Thanks for reporting this. I think the issue is in the executeworkflow command line tool, as I can replicate this with also with executeworkflow -inputfile - e.g. a Tool activity with "ls -al `pwd`/fred" will output in the Workbench:
lrwxrwxrwx 1 stain stain 17 Apr 27 10:52 /tmp/usecase2549370560835453456dir/fred -> /home/stain/2.ttl but run as executeworkflow fred.t2flow -inputfile fred /tmp/oa.html it will save a copy: -rw-rw-r-- 1 stain stain 171344 Apr 27 10:53 /tmp/usecase5592972701647292140dir/fred so it seems the command line is not providing the input files as File references for the Tool activity to recognize - thus Tool is forced to save them as new files. I think in Taverna 3 the file will actually be copied twice - once into the input DataBundle, and then out to the tool activity. Relevant code: https://github.com/apache/incubator-taverna-common-activities/blob/master/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/local/LocalUseCaseInvocation.java#L142 https://github.com/apache/incubator-taverna-commandline/blob/master/taverna-commandline-common/src/main/java/org/apache/taverna/commandline/CommandLineTool.java#L234 https://github.com/apache/incubator-taverna-commandline/blob/master/taverna-commandline-common/src/main/java/org/apache/taverna/commandline/data/InputsHandler.java#L168 2.5 code as well: https://github.com/apache/incubator-taverna-commandline/blob/old/taverna-commandline-1.5/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/InputsHandler.java#L190 Both of these seems to read the file into memory (!) - even though (in Taverna 3) setValue() supports File and URL forwarded on to DataBundles.setReference(). I think URL can then be converted back to File by Tool if it starts with file:/// - worth checking in ToolActivity. On 26 April 2016 at 22:39, Daniele Tartarini <[email protected]> wrote: > Hi, > > I am using a Taverna server to run a workflow based on Taverna tools > service. > > I can run execution correctly following the API here: > http://dev.mygrid.org.uk/wiki/display/tav250/Conceptual+Interface > > The test workflow is very simple, taking a single input file. > > I noted that when I upload to the server the input file using: > POST to > https://myserver.ac.uk/taverna-server/rest/runs/42d06756-b9c4-45ef-b69d-a141c69499be//wd/IN > > and then associating the port to the file using: > > PUT to > https://myserver.ac.uk/taverna-server/rest/runs/42d06756-b9c4-45ef-b69d-a141c69499be/input/input/input_file_text > with data > <t2sr:runInput xmlns:t2sr="http://ns.taverna.org.uk/2010/xml/server/rest/";> > <t2sr:file>IN/myfile.txt</t2sr:file> </t2sr:runInput> > > execution is correct but input files are copied from the > /tmp/42d06756-b9c4-45ef-b69d-a141c69499be > to the Taverna Tool service working folder 'usecase....dir' > > I would like to avoid this copy because I would be dealing to substantial > inputs and on a parameter sweep can affect performance. > > In Taverna Workbench this issue is solved in a elegant way using the "Set > File Location" tab in the form input window. Files are not copied but > replaced by symbolic links. > > *How can I achieve the same result via Taverna server API or a baclava (I > noted the Set file location information is not saved inside the baclava)?* > > I tried to use the Taverna server API setting the input as reference as > documented in: > http://dev.mygrid.org.uk/wiki/display/tav250/Conceptual+Interface section: > "Using a File Already on the Taverna Server Installation" > > Using: > PUT > https://myserver.ac.uk:8444/taverna-server/rest/runs/88f79b84-6451-4aed-b151-6b051328d922 > /input/input/input_file_text > > with data ({'content-type': 'application/xml'}): > > <t2sr:runInput xmlns:t2sr="http://ns.taverna.org.uk/2010/xml/server/rest/";> > <t2sr:reference> > > https://myserver.ac.uk:8444/taverna-server/rest/runs/88f79b84-6451-4aed-b151-6b051328d922/wd/IN/myfile.txt > </t2sr:reference> > </t2sr:runInput> > > > I get the following 403 error: filename may not be absolute > > *Any Idea how to solve both issues?* > > Many thanks in advance. > > Cheers > > Daniele > > > -- > -- > Daniele Tartarini > > Post-Doctoral Research Associate > Dept. Mechanical Engineering & > INSIGNEO, institute for *in silico* medicine, > University of Sheffield, Sheffield, UK > linkedIn <http://uk.linkedin.com/in/danieletartarini> -- Stian Soiland-Reyes Apache Taverna (incubating), Apache Commons RDF (incubating) http://orcid.org/0000-0001-9842-9718
