inab · nicodr97 · Nov 28, 2025 · Nov 28, 2025 · Dec 2, 2025 · Dec 3, 2025
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -138,6 +138,8 @@ services:
       - net_vre
     ports:
       - "6444:6444"
+    extra_hosts:
+      - "front_end:172.21.0.14"
     restart: on-failure:2
 
 volumes:

diff --git a/front_end/Dockerfile b/front_end/Dockerfile
@@ -24,9 +24,9 @@ RUN apt-get update && apt-get install -y libmcrypt-dev \
     && docker-php-ext-configure gd --with-freetype=/usr/include/ --with-jpeg=/usr/include/ \
     && docker-php-ext-install gd 
 
-RUN apt-get update && apt-get install gnupg curl
-RUN curl -fsSL https://www.mongodb.org/static/pgp/server-7.0.asc |gpg -o /usr/share/keyrings/mongodb-server-7.0.gpg --dearmor
-RUN echo "deb [ signed-by=/usr/share/keyrings/mongodb-server-7.0.gpg ] http://repo.mongodb.org/apt/debian bookworm/mongodb-org/7.0 main" | tee /etc/apt/sources.list.d/mongodb-org-7.0.list
+RUN apt-get update && apt-get install -y gnupg curl
+RUN curl -fsSL https://www.mongodb.org/static/pgp/server-8.0.asc |gpg -o /usr/share/keyrings/mongodb-server-8.0.gpg --dearmor
+RUN echo "deb [ signed-by=/usr/share/keyrings/mongodb-server-8.0.gpg ] http://repo.mongodb.org/apt/debian bookworm/mongodb-org/8.0 main" | tee /etc/apt/sources.list.d/mongodb-org-8.0.list
 RUN apt-get update
 RUN apt-get install -y mongodb-org
 

diff --git a/front_end/openVRE/composer.json b/front_end/openVRE/composer.json
@@ -3,12 +3,14 @@
     "ext-openssl": "*",
     "auth0/auth0-php": "^8.0",
     "chadicus/slim-oauth2": "^3.1",
+    "erusev/parsedown": "^1.7",
     "firebase/php-jwt": "^6.11",
     "guzzlehttp/guzzle": "*",
     "justinrainbow/json-schema": "^5.2",
     "league/oauth2-google": "^2.0",
     "mongodb/mongodb": "^2.1",
-    "monolog/monolog": "^2.5",
+    "monolog/monolog": "^3.9",
+    "phpmailer/phpmailer": "^7.0.0",
     "phpseclib/phpseclib": "~3.0",
     "slim/extras": "*",
     "slim/http": "^1.3.0",
@@ -20,11 +22,7 @@
   },
   "autoload": {
     "psr-4": {
-      "App\\": "app/",
-      "App\\Controllers\\": "app/controllers",
-      "App\\Models\\": "app/models",
-      "App\\Middleware\\": "app/Middleware",
-      "App\\Handlers\\": "app/Handlers"
+      "OpenVRE\\": "public/phplib/classes/"
     }
   },
   "autoload-dev": {

diff --git a/front_end/openVRE/config/bootstrap.php b/front_end/openVRE/config/bootstrap.php
@@ -1,21 +1,42 @@
 <?php
 
+// import vendor libs
+require dirname(__FILE__) . "/../vendor/autoload.php";
+
+use OpenVRE\LoggerFactory;
+
+set_exception_handler(function (Throwable $e) {
+    #$_SESSION['errorData']['Error'][] = $e->getMessage();
+    $logger = LoggerFactory::getLogger("Bootstrap interface");
+    $logger->error($e->getTraceAsString());
+    $logger->error(sprintf(
+        "%s in %s:%d",
+        $e->getMessage(),
+        $e->getFile(),
+        $e->getLine()
+    ));
+
+    http_response_code(500);
+    echo "<!DOCTYPE html><html><body>";
+    echo "<h1>Application error</h1>";
+    echo "<div class='alert alert-danger'>"
+        . htmlspecialchars($e->getMessage(), ENT_QUOTES, 'UTF-8')
+        . "</div>";
+    echo "</body></html>";
+
+    exit;
+});
+
 // set up app settings
-require dirname(__FILE__)."/../config/globals.inc.php";
+require dirname(__FILE__) . "/../config/globals.inc.php";
 
 // import vendor libs
-require dirname(__FILE__)."/../vendor/autoload.php"; 
+require dirname(__FILE__) . "/../vendor/autoload.php";
 
