X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/16f704326f44fd1e5e5e60b936c9b5895d6a6ff8..c68e4ba51336a871dff26ae9f8dc7eb7e316083d:/sdk/R/man/ArvadosFile.Rd
diff --git a/sdk/R/man/ArvadosFile.Rd b/sdk/R/man/ArvadosFile.Rd
index 514e9e846d..81c25af5f1 100644
--- a/sdk/R/man/ArvadosFile.Rd
+++ b/sdk/R/man/ArvadosFile.Rd
@@ -1,58 +1,475 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ArvadosFile.R
-\name{ArvadosFile}
-\alias{ArvadosFile}
-\title{ArvadosFile}
-\description{
-ArvadosFile class represents a file inside Arvados collection.
-}
-\section{Usage}{
-
-\preformatted{file = ArvadosFile$new(name)}
-}
-
-\section{Arguments}{
-
-\describe{
- \item{name}{Name of the file.}
-}
-}
-
-\section{Methods}{
-
-\describe{
- \item{getName()}{Returns name of the file.}
- \item{getRelativePath()}{Returns file path relative to the root.}
- \item{read(contentType = "raw", offset = 0, length = 0)}{Read file content.}
- \item{write(content, contentType = "text/html")}{Write to file (override current content of the file).}
- \item{connection(rw)}{Get connection opened in "read" or "write" mode.}
- \item{flush()}{Write connections content to a file (override current content of the file).}
- \item{remove(name)}{Removes ArvadosFile or Subcollection specified by name from the subcollection.}
- \item{getSizeInBytes()}{Returns file size in bytes.}
- \item{move(destination)}{Moves file to a new location inside collection.}
- \item{copy(destination)}{Copies file to a new location inside collection.}
-}
-}
-
-\examples{
-\dontrun{
-myFile <- ArvadosFile$new("myFile")
-
-myFile$write("This is new file content")
-fileContent <- myFile$read()
-fileContent <- myFile$read("text")
-fileContent <- myFile$read("raw", offset = 8, length = 4)
-
-#Write a table:
-arvConnection <- myFile$connection("w")
-write.table(mytable, arvConnection)
-arvadosFile$flush()
-
-#Read a table:
-arvConnection <- myFile$connection("r")
-mytable <- read.table(arvConnection)
-
-myFile$move("newFolder/myFile")
-myFile$copy("newFolder/myFile")
-}
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ArvadosFile.R
+\name{ArvadosFile}
+\alias{ArvadosFile}
+\title{R6 Class Representing a ArvadosFile}
+\description{
+ArvadosFile class represents a file inside Arvados collection.
+}
+\examples{
+
+## ------------------------------------------------
+## Method `ArvadosFile$new`
+## ------------------------------------------------
+
+\dontrun{
+myFile <- ArvadosFile$new("myFile")
+}
+
+## ------------------------------------------------
+## Method `ArvadosFile$getName`
+## ------------------------------------------------
+
+\dontrun{
+arvadosFile$getName()
+}
+
+## ------------------------------------------------
+## Method `ArvadosFile$getFileListing`
+## ------------------------------------------------
+
+\dontrun{
+arvadosFile$getFileListing()
+}
+
+## ------------------------------------------------
+## Method `ArvadosFile$getSizeInBytes`
+## ------------------------------------------------
+
+\dontrun{
+arvadosFile$getSizeInBytes()
+}
+
+## ------------------------------------------------
+## Method `ArvadosFile$read`
+## ------------------------------------------------
+
+\dontrun{
+collection <- Collection$new(arv, collectionUUID)
+arvadosFile <- collection$get(fileName)
+fileContent <- arvadosFile$read("text")
+}
+
+## ------------------------------------------------
+## Method `ArvadosFile$connection`
+## ------------------------------------------------
+
+\dontrun{
+collection <- Collection$new(arv, collectionUUID)
+arvadosFile <- collection$get(fileName)
+arvConnection <- arvadosFile$connection("w")
+}
+
+## ------------------------------------------------
+## Method `ArvadosFile$flush`
+## ------------------------------------------------
+
+\dontrun{
+collection <- Collection$new(arv, collectionUUID)
+arvadosFile <- collection$get(fileName)
+myFile$write("This is new file content")
+arvadosFile$flush()
+}
+
+## ------------------------------------------------
+## Method `ArvadosFile$write`
+## ------------------------------------------------
+
+\dontrun{
+collection <- Collection$new(arv, collectionUUID)
+arvadosFile <- collection$get(fileName)
+myFile$write("This is new file content")
+}
+
+## ------------------------------------------------
+## Method `ArvadosFile$move`
