X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/29659ffa9e00efe7a845aa303c70ba543c23174d..c68e4ba51336a871dff26ae9f8dc7eb7e316083d:/sdk/R/man/Collection.Rd

diff --git a/sdk/R/man/Collection.Rd b/sdk/R/man/Collection.Rd
index add30b1440..0de9a842e6 100644
--- a/sdk/R/man/Collection.Rd
+++ b/sdk/R/man/Collection.Rd
@@ -1,67 +1,480 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/arvados_objects.R
-\name{Collection}
-\alias{Collection}
-\title{Collection Object}
-\usage{
-Collection(uuid = NULL, etag = NULL, owner_uuid = NULL,
-  created_at = NULL, modified_by_client_uuid = NULL,
-  modified_by_user_uuid = NULL, modified_at = NULL,
-  portable_data_hash = NULL, replication_desired = NULL,
-  replication_confirmed_at = NULL, replication_confirmed = NULL,
-  updated_at = NULL, manifest_text = NULL, name = NULL,
-  description = NULL, properties = NULL, delete_at = NULL,
-  file_names = NULL, trash_at = NULL, is_trashed = NULL)
-}
-\arguments{
-\item{uuid}{Object ID}
-
-\item{etag}{Object version}
-
-\item{owner_uuid}{No description}
-
-\item{created_at}{No description}
-
-\item{modified_by_client_uuid}{No description}
-
-\item{modified_by_user_uuid}{No description}
-
-\item{modified_at}{No description}
-
-\item{portable_data_hash}{No description}
-
-\item{replication_desired}{No description}
-
-\item{replication_confirmed_at}{No description}
-
-\item{replication_confirmed}{No description}
-
-\item{updated_at}{No description}
-
-\item{manifest_text}{No description}
-
-\item{name}{No description}
-
-\item{description}{No description}
-
-\item{properties}{No description}
-
-\item{delete_at}{No description}
-
-\item{file_names}{No description}
-
-\item{trash_at}{No description}
-
-\item{is_trashed}{No description}
-}
-\value{
-Collection object
-}
-\description{
-Collection Object
-}
-\details{
-Todo: Update description
-Collection
-}
-\concept{Collection functions}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/Collection.R
+\name{Collection}
+\alias{Collection}
+\title{R6 Class Representing Arvados Collection}
+\description{
+Collection class provides interface for working with Arvados collections,
+for exaplme actions like creating, updating, moving or removing are possible.
+}
+\examples{
+
+## ------------------------------------------------
+## Method `Collection$new`
+## ------------------------------------------------
+
+\dontrun{
+collection <- Collection$new(arv, CollectionUUID)
+}
+
+## ------------------------------------------------
+## Method `Collection$readArvFile`
+## ------------------------------------------------
+
+\dontrun{
+collection <- Collection$new(arv, collectionUUID)
+readFile <- collection$readArvFile(arvadosFile, istable = 'yes')                    # table
+readFile <- collection$readArvFile(arvadosFile, istable = 'no')                     # text
+readFile <- collection$readArvFile(arvadosFile)                                     # xlsx, csv, tsv, rds, rdata
+readFile <- collection$readArvFile(arvadosFile, fileclass = 'fasta')                # fasta
+readFile <- collection$readArvFile(arvadosFile, Ncol= 4, Nrow = 32)                 # binary, only numbers
+readFile <- collection$readArvFile(arvadosFile, Ncol = 5, Nrow = 150, istable = "factor") # binary with factor or text
+}
+
+## ------------------------------------------------
+## Method `Collection$writeFile`
+## ------------------------------------------------
+
+\dontrun{
+collection <- Collection$new(arv, collectionUUID)
+writeFile <- collection$writeFile(name = "myoutput.csv", file = file, fileFormat = "csv", istable = NULL, collectionUUID = collectionUUID)             # csv
+writeFile <- collection$writeFile(name = "myoutput.tsv", file = file, fileFormat = "tsv", istable = NULL, collectionUUID = collectionUUID)             # tsv
+writeFile <- collection$writeFile(name = "myoutput.fasta", file = file, fileFormat = "fasta", istable = NULL, collectionUUID = collectionUUID)         # fasta
+writeFile <- collection$writeFile(name = "myoutputtable.txt", file = file, fileFormat = "txt", istable = "yes", collectionUUID = collectionUUID)       # txt table
+writeFile <- collection$writeFile(name = "myoutputtext.txt", file = file, fileFormat = "txt", istable = "no", collectionUUID = collectionUUID)         # txt text
+writeFile <- collection$writeFile(name = "myoutputbinary.dat", file = file, fileFormat = "dat", collectionUUID = collectionUUID)                       # binary
+writeFile <- collection$writeFile(name = "myoutputxlsx.xlsx", file = file, fileFormat = "xlsx", collectionUUID = collectionUUID)                       # xlsx
+}
+
+## ------------------------------------------------
+## Method `Collection$create`
+## ------------------------------------------------
+
+\dontrun{
+collection <- arv$collections_create(name = collectionTitle, description = collectionDescription, owner_uuid = collectionOwner, properties = list("ROX37196928443768648" = "ROX37742976443830153"))
+}
+
+## ------------------------------------------------
+## Method `Collection$remove`
+## ------------------------------------------------
+
+\dontrun{
+collection$remove(fileName.format)
+}
+
+## ------------------------------------------------
+## Method `Collection$move`
+## ------------------------------------------------
+
+\dontrun{
+collection$move("fileName.format", path)
+}
+
+## ------------------------------------------------
+## Method `Collection$copy`
