+++ /dev/null
-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.
--- /dev/null
+## 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.
projects / arvados.git / commitdiff