-dev] ensembl code Message-ID: <6CA04E21-058F-4379-B944-6C3C1187AA2E@roslin.ed.ac.uk> Andreas, Did the (old, defunct) Ensembl code make the transition from cvs to svn? The reason that I ask is that I'm putting in a proposal to fund a body to resurrect it and it will look more professional if I actually know where it is. I would look myself, but our internet access is screwed completely today (and the University IT staff are on holiday). Email seems to be working but bu**er-all else is. Later, Andy -------- Yada, yada, yada... The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336 Disclaimer: This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. From andreas.prlic at gmail.com Thu Sep 24 11:10:38 2009 From: andreas.prlic at gmail.com (Andreas Prlic) Date: Thu, 24 Sep 2009 08:10:38 -0700 Subject: [Biojava-dev] Moving web blast stuff to the new mavenized code tree In-Reply-To: References: Message-ID: <59a41c430909240810o61228e27ja65289eb33a7fa1c@mail.gmail.com> Hi Sylvain, It is best to get a current checkout at a new location on your disc. Did you commit it to svn prior to the maven move? Then it got moved by me. Otherwise the package naming did not get changed and it should be relatively straightforward to copy over the files. For eclipse based developers I recommend getting the latest SVN plugin and m2eclipse for maven. Then it is possible to browse through the biojava svn repository, right click on the biojava-live/trunk folder and ->Check out as Maven project. Perhaps somebody using other IDEs could comment on what's the best strategy to get the basic checkout there? Andreas On Thu, Sep 24, 2009 at 7:54 AM, Sylvain Foisy wrote: > Hi Andreas, > > How could the code I wrote a few weeks back be moved to the new tree? I > would like to continue working on this but I see no point of doing so > outside of the new tree... > > Best regards > > Sylvain > > > ================================================================== > > Sylvain Foisy, Ph. D. > Charg? de projet / Project Manager > Bio-informatique > > Adresse postale: > > Laboratoire de genetique et medecine genomique de l'inflammation > Institut de cardiologie de Montreal > 5000 Belanger > Montreal, Qc > H1T 1C8 > > T: 514-376-3330 x.2299 | F: 514-593-2539 > M: sylvain.foisy at inflammgen.org > W: http://www.inflammgen.org > > ================================================================== > > > From simpleyrx at 163.com Wed Sep 30 00:56:46 2009 From: simpleyrx at 163.com (simpleyrx) Date: Wed, 30 Sep 2009 12:56:46 +0800 (CST) Subject: [Biojava-dev] what is the default parameters of Message-ID: <27727343.508701254286606200.JavaMail.coremail@bj163app55.163.com> Dear experts, NeedlemanWunsch's constructive funtion in biojava is as below: public NeedlemanWunsch(short?match, short?replace, short?insert, short?delete, short?gapExtend, SubstitutionMatrix?subMat) I would like to know what are the default values to used NeedlemanWunsch. Such as how select match ,replace,insert,delete,gapExtend or subMat parameters ? -- Renxiang Yan From andreas.prlic at gmail.com Wed Sep 30 23:48:11 2009 From: andreas.prlic at gmail.com (Andreas Prlic) Date: Wed, 30 Sep 2009 20:48:11 -0700 Subject: [Biojava-dev] what is the default parameters of In-Reply-To: <27727343.508701254286606200.JavaMail.coremail@bj163app55.163.com> References: <27727343.508701254286606200.JavaMail.coremail@bj163app55.163.com> Message-ID: <59a41c430909302048g14712d53tefdef1f1d64edfb3@mail.gmail.com> Hi, That depends on several things. E.g. on the substitution matrix being used, also on what you want to align. Here a site that suggests a combination of substitution matrix and gap penalties: ( BLOSUM62 matrix with gap opening penalty of 10 and a gap extension penalty of 0.5) http://hydra.icgeb.trieste.it/benchmark_previous/index.php?experiment=13 To also advertise some related, but ancient work of myself ;-) see: at: http://peds.oxfordjournals.org/cgi/content/full/13/8/545 Andreas http://hydra.icgeb.trieste.it/benchmark_previous/index.php?experiment=13 2009/9/29 simpleyrx : > > Dear experts, > > > NeedlemanWunsch's constructive funtion in biojava is as below: > public NeedlemanWunsch(short?match, > ? ? ? ? ? ? ? ? ? ? ? short?replace, > ? ? ? ? ? ? ? ? ? ? ? short?insert, > ? ? ? ? ? ? ? ? ? ? ? short?delete, > ? ? ? ? ? ? ? ? ? ? ? short?gapExtend, > ? ? ? ? ? ? ? ? ? ? ? SubstitutionMatrix?subMat) > I would like to know what are the default values to used NeedlemanWunsch. Such as how select match ,replace,insert,delete,gapExtend or subMat parameters ? > > > -- > > > Renxiang Yan > > > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > > From andreas at sdsc.edu Tue Sep 1 04:03:14 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Mon, 31 Aug 2009 21:03:14 -0700 Subject: [Biojava-dev] maven progress In-Reply-To: References: <59a41c430908301823s6e2e3d7fi6caffc47e1a8c0ff@mail.gmail.com> Message-ID: <59a41c430908312103w7ba30a83s12d48884957be371@mail.gmail.com> >> The new SVN location is emerging here: >> >> http://dev.open-bio.org/home/svn-repositories/biojava/biojava-live/biojava > > That seems like an odd place for it, at the same level as branches, tags, > and trunk? > > If you've branched for 1.7 and called for the freeze on trunk, I don't see > any reason not to do this work on trunk. ok. makes sense. It is easy to flip locations around in svn.. I can move the old trunk e.g. to a tag folder for archive purposes and make what is called biojava right now the future trunk. (in svn this moves or copy operations are cheap) For the moment things are not stabilized yet and I will do this once things are there... At the moment I am chasing an "interesting" problem. When I run the junit tests on the new core module in eclipse, they run fine. When I do the same via a mvn test I get several issues like the one below. Anybody got an idea? ------------------------------------------------------------------------------- Test set: org.biojava.bio.seq.project.ProjectedFeatureHolderTest ------------------------------------------------------------------------------- Tests run: 6, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.036 sec <<< FAILURE! testFeatureChangeEvent(org.biojava.bio.seq.project.ProjectedFeatureHolderTest) Time elapsed: 0.011 sec <<< ERROR! java.lang.AssertionError: firePreChangeEvent must be called in a synchronized block locking the ChangeSupport at org.biojava.utils.ChangeSupport.firePreChangeEvent(ChangeSupport.java:281) at org.biojava.bio.seq.projection.ReparentContext$PFChangeForwarder.preChange(ReparentContext.java:299) at org.biojava.utils.ChangeSupport.firePreChangeEvent(ChangeSupport.java:297) at org.biojava.bio.seq.impl.SimpleFeature.setLocation(SimpleFeature.java:173) at org.biojava.bio.seq.project.ProjectedFeatureHolderTest.testFeatureChangeEvent(ProjectedFeatureHolderTest.java:297) Andreas From heuermh at acm.org Tue Sep 1 04:12:38 2009 From: heuermh at acm.org (Michael Heuer) Date: Tue, 1 Sep 2009 00:12:38 -0400 (EDT) Subject: [Biojava-dev] maven progress In-Reply-To: <59a41c430908312103w7ba30a83s12d48884957be371@mail.gmail.com> Message-ID: Andreas Prlic wrote: > >> The new SVN location is emerging here: > >> > >> http://dev.open-bio.org/home/svn-repositories/biojava/biojava-live/biojava > > > > That seems like an odd place for it, at the same level as branches, tags, > > and trunk? > > > > If you've branched for 1.7 and called for the freeze on trunk, I don't see > > any reason not to do this work on trunk. > > ok. makes sense. It is easy to flip locations around in svn.. I can > move the old trunk e.g. to a tag folder for archive purposes and make > what is called biojava right now the future trunk. (in svn this moves > or copy operations are cheap) For the moment things are not > stabilized yet and I will do this once things are there... That's cool. I wanted to check in some preliminary fastq stuff and wasn't sure where it should go. I'm in the biojava3 branch for now, and will move to the right place once things settle. > At the moment I am chasing an "interesting" problem. When I run the > junit tests on the new core module in eclipse, they run fine. When I > do the same via a mvn test I get several issues like the one below. > Anybody got an idea? > > ------------------------------------------------------------------------------- > Test set: org.biojava.bio.seq.project.ProjectedFeatureHolderTest > ------------------------------------------------------------------------------- > Tests run: 6, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.036 > sec <<< FAILURE! > testFeatureChangeEvent(org.biojava.bio.seq.project.ProjectedFeatureHolderTest) > Time elapsed: 0.011 sec <<< ERROR! > java.lang.AssertionError: firePreChangeEvent must be called in a > synchronized block locking the ChangeSupport > at org.biojava.utils.ChangeSupport.firePreChangeEvent(ChangeSupport.java:281) > at org.biojava.bio.seq.projection.ReparentContext$PFChangeForwarder.preChange(ReparentContext.java:299) > at org.biojava.utils.ChangeSupport.firePreChangeEvent(ChangeSupport.java:297) > at org.biojava.bio.seq.impl.SimpleFeature.setLocation(SimpleFeature.java:173) > at org.biojava.bio.seq.project.ProjectedFeatureHolderTest.testFeatureChangeEvent(ProjectedFeatureHolderTest.java:297) I've always disliked the change stuff, how about get rid of it all and make everything immutable? ;) michael From andreas at sdsc.edu Tue Sep 1 04:17:47 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Mon, 31 Aug 2009 21:17:47 -0700 Subject: [Biojava-dev] maven progress In-Reply-To: References: <59a41c430908312103w7ba30a83s12d48884957be371@mail.gmail.com> Message-ID: <59a41c430908312117x641453c0yc26be5cb669b4396@mail.gmail.com> Can you start using the biojava-live/biojava/sequencing module for the fastq stuff? that way we can already be in sync. I will do svn updates every time before I start working on something and commits when I stop.... Andreas On Mon, Aug 31, 2009 at 9:12 PM, Michael Heuer wrote: > Andreas Prlic wrote: > >> >> The new SVN location is emerging here: >> >> >> >> http://dev.open-bio.org/home/svn-repositories/biojava/biojava-live/biojava >> > >> > That seems like an odd place for it, at the same level as branches, tags, >> > and trunk? >> > >> > If you've branched for 1.7 and called for the freeze on trunk, I don't see >> > any reason not to do this work on trunk. >> >> ok. makes sense. ?It is easy to flip locations around in svn.. ?I can >> move the old trunk ?e.g. to a tag folder for archive purposes and make >> what is called biojava right now the future trunk. (in svn this moves >> or copy operations are cheap) ?For the moment things are not >> stabilized yet and I will do this once things are there... > > That's cool. ?I wanted to check in some preliminary fastq stuff and wasn't > sure where it should go. ?I'm in the biojava3 branch for now, and will > move to the right place once things settle. > > >> At the moment I am chasing an "interesting" problem. When I run the >> junit tests on the new core module in eclipse, they run fine. ? When I >> do the same via a mvn test I get several issues like the one below. >> Anybody got an idea? >> >> ------------------------------------------------------------------------------- >> Test set: org.biojava.bio.seq.project.ProjectedFeatureHolderTest >> ------------------------------------------------------------------------------- >> Tests run: 6, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.036 >> sec <<< FAILURE! >> testFeatureChangeEvent(org.biojava.bio.seq.project.ProjectedFeatureHolderTest) >> ?Time elapsed: 0.011 sec ?