Changeset 102 for branches/omero

Timestamp:

06/09/05 12:08:03 (4 years ago)

Author:

jmoore

Message:

Ha Ha. Things are working.

---

Unit/Integration testing works on a switch in maven "maven.test.mode"
All current tests passed, though there will be issues with nulls in
the returned objects.

Location:

branches/omero

Files:

• components/client/.springBeans (modified) (1 diff)
• components/client/src/client.properties (deleted)
• components/client/test/org/openmicroscopy/omero/client/itests/OmeroGrinderTest.java (moved) (moved from branches/omero/components/client/test/org/openmicroscopy/omero/client/OmeroGrinderTest.java) (2 diffs)
• components/client/test/org/openmicroscopy/omero/client/itests/OmeroHierarchyBrowsingIntegrationTest.java (moved) (moved from branches/omero/components/client/test/org/openmicroscopy/omero/client/OmeroHierarchyBrowsingIntegrationTest.java) (1 diff)
• components/client/test/org/openmicroscopy/omero/client/itests/test.xml (moved) (moved from branches/omero/components/client/test/org/openmicroscopy/omero/client/test.xml) (1 diff)
• components/client/test/org/openmicroscopy/omero/client/tests (deleted)
• components/server/.classpath (modified) (2 diffs)
• components/server/maven.xml (modified) (1 diff)
• components/server/project.xml (modified) (3 diffs)
• components/server/src/org/openmicroscopy/omero/logic/HierarchyBrowsingImpl.java (modified) (10 diffs)
• components/server/src/org/openmicroscopy/omero/logic/queries.hbm.xml (modified) (2 diffs)
• components/server/src/spring.properties (modified) (1 diff)
• components/server/test/org/openmicroscopy/omero/server/itests/OmeroServiceTest.java (modified) (1 diff)
• components/server/test/org/openmicroscopy/omero/server/utests/HierarchyBrowsingUnitTest.java (modified) (1 diff)
• components/server/web/WEB-INF/config-test.xml (modified) (1 diff)
• components/server/web/WEB-INF/data.xml (modified) (1 diff)
• components/server/web/WEB-INF/web.xml (modified) (1 diff)
• maven.xml (modified) (2 diffs)

branches/omero/components/client/.springBeans

@@ -2 +2 @@
 <beansProjectDescription>
         <configs>
-                <config>test/org/openmicroscopy/omero/tests/client/test.xml</config>
+                <config>test/org/openmicroscopy/omero/client/itests/test.xml</config>
                 <config>src/org/openmicroscopy/omero/client/spring.xml</config>
         </configs>

branches/omero/components/client/test/org/openmicroscopy/omero/client/itests/OmeroGrinderTest.java

@@ -2 +2 @@
  * Created on Jun 7, 2005
  */
-package org.openmicroscopy.omero.tests.client;
+package org.openmicroscopy.omero.client.itests;
 
 import org.openmicroscopy.omero.tests.AbstractOmeroHierarchyBrowserIntegrationTest;
@@ -21 +21 @@
         return new String[]{
                 "org/openmicroscopy/omero/client/spring.xml",
-                "org/openmicroscopy/omero/tests/client/test.xml"}; 
+                "org/openmicroscopy/omero/client/itests/test.xml"}; 
     }
     

branches/omero/components/client/test/org/openmicroscopy/omero/client/itests/OmeroHierarchyBrowsingIntegrationTest.java

@@ -2 +2 @@
  * Created on Jun 7, 2005
 */
-package org.openmicroscopy.omero.tests.client;
+package org.openmicroscopy.omero.client.itests;
 
 import java.util.HashSet;

branches/omero/components/client/test/org/openmicroscopy/omero/client/itests/test.xml

