sdk/R/README

   1 R SDK for Arvados
   2
   3 Examples of usage:
   4
   5 --------------------------------------------------------------------------------------------------------------------------------
   6
   7 #Initialize API:
   8
   9 arv <- Arvados$new("insert_token", "insert_host_name")
  10
  11 --------------------------------------------------------------------------------------------------------------------------------
  12
  13 #Get collection:
  14
  15 arv$getCollection("uuid")
  16
  17 --------------------------------------------------------------------------------------------------------------------------------
  18
  19 #List collections:
  20
  21 collectionList <- arv$listCollections(list("uuid", "=" "aaaaa-bbbbb-ccccccccccccccc"), limit = 10, offset = 2)
  22
  23 --------------------------------------------------------------------------------------------------------------------------------
  24
  25 #Delete collection:
  26
  27 deletedCollection <- arv$deleteCollection("uuid")
  28
  29 --------------------------------------------------------------------------------------------------------------------------------
  30
  31 #Update collection:
  32
  33 updatedCollection <- arv$updateCollection("uuid", list((name = "new_name", description = "new_desciption")))
  34
  35 --------------------------------------------------------------------------------------------------------------------------------
  36
  37 #Create collection:
  38
  39 cratedCollection <- arv$createCollection(list(list(name = "new_name", description = "new_desciption")))
  40
  41 --------------------------------------------------------------------------------------------------------------------------------
  42
  43 --------------------------------------------------------------------------------------------------------------------------------
  44
  45 #Collection content manipulation:
  46
  47 --------------------------------------------------------------------------------------------------------------------------------
  48
  49 --------------------------------------------------------------------------------------------------------------------------------
  50
  51 #Create collection object:
  52
  53 arv <- Arvados$new("insert_token", "insert_host_name")
  54 collection <- Collection$new(arv, "uuid")
  55
  56 --------------------------------------------------------------------------------------------------------------------------------
  57
  58 #Get file/folder content as character vector
  59
  60 collection$getFileContent()
  61
  62 --------------------------------------------------------------------------------------------------------------------------------
  63
  64 #This will return ArvadosFile or Subcollection from internal tree-like structure.
  65
  66 arvadosFile <- collection$get("location/to/my/file.cpp")
  67
  68 #or
  69
  70 arvadosSubcollection <- collection$get("location/to/my/directory/")
  71
  72 --------------------------------------------------------------------------------------------------------------------------------
  73
  74 #Read whole file or just a portion of it.
  75
  76 fileContent <- arvadosFile$read(offset = 1024, length = 512)
  77
  78 --------------------------------------------------------------------------------------------------------------------------------
  79
  80 #Get ArvadosFile or Subcollection size
  81
  82 size <- arvadosFile$getSizeInBytes()
  83 size <- arvadosSubcollection$getSizeInBytes()
  84
  85 --------------------------------------------------------------------------------------------------------------------------------
  86
  87 #Create new file in a collection
  88
  89 #Call structure
  90
  91 collection$add(arvadosFileOrSubcollectionOrFileName, optionalRelativePath)
  92
  93 #Example
  94
  95 collection$add("main.cpp", "cpp/src/")
  96
  97 #or
  98
  99 folder <- Subcollection$new("src")
 100 file <- ArvadosFile$new("main.cpp")
 101 folder$add(file)
 102
 103 collection$add(folder, "cpp")
 104
 105 #Both examples will add file "main.cpp" in "./cpp/src/" folder if folder exists.
 106 #If subcollection contains more files or folders they will be added recursively.
 107
 108 #You can also add multiple files
 109
 110 collection$add(c("path/to/my/file.cpp", "path/to/other/file.cpp"))
 111
 112 --------------------------------------------------------------------------------------------------------------------------------
 113
 114 #Write to existing file (Override current content of the file)
 115
 116 arvadosFile <- collection$get("location/to/my/file.cpp")
 117
 118 arvadosFile$write("This is new file content")
 119
 120 --------------------------------------------------------------------------------------------------------------------------------
 121
 122 #Delete file from a collection
 123
 124 file <- collection$get("location/to/my/file.cpp")
 125
 126 file$removeFromCollection()
 127
 128 #Or
 129
 130 collection$remove(file)
 131
 132 #Both examples will remove file "file.cpp" from a collection
 133 #If subcollection contains more files or folders they will be removed recursively.
 134
 135 #You can also remove multiple files
 136
 137 collection$remove(c("path/to/my/file.cpp", "path/to/other/file.cpp"))
 138
 139 --------------------------------------------------------------------------------------------------------------------------------
 140
 141 --------------------------------------------------------------------------------------------------------------------------------
 142
 143 #Get project:
 144
 145 arv$getProject("uuid")
 146
 147 --------------------------------------------------------------------------------------------------------------------------------
 148
 149 #List projects:
 150
 151 projects <- arv$listProjects(list("uuid", "=" "aaaaa-bbbbb-ccccccccccccccc"), limit = 10, offset = 2)
 152
 153 --------------------------------------------------------------------------------------------------------------------------------
 154
 155 #Delete project:
 156
 157 deletedProject <- arv$deleteProject("uuid")
 158
 159 --------------------------------------------------------------------------------------------------------------------------------
 160
 161 #Update project:
 162
 163 updatedProject <- arv$updateProject("uuid", list((name = "new_name", description = "new_desciption")))
 164
 165 --------------------------------------------------------------------------------------------------------------------------------
 166
 167 #Create project:
 168
 169 cratedProject <- arv$createProject(list(list(name = "project_name", description = "project_desciption")))
 170
 171 --------------------------------------------------------------------------------------------------------------------------------