/**
* Iterate through each Organism in the World, created as a 2D array.
* Check surroundings of each Organism and do some operations.
*
* @return $this
*/
public function live()
{
if ($this->table) {
$this->table();
}
for ($i = 0; $i < $this->iterations; $i++) {
$this->operations = [];
for ($x = 0; $x < $this->cells; $x++) {
for ($y = 0; $y < $this->cells; $y++) {
// Calculate operation
$operation = !isset($this->life[$x][$y]) ? Organism::canBeBirthable($x, $y, $this->life) : $this->life[$x][$y]->whatShouldIDo($this->life);
if ($operation) {
$this->operations[] = array_merge($operation, ['x' => $x, 'y' => $y]);
}
}
}
// After iteration is done, process all operations.
$this->process();
// Add current iteration life to output for simulation
$this->addOrganismsToSimulation($i);
if ($this->table) {
$this->table($i);
}
}
return $this;
}
/**
* Store a newly created resource in storage.
*
* @return Response
*/
public function store()
{
$action = Input::get('action');
$user_id = Auth::user()->id;
$test = Input::get('test');
$organism = Input::get('organism');
$drug = Input::get('drug');
$zone = Input::get('zone');
$interpretation = Input::get('interpretation');
for ($i = 0; $i < count($test); $i++) {
$sensitivity = Susceptibility::getDrugSusceptibility($test[$i], $organism[$i], $drug[$i]);
if (count($sensitivity) > 0) {
$drugSusceptibility = Susceptibility::find($sensitivity->id);
$drugSusceptibility->user_id = $user_id;
$drugSusceptibility->test_id = $test[$i];
$drugSusceptibility->organism_id = $organism[$i];
$drugSusceptibility->drug_id = $drug[$i];
$drugSusceptibility->zone = $zone[$i];
$drugSusceptibility->interpretation = $interpretation[$i];
$drugSusceptibility->save();
} else {
$drugSusceptibility = new Susceptibility();
$drugSusceptibility->user_id = $user_id;
$drugSusceptibility->test_id = $test[$i];
$drugSusceptibility->organism_id = $organism[$i];
$drugSusceptibility->drug_id = $drug[$i];
$drugSusceptibility->zone = $zone[$i];
$drugSusceptibility->interpretation = $interpretation[$i];
$drugSusceptibility->save();
}
}
if ($action == "results") {
$test_id = Input::get('testId');
$organism_id = Input::get('organismId');
$susceptibility = Susceptibility::where('test_id', $test_id)->where('organism_id', $organism_id)->where('zone', '!=', 0)->get();
foreach ($susceptibility as $drugSusceptibility) {
$drugSusceptibility->drugName = Drug::find($drugSusceptibility->drug_id)->name;
$drugSusceptibility->pathogen = Organism::find($drugSusceptibility->organism_id)->name;
if ($drugSusceptibility->interpretation == 'I') {
$drugSusceptibility->sensitivity = 'Intermediate';
} else {
if ($drugSusceptibility->interpretation == 'R') {
$drugSusceptibility->sensitivity = 'Resistant';
} else {
if ($drugSusceptibility->interpretation == 'S') {
$drugSusceptibility->sensitivity = 'Sestitive';
}
}
}
}
return json_encode($susceptibility);
}
}
/**
* Tests the update function in the OrganismController
* @param void
* @return void
*/
public function testUpdate()
{
Input::replace($this->organismData);
$organism = new OrganismController();
$organism->store();
$organismStored = Organism::orderBy('id', 'desc')->take(1)->get()->toArray();
Input::replace($this->organismDataUpdate);
$organism->update($organismStored[0]['id']);
$organismSavedUpdated = Organism::find($organismStored[0]['id']);
$this->assertEquals($organismSavedUpdated->name, $this->organismDataUpdate['name']);
$this->assertEquals($organismSavedUpdated->description, $this->organismDataUpdate['description']);
//Getting the drugs related to the organism
/*$organismDrugUpdated = Organism::find($organismStored[0]['id'])->drugs->toArray();
$this->assertEquals(12, $this->organismDataUpdate['drugs'][0]);*/
}
public function run()
{
//Seed for drugs
$penicillin = Drug::create(array('name' => "PENICILLIN"));
$ampicillin = Drug::create(array('name' => "AMPICILLIN"));
$clindamycin = Drug::create(array('name' => "CLINDAMYCIN"));
$tetracycline = Drug::create(array('name' => "TETRACYCLINE"));
$ciprofloxacin = Drug::create(array('name' => "CIPROFLOXACIN"));
$trimeth = Drug::create(array('name' => "TRIMETHOPRIM/SULFA"));
$nitrofurantoin = Drug::create(array('name' => "NITROFURANTOIN"));
$chloramphenicol = Drug::create(array('name' => "CHLORAMPHENICOL"));
$cefazolin = Drug::create(array('name' => "CEFAZOLIN"));
$gentamicin = Drug::create(array('name' => "GENTAMICIN"));
$amoxicillin = Drug::create(array('name' => "AMOXICILLIN-CLAV"));
