feat: Support creating Lightcycler Sample Sheets for Absolute Quantification

CHANGELOG.md

@@ -9,6 +9,12 @@ See [GitHub releases](https://github.com/mll-lab/php-utils/releases).
 
 ## Unreleased
 
+## v5.17.0
+
+### Added
+
+- Support creating Lightcycler Sample Sheets for Absolute Quantification
+
 ## v5.16.0
 
 ### Added

src/LightcyclerSampleSheet/AbsoluteQuantificationSample.php

@@ -0,0 +1,57 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\LightcyclerSampleSheet;
+
+use MLL\Utils\Microplate\Coordinates;
+use MLL\Utils\Microplate\CoordinateSystem12x8;
+
+class AbsoluteQuantificationSample
+{
+    public string $sampleName;
+
+    public string $filterCombination;
+
+    public string $hexColor;
+
+    public string $sampleType;
+
+    public string $concentration;
+
+    /** @var Coordinates<CoordinateSystem12x8>|null */
+    public ?Coordinates $replicationOf;
+
+    /** @param Coordinates<CoordinateSystem12x8>|null $replicationOf */
+    public function __construct(
+        string $sampleName,
+        string $filterCombination,
+        string $hexColor,
+        string $sampleType,
+        string $concentration,
+        ?Coordinates $replicationOf = null
+    ) {
+        $this->sampleName = $sampleName;
+        $this->filterCombination = $filterCombination;
+        $this->hexColor = $hexColor;
+        $this->sampleType = $sampleType;
+        $this->concentration = $concentration;
+        $this->replicationOf = $replicationOf;
+    }
+
+    /** @return list<string> */
+    public function toSerializableArray(string $coordinatesString): array
+    {
+        $replicationOf = $this->replicationOf instanceof Coordinates
+            ? "\"{$this->replicationOf->toString()}\""
+            : '""';
+
+        return [
+            Coordinates::fromString($coordinatesString, new CoordinateSystem12x8())->toString(),
+            "\"{$this->sampleName}\"",
+            $replicationOf,
+            $this->filterCombination,
+            "$00{$this->hexColor}",
+            "\"{$this->sampleType}\"",
+            "\"{$this->concentration}\"",
+        ];
+    }
+}

src/LightcyclerSampleSheet/AbsoluteQuantificationSheet.php

@@ -0,0 +1,30 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\LightcyclerSampleSheet;
+
+use Illuminate\Support\Collection;
+use MLL\Utils\StringUtil;
+
+class AbsoluteQuantificationSheet
+{
+    public const HEADER_COLUMNS = [
+        '"General:Pos"',
+        '"General:Sample Name"',
+        '"General:Repl. Of"',
+        '"General:Filt. Comb."',
+        '"Sample Preferences:Color"',
+        '"Abs Quant:Sample Type"',
+        '"Abs Quant:Concentration"',
+    ];
+
+    /** @param Collection<string, AbsoluteQuantificationSample> $samples */
+    public function generate(Collection $samples): string
+    {
+        return $samples
+            ->map(fn (AbsoluteQuantificationSample $well, string $coordinateFromKey): array => $well->toSerializableArray($coordinateFromKey))
+            ->prepend(self::HEADER_COLUMNS)
+            ->map(fn (array $row): string => implode(StringUtil::TAB, $row))
+            ->implode(StringUtil::WINDOWS_NEW_LINE)
+            . StringUtil::WINDOWS_NEW_LINE;
+    }
+}

src/LightcyclerSampleSheet/RelativeQuantificationSheet.php

@@ -3,11 +3,10 @@
 namespace MLL\Utils\LightcyclerSampleSheet;
 
 use Illuminate\Support\Collection;
+use MLL\Utils\StringUtil;
 
 class RelativeQuantificationSheet
 {
-    protected const WINDOWS_NEW_LINE = "\r\n";
-    protected const TAB_SEPARATOR = "\t";
     public const HEADER_COLUMNS = [
         '"General:Pos"',
         '"General:Sample Name"',
@@ -22,8 +21,8 @@ public function generate(Collection $samples): string
         return $samples
             ->map(fn (RelativeQuantificationSample $well, string $coordinateFromKey): array => $well->toSerializableArray($coordinateFromKey))
             ->prepend(self::HEADER_COLUMNS)
-            ->map(fn (array $row): string => implode(self::TAB_SEPARATOR, $row))
-            ->implode(self::WINDOWS_NEW_LINE)
-            . self::WINDOWS_NEW_LINE;
+            ->map(fn (array $row): string => implode(StringUtil::TAB, $row))
+            ->implode(StringUtil::WINDOWS_NEW_LINE)
+            . StringUtil::WINDOWS_NEW_LINE;
     }
 }

src/StringUtil.php

@@ -6,6 +6,10 @@
 
 class StringUtil
 {
+    public const WINDOWS_NEW_LINE = "\r\n";
+
+    public const TAB = "\t";
+
     /** https://en.wikipedia.org/wiki/Byte_order_mark#UTF-8 */
     public const UTF_8_BOM = "\xEF\xBB\xBF";
 

