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Merge pull request #167 from srbcheema1/unused_options
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warn for unused parameters

This PR is to fix #165. vcf_validator will show a warning if any of the parameters went unused or unrecognised. 
```
$ ./vcf_validator -i a.vcf -r summary, text
[warning] unused parameter: text
[info] Reading from input file...
[info] Summary report written to : stdin.errors_summary.1537119684362.txt
[info] According to the VCF specification, the input file is not valid
```
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@jmmut
jmmut authored Sep 27, 2018
2 parents 6118f3e + 3c36b54 commit 97ffaed
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Showing 4 changed files with 143 additions and 116 deletions.
72 changes: 72 additions & 0 deletions inc/util/cli_utils.hpp
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@@ -0,0 +1,72 @@
/**
* Copyright 2017 EMBL - European Bioinformatics Institute
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/

#ifndef UTIL_CLI_UTILS_HPP
#define UTIL_CLI_UTILS_HPP

#include <string>
#include <vector>

#include <boost/program_options.hpp>
#include <boost/filesystem/operations.hpp>

#include "util/logger.hpp"

namespace ebi
{
namespace util
{
namespace po = boost::program_options;

po::variables_map build_variables_map(int argc, char** argv, const po::options_description & desc)
{
po::variables_map vm;
po::parsed_options parsed = po::command_line_parser(argc, argv).options(desc).allow_unregistered().run();
po::store(parsed,vm);
std::vector<std::string> unrecognised_parameters = collect_unrecognized(parsed.options, po::include_positional);

for (auto & parameter: unrecognised_parameters) {
BOOST_LOG_TRIVIAL(warning) << "unused parameter: " << parameter;
}

po::notify(vm);
return vm;
}

std::string get_output_path(const std::string &outdir, const std::string &file_path)
{
if (outdir == "") {
return file_path;
}

boost::filesystem::path file_boost_path{file_path};
boost::filesystem::path outdir_boost_path{outdir};
if (!boost::filesystem::exists(outdir_boost_path)) {
throw std::invalid_argument{"Directory not found: " + outdir_boost_path.string()};
}
if (!boost::filesystem::is_directory(outdir_boost_path)) {
throw std::invalid_argument{"outdir should be a directory, not a file: " + outdir_boost_path.string()};
}

outdir_boost_path /= file_boost_path.filename();

return outdir_boost_path.string();
}

}
}

#endif // UTIL_CLI_UTILS_HPP
30 changes: 5 additions & 25 deletions src/assembly_checker_main.cpp
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Expand Up @@ -18,10 +18,11 @@
#include <boost/program_options.hpp>

#include "cmake_config.hpp"
#include "util/cli_utils.hpp"
#include "util/logger.hpp"
#include "vcf/assembly_checker.hpp"
#include "vcf/assembly_report_writer.hpp"
#include "vcf/string_constants.hpp"
#include "util/logger.hpp"

namespace
{
Expand Down Expand Up @@ -73,26 +74,6 @@ namespace
return 0;
}

std::string get_output_path(const std::string &outdir, const std::string &file_path)
{
if (outdir == "") {
return file_path;
}

boost::filesystem::path file_boost_path{file_path};
boost::filesystem::path outdir_boost_path{outdir};
if (!boost::filesystem::exists(outdir_boost_path)) {
throw std::invalid_argument{"Directory not found: " + outdir_boost_path.string()};
}
if (!boost::filesystem::is_directory(outdir_boost_path)) {
throw std::invalid_argument{"outdir should be a directory, not a file: " + outdir_boost_path.string()};
}

outdir_boost_path /= file_boost_path.filename();

return outdir_boost_path.string();
}

std::vector<std::unique_ptr<ebi::vcf::AssemblyReportWriter>> get_outputs(std::string const &output_str,
std::string const &input)
{
Expand Down Expand Up @@ -152,10 +133,9 @@ namespace
int main(int argc, char** argv)
{
ebi::util::init_boost_loggers();

po::options_description desc = build_command_line_options();
po::variables_map vm;
po::store(po::parse_command_line(argc, argv, desc), vm);
po::notify(vm);
po::variables_map vm = ebi::util::build_variables_map(argc, argv, desc);

int check_options = check_command_line_options(vm, desc);
if (check_options < 0) { return 0; }
Expand All @@ -165,7 +145,7 @@ int main(int argc, char** argv)
auto vcf_path = vm[ebi::vcf::INPUT].as<std::string>();
auto fasta_path = vm[ebi::vcf::FASTA].as<std::string>();
auto fasta_index_path = fasta_path + ".fai";
auto outdir = get_output_path(vm[ebi::vcf::OUTDIR].as<std::string>(), vcf_path);
auto outdir = ebi::util::get_output_path(vm[ebi::vcf::OUTDIR].as<std::string>(), vcf_path);
auto outputs = get_outputs(vm[ebi::vcf::REPORT].as<std::string>(), outdir);

