Merge branch 'release/v0.21.0'

Author: rubenarslan

.gitignore

@@ -30,9 +30,9 @@ nohup.out
 webroot/*.html
 webroot/assets/*.mp4
 webroot/assets/*.html
-webroot/assets/bower_components
 webroot/assets/lib/bower_components
 /bin/migra.php
 /*.key
+formr.feature_dockerprep.version
 webroot/study
-bin/create-named-sessions.php
+bin/create-named-sessions.php

.zenodo.json

@@ -3,7 +3,7 @@
     "upload_type": "software",
     "creators": [
         {
-            "affiliation": "Center for Adaptive Rationality, Max Planck Institute for Human Development",
+            "affiliation": "Wilhelm Wundt Institute of Psychology, University of Leipzig",
             "name": "Ruben C. Arslan",
             "orcid": "0000-0002-6670-5658"
         },

application/Controller/AdminAccountController.php

@@ -13,7 +13,7 @@ public function __construct(Site &$site) {
     public function indexAction() {
         if (!$this->user->loggedIn()) {
             alert('You need to be logged in to go here.', 'alert-info');
-            $this->request->redirect('login');
+            $this->request->redirect('admin/account/login');
         }
 
         $vars = array('showform' => false);
@@ -128,7 +128,7 @@ public function registerAction() {
         if ($this->request->isHTTPPostRequest() && $site->request->str('email') && filter_var($this->request->str('email'), FILTER_VALIDATE_EMAIL)) {
             if (!Session::canValidateRequestToken($site->request) || Site::getSettings('signup:allow', 'true') !== 'true') {
                 alert('Could not process your request please try again later', 'alert-danger');
-                return $this->request->redirect('register');
+                return $this->request->redirect('admin/account/register');
             }
 
 
@@ -156,13 +156,13 @@ public function verifyEmailAction() {
 
         if ($this->request->isHTTPGetRequest() && $this->request->str('token')) {
             $user->resendVerificationEmail($this->request->str('token'));
-            $this->request->redirect('login');
+            $this->request->redirect('admin/account/login');
         } elseif (!$verification_token || !$email) {
             alert("You need to follow the link you received in your verification mail.");
-            $this->request->redirect('login');
+            $this->request->redirect('admin/account/login');
         } else {
             $user->verifyEmail($email, $verification_token);
-            $this->request->redirect('login');
+            $this->request->redirect('admin/account/login');
         };
     }
 
@@ -188,7 +188,7 @@ public function resetPasswordAction() {
 
         if ($this->request->isHTTPGetRequest() && (!$this->request->str('email') || !$this->request->str('reset_token')) && !$this->request->str('ok')) {
             alert('You need to follow the link you received in your password reset mail');
-            $this->request->redirect('forgot_password');
+            $this->request->redirect('admin/account/forgot-password');
         } elseif ($this->request->isHTTPPostRequest()) {
             $postRequest = new Request($_POST);
             $info = array(
@@ -198,7 +198,7 @@ public function resetPasswordAction() {
                 'new_password_confirm' => $postRequest->str('new_password_c'),
             );
             if (($done = $user->resetPassword($info))) {
-                $this->request->redirect('forgot_password');
+                $this->request->redirect('admin/account/forgot-password');
             }
         }
 

application/Controller/AdminController.php

@@ -93,7 +93,7 @@ protected function setView($template, $vars = array()) {
     protected function header() {
         if (!($cookie = Session::getAdminCookie())) {
             alert('You need to login to access the admin section', 'alert-warning');
-            $this->request->redirect('login');
+            $this->request->redirect('admin/account/login');
         }
 
         $this->user = new User($cookie[0], $cookie[1]);

application/Controller/ApiController.php

@@ -82,7 +82,7 @@ public function osfAction($do = '') {
         $user = Site::getCurrentUser();
         if (!$user->loggedIn()) {
             alert('You need to login to access this section', 'alert-warning');
-            redirect_to('login');
+            redirect_to('admin/account/login');
         }
 
         $osfconfg = Config::get('osf');

application/Functions.php

@@ -27,7 +27,11 @@ function formr_log_exception(Exception $e, $prefix = '', $debug_data = null) {
 }
 
 function get_log_file($filename) {
-    return APPLICATION_ROOT . "tmp/logs/$filename";
+    if(Config::get('error_to_stderr') == 1) {
+        return "php://stderr";
+    } else {
+        return APPLICATION_ROOT . "tmp/logs/$filename";
+    }
 }
 
 function alert($msg, $class = 'alert-warning', $dismissable = true) { // shorthand
@@ -756,15 +760,17 @@ function run_url($name = '', $action = '', $params = array()) {
         return site_url('run/' . $name . '/' . $action);
     }
 
