R/class-tool.R

In sevenbridges: Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R

# SBG extesion
.sbg.items <- c(
  "sbg:homepage",
  "sbg:validationErrors",
  "sbg:sbgMaintained",
  "sbg:latestRevision",
  "sbg:job",
  "sbg:toolAuthor",
  "sbg:copyOf",
  "sbg:createdOn",
  "sbg:categories",
  "sbg:contributors",
  "sbg:links",
  "sbg:project",
  "sbg:createdBy",
  "sbg:toolkitVersion",
  "sbg:id",
  "sbg:license",
  "sbg:revision",
  "sbg:cmdPreview",
  "sbg:modifiedOn",
  "sbg:modifiedBy",
  "sbg:revisionInfo",
  "sbg:revisionNotes",
  "sbg:toolkit",
  "sbg:projectId",
  "sbg:image_url",
  "sbg:appVersion",
  "sbg:projectName",
  "sbg:publisher",
  "cwlVersion",
  "appUrl",
  "x"
)

.sbg.fld <- gsub("sbg:", "", .sbg.items)

SBG <- setRefClass(
  "SBG",
  contains = "CWL",

  fields = list(
    "sbg:homepage" = "characterORNULL",
    "sbg:validationErrors" = "listORNULL",
    "sbg:sbgMaintained" = "logicalORNULL",
    "sbg:latestRevision" = "integerORNULL",
    "sbg:job" = "listORNULL",
    "sbg:toolAuthor" = "characterORNULL",
    "sbg:copyOf" = "characterORNULL",
    "sbg:createdOn" = "integerORNULL",
    "sbg:categories" = "characterORlistORNULL",
    "sbg:contributors" = "listORNULL",
    "sbg:links" = "listORNULL",
    "sbg:project" = "characterORNULL",
    "sbg:projectId" = "characterORNULL",
    "sbg:createdBy" = "characterORNULL",
    "sbg:toolkitVersion" = "characterORNULL",
    "sbg:id" = "characterORNULL",
    "sbg:license" = "characterORNULL",
    "sbg:revision" = "integerORNULL",
    "sbg:revisionNotes" = "characterORNULL",
    "sbg:cmdPreview" = "characterORNULL",
    "sbg:modifiedOn" = "integerORNULL",
    "sbg:modifiedBy" = "characterORNULL",
    "sbg:revisionsInfo" = "listORNULL",
    "sbg:toolkit" = "characterORNULL",
    "sbg:image_url" = "characterORNULL",
    "sbg:updateRevisionNotes" = "characterORNULL",
    "sbg:updateModifiedBy" = "characterORNULL",
    "sbg:update" = "characterORNULL",
    "sbg:appVersion" = "listORNULL",
    "sbg:projectName" = "characterORNULL",
    "sbg:publisher" = "characterORNULL",
    "cwlVersion" = "characterORNULL",
    "$namespaces" = "listORNULL",
    "sbg:expand_workflow" = "logicalORNULL",
    "doc" = "characterORNULL", # added in CWL v1.0
    "appUrl" = "characterORNULL",
    "sbg:wrapperAuthor" = "characterORNULL"
  ),

  methods = list(
    initialize = function(homepage = NULL,
                              validationErrors = NULL,
                              sbgMaintained = NULL,
                              latestRevision = NULL,
                              job = NULL,
                              toolAuthor = NULL,
                              copyOf = NULL,
                              createdOn = NULL,
                              categories = NULL,
                              contributors = NULL,
                              links = NULL,
                              project = NULL,
                              createdBy = NULL,
                              toolkitVersion = NULL,
                              id = NULL,
                              license = NULL,
                              revision = NULL,
                              cmdPreview = NULL,
                              modifiedOn = NULL,
                              modifiedBy = NULL,
                              revisionsInfo = NULL,
                              toolkit = NULL,
                              revisionNotes = NULL,
                              updateRevisionNote = NULL,
                              updateModifiedBy = NULL,
                              update = NULL,
                              appVersion = NULL,
                              projectName = NULL,
                              publisher = NULL,
                              cwlVersion = NULL,
                              namespaces = NULL,
                              expand_workflow = NULL,
                              doc = NULL,
                              appUrl = NULL,
                              wrapperAuthor = NULL,
                              ...) {
      args <- mget(names(formals()), sys.frame(sys.nframe()))
      nms <- names(args)
      for (nm in nms) .self$field(paste0("sbg:", nm), args[[nm]])

      callSuper(...)
    }
  )
)

