R/dataenv.R

In tgirke/systemPipeRdata: systemPipeRdata: Workflow templates and sample data

#################################
## Obtain paths to sample data ##
#################################
pathList <- function() {
  list(
    targets=system.file("extdata/param", "targets.txt", package="systemPipeRdata", mustWork=TRUE),
    targetsPE=system.file("extdata/param", "targetsPE.txt", package="systemPipeRdata", mustWork=TRUE),
    annotationdir=system.file("extdata/annotation", "", package="systemPipeRdata", mustWork=TRUE),
    fastqdir=system.file("extdata/fastq", "", package="systemPipeRdata", mustWork=TRUE),
    bamdir=system.file("extdata/bam", "", package="systemPipeRdata", mustWork=TRUE),
    paramdir=system.file("extdata/param", "", package="systemPipeRdata", mustWork=TRUE)
  )
}
wf_name_map <- list(
  "chipseq" = "ChIP-seq",
  "new" = "New Empty Workflow",
  "riboseq" = "Ribosome Profiling",
  "rnaseq" = "RNA-seq",
  "SPblast" = "BLAST",
  "SPcheminfo" = "Chemical Informatics",
  "SPscrna" = "Single-cell RNA-seq",
  "varseq" = "Variant Calling"
)
#########################################
## Generate environments for workflows ##
#########################################
genWorkenvir <- function(
    workflow,
    mydirname=NULL,
    bam=FALSE
    # ref="master",
    # subdir=NULL,
    # url=NULL,
    # urlname=NULL
    ) {
  url <- NULL
  ## Input validity check
  if(FALSE) {
  # if(grepl("/", workflow)==TRUE) {
    ## if the package is defined it
    mydirname2 <- .genWorkenvirPKG(package_repo=workflow, ref=ref, subdir=subdir, mydirname=mydirname, build_env=TRUE, silent=TRUE)
    genWorkdata(path = mydirname2)
  } else {
    check_workflow <- dir(system.file("extdata/workflows", "", package="systemPipeRdata", mustWork=TRUE))
    workflow <- match.arg(workflow, check_workflow)
    if(workflow=="new" && is.null(mydirname)) warning("It is recommended to specify the workflow directory name, using 'mydirname' argument")
    if(all(!c(is.null(mydirname), is.character(mydirname)))) stop("mydirname can only be assigned 'NULL' or a character vector of length 1")
    if(is.null(mydirname)) {
      mydirname2 <- workflow
    } else {
      mydirname2 <- mydirname
    }
    ## Generate temp workflow directory
    mydirname2temp <- paste0(mydirname2, "_temp", paste(sample(0:9, 4), collapse=""))
    if(dir.exists(mydirname2) | dir.exists(mydirname2temp)) stop("Directory name assigned to 'mydirname' or its temp variant exists already. Please assign to 'mydirname' a different name or rename/delete existing one.")
    dir.create(mydirname2temp)
    ## Move workflow templates into workflow directory
    file.copy(system.file("extdata/workflows/", workflow, package="systemPipeRdata", mustWork=TRUE), mydirname2temp, recursive=TRUE)
    file.rename(paste0(normalizePath(mydirname2temp), "/", workflow), mydirname2) # generates final dir
    unlink(mydirname2temp, recursive=TRUE) # removes temp dir
    ## Moving data and param common files
    if(workflow != "new") {
      file.copy(normalizePath(list.files(pathList()$fastqdir, "*", full.names=TRUE)), paste0(mydirname2, "/data"), overwrite=TRUE, recursive=TRUE)
      file.copy(normalizePath(list.files(pathList()$annotationdir, "*", full.names=TRUE)), paste0(mydirname2, "/data"), overwrite=TRUE, recursive=TRUE)
    }
    file.copy(c(normalizePath(paste0(pathList()$paramdir, "/targetsPE.txt")), normalizePath(paste0(pathList()$paramdir, "/targets.txt"))), paste0(mydirname2, "/"))
    file.copy(c(paste0(pathList()$paramdir, "bibtex.bib")), paste0(mydirname2, "/bibtex.bib"), overwrite=TRUE)
    if(bam==TRUE) file.copy(normalizePath(list.files(pathList()$bamdir, "*", full.names=TRUE)), paste0(mydirname2, "/results"), overwrite=TRUE, recursive=TRUE)
    file.copy(pathList()$paramdir, paste0(mydirname2, "/"), recursive=TRUE)
    file.copy(c(file.path(pathList()$paramdir, "batchtools.slurm.tmpl"), file.path(pathList()$paramdir, ".batchtools.conf.R")), paste0(mydirname2, "/"))
  }
  # if(all(c(!is.null(url), is.null(urlname)))) stop("argument 'urlname' missing. The argument can only be assigned 'NULL' when no url is provided. The argument should be assigned as a character vector of length 1")
  # if(!is.null(url)){
  #   download.file(url=url, destfile = paste0("./", mydirname2, "/", urlname), quiet = TRUE)
  # }
  print(paste("Generated", mydirname2, "directory. Next run in", workflow, "directory, the R code from *.Rmd template interactively. Alternatively, workflows can be exectued with a single command as instructed in the vignette."))
}
## Usage:
#genWorkenvir(workflow="systemPipeR/SPvarseq", mydirname="varseq")
# genWorkenvir(workflow="systemPipeR/SPrnaseq", mydirname="rnaseq",
# url = "https://raw.githubusercontent.com/systemPipeR/systemPipeRNAseq/cluster/vignettes/systemPipeRNAseq.Rmd",
# urlname = "rnaseq_V-cluster.Rmd")

