[ARVADOS] updated: 1.1.2-267-g1e00053
Git user
git at public.curoverse.com
Wed Feb 7 11:44:32 EST 2018
Summary of changes:
sdk/R/R/Arvados.R | 57 ++++++++--
sdk/R/R/ArvadosFile.R | 51 ++++++++-
sdk/R/R/Collection.R | 44 +++++++-
sdk/R/R/Subcollection.R | 41 +++++++-
sdk/R/README | 251 ---------------------------------------------
sdk/R/README.Rmd | 209 +++++++++++++++++++++++++++++++++++++
sdk/R/man/Arvados.Rd | 61 ++++++++---
sdk/R/man/ArvadosFile.Rd | 59 +++++++++--
sdk/R/man/Collection.Rd | 50 +++++++--
sdk/R/man/Subcollection.Rd | 49 +++++++--
10 files changed, 567 insertions(+), 305 deletions(-)
delete mode 100644 sdk/R/README
create mode 100644 sdk/R/README.Rmd
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commit 1e00053e7bc962a827ae960c1953ac9bd63d503b
Author: Fuad Muhic <fmuhic at capeannenterprises.com>
Date: Wed Feb 7 17:42:56 2018 +0100
Added documentation to each public class of SDK.
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic at capeannenterprises.com>
diff --git a/sdk/R/R/Arvados.R b/sdk/R/R/Arvados.R
index ea4384b..d9bd091 100644
--- a/sdk/R/R/Arvados.R
+++ b/sdk/R/R/Arvados.R
@@ -2,14 +2,59 @@ source("./R/RESTService.R")
source("./R/HttpRequest.R")
source("./R/HttpParser.R")
-#' Arvados SDK Object
+#' Arvados
+#'
+#' Arvados class gives users ability to manipulate collections and projects.
+#'
+#' @section Usage:
+#' \preformatted{arv = Arvados$new(authToken, hostName, numRetries = 0)}
#'
-#' All Arvados logic is inside this class
+#' @section Arguments:
+#' \describe{
+#' \item{authToken}{Authentification token. If not specified ARVADOS_API_TOKEN environment variable will be used.}
+#' \item{hostName}{Host name. If not specified ARVADOS_API_HOST environment variable will be used.}
+#' \item{numRetries}{Number which specifies how many times to retry failed service requests.}
+#' }
+#'
+#' @section Methods:
+#' \describe{
+#' \item{getToken()}{Returns authentification token currently in use.}
+#' \item{getHostName()}{Returns host name currently in use.}
+#' \item{getNumRetries()}{Returns number which specifies how many times to retry failed service requests.}
+#' \item{setNumRetries(newNumOfRetries)}{Sets number which specifies how many times to retry failed service requests.}
+#' \item{getCollection(uuid)}{Get collection with specified UUID.}
+#' \item{listCollections(filters = NULL, limit = 100, offset = 0)}{Returns list of collections based on filters parameter.}
+#' \item{listAllCollections(filters = NULL)}{Lists all collections, based on filters parameter, even if the number of items is greater than maximum API limit.}
+#' \item{deleteCollection(uuid)}{Deletes collection with specified UUID.}
+#' \item{updateCollection(uuid, newContent)}{Updates collection with specified UUID.}
+#' \item{createCollection(content)}{Creates new collection.}
+#' \item{getProject(uuid)}{Get project with specified UUID.}
+#' \item{listProjects(filters = NULL, limit = 100, offset = 0)}{Returns list of projects based on filters parameter.}
+#' \item{listAllProjects(filters = NULL)}{Lists all projects, based on filters parameter, even if the number of items is greater than maximum API limit.}
+#' \item{deleteProject(uuid)}{Deletes project with specified UUID.}
+#' \item{updateProject(uuid, newContent)}{Updates project with specified UUID.}
+#' \item{createProject(content)}{Creates new project.}
+#' }
#'
-#' @field token Token represents user authentification token.
-#' @field host Host represents server name we wish to connect to.
-#' @examples arv = Arvados$new("token", "host_name")
-#' @export Arvados
+#' @name Arvados
+#' @examples
+#' \dontrun{
+#' arv <- Arvados$new("your Arvados token", "example.arvadosapi.com")
+#'
+#' collection <- arv$getCollection("uuid")
+#'
+#' collectionList <- arv$listCollections(list(list("name", "like", "Test%")))
+#' collectionList <- arv$listAllCollections(list(list("name", "like", "Test%")))
+#'
+#' deletedCollection <- arv$deleteCollection("uuid")
+#'
+#' updatedCollection <- arv$updateCollection("uuid", list(name = "New name", description = "New description"))
+#'
+#' createdCollection <- arv$createCollection(list(name = "Example", description = "This is a test collection"))
+#' }
+NULL
+
+#' @export
Arvados <- R6::R6Class(
"Arvados",
diff --git a/sdk/R/R/ArvadosFile.R b/sdk/R/R/ArvadosFile.R
index 3437933..53321ef 100644
--- a/sdk/R/R/ArvadosFile.R
+++ b/sdk/R/R/ArvadosFile.R
@@ -1,10 +1,55 @@
source("./R/util.R")
-#' ArvadosFile Object
+#' ArvadosFile
+#'
+#' ArvadosFile class represents a file inside Arvados collection.
