Hi Jits: Thanks for you information. Can you please provide more details on how to install it and use it?
Thanks again for your help. Jamal ----- Original Message ----- From: [email protected] To: [email protected] Sent: Friday, January 29, 2010 5:09:12 AM (GMT-0500) Auto-Detected Subject: taverna-users Digest, Vol 44, Issue 11 Send taverna-users mailing list submissions to [email protected] To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/taverna-users 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-users digest..." Today's Topics: 1. Re: error in web service (Stuart Owen) 2. Re: Taverna 2.1 error message (Alan Williams) 3. Display the visual representation of the workflow (Jamal Alhiyafi) 4. Re: error in web service (Stian Soiland-Reyes) 5. Re: Display the visual representation of the workflow (Jiten Bhagat) 6. Re: Taverna 2.1 error message (Stian Soiland-Reyes) 7. Re: Taverna 2.1 error message (Paul Fisher) 8. Complex iteration in T2 (Peter Li) ---------------------------------------------------------------------- Message: 1 Date: Wed, 27 Jan 2010 13:17:17 +0000 From: Stuart Owen <[email protected]> Subject: Re: [Taverna-users] error in web service To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset="iso-8859-1" Hi Shady, I'm unable to test the service "getids" without having a valid jobid. Would it be possible to send me your workflow, or send me a pre-existing jobId from a previous execution if it is persitant. You can send it privately direct to my email if you would prefer. thanks, Stuart. On 27/01/10 12:15, Shady Alaa wrote: > I am using taverna v1.7.2.1 > > > ------------------------------------------------------------------------------ > The Planet: dedicated and managed hosting, cloud storage, colocation > Stay online with enterprise data centers and the best network in the business > Choose flexible plans and management services without long-term contracts > Personal 24x7 support from experience hosting pros just a phone call away. > http://p.sf.net/sfu/theplanet-com > > > _______________________________________________ > taverna-users mailing list > [email protected] > [email protected] > Web site: http://www.taverna.org.uk > Mailing lists: http://www.taverna.org.uk/taverna-mailing-lists/ > -------------- next part -------------- An HTML attachment was scrubbed... ------------------------------ Message: 2 Date: Wed, 27 Jan 2010 13:59:13 +0000 From: Alan Williams <[email protected]> Subject: Re: [Taverna-users] Taverna 2.1 error message To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Paul Fisher wrote: > Hello, [snip] > Does anyone know what the error message means? The problem is being caused by one thread in Taverna trying to read from a list (a list within the Taverna code not within your workflow) while another is adding to that list. It is most likely caused by nested workflows starting off when a service is registering data. I've put the bug into Jira as http://www.mygrid.org.uk/dev/issues/browse/T2-1124 to be fixed for 2.1.1 I can't think of a workaround - sorry :( Maybe someone else can. > cheers, > Paul. Alan ------------------------------ Message: 3 Date: Wed, 27 Jan 2010 20:50:53 -0500 (EST) From: Jamal Alhiyafi <[email protected]> Subject: [Taverna-users] Display the visual representation of the workflow To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset=utf-8 Hi: I have a taverna workflow (.xml). Is there a command that I can execute and pass the .xml file as a parameter and it will display the visual representation of the workflow (not execute it) .. just rendering it or creating the png image for it and displaying it on the screen. Thanks, Jamal ------------------------------ Message: 4 Date: Thu, 28 Jan 2010 10:56:54 +0000 From: Stian Soiland-Reyes <[email protected]> Subject: Re: [Taverna-users] error in web service To: taverna-users <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset=UTF-8 On Wed, Jan 27, 2010 at 12:15, Shady Alaa <[email protected]> wrote: > I am using taverna v1.7.2.1 Out of curiosity, might I ask why you prefer to stay with version 1.7 instead of 2.1..? We need to know what blocks people from upgrading! :) -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester ------------------------------ Message: 5 Date: Thu, 28 Jan 2010 11:01:50 +0000 From: Jiten Bhagat <[email protected]> Subject: Re: [Taverna-users] Display the visual representation of the workflow To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset=ISO-8859-1 Hello, If you're familiar with Ruby (or don't mind learning it), you can use the Taverna 1 & 2 RubyGems that we use in myExperiment to automatically generate the preview images. For Taverna 1 (SCUFL): http://github.com/mannie/taverna1-gem/ For Taverna 2 (t2flow): http://github.com/mannie/taverna2-gem/ Let me know if you need some example code on how to use these. Cheers, Jits Jamal Alhiyafi wrote: > Hi: > > I have a taverna workflow (.xml). Is there a command that I can execute and > pass the .xml file as a parameter and it will display the visual > representation of the workflow (not execute it) .. just rendering it or > creating the png image for it and displaying it on the screen. > > > Thanks, > Jamal > > ------------------------------------------------------------------------------ > The Planet: dedicated and managed hosting, cloud storage, colocation > Stay online with enterprise data centers and the best network in the business > Choose flexible plans and management services without long-term contracts > Personal 24x7 support from experience hosting pros just a phone call away. > http://p.sf.net/sfu/theplanet-com > _______________________________________________ > taverna-users mailing list > [email protected] > [email protected] > Web site: http://www.taverna.org.uk > Mailing lists: http://www.taverna.org.uk/taverna-mailing-lists/ > ------------------------------ Message: 6 Date: Thu, 28 Jan 2010 11:02:05 +0000 From: Stian Soiland-Reyes <[email protected]> Subject: Re: [Taverna-users] Taverna 