LineWise-class: Class '"LineWise"'
In tgirke/systemPipeR: systemPipeR: Workflow Environment for Data Analysis and Report Generation

LineWise-class

R Documentation

Class `"LineWise"`

Description

S4 class container for storing R-based code for a workflow step. LineWise class instances are constructed by the LineWise function, based on the R-based code, step name, and dependency tree. When the container is built from the R Markdown, using importWF function, two other slots are populated: codeChunkStart and rmdPath. codeChunkStart will store the first line of each R chunk, and rmdPath will store the R Markdown file path.

Usage

## Constructor

LineWise(code, step_name = "default", codeChunkStart = integer(), 
            rmdPath = character(), dependency="", 
            run_step = "mandatory",
            run_session = "management", 
            run_remote_resources = NULL)

Arguments

`code`	R code separated either by a semi-colon (`\;`), or by a newline, and enclosed by braces (`{ }`).
`step_name`	character. Step name needs to be unique and is required when appending this step to the workflow.
`codeChunkStart`	integer. R Markdown code chunk line start. This element will be populated when the object is built by `importWF`.
`rmdPath`	character. Path of R Markdown file used by `importWF`.
`dependency`	character. Dependency tree, required when appending this step to the workflow. Character name of a previous step in the workflow. Default is empty string `""`.
`run_step`	character. If the step has "mandatory" or "optional" flag for the execution.
`run_session`	character. If the step has "management" or "compute" flag for the execution.
`run_remote_resources`	`List` for reserving for each cluster job sufficient computing resources including memory (Megabyte), number of nodes, CPU cores, walltime (minutes), etc. It is necessary two aditional files: `conffile` and `template`. `conffile` is the path to conf file (default location `./.batchtools.conf.R`). This file contains in its simplest form just one command, such as this line for the Slurm scheduler: `cluster.functions <- makeClusterFunctionsSlurm(template="batchtools.slurm.tmpl")`. For more detailed information visit this page: https://mllg.github.io/batchtools/index.html `template` The template files for a specific queueing/scheduling systems can be downloaded from here: https://github.com/mllg/batchtools/tree/master/inst/templates. Slurm, PBS/Torque, and Sun Grid Engine (SGE) templates are provided

Objects from the Class

Objects can be created by calls of the form new("LineWise", ...).

Slots

codeLine:: Object of class "expression" storing R-based code.
codeChunkStart:: Object of class "interger" storing start line from the rmdPath file, when the "LineWise" is built from R Markdown.
stepName:: Object of class "character" storing step name.
dependency:: Object of class "list" storing dependency tree.
status:: Object of class "list" storing status steps.
files:: Object of class "list" storing file for R Markdown file and the file containing stdout and stderr after running the R-based code.
runInfo:: Object of class "list" storing all the runInfo information of the workflow

Functions and Methods

See 'Usage' for details on invocation.

Constructor:

LineWise:: Returns a LineWise object.

Accessors:

codeLine: Printing method for the CodeLine slot.
codeChunkStart: Extract start line of the R Markdown R chunk.
rmdPath: Extract Rmarkdown file path.
stepName: Extract the step name.
dependency: Extract the dependency tree.
status: Extract status of the step.
files: Extract log file path storing stdout and stderr after running step.
appendCodeLine<-: Replacement method for append a R code line.
replaceCodeLine<-: Replacement method for replace a R code line.

Methods:

[: Return a new LineWise object made of the selected R code lines.
[[: Extract the slot information from LineWine object.
[[<-: Replacement method for LineWine slots.
$: Extract slots elements by name.
length: Extract number of R-based code lines.
names: Extract slot names.
show: Summary view of LineWise elements.
coerce: signature(from = "LineWise", to = "list")as(LineWise, "list")
coerce: signature(from = "list", to = "LineWise")as(list, "LineWise")
linewise: Coerce back to list as(LineWise, "list")

Author(s)

Daniela Cassol

Examples

showClass("LineWise")
lw <- LineWise(code = {
              log_out <- log(10)
              },
              step_name = "R_log")

codeLine(lw)

## ImportWF option
file_path <- system.file("extdata/spr_simple_lw.Rmd", package="systemPipeR")
sal <- SPRproject(overwrite = TRUE)
# file_path <- "../inst/extdata/spr_simple_lw.Rmd"
sal <- importWF(sal, file_path)
sal <- runWF(sal)
lw2 <- sal$stepsWF[[2]]
lw2
names(lw2)
length(lw2)

## Accessors
codeLine(lw2)
codeChunkStart(lw2)
rmdPath(lw2)
stepName(lw2)
dependency(lw2)
status(lw2)
files(lw2)

## Replacement
appendCodeLine(lw2, after = 0) <- "log <- log(10)"
codeLine(lw2)
replaceCodeLine(lw2, 1) <- "plot(iris)"
codeLine(lw2)

## Coerce
lw2 <- linewise(lw2) ## OR lw2 <- as(lw2, "list") 
lw2 <- as(lw2, "LineWise")

tgirke/systemPipeR documentation built on Sept. 24, 2024, 9:48 a.m.