-    $protocol = Config::get('define_root.protocol');
-    $domain = trim(Config::get('define_root.doc_root', ''), "\/\\");
+    $protocol = Config::get('protocol');
+    # use different domain for studies if set, independent of wildcard subdomain setting
+    $domain = trim(Config::get('study_domain', ''), "*\/\\");
     $subdomain = null;
+    
     if (Config::get('use_study_subdomains')) {
-        $domain = Config::get('define_root.study_domain', $domain); # use different domain for studies if set
-        $subdomain = strtolower($name) . '.';
+        $subdomain = strtolower($name);
     } else {
         $domain .= '/' . $name;
     }
+
     $url = $protocol . $subdomain . $domain;
     if ($action) {
         $action = trim($action, "\/\\");
@@ -1348,7 +1354,7 @@ function opencpu_debug($session, OpenCPU $ocpu = null, $rtype = 'json') {
                 }
             }
 
-            $urls = $session->getResponsePathsAsLinks();
+            $urls = $session->getFiles();
             if (!$session->hasError() AND!empty($urls)) {
                 $locations = '';
                 foreach ($urls AS $path => $link) {

application/Services/OpenCPU.php

@@ -1,8 +1,12 @@
 <?php
-
+// todo:
+// differentiate calls into those that need auth and those that don't
+// in the call function, check whether opencpu server was set up with auth
+// 
 class OpenCPU {
 
-    protected $baseUrl = 'https://public.opencpu.org';
+    protected $localUrl = null;
+    protected $publicUrl = null;
     protected $libUri = '/ocpu/library';
     protected $last_message = null;
     protected $rLibPath = '/usr/local/lib/R/site-library';
@@ -52,40 +56,35 @@ protected function __construct($instance) {
         foreach ($config as $key => $value) {
             $property = lcfirst(preg_replace('/\s+/', '', ucwords(str_replace('_', ' ', $key))));
             if (property_exists($this, $property)) {
-                $this->{$property} = $value;
+                $this->{$property} = rtrim($value, "/");
             }
         }
+        
+        if(!empty($config["base_url"]) && empty($config['public_url'])
+            && empty($config['local_url'])) {
+            $this->localUrl = $config["base_url"];
+            $this->publicUrl = $config["base_url"];
+        }
 
         $this->curl_opts = $this->curl_opts + array_val($config, 'curl_opts', array());
     }
 
-    /**
-     * @param string $baseUrl
-     */
-    public function setBaseUrl($baseUrl) {
-        if ($baseUrl) {
-            $baseUrl = rtrim($baseUrl, "/");
-            $this->baseUrl = $baseUrl;
-        }
+    public function getPublicUrl() {
+        return $this->publicUrl;
     }
 
-    public function getBaseUrl() {
-        return $this->baseUrl;
+    public function getLocalUrl() {
+        return $this->localUrl;
     }
 
     public function getRLibPath() {
         return $this->rLibPath;
     }
 
-    public function getRTempBaseUrl() {
+    public function getRTempPublicUrl() {
         return self::TEMP_BASE_URL;
     }
 
-    public function setLibUrl($libUri) {
-        $libUri = trim($libUri, "/");
-        $this->libUri = '/' . $libUri;
-    }
-
     public function getLibUri() {
         return $this->libUri;
     }
@@ -135,9 +134,9 @@ public function getRequestInfo($item = null) {
      * @throws OpenCPU_Exception
      */
     private function call($uri = '', $params = array(), $method = CURL::HTTP_METHOD_GET) {
-        if ($uri && strstr($uri, $this->baseUrl) === false) {
+        if ($uri && strstr($uri, $this->localUrl) === false) {
             $uri = "/" . ltrim($uri, "/");
-            $url = $this->baseUrl . $this->libUri . $uri;
+            $url = $this->localUrl . $this->libUri . $uri;
         } else {
             $url = $uri;
         }
@@ -168,7 +167,7 @@ private function call($uri = '', $params = array(), $method = CURL::HTTP_METHOD_
             return new OpenCPU_Session(null, null, $results, $this);
         } elseif ($this->curl_info['http_code'] < 200 || $this->curl_info['http_code'] > 302) {
             if (!$results) {
-                $results = "OpenCPU server '{$this->baseUrl}' could not be contacted";
+                $results = "OpenCPU server '{$this->publicUrl}' could not be contacted";
             }
             throw new OpenCPU_Exception($results, $this->curl_info['http_code']);
         }
@@ -307,14 +306,19 @@ public function getKey() {
      * Get an array of files present in current session
      *
      * @param string $match You can match only files with some slug in the path name
-     * @param string $baseURL URL segment to prepend to paths
+     * @param string $localUrl URL segment to prepend to paths
      * @return array
      */
-    public function getFiles($match = '/files/', $baseURL = null) {
+    public function getFiles($match = '/files/', $baseUrl = null) {
         if (!$this->key) {
             return null;
         }
 
