From 57fccb68b5564bce605d44328cd97b4c8e2c0544 Mon Sep 17 00:00:00 2001
From: Simon Bigelmayr <simon.bigelmayr@mll.com>
Date: Wed, 18 Sep 2024 14:32:27 +0200
Subject: [PATCH] feat: Add `Mix`-command to tecan worklist
---
phpunit.xml | 3 +
src/Tecan/AdvancedCommands/Mix.php | 69 +++++++++++
src/Tecan/AdvancedCommands/Str.php | 12 ++
src/Tecan/AdvancedCommands/Volumes.php | 68 +++++++++++
src/Tecan/AdvancedCommands/WellSelection.php | 84 ++++++++++++++
tests/Tecan/AdvancedCommands/MixTest.php | 43 +++++++
tests/Tecan/AdvancedCommands/VolumesTest.php | 47 ++++++++
.../AdvancedCommands/WellSelectionTest.php | 109 ++++++++++++++++++
8 files changed, 435 insertions(+)
create mode 100644 src/Tecan/AdvancedCommands/Mix.php
create mode 100644 src/Tecan/AdvancedCommands/Str.php
create mode 100644 src/Tecan/AdvancedCommands/Volumes.php
create mode 100644 src/Tecan/AdvancedCommands/WellSelection.php
create mode 100644 tests/Tecan/AdvancedCommands/MixTest.php
create mode 100644 tests/Tecan/AdvancedCommands/VolumesTest.php
create mode 100644 tests/Tecan/AdvancedCommands/WellSelectionTest.php
diff --git a/phpunit.xml b/phpunit.xml
index 2b57a08..acb7da4 100644
--- a/phpunit.xml
+++ b/phpunit.xml
@@ -3,6 +3,9 @@
xsi:noNamespaceSchemaLocation="vendor/phpunit/phpunit/phpunit.xsd"
bootstrap="vendor/autoload.php"
colors="true"
+ displayDetailsOnTestsThatTriggerWarnings="true"
+ displayDetailsOnTestsThatTriggerDeprecations="true"
+ displayDetailsOnPhpunitDeprecations="true"
>
<source>
<include>
diff --git a/src/Tecan/AdvancedCommands/Mix.php b/src/Tecan/AdvancedCommands/Mix.php
new file mode 100644
index 0000000..92382bf
--- /dev/null
+++ b/src/Tecan/AdvancedCommands/Mix.php
@@ -0,0 +1,69 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Tecan\AdvancedCommands;
+
+use MLL\Utils\Tecan\BasicCommands\Command;
+use MLL\Utils\Tecan\TecanException;
+
+class Mix extends Command
+{
+ private string $liquidClass;
+
+ private Volumes $volumes;
+
+ private int $grid;
+
+ private int $site;
+
+ private int $spacing;
+
+ private string $wellSelection;
+
+ private int $cycles;
+
+ private int $noOfLoopOptions = 0;
+
+ private int $arm;
+
+ public function __construct(
+ string $liquidClass,
+ Volumes $volumes,
+ int $grid,
+ int $site,
+ int $spacing,
+ WellSelection $wellSelection,
+ int $cycles,
+ int $arm = 0
+ ) {
+ $this->liquidClass = $liquidClass;
+ $this->volumes = $volumes;
+ $this->grid = $grid;
+ $this->site = $site;
+ $this->spacing = $spacing;
+ $this->wellSelection = $wellSelection->toString();
+ $this->cycles = $cycles;
+ $this->arm = $arm;
+ }
+
+ public function toString(): string
+ {
+ if ($this->noOfLoopOptions !== 0) {
+ throw new TecanException('Loop options are not yet supported');
+ }
+
+ $mixParameters = implode(',', [
+ $this->volumes->tipMask(),
+ Str::encloseWithDoubleQuotes($this->liquidClass),
+ $this->volumes->volumeString(),
+ $this->grid,
+ $this->site,
+ $this->spacing,
+ Str::encloseWithDoubleQuotes($this->wellSelection),
+ $this->cycles,
+ $this->noOfLoopOptions,
+ $this->arm,
+ ]);
+
+ return "Mix({$mixParameters})";
+ }
+}
diff --git a/src/Tecan/AdvancedCommands/Str.php b/src/Tecan/AdvancedCommands/Str.php
new file mode 100644
index 0000000..ba4f17f
--- /dev/null
+++ b/src/Tecan/AdvancedCommands/Str.php
@@ -0,0 +1,12 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Tecan\AdvancedCommands;