+## ------------------------------------------------
+
+\dontrun{
+copied <- collection$copy("oldName.format", "newName.format")
+}
+
+## ------------------------------------------------
+## Method `Collection$refresh`
+## ------------------------------------------------
+
+\dontrun{
+collection$refresh()
+}
+
+## ------------------------------------------------
+## Method `Collection$getFileListing`
+## ------------------------------------------------
+
+\dontrun{
+list <- collection$getFileListing()
+}
+
+## ------------------------------------------------
+## Method `Collection$get`
+## ------------------------------------------------
+
+\dontrun{
+arvadosFile <- collection$get(fileName)
+}
+}
+\seealso{
+https://git.arvados.org/arvados.git/tree/HEAD:/sdk/R
+}
+\section{Public fields}{
+\if{html}{\out{<div class="r6-fields">}}
+\describe{
+\item{\code{uuid}}{Autentic for Collection UUID.}
+}
+\if{html}{\out{</div>}}
+}
+\section{Methods}{
+\subsection{Public methods}{
+\itemize{
+\item \href{#method-Collection-new}{\code{Collection$new()}}
+\item \href{#method-Collection-add}{\code{Collection$add()}}
+\item \href{#method-Collection-readArvFile}{\code{Collection$readArvFile()}}
+\item \href{#method-Collection-writeFile}{\code{Collection$writeFile()}}
+\item \href{#method-Collection-create}{\code{Collection$create()}}
+\item \href{#method-Collection-remove}{\code{Collection$remove()}}
+\item \href{#method-Collection-move}{\code{Collection$move()}}
+\item \href{#method-Collection-copy}{\code{Collection$copy()}}
+\item \href{#method-Collection-refresh}{\code{Collection$refresh()}}
+\item \href{#method-Collection-getFileListing}{\code{Collection$getFileListing()}}
+\item \href{#method-Collection-get}{\code{Collection$get()}}
+\item \href{#method-Collection-getRESTService}{\code{Collection$getRESTService()}}
+\item \href{#method-Collection-setRESTService}{\code{Collection$setRESTService()}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-Collection-new"></a>}}
+\if{latex}{\out{\hypertarget{method-Collection-new}{}}}
+\subsection{Method \code{new()}}{
+Initialize new enviroment.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Collection$new(api, uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{api}}{Arvados enviroment.}
+
+\item{\code{uuid}}{The UUID Autentic for Collection UUID.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Returns}{
+A new `Collection` object.
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{\dontrun{
+collection <- Collection$new(arv, CollectionUUID)
+}
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-Collection-add"></a>}}
+\if{latex}{\out{\hypertarget{method-Collection-add}{}}}
+\subsection{Method \code{add()}}{
+Adds ArvadosFile or Subcollection specified by content to the collection. Used only with ArvadosFile or Subcollection.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Collection$add(content, relativePath = "")}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{content}}{Content to be added.}
+
+\item{\code{relativePath}}{Path to add content.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-Collection-readArvFile"></a>}}
+\if{latex}{\out{\hypertarget{method-Collection-readArvFile}{}}}
+\subsection{Method \code{readArvFile()}}{
+Read file content.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Collection$readArvFile(
+  file,
+  con,
+  sep = ",",
+  istable = NULL,
+  fileclass = "SeqFastadna",
+  Ncol = NULL,
+  Nrow = NULL,
+  wantedFunction = NULL
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{file}}{Name of the file.}
+
+\item{\code{sep}}{Separator used in reading tsv, csv file format.}
+
+\item{\code{istable}}{Used in reading txt file to check if the file is table or not.}
+
+\item{\code{fileclass}}{Used in reading fasta file to set file class.}
+
+\item{\code{Ncol}}{Used in reading binary file to set numbers of columns in data.frame.}
+
+\item{\code{Nrow}}{Used in reading binary file to set numbers of rows in data.frame size.}
+
+\item{\code{col}}{Collection from which the file is read.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{\dontrun{
+collection <- Collection$new(arv, collectionUUID)
+readFile <- collection$readArvFile(arvadosFile, istable = 'yes')                    # table
+readFile <- collection$readArvFile(arvadosFile, istable = 'no')                     # text
+readFile <- collection$readArvFile(arvadosFile)                                     # xlsx, csv, tsv, rds, rdata
+readFile <- collection$readArvFile(arvadosFile, fileclass = 'fasta')                # fasta
+readFile <- collection$readArvFile(arvadosFile, Ncol= 4, Nrow = 32)                 # binary, only numbers
+readFile <- collection$readArvFile(arvadosFile, Ncol = 5, Nrow = 150, istable = "factor") # binary with factor or text
+}
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-Collection-writeFile"></a>}}
+\if{latex}{\out{\hypertarget{method-Collection-writeFile}{}}}
+\subsection{Method \code{writeFile()}}{
+Write file content
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Collection$writeFile(
+  name,
+  file,
+  collectionUUID,
+  fileFormat,
+  istable = NULL,
+  seqName = NULL
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{name}}{Name of the file.}
+
+\item{\code{file}}{File to be saved.}
+
+\item{\code{istable}}{Used in writing txt file to check if the file is table or not.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{\dontrun{
+collection <- Collection$new(arv, collectionUUID)
