MLL

src/Tecan/CustomCommands/MLLReagentDistribution.php

@@ -0,0 +1,61 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Tecan\CustomCommands;
+
+use MLL\Utils\Tecan\BasicCommands\Command;
+use MLL\Utils\Tecan\BasicCommands\ReagentDistribution;
+use MLL\Utils\Tecan\LiquidClass\LiquidClass;
+use MLL\Utils\Tecan\ReagentDistribution\ReagentDistributionDirection;
+
+final class MLLReagentDistribution extends Command
+{
+    public const NUMBER_OF_DITI_REUSES = 6;
+    public const NUMBER_OF_MULTI_DISP = 1;
+
+    private AspirateParameters $source;
+
+    private DispenseParameters $target;
+
+    private float $volume;
+
+    private LiquidClass $liquidClass;
+
+    public function __construct(
+        AspirateParameters $source,
+        DispenseParameters $target,
+        float $dispenseVolume,
+        LiquidClass $liquidClass
+    ) {
+        $this->source = $source;
+        $this->target = $target;
+        $this->volume = $dispenseVolume;
+        $this->liquidClass = $liquidClass;
+    }
+
+    public function toString(): string
+    {
+        $reagentDistribution = new ReagentDistribution(
+            $this->source->formatToAspirateAndDispenseParameters(),
+            $this->target->formatToAspirateAndDispenseParameters(),
+            $this->volume,
+            $this->liquidClass,
+            self::NUMBER_OF_DITI_REUSES,
+            self::NUMBER_OF_MULTI_DISP,
+            ReagentDistributionDirection::LEFT_TO_RIGHT(),
+            $this->excludedWells(),
+        );
+
+        return $reagentDistribution->toString();
+    }
+
+    /** @return array<int, int> */
+    private function excludedWells(): array
+    {
+        $min = min($this->target->dispensePositions);
+        $max = max($this->target->dispensePositions);
+
+        $allWellsFromStartToEnd = range($min, $max);
+
+        return array_diff($allWellsFromStartToEnd, $this->target->dispensePositions);
+    }
+}

src/Tecan/LiquidClass/MLLLiquidClass.php

@@ -0,0 +1,49 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Tecan\LiquidClass;
+
+class MLLLiquidClass implements LiquidClass
+{
+    public const DNA_DILUTION = 'DNA_Dilution';
+    public const DNA_DILUTION_WATER = 'DNA_Dilution_Water';
+    public const TRANSFER_PCR_PRODUKT = 'Transfer_PCR_Produkt';
+    public const TRANSFER_MASTERMIX_MP = 'Transfer_Mastermix_MP';
+    public const TRANSFER_TEMPLATE = 'Transfer_Template'; // DNA-templates and BUFFER!
+
+    public string $value;
+
+    public function __construct(string $value)
+    {
+        $this->value = $value;
+    }
+
+    public static function DNA_DILUTION(): self
+    {
+        return new self(self::DNA_DILUTION);
+    }
+
+    public static function DNA_DILUTION_WATER(): self
+    {
+        return new self(self::DNA_DILUTION_WATER);
+    }
+
+    public static function TRANSFER_PCR_PRODUKT(): self
+    {
+        return new self(self::TRANSFER_PCR_PRODUKT);
+    }
+
+    public static function TRANSFER_MASTERMIX_MP(): self
+    {
+        return new self(self::TRANSFER_MASTERMIX_MP);
+    }
+
+    public static function TRANSFER_TEMPLATE(): self
+    {
+        return new self(self::TRANSFER_TEMPLATE);
+    }
+
+    public function name(): string
+    {
+        return $this->value;
+    }
+}

