Merge pull request #12 from Sage-Bionetworks/synapser

Use synapser

DESCRIPTION

@@ -1,16 +1,18 @@
 Package: knit2synapse
 Type: Package
 Title: Knit RMarkdown to a Synapse Wiki page.
-Version: 0.0.0.9000
+Version: 0.1
 Date: 2015-04-27
 Authors@R: c(
     person("Brian", "Bot", email = "[email protected]", role = "cre"),
-    person("Kenneth", "Daily", email = "[email protected]", role = "aut"))
-Maintainer: Kenneth Daily <[email protected]>
+    person("Kenneth", "Daily", email = "[email protected]", role = "aut"),
+    person("Thanneer", "Perumal", email = "[email protected]", role = "aut"))
+Maintainer: Kenneth Daily <[email protected]>
 Description: Knit RMarkdown to Synapse Wiki page.
 License: CC0
 Imports: knitr,
     RCurl,
     stringr,
     tools,
-    synapseClient
+    synapser
+RoxygenNote: 6.0.1

NAMESPACE

@@ -1 +1,5 @@
-exportPattern("^[[:alpha:]]+")
+# Generated by roxygen2: do not edit by hand
+
+export(createAndKnitToFileEntity)
+export(createAndKnitToFolderEntity)
+export(knitfile2synapse)

R/knitfile2synapse.R

@@ -26,7 +26,7 @@ knitfile2synapse <- function(file, owner, parentWikiId=NULL, wikiName=NULL, over
 
   ## IF OWNER IS CHARACTER, TRY TO GET FROM SYNAPSE
   if( is.character(owner) & length(owner) == 1 ){
-    owner <- synapseClient::synGet(owner, downloadFile=FALSE)
+    owner <- synapser::synGet(owner, downloadFile=FALSE)
   }
 
   #####
@@ -66,42 +66,32 @@ knitfile2synapse <- function(file, owner, parentWikiId=NULL, wikiName=NULL, over
   } else {
     stop(sprintf("markdown file %s does not exist at this location: %s", basename(mdName), mdName))
   }
-    att <- list.files(knitPlotDir, full.names=TRUE)
-
+  att <- as.list(list.files(knitPlotDir, full.names=TRUE))
+
+  ## New wiki page
+
+  newWiki <- synapser::Wiki(owner=owner,
+                            title=wikiName,
+                            markdownFile=mdFile,
+                            attachments=att,
+                            parentWikiId=as.character(parentWikiId))
   ## Create/retrieve and store Wiki markdown to Synapse
-  w <- try(synapseClient::synGetWiki(owner),silent=T)
+  w <- try(synapser::synGetWiki(owner),silent=T)
 
   ## create new wiki if doesn't exist
-  if (class(w) == 'try-error') {
-    w <- synapseClient::WikiPage(owner=owner,
-                                 title=wikiName,
-                                 markdown=readChar(mdFile, file.info(mdFile)$size))
-  # delete existing wiki along with history
+  if (class(w)[1] == 'try-error') {
+    w <- newWiki
+    # delete existing wiki along with history
   } else if (overwrite) {
-    w <- synapseClient::synGetWiki(owner)
-    w <- synapseClient::synDelete(w)
-    w <- synapseClient::WikiPage(owner=owner,
-                                 title=wikiName,
-                                 markdown=readChar(mdFile, file.info(mdFile)$size))
+    w <- synapser::synDelete(w)
+    w <- newWiki
     # update existing wiki
   } else {
-    w <- synapseClient::synGetWiki(owner)    
-    w@properties$title <- wikiName
-    w@properties$markdown <- readChar(mdFile, file.info(mdFile)$size)
-  }
-
-  ## Add the attachments
-  if (length(att) > 0 ){
-    w@attachments <- as.list(att)
-  }
-
-  ## Set the parent wiki id, if one provided
-  if(!is.null(parentWikiId)){
-    w@properties$parentWikiId <- parentWikiId
+    w <- newWiki
   }
 
   ## Store to Synapse 
-  w <- synapseClient::synStore(w)
+  w <- synapser::synStore(w)
 
   # Undo changes to options
   knitr::opts_chunk$restore(old_knitr_opts)
@@ -111,56 +101,45 @@ knitfile2synapse <- function(file, owner, parentWikiId=NULL, wikiName=NULL, over
   return(w)
 }
 
-#' storeAndKnitToFileEntity
+#' 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 owner A Synapse entity (or Synapse ID of an entity) 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). 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
-storeAndKnitToFileEntity <- function(file, parentId, fileName=NULL, owner=NULL, parentWikiId=NULL,
-                                     wikiName=NULL, overwrite=FALSE, knitmd=TRUE, ...) {
+createAndKnitToFileEntity <- function(file, parentId, fileName=NULL, wikiName=NULL, overwrite=FALSE, knitmd=TRUE, ...) {
 
-  if (is.null(owner)) {
-    entity <- synapseClient::File(file, parentId=parentId, name=fileName)
-    entity <- synapseClient::synStore(entity, ...)
-    owner <- entity
-  }
-
-  knitfile2synapse(file=file, owner=owner, parentWikiId=parentWikiId, wikiName=wikiName,
+  entity <- synapser::File(file, parentId=parentId, name=fileName)
+  entity <- synapser::synStore(entity, ...)
+
+  knitfile2synapse(file=file, owner=entity, wikiName=wikiName,
                    overwrite=overwrite, knitmd=knitmd)
 }
 
-#' knitToFolderEntity
+#' 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 owner A Synapse entity (or Synapse ID of an entity) which will own the resulting WikiPage (usually a synapseClient::Project, synapseClient::Folder, or synapseClient::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). 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
-knitToFolderEntity <- function(file, parentId, folderName, owner=NULL, parentWikiId=NULL,
-                               wikiName=NULL, overwrite=FALSE, knitmd=TRUE, ...) {
+createAndKnitToFolderEntity <- function(file, parentId, folderName,
+                                        wikiName=NULL, overwrite=FALSE, knitmd=TRUE, ...) {
 
-  if (is.null(owner)) {
-    entity <- synapseClient::Folder(parentId=parentId, name=folderName)
-    entity <- synapseClient::synStore(entity, ...)
-    owner <- entity
-  }
-
-  knitfile2synapse(file=file, owner=owner, parentWikiId=parentWikiId, wikiName=wikiName,
+  entity <- synapser::Folder(parentId=parentId, name=folderName)
+  entity <- synapser::synStore(entity, ...)
+
+  knitfile2synapse(file=file, owner=entity, wikiName=wikiName, 
                    overwrite=overwrite, knitmd=knitmd)
 }

README.md

@@ -1,8 +1,16 @@
 ## knit2synapse: Knit RMarkdown files to Synapse wikis.
 
+> This version has [synapser](https://github.com/Sage-Bionetworks/synapser) as a dependency. The last version of this package to use the [rSynapseClient](https://github.com/Sage-Bionetworks/rSynapseClient) is `v0.1`. 
+
 ### Installing
 
-Using `devtools`:
+First, install the `synapser` package:
+
+```
+install.packages("synapser", repos=c("https://sage-bionetworks.github.io/staging-ran", "http://cran.fhcrc.org"))
+```
+
+The, using `devtools`:
 
 ```
 devtools::install_github("Sage-Bionetworks/knit2synapse")

knit2synapse.Rproj

@@ -15,4 +15,4 @@ LaTeX: pdfLaTeX
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
-PackageRoxygenize: rd
+PackageRoxygenize: rd,collate,namespace,vignette