R SDK for Arvados

Installation from source

1. Dependencies

libxml2-dev, libssl-dev, curl

2. Build the ArvadosR package tarball

cd arvados/sdk
R CMD build R

That will create a tarball of the Arvados package in the current directory.

3. Install the R package and its dependencies

Then start R. Assuming the generated tarball is named `ArvadosR_0.0.1.tar.gz`,
install it like this:

> install.packages(c('R6', 'httr', 'stringr', 'jsonlite', 'curl', 'XML'))
> install.packages('./ArvadosR_0.0.1.tar.gz', repos = NULL, type="source", dependencies = TRUE)
> library('ArvadosR')

4. Examples of usage:

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#Initialize API:

arv <- Arvados$new("insert_token", "insert_host_name")

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#Get collection:

arv$getCollection("uuid")

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#List collections:
collectionList <- arv$listCollections(list(list("uuid", "=", "aaaaa-4zz18-ccccccccccccccc")), limit = 10, offset = 2)

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#Delete collection:

deletedCollection <- arv$deleteCollection("uuid")

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#Update collection:

updatedCollection <- arv$updateCollection("uuid", list(list(name = "new_name", description = "new_desciption")))

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#Create collection:

createdCollection <- arv$createCollection(list(list(name = "new_name", description = "new_desciption")))

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#Collection content manipulation:

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#Create collection object:

collection <- Collection$new(arv, "uuid")

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#Get file/folder content as character vector

collection$getFileContent()

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#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/")

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#Read whole file or just a portion of it.

fileContent <- arvadosFile$read(offset = 1024, length = 512)

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#Get ArvadosFile or Subcollection size 

size <- arvadosFile$getSizeInBytes()
size <- arvadosSubcollection$getSizeInBytes()

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#Create new file in a collection

#Call structure

collection$add(arvadosFileOrSubcollectionOrFileName, optionalRelativePath)

#Example

collection$add("main.cpp", "cpp/src/")

#or

folder <- Subcollection$new("src")
file <- ArvadosFile$new("main.cpp")
folder$add(file)

collection$add(folder, "cpp")

#Both 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.

#You can also add multiple files

collection$add(c("path/to/my/file.cpp", "path/to/other/file.cpp"))

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#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")

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#Delete file from a collection

file <- collection$get("location/to/my/file.cpp")

file$removeFromCollection()

#Or

collection$remove(file)

#Both examples will remove file "file.cpp" from a collection
#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"))

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#Move file or folder inside collection

file <- collection$get("location/to/my/file.cpp")

file$move("destination/file.cpp")

#Or subcollections

subcollection <- collection$get("location/to/folder")

subcollection$move("destination/folder")

#Make sure to include folder name in destination
#For example
#file$move("destination/") will not work

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# Working with projects:

#Get project:

arv$getProject("uuid")

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#List projects:
projects <- arv$listProjects(list(list("uuid", "=", "aaaaa-j7d0g-ccccccccccccccc")), limit = 10, offset = 2)

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#Delete project:

deletedProject <- arv$deleteProject("uuid")

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#Update project:

updatedProject <- arv$updateProject("uuid", list(list(name = "new_name", description = "new_desciption")))

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#Create project:

createdProject <- arv$createProject(list(list(name = "project_name", description = "project_desciption")))

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