bd2kccd / causal-web Goto Github PK

CCD web application.

Java 41.77% CSS 1.02% JavaScript 5.66% HTML 51.55%

causal-web's Introduction

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 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.

Building the software

Prerequisites - You must have the following installed to build/install causal-web

Oracle Java 1.8 - (http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html)
Maven 3.x -(https://maven.apache.org/download.cgi)
For production install MySQL 5.x - (http://dev.mysql.com/downloads/)
You will need a GMail account. GMail will be used to send out account activation links and feedbacks.

Download the source code

Dependencies

Download and uncompress the source code for each of following dependencies:

ccd-job-queue-0.1.8
ccd-mail-0.2.4
ccd-db-0.6.7
ccd-commons-0.3.1 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-1.3.7. To compile and build the application, go to the directory causal-web-1.3.7 and type mvn package.

External Dependencies

causal-cmd-0.2.1-jar-with-dependencies.jar

Configure the software

Setup the directory structure and copy libraries

First, you need to create a workspace for the application to work in. Create a directory called workspace, for an example /home/tuser/workspace.
Inside the workspace directory, create another folder called lib, for example /home/tuser/workspace/lib.

Copy the causal-cmd-0.2.1-jar-with-dependencies.jar to the workspace/lib folder.

Configure

There are 4 configuration files to configure located in causal-web-1.3.7/src/main/resources folder:

application-hsqldb.properties: HSQLDB database configurations (for testing only).
application-mysql.properties: MySQL database configurations
application.properties: Spring Boot configurations
ccd.properties: CCD web application related configurations

Workspace Configuration

Set the property ccd.server.workspace in the ccd.properties file to the workspace location.

// based on the above example
ccd.server.workspace=/home/tuser/workspace

Mail Configuration

Set the following properties in the application.properties file:

// add gmail account
spring.mail.username=<gmail username>
spring.mail.password=<gmail username>

Testing Configuration

Set the following properties in the application.properties file:

spring.profiles.active=scheduler,hsqldb

Production Configuration

Set the following properties in the application.properties file:

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 causal-web directory and run the command mvn clean package. This will create a jar file called causal-web-1.3.7.jar in the /target folder.

Launch the Program

java -jar causal-web-1.3.7.jar

To give the program 4GB of memory to run on, type the follow, using the jvm options:

java -Xmx4G -jar causal-web-1.3.7.jar

To launch app in the browser

http://localhost:[port]/ccd       // default port is 8080, otherwise change to specified port

causal-web's People

Contributors

Stargazers

Watchers

Forkers

the-alchemist azzaea

causal-web's Issues

workspace file chooser bombs on symlink with no destination

The workspace file browser blew up on me.

I think the problem had to do with the reading of a file that was a dangling reference sym link - ie, the link existed, but the target file did not.

Probably best to revise the iteration code to skip over anything that comes up in the directory list of files but then has a NoSuchFile problem.

2015-07-06 13:15:13.137 INFO 14599 --- [ main] edu.pitt.dbmi.ccd.web.CCDWebApplication : Started CCDWebApplication in 13.103 seconds (JVM running for 13.749)
Hibernate: select useraccoun0_."id" as id1_2_, useraccoun0_."active" as active2_2_, useraccoun0_."created_date" as created_3_2_, useraccoun0_."last_login_date" as last_log4_2_, useraccoun0_."password" as password5_2_, useraccoun0_.person_id as person_i7_2_, useraccoun0_."username" as username6_2_ from "user_account" useraccoun0_ where useraccoun0_."username"=?
java.nio.file.NoSuchFileException: /Users/harry/Documents/research/projects/bart-phoenix
at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86)
at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
at sun.nio.fs.UnixFileAttributeViews$Basic.readAttributes(UnixFileAttributeViews.java:55)
at sun.nio.fs.UnixFileSystemProvider.readAttributes(UnixFileSystemProvider.java:144)
at java.nio.file.Files.readAttributes(Files.java:1737)
at edu.pitt.dbmi.ccd.web.util.FileUtility.getDirListing(FileUtility.java:121)
at edu.pitt.dbmi.ccd.web.ctrl.UserAccountController.browsingServerSideDirectory(UserAccountController.java:225)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:221)
at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:137)
at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:110)
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandleMethod(RequestMappingHandlerAdapter.java:776)
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:705)
at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:85)
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:959)
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:893)
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:966)

