public function img($id)
 {
     //
     $Library_Samples = Library_Samples::find($id);
     $filepath = $Library_Samples->figure_Path;
     return response()->download($filepath);
 }
Example #2
0
 /**
  * Update the specified resource in storage.
  *
  * @param  Request  $request
  * @param  int  $id
  * @return Response
  */
 public function update(SeqencingCreateFormRequest $request)
 {
     $POrecord = POcase::findOrFail($request->get('POrecord_id'));
     Sequencing::where('POrecord_id', '=', $POrecord->id)->delete();
     $sampleName = $request->get('sampleName');
     $indexNo = $request->get('indexNo');
     $barcode = $request->get('barcode');
     $sequencer = $request->get('sequencer');
     $sequencerNote = $request->get('sequencerNote');
     $length_bp = $request->get('length_bp');
     $type = $request->get('type');
     $targetQuantity = $request->get('targetQuantity');
     $quantityUnit = $request->get('quantityUnit');
     $operator = $request->get('operator');
     $operatorDate = $request->get('operatorDate');
     $note = $request->get('note');
     $Library_Sample_id = $request->get('Library_Sample_id');
     $max = sizeof($sampleName);
     for ($i = 0; $i < $max; $i++) {
         if (!empty($sampleName[$i])) {
             $targetQuantityBp = '';
             if ($quantityUnit[$i] == 'M Reads') {
                 if ($type[$i] == 'SE') {
                     $targetQuantityBp = $length_bp[$i] * $targetQuantity[$i] * 1000000;
                 } elseif ($type[$i] == 'PE') {
                     $targetQuantityBp = $length_bp[$i] * $targetQuantity[$i] * 1000000 * 2;
                 }
             } elseif ($quantityUnit[$i] == 'Gb') {
                 $targetQuantityBp = $targetQuantity[$i] * 1000000000;
             } elseif ($quantityUnit[$i] == 'Lane') {
                 if ($sequencer[$i] == 'Illumina - Hiseq X Ten (SINGLE FLOW CELL)') {
                     if ($type[$i] == 'PE') {
                         if ($length_bp[$i] == '150 ') {
                             $targetQuantityBp = $targetQuantity[$i] * 800 * 1000000000;
                         }
                     }
                 } elseif ($sequencer[$i] == 'Illumina - Hiseq X Ten (DUAL FLOW CELL)') {
                     if ($type[$i] == 'PE') {
                         if ($length_bp[$i] == '150 ') {
                             $targetQuantityBp = $targetQuantity[$i] * 1600 * 1000000000;
                         }
                     }
                 }
             } elseif ($quantityUnit[$i] == 'Run') {
                 if ($sequencer[$i] == 'Illumina - Miseq (V2 KIT)') {
                     if ($type[$i] == 'PE') {
                         if ($length_bp[$i] == '150') {
                             $targetQuantityBp = 4.5 * 1000000000;
                         } elseif ($length_bp[$i] == '250') {
                             $targetQuantityBp = 7.5 * 1000000000;
                         }
                     }
                 } elseif ($sequencer[$i] == 'Illumina - Miseq (V3 KIT)') {
                     if ($type[$i] == 'PE') {
                         if ($length_bp[$i] == '75') {
                             $targetQuantityBp = 3.3 * 1000000000;
                         } elseif ($length_bp[$i] == '300') {
                             $targetQuantityBp = 13.2 * 1000000000;
                         }
                     }
                 } elseif ($sequencer[$i] == 'Illumina - NextSeq 500 (HIGH OUTPUT KIT)') {
                     if ($type[$i] == 'PE') {
                         if ($length_bp[$i] == '75') {
                             $targetQuantityBp = 50 * 1000000000;
                         } elseif ($length_bp[$i] == '150') {
                             $targetQuantityBp = 100 * 1000000000;
                         }
                     } elseif ($type[$i] == 'SE') {
                         if ($length_bp[$i] == '75') {
                             $targetQuantityBp = 25 * 1000000000;
                         }
                     }
                 } elseif ($sequencer[$i] == 'Illumina - NextSeq 500 (MID OUTPUT KIT)') {
                     if ($type[$i] == 'PE') {
                         if ($length_bp[$i] == '75') {
                             $targetQuantityBp = 16.25 * 1000000000;
                         } elseif ($length_bp[$i] == '150') {
                             $targetQuantityBp = 32.5 * 1000000000;
                         }
                     }
                 } elseif ($sequencer[$i] == 'Illumina - Hiseq X Ten (SINGLE FLOW CELL)') {
                     if ($type[$i] == 'PE') {
                         if ($length_bp[$i] == '150 ') {
                             $targetQuantityBp = 800 * 1000000000;
                         }
                     }
                 } elseif ($sequencer[$i] == 'Illumina - Hiseq X Ten (DUAL FLOW CELL)') {
                     if ($type[$i] == 'PE') {
                         if ($length_bp[$i] == '150 ') {
                             $targetQuantityBp = 1600 * 1000000000;
                         }
                     }
                 }
             }
             $Sequencing = new Sequencing(array('sampleName' => $sampleName[$i], 'indexNo' => $indexNo[$i], 'barcode' => $barcode[$i], 'sequencer' => $sequencer[$i], 'sequencerNote' => $sequencerNote[$i], 'length_bp' => $length_bp[$i], 'type' => $type[$i], 'targetQuantity' => $targetQuantity[$i], 'quantityUnit' => $quantityUnit[$i], 'operatorDate' => $operatorDate[$i], 'note' => $note[$i], 'targetQuantityBp' => $targetQuantityBp));
             $Sequencing->POrecord()->associate($POrecord);
             $sampleOperator = User::findOrFail($operator[$i]);
             $Sequencing->operator()->associate($sampleOperator);
             $library_Samples = Library_Samples::findOrFail($Library_Sample_id[$i]);
             $Sequencing->Library_Samples()->associate($library_Samples);
             $Sequencing->save();
         }
     }
     return \Redirect::to('research/ngs/projects/show/' . $POrecord->project->id)->with('message', 'Your Sequencing has been updated!');
 }
Example #3
0
 /**
  * Remove the specified resource from storage.
  *
  * @param  int  $id
  * @return Response
  */
 public function destroy($id)
 {
     //
     $user = \Auth::user();
     $library = Library::findOrFail($id);
     $POrecord = $library->POrecord;
     $POrecord->status = 'QualityControl';
     $POrecord->save();
     $project = $POrecord->project;
     Library_Samples::where('library_id', '=', $library->id)->delete();
     $library->delete();
     return \Redirect::to('research/ngs/projects/show/' . $project->id)->with('message', 'Your Library has been deleted!');
 }