sorted out some issues integrating into tomcat.

giffordlabcvr · Jul 29, 2015 · d27090f · d27090f
1 parent 3d4ace7
commit d27090f
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Showing 28 changed files with 648 additions and 108 deletions.
diff --git a/.classpath b/.classpath
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="output" path="bin"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER" exported="true"/>
+</classpath>
diff --git a/.gradle/2.4/taskArtifacts/cache.properties.lock b/.gradle/2.4/taskArtifacts/cache.properties.lock
diff --git a/.gradle/2.4/taskArtifacts/fileHashes.bin b/.gradle/2.4/taskArtifacts/fileHashes.bin
diff --git a/.gradle/2.4/taskArtifacts/fileSnapshots.bin b/.gradle/2.4/taskArtifacts/fileSnapshots.bin
diff --git a/.gradle/2.4/taskArtifacts/outputFileStates.bin b/.gradle/2.4/taskArtifacts/outputFileStates.bin
diff --git a/.gradle/2.4/taskArtifacts/taskArtifacts.bin b/.gradle/2.4/taskArtifacts/taskArtifacts.bin
diff --git a/.project b/.project
@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>gluetools</name>
+	<comment/>
+	<projects/>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.eclipse.wst.common.project.facet.core.nature</nature>
+		<nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
+		<nature>org.eclipse.jem.workbench.JavaEMFNature</nature>
+	</natures>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments/>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.wst.common.project.facet.core.builder</name>
+			<arguments/>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.wst.validation.validationbuilder</name>
+			<arguments/>
+		</buildCommand>
+	</buildSpec>
+	<linkedResources/>
+</projectDescription>
diff --git a/.settings/org.eclipse.jdt.core.prefs b/.settings/org.eclipse.jdt.core.prefs
@@ -0,0 +1,13 @@
+#
+#Wed Jul 29 13:36:23 BST 2015
+org.eclipse.jdt.core.compiler.debug.localVariable=generate
+org.eclipse.jdt.core.compiler.compliance=1.8
+org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
+org.eclipse.jdt.core.compiler.debug.sourceFile=generate
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
+org.eclipse.jdt.core.compiler.debug.lineNumber=generate
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
+org.eclipse.jdt.core.compiler.source=1.8
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
diff --git a/.settings/org.eclipse.wst.common.component b/.settings/org.eclipse.wst.common.component
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project-modules id="moduleCoreId" project-version="2.0">
+	<wb-module deploy-name="gluetools"/>
+</project-modules>
diff --git a/.settings/org.eclipse.wst.common.project.facet.core.xml b/.settings/org.eclipse.wst.common.project.facet.core.xml
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<faceted-project>
+	<fixed facet="jst.java"/>
+	<installed facet="jst.utility" version="1.0"/>
+	<installed facet="jst.java" version="1.8"/>
+</faceted-project>
diff --git a/.settings/org.eclipse.wst.validation.prefs b/.settings/org.eclipse.wst.validation.prefs
@@ -0,0 +1,11 @@
+DELEGATES_PREFERENCE=delegateValidatorList
+USER_BUILD_PREFERENCE=enabledBuildValidatorList
+USER_MANUAL_PREFERENCE=enabledManualValidatorList
+USER_PREFERENCE=overrideGlobalPreferencestruedisableAllValidationfalseversion1.2.600.v201501211647
+eclipse.preferences.version=1
+override=true
+suspend=false
+vals/org.eclipse.angularjs.core.HTMLAngularValidator/global=FF01
+vals/org.eclipse.wst.html.core.HTMLValidator/global=FF01
+vals/org.eclipse.wst.xml.core.xml/global=FF03
+vf.version=3
diff --git a/build.gradle b/build.gradle
@@ -1,7 +1,36 @@
+apply plugin: 'java'
+apply plugin: 'eclipse-wtp'
+
 project('gluetools-core') {
+	apply plugin: 'java'
+	apply plugin: 'eclipse-wtp'
 
 }
 
 project('gluetools-ws') {
+	apply plugin: 'java'
+	apply plugin: 'eclipse-wtp'
+
+}
 