Test SLURM Client on EC2 within causal web

Causal Web: Job Queue Hangs

It seems like the job queue hangs after a while. Unable to delete and add new jobs. Had to restart the causal web service.

Compilation error

Hello again,
I thought I make a new issue since this is not strictly a dependency problem. I hope you don't mind.

Now that all my dependencies are in place, I went ahead and downloaded a hqsldb for testing out. I set the options in the HypersqlDB Manager as per the default options in the causal-web-1.3.7/src/main/resources/application-hsqldb.properties (figure below).

Yet, no luck with actually running java -jar target/causal-web-1.3.7.jar &> java.error.txt. I'm afraid I can't really understand why this one is failing (or, where to place the seemingly missing log4j2 configuration file). Would you kindly be able to help?

Thank you in advance for any pointers you may be able to provide

Deploy to production vm

File upload error with file file data_%20.txt

I tried to upload a file named "data_%20.txt" and it was uploaded, and then I summarized this data file. But when I clicked the link of this file name to view more info, it says nothing.

I'm guessing it has something to do with the file name.

"Error: Invalid or corrupt jarfile /private/tmp/workspace/lib": missing instructions for property ccd.jar.algorithm

File ccd.properties comes with a blank ccd.jar.algorithm property: https://github.com/bd2kccd/causal-web/blob/development/src/main/resources/ccd.properties#L19

However, this property is not optional, and if you leave the default, you'll get:

Error: Invalid or corrupt jarfile /private/tmp/workspace/lib

...because the property is left blank.

What's the recommendation to get causal-web running? ccd-algorithm is deprecated in favor of Tetrad, but I don't know if tetrad-lib supports the command-line options that causal-web uses.

Any pointer or suggestions would be greatly appreciated. :)

Causal Web not working

Hello,

I am trying to use the "Causal Web" program, clicking on the URL found on the CCD's site: https://cloud.ccd.pitt.edu/ccd-web. Unfortunately, I got this message: "Service Temporarily Unavailable"

Then, as User Guide suggests, I visited another URL: https://ccd4.vm.bridges.psc.edu/ccd/, but again the site can't be reached.

Do you have any idea about what is going on?

Thank you in advance!

Version error

a ccd user tried causal web and got this error message. Any idea what's up and how we can fix it?

Exception in thread "main" java.lang.UnsupportedClassVersionError: edu/pitt/dbmi/causal/cmd/CausalCmdApplication : Unsupported major.minor version 52.0
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:800)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)

Automate EBS backup in cluster

Since the EBS volume has been mounted and tested with cfncluster #14, we wanted to use a script to automate the EBS snapshot instead of manually create the snapshot.

Causal Web: Add GFCI Discrete

job titles don't relate back to input file

How do I know which job was associated with which input file?

Configure causal web to work with EC2

Time out error in large datasets

Hi,

This came up in the ccd-helpdesk:

"I can successfully upload my datasets, specify constraints (prior knowledge), and it seems to work out for smaller datasets. But, for some larger datasets (I have ones with 1,054 and 1,212 columns), I keep getting a timeout error message after one hour from launching each job"

This is the error the user gets:

SLURM Job_id=662001 Name=causal-cmd ccd2 charmgil Failed, Run time 01:00:01, TIMEOUT

Any ideas ?

allow selecting of knowledge file in run algorithm

Disable Annotation Icon When Annotation Service is Disabled

I disabled the annotation service profile in application.properties but the annotation icon still shows up in the Causal Web UI.

