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feature: add QxManager sample sheet (#8)
* feature: add `QxManager` sample sheet
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‎CHANGELOG.md

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@@ -9,6 +9,12 @@ See [GitHub releases](https://github.com/mll-lab/php-utils/releases).
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## Unreleased
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## v1.7.0
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### Added
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- Add `QxManagerSampleSheet::toCsvString(...)`
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## v1.6.1
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### Fixed

‎composer.json

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"require": {
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"php": "^7.4 || ^8",
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"illuminate/support": "^8.73 || ^9 || ^10",
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"mll-lab/microplate": "^6",
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"mll-lab/str_putcsv": "^1",
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"thecodingmachine/safe": "^1 || ^2"
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},
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"infection/infection": "^0.26 || ^0.27",
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"jangregor/phpstan-prophecy": "^1",
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"mll-lab/php-cs-fixer-config": "^5",
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"nesbot/carbon": "^2.62.1",
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"phpstan/extension-installer": "^1",
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"phpstan/phpstan": "^1",
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"phpstan/phpstan-deprecation-rules": "^1",

‎src/QxManager/EmptyRow.php

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<?php declare(strict_types=1);
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namespace MLL\Utils\QxManager;
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class EmptyRow
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{
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public function toString(): string
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{
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return implode(QxManagerSampleSheet::DELIMITER, [
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'No',
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...array_fill(0, 16, null),
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]);
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}
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}

‎src/QxManager/FilledRow.php

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<?php declare(strict_types=1);
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namespace MLL\Utils\QxManager;
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class FilledRow
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{
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private string $experimentType;
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private string $supermixName;
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private string $assayType;
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private string $targetType;
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private string $plot;
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private string $targetName;
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private string $signalCh1;
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private string $signalCh2;
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private string $sampleDescription1;
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private ?string $sampleDescription2;
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private ?string $sampleDescription3;
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private ?string $sampleDescription4;
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private string $sampleType;
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private ?int $referenceCopies;
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private ?string $wellNotes;
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private ?string $rdqConversionFactor;
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public function __construct(
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string $sampleDescription1,
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?string $sampleDescription2,
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?string $sampleDescription3,
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?string $sampleDescription4,
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string $sampleType,
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string $experimentType,
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string $supermixName,
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string $assayType,
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string $targetType,
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string $plot,
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string $targetName,
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string $signalCh1,
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string $signalCh2,
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int $referenceCopies = null,
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string $wellNotes = null,
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string $rdqConversionFactor = null
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) {
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$this->targetName = $targetName;
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$this->signalCh1 = $signalCh1;
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$this->signalCh2 = $signalCh2;
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$this->sampleDescription1 = $sampleDescription1;
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$this->sampleDescription2 = $sampleDescription2;
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$this->sampleDescription3 = $sampleDescription3;
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$this->sampleDescription4 = $sampleDescription4;
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$this->sampleType = $sampleType;
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$this->experimentType = $experimentType;
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$this->supermixName = $supermixName;
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$this->assayType = $assayType;
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$this->targetType = $targetType;
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$this->plot = $plot;
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$this->referenceCopies = $referenceCopies;
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$this->wellNotes = $wellNotes;
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$this->rdqConversionFactor = $rdqConversionFactor;
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}
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public function toString(): string
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{
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return implode(QxManagerSampleSheet::DELIMITER, [
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'Yes',
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$this->experimentType,
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$this->sampleDescription1,
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$this->sampleDescription2,
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$this->sampleDescription3,
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$this->sampleDescription4,
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$this->sampleType,
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$this->supermixName,
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$this->assayType,
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$this->targetName,
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$this->targetType,
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$this->signalCh1,
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$this->signalCh2,
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$this->referenceCopies,
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$this->wellNotes,
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$this->plot,
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$this->rdqConversionFactor,
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]);
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}
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}

‎src/QxManager/FilledWell.php

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<?php declare(strict_types=1);
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namespace MLL\Utils\QxManager;
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use Mll\Microplate\Coordinates;
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use Mll\Microplate\CoordinateSystem96Well;
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class FilledWell
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{
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private FilledRow $famRow;
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private FilledRow $hexRow;
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public function __construct(FilledRow $famRow, FilledRow $hexRow)
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{
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$this->famRow = $famRow;
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$this->hexRow = $hexRow;
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}
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/** @param Coordinates<CoordinateSystem96Well> $coordinates */
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public function toString(Coordinates $coordinates): string
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{
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return $coordinates->toPaddedString() . QxManagerSampleSheet::DELIMITER . $this->famRow->toString() . QxManagerSampleSheet::EOL
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. $coordinates->toPaddedString() . QxManagerSampleSheet::DELIMITER . $this->hexRow->toString();
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}
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}

