J21tc9

Model/lib/conifer/roles/conifer/vars/default.yml

@@ -34,24 +34,27 @@ _host_frontends:
   w2: ''
 
 _userdb_link_map:
-  apicomms:    prods.login_comment
-  apicommn:    prodn.login_comment
-  apicommbetas: betas.login_comment
-  apicommbetan: betan.login_comment
-  apicommdevs: devs.login_comment
-  apicommdevn: devn.login_comment
+  apicomms:       prods.login_comment
+  apicommn:       prodn.login_comment
+  apicommbetas:   betas.login_comment
+  apicommbetan:   betan.login_comment
+  apicommdevs:    devs.login_comment
+  apicommdevn:    devn.login_comment
+  apicommd:       devn.login_comment  # local dev
   apicommlegacys: legacys.login_comment
   apicommlegacyn: legacyn.login_comment
-  cecomms:     ceprods.login_comment
-  cecommn:     ceprodn.login_comment
-  cecommdevs:  cedevs.login_comment
-  cecommdevn:  cedevn.login_comment
-  userdb:      vm.userdb
+  cecomms:        ceprods.login_comment
+  cecommn:        ceprodn.login_comment
+  cecommdevs:     cedevs.login_comment
+  cecommdevn:     cedevn.login_comment
+  cecommd:        cedevn.login_comment  # local dev
+  userdb:         vm.userdb
 
 _acctdb_link_map:
   acctdbn: acctdbN.profile
   acctdbs: acctdbS.profile
-  acctdb:  vm.acctdb # savm
+  acctdb: acctdbN.profile  # local dev
+#  acctdb:  vm.acctdb # savm
 
 modelconfig_modelName: =c= WDK model name, e.g. ToxoDB
 

Model/pom.xml

@@ -82,7 +82,7 @@
 
     <dependency>
       <groupId>javax.servlet</groupId>
-      <artifactId>servlet-api</artifactId>
+      <artifactId>javax.servlet-api</artifactId>
       <scope>provided</scope>
     </dependency>
 
@@ -151,10 +151,11 @@
     </dependency>
 
     <!-- Contains context listener used to prevent classloader memory leaks (used by web.xmls) -->
+    <!-- This is throwing errors and want to eliminate it as a possible error cause
     <dependency>
       <groupId>se.jiderhamn.classloader-leak-prevention</groupId>
-      <artifactId>classloader-leak-prevention-servlet</artifactId>
-    </dependency>
+      <artifactId>classloader-leak-prevention-servlet3</artifactId>
+    </dependency>-->
 
     <dependency>
       <groupId>junit</groupId>

Model/src/main/java/org/eupathdb/common/db/EuPathDbDriverInitializer.java

@@ -5,6 +5,7 @@
 import java.util.Properties;
 
 import org.apache.log4j.Logger;
+import org.gusdb.fgputil.db.platform.SupportedPlatform;
 import org.gusdb.fgputil.db.pool.ConnectionPoolConfig;
 import org.gusdb.fgputil.db.pool.DbDriverInitializer;
 import org.gusdb.fgputil.db.runner.SQLRunner;
@@ -55,8 +56,10 @@ public void closeConnection(Connection connection, ConnectionPoolConfig dbConfig
     if (dbConfig instanceof ModelConfigAppDB) {
       connection.setAutoCommit(true);
       ModelConfigAppDB appDbConfig = (ModelConfigAppDB)dbConfig;
-      closeDbLink(connection, appDbConfig.getUserDbLink());
-      closeDbLink(connection, appDbConfig.getAcctDbLink());
+      if (appDbConfig.getPlatformEnum() == SupportedPlatform.ORACLE) {
+        closeDbLink(connection, appDbConfig.getUserDbLink());
+        closeDbLink(connection, appDbConfig.getAcctDbLink());
+      }
     }
     // set auto-commit back to what it was
     connection.setAutoCommit(incomingAutoCommit);

Site/dashboard/autoload.php

@@ -0,0 +1,18 @@
+<?php
+
+function rglob(string $path): void {
+  foreach (glob($path . "/*") as $subpath) {
+    if (is_dir($subpath)) {
+      rglob($subpath);
+    } elseif (basename($subpath) == "functions.php") {
+      require_once $subpath;
+    }
+  }
+}
+
+rglob(__DIR__ . "/lib");
+
+spl_autoload_extensions(".php");
+spl_autoload_register(function(string $class) {
+  require_once str_replace("\\", "/", $class) . ".php";
+});