@@ -13 +13 @@
             <property name="driverClassName"><value>${database.driver}</value></property>
         <property name="url"><value>${database.url}</value></property>
-            <property name="username"><value>${database.user}</value></property>
+            <property name="username"><value>${database.username}</value></property>
             <property name="password"><value>${database.password}</value></property>
         </bean>

branches/omero/components/server/.classpath

@@ -1 +1 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-        <classpathentry kind="src" path="src"/>
-        <classpathentry kind="src" path="web/WEB-INF"/>
-        <classpathentry excluding="WEB-INF/|WEB-INF/" kind="src" path="web"/>
-        <classpathentry output="target/test-classes" kind="src" path="test"/>
-        <classpathentry output="target/test-classes" kind="src" path="itest"/>
+        <classpathentry excluding=".svn" kind="src" path="src"/>
+        <classpathentry excluding=".svn" kind="src" path="web"/>
+        <classpathentry excluding=".svn" kind="src" path="test"/>
         <classpathentry kind="var" path="MAVEN_REPO/junit/jars/junit-3.8.1.jar"/>
         <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
@@ -33 +31 @@
         <classpathentry kind="var" path="MAVEN_REPO/dbunit/jars/dbunit-2.1.jar"/>
         <classpathentry kind="var" path="MAVEN_REPO/groovy/jars/groovy-all-1.0-beta-10.jar"/>
-        <classpathentry kind="output" path="target/classes"/>
+        <classpathentry kind="output" path="target/eclipse"/>
 </classpath>

branches/omero/components/server/maven.xml

@@ -14 +14 @@
    <attainGoal name="tomcat:install"/>
  </goal>
-
-  <!-- For internal development. TODO -->
-  <preGoal name="war:war">
-    <attainGoal name="jar:install"/>
-  </preGoal>
 
  <!-- DB STUFF: TODO Perhaps in a build.xml (or use appfuses) -->

branches/omero/components/server/project.xml

@@ -179 +179 @@
     </dependency>
     <dependency>
+      <groupId>commons-lang</groupId>
+      <artifactId>commons-lang</artifactId>
+      <version>2.0</version>
+    </dependency>
+    <dependency>
       <groupId>commons-pool</groupId>
       <artifactId>commons-pool</artifactId>
@@ -247 +252 @@
         <include>**/*Test.java</include>
       </includes>
+      <resources>
+        <resource>
+          <directory>${pom.build.unitTestSourceDirectory}</directory>
+          <includes>
+            <include>**/*.xml</include>
+            <include>**/*.properties</include>
+          </includes>
+        </resource>
+      </resources>
     </unitTest>
     <resources>
@@ -253 +267 @@
         <includes>
           <include>**/*.hbm.xml</include>
+          <include>**/*.properties</include>
+        </includes>
+      </resource>
+      <resource>
+        <directory>web</directory>
+        <includes>
+          <include>**/*.xml</include>
         </includes>
       </resource>

branches/omero/components/server/src/org/openmicroscopy/omero/logic/HierarchyBrowsingImpl.java

@@ -38 +38 @@
 
 //Java imports
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -46 +48 @@
 
 //Third-party libraries
-
+import org.hibernate.Hibernate;
 
 //Application-internal dependencies
@@ -100 +102 @@
         }
 
-        return containerDao.loadHierarchy(arg0, arg1);
+        return clean(containerDao.loadHierarchy(arg0, arg1));
 
     }
@@ -115 +117 @@
         }
 
-        return containerDao.loadHierarchy(arg0, arg1);
+        return clean(containerDao.loadHierarchy(arg0, arg1));
 
     }
@@ -174 +176 @@
         }
 
-        return hierarchies;
+        return (Set) clean(hierarchies);
 
     }
@@ -239 +241 @@
         }
 
-        return hierarchies;
+        return (Set) clean(hierarchies);
     }
 
@@ -253 +255 @@
 
         List result = annotationDao.findImageAnnotations(arg0);
-        return sortImageAnnotations(result);
+        return (Map) clean(sortImageAnnotations(result));
 
     }
@@ -270 +272 @@
         List result = annotationDao.findImageAnnotationsForExperimenter(arg0,
                 arg1);
-        return sortImageAnnotations(result);
+        return (Map) clean(sortImageAnnotations(result));
 
