Merge pull request #116 from liberu-genealogy/sweep/_de62a

Sweep:  (✓ Sandbox Passed)

src/Snps/ReferenceSequence.php

@@ -9,12 +9,12 @@ class ReferenceSequence
 {
 
     public function __construct(
-        private readonly string $ID = "",
-        private readonly string $url = "",
-        private readonly string $path = "",
-        private readonly string $assembly = "",
-        private readonly string $species = "",
-        private readonly string $taxonomy = ""
+        private string $ID = "",
+        private string $url = "",
+        private string $path = "",
+        private string $assembly = "",
+        private string $species = "",
+        private string $taxonomy = ""
     ) {
         $this->sequence = [];
         $this->md5 = "";
@@ -37,7 +37,7 @@ public function __toString()
      */
     public function getID(): string
     {
-        return $this->_ID;
+        return $this->ID;
     }
 
     /**
@@ -47,7 +47,7 @@ public function getID(): string
      */
     public function getChrom(): string
     {
-        return $this->_ID;
+        return $this->ID;
     }
 
     /**
@@ -57,7 +57,7 @@ public function getChrom(): string
      */
     public function getUrl(): string
     {
-        return $this->_url;
+        return $this->url;
     }
 
     /**
@@ -67,7 +67,7 @@ public function getUrl(): string
      */
     public function getPath(): string
     {
-        return $this->_path;
+        return $this->path;
     }
 
     /**
@@ -77,7 +77,7 @@ public function getPath(): string
      */
     public function getAssembly(): string
     {
-        return $this->_assembly;
+        return $this->assembly;
     }
 
     /**
@@ -87,7 +87,7 @@ public function getAssembly(): string
      */
     public function getBuild(): string
     {
-        return "B" . substr($this->_assembly, -2);
+        return "B" . substr($this->assembly, -2);
     }
     /**
      * Returns the species of the reference sequence.
@@ -96,7 +96,7 @@ public function getBuild(): string
      */
     public function getSpecies(): string
     {
-        return $this->_species;
+        return $this->species;
     }
 
     /**
@@ -106,7 +106,7 @@ public function getSpecies(): string
      */
     public function getTaxonomy(): string
     {
-        return $this->_taxonomy;
+        return $this->taxonomy;
     }
 
     /**
@@ -167,7 +167,7 @@ private function loadSequence(): void
     {
         if (!count($this->sequence)) {
             // Decompress and read file
-            $data = file_get_contents($this->_path);
+            $data = file_get_contents($this->path);
 
             // check if file is gzipped
             if (str_starts_with($data, "\x1f\x8b")) {

src/Snps/Resources.php

@@ -0,0 +1,52 @@
+<?php
+
+namespace Dna\Snps;
+
+use GuzzleHttp\Client;
+
+class Resources
+{
+    private string $baseUrl;
+    private string $localResourceDir;
+    private Client $httpClient;
+
+    public function __construct(string $baseUrl, string $localResourceDir)
+    {
+        $this->baseUrl = $baseUrl;
+        $this->localResourceDir = $localResourceDir;
+        $this->httpClient = new Client();
+    }
+
+    public function downloadResource(string $url, string $destinationPath): void
+    {
+        $response = $this->httpClient->get($url);
+        file_put_contents($destinationPath, $response->getBody());
+    }
+
+    public function loadDataFromFile(string $filePath)
+    {
+        return file_get_contents($filePath);
+    }
+
+    public function getReferenceSequence(string $id): ReferenceSequence
+    {
+        $filePath = $this->getLocalPathForResource($id);
+        $sequenceData = $this->loadDataFromFile($filePath);
+        return new ReferenceSequence($id, $sequenceData);
+    }
+
+    public function getAssemblyMappingData(string $id)
+    {
+        // Implementation for fetching assembly mapping data
+    }
+
+    public function getExampleDataset(string $id)
+    {
+        // Implementation for fetching example datasets
+    }
+
+    private function getLocalPathForResource(string $resourceId): string
+    {
+        return $this->localResourceDir . DIRECTORY_SEPARATOR . $resourceId;
+    }
+}