#' project_exist enables checking if the project with such a UUID exist.
#' @param uuid The UUID of a project or a file.
#' @examples
- #' arv$project_exist(uuid = projectUUID)
+ #' \dontrun{
+ #' arv$project_exist(uuid = "projectUUID")
+ #' }
project_exist = function(uuid)
{
proj <- self$project_list(list(list("uuid", '=', uuid)))
#' project_get returns the demanded project.
#' @param uuid The UUID of the Group in question.
#' @examples
- #' project <- arv$project_get(uuid = projectUUID)
+ #' \dontrun{
+ #' project <- arv$project_get(uuid = 'projectUUID')
+ #' }
project_get = function(uuid)
{
self$groups_get(uuid)
#' @param properties List of the properties of the project.
#' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
#' @examples
+ #' \dontrun{
#' Properties <- list() # should contain a list of new properties to be added
#' new_project <- arv$project_create(name = "project name", description = "project description", owner_uuid = "project UUID", properties = NULL, ensureUniqueName = "false")
+ #' }
project_create = function(name, description, ownerUUID, properties = NULL, ensureUniqueName = "false")
{
group <- list(name = name, description = description, owner_uuid = ownerUUID, properties = properties)
#' @param listProperties List of new properties.
#' @param uuid The UUID of a project or a file.
#' @examples
+ #' \dontrun{
#' Properties <- list() # should contain a list of new properties to be added
#' arv$project_properties_set(Properties, uuid)
+ #' }
project_properties_set = function(listProperties, uuid)
{
group <- c("group_class" = "project", list("properties" = listProperties))
#' @description
#' project_properties_append is a method defined in Arvados class that enables appending properties. Allows to add new properties.
- #' @param listOfNewProperties List of new properties.
+ #' @param properties List of new properties.
#' @param uuid The UUID of a project or a file.
#' @examples
+ #' \dontrun{
#' newProperties <- list() # should contain a list of new properties to be added
#' arv$project_properties_append(properties = newProperties, uuid)
+ #' }
project_properties_append = function(properties, uuid)
{
proj <- self$project_list(list(list('uuid', '=', uuid)))
#' project_properties_get is a method defined in Arvados class that returns properties.
#' @param uuid The UUID of a project or a file.
#' @examples
+ #' \dontrun{
#' arv$project_properties_get(projectUUID)
+ #' }
project_properties_get = function(uuid)
{
proj <- self$project_list(list(list('uuid', '=', uuid)))
#' @param oneProp Property to be deleted.
#' @param uuid The UUID of a project or a file.
#' @examples
+ #' \dontrun{
#' Properties <- list() # should contain a list of new properties to be added
#' arv$project_properties_delete(Properties, projectUUID)
+ #' }
project_properties_delete = function(oneProp, uuid)
{
proj <- self$project_list(list(list('uuid', '=', uuid))) # find project
#' @param ... Feature to be updated (name, description, properties).
#' @param uuid The UUID of a project in question.
#' @examples
+ #' \dontrun{
#' newProperties <- list() # should contain a list of new properties to be added
#' arv$project_update(name = "new project name", properties = newProperties, uuid = projectUUID)
+ #' }
project_update = function(..., uuid) {
vec <- list(...)
for (i in 1:length(vec))
#' @param uuid The UUID of a project in question.
#' @param recursive Include contents from child groups recursively.
#' @examples
+ #' \dontrun{
#' listOfprojects <- arv$project_list(list(list("owner_uuid", "=", projectUUID))) # Sample query which show projects within the project of a given UUID
+ #' }
project_list = function(filters = NULL, where = NULL,
order = NULL, select = NULL, distinct = NULL,
limit = "100", offset = "0", count = "exact",
#' @description
#' project_delete trashes project of a given uuid. It can be restored from trash or deleted permanently.
#' @param uuid The UUID of the Group in question.
+ #' @examples
+ #' \dontrun{
+ #' arv$project_delete(uuid = 'projectUUID')
+ #' }
project_delete = function(uuid)
{
self$groups_delete(uuid)
#' @description
#' collections_get is a method defined in Arvados class.
#' @param uuid The UUID of the Collection in question.
