X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/f67c59f3fea793ed3ccea7f5a8106014ec2dc108..44ab8ee44302102a7cd5289ef7336d7a94594558:/sdk/R/README diff --git a/sdk/R/README b/sdk/R/README index 344deab78d..8a0c31dce6 100644 --- a/sdk/R/README +++ b/sdk/R/README @@ -1,85 +1,117 @@ R SDK for Arvados -Examples of usage: +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 -#Initialize API: +2. Install the ArvardosR package -arv <- Arvados$new("insert_token", "insert_host_name") + > install.packages('/path/to/ArvadosR_0.0.2.tar.gz', repos = NULL, type="source", dependencies = TRUE) + + +EXAMPLES OF USAGE + + +#Load Library and Initialize API: + +library('ArvadosR') +arv <- Arvados$new() # uses environment variables ARVADOS_API_TOKEN and ARVADOS_API_HOST +arv <- Arvados$new("your Arvados token", "example.arvadosapi.com") -------------------------------------------------------------------------------------------------------------------------------- -#Get collection: +#Get a collection: arv$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 -collectionList <- arv$listCollections(list("uuid", "=" "aaaaa-bbbbb-ccccccccccccccc"), limit = 10, offset = 2) +#Next example will list all collections even when the number of items is greater than maximum API limit + +collectionList <- arv$listAllCollections(list(list("name", "like", "Test%"))) -------------------------------------------------------------------------------------------------------------------------------- -#Delete collection: +#Delete a collection: deletedCollection <- arv$deleteCollection("uuid") -------------------------------------------------------------------------------------------------------------------------------- -#Update collection: +#Update a collection's metadata: -updatedCollection <- arv$updateCollection("uuid", list(collection = list(name = "new_name", description = "new_desciption"))) +updatedCollection <- arv$updateCollection("uuid", list(name = "New name", description = "New description")) -------------------------------------------------------------------------------------------------------------------------------- #Create collection: -updatedCollection <- arv$createCollection("uuid", list(collection = list(name = "new_name", description = "new_desciption"))) - --------------------------------------------------------------------------------------------------------------------------------- - --------------------------------------------------------------------------------------------------------------------------------- +createdCollection <- arv$createCollection(list(name = "Example", description = "This is a test collection")) -#Collection manipulation: -------------------------------------------------------------------------------------------------------------------------------- - +COLLECTION CONTENT MANIPULATION -------------------------------------------------------------------------------------------------------------------------------- #Create collection object: -arv <- Arvados$new("insert_token", "insert_host_name") collection <- Collection$new(arv, "uuid") -------------------------------------------------------------------------------------------------------------------------------- -#Print content of the collection (directory/folder tree structure) +#Get list of files -collection$printFileContent() +collection$getFileListing() -------------------------------------------------------------------------------------------------------------------------------- -#Get file/folder content as character vector +#This will return ArvadosFile or Subcollection from internal tree-like structure. + +arvadosFile <- collection$get("location/to/my/file.cpp") + +#or -collection$getFileContent() +arvadosSubcollection <- collection$get("location/to/my/directory/") -------------------------------------------------------------------------------------------------------------------------------- -#This will return ArvadosFile or Subcollection from internal tree-like structure. +#Read a table -arvadosFile <- collection$get("location/to/my/file.cpp") +arvadosFile <- collection$get("myinput.txt") +arvConnection <- arvadosFile$connection("r") +mytable <- read.table(arvConnection) -#or +#Write a table -arvadosSubcollection <- collection.get("location/to/my/directory/") +arvadosFile <- collection$create("myoutput.txt") +arvConnection <- arvadosFile$connection("w") +write.table(mytable, arvConnection) +arvadosFile$flush() -------------------------------------------------------------------------------------------------------------------------------- #Read whole file or just a portion of it. -fileContent <- arvadosFile$read(offset = 1024, length = 512) +fileContent <- arvadosFile$read() +fileContent <- arvadosFile$read("text") +fileContent <- arvadosFile$read("raw", offset = 1024, length = 512) -------------------------------------------------------------------------------------------------------------------------------- @@ -89,3 +121,121 @@ 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.