<<< ERROR! >> java.lang.AssertionError: firePreChangeEvent must be called in a >> synchronized block locking the ChangeSupport >> ? ? ? at org.biojava.utils.ChangeSupport.firePreChangeEvent(ChangeSupport.java:281) >> ? ? ? at org.biojava.bio.seq.projection.ReparentContext$PFChangeForwarder.preChange(ReparentContext.java:299) >> ? ? ? at org.biojava.utils.ChangeSupport.firePreChangeEvent(ChangeSupport.java:297) >> ? ? ? at org.biojava.bio.seq.impl.SimpleFeature.setLocation(SimpleFeature.java:173) >> ? ? ? at org.biojava.bio.seq.project.ProjectedFeatureHolderTest.testFeatureChangeEvent(ProjectedFeatureHolderTest.java:297) > > I've always disliked the change stuff, how about get rid of it all and > make everything immutable? ?;) > > ? michael > > From heuermh at acm.org Tue Sep 1 04:27:19 2009 From: heuermh at acm.org (Michael Heuer) Date: Tue, 1 Sep 2009 00:27:19 -0400 (EDT) Subject: [Biojava-dev] maven progress In-Reply-To: <59a41c430908312117x641453c0yc26be5cb669b4396@mail.gmail.com> Message-ID: Andreas Prlic wrote: > Can you start using the biojava-live/biojava/sequencing module for the > fastq stuff? that way we can already be in sync. I will do svn updates > every time before I start working on something and commits when I > stop.... The build for the fastq stuff is currently fully self-contained, since I've been away from biojava development for some time and prefer to do things "my way" . . . it will take me a while to merge it back into the biojava way of doing things, and that is after the funtionality is complete. michael From andreas at sdsc.edu Tue Sep 1 14:37:57 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Tue, 1 Sep 2009 07:37:57 -0700 Subject: [Biojava-dev] maven progress In-Reply-To: References: <59a41c430908301823s6e2e3d7fi6caffc47e1a8c0ff@mail.gmail.com> <59a41c430908312103w7ba30a83s12d48884957be371@mail.gmail.com> Message-ID: <59a41c430909010737r731f9b58p2a96bf8558822de3@mail.gmail.com> Hi Andy, this repository location is ssh protected. Anonymous checkouts are possible via svn://code.open-bio.org/biojava/biojava-live/biojava viewing in your web browser is possible at http://code.open-bio.org/svnweb/index.cgi/biojava/browse/biojava-live/biojava Andreas >>>> The new SVN location is emerging here: >>>> >>>> >>>> http://dev.open-bio.org/home/svn-repositories/biojava/biojava-live/biojava > > > I can't see that from where I'm sitting. Is the server down or are there > firewalls or other corporateness blocking me out? > > >> >> At the moment I am chasing an "interesting" problem. When I run the >> junit tests on the new core module in eclipse, they run fine. ? When I >> do the same via a mvn test I get several issues like the one below. >> Anybody got an idea? >> >> >> ------------------------------------------------------------------------------- >> Test set: org.biojava.bio.seq.project.ProjectedFeatureHolderTest >> >> ------------------------------------------------------------------------------- >> Tests run: 6, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.036 >> sec <<< FAILURE! >> >> testFeatureChangeEvent(org.biojava.bio.seq.project.ProjectedFeatureHolderTest) >> Time elapsed: 0.011 sec ?<<< ERROR! >> java.lang.AssertionError: firePreChangeEvent must be called in a >> synchronized block locking the ChangeSupport >> ? ? ? ?at >> org.biojava.utils.ChangeSupport.firePreChangeEvent(ChangeSupport.java:281) >> ? ? ? ?at >> org.biojava.bio.seq.projection.ReparentContext$PFChangeForwarder.preChange(ReparentContext.java:299) >> ? ? ? ?at >> org.biojava.utils.ChangeSupport.firePreChangeEvent(ChangeSupport.java:297) >> ? ? ? ?at >> org.biojava.bio.seq.impl.SimpleFeature.setLocation(SimpleFeature.java:173) >> ? ? ? ?at >> org.biojava.bio.seq.project.ProjectedFeatureHolderTest.testFeatureChangeEvent(ProjectedFeatureHolderTest.java:297) >> > > > That's certainly not one that I've ever seen, but then I probably don't > write code that is as complicated as BioJava :o} > > If I could get a checkout (see above) then I would try it out in NetBeans to > see if it is something that Eclipse is doing to "protect" against the > synchronisation problem. But I can't get the code so I can't test it :o{ > > > > > Later, > > Andy > -------- > Yada, yada, yada... > The University of Edinburgh is a charitable body, registered in Scotland, > with registration number SC005336 > Disclaimer: This e-mail and any attachments are confidential and intended > solely for the use of the recipient(s) to whom they are addressed. If you > have received it in error, please destroy all copies and inform the sender. > > > > From andy.law at roslin.ed.ac.uk Tue Sep 1 16:30:32 2009 From: andy.law at roslin.ed.ac.uk (Andy Law (RI)) Date: Tue, 1 Sep 2009 17:30:32 +0100 Subject: [Biojava-dev] maven progress In-Reply-To: <59a41c430909010737r731f9b58p2a96bf8558822de3@mail.gmail.com> References: <59a41c430908301823s6e2e3d7fi6caffc47e1a8c0ff@mail.gmail.com> <59a41c430908312103w7ba30a83s12d48884957be371@mail.gmail.com> <59a41c430909010737r731f9b58p2a96bf8558822de3@mail.gmail.com> Message-ID: <32C14A50-465E-423B-9816-F1B995CBDC16@roslin.ed.ac.uk> On 1 Sep 2009, at 15:37, Andreas Prlic wrote: > Hi Andy, > > this repository location is ssh protected. Anonymous checkouts are > possible via > > svn://code.open-bio.org/biojava/biojava-live/biojava OK. I've got a checkout from there thanks. I trip up over a dependency on bytecode version 3.0. That will need to either be incorporated into the tree or published to maven central before the system works as it should (version 1.5 is on the maven central repo but I couldn't find a later version) >>> >>> At the moment I am chasing an "interesting" problem. When I run the >>> junit tests on the new core module in eclipse, they run fine. >>> When I >>> do the same via a mvn test I get several issues like the one below. >>> Anybody got an idea? >>> >>> >>> ------------------------------------------------------------------------------- >>> Test set: org.biojava.bio.seq.project.ProjectedFeatureHolderTest >>> >>> ------------------------------------------------------------------------------- >>> Tests run: 6, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: >>> 0.036 >>> sec <<< FAILURE! >>> >>> testFeatureChangeEvent >>> (org.biojava.bio.seq.project.ProjectedFeatureHolderTest) >>> Time elapsed: 0.011 sec <<< ERROR! >>> java.lang.AssertionError: firePreChangeEvent must be called in a >>> synchronized block locking the ChangeSupport >>> at >>> org >>> .biojava.utils.ChangeSupport.firePreChangeEvent(ChangeSupport.java: >>> 281) >>> at >>> org.biojava.bio.seq.projection.ReparentContext >>> $PFChangeForwarder.preChange(ReparentContext.java:299) >>> at >>> org >>> .biojava.utils.ChangeSupport.firePreChangeEvent(ChangeSupport.java: >>> 297) >>> at >>> org >>> .biojava.bio.seq.impl.SimpleFeature.setLocation(SimpleFeature.java: >>> 173) >>> at >>> org >>> .biojava >>> .bio >>> .seq >>> .project >>> .ProjectedFeatureHolderTest >>> .testFeatureChangeEvent(ProjectedFeatureHolderTest.java:297) >>> >> >> >> That's certainly not one that I've ever seen, but then I probably >> don't >> write code that is as complicated as BioJava :o} >> >> If I could get a checkout (see above) then I would try it out in >> NetBeans to >> see if it is something that Eclipse is doing to "protect" against the >> synchronisation problem. But I can't get the code so I can't test >> it :o{ >> Thos error messages *do* appear when running the tests from inside Netbeans, so clearly something that Eclipse is doing must be hiding the errors from you :o} From what I can tell, there are instances in the code that fire off preChange()/postChange() in ChangeListeners without first locking down the ChangeSupport object (whatever that is - this is the first real delve that I've had in the BioJava guts). For example, SimpleSequence.java contains a private class called FeatureForwarder that implements ChangeListener (lines 322:332) This currently reads: private class FeatureForwarder implements ChangeListener { public void preChange(ChangeEvent cev) throws ChangeVetoException { getChangeSupport(cev.getType()).firePreChangeEvent(cev); } public void postChange(ChangeEvent cev) { getChangeSupport(cev.getType()).firePostChangeEvent(cev); } } I think that it *should* read something like private class FeatureForwarder implements ChangeListener { public void preChange(ChangeEvent cev) throws ChangeVetoException { ChangeSupport cs = getChangeSupport(cev.getType()); synchronized(cs) { cs.firePreChangeEvent(cev); } } public void postChange(ChangeEvent cev) { ChangeSupport cs = getChangeSupport(cev.getType()); synchronized(cs) { cs.firePostChangeEvent(cev); } } } and when I change my local copy to this, the problems go away (for at least one section of the tests). I still get the same error cropping up in other parts (where the code funnels through different ChangeListener implementations which all have the same style as the first version above but that, I guess, is to be expected. There are test problems relating to file paths too - but I presume that you knew that stuff already. Later, Andy -------- Yada, yada, yada... The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336 Disclaimer: This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. From andreas at sdsc.edu Tue Sep 1 17:12:16 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Tue, 1 Sep 2009 10:12:16 -0700 Subject: [Biojava-dev] maven progress In-Reply-To: <32C14A50-465E-423B-9816-F1B995CBDC16@roslin.ed.ac.uk> References: <59a41c430908301823s6e2e3d7fi6caffc47e1a8c0ff@mail.gmail.com> <59a41c430908312103w7ba30a83s12d48884957be371@mail.gmail.com> <59a41c430909010737r731f9b58p2a96bf8558822de3@mail.gmail.com> <32C14A50-465E-423B-9816-F1B995CBDC16@roslin.ed.ac.uk> Message-ID: <59a41c430909011012t69fa1837sc92bb654434dd9a7@mail.gmail.com> Thanks, Andy I will try to chase up the calls and make sure they get properly synchronized. Not sure why those issues did not get detected already earlier! The broken file paths I am aware of. That has to do with me moving the files around to make the organization of the directories maven standard compliant. probably will get fixed by tonight (west coast) ... Andreas On Tue, Sep 1, 2009 at 9:30 AM, Andy Law (RI) wrote: > > On 1 Sep 2009, at 15:37, Andreas Prlic wrote: > >> Hi Andy, >> >> this repository location is ssh protected. ?Anonymous checkouts are >> possible via >> >> svn://code.open-bio.org/biojava/biojava-live/biojava > > > OK. I've got a checkout from there thanks. > > I trip up over a dependency on bytecode version 3.0. That will need to > either be incorporated into the tree or published to maven central before > the system works as it should (version 1.5 is on the maven central repo but > I couldn't find a later version) > > > >>>> >>>> At the moment I am chasing an "interesting" problem. When I run the >>>> junit tests on the new core module in eclipse, they run fine. ? When I >>>> do the same via a mvn test I get several issues like the one below. >>>> Anybody got an idea? >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------- >>>> Test set: org.biojava.bio.seq.project.ProjectedFeatureHolderTest >>>> >>>> >>>> ------------------------------------------------------------------------------- >>>> Tests run: 6, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.036 >>>> sec <<< FAILURE! >>>> >>>> >>>> testFeatureChangeEvent(org.biojava.bio.seq.project.ProjectedFeatureHolderTest) >>>> Time elapsed: 0.011 sec ?<<< ERROR! >>>> java.lang.AssertionError: firePreChangeEvent must be called in a >>>> synchronized block locking the ChangeSupport >>>> ? ? ? at >>>> >>>> org.biojava.utils.ChangeSupport.firePreChangeEvent(ChangeSupport.java:281) >>>> ? ? ? at >>>> >>>> org.biojava.bio.seq.projection.ReparentContext$PFChangeForwarder.preChange(ReparentContext.java:299) >>>> ? ? ? at >>>> >>>> org.biojava.utils.ChangeSupport.firePreChangeEvent(ChangeSupport.java:297) >>>> ? ? ? at >>>> >>>> org.biojava.bio.seq.impl.SimpleFeature.setLocation(SimpleFeature.java:173) >>>> ? ? ? at >>>> >>>> org.biojava.bio.seq.project.ProjectedFeatureHolderTest.testFeatureChangeEvent(ProjectedFeatureHolderTest.java:297) >>>> >>> >>> >>> That's certainly not one that I've ever seen, but then I probably don't >>> write code that is as complicated as BioJava :o} >>> >>> If I could get a checkout (see above) then I would try it out in NetBeans >>> to >>> see if it is something that Eclipse is doing to "protect" against the >>> synchronisation problem. But I can't get the code so I can't test it :o{ >>> > > > > Thos error messages *do* appear when running the tests from inside Netbeans, > so clearly something that Eclipse is doing must be hiding the errors from > you :o} > > From what I can tell, there are instances in the code that fire off > preChange()/postChange() in ChangeListeners without first locking down the > ChangeSupport object (whatever that is - this is the first real delve that > I've had in the BioJava guts). > > For example, SimpleSequence.java contains a private class called > FeatureForwarder that implements ChangeListener (lines 322:332) > This currently reads: > > ? ?private class FeatureForwarder implements ChangeListener { > ? ? ?public void preChange(ChangeEvent cev) > ? ? ?throws ChangeVetoException > ? ? ?{ > ? ? ? ?getChangeSupport(cev.getType()).firePreChangeEvent(cev); > ? ? ? ? ?} > > ? ? ?public void postChange(ChangeEvent cev) { > ? ? ? ?getChangeSupport(cev.getType()).firePostChangeEvent(cev); > ? ? ? ? ?} > ? ?} > > > > I think that it *should* read something like > > ? ?private class FeatureForwarder implements ChangeListener { > ? ? ?public void preChange(ChangeEvent cev) > ? ? ?throws ChangeVetoException > ? ? ?{ > ? ? ? ? ?ChangeSupport cs = getChangeSupport(cev.getType()); > ? ? ? ? ?synchronized(cs) { > ? ? ? ?cs.firePreChangeEvent(cev); > ? ? ? ? ?} > ? ? ?} > > ? ? ?public void postChange(ChangeEvent cev) { > ? ? ? ?ChangeSupport cs = getChangeSupport(cev.getType()); > ? ? ? ? ?synchronized(cs) { > ? ? ? ?cs.firePostChangeEvent(cev); > ? ? ? ? ?} > ? ? ?} > ? ?} > > and when I change my local copy to this, the problems go away (for at least > one section of the tests). I still get the same error cropping up in other > parts (where the code funnels through different ChangeListener > implementations which all have the same style as the first version above but > that, I guess, is to be expected. > > There are test problems relating to file paths too - but I presume that you > knew that stuff already. > > Later, > > Andy > -------- > Yada, yada, yada... > The University of Edinburgh is a charitable body, registered in Scotland, > with registration number SC005336 > Disclaimer: This e-mail and any attachments are confidential and intended > solely for the use of the recipient(s) to whom they are addressed. If you > have received it in error, please destroy all copies and inform the sender. > > > > From andreas at sdsc.edu Wed Sep 2 02:39:37 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Tue, 1 Sep 2009 19:39:37 -0700 Subject: [Biojava-dev] today's update Message-ID: <59a41c430909011939q13caf8e1p5487ba8ae4d33ccf@mail.gmail.com> * fixed the synchronisation problems with the JUnit tests. * started to work on the das module * general refactoring. The whole feels much more stable now. Still missing: * demos and apps subdirectories. Shall I move them to a biojava-demos module? * Can we drop the docs dir? if this is relevant it should be moved to the wiki. * refactor the biosql code to its module * signing - need to re-enable the digital signature * need to update cruisecontrol to use maven instead of ant Done: The following modules have been refactored and mavenized so far: * alignment, blast, structure, phylo, sequence, sequencing Did I miss anything? Andreas From markjschreiber at gmail.com Wed Sep 2 02:51:32 2009 From: markjschreiber at gmail.com (Mark Schreiber) Date: Wed, 2 Sep 2009 10:51:32 +0800 Subject: [Biojava-dev] today's update In-Reply-To: <59a41c430909011939q13caf8e1p5487ba8ae4d33ccf@mail.gmail.com> References: <59a41c430909011939q13caf8e1p5487ba8ae4d33ccf@mail.gmail.com> Message-ID: <93b45ca50909011951t74440edaye427625d6986acec@mail.gmail.com> I think the demos apps and docs dirs are all badly out of date and should be dropped. Going forward material like this should go to the wiki. On Sep 2, 2009 10:44 AM, "Andreas Prlic" wrote: * fixed the synchronisation problems with the JUnit tests. * started to work on the das module * general refactoring. The whole feels much more stable now. Still missing: * demos and apps subdirectories. Shall I move them to a biojava-demos module? * Can we drop the docs dir? if this is relevant it should be moved to the wiki. * refactor the biosql code to its module * signing - need to re-enable the digital signature * need to update cruisecontrol to use maven instead of ant Done: The following modules have been refactored and mavenized so far: * alignment, blast, structure, phylo, sequence, sequencing Did I miss anything? Andreas _______________________________________________ biojava-dev mailing list biojava-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-dev From andy.law at roslin.ed.ac.uk Wed Sep 2 08:45:03 2009 From: andy.law at roslin.ed.ac.uk (Andy Law (RI)) Date: Wed, 2 Sep 2009 09:45:03 +0100 Subject: [Biojava-dev] today's update In-Reply-To: <93b45ca50909011951t74440edaye427625d6986acec@mail.gmail.com> References: <59a41c430909011939q13caf8e1p5487ba8ae4d33ccf@mail.gmail.com> <93b45ca50909011951t74440edaye427625d6986acec@mail.gmail.com> Message-ID: <0BCEDF5F-6857-43D3-8025-329E4F50A37E@roslin.ed.ac.uk> On 2 Sep 2009, at 03:51, Mark Schreiber wrote: > I think the demos apps and docs dirs are all badly out of date and > should be > dropped. Going forward material like this should go to the wiki. Docs should get autogenerated from the javadoc. Maven will do this for you (maven-javadoc-plugin, goal site:site). I would argue that the demos are (will be) useful to newcomers. There is nothing like code to get you to understand how the bits fit together. Wiki pages just don't cut it for me. Plus, with maven and a decent set of test routines you can be certain that your demos are up- to-date going forward. But then I'm *not* volunteering to make sure that the demos actually work from the off so my opinion counts for nothing :o} Later, Andy -------- Yada, yada, yada... The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336 Disclaimer: This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. From HWillis at scripps.edu Wed Sep 2 14:45:57 2009 From: HWillis at scripps.edu (Scooter Willis) Date: Wed, 2 Sep 2009 10:45:57 -0400 Subject: [Biojava-dev] today's update In-Reply-To: <59a41c430909011939q13caf8e1p5487ba8ae4d33ccf@mail.gmail.com> Message-ID: Andreas Looks like you are getting close! One advantage of hosting the BioJava demo code with detailed tutorial on the web site is the ability to gather information about what modules or source code is of the most interest to developers. The download could include jars for the module with java doc and demo code to test. The tutorial related content would remain hosted as a way of measuring usage/interest. Scooter On 9/1/09 10:39 PM, "Andreas Prlic" wrote: * fixed the synchronisation problems with the JUnit tests. * started to work on the das module * general refactoring. The whole feels much more stable now. Still missing: * demos and apps subdirectories. Shall I move them to a biojava-demos module? * Can we drop the docs dir? if this is relevant it should be moved to the wiki. * refactor the biosql code to its module * signing - need to re-enable the digital signature * need to update cruisecontrol to use maven instead of ant Done: The following modules have been refactored and mavenized so far: * alignment, blast, structure, phylo, sequence, sequencing Did I miss anything? Andreas _______________________________________________ biojava-dev mailing list biojava-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-dev From andreas at sdsc.edu Thu Sep 3 06:25:58 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Wed, 2 Sep 2009 23:25:58 -0700 Subject: [Biojava-dev] today's update In-Reply-To: References: <59a41c430909011939q13caf8e1p5487ba8ae4d33ccf@mail.gmail.com> Message-ID: <59a41c430909022325n753d8c5dvcc4643ba2acbdc6b@mail.gmail.com> > One advantage of hosting the BioJava demo code with detailed tutorial on the > web site is the ability to gather information about what modules or source > code is of the most interest to developers. The download could include jars > for the module with java doc and demo code to test. The tutorial related > content would remain hosted as a way of measuring usage/interest. interesting point. I see it is easy to create javadoc via maven. Any suggestions for a plugin to create doc jars? Andreas From andreas at sdsc.edu Fri Sep 4 06:53:11 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Thu, 3 Sep 2009 23:53:11 -0700 Subject: [Biojava-dev] more updates... Message-ID: <59a41c430909032353m1a4cc116o62a98e1673da0243@mail.gmail.com> Hi, quick update: new modules: biojava-biosql and biojava-gui biojava-das compiles, still talking off list with Jonathan about details. mvn install works fine for me on the current svn. With this the most critical part of the reorganization should be done and it is time for more eyes to take a look and perhaps do some more refinement. It would be good if the module maintainers would start to take a look at their modules and see if they work for them like that. I also started to use some of the modules in a real project and looks good so far. Andreas From andy.law at roslin.ed.ac.uk Fri Sep 4 10:03:12 2009 From: andy.law at roslin.ed.ac.uk (Andy Law (RI)) Date: Fri, 4 Sep 2009 11:03:12 +0100 Subject: [Biojava-dev] more updates... In-Reply-To: <59a41c430909032353m1a4cc116o62a98e1673da0243@mail.gmail.com> References: <59a41c430909032353m1a4cc116o62a98e1673da0243@mail.gmail.com> Message-ID: <7DF95F57-F3EF-4ACB-B1FE-13CD82595341@roslin.ed.ac.uk> Andreas, On 4 Sep 2009, at 07:53, Andreas Prlic wrote: > Hi, > > quick update: new modules: > biojava-biosql and > biojava-gui > biojava-das compiles, still talking off list with Jonathan about > details. > > mvn install works fine for me on the current svn. We can't get a clean check-out to build on our systems at Roslin. I have Trevor Paterson (my local maven maven) working on detailing why not - he'll be joining us later on the list to give us a rundown. First issue is the bytecode jar. I recognise that you have stuck it into a folder with a README file, but that is not a good solution. The folder that you have put it in is not displayed in the Project view of the Netbeans IDE because it is not a standard maven location. Obviously the best solution would be to include the bytecode source as a subproject and have it build or alternatively to publish the bytecode jar into a publicly accessible (central) maven repository. Having got that in place, we then descend into jaxb hell. At that point I gave up and handed the baton to Trevor. Later, Andy -------- Yada, yada, yada... The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336 Disclaimer: This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. From trevor.paterson at roslin.ed.ac.uk Fri Sep 4 10:28:48 2009 From: trevor.paterson at roslin.ed.ac.uk (trevor paterson (RI)) Date: Fri, 4 Sep 2009 11:28:48 +0100 Subject: [Biojava-dev] JAXB plugin dependencies in sequence-blastxml module Message-ID: <050C9A545DC1D84BAC7A678B76A56C3C15CE0B48FD@ebrcexch1.ebrc.bbsrc.ac.uk> Hi Andreas I have been looking at compiling the maven project with Andy and am getting stuck at the maven-jaxb2-plugin specified for the sequence-balstxml module This is lacking a required version identifier - ( I seem to recall that only core maven plugins can skip the version) I tried a couple of the available plugins (see http://download.java.net/maven/2/org/jvnet/jaxb2/maven2/maven-jaxb2-plugin/ ) But these were failing for other non standard artifact dependencies.. e.g version 0.6.0 Path to dependency: 1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.6.0 2) org.jvnet.jaxb2_commons:jaxb-xjc:jar:2.1.6 3) org.kohsuke.rngom:rngom:jar:20061207 Path to dependency: 1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.6.0 2) org.jfrog.maven.annomojo:maven-plugin-anno:jar:1.2.4 e.g version 0.7.1 Path to dependency: 1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.7.1 2) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin-raw:jar:0.7.1 3) org.jfrog.maven.annomojo:maven-plugin-anno:jar:1.3.1 Path to dependency: 1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.7.1 2) org.jvnet.jaxb2_commons:jaxb-xjc:jar:2.1.10 3) org.kohsuke.rngom:rngom:jar:20061207 Which version of the maven-jaxb2-plugin should the build be using? And am I missing a required repository for the dependencies for the maven-jaxb2-plugin Or is it necessary to find these dependencies manually and install them locally? We are currently configured system wide to use the following repos ( and whatever plugin repos etc you add in project POMs) Central Repository http://repo1.maven.org/maven2 Java.net Repository http://download.java.net/maven/2/ Netbeans