Merge pull request #3 from mll-lab/fixes_for_handling

feat: Add predefined classes that implement `Rack`- and `LiquidClass`…

CHANGELOG.md

@@ -7,6 +7,21 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## Unreleased
 
+## v2.0.0
+
+### Added
+
+- Add predefined classes that implement `Rack`- and `LiquidClass`-interface
+- Add `fileName`-method on `TecanProtocol`
+
+### Breaking
+
+- delete superfluous semicolon after TipMask
+- `PositionLocation` returns `$rack->name`
+- `BarcodeLocation` does not return `$rack->name`
+- Move `Rack`- and `LiquidClass`-interface to subdirectory
+- Change signature of `TransferWithAutoWash`-class
+
 ## v1.1.0
 
 ### Added

src/Tecan/BasicCommands/Aspirate.php

@@ -2,11 +2,16 @@
 
 namespace Mll\LiquidHandlingRobotics\Tecan\BasicCommands;
 
-use Mll\LiquidHandlingRobotics\Tecan\LiquidClass;
+use Mll\LiquidHandlingRobotics\Tecan\LiquidClass\LiquidClass;
 use Mll\LiquidHandlingRobotics\Tecan\Location\Location;
 
 final class Aspirate extends BasicPipettingActionCommand implements Command
 {
+    /**
+     * @param float $volume Floating point values are accepted and do not cause an error,
+     * but they will be rounded before being used. In such cases, it is recommended to use
+     * integer calculations to avoid unexpected results.
+     */
     public function __construct(float $volume, Location $location, LiquidClass $liquidClass)
     {
         $this->volume = $volume;

src/Tecan/BasicCommands/BasicPipettingActionCommand.php

@@ -2,7 +2,7 @@
 
 namespace Mll\LiquidHandlingRobotics\Tecan\BasicCommands;
 
-use Mll\LiquidHandlingRobotics\Tecan\LiquidClass;
+use Mll\LiquidHandlingRobotics\Tecan\LiquidClass\LiquidClass;
 use Mll\LiquidHandlingRobotics\Tecan\Location\Location;
 
 abstract class BasicPipettingActionCommand implements PipettingActionCommand
@@ -17,7 +17,7 @@ abstract class BasicPipettingActionCommand implements PipettingActionCommand
 
     abstract public static function commandLetter(): string;
 
-    public function toString(): string
+    public function formatToString(): string
     {
         return
             static::commandLetter() . ';'
@@ -29,7 +29,7 @@ public function toString(): string
             . $this->volume . ';'
             . $this->liquidClass->name() . ';'
             . ';' // tipType
-            . $this->getTipMask() . ';'
+            . $this->getTipMask()
         ;
     }
 

src/Tecan/BasicCommands/BreakCommand.php

@@ -4,13 +4,8 @@
 
 final class BreakCommand implements Command
 {
-    public static function commandLetter(): string
+    public function formatToString(): string
     {
         return 'B;';
     }
-
-    public function toString(): string
-    {
-        return static::commandLetter();
-    }
 }

src/Tecan/BasicCommands/Command.php

@@ -4,7 +4,5 @@
 
 interface Command
 {
-    public static function commandLetter(): string;
-
-    public function toString(): string;
+    public function formatToString(): string;
 }

src/Tecan/BasicCommands/Dispense.php

@@ -2,12 +2,17 @@
 
 namespace Mll\LiquidHandlingRobotics\Tecan\BasicCommands;
 
-use Mll\LiquidHandlingRobotics\Tecan\LiquidClass;
+use Mll\LiquidHandlingRobotics\Tecan\LiquidClass\LiquidClass;
 use Mll\LiquidHandlingRobotics\Tecan\Location\Location;
 
 final class Dispense extends BasicPipettingActionCommand implements Command
 {
-    public function __construct(int $volume, Location $location, LiquidClass $liquidClass)
+    /**
+     * @param float $volume Floating point values are accepted and do not cause an error,
+     * but they will be rounded before being used. In such cases, it is recommended to use
+     * integer calculations to avoid unexpected results.
+     */
+    public function __construct(float $volume, Location $location, LiquidClass $liquidClass)
     {
         $this->volume = $volume;
         $this->location = $location;

src/Tecan/BasicCommands/Wash.php

@@ -4,13 +4,8 @@
 
 final class Wash implements Command
 {
-    public static function commandLetter(): string
+    public function formatToString(): string
     {
         return 'W;';
     }
-
-    public function toString(): string
-    {
-        return static::commandLetter();
-    }
 }

src/Tecan/CustomCommand/TransferWithAutoWash.php

@@ -5,6 +5,9 @@
 use Mll\LiquidHandlingRobotics\Tecan\BasicCommands\Aspirate;
 use Mll\LiquidHandlingRobotics\Tecan\BasicCommands\Dispense;
 use Mll\LiquidHandlingRobotics\Tecan\BasicCommands\PipettingActionCommand;
+use Mll\LiquidHandlingRobotics\Tecan\BasicCommands\Wash;
+use Mll\LiquidHandlingRobotics\Tecan\LiquidClass\LiquidClass;
+use Mll\LiquidHandlingRobotics\Tecan\Location\Location;
 use Mll\LiquidHandlingRobotics\Tecan\TecanProtocol;
 
 final class TransferWithAutoWash implements PipettingActionCommand
@@ -13,25 +16,20 @@ final class TransferWithAutoWash implements PipettingActionCommand
 
     private Dispense $dispense;
 
