public function img($id)
{
//
$Library_Samples = Library_Samples::find($id);
$filepath = $Library_Samples->figure_Path;
return response()->download($filepath);
}
/**
* 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!');
}
/**
* 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!');
}
