R SDK for Arvados
-Installation from source
+This SDK focuses on providing support for accessing Arvados projects, collections, and the files within collections.
-1. Dependencies
+The API is not final and feedback is solicited from users on ways in which it could be improved.
-libxml2-dev, libssl-dev, curl
+INSTALLATION
-2. Build the ArvadosR package tarball
+1. Install the dependencies
-cd arvados/sdk
-R CMD build R
+ > install.packages(c('R6', 'httr', 'stringr', 'jsonlite', 'curl', 'XML'))
-That will create a tarball of the Arvados package in the current directory.
+If needed, you may have to install the supporting packages first. On Linux, these are:
-3. Install the R package and its dependencies
+ libxml2-dev, libssl-dev, libcurl4-gnutls-dev or libcurl4-openssl-dev
-Then start R. Assuming the generated tarball is named `ArvadosR_0.0.1.tar.gz`,
-install it like this:
+2. Install the ArvardosR package
-> 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')
+ > install.packages('/path/to/ArvadosR_0.0.2.tar.gz', repos = NULL, type="source", dependencies = TRUE)
-4. Examples of usage:
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+EXAMPLES OF USAGE
-#Initialize API:
-arv <- Arvados$new("insert_token", "insert_host_name")
+#Load Library and Initialize API:
+
+library('ArvadosR')
+arv <- Arvados$new() # uses environment variables ARVADOS_API_TOKEN and ARVADOS_API_HOST
+arv <- Arvados$new("your Arvados token", "example.arvadosapi.com")
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-#Get collection:
+#Get a collection:
arv$getCollection("uuid")
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#List collections:
-collectionList <- arv$listCollections(list(list("uuid", "=", "aaaaa-4zz18-ccccccccccccccc")), limit = 10, offset = 2)
+collectionList <- arv$listCollections(list(list("name", "like", "Test%"))) # offset of 0 and default limit of 100
+collectionList <- arv$listCollections(list(list("name", "like", "Test%")), limit = 10, offset = 2)
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+collectionList$items_available # count of total number of items (may be more than returned due to paging)
+collectionList$items # items which match the filter criteria
-#Delete collection:
+#Next example will list all collections even when the number of items is greater than maximum API limit
-deletedCollection <- arv$deleteCollection("uuid")
+collectionList <- arv$listAllCollections(list(list("name", "like", "Test%")))
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-#Update collection:
+#Delete a collection:
-updatedCollection <- arv$updateCollection("uuid", list(name = "new_name", description = "new_desciption"))
+deletedCollection <- arv$deleteCollection("uuid")
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-#Create collection:
+#Update a collection's metadata:
-createdCollection <- arv$createCollection(list(name = "new_name", description = "new_desciption"))
+updatedCollection <- arv$updateCollection("uuid", list(name = "New name", description = "New description"))
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+#Create collection:
-#Collection content manipulation:
+createdCollection <- arv$createCollection(list(name = "Example", description = "This is a test collection"))
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+--------------------------------------------------------------------------------------------------------------------------------
+COLLECTION CONTENT MANIPULATION
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#Create collection object:
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-#Get file/folder content as character vector
+#Get list of files
-collection$getFileContent()
+collection$getFileListing()
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+#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()
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-#Get ArvadosFile or Subcollection size
+#Get ArvadosFile or Subcollection size
size <- arvadosFile$getSizeInBytes()
size <- arvadosSubcollection$getSizeInBytes()
#Create new file in a collection
-#Call structure
-
-collection$add(arvadosFileOrSubcollectionOrFileName, optionalRelativePath)
+collection$create(fileNames, optionalRelativePath)
#Example
-collection$add("main.cpp", "cpp/src/")
+mainFile <- collection$create("main.cpp", "cpp/src/")
+fileList <- collection$create(c("main.cpp", lib.dll), "cpp/src/")
-#or
+--------------------------------------------------------------------------------------------------------------------------------
+
+#Add existing ArvadosFile or Subcollection to a collection
folder <- Subcollection$new("src")
-file <- ArvadosFile$new("main.cpp")
+file <- ArvadosFile$new("main.cpp")
folder$add(file)
collection$add(folder, "cpp")
-#Both examples will add file "main.cpp" in "./cpp/src/" folder if folder exists.
+#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.
-#You can also add multiple files
-
-collection$add(c("path/to/my/file.cpp", "path/to/other/file.cpp"))
-
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#Write to existing file (Override current content of the file)
#Delete file from a collection
-file <- collection$get("location/to/my/file.cpp")
-
-file$removeFromCollection()
-
-#Or
+collection$remove("location/to/my/file.cpp")
-collection$remove(file)
-
-#Both examples will remove file "file.cpp" from a collection
+#You can remove both Subcollection and ArvadosFile
#If subcollection contains more files or folders they will be removed recursively.
#You can also remove multiple files
collection$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$remove("folderInsideSubcollection/")
+
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#Move file or folder inside collection
-file <- collection$get("location/to/my/file.cpp")
+#Directley from collection
-file$move("destination/file.cpp")
+collection$move("folder/file.cpp", "file.cpp")
-#Or subcollections
+#Or from file
-subcollection <- collection$get("location/to/folder")
+file <- collection$get("location/to/my/file.cpp")
+file$move("newDestination/file.cpp")
-subcollection$move("destination/folder")
+#Or from subcollection
-#Make sure to include folder name in destination
-#For example
-#file$move("destination/") will not work
+subcollection <- collection$get("location/to/folder")
+subcollection$move("newDestination/folder")
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+#Make sure to include new file name in destination
+#In second example file$move("newDestination/") will not work
+--------------------------------------------------------------------------------------------------------------------------------
+WORKING WITH ARVADOS PROJECTS
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-# Working with projects:
-
-#Get project:
+#Get a project:
arv$getProject("uuid")
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#List projects:
-projects <- arv$listProjects(list(list("uuid", "=", "aaaaa-j7d0g-ccccccccccccccc")), limit = 10, offset = 2)
+
+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$listAllProjects(list(list("name","like","Example%")))
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-#Delete project:
+#Delete a project:
deletedProject <- arv$deleteProject("uuid")
#Update project:
-updatedProject <- arv$updateProject("uuid", list(name = "new_name", description = "new_desciption"))
+updatedProject <- arv$updateProject("uuid", list(name = "new_name", description = "new description"))
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#Create project:
-createdProject <- arv$createProject(list(name = "project_name", description = "project_desciption"))
+createdProject <- arv$createProject(list(name = "project_name", description = "project description"))
+
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+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 / blobdiff