Repository http://deadlock.netbeans.org/maven2/ Trevor Paterson PhD new email trevor.paterson at roslin.ed.ac.uk Bioinformatics The Roslin Institute Edinburgh University Scotland EH25 9PS phone +44 (0)131 5274402 http://www.roslin.ed.ac.uk http://www.comparagrid.org http://www.thearkdb.org Please consider the environment before printing this e-mail The University of Edinburgh is a charitable body, registered in Scotland with registration number SC005336 Disclaimer:This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. From trevor.paterson at roslin.ed.ac.uk Fri Sep 4 10:59:58 2009 From: trevor.paterson at roslin.ed.ac.uk (trevor paterson (RI)) Date: Fri, 4 Sep 2009 11:59:58 +0100 Subject: [Biojava-dev] JAXB plugin dependencies in sequence-blastxml module In-Reply-To: <050C9A545DC1D84BAC7A678B76A56C3C15CE0B48FD@ebrcexch1.ebrc.bbsrc.ac.uk> Message-ID: <050C9A545DC1D84BAC7A678B76A56C3C15CE0B48FE@ebrcexch1.ebrc.bbsrc.ac.uk> Apologies It looks like we are failing to get these dependencies because we use a local Archiva repository to mirror the external world.... and for some reason it is failing to pull down these dependencies which have checksum failures ( even though Archiva is set to Ignore checksum failures ) When we don't use archiva as a mirror we can get the dependencies... Trevor Paterson PhD new email trevor.paterson at roslin.ed.ac.uk Bioinformatics The Roslin Institute Edinburgh University Scotland EH25 9PS phone +44 (0)131 5274402 http://www.roslin.ed.ac.uk http://www.comparagrid.org http://www.thearkdb.org Please consider the environment before printing this e-mail The University of Edinburgh is a charitable body, registered in Scotland with registration number SC005336 Disclaimer:This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. -----Original Message----- From: biojava-dev-bounces at lists.open-bio.org [mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of trevor paterson (RI) Sent: 04 September 2009 11:29 To: 'biojava-dev at biojava.org' Subject: [Biojava-dev] JAXB plugin dependencies in sequence-blastxml module Hi Andreas I have been looking at compiling the maven project with Andy and am getting stuck at the maven-jaxb2-plugin specified for the sequence-balstxml module This is lacking a required version identifier - ( I seem to recall that only core maven plugins can skip the version) I tried a couple of the available plugins (see http://download.java.net/maven/2/org/jvnet/jaxb2/maven2/maven-jaxb2-plugin/ ) But these were failing for other non standard artifact dependencies.. e.g version 0.6.0 Path to dependency: 1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.6.0 2) org.jvnet.jaxb2_commons:jaxb-xjc:jar:2.1.6 3) org.kohsuke.rngom:rngom:jar:20061207 Path to dependency: 1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.6.0 2) org.jfrog.maven.annomojo:maven-plugin-anno:jar:1.2.4 e.g version 0.7.1 Path to dependency: 1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.7.1 2) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin-raw:jar:0.7.1 3) org.jfrog.maven.annomojo:maven-plugin-anno:jar:1.3.1 Path to dependency: 1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.7.1 2) org.jvnet.jaxb2_commons:jaxb-xjc:jar:2.1.10 3) org.kohsuke.rngom:rngom:jar:20061207 Which version of the maven-jaxb2-plugin should the build be using? And am I missing a required repository for the dependencies for the maven-jaxb2-plugin Or is it necessary to find these dependencies manually and install them locally? We are currently configured system wide to use the following repos ( and whatever plugin repos etc you add in project POMs) Central Repository http://repo1.maven.org/maven2 Java.net Repository http://download.java.net/maven/2/ Netbeans Repository http://deadlock.netbeans.org/maven2/ Trevor Paterson PhD new email trevor.paterson at roslin.ed.ac.uk Bioinformatics The Roslin Institute Edinburgh University Scotland EH25 9PS phone +44 (0)131 5274402 http://www.roslin.ed.ac.uk http://www.comparagrid.org http://www.thearkdb.org Please consider the environment before printing this e-mail The University of Edinburgh is a charitable body, registered in Scotland with registration number SC005336 Disclaimer:This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. _______________________________________________ biojava-dev mailing list biojava-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-dev From andy.law at roslin.ed.ac.uk Fri Sep 4 11:57:10 2009 From: andy.law at roslin.ed.ac.uk (Andy Law (RI)) Date: Fri, 4 Sep 2009 12:57:10 +0100 Subject: [Biojava-dev] more updates... In-Reply-To: <59a41c430909032353m1a4cc116o62a98e1673da0243@mail.gmail.com> References: <59a41c430909032353m1a4cc116o62a98e1673da0243@mail.gmail.com> Message-ID: Andreas, The pom.xml file under the sequence module says that its name is 'biojava'. I think this should be 'sequence' (line 8). This causes bad things to happen in NetBeans. Can you add 'svn:ignore target' properties to all the module top-level folders please? I still do not believe that there is a DEPENDENCY on the maven- dependency-plugin (in top-level pom.xml and sequence/pom.xml). I can remove those and still have everything compile cleanly either on the command line or in netbeans. The plugin may be being used as a plugin, but it is NOT a dependency. What are other people seeing? ...and our archiva system is *still* not behaving and making us look silly (but you can't do anything about that from where you are sat) :o} On 4 Sep 2009, at 07:53, Andreas Prlic wrote: > Hi, > > quick update: new modules: > biojava-biosql and > biojava-gui > biojava-das compiles, still talking off list with Jonathan about > details. > > mvn install works fine for me on the current svn. > > With this the most critical part of the reorganization should be done > and it is time for more eyes to take a look and perhaps do some more > refinement. > It would be good if the module maintainers would start to take a look > at their modules and see if they work for them like that. > > I also started to use some of the modules in a real project and looks > good so far. Later, Andy -------- Yada, yada, yada... The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336 Disclaimer: This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. From trevor.paterson at roslin.ed.ac.uk Fri Sep 4 14:13:56 2009 From: trevor.paterson at roslin.ed.ac.uk (trevor paterson (RI)) Date: Fri, 4 Sep 2009 15:13:56 +0100 Subject: [Biojava-dev] JAXB plugin dependencies in sequence-blastxml module In-Reply-To: <050C9A545DC1D84BAC7A678B76A56C3C15CE0B48FE@ebrcexch1.ebrc.bbsrc.ac.uk> Message-ID: <050C9A545DC1D84BAC7A678B76A56C3C15CE0B4900@ebrcexch1.ebrc.bbsrc.ac.uk> I managed to fix the Archiva configuration by adding '**/*' to the whitelist for http://download.java.net/maven/2/ Somehow available artifacts had been added to the whitelist (in my world you would expect unavailable artifacts to be added to the blacklist...;) So I can almost get the whole project to compile on linux/netbeans The remaining bug is with the jaxb-api, the pom includes v2.2 as a dependency, but netbeans seems to have an internal version of v2.0 which it bootstraps with - so wont use 2.2 ( as far as I can tell java1.6 includes v2.2 - but as an internal ??runtime only?? Library) I am trying to kill this somehow - or put the correct version in lib/endorsed Trevor Paterson PhD new email trevor.paterson at roslin.ed.ac.uk Bioinformatics The Roslin Institute Edinburgh University Scotland EH25 9PS phone +44 (0)131 5274402 http://www.roslin.ed.ac.uk http://www.comparagrid.org http://www.thearkdb.org Please consider the environment before printing this e-mail The University of Edinburgh is a charitable body, registered in Scotland with registration number SC005336 Disclaimer:This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. -----Original Message----- From: biojava-dev-bounces at lists.open-bio.org [mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of trevor paterson (RI) Sent: 04 September 2009 12:00 To: 'biojava-dev at biojava.org' Subject: Re: [Biojava-dev] JAXB plugin dependencies in sequence-blastxml module Apologies It looks like we are failing to get these dependencies because we use a local Archiva repository to mirror the external world.... and for some reason it is failing to pull down these dependencies which have checksum failures ( even though Archiva is set to Ignore checksum failures ) When we don't use archiva as a mirror we can get the dependencies... Trevor Paterson PhD new email trevor.paterson at roslin.ed.ac.uk Bioinformatics The Roslin Institute Edinburgh University Scotland EH25 9PS phone +44 (0)131 5274402 http://www.roslin.ed.ac.uk http://www.comparagrid.org http://www.thearkdb.org Please consider the environment before printing this e-mail The University of Edinburgh is a charitable body, registered in Scotland with registration number SC005336 Disclaimer:This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. -----Original Message----- From: biojava-dev-bounces at lists.open-bio.org [mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of trevor paterson (RI) Sent: 04 September 2009 11:29 To: 'biojava-dev at biojava.org' Subject: [Biojava-dev] JAXB plugin dependencies in sequence-blastxml module Hi Andreas I have been looking at compiling the maven project with Andy and am getting stuck at the maven-jaxb2-plugin specified for the sequence-balstxml module This is lacking a required version identifier - ( I seem to recall that only core maven plugins can skip the version) I tried a couple of the available plugins (see http://download.java.net/maven/2/org/jvnet/jaxb2/maven2/maven-jaxb2-plugin/ ) But these were failing for other non standard artifact dependencies.. e.g version 0.6.0 Path to dependency: 1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.6.0 2) org.jvnet.jaxb2_commons:jaxb-xjc:jar:2.1.6 3) org.kohsuke.rngom:rngom:jar:20061207 Path to dependency: 1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.6.0 2) org.jfrog.maven.annomojo:maven-plugin-anno:jar:1.2.4 e.g version 0.7.1 Path to dependency: 1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.7.1 2) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin-raw:jar:0.7.1 3) org.jfrog.maven.annomojo:maven-plugin-anno:jar:1.3.1 Path to dependency: 1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.7.1 2) org.jvnet.jaxb2_commons:jaxb-xjc:jar:2.1.10 3) org.kohsuke.rngom:rngom:jar:20061207 Which version of the maven-jaxb2-plugin should the build be using? And am I missing a required repository for the dependencies for the maven-jaxb2-plugin Or is it necessary to find these dependencies manually and install them locally? We are currently configured system wide to use the following repos ( and whatever plugin repos etc you add in project POMs) Central Repository http://repo1.maven.org/maven2 Java.net Repository http://download.java.net/maven/2/ Netbeans Repository http://deadlock.netbeans.org/maven2/ Trevor Paterson PhD new email trevor.paterson at roslin.ed.ac.uk Bioinformatics The Roslin Institute Edinburgh University Scotland EH25 9PS phone +44 (0)131 5274402 http://www.roslin.ed.ac.uk http://www.comparagrid.org http://www.thearkdb.org Please consider the environment before printing this e-mail The University of Edinburgh is a charitable body, registered in Scotland with registration number SC005336 Disclaimer:This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. _______________________________________________ biojava-dev mailing list biojava-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-dev _______________________________________________ biojava-dev mailing list biojava-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-dev From trevor.paterson at roslin.ed.ac.uk Fri Sep 4 16:12:47 2009 From: trevor.paterson at roslin.ed.ac.uk (trevor paterson (RI)) Date: Fri, 4 Sep 2009 17:12:47 +0100 Subject: [Biojava-dev] JAXB plugin dependencies in sequence-blastxml module In-Reply-To: <050C9A545DC1D84BAC7A678B76A56C3C15CE0B4900@ebrcexch1.ebrc.bbsrc.ac.uk> Message-ID: <050C9A545DC1D84BAC7A678B76A56C3C15CE0B4901@ebrcexch1.ebrc.bbsrc.ac.uk> [ONLY OF INTEREST TO NETBEANS USERS] I can't find a way to configure Netbeans6.5 to not use its bundled jaxb-api, so am having to use the endorsed libraries