FYI @marksilvis I've talked to @kvb2univpitt and he said he'll make the change in causal web. Just wanted to track this on github.

Add PAGs Coloring

Have d3.js shows different color edge for different PAG edge types.

Invalid SSL Certifiate

I went to https://dxcvm26.psc.edu/ccd by following the README, and got the SSL error in both Google Chrome and Firefox.

Then I tested the plain http at http://dxcvm26.psc.edu/ccd and it worked.

Missing dependency

Hello,

Thank you for your efforts packaging many important causal reasoning algorithms via these suits of programs.

I'm trying to install causal web as a dependency for the Causal Rest API, but stuck at the stage of installing ccd-job-queue-0.1.8. First, it gave me this error:

ERROR] Failed to execute goal on project ccd-job-queue: Could not resolve dependencies for project edu.pitt.dbmi:ccd-job-queue:jar:0.1.8: The following artifacts could not be resolved: edu.pitt.dbmi:ccd-db:jar:0.6.5, edu.pitt.dbmi.isg:remoteSchedulerClient:jar:0.1.4: Failure to find edu.pitt.dbmi:ccd-db:jar:0.6.5 in https://repo.maven.apache.org/maven2 was cached in the local repository, resolution will not be reattempted until the update interval of central has elapsed or updates are forced -> [Help 1]

To which a partial fix is installing the older version of ccd-db-0.6.5 (along with the recent version suggested in the README file of this repo. Now, I get the following error:

[ERROR] Failed to execute goal on project ccd-job-queue: Could not resolve dependencies for project edu.pitt.dbmi:ccd-job-queue:jar:0.1.8: Failure to find edu.pitt.dbmi.isg:remoteSchedulerClient:jar:0.1.4 in https://repo.maven.apache.org/maven2 was cached in the local repository, resolution will not be reattempted until the update interval of central has elapsed or updates are forced -> [Help 1]

I'm not sure where this jar file is, and would really appreciate any pointers you may be able to share.

Thank you,
Azza

Deploy causal web with FGSd to test vm

ccd-web-1.2.1 not found

On the readme file (https://github.com/bd2kccd/causal-web#application) it says to use ccd-web-1.2.1, after clicking the link, it says not found. The latest release is 1.2.0.

Can't get sign up email

I installed CCD-Web 1.2.0 and specified the gmail username and password. But after I went through the sign up new account process, I got this error:

[2016-03-16 14:17:56.707] boot - 30419  INFO [main] --- CcdWebApplication: Started CcdWebApplication in 14.536 seconds (JVM running for 14.927)
Exception in thread "Thread-16" org.springframework.mail.MailAuthenticationException: Authentication failed; nested exception is javax.mail.AuthenticationFailedException: failed to connect, no password specified?
    at org.springframework.mail.javamail.JavaMailSenderImpl.doSend(JavaMailSenderImpl.java:409)
    at org.springframework.mail.javamail.JavaMailSenderImpl.send(JavaMailSenderImpl.java:345)
    at org.springframework.mail.javamail.JavaMailSenderImpl.send(JavaMailSenderImpl.java:362)
    at org.springframework.mail.javamail.JavaMailSenderImpl.send(JavaMailSenderImpl.java:350)
    at edu.pitt.dbmi.ccd.mail.AbstractBasicMail.send(AbstractBasicMail.java:40)
    at edu.pitt.dbmi.ccd.mail.service.SimpleUserMailService.sendRegistrationActivation(SimpleUserMailService.java:60)
    at edu.pitt.dbmi.ccd.web.service.mail.MailService.sendRegistrationActivation(MailService.java:58)
    at edu.pitt.dbmi.ccd.web.service.UserService.lambda$registerNewUser$24(UserService.java:123)
    at java.lang.Thread.run(Thread.java:745)
Caused by: javax.mail.AuthenticationFailedException: failed to connect, no password specified?
    at javax.mail.Service.connect(Service.java:398)
    at org.springframework.mail.javamail.JavaMailSenderImpl.connectTransport(JavaMailSenderImpl.java:486)
    at org.springframework.mail.javamail.JavaMailSenderImpl.doSend(JavaMailSenderImpl.java:406)
    ... 8 more

I had this work couple months ago and since the ccd-mail master branch hasn't been updated since 4 months, I suspect something is not right in CCD-Web.