Site/dashboard/config/module.php

@@ -2,48 +2,61 @@
 // keyworkd, module, and whether a menu tab should be made
 // exclude_hosts is an optional regex matching against
 // $_SERVER['SERVER_NAME']
-$pageMap = array(
-    'Databases' => array(
-        'module' => "view/databaseInfo.php",
-        'tab' => 1),
-    'Database Connection Pool' => array(
-        'module' => "view/dbConnectionPool.php",
-        'tab' => 0),
-    'WDK State' => array(
-        'module' => "view/stateInfo.php",
-        'tab' => 1),
-    'Configuration' => array(
-        'module' => "view/configurationInfo.php",
-        'tab' => 1),
-    'Tomcat' => array(
-        'module' => "view/tomcatInfo.php",
-        'tab' => 1),
-    'Apache' => array(
-        'module' => "view/apacheInfo.php",
-        'tab' => 1),
-    'Proxy' => array(
-        'module' => "view/proxyInfo.php",
-        'tab' => 1),
-    'Build' => array(
-        'module' => "view/buildInfo.php",
-        'tab' => 1),
-    'Announcements' => array(
-        'module' => "/cgi-bin/admin/messageConsole.pl",
-        'tab' => 1),
-    'Performance' => array(
-        'module' => 'view/performance.php',
-        'tab' => 1),
-    'Services' => array(
-        'module' => 'view/services.php',
-        'tab' => 1),
-    'JSLint' => array(
-        'module' => 'view/jslint.php',
-        'tab' => 0),
-    'Logger'  => array(
-        'module' => "view/logger.php",
-        'tab' => 0),
-    'About'  => array(
-        'module' => "view/about.php",
-        'tab' => 0),
-   );
-?>
+return [
+  'Databases'          => [
+    'module' => "view/databaseInfo.php",
+    'tab'    => 1
+  ],
+  'DB Connection Pool' => [
+    'module' => "view/dbConnectionPool.php",
+    'tab'    => 0
+  ],
+  'WDK State'          => [
+    'module' => "view/stateInfo.php",
+    'tab'    => 1
+  ],
+  'Configuration'      => [
+    'module' => "view/configurationInfo.php",
+    'tab'    => 1
+  ],
+  'Tomcat'             => [
+    'module' => "view/tomcatInfo.php",
+    'tab'    => 1
+  ],
+  'HTTP Server'        => [
+    'module' => "view/serverInfo.php",
+    'tab'    => 1
+  ],
+  'Proxy'              => [
+    'module' => "view/proxyInfo.php",
+    'tab'    => 1
+  ],
+  'Build'              => [
+    'module' => "view/buildInfo.php",
+    'tab'    => 1
+  ],
+  'Announcements'      => [
+    'module' => "/cgi-bin/admin/messageConsole.pl",
+    'tab'    => 1
+  ],
+  'Performance'        => [
+    'module' => 'view/performance.php',
+    'tab'    => 1
+  ],
+  'Services'           => [
+    'module' => 'view/services.php',
+    'tab'    => 1
+  ],
+  'JSLint'             => [
+    'module' => 'view/jslint.php',
+    'tab'    => 0
+  ],
+  'Logger'             => [
+    'module' => "view/logger.php",
+    'tab'    => 0
+  ],
+  'About'              => [
+    'module' => "view/about.php",
+    'tab'    => 0
+  ],
+];

Site/dashboard/head.php.inc

@@ -1,25 +1,25 @@
 <head>
-    <title><?php print $_SERVER['HTTP_HOST'] ?> /dashboard</title>
-    <meta http-equiv="content-type" content="text/html; charset=iso-8859-1" />
+  <title><?=$_SERVER['HTTP_HOST']?>/dashboard</title>
+  <meta http-equiv="content-type" content="text/html; charset=iso-8859-1"/>
 
-    <link rel="stylesheet" type="text/css" href="css/ui-lightness/jquery-ui-1.8.21.custom.css" />
-    <link rel="stylesheet" type="text/css" href="js/DataTables/media/css/jquery.dataTables.min.css">  
-    <link rel="stylesheet" type="text/css" href="css/main.css" />
-    <!-- use local JS files. Do not make client fetch from  Google because site might be hosted on a virtual machine with no internet acdess -->
-    <script type='text/javascript' src='js/jquery.min.js'></script>
-    <script type='text/javascript' src='js/jquery-ui.min.js'></script>
-    <script type='text/javascript' src='js/overlib.js'></script>
-    <script type='text/javascript' src='js/main.js'></script>
-    <script type="text/javascript" charset="utf8" src="js/DataTables/media/js/jquery.dataTables.min.js"></script>
+  <link rel="stylesheet" type="text/css" href="css/ui-lightness/jquery-ui-1.8.21.custom.css"/>
+  <link rel="stylesheet" type="text/css" href="js/DataTables/media/css/jquery.dataTables.min.css">
+  <link rel="stylesheet" type="text/css" href="css/main.css"/>
+  <!-- use local JS files. Do not make client fetch from  Google because site might be hosted on a virtual machine with no internet acdess -->
+  <script type='text/javascript' src='js/jquery.min.js'></script>
+  <script type='text/javascript' src='js/jquery-ui.min.js'></script>
+  <script type='text/javascript' src='js/overlib.js'></script>
+  <script type='text/javascript' src='js/main.js'></script>
+  <script type="text/javascript" charset="utf8" src="js/DataTables/media/js/jquery.dataTables.min.js"></script>
 
-    <script type="text/javascript">
-      var ol_textcolor = "#003366";
-      var ol_fgcolor = "#ffffff";
-      var ol_bgcolor = "#003366";
-      var ol_texsize = "11px";
-      var ol_cellpad = "5";
-      var ol_height = -1;
-      var ol_vpos = ABOVE;
-    </script>
+  <script type="text/javascript">
+    const ol_textcolor = "#003366";
+    const ol_fgcolor = "#ffffff";
+    const ol_bgcolor = "#003366";
+    const ol_texsize = "11px";
+    const ol_cellpad = "5";
+    const ol_height = -1;
+    const ol_vpos = ABOVE;
+  </script>
 </head>