sdk/R/README

   1 R SDK for Arvados
   2
   3 This SDK focuses on providing support for accessing Arvados projects, collections, and the files within collections.
   4
   5 The API is not final and feedback is solicited from users on ways in which it could be improved.
   6
   7 INSTALLATION
   8
   9 1. Install the dependencies
  10
  11     > install.packages(c('R6', 'httr', 'stringr', 'jsonlite', 'curl', 'XML'))
  12
  13 If needed, you may have to install the supporting packages first. On Linux, these are:
  14
  15     libxml2-dev, libssl-dev, curl
  16
  17 2. Install the ArvardosR package
  18
  19     > install.packages('/path/to/ArvadosR_0.0.1.tar.gz', repos = NULL, type="source", dependencies = TRUE)
  20
  21
  22 EXAMPLES OF USAGE
  23
  24
  25 #Load Library and Initialize API:
  26
  27 library('ArvadosR')
  28 arv <- Arvados$new() # uses environment variables ARVADOS_API_TOKEN and ARVADOS_API_HOST
  29 arv <- Arvados$new("your Arvados token", "example.arvadosapi.com")
  30
  31 --------------------------------------------------------------------------------------------------------------------------------
  32
  33 #Get a collection:
  34
  35 arv$getCollection("uuid")
  36
  37 --------------------------------------------------------------------------------------------------------------------------------
  38
  39 #List collections:
  40 collectionList <- arv$listCollections(list(list("name", "like", "Test%"))) # offset of 0 and default limit of 100
  41 collectionList <- arv$listCollections(list(list("name", "like", "Test%")), limit = 10, offset = 2)
  42
  43 collectionList$items_available # count of total number of items (may be more than returned due to paging)
  44 collectionList$items # items which match the filter criteria
  45
  46 --------------------------------------------------------------------------------------------------------------------------------
  47
  48 #Delete a collection:
  49
  50 deletedCollection <- arv$deleteCollection("uuid")
  51
  52 --------------------------------------------------------------------------------------------------------------------------------
  53
  54 #Update a collection's metadata:
  55
  56 updatedCollection <- arv$updateCollection("uuid", list(name = "My new name", description = "a brand new description"))
  57
  58 --------------------------------------------------------------------------------------------------------------------------------
  59
  60 #Create collection:
  61
  62 createdCollection <- arv$createCollection(list(name = "Example", description = "This is a test collection"))
  63
  64
  65 --------------------------------------------------------------------------------------------------------------------------------
  66 COLLECTION CONTENT MANIPULATION
  67 --------------------------------------------------------------------------------------------------------------------------------
  68
  69 #Create collection object:
  70
  71 collection <- Collection$new(arv, "uuid")
  72
  73 --------------------------------------------------------------------------------------------------------------------------------
  74
  75 #Get file/folder content as character vector
  76
  77 collection$getFileContent()
  78
  79 --------------------------------------------------------------------------------------------------------------------------------
  80
  81 #This will return ArvadosFile or Subcollection from internal tree-like structure.
  82
  83 arvadosFile <- collection$get("location/to/my/file.cpp")
  84
  85 #or
  86
  87 arvadosSubcollection <- collection$get("location/to/my/directory/")
  88
  89 --------------------------------------------------------------------------------------------------------------------------------
  90
  91 #Read whole file or just a portion of it.
  92
  93 fileContent <- arvadosFile$read()
  94 fileContent <- arvadosFile$read("text")
  95 fileContent <- arvadosFile$read("raw", offset = 1024, length = 512)
  96
  97 --------------------------------------------------------------------------------------------------------------------------------
  98
  99 #Get ArvadosFile or Subcollection size
 100
 101 size <- arvadosFile$getSizeInBytes()
 102 size <- arvadosSubcollection$getSizeInBytes()
 103
 104 --------------------------------------------------------------------------------------------------------------------------------
 105
 106 #Create new file in a collection
 107
 108 collection$create(fileNames, optionalRelativePath)
 109
 110 #Example
 111
 112 mainFile <- collection$create("main.cpp", "cpp/src/")
 113 fileList <- collection$create(c("main.cpp", lib.dll), "cpp/src/")
 114
 115 --------------------------------------------------------------------------------------------------------------------------------
 116
 117 #Add existing ArvadosFile or Subcollection to a collection
 118
 119 folder <- Subcollection$new("src")
 120 file <- ArvadosFile$new("main.cpp")
 121 folder$add(file)
 122
 123 collection$add(folder, "cpp")
 124
 125 #This examples will add file "main.cpp" in "./cpp/src/" folder if folder exists.
 126 #If subcollection contains more files or folders they will be added recursively.
 127
 128 --------------------------------------------------------------------------------------------------------------------------------
 129
 130 #Write to existing file (Override current content of the file)
 131
 132 arvadosFile <- collection$get("location/to/my/file.cpp")
 133
 134 arvadosFile$write("This is new file content")
 135
 136 --------------------------------------------------------------------------------------------------------------------------------
 137
 138 #Delete file from a collection
 139
 140 file <- collection$get("location/to/my/file.cpp")
 141
 142 file$removeFromCollection()
 143
 144 #Or
 145
 146 collection$remove(file)
 147
 148 #Both examples will remove file "file.cpp" from a collection
 149 #If subcollection contains more files or folders they will be removed recursively.
 150
 151 #You can also remove multiple files
 152
 153 collection$remove(c("path/to/my/file.cpp", "path/to/other/file.cpp"))
 154
 155 --------------------------------------------------------------------------------------------------------------------------------
 156
 157 #Move file or folder inside collection
 158
 159 file <- collection$get("location/to/my/file.cpp")
 160
 161 file$move("destination/file.cpp")
 162
 163 #Or subcollections
 164
 165 subcollection <- collection$get("location/to/folder")
 166
 167 subcollection$move("destination/folder")
 168
 169 #Make sure to include folder name in destination
 170 #For example
 171 #file$move("destination/") will not work
 172
 173
 174 --------------------------------------------------------------------------------------------------------------------------------
 175 WORKING WITH ARVADOS PROJECTS
 176 --------------------------------------------------------------------------------------------------------------------------------
 177
 178 #Get a project:
 179
 180 arv$getProject("uuid")
 181
 182 --------------------------------------------------------------------------------------------------------------------------------
 183
 184 #List projects:
 185
 186 projects <- arv$listProjects(list(list("owner_uuid", "=", "aaaaa-j7d0g-ccccccccccccccc"))) # list subprojects of a project
 187 arv$listProjects(list(list("name","like","Example%"))) # list projects which have names beginning with Example
 188
 189 --------------------------------------------------------------------------------------------------------------------------------
 190
 191 #Delete a project:
 192
 193 deletedProject <- arv$deleteProject("uuid")
 194
 195 --------------------------------------------------------------------------------------------------------------------------------
 196
 197 #Update project:
 198
 199 updatedProject <- arv$updateProject("uuid", list(name = "new_name", description = "new description"))
 200
 201 --------------------------------------------------------------------------------------------------------------------------------
 202
 203 #Create project:
 204
 205 createdProject <- arv$createProject(list(name = "project_name", description = "project description"))
 206
 207
 208 --------------------------------------------------------------------------------------------------------------------------------
 209 BUILDING THE ARVADOS SDK TARBALL
 210 --------------------------------------------------------------------------------------------------------------------------------
 211
 212
 213 cd arvados/sdk
 214 R CMD build R
 215
 216 This will create a tarball of the Arvados package in the current directory.