#' Class Tool
#'
#' code{Tool} class extends \code{CommandLineTool}
#' with more seven bridges flabored fields the \code{SBG} class.
#' \code{obj$toJSON()}, \code{obj$toJSON(pretty = TRUE)} or
#' \code{obj$toYAML()} will convert a
#' \code{Tool} object into a text JSON/YAML file.
#'
#' @field context [character] by default:
#' \url{http://www.commonwl.org/draft-2/}
#' @field owner [list] a list of owner names.
#' @field contributor [list] a list of contributor names.
#'
#' @export Tool
#' @return a Tool object.
#' @exportClass Tool
#' @examples
#' t1 <- system.file("extdata/app", "tool_star.json", package = "sevenbridges")
#' # convert json file into a Tool object
#' t1 <- convert_app(t1)
#' # get input type information
#' t1$input_type()
#' # get output type information
#' t1$output_type()
#' # return a input matrix with more informtion
#' t1$input_matrix()
#' # return only a few fields
#' t1$input_matrix(c("id", "type", "required"))
#' # return only required
#' t1$input_matrix(required = TRUE)
#' # return everything
#' t1$input_matrix(NULL)
#' # return a output matrix with more informtion
#' t1$output_matrix()
#' # return only a few fields
#' t1$output_matrix(c("id", "type"))
#' # return everything
#' t1$output_matrix(NULL)
#' # get input id
#' t1$input_id()
#' # get full input id with Tool name
#' t1$input_id(TRUE)
#' # get output id
#' t1$output_id()
#' # get full output id
#' t1$output_id(TRUE)
#' # get required input id
#' t1$get_required()
#' # set input required
#' t1$set_required(c("#reads", "winFlankNbins"))
#' t1$get_required()
#' t1$set_required("reads", FALSE)
#' t1$get_required()
#' t1$get_input(name = "ins")
#' t1$get_input(id = "#winFlankNbins")
#' t1$get_output(name = "gene")
#' t1$get_output(id = "#aligned_reads")
#' # get a tool from a flow
#' f1 <- system.file("extdata/app", "flow_star.json", package = "sevenbridges")
#' # convert json file into a Tool object
#' f1 <- convert_app(f1)
#' t2 <- f1$get_tool("STAR$")
#' oid <- t2$get_input_port()
#' oid
#' # set new ports
#' t2$input_id()
#' t2$set_input_port("#chimScoreSeparation")
#' t2$get_input_port()
#' t2$set_input_port("#chimScoreSeparation", FALSE)
#' t2$get_input_port()
#' # run the tool locally with example data
#' \dontrun{
#' t3 <- system.file("extdata/app/dna2protein", "translate.cwl.json", package = "sevenbridges")
#' t3 <- convert_app(t3)
#' fl <- system.file("extdata/app/dna2protein/data", "input.txt", package = "sevenbridges")
#' set_test_env("dind", "tengfei/testenv", "~/mounts")
#' t3$input_type()
#' t3$run(list(input_file = Files(fl)))  # Not File}
Tool <- setRefClass(
  "Tool",
  contains = c("CommandLineTool", "SBG"),

  fields = list(
    context = "characterORNULL",
    x = "numericORNULL",
    y = "numericORNULL"
  ),

  methods = list(
    initialize = function(...,
                              id = NULL,
                              label = NULL,
                              inputs = NULL,
                              outputs = NULL,
                              x = NULL,
                              y = NULL) {
      stopifnot(!is.null(id))

      if (is.null(label)) {
        .label <- id
      } else {
        .label <- label
      }

      if (is(inputs, "InputParameterList") ||
        (is.list(inputs) &&
          all(sapply(inputs, is, "InputParameter")))) {
        if (is.list(inputs) &&
          all(sapply(inputs, is, "InputParameter"))) {
          inputs <<- IPList(inputs)
        }