############################################
## Generate data/param for SPR_packages ##
############################################
genWorkdata <- function(path=getwd(), data=TRUE, param=TRUE){
  ## TODO: we can add a check if it is a spr_project
  suppressWarnings({
    data.path <- normalizePath(paste0(path, "/data/"))
    param.path <- normalizePath(paste0(path, "/param/"))
  })
  if(data==TRUE){
    if (dir.exists(data.path) == FALSE) (dir.create(data.path))
    file.copy(normalizePath(list.files(pathList()$fastqdir, "*", full.names=TRUE)), data.path, overwrite=TRUE, recursive=TRUE)
    file.copy(normalizePath(list.files(pathList()$annotationdir, "*", full.names=TRUE)), data.path, overwrite=TRUE, recursive=TRUE)
    print("The 'demo data'was successfully copied to your project.")
  }
  if (param==TRUE){
    if (dir.exists(param.path) == FALSE) (dir.create(param.path))
    file.copy(pathList()$paramdir, normalizePath(path), recursive=TRUE)
    print("The 'param' directory was successfully copied to your project.")
  }
  file.copy(c(file.path(pathList()$paramdir, "batchtools.slurm.tmpl"), file.path(pathList()$paramdir, ".batchtools.conf.R")), path)
}

## Usage:
# genWorkdata()

############################################
## Generate environments for SPR_packages ##
############################################
# This function installs packages from GitHub. Internally, it is used remotes::install_github(), which also requires remotes to be installed.
## Arguments
# package_repo Repository Github address in the format `username/repo`.
# ref Desired GitHub reference for the `"branch"` name. Default to `"master"`.
# subdir subdirectory within GitHub repo that contains the R package.
# mydirname Specifies the name of the workflow directory and the *Rmd file. Default is NULL, using the workflow/package name.
# build_env Internally the function uses rmarkdown::draft function to populate the directory with all the files,  the same way if it is used the Rstudio create a new file. Default is TRUE.
# silent If TRUE, suppress output.
# Details
# For an interactive() session, the readline() function is used to choose between `yes` or `no`.
# For non-interactive use, if there is no package install, the option YES will be chosen.

.genWorkenvirPKG <- function(package_repo, ref="master", subdir=NULL, mydirname=NULL, build_env=TRUE, silent=FALSE){
  ## Check if pkg is installed
  pkgs <- c("remotes", sub('.*/', '', package_repo))
  pkg_name <- sub('.*/', '', package_repo)
  pkg_req <- sapply(pkgs, function(x) !requireNamespace(x, quietly=TRUE))
  ## If 'mydirname' is NULL (default) use value assigned to 'pkg_name' as directory/*Rmd name
  if(is.null(mydirname)) {
    mydirname2 <- pkg_name
  } else {
    mydirname2 <- mydirname
  }
  ## Question
  if(any(pkg_req)) {
    ## For an interactive() session
    if(interactive()){
      pkg_install <- readline(cat("There is no package called", paste0(pkgs, collapse = " OR "), "\n",
                    "Would you like to install this package now? Type a number: \n 1. Yes \n 2. No \n"))
    } else {
      ## For an non-interactive session
      pkg_install <-"1"
    }
    print(paste("Installing package", pkg_name))
    for(i in which(pkg_req)){
      if (pkg_install == "1"){
        if (!requireNamespace("remotes", quietly=TRUE))
          install.packages("remotes", quiet = TRUE)
        remotes::install_github(repo=package_repo, ref=ref, subdir=subdir, quiet = TRUE, upgrade = "ask", build_vignettes=TRUE, dependencies=TRUE)
      } else if (pkg_install == 2)
        stop (paste("The", pkg_name, "package is required, you can install the package and come back later!"))
    }
  }
  print(paste("Package", pkg_name, "is successfully installed!"))
  if(build_env==TRUE){
    rmarkdown::draft(paste0(mydirname2, ".Rmd"), template = pkg_name, package = pkg_name, edit=FALSE)
    if(silent != TRUE) print(paste("Generated", mydirname2, "directory. Next run in", pkg_name, "directory, the R code from *.Rmd template interactively. Alternatively, workflows can be exectued with a single command as instructed in the vignette."))
  } else {
    dump <- "do nothing"
  }
  return(mydirname2)
}

