Place these two files in the ./lib directory of your Taverna installation. Be sure that this modified version of the JRClient is before the original version in the java classpath. If you don't know how to do this, you can simply delete the old JRClientXXX.jar file in the ./lib directory, since the new one is backwards compatible with the original library.
The R scripts can be executed on an external server. It is also possible to executed them localy. Therefore, you need a local installation of R and an installation of the Rserve server. These can be found below:
| The factory for making Rshell processes is available in the service explorer, which is the frame with the title "Available Services". To create a new Rshell process, select the Rshell symbol and drag it to the "Advanced model explorer". |  |
| For setting the script, adding ports or modifying connection settings, the Rshell needs to be configured. In order to do this, right-click on the Rshell process in the "Advanced Model Explorer" and select "Configure Rshell...". |  |
| The script-tab is used for typing the R-script to be executed by the Rshell process. The script can be typed manually, or can be read from an R-file (ending with ".R"). The input and output variables do not have to be declared here, since this is done in the input port tab and output port tab. In our example, the Rshell generates a list of random numbers. The length of the list is equal to numberOfRandomValues. |  |
| To add a new input port, click on the "Create input port" button. Now, a popup box will appear, where one can enter the port name. When the name is entered, the created port will appear in the port table. |  |
| By default, a port is of type "R-expression". To modify the type, one can click on the current port type. Now, a drop-down list will appear. One can select one of the types in this drop-down list. |  |
| Output ports are used for passing data to other processes in Taverna. They represent the processors output. Creating and modifying the output port is done in the same way as input ports are created adn modified. The name of the output port is also the variable representing the output port. Only the last assignment to the variable representing the output port is passed to the Taverna. |  |
| By default, the Rshell is configured for making connections
with a Rserv on the same computer, in other words localhost. It can
be the case that the Rserve is on another system. Then one has to
change the connection settings.
The connection settings are:
Besides these settings, there is an option called "Keep session alive". If this option is selected, then for all Rshell processes where this option is selected and which have the same connection settings, including username and password, share the same connection. The connection will be closed when all running workflows are finished. This option is usefull to keep and to reuse variables stored at the Rserve. Normally when a connection is closed, all variables are thrown away or in other words, the session is closed. This can be used to prevent transfering huge amounts of data between Rshell processes. When a Rshell A process needs variables created in an other Rshell, named it B, then one needs to add a constraint between the processes A and B. This constraint prevents process A being executed before process B is finished. |
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| Rshell supports transfering images to Taverna. This is done using normal ports. To do this, a port needs to be added with the name corresponding to the image. |  |
An example of the script is given below:
png(PNGRandomPlot); plot(rnorm(1:100)); dev.off()
The result of the script is given in the image below.