+#'
+#' @section Usage:
+#' \preformatted{file = ArvadosFile$new(name)}
#'
-#' Update description
+#' @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 content of the connecitons buffer 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(newLocation)}{Moves file to a new location inside collection.}
+#' }
#'
-#' @export ArvadosFile
+#' @name ArvadosFile
+#' @examples
+#' \dontrun{
+#' myFile <- ArvadosFile$new("myFile")
+#'
+#' myFile$write("This is new file content")
+#' fileContent <- myFile$read()
+#' fileContent <- myFile$read("text")
+#' fileContent <- myFile$read("raw", offset = 1024, length = 512)
+#'
+#'
+#' #Write a table:
+#' arvConnection <- myFile$connection("w")
+#' write.table(mytable, arvConnection)
+#' arvadosFile$flush()
+#'
+#' #Read a table:
+#' arvConnection <- myFile$connection("r")
+#' mytable <- read.table(arvConnection)
+#'
+#' myFile$move("newFolder/myFile")
+#' }
+NULL
+
+#' @export
ArvadosFile <- R6::R6Class(
"ArvadosFile",
diff --git a/sdk/R/R/Collection.R b/sdk/R/R/Collection.R
index 47d88ac..b788f9c 100644
--- a/sdk/R/R/Collection.R
+++ b/sdk/R/R/Collection.R
@@ -3,12 +3,48 @@ source("./R/ArvadosFile.R")
source("./R/RESTService.R")
source("./R/util.R")
-#' Arvados Collection Object
+#' Collection
+#'
+#' Collection class provides interface for working with Arvados collections.
+#'
+#' @section Usage:
+#' \preformatted{collection = Collection$new(arv, uuid)}
#'
-#' Update description
+#' @section Arguments:
+#' \describe{
+#' \item{arv}{Arvados object.}
+#' \item{uuid}{UUID of a collection.}
+#' }
+#'
+#' @section Methods:
+#' \describe{
+#' \item{add(content)}{Adds ArvadosFile or Subcollection specified by content to the collection.}
+#' \item{create(fileNames, relativePath = "")}{Creates one or more ArvadosFiles and adds them to the collection at specified path.}
+#' \item{remove(fileNames)}{Remove one or more files from the collection.}
+#' \item{move(content, newLocation)}{Moves ArvadosFile or Subcollection to another location in the collection.}
+#' \item{getFileListing()}{Returns collections file content as character vector.}
+#' \item{get(relativePath)}{If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.}
+#' }
#'
-#' @examples arv = Collection$new(api, uuid)
-#' @export Collection
+#' @name Collection
+#' @examples
+#' \dontrun{
+#' collection <- Collection$new(arv, "uuid")
+#'
+#' collection$add(existingArvadosFile, "cpp")
+#'
+#' createdFiles <- collection$create(c("main.cpp", lib.dll), "cpp/src/")
+#'
+#' collection$remove("location/to/my/file.cpp")
+#'
+#' collection$move("folder/file.cpp", "file.cpp")
+#'
+#' arvadosFile <- collection$get("location/to/my/file.cpp")
+#' arvadosSubcollection <- collection$get("location/to/my/directory/")
+#' }
+NULL
+
+#' @export
Collection <- R6::R6Class(
"Collection",
diff --git a/sdk/R/R/Subcollection.R b/sdk/R/R/Subcollection.R
index d580695..179bbcd 100644
--- a/sdk/R/R/Subcollection.R
+++ b/sdk/R/R/Subcollection.R
@@ -1,10 +1,45 @@
source("./R/util.R")
-#' Arvados SubCollection Object
+#' Subcollection
+#'
+#' Subcollection class represents a folder inside Arvados collection.
+#' It is essentially a composite of ArvadosFiles and other Subcollections.
