Sweep: convert python about php-dna

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GitHub Actions✓

Here are the GitHub Actions logs prior to making any changes:

Sandbox logs for 78a634f

Checking src/Snps/SNPs.php for syntax errors... ✅ src/Snps/SNPs.php has no syntax errors! 1/1 ✓

Checking src/Snps/SNPs.php for syntax errors...
✅ src/Snps/SNPs.php has no syntax errors!

Sandbox passed on the latest main, so sandbox checks will be enabled for this issue.

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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/Snps/EnsemblRestClient.php

Lines 1 to 79 in b437c4a

	<?php
	namespace Dna\Snps;
	use Exception;
	class EnsemblRestClient
	{
	private string $server;
	private int $reqs_per_sec;
	private int $req_count;
	private float $last_req;
	public function __construct(string $server = "https://rest.ensembl.org", int $reqs_per_sec = 15)
	{
	$this->server = $server;
	$this->reqs_per_sec = $reqs_per_sec;
	$this->req_count = 0;
	$this->last_req = 0;
	}
	public function perform_rest_action(string $endpoint, ?array $hdrs = null, ?array $params = null): ?array
	{
	if ($hdrs === null) {
	$hdrs = [];
	}
	if (!array_key_exists("Content-Type", $hdrs)) {
	$hdrs["Content-Type"] = "application/json";
	}
	if ($params) {
	$endpoint .= "?" . http_build_query($params);
	}
	$data = null;
	// check if we need to rate limit ourselves
	if ($this->req_count >= $this->reqs_per_sec) {
	$delta = microtime(true) - $this->last_req;
	if ($delta < 1) {
	usleep((1 - $delta) * 1000000);
	}
	$this->last_req = microtime(true);
	$this->req_count = 0;
	}
	$client = new \Symfony\Component\HttpClient\HttpClient();
	$url = $this->server . $endpoint;
	$options = [
	'headers' => $hdrs,
	'query' => $params,
	];
	try {
	$response = $client->request('GET', $url, $options);
	$statusCode = $response->getStatusCode();
	if ($statusCode === 200) {
	$data = $response->toArray();
	} else {
	throw new Exception("HTTP request failed with status code {$statusCode}.");
	}
	$this->req_count++;
	} catch (Exception $e) {
	if ($statusCode == 429) {
	$retryAfter = $response->getHeaders()['retry-after'][0] ?? 0;
	sleep($retryAfter);
	return $this->perform_rest_action($endpoint, $hdrs, $params);
	} else {
	error_log("Request failed for {$endpoint}: Status code: {$statusCode} Reason: {$e->getMessage()}\n");
	}
	}
	return $data;
	}
	}