+## ------------------------------------------------
+
+\dontrun{
+arvadosFile$move(newPath)
+}
+
+## ------------------------------------------------
+## Method `ArvadosFile$copy`
+## ------------------------------------------------
+
+\dontrun{
+arvadosFile$copy("NewName.format")
+}
+}
+\section{Methods}{
+\subsection{Public methods}{
+\itemize{
+\item \href{#method-ArvadosFile-new}{\code{ArvadosFile$new()}}
+\item \href{#method-ArvadosFile-getName}{\code{ArvadosFile$getName()}}
+\item \href{#method-ArvadosFile-getFileListing}{\code{ArvadosFile$getFileListing()}}
+\item \href{#method-ArvadosFile-getSizeInBytes}{\code{ArvadosFile$getSizeInBytes()}}
+\item \href{#method-ArvadosFile-get}{\code{ArvadosFile$get()}}
+\item \href{#method-ArvadosFile-getFirst}{\code{ArvadosFile$getFirst()}}
+\item \href{#method-ArvadosFile-getCollection}{\code{ArvadosFile$getCollection()}}
+\item \href{#method-ArvadosFile-setCollection}{\code{ArvadosFile$setCollection()}}
+\item \href{#method-ArvadosFile-getRelativePath}{\code{ArvadosFile$getRelativePath()}}
+\item \href{#method-ArvadosFile-getParent}{\code{ArvadosFile$getParent()}}
+\item \href{#method-ArvadosFile-setParent}{\code{ArvadosFile$setParent()}}
+\item \href{#method-ArvadosFile-read}{\code{ArvadosFile$read()}}
+\item \href{#method-ArvadosFile-connection}{\code{ArvadosFile$connection()}}
+\item \href{#method-ArvadosFile-flush}{\code{ArvadosFile$flush()}}
+\item \href{#method-ArvadosFile-write}{\code{ArvadosFile$write()}}
+\item \href{#method-ArvadosFile-move}{\code{ArvadosFile$move()}}
+\item \href{#method-ArvadosFile-copy}{\code{ArvadosFile$copy()}}
+\item \href{#method-ArvadosFile-duplicate}{\code{ArvadosFile$duplicate()}}
+}
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-new}{}}}
+\subsection{Method \code{new()}}{
+Initialize new enviroment.
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{ArvadosFile$new(name)}\if{html}{\out{
}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{}}
+\describe{
+\item{\code{name}}{Name of the new enviroment.}
+}
+\if{html}{\out{
}}
+}
+\subsection{Returns}{
+A new `ArvadosFile` object.
+}
+\subsection{Examples}{
+\if{html}{\out{}}
+\preformatted{\dontrun{
+myFile <- ArvadosFile$new("myFile")
+}
+}
+\if{html}{\out{
}}
+
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-getName}{}}}
+\subsection{Method \code{getName()}}{
+Returns name of the file.
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{ArvadosFile$getName()}\if{html}{\out{
}}
+}
+
+\subsection{Examples}{
+\if{html}{\out{}}
+\preformatted{\dontrun{
+arvadosFile$getName()
+}
+}
+\if{html}{\out{
}}
+
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-getFileListing}{}}}
+\subsection{Method \code{getFileListing()}}{
+Returns collections file content as character vector.
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{ArvadosFile$getFileListing(fullpath = TRUE)}\if{html}{\out{
}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{}}
+\describe{
+\item{\code{fullPath}}{Checking if TRUE.}
+}
+\if{html}{\out{
}}
+}
+\subsection{Examples}{
+\if{html}{\out{}}
+\preformatted{\dontrun{
+arvadosFile$getFileListing()
+}
+}
+\if{html}{\out{
}}
+
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-getSizeInBytes}{}}}
+\subsection{Method \code{getSizeInBytes()}}{
+Returns collections content size in bytes.
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{ArvadosFile$getSizeInBytes()}\if{html}{\out{
}}
+}
+
+\subsection{Examples}{
+\if{html}{\out{}}
+\preformatted{\dontrun{
+arvadosFile$getSizeInBytes()
+}
+}
+\if{html}{\out{
}}
+
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-get}{}}}
+\subsection{Method \code{get()}}{
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{ArvadosFile$get(fileLikeObjectName)}\if{html}{\out{
}}
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-getFirst}{}}}
+\subsection{Method \code{getFirst()}}{
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{ArvadosFile$getFirst()}\if{html}{\out{
}}
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-getCollection}{}}}
+\subsection{Method \code{getCollection()}}{
+Returns collection UUID.
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{ArvadosFile$getCollection()}\if{html}{\out{
}}
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-setCollection}{}}}
+\subsection{Method \code{setCollection()}}{
+Sets new collection.
