merge spring-data-jpa

.gitignore

@@ -1,17 +1,20 @@
-
+.DS_Store
+.checkstyle
 *.iml
 web/src/main/webapp/WEB-INF/data/config/schema_plugins/*/schematron/schematron*.xsl
 web/src/main/webapp/WEB-INF/data/config/schemaplugin-uri-catalog.xml
 web/src/main/webapp/WEB-INF/classes/JZKitConfig.xml
 web/src/main/webapp/scripts/lib/*
 web/src/main/webapp/images/logos/*
+web/src/main/webapp/images/statTmp
 web/logs/
 web/jcs_caching/
-geonetwork*.db
-geonetwork-*
+web/geonetwork*.db
+/geonetwork*
 changes-*
 web/coverage.ec
 */target/
+*/.externalToolBuilders
 web/src/main/webapp/data/
 web/src/main/webapp/WEB-INF/lucene/
 web/src/main/webapp/WEB-INF/metadata_subversion/
@@ -31,10 +34,24 @@ web-client/src/main/resources/apps/html5ui/js/App-mini.js
 *.iml
 .idea/
 eclipse/
-web/src/main/webapp/WEB-INF/data/data
+web/src/main/webapp/WEB-INF/data/data/metadata_data
+web/src/main/webapp/WEB-INF/data/data/metadata_subversion
+web/src/main/webapp/WEB-INF/data/data/resources
 web/src/main/webapp/WEB-INF/data/index
 web-itest/jcs_caching
 bin/config_delawen.sh
 web-client/src/main/resources/apps/geocatch/js/App-mini.js
 web/dev-config/log4j-delawen.cfg
 
+datadir/
+*.factorypath
+web/src/main/webapp/WEB-INF/data/removed/
+web/.springBeans
+web/images/
+*.launch
+idea/
+web/src/main/webapp/WEB-INF/data/0*
+jcs_caching/
+web-ui/src/main/resources/catalog/lib/gn*.min.js
+web-ui/src/main/resources/catalog/style/gn*.css
+web-ui/src/main/resources/catalog/style/gn.css

README.md

@@ -1,5 +1,4 @@
-Features
---------
+# Features
 
 * Immediate search access to local and distributed geospatial catalogues
 * Up- and downloading of data, graphics, documents, pdf files and any other content type
@@ -8,4 +7,49 @@ Features
 * Scheduled harvesting and synchronization of metadata between distributed catalogs
 * Support for OGC-CSW 2.0.2 ISO Profile, OAI-PMH, Z39.50 protocols
 * Fine-grained access control with group and user management
-* Multi-lingual user interface
+* Multi-lingual user interface
+
+# Documentation
+
+User documentation is in the docs submodule in the current repository and is compiled into html pages during a release for publishing on
+a website.
+
+Developer documentation is also in the docs submodule but is being migrated out of that project into the Readme files in each module
+in the project.  General documentation for the project as a whole is in this Readme and module specific documentation can be found in
+each module (assuming there is module specific documentation required).
+
+# Software Development
+
+Instructions for setting up a development environment/building Geonetwork/compiling user documentation/making a release see:
+[Software Development Documentation](/software_development/)
+
+# Testing
+
+With regards to testing Geonetwork is a standard Java project and primarily depends on JUnit for testing.  However there is a very important
+issue to consider when writing JUnit tests in Geonetwork and that is the separation between unit tests and integration tests
+
+* *Unit Tests* - In Geonetwork unit tests should be very very quick to execute and not start up any subsystems of the application in order to keep
+    the execution time of the unit tests very short.  Integration tests do not require super classes and any assistance methods can be static
+    imports, for example statically importing org.junit.Assert or org.junit.Assume or org.fao.geonet.Assert.
+* *Integration Tests* - Integration Test typically start much or all of Geonetwork as part of the test and will take longer to run than
+    a unit test.  However, even though the tests take longer they should still be implemented in such a way to be as efficient as possible.
+    Starting Geonetwork in a way that isolates each integration test from each other integration test is non-trivial.  Because of this
+    there are `abstract` super classes to assist with this.  Many modules have module specific Abstract classes.  For example at the time
+    that this is being written `domain`, `core`, `harvesters` and `services` modules all have module specific super classes that need to
+    be used.  (`harvesting` has 2 superclasses depending on what is to be tested.)
+    The easiest way to learn how to implement an integration test is to search for other integration tests in the same module as the class
+    you want to test.  The following list provides a few tips:
+    * *IMPORTANT*: All Integrations tests *must* end in IntegrationTest.  The build system assumes all tests ending in IntegrationTest is
+        an integration test and runs them in a build phase after unit tests.  All other tests are assumed to be unit tests.
+    * Prefer unit tests over Integration Tests because they are faster.
+    * Search the current module for IntegrationTest to find tests to model your integration test against
+    * This you might want integration tests for are:
+        * Services: If the service already exists and you quick need to write a test to debug/fix its behaviour.
+                    If you are writing a new service it is better to use Mockito to mock the dependencies of the service so the test is
+                    a unit test.
+        * Harvesters
+        * A behaviour that crosses much of the full system
+
+*org.fao.geonet.utils.GeonetHttpRequestFactory*: When making Http requests you should use org.fao.geonet.utils.GeonetHttpRequestFactory instead
+    of directly using HttpClient.  This is because there are mock instances of org.fao.geonet.utils.GeonetHttpRequestFactory that can
+    be used to mock responses when performing tests.

