add Rd files

DESCRIPTION

@@ -8,7 +8,7 @@ Maintainer: Kimyen Ladia <kimyen.ladia@sageabse.org>
 Description: Provides convenience R functions for interacting with Synapse.
 License: Apache License 2.0
 Encoding: UTF-8
-Depends: synapser (>= 0.1.25)
+Depends: synapser (>= 0.2)
 Suggests: testthat, knitr, rmarkdown
 URL: https://www.sagebase.org
 BugReports: https://github.com/Sage-Bionetworks/synapserutils/issues

R/shared.R

@@ -0,0 +1,8 @@
+.getSynapseUtilsFunctionInfo <- function(rootDir) {
+  pyImport("synapseutils")
+  pyExec("info = functionInfo.functionInfo(synapseutils)")
+  functionInfo <- pyGet("info")
+  result <- lapply(X = functionInfo, function(x) {
+    list(name = x$name, synName = x$name, functionContainerName = "synapseutils", args = x$args, doc = x$doc, title = x$name)
+  })
+}

R/zzz.R

@@ -2,15 +2,6 @@
   .defineUtilFunctions()
 }
 
-.getSynapseUtilsFunctionInfo <- function(rootDir) {
-  pyImport("synapseutils")
-  pyExec("info = functionInfo.functionInfo(synapseutils)")
-  functionInfo <- pyGet("info")
-  result <- lapply(X = functionInfo, function(x) {
-    list(name = x$name, synName = x$name, functionContainerName = "synapseutils", args = x$args, doc = x$doc, title = x$name)
-  })
-}
-
 .defineFunction <- function(synName, pyName, functionContainerName) {
   force(synName)
   force(pyName)

auto-man/changeFileMetaData.Rd

@@ -0,0 +1,49 @@
+%
+%  Auto-generated file, do not modify.
+%  Instead, copy this file to the man/ folder, remove this warning, and edit freely.
+%  Use Git to identify changes in this file which suggest where to change your edited copy.
+%
+\name{changeFileMetaData}
+\alias{changeFileMetaData}
+\docType{methods}
+\title{
+changeFileMetaData
+}
+\description{
+
+}
+\usage{
+changeFileMetaData(syn, entity, downloadAs=NA, contentType=NA)
+}
+\arguments{
+\item{syn}{}
+\item{entity}{        Synapse entity Id or object}
+\item{downloadAs}{    Specify filename to change the filename of a filehandle}
+\item{contentType}{   Specify content type to change the content type of a filehandle}
+}
+\details{
+% A detailed if possible precise description of the functionality provided, extending the basic information in the \description slot.
+}
+\value{
+              Synapse Entity
+}
+\references{
+% A section with references to the literature. Use \url{} or \href{}{} for web pointers.
+}
+\note{
+% Use this for a special note you want to have pointed out. 
+}
+\seealso{
+% Pointers to related R objects, using \code{\link{...}} to refer to them.
+}
+% Examples of how to use the function. 
+% Examples are not only useful for documentation purposes, but also provide test code used for diagnostic checking of R code. 
+% By default, text will be displayed in the output of the help page and run by example() and by R CMD check. 
+% You can use \dontrun{} for text that should only be shown, but not run, and \dontshow{} for extra commands 
+% for testing that should not be shown to users, but will be run by example(). 
+\examples{
+
+}
+
+
+

