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, libcurl4-gnutls-dev or libcurl4-openssl-dev
  16
  17 2. Install the ArvardosR package
  18
  19     > install.packages('/path/to/ArvadosR_0.0.2.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$items # items which match the filter criteria
  45
  46 #Next example will list all collections even when the number of items is greater than maximum API limit
  47
  48 collectionList <- arv$listAllCollections(list(list("name", "like", "Test%")))
  49
  50 --------------------------------------------------------------------------------------------------------------------------------
  51
  52 #Delete a collection:
  53
  54 deletedCollection <- arv$deleteCollection("uuid")
  55
  56 --------------------------------------------------------------------------------------------------------------------------------
  57
  58 #Update a collection's metadata:
  59
  60 updatedCollection <- arv$updateCollection("uuid", list(name = "New name", description = "New description"))
  61
  62 --------------------------------------------------------------------------------------------------------------------------------
  63
  64 #Create collection:
  65
  66 createdCollection <- arv$createCollection(list(name = "Example", description = "This is a test collection"))
  67
  68
  69 --------------------------------------------------------------------------------------------------------------------------------
  70 COLLECTION CONTENT MANIPULATION
  71 --------------------------------------------------------------------------------------------------------------------------------
  72
  73 #Create collection object:
  74
  75 collection <- Collection$new(arv, "uuid")
  76
  77 --------------------------------------------------------------------------------------------------------------------------------
  78
  79 #Get list of files
  80
  81 collection$getFileListing()
  82
  83 --------------------------------------------------------------------------------------------------------------------------------
  84
  85 #This will return ArvadosFile or Subcollection from internal tree-like structure.
  86
  87 arvadosFile <- collection$get("location/to/my/file.cpp")
  88
  89 #or
  90
  91 arvadosSubcollection <- collection$get("location/to/my/directory/")
  92
  93 --------------------------------------------------------------------------------------------------------------------------------
  94
  95 #Read a table
  96
  97 arvadosFile   <- collection$get("myinput.txt")
  98 arvConnection <- arvadosFile$connection("r")
  99 mytable       <- read.table(arvConnection)
 100
 101 #Write a table
 102
 103 arvadosFile   <- collection$create("myoutput.txt")
 104 arvConnection <- arvadosFile$connection("w")
 105 write.table(mytable, arvConnection)
 106 arvadosFile$flush()
 107
 108 --------------------------------------------------------------------------------------------------------------------------------
 109
 110 #Read whole file or just a portion of it.
 111
 112 fileContent <- arvadosFile$read()
 113 fileContent <- arvadosFile$read("text")
 114 fileContent <- arvadosFile$read("raw", offset = 1024, length = 512)
 115
 116 --------------------------------------------------------------------------------------------------------------------------------
 117
 118 #Get ArvadosFile or Subcollection size
 119
 120 size <- arvadosFile$getSizeInBytes()
 121 size <- arvadosSubcollection$getSizeInBytes()
 122
 123 --------------------------------------------------------------------------------------------------------------------------------
 124
 125 #Create new file in a collection
 126
 127 collection$create(fileNames, optionalRelativePath)
 128
 129 #Example
 130
 131 mainFile <- collection$create("main.cpp", "cpp/src/")
 132 fileList <- collection$create(c("main.cpp", lib.dll), "cpp/src/")
 133
 134 --------------------------------------------------------------------------------------------------------------------------------
 135
 136 #Add existing ArvadosFile or Subcollection to a collection
 137
 138 folder <- Subcollection$new("src")
 139 file   <- ArvadosFile$new("main.cpp")
 140 folder$add(file)
 141
 142 collection$add(folder, "cpp")
 143
 144 #This examples will add file "main.cpp" in "./cpp/src/" folder if folder exists.
 145 #If subcollection contains more files or folders they will be added recursively.
 146
 147 --------------------------------------------------------------------------------------------------------------------------------
 148
 149 #Write to existing file (Override current content of the file)
 150
 151 arvadosFile <- collection$get("location/to/my/file.cpp")
 152
 153 arvadosFile$write("This is new file content")
 154
 155 --------------------------------------------------------------------------------------------------------------------------------
 156
 157 #Delete file from a collection
 158
 159 collection$remove("location/to/my/file.cpp")
 160
 161 #You can remove both Subcollection and ArvadosFile
 162 #If subcollection contains more files or folders they will be removed recursively.
 163
 164 #You can also remove multiple files
 165
 166 collection$remove(c("path/to/my/file.cpp", "path/to/other/file.cpp"))
 167
 168 #Delete file or folder from a Subcollection
 169
 170 subcollection <- collection$get("mySubcollection/")
 171 subcollection$remove("fileInsideSubcollection.exe")
 172 subcollection$remove("folderInsideSubcollection/")
 173
 174 --------------------------------------------------------------------------------------------------------------------------------
 175
 176 #Move file or folder inside collection
 177
 178 #Directley from collection
 179
 180 collection$move("folder/file.cpp", "file.cpp")
 181
 182 #Or from file
 183
 184 file <- collection$get("location/to/my/file.cpp")
 185 file$move("newDestination/file.cpp")
 186
 187 #Or from subcollection
 188
 189 subcollection <- collection$get("location/to/folder")
 190 subcollection$move("newDestination/folder")
 191
 192 #Make sure to include new file name in destination
 193 #In second example file$move("newDestination/") will not work
 194
 195 --------------------------------------------------------------------------------------------------------------------------------
 196 WORKING WITH ARVADOS PROJECTS
 197 --------------------------------------------------------------------------------------------------------------------------------
 198
 199 #Get a project:
 200
 201 arv$getProject("uuid")
 202
 203 --------------------------------------------------------------------------------------------------------------------------------
 204
 205 #List projects:
 206
 207 projects <- arv$listProjects(list(list("owner_uuid", "=", "aaaaa-j7d0g-ccccccccccccccc"))) # list subprojects of a project
 208 arv$listProjects(list(list("name","like","Example%"))) # list projects which have names beginning with Example
 209
 210 #Next example will list all projects even when the number of items is greater than maximum API limit
 211
 212 collectionList <- arv$listAllProjects(list(list("name","like","Example%")))
 213
 214 --------------------------------------------------------------------------------------------------------------------------------
 215
 216 #Delete a project:
 217
 218 deletedProject <- arv$deleteProject("uuid")
 219
 220 --------------------------------------------------------------------------------------------------------------------------------
 221
 222 #Update project:
 223
 224 updatedProject <- arv$updateProject("uuid", list(name = "new_name", description = "new description"))
 225
 226 --------------------------------------------------------------------------------------------------------------------------------
 227
 228 #Create project:
 229
 230 createdProject <- arv$createProject(list(name = "project_name", description = "project description"))
 231
 232
 233 --------------------------------------------------------------------------------------------------------------------------------
 234 BUILDING THE ARVADOS SDK TARBALL
 235 --------------------------------------------------------------------------------------------------------------------------------
 236
 237
 238 cd arvados/sdk
 239 R CMD build R
 240
 241 This will create a tarball of the Arvados package in the current directory.