takane validation functions. More...

Namespaces
namespace	atomic_vector
	Definitions for atomic vectors.

namespace	bam_file
	Definitions for BAM files.

namespace	bcf_file
	Definitions for BCF files.

namespace	bed_file
	Definitions for BED files.

namespace	bigbed_file
	Definitions for bigBed files.

namespace	bigwig_file
	Definitions for bigWig files.

namespace	compressed_sparse_matrix
	Definitions for compressed sparse matrices.

namespace	csv_data_frame
	Definitions for CSV data frames.

namespace	data_frame_factor
	Definitions for data frame factors.

namespace	delayed_array
	Definitions for delayed arrays.

namespace	dense_array
	Definitions for dense arrays.

namespace	fasta_file
	Definitions for FASTA files.

namespace	fastq_file
	Definitions for FASTQ files.

namespace	genomic_ranges
	Definitions for genomic ranges.

namespace	gff_file
	Definitions for GFF files.

namespace	gmt_file
	Definitions for GMT files.

namespace	multi_sample_dataset
	Definitions for multi-sample datasets.

namespace	ranged_summarized_experiment
	Definitions for ranged summarized experiments.

namespace	rds_file
	Definitions for RDS files.

namespace	sequence_information
	Definitions for sequence information objects.

namespace	sequence_string_set
	Definitions for sequence string sets.

namespace	simple_list
	Definitions for simple lists.

namespace	single_cell_experiment
	Definitions for single cell experiments.

namespace	spatial_experiment
	Definitions for spatial experiments.

namespace	string_factor
	Definitions for string factors.

namespace	summarized_experiment
	Definitions for summarized experiments.

namespace	vcf_experiment
	Definitions for VCF experiments.

Classes
struct	CsvContents
	Contents of the parsed CSV. More...

struct	CsvFieldCreator
	Create `comservatory::Field` objects to capture column contents. More...

struct	DummyCsvFieldCreator
	Dummy column creator. More...

struct	ObjectMetadata
	Object metadata, including the type and other fields. More...

struct	Options
	Validation options. More...

Functions
bool	derived_from (const std::string &type, const std::string &base, const Options &options)

std::vector< size_t >	dimensions (const std::filesystem::path &path, const ObjectMetadata &metadata, Options &options)

std::vector< size_t >	dimensions (const std::filesystem::path &path, Options &options)

std::vector< size_t >	dimensions (const std::filesystem::path &path)

size_t	height (const std::filesystem::path &path, const ObjectMetadata &metadata, Options &options)

size_t	height (const std::filesystem::path &path, Options &options)

size_t	height (const std::filesystem::path &path)

bool	satisfies_interface (const std::string &type, const std::string &interface, const Options &options)

void	validate (const std::filesystem::path &path, const ObjectMetadata &metadata, Options &options)

void	validate (const std::filesystem::path &path, Options &options)

void	validate (const std::filesystem::path &path)

ObjectMetadata	reformat_object_metadata (millijson::Base *raw)

ObjectMetadata	read_object_metadata (const std::filesystem::path &path)

Detailed Description

takane validation functions.

Function Documentation

◆ derived_from()

bool takane::derived_from	(	const std::string &	type,
		const std::string &	base,
		const Options &	options
	)

inline

Check whether a particular object type is derived from a base object type. Derived types satisfy the same file requirements of the base type, but usually add more files to represent additional functionality. This can be used by specifications to check whether arbitrary objects satisfy the file structure expectations for a particular base type.

Applications can add their own derived types for a given base class in Options::custom_derived_from. This extends the default relationships whereby derived_from() will take the union of all derived object types in the default and custom sets. Note that derived types must be manually included in every base type's set, e.g., if B is derived from A and C is derived from B, C must be added to the sets for both A and B.

Parameters

type	Object type.
base	Base object type.
options	Validation options, containing custom derived/base relationships.

Returns: Whether type is derived from base or is equal to base.

◆ dimensions() [1/3]

std::vector< size_t > takane::dimensions ( const std::filesystem::path & path )

inline

Overload of dimensions() with default settings.

Parameters

path	Path to a directory containing an object.

Returns: The object's dimensions.

◆ dimensions() [2/3]

std::vector< size_t > takane::dimensions	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		Options &	options
	)

inline

Get the dimensions of a multi-dimensional object in a subdirectory, based on the supplied object type.

Applications can supply custom dimension functions for a given type via Options::custom_dimensions. If available, the supplied custom function will be used instead of the default.

