Merge branch 'v0.6.0'

README.md

@@ -8,23 +8,26 @@ The web version allows multiple users to run the algorithms on their dataset on
 ## How Can I Use It?
 ### Required Dependencies
 #### Algorithm Dependencies
+* ccd-algorithm-0.4.3.jar
 * colt-1.2.0.jar
 * commons-collections-3.1.jar
 * commons-math3-3.3.jar
 * jama-1.0.2.jar
-* lib-tetrad-0.3.jar
+* lib-tetrad-0.4.1.jar
 * mtj-0.9.14.jar
+* pal-1.5.1.jar
 * xom-1.1.jar
-* ccd-algorithm-0.3.jar
 
 #### Application Dependencies
-* ccd-db-0.4.jar
+* ccd-db-0.6.0.jar
+* ccd-commons-0.3.0.jar
+* ccd-ws-dto-0.3.0.jar
 
 #### Building the Application
 Since this is a maven project all the dependencies will be download from the Maven public repository when compiling. There is one dependency that must be built and installed manually, the database component.  
-* Download the [ccd-db-04](https://github.com/bd2kccd/ccd-db/tree/v0.4-alpha) project from GitHub.
-* In the ccd-db-04 directory run **mvn install** to build and install the ccd-db-0.4.jar library   
-* After ccd-db-0.4 has been successfully built and installed, go to the **ccd-web** directory and run **mvn package**. This will create a jar file called **ccd-web.jar** in the **/target** folder.
+* Download the [ccd-db-0.6.0](https://github.com/bd2kccd/ccd-db/releases/tag/v0.6.0),[ccd-commons-0.3.0](https://github.com/bd2kccd/ccd-commons/releases/tag/v0.3.0) and [ccd-ws-dto-0.3.0](https://github.com/bd2kccd/ccd-ws-dto/releases/tag/v0.3.0)  project from GitHub.
+* Go to each of these project directory and type **mvn clean install** to build and install the jar libraries.
+* After ccd-db-0.6.0 has been successfully built and installed, go to the **ccd-web** directory and run **mvn package**. This will create a jar file called **ccd-web.jar** in the **/target** folder.
 