-    public function __construct(Aspirate $aspirate, Dispense $dispense)
+    public function __construct(float $volume, LiquidClass $liquidClass, Location $aspirateLocation, Location $dispenseLocation)
     {
-        $this->aspirate = $aspirate;
-        $this->dispense = $dispense;
+        $this->aspirate = new Aspirate($volume, $aspirateLocation, $liquidClass);
+        $this->dispense = new Dispense($volume, $dispenseLocation, $liquidClass);
     }
 
-    public static function commandLetter(): string
-    {
-        return 'W;';
-    }
-
-    public function toString(): string
+    public function formatToString(): string
     {
         return
-            $this->aspirate->toString()
+            $this->aspirate->formatToString()
             . TecanProtocol::WINDOWS_NEW_LINE
-            . $this->dispense->toString()
+            . $this->dispense->formatToString()
             . TecanProtocol::WINDOWS_NEW_LINE
-            . static::commandLetter();
+            . (new Wash())->formatToString();
     }
 
     public function setTipMask(int $tipMask): void

src/Tecan/LiquidClass/CustomLiquidClass.php

@@ -0,0 +1,18 @@
+<?php declare(strict_types=1);
+
+namespace Mll\LiquidHandlingRobotics\Tecan\LiquidClass;
+
+final class CustomLiquidClass implements LiquidClass
+{
+    private string $name;
+
+    public function __construct(string $name)
+    {
+        $this->name = $name;
+    }
+
+    public function name(): string
+    {
+        return $this->name;
+    }
+}

src/Tecan/LiquidClass.php → src/Tecan/LiquidClass/LiquidClass.php

@@ -1,6 +1,6 @@
 <?php declare(strict_types=1);
 
-namespace Mll\LiquidHandlingRobotics\Tecan;
+namespace Mll\LiquidHandlingRobotics\Tecan\LiquidClass;
 
 interface LiquidClass
 {

src/Tecan/LiquidClass/MllLiquidClass.php

@@ -0,0 +1,28 @@
+<?php declare(strict_types=1);
+
+namespace Mll\LiquidHandlingRobotics\Tecan\LiquidClass;
+
+use BenSampo\Enum\Enum;
+
+/**
+ * @method static static DNA_DILUTION()
+ * @method static static DNA_DILUTION_WATER()
+ * @method static static TRANSFER_PCR_PRODUKT()
+ * @method static static TRANSFER_MASTERMIX_MP()
+ * @method static static TRANSFER_TEMPLATE()
+ */
+final class MllLiquidClass extends Enum 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 function name(): string
+    {
+        assert(is_string($this->value));
+
+        return $this->value;
+    }
+}

src/Tecan/Location/BarcodeLocation.php

@@ -2,7 +2,7 @@
 
 namespace Mll\LiquidHandlingRobotics\Tecan\Location;
 
-use Mll\LiquidHandlingRobotics\Tecan\Rack;
+use Mll\LiquidHandlingRobotics\Tecan\Rack\Rack;
 
 final class BarcodeLocation implements Location
 {
@@ -26,9 +26,9 @@ public function position(): ?string
         return null;
     }
 
-    public function rackName(): string
+    public function rackName(): ?string
     {
-        return $this->rack->name();
+        return null;
     }
 
     public function rackType(): string

src/Tecan/Location/PositionLocation.php

@@ -2,7 +2,7 @@
 
 namespace Mll\LiquidHandlingRobotics\Tecan\Location;
 
-use Mll\LiquidHandlingRobotics\Tecan\Rack;
+use Mll\LiquidHandlingRobotics\Tecan\Rack\Rack;
 
 final class PositionLocation implements Location
 {
@@ -28,7 +28,7 @@ public function position(): string
 
     public function rackName(): ?string
     {
-        return null;
+        return $this->rack->name();
     }
 
     public function rackType(): string

src/Tecan/Rack/CustomRack.php

@@ -0,0 +1,26 @@
+<?php declare(strict_types=1);
+
+namespace Mll\LiquidHandlingRobotics\Tecan\Rack;
+
+final class CustomRack implements Rack
+{
+    private string $name;
+
+    private string $type;
+
+    public function __construct(string $name, string $type)
+    {
+        $this->type = $type;
+        $this->name = $name;
+    }
+
+    public function name(): string
+    {
+        return $this->name;
+    }
+
+    public function type(): string
+    {
+        return $this->type;
+    }
+}

src/Tecan/Rack/MllLabWareRack.php

@@ -0,0 +1,63 @@
+<?php declare(strict_types=1);
+
+namespace Mll\LiquidHandlingRobotics\Tecan\Rack;
+
+use BenSampo\Enum\Enum;
+use Exception;
+
+/**
+ * @method static static A()
+ * @method static static MP_CDNA()
+ * @method static static MP_SAMPLE()
+ * @method static static MP_WATER()
+ * @method static static FLUID_X()
+ * @method static static MM()
+ * @method static static DEST_LC()
+ * @method static static DEST_PCR()
+ * @method static static DEST_TAQMAN()
+ */
+final class MllLabWareRack extends Enum 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 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 ' . $this->value);
+        }
+    }
+
+    public function name(): string
+    {
+        assert(is_string($this->value));
+
+        return $this->value;
+    }
+}

src/Tecan/Rack.php → src/Tecan/Rack/Rack.php

@@ -1,6 +1,6 @@
 <?php declare(strict_types=1);
 
-namespace Mll\LiquidHandlingRobotics\Tecan;
+namespace Mll\LiquidHandlingRobotics\Tecan\Rack;
 
 interface Rack
 {