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regression_test.cpp
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regression_test.cpp
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/* SpecUtils: a library to parse, save, and manipulate gamma spectrum data files.
Copyright 2018 National Technology & Engineering Solutions of Sandia, LLC
(NTESS). Under the terms of Contract DE-NA0003525 with NTESS, the U.S.
Government retains certain rights in this software.
For questions contact William Johnson via email at [email protected], or
alternative emails of [email protected], or [email protected].
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
*/
#include "SpecUtils_config.h"
#include <chrono>
#include <string>
#include <vector>
#include <iomanip>
#include <fstream>
#include <sstream>
#include <assert.h>
#include <iostream>
#include <algorithm>
#include "SpecUtils/SpecFile.h"
#include "SpecUtils/DateTime.h"
#include "SpecUtils/ParseUtils.h"
#include "SpecUtils/StringAlgo.h"
#include "SpecUtils/Filesystem.h"
#if( !SpecUtils_ENABLE_EQUALITY_CHECKS )
#error SpecUtils_ENABLE_EQUALITY_CHECKS must be enabled to compile regression_test
#endif
using namespace std;
//g_truth_n42_dirname: name of the sub-directory that truth N42 files will be
// stored in.
const string g_truth_n42_dirname = "truth_n42s";
//g_automated_mode: specifies whether being ran in an automated mode, or with
// user interaction.
bool g_automated_mode = false;
//g_sub_test_dir: specifies directory containing file types to be tested. All
// files if its empty.
string g_sub_test_dir = "";
//g_parse_time_filename: the name of the file written to the test base directory
// that stores the parse times for files. Not added to GIT.
const string g_parse_time_filename = "parsetimes.txt";
//open_spec_file(): uses the OS X 'open' command to open the spectrum file
// with InterSpec running on localport:8080.
void open_spec_file( const std::string &p );
//open_spec_file_in_textmate(): : uses the OS X 'open' command to open the
// spectrum file in textmate
void open_spec_file_in_textmate( const std::string &p );
//open_directory(): uses OS X 'open' command to open a finder window for the
// specified directory; if a file is passed in, its parent directory is opened.
void open_directory( const std::string &p );
//handle_no_truth_files(): interactively creates truth files, based on prompting
// user what actions should be taken (so they can decide it a truth file should
// be created or not).
void handle_no_truth_files( const string basedir );
//FixableErrors: types of errors that are non-fatal for parsing that might be
// expected to change over time, and hence you might want the truth level
// information to be updated.
enum FixableErrors
{
UuidError,
NumFixableErrors
};//enum FixableErrors
//get_compare_error_type(): searches the what() given by the exception thrown
// by MeasurmentInfo::equal_enough() to determine error type. Returns
// NumFixableErrors if it wasnt recognized or is not fixable.
FixableErrors get_compare_error_type( const string &msg );
//check_files_with_truth_n42(): check files that have a cooresponding truth n42
// file, to be sure that the original and truth n42 files parse to similar
// results using the 'equal_enough(...)' test.
void check_files_with_truth_n42( const string basedir );
//check_serialization_to_n42(): for test files (that have truth N42 files) this
// function tests that the oringal file can be read in, written out to a 2011
// N42, and then read back in and ensured its equal_enough() to the original.
void check_serialization_to_n42( const string basedir );
/** Checks the oeprator= to make sure copies are complete. */
void check_equality_operator( const string basedir );
//add_truth_n42(): adds a truth n42 file for the SpecUtils::SpecFile and path
// passed in. Will fail if a truth n42 file already exists, unless force is
// specified to be true. Checks the created n42 file to be sure it can be read
// back in and pass the 'equal_enough(...)' test, otherwise wont add truth n42
// file. Will add resulting added file (and possibly directory) to GIT.
