Dear Stian, Here you can find the bet solution we thought: http://myexperiment.elda.org/workflows/27/download?version=1
Any suggestion?? Thanks in advance 2011/9/12 Marta Villegas <[email protected]> > Thank you for your help and for a very detailed and useful answer. > > In fact, I agree all a) b) c) options have problems... > > in fact option C is not very good solution for us either because it would > pass the error to the following processor as you said. > > But it would be nice to have some beanshell option to detect elements with > errors in a list. So the beanshell designer can decide what to do with that > error: make the whole list fail, make an output list with correct values and > error values, skip the errors, etc. > > Thanks for opening the new feature request. > > > 2011/9/9 Stian Soiland-Reyes <[email protected]> > >> If the error is caused by the occasional failure, such as due to >> network variations, etc, then you can improve this by setting the >> Retry setting on services that call over the network: >> >> >> http://www.mygrid.org.uk/dev/wiki/display/taverna/Advanced+workflow+configuration+video#Advancedworkflowconfigurationvideo-Retries >> >> >> However, if the service for certain values always will fail, you would >> need a "filter/replace error" shim. This is unfortunately not >> currently easy to do with Beanshell script as Taverna by default >> prevents execution on data with errors. >> >> >> When we earlier talked to some users about what options they wanted >> for error handling, we considered: >> a) Removing errors from the list (skipping them) >> b) Replacing errors with a replacement input value, e.g. >> "myStandardGene", empty string, etc. >> c) Replacing calls on errors with a replacement output value, e.g. "-- >> ERROR HERE!!--" >> >> The consideration was not conclusive, but roughly each of these come >> with issues: >> a) Breaks the order of the list - result in position 5 might now come >> from position 7 in incoming list (5 & 6 were errors) - which makes it >> hard to use with later dot products >> >> b) Not sure which "fake input" would work well in many cases - and >> could end up with "fake data" sneaking its way into the results >> >> c) "Error message" values could be passed on to the next service, >> which don't know it's an error, and falls over with new errors or >> strange outputs, but these are no longer linked back to original >> error. >> >> >> As engineers we thought that we could address c) by giving out the >> replacement output as "An error with a replacement value". The service >> which could fail would have an error handling configuration with "[x] >> Substitute errors with __my_value______" >> >> Thus the default for downstream services would be to fail (as of now) >> - but with a possible error handling configuration to "[x] Allow error >> replacement values" which would run using the provided replacement >> value. We were not sure if the outputs of such processors should then >> be normal values or "errors with replacement values". >> >> We did not proceed with implementing any of these options, as they >> seemed to require a fair bit of effort and raised more open questions. >> >> >> >> Now - for your case I assume that as you are just concatenating >> strings as the final step, you are not overly concerned with these >> workflow implications for the general case, as you only want to deal >> with or handling the errors that have occurred before giving a single >> line-separated string back to the user. >> >> This is the kind of practical use case that we would have needed back >> then - this is much simpler to implement, but would unfortunately >> require writing a Taverna plugin or patch. >> >> I've registered this as a New Feature request: >> http://www.mygrid.org.uk/dev/issues/browse/T2-1991 >> .. but I can't give any promises as to when it would be implemented. >> >> >> The only workaround I can think of would be to use the "Failover" >> mechanism - specifying an alternate service to the one that >> occasionally fails. Unfortunately the Taverna 2 user interface does >> not yet show this feature - >> http://www.mygrid.org.uk/dev/issues/browse/T2-294 suggests creating >> that processor in Taverna 1 and then use Copy and Paste. See >> >> http://www.mygrid.org.uk/usermanual1.7/workbench_windows.html#ame_alternate_processors >> for Taverna 1 documentation. >> >> >> >> See attached where I have manually edited the .t2flow to add a string >> constant as an alternate service to "Sometime fails". (Note that the >> alternate service would need to provide values for all the service >> outputs - and at the same list depth) >> >> >> >> >> On Fri, Sep 9, 2011 at 10:03, Marta Villegas <[email protected]> >> wrote: >> > Hi, >> > >> > I'm using "merge string list to a string" component to concatenate a >> list of >> > outputs in most of our workflows. We do that because it's more user >> friendly >> > to copy that output with all results than coping each element of the >> list. >> > We work with lists with more than 500 elements. >> > >> > The problem comes when some elements have an error, then "merge string >> list" >> > is not able to create the concatenation and gives an error. >> > Here I attach an example workflow that shows the problem... >> > >> > the exected result without errors would be a list like: >> > String0 >> > String1 >> > String2 >> > String3 >> > .... >> > >> > with errors the result now is: >> > [an error message] >> > >> > I would like to have: >> > String0 >> > String1 >> > [error] >> > String3 >> > .... >> > >> > Is there any way to do this? >> > >> > Thanks in advance. >> > >> > >> > -- >> > Marta Villegas >> > [email protected] >> > >> > >> ------------------------------------------------------------------------------ >> > Why Cloud-Based Security and Archiving Make Sense >> > Osterman Research conducted this study that outlines how and why cloud >> > computing security and archiving is rapidly being adopted across the IT >> > space for its ease of implementation, lower cost, and increased >> > reliability. Learn more. >> http://www.accelacomm.com/jaw/sfnl/114/51425301/ >> > _______________________________________________ >> > taverna-users mailing list >> > [email protected] >> > [email protected] >> > Web site: http://www.taverna.org.uk >> > Mailing lists: http://www.taverna.org.uk/about/contact-us/ >> > >> > >> >> >> >> -- >> Stian Soiland-Reyes, myGrid team >> School of Computer Science >> The University of Manchester >> >> >> ------------------------------------------------------------------------------ >> Why Cloud-Based Security and Archiving Make Sense >> Osterman Research conducted this study that outlines how and why cloud >> computing security and archiving is rapidly being adopted across the IT >> space for its ease of implementation, lower cost, and increased >> reliability. Learn more. http://www.accelacomm.com/jaw/sfnl/114/51425301/ >> _______________________________________________ >> taverna-users mailing list >> [email protected] >> [email protected] >> Web site: http://www.taverna.org.uk >> Mailing lists: http://www.taverna.org.uk/about/contact-us/ >> >> > > > -- > Marta Villegas > [email protected] > -- Marta Villegas [email protected]
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