Improve installation script and various small fixes

.htaccess

@@ -1,5 +1,5 @@
 RewriteEngine on
 RewriteCond %{HTTP_HOST} ^ [NC,OR]
 RewriteCond %{HTTP_HOST} ^
-RewriteCond %{REQUEST_URI} !webroot/
+RewriteCond %{REQUEST_URI} !^/webroot/
 RewriteRule (.*) /webroot/$1 [L]

README.md

@@ -15,6 +15,7 @@ Systems evaluations are an important part of development and empirical research
 * PHP 5.6 or higher
 * Apache2 with active mod_rewrite 
 * Apache config `AllowOverride All` needs to be set
+* Git
 
 
 ### Installation procedure

api/v1/job.php

@@ -58,7 +58,7 @@ public function get() {
                 }
                 $filters = [];
                 if ($this->get['supports'] == 'demoall') { // demo mode to match all systems
-                    // we acceppt all systems now
+                    // we accept all systems now
                 } else {
                     $supports = Systems_Library::getArrayFromString($this->get['supports']);
                     $filters[] = new ContainFilter(Job::SYSTEM_ID, $supports);
@@ -103,22 +103,16 @@ public function get() {
 
         if (isset($this->get['withLog']) && $this->get['withLog'] == true) {
             $path = UPLOADED_DATA_PATH . '/log/' . $job->getId() . '.log';
-            if (file_exists($path)) {
-                // read log from file
-                $log = file_get_contents($path);
-                if ($log === false) {
-                    $data->log = "";
-                } else {
-                    $data->log = $log;
-                }
-            } else {
+            $log = Util::readFileContents($path);
+            if ($log === false) {
                 $data->log = "";
+            } else {
+                $data->log = $log;
             }
         }
         $this->add($data);
     }
 
-
     public $post_access = Auth_Library::A_PUBLIC;
 
     /**

controllers/admin.php

@@ -481,7 +481,11 @@ public function system() {
             $this->view->assign('system', $system);
             $systemLib = new System($system->getId());
             $results = json_decode($systemLib->getResultsAll(), true);
-            $this->view->assign('results', $results['elements']);
+            if ($results === null) {
+                $this->view->assign('results', []);
+            } else {
+                $this->view->assign('results', $results['elements']);
+            }
             $this->view->assign('identifier', $systemLib->getIdentifier());
             $users = Factory::getUserFactory()->filter([]);
             $this->view->assign('users', $users);

controllers/project.php

@@ -272,4 +272,4 @@ public function detail() {
             throw new Exception("No project id provided!");
         }
     }
-}
+}

core/autoloader.php

@@ -49,6 +49,9 @@ function loader($className) {
         $folder = '/core/';
     } else {
         //parse out filename where class should be located
+        if (!str_contains($className, '_')) {
+            die("Invalid class name for autoload");
+        }
         list($filename, $suffix) = preg_split('/_/', $className);
 
         //select the folder where class should be located based on suffix
@@ -86,4 +89,4 @@ function loader($className) {
     }
 }
 
-spl_autoload_register("loader");
+spl_autoload_register("loader");

core/element.php

@@ -36,10 +36,11 @@ class Element {
      */
     public function __construct($path) {
         $this->path = $path . "/";
-        if (!file_exists($this->path . "config.json")) {
+        $file = Util::readFileContents($this->path . "config.json");
+        if ($file === false) {
             throw new Exception("No config available for element '$this->path'!");
         }
-        $this->config = json_decode(file_get_contents($this->path . "config.json"), true);
+        $this->config = json_decode($file, true);
     }
 
     public function isValid() {

core/plot.php

@@ -38,10 +38,11 @@ class Plot {
      */
     public function __construct($path) {
         $this->path = $path . "/";
-        if (!file_exists($this->path . "config.json")) {
+        $file = Util::readFileContents($this->path . "config.json");
+        if ($file === false) {
             throw new Exception("No config available for plot '$this->path'!");
         }
-        $this->config = json_decode(file_get_contents($this->path . "config.json"), true);
+        $this->config = json_decode($file, true);
     }
 
     public function isValid() {

core/router.php

@@ -34,7 +34,7 @@
 $log->debug('query string: ' . $request);
 
 // if $request is empty (user called www.domain.tld) show home
-if ($request == '') {
+if ($request === '' or $request === '/') {
     $page = DEFAULT_CONTROLLER;
     $action = DEFAULT_ACTION;
     $getVars = [];
@@ -138,11 +138,11 @@
     }
 