bin/start.ps1

@@ -1,3 +1,7 @@
+param (
+	[string]$mode = "build"
+)
+
 $scriptPath = split-path -parent $MyInvocation.MyCommand.Definition
 . "$scriptPath\config.ps1"
 
@@ -14,16 +18,20 @@ if (!(test-path Env:\JREBEL_HOME)) {
 	echo "Env:JREBEL_HOME is found.  Configuring JRebel. JREBEL_OPTS = $JREBEL_OPTS"
 }
 
-$Env:MAVEN_OPTS=""
-
-cmd /c "cd $JEEVES_DIR && mvn install $args"
+if ($mode -eq "build") {
+	$Env:MAVEN_OPTS=""
 
-#if (  ]; then
-#    echo "[FAILURE] [deploy] Failed to execute 'jeeves' correctly"
-#    exit -1
-#fi
+	cmd /c "cd $scriptPath\..\common && mvn install $args"
+	cmd /c "cd $scriptPath\..\domain && mvn install $args"
+	cmd /c "cd $JEEVES_DIR && mvn install $args"
+	cmd /c "cd $scriptPath\..\core && mvn install $args"
+	cmd /c "cd $scriptPath\..\csw-server && mvn install $args"
+	cmd /c "cd $scriptPath\..\healthmonitor && mvn install $args"
+	cmd /c "cd $scriptPath\..\harvesters && mvn install $args"
+	cmd /c "cd $scriptPath\..\services && mvn install $args"
+}
 
-$Env:MAVEN_OPTS="$JREBEL_OPTS $DEBUG $OVERRIDES $MEMORY -Dgeonetwork.dir=$DATA_DIR $LOGGING -Dfile.encoding=UTF8"
+$Env:MAVEN_OPTS="$JREBEL_OPTS $DEBUG $OVERRIDES $MEMORY -Dgeonetwork.dir=$DATA_DIR -Dfile.encoding=UTF8"
 
-cmd /c "cd $WEB_DIR &&  mvn jetty:run -Penv-dev -Pwidgets $args"
-cd $scriptPath
+cmd /c "cd $WEB_DIR &&  mvn jetty:run -Penv-inspire $args"
+cd $scriptPath

cachingxslt/README.md

@@ -0,0 +1,2 @@
+The cachingxslt module contains an XSLT parser that will cache the compiled XSLT Style sheet to improve the performance of performing
+XSLT transformations.