src/Tecan/Rack/MLLLabWareRack.php

@@ -0,0 +1,116 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Tecan\Rack;
+
+class MLLLabWareRack implements Rack
+{
+    public const A = 'A';
+    public const MP_CDNA = 'MPCDNA';
+    public const MP_SAMPLE = 'MPSample';
+    public const MP_WATER = 'MPWasser';
+    public const FLUID_X = 'FluidX';
+    public const MM = 'MM';
+    public const DEST_LC = 'DestLC';
+    public const DEST_PCR = 'DestPCR';
+    public const DEST_TAQMAN = 'DestTaqMan';
+
+    public string $value;
+
+    public function __construct(string $value)
+    {
+        $this->value = $value;
+    }
+
+    public static function A(): self
+    {
+        return new self(self::A);
+    }
+
+    public static function MP_CDNA(): self
+    {
+        return new self(self::MP_CDNA);
+    }
+
+    public static function MP_SAMPLE(): self
+    {
+        return new self(self::MP_SAMPLE);
+    }
+
+    public static function MP_WATER(): self
+    {
+        return new self(self::MP_WATER);
+    }
+
+    public static function FLUID_X(): self
+    {
+        return new self(self::FLUID_X);
+    }
+
+    public static function MM(): self
+    {
+        return new self(self::MM);
+    }
+
+    public static function DEST_LC(): self
+    {
+        return new self(self::DEST_LC);
+    }
+
+    public static function DEST_PCR(): self
+    {
+        return new self(self::DEST_PCR);
+    }
+
+    public static function DEST_TAQMAN(): self
+    {
+        return new self(self::DEST_TAQMAN);
+    }
+
+    public function id(): ?string
+    {
+        return null;
+    }
+
+    public function name(): string
+    {
+        return $this->value;
+    }
+
+    public function type(): string
+    {
+        switch ($this->value) {
+            case self::A:
+                return 'Eppis 24x0.5 ml Cooled';
+            case self::MP_CDNA:
+                return 'MP cDNA';
+            case self::MP_SAMPLE:
+                return 'MP Microplate';
+            case self::MP_WATER:
+                return 'Trough 300ml MCA Portrait';
+            case self::FLUID_X:
+                return '96FluidX';
+            case self::MM:
+                return 'Eppis 32x1.5 ml Cooled';
+            case self::DEST_LC:
+                return '96 Well MP LightCycler480';
+            case self::DEST_PCR:
+                return '96 Well PCR ABI semi-skirted';
+            case self::DEST_TAQMAN:
+                return '96 Well PCR TaqMan';
+            default:
+                throw new \Exception('Type not defined for ' . $this->value);
+        }
+    }
+
+    public function toString(): string
+    {
+        return implode(
+            ';',
+            [
+                $this->name(),
+                $this->id(),
+                $this->type(),
+            ]
+        );
+    }
+}

tests/Tecan/BasicCommands/AspirateTest.php

@@ -4,11 +4,11 @@
 
 use MLL\Utils\Tecan\BasicCommands\Aspirate;
 use MLL\Utils\Tecan\LiquidClass\CustomLiquidClass;
-use MLL\Utils\Tecan\LiquidClass\MllLiquidClass;
+use MLL\Utils\Tecan\LiquidClass\MLLLiquidClass;
 use MLL\Utils\Tecan\Location\BarcodeLocation;
 use MLL\Utils\Tecan\Location\PositionLocation;
 use MLL\Utils\Tecan\Rack\CustomRack;
-use MLL\Utils\Tecan\Rack\MllLabWareRack;
+use MLL\Utils\Tecan\Rack\MLLLabWareRack;
 use PHPUnit\Framework\TestCase;
 
 final class AspirateTest extends TestCase
@@ -26,7 +26,7 @@ public function testAspirateWithPositionLocation(): void
     {
         $position = 7;
         $volume = 2.2;
-        $aspirate = new Aspirate($volume, new PositionLocation($position, MllLabWareRack::DEST_PCR()), MllLiquidClass::TRANSFER_TEMPLATE());
+        $aspirate = new Aspirate($volume, new PositionLocation($position, MLLLabWareRack::DEST_PCR()), MLLLiquidClass::TRANSFER_TEMPLATE());
         self::assertNull($aspirate->location->tubeID());
         self::assertSame((string) $position, $aspirate->location->position());
         self::assertSame('A;DestPCR;;96 Well PCR ABI semi-skirted;' . $position . ';;2.2;Transfer_Template;;', $aspirate->toString());

tests/Tecan/BasicCommands/DispenseTest.php

@@ -4,11 +4,11 @@
 
 use MLL\Utils\Tecan\BasicCommands\Dispense;
 use MLL\Utils\Tecan\LiquidClass\CustomLiquidClass;
-use MLL\Utils\Tecan\LiquidClass\MllLiquidClass;
+use MLL\Utils\Tecan\LiquidClass\MLLLiquidClass;
 use MLL\Utils\Tecan\Location\BarcodeLocation;
 use MLL\Utils\Tecan\Location\PositionLocation;
 use MLL\Utils\Tecan\Rack\CustomRack;
-use MLL\Utils\Tecan\Rack\MllLabWareRack;
+use MLL\Utils\Tecan\Rack\MLLLabWareRack;
 use PHPUnit\Framework\TestCase;
 
 final class DispenseTest extends TestCase
@@ -26,7 +26,7 @@ public function testDispenseWithPositionLocation(): void
     {
         $position = 7;
         $volume = 2.2;
-        $aspirate = new Dispense($volume, new PositionLocation($position, MllLabWareRack::DEST_LC()), MllLiquidClass::TRANSFER_TEMPLATE());
+        $aspirate = new Dispense($volume, new PositionLocation($position, MLLLabWareRack::DEST_LC()), MLLLiquidClass::TRANSFER_TEMPLATE());
         self::assertNull($aspirate->location->tubeID());
         self::assertSame((string) $position, $aspirate->location->position());
         self::assertSame("D;DestLC;;96 Well MP LightCycler480;{$position};;{$volume};Transfer_Template;;", $aspirate->toString());

tests/Tecan/BasicCommands/ReagentDistributionTest.php

@@ -4,8 +4,8 @@
 
 use MLL\Utils\Tecan\BasicCommands\AspirateAndDispenseParameters;
 use MLL\Utils\Tecan\BasicCommands\ReagentDistribution;
-use MLL\Utils\Tecan\LiquidClass\MllLiquidClass;
-use MLL\Utils\Tecan\Rack\MllLabWareRack;
+use MLL\Utils\Tecan\LiquidClass\MLLLiquidClass;
+use MLL\Utils\Tecan\Rack\MLLLabWareRack;
 use MLL\Utils\Tecan\ReagentDistribution\ReagentDistributionDirection;
 use PHPUnit\Framework\TestCase;
 
@@ -15,16 +15,16 @@ public function testFormatToString(): void
     {
         $sourceStartPosition = 13;
         $sourceEndPosition = 13;
-        $sourceRack = MllLabWareRack::MM();
+        $sourceRack = MLLLabWareRack::MM();
         $source = new AspirateAndDispenseParameters($sourceRack, $sourceStartPosition, $sourceEndPosition);
 
         $targetStartPosition = 48;
         $targetEndPosition = 73;
-        $targetRack = MllLabWareRack::DEST_PCR();
+        $targetRack = MLLLabWareRack::DEST_PCR();
         $target = new AspirateAndDispenseParameters($targetRack, $targetStartPosition, $targetEndPosition);
 
         $dispenseVolume = 24;
-        $liquidClass = MllLiquidClass::TRANSFER_MASTERMIX_MP();
+        $liquidClass = MLLLiquidClass::TRANSFER_MASTERMIX_MP();
 
         $numberOfDitiReuses = 6;
         $numberOfMultiDisp = 1;

tests/Tecan/CustomCommands/MLLReagentDistributionTest.php

@@ -0,0 +1,41 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Tests\Tecan\CustomCommands;
+
+use MLL\Utils\Tecan\CustomCommands\AspirateParameters;
+use MLL\Utils\Tecan\CustomCommands\DispenseParameters;
+use MLL\Utils\Tecan\CustomCommands\MLLReagentDistribution;
+use MLL\Utils\Tecan\LiquidClass\MLLLiquidClass;
+use MLL\Utils\Tecan\Rack\MLLLabWareRack;
+use PHPUnit\Framework\TestCase;
+
+final class MLLReagentDistributionTest extends TestCase
+{
+    public function testFormatToString(): void
+    {
+        $sourceStartPosition = 13;
+        $sourceRack = MLLLabWareRack::MM();
+        $source = new AspirateParameters($sourceRack, $sourceStartPosition);
+
+        $targetRack = MLLLabWareRack::DEST_PCR();
+        $target = new DispenseParameters($targetRack, [48, 49, 72, 73]);
+
+        $dispenseVolume = 24;
+        $liquidClass = MLLLiquidClass::TRANSFER_MASTERMIX_MP();
+
+        $command = new MLLReagentDistribution(
+            $source,
+            $target,
+            $dispenseVolume,
+            $liquidClass,
+        );
+
+        $numberOfDitiReuses = MLLReagentDistribution::NUMBER_OF_DITI_REUSES;
+        $numberOfMultiDisp = MLLReagentDistribution::NUMBER_OF_MULTI_DISP;
+
+        self::assertSame(
+            "R;{$sourceRack->name()};;{$sourceRack->type()};{$sourceStartPosition};{$sourceStartPosition};{$targetRack->name()};;{$targetRack->type()};48;73;{$dispenseVolume};{$liquidClass->name()};{$numberOfDitiReuses};{$numberOfMultiDisp};0;50;51;52;53;54;55;56;57;58;59;60;61;62;63;64;65;66;67;68;69;70;71",
+            $command->toString()
+        );
+    }
+}

tests/Tecan/LiquidClass/MLLLiquidClassTest.php

@@ -0,0 +1,18 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Tests\Tecan\LiquidClass;
+
+use MLL\Utils\Tecan\LiquidClass\MLLLiquidClass;
+use PHPUnit\Framework\TestCase;
+
+final class MLLLiquidClassTest extends TestCase
+{
+    public function testNameOfEnum(): void
+    {
+        self::assertSame('DNA_Dilution', MLLLiquidClass::DNA_DILUTION()->name());
+        self::assertSame('DNA_Dilution_Water', MLLLiquidClass::DNA_DILUTION_WATER()->name());
+        self::assertSame('Transfer_PCR_Produkt', MLLLiquidClass::TRANSFER_PCR_PRODUKT()->name());
+        self::assertSame('Transfer_Mastermix_MP', MLLLiquidClass::TRANSFER_MASTERMIX_MP()->name());
+        self::assertSame('Transfer_Template', MLLLiquidClass::TRANSFER_TEMPLATE()->name());
+    }
+}