feat: Default missing columns to empty strings instead of throwing in CSVArray::toArray (#48)

- Default missing columns to empty strings instead of throwing in CSVArray::toArray
- Ensure extensibility by using new static over new self everywhere

Author: simbig

CHANGELOG.md

@@ -9,6 +9,13 @@ See [GitHub releases](https://github.com/mll-lab/php-utils/releases).
 
 ## Unreleased
 
+## v5.12.0
+
+### Added
+
+- Default missing columns to empty strings instead of throwing in `CSVArray::toArray`
+- Ensure extensibility by using `new static` over `new self` everywhere
+
 ## v5.11.0
 
 ### Added

phpstan.neon

@@ -9,3 +9,6 @@ parameters:
   # Install https://plugins.jetbrains.com/plugin/7677-awesome-console to make those links clickable
   editorUrl: '%%relFile%%:%%line%%'
   editorUrlTitle: '%%relFile%%:%%line%%'
+  ignoreErrors:
+  # This is a library, so it should be extendable
+  - '#Unsafe usage of new static.*#'

src/CSVArray.php

@@ -7,6 +7,8 @@
 /** @phpstan-type CSVPrimitive bool|float|int|string|\Stringable|null */
 class CSVArray
 {
+    public const DEFAULT_EMPTY_VALUE = '';
+
     /**
      * TODO: fix parsing multiline-content in csv.
      *
@@ -36,12 +38,8 @@ public static function toArray(string $csv, string $delimiter = ';', string $enc
 
             /** @var array<int, string> $entries */
             $entries = str_getcsv($line, $delimiter, $enclosure, $escape);
-            if (count($entries) !== count($columnHeaders)) {
-                throw new \Exception("The number of columns in row {$index} does not match the headers in CSV: {$firstLine}");
-            }
-
             foreach ($columnHeaders as $columnIndex => $columnName) {
-                $result[$index + 1][$columnName] = $entries[$columnIndex];
+                $result[$index + 1][$columnName] = $entries[$columnIndex] ?? self::DEFAULT_EMPTY_VALUE;
             }
         }
 

src/IlluminaSampleSheet/V2/BclConvert/CycleType.php

@@ -18,21 +18,21 @@ public function __construct(string $value)
 
     public static function READ_CYCLE(): self
     {
-        return new self(self::READ_CYCLE);
+        return new static(self::READ_CYCLE);
     }
 
     public static function TRIMMED_CYCLE(): self
     {
-        return new self(self::TRIMMED_CYCLE);
+        return new static(self::TRIMMED_CYCLE);
     }
 
     public static function UMI_CYCLE(): self
     {
-        return new self(self::UMI_CYCLE);
+        return new static(self::UMI_CYCLE);
     }
 
     public static function INDEX_CYCLE(): self
     {
-        return new self(self::INDEX_CYCLE);
+        return new static(self::INDEX_CYCLE);
     }
 }

src/IlluminaSampleSheet/V2/Enums/FastQCompressionFormat.php

@@ -16,11 +16,11 @@ public function __construct(string $value)
 
     public static function GZIP(): self
     {
-        return new self(self::GZIP);
+        return new static(self::GZIP);
     }
 
     public static function DRAGEN(): self
     {
-        return new self(self::DRAGEN);
+        return new static(self::DRAGEN);
     }
 }

src/Microplate/Coordinates.php

@@ -54,7 +54,7 @@ public function __construct(string $row, int $column, CoordinateSystem $coordina
      */
     public static function fromArray(array $coordinates, CoordinateSystem $coordinateSystem): self
     {
-        return new self($coordinates['row'], $coordinates['column'], $coordinateSystem);
+        return new static($coordinates['row'], $coordinates['column'], $coordinateSystem);
     }
 
     /**
@@ -88,7 +88,7 @@ public static function fromString(string $coordinatesString, CoordinateSystem $c
             throw new \InvalidArgumentException("Expected coordinates between {$firstValidExample} and {$lastValidExample} for {$coordinateSystemClass}, got: {$coordinatesString}.");
         }
 
-        return new self($matches[1], (int) $matches[2], $coordinateSystem);
+        return new static($matches[1], (int) $matches[2], $coordinateSystem);
     }
 
     /**
@@ -104,14 +104,14 @@ public static function fromPosition(int $position, FlowDirection $direction, Coo
 
         switch ($direction->value) {
             case FlowDirection::COLUMN:
-                return new self(
+                return new static(
                     $coordinateSystem->rowForColumnFlowPosition($position),
                     $coordinateSystem->columnForColumnFlowPosition($position),
                     $coordinateSystem
                 );
 
             case FlowDirection::ROW:
-                return new self(
+                return new static(
                     $coordinateSystem->rowForRowFlowPosition($position),
                     $coordinateSystem->columnForRowFlowPosition($position),
                     $coordinateSystem

src/Microplate/Enums/FlowDirection.php

@@ -16,11 +16,11 @@ public function __construct(string $value)
 
     public static function ROW(): self
     {
-        return new self(self::ROW);
+        return new static(self::ROW);
     }
 
     public static function COLUMN(): self
     {
-        return new self(self::COLUMN);
+        return new static(self::COLUMN);
     }
 }

src/Tecan/LiquidClass/MLLLiquidClass.php

@@ -19,27 +19,27 @@ public function __construct(string $value)
 
     public static function DNA_DILUTION(): self
     {
-        return new self(self::DNA_DILUTION);
+        return new static(self::DNA_DILUTION);
     }
 
     public static function DNA_DILUTION_WATER(): self
     {
-        return new self(self::DNA_DILUTION_WATER);
+        return new static(self::DNA_DILUTION_WATER);
     }
 
     public static function TRANSFER_PCR_PRODUKT(): self
     {
-        return new self(self::TRANSFER_PCR_PRODUKT);
+        return new static(self::TRANSFER_PCR_PRODUKT);
     }
 
     public static function TRANSFER_MASTERMIX_MP(): self
     {
-        return new self(self::TRANSFER_MASTERMIX_MP);
+        return new static(self::TRANSFER_MASTERMIX_MP);
     }
 
     public static function TRANSFER_TEMPLATE(): self
     {
-        return new self(self::TRANSFER_TEMPLATE);
+        return new static(self::TRANSFER_TEMPLATE);
     }
 
     public function name(): string

src/Tecan/ReagentDistribution/ReagentDistributionDirection.php

@@ -16,11 +16,11 @@ public function __construct(int $value)
 
     public static function LEFT_TO_RIGHT(): self
     {
-        return new self(self::LEFT_TO_RIGHT);
+        return new static(self::LEFT_TO_RIGHT);
     }
 
     public static function RIGHT_TO_LEFT(): self
     {
-        return new self(self::RIGHT_TO_LEFT);
+        return new static(self::RIGHT_TO_LEFT);
     }
 }

src/Tecan/TipMask/TipMask.php

@@ -20,12 +20,12 @@ public function __construct(string $value)
 
     public static function FOUR_TIPS(): self
     {
-        return new self(self::FOUR_TIPS);
+        return new static(self::FOUR_TIPS);
     }
 
     public static function EIGHT_TIPS(): self
     {
-        return new self(self::EIGHT_TIPS);
+        return new static(self::EIGHT_TIPS);
     }
 
     public static function firstTip(): int