Create a jar resource with all dependencies

knowledge file upload

causal-web needs a way for user to upload a knowledge file that causal-cmd will use as input

add knowledge file upload in data management

Unable to compare result files that contain variable names with spaces.

Create a customized CloudFormation template to deploy the stack

CfnCluster CLI creates a CloudFormation template to deploy the cluster. We can modify the template https://github.com/awslabs/cfncluster/blob/master/cloudformation/cfncluster.cfn.json to ease future stack creation and update without installing CfnCluster CLI tool. This also gives us fine-grained configurations of the cluster.

lack of feedback when search fails

file that fails to provide any output leads to blank screen when viewing results. Users should get some feedback indicating that a graph cannot be drawn.

Update documentation

Prepare for FGSd release

wording on algorithmic options.

Rephrase FCI and similar checkbox arguments to avoid the "Yes if " construct.

Instead of "Yes if (one edge) faithfulness should be assumed", just use

"Assume (one edge) faithfulness?" ...etc.

Annotations UI/UX

The UI on the annotations page needs an overhaul. This includes replacing some slower jQuery calls with vanilla js.

GFCIm-CG

Added mixed data support for GFCI

Disable javascript call to annotation server when annotation is turned off

This issue is a side product of #36 and it's better to separate the discussion.

When annotation profile is turned off in causal web build, the client side javascript code still calls the annotation server for login.

Integrate Annotations REST services

The annotations page will be moved to making API calls to the annotations service from the server. This replaces the current method of making requests from JavaScript.

Annotation size limit

There should be a counter letting the user know how much of the maximum annotation size they have used so far (max 1000 characters).

FESCm-CG

Add mixed data support for FGES.

Error with new user registration when annotation is disabled

On AWS I disabled the annotation profile, but when registering new users, I still got this error related to "Column 'first_name' cannot be null":

The according log says:

2016-11-29 22:05:50.289 ERROR 8991 --- [qtp1313618488-13] o.h.e.j.s.SqlExceptionHelper             : Column 'first_name' cannot be null
2016-11-29 22:05:50.289 ERROR 8991 --- [qtp1313618488-13] e.p.d.c.w.s.a.UserRegistrationService    : Failed to register new user.

