Merge branch 'xdmod8.1' into coldfront_integration_lite

ubccr · Nov 9, 2018 · 196b1ad · 196b1ad
2 parents 882ef29 + 4552ced
commit 196b1ad
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diff --git a/Dockerfile b/Dockerfile
@@ -1 +1 @@
-FROM       tas-tools-ext-01.ccr.xdmod.org/xdmod-centos7:open7.5.1-v5
+FROM       tas-tools-ext-01.ccr.xdmod.org/xdmod-centos7:open8.0.0-v1
diff --git a/bin/xdmod-upgrade b/bin/xdmod-upgrade
@@ -26,8 +26,7 @@ ini_set('memory_limit', -1);
  * @var array
  */
 $supportedUpgrades = array(
-    '7.5.0' => '7.5.1',
-    '7.5.1' => '8.0.0',
+    '8.0.0' => '8.1.0',
 );
 
 /**

diff --git a/classes/Authentication/SAML/XDSamlAuthentication.php b/classes/Authentication/SAML/XDSamlAuthentication.php
@@ -37,8 +37,6 @@ class XDSamlAuthentication
 Name:              %s
 Username:          %s
 E-Mail:            %s
-Organization ID:   %s
-Organization Name: %s
 
 SAML Attributes ----------------------------------
 %s
@@ -244,71 +242,33 @@ public function getLoginLink()
      * @param array $samlAttributes the attributes that we received via SAML for this user.
      * @param boolean $linked whether or not we were able to link the SSO User with an XDMoD Person.
      * @throws Exception if there is a problem with notifying the user.
-     * @throws Exception if there is a problem retrieving the name for the users organization.
      */
     private function handleNotifications(XDUser $user, $samlAttributes, $linked)
     {
-        // We only notify admins iff we were unable to identify which organization the user should
-        // be associated with ( i.e. we had to assign them to the 'Unknown' organization ).
-        if ($user->getOrganizationID() === -1) {
-            $techSupportRecipient = \xd_utilities\getConfiguration('general', 'tech_support_recipient');
-            $senderEmail = \xd_utilities\getConfiguration('mailer', 'sender_email');
-
-            $userEmail = $user->getEmailAddress()
-                ? $user->getEmailAddress()
-                : $samlAttributes['email_address'][0];
-
-            $userOrganization = $user->getOrganizationID();
-
-            $emailBody = sprintf(
-                self::BASE_ADMIN_EMAIL,
-                $user->getFormalName(true),
-                $user->getUsername(),
-                $userEmail,
-                $userOrganization,
-                Organizations::getNameById($userOrganization),
-                json_encode($samlAttributes, JSON_PRETTY_PRINT)
-            );
+        if ($user->getOrganizationID() !== -1) {
+            // Only send email if we were unable to identify an organization for the user.
+            return;
+        }
 
-            $subject = sprintf(
-                'New %s Single Sign On User Created',
-                ($linked ? 'Linked' : 'Unlinked')
-            );
+        $subject = sprintf(
+            'New %s Single Sign On User Created',
+            ($linked ? 'Linked' : 'Unlinked')
+        );
 
-            $this->notify(
-                $techSupportRecipient,
-                $techSupportRecipient,
-                '',
-                $senderEmail,
-                $subject,
-                $emailBody
-            );
-        }
-    }
+        $body = sprintf(
+            self::BASE_ADMIN_EMAIL,
+            $user->getFormalName(true),
+            $user->getUsername(),
+            $user->getEmailAddress(),
+            json_encode($samlAttributes, JSON_PRETTY_PRINT)
+        );
 
-    /**
-     * Attempt to generate / send a notification email with the specified parameters.
-     *
-     * @param string $toAddress    the address that the notification will be sent to.
-     * @param string $fromAddress  the address that the notification will be sent from.
-     * @param string $fromName     A name to be used when identifying the `$fromAddress`
-     * @param string $replyAddress the address to be used when a user replies to the notification.
-     * @param string $subject      the subject of the notification.
-     * @param string $body         the body of the notification.
-     *
-     * @throws Exception if there is a problem sending the notification email.
-     */
-    public function notify($toAddress, $fromAddress, $fromName, $replyAddress, $subject, $body)
-    {
         try {
             MailWrapper::sendMail(
                 array(
                     'subject' => $subject,
                     'body' => $body,
-                    'toAddress' => $toAddress,
-                    'fromAddress' => $fromAddress,
-                    'fromName' => $fromName,
-                    'replyAddress' => $replyAddress
+                    'toAddress' => \xd_utilities\getConfiguration('general', 'tech_support_recipient')
                 )
             );
         } catch (Exception $e) {

diff --git a/classes/Rest/Controllers/WarehouseControllerProvider.php b/classes/Rest/Controllers/WarehouseControllerProvider.php
@@ -1482,8 +1482,15 @@ private function getJobData(Application $app, XDUser $user, $realm, $jobId, $act
      */
     private function getJobDataSet(XDUser $user, $realm, $jobId, $action)
     {
+        $config = \Xdmod\Config::factory();
+
+        $rawstats = $config['rawstatistics'];
+        if (!isset($rawstats['realms'][$realm])) {
+            throw new \DataWarehouse\Query\Exceptions\AccessDeniedException;
+        }
+
         $params = array(
-            new \DataWarehouse\Query\Model\Parameter('_id', '=', $jobId)
+            new \DataWarehouse\Query\Model\Parameter($rawstats['realms'][$realm]['primary_key'], '=', $jobId)
         );
 
