Stian Soiland-Reyes wrote: > On Thu, Jul 9, 2009 at 10:34, Stian > Soiland-Reyes<[email protected]> wrote: > >> Oh - if I Use the hsa:7097 as an input (Now I see it mentioned in your >> email! It was not set on the workflow port description or example) - >> then I do get lots of results and every box turns grey.. at least when >> I have turned off provenance from Preferences. >> >> These don't give any output, though: >> >> go_term_accession >> go_term >> go_term_definition >> publication_title >> publication_abstract >> publication_pubmed_id >> publication_author >> publication_journal_name >> >> >> There is a bug in that if an empty list is returned, nothing is shown >> (T2-618) - worth checking if this is the case for these ports. >> >> >> >> Stuart says the workflow file indicates it's been made with an earlier >> nightly snapshot or beta 1 - Eddie, has there been any recent Moby >> changes that could affect this workflow? Is it worth trying to build >> it from scratch in beta 2? (looks like a big job!) >> I've been trying it in the 2.1 beta 1, and get the same results as Stian. After adding some extra output port to see whats happening above those ports - its appears that things are working correctly, and the various Parse_Moby_Data_*'s are returning results. Even putting some trace in the downstream list flatteners indicates that they are working correctly. So something appears to be going wrong between within the results pane for these flattened lists.
Stuart. >> When I connect up an output port from Gene2PubMed_Publication (before >> the parser that makes publication_.*) I do get lots of items like: >> >> <moby:MOBY xmlns:moby="http://www.biomoby.org/moby";> >> <moby:mobyContent> >> <moby:mobyData moby:queryID="a28"> >> <moby:Simple moby:articleName="publications"> >> <moby:Publication moby:id="11724772" moby:namespace="PMID"> >> <moby:String moby:id="" moby:namespace="" >> moby:articleName="Author">Seiji Murakami</moby:String> >> <moby:String moby:id="" moby:namespace="" >> moby:articleName="Author">Daisuke Iwaki</moby:String> >> <moby:String moby:id="" moby:namespace="" >> moby:articleName="Author">Hiroaki Mitsuzawa</moby:String> >> <moby:String moby:id="" moby:namespace="" >> moby:articleName="Author">Hitomi Sano</moby:String> >> <moby:String moby:id="" moby:namespace="" >> moby:articleName="Author">Hiroki Takahashi</moby:String> >> <moby:String moby:id="" moby:namespace="" >> moby:articleName="Author">Dennis R Voelker</moby:String> >> <moby:String moby:id="" moby:namespace="" >> moby:articleName="Author">Toyoaki Akino</moby:String> >> <moby:String moby:id="" moby:namespace="" >> moby:articleName="Author">Yoshio Kuroki</moby:String> >> <moby:String moby:id="" moby:namespace="" >> moby:articleName="Year">2002</moby:String> >> <moby:String moby:id="" moby:namespace="" >> moby:articleName="Abstract">Pulmonary surfactant protein A (SP-A) >> plays an important role in modulation of the innate immune system of >> the lung. Peptidoglycan (PGN), a cell wall component of Gram-positive >> bacteria, is known to elicit excessive proinflammatory cytokine >> production from immune cells. In this study we investigated whether >> SP-A interacts with PGN and alters PGN-elicited cellular responses. >> Binding studies demonstrate that PGN is not a ligand for SP-A. >> However, SP-A significantly reduced PGN-elicited tumor necrosis factor >> alpha (TNF-alpha) secretion by U937 cells and rat alveolar >> macrophages. The inhibitory effect on TNF-alpha secretion was >> dependent upon SP-A concentrations in physiological range. >> Coincubation of SP-A and PGN with human embryonic kidney 293 cells >> that had been transiently transfected with the cDNA of Toll-like >> receptor 2 (TLR2), a cell signaling receptor for PGN, significantly >> attenuated PGN-induced nuclear factor-kappaB activity. SP-A directly >> bound to a soluble form of the recombinant extracellular TLR2 domain >> (sTLR2). Coincubation of sTLR2 with SP-A significantly reduced the >> binding of sTLR2 to PGN. These results indicate that the direct >> interaction of SP-A with TLR2 alters PGN-induced cell signaling. We >> propose that SP-A modulates inflammatory responses against the >> bacterial components by interactions with pattern-recognition >> receptors.