route.... Until netbeans 6.7 (which is allegedly still flakey) you can't alter the jdk for maven to use by default, it just uses whatever JAVA_HOME is. You can however add a -D property flag to any global or custom maven action. So you can either set to build with a different jdk (containing your endorsed libraries) Or you can just point at the ensdorsed libraries location itself i.e. -DEnv.JAVA_HOME=/nfs_netapp/paterson/MyJava6/jdk1.6.0_04/ -Djava.endorsed.dirs= /nfs_netapp/paterson/MyJava6/jdk1.6.0_04/jre/lib/endorsed You don't seem to be able to add these as as maven properties in a POM or settings.xml And I am not sure why andy is not getting this happenning in his OSX.5/MACJava worl - probably he has not installed some netbeans plugin module that wired in this jaxb version Trevor -----Original Message----- From: biojava-dev-bounces at lists.open-bio.org [mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of trevor paterson (RI) Sent: 04 September 2009 15:14 To: 'biojava-dev at biojava.org' Subject: Re: [Biojava-dev] JAXB plugin dependencies in sequence-blastxml module I managed to fix the Archiva configuration by adding '**/*' to the whitelist for http://download.java.net/maven/2/ Somehow available artifacts had been added to the whitelist (in my world you would expect unavailable artifacts to be added to the blacklist...;) So I can almost get the whole project to compile on linux/netbeans The remaining bug is with the jaxb-api, the pom includes v2.2 as a dependency, but netbeans seems to have an internal version of v2.0 which it bootstraps with - so wont use 2.2 ( as far as I can tell java1.6 includes v2.2 - but as an internal ??runtime only?? Library) I am trying to kill this somehow - or put the correct version in lib/endorsed Trevor Paterson -----Original Message----- From: biojava-dev-bounces at lists.open-bio.org [mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of trevor paterson (RI) Sent: 04 September 2009 12:00 To: 'biojava-dev at biojava.org' Subject: Re: [Biojava-dev] JAXB plugin dependencies in sequence-blastxml module Apologies It looks like we are failing to get these dependencies because we use a local Archiva repository to mirror the external world.... and for some reason it is failing to pull down these dependencies which have checksum failures ( even though Archiva is set to Ignore checksum failures ) When we don't use archiva as a mirror we can get the dependencies... Trevor Paterson -----Original Message----- From: biojava-dev-bounces at lists.open-bio.org [mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of trevor paterson (RI) Sent: 04 September 2009 11:29 To: 'biojava-dev at biojava.org' Subject: [Biojava-dev] JAXB plugin dependencies in sequence-blastxml module Hi Andreas I have been looking at compiling the maven project with Andy and am getting stuck at the maven-jaxb2-plugin specified for the sequence-balstxml module This is lacking a required version identifier - ( I seem to recall that only core maven plugins can skip the version) I tried a couple of the available plugins (see http://download.java.net/maven/2/org/jvnet/jaxb2/maven2/maven-jaxb2-plugin/ ) But these were failing for other non standard artifact dependencies.. e.g version 0.6.0 Path to dependency: 1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.6.0 2) org.jvnet.jaxb2_commons:jaxb-xjc:jar:2.1.6 3) org.kohsuke.rngom:rngom:jar:20061207 Path to dependency: 1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.6.0 2) org.jfrog.maven.annomojo:maven-plugin-anno:jar:1.2.4 e.g version 0.7.1 Path to dependency: 1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.7.1 2) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin-raw:jar:0.7.1 3) org.jfrog.maven.annomojo:maven-plugin-anno:jar:1.3.1 Path to dependency: 1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.7.1 2) org.jvnet.jaxb2_commons:jaxb-xjc:jar:2.1.10 3) org.kohsuke.rngom:rngom:jar:20061207 Which version of the maven-jaxb2-plugin should the build be using? And am I missing a required repository for the dependencies for the maven-jaxb2-plugin Or is it necessary to find these dependencies manually and install them locally? We are currently configured system wide to use the following repos ( and whatever plugin repos etc you add in project POMs) Central Repository http://repo1.maven.org/maven2 Java.net Repository http://download.java.net/maven/2/ Netbeans Repository http://deadlock.netbeans.org/maven2/ Trevor Paterson PhD new email trevor.paterson at roslin.ed.ac.uk Bioinformatics The Roslin Institute Edinburgh University Scotland EH25 9PS phone +44 (0)131 5274402 http://www.roslin.ed.ac.uk http://www.comparagrid.org http://www.thearkdb.org Please consider the environment before printing this e-mail The University of Edinburgh is a charitable body, registered in Scotland with registration number SC005336 Disclaimer:This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. _______________________________________________ biojava-dev mailing list biojava-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-dev _______________________________________________ biojava-dev mailing list biojava-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-dev _______________________________________________ biojava-dev mailing list biojava-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-dev From andreas at sdsc.edu Fri Sep 4 21:49:32 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Fri, 4 Sep 2009 14:49:32 -0700 Subject: [Biojava-dev] JAXB plugin dependencies in sequence-blastxml module In-Reply-To: <050C9A545DC1D84BAC7A678B76A56C3C15CE0B4900@ebrcexch1.ebrc.bbsrc.ac.uk> References: <050C9A545DC1D84BAC7A678B76A56C3C15CE0B48FE@ebrcexch1.ebrc.bbsrc.ac.uk> <050C9A545DC1D84BAC7A678B76A56C3C15CE0B4900@ebrcexch1.ebrc.bbsrc.ac.uk> Message-ID: <59a41c430909041449p24e90756l97aec6cd9fcbe6e6@mail.gmail.com> Hi Trevor and Andy, Thanks for the detailed feedback. To make sure nothing gets lost I added a todo list to the wiki. Feel free to add other action items... http://biojava.org/wiki/BioJava:MavenMigration * I understand the jaxb problem is mainly related to netbeans. I think we should support easy setup on all popular IDEs. Would it be of advantage to change the dependency to a different jaxb package? Seems there are many available... Richard, do you as the module lead have an opinion which version of jaxb to depend on? - I suppose you will say the latest... :-) Andreas From heuermh at acm.org Sat Sep 5 02:40:48 2009 From: heuermh at acm.org (Michael Heuer) Date: Fri, 4 Sep 2009 22:40:48 -0400 (EDT) Subject: [Biojava-dev] more updates... In-Reply-To: <7DF95F57-F3EF-4ACB-B1FE-13CD82595341@roslin.ed.ac.uk> Message-ID: Andy Law (RI) wrote: > Andreas, > > On 4 Sep 2009, at 07:53, Andreas Prlic wrote: > > > Hi, > > > > quick update: new modules: > > biojava-biosql and > > biojava-gui > > biojava-das compiles, still talking off list with Jonathan about > > details. > > > > mvn install works fine for me on the current svn. > > > We can't get a clean check-out to build on our systems at Roslin. > > I have Trevor Paterson (my local maven maven) working on detailing why > not - he'll be joining us later on the list to give us a rundown. > > First issue is the bytecode jar. I recognise that you have stuck it > into a folder with a README file, but that is not a good solution. The > folder that you have put it in is not displayed in the Project view of > the Netbeans IDE because it is not a standard maven location. > Obviously the best solution would be to include the bytecode source as > a subproject and have it build or alternatively to publish the > bytecode jar into a publicly accessible (central) maven repository. Perhaps the biojava code that depends on bytecode.jar should be refactored to use BCEL or some other third party bytecode generation library. michael From holland at eaglegenomics.com Sat Sep 5 09:12:32 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Sat, 5 Sep 2009 11:12:32 +0200 Subject: [Biojava-dev] JAXB plugin dependencies in sequence-blastxml module In-Reply-To: <59a41c430909041449p24e90756l97aec6cd9fcbe6e6@mail.gmail.com> References: <050C9A545DC1D84BAC7A678B76A56C3C15CE0B48FE@ebrcexch1.ebrc.bbsrc.ac.uk> <050C9A545DC1D84BAC7A678B76A56C3C15CE0B4900@ebrcexch1.ebrc.bbsrc.ac.uk> <59a41c430909041449p24e90756l97aec6cd9fcbe6e6@mail.gmail.com> Message-ID: <600E7D2C-179E-4BAE-B554-AA3E44A3C043@eaglegenomics.com> Yup I would say the latest but as I can see no specific feature in it which is required as a dependency, then any version will probably do. On 4 Sep 2009, at 23:49, Andreas Prlic wrote: > Hi Trevor and Andy, > > Thanks for the detailed feedback. To make sure nothing gets lost I > added a todo list to the wiki. Feel free to add other action items... > http://biojava.org/wiki/BioJava:MavenMigration > > * I understand the jaxb problem is mainly related to netbeans. I think > we should support easy setup on all popular IDEs. Would it be of > advantage to change the dependency to a different jaxb package? Seems > there are many available... > > Richard, do you as the module lead have an opinion which version of > jaxb to depend on? - I suppose you will say the latest... :-) > > Andreas > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From holland at eaglegenomics.com Sat Sep 5 09:13:49 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Sat, 5 Sep 2009 11:13:49 +0200 Subject: [Biojava-dev] more updates... In-Reply-To: References: Message-ID: <883EF3DE-E522-4121-A978-C13377CA2475@eaglegenomics.com> What bit of the code is it actually used for? Do we still need to do that? Either way, the easiest solution is to make bytecode.jar into its own separate maven/svn project. It's not really bio-specific and so could live quite happily as its own project. On 5 Sep 2009, at 04:40, Michael Heuer wrote: > Andy Law (RI) wrote: > >> Andreas, >> >> On 4 Sep 2009, at 07:53, Andreas Prlic wrote: >> >>> Hi, >>> >>> quick update: new modules: >>> biojava-biosql and >>> biojava-gui >>> biojava-das compiles, still talking off list with Jonathan about >>> details. >>> >>> mvn install works fine for me on the current svn. >> >> >> We can't get a clean check-out to build on our systems at Roslin. >> >> I have Trevor Paterson (my local maven maven) working on detailing >> why >> not - he'll be joining us later on the list to give us a rundown. >> >> First issue is the bytecode jar. I recognise that you have stuck it >> into a folder with a README file, but that is not a good solution. >> The >> folder that you have put it in is not displayed in the Project view >> of >> the Netbeans IDE because it is not a standard maven location. >> Obviously the best solution would be to include the bytecode source >> as >> a subproject and have it build or alternatively to publish the >> bytecode jar into a publicly accessible (central) maven repository. > > Perhaps the biojava code that depends on bytecode.jar should be > refactored > to use BCEL or some other third party bytecode generation library. > > michael > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From trevor.paterson at roslin.ed.ac.uk Mon Sep 7 08:13:34 2009 From: trevor.paterson at roslin.ed.ac.uk (trevor paterson (RI)) Date: Mon, 7 Sep 2009 09:13:34 +0100 Subject: [Biojava-dev] JAXB plugin dependencies in sequence-blastxml module In-Reply-To: <59a41c430909041449p24e90756l97aec6cd9fcbe6e6@mail.gmail.com> Message-ID: <050C9A545DC1D84BAC7A678B76A56C3C15CE0B4902@ebrcexch1.ebrc.bbsrc.ac.uk> Personally I think that the code should be independent of any IDE quirks - not tailored to work with every possible IDE. As we know what the issue is and how to avoid it I think the dependency should be left as it is. It looks like netbeans is supplying something equivalent to jaxb 2.0 which lacks the Marshaller.marshall(Object, File) method signature - found since version 2.1. - the sequence-blastxml BlastXMLTYools object uses this convenience method. Trevor Paterson PhD new email trevor.paterson at roslin.ed.ac.uk Bioinformatics The Roslin Institute Edinburgh University Scotland EH25 9PS phone +44 (0)131 5274402 http://www.roslin.ed.ac.uk http://www.comparagrid.org http://www.thearkdb.org Please consider the environment before printing this e-mail The University of Edinburgh