Hello,I am talking about BioMoby registreas that plug-in uses to get BioMoby artifacts (services, datatypes).Could you detail which repository should be removed, and which should be added? They are hardcoded in a java class "org.biomoby.registry.meta.RegistriesList". I have modified it in the BioMoby CVS repository, but to update a plugin it must be somehow compiled... BioMoby ant script has a taverna plug-in target, but it compiles v 1.1.1 plug-in and doesn't put it into BioMoby maven repository... Does this means that once I put a new v 1.1.5 plugin intoNote that [6] is a (weekly) mirror of [7] [9] http://biomoby.org/m2repo/org/biomoby/jmoby/ it will be copied into [6] http://www.mygrid.org.uk/maven/biomoby/biomoby.org/m2repo/ and could be used by taverna? What about already installed Tavernas? Could they be automatically updated? Kind Regards, Dmitry On 26/09/2011 13:22, Stian Soiland-Reyes wrote: On Mon, Sep 26, 2011 at 11:22, Dmitry <[email protected]> wrote:Could anybody change INB repository address in BioMoby Taverna plug-in please? The current plug-in points into developers repository and not to a production one. I already changed it in BioMoby repository, but unfortunately I have little knowledge how BioMoby Taverna plug-in is built. As far as I understand taverna uses it's own build scripts. Does it use BioMoby (OpenBio) repository? Why the plug-in itself is in Taverna maven repository and not in BioMoby maven?Could you detail which repository should be removed, and which should be added?See [1] for the current setting used by Taverna at runtime - and [2][3] for dependencies used at build-time - repositories for building are declared in [4][5] - that is also our mirror [6]. Note that [6] is a (weekly) mirror of [7] due to the repeated instability of the network connection (and future accessibility) of http://biomoby.org/ - done as: #!/bin/bash set -e # exit on error cd /local/www/mygrid/maven/biomoby wget --reject 'index.html*' --no-parent --random-wait --wait 0.1 --no-verbose --tries=3 --retry-connrefused --mirror http://biomoby.org/m2repo/ Please also note that the biomoby activity is depending on a slightly patched version of jmoby called 1.1.4-taverna which we host in our own repository [8]. Only the POM has been edited compared to jmoby 1.1.4 which was provided to us by Eddie Kawas from BioMoby. I don't know why he did not deploy this to [9] Also see below an email exchange with Ben Vandervalk who volunteered to bring our POM changes into the main jMoby codebase and do a 1.1.5 release. [1] http://www.mygrid.org.uk/taverna/updates/2.3.0/plugins/official/activities-2.3.0-20110905.xml [2] http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/trunk/biomoby-activity/pom.xml [3] http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/branches/maintenance/biomoby-activity/pom.xml [4] http://taverna.googlecode.com/svn/taverna/taverna-parent/trunk/pom.xml [5] http://taverna.googlecode.com/svn/taverna/taverna-parent/branches/maintenance/pom.xml [6] http://www.mygrid.org.uk/maven/biomoby/biomoby.org/m2repo/ [7] http://biomoby.org/m2repo [8] http://www.mygrid.org.uk/maven/repository/org/biomoby/jmoby/1.1.4-taverna/jmoby-1.1.4-taverna.pom [9] http://biomoby.org/m2repo/org/biomoby/jmoby/ On Fri, Aug 26, 2011 at 15:59, Stian Soiland-Reyes <[email protected]> wrote:I believe JMoby 1.1.2, 1.1.3 and 1.1.4 was made specifically for Taverna and probably not released as full Moby releases. Until 1.1.4 there was not a single CVS tag for any of these. They didn't get deployed properly as Eddie didn't have access to the Maven repository server at the time. So the next version now would be 1.1.5 - most certainly not another 1.1.2! See attached email exchange with Eddie in the bottom of this message. Also note that we had to make our own POM file as the Moby team refused our modifications upstream. So the -taverna versions in http://www.mygrid.org.uk/maven/repository/org/biomoby/jmoby/ and friends should be bytewise equal on the .jar as supplied by Moby, but with modifications of the POM. I don't remember the reason for not accepting our patch, but I believe it was due to some confusion about Maven warnings. I remember we had to use a different axis declarations. I think I also had to remove a dependency to really old Taverna jars in jmoby-desktop. Hopefully you would be able to pull in those POM changes for the 1.1.5 release - you can just do a diff of the POM files from our repository against what's in the CVS checkout. Feel free to ask me any questions, and .. I'll try to remember or dig up the emails for why we did it a certain way. Note that we no longer require Java 5 support, we use Java 6 now. (I assume this update is for Taverna 2.3). On Thu, Aug 25, 2011 at 14:34, Alan R Williams <[email protected]> wrote:Stian is looking up an e-mail exchange he had with Eddie when the current jar was created. Alan-- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester ---------- Forwarded message ---------- From: Stian Soiland-Reyes <[email protected]> Date: Thu, Sep 2, 2010 at 11:24 Subject: Re: FW: http://www.mygrid.org.uk/dev/issues/browse/T2-1496 To: Edward Kawas <[email protected]> Cc: Mark Wilkinson <[email protected]> We've already have two builds called 1.1.2 and 1.1.3 that I believe you provided. I believe 1.1.3 was just a rebuild of 1.1.2, as 1.1.2 was compiled for Java 6 instead of Java 5. I can't find any tags for any of these versions (and neither for 1.1.1) in :pserver:[email protected]:/home/repository/moby - does the code live somewhere else? This is all a bit messy - we need to know what version of jmoby to include in Taverna, but it seems like jMoby basically isn't versioned. When you say that 'the bugs that are reported against BioMoby in Taverna' are old bugs, which bugs do you mean? How can I verify that those bugs are fixed using the 1.1.1 JAR (or the build you are talking about making - would that be 1.1.4 then? From which code will it be built?). In which Taverna version did this work as expected..? Mark (cc): We're trying to clear up what JAR of jMoby is included in Taverna 2.2.0, and which it should be, as Eddie suspects it is the wrong one. On Wed, Sep 1, 2010 at 15:14, Edward Kawas <[email protected]> wrote:I think that you are right about only having a customized pom. In any case, the jar that shipped with the latest Taverna is not the same as older versions (probably because of the version number mess; my fault). I think that if you could, you should try a newer version (I can build it for you) and we could label it version 1.1.2 and you could host it in the mygrid repository. I have never been able to access the Biomoby.org one. I had to always depend on someone else deploying it for me. The bugs that are reported regarding Biomoby in taverna 2.2.0 are old ones and were fixed some time ago. That's why we believe that an older version got thrown in by accident somehow. Eddie-----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Stian Soiland-Reyes Sent: Wednesday, September 01, 2010 7:05 AM To: Edward Kawas Subject: Re: FW: http://www.mygrid.org.uk/dev/issues/browse/T2-1496 On Wed, Sep 1, 2010 at 14:52, Edward Kawas <[email protected]> wrote:Hi Stian, The latest one that I know about is here:http://biomoby.org/m2repo/org/biomoby/jmoby/1.1.1/>From what I remember, Taverna is using a custom version, hosted by you(not personally, of course, but your project) somewhere. That matches http://www.mygrid.org.uk/maven/repository/org/biomoby/jmoby/1.1.1- taverna/ I don't think we have customized the JAR, just the POM. -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester-- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester ---------- Forwarded message ---------- From: Stian Soiland-Reyes <[email protected]> Date: Fri, Sep 3, 2010 at 13:55 Subject: Re: FW: http://www.mygrid.org.uk/dev/issues/browse/T2-1496 To: Edward Kawas <[email protected]> Cc: Mark Wilkinson <[email protected]> On Thu, Sep 2, 2010 at 19:28, Edward Kawas <[email protected]> wrote:This is all a bit messy - we need to know what version of jmoby to include in Taverna, but it seems like jMoby basically isn't versioned.I thought that there were some version tags, but if you can't find them, I am obviously incorrect.I just had a quick look using Eclipse, tag discovery in CVS is inherently tricky, so I won't claim you are incorrect :)When you say that 'the bugs that are reported against BioMoby in Taverna' are old bugs, which bugs do you mean?The 'too many open' files bug. I believe that this was reported in version 1.7, but I can't find any reference to thatNo, I believe it was for 2.2.0.How can I verify that those bugs are fixed using the 1.1.1 JAR (or the build you are talking about making - would that be 1.1.4 then? From which code will it be