</moby:String> >> <moby:String moby:id="" moby:namespace="" >> moby:articleName="Title">Surfactant protein A inhibits >> peptidoglycan-induced tumor necrosis factor-alpha secretion in U937 >> cells and alveolar macrophages by direct interaction with toll-like >> receptor 2.</moby:String> >> <moby:String moby:id="" moby:namespace="" >> moby:articleName="Journal">The Journal of biological >> chemistry</moby:String> >> </moby:Publication> >> </moby:Simple> >> </moby:mobyData> >> </moby:mobyContent> >> </moby:MOBY> >> >> >> So it seems there might be a problem in the Moby parser. >> >> >> On Thu, Jul 9, 2009 at 10:10, Stian >> Soiland-Reyes<[email protected]> wrote: >> >>> On Wed, Jul 8, 2009 at 18:25, Mark Wilkinson<[email protected]> wrote: >>> >>> >>>> Another oddity just popped-up. Probably best if you run this workflow >>>> yourselves to see the problem (attached) - use input "hsa:7097" as the >>>> value >>>> for the input "id" slot. >>>> >>>> About half of the output bins contain no data, though the output of the >>>> node >>>> that feeds into that bin is clearly full and happy... I can't see any >>>> obvious difference between the bins that contain data and the bins that >>>> don't... >>>> >>> I had a similar problem the other day - some of the output ports >>> didn't show the result values - but when I clicked for the >>> intermediate results of the processor feeding to that port, there's >>> output there. Also if I add a dummy processor in the middle (Echo >>> list) before the workflow output port, then I do get to see the value. >>> >>> In the workflow I used the outputs came from an XML splitter, so all >>> the values should have come.. >>> >>> The workflow I used was using a caGrid plugin, so there's not much >>> point in sharing it here, but I can try to find a similar one. >>> >>> >>> Could it possibly have something to do with the 'Workflow finished' >>> sign? Do the output bins (good name, Mark!) stop receiving the outputs >>> at some point? >>> >>> >>> >>> I can replicate the empty bins, but I have no idea what KEGG ID to use >>> as no example was provided, I tried using "path:hsa05216". What I find >>> is that most of the processors don't seem to have run (they are not >>> greyed out) - but it still says 'Workflow complete'. >>> >>> Could there be something with error handling within the BioMoby >>> activity that is not working as expected? >>> >>> (Note developers - as this is a Moby workflow it's affected by T2-602 >>> and intermediate values don't work) >>> >>> It seems everything from ConvertSnp2EntrezGeneID and below don't run - >>> but I don't get any warnings or errors on the console, even though >>> I've turned up logging. >>> >>> We would need to run this one through a debugger to see what is really >>> going on.. I'll see if anyone here has time to do that. >>> >>> I've created a bug: http://www.mygrid.org.uk/dev/issues/browse/T2-694 >>> >>> >>> BTW Mark - why did you rename the workflow file from .t2flow to .xml ..? >>> >>> -- >>> Stian Soiland-Reyes, myGrid team >>> School of Computer Science >>> The University of Manchester >>> >>> >> >> -- >> Stian Soiland-Reyes, myGrid team >> School of Computer Science >> The University of Manchester >> >> > > > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------------ > Enter the BlackBerry Developer Challenge > This is your chance to win up to $100,000 in prizes! For a limited time, > vendors submitting new applications to BlackBerry App World(TM) will have > the opportunity to enter the BlackBerry Developer Challenge. 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