tests/LightcyclerSampleSheet/AbsoluteQuantificationSheetTest.php

@@ -0,0 +1,52 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Tests\LightcyclerSampleSheet;
+
+use Illuminate\Support\Collection;
+use MLL\Utils\LightcyclerSampleSheet\AbsoluteQuantificationSample;
+use MLL\Utils\LightcyclerSampleSheet\AbsoluteQuantificationSheet;
+use MLL\Utils\Microplate\Coordinates;
+use MLL\Utils\Microplate\CoordinateSystem12x8;
+use MLL\Utils\StringUtil;
+use PHPUnit\Framework\TestCase;
+
+final class AbsoluteQuantificationSheetTest extends TestCase
+{
+    public function testGenerateWithFakeData(): void
+    {
+        $coordinateSystem = new CoordinateSystem12x8();
+
+        $samples = Collection::make([
+            'A1' => new AbsoluteQuantificationSample('Standard_1', '485-520', 'FF0000', 'Standard', '1000.0', null),
+            'B1' => new AbsoluteQuantificationSample('Standard_1', '485-520', 'FF0001', 'Standard', '1000.0', Coordinates::fromString('A1', $coordinateSystem)),
+            'C1' => new AbsoluteQuantificationSample('Standard_2', '485-520', '00FF00', 'Standard', '100.0', null),
+            'D1' => new AbsoluteQuantificationSample('Standard_2', '485-520', '00FF01', 'Standard', '100.0', Coordinates::fromString('C1', $coordinateSystem)),
+            'E1' => new AbsoluteQuantificationSample('Sample_001', '485-520', '0000FF', 'Unknown', '', null),
+            'F1' => new AbsoluteQuantificationSample('Sample_001', '485-520', '0000FE', 'Unknown', '', Coordinates::fromString('E1', $coordinateSystem)),
+            'G1' => new AbsoluteQuantificationSample('Sample_002', '485-520', 'FFFF00', 'Unknown', '', null),
+            'H1' => new AbsoluteQuantificationSample('Sample_002', '485-520', 'FFFF01', 'Unknown', '', Coordinates::fromString('G1', $coordinateSystem)),
+            'A2' => new AbsoluteQuantificationSample('NTC', '485-520', '000000', 'Negative Control', '', null),
+            'B2' => new AbsoluteQuantificationSample('NTC', '485-520', '000001', 'Negative Control', '', Coordinates::fromString('A2', $coordinateSystem)),
+        ]);
+
+        $sheet = new AbsoluteQuantificationSheet();
+        $result = $sheet->generate($samples);
+
+        $expected = <<<EOT
+"General:Pos"\t"General:Sample Name"\t"General:Repl. Of"\t"General:Filt. Comb."\t"Sample Preferences:Color"\t"Abs Quant:Sample Type"\t"Abs Quant:Concentration"
+A1\t"Standard_1"\t""\t485-520\t$00FF0000\t"Standard"\t"1000.0"
+B1\t"Standard_1"\t"A1"\t485-520\t$00FF0001\t"Standard"\t"1000.0"
+C1\t"Standard_2"\t""\t485-520\t$0000FF00\t"Standard"\t"100.0"
+D1\t"Standard_2"\t"C1"\t485-520\t$0000FF01\t"Standard"\t"100.0"
+E1\t"Sample_001"\t""\t485-520\t$000000FF\t"Unknown"\t""
+F1\t"Sample_001"\t"E1"\t485-520\t$000000FE\t"Unknown"\t""
+G1\t"Sample_002"\t""\t485-520\t$00FFFF00\t"Unknown"\t""
+H1\t"Sample_002"\t"G1"\t485-520\t$00FFFF01\t"Unknown"\t""
+A2\t"NTC"\t""\t485-520\t$00000000\t"Negative Control"\t""
+B2\t"NTC"\t"A2"\t485-520\t$00000001\t"Negative Control"\t""
+
+EOT;
+
+        self::assertSame(StringUtil::normalizeLineEndings($expected), $result);
+    }
+}

tests/LightcyclerSampleSheet/RelativeQuantificationSheetTest.php

@@ -14,12 +14,14 @@ final class RelativeQuantificationSheetTest extends TestCase
 {
     public function testGenerate(): void
     {
+        $coordinateSystem = new CoordinateSystem12x8();
+
         $samples = Collection::make([
             'A1' => new RelativeQuantificationSample('Sample 1', '498-640', 'FF378A', null),
             'B1' => new RelativeQuantificationSample('Sample 2', '498-640', '4899D1', null),
             'C1' => new RelativeQuantificationSample('Sample 3', '498-640', '8528B9', null),
             'D1' => new RelativeQuantificationSample('Sample 4', '498-640', '8E05D9', null),
-            'E1' => new RelativeQuantificationSample('Sample 5', '498-640', '4080A5', Coordinates::fromString('C12', new CoordinateSystem12x8())),
+            'E1' => new RelativeQuantificationSample('Sample 5', '498-640', '4080A5', Coordinates::fromString('C12', $coordinateSystem)),
         ]);
 
         $sheet = new RelativeQuantificationSheet();