This SDK focuses on providing support for accessing Arvados projects, collections, and the files within collections.
The API is not final and feedback is solicited from users on ways in which it could be improved.
-### INSTALLATION
+### Installation
-`install.packages("ArvadosR", repos=c("http://r.arvados.org", getOption("repos")["CRAN"]), dependencies=TRUE)`
+```install.packages("ArvadosR", repos=c("http://r.arvados.org", getOption("repos")["CRAN"]), dependencies=TRUE)```
Note: on Linux, you may have to install supporting packages.
On Centos 7, this is:
-`yum install libxml2-devel openssl-devel curl-devel`
+```yum install libxml2-devel openssl-devel curl-devel```
On Debian, this is:
-`apt-get install build-essential libxml2-dev libssl-dev libcurl4-gnutls-dev`
+```apt-get install build-essential libxml2-dev libssl-dev libcurl4-gnutls-dev```
-### EXAMPLES OF USAGE
+### Usage
-#### INITIALIZING API
+#### Initializing API
+
+```{r include=FALSE}
+knitr::opts_chunk$set(eval = FALSE)
+```
* Load Library and Initialize API:
- `library('ArvadosR')`
- `arv <- Arvados$new() # uses environment variables ARVADOS_API_TOKEN and ARVADOS_API_HOST`
- `arv <- Arvados$new("your Arvados token", "example.arvadosapi.com")`
+ ```{r}
+ library('ArvadosR')
+ # use environment variables ARVADOS_API_TOKEN and ARVADOS_API_HOST
+ arv <- Arvados$new()
+
+ # provide them explicitly
+ arv <- Arvados$new("your Arvados token", "example.arvadosapi.com")
+ ```
Optionally, add numRetries parameter to specify number of times to retry failed service requests.
Default is 0.
- `arv <- Arvados$new("your Arvados token", "example.arvadosapi.com", numRetries = 3)`
+ ```{r}
+ arv <- Arvados$new("your Arvados token", "example.arvadosapi.com", numRetries = 3)
+ ```
This parameter can be set at any time using setNumRetries
- `arv$setNumRetries(5)`
+ ```{r}
+ arv$setNumRetries(5)
+ ```
-#### WORKING WITH COLLECTIONS
+#### Working with collections
* Get a collection:
- `collection <- arv$getCollection("uuid")`
+ ```{r}
+ collection <- arv$getCollection("uuid")
+ ```
* List collections:
- `collectionList <- arv$listCollections(list(list("name", "like", "Test%"))) # offset of 0 and default limit of 100`
- `collectionList <- arv$listCollections(list(list("name", "like", "Test%")), limit = 10, offset = 2)`
+ ```{r}
+ # offset of 0 and default limit of 100
+ collectionList <- arv$listCollections(list(list("name", "like", "Test%")))
+
+ collectionList <- arv$listCollections(list(list("name", "like", "Test%")), limit = 10, offset = 2)
+ ```
- `collectionList$items_available # count of total number of items (may be more than returned due to paging)`
- `collectionList$items # items which match the filter criteria`
+ ```{r}
+ # count of total number of items (may be more than returned due to paging)
+ collectionList$items_available
+
+ # items which match the filter criteria
+ collectionList$items
+ ```
* List all collections even if the number of items is greater than maximum API limit:
- `collectionList <- arv$listAllCollections(list(list("name", "like", "Test%")))`
+ ```{r}
+ collectionList <- arv$listAllCollections(list(list("name", "like", "Test%")))
+ ```
* Delete a collection:
- `deletedCollection <- arv$deleteCollection("uuid")`
+ ```{r}
+ deletedCollection <- arv$deleteCollection("uuid")
+ ```
* Update a collection's metadata:
- `updatedCollection <- arv$updateCollection("uuid", list(name = "New name", description = "New description"))`
+ ```{r}
+ updatedCollection <- arv$updateCollection("uuid", list(name = "New name", description = "New description"))
+ ```
* Create collection:
- `createdCollection <- arv$createCollection(list(name = "Example", description = "This is a test collection"))`
+ ```{r}
+ createdCollection <- arv$createCollection(list(name = "Example", description = "This is a test collection"))
+ ```
-#### MANIPULATIN COLLECTION CONTENT
+#### Manipulating collection content
* Create collection object:
- `collection <- Collection$new(arv, "uuid")`
+ ```{r}
+ collection <- Collection$new(arv, "uuid")
+ ```
* Get list of files:
- `files <- collection$getFileListing()`
+ ```{r}
+ files <- collection$getFileListing()
+ ```
* Get ArvadosFile or Subcollection from internal tree-like structure:
- `arvadosFile <- collection$get("location/to/my/file.cpp")`
+ ```{r}
+ arvadosFile <- collection$get("location/to/my/file.cpp")
+ ```
or
- `arvadosSubcollection <- collection$get("location/to/my/directory/")`
+ ```{r}
+ arvadosSubcollection <- collection$get("location/to/my/directory/")
+ ```
* Read a table:
- `arvadosFile <- collection$get("myinput.txt")`
- `arvConnection <- arvadosFile$connection("r")`
- `mytable <- read.table(arvConnection)`
+ ```{r}
+ arvadosFile <- collection$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()`
+ ```{r}
+ arvadosFile <- collection$create("myoutput.txt")
+ arvConnection <- arvadosFile$connection("w")