cachingxslt/pom.xml

@@ -19,19 +19,41 @@
   <description>
     Caching xslt project.
   </description>
-
-  <licenses>
-    <license>
-      <name>General Public License (GPL)</name>
-      <url>http://www.gnu.org/licenses/old-licenses/gpl-2.0.txt</url>
-      <distribution>repo</distribution>
-    </license>
-  </licenses>
-
-  <dependencies>
-    <dependency>
-      <groupId>net.sf.saxon</groupId>
-      <artifactId>saxon</artifactId>
-    </dependency>
-  </dependencies>
+
+	<licenses>
+		<license>
+			<name>General Public License (GPL)</name>
+			<url>http://www.gnu.org/licenses/old-licenses/gpl-2.0.txt</url>
+			<distribution>repo</distribution>
+		</license>
+	</licenses>
+
+	<dependencies>
+		<dependency>
+			<groupId>net.sf.saxon</groupId>
+			<artifactId>saxon</artifactId>
+		</dependency>
+	</dependencies>
+
+	<profiles>
+		<profile>
+			<id>run-static-analysis</id>
+			<activation>
+				<property>
+					<name>!skipTests</name>
+				</property>
+			</activation>
+			<build>
+				<plugins>
+					<plugin>
+						<groupId>org.codehaus.mojo</groupId>
+						<artifactId>findbugs-maven-plugin</artifactId>
+					</plugin>
+				</plugins>
+			</build>
+		</profile>
+	</profiles>
+	<properties>
+		<rootProjectDir>${basedir}/..</rootProjectDir>
+	</properties>
 </project>

cachingxslt/src/main/java/de/fzi/dbs/xml/transform/CachingTransformerFactory.java

@@ -29,13 +29,13 @@ public class CachingTransformerFactory extends TransformerFactoryImpl
   private static Map<String, TemplatesCacheEntry> templatesCache = new HashMap<String, TemplatesCacheEntry>();
 
   /** Factory logger. */
-  protected static Logger logger =
+  protected static final Logger logger =
     Logger.getLogger(CachingTransformerFactory.class);
 
   /** Active readers count. */
-  protected static int activeReaders = 0;
+  static int activeReaders = 0;
   /** Active writers count. */
-  protected static int activeWriters = 0;
+  static int activeWriters = 0;
 
 	/**
 	 * Clear the stylesheet cache. This is not part of the 
@@ -215,7 +215,7 @@ protected synchronized void afterWrite()
   /**
    * Private class to hold templates cache entry.
    */
-  private class TemplatesCacheEntry
+  private static final class TemplatesCacheEntry
   {
     /** When was the cached entry last modified. */
     private long lastModified;

code_quality/README.md

@@ -0,0 +1,3 @@
+The files in this directory are used for configuring IDEs or are used by the build tool to make certain code quality checks.
+
+For example findbugs-ecludes is used by both the build tool's findbugs implementation as well as IDES for running findbugs.

code_quality/checkstyle_checks.xml

@@ -32,7 +32,7 @@
     <module name="ParameterName"/>
     <module name="StaticVariableName"/>
     <module name="TypeName"/>
-    <module name="AvoidStarImport"/>
+    <!--<module name="AvoidStarImport"/>-->
     <module name="IllegalImport"/>
     <module name="RedundantImport"/>
     <module name="UnusedImports"/>
@@ -47,7 +47,7 @@
       <property name="tokens" value="BNOT,DEC,DOT,INC,LNOT,UNARY_MINUS,UNARY_PLUS"/>
     </module>
     <module name="NoWhitespaceBefore"/>
-    <module name="OperatorWrap"/>
+    <!--<module name="OperatorWrap"/>-->
     <module name="ParenPad"/>
     <module name="TypecastParenPad"/>
     <module name="WhitespaceAfter"/>
@@ -72,7 +72,7 @@
     </module>
     <module name="SimplifyBooleanExpression"/>
     <module name="SimplifyBooleanReturn"/>
-    <module name="DesignForExtension"/>
+    <!--<module name="DesignForExtension"/>-->
     <module name="FinalClass"/>
     <module name="HideUtilityClassConstructor"/>
     <module name="InterfaceIsType"/>

