Merge pull request #1417 from NCEAS/dev-2.12

Dev 2.12

README.md

@@ -1,6 +1,6 @@
 # Metacat: Data Preservation and Discovery System
 
-Version: 2.12.2 Release
+Version: 2.12.3 Release
 
 Send feedback and bugs to: [email protected]
                            http://github.com/NCEAS/metacat
@@ -67,6 +67,11 @@ for the next release.
 
 ## Release Notes
 
+### Release Notes for 2.12.3
+New features and bugs fixed in this release:
+* Return an invalid response to the call of cn.getLogRecords if some log records have a null ip address
+* Add the indication of completing the database upgrade process during configuration
+
 ### Release Notes for 2.12.2
 Bugs fixed in this release:
 * Modify the schema files of the format ids of portal and collections 

build.properties

@@ -2,7 +2,7 @@
 
 #Version of this build.  This needs to be a dotted numeric version.  For
 #instance 1.9.1 is okay.  1.9.1_rc1 is not.
-metacat.version=2.12.2
+metacat.version=2.12.3
 
 #This is for packaging purposes.  leave it blank for final production release.
 metacat.releaseCandidate=

docs/user/metacat/source/dataone.rst

@@ -328,17 +328,60 @@ These Apache directives are crucial for Metacat to function as a Tier 2+ Member
 ::
 
   ...
-  AllowEncodedSlashes On
-  AcceptPathInfo      On
-  JkOptions +ForwardURICompatUnparsed
-  SSLEngine on
-  SSLOptions +StrictRequire +StdEnvVars +ExportCertData
-  SSLVerifyClient optional
-  SSLVerifyDepth 10
-  SSLCertificateFile /etc/ssl/certs/<your_server_certificate>
-  SSLCertificateKeyFile /etc/ssl/private/<your_server_key>
-  SSLCertificateChainFile /etc/ssl/certs/<CA_chain_file>.crt
-  SSLCACertificatePath /etc/ssl/certs/
+  <VirtualHost XXX.XXX.XXX.XXX:443> 
+        DocumentRoot /var/www 
+        ServerName dev.nceas.ucsb.edu
+        ## Allow CORS requests from all origins to use cookies
+        SetEnvIf Origin "^(.*)$" ORIGIN_DOMAIN=$1
+        Header set Access-Control-Allow-Origin "%{ORIGIN_DOMAIN}e" env=ORIGIN_DOMAIN
+        Header set Access-Control-Allow-Headers "Authorization, Content-Type, Origin, Cache-Control"
+        Header set Access-Control-Allow-Methods "GET, POST, PUT, OPTIONS"
+        Header set Access-Control-Allow-Credentials "true"
+        ErrorLog /var/log/httpd/error_log 
+        CustomLog /var/log/httpd/access_log common 
+        ScriptAlias /cgi-bin/ "/var/www/cgi-bin/" 
+        <Directory /var/www/cgi-bin/> 
+          AllowOverride None 
+          Options ExecCGI 
+          Require all granted
+        </Directory> 
+        ScriptAlias /metacat/cgi-bin/ "/var/www/webapps/metacat/cgi-bin/" 
+        <Directory "/var/www/webapps/metacat/cgi-bin/"> 
+          AllowOverride None 
+          Options ExecCGI 
+          Require all granted
+        </Directory> 
+        <IfModule mod_rewrite.c>
+                RewriteEngine on
+                RewriteCond %{HTTP:Authorization} ^(.*)
+                RewriteRule .* - [e=HTTP_AUTHORIZATION:%1]
+        </IfModule>
+        JkMount /metacat ajp13 
+        JkMount /metacat/* ajp13 
+        JkMount /metacat/metacat ajp13 
+        JkUnMount /metacat/cgi-bin/* ajp13 
+        JkMount /metacatui ajp13 
+        JkMount /metacatui/* ajp13 
+        JkMount /*.jsp ajp13 
+        AllowEncodedSlashes On
+        AcceptPathInfo      On
+        JkOptions +ForwardURICompatUnparsed
+        SSLEngine on
+        SSLOptions +StrictRequire +StdEnvVars +ExportCertData
+        SSLVerifyClient optional
+        SSLVerifyDepth 10
+        SSLCertificateFile /etc/ssl/certs/<your_server_certificate>
+        SSLCertificateKeyFile /etc/ssl/private/<your_server_key>
+        SSLCertificateChainFile /etc/ssl/certs/<CA_chain_file>.crt
+        SSLCACertificatePath /etc/ssl/certs/
+        <Location "/metacat/d1/mn">
+                #SSLRenegBufferSize 10000000
+                #SSLOptions +OptRenegotiate
+                <If " ! ( %{HTTP_USER_AGENT} =~ /(windows|chrome|mozilla|safari|webkit|httr|julia|python)/i )">
+                        SSLVerifyClient optional
+                </If>
+        </Location>
+  </VirtualHost> 
   ...
   