// Returns true if the truth N42 file was created.
bool add_truth_n42( const SpecUtils::SpecFile &m, const std::string &p, const bool force );
//check_parse_time(): compares the parse times of files with truth n42 files
// against previous parse times. Parses the file 10 times and takes the
// minimum CPU time run as the parse time.
void check_parse_time( const string basedir );
//url_encode(): encodes a string appropriately to be passed as a URL argument.
string url_encode( const string &value );
//print_summary(): prints a reasonably brief summary to the provided stream.
void print_summary( const SpecUtils::SpecFile &info, std::ostream &out );
//print_one_line_summary(): prints a single line summary to the provided stream.
void print_one_line_summary( const SpecUtils::Measurement &info, std::ostream &out );
//candidate_test_files(): return all candidate files, regardless if they have a
// matching truth_n42.
vector<std::string> candidate_test_files( const string basedir );
//candidates_with_truth_n42_files(): returns only candidate files that have
// truth information as well.
vector<std::string> candidates_with_truth_n42_files( const string basedir );
//truth_n42_files(): return all truth_n42 files.
vector<std::string> truth_n42_files( const string basedir );
//candidates_without_truth_n42_files(): return files that do not have truthfiles
vector<std::string> candidates_without_truth_n42_files( const string basedir );
int main( int argc, char **argv )
{
//TODO: add test that ensures serializing to N42 and back again pass
// equal_enough(...) test.
//test_base_directory: the directory where the test file structure is based.
#if( !defined(WIN32) )
string test_base_directory = "/Users/wcjohns/rad_ana/SpectrumFileFormats/file_format_test_spectra";
#else
string test_base_directory = "Z:\\wcjohns\\rad_ana\\InterSpec\\testing\\SpectrumFileFormats\\file_format_test_spectra";
#endif
g_automated_mode = false;
g_sub_test_dir = "";
vector<string> actions;
// Do a very minimal command-line argument parser
try
{
for( int i = 1; i < argc; ++i )
{
const string arg = argv[i];
auto is_short_opt = []( const string &arg, const char test ) -> bool {
return ((arg.size() > 1) && ((arg[0] == '-') || (arg[0] == '/'))
&& (arg[1] == test) && ((arg.size() == 2) || (arg[2] == '=')) );
};
auto is_long_opt = []( const string &arg, const string &test ) -> bool {
return (((arg.size() >= (2+test.size()))
&& (arg[0] == '-') && (arg[1] == '-')
&& (arg.substr(2,test.size()) == test)
&& ((arg.size() == (2+test.size()))
|| (arg[2+test.size()] == '=')))
|| ((arg.size() >= (1+test.size())) //Windows specify option using '/' character instead of '--'
&& (arg[0] == '/')
&& SpecUtils::iequals_ascii(arg.substr(1,test.size()), test) //For Windows, allow to be case insensitive
&& ((arg.size() == (1+test.size()))
|| (arg[1+test.size()] == '=')))
);
};
auto get_arg_str_val = [&i,argv,argc,arg]() -> string {
const auto pos = arg.find("=");
if( pos != string::npos )
return arg.substr(pos+1);
if( (i+1) >= argc )
throw runtime_error( "No value specified for argument '" + arg + "'" );
string val = SpecUtils::trim_copy( argv[i+1] );
assert( !SpecUtils::istarts_with(val, "-") );
i += 1; //advance the argument position, so we dont try and interpret this value as an argument
cout << "Arg value: '" << val << "'" << endl;
return val;
};//auto get_arg_str_val()
auto get_arg_bool_val = [=]() -> bool {
using SpecUtils::iequals_ascii;
const string val = get_arg_str_val();
if( iequals_ascii(val,"0") || iequals_ascii(val,"false") || iequals_ascii(val,"no") )
return false;
else if( iequals_ascii(val,"1") || iequals_ascii(val,"true") || iequals_ascii(val,"yes") )
return true;
throw runtime_error( "Invalid boolean value '" + val + "'" );
return false;
};//get_arg_bool_val(...)
if( (arg == "-h") || (arg == "--help") )
{
cout << "Available options:\n"
"\thelp,h\t"
"produce help message\n"
"\tbatch,b\t"
"Run in non-interactive automated test mode.\n"
"\tbasedir,d\t"
"Directory where the test files are located.\n"
"\tsubdir,s\t"
"Sub-directory in 'basedir' of files to test.\n"
"action,a\t"
"Action to perform. Either 'n42test', 'regression' (or equivalently 'test'),\n"
"\t\t'addfiles', 'timing', or 'equality'. If blank defaults to 'test' if in\n"
"\t\tautomated mode, or 'n42test', 'addfiles', 'test', 'timing', 'equality' otherwise."
