/**
  * 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!');
 }
Exemple #4
0
 /**
  * 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!');
 }
Exemple #6
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 /**
  * 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!');
 }
Exemple #9
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 /**
  * 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!');
 }