is a charitable body, registered in Scotland with registration number SC005336 Disclaimer:This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. -----Original Message----- From: andreas.prlic at gmail.com [mailto:andreas.prlic at gmail.com] On Behalf Of Andreas Prlic Sent: 04 September 2009 22:50 To: trevor paterson (RI) Cc: biojava-dev at biojava.org; andy law (RI) Subject: Re: [Biojava-dev] JAXB plugin dependencies in sequence-blastxml module Hi Trevor and Andy, Thanks for the detailed feedback. To make sure nothing gets lost I added a todo list to the wiki. Feel free to add other action items... http://biojava.org/wiki/BioJava:MavenMigration * I understand the jaxb problem is mainly related to netbeans. I think we should support easy setup on all popular IDEs. Would it be of advantage to change the dependency to a different jaxb package? Seems there are many available... Richard, do you as the module lead have an opinion which version of jaxb to depend on? - I suppose you will say the latest... :-) Andreas From andy.law at roslin.ed.ac.uk Mon Sep 7 15:35:56 2009 From: andy.law at roslin.ed.ac.uk (Andy Law (RI)) Date: Mon, 7 Sep 2009 16:35:56 +0100 Subject: [Biojava-dev] File path problem Message-ID: All, Clean checkout of the code gives me multiple test failures (FileNotFoundException) if the path to the code includes spaces. Seems that calls to open test files are failing. The path to the file has been encoded with %20 instead of the spaces but the open file is failing - apparently inside of the Sun code in java.io.RandomAccessFile.open(Native Method). Anyone else seeing this on any other platform (I'm on a Mac) Later, Andy -------- Yada, yada, yada... The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336 Disclaimer: This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. From andreas at sdsc.edu Mon Sep 7 20:01:45 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Mon, 7 Sep 2009 13:01:45 -0700 Subject: [Biojava-dev] replacing trunk with new modules Message-ID: <59a41c430909071301x21885fb9m6b8d6af32ad43df6@mail.gmail.com> Hi, unless I hear any objections, I would like to replace the ("old") biojava-trunk with the new modularized svn location tomorrow evening (San Diego time). I will move the current trunk location to a tag directory in svn, so it is still possible to refer to it and compare with it. This is to avoid any confusion about where any new development should happen. Any objections? Andreas From andreas.prlic at gmail.com Mon Sep 7 20:03:35 2009 From: andreas.prlic at gmail.com (Andreas Prlic) Date: Mon, 7 Sep 2009 13:03:35 -0700 Subject: [Biojava-dev] File path problem In-Reply-To: References: Message-ID: <59a41c430909071303o347ef9au1b9a056ea2d606e9@mail.gmail.com> Hi Andy, Can you send me a few stacktraces / file locations that you are having problems with? works fine for me on OSX using eclipse and command line mvn... Andreas On Mon, Sep 7, 2009 at 8:35 AM, Andy Law (RI) wrote: > All, > > Clean checkout of the code gives me multiple test failures > (FileNotFoundException) if the path to the code includes spaces. Seems that > calls to open test files are failing. The path to the file has been encoded > with %20 instead of the spaces but the open file is failing - apparently > inside of the Sun code in java.io.RandomAccessFile.open(Native Method). > > Anyone else seeing this on any other platform (I'm on a Mac) > > Later, > > Andy > -------- > Yada, yada, yada... > The University of Edinburgh is a charitable body, registered in Scotland, > with registration number SC005336 > Disclaimer: This e-mail and any attachments are confidential and intended > solely for the use of the recipient(s) to whom they are addressed. If you > have received it in error, please destroy all copies and inform the sender. > > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From heuermh at acm.org Tue Sep 8 02:01:01 2009 From: heuermh at acm.org (Michael Heuer) Date: Mon, 7 Sep 2009 22:01:01 -0400 (EDT) Subject: [Biojava-dev] replacing trunk with new modules In-Reply-To: <59a41c430909071301x21885fb9m6b8d6af32ad43df6@mail.gmail.com> Message-ID: Andreas Prlic wrote: > unless I hear any objections, I would like to replace the ("old") > biojava-trunk with the new modularized svn location tomorrow evening > (San Diego time). I will move the current trunk location to a tag > directory in svn, so it is still possible to refer to it and compare > with it. This is to avoid any confusion about where any new > development should happen. I will need to get a 1.7.1 release out quickly for this FASTQ paper submission. Do you feel that we'd be able to get a 1.7.1 release built off the new structure without any problems, or is the modularized tree slated for a version 1.8? In that case, I can do a release from the 1.7 release branch no problem. michael From andreas at sdsc.edu Tue Sep 8 02:57:06 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Mon, 7 Sep 2009 19:57:06 -0700 Subject: [Biojava-dev] replacing trunk with new modules In-Reply-To: References: <59a41c430909071301x21885fb9m6b8d6af32ad43df6@mail.gmail.com> Message-ID: <59a41c430909071957kf7699cah7635f07efd1386af@mail.gmail.com> better do a 1.7.1 build from the current code in the trunk. the modularized new thingy probably should be called v. 3.0 and will only be ready at some point after the hackaton... do you need a full release or just some kind of jar file available for download? Andreas On Mon, Sep 7, 2009 at 7:01 PM, Michael Heuer wrote: > Andreas Prlic wrote: > >> unless I hear any objections, I would like to replace the ("old") >> biojava-trunk with the new modularized svn location tomorrow evening >> (San Diego time). I will move the current trunk location to a tag >> directory in svn, so it is still possible to refer to it and compare >> with it. This is to avoid any confusion about where any new >> development should happen. > > I will need to get a 1.7.1 release out quickly for this FASTQ paper > submission. ?Do you feel that we'd be able to get a 1.7.1 release built > off the new structure without any problems, or is the modularized tree > slated for a version 1.8? ?In that case, I can do a release from the 1.7 > release branch no problem. > > ? michael > > From andy.law at roslin.ed.ac.uk Tue Sep 8 09:26:25 2009 From: andy.law at roslin.ed.ac.uk (Andy Law (RI)) Date: Tue, 8 Sep 2009 10:26:25 +0100 Subject: [Biojava-dev] more updates... In-Reply-To: References: Message-ID: On 5 Sep 2009, at 03:40, Michael Heuer wrote: > Perhaps the biojava code that depends on bytecode.jar should be > refactored > to use BCEL or some other third party bytecode generation library. Where *is* the code that underpins this library? It's all org.biojava.util package so presumably it's lying around somewhere in the biojava vaults? Later, Andy -------- Yada, yada, yada... The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336 Disclaimer: This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. From andy.law at roslin.ed.ac.uk Tue Sep 8 09:43:48 2009 From: andy.law at roslin.ed.ac.uk (Andy Law (RI)) Date: Tue, 8 Sep 2009 10:43:48 +0100 Subject: [Biojava-dev] File path problem In-Reply-To: <59a41c430909071303o347ef9au1b9a056ea2d606e9@mail.gmail.com> References: <59a41c430909071303o347ef9au1b9a056ea2d606e9@mail.gmail.com> Message-ID: <2256B94E-ADF8-4781-9E60-DE5935C62973@roslin.ed.ac.uk> On 7 Sep 2009, at 21:03, Andreas Prlic wrote: > Hi Andy, > > Can you send me a few stacktraces / file locations that you are having > problems with? works fine for me on OSX using eclipse and command line > mvn... > http://tr.im/y8YT I have lots like this (generated from the command line). If I move the biojava folder to the Desktop (i.e. at "~/Desktop/ biojava/" rather than "~/Desktop/No Time Machine Backup/biojava/") then the problem goes away. Later, Andy -------- Yada, yada, yada... The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336 Disclaimer: This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. From phidias51 at gmail.com Tue Sep 8 16:08:40 2009 From: phidias51 at gmail.com (Mark Fortner) Date: Tue, 8 Sep 2009 09:08:40 -0700 Subject: [Biojava-dev] File path problem In-Reply-To: <2256B94E-ADF8-4781-9E60-DE5935C62973@roslin.ed.ac.uk> References: <59a41c430909071303o347ef9au1b9a056ea2d606e9@mail.gmail.com> <2256B94E-ADF8-4781-9E60-DE5935C62973@roslin.ed.ac.uk> Message-ID: <6e1d61f50909080908t7d982cb3oa844e902ad75a7aa@mail.gmail.com> Andreas & Andy, AFAIK this is a long-standing JVM/OS dependent issue. The only workaround I know of is to escape the spaces by preceding them with a backslash. You may be able to create a relative root directory from which all other subdirectories can be resolved. Andy, do you encounter a problem if you do something like this: File biojavaHome = new File("."); in the ~/Desktop/No Time Machine Backup/biojava directory? Does biojavaHome.exists() return true? If you don't, then it may be able to resolve subdirectories of the biojavaHome file object. You might also try to declare a biojava home env variable and use it throughout the unit tests. The other thing that you might try is the new File(new URI("blah")) constructor. According to the URI javadoc it apparently can deal with %20 spaces in file names. Hope this helps, Mark On Tue, Sep 8, 2009 at 2:43 AM, Andy Law (RI) wrote: > > On 7 Sep 2009, at 21:03, Andreas Prlic wrote: > > Hi Andy, >> >> Can you send me a few stacktraces / file locations that you are having >> problems with? works fine for me on OSX using eclipse and command line >> mvn... >> >> > > > http://tr.im/y8YT > > > I have lots like this (generated from the command line). > > If I move the biojava folder to the Desktop (i.e. at "~/Desktop/biojava/" > rather than "~/Desktop/No Time Machine Backup/biojava/") then the problem > goes away. > > > > > Later, > > Andy > -------- > Yada, yada, yada... > The University of Edinburgh is a charitable body, registered in Scotland, > with registration number SC005336 > Disclaimer: This e-mail and any attachments are confidential and intended > solely for the use of the recipient(s) to whom they are addressed. If you > have received it in error, please destroy all copies and inform the sender. > > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > -- Mark Fortner blog: http://feeds.feedburner.com/jroller/ideafactory From andreas.prlic at gmail.com Tue Sep 8 16:47:37 2009 From: andreas.prlic at gmail.com (Andreas Prlic) Date: Tue, 8 Sep 2009 09:47:37 -0700 Subject: [Biojava-dev] File path problem In-Reply-To: <6e1d61f50909080908t7d982cb3oa844e902ad75a7aa@mail.gmail.com> References: <59a41c430909071303o347ef9au1b9a056ea2d606e9@mail.gmail.com> <2256B94E-ADF8-4781-9E60-DE5935C62973@roslin.ed.ac.uk> <6e1d61f50909080908t7d982cb3oa844e902ad75a7aa@mail.gmail.com> Message-ID: <59a41c430909080947q7661b604j76d0f0e2c774aff3@mail.gmail.com> Another work around is to use symbolic links... The standard way to request files form the file system in biojava is like this: String resName = "org/biojava/bio/program/sax/blastxml/input.xml"; InputStream resStream = getClass().getClassLoader().getResourceAsStream(resName); Not sure if this will work with spaces in directory names.... Andreas On Tue, Sep 8, 2009 at 9:08 AM, Mark Fortner wrote: > Andreas & Andy, > AFAIK this is a long-standing JVM/OS dependent issue.? The only workaround I > know of is to escape the spaces by preceding them with a backslash. > > You may be able to create a relative root directory from which all other > subdirectories can be resolved.? Andy, do you encounter a problem if you do > something like this: > > File biojavaHome = new File("."); > > in the ~/Desktop/No Time Machine Backup/biojava directory?? Does > biojavaHome.exists() return true? > > If you don't, then it may be able to resolve subdirectories of the > biojavaHome file object.? You might also try to declare a biojava home env > variable and use it throughout the unit tests. > > The other thing that you might try is the new File(new URI("blah")) > constructor.? According to the URI javadoc? it apparently can deal with %20 > spaces in file names. > > Hope this helps, > > Mark > > On Tue, Sep 8, 2009 at 2:43 AM, Andy Law (RI) > wrote: >> >> On 7 Sep 2009, at 21:03, Andreas Prlic wrote: >> >>> Hi Andy, >>> >>> Can you