public function create()
{
$iSet = IndexSet::lists('name', 'id');
$iAll = IndexSet::all();
$i7 = I7Index::lists('index', 'id');
$i5 = I5Index::lists('index', 'id');
$pg = ProjectGroup::lists('name', 'id');
$user = Auth::user();
$batches = $user->batches->lists('batch_name', 'id');
return view('samples.create', ['iSet' => $iSet, 'iAll' => $iAll, 'i7' => $i7, 'i5' => $i5, 'pg' => $pg, 'user' => $user, 'batches' => $batches]);
}
public function create()
{
$iSet = IndexSet::lists('name', 'id');
$iAll = IndexSet::all();
$i7 = I7Index::lists('index', 'id');
$i5 = I5Index::lists('index', 'id');
$pg = ProjectGroup::lists('name', 'id');
$user = Auth::user();
$batches = Batch::where('user_id', $user->id)->orderBy('created_at', 'desc')->lists('batch_name', 'id');
return view('samples.create', ['iSet' => $iSet, 'iAll' => $iAll, 'i7' => $i7, 'i5' => $i5, 'pg' => $pg, 'user' => $user, 'batches' => $batches]);
}
/**
* @param Request $request
* @return mixed
*/
public function validateFile(ImportSampleRequest $request)
{
// Get form input and check if dupes are ok
$input = $request->all();
$dupes_ok = isset($input['dupes_ok']);
$instument_lane = 1;
$file = array('sampleFile' => Input::file('sampleFile'));
// setting up rules
/*$rules = array('sampleFile' => array('required', 'mimes:csv,txt'),
'plate' => array('regex:/^[a-zA-Z0-9-]{1,120}$/' , 'max:120'),
'well' => array('regex:/^[a-zA-Z0-9-]{1,120}$/', 'max:120'),
'description' => array('regex:/^[a-zA-Z0-9-]{1,120}$/' , 'max:120'),
'runs_remaining' => array('integer', 'between:1,60'),
'instrument_lane' => array('integer', 'between:1,8'),
);*/
//mimes:jpeg,bmp,png and for max size max:10000
// doing the validation, passing post data, rules and the messages
$rules = array();
$validator = Validator::make($file, $rules);
if ($validator->fails()) {
// send back to the page with the input data and errorBag
return Redirect::to('import')->withInput()->withErrors($validator);
} else {
// checking file is valid.
//dd(Request::file('sampleFile')->getExtension());
if (Input::file('sampleFile')->isValid()) {
$this->i7Indexes = I7Index::lists('sequence', 'index');
$this->i7IndexSetArray = I7Index::lists('index_set_id', 'index');
$this->i5Indexes = I5Index::lists('sequence', 'index');
$this->i5IndexSetArray = I5Index::lists('index_set_id', 'index');
$this->samplesList = DB::table('samples')->lists('sample_id');
$this->loadExistingSamples(Input::get()['batch_id']);
$this->csvToArray(Request::file('sampleFile'), ',', $dupes_ok);
$this->generateErrors();
if (Count($this->stringErrors)) {
Session::flash('error', $this->stringErrors);
} else {
if ($this->checkBatchCompatibility(Input::get()['batch_id'])) {
$this->addData(Request::file('sampleFile'), Input::get()['batch_id'], Input::get()['plate'], Input::get()['well'], Input::get()['description'], Input::get()['runs_remaining'], $instument_lane);
Session::flash('success', "File Upload Successful");
} else {
array_push($this->stringErrors, "File is not compatible with the batch selected.");
Session::flash('error', $this->stringErrors);
}
}
return Redirect::to('import')->withInput();
} else {
// sending back with error message.
array_push($this->stringErrors, "Upload file is not valid.");
Session::flash('error', $this->stringErrors);
return Redirect::to('import')->withInput();
}
}
}