## Usage:
# .genWorkenvirPKG(package_repo="systemPipeR/systemPipeRIBOseq")

############################################
## Check Workflow Templates Availability ##
############################################
# This function checks the workflow templates availability from systemPipeRdata package and
# also from GitHub.
## Arguments
# github if TRUE, it will return the available Workflow Templates packages from https://github.com/systemPipeR
## Note:
# We are assuming that workflow templates repositories under [systemPipeR Organization](https://github.com/systemPipeR/)
# content the keywords in the description "Workflow Template" and in "Topics" we expected "systempiper" and "release" or "development" words.

availableWF <- function(github = FALSE){
  check_workflow <- dir(system.file("extdata/workflows", "", package="systemPipeRdata", mustWork=TRUE))
  wf_list <- list(systemPipeRdata=check_workflow)
  if(github == TRUE){
    cat("Checking templates in systemPipeR GitHub, please wait ...\n")
    ## get all the repos
    tryCatch(get_repos <- jsonlite::fromJSON("https://api.github.com/orgs/systemPipeR/repos"),
         error = function(e){
           stop('You have reached the limit for GitHub API requests. The limit is 60 requests per hour.')
         }
    )
    WFrepos <- data.frame(workflow=get_repos$name, html=get_repos$html_url, description=get_repos$description)
    ## Keep repos with the right description
    WFrepos <- WFrepos[WFrepos$description %in% "Workflow Template", ]
    ## branches
    for(i in seq_along(WFrepos$workflow)){
      branches <- jsonlite::fromJSON(paste0("https://api.github.com/repos/systemPipeR/", WFrepos$workflow[i], "/branches"))$name
      WFrepos$branches[i] <- list(branches)
    }
    ## Searching for topics
    # release <- data.frame(workflow=jsonlite::fromJSON("https://api.github.com/search/repositories?q=topic:systempiper+topic:release")$items$name)
    devel <- data.frame(workflow=jsonlite::fromJSON("https://api.github.com/search/repositories?q=topic:systempiper+topic:development")$items$name)
    ## Merge topics and version
    WFrepos_devel <- cbind(merge(WFrepos, devel, by="workflow"), version=rep("devel"))
    # WFrepos_release <- cbind(merge(WFrepos, release, by="workflow"), version=rep("release"))
    ## final
    # WFrepos <- rbind(WFrepos_release, WFrepos_devel)
    WFrepos <- WFrepos_devel
    # WFrepos$workflow <- paste0("systemPipeR/", WFrepos$workflow)
    WFrepos <- WFrepos[c("workflow",  "html")]
    names(WFrepos) <- c("Workflow", "Download URL")
    WFrepos$`Download URL` <- paste0(WFrepos$`Download URL`, ".git")
    WFrepos <- WFrepos[!WFrepos$Workflow %in% c('SPrnaseq', 'SPchipseq', 'SPriboseq', 'SPvarseq', 'SPscrnaseq'), ]
    wf_list <- list(systemPipeRdata=check_workflow, github=WFrepos)
  }

  cat("Available Workflow Templates in systemPipeRdata:\n")
  cat("Name         Description\n")
  cat("------------------------------------\n")
  wf_name_map <- wf_name_map[wf_list$systemPipeRdata]
  cat(paste0(names(wf_name_map), strrep(" ", 12 - nchar(names(wf_name_map)) + 1), wf_name_map), sep = "\n")
  # cat(paste(names(wf_name_map), collapse = "\n"), sep = "")
  if(!is.null(wf_list$github)) {
    cat("Experimental Workflow Templates in systemPipeR GitHub Organization:\n")
    print(wf_list$github)
    cat("------------------------------------\n")
    cat("To install a workflow template from GitHub, use:\n")
    cat("git clone <URL>\n")
    cat("e.g. git clone https://github.com/systemPipeR/SPatacseq.git\n")
  }
  return(invisible(wf_list))
}

## Usage:
# availableWF()
# availableWF(github = TRUE)