+ write.table(mytable, arvConnection)
+ arvadosFile$flush()
+ ```
* Write to existing file (override current content of the file):
- `arvadosFile <- collection$get("location/to/my/file.cpp")`
- `arvadosFile$write("This is new file content")`
+ ```{r}
+ arvadosFile <- collection$get("location/to/my/file.cpp")
+ arvadosFile$write("This is new file content")
+ ```
* Read whole file or just a portion of it:
- `fileContent <- arvadosFile$read()`
- `fileContent <- arvadosFile$read("text")`
- `fileContent <- arvadosFile$read("raw", offset = 1024, length = 512)`
+ ```{r}
+ fileContent <- arvadosFile$read()
+ fileContent <- arvadosFile$read("text")
+ fileContent <- arvadosFile$read("raw", offset = 1024, length = 512)
+ ```
* Get ArvadosFile or Subcollection size:
- `size <- arvadosFile$getSizeInBytes()`
+ ```{r}
+ size <- arvadosFile$getSizeInBytes()
+ ```
or
- `size <- arvadosSubcollection$getSizeInBytes()`
+ ```{r}
+ size <- arvadosSubcollection$getSizeInBytes()
+ ```
* Create new file in a collection:
- `collection$create(fileNames, optionalRelativePath)`
+ ```{r}
+ collection$create(fileNames, optionalRelativePath)
+ ```
Example:
- `mainFile <- collection$create("main.cpp", "cpp/src/")`
- `fileList <- collection$create(c("main.cpp", lib.dll), "cpp/src/")`
+ ```{r}
+ mainFile <- collection$create("main.cpp", "cpp/src/")
+ fileList <- collection$create(c("main.cpp", lib.dll), "cpp/src/")
+ ```
* Add existing ArvadosFile or Subcollection to a collection:
- `folder <- Subcollection$new("src")`
- `file <- ArvadosFile$new("main.cpp")`
- `folder$add(file)`
+ ```{r}
+ folder <- Subcollection$new("src")
+ file <- ArvadosFile$new("main.cpp")
+ folder$add(file)
+ ```
- `collection$add(folder, "cpp")`
+ ```{r}
+ collection$add(folder, "cpp")
+ ```
This examples will add file "main.cpp" in "./cpp/src/" folder if folder exists.
If subcollection contains more files or folders they will be added recursively.
* Delete file from a collection:
- `collection$remove("location/to/my/file.cpp")`
+ ```{r}
+ collection$remove("location/to/my/file.cpp")
+ ```
You can remove both Subcollection and ArvadosFile.
If subcollection contains more files or folders they will be removed recursively.
You can also remove multiple files at once:
- `collection$remove(c("path/to/my/file.cpp", "path/to/other/file.cpp"))`
+ ```{r}
+ 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/")`
+ ```{r}
+ subcollection <- collection$get("mySubcollection/")
+ subcollection$remove("fileInsideSubcollection.exe")
+ subcollection$remove("folderInsideSubcollection/")
+ ```
* Move file or folder inside collection:
Directley from collection
- `collection$move("folder/file.cpp", "file.cpp")`
+ ```{r}
+ collection$move("folder/file.cpp", "file.cpp")
+ ```
Or from file
- `file <- collection$get("location/to/my/file.cpp")`
- `file$move("newDestination/file.cpp")`
+ ```{r}
+ file <- collection$get("location/to/my/file.cpp")
+ file$move("newDestination/file.cpp")
+ ```
Or from subcollection
- `subcollection <- collection$get("location/to/folder")`
- `subcollection$move("newDestination/folder")`
+ ```{r}
+ subcollection <- collection$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.
-#### WORKING WITH ARVADOS PROJECTS
+#### Working with Aravdos projects
* Get a project:
- `project <- arv$getProject("uuid")`
+ ```{r}
+ project <- arv$getProject("uuid")
+ ```
* List 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`
+ ```{r}
+ # list subprojects of a project
+ projects <- arv$listProjects(list(list("owner_uuid", "=", "aaaaa-j7d0g-ccccccccccccccc")))
+
+ # list projects which have names beginning with Example
+ arv$listProjects(list(list("name","like","Example%")))
+ ```
* List all projects even if the number of items is greater than maximum API limit:
- `collectionList <- arv$listAllProjects(list(list("name","like","Example%")))`
+ ```{r}
+ collectionList <- arv$listAllProjects(list(list("name","like","Example%")))
+ ```
* Delete a project:
- `deletedProject <- arv$deleteProject("uuid")`
+ ```{r}
+ deletedProject <- arv$deleteProject("uuid")
+ ```
* Update project:
- `updatedProject <- arv$updateProject("uuid", list(name = "new_name", description = "new description"))`
+ ```{r}
+ updatedProject <- arv$updateProject("uuid", list(name = "new_name", description = "new description"))
+ ```
* Create project:
- `createdProject <- arv$createProject(list(name = "project_name", description = "project description"))`
+ ```{r}
+ createdProject <- arv$createProject(list(name = "project_name", description = "project description"))
+ ```
-### BUILDING THE ARVADOS SDK TARBALL
+### Building the ArvadosR package
-cd arvados/sdk
-R CMD build R
+ ```
+ cd arvados/sdk && R CMD build R
+ ```
-This will create a tarball of the Arvados package in the current directory.
+This will create a tarball of the ArvadosR package in the current directory.
projects / arvados.git / commitdiff