auto-man/copy.Rd

@@ -0,0 +1,67 @@
+%
+%  Auto-generated file, do not modify.
+%  Instead, copy this file to the man/ folder, remove this warning, and edit freely.
+%  Use Git to identify changes in this file which suggest where to change your edited copy.
+%
+\name{copy}
+\alias{copy}
+\docType{methods}
+\title{
+copy
+}
+\description{
+- This function will assist users in copying entities (Tables, Links, Files, Folders, Projects),
+  and will recursively copy everything in directories.
+- A Mapping of the old entities to the new entities will be created and all the wikis of each entity
+  will also be copied over and links to synapse Ids will be updated.
+}
+\usage{
+copy(syn, entity, destinationId, skipCopyWikiPage=FALSE, skipCopyAnnotations=FALSE, version=NULL, updateExisting=NULL, setProvenance=NULL, excludeTypes=NULL)
+}
+\arguments{
+\item{syn}{                 A synapse object: syn = synapseclient.login()- Must be logged into synapse}
+\item{entity}{              A synapse entity ID}
+\item{destinationId}{       Synapse ID of a folder/project that the copied entity is being copied to}
+\item{skipCopyWikiPage}{    Skip copying the wiki pages\cr
+                            Default is False}
+\item{skipCopyAnnotations}{ Skips copying the annotations\cr
+                            Default is False}
+\item{version}{optional named parameter:          Can specify version of a file. \cr
+                        Default to None}
+\item{updateExisting}{optional named parameter:   When the destination has an entity that has the same name, \cr
+                        users can choose to update that entity.  \cr
+                        It must be the same entity type\cr
+                        Default to False}
+\item{setProvenance}{optional named parameter:    Has three values to set the provenance of the copied entity:\cr
+                            traceback: Sets to the source entity\cr
+                            existing: Sets to source entity's original provenance (if it exists)\cr
+                            None: No provenance is set}
+\item{excludeTypes}{optional named parameter:     Accepts a list of entity types (file, table, link) which determines which entity types to not copy.\cr
+                        Defaults to an empty list.}
+}
+\details{
+% A detailed if possible precise description of the functionality provided, extending the basic information in the \description slot.
+}
+\value{
+ a mapping between the original and copied entity: {'syn1234':'syn33455'}
+}
+\references{
+% A section with references to the literature. Use \url{} or \href{}{} for web pointers.
+}
+\note{
+% Use this for a special note you want to have pointed out. 
+}
+\seealso{
+% Pointers to related R objects, using \code{\link{...}} to refer to them.
+}
+% Examples of how to use the function. 
+% Examples are not only useful for documentation purposes, but also provide test code used for diagnostic checking of R code. 
+% By default, text will be displayed in the output of the help page and run by example() and by R CMD check. 
+% You can use \dontrun{} for text that should only be shown, but not run, and \dontshow{} for extra commands 
+% for testing that should not be shown to users, but will be run by example(). 
+\examples{
+
+}
+
+
+

auto-man/copyFileHandles.Rd

@@ -0,0 +1,51 @@
+%
+%  Auto-generated file, do not modify.
+%  Instead, copy this file to the man/ folder, remove this warning, and edit freely.
+%  Use Git to identify changes in this file which suggest where to change your edited copy.
+%
+\name{copyFileHandles}
+\alias{copyFileHandles}
+\docType{methods}
+\title{
+copyFileHandles
+}
+\description{
+Given a list of fileHandle Objects, copy the fileHandles
+}
+\usage{
+copyFileHandles(syn, fileHandles, associateObjectTypes, associateObjectIds, contentTypes, fileNames)
+}
+\arguments{
+\item{syn}{}
+\item{fileHandles}{          List of fileHandle Ids or Objects}
+\item{associateObjectTypes}{ List of associated object types: FileEntity, TableEntity, WikiAttachment, UserProfileAttachment, MessageAttachment, TeamAttachment, SubmissionAttachment, VerificationSubmission (Must be the same length as fileHandles)}
+\item{associateObjectIds}{   List of associated object Ids: If copying a file, the objectId is the synapse id, and if copying a wiki attachment, the object id is the wiki subpage id. (Must be the same length as fileHandles)}
+\item{contentTypes}{         List of content types (Can change a filetype of a filehandle).}
+\item{fileNames}{            List of filenames (Can change a filename of a filehandle).}
+}
+\details{
+% A detailed if possible precise description of the functionality provided, extending the basic information in the \description slot.
+}
+\value{
+                     List of batch filehandle copy results, can include failureCodes: UNAUTHORIZED and NOT_FOUND
+}
+\references{
+% A section with references to the literature. Use \url{} or \href{}{} for web pointers.
+}
+\note{
+% Use this for a special note you want to have pointed out. 
+}
+\seealso{
+% Pointers to related R objects, using \code{\link{...}} to refer to them.
+}
+% Examples of how to use the function. 
+% Examples are not only useful for documentation purposes, but also provide test code used for diagnostic checking of R code. 
+% By default, text will be displayed in the output of the help page and run by example() and by R CMD check. 
+% You can use \dontrun{} for text that should only be shown, but not run, and \dontshow{} for extra commands 
+% for testing that should not be shown to users, but will be run by example(). 
+\examples{
+
+}
+
+
+

