sdk/R/README

   1 R SDK for Arvados
   2
   3 Installation from source
   4
   5 1. Dependencies
   6
   7 libxml2-dev, libssl-dev, curl
   8
   9 2. Build the ArvadosR package tarball
  10
  11 cd arvados/sdk
  12 R CMD build R
  13
  14 That will create a tarball of the Arvados package in the current directory.
  15
  16 3. Install the R package and its dependencies
  17
  18 Then start R. Assuming the generated tarball is named `ArvadosR_0.0.1.tar.gz`,
  19 install it like this:
  20
  21 > install.packages(c('R6', 'httr', 'stringr', 'jsonlite', 'curl', 'XML'))
  22 > install.packages('./ArvadosR_0.0.1.tar.gz', repos = NULL, type="source", dependencies = TRUE)
  23 > library('ArvadosR')
  24
  25 4. Examples of usage:
  26
  27 --------------------------------------------------------------------------------------------------------------------------------
  28
  29 #Initialize API:
  30
  31 arv <- Arvados$new("insert_token", "insert_host_name")
  32
  33 --------------------------------------------------------------------------------------------------------------------------------
  34
  35 #Get collection:
  36
  37 arv$getCollection("uuid")
  38
  39 --------------------------------------------------------------------------------------------------------------------------------
  40
  41 #List collections:
  42 collectionList <- arv$listCollections(list(list("uuid", "=", "aaaaa-4zz18-ccccccccccccccc")), limit = 10, offset = 2)
  43
  44 --------------------------------------------------------------------------------------------------------------------------------
  45
  46 #Delete collection:
  47
  48 deletedCollection <- arv$deleteCollection("uuid")
  49
  50 --------------------------------------------------------------------------------------------------------------------------------
  51
  52 #Update collection:
  53
  54 updatedCollection <- arv$updateCollection("uuid", list(list(name = "new_name", description = "new_desciption")))
  55
  56 --------------------------------------------------------------------------------------------------------------------------------
  57
  58 #Create collection:
  59
  60 createdCollection <- arv$createCollection(list(list(name = "new_name", description = "new_desciption")))
  61
  62 --------------------------------------------------------------------------------------------------------------------------------
  63
  64 --------------------------------------------------------------------------------------------------------------------------------
  65
  66 #Collection content manipulation:
  67
  68 --------------------------------------------------------------------------------------------------------------------------------
  69
  70 --------------------------------------------------------------------------------------------------------------------------------
  71
  72 #Create collection object:
  73
  74 collection <- Collection$new(arv, "uuid")
  75
  76 --------------------------------------------------------------------------------------------------------------------------------
  77
  78 #Get file/folder content as character vector
  79
  80 collection$getFileContent()
  81
  82 --------------------------------------------------------------------------------------------------------------------------------
  83
  84 #This will return ArvadosFile or Subcollection from internal tree-like structure.
  85
  86 arvadosFile <- collection$get("location/to/my/file.cpp")
  87
  88 #or
  89
  90 arvadosSubcollection <- collection$get("location/to/my/directory/")
  91
  92 --------------------------------------------------------------------------------------------------------------------------------
  93
  94 #Read whole file or just a portion of it.
  95
  96 fileContent <- arvadosFile$read()
  97 fileContent <- arvadosFile$read("text")
  98 fileContent <- arvadosFile$read("raw", offset = 1024, length = 512)
  99
 100 --------------------------------------------------------------------------------------------------------------------------------
 101
 102 #Get ArvadosFile or Subcollection size
 103
 104 size <- arvadosFile$getSizeInBytes()
 105 size <- arvadosSubcollection$getSizeInBytes()
 106
 107 --------------------------------------------------------------------------------------------------------------------------------
 108
 109 #Create new file in a collection
 110
 111 #Call structure
 112
 113 collection$add(arvadosFileOrSubcollectionOrFileName, optionalRelativePath)
 114
 115 #Example
 116
 117 collection$add("main.cpp", "cpp/src/")
 118
 119 #or
 120
 121 folder <- Subcollection$new("src")
 122 file <- ArvadosFile$new("main.cpp")
 123 folder$add(file)
 124
 125 collection$add(folder, "cpp")
 126
 127 #Both examples will add file "main.cpp" in "./cpp/src/" folder if folder exists.
 128 #If subcollection contains more files or folders they will be added recursively.
 129
 130 #You can also add multiple files
 131
 132 collection$add(c("path/to/my/file.cpp", "path/to/other/file.cpp"))
 133
 134 --------------------------------------------------------------------------------------------------------------------------------
 135
 136 #Write to existing file (Override current content of the file)
 137
 138 arvadosFile <- collection$get("location/to/my/file.cpp")
 139
 140 arvadosFile$write("This is new file content")
 141
 142 --------------------------------------------------------------------------------------------------------------------------------
 143
 144 #Delete file from a collection
 145
 146 file <- collection$get("location/to/my/file.cpp")
 147
 148 file$removeFromCollection()
 149
 150 #Or
 151
 152 collection$remove(file)
 153
 154 #Both examples will remove file "file.cpp" from a collection
 155 #If subcollection contains more files or folders they will be removed recursively.
 156
 157 #You can also remove multiple files
 158
 159 collection$remove(c("path/to/my/file.cpp", "path/to/other/file.cpp"))
 160
 161 --------------------------------------------------------------------------------------------------------------------------------
 162
 163 #Move file or folder inside collection
 164
 165 file <- collection$get("location/to/my/file.cpp")
 166
 167 file$move("destination/file.cpp")
 168
 169 #Or subcollections
 170
 171 subcollection <- collection$get("location/to/folder")
 172
 173 subcollection$move("destination/folder")
 174
 175 #Make sure to include folder name in destination
 176 #For example
 177 #file$move("destination/") will not work
 178
 179 --------------------------------------------------------------------------------------------------------------------------------
 180
 181 --------------------------------------------------------------------------------------------------------------------------------
 182
 183 # Working with projects:
 184
 185 #Get project:
 186
 187 arv$getProject("uuid")
 188
 189 --------------------------------------------------------------------------------------------------------------------------------
 190
 191 #List projects:
 192 projects <- arv$listProjects(list(list("uuid", "=", "aaaaa-j7d0g-ccccccccccccccc")), limit = 10, offset = 2)
 193
 194 --------------------------------------------------------------------------------------------------------------------------------
 195
 196 #Delete project:
 197
 198 deletedProject <- arv$deleteProject("uuid")
 199
 200 --------------------------------------------------------------------------------------------------------------------------------
 201
 202 #Update project:
 203
 204 updatedProject <- arv$updateProject("uuid", list(list(name = "new_name", description = "new_desciption")))
 205
 206 --------------------------------------------------------------------------------------------------------------------------------
 207
 208 #Create project:
 209
 210 createdProject <- arv$createProject(list(list(name = "project_name", description = "project_desciption")))
 211
 212 --------------------------------------------------------------------------------------------------------------------------------