<< endl;
return EXIT_SUCCESS;
}else if( is_long_opt(arg, "batch") || is_short_opt(arg, 'b') )
{
g_automated_mode = get_arg_bool_val();
}else if( is_long_opt(arg, "basedir") || is_short_opt(arg, 'd') )
{
test_base_directory = get_arg_str_val();
}else if( is_long_opt(arg, "subdir") || is_short_opt(arg, 's') )
{
g_sub_test_dir = get_arg_str_val();
}else if( is_long_opt(arg, "action") || is_short_opt(arg, 'a') )
{
string arg = get_arg_str_val();
// We'll allow specifying a CSV list of values, like `--action=A,b,c,d`
vector<string> vals;
SpecUtils::split( vals, arg, "," );
actions.insert( end(actions), begin(vals), end(vals) );
// Or user could do something like `--action A b c d`
while( (i+1) < argc )
{
if( (argv[i+1][0] == '-') || (argv[i+1][0] == '/') )
break;
actions.push_back( argv[i+1] );
i += 1;
}//while( (i+1) < argc )
}else
{
throw runtime_error( "Unknown arg '" + arg + "'" );
}
}//for( int i = 1; i < argc; ++i )
}catch( std::exception &e )
{
cerr << "Error parsing command line arguments: " << e.what() << endl;
return EXIT_FAILURE;
}//try / catch to parse command line options
if( !SpecUtils::is_directory( test_base_directory ) )
{
cerr << "Base directory '" << test_base_directory << "' is not a valid "
<< "directory\n";
return EXIT_FAILURE;
}//if( base directory is invalid )
cout << "File base directory: '" << test_base_directory << "'\n";
if( g_automated_mode )
cout << "Testing in automated mode\n";
else
cout << "Testing in interactive mode\n";
if( !g_sub_test_dir.empty() )
{
test_base_directory
= SpecUtils::append_path( test_base_directory, g_sub_test_dir );
if( !SpecUtils::is_directory(test_base_directory) )
{
cerr << "Test sub directory '" << g_sub_test_dir << "' is not a valid"
<< " directory\n";
return EXIT_FAILURE;
}//if( sub directory is invalid )
cout << "Only testing files in the '" << g_sub_test_dir
<< "' subdirectory\n";
}//if( !g_sub_test_dir.empty() )
if( actions.empty() )
{
if( g_automated_mode )
actions.push_back( "test" );
else
actions = vector<string>{ "addfiles", "test", "timing", "n42test", "equality" };
}//if( vm.count("action") ) / else
for( string action : actions )
{
if( action == "n42test" )
check_serialization_to_n42( test_base_directory );
else if( action == "regression" || action == "test" )
check_files_with_truth_n42( test_base_directory );
else if( action == "addfiles" )
handle_no_truth_files( test_base_directory );
else if( action == "timing" )
check_parse_time( test_base_directory );
else if( action == "equality" )
check_equality_operator( test_base_directory );
else
{
cerr << "Invalid action type '" << action << "', valid options are "
<< "'n42test', 'regression', 'test', 'addfiles', 'timing', or blank\n";
return EXIT_FAILURE;
}
}//for( string action : actions )
return EXIT_SUCCESS;
}//int main( int argc, char **argv )
void open_spec_file( const std::string &p )
{
const string command = "open http://localhost:8080/?specfilename="
+ url_encode( p );
system( command.c_str() );
//The following wine comand crashes Peak Easy, but would be nice.