+ #' @examples
+ #' \dontrun{
#' collection <- arv$collections_get(uuid = collectionUUID)
+ #' }
collections_get = function(uuid)
{
endPoint <- stringr::str_interp("collections/${uuid}")
#' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
#' @param clusterID Create object on a remote federated cluster instead of the current one.
#' @examples
+ #' \dontrun{
#' Properties <- list() # should contain a list of new properties to be added
#' arv$collections_create(name = "collectionTitle", description = "collectionDescription", ownerUUID = "collectionOwner", properties = Properties)
+ #' }
collections_create = function(name, description, ownerUUID = NULL, properties = NULL, # name and description are obligatory
ensureUniqueName = "false", clusterID = NULL)
{
#' @param properties New list of properties of the collection.
#' @param uuid The UUID of the Collection in question.
#' @examples
+ #' \dontrun{
#' collection <- arv$collections_update(name = "newCollectionTitle", description = "newCollectionDescription", ownerUUID = "collectionOwner", properties = NULL, uuid = "collectionUUID")
+ #' }
collections_update = function(name, description, ownerUUID = NULL, properties = NULL, uuid)
{
endPoint <- stringr::str_interp("collections/${uuid}")
#' collections_delete is a method defined in Arvados class.
#' @param uuid The UUID of the Collection in question.
#' @examples
+ #' \dontrun{
#' arv$collection_delete(collectionUUID)
+ #' }
collections_delete = function(uuid)
{
endPoint <- stringr::str_interp("collections/${uuid}")
#' collections_provenance is a method defined in Arvados class, it returns the collection by uuid.
#' @param uuid The UUID of the Collection in question.
#' @examples
+ #' \dontrun{
#' collection <- arv$collections_provenance(collectionUUID)
+ #' }
collections_provenance = function(uuid)
{
endPoint <- stringr::str_interp("collections/${uuid}/provenance")
#' collections_trash is a method defined in Arvados class, it moves collection to trash.
#' @param uuid The UUID of the Collection in question.
#' @examples
+ #' \dontrun{
#' arv$collections_trash(collectionUUID)
+ #' }
collections_trash = function(uuid)
{
endPoint <- stringr::str_interp("collections/${uuid}/trash")
#' collections_untrash is a method defined in Arvados class, it moves collection from trash to project.
#' @param uuid The UUID of the Collection in question.
#' @examples
+ #' \dontrun{
#' arv$collections_untrash(collectionUUID)
+ #' }
collections_untrash = function(uuid)
{
endPoint <- stringr::str_interp("collections/${uuid}/untrash")
#' @param includeTrash Include collections whose is_trashed attribute is true.
#' @param includeOldVersions Include past collection versions.
#' @examples
+ #' \dontrun{
#' collectionList <- arv$collections_list(list(list("name", "=", "Example")))
+ #' }
collections_list = function(filters = NULL,
where = NULL, order = NULL, select = NULL,
distinct = NULL, limit = "100", offset = "0",
#' @param uuid The UUID of a project or a file.
#' @param user The UUID of the person that gets the permission.
#' @examples
+ #' \dontrun{
#' arv$project_permission_give(type = "can_read", uuid = objectUUID, user = userUUID)
+ #' }
project_permission_give = function(type, uuid, user)
{
endPoint <- stringr::str_interp("links")
#' @param uuid The UUID of a project or a file.
#' @param user The UUID of a person that permissions are taken from.
#' @examples
+ #' \dontrun{
#' arv$project_permission_refuse(type = "can_read", uuid = objectUUID, user = userUUID)
+ #' }
project_permission_refuse = function(type, uuid, user)
{
examples <- self$links_list(list(list("head_uuid","=", uuid)))
#' @param uuid The UUID of a project or a file.
#' @param user The UUID of the person that the permission is being updated.
#' @examples
+ #' \dontrun{
#' arv$project_permission_update(typeOld = "can_read", typeNew = "can_write", uuid = objectUUID, user = userUUID)
+ #' }
project_permission_update = function(typeOld, typeNew, uuid, user)
{
link <- list("name" = typeNew)
#' @param user The UUID of the person that the permission is being updated.