+
+class Str
+{
+ /** @param int|float|string $value */
+ public static function encloseWithDoubleQuotes($value): string
+ {
+ return "\"{$value}\"";
+ }
+}
diff --git a/src/Tecan/AdvancedCommands/Volumes.php b/src/Tecan/AdvancedCommands/Volumes.php
new file mode 100644
index 0000000..66f3088
--- /dev/null
+++ b/src/Tecan/AdvancedCommands/Volumes.php
@@ -0,0 +1,68 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Tecan\AdvancedCommands;
+
+class Volumes
+{
+ /** @var array{
+ * 0:float|int,
+ * 1:float|int,
+ * 2:float|int,
+ * 3:float|int,
+ * 4:float|int,
+ * 5:float|int,
+ * 6:float|int,
+ * 7:float|int,
+ * 8:float|int,
+ * 9:float|int,
+ * 10:float|int,
+ * 11:float|int,
+ * } */
+ private array $volumes;
+
+ /** @param array{
+ * 0:float|int,
+ * 1:float|int,
+ * 2:float|int,
+ * 3:float|int,
+ * 4:float|int,
+ * 5:float|int,
+ * 6:float|int,
+ * 7:float|int,
+ * 8:float|int,
+ * 9:float|int,
+ * 10:float|int,
+ * 11:float|int,
+ * } $volumes
+ */
+ public function __construct(array $volumes)
+ {
+ $this->volumes = $volumes;
+ }
+
+ public function volumeString(): string
+ {
+ $volumesArray = array_map(fn ($volume): string => $volume === 0.0 || $volume === 0
+ ? (string) $volume
+ : Str::encloseWithDoubleQuotes($volume), $this->volumes);
+
+ return implode(',', $volumesArray);
+ }
+
+ /**
+ * Generate tip bitmask from volumes.
+ *
+ * @return int Bitmask representing the tip mask
+ */
+ public function tipMask()
+ {
+ $bitmask = 0;
+ foreach ($this->volumes as $index => $volume) {
+ if ($volume > 0) {
+ $bitmask |= (1 << $index);
+ }
+ }
+
+ return $bitmask;
+ }
+}
diff --git a/src/Tecan/AdvancedCommands/WellSelection.php b/src/Tecan/AdvancedCommands/WellSelection.php
new file mode 100644
index 0000000..a6b3c7f
--- /dev/null
+++ b/src/Tecan/AdvancedCommands/WellSelection.php
@@ -0,0 +1,84 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Tecan\AdvancedCommands;
+
+class WellSelection
+{
+ public const MAX_ITEMS_PER_SUBARRAY = 7;
+
+ private int $xWells;
+
+ private int $yWells;
+
+ /** @var array<int, array<int, int>> */
+ private array $selFlag;
+
+ /** @param array<int> $positions */
+ public function __construct(int $xWells, int $yWells, array $positions)
+ {
+ $this->xWells = $xWells;
+ $this->yWells = $yWells;
+ $this->selFlag = WellSelection::transformPositionsToSelFlag($positions, $xWells, $yWells);
+ }
+
+ public function toString(): string
+ {
+ if ($this->xWells === 0 || $this->yWells === 0) {
+ return '0000';
+ }
+ $selString = sprintf('%02X%02X', $this->xWells, $this->yWells);
+
+ $bitCounter = 0;
+ $bitMask = 0;
+
+ $selFlag = $this->selFlag;
+
+ for ($x = 0; $x < $this->xWells; ++$x) {
+ for ($y = 0; $y < $this->yWells; ++$y) {
+ if (isset($selFlag[$x][$y]) && ($selFlag[$x][$y] & 1) !== 0) {
+ $bitMask |= (1 << $bitCounter);
+ }
+ if (++$bitCounter > 6) {
+ $selString .= chr(ord('0') + $bitMask);
+ $bitCounter = 0;
+ $bitMask = 0;
+ }
+ }
+ }
+
+ if ($bitCounter > 0) {
+ $selString .= chr(ord('0') + $bitMask);
+ }
+
+ return $selString;
+ }
+
+ /**
+ * @param array<int> $positions
+ *
+ * @return array<int, array<int, int>>
+ */
+ public static function transformPositionsToSelFlag(array $positions, int $xWells, int $yWells): array
+ {
+ // Calculate the total number of wells
+ $totalWells = $xWells * $yWells;