‎src/QxManager/QxManagerSampleSheet.php

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<?php declare(strict_types=1);
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namespace MLL\Utils\QxManager;
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use Carbon\CarbonInterface;
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use Mll\Microplate\Coordinates;
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use Mll\Microplate\CoordinateSystem96Well;
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use Mll\Microplate\Enums\FlowDirection;
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use Mll\Microplate\Microplate;
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use MLL\Utils\StringUtil;
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class QxManagerSampleSheet
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{
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public const EOL = "\r\n";
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public const DELIMITER = ',';
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/** @param Microplate<FilledWell, CoordinateSystem96Well> $microplate */
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public function toCsvString(Microplate $microplate, CarbonInterface $createdDate): string
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{
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$header = StringUtil::normalizeLineEndings(
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<<<CSV
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ddplate - DO NOT MODIFY THIS LINE,Version=1,ApplicationName=QX Manager Standard Edition,ApplicationVersion=2.0.0.665,ApplicationEdition=ResearchEmbedded,User=\QX User,CreatedDate={$createdDate->format('n/j/Y g:i:s A')},
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PlateSize=GCR96
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PlateNotes=
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Well,Perform Droplet Reading,ExperimentType,Sample description 1,Sample description 2,Sample description 3,Sample description 4,SampleType,SupermixName,AssayType,TargetName,TargetType,Signal Ch1,Signal Ch2,Reference Copies,Well Notes,Plot?,RdqConversionFactor
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CSV
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);
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return $header . $microplate->sortedWells(FlowDirection::ROW())
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->map(
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/** @param FilledWell|null $well */
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function ($well, string $coordinateString) use ($microplate): string {
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$coordinates = Coordinates::fromString($coordinateString, $microplate->coordinateSystem);
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if ($well instanceof FilledWell) {
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return $well->toString($coordinates);
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}
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return $coordinates->toPaddedString() . QxManagerSampleSheet::DELIMITER . (new EmptyRow())->toString();
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}
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)
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->join(self::EOL) . self::EOL;
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}
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}

‎tests/CSVArrayTest.php

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<?php declare(strict_types=1);
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namespace MLL\Utils\Tests\Unit;
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namespace MLL\Utils\Tests;
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use MLL\Utils\CSVArray;
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use PHPUnit\Framework\TestCase;

‎tests/QxManager/EmptyRowTest.php

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<?php declare(strict_types=1);
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namespace MLL\Utils\Tests\QxManager;
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use MLL\Utils\QxManager\EmptyRow;
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use PHPUnit\Framework\TestCase;
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final class EmptyRowTest extends TestCase
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{
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public function testToString(): void
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{
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self::assertSame('No,,,,,,,,,,,,,,,,', (new EmptyRow())->toString());
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}
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}

‎tests/QxManager/FilledRowTest.php

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<?php declare(strict_types=1);
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namespace MLL\Utils\Tests\Unit\QxManager;
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use MLL\Utils\QxManager\FilledRow;
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use PHPUnit\Framework\TestCase;
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final class FilledRowTest extends TestCase
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{
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public function testToString(): void
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{
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$filledRow = new FilledRow(
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'Sample 1',
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'Sample 2',
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null,
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null,
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'Sample Type',
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'Experiment Type',
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'Supermix Name',
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'Assay Type',
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'Target Type',
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'Plot',
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'Target Name',
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'Signal Ch1',
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'Signal Ch2',
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1000,
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'Well Notes',
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'RDQ Conversion Factor'
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);
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$expectedString = 'Yes,Experiment Type,Sample 1,Sample 2,,,Sample Type,Supermix Name,Assay Type,Target Name,Target Type,Signal Ch1,Signal Ch2,1000,Well Notes,Plot,RDQ Conversion Factor';
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self::assertSame($expectedString, $filledRow->toString());
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}
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public function testToStringWithNullValues(): void
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{
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$filledRow = new FilledRow(
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'Sample 1',
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null,
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null,
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null,
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'Sample Type',
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'Experiment Type',
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'Supermix Name',
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'Assay Type',
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'Target Type',
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'Plot',
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'Target Name',
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'Signal Ch1',
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'Signal Ch2'
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);
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$expectedString = 'Yes,Experiment Type,Sample 1,,,,Sample Type,Supermix Name,Assay Type,Target Name,Target Type,Signal Ch1,Signal Ch2,,,Plot,';
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self::assertSame($expectedString, $filledRow->toString());
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}
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}

‎tests/QxManager/FilledWellTest.php

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<?php declare(strict_types=1);
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namespace MLL\Utils\Tests\Unit\QxManager;
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use Mll\Microplate\Coordinates;
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use Mll\Microplate\CoordinateSystem96Well;
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use MLL\Utils\QxManager\FilledRow;
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use MLL\Utils\QxManager\FilledWell;
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use PHPUnit\Framework\TestCase;
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final class FilledWellTest extends TestCase
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{
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public function testToString(): void
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{
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$coordinates = Coordinates::fromString('C9', new CoordinateSystem96Well());
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$famRowMock = $this->createMock(FilledRow::class);
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$famRowMock->expects(self::once())
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->method('toString')
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->willReturn('FAM Row String');
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$hexRowMock = $this->createMock(FilledRow::class);
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$hexRowMock->expects(self::once())
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->method('toString')
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->willReturn('HEX Row String');
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$filledWell = new FilledWell($famRowMock, $hexRowMock);
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self::assertSame("C09,FAM Row String\r\nC09,HEX Row String", $filledWell->toString($coordinates));
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}
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}

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