auto-man/copyWiki.Rd

@@ -0,0 +1,60 @@
+%
+%  Auto-generated file, do not modify.
+%  Instead, copy this file to the man/ folder, remove this warning, and edit freely.
+%  Use Git to identify changes in this file which suggest where to change your edited copy.
+%
+\name{copyWiki}
+\alias{copyWiki}
+\docType{methods}
+\title{
+copyWiki
+}
+\description{
+Copies wikis and updates internal links
+}
+\usage{
+copyWiki(syn, entity, destinationId, entitySubPageId=NA, destinationSubPageId=NA, updateLinks=TRUE, updateSynIds=TRUE, entityMap=NA)
+}
+\arguments{
+\item{syn}{                     A synapse object: syn = synapseclient.login()- Must be logged into synapse}
+\item{entity}{                  A synapse ID of an entity whose wiki you want to copy}
+\item{destinationId}{           Synapse ID of a folder/project that the wiki wants to be copied to}
+\item{entitySubPageId}{         Can specify subPageId and copy all of its subwikis\cr
+                                Defaults to None, which copies the entire wiki\cr
+                                subPageId can be found: https://www.synapse.org/#!Synapse:syn123/wiki/1234\cr
+                                In this case, 1234 is the subPageId. }
+\item{destinationSubPageId}{    Can specify destination subPageId to copy wikis to\cr
+                                Defaults to None}
+\item{updateLinks}{             Update all the internal links. (e.g. syn1234/wiki/34345 becomes syn3345/wiki/49508)\cr
+                                Defaults to True}
+\item{updateSynIds}{            Update all the synapse ID's referenced in the wikis. (e.g. syn1234 becomes syn2345)\cr
+                                Defaults to True but needs an entityMap}
+\item{entityMap}{               An entity map {'oldSynId','newSynId'} to update the synapse IDs referenced in the wiki\cr
+                                Defaults to None }
+}
+\details{
+% A detailed if possible precise description of the functionality provided, extending the basic information in the \description slot.
+}
+\value{
+ A list of Objects with three fields: id, title and parentId.
+}
+\references{
+% A section with references to the literature. Use \url{} or \href{}{} for web pointers.
+}
+\note{
+% Use this for a special note you want to have pointed out. 
+}
+\seealso{
+% Pointers to related R objects, using \code{\link{...}} to refer to them.
+}
+% Examples of how to use the function. 
+% Examples are not only useful for documentation purposes, but also provide test code used for diagnostic checking of R code. 
+% By default, text will be displayed in the output of the help page and run by example() and by R CMD check. 
+% You can use \dontrun{} for text that should only be shown, but not run, and \dontshow{} for extra commands 
+% for testing that should not be shown to users, but will be run by example(). 
+\examples{
+
+}
+
+
+