+
+ // Calculate the number of sub-arrays needed, each with 7 elements
+ $numSubArrays = (int) ceil($totalWells / self::MAX_ITEMS_PER_SUBARRAY);
+
+ // Initialize the selFlag array with zeros
+ $selFlag = array_fill(0, $numSubArrays, array_fill(0, self::MAX_ITEMS_PER_SUBARRAY, 0));
+
+ // Iterate over the positions and set the corresponding selFlag positions to 1
+ foreach ($positions as $position) {
+ $index = $position - 1;
+ $subArrayIndex = intdiv($index, self::MAX_ITEMS_PER_SUBARRAY);
+ $bitIndex = $index % self::MAX_ITEMS_PER_SUBARRAY;
+ if ($subArrayIndex < $numSubArrays) {
+ $selFlag[$subArrayIndex][$bitIndex] = 1;
+ }
+ }
+
+ return $selFlag;
+ }
+}
diff --git a/tests/Tecan/AdvancedCommands/MixTest.php b/tests/Tecan/AdvancedCommands/MixTest.php
new file mode 100644
index 0000000..5d29123
--- /dev/null
+++ b/tests/Tecan/AdvancedCommands/MixTest.php
@@ -0,0 +1,43 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Tests\Tecan\AdvancedCommands;
+
+use MLL\Utils\Tecan\AdvancedCommands\Mix;
+use MLL\Utils\Tecan\AdvancedCommands\Volumes;
+use MLL\Utils\Tecan\AdvancedCommands\WellSelection;
+use PHPUnit\Framework\TestCase;
+
+class MixTest extends TestCase
+{
+ public function testMixCommandWithValidParameters(): void
+ {
+ $mix = new Mix(
+ 'Water',
+ new Volumes([5.5, 5.5, 4.5, 4.5, 0, 0, 0, 0, 0, 0, 0, 0]),
+ 15,
+ 2,
+ 1,
+ new WellSelection(12, 8, [1]),
+ 1,
+ );
+
+ $expected = 'Mix(15,"Water","5.5","5.5","4.5","4.5",0,0,0,0,0,0,0,0,15,2,1,"0C0810000000000000",1,0,0)';
+ self::assertEquals($expected, $mix->toString());
+ }
+
+ public function testMixCommandWithNoVolumes(): void
+ {
+ $mix = new Mix(
+ 'Water',
+ new Volumes([0, 0.0, 0.00000, 0, 0, 0, 0, 0, 0, 0, 0, 0]),
+ 15,
+ 2,
+ 1,
+ new WellSelection(12, 8, [1]),
+ 1,
+ );
+
+ $expected = 'Mix(0,"Water",0,0,0,0,0,0,0,0,0,0,0,0,15,2,1,"0C0810000000000000",1,0,0)';
+ self::assertEquals($expected, $mix->toString());
+ }
+}
diff --git a/tests/Tecan/AdvancedCommands/VolumesTest.php b/tests/Tecan/AdvancedCommands/VolumesTest.php
new file mode 100644
index 0000000..dd8cff3
--- /dev/null
+++ b/tests/Tecan/AdvancedCommands/VolumesTest.php
@@ -0,0 +1,47 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Tests\Tecan\AdvancedCommands;
+
+use MLL\Utils\Tecan\AdvancedCommands\Volumes;
+use PHPUnit\Framework\Attributes\DataProvider;
+use PHPUnit\Framework\TestCase;
+
+class VolumesTest extends TestCase
+{
+ /** @return iterable<array{0: array<int, float|int>, 1: string, 2: int}> */
+ public static function validVolumesProvider(): iterable
+ {
+ yield [[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], '0,0,0,0,0,0,0,0,0,0,0,0', 0];
+ yield [[1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], '"1",0,0,0,0,0,0,0,0,0,0,0', 1];
+ yield [[1, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], '"1","2",0,0,0,0,0,0,0,0,0,0', 3];
+ yield [[1, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0], '"1",0,"2",0,0,0,0,0,0,0,0,0', 5];
+ yield [[1, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0], '"1",0,0,"2",0,0,0,0,0,0,0,0', 9];
+
+ yield [[1, 0, 2.5, 0, 0, 3, 0, 4, 0, 0, 0, 0], '"1",0,"2.5",0,0,"3",0,"4",0,0,0,0', 165];
+ yield [[1, 2, 3, 4, 5, 6, 7, 8, 0, 0, 0, 0], '"1","2","3","4","5","6","7","8",0,0,0,0', 255];
+ }
+
+ /** @dataProvider validVolumesProvider
+ * @param array{
+ * 0:float|int,
