V1.3.0

README.md

@@ -1,7 +1,7 @@
 # causal-web
 Causal web is a Java web-based application that allows users to run causal modeling algorithms on their dataset.  The Center for Causal Discovery is hosting this application at the Pittsburgh Supercomputing Center and you can access it at https://ccd2.vm.bridges.psc.edu/ccd
 
-Documentation for using the web application can be found at [http://www.ccd.pitt.edu/wiki/index.php?title=Causal_Web_Application_Quick_Start_and_User_Guide](http://www.ccd.pitt.edu/wiki/index.php?title=Causal_Web_Application_Quick_Start_and_User_Guide) 
+Documentation for using the web application can be found at [https://bd2kccd.github.io/docs/causal-web/](https://bd2kccd.github.io/docs/causal-web/) 
 
 If you want to host the application with your own hardware, follow the instructions below for configuring, building and installing the application.
 
@@ -17,18 +17,17 @@ If you want to host the application with your own hardware, follow the instructi
 #### Dependencies
 Download and uncompress the source code for each of following dependencies:
 
-* [ccd-job-queue-0.1.4](https://github.com/bd2kccd/ccd-job-queue/releases/tag/v0.1.4)
-* [ccd-mail-0.2.0](https://github.com/bd2kccd/ccd-mail/releases/tag/v0.2.0)
-* [ccd-db-0.6.1](https://github.com/bd2kccd/ccd-db/releases/tag/v0.6.1)
+* [ccd-job-queue-0.1.5](https://github.com/bd2kccd/ccd-job-queue/releases/tag/v0.1.5)
+* [ccd-mail-0.2.1](https://github.com/bd2kccd/ccd-mail/releases/tag/v0.2.1)
+* [ccd-db-0.6.2](https://github.com/bd2kccd/ccd-db/releases/tag/v0.6.2)
 * [ccd-commons-0.3.1](https://github.com/bd2kccd/ccd-commons/releases/tag/v0.3.1)
-
 To install the dependencies, go to the top directory of each project and do a maven install by typing **mvn install**.
 
 #### Application
-Download and uncompress the application source code  [causal-web-1.2.2](https://github.com/bd2kccd/causal-web/releases/tag/v1.2.2).  To compile and build the application, go to the directory **causal-web-1.2.2** and type **mvn package**.
+Download and uncompress the application source code  [causal-web-1.3.0](https://github.com/bd2kccd/causal-web/releases/tag/v1.3.0).  To compile and build the application, go to the directory **causal-web-1.3.0** and type **mvn package**.
 
 #### External Dependencies
-* [causal-cmd-5.3.0.jar](https://github.com/cmu-phil/tetrad/releases/tag/v5.3.0-20160624)
+* [causal-cmd-6.0.0.jar](https://github.com/cmu-phil/tetrad/releases/tag/6.0.0-20161031)
 
 ## Configure the software
 
@@ -39,7 +38,7 @@ Inside the workspace directory, create another folder called **lib**, for exampl
 Copy the **causal-cmd-5.3.0.jar** to the  **workspace/lib** folder.
 
 ### Configure
-There are 4 configuration files to configure located in causal-web-1.2.2/src/main/resources folder:
+There are 4 configuration files to configure located in causal-web-1.3.0/src/main/resources folder:
 1. **application-hsqldb.properties**: HSQLDB database configurations (for testing only).
 2. **application-mysql.properties**: MySQL database configurations
 3. **application.properties**: Spring Boot configurations
@@ -59,11 +58,6 @@ Set the following properties in the **application.properties** file:
 spring.mail.username=<gmail username>
 spring.mail.password=<gmail username>
 ```
-Set the following properties in the **ccd.properties** file:
-```java
-// add gmail account
-ccd.mail.feedback.to=<gmail username>
-```
 
 #### Testing Configuration
 Set the following properties in the **application.properties** file:
@@ -80,18 +74,18 @@ spring.profiles.active=scheduler,mysql
 Make sure you set **ccd.server.workspace=/home/tuser/workspace** and **ccd.folder.lib=lib** in the **ccd.properties** file.
 
 ## Compile the Program
-Go to the **ccd-web** directory and run the command **mvn clean package**. This will create a jar file called **causal-web-1.2.2.jar** in the **/target** folder.
+Go to the **causal-web** directory and run the command **mvn clean package**. This will create a jar file called **causal-web-1.3.0.jar** in the **/target** folder.
 
 ### Launch the Program
 ```java
-java -jar causal-web-1.2.2.jar
+java -jar causal-web-1.3.0.jar
 ```
 To give the program 4GB of memory to run on, type the follow, using the jvm options:
 ```java
-java -Xmx4G -jar causal-web-1.2.2.jar
+java -Xmx4G -jar causal-web-1.3.0.jar
 ```
 
 To launch app in the browser
 ```
 http://localhost:[port]/ccd       // default port is 8080, otherwise change to specified port
-```
+```