php-dna/src/Snps/SNPs.php

Lines 1 to 157 in b437c4a

	<?php
	namespace Dna\Snps;
	use Countable;
	use Dna\Resources;
	use Dna\Snps\IO\IO;
	use Dna\Snps\IO\Reader;
	use Dna\Snps\IO\Writer;
	use Iterator;
	// You may need to find alternative libraries for numpy, pandas, and snps in PHP, as these libraries are specific to Python
	// For numpy, consider using a library such as MathPHP: https://github.com/markrogoyski/math-php
	// For pandas, you can use DataFrame from https://github.com/aberenyi/php-dataframe, though it is not as feature-rich as pandas
	// For snps, you'll need to find a suitable PHP alternative or adapt the Python code to PHP
	// import copy // In PHP, you don't need to import the 'copy' module, as objects are automatically copied when assigned to variables
	// from itertools import groupby, count // PHP has built-in support for array functions that can handle these operations natively
	// import logging // For logging in PHP, you can use Monolog: https://github.com/Seldaek/monolog
	// use Monolog\Logger;
	// use Monolog\Handler\StreamHandler;
	// import os, re, warnings
	// PHP has built-in support for file operations, regex, and error handling, so no need to import these modules
	// import numpy as np // See the note above about using MathPHP or another PHP library for numerical operations
	// import pandas as pd // See the note above about using php-dataframe or another PHP library for data manipulation
	// from pandas.api.types import CategoricalDtype // If using php-dataframe, check documentation for similar functionality
	// For snps.ensembl, snps.resources, snps.io, and snps.utils, you'll need to find suitable PHP alternatives or adapt the Python code
	// from snps.ensembl import EnsemblRestClient
	// from snps.resources import Resources
	// from snps.io import Reader, Writer, get_empty_snps_dataframe
	// from snps.utils import Parallelizer
	// Set up logging
	// $logger = new Logger('my_logger');
	// $logger->pushHandler(new StreamHandler('php://stderr', Logger::DEBUG));
	class SNPs implements Countable, Iterator
	{
	private array $_source = [];
	private array $_snps = [];
	private int $_build = 0;
	private ?bool $_phased = null;
	private ?bool $_build_detected = null;
	private ?Resources $_resources = null;
	private ?string $_chip = null;
	private ?string $_chip_version = null;
	private ?string $_cluster = null;
	private int $_position = 0;
	private array $_keys = [];
	private array $_duplicate;
	private array $_discrepant_XY;
	private array $_heterozygous_MT;
	private $_chip;
	private $_chip_version;
	private $_cluster;
	/**
	* SNPs constructor.
	*
	* @param string $file Input file path
	* @param bool $only_detect_source Flag to indicate whether to only detect the source
	* @param bool $assign_par_snps Flag to indicate whether to assign par_snps
	* @param string $output_dir Output directory path
	* @param string $resources_dir Resources directory path
	* @param bool $deduplicate Flag to indicate whether to deduplicate
	* @param bool $deduplicate_XY_chrom Flag to indicate whether to deduplicate XY chromosome
	* @param bool $deduplicate_MT_chrom Flag to indicate whether to deduplicate MT chromosome
	* @param bool $parallelize Flag to indicate whether to parallelize
	* @param int $processes Number of processes to use for parallelization
	* @param array $rsids Array of rsids
	*/
	public function __construct(
	private $file = "",
	private bool $only_detect_source = False,
	private bool $assign_par_snps = False,
	private string $output_dir = "output",
	private string $resources_dir = "resources",
	private bool $deduplicate = True,
	private bool $deduplicate_XY_chrom = True,
	private bool $deduplicate_MT_chrom = True,
	private bool $parallelize = False,
	private int $processes = 1, // cpu count
	private array $rsids = [],
	private $ensemblRestClient = null,
	) //, $only_detect_source, $output_dir, $resources_dir, $parallelize, $processes)
	{
	// $this->_only_detect_source = $only_detect_source;
	$this->setSNPs(IO::get_empty_snps_dataframe());
	$this->_duplicate = IO::get_empty_snps_dataframe();
	$this->_discrepant_XY = IO::get_empty_snps_dataframe();
	$this->_heterozygous_MT = IO::get_empty_snps_dataframe();
	// $this->_discrepant_vcf_position = $this->get_empty_snps_dataframe();
	// $this->_low_quality = $this->_snps->index;
	// $this->_discrepant_merge_positions = new DataFrame();
	// $this->_discrepant_merge_genotypes = new DataFrame();
	$this->_source = [];
	// $this->_phased = false;
	$this->_build = 0;
	$this->_build_detected = false;
	// $this->_output_dir = $output_dir;
	$this->_resources = new Resources($resources_dir);
	// $this->_parallelizer = new Parallelizer($parallelize, $processes);
	$this->_cluster = "";
	$this->_chip = "";
	$this->_chip_version = "";
	$this->ensemblRestClient = $ensemblRestClient ?? new EnsemblRestClient("https://api.ncbi.nlm.nih.gov", 1);
	if (!empty($file)) {
	$this->readFile();
	}
	}
	public function count(): int
	{
	return $this->get_count();
	}
	public function current(): SNPs
	{
	return $this->_snps[$this->_position];
	}
	public function key(): int
	{
	return $this->_position;
	}
	public function next(): void
	{
	++$this->_position;
	}
	public function rewind(): void
	{
	$this->_position = 0;
	}
	public function valid(): bool
	{
	return isset($this->_snps[$this->_position]);
	}
	/**
	* Get the SNPs as a DataFrame.
	*
	* @return SNPs[] The SNPs array