 Where ``<your_server_certificate>`` and ``<your_server_key>`` are the certificate/key pair used by Apache 

docs/user/metacat/source/install.rst

@@ -252,8 +252,8 @@ install and run the Metacat Registry or to use the Metacat Replication feature.
         DocumentRoot /var/www 
         ServerName dev.nceas.ucsb.edu
         ## Allow CORS requests from all origins to use cookies
-        #SetEnvIf Origin "^(.*)$" ORIGIN_DOMAIN=$1
-        #Header set Access-Control-Allow-Origin "%{ORIGIN_DOMAIN}e" env=ORIGIN_DOMAIN
+        SetEnvIf Origin "^(.*)$" ORIGIN_DOMAIN=$1
+        Header set Access-Control-Allow-Origin "%{ORIGIN_DOMAIN}e" env=ORIGIN_DOMAIN
         Header set Access-Control-Allow-Headers "Authorization, Content-Type, Origin, Cache-Control"
         Header set Access-Control-Allow-Methods "GET, POST, PUT, OPTIONS"
         Header set Access-Control-Allow-Credentials "true"
@@ -263,15 +263,13 @@ install and run the Metacat Registry or to use the Metacat Replication feature.
         <Directory /var/www/cgi-bin/> 
           AllowOverride None 
           Options ExecCGI 
-          Order allow,deny 
-          Allow from all 
+          Require all granted
         </Directory> 
         ScriptAlias /metacat/cgi-bin/ "/var/www/webapps/metacat/cgi-bin/" 
         <Directory "/var/www/webapps/metacat/cgi-bin/"> 
           AllowOverride None 
           Options ExecCGI 
-          Order allow,deny 
-          Allow from all 
+          Require all granted
         </Directory> 
         JkMount /metacat ajp13 
         JkMount /metacat/* ajp13 

lib/metacat.properties

@@ -14,6 +14,12 @@ configutil.geoserverConfigured=false
 configutil.dataoneConfigured=false
 configutil.ezidConfigured=bypassed
 
+#The property of configutil.upgrade.status depends on other status (database, java et al). 
+#If all of them are success, the property of configutil.upgrade will be successs; otherwise failure.
+configutil.upgrade.status=
+configutil.upgrade.database.status=
+configutil.upgrade.java.status=
+
 ############### Server Values #################
 
 server.name=localhost
@@ -25,7 +31,7 @@ server.internalPort=80
 ############### Application Values ############
 
 ## one of the few places where we use ANT tokens
-application.metacatVersion=2.12.2
+application.metacatVersion=2.12.3
 application.metacatReleaseInfo=-1
 application.readOnlyMode=false
 
@@ -119,6 +125,7 @@ database.upgradeVersion.2.11.1=upgrade-db-to-2.11.1
 database.upgradeVersion.2.12.0=upgrade-db-to-2.12.0
 database.upgradeVersion.2.12.1=upgrade-db-to-2.12.1
 database.upgradeVersion.2.12.2=upgrade-db-to-2.12.2
+database.upgradeVersion.2.12.3=upgrade-db-to-2.12.3
 
 ## for running java-based utilities
 database.upgradeUtility.1.5.0=edu.ucsb.nceas.metacat.admin.upgrade.Upgrade1_5_0

metacat-common/pom.xml

@@ -4,7 +4,7 @@
 	<groupId>edu.ucsb.nceas.metacat.common</groupId>
 	<artifactId>metacat-common</artifactId>
 	<packaging>jar</packaging>
-	<version>2.12.2</version>
+	<version>2.12.3</version>
 	<name>metacat-common</name>
 	<url>http://maven.apache.org</url>
 	<properties>

metacat-index/pom.xml

@@ -4,13 +4,13 @@
 	<groupId>edu.ucsb.nceas.metacat.index</groupId>
 	<artifactId>metacat-index</artifactId>
 	<packaging>war</packaging>
-	<version>2.12.2</version>
+	<version>2.12.3</version>
 	<name>metacat-index</name>
 	<url>http://maven.apache.org</url>
 
 	<properties>
         <d1_cn_index_processor_version>2.3.8</d1_cn_index_processor_version>
-        <metacat_common_version>2.12.2</metacat_common_version>
+        <metacat_common_version>2.12.3</metacat_common_version>
     </properties>
 
 	<repositories>

pom.xml

@@ -4,15 +4,15 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>org.ecoinformatics</groupId>
     <artifactId>metacat</artifactId>
-    <version>2.12.2</version>
+    <version>2.12.3</version>
     <name>metacat</name>
     <packaging>war</packaging>
     <url>http://maven.apache.org</url>
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <d1_libclient_version>2.3.1</d1_libclient_version>
         <d1_portal_version>2.3.1</d1_portal_version>
-        <metacat_common_version>2.12.2</metacat_common_version>            
+        <metacat_common_version>2.12.3</metacat_common_version>            
     </properties>
     <repositories>
         <repository>

src/edu/ucsb/nceas/metacat/EventLog.java

@@ -642,21 +642,38 @@ public Log getD1Report(String[] ipAddress, String[] principal, String[] docid,
 	            //process the result and return it            
 	            while (rs.next()) {
 	            	LogEntry logEntry = new LogEntry();
-	            	logEntry.setEntryId(rs.getString(1));
+	            	String logId = rs.getString(1);
+	            	if (logId == null || logId.trim().equals("")) {
+	            	    logId = "N/A";
+	            	}
+	            	logEntry.setEntryId(logId);
 