     }
@@ -309 +311 @@
 
         List result = annotationDao.findDataListAnnotations(arg0);
-        return sortDatasetAnnotations(result);
+        return (Map) clean(sortDatasetAnnotations(result));
 
     }
@@ -354 +356 @@
     }
 
+    /** top-level call. If this is not initialized abort */
+    Object clean(Object obj){
+        if (! Hibernate.isInitialized(obj)){
+            throw new IllegalStateException("If the return object is not initialized then we can't send it.");
+        }
+        Set done = new HashSet();
+        hessianClean(obj,done);
+        return obj;
+    }
+       
+    void hessianClean(Object obj, Set done) {
+        
+        if (null==obj) return;
+        if (done.contains(obj)) return;
+        done.add(obj);
+        
+        if (obj instanceof Map) {
+            Map map = (Map) obj;
+            for (Iterator i = map.values().iterator(); i.hasNext();) {
+                Object value = i.next();
+                hessianClean(value,done);
+            }
+        } else if (obj instanceof Set) {
+            Set set = (Set) obj;
+            for (Iterator i = set.iterator(); i.hasNext();) {
+                Object item = i.next();
+                hessianClean(item,done);
+            }
+        } else { // TODO can check for super class when implemented
+            Method[] methods = obj.getClass().getDeclaredMethods();
+            for (int i = 0; i < methods.length; i++) {
+                Method method = methods[i];
+                if (method.getName().startsWith("get")){
+                    if (0==method.getParameterTypes().length){
+                        Object result=invokeGetter(obj,method);
+                        if (! Hibernate.isInitialized(result)){
+                            Method setter = getSetterForGetter(methods,method);
+                            if (null==setter){
+                                throw new IllegalStateException("No setter for getter; this will explode");
+                            }
+                            setToNull(obj,setter);
+                        } else {
+                            hessianClean(result,done);
+                        }
+                    }
+                }
+            }
+            
+        }
+    }
+    
+    Method getSetterForGetter(Method[] methods, Method getter){
+        for (int i = 0; i < methods.length; i++) {
+            Method method = methods[i];
+            if (method.getName().startsWith("set")){
+                if (method.getName().substring(1).equals(getter.getName().substring(1))){
+                    return method;
+                }
+            }
+        }
+        return null;
+    }
+    
+    Object invokeGetter(Object target, Method getter){
+        Object result=null;
+        try {
+            result = getter.invoke(target,new Object[]{});
+        } catch (IllegalArgumentException e) {
+            // TODO Auto-generated catch block
+            e.printStackTrace();
+        } catch (IllegalAccessException e) {
+            // TODO Auto-generated catch block
+            e.printStackTrace();
+        } catch (InvocationTargetException e) {
+            // TODO Auto-generated catch block
+            e.printStackTrace();
+        }
+        return result;
+    }
+    
+    void setToNull(Object obj, Method setter){
+        RuntimeException re = new RuntimeException("Error trying to set to null"); 
+
+        try {
+            setter.invoke(obj,new Object[]{null});
+        } catch (IllegalArgumentException e) {
+            // TODO Auto-generated catch block
+            e.printStackTrace();
+            throw re;
+        } catch (IllegalAccessException e) {
+            // TODO Auto-generated catch block
+            e.printStackTrace();
+            throw re;
+        } catch (InvocationTargetException e) {
+            // TODO Auto-generated catch block
+            e.printStackTrace();
+            throw re;
+        }
+    }
 
 

branches/omero/components/server/src/org/openmicroscopy/omero/logic/queries.hbm.xml

@@ -6 +6 @@
 <hibernate-mapping>
   <!-- load*Hierarchy 
-        TODO if all ids where called *.getId() then we could merge these
+        TODO if all ids where called *.getId() then we could merge these 
         -->
         
@@ -31 +31 @@
   <!-- find*Hierarchies -->
   <query name="findPDI"><![CDATA[
-        from Image as i where i in (:img_list)
+        from Image as i join fetch i.datasets as ds join fetch ds.projects as prj 
+          where i in (:img_list)
   ]]></query>   
   
