Rack to object with positions

CHANGELOG.md

@@ -9,6 +9,19 @@ See [GitHub releases](https://github.com/mll-lab/php-utils/releases).
 
 ## Unreleased
 
+## v4.0.0
+
+### Added
+
+- Add specific class for each `MLLLabWareRack`-type that includes a `positions`-Collection
+
+### Changed
+
+- Breaking Change: Delete class `MLLLabWareRack`
+- Breaking Change: Delete class `CustomRack`
+- Breaking Change: Add method `positionCount` to interface `Rack`
+- Breaking Change: Limit the usage of `BarcodeLocation` to objects implementing `ScannedRack`
+
 ## v3.2.0
 
 ### Added

src/Tecan/BasicCommands/AspirateAndDispenseParameters.php

@@ -22,13 +22,10 @@ public function __construct(Rack $rack, int $startPosition, int $endPosition)
     /** Serializes the aspirate and dispense parameters as part of a reagent distribution according the gwl file format. */
     public function toString(): string
     {
-        return implode(
-            ';',
-            [
-                $this->rack->toString(),
-                $this->startPosition,
-                $this->endPosition,
-            ]
-        );
+        return implode(';', [
+            $this->rack->toString(),
+            $this->startPosition,
+            $this->endPosition,
+        ]);
     }
 }

src/Tecan/BasicCommands/BasicPipettingActionCommand.php

@@ -19,17 +19,14 @@ abstract public static function commandLetter(): string;
 
     public function toString(): string
     {
-        return implode(
-            ';',
-            [
-                static::commandLetter(),
-                $this->location->toString(),
-                $this->volume,
-                $this->liquidClass->name(),
-                null, // tipType
-                $this->getTipMask(),
-            ]
-        );
+        return implode(';', [
+            static::commandLetter(),
+            $this->location->toString(),
+            $this->volume,
+            $this->liquidClass->name(),
+            null, // tipType
+            $this->getTipMask(),
+        ]);
     }
 
     protected function getTipMask(): string

src/Tecan/BasicCommands/ReagentDistribution.php

@@ -52,20 +52,17 @@ public function __construct(
 
     public function toString(): string
     {
-        return implode(
-            ';',
-            [
-                'R',
-                $this->source->toString(),
-                $this->target->toString(),
-                $this->volume,
-                $this->liquidClass->name(),
-                $this->numberOfDitiReuses,
-                $this->numberOfMultiDisp,
-                $this->direction->value,
-                $this->excludedWells(),
-            ]
-        );
+        return implode(';', [
+            'R',
+            $this->source->toString(),
+            $this->target->toString(),
+            $this->volume,
+            $this->liquidClass->name(),
+            $this->numberOfDitiReuses,
+            $this->numberOfMultiDisp,
+            $this->direction->value,
+            $this->excludedWells(),
+        ]);
     }
 
     private function excludedWells(): string

src/Tecan/Location/BarcodeLocation.php

@@ -2,15 +2,15 @@
 
 namespace MLL\Utils\Tecan\Location;
 
-use MLL\Utils\Tecan\Rack\Rack;
+use MLL\Utils\Tecan\Rack\ScannedRack;
 
 class BarcodeLocation implements Location
 {
     private string $barcode;
 
-    private Rack $rack;
+    private ScannedRack $rack;
 
-    public function __construct(string $barcode, Rack $rack)
+    public function __construct(string $barcode, ScannedRack $rack)
     {
         $this->barcode = $barcode;
         $this->rack = $rack;
@@ -43,15 +43,12 @@ public function rackID(): ?string
 
     public function toString(): string
     {
-        return implode(
-            ';',
-            [
-                $this->rackName(),
-                $this->rackID(),
-                $this->rackType(),
-                $this->position(),
-                $this->tubeID(),
-            ]
-        );
+        return implode(';', [
+            $this->rackName(),
+            $this->rackID(),
+            $this->rackType(),
+            $this->position(),
+            $this->tubeID(),
+        ]);
     }
 }

