[Core/Refactor] Do not mangle request URI

modules/api/php/module.class.inc

@@ -68,7 +68,7 @@ class Module extends \Module
         }
 
         // Requests sent to this module must start with /api/$version
-        $url    = $request->getURI()->getPath();
+        $url    = $request->getAttribute("unhandledURI")->getPath();
         $pieces = [];
         if (preg_match(
             "/^\/?(v[0-9]+\.[0-9]+\.[0-9]+[^\/]*)\/(.*)/",

modules/biobank/php/endpoint.class.inc

@@ -95,7 +95,7 @@ abstract class Endpoint
         ServerRequestInterface $request,
         RequestHandlerInterface $handler
     ): ResponseInterface {
-        $path      = trim($request->getURI()->getPath(), "/");
+        $path      = trim($request->getAttribute("unhandledURI")->getPath(), "/");
         $pathparts = explode('/', $path);
 
         // Check if sub-handlers are supported

modules/biobank/php/module.class.inc

@@ -65,8 +65,8 @@ class Module extends \Module
     {
         $this->logger->debug("Module handle function called");
         $resp = parent::handle($request);
+        $path = $request->getAttribute("unhandledURI")->getPath();
         if ($resp->getStatusCode() != 404) {
-            $path = $request->getURI()->getPath();
             if (preg_match('/(\.css)$/', $path) == 1) {
                 $resp = $resp->withHeader(
                     "Content-Type",
@@ -84,7 +84,7 @@ class Module extends \Module
 
         $this->loris = $request->getAttribute("loris");
         $pagename    = $this->getName();
-        $path        = trim($request->getURI()->getPath(), "/");
+        $path        = trim($path, "/");
         if ($path == 'optionsendpoint'
             || $path == 'poolendpoint'
             || $path == 'containerendpoint'

modules/biobank/php/preparations.class.inc

@@ -132,7 +132,7 @@ class Preparations implements RequestHandlerInterface
         $this->loris = $request->getAttribute("loris");
 
         $db        = $this->loris->getDatabaseConnection();
-        $endpoint  = $request->getURI()->getPath();
+        $endpoint  = $request->getAttribute("unhandledURI")->getPath();
         $pathparts = explode('/', $endpoint);
         $db->delete(
             'biobank_specimen_preparation',

modules/candidate_profile/php/module.class.inc

@@ -23,7 +23,7 @@ class Module extends \Module
      */
     public function handle(ServerRequestInterface $request) : ResponseInterface
     {
-        $candIDStr = ltrim($request->getURI()->getPath(), '/');
+        $candIDStr = ltrim($request->getAttribute("unhandledURI")->getPath(), '/');
         try {
             $candID    = new CandID($candIDStr);
             $candidate = \Candidate::singleton($candID);

modules/conflict_resolver/php/module.class.inc

@@ -58,7 +58,7 @@ class Module extends \Module
      */
     public function handle(ServerRequestInterface $request) : ResponseInterface
     {
-        $path = trim($request->getURI()->getPath(), "/");
+        $path = trim($request->getAttribute("unhandledURI")->getPath(), "/");
         switch ($path) {
         case 'unresolved':
             $handler = new Endpoints\Unresolved($this->loris);

modules/instruments/php/module.class.inc

@@ -57,7 +57,7 @@ class Module extends \Module
             return $resp;
         }
 
-        $path           = $request->getURI()->getPath();
+        $path           = $request->getAttribute("unhandledURI")->getPath();
         $pathComponents = [];
 
         // Breakdown path information from the request.

modules/statistics/php/charts.class.inc

@@ -81,7 +81,11 @@ class Charts extends \NDB_Page
         // Strip any prefix of '/' to ensure that we don't have an empty string
         // when splitting the path, then there should be exactly 2 parts left,
         // "charts", and the endpoint requested.
-        $url       = ltrim($request->getURI()->getPath(), '/');
+        $url = ltrim(
+            $request->getAttribute("unhandledURI")->getURI()->getPath(),
+            '/'
+        );
+
         $pathparts = explode('/', $url);
         if (count($pathparts) != 2) {
             return new \LORIS\Http\Response\JSON\NotFound();

php/libraries/Module.class.inc

@@ -271,9 +271,11 @@ abstract class Module extends \LORIS\Router\PrefixRouter
     public function handle(ServerRequestInterface $request) : ResponseInterface
     {
         $this->logger->debug("Module handle function called");
-        $resp = parent::handle($request);
+        $moduleURI = $request->getAttribute("unhandledURI");
+        $resp      = parent::handle($request);
+
         if ($resp->getStatusCode() != 404) {
-            $path = $request->getURI()->getPath();
+            $path = $moduleURI->getPath();
             if (preg_match('/(\.css)$/', $path) == 1) {
                 $resp = $resp->withHeader(
                     "Content-Type",
@@ -290,7 +292,7 @@ abstract class Module extends \LORIS\Router\PrefixRouter
         }
 
         $pagename = $this->getName();
-        $path     = trim($request->getURI()->getPath(), "/");
+        $path     = trim($moduleURI->getPath(), "/");
         if (!empty($path)) {
             // There is a subpage
             $pagename = explode("/", $path)[0];

src/Router/BaseRouter.php

@@ -54,8 +54,9 @@ public function __construct(
      */
     public function handle(ServerRequestInterface $request) : ResponseInterface
     {
-        $uri  = $request->getUri();
-        $path = $uri->getPath();
+        $request = $request->withAttribute("unhandledURI", $request->getURI());
+        $uri     = $request->getUri();
+        $path    = $uri->getPath();
 
         // Replace multiple slashes in the URL with a single slash
         $path = preg_replace("/\/+/", "/", $path);
@@ -157,7 +158,8 @@ public function handle(ServerRequestInterface $request) : ResponseInterface
                 $module->setLogger(new \PSR\Log\NullLogger);
             }
             $mr      = new ModuleRouter($module);
-            $request = $request->withURI($suburi);
+            $request = $request->withAttribute("unhandledURI", $suburi);
+
             return $ehandler->process($request, $mr);
         }
         // Legacy from .htaccess. A CandID goes to the timepoint_list

src/Router/ModuleFileRouter.php

@@ -76,12 +76,15 @@ public function __construct(\Module $module, string $moduledir, string $subdir,
      */
     public function handle(ServerRequestInterface $request) : ResponseInterface
     {
+        $uri  = $request->getAttribute("unhandledURI");
+        $path = !empty($uri) ? $uri->getPath() : $request->getURI()->getPath();
+
         $fullpath = (
             $this->moduledir .
             "/" .
             $this->subdir .
             "/"
-            . $request->getURI()->getPath()
+            . $path
         );
 
         if (is_file($fullpath)) {

src/Router/PrefixRouter.php

@@ -92,11 +92,11 @@ protected function stripPrefix(string $prefix, URIInterface $uri) : URIInterface
      */
     public function handle(ServerRequestInterface $request) : ResponseInterface
     {
+        $uri = $request->getAttribute("unhandledURI");
         foreach ($this->paths as $path => $subhandler) {
-            if ($this->hasPrefix($path, $request->getURI())) {
-                // Strip the prefix before passing it to the subhandler.
-                $newURI  = $this->stripPrefix($path, $request->getURI());
-                $request = $request->withURI($newURI);
+            if ($this->hasPrefix($path, $uri)) {
+                $newURI  = $this->stripPrefix($path, $uri);
+                $request = $request->withAttribute("unhandledURI", $newURI);
                 return $subhandler->handle($request);
             }
         }