         $QueryClass = "\\DataWarehouse\\Query\\$realm\\JobDataset";
@@ -1761,17 +1768,27 @@ private function processHistoryRequest(Application $app, XDUser $user, $realm, $
      */
     private function processHistoryDefaultRealmRequest(Application $app, $action)
     {
+        $config = \Xdmod\Config::factory();
+
+        $rawstats = $config['rawstatistics'];
+
+        $results = array();
+
+        if (isset($rawstats['realms'])) {
+            foreach($rawstats['realms'] as $realm => $realmconfig) {
+                $results[] = array(
+                    'dtype' => 'realm',
+                    'realm' => $realm,
+                    'text' => $realmconfig['name']
+                );
+            }
+        }
+
         return $app->json(
             array(
                 'success' => true,
                 'action' => $action,
-                'results' => array(
-                    array(
-                        'dtype' => 'realm',
-                        'realm' => 'SUPREMM',
-                        'text' => 'SUPREMM'
-                    )
-                )
+                'results' => $results
             )
         );
     }
@@ -2062,14 +2079,21 @@ private function getJobTimeSeriesData(Application $app, Request $request, \XDUse
      */
     private function getJobByPrimaryKey(Application $app, \XDUser $user, $realm, $searchparams)
     {
+        $config = \Xdmod\Config::factory();
+
+        $rawstats = $config['rawstatistics'];
+        if (!isset($rawstats['realms'][$realm])) {
+            throw new \DataWarehouse\Query\Exceptions\AccessDeniedException;
+        }
+
         if (isset($searchparams['jobref'])) {
             $params = array(
-                new \DataWarehouse\Query\Model\Parameter('_id', '=', $searchparams['jobref'])
+                new \DataWarehouse\Query\Model\Parameter($rawstats['realms'][$realm]['primary_key'], '=', $searchparams['jobref'])
             );
         } else {
             $params = array(
                 new \DataWarehouse\Query\Model\Parameter("resource_id", "=", $searchparams['resource_id']),
-                new \DataWarehouse\Query\Model\Parameter("local_job_id", "=", $searchparams['local_job_id'])
+                new \DataWarehouse\Query\Model\Parameter($rawstats['realms'][$realm]['ident_key'], "=", $searchparams['local_job_id'])
             );
         }
 

diff --git a/configuration/portal_settings.ini b/configuration/portal_settings.ini
@@ -6,7 +6,7 @@ contact_page_recipient = ""
 tech_support_recipient = ""
 
 ; The version number is updated during the upgrade process.
-version = "8.0.0"
+version = "8.1.0"
 
 debug_mode = "off"
 debug_recipient = ""

diff --git a/configuration/rawstatistics.d/.gitignore b/configuration/rawstatistics.d/.gitignore
diff --git a/configuration/rawstatistics.json b/configuration/rawstatistics.json
@@ -0,0 +1,3 @@
+{
+    "realms": []
+}
diff --git a/etl/js/lib/dataset_processor.js b/etl/js/lib/dataset_processor.js
@@ -240,16 +240,17 @@ DatasetProcessor.prototype.process = function (totalCores, coreIndex) {
     var self = this;
     var multiCore = totalCores !== undefined && coreIndex !== undefined;
     if (this.dataset.input.dbEngine == 'mongodb') {
-        var uri_decode_auth = this.dataset.input.config.uri.indexOf('@') > -1;
-
-        MongoClient.connect(self.dataset.input.config.uri, {native_parser: true, uri_decode_auth: uri_decode_auth}, function(err, db) {
+        MongoClient.connect(self.dataset.input.config.uri, { useNewUrlParser: true }, function (err, client) {
             if (err) {
                 self.emit("error", self.dataset.name + ': ' + "MongoClient Open Error: " + util.inspect(err));
                 self._processEnded = true;
                 self.onEndProcess();
                 return;
             }
 
+            self.client = client;
+            var db = client.db();
+
             self.emit('message', self.dataset.name + ': connected to database \'' + db.databaseName + '\'');
 
             //look for jobs that haven't been processed yet,
@@ -267,8 +268,7 @@ DatasetProcessor.prototype.process = function (totalCores, coreIndex) {
                 return;
             }
 
-            self.db = db;
-            self.collection = self.db.collection(self.dataset.input.config.collection);
+            self.collection = db.collection(self.dataset.input.config.collection);
 
             // Ensure the query is indexed
             var indexParams = {};
@@ -378,8 +378,8 @@ DatasetProcessor.prototype.onEndProcess = function () {
     if (this.stats.currentlyMarking === 0) {
         this.mysqlPool.end();
         this.emit('message', this.dataset.name + ': mysqlPool closed');
-        if (this.db) {
-            this.db.close();
+        if (this.client) {
+            this.client.close(true);
             this.emit('message', this.dataset.name + ': mongo connection closed');
         }
 

diff --git a/etl/js/package.json b/etl/js/package.json
@@ -8,7 +8,7 @@
     "dependencies": {
         "cloneextend": "0.0.x",
         "ini": "1.2.x",
-        "mongodb": "2.1.x",
+        "mongodb": "3.1.x",
         "mysql": "2.2.x",
         "tv4": "^1.0.13",
         "winston": "0.7.x",

diff --git a/html/gui/js/modules/job_viewer/JobViewer.js b/html/gui/js/modules/job_viewer/JobViewer.js
@@ -216,7 +216,9 @@ XDMoD.Module.JobViewer = Ext.extend(XDMoD.PortalModule, {
             modal: true,
             title: 'Search',
             layout: 'fit',
-            resizable: false,
+            resizable: true,
+            boxMaxHeight: 641,
+            boxMaxWidth: 1014,
             items: [searchPanel]
         });
         searchPanel.relayEvents(self.searchWindow, ['show', 'hide', 'move']);