Parameters

path	Path to a directory representing an object.
metadata	Metadata for the object, typically determined from its `OBJECT` file.
options	Validation options.

Returns: Vector containing the object's dimensions.

◆ dimensions() [3/3]

std::vector< size_t > takane::dimensions	(	const std::filesystem::path &	path,
		Options &	options
	)

inline

Get the dimensions of an object in a subdirectory, using its OBJECT file to automatically determine the type.

Parameters

path	Path to a directory containing an object.
options	Validation options.

Returns: The object's dimensions.

◆ height() [1/3]

size_t takane::height ( const std::filesystem::path & path )

inline

Overload of height() with default settings.

Parameters

path	Path to a directory containing an object.

Returns: The object's height.

◆ height() [2/3]

size_t takane::height	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		Options &	options
	)

inline

Get the height of an object in a subdirectory, based on the supplied object type.

height() is used to check the shape of objects stored in vertical containers, e.g., columns of a data_frame. For vectors or other 1-dimensional objects, the height is usually just the length of the object (for some object-specific definition of "length"). For higher-dimensional objects, the height is usually the extent of the first dimension.

Applications can supply custom height functions for a given type via Options::custom_height. If available, the supplied custom function will be used instead of the default.

Parameters

path	Path to a directory representing an object.
metadata	Metadata for the object, typically determined from its `OBJECT` file.
options	Validation options.

Returns: The object's height.

◆ height() [3/3]

size_t takane::height	(	const std::filesystem::path &	path,
		Options &	options
	)

inline

Get the height of an object in a subdirectory, using its OBJECT file to automatically determine the type.

Parameters

path	Path to a directory containing an object.
options	Validation options.

Returns: The object's height.

◆ read_object_metadata()

ObjectMetadata takane::read_object_metadata ( const std::filesystem::path & path )

inline

Reads the OBJECT file inside a directory to determine the object type.

Parameters

path	Path to a directory containing an object.

Returns: Object metadata, including the type and other fields.

◆ reformat_object_metadata()

ObjectMetadata takane::reformat_object_metadata ( millijson::Base * raw )

inline

Parses a JSON object to obtain the object metadata.

Parameters

raw	Raw JSON object, typically obtained by `millijson::parse_file`. Note that `raw` is consumed by this function and should no longer be used by the caller.

Returns: Object metadata, including the type and other fields.

◆ satisfies_interface()

bool takane::satisfies_interface	(	const std::string &	type,
		const std::string &	interface,
		const Options &	options
	)

inline

Check whether a particular object type satisfies a particular object interface. This can be used by specifications to check that child components satisfy certain user-level expectations for an abstract object (e.g., data frames, lists).

Applications can extend the takane framework by adding custom types to Options::custom_satisfies_interface. This extends the default relationships whereby satisfies_interface() will take the union of all object types in the default and custom sets. Note that, if a type is included in a particular set, it is not necessary to add its derived types, as satisfies_interface() will automatically call derived_from().

Parameters

type	Object type.
interface	Interface type.
options	Validation options, containing custom object interface relationships.

Returns: Whether type satisfies interface.

◆ validate() [1/3]

void takane::validate ( const std::filesystem::path & path )

inline

Overload of validate() with default settings.

Parameters

path	Path to a directory containing an object.

◆ validate() [2/3]

void takane::validate	(	const std::filesystem::path &	path,
		const ObjectMetadata &	metadata,
		Options &	options
	)

inline

Validate an object in a subdirectory, based on the supplied object type.

Applications can supply custom validation functions for a given type via Options::custom_validate. If available, the supplied custom function will be used instead of the default.

Parameters

path	Path to a directory representing an object.
metadata	Metadata for the object, typically determined from its `OBJECT` file.
options	Validation options.

◆ validate() [3/3]

void takane::validate	(	const std::filesystem::path &	path,
		Options &	options
	)

inline

Validate an object in a subdirectory, using its OBJECT file to automatically determine the type.

Parameters

path	Path to a directory containing an object.
options	Validation options.

Namespaces

Classes

Functions

Detailed Description

Function Documentation

◆ derived_from()

◆ dimensions() [1/3]

◆ dimensions() [2/3]

◆ dimensions() [3/3]

◆ height() [1/3]

◆ height() [2/3]

◆ height() [3/3]

◆ read_object_metadata()

◆ reformat_object_metadata()

◆ satisfies_interface()

◆ validate() [1/3]

◆ validate() [2/3]

◆ validate() [3/3]