org.springframework.dao.DataIntegrityViolationException: could not execute statement; SQL [n/a]; constraint [null]; nested exception is org.hibernate.exception.ConstraintViolationException: could not execute statement
	at org.springframework.orm.jpa.vendor.HibernateJpaDialect.convertHibernateAccessException(HibernateJpaDialect.java:278) ~[spring-orm-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.orm.jpa.vendor.HibernateJpaDialect.translateExceptionIfPossible(HibernateJpaDialect.java:244) ~[spring-orm-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.translateExceptionIfPossible(AbstractEntityManagerFactoryBean.java:491) ~[spring-orm-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.dao.support.ChainedPersistenceExceptionTranslator.translateExceptionIfPossible(ChainedPersistenceExceptionTranslator.java:59) ~[spring-tx-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.dao.support.DataAccessUtils.translateIfNecessary(DataAccessUtils.java:213) ~[spring-tx-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(PersistenceExceptionTranslationInterceptor.java:147) ~[spring-tx-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) ~[spring-aop-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.data.jpa.repository.support.CrudMethodMetadataPostProcessor$CrudMethodMetadataPopulatingMethodInterceptor.invoke(CrudMethodMetadataPostProcessor.java:133) ~[spring-data-jpa-1.10.3.RELEASE.jar!/:?]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) ~[spring-aop-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:92) ~[spring-aop-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) ~[spring-aop-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) ~[spring-aop-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at com.sun.proxy.$Proxy113.save(Unknown Source) ~[?:?]
	at edu.pitt.dbmi.ccd.db.service.UserAccountService.save(UserAccountService.java:99) ~[ccd-db-0.6.2.jar!/:0.6.2]
	at edu.pitt.dbmi.ccd.db.service.UserAccountService.createNewAccount(UserAccountService.java:116) ~[ccd-db-0.6.2.jar!/:0.6.2]
	at edu.pitt.dbmi.ccd.web.service.account.UserRegistrationService.regesterUser(UserRegistrationService.java:166) [classes!/:1.3.1]
	at edu.pitt.dbmi.ccd.web.service.account.UserRegistrationService.registerNewRegularUser(UserRegistrationService.java:111) [classes!/:1.3.1]
	at edu.pitt.dbmi.ccd.web.ctrl.account.UserRegistrationController.registerNewRegularUser(UserRegistrationController.java:136) [classes!/:1.3.1]
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:1.8.0_101]
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[?:1.8.0_101]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:1.8.0_101]
	at java.lang.reflect.Method.invoke(Method.java:498) ~[?:1.8.0_101]
	at org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:221) [spring-web-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:136) [spring-web-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:114) [spring-webmvc-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:827) [spring-webmvc-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:738) [spring-webmvc-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:85) [spring-webmvc-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:963) [spring-webmvc-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:897) [spring-webmvc-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:970) [spring-webmvc-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:872) [spring-webmvc-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:707) [javax.servlet-api-3.1.0.jar!/:3.1.0]
	at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:846) [spring-webmvc-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:790) [javax.servlet-api-3.1.0.jar!/:3.1.0]
	at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:845) [jetty-servlet-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1689) [jetty-servlet-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.websocket.server.WebSocketUpgradeFilter.doFilter(WebSocketUpgradeFilter.java:225) [websocket-server-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1676) [jetty-servlet-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.springframework.boot.web.filter.ApplicationContextHeaderFilter.doFilterInternal(ApplicationContextHeaderFilter.java:55) [spring-boot-1.4.1.RELEASE.jar!/:1.4.1.RELEASE]
	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1676) [jetty-servlet-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:449) [shiro-web-1.3.2.jar!/:1.3.2]
	at org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:365) [shiro-web-1.3.2.jar!/:1.3.2]
	at org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90) [shiro-core-1.3.2.jar!/:1.3.2]
	at org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83) [shiro-core-1.3.2.jar!/:1.3.2]
	at org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:383) [shiro-core-1.3.2.jar!/:1.3.2]
	at org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:362) [shiro-web-1.3.2.jar!/:1.3.2]
	at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125) [shiro-web-1.3.2.jar!/:1.3.2]
	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1676) [jetty-servlet-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.springframework.boot.actuate.trace.WebRequestTraceFilter.doFilterInternal(WebRequestTraceFilter.java:105) [spring-boot-actuator-1.4.1.RELEASE.jar!/:1.4.1.RELEASE]
	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1676) [jetty-servlet-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.springframework.web.filter.RequestContextFilter.doFilterInternal(RequestContextFilter.java:99) [spring-web-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1676) [jetty-servlet-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.springframework.web.filter.HttpPutFormContentFilter.doFilterInternal(HttpPutFormContentFilter.java:89) [spring-web-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1676) [jetty-servlet-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.springframework.web.filter.HiddenHttpMethodFilter.doFilterInternal(HiddenHttpMethodFilter.java:77) [spring-web-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1676) [jetty-servlet-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:197) [spring-web-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1676) [jetty-servlet-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.springframework.boot.actuate.autoconfigure.MetricsFilter.doFilterInternal(MetricsFilter.java:107) [spring-boot-actuator-1.4.1.RELEASE.jar!/:1.4.1.RELEASE]