src/Tecan/Location/PositionLocation.php

@@ -43,15 +43,12 @@ public function rackID(): ?string
 
     public function toString(): string
     {
-        return implode(
-            ';',
-            [
-                $this->rackName(),
-                $this->rackID(),
-                $this->rackType(),
-                $this->position(),
-                $this->tubeID(),
-            ]
-        );
+        return implode(';', [
+            $this->rackName(),
+            $this->rackID(),
+            $this->rackType(),
+            $this->position(),
+            $this->tubeID(),
+        ]);
     }
 }

src/Tecan/Rack/AlublockA.php

@@ -0,0 +1,21 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Tecan\Rack;
+
+class AlublockA extends BaseRack
+{
+    public function type(): string
+    {
+        return 'Eppis 24x0.5 ml Cooled';
+    }
+
+    public function name(): string
+    {
+        return 'A';
+    }
+
+    public function positionCount(): int
+    {
+        return 24;
+    }
+}

src/Tecan/Rack/BaseRack.php

@@ -0,0 +1,85 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Tecan\Rack;
+
+use Illuminate\Support\Collection;
+
+abstract class BaseRack implements Rack
+{
+    public const EMPTY_POSITION = null;
+
+    /** @var Collection<int, mixed> */
+    public Collection $positions;
+
+    public function __construct()
+    {
+        $this->positions = Collection::times($this->positionCount(), fn () => self::EMPTY_POSITION)
+            ->mapWithKeys(fn ($content, int $position): array => [$position + 1 => $content]);
+    }
+
+    public function id(): ?string
+    {
+        return null;
+    }
+
+    public function toString(): string
+    {
+        return implode(';', [
+            $this->name(),
+            $this->id(),
+            $this->type(),
+        ]);
+    }
+
+    /** @param mixed $content Anything goes, null is considered empty */
+    public function assignFirstEmptyPosition($content): int
+    {
+        return $this->assignPosition($content, $this->findFirstEmptyPosition());
+    }
+
+    /** @param mixed $content Anything goes, null is considered empty */
+    public function assignLastEmptyPosition($content): int
+    {
+        return $this->assignPosition($content, $this->findLastEmptyPosition());
+    }
+
+    public function findFirstEmptyPosition(): int
+    {
+        $firstEmpty = $this->positions
+            ->filter(fn ($content): bool => $content === self::EMPTY_POSITION)
+            ->keys()
+            ->first();
+
+        if ($firstEmpty === null) {
+            throw new NoEmptyPositionOnRack();
+        }
+
+        return $firstEmpty;
+    }
+
+    public function findLastEmptyPosition(): int
+    {
+        $lastEmpty = $this->positions
+            ->filter(fn ($content): bool => $content === self::EMPTY_POSITION)
+            ->keys()
+            ->last();
+
+        if ($lastEmpty === null) {
+            throw new NoEmptyPositionOnRack();
+        }
+
+        return $lastEmpty;
+    }
+
+    /** @param mixed $content Anything goes, null is considered empty */
+    public function assignPosition($content, int $position): int
+    {
+        if (! $this->positions->has($position)) {
+            throw new InvalidPositionOnRack($position, $this);
+        }
+
+        $this->positions[$position] = $content;
+
+        return $position;
+    }
+}

src/Tecan/Rack/DestLC.php

@@ -0,0 +1,21 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Tecan\Rack;
+
+class DestLC extends BaseRack
+{
+    public function type(): string
+    {
+        return '96 Well MP LightCycler480';
+    }
+
+    public function name(): string
+    {
+        return 'DestLC';
+    }
+
+    public function positionCount(): int
+    {
+        return 96;
+    }
+}

src/Tecan/Rack/DestPCR.php

@@ -0,0 +1,21 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Tecan\Rack;
+
+class DestPCR extends BaseRack
+{
+    public function type(): string
+    {
+        return '96 Well PCR ABI semi-skirted';
+    }
+
+    public function name(): string
+    {
+        return 'DestPCR';
+    }
+
+    public function positionCount(): int
+    {
+        return 96;
+    }
+}

src/Tecan/Rack/DestTaqMan.php

@@ -0,0 +1,21 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Tecan\Rack;
+
+class DestTaqMan extends BaseRack
+{
+    public function type(): string
+    {
+        return '96 Well PCR TaqMan';
+    }
+
+    public function name(): string
+    {
+        return 'DestTaqMan';
+    }
+
+    public function positionCount(): int
+    {
+        return 96;
+    }
+}