#' @param type Possible options are can_read or can_write or can_manage.
#' @examples
+ #' \dontrun{
#' arv$project_permission_check(type = "can_read", uuid = objectUUID, user = userUUID)
+ #' }
project_permission_check = function(uuid, user, type = NULL)
{
examples <- self$links_list(list(list("head_uuid","=", uuid)))
#' @param name Name of the new enviroment.
#' @return A new `ArvadosFile` object.
#' @examples
+ #' \dontrun{
#' myFile <- ArvadosFile$new("myFile")
+ #' }
initialize = function(name)
{
if(name == "")
#' @description
#' Returns name of the file.
#' @examples
+ #' \dontrun{
#' arvadosFile$getName()
+ #' }
getName = function() private$name,
#' @description
#' Returns collections file content as character vector.
#' @param fullPath Checking if TRUE.
#' @examples
+ #' \dontrun{
#' arvadosFile$getFileListing()
+ #' }
getFileListing = function(fullpath = TRUE)
{
self$getName()
#' @description
#' Returns collections content size in bytes.
#' @examples
+ #' \dontrun{
#' arvadosFile$getSizeInBytes()
+ #' }
getSizeInBytes = function()
{
if(is.null(private$collection))
#' @param offset Describes the location of a piece of data compared to another location
#' @param length Length of content
#' @examples
+ #' \dontrun{
#' collection <- Collection$new(arv, collectionUUID)
#' arvadosFile <- collection$get(fileName)
#' fileContent <- arvadosFile$read("text")
+ #' }
read = function(contentType = "raw", offset = 0, length = 0)
{
if(is.null(private$collection))
#' Get connection opened in "read" or "write" mode.
#' @param rw Type of connection.
#' @examples
+ #' \dontrun{
#' collection <- Collection$new(arv, collectionUUID)
#' arvadosFile <- collection$get(fileName)
#' arvConnection <- arvadosFile$connection("w")
+ #' }
connection = function(rw)
{
if (rw == "r" || rw == "rb")
#' @description
#' Write connections content to a file or override current content of the file.
#' @examples
+ #' \dontrun{
#' collection <- Collection$new(arv, collectionUUID)
#' arvadosFile <- collection$get(fileName)
#' myFile$write("This is new file content")
#' arvadosFile$flush()
+ #' }
flush = function()
{
v <- textConnectionValue(private$buffer)
#' @param content File to write.
#' @param contentType Type of content. Possible is "text", "raw".
#' @examples
+ #' \dontrun{
#' collection <- Collection$new(arv, collectionUUID)
#' arvadosFile <- collection$get(fileName)
#' myFile$write("This is new file content")
+ #' }
write = function(content, contentType = "text/html")
{
if(is.null(private$collection))
#' Moves file to a new location inside collection.
#' @param destination Path to new folder.
#' @examples
+ #' \dontrun{
#' arvadosFile$move(newPath)
+ #' }
move = function(destination)
{
if(is.null(private$collection))
#' Copies file to a new location inside collection.
#' @param destination Path to new folder.
#' @examples
+ #' \dontrun{
#' arvadosFile$copy("NewName.format")
+ #' }
copy = function(destination)
{
if(is.null(private$collection))
#' @param uuid The UUID Autentic for Collection UUID.
#' @return A new `Collection` object.
#' @examples
+ #' \dontrun{
#' collection <- Collection$new(arv, CollectionUUID)
+ #' }
initialize = function(api, uuid)
{
private$REST <- api$getRESTService()
#' @param Ncol Used in reading binary file to set numbers of columns in data.frame.
#' @param Nrow Used in reading binary file to set numbers of rows in data.frame size.
#' @examples
+ #' \dontrun{
#' collection <- Collection$new(arv, collectionUUID)
#' readFile <- collection$readArvFile(arvadosFile, istable = 'yes') # table
#' readFile <- collection$readArvFile(arvadosFile, istable = 'no') # text
#' readFile <- collection$readArvFile(arvadosFile, fileclass = 'fasta') # fasta
#' readFile <- collection$readArvFile(arvadosFile, Ncol= 4, Nrow = 32) # binary, only numbers
#' readFile <- collection$readArvFile(arvadosFile, Ncol = 5, Nrow = 150, istable = "factor") # binary with factor or text
+ #' }
readArvFile = function(file, con, sep = ',', istable = NULL, fileclass = "SeqFastadna", Ncol = NULL, Nrow = NULL, wantedFunction = NULL)
{
arvFile <- self$get(file)
#' @param file File to be saved.