// command = "wine '/Users/wcjohns/Desktop/triage_spectra/PeakEasy 4.74/PeakEasy 4.74.exe' '" + path + "' &"
// system( command.c_str() );
}//void open_spec_file( const path &p )
void open_spec_file_in_textmate( const std::string &p )
{
//const string command = "open -a TextMate '" + p.string<string>() + "'";
const string command = "/usr/local/bin/code '" + p + "'";
system( command.c_str() );
}//void open_spec_file_in_textmate( const std::string &p )
void open_directory( const std::string &p )
{
string command = "open '";
if( !SpecUtils::is_file(p) )
command += p + "'";
else
command += SpecUtils::parent_path(p) + "'";
system( command.c_str() );
}//void open_directory( const std::string &p )
void check_parse_time( const string basedir )
{
const int ntimes_parse = 10;
map<std::string,double> cpu_parse_times, wall_parse_times;
const vector<std::string> with_truth = candidates_with_truth_n42_files( basedir );
const SpecUtils::time_point_t start_time = std::chrono::time_point_cast<std::chrono::microseconds>(std::chrono::system_clock::now());
for( const std::string &fpath : with_truth )
{
const string extention = SpecUtils::file_extension(fpath);
for( int i = 0; i < ntimes_parse; ++i )
{
SpecUtils::SpecFile info;
const double orig_wall_time = SpecUtils::get_wall_time();
const double orig_cpu_time = SpecUtils::get_cpu_time();
const bool parsed = info.load_file( fpath, SpecUtils::ParserType::Auto, extention );
const double final_cpu_time = SpecUtils::get_cpu_time();
const double final_wall_time = SpecUtils::get_wall_time();
if( parsed && orig_cpu_time > 0.0 && final_cpu_time > 0.0 )
{
double cpu_dt = final_cpu_time - orig_cpu_time;
double wall_dt = final_wall_time - orig_wall_time;
const map<string,double>::const_iterator pos = cpu_parse_times.find( fpath );
if( pos != cpu_parse_times.end() && (pos->second < cpu_dt) )
{
cpu_dt = pos->second;
wall_dt = wall_parse_times[pos->first];
}
cpu_parse_times[fpath] = cpu_dt;
wall_parse_times[fpath] = wall_dt;
}//if( parsed && orig_cpu_time > 0.0 && final_cpu_time > 0.0 )
}//for( int i = 0; i < ntimes_parse; ++i )
}//for( const string &fpath : with_truth )
string prevtimestr;
map<string,double> previous_cpu_parse_times, previous_wall_parse_times;
const string timingname
= SpecUtils::append_path( basedir, g_parse_time_filename );
{//begin read parsetimes
ifstream parsetimes( timingname.c_str(), ios::in | ios::binary );
if( parsetimes.is_open() && parsetimes.good() )
{
string filename;
SpecUtils::safe_get_line( parsetimes, prevtimestr );
while( SpecUtils::safe_get_line( parsetimes, filename ) )
{
if( filename.size() == 0 )
continue;
string times;
SpecUtils::safe_get_line( parsetimes, times );
double cputime, walltime;
const int n = sscanf( times.c_str(), "%lf %lf", &cputime, &walltime );
if( n != 2 )
{
cerr << "Error reading times for file '" << filename << "'\n"
<< "Stopping parsing timing file.\n";
break;
}//if( n != 2 )
previous_cpu_parse_times[filename] = cputime;
previous_wall_parse_times[filename] = walltime;
}//while( SpecUtils::safeGetline( parsetimes, line ) )
}//if( parsetimes.is_open() && parsetimes.good() )
}//end read parsetimes
//print comparison
double prev_cpu_total = 0.0, prev_wall_total = 0.0;
double current_cpu_total = 0.0, current_wall_total = 0.0;
bool previous_had_all = true;