+#'
+#' @section Usage:
+#' \preformatted{subcollection = Subcollection$new(name)}
#'
-#' Update description
+#' @section Arguments:
+#' \describe{
+#' \item{name}{Name of the subcollection.}
+#' }
+#'
+#' @section Methods:
+#' \describe{
+#' \item{getName()}{Returns name of the subcollection.}
+#' \item{getRelativePath()}{Returns subcollection path relative to the root.}
+#' \item{add(content)}{Adds ArvadosFile or Subcollection specified by content to the subcollection.}
+#' \item{remove(name)}{Removes ArvadosFile or Subcollection specified by name from the subcollection.}
+#' \item{get(relativePath)}{If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.}
+#' \item{getFileListing()}{Returns subcollections file content as character vector.}
+#' \item{getSizeInBytes()}{Returns subcollections content size in bytes.}
+#' \item{move(newLocation)}{Moves subcollection to a new location inside collection.}
+#' }
#'
-#' @export Subcollection
+#' @name Subcollection
+#' @examples
+#' \dontrun{
+#' myFolder <- Subcollection$new("myFolder")
+#' myFile <- ArvadosFile$new("myFile")
+#'
+#' myFolder$add(myFile)
+#' myFolder$get("myFile")
+#' myFolder$remove("myFile")
+#'
+#' myFolder$move("newLocation/myFolder")
+#' }
+NULL
+
+#' @export
Subcollection <- R6::R6Class(
"Subcollection",
diff --git a/sdk/R/README.Rmd b/sdk/R/README.Rmd
index ebf591c..6315ddd 100644
--- a/sdk/R/README.Rmd
+++ b/sdk/R/README.Rmd
@@ -51,7 +51,7 @@ The API is not final and feedback is solicited from users on ways in which it co
`collectionList$items_available # count of total number of items (may be more than returned due to paging)`
`collectionList$items # items which match the filter criteria`
-* List all collections even when the number of items is greater than maximum API limit:
+* List all collections even if the number of items is greater than maximum API limit:
`collectionList <- arv$listAllCollections(list(list("name", "like", "Test%")))`
@@ -98,6 +98,11 @@ The API is not final and feedback is solicited from users on ways in which it co
`arvConnection <- arvadosFile$connection("w")`
`write.table(mytable, arvConnection)`
`arvadosFile$flush()`
+
+* Write to existing file (override current content of the file):
+
+ `arvadosFile <- collection$get("location/to/my/file.cpp")`
+ `arvadosFile$write("This is new file content")`
* Read whole file or just a portion of it:
@@ -133,11 +138,6 @@ The API is not final and feedback is solicited from users on ways in which it co
This examples will add file "main.cpp" in "./cpp/src/" folder if folder exists.
If subcollection contains more files or folders they will be added recursively.
-* Write to existing file (override current content of the file):
-
- `arvadosFile <- collection$get("location/to/my/file.cpp")`
- `arvadosFile$write("This is new file content")`
-
* Delete file from a collection:
`collection$remove("location/to/my/file.cpp")`
@@ -185,7 +185,7 @@ The API is not final and feedback is solicited from users on ways in which it co
`projects <- arv$listProjects(list(list("owner_uuid", "=", "aaaaa-j7d0g-ccccccccccccccc"))) # list subprojects of a project`
`arv$listProjects(list(list("name","like","Example%"))) # list projects which have names beginning with Example`
-* List all projects even when the number of items is greater than maximum API limit:
+* List all projects even if the number of items is greater than maximum API limit:
`collectionList <- arv$listAllProjects(list(list("name","like","Example%")))`
diff --git a/sdk/R/man/Arvados.Rd b/sdk/R/man/Arvados.Rd
index 6dfb0ce..9173830 100644
--- a/sdk/R/man/Arvados.Rd
+++ b/sdk/R/man/Arvados.Rd
@@ -1,25 +1,60 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/Arvados.R
-\docType{data}
\name{Arvados}
\alias{Arvados}
-\title{Arvados SDK Object}
-\format{An object of class \code{R6ClassGenerator} of length 24.}
-\usage{
-Arvados
-}
+\title{Arvados}
\description{
-All Arvados logic is inside this class
+Arvados class gives users ability to manipulate collections and projects.