+        if($baseUrl !== null) {
+            $baseUrl = str_replace($this->caller()->getLocalUrl(), 
+                        $this->caller()->getPublicUrl(), $baseUrl);
+        }
+
         $files = array();
         $result = explode("\n", $this->raw_result);
         foreach ($result as $path) {
@@ -323,38 +327,7 @@ public function getFiles($match = '/files/', $baseURL = null) {
             }
 
             $id = basename($path);
-            $files[$id] = $baseURL ? $baseURL . $path : $this->getResponsePath($path);
-        }
-        return $files;
-    }
-
-    /**
-     * Get absolute URLs of all resources in the response
-     *
-     * @return array
-     */
-    public function getResponsePaths() {
-        if (!$this->key || $this->isJSONResult()) {
-            return null;
-        }
-
-        $result = explode("\n", $this->raw_result);
-        $files = array();
-        foreach ($result as $id => $path) {
-            $files[$id] = $this->getResponsePath($path);
-        }
-        return $files;
-    }
-
-    public function getResponsePathsAsLinks() {
-        if (!$this->key || $this->isJSONResult()) {
-            return null;
-        }
-
-        $result = explode("\n", $this->raw_result);
-        $files = array();
-        foreach ($result as $path) {
-            $files[$path] = $this->getResponsePath($path);
+            $files[$id] = $baseUrl ? $baseUrl . $path : $this->getResponsePath($path);
         }
         return $files;
     }
@@ -363,8 +336,9 @@ public function getLocation() {
         return $this->location;
     }
 
-    public function getFileURL($path) {
-        return $this->getResponsePath('/files/' . $path);
+    public function getPublicLocation() {
+        return str_replace($this->caller()->getLocalUrl(), 
+                        $this->caller()->getPublicUrl(), $this->location);
     }
 
     public function getObject($name = 'json', $params = array()) {
@@ -379,8 +353,8 @@ public function getObject($name = 'json', $params = array()) {
             $object = $this->getJSONObject($object);
         }
         if (is_string($object)) {
-            $object = str_replace($this->ocpu->getRLibPath(), $this->getBaseUrl() . $this->ocpu->getLibUri(), $object);
-            return str_replace($this->ocpu->getRTempBaseUrl(), $this->getLocation() . 'files/', $object);
+            $object = str_replace($this->ocpu->getRLibPath(), $this->getPublicUrl() . $this->ocpu->getLibUri(), $object);
+            return str_replace($this->ocpu->getRTempPublicUrl(), $this->getPublicLocation() . 'files/', $object);
         }
 
         return $object;
@@ -399,8 +373,8 @@ public function getJSONObject($string = null, $as_assoc = true) {
         // if decoded object is a non-empty array, get it's first element
         if (is_array($json) && array_key_exists(0, $json)) {
             if (is_string($json[0])) {
-                $string = str_replace($this->ocpu->getRLibPath(), $this->getBaseUrl() . $this->ocpu->getLibUri(), $json[0]);
-                return str_replace($this->ocpu->getRTempBaseUrl(), $this->getLocation() . 'files/', $string);
+                $string = str_replace($this->ocpu->getRLibPath(), $this->getLocalUrl() . $this->ocpu->getLibUri(), $json[0]);
+                return str_replace($this->ocpu->getRTempPublicUrl(), $this->getPublicLocation() . 'files/', $string);
             }
             return $json[0];
         }
@@ -464,12 +438,16 @@ public function getResponseHeaders() {
         return $this->caller()->getResponseHeaders();
     }
 
-    public function getBaseUrl() {
-        return $this->caller()->getBaseUrl();
+    public function getPublicUrl() {
+        return $this->caller()->getPublicUrl();
+    }
+
+    public function getLocalUrl() {
+        return $this->caller()->getLocalUrl();
     }
 
     protected function getResponsePath($path) {
-        return $this->caller()->getBaseUrl() . $path;
+        return $this->caller()->getPublicUrl() . $path;
     }
 
 }