cout << "Previous parse time: " << prevtimestr << endl;
for( map<string,double>::iterator i = cpu_parse_times.begin();
i != cpu_parse_times.end(); ++i )
{
const double cputime = i->second;
const double walltime = wall_parse_times[i->first];
current_cpu_total += cputime;
current_wall_total +=walltime;
string name = SpecUtils::filename(i->first);
if( name.size() > 30 )
name = name.substr( 0, 27 ) + "...";
cout << std::setw(31) << std::left << name << ": {cpu: "
<< setprecision(6) << std::fixed << cputime << ", wall: "
<< setprecision(6) << walltime << "}"
<< ", size: " << (SpecUtils::file_size(i->first) / 1024) << " kb\n";
if( previous_cpu_parse_times.count(i->first) )
{
prev_cpu_total += previous_cpu_parse_times[i->first];
prev_wall_total += previous_wall_parse_times[i->first];
cout << " previous : {cpu: "
<< setprecision(6) << previous_cpu_parse_times[i->first]
<< ", wall: "
<< setprecision(6) << previous_wall_parse_times[i->first] << "}\n";
}else
{
previous_had_all = false;
cout << " no previous \n";
}
cout << "\n";
}//for( loop over parse times )
cout << "Current total : {cpu: " << setprecision(6) << current_cpu_total
<< ", wall: " << setprecision(6) << prev_wall_total << "}\n";
if( previous_had_all )
cout << "Previous total : {cpu: " << setprecision(6) << prev_cpu_total
<< ", wall: " << setprecision(6) << prev_wall_total << "}\n\n";
else
cout << "Did not have previous timings for all the files\n\n";
//Decide if we should save the current results.
char action = (g_automated_mode ? 'n' : '\0');
while( action != 'y' && action != 'n' )
{
cout << "Would you like to save these latest timings? y/n\n";
cin >> action;
}//while( user hasnt entered valid answer )
if( action == 'y' )
{
ofstream file( timingname.c_str(), ios::out | ios::binary );
if( file.is_open() )
{
file << SpecUtils::to_extended_iso_string( start_time ) << endl;
for( map<string,double>::iterator i = cpu_parse_times.begin();
i != cpu_parse_times.end(); ++i )
{
file << i->first << endl << i->second
<< " " << wall_parse_times[i->first] << endl;
}
cout << "Saved timings to '" << timingname << "'" << endl;
}else
{
cerr << "Failed to open '" << timingname << "' for writing times\n";
}
}//if( action == 'y' )
}//void compare_parse_time( const string basedir )
FixableErrors get_compare_error_type( const string &msg )
{
if( SpecUtils::icontains( msg, "UUID of LHS" ) )
return UuidError;
return NumFixableErrors;
}//FixableErrors get_compare_error_type( const string &msg )
void check_files_with_truth_n42( const string basedir )
{
int initial = 0, initial_parsed = 0, failed_original_parsed = 0;
int failed_truth_parsed = 0, initial_with_truth = 0, passed_tests = 0;
int failed_tests = 0, updated_truths = 0, truths_failed_to_update = 0;
const vector<string> with_truth = candidates_with_truth_n42_files( basedir );
map<string,double> parse_times;
for( size_t file_index = 0; file_index < with_truth.size(); ++file_index )
{
const string &fpath = with_truth[file_index];
++initial;
const string filename = SpecUtils::filename(fpath);
const string originalpath = fpath;
const string originalext = SpecUtils::file_extension(fpath);
//A little hack to only look at certain files when debugging; insert part of the filename
// into 'files_interested_in' and re-compile.