$cephalothin = Drug::create(array('name' => "CEPHALOTHIN"));
$cefuroxime = Drug::create(array('name' => "CEFUROXIME"));
$cefotaxime = Drug::create(array('name' => "CEFOTAXIME"));
$piperacillin = Drug::create(array('name' => "PIPERACILLIN"));
$cefixime = Drug::create(array('name' => "CEFIXIME"));
$ceftazidime = Drug::create(array('name' => "CEFTAZIDIME"));
$cefriaxone = Drug::create(array('name' => "CEFRIAXONE"));
$levofloxacin = Drug::create(array('name' => "LEVOFLOXACIN"));
$merodenem = Drug::create(array('name' => "MERODENEM"));
$tazo = Drug::create(array('name' => "PIPERACILLIN/TAZO"));
$imedenem = Drug::create(array('name' => "IMEDENEM"));
$oxacillin = Drug::create(array('name' => "OXACILLIN (CEFOXITIN)"));
$erythromycin = Drug::create(array('name' => "ERYTHROMYCIN"));
$vancomycin = Drug::create(array('name' => "VANCOMYCIN"));
$cefoxitin = Drug::create(array('name' => "CEFOXITIN"));
$tobramycin = Drug::create(array('name' => "TOBRAMYCIN"));
$sulbactam = Drug::create(array('name' => "AMPICILLIN-SULBACTAM"));
$this->command->info('Drugs table seeded');
//Seed for organisims
$staphylococci = Organism::create(array('name' => "Staphylococci species"));
$gramnegative = Organism::create(array('name' => "Gram negative cocci"));
$pseudomonas = Organism::create(array('name' => "Pseudomonas aeruginosa"));
$enterococcus = Organism::create(array('name' => "Enterococcus species"));
$pneumoniae = Organism::create(array('name' => "Streptococcus pneumoniae"));
$streptococcus = Organism::create(array('name' => "Streptococcus species viridans group"));
$beta = Organism::create(array('name' => "Beta-haemolytic streptococci"));
$haemophilus = Organism::create(array('name' => "Haemophilus influenzae"));
$naisseria = Organism::create(array('name' => "Naisseria menengitidis"));
$salmonella = Organism::create(array('name' => "Salmonella species"));
$shigella = Organism::create(array('name' => "Shigella"));
$vibrio = Organism::create(array('name' => "Vibrio cholerae"));
$grampositive = Organism::create(array('name' => "Gram positive cocci"));
$this->command->info('Organisms table seeded');
// Seed for organism_drugs
// Staphylococci species
DB::table('organism_drugs')->insert(array("organism_id" => $staphylococci->id, "drug_id" => $penicillin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $staphylococci->id, "drug_id" => $oxacillin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $staphylococci->id, "drug_id" => $cefoxitin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $staphylococci->id, "drug_id" => $erythromycin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $staphylococci->id, "drug_id" => $clindamycin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $staphylococci->id, "drug_id" => $trimeth->id));
DB::table('organism_drugs')->insert(array("organism_id" => $staphylococci->id, "drug_id" => $cefazolin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $staphylococci->id, "drug_id" => $cephalothin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $staphylococci->id, "drug_id" => $chloramphenicol->id));
DB::table('organism_drugs')->insert(array("organism_id" => $staphylococci->id, "drug_id" => $nitrofurantoin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $staphylococci->id, "drug_id" => $tetracycline->id));
DB::table('organism_drugs')->insert(array("organism_id" => $staphylococci->id, "drug_id" => $vancomycin->id));
$this->command->info('Staphylococci species seeded');
// Gram negative cocci
DB::table('organism_drugs')->insert(array("organism_id" => $gramnegative->id, "drug_id" => $ampicillin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $gramnegative->id, "drug_id" => $cefazolin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $gramnegative->id, "drug_id" => $gentamicin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $gramnegative->id, "drug_id" => $amoxicillin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $gramnegative->id, "drug_id" => $cephalothin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $gramnegative->id, "drug_id" => $cefuroxime->id));
DB::table('organism_drugs')->insert(array("organism_id" => $gramnegative->id, "drug_id" => $cefotaxime->id));
DB::table('organism_drugs')->insert(array("organism_id" => $gramnegative->id, "drug_id" => $ciprofloxacin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $gramnegative->id, "drug_id" => $trimeth->id));
