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

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

#include <seqan3/argument_parser/validators.hpp>

+ Inheritance diagram for seqan3::input_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 an existing regular file and is readable.
 
Constructors, destructor and assignment
 input_file_validator ()
 Default constructor.
 
 input_file_validator (input_file_validator const &)=default
 Defaulted.
 
 input_file_validator (input_file_validator &&)=default
 Defaulted.
 
input_file_validatoroperator= (input_file_validator const &)=default
 Defaulted.
 
input_file_validatoroperator= (input_file_validator &&)=default
 Defaulted.
 
virtual ~input_file_validator ()=default
 Virtual destructor.
 
 input_file_validator (std::vector< std::string > extensions)
 Constructs from a given collection 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
 

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::input_file_validator< file_t >

A validator that checks if a given path is a valid input 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::filesystem::path) is not in the given list of valid file extensions, if the file does not exist, or if the file does not have the proper read permissions.

// 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
myparser.add_option(myfile,
'f',
"file",
"The input file containing the sequences.",
seqan3::input_file_validator{{"fa", "fasta"}});
// an exception will be thrown if the user specifies a filename
// that does not have one of the extensions ["fa","fasta"] or if the file does not exist/is not readable.
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 input file.
Definition validators.hpp:514
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
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::input_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 input file.
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_input 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

◆ input_file_validator() [1/2]

template<typename file_t = void>
seqan3::input_file_validator< file_t >::input_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.

◆ input_file_validator() [2/2]

template<typename file_t = void>
seqan3::input_file_validator< file_t >::input_file_validator ( std::vector< std::string extensions)
inlineexplicit

Constructs from a given collection of valid extensions.

Parameters
[in]extensionsThe valid extensions to validate for.

This constructor is only available if file_t does not name a valid seqan3 file type that contains a static member valid_formats.

Member Function Documentation

◆ get_help_page_message()

template<typename file_t = void>
std::string seqan3::input_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::input_file_validator< file_t >::operator() ( std::filesystem::path const &  file) const
inlineoverridevirtual

Tests whether path is an existing regular file and is readable.

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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