send me a few stacktraces / file locations that you are having >>> problems with? works fine for me on OSX using eclipse and command line >>> mvn... >>> >> >> >> >> http://tr.im/y8YT >> >> >> I have lots like this (generated from the command line). >> >> If I move the biojava folder to the Desktop (i.e. at "~/Desktop/biojava/" >> rather than "~/Desktop/No Time Machine Backup/biojava/") then the problem >> goes away. >> >> >> >> Later, >> >> Andy >> -------- >> Yada, yada, yada... >> The University of Edinburgh is a charitable body, registered in Scotland, >> with registration number SC005336 >> Disclaimer: This e-mail and any attachments are confidential and intended >> solely for the use of the recipient(s) to whom they are addressed. If you >> have received it in error, please destroy all copies and inform the sender. >> >> >> >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev > > > > -- > Mark Fortner > > blog: http://feeds.feedburner.com/jroller/ideafactory > From andreas at sdsc.edu Tue Sep 8 17:03:11 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Tue, 8 Sep 2009 10:03:11 -0700 Subject: [Biojava-dev] more updates... In-Reply-To: References: Message-ID: <59a41c430909081003v267cd167ofb3d4f9adaa26e9b@mail.gmail.com> The bytecode.jar source is in a different location in SVN: http://code.open-bio.org/svnweb/index.cgi/biojava/browse/bytecode/trunk Not sure how this one will go, since it seems to be a bit special, but I will try to make this another maven module, so things are consistent. Andreas On Tue, Sep 8, 2009 at 2:26 AM, Andy Law (RI) wrote: > > On 5 Sep 2009, at 03:40, Michael Heuer wrote: > >> Perhaps the biojava code that depends on bytecode.jar should be refactored >> to use BCEL or some other third party bytecode generation library. > > Where *is* the code that underpins this library? It's all org.biojava.util > package so presumably it's lying around somewhere in the biojava vaults? > > Later, > > Andy > -------- > Yada, yada, yada... > The University of Edinburgh is a charitable body, registered in Scotland, > with registration number SC005336 > Disclaimer: This e-mail and any attachments are confidential and intended > solely for the use of the recipient(s) to whom they are addressed. If you > have received it in error, please destroy all copies and inform the sender. > > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From andreas at sdsc.edu Wed Sep 9 04:05:07 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Tue, 8 Sep 2009 21:05:07 -0700 Subject: [Biojava-dev] bytecode module (was: more updates...) Message-ID: <59a41c430909082105v4ee83c0bmeb29b7f80bd5ad16@mail.gmail.com> To follow up on the bytecode module: Turned out it was easy to move the code into its own module. The core module is now set up correctly and does not require any local installations of bytecode.jar any longer. Andreas On Tue, Sep 8, 2009 at 10:03 AM, Andreas Prlic wrote: > The bytecode.jar source is in a different location in SVN: > > http://code.open-bio.org/svnweb/index.cgi/biojava/browse/bytecode/trunk > > Not sure how this one will go, since it seems to be a bit special, but > I will try to ?make this another maven module, so things are > consistent. > > Andreas > > > > On Tue, Sep 8, 2009 at 2:26 AM, Andy Law (RI) wrote: >> >> On 5 Sep 2009, at 03:40, Michael Heuer wrote: >> >>> Perhaps the biojava code that depends on bytecode.jar should be refactored >>> to use BCEL or some other third party bytecode generation library. >> >> Where *is* the code that underpins this library? It's all org.biojava.util >> package so presumably it's lying around somewhere in the biojava vaults? >> >> Later, >> >> Andy >> -------- >> Yada, yada, yada... >> The University of Edinburgh is a charitable body, registered in Scotland, >> with registration number SC005336 >> Disclaimer: This e-mail and any attachments are confidential and intended >> solely for the use of the recipient(s) to whom they are addressed. If you >> have received it in error, please destroy all copies and inform the sender. >> >> >> >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev >> > From andy.law at roslin.ed.ac.uk Wed Sep 9 10:30:40 2009 From: andy.law at roslin.ed.ac.uk (Andy Law (RI)) Date: Wed, 9 Sep 2009 11:30:40 +0100 Subject: [Biojava-dev] File path problem In-Reply-To: <6e1d61f50909080908t7d982cb3oa844e902ad75a7aa@mail.gmail.com> References: <59a41c430909071303o347ef9au1b9a056ea2d606e9@mail.gmail.com> <2256B94E-ADF8-4781-9E60-DE5935C62973@roslin.ed.ac.uk> <6e1d61f50909080908t7d982cb3oa844e902ad75a7aa@mail.gmail.com> Message-ID: <58E00A8B-DAD7-46D2-AAF8-424C9F896C40@roslin.ed.ac.uk> The problem appears not to be in accessing the file - the test code generates File objects correctly with the paths escaped to contain %20 instead of spaces. If I modify the source code of the test so that the names of the files are incorrect then the failure is that the File object is returned as null. I am confident that this part of the code is working. The problem arises when the biojava code asks for a biojava RAF object to be constructed from the File object. RAF is a wrapper around java.io.RandomAccessFile, seemingly simply to allow access to the File object although java.io.RandomAccessFile does provide access to a FileDescriptor. The RAF constructor calls the RandomAccessFile constructor passing it the (perfectly valid) File object it was itself handed. The failure occurs inside the RandomAccessFile constructor. I suspect that this occurs in the call to 'open' in the constructor which is - obviously - a platform-specific piece of code. Thus we seem to have tripped over a bug in the Apple implementation of the JVM. I will look into this further if/when time permits. It may be possible to workaround it by manipulating the path in the RAF constructor on a platform-by-platform basis but that kind of hacking should only be a short-term solution. On 8 Sep 2009, at 17:08, Mark Fortner wrote: > Andreas & Andy, > AFAIK this is a long-standing JVM/OS dependent issue. The only > workaround I know of is to escape the spaces by preceding them with > a backslash. > > You may be able to create a relative root directory from which all > other subdirectories can be resolved. Andy, do you encounter a > problem if you do something like this: > > File biojavaHome = new File("."); > > in the ~/Desktop/No Time Machine Backup/biojava directory? Does > biojavaHome.exists() return true? > > If you don't, then it may be able to resolve subdirectories of the > biojavaHome file object. You might also try to declare a biojava > home env variable and use it throughout the unit tests. > > The other thing that you might try is the new File(new URI("blah")) > constructor. According to the URI javadoc it apparently can deal > with %20 spaces in file names. > > Hope this helps, > > Mark > > On Tue, Sep 8, 2009 at 2:43 AM, Andy Law (RI) > wrote: > > On 7 Sep 2009, at 21:03, Andreas Prlic wrote: > > Hi Andy, > > Can you send me a few stacktraces / file locations that you are having > problems with? works fine for me on OSX using eclipse and command line > mvn... > > > > > http://tr.im/y8YT > > > I have lots like this (generated from the command line). > > If I move the biojava folder to the Desktop (i.e. at "~/Desktop/ > biojava/" rather than "~/Desktop/No Time Machine Backup/biojava/") > then the problem goes away. > > > > > Later, > > Andy > -------- > Yada, yada, yada... > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336 > Disclaimer: This e-mail and any attachments are confidential and > intended solely for the use of the recipient(s) to whom they are > addressed. If you have received it in error, please destroy all > copies and inform the sender. > > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > > > > -- > Mark Fortner > > blog: http://feeds.feedburner.com/jroller/ideafactory Later, Andy -------- Yada, yada, yada... The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336 Disclaimer: This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. From andy.law at roslin.ed.ac.uk Thu Sep 10 15:00:53 2009 From: andy.law at roslin.ed.ac.uk (Andy Law (RI)) Date: Thu, 10 Sep 2009 16:00:53 +0100 Subject: [Biojava-dev] Spaces in file paths - resolved Message-ID: All, I've been digging about in the bowels of the java.io libraries and the biojava core tests and I have a fix. From what I can tell, the problem with spaces in file paths is NOT a Mac-specific thing. I threw together some tests (attached as a tgz version of the maven project) that demonstrate the problem on the Mac but then when I ran them on the linux box, the same tests failed so I think it is a general issue. However, in doing so I was able to get to grips with why it is failing and how to work around it. The problem stems from the RandomAccessFile constructor being given a File whose path contains encoded spaces. The File objects in question are constructed (in the tests) using the file path extracted from a URL object i.e. the MO of the tests is: (1) create URL pointing at the file (2) create a File from that (using the *path* extracted from the URL [via getFile()! go figure]) (3) create a RandomAccessFile from the File There are similar problems creating Streams from the File object but points (1) and (2) are the same in that situation. However, it is possible to construct a File from a URI (note UR*I* not UR*L*) and it is possible to extract a URI from a URL. The File generated this way seems to have the path escaped or handled properly. Thus if we replace step (2) with "create a File from a URI extracted from the URL" then all seems to be well. Changes required: Change .getFile() to .getURI() at: Line 196: biojava/core/src/test/java/org/biojava/bio/program/indexdb/ IndexToolsTest.java Line 53: biojava/core/src/test/java/org/biojava/bio/seq/db/emblcd/ DivisionLkpReaderTest.java Line 58: biojava/core/src/test/java/org/biojava/bio/seq/db/emblcd/ EntryNamIdxReaderTest.java Line 54: biojava/core/src/test/java/org/biojava/bio/seq/db/emblcd/ EntryNamRandomAccessTest.java Line 70: biojava/core/src/test/java/org/biojava/bio/seq/db/ EmblCDROMIndexStoreTest.java Line 71: biojava/core/src/test/java/org/biojava/bio/seq/db/ EmblCDROMIndexStoreTest.java Hope that helps. Later, Andy -------- Yada, yada, yada... The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336 Disclaimer: This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. -------------- next part -------------- A non-text attachment was scrubbed... Name: testfiles.tgz Type: application/octet-stream Size: 1749 bytes Desc: not available URL: From andreas at sdsc.edu Thu Sep 10 21:38:22 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Thu, 10 Sep 2009 14:38:22 -0700 Subject: [Biojava-dev] Spaces in file paths - resolved In-Reply-To: References: Message-ID: <59a41c430909101438r3b3a572au6efa15fcba1af63b@mail.gmail.com> Hi Andy, thanks for figuring this out. I committed the patches to SVN. what used to read URL url = EntryNamRandomAccessTest.class.getResource("entrynam.idx"); File f = new File(url.getFile()); now reads: URL url = EntryNamRandomAccessTest.class.getResource("entrynam.idx"); File f = new File(new URI("file://"+url.getFile())); Andreas On Thu, Sep 10, 2009 at 8:00 AM, Andy Law (RI) wrote: > All, > > I've been digging about in the bowels of the java.io libraries and the > biojava core tests and I have a fix. > > From what I can tell, the problem with spaces in file paths is NOT a > Mac-specific thing. I threw together some tests (attached as a tgz version > of the maven project) that demonstrate the problem on the Mac but then when > I ran them on the linux box, the same tests failed so I think it is a > general issue. However, in doing so I was able to get to grips with why it > is failing and how to work around it. > > The problem stems from the RandomAccessFile constructor being given a File > whose path contains encoded spaces. The File objects in question are > constructed (in the tests) using the file path extracted from a URL object > i.e. the MO of the tests is: > > (1) create URL pointing at the file > (2) create a File from that (using the *path* extracted from the URL [via > getFile()! go figure]) > (3) create a RandomAccessFile from the File > > There are similar problems creating Streams