+ * 1:float|int,
+ * 2:float|int,
+ * 3:float|int,
+ * 4:float|int,
+ * 5:float|int,
+ * 6:float|int,
+ * 7:float|int,
+ * 8:float|int,
+ * 9:float|int,
+ * 10:float|int,
+ * 11:float|int,
+ * } $volumes
+ */
+ #[DataProvider('validVolumesProvider')]
+ public function testVolumesStringAndTipMask(array $volumes, string $expectedString, int $expectedMask): void
+ {
+ $volumesObj = new Volumes($volumes);
+ self::assertSame($expectedString, $volumesObj->volumeString());
+ self::assertSame($expectedMask, $volumesObj->tipMask());
+ }
+}
diff --git a/tests/Tecan/AdvancedCommands/WellSelectionTest.php b/tests/Tecan/AdvancedCommands/WellSelectionTest.php
new file mode 100644
index 0000000..9c29e74
--- /dev/null
+++ b/tests/Tecan/AdvancedCommands/WellSelectionTest.php
@@ -0,0 +1,109 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Tests\Tecan\AdvancedCommands;
+
+use MLL\Utils\Tecan\AdvancedCommands\WellSelection;
+use PHPUnit\Framework\Attributes\DataProvider;
+use PHPUnit\Framework\TestCase;
+
+class WellSelectionTest extends TestCase
+{
+ /** @return iterable<array{0: int, 1: int, 2: array<int>, 3: string}> */
+ public static function wellSelectionProvider(): iterable
+ {
+ yield 'returns0000WhenXWellsIsZero' => [0, 5, [], '0000'];
+ yield 'returns0000WhenYWellsIsZero' => [5, 0, [], '0000'];
+ yield 'A1 pos 1' => [12, 8, [1], '0C0810000000000000'];
+ yield 'B1 pos 2' => [12, 8, [2], '0C0820000000000000'];
+ yield 'C1 pos 3' => [12, 8, [3], '0C0840000000000000'];
+ yield 'D1 pos 4' => [12, 8, [4], '0C0880000000000000'];
+ yield 'E1 pos 5' => [12, 8, [5], '0C08@0000000000000'];
+ yield 'F1 pos 6' => [12, 8, [6], '0C08P0000000000000'];
+ yield 'G1 pos 7' => [12, 8, [7], '0C08p0000000000000'];
+ yield 'A1 + E1 pos 1 + 5' => [12, 8, [1, 5], '0C08A0000000000000'];
+ yield 'no wells selected' => [12, 8, [], '0C0800000000000000'];
+ }
+
+ /**
+ * @dataProvider wellSelectionProvider
+ *
+ * @param array<int, int> $positions
+ */
+ #[DataProvider('wellSelectionProvider')]
+ public function testWellSelection(int $xWells, int $yWells, array $positions, string $expected): void
+ {
+ $wellSelection = new WellSelection($xWells, $yWells, $positions);
+ self::assertEquals($expected, $wellSelection->toString());
+ }
+
+ /** @return iterable<array{0: array<int>, 1: int, 2: int, 3: array<int, array<int, int>>}> */
+ public static function transformPositionsToSelFlagProvider(): iterable
+ {
+ yield [
+ [1, 5], 12, 8, [
+ [1, 0, 0, 0, 1, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ ],
+ ];
+ yield [
+ [8, 96], 12, 8, [
+ [0, 0, 0, 0, 0, 0, 0],
+ [1, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 1, 0, 0],
+ ],
+ ];
+ yield [
+ [15, 40], 12, 8, [
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [1, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 1, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ [0, 0, 0, 0, 0, 0, 0],
+ ],
+ ];
+ }
+
+ /**
+ * @dataProvider transformPositionsToSelFlagProvider
+ *
+ * @param array<int> $positions
+ * @param array<int, array<int, int>> $expected
+ */
+ #[DataProvider('transformPositionsToSelFlagProvider')]
+ public function testTransformPositionsToSelFlag(array $positions, int $xWells, int $yWells, array $expected): void
+ {
+ self::assertEquals($expected, WellSelection::transformPositionsToSelFlag($positions, $xWells, $yWells));
+ }
+}