utility_functions/knitfile2synapse.R

In jgockley62/UW_RNASeq: Identify differentially expressed genes counts data

#' knitfile2synapseClient ' ' Allow users to leverage knitr when constructing Synapse Wiki content ' ' 
#@export ' @param file path to a local .Rmd file which to knit ' @param owner A Synapse object which will 
#own the resulting WikiPage (usually a Project, Folder, or File) ' @param parentWikiId If the resulting 
#WikiPage is to be a subpage of another WikiPage, this is the id for the parent WikiPage (NOTE: owner is 
#still required) ' @param wikiName A title for the resulting WikiPage - will default to the file name 
#without the .Rmd extension ' @param overwrite Only if owner specified and parentWikiId is NULL - flag for 
#whether or not to overwrite the previous root WikiPage (if it exists) ' @param knitmd Flag for whether or 
#not to knit; if false and file already exists, don't knit it again ' @return a synapseClient::WikiPage 
#object
knitfile2synapseClient <- function(file, owner, parentWikiId=NULL, wikiName=NULL, overwrite=FALSE, 
knitmd=TRUE){
  ## CHECK TO MAKE SURE FILE EXISTS
  file <- path.expand(file)
  if( !file.exists(file) ){
    stop(sprintf("file %s does not exist at this location:\n", basename(f), f))
  }
  
  ## IF NO WIKI NAME GIVEN, DEFAULT TO FILE NAME WITHOUT EXTENSION
  fName <- basename(tools::file_path_sans_ext(file))
  if( is.null(wikiName) ){
    wikiName <- fName
  }
  
  ## IF OWNER IS CHARACTER, TRY TO GET FROM SYNAPSE
  if( is.character(owner) & length(owner) == 1 ){
    owner <- syn_temp$get(owner, downloadFile=FALSE)
  }
  
  #####
  ## Set Synapse-specific markdown hooks
  #####
  knitr::render_markdown()
  
  ## Set plotting and knitr options
  old_knitr_opts <- knitr::opts_chunk$get()
  knitr::opts_chunk$set(tidy=FALSE, error=FALSE)
  
  old_knitr_hooks <- knitr::knit_hooks$get()
  knitr::knit_hooks$set(plot=hook_synapseMdSyntax_plot)
  
  ## Create temporary output directory for Markdown and plots If a cache directory exists, then do not 
  ## create a new one
  knitDir <- paste(tools::file_path_sans_ext(file),'cache',sep='_')
  if (!file.exists(paste(tools::file_path_sans_ext(file),'cache',sep='_')))
    dir.create(knitDir)
  
  ## Create plots directory
  knitPlotDir <- file.path(knitDir, "plots/")
  if (!file.exists(knitPlotDir))
    dir.create(knitPlotDir)
  knitr::opts_chunk$set(fig.path = knitPlotDir)
  
  ## File name
  mdName <- file.path(knitDir, paste(fName, ".md", sep=""))
  
  ## Knit file to markdown
  if (knitmd) {
    mdFile <- knitr::knit(file,
                          envir = parent.frame(n=2),
                          output = mdName)
  } else if (file.exists(mdName)) { # if knitmd is false check already markdown exists
    mdFile <- mdName
  } else {
    stop(sprintf("markdown file %s does not exist at this location: %s", basename(mdName), mdName))
  }
  att <- as.list(list.files(knitPlotDir, full.names=TRUE))
  
  # New wiki page
  
  # A quick fix for SYNR-1270/SYNPY-689 https://sagebionetworks.jira.com/browse/SYNPY-689 R-to-Python 
  # conversion of an empty list isn't working properly in the case that there are no attachments
  if(length(att) == 0) {
    
    newWiki <- synapseclient$Wiki(
                              owner=owner,
                              title=wikiName,
                              markdownFile=mdFile
                            )
  }
  else {
    
    #synapser::Wiki -> synapse$Wiki
    newWiki <- synapseclient$Wiki(
                              owner=owner,
                              title=wikiName,
                              markdownFile=mdFile,
                              attachments=att
                            )
  }
  ## Create/retrieve and store Wiki markdown to Synapse
  w <- try(syn_temp$getWiki(owner),silent=T)
  
  ## create new wiki if doesn't exist
  if (class(w)[1] == 'try-error') {
    w <- newWiki
    # delete existing wiki along with history
  } else if (overwrite && is.na(parentWikiId)) {
    w <- syn$delete(w)
    w <- newWiki
    # update existing wiki
  } else {
    w <- newWiki
  }
  
  ## Store to Synapse
  w <- syn_temp$store(w)
  
  # Undo changes to options
  knitr::opts_chunk$restore(old_knitr_opts)
  knitr::knit_hooks$restore(old_knitr_hooks)
  
  cat(paste("built wiki: '", wikiName, "'\n", sep=""))
  return(w)
}
#' createAndKnitToFileEntity ' ' Store a local RMarkdown file to Synapse and then knit it to that file's 
#WikiPage. ' ' @export ' @param file path to a local .Rmd file which to knit ' @param parentId A 
#synapseClient::Project or synapseClient::Folder entity (or Synapse ID of an entity) where the File will be 
#created ' @param fileName Name of the synapseClient::File to create ' @param wikiName A title for the 
#resulting WikiPage - will default to the file name without the .Rmd extension ' @param overwrite Only if 
#owner specified and parentWikiId is NULL - flag for whether or not to overwrite the previous root WikiPage 
#(if it exists). This will remove the history of changes for this Wiki page. ' @param knitmd Flag for 
#whether or not to knit; if FALSE and file already exists, don't knit it again ' @return a 
#synapseClient::WikiPage object
createAndKnitToFileEntityClient <- function(file, parentId, fileName=NULL, wikiName=NULL, overwrite=FALSE, 
knitmd=TRUE, ...) {
  
  entity <- syn_temp$store(
    synapseclient$File(
      name = folderName,
      parentId = parentId
    )
  )
  knitfile2synapseClient(file=file, owner=entity, wikiName=wikiName,
                   overwrite=overwrite, knitmd=knitmd)
}
#' createAndKnitToFolderEntity ' ' Create a Synapse Folder entity and knit a local RMarkdown file to it's 
#WikiPage. ' ' @export ' @param file path to a local .Rmd file which to knit ' @param parentId A 
#synapseClient::Project or synapseClient::Folder entity (or Synapse ID of an entity) where the Folder will 
#be created ' @param folderName Name of the synapseClient::Folder to create ' @param wikiName A title for 
#the resulting WikiPage - will default to the file name without the .Rmd extension ' @param overwrite Only 
#if owner specified and parentWikiId is NULL - flag for whether or not to overwrite the previous root 
#WikiPage (if it exists). This will remove the history of changes for this Wiki page. ' @param knitmd Flag 
#for whether or not to knit; if FALSE and file already exists, don't knit it again ' @return a 
#synapseClient::WikiPage entity object
createAndKnitToFolderEntityClient <- function(file, parentId, folderName,
                                        wikiName=NULL, overwrite=FALSE, knitmd=TRUE, ...) {
  entity <- syn_temp$store(
    synapseclient$Folder(
      name = folderName,
      parentId = parentId
    )
  )
  knitfile2synapseClient(file=file, owner=entity, wikiName=wikiName,
                   overwrite=overwrite, knitmd=knitmd)
}