comparison w4mcorcov_input.R @ 5:50f60f94c034 draft

planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f

4:8bba31f628da

       || ! ( xcms_data_type %in% c("sampleMetadata", "variableMetadata", "dataMatrix") ) 
  ) {
    my_failure_action( sprintf("bad parameter xcms_data_type '%s'", xcms_data_type) )
    return ( FALSE )
  }
  if ( is.character(xcms_data_in) ){
    # case: xcms_data_in is a path to a file
    xcms_data_input_env <- read_data_frame( xcms_data_in, sprintf("%s input", xcms_data_type) )
    if (!xcms_data_input_env$success) {
      my_failure_action(xcms_data_input_env$msg)
      return ( FALSE )
    }
    return ( xcms_data_input_env$data )
    # commenting out pasted code that is not tested here
    # } else if ( is.data.frame(xcms_data_in) || is.matrix(xcms_data_in) ) {
    #   # case: xcms_data_in is a data.frame or matrix
    #   return(xcms_data_in)
    # } else if ( is.list(xcms_data_in) || is.environment(xcms_data_in) ) {
    #   # NOTE WELL: is.list succeeds for data.frame, so the is.data.frame test must appear before the is.list test
    #   # case: xcms_data_in is a list
    #   if ( ! exists(xcms_data_type, where = xcms_data_in) ) {
    #     my_failure_action(sprintf("%s xcms_data_in is missing member '%s'"), ifelse(is.environment(xcms_data_in),"environment","list"), xcms_data_type)
    #     return ( FALSE )
    #   }
    #   prospect <- getElement(name = xcms_data_type, object = xcms_data_in)
    #   if ( ! is.data.frame(prospect) && ! is.matrix(prospect) ) {
    #     utils::str("list - str(prospect)")
    #     utils::str(prospect)
    #     if ( is.list(xcms_data_in) ) {
    #       my_failure_action(sprintf("the first member of xcms_data_in['%s'] is neither a data.frame nor a matrix but is a %s", xcms_data_type, typeof(prospect)))
    #     } else {
    #       my_failure_action(sprintf("the first member of xcms_data_in$%s is neither a data.frame nor a matrix but is a %s", xcms_data_type, typeof(prospect)))
    #     }
    #     return ( prospect )
    #   }
    #   # stop("stopping here for a snapshot")
    #   return ( prospect ) 
  } else {
    # case: xcms_data_in is invalid
    my_failure_action( sprintf("xcms_data_in has unexpected type %s", typeof(xcms_data_in)) )
    return ( FALSE )
  }

5:50f60f94c034

       || ! ( xcms_data_type %in% c("sampleMetadata", "variableMetadata", "dataMatrix") ) 
  ) {
    my_failure_action( sprintf("bad parameter xcms_data_type '%s'", xcms_data_type) )
    return ( FALSE )
  }
  if ( is.character(xcms_data_in) ) {
    # case: xcms_data_in is a path to a file
    xcms_data_input_env <- read_data_frame( xcms_data_in, sprintf("%s input", xcms_data_type) )
    if (!xcms_data_input_env$success) {
      my_failure_action(xcms_data_input_env$msg)
      return ( FALSE )
    }
    return ( xcms_data_input_env$data )
  } else {
    # case: xcms_data_in is invalid
    my_failure_action( sprintf("xcms_data_in has unexpected type %s", typeof(xcms_data_in)) )
    return ( FALSE )
  }