Program Listing for File end_to_end.test.cc¶
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#include <fstream>
#include <algorithm>
#include <array>
#include <string>
#include "../native/symbulation.cc"
using namespace std;
void Test(std::string expected_result_file, int seed = 10, int data_int = 100, double mutation_rate = 0.002,
double synergy = 5, double vertical_transmission = 1, double host_int = 0,
double sym_int = 0, int grid_x = 5, int grid_y = 5, int updates = 1,
int sym_limit = 1, bool lysis = 0, bool horiz_trans = 0, int burst_size = 10,
int burst_time = 10, double host_repro_res = 1000,double sym_lysis_res = 1,
double sym_horiz_trans_res = 100, int start_moi = 1, bool grid = 0) {
SymConfigBase config;
config.SEED(seed); //What value should the random seed be? If seed <= 0, then it is randomly re-chosen.
config.DATA_INT(data_int); //How frequently data should be written
config.MUTATION_RATE(mutation_rate); //Standard deviation of the distribution to mutate by
config.SYNERGY(synergy); //Amount symbiont's returned resources should be multiplied by
config.VERTICAL_TRANSMISSION(vertical_transmission); //Value 0 to 1 of probability of symbiont vertically transmitting when host reproduces
config.HOST_INT(host_int); //Interaction value from -1 to 1 that hosts should have initially, -2 for random
config.SYM_INT(sym_int); //Interaction value from -1 to 1 that symbionts should have initially, -2 for random
config.GRID_X(grid_x); //Width of the world, just multiplied by the height to get total size
config.GRID_Y(grid_y); //Height of world, just multiplied by width to get total size
config.UPDATES(updates); //Number of updates to run before quitting
config.SYM_LIMIT(sym_limit); //Number of symbiont allowed to infect a single host
config.LYSIS(lysis); //Should lysis occur? 0 for no, 1 for yes
config.HORIZ_TRANS(horiz_trans); //Should non-lytic horizontal transmission occur? 0 for no, 1 for yes
config.BURST_SIZE(burst_size); //If there is lysis, this is how many symbionts should be produced during lysis. This will be divided by burst_time and that many symbionts will be produced every update
config.BURST_TIME(burst_time); //If lysis enabled, this is how many updates will pass before lysis occurs
config.HOST_REPRO_RES(host_repro_res); //How many resources required for host reproduction
config.SYM_LYSIS_RES(sym_lysis_res); //How many resources required for symbiont to create offspring for lysis each update
config.SYM_HORIZ_TRANS_RES(sym_horiz_trans_res); //How many resources required for symbiont non-lytic horizontal transmission
config.START_MOI(start_moi); //How many symbionts per host to start
config.GRID(grid); //Do offspring get placed immediately next to parents on grid, same for symbiont spreading
config.FILE_PATH(""); //Output file location, leave blank for current folder
config.FILE_NAME("_Test"); //Root output file name
GIVEN( string("The configuration {") +
string(" seed = ") + to_string(seed) +
string(" data_int = ") + to_string(data_int) +
string(" mutation_rate = ") + to_string(mutation_rate) +
string(" synergy = ") + to_string(synergy) +
string(" vertical_transmission = ") + to_string(vertical_transmission) +
string(" host_int = ") + to_string(host_int) +
string(" sym_int = ") + to_string(sym_int) +
string(" grid_x = ") + to_string(grid_x) +
string(" grid_y = ") + to_string(grid_y) +
string(" updates = ") + to_string(updates) +
string(" sym_limit = ") + to_string(sym_limit) +
string(" lysis = ") + to_string(lysis) +
string(" horiz_trans = ") + to_string(horiz_trans) +
string(" burst_size = ") + to_string(burst_size) +
string(" burst_time = ") + to_string(burst_time) +
string(" host_repro_res = ") + to_string(host_repro_res) +
string(" sym_lysis_res = ") + to_string(sym_lysis_res) +
string(" sym_horiz_trans_res = ") + to_string(sym_horiz_trans_res) +
string(" start_moi = ") + to_string(start_moi) +
string(" grid = ") + to_string(grid) + " }") {
config.Write("SymSettings.cfg");
THEN( "Symublation runs without error" ) {
symbulation_main(0, NULL);
}
string type;
for(int i = 0; i < 2; i++) {
if(i == 0)
type = "SymVals";
else
type = "HostVals";
string path = "source/end_to_end_test_data/"+type+"_"+expected_result_file+".data";
THEN( "Symbulation's actual "+type+" output found at \"" + type + "_Test.data\" matches the expected output at \"" + path + "\"" ) {
ifstream actual, expected;
actual.open(type + "_Test.data", ios::in);
expected.open(path, ios::in);
REQUIRE(actual.is_open());
REQUIRE(expected.is_open());
//Is this a good length of text to display to the user?
const int chunk_length = 1000;
char actual_buffer[chunk_length];
char expected_buffer[chunk_length];
while (!(actual.eof() && expected.eof())) {
actual >> actual_buffer;
expected >> expected_buffer;
//This provides a nice error with context when they don't match.
// array<char, chunk_length> actual_chunk;
// move(begin(actual_buffer), end(actual_buffer), actual_chunk.begin());
// array<char, chunk_length> expected_chunk;
// move(begin(expected_buffer), end(expected_buffer), expected_chunk.begin());
string actual_chunk = string(actual_buffer);
string expected_chunk = string(expected_buffer);
REQUIRE(actual_chunk == expected_chunk);
}
actual.close();
expected.close();
}//THEN
}//type loop
}//GIVEN
}//void Test(.........)
/*Test(std::string expected_result_file, int seed = 10, int data_int = 100, double mutation_rate = 0.002,
double synergy = 5, double vertical_transmission = 1, double host_int = 0,
double sym_int = 0, int grid_x = 5, int grid_y = 5, int updates = 1,
int sym_limit = 1, bool lysis = 0, bool horiz_trans = 0, int burst_size = 10,
int burst_time = 10, double host_repro_res = 1000,double sym_lysis_res = 1,
double sym_horiz_trans_res = 100, int start_moi = 1, bool grid = 0)
*/
TEST_CASE( "End To End" ) {
Test("vert_trans_0", 17, 100, 0.002, 5, 0, -2, -2, 100, 100, 1001, 1, 0, 1, 4, 2, 1000, 0.3, 100, 1, 0);
Test("vert_trans_0.5", 17, 100, 0.002, 5, 0.5, -2, -2, 100, 100, 1001, 1, 0, 1, 4, 2, 1000, 0.3, 100, 1, 0);
Test("vert_trans_1", 17, 100, 0.002, 5, 1, -2, -2, 100, 100, 1001, 1, 0, 1, 4, 2, 1000, 0.3, 100, 1, 0);
Test("vert_trans_0.1", 17, 100, 0.002, 5, 0.1, -2, -2, 100, 100, 1001, 1, 0, 1, 4, 2, 1000, 0.3, 100, 1, 0);
}