I also found the following external resources that might be helpful:

Summaries of links found in the content:

https://raw.githubusercontent.com/apriha/snps/master/src/snps/ensembl.py:

The given page is a Python script that serves as a client for the Ensembl REST API. It includes a class called EnsemblRestClient that initializes the server URL and the number of requests per second. The class has a method called perform_rest_action that takes an endpoint, headers, and parameters as input. It makes a request to the Ensembl server using the urllib library and returns the response content as JSON data.

To solve the problem of converting the Python script into PHP, the user needs to create a corresponding PHP class called Ensembl in the Snps namespace. The PHP class should have a method similar to perform_rest_action that makes HTTP requests to the Ensembl server using the file_get_contents function or a similar method. The Python code snippets need to be translated into their equivalent PHP code.

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Step 2: ⌨️ Coding

• Create src/Snps/Ensembl.php ✓ 2a154aa Edit

Create src/Snps/Ensembl.php with contents:
• Create a new PHP class file named `Ensembl.php` within the `src/Snps/` directory. This file will contain a class `Ensembl` that mirrors the functionality provided by the Python `EnsemblRestClient` script.
• At the top of `Ensembl.php`, declare the namespace `Dna\Snps;` to align with the project's structure.
• Import necessary classes and namespaces at the beginning of the file, including `Exception` for error handling and any relevant HTTP client classes from Symfony or another library already used within the project for making HTTP requests.
• Define the `Ensembl` class with private properties for server URL, requests per second, request count, and last request time, similar to the Python script's structure.
• Implement a constructor `__construct` that initializes the server URL to "https://rest.ensembl.org" and sets default values for requests per second, request count, and last request time.
• Add a method `performRestAction` that takes parameters for the endpoint, headers, and query parameters. This method should handle building the request URL, adding default headers if not provided, rate limiting based on the requests per second property, making the HTTP request, and handling responses including retry logic for rate-limited requests.
• Ensure that the `performRestAction` method uses modern PHP features for handling HTTP requests and responses, such as the Symfony HTTP client or similar, and leverages PHP 8.3 features for improved type declarations and error handling.

• Running GitHub Actions for src/Snps/Ensembl.php ✓ Edit

Check src/Snps/Ensembl.php with contents:

Ran GitHub Actions for 2a154aa40101da0fb36a66159aa18d7cb72123b1:

• Modify src/Snps/SNPs.php ✓ 2e0e401 Edit

Modify src/Snps/SNPs.php with contents:
• Replace the comment line that mentions importing `EnsemblRestClient` from Python with a PHP `use` statement that imports the newly created `Ensembl` class: `use Dna\Snps\Ensembl;`.
• This change ensures that the `SNPs` class can utilize the new `Ensembl` class for making requests to the Ensembl REST API, aligning with the functionality previously expected from the Python script.

--- 
+++ 
@@ -32,7 +32,7 @@
 // from pandas.api.types import CategoricalDtype // If using php-dataframe, check documentation for similar functionality
 
 // For snps.ensembl, snps.resources, snps.io, and snps.utils, you'll need to find suitable PHP alternatives or adapt the Python code
-// from snps.ensembl import EnsemblRestClient
+use Dna\Snps\Ensembl;
 // from snps.resources import Resources
 // from snps.io import Reader, Writer, get_empty_snps_dataframe
 // from snps.utils import Parallelizer

• Running GitHub Actions for src/Snps/SNPs.php ✓ Edit

Check src/Snps/SNPs.php with contents:

Ran GitHub Actions for 2e0e4014eb45103665126bbc81a2972298177146:

• Modify src/Snps/SNPs.php ✓ 105410c Edit

Modify src/Snps/SNPs.php with contents:
• Modify the instantiation of `EnsemblRestClient` within the `SNPs` constructor to use the new `Ensembl` class instead. Change the line to `$this->ensemblRestClient = $ensemblRestClient ?? new Ensembl("https://api.ncbi.nlm.nih.gov", 1);`.
• This adjustment ensures that the `SNPs` class leverages the new `Ensembl` class for interacting with the Ensembl REST API, providing a direct replacement for the functionality described in the issue.