+subprojects {
+	dependencies {
+	    compile group: 'org.apache.httpcomponents', name: 'httpclient', version: '4.4.1'
+	    compile group: 'org.apache.cayenne', name: 'cayenne-server', version:'3.1'
+	    compile group: 'org.apache.cayenne', name: 'cayenne-project', version:'3.1'
+	    compile group: 'org.biojava', name: 'biojava-core', version: '4.0.0'
+	    compile group: 'org.apache.commons', name: 'commons-io', version: '1.3.2'
+	    compile group: 'org.freemarker', name: 'freemarker', version: '2.3.20'
+	    compile group: 'commons-collections', name: 'commons-collections', version: '3.2'
+	    compile group: 'mysql', name: 'mysql-connector-java', version: '5.1.35'
+	    compile group: 'org.apache.derby', name: 'derby', version: '10.5.3.0_1'
+	    compile group: 'jline', name: 'jline', version: '2.12.1'
+	    compile group: 'com.brsanthu', name: 'data-exporter', version: '1.0.4'
+	    // compile group: 'dnl.utils', name: 'j-text-utils', version: '0.3.3'
+	    compile group: 'com.offbytwo', name:'docopt', version:'0.6.0.20150202'
+	    compile group: 'javax.json', name:'javax.json-api', version:'1.0'
+	    compile group: 'org.glassfish', name:'javax.json', version:'1.0.4'
+
+	    testCompile group: 'junit', name: 'junit', version: '4.+'
+	}
 }
diff --git a/derby.log b/derby.log
@@ -0,0 +1,6 @@
+----------------------------------------------------------------
+2015-07-29 12:39:32.729 GMT:
+ Booting Derby version The Apache Software Foundation - Apache Derby - 10.5.3.0 - (802917): instance a816c00e-014e-d9d3-2e25-00000d2d4400
+on database directory memory:/Users/joshsinger/gitrepos/gluetools/testdb  
+
+Database Class Loader started - derby.database.classpath=''
diff --git a/gluetools-core/.classpath b/gluetools-core/.classpath
diff --git a/gluetools-core/build.gradle b/gluetools-core/build.gradle
@@ -1,5 +1,5 @@
 apply plugin: 'java'
-apply plugin: 'eclipse'
+apply plugin: 'eclipse-wtp'
 
 sourceCompatibility = 1.8
 version = '1.0'
@@ -62,25 +62,7 @@ task datamodel(dependsOn: 'checkCayenneTools') << {
 }
 
 dependencies {
-    compile group: 'org.apache.httpcomponents', name: 'httpclient', version: '4.4.1'
-    compile group: 'org.apache.cayenne', name: 'cayenne-server', version:'3.1'
-    compile group: 'org.apache.cayenne', name: 'cayenne-project', version:'3.1'
-    compile group: 'org.biojava', name: 'biojava-core', version: '4.0.0'
-    compile group: 'org.apache.commons', name: 'commons-io', version: '1.3.2'
-    compile group: 'org.freemarker', name: 'freemarker', version: '2.3.20'
-    compile group: 'commons-collections', name: 'commons-collections', version: '3.2'
-    compile group: 'mysql', name: 'mysql-connector-java', version: '5.1.35'
-    compile group: 'org.apache.derby', name: 'derby', version: '10.5.3.0_1'
-    compile group: 'jline', name: 'jline', version: '2.12.1'
-    compile group: 'com.brsanthu', name: 'data-exporter', version: '1.0.4'
-    // compile group: 'dnl.utils', name: 'j-text-utils', version: '0.3.3'
-    compile group: 'com.offbytwo', name:'docopt', version:'0.6.0.20150202'
-    compile group: 'javax.json', name:'javax.json-api', version:'1.0'
-    compile group: 'org.glassfish', name:'javax.json', version:'1.0.4'
    	compile group: 'javax.ws.rs', name: 'javax.ws.rs-api', version: '2.0.1'
-
-
-    testCompile group: 'junit', name: 'junit', version: '4.+'
     cgen group: 'org.apache.cayenne', name: 'cayenne-tools', version: '3.1'
 }
 

diff --git a/gluetools-core/src/main/java/uk/ac/gla/cvr/gluetools/core/GluetoolsEngine.java b/gluetools-core/src/main/java/uk/ac/gla/cvr/gluetools/core/GluetoolsEngine.java
@@ -1,7 +1,6 @@
 package uk.ac.gla.cvr.gluetools.core;
 
