2. Install the ArvardosR package
- > install.packages('/path/to/ArvadosR_0.0.1.tar.gz', repos = NULL, type="source", dependencies = TRUE)
+ > install.packages('/path/to/ArvadosR_0.0.2.tar.gz', repos = NULL, type="source", dependencies = TRUE)
EXAMPLES OF USAGE
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$listAllCollections(list(list("name", "like", "Test%")))
+
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#Delete a collection:
#Update a collection's metadata:
-updatedCollection <- arv$updateCollection("uuid", list(name = "My new name", description = "a brand new description"))
+updatedCollection <- arv$updateCollection("uuid", list(name = "New name", description = "New description"))
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-#Get file/folder content as character vector
+#Get list of files
-collection$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$read()
#Add existing ArvadosFile or Subcollection to a collection
folder <- Subcollection$new("src")
-file <- ArvadosFile$new("main.cpp")
+file <- ArvadosFile$new("main.cpp")
folder$add(file)
collection$add(folder, "cpp")
#Delete file from a collection
-file <- collection$get("location/to/my/file.cpp")
-
-file$removeFromCollection()
+collection$remove("location/to/my/file.cpp")
-#Or
-
-collection$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")
+#Make sure to include new file name in destination
+#In second example file$move("newDestination/") will not work
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WORKING WITH ARVADOS PROJECTS
projects <- arv$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%")))
+
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#Delete a project: