public function run()
{
if (class_exists('Faker\\Factory')) {
$faker = Faker\Factory::create();
$specimens = Specimen::all()->all();
$museums = Museum::all()->all();
$authors = Author::all()->all();
$animalGroups = AnimalGroup::all()->all();
for ($i = 1; $i <= 500; $i++) {
Scan::create(['scanId' => $faker->randomNumber(5), 'scanQuality' => $faker->randomElement(['low', 'medium', 'high']), 'fileDirectory' => '//scan' . $faker->randomNumber(2), 'location' => $faker->country, 'scanTime' => $faker->dateTime, 'voltage' => $faker->randomFloat(2, 1, 20), 'voxelSize' => $faker->randomFloat(1, 0, 1) . 'mm', 'imageCount' => $faker->randomNumber(4), 'current' => '120v', 'sequence' => $faker->randomNumber(4), 'specimenId' => $faker->randomElement($specimens)->id, 'museumId' => $faker->randomElement($museums)->id, 'authorId' => $faker->randomElement($authors)->id, 'animalGroupId' => $faker->randomElement($animalGroups)->id]);
}
}
}
public function run()
{
$rawData = array_map('str_getcsv', file(__DIR__ . '/../data/specimens.csv'));
$headers = array_shift($rawData);
$items = array_map(function ($row) use($headers) {
return array_combine($headers, $row);
}, $rawData);
if (!array_walk($items, function ($item) {
Specimen::updateOrCreate(['id' => $item['id']], $item);
})) {
throw new Exception('There was an issue importing specimens.');
}
}
/**
* Returns grouped specimen Counts with optional gender, age range, date range
*
* @param $gender, $ageRange, $from, $to
*/
public function groupedSpecimenCount($gender = null, $ageRange = null, $from = null, $to = null)
{
$specimens = Specimen::where('specimen_type_id', $this->id)->whereIn('specimen_status_id', [Specimen::ACCEPTED]);
if ($to && $from) {
$specimens = $specimens->whereBetween('time_accepted', [$from, $to]);
}
if ($gender) {
$specimens = $specimens->join('tests', 'specimens.id', '=', 'tests.specimen_id')->join('visits', 'tests.visit_id', '=', 'visits.id')->join('patients', 'visits.patient_id', '=', 'patients.id')->whereIn('gender', $gender);
}
if ($ageRange) {
$ageRange = explode('-', $ageRange);
$ageStart = $ageRange[0];
$ageEnd = $ageRange[1];
$now = new DateTime('now');
$finishDate = $now->sub(new DateInterval('P' . $ageStart . 'Y'))->format('Y-m-d');
$startDate = $now->sub(new DateInterval('P' . $ageEnd . 'Y'))->format('Y-m-d');
$specimens = $specimens->whereBetween('dob', [$startDate, $finishDate]);
}
return $specimens->count();
}
public function testWaitTime()
{
$specIDs = Specimen::where('specimen_status_id', '!=', Specimen::NOT_COLLECTED)->lists('id');
if (count($specIDs) == 0) {
$this->assertTrue(false);
}
foreach ($specIDs as $id) {
$test = Specimen::find($id)->test()->first();
$this->assertTrue($test->getWaitTime() >= 0);
}
}
public function testIsNotRejected()
{
$specimenRejected = Specimen::where('specimen_status_id', '!=', Specimen::REJECTED)->first();
$this->assertEquals($specimenRejected->isRejected(), false);
}
/**
* Display specimen rejection chart
*
* @return Response
*/
public static function specimenRejectionChart($testTypeID = 0)
{
$from = Input::get('start');
$to = Input::get('end');
$spec_type = Input::get('specimen_type');
$months = json_decode(self::getMonths($from, $to));
// Get specimen rejection reasons available in the time period
$rr = Specimen::select(DB::raw('DISTINCT(reason) AS rr, rejection_reason_id'))->join('rejection_reasons', 'rejection_reasons.id', '=', 'specimens.rejection_reason_id')->whereBetween('time_rejected', [$from, $to])->groupBy('rr')->get();
$options = '{
"chart": {
"type": "spline"
},
"title": {
"text":"Rejected Specimen per Reason Overtime"
},
"subtitle": {
"text":';
if ($from == $to) {
$options .= '"' . trans('messages.for-the-year') . ' ' . date('Y') . '"';
} else {
$options .= '"' . trans('messages.from') . ' ' . $from . ' ' . trans('messages.to') . ' ' . $to . '"';
}
$options .= '},
"credits": {
"enabled": false
},
"navigation": {
"buttonOptions": {
"align": "right"
}
},
"series": [';
$counts = count($rr);
foreach ($rr as $rrr) {
$options .= '{
"name": "' . $rrr->rr . '","data": [';
$counter = count($months);
foreach ($months as $month) {
$data = Specimen::where('rejection_reason_id', $rrr->rejection_reason_id)->whereRaw('MONTH(time_rejected)=' . $month->months);
if ($spec_type) {
$data = $data->where('specimen_type_id', $spec_type);
}
$data = $data->count();
$options .= $data;
if ($counter == 1) {
$options .= '';
} else {
$options .= ',';
}
$counter--;
}
$options .= ']';
if ($counts == 1) {
$options .= '}';
} else {
$options .= '},';
}
$counts--;
}
$options .= '],
"xAxis": {
"categories": [';
$count = count($months);
foreach ($months as $month) {
$options .= '"' . $month->label . " " . $month->annum;
if ($count == 1) {
$options .= '" ';
} else {
$options .= '" ,';
}
$count--;
}
$options .= ']
},
"yAxis": {
"title": {
"text": "No. of Rejected Specimen"
}
}
}';
return view('reports.rejection.index')->with('options', $options)->withInput(Input::all());
}
/**
* generate barcode
*
* @param int $id
* @return Response
*/
public function barcode()
{
$id = Input::get('sId');
$spec = Specimen::find($id);
return $spec->barcode();
}
public function createSpecimen($testStatus, $specimenStatus, $specimenTypeID, $acceptor = 0, $rejector = 0, $rejectReason = "")
{
$values["specimen_type_id"] = $specimenTypeID;
$values["specimen_status_id"] = $specimenStatus;
if ($specimenStatus == Specimen::ACCEPTED) {
$values["accepted_by"] = $acceptor;
$values["time_accepted"] = date('Y-m-d H:i:s');
}
if ($specimenStatus == Specimen::REJECTED) {
$values["rejected_by"] = $rejector;
$values["rejection_reason_id"] = $rejectReason;
$values["time_rejected"] = date('Y-m-d H:i:s');
}
$specimen = Specimen::create($values);
return $specimen->id;
}
/**
* Function for processing the requests we receive from the external system
* and putting the data into our system.
*
* @var array lab_requests
*/
public function process($labRequest)
{
//First: Check if patient exists, if true dont save again
$patient = Patient::where('external_patient_number', '=', $labRequest->patient->id)->get();
if (!$patient->first()) {
$patient = new Patient();
$patient->external_patient_number = $labRequest->patient->id;
$patient->patient_number = $labRequest->patient->id;
$patient->name = $labRequest->patient->fullName;
$gender = array('Male' => Patient::MALE, 'Female' => Patient::FEMALE);
$patient->gender = $gender[$labRequest->patient->gender];
$patient->dob = $labRequest->patient->dateOfBirth;
$patient->address = $labRequest->address->address;
$patient->phone_number = $labRequest->address->phoneNumber;
$patient->created_by = User::EXTERNAL_SYSTEM_USER;
$patient->save();
} else {
$patient = $patient->first();
}
//We check if the test exists in our system if not we just save the request in stagingTable
if ($labRequest->parentLabNo == '0') {
$testTypeId = TestType::getTestTypeIdByTestName($labRequest->investigation);
} else {
$testTypeId = null;
}
if (is_null($testTypeId) && $labRequest->parentLabNo == '0') {
$this->saveToExternalDump($labRequest, ExternalDump::TEST_NOT_FOUND);
return;
}
//Check if visit exists, if true dont save again
$visitType = array('ip' => 'In-patient', 'op' => 'Out-patient');
//Should be a constant
$visit = Visit::where('visit_number', '=', $labRequest->patientVisitNumber)->where('visit_type', '=', $visitType[$labRequest->orderStage])->get();
if (!$visit->first()) {
$visit = new Visit();
$visit->patient_id = $patient->id;
$visit->visit_type = $visitType[$labRequest->orderStage];
$visit->visit_number = $labRequest->patientVisitNumber;
// We'll save Visit in a transaction a little bit below
} else {
$visit = $visit->first();
if (strcmp($visitType[$labRequest->orderStage], $visit->visit_type) != 0) {
$visit = new Visit();
$visit->patient_id = $patient->id;
$visit->visit_type = $visitType[$labRequest->orderStage];
$visit->visit_number = $labRequest->patientVisitNumber;
}
}
$test = null;
//Check if parentLabNO is 0 thus its the main test and not a measure
if ($labRequest->parentLabNo == '0') {
//Check via the labno, if this is a duplicate request and we already saved the test
$test = Test::where('external_id', '=', $labRequest->labNo)->get();
if (!$test->first()) {
//Specimen
$specimen = new Specimen();
$specimen->specimen_type_id = TestType::find($testTypeId)->specimenTypes->lists('id')[0];
// We'll save the Specimen in a transaction a little bit below
$test = new Test();
$test->test_type_id = $testTypeId;
$test->test_status_id = Test::NOT_RECEIVED;
$test->created_by = User::EXTERNAL_SYSTEM_USER;
//Created by external system 0
$test->requested_by = $labRequest->requestingClinician;
$test->external_id = $labRequest->labNo;
DB::transaction(function () use($visit, $specimen, $test) {
$visit->save();
$specimen->save();
$test->visit_id = $visit->id;
$test->specimen_id = $specimen->id;
$test->save();
});
$this->saveToExternalDump($labRequest, $test->id);
return;
}
}
$this->saveToExternalDump($labRequest, null);
}
/**
* Get the specimen registered by a user
*
* @return db resultset
*/
public static function getSpecimensRegistered($from, $to, $userID = 0)
{
$specimens = Specimen::select(['id'])->whereBetween('time_accepted', [$from, $to]);
if ($userID > 0) {
$specimens = $specimens->where('accepted_by', '=', $userID);
}
return $specimens->get();
}