BOOST_LOG_TRIVIAL(info) << "Reading from input FASTA file...";
Expand Down
115 changes: 56 additions & 59 deletions src/debugulator_main.cpp
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Expand Up @@ -20,78 +20,75 @@
#include <boost/program_options.hpp>

#include "cmake_config.hpp"
#include "util/cli_utils.hpp"
#include "util/logger.hpp"
#include "vcf/debugulator.hpp"
#include "vcf/odb_report.hpp"
#include "vcf/string_constants.hpp"
#include "vcf/debugulator.hpp"

namespace
{
namespace po = boost::program_options;

enum class ValidationLevel
{
error, warning, stop
};

const std::string version_info = "vcf-debugulator version " + std::to_string(VERSION_MAJOR) + "."
+ std::to_string(VERSION_MINOR);

po::options_description build_command_line_options()
{
po::options_description description(version_info + "\n\nUsage: vcf-debugulator [OPTIONS] [< input_file]\nAllowed options");

description.add_options()
(ebi::vcf::HELP_OPTION, "Display this help")
(ebi::vcf::VERSION_OPTION, "Display version of the debugulator")
(ebi::vcf::INPUT_OPTION, po::value<std::string>()->default_value(ebi::vcf::STDIN), "Path to the input VCF file, or stdin")
(ebi::vcf::ERRORS_OPTION, po::value<std::string>(), "Path to the errors report from the input VCF file")
(ebi::vcf::LEVEL_OPTION, po::value<std::string>()->default_value(ebi::vcf::WARNING_LEVEL), "Validation level (error, warning, stop)")
(ebi::vcf::OUTPUT_OPTION, po::value<std::string>()->default_value(ebi::vcf::STDOUT), "Write to a file or stdout")
;

return description;
}

int check_command_line_options(po::variables_map const &vm, po::options_description const &desc)
{
if (vm.count(ebi::vcf::HELP)) {
std::cout << desc << std::endl;
return -1;
}

if (vm.count(ebi::vcf::VERSION)) {
std::cout << version_info << std::endl;
return -1;
}

std::string level = vm[ebi::vcf::LEVEL].as<std::string>();
if (level != ebi::vcf::ERROR_LEVEL && level != ebi::vcf::WARNING_LEVEL && level != ebi::vcf::STOP_LEVEL) {
std::cout << desc << std::endl;
BOOST_LOG_TRIVIAL(error) << "Please choose one of the accepted validation levels";
return 1;
}

if (!vm.count(ebi::vcf::ERRORS)) {
std::cout << desc << std::endl;
BOOST_LOG_TRIVIAL(error) << "Please specify the path to the errors report (--errors)";
return 1;
}

return 0;
}
namespace po = boost::program_options;

enum class ValidationLevel
{
error, warning, stop
};

const std::string version_info = "vcf-debugulator version " + std::to_string(VERSION_MAJOR) + "."
+ std::to_string(VERSION_MINOR);

po::options_description build_command_line_options()
{
po::options_description description(version_info + "\n\nUsage: vcf-debugulator [OPTIONS] [< input_file]\nAllowed options");

description.add_options()
(ebi::vcf::HELP_OPTION, "Display this help")
(ebi::vcf::VERSION_OPTION, "Display version of the debugulator")
(ebi::vcf::INPUT_OPTION, po::value<std::string>()->default_value(ebi::vcf::STDIN), "Path to the input VCF file, or stdin")
(ebi::vcf::ERRORS_OPTION, po::value<std::string>(), "Path to the errors report from the input VCF file")
(ebi::vcf::LEVEL_OPTION, po::value<std::string>()->default_value(ebi::vcf::WARNING_LEVEL), "Validation level (error, warning, stop)")
(ebi::vcf::OUTPUT_OPTION, po::value<std::string>()->default_value(ebi::vcf::STDOUT), "Write to a file or stdout")
;

return description;
}

int check_command_line_options(po::variables_map const &vm, po::options_description const &desc)
{
if (vm.count(ebi::vcf::HELP)) {
std::cout << desc << std::endl;
return -1;
}