code_quality/checkstyle_suppressions.xml

@@ -7,5 +7,17 @@
 <suppressions>
     <suppress files=".*Test.*\.java" checks="[a-zA-Z0-9]*"/>
     <suppress files=".*DummyGraph\.java" checks="[a-zA-Z0-9]*"/>
-    <suppress files=".*" checks="[a-zA-Z0-9]*"/>
+    <suppress files="core/.*" checks="[a-zA-Z0-9]*"/>
+    <suppress files="cachingxslt/.*" checks="[a-zA-Z0-9]*"/>
+    <suppress files="csw-server/.*" checks="[a-zA-Z0-9]*"/>
+    <suppress files="dummy-api/.*" checks="[a-zA-Z0-9]*"/>
+    <suppress files="harvesters/.*" checks="[a-zA-Z0-9]*"/>
+    <suppress files="health-monitor/.*" checks="[a-zA-Z0-9]*"/>
+    <suppress files="jeeves/.*" checks="[a-zA-Z0-9]*"/>
+    <suppress files="oaipmh/.*" checks="[a-zA-Z0-9]*"/>
+    <suppress files="services/.*" checks="[a-zA-Z0-9]*"/>
+    <suppress files="web-app/.*" checks="[a-zA-Z0-9]*"/>
+    <suppress files="common/.*" checks="[a-zA-Z0-9]*"/>
+    <suppress files="domain/.*_.java" checks="[a-zA-Z0-9]*"/>
+    <suppress files="domain/.*" checks="DesignForExtension"/>
 </suppressions>

code_quality/findbugs-excludes.xml

@@ -7,7 +7,17 @@
 	<Match>
 		<Class name="~.*\..*Test" />
 	</Match>
-
+
+    <!-- 			Domain Exceptions 					-->
+	<Match>
+		<Class name="~org\.fao\.geonet\.domain\.\S+_$" />
+	</Match>
+    <!-- 			Oaipmh Exceptions 					-->
+	<Match>
+		<Class name="org.fao.oaipmh.util.ISODate" />
+		<Bug pattern="REC_CATCH_EXCEPTION" />
+	</Match>
+
 	<!--              Jeeves  Exceptions                 -->
 	<Match>
 		<Class name="jeeves.server.JeevesEngine" />
@@ -72,6 +82,10 @@
 		<Bug pattern="RCN_REDUNDANT_NULLCHECK_OF_NONNULL_VALUE" />
 		<Method name="processCQLTermNode"/>
 	</Match>
+	<Match>
+		<Class name="de.fzi.dbs.xml.transform.CachingTransformerFactory" />
+		<Bug pattern="RCN_REDUNDANT_NULLCHECK_OF_NONNULL_VALUE" />
+	</Match>
 	<Match>
 		<Class name="org.fao.geonet.services.metadata.BatchVersion" />
 		<Bug pattern="RCN_REDUNDANT_NULLCHECK_OF_NONNULL_VALUE" />
@@ -82,25 +96,25 @@
 		<Bug pattern="RCN_REDUNDANT_NULLCHECK_OF_NONNULL_VALUE" />
 		<Method name="serviceSpecificExec"/>
 	</Match>
-	<Match>
-		<Bug pattern="SE_COMPARATOR_SHOULD_BE_SERIALIZABLE" />
-	</Match>
-
-	<Match>
-		<Or>
-			<Class name="org.fao.geonet.services.extent.ExtentManager" />
-			<Class name="org.fao.geonet.services.extent.Update" />
-		</Or>
-		<Bug pattern="LG_LOST_LOGGER_DUE_TO_WEAK_REFERENCE " />
-	</Match>
+    <Match>
+        <Class name="org.fao.geonet.DatabaseMigration" />
+        <Bug pattern="SQL_NONCONSTANT_STRING_PASSED_TO_EXECUTE" />
+        <Method name="newLookup"/>
+    </Match>
+    <Match>
+        <Bug pattern="SE_COMPARATOR_SHOULD_BE_SERIALIZABLE" />
+    </Match>
+    <Match>
+        <Class name="org.fao.geonet.services.ownership.OwnershipUtils$1" />
+    </Match>
+
 
 <!-- The following bugs are hard to fix should be fixed because they can cause problems in servers with multiple geonetworks running -->	
 	<Match>
 		<Or>
 			<Class name="org.fao.geonet.kernel.search.LuceneSearcher" />
 			<Class name="org.fao.geonet.kernel.search.spatial.SpatialIndexWriter" />
 			<Class name="org.fao.geonet.kernel.search.SearchManager" />
-			<Class name="org.fao.geonet.services.extent.ExtentManager" />
 		</Or>
 		<Bug pattern="ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD" />
 	</Match>

common/README.md

@@ -0,0 +1,2 @@
+The common module contains very basic utilities that are useful for all projects.  For example utilities for assisting with parsing
+and encoding XML or making HTTP requests.