/**
* Store a newly created resource in storage.
*
* @param Request $request
* @return Response
*/
public function store(CaseClosedCreateFormRequest $request)
{
//
$caseClosed = new CaseClosed(array('status' => $request->get('status'), 'status_note' => $request->get('status_note')));
$user = \Auth::user();
$caseClosed->creater()->associate($user);
$POrecord = POcase::findOrFail($request->get('POrecord_id'));
$POrecord->status = 'CaseClosed';
$POrecord->save();
$caseClosed->POrecord()->associate($POrecord);
$caseClosed->save();
return \Redirect::to('research/ngs/projects/show/' . $POrecord->project->id)->with('message', 'Your Case Closed has been updated!');
}
/**
* Update the specified resource in storage.
*
* @param Request $request
* @param int $id
* @return Response
*/
public function update(ReportCheckCreateFormRequest $request, $id)
{
//
$reportCheck = ReportCheck::findOrFail($id);
$reportCheck->update(array('reviewDate' => $request->get('reviewDate'), 'note' => $request->get('note'), 'reviewer_id' => $request->get('reviewer')));
$reviewer = User::findOrFail($request->get('reviewer'));
$reportCheck->reviewer()->associate($reviewer);
$analysis = Analysis::findOrFail($request->get('analysis_id'));
$reportCheck->analysis()->associate($analysis);
$POrecord = POcase::findOrFail($request->get('POrecord_id'));
$reportCheck->POrecord()->associate($POrecord);
$reportCheck->save();
return \Redirect::to('research/ngs/projects/show/' . $POrecord->project->id)->with('message', 'Your Report Check has been updated!');
}
public function storeStatus(Request $request)
{
//
$POrecord = POcase::findOrFail($request->get('POrecord_id'));
$Sequencings = Sequencing::where('POrecord_id', '=', $POrecord->id)->get()->all();
foreach ($Sequencings as $Sequencing) {
$Sequencing->status = $request->get('status');
$Sequencing->status_note = $request->get('status_note');
$Sequencing->save();
}
return \Redirect::to('research/ngs/projects/show/' . $POrecord->project->id)->with('message', 'Your Sequencing has been updated!');
}
/**
* Update the specified resource in storage.
*
* @param Request $request
* @param int $id
* @return Response
*/
public function update(AnalysisCreateFormRequest $request, $id)
{
//
$Analysis = Analysis::findOrFail($id);
foreach ($request->get('analysisDetail') as &$Detail) {
if (empty($analysisDetail)) {
$analysisDetail = $Detail;
} else {
$analysisDetail = $analysisDetail . "|" . $Detail;
}
}
$Analysis->update(array('caseType' => $request->get('caseType'), 'analysisDetail' => $analysisDetail, 'is_assignDB' => $request->get('is_assignDB'), 'assignDBver' => $request->get('assignDBver'), 'analysisDB' => $request->get('analysisDB'), 'analysisMethod' => $request->get('analysisMethod'), 'analyst' => $request->get('analyst'), 'analysisDate' => $request->get('analysisDate'), 'analysisHour' => $request->get('analysisHour'), 'runHour' => $request->get('runHour'), 'description' => $request->get('description'), 'downloadLink' => $request->get('downloadLink')));
$POrecord = POcase::findOrFail($request->get('POrecord_id'));
return \Redirect::to('research/ngs/projects/show/' . $POrecord->project->id)->with('message', 'Your Analysis has been updated!');
}
/**
* Update the specified resource in storage.