built?). In which Taverna version did this work as expected..?The recent Biomoby errors in Taverna 2.2.0 won't occur on *nix machines. The library would be built from the latest Biomoby source. I may be wrong, but if you use an older version of Taverna, with the same jmoby version as is shipped with Taverna 2.2.0, the errors do not occur.So in Taverna 2.1.2 there is no problem, and the 'Moby Objects' folder appear - even if the jMoby JAR there is byte-wise exactly the same? Let's do a new build of jMoby, you call it 1.1.4 and make sure it's tagged, and then I can add it to our repository with the updated POM. We can then either wait till Taverna 2.3 (rougly scheduled end of October) to release it, or do it as an online update, which should not be too much work. I would suggest waiting until 2.3 if the current installation still works, but just has an error-popup now and then, but if it is true that the 'Moby Objects' folder is missing, we should do it as an online update. I'm unable to reproduce on my Ubuntu, but another colleague here has also seen the pop-up now and then, so we can test your new JAR there. Just one thing - remember to compile it for Java 5, not java 6! (From Taverna 2.3 Java 6-style should be OK, but not for a 2.2 update) -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester ---------- Forwarded message ---------- From: Edward Kawas <[email protected]> Date: Thu, Sep 9, 2010 at 16:11 Subject: RE: FW: http://www.mygrid.org.uk/dev/issues/browse/T2-1496 To: Stian Soiland-Reyes <[email protected]> Cc: Mark Wilkinson <[email protected]> Hi Stian, I added a tag to the moby cvs java/main branch and generated 2 jars (target=1.5) for Taverna. I have attached them here. An immediate update would be best, because I think that running Biomoby services is broken too when the error is encountered. Please let me know if I can be of further assistance. Thanks, Eddie-----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Stian Soiland-Reyes Sent: Friday, September 03, 2010 5:56 AM To: Edward Kawas Cc: Mark Wilkinson Subject: Re: FW: http://www.mygrid.org.uk/dev/issues/browse/T2-1496 On Thu, Sep 2, 2010 at 19:28, Edward Kawas <[email protected]> wrote:This is all a bit messy - we need to know what version of jmoby to include in Taverna, but it seems like jMoby basically isn't versioned.I thought that there were some version tags, but if you can't find them, Iam obviously incorrect. I just had a quick look using Eclipse, tag discovery in CVS is inherently tricky, so I won't claim you are incorrect :)When you say that 'the bugs that are reported against BioMoby inTaverna'are old bugs, which bugs do you mean?The 'too many open' files bug. I believe that this was reported in version 1.7, but I can't find any reference to thatNo, I believe it was for 2.2.0.How can I verify that those bugs are fixed using the 1.1.1 JAR (or the build you are talking about making - would that be 1.1.4 then? >From which code will it be built?). In which Taverna version did this workas expected..?The recent Biomoby errors in Taverna 2.2.0 won't occur on *nix machines.The library would be built from the latest Biomoby source. I may be wrong, but if you use an older version of Taverna, with the same jmoby version as is shipped with Taverna 2.2.0, the errors do not occur. So in Taverna 2.1.2 there is no problem, and the 'Moby Objects' folder appear - even if the jMoby JAR there is byte-wise exactly the same? Let's do a new build of jMoby, you call it 1.1.4 and make sure it's tagged, and then I can add it to our repository with the updated POM. We can then either wait till Taverna 2.3 (rougly scheduled end of October) to release it, or do it as an online update, which should not be too much work. I would suggest waiting until 2.3 if the current installation still works, but just has an error-popup now and then, but if it is true that the 'Moby Objects' folder is missing, we should do it as an online update. I'm unable to reproduce on my Ubuntu, but another colleague here has also seen the pop-up now and then, so we can test your new JAR there. Just one thing - remember to compile it for Java 5, not java 6! (From Taverna 2.3 Java 6-style should be OK, but not for a 2.2 update) -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester-- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester --
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