2.1 error message To: taverna-users <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset=UTF-8 On Wed, Jan 27, 2010 at 13:59, Alan Williams <[email protected]> wrote: > I've put the bug into Jira as > http://www.mygrid.org.uk/dev/issues/browse/T2-1124 to be fixed for 2.1.1 We've found that we'll have to release an update (2.1.1) next week to fix this bug, which can affect any workflow with nested workflows. We'll try to do this as an online update. See http://tinyurl.com/tav-2-1-1 for issues scheduled to be fixed for 2.1.1. -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester ------------------------------ Message: 7 Date: Thu, 28 Jan 2010 11:15:29 +0000 From: Paul Fisher <[email protected]> Subject: Re: [Taverna-users] Taverna 2.1 error message To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Excellent. Thank you very much. Paul. Stian Soiland-Reyes wrote: > On Wed, Jan 27, 2010 at 13:59, Alan Williams <[email protected]> wrote: > >> I've put the bug into Jira as >> http://www.mygrid.org.uk/dev/issues/browse/T2-1124 to be fixed for 2.1.1 >> > > We've found that we'll have to release an update (2.1.1) next week to > fix this bug, which can affect any workflow with nested workflows. > > We'll try to do this as an online update. > > See http://tinyurl.com/tav-2-1-1 for issues scheduled to be fixed for 2.1.1. > > ------------------------------ Message: 8 Date: Fri, 29 Jan 2010 10:09:01 +0000 From: Peter Li <[email protected]> Subject: [Taverna-users] Complex iteration in T2 To: <[email protected]> Message-ID: <c788643d.49dc%[email protected]> Content-Type: text/plain; charset="US-ASCII" Hi there, I'm needing to perform the same type of iteration on data as Marco describes in the email below. http://markmail.org/message/hwoipvurcgsi6dey Is there now a way of doing this in without having to use the echo list processor and a nested workflow by configuring a processor's list handling functionality in Taverna 2? Thanks, Peter. -- Marco Roos wrote: Dear Taverna user, Issue 1: Complex iteration I would like to perform an iteration including a dot product between a list and a list of lists; example: Input: [1] [A,B,C] [[a,b],[c,d],[e,f]] Desired output: [1Aa, 1Ab, 1Bc, 1Bd, 1Ce, 1Cf] Is this possible? If so, how can I achieve this? Yes, but not directly. This is actually the reason for the new T2 feature called 'staged iteration'. The issue is that assuming you iterate down to single items (which appears to be the case) you want to go half way with a dot product and then use a cross product. As the iteration strategies always (in the current code) drill down to the final thing you're asking for you can't do this, at least you can't do it without a trick... So... the trick : First off the [1] is a red herring, that's the easy bit! it doesn't matter where you put that in as it'll always be added onto every single job. So you now have a list and a list of lists, you want to combine item 'n' in the first list with all the items of list 'n' in the second. Firstly you'll need a nested workflow into which you put your processor, the trick being that you also put in an 'echo list' operation. Connect the echo list output to the input of your processor being fed needing the list of lists and the echo list input to a workflow input. Connect the other input (the list) of your processor to a workflow input. The workflow inputs will have type of 'single item' and 'list' as the workflow inputs copy the types of the inputs they're connected to. It should be obvious that if you give this nested workflow the inputs 'A' and [a,b] it'll iterate and give you [f(A*a),f(A*b]. Also note that now the nested workflow mismatches by the same level on both inputs - it has one input with a single item type which you'll feed it a list and another of a list where you feed it a list of lists. This means you can set a dot iteration strategy over the nested workflow with the cross product (default) iteration strategy over the processor within it. This nested workflow will now produce the result you want; it will be called three times with : [A*[a,b], B*[c,d], C*[e,f]] Each one of these then creates a cross product iteration within the nested workflow, so the output is : [f(A*a),f(A*b)],[f(B*c),f(B*d)],[f(C*e),f(C*f)]] Passing the output through a list flatten operation then gives you (leaving out the 'F(x)' and replacing with 'x') : [Aa,Ab,Bc,Bd,Ce,Cf] which is what I believe you wanted? :) Adding the [1] bit in is easy from there! We actually did this exact thing some time ago for Paul, he had a structure he was viewing as two lists of directories where the lists were the same length but the directories could have any number of items in, he wanted a comparison between every item in directory 'n' from list 1 and every item in directory 'n' from list 2. Hope that helps, if you were wondering why we have a superficially pointless 'echo list' local worker now you know :) Tom _______________________________________________ Taverna-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/taverna-users Documentation: http://www.mygrid.org.uk/usermanual1.6/ FAQ: http://www.mygrid.org.uk/wiki/Mygrid/TavernaFaq Biological Services: http://www.mygrid.org.uk/wiki/Mygrid/BiologicalWebServices ------------------------------ ------------------------------------------------------------------------------ The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com ------------------------------ _______________________________________________ taverna-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/taverna-users End of taverna-users Digest, Vol 44, Issue 11 ********************************************* ------------------------------------------------------------------------------ The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com _______________________________________________ taverna-users mailing list [email protected] [email protected] Web site: http://www.taverna.org.uk Mailing lists: http://www.taverna.org.uk/taverna-mailing-lists/