if (vm.count(ebi::vcf::VERSION)) {
std::cout << version_info << std::endl;
return -1;
}

std::string level = vm[ebi::vcf::LEVEL].as<std::string>();
if (level != ebi::vcf::ERROR_LEVEL && level != ebi::vcf::WARNING_LEVEL && level != ebi::vcf::STOP_LEVEL) {
std::cout << desc << std::endl;
BOOST_LOG_TRIVIAL(error) << "Please choose one of the accepted validation levels";
return 1;
}

if (!vm.count(ebi::vcf::ERRORS)) {
std::cout << desc << std::endl;
BOOST_LOG_TRIVIAL(error) << "Please specify the path to the errors report (--errors)";
return 1;
}

return 0;
}
}

int main(int argc, char **argv)
{
ebi::util::init_boost_loggers();

namespace po = boost::program_options;

po::options_description desc = build_command_line_options();
po::variables_map vm;
po::store(po::parse_command_line(argc, argv, desc), vm);
po::notify(vm);
po::variables_map vm = ebi::util::build_variables_map(argc, argv, desc);

int check_options = check_command_line_options(vm, desc);
if (check_options < 0) { return 0; }
Expand Down
42 changes: 10 additions & 32 deletions src/validator_main.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -14,25 +14,26 @@
* limitations under the License.
*/

#include <iostream>
#include <chrono>
#include <fstream>
#include <iomanip>
#include <iostream>
#include <memory>
#include <stdexcept>
#include <string>
#include <vector>
#include <stdexcept>
#include <chrono>
#include <iomanip>

#include <boost/program_options.hpp>
#include <boost/filesystem/operations.hpp>

#include "cmake_config.hpp"
#include "util/cli_utils.hpp"
#include "util/logger.hpp"
#include "vcf/file_structure.hpp"
#include "vcf/validator.hpp"
#include "vcf/report_writer.hpp"
#include "vcf/odb_report.hpp"
#include "vcf/report_writer.hpp"
#include "vcf/summary_report_writer.hpp"
#include "vcf/validator.hpp"

namespace
{
Expand Down Expand Up @@ -92,27 +93,8 @@ namespace
throw std::invalid_argument{"Please choose one of the accepted validation levels"};
}

std::string get_output_path(const std::string &outdir, const std::string &file_path)
std::vector<std::unique_ptr<ebi::vcf::ReportWriter>> get_outputs(std::string const &output_str, std::string const &input)
{
if (outdir == "") {
return file_path;
}

boost::filesystem::path file_boost_path{file_path};
boost::filesystem::path outdir_boost_path{outdir};
if (!boost::filesystem::exists(outdir_boost_path)) {
throw std::invalid_argument{"Directory not found: " + outdir_boost_path.string()};
}
if (!boost::filesystem::is_directory(outdir_boost_path)) {
throw std::invalid_argument{"outdir should be a directory, not a file: " + outdir_boost_path.string()};
}

outdir_boost_path /= file_boost_path.filename();

return outdir_boost_path.string();
}

std::vector<std::unique_ptr<ebi::vcf::ReportWriter>> get_outputs(std::string const &output_str, std::string const &input) {
std::vector<std::string> outs;
ebi::util::string_split(output_str, ",", outs);
size_t initial_size = outs.size();
Expand Down Expand Up @@ -159,21 +141,17 @@ int main(int argc, char** argv)
ebi::util::init_boost_loggers();

po::options_description desc = build_command_line_options();
po::variables_map vm;
po::store(po::parse_command_line(argc, argv, desc), vm);
po::notify(vm);

po::variables_map vm = ebi::util::build_variables_map(argc, argv, desc);
int check_options = check_command_line_options(vm, desc);
if (check_options < 0) { return 0; }
if (check_options > 0) { return check_options; }

bool is_valid;

try {
auto path = vm[ebi::vcf::INPUT].as<std::string>();
auto level = vm[ebi::vcf::LEVEL].as<std::string>();
ebi::vcf::ValidationLevel validationLevel = get_validation_level(level);
auto outdir = get_output_path(vm[ebi::vcf::OUTDIR].as<std::string>(), path);
auto outdir = ebi::util::get_output_path(vm[ebi::vcf::OUTDIR].as<std::string>(), path);
auto outputs = get_outputs(vm[ebi::vcf::REPORT].as<std::string>(), outdir);

if (path == ebi::vcf::STDIN) {
Expand Down

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