pom.xml

@@ -5,7 +5,7 @@
 
     <groupId>edu.pitt.dbmi</groupId>
     <artifactId>causal-web</artifactId>
-    <version>1.2.2</version>
+    <version>1.3.0</version>
     <packaging>jar</packaging>
 
     <name>causal-web</name>
@@ -14,14 +14,14 @@
     <parent>
         <groupId>org.springframework.boot</groupId>
         <artifactId>spring-boot-starter-parent</artifactId>
-        <version>1.3.5.RELEASE</version>
+        <version>1.4.1.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>1.2.4</shiro.version>
+        <shiro.version>1.3.2</shiro.version>
         <maven.compiler.source>1.8</maven.compiler.source>
         <maven.compiler.target>1.8</maven.compiler.target>
     </properties>
@@ -53,7 +53,7 @@
         </dependency>
         <dependency>
             <groupId>org.springframework.boot</groupId>
-            <artifactId>spring-boot-starter-log4j</artifactId>
+            <artifactId>spring-boot-starter-log4j2</artifactId>
         </dependency>
         <dependency>
             <groupId>org.springframework.boot</groupId>
@@ -77,26 +77,42 @@
             <version>${shiro.version}</version>
         </dependency>
 
+        <dependency>
+            <groupId>com.auth0</groupId>
+            <artifactId>auth0-spring-mvc</artifactId>
+            <version>1.1.1</version>
+        </dependency>
+
         <dependency>
             <groupId>edu.pitt.dbmi</groupId>
             <artifactId>ccd-job-queue</artifactId>
-            <version>0.1.4</version>
+            <version>0.1.5</version>
+            <exclusions>
+                <exclusion>
+                    <groupId>edu.pitt.dbmi</groupId>
+                    <artifactId>ccd-db</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
         <dependency>
             <groupId>edu.pitt.dbmi</groupId>
             <artifactId>ccd-mail</artifactId>
-            <version>0.2.0</version>
+            <version>0.2.1</version>
         </dependency>
         <dependency>
             <groupId>edu.pitt.dbmi</groupId>
             <artifactId>ccd-db</artifactId>
-            <version>0.6.1</version>
+            <version>0.6.2</version>
         </dependency>
         <dependency>
             <groupId>edu.pitt.dbmi</groupId>
             <artifactId>ccd-commons</artifactId>
             <version>0.3.1</version>
         </dependency>
+        <dependency>
+            <groupId>org.json</groupId>
+            <artifactId>json</artifactId>
+        </dependency>
     </dependencies>
 
     <build>

src/main/java/edu/pitt/dbmi/ccd/web/CcdWebApplication.java

@@ -18,15 +18,16 @@
  */
 package edu.pitt.dbmi.ccd.web;
 
-import edu.pitt.dbmi.ccd.db.CCDDatabaseApplication;
-import edu.pitt.dbmi.ccd.mail.CCDMailApplication;
-import edu.pitt.dbmi.ccd.queue.CCDJobQueueApplication;
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
 import org.springframework.context.annotation.Import;
 import org.springframework.context.annotation.PropertySource;
 import org.springframework.scheduling.annotation.EnableAsync;
 