set<string> files_interested_in, files_to_skip;
//files_interested_in.insert( "T10011_CS01C_D20070418_T181528_O0019_U.n42" );
bool interested_in = files_interested_in.empty();
for( const string &namesubstr : files_interested_in )
interested_in |= (filename.find(namesubstr) != string::npos);
//files_to_skip.insert( "some_filename_to_skip.n42" );
for( const auto &namesubstr : files_to_skip )
interested_in &= (filename.find(namesubstr) == string::npos);
if( !interested_in )
{
cerr << "Warning: skipping '" << filename << "' as requested in check_files_with_truth_n42\n";
continue;
}
SpecUtils::SpecFile original;
const bool originalstatus
= original.load_file( originalpath, SpecUtils::ParserType::Auto, originalext );
if( !originalstatus )
{
++failed_original_parsed;
cerr << "Failed to parse original file " << fpath << "\n\tskipping; type 'c' and enter to continue.\n\n";
char awk = (g_automated_mode ? 'c' : 'n');
while( awk != 'c' )
cin >> awk;
continue;
}
++initial_parsed;
const string tpath = SpecUtils::append_path( SpecUtils::append_path( SpecUtils::parent_path(fpath), g_truth_n42_dirname ), (filename + ".n42") );
if( !SpecUtils::is_file(tpath) )
{
cerr << "Fatal error: " << fpath << " doesnt have truth file at "
<< tpath << "\n\n";
exit( EXIT_FAILURE );
}
SpecUtils::SpecFile truth;
const bool truthstat = truth.load_file( tpath, SpecUtils::ParserType::N42_2012, "" );
if( !truthstat )
{
++failed_truth_parsed;
cerr << "Failed to parse truth file '" << tpath << "'\n\tskipping.\n\n";
continue;
}
++initial_with_truth;
truth.set_filename( original.filename() );
try
{
SpecUtils::SpecFile::equal_enough( original, truth );
++passed_tests;
}catch( std::exception &e )
{
++failed_tests;
cerr << "(on file " << file_index+1 << " of " << with_truth.size() << " )" << endl;
const string description = e.what();
vector<string> errors;
SpecUtils::split(errors, e.what(), "\n\r");
cerr << "\n" << fpath << "\nfailed comparison with previous parsing:\n";
for( const string &err : errors )
cerr << "\t" << err << endl;
cerr << "\n\t\t(Current parse is LHS, previous parse is RHS)\n"
<< "\n\tWhat would like to do?"
<< "\n";
const FixableErrors errortype = get_compare_error_type( description );
char action = (g_automated_mode ? 'i' : '\0');
while( (action != 'i') && (action != 'u') )
{
cout << "\ti: ignore\n"
<< "\to: open original file\n"
<< "\tt: open truth n42\n"
<< "\td: open contiaing directory\n"
<< "\tp: print summary of current parsing\n"
<< "\tq: print summary of truth\n"
<< "\tu: update truth\n";
if( errortype != NumFixableErrors )
cout << "\ts: set new error value to old parsing and try again\n";
cin >> action;
switch( action )
{
case 'i': break;
case 'o': open_spec_file( fpath ); break;
case 't': open_spec_file( tpath ); break;
case 'd': open_directory( fpath ); break;
case 'p': print_summary( original, cout ); break;
case 'q': print_summary( truth, cout ); break;
case 'u':
if( add_truth_n42( original, fpath, true ) )
{
++updated_truths;
cout << "\nUpdated truth info file.\n\n";
}else
{
++truths_failed_to_update;
cout << "\nFailed to updated truth info file.\n\n";
}
break;
case 's':
{
try
{
switch( errortype )
{
case UuidError:
truth.set_uuid( original.uuid() );
break;
case NumFixableErrors:
assert( 0 );
break;
}//switch( errortype )
SpecUtils::SpecFile::equal_enough( original, truth );
cout << "\nFixing the issue allowed the comparison test to pass."
<< "\nWould you like to update the truth level information?"
