We are due to restructure the code, and probably move to Github, some time this autumn, in particular to make it simpler to use.
One big question here is what would the individual checkouts consist of. We know that Taverna is too big for a single project, (in particular to handle updates and tagging), but we also know that the modules currently in SVN are too fine grained. For Taverna 2 we used an SVN trick with svn externals to bind it all together for a single checkout, as you say. http://taverna.googlecode.com/svn/taverna/builds/taverna-workbench/branches/maintenance/ shows this for Taverna 2. (On checkout you would find say engine/net.sf.taverna.t2.core checked out from the external http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.core/branches/maintenance/ ) I am not sure if David has made such a build tree for Taverna 3, but it would generally follow the same structure. http://dev.mygrid.org.uk/wiki/display/developer/Maven+Modules explains the modules of Taverna 2, which generally apply to Taverna 3 as well. You would not need anything (I believe) from the UI modules as we have not yet got an official Taverna 3 workbench. http://dev.mygrid.org.uk/wiki/display/tav/Building+Taverna+Platform explains how to build the platform, but it has not been updated since last year, so it might not be a perfect description of the situation today. David - are there any big changes? On Tue, Jul 24, 2012 at 1:42 PM, Schenck, Martin <[email protected]> wrote: > Hi, > > the folder structure is just too confusing ... "unsorted", "taverna", > "platform", ... I would like to check out one folder with all its > contents/sub-folders which represents the up-to-date version of the Taverna 3 > development (and then build that using maven). > > Like with the SCUFL2 API at http://taverna.googlecode.com/svn/scufl2/trunk/ > > > Thanks, > > Martin > > > -- > Martin Schenck > > Room: > EN-740 > Phone: > +49 30 314-24122 > Email: > [email protected] > Address: > TU Berlin Fak. IV > Sekretariat EN7 > Einsteinufer 17 > 10587 Berlin > > -----Original Message----- > From: [email protected] > [mailto:[email protected]] > Sent: Tuesday, July 24, 2012 2:01 PM > To: [email protected] > Subject: taverna-hackers Digest, Vol 72, Issue 3 > > Send taverna-hackers mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/taverna-hackers > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific than "Re: > Contents of taverna-hackers digest..." > > > Today's Topics: > > 1. Taverna 3 Source Code (Schenck, Martin) > 2. Re: Taverna 3 Source Code (David Withers) > 3. Re: segmentation fault / uncaught exception (Alan R Williams) > 4. Re: segmentation fault / uncaught exception (Jorge de Jesus) > 5. Re: segmentation fault / uncaught exception (Jorge de Jesus) > 6. Re: segmentation fault / uncaught exception (Alan R Williams) > 7. Baclava Library (Markus Plangg) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 23 Jul 2012 15:46:32 +0000 > From: "Schenck, Martin" <[email protected]> > Subject: [Taverna-hackers] Taverna 3 Source Code > To: "[email protected]" > <[email protected]> > Message-ID: > > <a133ffa97e411c4499915386e8c78c6523970...@ex-mb3.tubit.win.tu-berlin.de> > > Content-Type: text/plain; charset="us-ascii" > > Hi, > > I need the Taverna 3 source code in order to develop the Taverna to Hadoop > conversion for the SCAPE project. Where/how is that source code accessible? > > > Cheers, > > Martin > > > -- > Martin Schenck > > Room: > EN-740 > Phone: > +49 30 314-24122 > Email: > [email protected] > Address: > TU Berlin Fak. IV > Sekretariat EN7 > Einsteinufer 17 > 10587 Berlin > > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > Message: 2 > Date: Mon, 23 Jul 2012 17:17:21 +0100 > From: David Withers <[email protected]> > Subject: Re: [Taverna-hackers] Taverna 3 Source Code > To: List for general discussion and hacking of the Taverna project > <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=us-ascii > > Hi Martin, > > The source code is on the trunk of http://taverna.googlecode.com/svn/ > > The work on executing Taverna workflows on Hadoop would be an implementation > of the execution api of the Taverna 3 Platform : > http://taverna.googlecode.com/svn/unsorted/platform/trunk/platform/taverna-execution-api > > You will also need the scufl2 api : > http://taverna.googlecode.com/svn/scufl2/trunk/scufl2-api > > David. > > On 23 Jul 2012, at 16:46, Schenck, Martin wrote: > >> Hi, >> >> I need the Taverna 3 source code in order to develop the Taverna to Hadoop >> conversion for the SCAPE project. Where/how is that source code accessible? >> >> >> Cheers, >> >> Martin >> >> >> -- >> Martin Schenck >> >> Room: >> EN-740 >> Phone: >> +49 30 314-24122 >> Email: >> [email protected] >> Address: >> TU Berlin Fak. IV >> Sekretariat EN7 >> Einsteinufer 17 >> 10587 Berlin >> >> ---------------------------------------------------------------------- >> -------- >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. >> Discussions will include endpoint security, mobile security and the >> latest in malware threats. >> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_____________ >> __________________________________ >> taverna-hackers mailing list >> [email protected] >> Web site: http://www.taverna.org.uk >> Mailing lists: http://www.taverna.org.uk/about/contact-us/ >> Developers Guide: http://www.taverna.org.uk/developers/ > > -- > David Withers > School of Computer Science, University of Manchester, Oxford Road, > Manchester, M13 9PL, UK. > +44 (0)161 275 0683 > > > > > > > > ------------------------------ > > Message: 3 > Date: Mon, 23 Jul 2012 18:13:01 +0100 > From: Alan R Williams <[email protected]> > Subject: Re: [Taverna-hackers] segmentation fault / uncaught exception > To: List for general discussion and hacking of the Taverna project > <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 23/07/2012 16:02, Alan R Williams wrote: > > [snip] > >> I'm trying it with SoapUI to see what it thinks. Then I'll load up >> Taverna in a debugger and see where it crashes. > > SoapUI is OK with it. When I debug Taverna in Eclipse I just get the > scary message > > "Invalid access of stack red zone 0x14ca07fd0 rip=0x12df1588e" > > which apparently could be a class loader issue (waves at Raven) or stack > overflow. This is probably not going to be easy to track down. > >>> Jorge >> >> Alan > > Alan > > > > > > ------------------------------ > > Message: 4 > Date: Tue, 24 Jul 2012 10:01:42 +0100 > From: Jorge de Jesus <[email protected]> > Subject: Re: [Taverna-hackers] segmentation fault / uncaught exception > To: [email protected] > Message-ID: <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Alan > > Thank you for giving it a look. I was surprised to see different > systems, and differente taverna versions to have the same problem, most > interesting is that the problem started more or less on Monday . I > wonder if the OGC schemas being used in the WSDL file have been changed > and are now causing the stack overflow. > > Please let me know what is going on > Jorge > > > On 23/07/12 18:13, Alan R Williams wrote: >> On 23/07/2012 16:02, Alan R Williams wrote: >> >> [snip] >> >>> I'm trying it with SoapUI to see what it thinks. Then I'll load up >>> Taverna in a debugger and see where it crashes. >> SoapUI is OK with it. When I debug Taverna in Eclipse I just get the >> scary message >> >> "Invalid access of stack red zone 0x14ca07fd0 rip=0x12df1588e" >> >> which apparently could be a class loader issue (waves at Raven) or stack >> overflow. This is probably not going to be easy to track down. >> >>>> Jorge >>> Alan >> Alan >> >> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> taverna-hackers mailing list >> [email protected] >> Web site: http://www.taverna.org.uk >> Mailing lists: http://www.taverna.org.uk/about/contact-us/ >> Developers Guide: http://www.taverna.org.uk/developers/ > > > -- > PGP public key: 0x595FF9D3 > > > > > ------------------------------ > > Message: 5 > Date: Tue, 24 Jul 2012 10:37:37 +0100 > From: Jorge de Jesus <[email protected]> > Subject: Re: [Taverna-hackers] segmentation fault / uncaught exception > To: List for general discussion and hacking of the Taverna project > <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi > > I've asked around and yes there was a change during the weekend > concerning xlink > > http://www.spatineo.com/2012/04/ogc-to-switch-to-wc3-xlink-in-july-2012/ > > Basically the OGC schemas have moved from a OGC-scpecific XLink > definition into a W3C compliant Xlink. So the problem could be something > wrong with