#' @param istable Used in writing txt file to check if the file is table or not.
#' @examples
+ #' \dontrun{
#' collection <- Collection$new(arv, collectionUUID)
#' writeFile <- collection$writeFile(name = "myoutput.csv", file = file, fileFormat = "csv", istable = NULL, collectionUUID = collectionUUID) # csv
#' writeFile <- collection$writeFile(name = "myoutput.tsv", file = file, fileFormat = "tsv", istable = NULL, collectionUUID = collectionUUID) # tsv
#' writeFile <- collection$writeFile(name = "myoutputtext.txt", file = file, fileFormat = "txt", istable = "no", collectionUUID = collectionUUID) # txt text
#' writeFile <- collection$writeFile(name = "myoutputbinary.dat", file = file, fileFormat = "dat", collectionUUID = collectionUUID) # binary
#' writeFile <- collection$writeFile(name = "myoutputxlsx.xlsx", file = file, fileFormat = "xlsx", collectionUUID = collectionUUID) # xlsx
- writeFile = function(name, file, collectionUUID, fileFormat, istable = NULL, seqName = NULL) {
-
+ #' }
+ writeFile = function(name, file, collectionUUID, fileFormat, istable = NULL, seqName = NULL)
+ {
# set enviroment
ARVADOS_API_TOKEN <- Sys.getenv("ARVADOS_API_TOKEN")
ARVADOS_API_HOST <- Sys.getenv("ARVADOS_API_HOST")
#' Creates one or more ArvadosFiles and adds them to the collection at specified path.
#' @param files Content to be created.
#' @examples
+ #' \dontrun{
#' collection <- arv$collections_create(name = collectionTitle, description = collectionDescription, owner_uuid = collectionOwner, properties = list("ROX37196928443768648" = "ROX37742976443830153"))
+ #' }
create = function(files)
{
if(is.null(private$tree))
#' Remove one or more files from the collection.
#' @param paths Content to be removed.
#' @examples
+ #' \dontrun{
#' collection$remove(fileName.format)
+ #' }
remove = function(paths)
{
if(is.null(private$tree))
#' @param content Content to be moved.
#' @param destination Path to move content.
#' @examples
+ #' \dontrun{
#' collection$move("fileName.format", path)
+ #' }
move = function(content, destination)
{
if(is.null(private$tree))
#' @param content Content to be moved.
#' @param destination Path to move content.
#' @examples
+ #' \dontrun{
#' copied <- collection$copy("oldName.format", "newName.format")
+ #' }
copy = function(content, destination)
{
if(is.null(private$tree))
#' @description
#' Refreshes the environment.
#' @examples
+ #' \dontrun{
#' collection$refresh()
+ #' }
refresh = function()
{
if(!is.null(private$tree))
#' @description
#' Returns collections file content as character vector.
#' @examples
+ #' \dontrun{
#' list <- collection$getFileListing()
+ #' }
getFileListing = function()
{
if(is.null(private$tree))
#' If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.
#' @param relativePath Path from content is taken.
#' @examples
+ #' \dontrun{
#' arvadosFile <- collection$get(fileName)
+ #' }
get = function(relativePath)
{
if(is.null(private$tree))
arv$setNumRetries(5)
```
-### Working with collections
+### Working with Aravdos projects
-#### Get a collection:
+##### Create project:
```r
-collection <- arv$collections_get("uuid")
+newProject <- arv$project_create(name = "project name", description = "project description", owner_uuid = "project UUID", properties = NULL, ensureUniqueName = "false")
```
-Be aware that the result from `collections_get` is not a Collection class. The object returned from this method lets you access collection fields like “name” and “description”. The Collection class lets you access the files in the collection for reading and writing, and is described in the next section.