<< " (y/n)\n";
cin >> action;
if( action == 'y' )
{
if( add_truth_n42( original, fpath, true ) )
{
++updated_truths;
cout << "\nUpdated truth info file.\n\n";
}else
{
++truths_failed_to_update;
cout << "\nFailed to updated truth info file.\n\n";
}
action = 'u';
}//if( action == 'y' )
}catch( std::exception &e )
{
cout << "\nAfter fixing error, there was another error: \n\t"
<< e.what() << "\nNot updating truth information.\n\n";
}
break;
}//case 's':
default: break;
}//switch( action )
}//while( action != 'i' && action != 'u' )
}//try / catch
}//for( const string &path : with_truth )
cout << "Of the " << initial << " initial test files " << initial_parsed
<< " were parsable (" << failed_original_parsed << " failed).\n"
<< failed_truth_parsed << " of the truth N42 files failed to parse.\n"
<< "Of the " << initial_with_truth << " parsible original files with "
<< "valid truth N42 files: \n"
<< "\t" << passed_tests << " passed comparison\n"
<< "\t" << failed_tests << " failed comaprison, with "
<< updated_truths << " truth N42 files updated.\n";
if( truths_failed_to_update )
cerr << truths_failed_to_update << " truth n42 files failed to update!\n";
}//void check_files_with_truth_n42( const string basedir )
void check_serialization_to_n42( const string basedir )
{
size_t ninitial = 0, nOrigFileFailParse = 0,
nFailToSerialize = 0, nSerializedFileFailParse = 0,
npassed = 0, nfailed = 0;
vector<string> failedcompare;
const string tempdir = SpecUtils::temp_dir();
const vector<string> with_truth = candidates_with_truth_n42_files( basedir );
for( const string &fpath : with_truth )
{
++ninitial;
const string filename = SpecUtils::filename(fpath);
const string originalpath = fpath;
const string originalext = SpecUtils::file_extension(fpath);
SpecUtils::SpecFile info;
bool status = info.load_file( originalpath, SpecUtils::ParserType::Auto, originalext );
if( !status )
{
++nOrigFileFailParse;
cerr << "N42 Serialization Test: Failed to parse input file " << fpath
<< "\n\n";
continue;
}//if( !status )
const string tempname = SpecUtils::temp_file_name( filename, tempdir );
{//Begin codeblock to serialize to temporary file
ofstream output( tempname.c_str() );
if( !output )
{
++nFailToSerialize;
cerr << "N42 Serialization Test: Couldnt open temporary file "
<< tempname << "\n\n";
SpecUtils::remove_file( tempname.c_str() );
continue;
}
status = info.write_2012_N42( output );
if( !status )
{
++nFailToSerialize;
cerr << "N42 Serialization Test: Couldnt serialize " << fpath
<< " to temp file " << tempname << "\n\n";
SpecUtils::remove_file( tempname.c_str() );
continue;
}//if( !status )
}//End codeblock to serialize to temporary file
SpecUtils::SpecFile reread;
status = reread.load_file( tempname.c_str(), SpecUtils::ParserType::N42_2012, "" );
if( !status )
{
++nSerializedFileFailParse;
cerr << "N42 Serialization Test: Couldnt parse serialized N42 file for "
<< fpath << "\n\n";
SpecUtils::remove_file( tempname.c_str() );
continue;
}//if( !status )
reread.set_filename( info.filename() );
try
{
SpecUtils::SpecFile::equal_enough( info, reread );
++npassed;
}catch( std::exception &e )
{
const string error_msg = e.what();
++nfailed;
failedcompare.push_back( fpath );
cerr << "N42 Serialization Test: comparison test for " << fpath
<< " failed with error:\n\t" << error_msg << "\n"
<< "\t(LHS is original parse, RHS is re-ad back in)\n\n";
if( SpecUtils::contains(error_msg, " SpecUtils::SpecFile: Number of remarks in LHS") )
{
for( const string r : info.remarks() )
cout << "\t\tLHS remark: '" << r << "'" << endl;
for( const string r : reread.remarks() )
cout << "\t\tRHS remark: '" << r << "'" << endl;
}
}//try / catch
SpecUtils::remove_file( tempname.c_str() );
}//for( const string &fpath : with_truth )
cout << "N42 Serialization Test Results:\n"
<< "\tNumber of input files: " << ninitial << "\n"
<< "\tNumber of input files that failed to parse: " << nOrigFileFailParse
<< "\n\tNumber of files that failed to serialize to N42: "
<< nFailToSerialize
<< "\n\tNumber of serialed files that couldnt be parsed: "
<< nSerializedFileFailParse
<< "\n\tNumber of files that failed comparison: " << nfailed
<< "\n\tNumber of files that passed comparison: " << npassed
<< "\n\n";
if( failedcompare.size() )
{
cout << "Files failing comparison:\n";
for( const string &p : failedcompare )
cout << "\t'" << p << "'" << endl;
cout << endl << endl;
}
if( !g_automated_mode && (nFailToSerialize || nSerializedFileFailParse || nfailed) )
{
char dummy;
cout << "There was an error, enter 'x' to exit the app, or any other key"
<< " to continue.\n";
cin >> dummy;
if( dummy == 'x' )
exit( EXIT_FAILURE );
}//if( !g_automated_mode )
}//void check_serialization_to_n42( const string basedir )
void check_equality_operator( const string basedir )
{
size_t ninitial = 0, nOrigFileFailParse = 0,
npassed = 0, nfailed = 0;
vector<string> failedcompare;
// We'll only test on files with a truth-level N42 file to make sure we only
// check files known to be good spectrum files.