+import edu.pitt.dbmi.ccd.db.CCDDatabaseApplication;
+import edu.pitt.dbmi.ccd.mail.CcdMailApplication;
+import edu.pitt.dbmi.ccd.queue.CCDJobQueueApplication;
+
 /**
  *
  * Aug 5, 2015 1:27:02 PM
@@ -35,7 +36,7 @@
  */
 @SpringBootApplication
 @EnableAsync
-@Import({CCDDatabaseApplication.class, CCDJobQueueApplication.class, CCDMailApplication.class})
+@Import({CCDDatabaseApplication.class, CCDJobQueueApplication.class, CcdMailApplication.class})
 @PropertySource("classpath:ccd.properties")
 public class CcdWebApplication {
 

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

@@ -18,9 +18,7 @@
  */
 package edu.pitt.dbmi.ccd.web.conf;
 
-import org.springframework.boot.context.embedded.ConfigurableEmbeddedServletContainer;
-import org.springframework.boot.context.embedded.EmbeddedServletContainerCustomizer;
-import org.springframework.boot.context.embedded.ErrorPage;
+import org.springframework.boot.web.servlet.ErrorPageRegistrar;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.http.HttpStatus;
@@ -37,14 +35,14 @@
 public class ApplicationConfigurer extends WebMvcConfigurerAdapter {
 
     @Bean
-    public EmbeddedServletContainerCustomizer webappEmbeddedServletContainerCustomizer() {
-        return (ConfigurableEmbeddedServletContainer container) -> {
-            ErrorPage[] errorPages = {
-                new ErrorPage(HttpStatus.NOT_FOUND, "/404"),
-                new ErrorPage(HttpStatus.UNAUTHORIZED, "/401"),
-                new ErrorPage(HttpStatus.INTERNAL_SERVER_ERROR, "/500")
-            };
-            container.addErrorPages(errorPages);
+    public ErrorPageRegistrar errorPageRegistrar() {
+        return registry -> {
+            registry.addErrorPages(
+                    new org.springframework.boot.web.servlet.ErrorPage(HttpStatus.BAD_REQUEST, "/400"),
+                    new org.springframework.boot.web.servlet.ErrorPage(HttpStatus.NOT_FOUND, "/404"),
+                    new org.springframework.boot.web.servlet.ErrorPage(HttpStatus.UNAUTHORIZED, "/401"),
+                    new org.springframework.boot.web.servlet.ErrorPage(HttpStatus.INTERNAL_SERVER_ERROR, "/500")
+            );
         };
     }
 

src/main/java/edu/pitt/dbmi/ccd/web/conf/Auth0Configurer.java

@@ -0,0 +1,53 @@
+/*
+ * Copyright (C) 2016 University of Pittsburgh.
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301  USA
+ */
+package edu.pitt.dbmi.ccd.web.conf;
+
+import com.auth0.web.Auth0Config;
+import com.auth0.web.Auth0Filter;
+import org.springframework.boot.autoconfigure.EnableAutoConfiguration;
+import org.springframework.boot.web.servlet.FilterRegistrationBean;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.ComponentScan;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Profile;
+
+/**
+ *
+ * Oct 6, 2016 3:47:55 PM
+ *
+ * @author Kevin V. Bui ([email protected])
+ */
+@Profile("auth0")
+@Configuration
+@ComponentScan(basePackages = {"com.auth0.web"})
+@EnableAutoConfiguration
+public class Auth0Configurer {
+
+    @Bean
+    public FilterRegistrationBean filterRegistration(Auth0Config auth0Config) {
+        final FilterRegistrationBean registration = new FilterRegistrationBean();
+        registration.setFilter(new Auth0Filter(auth0Config));
+        registration.addUrlPatterns(auth0Config.getSecuredRoute());
+        registration.addInitParameter("redirectOnAuthError", auth0Config.getLoginRedirectOnFail());
+        registration.setName("Auth0Filter");
+
+        return registration;
+    }
+
+}

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

@@ -40,7 +40,6 @@
 public class ShiroConfigurer {
 
     private static final String AUTHC = "authc";
-    private static final String ANON = "anon";
 
     @Bean(name = "passwordService")
     public DefaultPasswordService passwordService() {