+##### Update project:
-#### List collections:
+```r
+updatedProject <- arv$project_update(name = "new project name", properties = newProperties, uuid = "projectUUID")
+```
+
+##### Delete a project:
```r
-# offset of 0 and default limit of 100
-collectionList <- arv$collections_list(list(list("name", "like", "Test%")))
+deletedProject <- arv$project_delete("uuid")
+```
-collectionList <- arv$collections_list(list(list("name", "like", "Test%")), limit = 10, offset = 2)
+#### Find a project:
-# count of total number of items (may be more than returned due to paging)
-collectionList$items_available
+##### Get a project:
-# items which match the filter criteria
-collectionList$items
+```r
+project <- arv$project_get("uuid")
```
-#### List all collections even if the number of items is greater than maximum API limit:
+##### List projects:
```r
-collectionList <- listAll(arv$collections_list, list(list("name", "like", "Test%")))
+list subprojects of a project
+projects <- arv$project_list(list(list("owner_uuid", "=", "aaaaa-j7d0g-ccccccccccccccc")))
+
+list projects which have names beginning with Example
+examples <- arv$project_list(list(list("name","like","Example%")))
```
-#### Delete a collection:
+##### List all projects even if the number of items is greater than maximum API limit:
```r
-deletedCollection <- arv$collections_delete("uuid")
+projects <- listAll(arv$project_list, list(list("name","like","Example%")))
+```
+
+### Working with collections
+
+#### Create a new collection:
+
+```r
+newCollection <- arv$collections_create(name = "collectionTitle", description = "collectionDescription", ownerUUID = "collectionOwner", properties = Properties)
```
#### Update a collection’s metadata:
collection <- arv$collections_update(name = "newCollectionTitle", description = "newCollectionDescription", ownerUUID = "collectionOwner", properties = NULL, uuid = "collectionUUID")
```
-#### Create a new collection:
+#### Delete a collection:
```r
-newCollection <- arv$collections_create(name = "collectionTitle", description = "collectionDescription", ownerUUID = "collectionOwner", properties = Properties)
+deletedCollection <- arv$collections_delete("uuid")
+```
+
+#### Find a collection:
+
+#### Get a collection:
+
+```r
+collection <- arv$collections_get("uuid")
+```
+
+Be aware that the result from `collections_get` is not a Collection class. The object returned from this method lets you access collection fields like “name” and “description”. The Collection class lets you access the files in the collection for reading and writing, and is described in the next section.
+
+#### List collections:
+
+```r
+# offset of 0 and default limit of 100
+collectionList <- arv$collections_list(list(list("name", "like", "Test%")))
+
+collectionList <- arv$collections_list(list(list("name", "like", "Test%")), limit = 10, offset = 2)
+
+# count of total number of items (may be more than returned due to paging)
+collectionList$items_available
+
+# items which match the filter criteria
+collectionList$items
+```
+
+#### List all collections even if the number of items is greater than maximum API limit:
+
+```r
+collectionList <- listAll(arv$collections_list, list(list("name", "like", "Test%")))
```
### Manipulating collection content
subcollection$copy("destination/folder")
```
-### Working with Aravdos projects
-
-#### Get a project:
-
-```r
-project <- arv$project_get("uuid")
-```
-
-#### List projects:
-
-```r
-list subprojects of a project
-projects <- arv$project_list(list(list("owner_uuid", "=", "aaaaa-j7d0g-ccccccccccccccc")))
-
-list projects which have names beginning with Example
-examples <- arv$project_list(list(list("name","like","Example%")))
-```
-
-#### List all projects even if the number of items is greater than maximum API limit:
-
-```r
-projects <- listAll(arv$project_list, list(list("name","like","Example%")))
-```
-
-##### Delete a project:
-
-```r
-deletedProject <- arv$project_delete("uuid")
-```
-
-##### Update project:
-
-```r
-updatedProject <- arv$project_update(name = "new project name", properties = newProperties, uuid = "projectUUID")
-```
-
-##### Create project:
-
-```r
-newProject <- arv$project_create(name = "project name", description = "project description", owner_uuid = "project UUID", properties = NULL, ensureUniqueName = "false")
-```
### Help
projects / arvados.git / commitdiff