Interface RExecutor

    • Method Detail

      • getName

        String getName()
        Get the name of the RExecutor.
        Returns:
        the name of the RExecutor
      • openConnection

        void openConnection()
                     throws IOException
        Open the connection.
        Throws:
        IOException - if an error occurs while opening the connection
      • closeConnection

        void closeConnection()
                      throws IOException
        Close the connection.
        Throws:
        IOException - if an error occurs while closing the connection
      • putInputFile

        void putInputFile​(DataFile inputFile)
                   throws IOException
        Put a file for the analysis.
        Parameters:
        inputFile - the input file
        Throws:
        IOException - if an error occurs while putting the file
      • putInputFile

        void putInputFile​(DataFile inputFile,
                          String outputFilename)
                   throws IOException
        Put a file.
        Parameters:
        inputFile - the file to put
        outputFilename - the output filename
        Throws:
        IOException - if an exception occurs while putting a file
      • writerFile

        void writerFile​(String content,
                        String outputFilename)
                 throws IOException
        Write a file.
        Parameters:
        content - the content of the file
        outputFilename - the output filename
        Throws:
        IOException - if an exception occurs while writing a file
      • executeRScript

        void executeRScript​(String rScript,
                            boolean sweave,
                            String sweaveOutput,
                            boolean saveRscript,
                            String description,
                            DataFile workflowOutputDir,
                            String... scriptArguments)
                     throws IOException
        Execute a R script.
        Parameters:
        rScript - the source of the script to execute
        sweave - true if the script is a Sweave script
        sweaveOutput - Sweave output file
        saveRscript - true to keep the R script
        description - description of the R script
        workflowOutputDir - workflow output directory
        scriptArguments - script arguments
        Throws:
        IOException - if an error occurs while executing the script
      • removeInputFiles

        void removeInputFiles()
                       throws IOException
        Remove input files.
        Throws:
        IOException - if an error occurs while removing the files
      • getOutputFiles

        void getOutputFiles()
                     throws IOException
        Get the output files of the analysis
        Throws:
        IOException - if an error occurs while getting the output files