SeqAn3 3.4.0-rc.1
The Modern C++ library for sequence analysis.
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seqan3::output_file_validator< file_t > Class Template Reference

A validator that checks if a given path is a valid output file. More...

#include <seqan3/argument_parser/validators.hpp>

+ Inheritance diagram for seqan3::output_file_validator< file_t >:

Public Types

using option_value_type = std::string
 Type of values that are tested by validator.
 
- Public Types inherited from seqan3::file_validator_base
using option_value_type = std::string
 Type of values that are tested by validator.
 

Public Member Functions

std::string get_help_page_message () const
 Returns a message that can be appended to the (positional) options help page info.
 
virtual void operator() (std::filesystem::path const &file) const override
 Tests whether path is does not already exists and is writable.
 
Constructors, destructor and assignment
 output_file_validator ()
 Default constructor.
 
 output_file_validator (output_file_validator const &)=default
 Defaulted.
 
 output_file_validator (output_file_validator &&)=default
 Defaulted.
 
output_file_validatoroperator= (output_file_validator const &)=default
 Defaulted.
 
output_file_validatoroperator= (output_file_validator &&)=default
 Defaulted.
 
virtual ~output_file_validator ()=default
 Virtual Destructor.
 
 output_file_validator (output_file_open_options const mode, std::vector< std::string > extensions=default_extensions())
 Constructs from a given overwrite mode and a list of valid extensions.
 
 file_validator_base ()=default
 Defaulted.
 
 file_validator_base (file_validator_base const &)=default
 Defaulted.
 
 file_validator_base (file_validator_base &&)=default
 Defaulted.
 
- Public Member Functions inherited from seqan3::file_validator_base
template<std::ranges::forward_range range_type>
requires (std::convertible_to<std::ranges::range_value_t<range_type>, std::filesystem::path const &> && !std::convertible_to<range_type, std::filesystem::path const &>)
void operator() (range_type const &v) const
 Tests whether every path in list v passes validation. See operator()(option_value_type const & value) for further information.
 
 file_validator_base ()=default
 Defaulted.
 
 file_validator_base (file_validator_base const &)=default
 Defaulted.
 
 file_validator_base (file_validator_base &&)=default
 Defaulted.
 
file_validator_baseoperator= (file_validator_base const &)=default
 Defaulted.
 
file_validator_baseoperator= (file_validator_base &&)=default
 Defaulted.
 
virtual ~file_validator_base ()=default
 

Static Public Member Functions

static std::vector< std::stringdefault_extensions ()
 The default extensions of file_t.
 

Additional Inherited Members

- Protected Member Functions inherited from seqan3::file_validator_base
bool case_insensitive_string_ends_with (std::string_view str, std::string_view suffix) const
 Helper function that checks if a string is a suffix of another string. Case insensitive.
 
std::string valid_extensions_help_page_message () const
 Returns the information of valid file extensions.
 
void validate_filename (std::filesystem::path const &path) const
 Validates the given filename path based on the specified extensions.
 
void validate_readability (std::filesystem::path const &path) const
 Checks if the given path is readable.
 
void validate_writeability (std::filesystem::path const &path) const
 Checks if the given path is writable.
 
- Protected Attributes inherited from seqan3::file_validator_base
std::vector< std::stringextensions {}
 Stores the extensions.
 

Detailed Description

template<typename file_t = void>
class seqan3::output_file_validator< file_t >

A validator that checks if a given path is a valid output file.

Template Parameters
file_tThe type of the file to get the valid extensions for; void on default.

On construction, the validator can receive a list (std::vector over std::string) of valid file extensions. The class acts as a functor that throws a seqan3::validation_error exception whenever a given filename's extension (std::string) is not in the given list of valid file extensions, or if the parent path does not have the proper writer permissions. In addition, the validator receives a seqan3::output_file_open_options which allows you to specify what to do if your output file already exists. seqan3::output_file_open_options::create_new will throw a seqan3::validation_error exception if it already exists and seqan3::output_file_open_options::open_or_create will skip this check (that means you are allowed to overwrite the existing file).