+}
+\section{Usage}{
+
+\preformatted{arv = Arvados$new(authToken, hostName, numRetries = 0)}
}
-\section{Fields}{
+
+\section{Arguments}{
\describe{
-\item{\code{token}}{Token represents user authentification token.}
+ \item{authToken}{Authentification token. If not specified ARVADOS_API_TOKEN environment variable will be used.}
+ \item{hostName}{Host name. If not specified ARVADOS_API_HOST environment variable will be used.}
+ \item{numRetries}{Number which specifies how many times to retry failed service requests.}
+}
+}
-\item{\code{host}}{Host represents server name we wish to connect to.}
-}}
+\section{Methods}{
+
+\describe{
+ \item{getToken()}{Returns authentification token currently in use.}
+ \item{getHostName()}{Returns host name currently in use.}
+ \item{getNumRetries()}{Returns number which specifies how many times to retry failed service requests.}
+ \item{setNumRetries(newNumOfRetries)}{Sets number which specifies how many times to retry failed service requests.}
+ \item{getCollection(uuid)}{Get collection with specified UUID.}
+ \item{listCollections(filters = NULL, limit = 100, offset = 0)}{Returns list of collections based on filters parameter.}
+ \item{listAllCollections(filters = NULL)}{Lists all collections, based on filters parameter, even if the number of items is greater than maximum API limit.}
+ \item{deleteCollection(uuid)}{Deletes collection with specified UUID.}
+ \item{updateCollection(uuid, newContent)}{Updates collection with specified UUID.}
+ \item{createCollection(content)}{Creates new collection.}
+ \item{getProject(uuid)}{Get project with specified UUID.}
+ \item{listProjects(filters = NULL, limit = 100, offset = 0)}{Returns list of projects based on filters parameter.}
+ \item{listAllProjects(filters = NULL)}{Lists all projects, based on filters parameter, even if the number of items is greater than maximum API limit.}
+ \item{deleteProject(uuid)}{Deletes project with specified UUID.}
+ \item{updateProject(uuid, newContent)}{Updates project with specified UUID.}
+ \item{createProject(content)}{Creates new project.}
+}
+}
\examples{
-arv = Arvados$new("token", "host_name")
+\dontrun{
+arv <- Arvados$new("your Arvados token", "example.arvadosapi.com")
+
+collection <- arv$getCollection("uuid")
+
+collectionList <- arv$listCollections(list(list("name", "like", "Test\%")))
+collectionList <- arv$listAllCollections(list(list("name", "like", "Test\%")))
+
+deletedCollection <- arv$deleteCollection("uuid")
+
+updatedCollection <- arv$updateCollection("uuid", list(name = "New name", description = "New description"))
+
+createdCollection <- arv$createCollection(list(name = "Example", description = "This is a test collection"))
+}
}
-\keyword{datasets}
diff --git a/sdk/R/man/ArvadosFile.Rd b/sdk/R/man/ArvadosFile.Rd
index f48a71f..41f68bc 100644
--- a/sdk/R/man/ArvadosFile.Rd
+++ b/sdk/R/man/ArvadosFile.Rd
@@ -1,14 +1,57 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/ArvadosFile.R
-\docType{data}
\name{ArvadosFile}
\alias{ArvadosFile}
-\title{ArvadosFile Object}
-\format{An object of class \code{R6ClassGenerator} of length 24.}
-\usage{
-ArvadosFile
-}
+\title{ArvadosFile}
\description{
-Update description
+ArvadosFile class represents a file inside Arvados collection.
+}
+\section{Usage}{
+
+\preformatted{file = ArvadosFile$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 content of the connecitons buffer 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(newLocation)}{Moves 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$read("raw", offset = 1024, length = 512)
+
+
+#Write a table:
+arvConnection <- myFile$connection("w")
+write.table(mytable, arvConnection)
+arvadosFile$flush()
+
+#Read a table:
+arvConnection <- myFile$connection("r")
+mytable <- read.table(arvConnection)
+
+myFile$move("newFolder/myFile")
+}
}
-\keyword{datasets}
diff --git a/sdk/R/man/Collection.Rd b/sdk/R/man/Collection.Rd
index 46c76cb..4e96b7c 100644
--- a/sdk/R/man/Collection.Rd
+++ b/sdk/R/man/Collection.Rd
@@ -1,17 +1,49 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/Collection.R
-\docType{data}
\name{Collection}
\alias{Collection}
-\title{Arvados Collection Object}
-\format{An object of class \code{R6ClassGenerator} of length 24.}
-\usage{
-Collection
-}
+\title{Collection}
\description{
-Update description
+Collection class provides interface for working with Arvados collections.
