/**
* Show the form for editing the specified resource.
*
* @param int $id
* @return Response
*/
public function edit($id)
{
//
$caseClosed = CaseClosed::findOrFail($id);
$POrecord = $caseClosed->POrecord;
$project_id = $POrecord->project->id;
$customersJoinQuery = DB::table('customers')->select(DB::raw('id AS c_id'), 'institute', 'department', 'c_name');
$usersJoinQuery = DB::table('users')->select(DB::raw('id AS u_id'), 'name');
$project = DB::table('projects')->leftJoin(DB::raw('(' . $customersJoinQuery->toSql() . ') i'), function ($join) {
$join->on('projects.Customer_id', '=', 'i.c_id');
})->leftJoin(DB::raw('(' . $usersJoinQuery->toSql() . ') j'), function ($join) {
$join->on('projects.salesman', '=', 'u_id');
})->where('projects.id', $project_id)->first();
$labmans = DB::table('users')->select('id', 'name')->get();
$user = User::find(\Auth::id());
$qualityControl = QualityControl::where('POrecord_id', '=', $POrecord->id)->first();
if ($qualityControl->QCtype == 'DNA') {
$qcReportUrl = url('research/ngs/qualityControl/dnareport') . '/' . $qualityControl->id;
} elseif ($qualityControl->QCtype == 'RNA') {
$qcReportUrl = url('research/ngs/qualityControl/rnareport') . '/' . $qualityControl->id;
}
$library = Library::where('POrecord_id', '=', $POrecord->id)->first();
$libraryReportUrl = url('research/ngs/library/report') . '/' . $library->id;
return view('research.caseClosed.edit')->with('user', $user)->with('project', $project)->with('labmans', $labmans)->with('POrecord', $POrecord)->with('qcReportUrl', $qcReportUrl)->with('libraryReportUrl', $libraryReportUrl)->with('caseClosed', $caseClosed);
}
/**
* Store a newly created resource in storage.
*
* @param Request $request
* @return Response
*/
public function store(Request $request)
{
//
$rules = ['QCtype' => 'required', 'operatorDate' => 'required|before:tomorrow', 'measureTool' => 'required', 'fragmentSize' => 'required', 'operator' => 'required', 'figure_1_Path' => 'image', 'figure_2_Path' => 'image', 'figure_3_Path' => 'image', 'figure_4_Path' => 'image', 'figure_nanodrop_Path' => 'image'];
$validator = Validator::make($request->all(), $rules);
if ($validator->fails()) {
return back()->withErrors($validator)->withInput();
}
$na_flag = 0;
foreach ($request->get('measureTool') as &$tool) {
if ($tool == 'N/A') {
$na_flag = 1;
}
if (empty($measureTools)) {
$measureTools = $tool;
} else {
$measureTools = $measureTools . "|" . $tool;
}
}
if ($na_flag == 1 && count($request->get('measureTool')) > 1) {
return back()->withErrors(['measureTool' => 'measureTool can not choose N/A with other option.'])->withInput();
}
if ($request->get('QCtype') == 'DNA') {
$qualityControl = new QualityControl(array('QCtype' => $request->get('QCtype'), 'operatorDate' => $request->get('operatorDate'), 'measureTool' => $measureTools, 'fragmentSize' => $request->get('fragmentSize'), 'measureNote' => $request->get('measureNote'), 'reportDescription' => $request->get('reportDescription'), 'note' => $request->get('note'), 'operator' => $request->get('operator')));
} elseif ($request->get('QCtype') == 'RNA') {
if (empty($request->get('is_differentMethods'))) {
$is_differentMethods = '';
} else {
$is_differentMethods = $request->get('is_differentMethods');
}
if (empty($request->get('is_interpretation'))) {
$is_interpretation = '';
} else {
$is_interpretation = $request->get('is_interpretation');
}
$qualityControl = new QualityControl(array('QCtype' => $request->get('QCtype'), 'operatorDate' => $request->get('operatorDate'), 'measureTool' => $measureTools, 'fragmentSize' => $request->get('fragmentSize'), 'measureNote' => $request->get('measureNote'), 'rin_28S18S_measure' => $request->get('rin_28S18S_measure'), 'is_differentMethods' => $is_differentMethods, 'is_interpretation' => $is_interpretation, 'reportDescription' => $request->get('reportDescription'), 'note' => $request->get('note'), 'operator' => $request->get('operator')));
}
$operator = User::findOrFail($request->get('operator'));
$qualityControl->operator()->associate($operator);
$POrecord = POcase::findOrFail($request->get('POrecord_id'));
$POrecord->status = 'QualityControl';
$POrecord->save();
$qualityControl->POrecord()->associate($POrecord);
$qualityControl->save();
if (empty($request->file('figure_1_Path'))) {
$figure_1_Path = null;
} else {
$fileName_1 = $qualityControl->id . '_1.' . $request->file('figure_1_Path')->getClientOriginalExtension();