from the File object but points > (1) and (2) are the same in that situation. > > However, it is possible to construct a File from a URI (note UR*I* not > UR*L*) and it is possible to extract a URI from a URL. The File generated > this way seems to have the path escaped or handled properly. Thus if we > replace step (2) with "create a File from a URI extracted from the URL" then > all seems to be well. > > > > Changes required: > > Change .getFile() to .getURI() at: > > Line 196: > biojava/core/src/test/java/org/biojava/bio/program/indexdb/IndexToolsTest.java > Line ?53: > biojava/core/src/test/java/org/biojava/bio/seq/db/emblcd/DivisionLkpReaderTest.java > Line ?58: > biojava/core/src/test/java/org/biojava/bio/seq/db/emblcd/EntryNamIdxReaderTest.java > Line ?54: > biojava/core/src/test/java/org/biojava/bio/seq/db/emblcd/EntryNamRandomAccessTest.java > Line ?70: > biojava/core/src/test/java/org/biojava/bio/seq/db/EmblCDROMIndexStoreTest.java > Line ?71: > biojava/core/src/test/java/org/biojava/bio/seq/db/EmblCDROMIndexStoreTest.java > > > > Hope that helps. > > > Later, > > Andy > -------- > Yada, yada, yada... > The University of Edinburgh is a charitable body, registered in Scotland, > with registration number SC005336 > Disclaimer: This e-mail and any attachments are confidential and intended > solely for the use of the recipient(s) to whom they are addressed. If you > have received it in error, please destroy all copies and inform the sender. > > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > > From holland at eaglegenomics.com Mon Sep 14 08:44:57 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Mon, 14 Sep 2009 09:44:57 +0100 Subject: [Biojava-dev] BioJava Hackathon in January Message-ID: <844D84C0-3363-4A3E-84B5-472C1E296B0E@eaglegenomics.com> Hi all, The January hackathon is now confirmed. It will take place from January 18th-22nd 2010, at the Wellcome Trust Genome Campus (at Hinxton, near Cambridge). Exact location on the campus will be determined nearer the time as it will depend on final numbers attending. If you will definitely be attending, _please email me_ to let me know as soon as possible so that I can ensure we get a big enough room. This is also important because unless I know you're coming, I won't be able to arrange you a security pass to get onto the campus. No funding is available at present so attendance will be at your own cost (or your employer's if you can persuade them!). If this changes I will let you know but don't hold your hopes too high! There is no accommodation near the campus itself but there is a free bus shuttle linking it to central Cambridge where you can find hotels and hostels of all kinds and for all budgets. The purpose of the hackathon is to make progress towards achieving the goals listed on this wiki page, which Andreas Prlic is maintaining: http://biojava.org/wiki/BioJava:Modules cheers, Richard -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From HWillis at scripps.edu Mon Sep 14 13:33:43 2009 From: HWillis at scripps.edu (Scooter Willis) Date: Mon, 14 Sep 2009 09:33:43 -0400 Subject: [Biojava-dev] BioJava Hackathon in January In-Reply-To: <844D84C0-3363-4A3E-84B5-472C1E296B0E@eaglegenomics.com> Message-ID: Richard Count me in! Thanks Scooter On 9/14/09 4:44 AM, "Richard Holland" wrote: Hi all, The January hackathon is now confirmed. It will take place from January 18th-22nd 2010, at the Wellcome Trust Genome Campus (at Hinxton, near Cambridge). Exact location on the campus will be determined nearer the time as it will depend on final numbers attending. If you will definitely be attending, _please email me_ to let me know as soon as possible so that I can ensure we get a big enough room. This is also important because unless I know you're coming, I won't be able to arrange you a security pass to get onto the campus. No funding is available at present so attendance will be at your own cost (or your employer's if you can persuade them!). If this changes I will let you know but don't hold your hopes too high! There is no accommodation near the campus itself but there is a free bus shuttle linking it to central Cambridge where you can find hotels and hostels of all kinds and for all budgets. The purpose of the hackathon is to make progress towards achieving the goals listed on this wiki page, which Andreas Prlic is maintaining: http://biojava.org/wiki/BioJava:Modules cheers, Richard -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ _______________________________________________ biojava-dev mailing list biojava-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-dev From andreas at sdsc.edu Mon Sep 14 15:33:27 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Mon, 14 Sep 2009 08:33:27 -0700 Subject: [Biojava-dev] BioJava Hackathon in January In-Reply-To: <844D84C0-3363-4A3E-84B5-472C1E296B0E@eaglegenomics.com> References: <844D84C0-3363-4A3E-84B5-472C1E296B0E@eaglegenomics.com> Message-ID: <59a41c430909140833i2827cd30g5ac83f134a1b5f21@mail.gmail.com> Excellent, thanks for organizing this, Richard! Looking forward to meeting you all in Cambridge! Andreas On Mon, Sep 14, 2009 at 1:44 AM, Richard Holland wrote: > Hi all, > > The January hackathon is now confirmed. It will take place from January > 18th-22nd 2010, at the Wellcome Trust Genome Campus (at Hinxton, near > Cambridge). Exact location on the campus will be determined nearer the time > as it will depend on final numbers attending. > > If you will definitely be attending, _please email me_ to let me know as > soon as possible so that I can ensure we get a big enough room. This is also > important because unless I know you're coming, I won't be able to arrange > you a security pass to get onto the campus. > > No funding is available at present so attendance will be at your own cost > (or your employer's if you can persuade them!). If this changes I will let > you know but don't hold your hopes too high! > > There is no accommodation near the campus itself but there is a free bus > shuttle linking it to central Cambridge where you can find hotels and > hostels of all kinds and for all budgets. > > The purpose of the hackathon is to make progress towards achieving the goals > listed on this wiki page, which Andreas Prlic is maintaining: > > ?http://biojava.org/wiki/BioJava:Modules > > cheers, > Richard > > -- > Richard Holland, BSc MBCS > Operations and Delivery Director, Eagle Genomics Ltd > T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com > http://www.eaglegenomics.com/ > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From andreas at sdsc.edu Tue Sep 15 16:22:36 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Tue, 15 Sep 2009 09:22:36 -0700 Subject: [Biojava-dev] trunk now mavenized Message-ID: <59a41c430909150922l1b19a597g12f0b893930194f7@mail.gmail.com> Hi, The Biojava - trunk is now pointing to the new mavenized and modularized code. The old ant-based trunk has been moved to a branch ( biojava-live/branches/trunk_1_7_ant ) so it is still easy to find. Seems we have only found minor issues with the new modules so far and they are ready for more people to try the checkouts. More feedback is welcome. Andreas From jacobsen at ebi.ac.uk Wed Sep 16 16:43:44 2009 From: jacobsen at ebi.ac.uk (Jules Jacobsen) Date: Wed, 16 Sep 2009 17:43:44 +0100 Subject: [Biojava-dev] BioJava Hackathon in January In-Reply-To: <844D84C0-3363-4A3E-84B5-472C1E296B0E@eaglegenomics.com> References: <844D84C0-3363-4A3E-84B5-472C1E296B0E@eaglegenomics.com> Message-ID: <12c279870909160943x15d5ff76q488f6696f597d121@mail.gmail.com> Hi Richard, Sounds cool - count me in. Jules On Mon, Sep 14, 2009 at 9:44 AM, Richard Holland wrote: > Hi all, > > The January hackathon is now confirmed. It will take place from January > 18th-22nd 2010, at the Wellcome Trust Genome Campus (at Hinxton, near > Cambridge). Exact location on the campus will be determined nearer the time > as it will depend on final numbers attending. > > If you will definitely be attending, _please email me_ to let me know as > soon as possible so that I can ensure we get a big enough room. This is also > important because unless I know you're coming, I won't be able to arrange > you a security pass to get onto the campus. > > No funding is available at present so attendance will be at your own cost > (or your employer's if you can persuade them!). If this changes I will let > you know but don't hold your hopes too high! > > There is no accommodation near the campus itself but there is a free bus > shuttle linking it to central Cambridge where you can find hotels and > hostels of all kinds and for all budgets. > > The purpose of the hackathon is to make progress towards achieving the goals > listed on this wiki page, which Andreas Prlic is maintaining: > > ?http://biojava.org/wiki/BioJava:Modules > > cheers, > Richard > > -- > Richard Holland, BSc MBCS > Operations and Delivery Director, Eagle Genomics Ltd > T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com > http://www.eaglegenomics.com/ > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From andy.law at roslin.ed.ac.uk Mon Sep 21 13:36:39 2009 From: andy.law at roslin.ed.ac.uk (Andy Law (RI)) Date: Mon, 21 Sep 2009 14:36:39 +0100 Subject: [Biojava-dev] ensembl code Message-ID: <6CA04E21-058F-4379-B944-6C3C1187AA2E@roslin.ed.ac.uk> Andreas, Did the (old, defunct) Ensembl code make the transition from cvs to svn? The reason that I ask is that I'm putting in a proposal to fund a body to resurrect it and it will look more professional if I actually know where it is. I would look myself, but our internet access is screwed completely today (and the University IT staff are on holiday). Email seems to be working but bu**er-all else is. Later, Andy -------- Yada, yada, yada... The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336 Disclaimer: This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. From andreas.prlic at gmail.com Thu Sep 24 15:10:38 2009 From: andreas.prlic at gmail.com (Andreas Prlic) Date: Thu, 24 Sep 2009 08:10:38 -0700 Subject: [Biojava-dev] Moving web blast stuff to the new mavenized code tree In-Reply-To: References: Message-ID: <59a41c430909240810o61228e27ja65289eb33a7fa1c@mail.gmail.com> Hi Sylvain, It is best to get a current checkout at a new location on your disc. Did you commit it to svn prior to the maven move? Then it got moved by me. Otherwise the package naming did not get changed and it should be relatively straightforward to copy over the files. For eclipse based developers I recommend getting the latest SVN plugin and m2eclipse for maven. Then it is possible to browse through the biojava svn repository, right click on the biojava-live/trunk folder and ->Check out as Maven project. Perhaps somebody using other IDEs could comment on what's the best strategy to get the basic checkout there? Andreas On Thu, Sep 24, 2009 at 7:54 AM, Sylvain Foisy wrote: > Hi Andreas, > > How could the code I wrote a few weeks back be moved to the new tree? I > would like to continue working on this but I see no point of doing so > outside of the new tree... > > Best regards > > Sylvain > > > ================================================================== > > Sylvain Foisy, Ph. D. > Charg? de projet / Project Manager > Bio-informatique > > Adresse postale: > > Laboratoire de genetique et medecine genomique de l'inflammation > Institut de cardiologie de Montreal > 5000 Belanger > Montreal, Qc > H1T 1C8 > > T: 514-376-3330 x.2299 | F: 514-593-2539 > M: sylvain.foisy at inflammgen.org > W: http://www.inflammgen.org > > ================================================================== > > > From simpleyrx at 163.com Wed Sep 30 04:56:46 2009 From: simpleyrx at 163.com (simpleyrx) Date: Wed, 30 Sep 2009 12:56:46 +0800 (CST) Subject: [Biojava-dev] what is the default parameters of Message-ID: <27727343.508701254286606200.JavaMail.coremail@bj163app55.163.com> Dear experts, NeedlemanWunsch's constructive funtion in biojava is as below: public NeedlemanWunsch(short?match, short?replace, short?insert, short?delete, short?gapExtend, SubstitutionMatrix?subMat) I would like to know what are the default values to used NeedlemanWunsch. Such as how select match ,replace,insert,delete,gapExtend or subMat parameters ? -- Renxiang Yan