Hi Donal! Thanks for looking into this.
Unfortunately, these strings come from input examples in workflows (from myExperiment) so I don't really have access to the initial strings. Of course I could change them internally. Having said that, passing: 'transmembrane proteins' AND amyloid gives the same results as: transmembrane proteins AND amyloid thus not what we want. That is the case in both the workbench and via the API of the client. The intended input: "transmembrane proteins" AND amyloid only seems to work from the workbench. Is some kind of escaping taking place that makes the beanshell happy which doesn't happen from the client? Cheers, Kostas On 28 February 2011 17:41, Donal K. Fellows <[email protected]> wrote: > On 28/02/2011 11:08, Kostas Karasavvas wrote: >> >> I do not really put the parameters from the prompt but using the >> run.set_input method. >> >> What makes sense is passing just: "transmembrane proteins" AND amyloid >> No escaping should be necessary (as far as I can tell). However, that >> produces the error I included at the end of the email. >> >> Would it be possible to see how the workbench code escapes the double >> quotes? Or to see exactly why that beanshell script fails? > > I've investigated this, and I can say that the value is getting conveyed > into the CommandLineLauncher class as exactly one argument without extra > quoting, but I don't know the Taverna sources well enough to trace what > happens after that. If anyone is testing, the easiest method is to add > 'single quotes' around any values passed in, as that disables all shell > mangling of the contents. > > Donal (v. puzzled by all this). > ------------------------------------------------------------------------------ Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev _______________________________________________ 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/