-// import local classes
-foreach(glob(dirname(__FILE__)."/../public/phplib/classes/*.php") as $lib){
-    require $lib;
-}
 // import local libs
-foreach(glob(dirname(__FILE__)."/../public/phplib/*.php") as $lib){
+foreach (glob(dirname(__FILE__) . "/../public/phplib/*.php") as $lib) {
     require $lib;
 }
 
 // initialize session
-require dirname(__FILE__)."/../public/phplib/session.inc";
-
-?>
+require dirname(__FILE__) . "/../public/phplib/session.inc";
diff --git a/front_end/openVRE/config/globals.inc.php.sample b/front_end/openVRE/config/globals.inc.php.sample
@@ -157,44 +157,7 @@ $GLOBALS['clouds'] = Array(
                         "pubDir_virtual"    => $GLOBALS['pubDir'],
                         "dataDir_host"    => $GLOBALS["host_path"].$GLOBALS['dataDir'],
                         "pubDir_host"    => $GLOBALS["host_path"].$GLOBALS['pubDir'],
-                        "PMESserver_domain" => "pmes.mydomain.com",
-                        "PMESserver_port"   => "80",
-                        "PMESserver_address"=> "/",
                         "imageTypes"        => array(),                      // list of cloud OCCI templates indexed by RAM (GB)
                         "auth"              => array("required" => False)
-                ),
-		'my_remote_2' => array(
-			"http_host"	    => "www.mydomain2.com",	      // used in getCurrentCloud
-			"dataDir_fs"   	    => "/NFS/export/path2/userdata/", // export path for NFS server
-			"pubDir_fs"	    => "/NFS/export/path2/public/",   // export path for NFS server
-			"dataDir_virtual"   => "/shared/path/for/userdata",
-			"pubDir_virtual"    => "/shared/path/for/public",
-			"PMESserver_domain" => "pmes.mydomain2.com",
-			"PMESserver_port"   => "8080",
-			"PMESserver_address"=> "/",
-			"imageTypes"	=>  array(                           // list of cloud OCCI templates indexed by RAM (GB)
-				"2"  => array(
-					"1"  => array("id" => "small", "disk" => null, "name" => "small"),
-					"8"  => array("id" => "large-small", "disk" => null, "name" => "large-small"),
-					"16" => array("id" => "extra_large-small", "disk" => null, "name" => "large-small")
-				    ),
-				"4"  => array(
-					"2"  => array("id" => "medium", "disk" => null, "name" => "medium"),
-					"4"  => array("id" => "medium-medium", "disk" => null, "name" => "medium-medium"),
-					"8"  => array("id" => "large-medium", "disk" => null, "name" => "large-medium"),
-					"16" => array("id" => "extra_large-medium", "disk" => null, "name" => "extra_large-medium")
-				    )
-			),
-			"auth"  => array(
-				"required"       => True,
-				"OS_NO_CACHE"    => "True",
-				"OS_CLOUDNAME"   => "overcloud",
-				"OS_AUTH_URL"    => "https://extcloud05.ebi.ac.uk:13000/v2.0",
-				"NOVA_VERSION"   => "1.2",
-				"COMPUTE_API_VERSION" => "1.2",
-				"OS_USERNAME"    => "username@mail.es",
-				"OS_PASSWORD"    => "s3cr3t",
-				"OS_TENANT_NAME" => "tenancy_name"
-			)
-	    )
+                )
 );
diff --git a/front_end/openVRE/data/sampleData/basic/.sample_metadata.json b/front_end/openVRE/data/sampleData/basic/.sample_metadata.json
@@ -1,8 +1,7 @@
 [
     {
-        "file_path": "uploads",
+        "path": "uploads",
         "type":"dir",
-        "sources": [0],
         "meta_data": {
             "expiration":-1,
             "description": "Uploaded personal data",

diff --git a/front_end/openVRE/data/sampleData/basic/uploads/.sample_metadata.json b/front_end/openVRE/data/sampleData/basic/uploads/.sample_metadata.json
@@ -1,12 +1,9 @@
 [
     {
-        "file_path": "uploads/README.md",
+        "path": "uploads/README.md",
         "data_type": "configuration_file",
-        "file_type": "TXT",
+        "format": "TXT",
         "type": "file",
-        "sources": [
-            0
-        ],
         "meta_data": {
             "expiration": -1,
             "description": "my first VRE file"