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feat: QiaxcelImport allows to create an import file for a Qiaxcel device from Qiagen
feat: QiaxcelImport allows to create an import file for a Qiaxcel device from Qiagen
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‎.github/CONTRIBUTING.md‎

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‎CONTRIBUTING.md‎

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# Commit Message Convention
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# CONTRIBUTING
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This project uses [Conventional Commits](https://conventionalcommits.org/) for automated version management and release notes generation.
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We are using [GitHub Actions](https://github.com/features/actions) as a continuous integration system.
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## Format
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For details, see [`workflows`](.github/workflows).
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## Code Style
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We are using [`friendsofphp/php-cs-fixer`](https://github.com/friendsofphp/php-cs-fixer) to automatically format the code.
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Run
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```bash
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make fix
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```
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to automatically format the code.
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## Static Code Analysis
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We are using [`phpstan/phpstan`](https://github.com/phpstan/phpstan) to statically analyze the code.
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Run
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```bash
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make stan
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```
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to run a static code analysis.
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## Tests
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We are using [`phpunit/phpunit`](https://github.com/sebastianbergmann/phpunit) to drive the development.
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Run
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```bash
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make test
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```
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to run all the tests.
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## Extra lazy?
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Run
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```bash
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make
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```
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to enforce coding standards, perform a static code analysis, and run tests!
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:bulb: Run
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```bash
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make help
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```
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to display a list of available targets with corresponding descriptions.
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## Commit Message Convention
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This project uses [Conventional Commits](https://conventionalcommits.org) for automated version management and release notes generation.
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### Format
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```
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<type>[optional scope]: <description>
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[optional footer(s)]
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```
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## Types
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### Types
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- **feat**: A new feature (triggers a minor version bump)
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- **fix**: A bug fix (triggers a patch version bump)
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- **test**: Adding missing tests or correcting existing tests
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- **chore**: Changes to the build process or auxiliary tools and libraries
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## Breaking Changes
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### Breaking Changes
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Add `BREAKING CHANGE:` in the footer or append `!` after the type/scope to indicate breaking changes (triggers a major version bump).
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## Examples
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### Examples
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```
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feat: add support for PHP 8.4
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BREAKING CHANGE: PHP 7.4 is no longer supported
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```
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## Scopes (optional)
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### Scopes (optional)
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You can use scopes to specify which part of the codebase is affected:
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- `csv`: CSV-related functionality

‎Makefile‎

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vendor/bin/phpunit --cache-directory=.build/phpunit
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vendor: composer.json
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composer validate --strict
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composer update
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composer validate --strict
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composer normalize

‎composer.json‎

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"mll-lab/graphql-php-scalars": "^6.4",
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"mll-lab/php-cs-fixer-config": "^5.10",
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"orchestra/testbench": "^6.47.1 || ^7.52 || ^8.33 || ^9.11 || ^10",
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"phpoffice/phpspreadsheet": "^1.2 || ^5.1",
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"phpstan/extension-installer": "^1",
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"phpstan/phpstan": "^1.8.11 || ^2.1.6",
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"phpstan/phpstan-deprecation-rules": "^1 || ^2.0.1",
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},
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"suggest": {
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"mll-lab/graphql-php-scalars": "To use the provided scalar types for GraphQL servers, requires version ^6.3",
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"phpoffice/phpspreadsheet": "Required if using QiaxcelImport",
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"spaze/phpstan-disallowed-calls": "Required when using the PHPStan configuration from rules.neon directly or through the extension installer"
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},
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"autoload": {

‎src/Microplate/AbstractMicroplate.php‎

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{
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return $this->wells()->sortBy(
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/** @param TWell $content */
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function ($content, string $key) use ($flowDirection): string { /** @phpstan-ignore missingType.parameter (is in template context) */
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function ($content, string $key) use ($flowDirection): string { // @phpstan-ignore missingType.parameter (is in template context)
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switch ($flowDirection->value) {
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case FlowDirection::ROW:
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return $key;
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/** @return Collection<string, null> */
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public function freeWells(): Collection
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{
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return $this->wells()->filter(
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return $this->wells()->filter( // @phpstan-ignore return.type (generic wrongly interpreted)
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/** @param TWell $content */
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static fn ($content): bool => $content === self::EMPTY_WELL /** @phpstan-ignore missingType.parameter (is in template context) */
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static fn ($content): bool => $content === self::EMPTY_WELL // @phpstan-ignore missingType.parameter (is in template context)
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);
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}
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{
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return $this->wells()->filter(
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/** @param TWell $content */
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static fn ($content): bool => $content !== self::EMPTY_WELL /** @phpstan-ignore missingType.parameter (is in template context) */
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static fn ($content): bool => $content !== self::EMPTY_WELL // @phpstan-ignore missingType.parameter (is in template context)
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);
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}
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/** @return callable(TWell|null $content, string $coordinatesString): bool */
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public function matchRow(string $row): callable
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{
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return function ($content, string $coordinatesString) use ($row): bool { /** @phpstan-ignore missingType.parameter (is in template context) */
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return function ($content, string $coordinatesString) use ($row): bool { // @phpstan-ignore missingType.parameter (is in template context)
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$coordinates = Coordinates::fromString($coordinatesString, $this->coordinateSystem);
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return $coordinates->row === $row;
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/** @return callable(TWell|null $content, string $coordinatesString): bool */
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public function matchColumn(int $column): callable
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{
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return function ($content, string $coordinatesString) use ($column): bool { /** @phpstan-ignore missingType.parameter (is in template context) */
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return function ($content, string $coordinatesString) use ($column): bool { // @phpstan-ignore missingType.parameter (is in template context)
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$coordinates = Coordinates::fromString($coordinatesString, $this->coordinateSystem);
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public function toWellWithCoordinatesMapper(): callable
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return fn ($content, string $coordinatesString): WellWithCoordinates => new WellWithCoordinates( /** @phpstan-ignore missingType.parameter (is in template context) */
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return fn ($content, string $coordinatesString): WellWithCoordinates => new WellWithCoordinates( // @phpstan-ignore missingType.parameter (is in template context)
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$content,
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Coordinates::fromString($coordinatesString, $this->coordinateSystem)
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);

