[Core/Refactor] Do not mangle request URI

The BaseRouter/Prefix router stripped off the handled part of the URI
before passing it to other handlers. The reasoning was that then the
modules could treat the request without regard to the location that LORIS
is being served for and act as if it's always the root.

However, in practice this causes more problems than it solves. The original
URI is lost completely, so middleware, error pages, and http headers that may
need it do not have access to it without reconstructing it.

This updates the handled part of the URI to go into an "unhandledURI" attribute
while leaving the request->getURI untouched. Doing so allows us to access
the original URI when needed and if ie. you print $request->getURI() in an
error message you will get the correct value.

Author: Dave MacFarlane

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