Not sure why you would want to use Taverna for such a problem.. You can solve this problem in two lines using a scripting language like Python.
In fact you could do it in a Beanshell script inside a Taverna workflow, but your workflow would not be doing much flowing.. On Tue, Oct 13, 2009 at 09:53, Sudharshan Krishnan <[email protected]> wrote: > Hi Fellow tavernas, > > Nice to get in touch with you.Let me introduce myself first-I am sudan,doing > my masters in IT at Syracuse University. I just started playing around with > taverna and it feels good. I was assigned a problem from my professor which > is as follows: > > Consider a list [(a,1,2,3),(b,1,2,3),(b,2,4,6)....] where a and b are like > indices of a list. If there are similar indices, then the output should > display the average of the corresponding numbers in each list.For instance in > this example we have 2 b's and so the result will be: > [(a,1,2,3),(b,1.5,3,4.5)...].Can someone please guide me in solving this > problem? > I think I need to create a plugin in taverna to implement this functionality. > > > > -----Original Message----- > From: [email protected] > [mailto:[email protected]] > Sent: Monday, October 12, 2009 11:06 AM > To: [email protected] > Subject: taverna-hackers Digest, Vol 41, 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. Re: Java 1.5 support (Jerzy Orlowski) > 2. Taverna Server documentation (Dinanath Sulakhe) > 3. Re: API usage for plugin development (Stian Soiland-Reyes) > 4. Provenance Plugin for Taverna (Girish Subramanian) > 5. Provenance Plugin for Taverna (Girish Subramanian) > 6. Re: Provenance Plugin for Taverna (Alan Williams) > 7. Re: Taverna Server documentation (Alexandra Nenadic) > 8. Re: Provenance Plugin for Taverna (Ian Dunlop) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 09 Oct 2009 14:02:21 +0100 > From: Jerzy Orlowski <[email protected]> > Subject: Re: [Taverna-hackers] Java 1.5 support > 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 > > I've never used 1.5 for Taverna and it worked. > Didn't even know about the issue > > Jerzy Orlowski > > Egon Willighagen pisze: >> On Thu, Oct 8, 2009 at 9:36 AM, Egon Willighagen >> <[email protected]> wrote: >> >>> On Mon, Oct 5, 2009 at 11:27 AM, Alan Williams <[email protected]> wrote: >>> >>>> At the moment Taverna is still using Java 1.5 because of lack of support >>>> for Java 1.6 on 32bit Macs. I was wondering what people's opinions are >>>> on switching to Java 1.6. >>>> >>> Java5 will not be available from archives for Ubuntu 10.04. >>> >> >> Umm... that's for 9.10 already. Sorry. >> >> Egon >> >> > > > > > ------------------------------ > > Message: 2 > Date: Fri, 9 Oct 2009 13:21:34 -0500 > From: Dinanath Sulakhe <[email protected]> > Subject: [Taverna-hackers] Taverna Server documentation > To: List for general discussion and hacking of the Taverna project > <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Hi, > > Is there any documentation on how to submit a workflow for execution, > once I stand a Taverna Server in Tomcat. > > I can't find any docs on how to submit and execute a workflow here: > http://www.mygrid.org.uk/dev/taverna-server > > Please let me know. > > Thanks > > -------------------------- > Dinanath Sulakhe > The Globus Alliance > Computation Institute, University of Chicago & > Math and Computer Science Division, Argonne National Laboratory. > Ph: (630) 252-7856 > > > > > > > ------------------------------ > > Message: 3 > Date: Fri, 9 Oct 2009 23:22:33 +0100 > From: Stian Soiland-Reyes <[email protected]> > Subject: Re: [Taverna-hackers] API usage for plugin development > To: List for general discussion and hacking of the Taverna project > <[email protected]> > Message-ID: > <[email protected]> > Content-Type: text/plain; charset=UTF-8 > > On Thu, Oct 8, 2009 at 12:21, Alan Williams <[email protected]> wrote: > >> In the executeAsynch method of your activity, you create a Runnable >> (normally a Thread) that will actually run the service for the activity >> e.g. executes the beanshell script or queries the BioMart database. ?You >> then do >> >> ? ? ? ?theCallback.requestRun(theRunnable) >> >> which asks Taverna to run the activity. > > No, as pointed out to me by Tom, you should *not* make a Thread to > create a Runnable. You should just make a Runnable. > > requestRun() will take care of making the actual thread. > > > (Supposedly the never-started threads would just hang around leaking > memory, as requestRun() would just call their run() method from the > Runnable interface.) > > -- > Stian Soiland-Reyes, myGrid team > School of Computer Science > The University of Manchester > > > > ------------------------------ > > Message: 4 > Date: Sat, 10 Oct 2009 04:33:11 -0400 > From: "Girish Subramanian" <[email protected]> > Subject: [Taverna-hackers] Provenance Plugin for Taverna > To: <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset="utf-8" > > Hi all, > > I am planning