DB::table('organism_drugs')->insert(array("organism_id" => $gramnegative->id, "drug_id" => $nitrofurantoin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $gramnegative->id, "drug_id" => $chloramphenicol->id));
DB::table('organism_drugs')->insert(array("organism_id" => $gramnegative->id, "drug_id" => $tetracycline->id));
$this->command->info('Gram negative cocci seeded');
// Pseudomonas aeruginosa
DB::table('organism_drugs')->insert(array("organism_id" => $pseudomonas->id, "drug_id" => $ceftazidime->id));
DB::table('organism_drugs')->insert(array("organism_id" => $pseudomonas->id, "drug_id" => $gentamicin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $pseudomonas->id, "drug_id" => $tobramycin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $pseudomonas->id, "drug_id" => $piperacillin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $pseudomonas->id, "drug_id" => $ciprofloxacin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $pseudomonas->id, "drug_id" => $merodenem->id));
DB::table('organism_drugs')->insert(array("organism_id" => $pseudomonas->id, "drug_id" => $tazo->id));
$this->command->info('Pseudomonas aeruginosa seeded');
// Enterococcus species
DB::table('organism_drugs')->insert(array("organism_id" => $enterococcus->id, "drug_id" => $ampicillin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $enterococcus->id, "drug_id" => $gentamicin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $enterococcus->id, "drug_id" => $nitrofurantoin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $enterococcus->id, "drug_id" => $ciprofloxacin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $enterococcus->id, "drug_id" => $tetracycline->id));
DB::table('organism_drugs')->insert(array("organism_id" => $enterococcus->id, "drug_id" => $chloramphenicol->id));
DB::table('organism_drugs')->insert(array("organism_id" => $enterococcus->id, "drug_id" => $vancomycin->id));
$this->command->info('Enterococcus species seeded');
// Streptococcus pneumoniae
DB::table('organism_drugs')->insert(array("organism_id" => $pneumoniae->id, "drug_id" => $penicillin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $pneumoniae->id, "drug_id" => $cefriaxone->id));
DB::table('organism_drugs')->insert(array("organism_id" => $pneumoniae->id, "drug_id" => $cefuroxime->id));
DB::table('organism_drugs')->insert(array("organism_id" => $pneumoniae->id, "drug_id" => $erythromycin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $pneumoniae->id, "drug_id" => $trimeth->id));
DB::table('organism_drugs')->insert(array("organism_id" => $pneumoniae->id, "drug_id" => $chloramphenicol->id));
DB::table('organism_drugs')->insert(array("organism_id" => $pneumoniae->id, "drug_id" => $tetracycline->id));
DB::table('organism_drugs')->insert(array("organism_id" => $pneumoniae->id, "drug_id" => $levofloxacin->id));
$this->command->info('Streptococcus pneumoniae seeded');
// Streptococcus species viridans group
DB::table('organism_drugs')->insert(array("organism_id" => $streptococcus->id, "drug_id" => $penicillin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $streptococcus->id, "drug_id" => $cefriaxone->id));
DB::table('organism_drugs')->insert(array("organism_id" => $streptococcus->id, "drug_id" => $vancomycin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $streptococcus->id, "drug_id" => $chloramphenicol->id));
DB::table('organism_drugs')->insert(array("organism_id" => $streptococcus->id, "drug_id" => $clindamycin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $streptococcus->id, "drug_id" => $erythromycin->id));
$this->command->info('Streptococcus species viridans group seeded');
// Beta-haemolytic streptococci
DB::table('organism_drugs')->insert(array("organism_id" => $beta->id, "drug_id" => $penicillin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $beta->id, "drug_id" => $erythromycin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $beta->id, "drug_id" => $clindamycin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $beta->id, "drug_id" => $cefriaxone->id));
DB::table('organism_drugs')->insert(array("organism_id" => $beta->id, "drug_id" => $chloramphenicol->id));
DB::table('organism_drugs')->insert(array("organism_id" => $beta->id, "drug_id" => $vancomycin->id));
$this->command->info('Beta-haemolytic streptococci seeded');
// Haemophilus influenzae
DB::table('organism_drugs')->insert(array("organism_id" => $haemophilus->id, "drug_id" => $ampicillin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $haemophilus->id, "drug_id" => $trimeth->id));