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
#include <filesystem>
int main(int argc, char const ** argv)
{
seqan3::argument_parser myparser{"Test", argc, argv}; // initialize
// Use the seqan3::output_file_open_options to indicate that you allow overwriting existing output files, ...
myparser.add_option(
myfile,
'f',
"file",
"Output file containing the processed sequences.",
// ... or that you will throw a seqan3::validation_error if the user specified output file already exists
myparser.add_option(myfile,
'g',
"file2",
"Output file containing the processed sequences.",
// an exception will be thrown if the user specifies a filename
// that does not have one of the extensions ["fa","fasta"],
// if the file already exists, or if the file is not writable.
try
{
myparser.parse();
}
catch (seqan3::argument_parser_error const & ext) // the user did something wrong
{
std::cerr << "[PARSER ERROR] " << ext.what() << "\n"; // customize your error message
return -1;
}
seqan3::debug_stream << "filename given by user passed validation: " << myfile << "\n";
return 0;
}
Meta-header for the Argument Parser module .
Argument parser exception that is thrown whenever there is an error while parsing the command line ar...
Definition exceptions.hpp:37
The SeqAn command line parser.
Definition argument_parser.hpp:145
A validator that checks if a given path is a valid output file.
Definition validators.hpp:644
Provides seqan3::debug_stream and related types.
@ standard
The default were no checking or special displaying is happening.
Definition auxiliary.hpp:242
debug_stream_type debug_stream
A global instance of seqan3::debug_stream_type.
Definition debug_stream.hpp:37
@ create_new
Forbid overwriting the output file.
@ open_or_create
Allow to overwrite the output file.
T what(T... args)

The valid extensions can also be obtained from a seqan3 formatted file type, e.g. seqan3::sequence_input_file, if it is given as template argument to this class. The following snippet demonstrates the different ways to instantiate the seqan3::output_file_validator.

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
int main()
{
// Default constructed validator has an empty extension list.
seqan3::debug_stream << validator1.get_help_page_message() << '\n';
// Specify your own extensions for the output file.
std::vector{std::string{"exe"}, std::string{"fasta"}}};
seqan3::debug_stream << validator2.get_help_page_message() << '\n';
// Give the seqan3 file type as a template argument to get all valid extensions for this file.
seqan3::debug_stream << validator3.get_help_page_message() << '\n';
return 0;
}
Provides seqan3::sequence_file_output and corresponding traits classes.
Provides some standard validators for (positional) options.
Note
The validator works on every type that can be implicitly converted to std::filesystem::path.
Remarks
For a complete overview, take a look at Argument Parser

Constructor & Destructor Documentation

◆ output_file_validator() [1/2]

template<typename file_t = void>
seqan3::output_file_validator< file_t >::output_file_validator ( )
inline

Default constructor.

If the class' template argument file_t names a valid seqan3 file type that contains a static member valid_formats, e.g. seqan3::sequence_input_file::valid_formats, then it generates the list of valid extensions from this file. Otherwise the extensions list is empty.

◆ output_file_validator() [2/2]

template<typename file_t = void>
seqan3::output_file_validator< file_t >::output_file_validator ( output_file_open_options const  mode,
std::vector< std::string extensions = default_extensions() 
)
inlineexplicit

Constructs from a given overwrite mode and a list of valid extensions.

Parameters
[in]modeA seqan3::output_file_open_options indicating whether the validator throws if a file already exists.
[in]extensionsThe valid extensions to validate for. Defaults to seqan3::output_file_validator::default_extensions.

Member Function Documentation

◆ default_extensions()

template<typename file_t = void>
static std::vector< std::string > seqan3::output_file_validator< file_t >::default_extensions ( )
inlinestatic

The default extensions of file_t.

Returns
A list of default extensions for file_t, will be empty if file_t is void.

If file_t does name a valid seqan3 file type that contains a static member valid_formats returns the extensions of that file_t type. Otherwise returns an empty list.

◆ get_help_page_message()

template<typename file_t = void>
std::string seqan3::output_file_validator< file_t >::get_help_page_message ( ) const
inline

Returns a message that can be appended to the (positional) options help page info.

Implements validator.

◆ operator()()

template<typename file_t = void>
virtual void seqan3::output_file_validator< file_t >::operator() ( std::filesystem::path const &  file) const
inlineoverridevirtual

Tests whether path is does not already exists and is writable.

Parameters
fileThe input value to check.
Exceptions
seqan3::validation_errorif the validation process failed. Might be nested with std::filesystem::filesystem_error on unhandled OS API errors.

Implements seqan3::file_validator_base.


The documentation for this class was generated from the following file:
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