*
* @param Request $request
* @param int $id
* @return Response
*/
public function update(Request $request, $id)
{
//
$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();
}
$qualityControl = qualityControl::findOrFail($id);
$na_flag = 0;
foreach ($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->update(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') {
$qualityControl->update(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' => $request->get('is_differentMethods'), 'is_interpretation' => $request->get('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'));
$qualityControl->POrecord()->associate($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;
$qualityControl->update(['figure_1_Path' => $figure_1_Path]);
}
if (empty($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;
$qualityControl->update(['figure_2_Path' => $figure_2_Path]);
}
if (empty($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;
$qualityControl->update(['figure_3_Path' => $figure_3_Path]);
}
if (empty($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;
$qualityControl->update(['figure_4_Path' => $figure_4_Path]);
}
if (empty($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_nanodrop_Path' => $figure_nanodrop_Path]);
}
$old_QC_Samples = QC_Samples::where('qualityControl_id', '=', $qualityControl->id)->get();
if (!empty($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)) {
if (empty($old_QC_Samples)) {
$figure_Path = null;
} else {
if ($i <= count($old_QC_Samples)) {
if (!empty($old_QC_Samples[$i - 1]->figure_Path)) {
if (preg_match("/\\.(.+)/", $old_QC_Samples[$i - 1]->figure_Path, $matches)) {
// Valid match
$fileExtesion = $matches[1];
}
$fileName = $QC_Samples->id . '.' . $fileExtesion;
$flag = \File::move($old_QC_Samples[$i - 1]->figure_Path, base_path() . '/storeFiles/ngs/QC_Samples/' . $fileName);
$figure_Path = base_path() . '/storeFiles/ngs/QC_Samples/' . $fileName;
}
} else {
$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' => $figure_Path]);
}
}
}
}
foreach ($old_QC_Samples as $old_QC_Sample) {
if (!empty($old_QC_Sample->figure_Path)) {
if (\File::exists($old_QC_Sample->figure_Path)) {
\File::delete($old_QC_Sample->figure_Path);
}
}
$old_QC_Sample->delete();
}
return \Redirect::to('research/ngs/projects/show/' . $POrecord->project->id)->with('message', 'Your Quality Control has been updated!');
}
/**
* Remove the specified resource from storage.
*
* @param int $id
* @return Response
*/
public function destroy($id)
{
//
$user = \Auth::user();
$POcase = POcase::findOrFail($id);
$project = $POcase->project;
$POcase->delete();
return \Redirect::to('research/ngs/projects/show/' . $project->id)->with('message', 'Your Case has been deleted!');
}
/**
* Update the specified resource in storage.
*
* @param Request $request
* @param int $id
* @return Response
*/
public function update(ExaminationCreateFormRequest $request)
{
$POrecord = POcase::findOrFail($request->get('POrecord_id'));
Examination::where('POrecord_id', '=', $POrecord->id)->delete();
$sampleName = $request->get('sampleName');
$indexNo = $request->get('indexNo');
$barcode = $request->get('barcode');
$sequencingDate = $request->get('sequencingDate');
$afterQuantity = $request->get('afterQuantity');
$Q20 = $request->get('Q20');
$Q30 = $request->get('Q30');
$operator = $request->get('operator');
$operatorDate = $request->get('operatorDate');
$note = $request->get('note');
$Sequencing_id = $request->get('Sequencing_id');
$max = sizeof($sampleName);
for ($i = 0; $i < $max; $i++) {
if (!empty($sampleName[$i])) {
$Examination = new Examination(array('sampleName' => $sampleName[$i], 'indexNo' => $indexNo[$i], 'barcode' => $barcode[$i], 'sequencingDate' => $sequencingDate[$i], 'afterQuantity' => $afterQuantity[$i], 'Q20' => $Q20[$i], 'Q30' => $Q30[$i], 'operatorDate' => $operatorDate[$i], 'note' => $note[$i]));
$Examination->POrecord()->associate($POrecord);
$sampleOperator = User::findOrFail($operator[$i]);
$Examination->operator()->associate($sampleOperator);
$Sequencing = Sequencing::findOrFail($Sequencing_id[$i]);
$Examination->Sequencing()->associate($Sequencing);
$Examination->save();
}
}
return \Redirect::to('research/ngs/examination/edit/' . $POrecord->project->id)->with('message', 'Your Examination has been updated!');
}
/**
* Update the specified resource in storage.
