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!) 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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