 
 ## Run As a Desktop Application
@@ -63,4 +66,50 @@ To launch app in the browser
 http://localhost:[port]/ccd       // default port is 8080, otherwise change to specified port
 ```
 
-******
+******
+
+## Build a Windows executable application
+Add this launch4j configuarion below to the pom.xml in the build/plugins entity. 
+
+```
+<plugin>
+	<groupId>com.akathist.maven.plugins.launch4j</groupId>
+	<artifactId>launch4j-maven-plugin</artifactId>
+	<executions>
+		<execution>
+			<id>l4j-ccd-web-windows</id>
+			<phase>package</phase>
+			<goals>
+				<goal>launch4j</goal>
+			</goals>
+			<configuration>
+				<headerType>console</headerType>
+				<outfile>target/ccd-desktop-windows.exe</outfile>
+				<jar>target/ccd-web.jar</jar>
+				<errTitle>CCD</errTitle>
+				<classPath>
+					<mainClass>org.springframework.boot.loader.JarLauncher</mainClass>
+					<addDependencies>false</addDependencies>
+				</classPath>
+				<jre>
+					<minVersion>1.8.0</minVersion>
+					<maxHeapSize>4096</maxHeapSize>
+				</jre>
+				<versionInfo>
+					<fileVersion>0.5.2.0</fileVersion>
+					<txtFileVersion>0.5.2.0</txtFileVersion>
+					<fileDescription>CCD Desktop Windows
+						Application</fileDescription>
+					<copyright>University of Pittsburgh and Carnegie Mellon University</copyright>
+					<productVersion>0.5.2.0</productVersion>
+					<txtProductVersion>0.5.2.0</txtProductVersion>
+					<productName>CCD-Desktop</productName>
+					<internalName>ccd-web</internalName>
+					<originalFilename>ccd-desktop-windows-0.5.2.exe</originalFilename>
+				</versionInfo>
+			</configuration>
+		</execution>
+	</executions>
+</plugin>
+
+```

pom.xml

@@ -5,7 +5,7 @@
 
     <groupId>edu.pitt.dbmi</groupId>
     <artifactId>ccd-web</artifactId>
-    <version>0.5.2</version>
+    <version>0.6.0</version>
     <packaging>jar</packaging>
 
     <name>ccd-web</name>
@@ -14,14 +14,14 @@
     <parent>
         <groupId>org.springframework.boot</groupId>
         <artifactId>spring-boot-starter-parent</artifactId>
-        <version>1.2.5.RELEASE</version>
+        <version>1.2.7.RELEASE</version>
         <relativePath/> <!-- lookup parent from repository -->
     </parent>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <java.version>1.8</java.version>
-        <shiro.version>1.2.3</shiro.version>
+        <shiro.version>1.2.4</shiro.version>
         <maven.compiler.source>1.8</maven.compiler.source>
         <maven.compiler.target>1.8</maven.compiler.target>
     </properties>
@@ -79,12 +79,17 @@
         <dependency>
             <groupId>edu.pitt.dbmi</groupId>
             <artifactId>ccd-job-queue</artifactId>
-            <version>0.1.2</version>
+            <version>0.1.3</version>
+        </dependency>
+        <dependency>
+            <groupId>edu.pitt.dbmi</groupId>
+            <artifactId>ccd-ws-dto</artifactId>
+            <version>0.3.0</version>
         </dependency>
         <dependency>
             <groupId>edu.pitt.dbmi</groupId>
             <artifactId>ccd-mail</artifactId>
-            <version>0.1.1</version>
+            <version>0.1.2</version>
             <exclusions>
                 <exclusion>
                     <groupId>com.sun.mail</groupId>
@@ -95,17 +100,17 @@
         <dependency>
             <groupId>edu.pitt.dbmi</groupId>
             <artifactId>ccd-db</artifactId>
-            <version>0.5.0</version>
+            <version>0.6.0</version>
         </dependency>
         <dependency>
             <groupId>edu.pitt.dbmi</groupId>
             <artifactId>ccd-commons</artifactId>
-            <version>0.2.0</version>
+            <version>0.3.0</version>
         </dependency>
     </dependencies>
 
     <build>
-        <finalName>ccd</finalName>
+        <finalName>ccd-web</finalName>
         <plugins>
             <plugin>
                 <groupId>org.springframework.boot</groupId>

src/main/java/edu/pitt/dbmi/ccd/web/conf/ApplicationConfigurer.java

@@ -59,7 +59,6 @@ public EmbeddedServletContainerCustomizer webappEmbeddedServletContainerCustomiz
             };
             container.addErrorPages(errorPages);
             container.setContextPath("/ccd");
-            container.setSessionTimeout(-1);
         };
     }
 

src/main/java/edu/pitt/dbmi/ccd/web/ctrl/ApplicationController.java

@@ -21,7 +21,6 @@
 import edu.pitt.dbmi.ccd.db.entity.UserAccount;
 import edu.pitt.dbmi.ccd.db.service.DataFileService;
 import edu.pitt.dbmi.ccd.db.service.UserAccountService;
-import static edu.pitt.dbmi.ccd.web.ctrl.ViewPath.LOGIN;
 import edu.pitt.dbmi.ccd.web.domain.AppUser;
 import edu.pitt.dbmi.ccd.web.service.AppUserService;
 import edu.pitt.dbmi.ccd.web.service.result.algorithm.AlgorithmResultService;

src/main/java/edu/pitt/dbmi/ccd/web/ctrl/ViewPath.java

@@ -48,6 +48,9 @@ public interface ViewPath {
     public static final String USER_PROFILE_VIEW = "user/userProfile";
     public static final String REDIRECT_USER_PROFILE = "redirect:/user/profile";
 
+    public static final String USER_SETTINGS_VIEW = "user/settings/userSettings";
+    public static final String REDIRECT_USER_SETTINGS = "redirect:/user/settings";
+
     public static final String DATA_SUMMARY = "dataSummary";
     public static final String DATA_SUMMARY_VIEW = "data/dataSummary";
 
@@ -62,6 +65,8 @@ public interface ViewPath {
 
     public static final String GES_VIEW = "algorithm/ges";
 
+    public static final String FGS_VIEW = "algorithm/fgs";
+
     public static final String FAST_IMAGES_VIEW = "algorithm/fastImages";
 
     public static final String ALGO_RUN_CONFIRM_VIEW = "algorithm/algoRunConfirm";

src/main/java/edu/pitt/dbmi/ccd/web/ctrl/algo/AlgorithmResultController.java

@@ -90,6 +90,7 @@ public String showPlot(
         String url = String.format("/algorithm/results/d3graph?file=%s&remote=%s", fileName, remote);
         model.addAttribute("plot", fileName);
         model.addAttribute("link", url);
+        model.addAttribute("datasets", algorithmResultService.getDatasets(fileName, remote, appUser));
         model.addAttribute("parameters", algorithmResultService.getPlotParameters(fileName, remote, appUser));
 
         return PLOT_VIEW;