to write a provenance plugin for Taverna. I have the following > questions : > > 1. The SVN repository that I am using is > http://taverna.googlecode.com/svn/taverna/ . I guess this is the latest > ones. Please correct me if I am wrong. > > 2. For my provenance collection part I need some callback mechanism which > gets invoked , before invoking or executing any of the nodes in the > workflows. Do we have such a framework built in Taverna engine, else what is > the work around ? Can someone guide me through the classes that I should > look into to get this done . > > 3. Is there any documentation which points out how to create a new plugin > for tavern. > > Thanks, > Girish Subramanian > > > > > ------------------------------ > > Message: 5 > Date: Sat, 10 Oct 2009 04:50:51 -0400 > From: "Girish Subramanian" <[email protected]> > Subject: [Taverna-hackers] Provenance Plugin for Taverna > To: <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset="utf-8" > > > Hi all, > > I am planning to write a provenance plugin for Taverna. I have the following > questions : > > 1. The SVN repository that I am using is > http://taverna.googlecode.com/svn/taverna/ . I guess this is the latest > ones. Please correct me if I am wrong. > > 2. For my provenance collection part I need some callback mechanism which > gets invoked , before invoking or executing any of the nodes in the > workflows. Do we have such a framework built in Taverna engine, else what is > the work around ? Can someone guide me through the classes that I should > look into to get this done . > > 3. Is there any documentation which points out how to create a new plugin > for tavern. > > Thanks, > Girish Subramanian > > > > > > ------------------------------ > > Message: 6 > Date: Mon, 12 Oct 2009 10:22:26 +0100 > From: Alan Williams <[email protected]> > Subject: Re: [Taverna-hackers] Provenance Plugin for Taverna > 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 > > Girish Subramanian wrote: >> Hi all, > > Hello, > >> I am planning to write a provenance plugin for Taverna. > > Have you looked at the provenance capture that is already in Taverna? > In 2.1 beta 2 the information about the run is captured in a database > and it is this data which is used to produce the "intermediate results" > information. > > For 2.1, Paolo Missier, Ian Dunlop and Stuart Owen have been working on > improving the provenance capture. This includes OPM support and an API > to allow out-of-Taverna access to the provenance data. > >> I have the following >> questions : >> >> 1. The SVN repository that I am using is >> http://taverna.googlecode.com/svn/taverna/ . I guess this is the latest >> ones. Please correct me if I am wrong. > > Yes, that is the code repository. > >> 2. For my provenance collection part I need some callback mechanism which >> gets invoked , before invoking or executing any of the nodes in the >> workflows. Do we have such a framework built in Taverna engine, else what is >> the work around ? Can someone guide me through the classes that I should >> look into to get this done . > > The relevant packages are under net.sf.taverna.t2.provenance. > net.sf.taverna.t2.provenance.lineageservice.Provenance takes events and > passes them to net.sf.taverna.t2.provenance.lineageservice.EventProcessor > > You would probably want to implement your own EventProcessor. Paolo and > Ian can give more details. > >> 3. Is there any documentation which points out how to create a new plugin >> for tavern. > > There will be archetypes available, certainly for activity plugins, for 2.1. > >> Thanks, >> Girish Subramanian > > Alan > > > > ------------------------------ > > Message: 7 > Date: Mon, 12 Oct 2009 13:04:06 +0100 > From: Alexandra Nenadic <[email protected]> > Subject: Re: [Taverna-hackers] Taverna Server documentation > 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 > > Hi Dina, > > There is no official documentation on the Taverna 2 Server - it is in > the alpha stage at the moment - but if you download the source code from: > > http://taverna.googlecode.com/svn/taverna/products/net.sf.taverna.t2.taverna-server/ > > there is a good test code that will help you understand how to use its > REST interface. > > Regards, > Alex > > > Dinanath Sulakhe wrote: >> Hi, >> >> Is there any documentation on how to submit a workflow for execution, >> once I stand a Taverna Server in Tomcat. >> >> I can't find any docs on how to submit and execute a workflow here: >> http://www.mygrid.org.uk/dev/taverna-server >> >> Please let me know. >> >> Thanks >> >> -------------------------- >> Dinanath Sulakhe >> The Globus Alliance >> Computation Institute, University of Chicago & >> Math and Computer Science Division, Argonne National Laboratory. >> Ph: (630) 252-7856 >> >> > > > > > ------------------------------ > > Message: 8 > Date: Mon, 12 Oct 2009 16:06:06 +0100 > From: Ian Dunlop <[email protected]> > Subject: Re: [Taverna-hackers] Provenance