[ARVADOS] updated: 1.1.2-271-g24e302c
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Fri Feb 9 09:37:13 EST 2018
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sdk/R/README.Rmd | 280 +++++++++++++++++++++++++++----------------------------
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commit 24e302ceb24fcf9f00340e1896729de45cde45dd
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date: Fri Feb 9 09:36:34 2018 -0500
11876: Update install instructions to r.arvados.org
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
diff --git a/sdk/R/README.Rmd b/sdk/R/README.Rmd
index 6315ddd..8e14058 100644
--- a/sdk/R/README.Rmd
+++ b/sdk/R/README.Rmd
@@ -9,198 +9,198 @@ The API is not final and feedback is solicited from users on ways in which it co
`install.packages(c('R6', 'httr', 'stringr', 'jsonlite', 'curl', 'XML'))`
- If needed, you may have to install the supporting packages first.
+ If needed, you may have to install the supporting packages first.
On Linux, these are: libxml2-dev, libssl-dev, libcurl4-gnutls-dev or libcurl4-openssl-dev
-
+
2. Install the ArvardosR package
- `install.packages('/path/to/ArvadosR_0.0.2.tar.gz', repos = NULL, type="source", dependencies = TRUE)`
-
+ `install.packages('http://r.arvados.org/ArvadosR_0.0.3.tar.gz', repos=NULL, type='source')`
+
### EXAMPLES OF USAGE
#### INITIALIZING API
* 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")`
-
- Optionally, add numRetries parameter to specify number of times to retry failed service requests.
- Default is 0.
-
- `arv <- Arvados$new("your Arvados token", "example.arvadosapi.com", numRetries = 3)`
-
- This parameter can be set at any time using setNumRetries
-
- `arv$setNumRetries(5)`
-
+ `library('ArvadosR')`
+ `arv <- Arvados$new() # uses environment variables ARVADOS_API_TOKEN and ARVADOS_API_HOST`
+ `arv <- Arvados$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$new("your Arvados token", "example.arvadosapi.com", numRetries = 3)`
+
+ This parameter can be set at any time using setNumRetries
+
+ `arv$setNumRetries(5)`
+
#### WORKING WITH COLLECTIONS
* Get a collection:
-
- `collection <- arv$getCollection("uuid")`
-
+
+ `collection <- arv$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)`
-
- `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`
-
+ `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)`
+
+ `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`
+
* List all collections even if the number of items is greater than maximum API limit:
-
- `collectionList <- arv$listAllCollections(list(list("name", "like", "Test%")))`
-
+
+ `collectionList <- arv$listAllCollections(list(list("name", "like", "Test%")))`
+
* Delete a collection:
-
- `deletedCollection <- arv$deleteCollection("uuid")`
-
+
+ `deletedCollection <- arv$deleteCollection("uuid")`
+
* Update a collection's metadata:
-
- `updatedCollection <- arv$updateCollection("uuid", list(name = "New name", description = "New description"))`
-
+
+ `updatedCollection <- arv$updateCollection("uuid", list(name = "New name", description = "New description"))`
+
* Create collection:
-
+
`createdCollection <- arv$createCollection(list(name = "Example", description = "This is a test collection"))`
-
-
+
+
#### MANIPULATIN COLLECTION CONTENT
* Create collection object:
-
- `collection <- Collection$new(arv, "uuid")`
-
+
+ `collection <- Collection$new(arv, "uuid")`
+
* Get list of files:
-
- `files <- collection$getFileListing()`
-
+
+ `files <- collection$getFileListing()`
+
* Get ArvadosFile or Subcollection from internal tree-like structure:
-
- `arvadosFile <- collection$get("location/to/my/file.cpp")`
-
- or
-
- `arvadosSubcollection <- collection$get("location/to/my/directory/")`
-
+
+ `arvadosFile <- collection$get("location/to/my/file.cpp")`
+
+ or
+
+ `arvadosSubcollection <- collection$get("location/to/my/directory/")`
+
* Read a table:
-