+}
+\section{Usage}{
+
+\preformatted{collection = Collection$new(arv, uuid)}
+}
+
+\section{Arguments}{
+
+\describe{
+ \item{arv}{Arvados object.}
+ \item{uuid}{UUID of a collection.}
+}
}
+
+\section{Methods}{
+
+\describe{
+ \item{add(content)}{Adds ArvadosFile or Subcollection specified by content to the collection.}
+ \item{create(fileNames, relativePath = "")}{Creates one or more ArvadosFiles and adds them to the collection at specified path.}
+ \item{remove(fileNames)}{Remove one or more files from the collection.}
+ \item{move(content, newLocation)}{Moves ArvadosFile or Subcollection to another location in the collection.}
+ \item{getFileListing()}{Returns collections file content as character vector.}
+ \item{get(relativePath)}{If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.}
+}
+}
+
\examples{
-arv = Collection$new(api, uuid)
+\dontrun{
+collection <- Collection$new(arv, "uuid")
+
+collection$add(existingArvadosFile, "cpp")
+
+createdFiles <- collection$create(c("main.cpp", lib.dll), "cpp/src/")
+
+collection$remove("location/to/my/file.cpp")
+
+collection$move("folder/file.cpp", "file.cpp")
+
+arvadosFile <- collection$get("location/to/my/file.cpp")
+arvadosSubcollection <- collection$get("location/to/my/directory/")
+}
}
-\keyword{datasets}
diff --git a/sdk/R/man/Subcollection.Rd b/sdk/R/man/Subcollection.Rd
index e644e02..df0970b 100644
--- a/sdk/R/man/Subcollection.Rd
+++ b/sdk/R/man/Subcollection.Rd
@@ -1,14 +1,47 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/Subcollection.R
-\docType{data}
\name{Subcollection}
\alias{Subcollection}
-\title{Arvados SubCollection Object}
-\format{An object of class \code{R6ClassGenerator} of length 24.}
-\usage{
-Subcollection
-}
+\title{Subcollection}
\description{
-Update description
+Subcollection class represents a folder inside Arvados collection.
+It is essentially a composite of ArvadosFiles and other Subcollections.
+}
+\section{Usage}{
+
+\preformatted{subcollection = Subcollection$new(name)}
+}
+
+\section{Arguments}{
+
+\describe{
+ \item{name}{Name of the subcollection.}
+}
+}
+
+\section{Methods}{
+
+\describe{
+ \item{getName()}{Returns name of the subcollection.}
+ \item{getRelativePath()}{Returns subcollection path relative to the root.}
+ \item{add(content)}{Adds ArvadosFile or Subcollection specified by content to the subcollection.}
+ \item{remove(name)}{Removes ArvadosFile or Subcollection specified by name from the subcollection.}
+ \item{get(relativePath)}{If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.}
+ \item{getFileListing()}{Returns subcollections file content as character vector.}
+ \item{getSizeInBytes()}{Returns subcollections content size in bytes.}
+ \item{move(newLocation)}{Moves subcollection to a new location inside collection.}
+}
+}
+
+\examples{
+\dontrun{
+myFolder <- Subcollection$new("myFolder")
+myFile <- ArvadosFile$new("myFile")
+
+myFolder$add(myFile)
+myFolder$get("myFile")
+myFolder$remove("myFile")
+
+myFolder$move("newLocation/myFolder")
+}
}
-\keyword{datasets}
commit 4c7c4c13f51f99de535905ad02fe9239490a7956
Author: Fuad Muhic <fmuhic at capeannenterprises.com>
Date: Wed Feb 7 12:19:25 2018 +0100
Replaced README with README.Rmd
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic at capeannenterprises.com>
diff --git a/sdk/R/README b/sdk/R/README
deleted file mode 100644
index 4c99c75..0000000
--- a/sdk/R/README
+++ /dev/null
@@ -1,251 +0,0 @@
-R SDK for Arvados
-
-This SDK focuses on providing support for accessing Arvados projects, collections, and the files within collections.
-
-The API is not final and feedback is solicited from users on ways in which it could be improved.
-
-INSTALLATION
-
-1. Install the dependencies
-
- > install.packages(c('R6', 'httr', 'stringr', 'jsonlite', 'curl', 'XML'))
-
-If needed, you may have to install the supporting packages first. On Linux, these are:
-
- libxml2-dev, libssl-dev, libcurl4-gnutls-dev or libcurl4-openssl-dev
-
-2. Install the ArvardosR package
-
- > install.packages('/path/to/ArvadosR_0.0.2.tar.gz', repos = NULL, type="source", dependencies = TRUE)
-
-
-EXAMPLES OF USAGE
-
-
-#Load Library and Initialize API:
-
-library('ArvadosR')
-arv <- Arvados$new() # uses environment variables ARVADOS_API_TOKEN and ARVADOS_API_HOST
-arv <- Arvados$new("your Arvados token", "example.arvadosapi.com")
-
-
-#Optionally, add numRetries parameter to specify number of times to retry failed service requests.
-#Default is 0.