*
* @param Request $request
* @param int $id
* @return Response
*/
public function update(Request $request, $id)
{
//
$rules = array('speices' => 'required', 'classify' => 'required', 'type' => 'required', 'condition' => 'required', 'SampleExtration' => 'required', 'ribosomalDepletion' => 'required', 'operator' => 'required', 'sender' => 'required', 'sampleNum' => 'required', 'shippingCondition' => 'required', 'salesman' => 'required_with:salesmanGetDate', 'labman' => 'required_with:labmanGetDate', 'salesmanGetDate' => 'date|required_without:labmanGetDate|required_with:salesman|before:tomorrow', 'labmanGetDate' => 'date|required_without:salesmanGetDate|required_with:labman|before:tomorrow');
if (empty($request->get('salesmanGetDate'))) {
$rules['sampleGetDate'] = 'required|date|before:labmanGetDate';
} elseif (empty($request->get('labmanGetDate'))) {
$rules['sampleGetDate'] = 'required|date|before:salesmanGetDate';
} else {
if ($request->get('salesmanGetDate') > $request->get('labmanGetDate')) {
$rules['sampleGetDate'] = 'required|date|before:labmanGetDate';
} else {
$rules['sampleGetDate'] = 'required|date|before:salesmanGetDate';
}
}
$validator = Validator::make($request->all(), $rules);
if ($validator->fails()) {
return back()->withErrors($validator)->withInput();
}
$extraction = Extraction::findOrFail($id);
$extraction->update(['speices' => $request->get('speices'), 'classify' => $request->get('classify'), 'type' => $request->get('type'), 'condition' => $request->get('condition'), 'is_treatRNase' => $request->get('is_treatRNase'), 'RNAisolationMethod' => $request->get('RNAisolationMethod'), 'note' => $request->get('note'), 'SampleExtration' => $request->get('SampleExtration'), 'ribosomalDepletion' => $request->get('ribosomalDepletion'), 'operator' => $request->get('operator'), 'create_at' => $request->get('create_at')]);
$operator = User::findOrFail($request->get('operator'));
$extraction->operator()->associate($operator);
$POrecord = POcase::findOrFail($request->get('POrecord_id'));
$extraction->POrecord()->associate($POrecord);
$Shipment = new Shipment(array('sender' => $request->get('sender'), 'sampleGetDate' => $request->get('sampleGetDate'), 'sampleNum' => $request->get('sampleNum'), 'salesman' => $request->get('salesman'), 'salesmanGetDate' => $request->get('salesmanGetDate'), 'shippingCondition' => $request->get('shippingCondition'), 'labman' => $request->get('labman'), 'labmanGetDate' => $request->get('labmanGetDate')));
$user = User::find(\Auth::id());
$Shipment->creater()->associate($user);
$Shipment->extraction()->associate($extraction);
$Shipment->save();
$extraction->Shipment_id = $Shipment->id;
$extraction->save();
$POrecord->save();
return \Redirect::to('research/ngs/projects/show/' . $POrecord->project->id)->with('message', 'Your Extraction has been updated!');
}
/**
* Update the specified resource in storage.