‎src/Qiaxcel/QiaxcelImport.php‎

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<?php declare(strict_types=1);
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namespace MLL\Utils\Qiaxcel;
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use Illuminate\Support\Str;
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use PhpOffice\PhpSpreadsheet\Cell\Cell;
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use PhpOffice\PhpSpreadsheet\IOFactory;
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use PhpOffice\PhpSpreadsheet\Spreadsheet;
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class QiaxcelImport
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{
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public string $fileName;
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/** @var list<string> */
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protected array $entries;
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public string $valueForEmptyCell;
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/** @param list<string> $entries */
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public function __construct(
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string $fileName,
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array $entries,
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string $valueForEmptyCell = 'Leer'
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) {
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$this->fileName = $fileName;
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$this->entries = $entries;
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$this->valueForEmptyCell = $valueForEmptyCell;
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}
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public function generate(): SpreadSheet
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{
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$sampleSheetData = [];
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foreach (array_chunk($this->entries, 12) as $entryChunks) {
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$sampleSheetRow = [];
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foreach ($entryChunks as $entryChunk) {
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$sampleSheetRow[] = Str::substr($entryChunk, 0, 36); // Maximum 36 characters in Qiaxcel
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}
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$sampleSheetData[] = $sampleSheetRow;
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}
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$spreadsheet = new Spreadsheet();
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$spreadsheet->getActiveSheet()->fromArray($sampleSheetData);
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$this->fillEmptyCells($spreadsheet);
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return $spreadsheet;
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}
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public function generateAndSaveImportFile(): void
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{
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$spreadsheet = $this->generate();
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self::saveSampleSheet($this->fileName, $spreadsheet);
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}
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public static function saveSampleSheet(string $fileName, Spreadsheet $spreadsheet): void
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{
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$writer = IOFactory::createWriter($spreadsheet, 'Xlsx');
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$writer->save($fileName);
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}
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private function fillEmptyCells(Spreadsheet &$spreadsheet): void
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{
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foreach (range(1, 8) as $number) {
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foreach (range('A', 'L') as $letter) {
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$cell = $spreadsheet->getActiveSheet()->getCell("{$letter}{$number}");
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if ($cell instanceof Cell) { // @phpstan-ignore instanceof.alwaysTrue
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$value = $cell->getValue();
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if ($value === '' || $value === null) {
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$cell->setValue($this->valueForEmptyCell);
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}
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}
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}
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}
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}
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}

‎tests/Qiaxcel/QiaxcelImportTest.php‎

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<?php declare(strict_types=1);
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namespace MLL\Utils\Tests\Qiaxcel;
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use MLL\Utils\Qiaxcel\QiaxcelImport;
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use PHPUnit\Framework\TestCase;
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final class QiaxcelImportTest extends TestCase
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{
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public function testGenerate(): void
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{
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$entries = [];
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foreach (range(1, 13) as $i) {
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$entries[] = "Test-Eintrag {$i}";
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}
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$newQiaxcelImport = new QiaxcelImport('test.xlsx', $entries);
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$spreadsheet = $newQiaxcelImport->generate();
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$worksheet = $spreadsheet->getActiveSheet();
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$cellA1 = $worksheet->getCell('A1');
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self::assertNotNull($cellA1); // @phpstan-ignore staticMethod.alreadyNarrowedType
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self::assertEquals('Test-Eintrag 1', $cellA1->getValue());
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$cellL1 = $worksheet->getCell('L1');
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self::assertNotNull($cellL1); // @phpstan-ignore staticMethod.alreadyNarrowedType
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self::assertSame('Test-Eintrag 12', $cellL1->getValue());
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$cellA2 = $worksheet->getCell('A2');
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self::assertNotNull($cellA2); // @phpstan-ignore staticMethod.alreadyNarrowedType
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self::assertSame('Test-Eintrag 13', $cellA2->getValue());
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$cellB2 = $worksheet->getCell('B2');
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self::assertNotNull($cellB2); // @phpstan-ignore staticMethod.alreadyNarrowedType
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self::assertSame('Leer', $cellB2->getValue());
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$cellL8 = $worksheet->getCell('L8');
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self::assertNotNull($cellL8); // @phpstan-ignore staticMethod.alreadyNarrowedType
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self::assertSame('Leer', $cellL8->getValue());
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}
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}

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