-
-arv <- Arvados$new("your Arvados token", "example.arvadosapi.com", numRetries = 3)
-
-#This parameter can be set at any time using setNumRetries
-
-arv$setNumRetries(5)
-
---------------------------------------------------------------------------------------------------------------------------------
-
-#Get a collection:
-
-arv$getCollection("uuid")
-
---------------------------------------------------------------------------------------------------------------------------------
-
-#List collections:
-collectionList <- arv$listCollections(list(list("name", "like", "Test%"))) # offset of 0 and default limit of 100
-collectionList <- arv$listCollections(list(list("name", "like", "Test%")), limit = 10, offset = 2)
-
-collectionList$items_available # count of total number of items (may be more than returned due to paging)
-collectionList$items # items which match the filter criteria
-
-#Next example will list all collections even when the number of items is greater than maximum API limit
-
-collectionList <- arv$listAllCollections(list(list("name", "like", "Test%")))
-
---------------------------------------------------------------------------------------------------------------------------------
-
-#Delete a collection:
-
-deletedCollection <- arv$deleteCollection("uuid")
-
---------------------------------------------------------------------------------------------------------------------------------
-
-#Update a collection's metadata:
-
-updatedCollection <- arv$updateCollection("uuid", list(name = "New name", description = "New description"))
-
---------------------------------------------------------------------------------------------------------------------------------
-
-#Create collection:
-
-createdCollection <- arv$createCollection(list(name = "Example", description = "This is a test collection"))
-
-
---------------------------------------------------------------------------------------------------------------------------------
-COLLECTION CONTENT MANIPULATION
---------------------------------------------------------------------------------------------------------------------------------
-
-#Create collection object:
-
-collection <- Collection$new(arv, "uuid")
-
---------------------------------------------------------------------------------------------------------------------------------
-
-#Get list of files
-
-collection$getFileListing()
-
---------------------------------------------------------------------------------------------------------------------------------
-
-#This will return ArvadosFile or Subcollection from internal tree-like structure.
-
-arvadosFile <- collection$get("location/to/my/file.cpp")
-
-#or
-
-arvadosSubcollection <- collection$get("location/to/my/directory/")
-
---------------------------------------------------------------------------------------------------------------------------------
-
-#Read a table
-
-arvadosFile <- collection$get("myinput.txt")
-arvConnection <- arvadosFile$connection("r")
-mytable <- read.table(arvConnection)
-
-#Write a table
-
-arvadosFile <- collection$create("myoutput.txt")
-arvConnection <- arvadosFile$connection("w")
-write.table(mytable, arvConnection)
-arvadosFile$flush()
-
---------------------------------------------------------------------------------------------------------------------------------
-
-#Read whole file or just a portion of it.
-
-fileContent <- arvadosFile$read()
-fileContent <- arvadosFile$read("text")
-fileContent <- arvadosFile$read("raw", offset = 1024, length = 512)
-
---------------------------------------------------------------------------------------------------------------------------------
-
-#Get ArvadosFile or Subcollection size
-
-size <- arvadosFile$getSizeInBytes()
-size <- arvadosSubcollection$getSizeInBytes()
-
---------------------------------------------------------------------------------------------------------------------------------
-
-#Create new file in a collection
-
-collection$create(fileNames, optionalRelativePath)
-
-#Example
-
-mainFile <- collection$create("main.cpp", "cpp/src/")
-fileList <- collection$create(c("main.cpp", lib.dll), "cpp/src/")
-
---------------------------------------------------------------------------------------------------------------------------------
-
-#Add existing ArvadosFile or Subcollection to a collection
-
-folder <- Subcollection$new("src")
-file <- ArvadosFile$new("main.cpp")
-folder$add(file)
-
-collection$add(folder, "cpp")
-
-#This examples will add file "main.cpp" in "./cpp/src/" folder if folder exists.
-#If subcollection contains more files or folders they will be added recursively.
-
---------------------------------------------------------------------------------------------------------------------------------
-
-#Write to existing file (Override current content of the file)
-
-arvadosFile <- collection$get("location/to/my/file.cpp")
-
-arvadosFile$write("This is new file content")
-
---------------------------------------------------------------------------------------------------------------------------------
-
-#Delete file from a collection
-
-collection$remove("location/to/my/file.cpp")
-
-#You can remove both Subcollection and ArvadosFile
-#If subcollection contains more files or folders they will be removed recursively.
