Cloning

Objects can be cloned (copied) from one data container (including projects) to another once they are in the "closed" state. Cloning requires VIEW or greater access to the source container and UPLOAD or greater access to the destination container. Moreover, the source container must not have the RESTRICTED flag set. Cloning generates a new copy of the user-provided metadata in the destination container, and access to that metadata and the underlying data object will abide by the permission list of the destination container; it will not be associated to the original object in any sense. (For example, if the original object is removed from the source container, that does not affect the cloned object. Similarly, if the cloned object’s metadata is modified, that does not affect the original; the cloned object should be thought of as a true copy).

API method: /class-xxxx/clone

Specification

Clones one or more objects and/or folders from a source container into a destination container (and optionally into a destination folder). Links in the details of the cloned objects will be followed, and any hidden objects they point to and are available in the source container will also be cloned. The process will continue recursively if the hidden linked objects also have outgoing links pointing to additional hidden objects. Note that if an object links to a hidden object that is not in the source container but which points to a hidden object that is available, this second hidden object will not be cloned as well. (The assumption is that it may lose its usefulness or meaning without its parent object.) If a folder is listed in "folders" and is successfully cloned, a new folder is created in the destination folder with the same name and with its contents set to the clones of the source folder’s contents. Any hidden objects contained in a folder to be cloned are only cloned if a visible ancestor is also cloned.

For an applet, if its run specification includes links to objects in its bundledDepends field, these objects will also be considered as an essential part of the data object and cloned with the applet.

If the root folder "/" is specified in "folders", then all of its contents will be cloned into the destination folder. Note that in all other cases, the contents of a folder (e.g. "/foo") specified to be cloned will be cloned into a new folder under the destination folder (e.g. "/destination/foo"), not into the destination folder itself.

If the same object appears multiple times in the "objects" input array, it is cloned only once. Similarly, if an extra object is encountered multiple times during the cloning process (for example, because it is a hidden object linked by multiple objects in the input, and includeHiddenLinks is set to true), it is also cloned only once.

If a hidden object is to be cloned as part of a folder, it will be cloned to a destination that is the same relative to the cloned folder as it was in the source container. Otherwise, it will be placed in the destination folder.

If an object represented in "objects" already exists in the destination container, no action is taken for that object. The object ID is returned in the array "exists". Note that as a result, a request to clone a set of objects into a particular folder in the container may succeed (in that no error is returned), but the destination folder may not contain all of the requested objects if one of the objects already exists in another folder in the same container. If the object needs to be in the specified folder, a "/move" call needs to be made. An object can appear in at most one folder in a container.

If a workflow is to be cloned, the result will depend upon the workflow's state. If the source workflow is open, a new replica workflow object will be created in the destination. If the source workflow is closed, the source workflow will be cloned to its destination.

Inputs

  • objects array of strings (optional) List of object IDs (strings of the form "class-xxxx") in the source container to be cloned
  • folders array of strings (optional) List of folders in the source container to be cloned
  • project string ID of the destination container
  • destination string (optional, default "/") The destination folder in project
  • parents boolean (optional, default false) Whether the destination folder and/or parent folders should be created if they do not exist

Outputs

  • id string ID of the source container
  • project string ID of the modified destination container
  • exists array of strings List of object IDs that could not be cloned because they already exist in the destination container

Errors

  • InvalidInput
    • objects (if provided) is not an array of nonempty strings
    • folders (if provided) is not an array of nonempty strings
    • Two of the folders in folders have the same name but different paths
    • project is missing or is not a nonempty string unequal to the source container
    • destination (if provided) is not a nonempty string starting with "/"
    • parents if provided is not a boolean
    • project must be in the same region as the source containers of all specified objects.
  • InvalidType
    • project is not a container ID
  • ResourceNotFound
    • The container specified in the URL does not exist
    • The container specified in project does not exist
    • One or more objects or folder routes in objects and folders were not found or were not in the source container
    • The folder specified in destination does not exist in the destination container)
  • PermissionDenied
    • VIEW access is required in the source container
    • UPLOAD access is required in the destination container
    • RESTRICTED flag must not be set in the source container
    • The source and destination containers must have the same region. For more information about regions, see Regions.
  • InvalidState
    • One or more of the input objects is not in the "closed" state
    • There exists a folder in the destination folder destination which has the same name as a folder listed in folders
    • The destination project is third-party sponsored and one or more of the input objects is DNAnexus-sponsored
    • The destination project is third-party sponsored and one or more of the input objects is already third-party sponsored in another project. When this error is thrown, the error details is of the form {alreadySponsored: [{id: ..., project: ...}, ...]} indicating the ID and sponsoring project of each object that was already third-party sponsored.
  • SpendingLimitExceeded
    • The billTo of the destination project has already reached its spending limit and is different from the billTo of the source project

API method: /class-xxxx/listProjects

Specification

Returns a list of projects that contain the object specified and for which the user has permissions to access. If the token is not full scope, the projects that are returned are additionally filtered to those that the token has at least VIEW access to.

Inputs

  • None

Outputs

  • key ID of a project that contains the specified object
  • value string Permission level that the user has in the project

Errors

  • ResourceNotFound (the specified object does not exist)

Last edited by Sean King, 2016-06-23 22:52:54

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