Validate an object's on-disk representation

Validate an object's on-disk representation against the takane specifications. This is done by dispatching to an appropriate validation function based on the type in the OBJECT file.

validateObject(path, metadata = NULL)

registerValidateObjectFunction(type, fun, existing = c("old", "new", "error"))

registerValidateObjectHeightFunction(
  type,
  fun,
  existing = c("old", "new", "error")
)

registerValidateObjectDimensionsFunction(
  type,
  fun,
  existing = c("old", "new", "error")
)

registerValidateObjectSatisfiesInterface(
  type,
  interface,
  action = c("add", "remove")
)

registerValidateObjectDerivedFrom(type, parent, action = c("add", "remove"))

Arguments

path

String containing a path to a directory, itself created with a saveObject method.

metadata

List containing metadata for the object. If this is not supplied, it is automatically read from the OBJECT file inside path.

type

String specifying the name of type of the object.

fun

For registerValidateObjectFunction, a function that accepts path and metadata, and raises an error if the object at path is invalid. It can be assumed that metadata is a list created by reading OBJECT.

For registerValidateObjectHeightFunction, a function that accepts path and metadata, and returns an integer specifying the “height” of the object. This is usually the length for vector-like or 1-dimensional objects, and the extent of the first dimension for higher-dimensional objects.

For registerValidateObjectDimensionsFunction, a function that accepts path and metadata, and returns an integer vector specifying the dimensions of the object.

This may also be NULL to delete an existing registry from any of the functions mentioned above.

existing

Logical scalar indicating the action to take if a function has already been registered for type - keep the old or new function, or throw an error.

interface

String specifying the name of the interface that is represented by type.

action

String specifying whether to add or remove type from the list of types that implements interface or is derived from parent.

parent

String specifying the parent object from which type is derived.

Value

For validateObject, NULL is returned invisibly upon success, otherwise an error is raised.

For the registerValidObject*Function functions, the supplied fun is added to the corresponding registry for type. If fun = NULL, any existing entry for type is removed; a logical scalar is returned indicating whether removal was performed.

For the registerValidateObjectSatisfiesInterface and registerValidateObjectDerivedFrom functions, type is added to or removed from relevant list of types. A logical scalar is returned indicating whether the type was added or removed - this may be FALSE if type was already present or absent, respectively.

See also

https://github.com/ArtifactDB/takane, for detailed specifications of the on-disk representation for various Bioconductor objects.

Author

Aaron Lun

Examples

library(S4Vectors)
df <- DataFrame(A=1:10, B=LETTERS[1:10])

tmp <- tempfile()
saveObject(df, tmp)
validateObject(tmp)