Plugin for Taverna > 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" > > Hello, > > The provenance capture in T2 captures 'everything' that happens when > workflows are invoked. The events that flow through your workflow are > captured as ProvenanceItems and sent across to the > ProvenanceReporter/Provenanceconnector plugin for processing. It is here > where you can change what happens to these events. > You would need to create your own ProvenanceConnector, have a look at the > DerbyProvenanceConnector in the SVN for ideas and also how to plugin your > own. It's really just a case of subclassing ProvenanceConnector and > overriding the addProvenanceItem method. You will also need the magic SPI > files in src/main/resources/META-INF/services to make sure your version can > be found by taverna. Taverna creates them through a factory so you also > need to create that class. > > Cheers, > > Ian > > 2009/10/12 Alan Williams <[email protected]> > >> Girish Subramanian wrote: >> > Hi all, >> >> Hello, >> >> > I am planning to write a provenance plugin for Taverna. >> >> Have you looked at the provenance capture that is already in Taverna? >> In 2.1 beta 2 the information about the run is captured in a database >> and it is this data which is used to produce the "intermediate results" >> information. >> >> For 2.1, Paolo Missier, Ian Dunlop and Stuart Owen have been working on >> improving the provenance capture. This includes OPM support and an API >> to allow out-of-Taverna access to the provenance data. >> >> > I have the following >> > questions : >> > >> > 1. The SVN repository that I am using is >> > http://taverna.googlecode.com/svn/taverna/ . I guess this is the latest >> > ones. Please correct me if I am wrong. >> >> Yes, that is the code repository. >> >> > 2. For my provenance collection part I need some callback mechanism which >> > gets invoked , before invoking or executing any of the nodes in the >> > workflows. Do we have such a framework built in Taverna engine, else what >> is >> > the work around ? Can someone guide me through the classes that I should >> > look into to get this done . >> >> The relevant packages are under net.sf.taverna.t2.provenance. >> net.sf.taverna.t2.provenance.lineageservice.Provenance takes events and >> passes them to net.sf.taverna.t2.provenance.lineageservice.EventProcessor >> >> You would probably want to implement your own EventProcessor. Paolo and >> Ian can give more details. >> >> > 3. Is there any documentation which points out how to create a new plugin >> > for tavern. >> >> There will be archetypes available, certainly for activity plugins, for >> 2.1. >> >> > Thanks, >> > Girish Subramanian >> >> Alan >> >> >> ------------------------------------------------------------------------------ >> Come build with us! The BlackBerry(R) Developer Conference in SF, CA >> is the only developer event you need to attend this year. Jumpstart your >> developing skills, take BlackBerry mobile applications to market and stay >> ahead of the curve. Join us from November 9 - 12, 2009. Register now! >> http://p.sf.net/sfu/devconference >> _______________________________________________ >> taverna-hackers mailing list >> [email protected] >> Web site: http://www.taverna.org.uk >> Mailing lists: http://www.taverna.org.uk/taverna-mailing-lists/ >> Developers Guide: http://www.mygrid.org.uk/tools/developer-information >> > > > > -- > Ian Dunlop > myGrid Team > School of Computer Science > University of Manchester > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry(R) Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart your > developing skills, take BlackBerry mobile applications to market and stay > ahead of the curve. Join us from November 9 - 12, 2009. Register now! > http://p.sf.net/sfu/devconference > > ------------------------------ > > _______________________________________________ > taverna-hackers mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/taverna-hackers > > > End of taverna-hackers Digest, Vol 41, Issue 3 > ********************************************** > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry(R) Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart your > developing skills, take BlackBerry mobile applications to market and stay > ahead of the curve. Join us from November 9 - 12, 2009. Register now! > http://p.sf.net/sfu/devconference > _______________________________________________ > taverna-hackers mailing list > [email protected] > Web site: http://www.taverna.org.uk > Mailing lists: http://www.taverna.org.uk/taverna-mailing-lists/ > Developers Guide: http://www.mygrid.org.uk/tools/developer-information > -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ taverna-hackers mailing list [email protected] Web site: http://www.taverna.org.uk Mailing lists: http://www.taverna.org.uk/taverna-mailing-lists/ Developers Guide: http://www.mygrid.org.uk/tools/developer-information
