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/