--- 
+++ 
@@ -32,7 +32,7 @@
 // from pandas.api.types import CategoricalDtype // If using php-dataframe, check documentation for similar functionality
 
 // For snps.ensembl, snps.resources, snps.io, and snps.utils, you'll need to find suitable PHP alternatives or adapt the Python code
-// from snps.ensembl import EnsemblRestClient
+use Dna\Snps\Ensembl;
 // from snps.resources import Resources
 // from snps.io import Reader, Writer, get_empty_snps_dataframe
 // from snps.utils import Parallelizer
@@ -92,29 +92,29 @@
         private int $processes = 1, // cpu count
         private array $rsids = [],
         private $ensemblRestClient = null,
-    ) //, $only_detect_source, $output_dir, $resources_dir, $parallelize, $processes)
-    {
-        // $this->_only_detect_source = $only_detect_source;
-        $this->setSNPs(IO::get_empty_snps_dataframe());
-        $this->_duplicate = IO::get_empty_snps_dataframe();
-        $this->_discrepant_XY = IO::get_empty_snps_dataframe();
-        $this->_heterozygous_MT = IO::get_empty_snps_dataframe();
-        // $this->_discrepant_vcf_position = $this->get_empty_snps_dataframe();
-        // $this->_low_quality = $this->_snps->index;
-        // $this->_discrepant_merge_positions = new DataFrame();
-        // $this->_discrepant_merge_genotypes = new DataFrame();
-        $this->_source = [];
-        // $this->_phased = false;
-        $this->_build = 0;
-        $this->_build_detected = false;
-        // $this->_output_dir = $output_dir;
-        $this->_resources = new Resources($resources_dir);
-        // $this->_parallelizer = new Parallelizer($parallelize, $processes);
-        $this->_cluster = "";
-        $this->_chip = "";
-        $this->_chip_version = "";
-
-        $this->ensemblRestClient = $ensemblRestClient ?? new EnsemblRestClient("https://api.ncbi.nlm.nih.gov", 1);
+            ) //, $only_detect_source, $output_dir, $resources_dir, $parallelize, $processes)
+            {
+                // $this->_only_detect_source = $only_detect_source;
+                $this->setSNPs(IO::get_empty_snps_dataframe());
+                $this->_duplicate = IO::get_empty_snps_dataframe();
+                $this->_discrepant_XY = IO::get_empty_snps_dataframe();
+                $this->_heterozygous_MT = IO::get_empty_snps_dataframe();
+                // $this->_discrepant_vcf_position = $this->get_empty_snps_dataframe();
+                // $this->_low_quality = $this->_snps->index;
+                // $this->_discrepant_merge_positions = new DataFrame();
+                // $this->_discrepant_merge_genotypes = new DataFrame();
+                $this->_source = [];
+                // $this->_phased = false;
+                $this->_build = 0;
+                $this->_build_detected = false;
+                // $this->_output_dir = $output_dir;
+                $this->_resources = new Resources($resources_dir);
+                // $this->_parallelizer = new Parallelizer($parallelize, $processes);
+                $this->_cluster = "";
+                $this->_chip = "";
+                $this->_chip_version = "";
+        
+                $this->ensemblRestClient = $ensemblRestClient ?? new Ensembl("https://api.ncbi.nlm.nih.gov", 1);
 
         if (!empty($file)) {
             $this->readFile();

• Running GitHub Actions for src/Snps/SNPs.php ✓ Edit

Check src/Snps/SNPs.php with contents:

Ran GitHub Actions for 105410c2e37d377123d3e27178881ea00852b618:

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Step 3: 🔁 Code Review

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

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