Sweep: Sweep: Refactor triangulation.php and use latest features modularization of the code about php-dna

[sweep-ai]

🚀 Here's the PR! #154

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Actions (click)

• ↻ Restart Sweep

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Step 1: 🔎 Searching

I found the following snippets in your repository. I will now analyze these snippets and come up with a plan.

Some code snippets I think are relevant in decreasing order of relevance (click to expand). If some file is missing from here, you can mention the path in the ticket description.

php-dna/src/Triangulation.php

Lines 1 to 27 in 88c916b

	<?php
	require_once 'SNPs.php';
	class Triangulation {
	public static function compareMultipleKits($kitsData) {
	$snpsLists = array_map(function($kit) { return $kit->getSnps(); }, $kitsData);
	$commonSnps = call_user_func_array('array_intersect_key', $snpsLists);
	foreach ($commonSnps as $key => $snp) {
	if (!self::isSnpCommonAcrossAllKits($snp, $kitsData)) {
	unset($commonSnps[$key]);
	}
	}
	return array_values($commonSnps);
	}
	private static function isSnpCommonAcrossAllKits($snp, $kitsData) {
	foreach ($kitsData as $kit) {
	$snps = $kit->getSnps();
	if (!array_key_exists($snp['pos'], $snps) || $snps[$snp['pos']]['genotype'] !== $snp['genotype']) {
	return false;
	}
	}
	return true;
	}
	}

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Step 2: ⌨️ Coding

• Modify src/Triangulation.php ✓ eb594b6 Edit

Modify src/Triangulation.php with contents: Refactor the compareMultipleKits method to break it into smaller methods.

<original_code>
public static function compareMultipleKits($kitsData) {
$snpsLists = array_map(function($kit) { return $kit->getSnps(); }, $kitsData);
$commonSnps = call_user_func_array('array_intersect_key', $snpsLists);
foreach ($commonSnps as $key => $snp) {
if (!self::isSnpCommonAcrossAllKits($snp, $kitsData)) {
unset($commonSnps[$key]);
}
}
return array_values($commonSnps);
}
</original_code>

<new_code>
public static function compareMultipleKits(array $kitsData): array {
$snpsLists = self::extractSnpLists($kitsData);
$commonSnps = self::findCommonSnps($snpsLists);
return self::filterNonCommonSnps($commonSnps, $kitsData);
}

private static function extractSnpLists(array $kitsData): array {
    return array_map(function($kit) { return $kit->getSnps(); }, $kitsData);
}

private static function findCommonSnps(array $snpsLists): array {
    return call_user_func_array('array_intersect_key', $snpsLists);
}

private static function filterNonCommonSnps(array $commonSnps, array $kitsData): array {
    return array_filter($commonSnps, function($snp) use ($kitsData) {
        return self::isSnpCommonAcrossAllKits($snp, $kitsData);
    });
}

</new_code>

• Modify src/Triangulation.php ✓ eb594b6 Edit

Modify src/Triangulation.php with contents:

Simplify the isSnpCommonAcrossAllKits method using array_filter.

<original_code>
private static function isSnpCommonAcrossAllKits($snp, $kitsData) {
foreach ($kitsData as $kit) {
$snps = $kit->getSnps();
if (!array_key_exists($snp['pos'], $snps) || $snps[$snp['pos']]['genotype'] !== $snp['genotype']) {
return false;
}
}
return true;
}
</original_code>

<new_code>
private static function isSnpCommonAcrossAllKits(array $snp, array $kitsData): bool {
return count(array_filter($kitsData, function($kit) use ($snp) {
$snps = $kit->getSnps();
return isset($snps[$snp['pos']]) && $snps[$snp['pos']]['genotype'] === $snp['genotype'];
})) === count($kitsData);
}
</new_code>

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Step 3: 🔁 Code Review

I have finished reviewing the code for completeness. I did not find errors for sweep/sweep_refactor_triangulationphp_and_use.

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