$request->file('figure_1_Path')->move(base_path() . '/storeFiles/ngs/qualityControl/', $fileName_1);
$figure_1_Path = base_path() . '/storeFiles/ngs/qualityControl/' . $fileName_1;
}
if (empty($request->file('figure_2_Path'))) {
$figure_2_Path = null;
} else {
$fileName_2 = $qualityControl->id . '_2.' . $request->file('figure_2_Path')->getClientOriginalExtension();
$request->file('figure_2_Path')->move(base_path() . '/storeFiles/ngs/qualityControl/', $fileName_2);
$figure_2_Path = base_path() . '/storeFiles/ngs/qualityControl/' . $fileName_2;
}
if (empty($request->file('figure_3_Path'))) {
$figure_3_Path = null;
} else {
$fileName_3 = $qualityControl->id . '_3.' . $request->file('figure_3_Path')->getClientOriginalExtension();
$request->file('figure_3_Path')->move(base_path() . '/storeFiles/ngs/qualityControl/', $fileName_3);
$figure_3_Path = base_path() . '/storeFiles/ngs/qualityControl/' . $fileName_3;
}
if (empty($request->file('figure_4_Path'))) {
$figure_4_Path = null;
} else {
$fileName_4 = $qualityControl->id . '_4.' . $request->file('figure_4_Path')->getClientOriginalExtension();
$request->file('figure_4_Path')->move(base_path() . '/storeFiles/ngs/qualityControl/', $fileName_4);
$figure_4_Path = base_path() . '/storeFiles/ngs/qualityControl/' . $fileName_4;
}
if (empty($request->file('figure_nanodrop_Path'))) {
$figure_nanodrop_Path = null;
} else {
$fileName_nanodrop = $qualityControl->id . '_nanodrop.' . $request->file('figure_nanodrop_Path')->getClientOriginalExtension();
$request->file('figure_nanodrop_Path')->move(base_path() . '/storeFiles/ngs/qualityControl/', $fileName_nanodrop);
$figure_nanodrop_Path = base_path() . '/storeFiles/ngs/qualityControl/' . $fileName_nanodrop;
}
$qualityControl->update(['figure_1_Path' => $figure_1_Path, 'figure_2_Path' => $figure_2_Path, 'figure_3_Path' => $figure_3_Path, 'figure_4_Path' => $figure_4_Path, 'figure_nanodrop_Path' => $figure_nanodrop_Path]);
if (!empty($request->get('sampleName'))) {
$sampleName = $request->get('sampleName');
$vol_ul = $request->get('vol_ul');
$conc_ng = $request->get('conc_ng');
$qty_ng = $request->get('qty_ng');
$_260_280 = $request->get('260_280');
$_260_230 = $request->get('260_230');
$_28S_18S = $request->get('28S_18S');
$rin = $request->get('rin');
$lane = $request->get('lane');
$comment = $request->get('comment');
$is_buildLibrary = $request->get('is_buildLibrary');
$figure_Path = $request->file('figure_Path');
$max = 0;
$indexs = array_keys($sampleName);
foreach ($indexs as $index) {
if ($index > $max) {
$max = $index;
}
}
for ($i = 1; $i <= $max; $i++) {
if (!empty($sampleName[$i])) {
if ($request->get('QCtype') == 'DNA') {
$QC_Samples = new QC_Samples(array('sampleName' => $sampleName[$i], 'vol_ul' => $vol_ul[$i], 'conc_ng' => $conc_ng[$i], 'qty_ng' => $qty_ng[$i], '260_280' => $_260_280[$i], '260_230' => $_260_230[$i], 'lane' => $lane[$i], 'comment' => $comment[$i], 'is_buildLibrary' => $is_buildLibrary[$i], 'operator_id' => $request->get('operator')));
} elseif ($request->get('QCtype') == 'RNA') {
$QC_Samples = new QC_Samples(array('sampleName' => $sampleName[$i], 'vol_ul' => $vol_ul[$i], 'conc_ng' => $conc_ng[$i], 'qty_ng' => $qty_ng[$i], '260_280' => $_260_280[$i], '260_230' => $_260_230[$i], '28S_18S' => $_28S_18S[$i], 'rin' => $rin[$i], 'lane' => $lane[$i], 'comment' => $comment[$i], 'is_buildLibrary' => $is_buildLibrary[$i], 'operator_id' => $request->get('operator')));
}
$QC_Samples->qualityControl()->associate($qualityControl);
$QC_Samples->operator()->associate($operator);
$user = \Auth::user();
$QC_Samples->creater()->associate($user);
$QC_Samples->save();
$images = glob(base_path() . '/storeFiles/ngs/tmpImage' . \Auth::id() . '/' . $i . '/' . '{*.gif,*.jpg,*.png}', GLOB_BRACE);
if (empty($images[0])) {
$figure_Path = null;
} else {
if (preg_match("/\\.(.+)/", $images[0], $matches)) {
// Valid match
$fileExtesion = $matches[1];
}
$fileName = $QC_Samples->id . '.' . $fileExtesion;
$flag = \File::move($images[0], base_path() . '/storeFiles/ngs/QC_Samples/' . $fileName);
$figure_Path = base_path() . '/storeFiles/ngs/QC_Samples/' . $fileName;
}
if (!empty($figure_Path)) {
$QC_Samples->update(['figure_Path' => $figure_Path]);
}
}
}
}
return \Redirect::to('research/ngs/projects/show/' . $POrecord->project->id)->with('message', 'Your Quality Control has been created!');
}