     // check if function exists
-    if (!method_exists($controller, $action)) {
+    if ($action === null or !method_exists($controller, $action)) {
         // function does not exist!
         $found = false;
         $log->debug('=> class found, but action does not exist: ' . $action);
-        die('=> class found, but action does not exist: ' . $action);
+        die('class found, but action does not exist: ' . $action);
     }
     $log->debug('controller found and instantiated: ' . $class);
 } else {

core/system.php

@@ -49,10 +49,11 @@ public function __construct($systemId) {
             throw new Exception("Failed to load system with ID $systemId!");
         }
         $this->path = SERVER_ROOT . "/webroot/systems/" . $this->model->getId() . "/";
-        if (!file_exists($this->path . "config.json")) {
+        $content = Util::readFileContents($this->path . System::CONFIG);
+        if ($content === false) {
             throw new Exception("Failed to load config for system with ID " . $this->model->getId());
         }
-        $this->config = json_decode(file_get_contents($this->path . System::CONFIG), true);
+        $this->config = json_decode($content, true);
     }
 
     public function getName() {
@@ -106,18 +107,19 @@ public function getViews() {
     }
 
     public function getParameters() {
-        if (!file_exists($this->path . System::PARAMETERS)) {
+        $contents = Util::readFileContents($this->path . System::PARAMETERS);
+        if ($contents === false) {
             return "{}";
         }
-        return file_get_contents($this->path . System::PARAMETERS);
+        return $contents;
     }
 
     public function getResultsAll($resultId = "") {
-        if (!file_exists($this->path . System::RESULTS)) {
+        $data = Util::readFileContents($this->path . System::RESULTS);
+        if ($data === false) {
             $this->convertResults();
+            $data = Util::readFileContents($this->path . System::RESULTS);
         }
-
-        $data = file_get_contents($this->path . System::RESULTS);
         if ($resultId != "") {
             $json = json_decode($data, true);
             if (!isset($json["elements"][$resultId])) {
@@ -130,32 +132,36 @@ public function getResultsAll($resultId = "") {
     }
 
     private function convertResults() {
-        if (!file_exists($this->path . System::RESULTS_JOB)) {
+        $dataJob = Util::readFileContents($this->path . System::RESULTS_JOB);
+        $dataAll = Util::readFileContents($this->path . System::RESULTS_ALL);
+        if ($dataJob === false) {
             $dataJob = "{}";
-        } else {
-            $dataJob = file_get_contents($this->path . System::RESULTS_JOB);
         }
-        if (!file_exists($this->path . System::RESULTS_ALL)) {
+        if ($dataAll === false) {
             $dataAll = "{}";
-        } else {
-            $dataAll = file_get_contents($this->path . System::RESULTS_ALL);
         }
         $jsonJob = json_decode($dataJob, true);
         $jsonAll = json_decode($dataAll, true);
 
         $json = ["version" => "1.0", "elements" => ["system-1" => ["job" => $jsonJob, "all" => $jsonAll, "name" => "Default"]]];
         $this->setResultsAll(json_encode($json));
-        unlink($this->path . System::RESULTS_ALL);
-        unlink($this->path . System::RESULTS_JOB);
-        sleep(1);
+        if (file_exists($this->path . System::RESULTS_ALL)) {
+            unlink($this->path . System::RESULTS_ALL);
+        }
+        if (file_exists($this->path . System::RESULTS_JOB)) {
+            unlink($this->path . System::RESULTS_JOB);
+        }
+	sleep(1);
     }
 
     public function getResultsJob($resultId = "") {
-        if (!file_exists($this->path . System::RESULTS)) {
+        $data = file_get_contents($this->path . System::RESULTS);
+
+        if ($data === false) {
             $this->convertResults();
+            $data = file_get_contents($this->path . System::RESULTS);
         }
 
-        $data = file_get_contents($this->path . System::RESULTS);
         if ($resultId != "") {
             $json = json_decode($data, true);
             if (!isset($json["elements"][$resultId])) {
@@ -219,4 +225,4 @@ public function deleteResults($resultId) {
         file_put_contents($this->path . System::RESULTS, json_encode($data));
         VCS_Library::commit($this->path, "Deleted results ID: $resultId");
     }
-}
+}

core/util.php

@@ -186,7 +186,7 @@ public static function mergeJobs($jobs, $parameter) {
      * @throws Exception
      */
     public static function scanForPlots($path) {
-        if (!file_exists($path) || !is_dir($path)) {
+        if (!is_dir($path)) {
             return [];
         }
         $dir = scandir($path);
@@ -245,6 +245,16 @@ public static function recursiveCopy($src, $dst) {
         closedir($dir);
     }
 
+    public static function readFileContents(string $file): string|false {
+        // There is still a window where the file can be deleted, and
+        // file_get_contents prints a warning to the page.  But when there
+        // is a way without that, only this helper needs to be changed.
+        if (file_exists($file)) {
+            return file_get_contents($file);
+        }
+        return false;
+    }
+
     public static function getObjectFromPhasesBitMask($bitMask, $obj = null) {
         if ($obj == null) {
             $obj = new stdClass();
@@ -456,15 +466,4 @@ public static function getNextIdForSystemResults($systemId) {
         return $newId;
     }
 
-    public static function updateSumsAndCounts($array, &$sums, &$counts) {
-        foreach ($array as $index => $value) {
-            if (isset($sums[$index])) {
-                $sums[$index] += $value;
-                $counts[$index] += 1;
-            } else {
-                $sums[$index] = $value;
-                $counts[$index] = 1;
-            }
-        }
-    }
-}
+}