Dear Stian, reply is in line:
> Should we raise that as a new Jira issue? yes, thanks. > I propose support for input overrides should be in the order: > -inputbundle > -inputdoc > -inputfile > -inputvalue > ? Sounds good. Best regards, Simone. ----- Messaggio originale ----- Da: "Stian Soiland-Reyes" <[email protected]> A: "Simone Bnà" <[email protected]> Cc: "Apache Dev" <[email protected]>, "VPHHF" <[email protected]> Inviato: Giovedì, 9 giugno 2016 9:13:28 Oggetto: Re: baclava port value overriding Hi! I think what you are describing is a new feature - currently the Taverna server and the command line will use the baclava / -inputdoc option "as gospel" and ignore any individual parameters set. Should we raise that as a new Jira issue? So you would have to either set each of the remaining inputs individually (but then no longer being able to do list of lists, etc), or hand-cook a modified baclava document to include the downloaded data - note that Baclava uses base64-encoding so this could get a bit big depending on the file. Adding support for this in our code would perhaps be a better solution.. Relevant Taverna 3 code: See https://github.com/apache/incubator-taverna-commandline/blob/master/taverna-commandline-common/src/main/java/org/apache/taverna/commandline/data/InputsHandler.java Note that this code in Taverna 3 expects a Data Bundle ZIP with -inputbundle, rather than a baclava document with -inputdoc. Support for Baclava (reintroducing -inputdoc) could be added there, and could use https://github.com/apache/incubator-taverna-language/blob/master/taverna-baclava-language/src/main/java/org/apache/taverna/baclava/BaclavaReader.java I propose support for input overrides should be in the order: -inputbundle -inputdoc -inputfile -inputvalue ? Being able to reference an input by URL from within the input document would probably help your use-case; which the Data Bundle support in Taverna 3 can already handle if you register it with https://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/databundle/DataBundles.html#setReference-java.nio.file.Path-java.net.URI- e.g. something like: try (Bundle b = DataBundles.createBundle()) { Path inputs = DataBundles.getInputs(b); Path portA = DataBundles.getPort(inputs, "thatone"); DataBundles.setReference(portA, URI.create("http://example.com/file.txt";)); DataBundles.closeAndSaveBundle(b, Paths.get("/home/alice/input.bundle.zip")); } On 8 June 2016 at 14:52, Simone Bnà <[email protected]> wrote: > Dear Taverna team, > > I developed a middleware for taverna that receives a baclava file as input. > > The middleware parses the baclava and if a port value is a URL it downloads > the file corresponding to that URL > and upload it to taverna using a POST request to "rest/runs/<uuid>/wd/IN". > > Then, I upload the baclava as is and make a PUT to > "rest/runs/<uuid>/input/baclava". > > In the next step I override the port value specified in the baclava as a URL > with the file description > making a PUT request to "rest/runs/<uuid>/input/input/<filename>" (payload > == """<t2sr:runInput > xmlns:t2sr="http://ns.taverna.org.uk/2010/xml/server/rest/";> > <t2sr:file>%s</t2sr:file> </t2sr:runInput>""" % filename ) > > What I noticed is that the overriding of the port does not work. The values > specified in the baclava are always evaluated during the run. > > If I do not make the PUT request to "rest/runs/<uuid>/input/baclava" the > update of the port is performed > but the other values specified in the baclava are not evaluated at all. > > > My question is: > > how can I override some port values reported in the baclava file using a REST > API and > telling taverna to take the port values in the baclava file if they are not > overridden? > > > Best regards, > > Simone. > > -- > Simone Bnà, PhD > C++ Software Developer, CINECA > Via Magnanelli 6/3, 40033 Casalecchio di Reno, Italy > office: +39-0516171938 > email: [email protected]/[email protected] -- Stian Soiland-Reyes Apache Taverna (incubating) http://orcid.org/0000-0001-9842-9718 -- Simone Bnà, PhD C++ Software Developer, CINECA Via Magnanelli 6/3, 40033 Casalecchio di Reno, Italy office: +39-0516171938 email: [email protected]/[email protected]