auto-man/notifyMe.Rd

@@ -0,0 +1,71 @@
+%
+%  Auto-generated file, do not modify.
+%  Instead, copy this file to the man/ folder, remove this warning, and edit freely.
+%  Use Git to identify changes in this file which suggest where to change your edited copy.
+%
+\name{notifyMe}
+\alias{notifyMe}
+\docType{methods}
+\title{
+notifyMe
+}
+\description{
+Function decorator that notifies you via email whenever an function completes running or 
+there is a failure.
+}
+\usage{
+notifyMe(syn, messageSubject=, retries=0)
+}
+\arguments{
+\item{syn}{    A synapse object as obtained with syn = synapseclient.login()}
+\item{messageSubject}{ A string with subject line for sent out messages.}
+\item{retries}{ Number of retries to attempt on failure (default=0)}
+}
+\details{
+% A detailed if possible precise description of the functionality provided, extending the basic information in the \description slot.
+}
+\value{
+
+}
+\references{
+% A section with references to the literature. Use \url{} or \href{}{} for web pointers.
+}
+\note{
+% Use this for a special note you want to have pointed out. 
+}
+\seealso{
+% Pointers to related R objects, using \code{\link{...}} to refer to them.
+}
+% Examples of how to use the function. 
+% Examples are not only useful for documentation purposes, but also provide test code used for diagnostic checking of R code. 
+% By default, text will be displayed in the output of the help page and run by example() and by R CMD check. 
+% You can use \dontrun{} for text that should only be shown, but not run, and \dontshow{} for extra commands 
+% for testing that should not be shown to users, but will be run by example(). 
+\examples{
+%\dontrun{
+%    # to decorate a function that you define
+%    from synapseutils import notifyMe
+%    import synapseclient
+%    syn = synapseclient.login()
+%    
+%    @notifyMe(syn, 'Long running function', retries=2)
+%    def my_function(x):
+%        doing_something()
+%        return long_runtime_func(x)
+%    
+%    my_function(123)
+%    
+%    #############################
+%    # to wrap a function that already exists
+%    from synapseutils import notifyMe
+%    import synapseclient
+%    syn = synapseclient.login()
+%    
+%    notify_decorator = notifyMe(syn, 'Long running query', retries=2)
+%    my_query = notify_decorator(syn.tableQuery)
+%    results = my_query("select id from syn1223")
+%}
+}
+
+
+

auto-man/syncFromSynapse.Rd

@@ -0,0 +1,56 @@
+%
+%  Auto-generated file, do not modify.
+%  Instead, copy this file to the man/ folder, remove this warning, and edit freely.
+%  Use Git to identify changes in this file which suggest where to change your edited copy.
+%
+\name{syncFromSynapse}
+\alias{syncFromSynapse}
+\docType{methods}
+\title{
+syncFromSynapse
+}
+\description{
+Synchronizes all the files in a folder (including subfolders) from Synapse and adds a readme manifest with file metadata.
+}
+\usage{
+syncFromSynapse(syn, entity, path=NULL, ifcollision=overwrite.local, allFiles=NULL, followLink=FALSE)
+}
+\arguments{
+\item{syn}{    A synapse object as obtained with syn = synapseclient.login()}
+\item{entity}{  A Synapse ID, a Synapse Entity object of type folder or project.}
+\item{path}{ An optional path where the file hierarchy will be\cr
+             reproduced.  If not specified the files will by default\cr
+             be placed in the synapseCache.}
+\item{ifcollision}{   Determines how to handle file collisions.\cr
+                      May be "overwrite.local", "keep.local", or "keep.both".\cr
+                      Defaults to "overwrite.local".}
+\item{allFiles}{}
+\item{followLink}{  Determines whether the link returns the target Entity.\cr
+                    Defaults to False}
+}
+\details{
+% A detailed if possible precise description of the functionality provided, extending the basic information in the \description slot.
+}
+\value{
+ list of entities (files, tables, links)
+}
+\references{
+% A section with references to the literature. Use \url{} or \href{}{} for web pointers.
+}
+\note{
+% Use this for a special note you want to have pointed out. 
+}
+\seealso{
+% Pointers to related R objects, using \code{\link{...}} to refer to them.
+}
+% Examples of how to use the function. 
+% Examples are not only useful for documentation purposes, but also provide test code used for diagnostic checking of R code. 
+% By default, text will be displayed in the output of the help page and run by example() and by R CMD check. 
+% You can use \dontrun{} for text that should only be shown, but not run, and \dontshow{} for extra commands 
+% for testing that should not be shown to users, but will be run by example(). 
+\examples{
+
+}
+
+
+