 import java.io.File;
-import java.net.URL;
 import java.util.logging.Logger;
 
 import org.apache.cayenne.ObjectContext;
@@ -23,7 +22,6 @@
 import uk.ac.gla.cvr.gluetools.core.plugins.Plugin;
 import uk.ac.gla.cvr.gluetools.core.plugins.PluginConfigContext;
 import uk.ac.gla.cvr.gluetools.core.plugins.PluginUtils;
-import uk.ac.gla.cvr.gluetools.core.resource.GlueURLStreamHandlerFactory;
 import uk.ac.gla.cvr.gluetools.utils.XmlUtils;
 import freemarker.template.Configuration;
 
@@ -58,7 +56,6 @@ public static synchronized GluetoolsEngine getInstance() {
 
 	private GluetoolsEngine(String configFilePath) {
 		freemarkerConfiguration = new Configuration();
-		URL.setURLStreamHandlerFactory(new GlueURLStreamHandlerFactory());
 		Document configDocument = null;
 		if(configFilePath != null) {
 			try {
@@ -132,5 +129,17 @@ public String getDbSchemaVersion() {
 		return dbSchemaVersion;
 	}
 
-
+	public synchronized static void shutdown() {
+		if(instance != null) {
+			instance.dispose();
+			instance = null;
+		}
+	}
+
+	private void dispose() {
+		rootServerRuntime.shutdown();
+	}
+
+
+
 }
diff --git a/gluetools-core/src/main/java/uk/ac/gla/cvr/gluetools/core/command/CommandMode.java b/gluetools-core/src/main/java/uk/ac/gla/cvr/gluetools/core/command/CommandMode.java
@@ -60,7 +60,7 @@ void setParentCommandMode(CommandMode parentCommandMode) {
 		this.parentCommandMode = parentCommandMode;
 	}
 
-	void exit() {
+	public void exit() {
 		if(serverRuntime != null) {
 			serverRuntime.shutdown();
 		}

diff --git a/gluetools-core/src/main/java/uk/ac/gla/cvr/gluetools/core/command/root/RootCommandMode.java b/gluetools-core/src/main/java/uk/ac/gla/cvr/gluetools/core/command/root/RootCommandMode.java
@@ -1,5 +1,7 @@
 package uk.ac.gla.cvr.gluetools.core.command.root;
 
+import javax.ws.rs.Path;
+
 import org.apache.cayenne.configuration.server.ServerRuntime;
 
 import uk.ac.gla.cvr.gluetools.core.command.CommandFactory;
@@ -11,5 +13,5 @@ public RootCommandMode(ServerRuntime serverRuntime) {
 		super("GLUE", CommandFactory.get(RootCommandFactory.creator));
 		setServerRuntime(serverRuntime);
 	}
-
+	
 }
diff --git a/gluetools-core/src/main/java/uk/ac/gla/cvr/gluetools/core/console/Console.java b/gluetools-core/src/main/java/uk/ac/gla/cvr/gluetools/core/console/Console.java
@@ -303,7 +303,7 @@ private void shutdown() {
 		while(!(commandContext.peekCommandMode() instanceof RootCommandMode)) {
 			commandContext.popCommandMode();
 		}
-		commandContext.popCommandMode();
+		GluetoolsEngine.shutdown();
 	}
 
 	private void runBatchFile(Object fileString) {

diff --git a/gluetools-core/src/main/java/uk/ac/gla/cvr/gluetools/core/resource/GlueResource.java b/gluetools-core/src/main/java/uk/ac/gla/cvr/gluetools/core/resource/GlueResource.java
@@ -17,7 +17,7 @@ public GlueResource(String fileName) {
 	@Override
 	public URL getURL() {
 		try {
-			return new URL("glue", "host", "/"+fileName);
+			return new URL("glue", "host", 9999, "/"+fileName, new GlueURLStreamHandler());
 		} catch (MalformedURLException e) {
 			throw new RuntimeException(e);
 		}

diff --git a/...core/src/main/java/uk/ac/gla/cvr/gluetools/core/resource/GlueURLStreamHandlerFactory.java b/...core/src/main/java/uk/ac/gla/cvr/gluetools/core/resource/GlueURLStreamHandlerFactory.java