the schemas and not with Taverna (even if Taverna crashes) > > I'll continue to give it a look > > Jorge > > On 24/07/12 10:01, Jorge de Jesus wrote: >> Hi Alan >> >> Thank you for giving it a look. I was surprised to see different >> systems, and differente taverna versions to have the same problem, most >> interesting is that the problem started more or less on Monday . I >> wonder if the OGC schemas being used in the WSDL file have been changed >> and are now causing the stack overflow. >> >> Please let me know what is going on >> Jorge >> >> >> On 23/07/12 18:13, Alan R Williams wrote: >>> On 23/07/2012 16:02, Alan R Williams wrote: >>> >>> [snip] >>> >>>> I'm trying it with SoapUI to see what it thinks. Then I'll load up >>>> Taverna in a debugger and see where it crashes. >>> SoapUI is OK with it. When I debug Taverna in Eclipse I just get the >>> scary message >>> >>> "Invalid access of stack red zone 0x14ca07fd0 rip=0x12df1588e" >>> >>> which apparently could be a class loader issue (waves at Raven) or stack >>> overflow. This is probably not going to be easy to track down. >>> >>>>> Jorge >>>> Alan >>> Alan >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Live Security Virtual Conference >>> Exclusive live event will cover all the ways today's security and >>> threat landscape has changed and how IT managers can respond. Discussions >>> will include endpoint security, mobile security and the latest in malware >>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>> _______________________________________________ >>> taverna-hackers mailing list >>> [email protected] >>> Web site: http://www.taverna.org.uk >>> Mailing lists: http://www.taverna.org.uk/about/contact-us/ >>> Developers Guide: http://www.taverna.org.uk/developers/ >> > > > -- > PGP public key: 0x595FF9D3 > > > > > ------------------------------ > > Message: 6 > Date: Tue, 24 Jul 2012 10:59:42 +0100 > From: Alan R Williams <[email protected]> > Subject: Re: [Taverna-hackers] segmentation fault / uncaught exception > To: [email protected] > Message-ID: <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 24/07/2012 10:37, Jorge de Jesus wrote: >> Hi >> >> I've asked around and yes there was a change during the weekend >> concerning xlink >> >> http://www.spatineo.com/2012/04/ogc-to-switch-to-wc3-xlink-in-july-2012/ >> >> Basically the OGC schemas have moved from a OGC-scpecific XLink >> definition into a W3C compliant Xlink. So the problem could be something >> wrong with the schemas and not with Taverna (even if Taverna crashes) >> >> I'll continue to give it a look > > Thanks Jorge. I guess we know the reason now, although not what it is > doing in Taverna. > >> Jorge > > Alan > > > > > ------------------------------ > > Message: 7 > Date: Tue, 24 Jul 2012 13:45:13 +0200 > From: Markus Plangg <[email protected]> > Subject: [Taverna-hackers] Baclava Library > To: [email protected] > Message-ID: <[email protected]> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > is there a Java library to read and write Baclava files? > > I saw that there is a package org.embl.ebi.escience.baclava on > http://build.mygrid.org.uk/taverna/api/org/embl/ebi/escience/baclava/package-use.html > but taverna also has something similar at > https://code.google.com/p/taverna/source/browse/taverna/utils/baclava/. > If I wanted to write and read Baclava files to use with Taverna which > library would be best to use? > > Cheers, > Markus > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > > ------------------------------ > > _______________________________________________ > taverna-hackers mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/taverna-hackers > > > End of taverna-hackers Digest, Vol 72, Issue 3 > ********************************************** > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > taverna-hackers mailing list > [email protected] > Web site: http://www.taverna.org.uk > Mailing lists: http://www.taverna.org.uk/about/contact-us/ > Developers Guide: http://www.taverna.org.uk/developers/ -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ taverna-hackers mailing list [email protected] Web site: http://www.taverna.org.uk Mailing lists: http://www.taverna.org.uk/about/contact-us/ Developers Guide: http://www.taverna.org.uk/developers/