-
-#You can also remove multiple files
-
-collection$remove(c("path/to/my/file.cpp", "path/to/other/file.cpp"))
-
-#Delete file or folder from a Subcollection
-
-subcollection <- collection$get("mySubcollection/")
-subcollection$remove("fileInsideSubcollection.exe")
-subcollection$remove("folderInsideSubcollection/")
-
---------------------------------------------------------------------------------------------------------------------------------
-
-#Move file or folder inside collection
-
-#Directley from collection
-
-collection$move("folder/file.cpp", "file.cpp")
-
-#Or from file
-
-file <- collection$get("location/to/my/file.cpp")
-file$move("newDestination/file.cpp")
-
-#Or from subcollection
-
-subcollection <- collection$get("location/to/folder")
-subcollection$move("newDestination/folder")
-
-#Make sure to include new file name in destination
-#In second example file$move("newDestination/") will not work
-
---------------------------------------------------------------------------------------------------------------------------------
-WORKING WITH ARVADOS PROJECTS
---------------------------------------------------------------------------------------------------------------------------------
-
-#Get a project:
-
-arv$getProject("uuid")
-
---------------------------------------------------------------------------------------------------------------------------------
-
-#List projects:
-
-projects <- arv$listProjects(list(list("owner_uuid", "=", "aaaaa-j7d0g-ccccccccccccccc"))) # list subprojects of a project
-arv$listProjects(list(list("name","like","Example%"))) # list projects which have names beginning with Example
-
-#Next example will list all projects even when the number of items is greater than maximum API limit
-
-collectionList <- arv$listAllProjects(list(list("name","like","Example%")))
-
---------------------------------------------------------------------------------------------------------------------------------
-
-#Delete a project:
-
-deletedProject <- arv$deleteProject("uuid")
-
---------------------------------------------------------------------------------------------------------------------------------
-
-#Update project:
-
-updatedProject <- arv$updateProject("uuid", list(name = "new_name", description = "new description"))
-
---------------------------------------------------------------------------------------------------------------------------------
-
-#Create project:
-
-createdProject <- arv$createProject(list(name = "project_name", description = "project description"))
-
-
---------------------------------------------------------------------------------------------------------------------------------
-BUILDING THE ARVADOS SDK TARBALL
---------------------------------------------------------------------------------------------------------------------------------
-
-
-cd arvados/sdk
-R CMD build R
-
-This will create a tarball of the Arvados package in the current directory.
diff --git a/sdk/R/README.Rmd b/sdk/R/README.Rmd
new file mode 100644
index 0000000..ebf591c
--- /dev/null
+++ b/sdk/R/README.Rmd
@@ -0,0 +1,209 @@
+## R SDK for Arvados
+
+This SDK focuses on providing support for accessing Arvados projects, collections, and the files within collections.
+The API is not final and feedback is solicited from users on ways in which it could be improved.
+
+### INSTALLATION
+
+1. Install the dependencies
+
+ `install.packages(c('R6', 'httr', 'stringr', 'jsonlite', 'curl', 'XML'))`
+
+ If needed, you may have to install the supporting packages first.
+ On Linux, these are: libxml2-dev, libssl-dev, libcurl4-gnutls-dev or libcurl4-openssl-dev
+
+
+2. Install the ArvardosR package
+
+ `install.packages('/path/to/ArvadosR_0.0.2.tar.gz', repos = NULL, type="source", dependencies = TRUE)`
+
+### EXAMPLES OF USAGE
+
+#### INITIALIZING API
+
+* Load Library and Initialize API:
+
+ `library('ArvadosR')`
+ `arv <- Arvados$new() # uses environment variables ARVADOS_API_TOKEN and ARVADOS_API_HOST`
+ `arv <- Arvados$new("your Arvados token", "example.arvadosapi.com")`
+
+ Optionally, add numRetries parameter to specify number of times to retry failed service requests.
+ Default is 0.