*
* @param Request $request
* @param int $id
* @return Response
*/
public function update(Request $request, $id)
{
$rules = ['libraryKit' => 'required', 'operatorDate' => 'required', 'measureTool' => 'required', 'fragmentSize' => 'required', 'operator' => 'required'];
$validator = Validator::make($request->all(), $rules);
if ($validator->fails()) {
return back()->withErrors($validator)->withInput();
}
$library = Library::findOrFail($id);
$library->update(array('libraryKit' => $request->get('libraryKit'), 'operatorDate' => $request->get('operatorDate'), 'measureTool' => $request->get('measureTool'), 'fragmentSize' => $request->get('fragmentSize'), 'measureNote' => $request->get('measureNote'), 'reportDescription' => $request->get('reportDescription'), 'note' => $request->get('note'), 'operator' => $request->get('operator')));
$operator = User::findOrFail($request->get('operator'));
$library->operator()->associate($operator);
$POrecord = POcase::findOrFail($request->get('POrecord_id'));
$library->POrecord()->associate($POrecord);
$library->save();
$old_library_Samples = Library_Samples::where('library_id', '=', $library->id)->get();
if (!empty($request->get('sampleName'))) {
$sampleName = $request->get('sampleName');
$vol = $request->get('vol');
$index = $request->get('index');
$barcode = $request->get('barcode');
$Qubit_ngul = $request->get('Qubit_ngul');
$B_TS_bp = $request->get('B_TS_bp');
$B_TS_ngul = $request->get('B_TS_ngul');
$B_TS_nM = $request->get('B_TS_nM');
$ND_ngul = $request->get('ND_ngul');
$OD_260_280 = $request->get('OD_260_280');
$OD_260_230 = $request->get('OD_260_230');
$result = $request->get('result');
$figure_Path = $request->file('figure_Path');
$max = 0;
$sampleIndexs = array_keys($sampleName);
foreach ($sampleIndexs as $sampleIndex) {
if ($sampleIndex > $max) {
$max = $sampleIndex;
}
}
for ($i = 1; $i <= $max; $i++) {
if (!empty($sampleName[$i])) {
$library_Samples = new Library_Samples(array('sampleName' => $sampleName[$i], 'vol' => $vol[$i], 'index' => $index[$i], 'barcode' => $barcode[$i], 'Qubit_ngul' => $Qubit_ngul[$i], 'B_TS_bp' => $B_TS_bp[$i], 'B_TS_ngul' => $B_TS_ngul[$i], 'B_TS_nM' => $B_TS_nM[$i], 'ND_ngul' => $ND_ngul[$i], 'OD_260_280' => $OD_260_280[$i], 'OD_260_230' => $OD_260_230[$i], 'result' => $result[$i]));
$library_Samples->library()->associate($library);
$user = \Auth::user();
$library_Samples->creater()->associate($user);
$library_Samples->save();
$images = glob(base_path() . '/storeFiles/ngs/tmpImage' . \Auth::id() . '/' . $i . '/' . '{*.gif,*.jpg,*.png}', GLOB_BRACE);
if (empty($images)) {
if (empty($old_library_Samples)) {
$figure_Path = null;
} else {
if ($i <= count($old_library_Samples)) {
if (!empty($old_library_Samples[$i - 1]->figure_Path)) {
if (preg_match("/\\.(.+)/", $old_library_Samples[$i - 1]->figure_Path, $matches)) {
// Valid match
$fileExtesion = $matches[1];
}
$fileName = $library_Samples->id . '.' . $fileExtesion;
$flag = \File::move($old_library_Samples[$i - 1]->figure_Path, base_path() . '/storeFiles/ngs/library_Samples/' . $fileName);
$figure_Path = base_path() . '/storeFiles/ngs/library_Samples/' . $fileName;
}
} else {
$figure_Path = null;
}
}
} else {
if (preg_match("/\\.(.+)/", $images[0], $matches)) {
// Valid match
$fileExtesion = $matches[1];
}
$fileName = $library_Samples->id . '.' . $fileExtesion;
$flag = \File::move($images[0], base_path() . '/storeFiles/ngs/library_Samples/' . $fileName);
$figure_Path = base_path() . '/storeFiles/ngs/library_Samples/' . $fileName;
}
if (!empty($figure_Path)) {
$library_Samples->update(['figure_Path' => $figure_Path]);
}
}
}
}
foreach ($old_library_Samples as $old_library_Sample) {
if (!empty($old_library_Sample->figure_Path)) {
if (\File::exists($old_library_Sample->figure_Path)) {
\File::delete($old_library_Sample->figure_Path);
}
}
$old_library_Sample->delete();
}
return \Redirect::to('research/ngs/projects/show/' . $POrecord->project->id)->with('message', 'Your Library has been updated!');
}