const vector<string> with_truth = candidates_with_truth_n42_files( basedir );
for( const string &fpath : with_truth )
{
++ninitial;
const string filename = SpecUtils::filename(fpath);
const string originalpath = fpath;
const string originalext = SpecUtils::file_extension(fpath);
SpecUtils::SpecFile info;
bool status = info.load_file( originalpath, SpecUtils::ParserType::Auto, originalext );
if( !status )
{
++nOrigFileFailParse;
cerr << "Equality Operator Test: Failed to parse input file " << fpath
<< "\n\n";
continue;
}//if( !status )
SpecUtils::SpecFile info_copy;
info_copy = info;
try
{
SpecUtils::SpecFile::equal_enough( info, info_copy );
++npassed;
}catch( std::exception &e )
{
const string error_msg = e.what();
++nfailed;
failedcompare.push_back( fpath );
cerr << "Equality Operator Test: comparison test for " << fpath
<< " failed with error:\n\t" << error_msg << "\n"
<< "\t(LHS is original parse, RHS is assigned copy)\n\n";
}//try / catch
}//for( const string &fpath : with_truth )
cout << "Equality Operator Test Results:\n"
<< "\tNumber of input files: " << ninitial << "\n"
<< "\tNumber of input files that failed to parse: " << nOrigFileFailParse
<< "\n\tNumber of files that failed comparison: " << nfailed
<< "\n\tNumber of files that passed comparison: " << npassed
<< "\n\n";
if( failedcompare.size() )
{
cout << "Files failing operator= comparison:\n";
for( const string &p : failedcompare )
cout << "\t" << p << endl;
cout << endl << endl;
}
if( !g_automated_mode && nfailed )
{
char dummy;
cout << "There was an error, enter 'x' to exit the app, or any other key"
<< " to continue.\n";
cin >> dummy;
if( dummy == 'x' )
exit( EXIT_FAILURE );
}//if( !g_automated_mode )
}//void check_equality_operator( const string basedir )
bool add_truth_n42( const SpecUtils::SpecFile &info, const string &p,
const bool force )
{
const string parentdir = SpecUtils::parent_path(p);
const string truthdir = SpecUtils::append_path(parentdir, g_truth_n42_dirname);
const string truth_n42 = SpecUtils::append_path(truthdir, (SpecUtils::filename(p) + ".n42"));
string old_n42;
const bool prevexist = SpecUtils::is_file( truth_n42 );
if( !force && prevexist )
{
cerr << "File " << truth_n42 << " already exits, not re-creating\n";
return false;
}if( prevexist )
{
old_n42 = truth_n42 + ".prev";
SpecUtils::rename_file( truth_n42, old_n42 );
}
try
{
if( !SpecUtils::is_directory( truthdir ) )
{
try
{
SpecUtils::create_directory( truthdir );
const string command = "git add '" + truthdir + "'";
const int val = system( command.c_str() );
if( val != 0 )
cerr << "\n\nThere may have been an issue adding " << truthdir
<< " to the GIT repository. Return code " << val << "\n";
}catch( std::exception &e )
{
throw runtime_error( "Couldnt create directory " + truthdir + ", so skipping file" );
}
}//if( !SpecUtils::is_directory( truthdir ) )
{//begin write file
ofstream output( truth_n42.c_str() );
if( !output )
throw runtime_error( "Couldnt create file " + truth_n42 + ", so skipping file" );
const bool status = info.write_2012_N42( output );