   <query name="findCGCI"><![CDATA[
-        from Image as i where i in (:img_list)
+        from Image as i join fetch i.classifications as cla 
+          where i in (:img_list)
   ]]></query>   
   

branches/omero/components/server/src/spring.properties

@@ +1 @@
+# Database and Server properties generated from build properties TODO remove from svn
+#Wed Jun 08 22:55:04 CEST 2005
+database.username=josh
 TODO=deprecate
-db.url=jdbc:postgresql://localhost/ome
+server.host=localhost
+db.url=jdbc\:postgresql\://localhost/ome
+database.show_sql=true
+database.url=jdbc\:postgresql\://localhost/ome
+local.path=/home/josh/code/omero/components/server/target/classes
+db.driver=org.postgresql.Driver
+server.port=8080
+db.dialect=org.hibernate.dialect.PostgreSQLDialect
+database.password=""
+database.dialect=org.hibernate.dialect.PostgreSQLDialect
 db.user=josh
+database.driver=org.postgresql.Driver
 db.password=""
-db.driver=org.postgresql.Driver
-db.dialect=org.hibernate.dialect.PostgreSQLDialect
-#show_sql=false

branches/omero/components/server/test/org/openmicroscopy/omero/server/itests/OmeroServiceTest.java

@@ -19 +19 @@
      */
     protected String[] getConfigLocations() {
-        System.out.println(System.getProperty("user.dir"));
+
         return new String[]{
                 "WEB-INF/services.xml",
-                "org/openmicroscopy/omero/tests/client/test.xml",
-                "WEB-INF/dao.xml"}; 
+                "WEB-INF/dao.xml",
+                "WEB-INF/data.xml",
+                "WEB-INF/config-test.xml"}; 
     }
     

branches/omero/components/server/test/org/openmicroscopy/omero/server/utests/HierarchyBrowsingUnitTest.java

@@ -1 @@
-package org.openmicroscopy.omero.tests;
+package org.openmicroscopy.omero.server.utests;
 
 import java.util.ArrayList;

branches/omero/components/server/web/WEB-INF/config-test.xml

@@ -9 +9 @@
                 <property name="locations">
                 <list>
-                        <value>target/classes/spring.properties</value>
+                        <value>spring.properties</value>
                 </list>
                 </property>
         </bean>
 
+        <!-- Add this config file to the getConfigLocations() of your tests
+                if you want data and interfaces injected -->
+        <bean id="data" class="org.openmicroscopy.omero.tests.OMEPerformanceData" init-method="init">
+                <property name="dataSource" ref="dataSource"/>
+        </bean>
+
 </beans>

branches/omero/components/server/web/WEB-INF/data.xml

@@ -46 +46 @@
             <property name="driverClassName"><value>${database.driver}</value></property>
         <property name="url"><value>${database.url}</value></property>
-            <property name="username"><value>${database.user}</value></property>
+            <property name="username"><value>${database.username}</value></property>
             <property name="password"><value>${database.password}</value></property>
         </bean>

branches/omero/components/server/web/WEB-INF/web.xml

@@ -58 +58 @@
                 /WEB-INF/services.xml 
                 /WEB-INF/dao.xml                        
+                /WEB-INF/data.xml                       
 <!--                    /WEB-INF/security.xml -->
         </param-value>

branches/omero/maven.xml

@@ -43 +43 @@
       <ant:mkdir dir="${maven.build.dest}"/>
       <ant:propertyfile 
-        comment=" Database and Server properties generated from build properties" 
-                        file="${maven.build.dest}/spring.properties">
+        comment=" Database and Server properties generated from build
+properties TODO remove from svn" 
+                        file="${basedir}/src/spring.properties">
          <ant:entry key="database.driver" value="${database.driver}"/>
          <ant:entry key="database.url" value="${database.url}"/>
@@ -67 +68 @@
    </goal>
 
+ <!-- from: http://java2.5341.com/msg/33178.html -->
   <goal name="filterTests">
    <j:set var="testModeX" value="${maven.test.mode}X" />