+writeFile <- collection$writeFile(name = "myoutput.csv", file = file, fileFormat = "csv", istable = NULL, collectionUUID = collectionUUID)             # csv
+writeFile <- collection$writeFile(name = "myoutput.tsv", file = file, fileFormat = "tsv", istable = NULL, collectionUUID = collectionUUID)             # tsv
+writeFile <- collection$writeFile(name = "myoutput.fasta", file = file, fileFormat = "fasta", istable = NULL, collectionUUID = collectionUUID)         # fasta
+writeFile <- collection$writeFile(name = "myoutputtable.txt", file = file, fileFormat = "txt", istable = "yes", collectionUUID = collectionUUID)       # txt table
+writeFile <- collection$writeFile(name = "myoutputtext.txt", file = file, fileFormat = "txt", istable = "no", collectionUUID = collectionUUID)         # txt text
+writeFile <- collection$writeFile(name = "myoutputbinary.dat", file = file, fileFormat = "dat", collectionUUID = collectionUUID)                       # binary
+writeFile <- collection$writeFile(name = "myoutputxlsx.xlsx", file = file, fileFormat = "xlsx", collectionUUID = collectionUUID)                       # xlsx
+}
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-Collection-create"></a>}}
+\if{latex}{\out{\hypertarget{method-Collection-create}{}}}
+\subsection{Method \code{create()}}{
+Creates one or more ArvadosFiles and adds them to the collection at specified path.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Collection$create(files)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{files}}{Content to be created.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{\dontrun{
+collection <- arv$collections_create(name = collectionTitle, description = collectionDescription, owner_uuid = collectionOwner, properties = list("ROX37196928443768648" = "ROX37742976443830153"))
+}
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-Collection-remove"></a>}}
+\if{latex}{\out{\hypertarget{method-Collection-remove}{}}}
+\subsection{Method \code{remove()}}{
+Remove one or more files from the collection.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Collection$remove(paths)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{paths}}{Content to be removed.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{\dontrun{
+collection$remove(fileName.format)
+}
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-Collection-move"></a>}}
+\if{latex}{\out{\hypertarget{method-Collection-move}{}}}
+\subsection{Method \code{move()}}{
+Moves ArvadosFile or Subcollection to another location in the collection.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Collection$move(content, destination)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{content}}{Content to be moved.}
+
+\item{\code{destination}}{Path to move content.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{\dontrun{
+collection$move("fileName.format", path)
+}
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-Collection-copy"></a>}}
+\if{latex}{\out{\hypertarget{method-Collection-copy}{}}}
+\subsection{Method \code{copy()}}{
+Copies ArvadosFile or Subcollection to another location in the collection.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Collection$copy(content, destination)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{content}}{Content to be moved.}
+
+\item{\code{destination}}{Path to move content.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{\dontrun{
+copied <- collection$copy("oldName.format", "newName.format")
+}
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-Collection-refresh"></a>}}
+\if{latex}{\out{\hypertarget{method-Collection-refresh}{}}}
+\subsection{Method \code{refresh()}}{
+Refreshes the environment.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Collection$refresh()}\if{html}{\out{</div>}}
+}
+
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{\dontrun{
+collection$refresh()
+}
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-Collection-getFileListing"></a>}}
+\if{latex}{\out{\hypertarget{method-Collection-getFileListing}{}}}
+\subsection{Method \code{getFileListing()}}{
+Returns collections file content as character vector.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Collection$getFileListing()}\if{html}{\out{</div>}}
+}
+
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{\dontrun{
+list <- collection$getFileListing()
+}
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-Collection-get"></a>}}
+\if{latex}{\out{\hypertarget{method-Collection-get}{}}}
+\subsection{Method \code{get()}}{
+If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Collection$get(relativePath)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{relativePath}}{Path from content is taken.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{\dontrun{
+arvadosFile <- collection$get(fileName)
+}
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-Collection-getRESTService"></a>}}
+\if{latex}{\out{\hypertarget{method-Collection-getRESTService}{}}}
+\subsection{Method \code{getRESTService()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Collection$getRESTService()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-Collection-setRESTService"></a>}}
+\if{latex}{\out{\hypertarget{method-Collection-setRESTService}{}}}
+\subsection{Method \code{setRESTService()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Collection$setRESTService(newRESTService)}\if{html}{\out{</div>}}
+}
+
+}
+}