 	            	Identifier identifier = new Identifier();
-	            	identifier.setValue(rs.getString(2));
+	            	String id = rs.getString(2);
+	            	if (id == null || id.trim().equals("")) {
+	            	    id = "N/A";
+	            	}
+	            	identifier.setValue(id);
 					logEntry.setIdentifier(identifier);
 
-	            	logEntry.setIpAddress(anonymous ? "N/A" : rs.getString(3));
+	            String ip = rs.getString(3);
+	            if (ip == null || ip.trim().equals("")) {
+	                ip = "N/A";
+	            }
+	            	logEntry.setIpAddress(anonymous ? "N/A" : ip);
+
 	            	String userAgent = "N/A";
 	            	if (rs.getString(4) != null) {
 	            		userAgent = rs.getString(4);
 	            	}
 	            	logEntry.setUserAgent(userAgent);
 
 	            	Subject subject = new Subject();
-	            	subject.setValue(anonymous ? "N/A" : rs.getString(5));
+	            	String subjectStr = rs.getString(5);
+	            	if (subjectStr == null || subjectStr.trim().equals("")) {
+	            	    subjectStr = "N/A";
+	            	}
+	            	subject.setValue(anonymous ? "N/A" : subjectStr);
 					logEntry.setSubject(subject);
 
 					String logEventString = rs.getString(6);

src/edu/ucsb/nceas/metacat/MetaCatServlet.java

@@ -1056,9 +1056,20 @@ private void handleGetOrPost(HttpServletRequest request,
 				out.close();
 			} else if (action.equals("getversion")) {
 				response.setContentType("text/xml");
-				PrintWriter out = response.getWriter();
-				out.println(MetacatVersion.getVersionAsXml());
-				out.close();
+				String version = null;
+				try {
+				    version = MetacatVersion.getVersionAsXml();
+				    PrintWriter out = response.getWriter();
+	                out.println(version);
+	                out.close();
+				} catch (SQLException e) {
+				    PrintWriter out = response.getWriter();
+				    out.println("<?xml version=\"1.0\"?>");
+                    out.println("<erorr>");
+                    out.println(StringEscapeUtils.escapeXml(e.getMessage()));
+                    out.println("</erorr>");
+                    out.close();
+				}
 			} else if (action.equals("getlog")) {
 				handler.handleGetLogAction(params, request, response, userName, groupNames, sessionId);
 			} else if (action.equals("getloggedinuserinfo")) {

src/edu/ucsb/nceas/metacat/MetacatVersion.java

@@ -23,6 +23,14 @@
  */
 package edu.ucsb.nceas.metacat;
 
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.sql.Timestamp;
+import java.util.Date;
+
+import edu.ucsb.nceas.metacat.database.DBConnection;
+import edu.ucsb.nceas.metacat.database.DBConnectionPool;
 import edu.ucsb.nceas.metacat.properties.PropertyService;
 import edu.ucsb.nceas.utilities.PropertyNotFoundException;
 
@@ -52,12 +60,53 @@ public static String getVersionID() throws PropertyNotFoundException {
 	 * 
 	 * @return the version wrapped in an XML document
 	 */
-    public static String getVersionAsXml() throws PropertyNotFoundException {
+    public static String getVersionAsXml() throws SQLException {
         StringBuffer sb = new StringBuffer();
         sb.append("<?xml version=\"1.0\"?>");
         sb.append("<version>");
-        sb.append(getVersionID());
+        sb.append(getVersionFromDB());
         sb.append("</version>");
         return sb.toString();
     }
+
+
+    /**
+     * Get the version number from DB
+     * @return  a string of the Metacat version from DB
+     * @throws SQLException
+     */
+    public static String getVersionFromDB() throws SQLException {
+        DBConnection conn = null;
+        PreparedStatement pstmt = null;
+        ResultSet rs = null;
+        String version = null;
+        int serialNumber = -1;
+        try {
+            // check out DBConnection
+            conn = DBConnectionPool.getDBConnection("MetacatVersion.getVersionFromDB()");
+            serialNumber = conn.getCheckOutSerialNumber();
+            pstmt = conn.prepareStatement("SELECT version FROM db_version WHERE status = ?");
+            pstmt.setInt(1, 1);
+            rs = pstmt.executeQuery();
+            if(rs.next()) {
+                version = rs.getString(1);
+            }
+            pstmt.close();
+            rs.close();
+        } catch (SQLException e) {
+            throw new SQLException("MetacatVersion.getVersionFromDB - sql error: " + e.getMessage());
+        }finally {
+            try {
+                if (pstmt != null) {
+                    pstmt.close();
+                }
+                if (rs != null) {
+                    rs.close();
+                }
+            } finally {
+                DBConnectionPool.returnDBConnection(conn, serialNumber);
+            }
+        }
+        return version;
+    }
 }