DB::table('organism_drugs')->insert(array("organism_id" => $haemophilus->id, "drug_id" => $sulbactam->id));
DB::table('organism_drugs')->insert(array("organism_id" => $haemophilus->id, "drug_id" => $cefriaxone->id));
DB::table('organism_drugs')->insert(array("organism_id" => $haemophilus->id, "drug_id" => $chloramphenicol->id));
$this->command->info('Haemophilus influenzae seeded');
// Naisseria menengitidis
DB::table('organism_drugs')->insert(array("organism_id" => $naisseria->id, "drug_id" => $penicillin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $naisseria->id, "drug_id" => $cefriaxone->id));
DB::table('organism_drugs')->insert(array("organism_id" => $naisseria->id, "drug_id" => $chloramphenicol->id));
$this->command->info('Neisseria menengitidis seeded');
// Salmonella species
DB::table('organism_drugs')->insert(array("organism_id" => $salmonella->id, "drug_id" => $ampicillin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $salmonella->id, "drug_id" => $ciprofloxacin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $salmonella->id, "drug_id" => $trimeth->id));
$this->command->info('Salmonella species seeded');
// Shigella
DB::table('organism_drugs')->insert(array("organism_id" => $shigella->id, "drug_id" => $ampicillin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $shigella->id, "drug_id" => $ciprofloxacin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $shigella->id, "drug_id" => $trimeth->id));
$this->command->info('Shigella seeded');
// Vibrio cholerae
DB::table('organism_drugs')->insert(array("organism_id" => $vibrio->id, "drug_id" => $ampicillin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $vibrio->id, "drug_id" => $ciprofloxacin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $vibrio->id, "drug_id" => $trimeth->id));
$this->command->info('Vibrio cholerae seeded');
// Gram positive cocci
DB::table('organism_drugs')->insert(array("organism_id" => $grampositive->id, "drug_id" => $cefoxitin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $grampositive->id, "drug_id" => $clindamycin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $grampositive->id, "drug_id" => $erythromycin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $grampositive->id, "drug_id" => $oxacillin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $grampositive->id, "drug_id" => $penicillin->id));
DB::table('organism_drugs')->insert(array("organism_id" => $grampositive->id, "drug_id" => $tetracycline->id));
DB::table('organism_drugs')->insert(array("organism_id" => $grampositive->id, "drug_id" => $trimeth->id));
DB::table('organism_drugs')->insert(array("organism_id" => $grampositive->id, "drug_id" => $vancomycin->id));
$this->command->info('Gram positive cocci seeded');
}
/**
* Return parents if dead organism can be birthable
*
* @param $x
* @param $y
* @param $life
* @return int
*/
public static function canBeBirthable($x, $y, $life)
{
$organism = new Organism($x, $y);
$organism->getSurroundings($life);
if ($parent = $organism->isBirthAble()) {
return ['result' => Result::BIRTH, 'parent' => $parent];
}
return FALSE;
}
/**
* Remove the specified resource from storage (soft delete).
*
* @param int $id
* @return Response
*/
public function delete($id)
{
//Soft delete the organism
$organism = Organism::find($id);
/*$testCategoryInUse = TestType::where('test_category_id', '=', $id)->first();
if (empty($testCategoryInUse)) {
// The test category is not in use
$testcategory->delete();
} else {
// The test category is in use
$url = Session::get('SOURCE_URL');
return Redirect::to($url)
->with('message', trans('messages.failure-test-category-in-use'));
}*/
// redirect
$url = Session::get('SOURCE_URL');
return Redirect::to($url)->with('message', trans('messages.success-deleting-organism'));
}
/**
* Show the form for editing the specified resource.
*
* @param int $id
* @return Response
*/
public function edit($id)
{
//Get the testtype
$testtype = TestType::find($id);
$measures = Measure::all();
$measuretype = MeasureType::all()->sortBy('id');
$specimentypes = SpecimenType::orderBy('name')->get();
$testcategory = TestCategory::all();
$organisms = Organism::orderBy('name')->get();
//Open the Edit View and pass to it the $testtype
return View::make('testtype.edit')->with('testtype', $testtype)->with('testcategory', $testcategory)->with('measures', $measures)->with('measuretype', $measuretype)->with('specimentypes', $specimentypes)->with('organisms', $organisms);
}