        if (is(inputs, "InputParameterList")) {
          inputs <<- inputs
        }
      } else if (is.data.frame(inputs)) {
        lst <- lapply(1:nrow(inputs), function(i) {
          para <- as.list(inputs[i, ])
          lst <- lapply(para, function(x) {
            if (is.factor(x)) {
              return(as.character(x))
            } else {
              return(x)
            }
          })
          do.call(input, lst)
        })
        inputs <<- IPList(lst)
      } else if (is(inputs, "InputParameter")) {
        inputs <<- IPList(inputs)
      } else if (is.null(inputs)) {
        inputs <<- IPList()
      } else {
        stop("wrong inputs type")
      }
      # now inputs should be a IPList,
      # outputs
      if (is(outputs, "OutputParameterList") ||
        (is.list(outputs) &&
          all(sapply(outputs, is, "OutputParameter")))) {
        if (is.list(outputs) &&
          all(sapply(outputs, is, "OutputParameter"))) {
          outputs <<- OPList(outputs)
        }

        if (is(outputs, "OutputParameterList")) {
          outputs <<- outputs
        }
      } else if (is.data.frame(outputs)) {
        lst <- lapply(1:nrow(outputs), function(i) {
          para <- as.list(outputs[i, ])
          lst <- lapply(para, function(x) {
            if (is.factor(x)) {
              return(as.character(x))
            } else {
              return(x)
            }
          })
          do.call(output, lst)
        })
        outputs <<- OPList(lst)
      } else if (is(outputs, "OutputParameter")) {
        outputs <<- OPList(outputs)
      } else if (is.null(outputs)) {
        outputs <<- OPList()
      } else {
        stop("wrong output")
      }
      x <<- x
      y <<- y
      res <- callSuper(id = id, label = .label, ...)
      res$field("sbg:id", id)
      res
    },

    input_type = function() {
      "this return a vector of types, names of them are input id"
      getInputType(toList())
    },

    output_type = function() {
      "this return a vector of types, names of them are output id"
      getOutputType(toList())
    },

    input_matrix = function(new.order = c("id", "label", "type", "required", "prefix", "fileTypes"), required = NULL) {
      "This return a matrix of input parameters, by default, following the order id, label, type, required, prefix, fileTypes. new.order accept names of column you want to print, but it has to be a field of inputs. When its set to NULL, it prints all fields. When required = TRUE, only print required field."
      res <- suppressWarnings(as(inputs, "data.frame"))
      if (!is.null(required)) {
        stopifnot(is.logical(required))
        res <- res[res$required == required, ]
        if (!nrow(res)) {
          return(NULL)
        }
      }
      if (!is.null(new.order)) {
        new.order <- intersect(new.order, names(res))
        res[, new.order]
      } else {
        res
      }
    },

    output_matrix = function(new.order = c("id", "label", "type", "fileTypes")) {
      "This return a matrix of output parameters, by default, following the order id, label, type, fileTypes. new.order accept names of column you want to print, but it has to be a field of outputs. When its set to NULL, it prints all fields. when required = TRUE, only print required field."

      res <- suppressWarnings(as(outputs, "data.frame"))
      if (!is.null(new.order)) {
        new.order <- intersect(new.order, names(res))
        res[, new.order]
      } else {
        res
      }
    },

    input_id = function(full = FALSE, requiredOnly = FALSE) {
      "Get input id from a Tool, when full = TRUE, connect tool id with input id. e.g. If requiredOnly = TRUE, return required field only."
      tool.name <- get_id_from_label(label)
      if (requiredOnly) {
        idx <- sapply(inputs, function(i) {
          i$required
        })
        if (length(idx)) {
          .inputs <- inputs[idx]
        } else {
          return(NULL)
        }
      } else {
        .inputs <- inputs
      }
      res <- sapply(.inputs, function(i) {
        if (full) {
          res <- paste0(tool.name, ".", de_sharp(i$id))
          names(res) <- .make_type(i$toList()$type)
          res
        } else {
          res <- i$id
          names(res) <- tool.name
          res
        }
      })
      res
    },

    output_id = function(full = FALSE) {
      "Get output id from a Tool, when full = TRUE, connect tool id with input id."
      tool.name <- get_id_from_label(label)
      res <- sapply(outputs, function(o) {
        if (full) {
          res <- paste0(tool.name, ".", de_sharp(o$id))
          names(res) <- .make_type(o$toList()$type)
          res
        } else {
          res <- o$id
          names(res) <- tool.name
          res
        }
      })
      res
    },