+
+ `arv <- Arvados$new("your Arvados token", "example.arvadosapi.com", numRetries = 3)`
+
+ This parameter can be set at any time using setNumRetries
+
+ `arv$setNumRetries(5)`
+
+
+#### WORKING WITH COLLECTIONS
+
+* Get a collection:
+
+ `collection <- arv$getCollection("uuid")`
+
+* List collections:
+
+ `collectionList <- arv$listCollections(list(list("name", "like", "Test%"))) # offset of 0 and default limit of 100`
+ `collectionList <- arv$listCollections(list(list("name", "like", "Test%")), limit = 10, offset = 2)`
+
+ `collectionList$items_available # count of total number of items (may be more than returned due to paging)`
+ `collectionList$items # items which match the filter criteria`
+
+* List all collections even when the number of items is greater than maximum API limit:
+
+ `collectionList <- arv$listAllCollections(list(list("name", "like", "Test%")))`
+
+* Delete a collection:
+
+ `deletedCollection <- arv$deleteCollection("uuid")`
+
+* Update a collection's metadata:
+
+ `updatedCollection <- arv$updateCollection("uuid", list(name = "New name", description = "New description"))`
+
+* Create collection:
+
+ `createdCollection <- arv$createCollection(list(name = "Example", description = "This is a test collection"))`
+
+
+#### MANIPULATIN COLLECTION CONTENT
+
+* Create collection object:
+
+ `collection <- Collection$new(arv, "uuid")`
+
+* Get list of files:
+
+ `files <- collection$getFileListing()`
+
+* Get ArvadosFile or Subcollection from internal tree-like structure:
+
+ `arvadosFile <- collection$get("location/to/my/file.cpp")`
+
+ or
+
+ `arvadosSubcollection <- collection$get("location/to/my/directory/")`
+
+* Read a table:
+
+ `arvadosFile <- collection$get("myinput.txt")`
+ `arvConnection <- arvadosFile$connection("r")`
+ `mytable <- read.table(arvConnection)`
+
+* Write a table:
+
+ `arvadosFile <- collection$create("myoutput.txt")`
+ `arvConnection <- arvadosFile$connection("w")`
+ `write.table(mytable, arvConnection)`
+ `arvadosFile$flush()`
+
+* Read whole file or just a portion of it:
+
+ `fileContent <- arvadosFile$read()`
+ `fileContent <- arvadosFile$read("text")`
+ `fileContent <- arvadosFile$read("raw", offset = 1024, length = 512)`
+
+* Get ArvadosFile or Subcollection size:
+
+ `size <- arvadosFile$getSizeInBytes()`
+
+ or
+
+ `size <- arvadosSubcollection$getSizeInBytes()`
+
+* Create new file in a collection:
+
+ `collection$create(fileNames, optionalRelativePath)`
+
+ Example:
+
+ `mainFile <- collection$create("main.cpp", "cpp/src/")`
+ `fileList <- collection$create(c("main.cpp", lib.dll), "cpp/src/")`
+
+* Add existing ArvadosFile or Subcollection to a collection:
+
+ `folder <- Subcollection$new("src")`
+ `file <- ArvadosFile$new("main.cpp")`
+ `folder$add(file)`
+
+ `collection$add(folder, "cpp")`
+
+ This examples will add file "main.cpp" in "./cpp/src/" folder if folder exists.
+ If subcollection contains more files or folders they will be added recursively.
+
+* Write to existing file (override current content of the file):
+
+ `arvadosFile <- collection$get("location/to/my/file.cpp")`
+ `arvadosFile$write("This is new file content")`
+
+* Delete file from a collection:
+
+ `collection$remove("location/to/my/file.cpp")`
+
+ You can remove both Subcollection and ArvadosFile.
+ If subcollection contains more files or folders they will be removed recursively.
+
+ You can also remove multiple files at once:
+
+ `collection$remove(c("path/to/my/file.cpp", "path/to/other/file.cpp"))`
+
+* Delete file or folder from a Subcollection:
+
+ `subcollection <- collection$get("mySubcollection/")`
+ `subcollection$remove("fileInsideSubcollection.exe")`
+ `subcollection$remove("folderInsideSubcollection/")`
+
+* Move file or folder inside collection:
+
+ Directley from collection
+
+ `collection$move("folder/file.cpp", "file.cpp")`
+
+ Or from file
+
+ `file <- collection$get("location/to/my/file.cpp")`
+ `file$move("newDestination/file.cpp")`
+
+ Or from subcollection
+
+ `subcollection <- collection$get("location/to/folder")`
+ `subcollection$move("newDestination/folder")`
+
+ Make sure to include new file name in destination.
+ In second example file$move("newDestination/") will not work.
+
+#### WORKING WITH ARVADOS PROJECTS
+
+* Get a project:
+
+ `project <- arv$getProject("uuid")`
+
+* List projects:
+
+ `projects <- arv$listProjects(list(list("owner_uuid", "=", "aaaaa-j7d0g-ccccccccccccccc"))) # list subprojects of a project`
+ `arv$listProjects(list(list("name","like","Example%"))) # list projects which have names beginning with Example`
+
+* List all projects even when the number of items is greater than maximum API limit:
+
+ `collectionList <- arv$listAllProjects(list(list("name","like","Example%")))`
+
+* Delete a project:
+
+ `deletedProject <- arv$deleteProject("uuid")`
+
+* Update project:
+
+ `updatedProject <- arv$updateProject("uuid", list(name = "new_name", description = "new description"))`
+
+* Create project:
+
+ `createdProject <- arv$createProject(list(name = "project_name", description = "project description"))`
+
+### BUILDING THE ARVADOS SDK TARBALL
+
+cd arvados/sdk
+R CMD build R
+
+This will create a tarball of the Arvados package in the current directory.
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