- `arvadosFile <- collection$get("myinput.txt")`
- `arvConnection <- arvadosFile$connection("r")`
- `mytable <- read.table(arvConnection)`
-
+
+ `arvadosFile <- collection$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()`
+
+ `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$write("This is new file content")`
-
+
+ `arvadosFile <- collection$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)`
-
+
+ `fileContent <- arvadosFile$read()`
+ `fileContent <- arvadosFile$read("text")`
+ `fileContent <- arvadosFile$read("raw", offset = 1024, length = 512)`
+
* Get ArvadosFile or Subcollection size:
-
- `size <- arvadosFile$getSizeInBytes()`
-
- or
-
+
+ `size <- arvadosFile$getSizeInBytes()`
+
+ or
+
`size <- arvadosSubcollection$getSizeInBytes()`
-
+
* Create new file in a collection:
-
- `collection$create(fileNames, optionalRelativePath)`
-
+
+ `collection$create(fileNames, optionalRelativePath)`
+
Example:
-
- `mainFile <- collection$create("main.cpp", "cpp/src/")`
- `fileList <- collection$create(c("main.cpp", lib.dll), "cpp/src/")`
-
+
+ `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$add(file)`
-
- `collection$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.
-
+
+ `folder <- Subcollection$new("src")`
+ `file <- ArvadosFile$new("main.cpp")`
+ `folder$add(file)`
+
+ `collection$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$remove("location/to/my/file.cpp")`
-
- You can remove both Subcollection and ArvadosFile.
- If subcollection contains more files or folders they will be removed recursively.
-
- You can also remove multiple files at once:
-
- `collection$remove(c("path/to/my/file.cpp", "path/to/other/file.cpp"))`
-
+
+ `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"))`
+
* Delete file or folder from a Subcollection:
-
- `subcollection <- collection$get("mySubcollection/")`
- `subcollection$remove("fileInsideSubcollection.exe")`
- `subcollection$remove("folderInsideSubcollection/")`
-
+
+ `subcollection <- collection$get("mySubcollection/")`
+ `subcollection$remove("fileInsideSubcollection.exe")`
+ `subcollection$remove("folderInsideSubcollection/")`
+
* Move file or folder inside collection:
-
- Directley from collection
-
- `collection$move("folder/file.cpp", "file.cpp")`
-
+
+ Directley from collection
+
+ `collection$move("folder/file.cpp", "file.cpp")`
+
Or from file
-
- `file <- collection$get("location/to/my/file.cpp")`
- `file$move("newDestination/file.cpp")`
-
+
+ `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")`
-
+
+ `subcollection <- collection$get("location/to/folder")`
+ `subcollection$move("newDestination/folder")`
+
Make sure to include new file name in destination.
- In second example file$move("newDestination/") will not work.
+ In second example file$move("newDestination/") will not work.
#### WORKING WITH ARVADOS PROJECTS
* Get a project:
-
- `project <- arv$getProject("uuid")`
-
+
+ `project <- arv$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`
-
+
+ `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`
+
* List all projects even if the number of items is greater than maximum API limit:
-
- `collectionList <- arv$listAllProjects(list(list("name","like","Example%")))`
-
+
+ `collectionList <- arv$listAllProjects(list(list("name","like","Example%")))`
+
* Delete a project:
-
- `deletedProject <- arv$deleteProject("uuid")`
-
+
+ `deletedProject <- arv$deleteProject("uuid")`
+
* Update project:
-
+
`updatedProject <- arv$updateProject("uuid", list(name = "new_name", description = "new description"))`
-
+
* Create project:
-
- `createdProject <- arv$createProject(list(name = "project_name", description = "project description"))`
-
+
+ `createdProject <- arv$createProject(list(name = "project_name", description = "project description"))`
+
### BUILDING THE ARVADOS SDK TARBALL
cd arvados/sdk
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