    get_required = function() {
      "return required input fields types, names of them are input id"
      res <- unname(unlist(sapply(inputs, function(i) {
        if (i$required) {
          return(i$id)
        } else {
          return(NULL)
        }
      })))
      if (length(res)) {
        res <- de_sharp(res)
        it <- input_type()
        enms <- names(it)

        it[enms %in% res]
      } else {
        return(NULL)
      }
    },

    set_required = function(ids, required = TRUE) {
      "Set an input node required or not required. The first parameter takes single input id or more than one ids. The second parameters required is the value you want to set to inputs. TRUE means set to required."
      message("not implemented yet!")
      # iid <- input_id()
      # ids <- addIdNum(ids)
      # idx = ids %in% iid
      # if (any(!idx)) {
      #     stop("mistyped id name: ", paste(ids[!idx], collapse = " "))
      # }

      # sapply(match(ids, iid), function(id) {
      #
      #   if(required){
      #     if(!.is_required(inputs[[id]])){
      #       print(inputs[[id]]$type)
      #       inputs[[id]]$type <<- c(DSCList("null"), inputs[[id]]$type)
      #     }
      #   }else{
      #
      #     if(.is_required(inputs[[id]])){
      #       inputs[[id]]$type <<- inputs[[id]]$type[-1]
      #     }
      #   }
      # })
    },

    get_input_port = function() {
      "the inputs node with \\code{sbg:includeInPorts} equals \\code{TRUE}"
      res <- sapply(inputs, function(i) {
        if (is.null(i$"sbg:includeInPorts")) {
          return(FALSE)
        } else {
          return(i$"sbg:includeInPorts")
        }
      })
      idx <- which(res)
      if (length(idx)) {
        input_id()[idx]
      } else {
        return(NULL)
      }
    },

    set_input_port = function(ids, include = TRUE) {
      "Set inputs ports field sbg:includeInPorts to the value of include, default is TRUE."
      idx <- match(ids, input_id())
      if (length(idx)) {
        for (i in idx) {
          inputs[[i]]$"sbg:includeInPorts" <<- include
        }
      }
    },

    get_input = function(name = NULL, id = NULL) {
      "get input objects by names or id"
      if (is.null(name) && is.null(id)) {
        stop("please provide name or id")
      }

      if (!is.null(name)) {
        idx <- which(grepl(name, sapply(inputs, function(i) i$label)))
      }
      if (!is.null(id)) {
        idx <- which(id == sapply(inputs, function(i) i$id))
      }
      if (length(idx) == 0) {
        return(NULL)
      } else if (length(idx) == 1) {
        return(inputs[[idx]])
      } else if (length(idx) > 1) {
        return(inputs[idx])
      }
    },

    get_output = function(name = NULL, id = NULL) {
      "get output objects by names or id"
      if (is.null(name) && is.null(id)) {
        stop("please provide name or id")
      }

      if (!is.null(name)) {
        idx <- which(grepl(name, sapply(outputs, function(i) i$label)))
      }
      if (!is.null(id)) {
        idx <- which(grepl(id, sapply(outputs, function(i) i$id)))
      }
      if (length(idx) == 0) {
        return(NULL)
      } else if (length(idx) == 1) {
        return(outputs[[idx]])
      } else if (length(idx) > 1) {
        return(outputs[idx])
      }
    },

    copy_obj = function() {
      "this is a hack to make copy of reference cwl object"
      tmp <- tempfile()
      write(toJSON(pretty = TRUE), tmp)
      res <- convert_app(tmp)
      file.remove(tmp)
      res
    },
    run = function(run_inputs = list(), engine = c("bunny", "rabix", "cwlrun")) {
      "Run this tool with inputs locally. Engines supported: bunny, rabix, cwlrun. Inputs accept list or JSON."
      engine <- match.arg(engine)
      # convert
      run_inputs <- lapply(run_inputs, asTaskInput)
      switch(engine,
        bunny = {
          test_tool_bunny(.self, run_inputs)
        },
        cwlrun = {
          test_tool_cwlrun(.self, run_inputs)
        },
        rabix = {
          test_tool_rabix(.self, run_inputs)
        }
      )
    }
  )
)