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{ArvadosFile$setCollection(collection, setRecursively = TRUE)}\if{html}{\out{
}}
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-getRelativePath}{}}}
+\subsection{Method \code{getRelativePath()}}{
+Returns file path relative to the root.
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{ArvadosFile$getRelativePath()}\if{html}{\out{
}}
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-getParent}{}}}
+\subsection{Method \code{getParent()}}{
+Returns project UUID.
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{ArvadosFile$getParent()}\if{html}{\out{
}}
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-setParent}{}}}
+\subsection{Method \code{setParent()}}{
+Sets project collection.
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{ArvadosFile$setParent(newParent)}\if{html}{\out{
}}
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-read}{}}}
+\subsection{Method \code{read()}}{
+Read file content.
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{ArvadosFile$read(contentType = "raw", offset = 0, length = 0)}\if{html}{\out{
}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{}}
+\describe{
+\item{\code{contentType}}{Type of content. Possible is "text", "raw".}
+
+\item{\code{offset}}{Describes the location of a piece of data compared to another location}
+
+\item{\code{length}}{Length of content}
+}
+\if{html}{\out{
}}
+}
+\subsection{Examples}{
+\if{html}{\out{}}
+\preformatted{\dontrun{
+collection <- Collection$new(arv, collectionUUID)
+arvadosFile <- collection$get(fileName)
+fileContent <- arvadosFile$read("text")
+}
+}
+\if{html}{\out{
}}
+
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-connection}{}}}
+\subsection{Method \code{connection()}}{
+Get connection opened in "read" or "write" mode.
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{ArvadosFile$connection(rw)}\if{html}{\out{
}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{}}
+\describe{
+\item{\code{rw}}{Type of connection.}
+}
+\if{html}{\out{
}}
+}
+\subsection{Examples}{
+\if{html}{\out{}}
+\preformatted{\dontrun{
+collection <- Collection$new(arv, collectionUUID)
+arvadosFile <- collection$get(fileName)
+arvConnection <- arvadosFile$connection("w")
+}
+}
+\if{html}{\out{
}}
+
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-flush}{}}}
+\subsection{Method \code{flush()}}{
+Write connections content to a file or override current content of the file.
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{ArvadosFile$flush()}\if{html}{\out{
}}
+}
+
+\subsection{Examples}{
+\if{html}{\out{}}
+\preformatted{\dontrun{
+collection <- Collection$new(arv, collectionUUID)
+arvadosFile <- collection$get(fileName)
+myFile$write("This is new file content")
+arvadosFile$flush()
+}
+}
+\if{html}{\out{
}}
+
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-write}{}}}
+\subsection{Method \code{write()}}{
+Write to file or override current content of the file.
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{ArvadosFile$write(content, contentType = "text/html")}\if{html}{\out{
}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{}}
+\describe{
+\item{\code{content}}{File to write.}
+
+\item{\code{contentType}}{Type of content. Possible is "text", "raw".}
+}
+\if{html}{\out{
}}
+}
+\subsection{Examples}{
+\if{html}{\out{}}
+\preformatted{\dontrun{
+collection <- Collection$new(arv, collectionUUID)
+arvadosFile <- collection$get(fileName)
+myFile$write("This is new file content")
+}
+}
+\if{html}{\out{
}}
+
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-move}{}}}
+\subsection{Method \code{move()}}{
+Moves file to a new location inside collection.
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{ArvadosFile$move(destination)}\if{html}{\out{
}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{}}
+\describe{
+\item{\code{destination}}{Path to new folder.}
+}
+\if{html}{\out{
}}
+}
+\subsection{Examples}{
+\if{html}{\out{}}
+\preformatted{\dontrun{
+arvadosFile$move(newPath)
+}
+}
+\if{html}{\out{
}}
+
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-copy}{}}}
+\subsection{Method \code{copy()}}{
+Copies file to a new location inside collection.
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{ArvadosFile$copy(destination)}\if{html}{\out{
}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{}}
+\describe{
+\item{\code{destination}}{Path to new folder.}
+}
+\if{html}{\out{
}}
+}
+\subsection{Examples}{
+\if{html}{\out{}}
+\preformatted{\dontrun{
+arvadosFile$copy("NewName.format")
+}
+}
+\if{html}{\out{
}}
+
+}
+
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-duplicate}{}}}
+\subsection{Method \code{duplicate()}}{
+Duplicate file and gives it a new name.
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{ArvadosFile$duplicate(newName = NULL)}\if{html}{\out{
}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{}}
+\describe{
+\item{\code{newName}}{New name for duplicated file.}
+}
+\if{html}{\out{
}}
+}
+}
+}