	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1676) [jetty-servlet-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:581) [jetty-servlet-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143) [jetty-server-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:548) [jetty-security-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:226) [jetty-server-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1180) [jetty-server-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:511) [jetty-servlet-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:185) [jetty-server-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1112) [jetty-server-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141) [jetty-server-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:134) [jetty-server-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.server.Server.handle(Server.java:524) [jetty-server-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:319) [jetty-server-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:253) [jetty-server-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:273) [jetty-io-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:95) [jetty-io-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.io.SelectChannelEndPoint$2.run(SelectChannelEndPoint.java:93) [jetty-io-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.util.thread.strategy.ExecuteProduceConsume.executeProduceConsume(ExecuteProduceConsume.java:303) [jetty-util-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.util.thread.strategy.ExecuteProduceConsume.produceConsume(ExecuteProduceConsume.java:148) [jetty-util-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.util.thread.strategy.ExecuteProduceConsume.run(ExecuteProduceConsume.java:136) [jetty-util-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:671) [jetty-util-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.util.thread.QueuedThreadPool$2.run(QueuedThreadPool.java:589) [jetty-util-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at java.lang.Thread.run(Thread.java:745) [?:1.8.0_101]
Caused by: org.hibernate.exception.ConstraintViolationException: could not execute statement
	at org.hibernate.exception.internal.SQLExceptionTypeDelegate.convert(SQLExceptionTypeDelegate.java:59) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:42) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:109) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:95) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.executeUpdate(ResultSetReturnImpl.java:207) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.dialect.identity.GetGeneratedKeysDelegate.executeAndExtract(GetGeneratedKeysDelegate.java:57) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.id.insert.AbstractReturningDelegate.performInsert(AbstractReturningDelegate.java:42) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2803) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:3374) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.action.internal.EntityIdentityInsertAction.execute(EntityIdentityInsertAction.java:81) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.engine.spi.ActionQueue.execute(ActionQueue.java:619) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.engine.spi.ActionQueue.addResolvedEntityInsertAction(ActionQueue.java:273) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.engine.spi.ActionQueue.addInsertAction(ActionQueue.java:254) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.engine.spi.ActionQueue.addAction(ActionQueue.java:299) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.event.internal.AbstractSaveEventListener.addInsertAction(AbstractSaveEventListener.java:317) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.event.internal.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:272) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.event.internal.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:178) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.event.internal.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:109) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.jpa.event.internal.core.JpaPersistEventListener.saveWithGeneratedId(JpaPersistEventListener.java:67) ~[hibernate-entitymanager-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.event.internal.DefaultPersistEventListener.entityIsTransient(DefaultPersistEventListener.java:189) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.event.internal.DefaultPersistEventListener.onPersist(DefaultPersistEventListener.java:132) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.event.internal.DefaultPersistEventListener.onPersist(DefaultPersistEventListener.java:58) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.internal.SessionImpl.firePersist(SessionImpl.java:775) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.internal.SessionImpl.persist(SessionImpl.java:748) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.internal.SessionImpl.persist(SessionImpl.java:753) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.jpa.spi.AbstractEntityManagerImpl.persist(AbstractEntityManagerImpl.java:1146) ~[hibernate-entitymanager-5.0.11.Final.jar!/:5.0.11.Final]
	at sun.reflect.GeneratedMethodAccessor231.invoke(Unknown Source) ~[?:?]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:1.8.0_101]
	at java.lang.reflect.Method.invoke(Method.java:498) ~[?:1.8.0_101]
	at org.springframework.orm.jpa.ExtendedEntityManagerCreator$ExtendedEntityManagerInvocationHandler.invoke(ExtendedEntityManagerCreator.java:347) ~[spring-orm-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at com.sun.proxy.$Proxy108.persist(Unknown Source) ~[?:?]
	at sun.reflect.GeneratedMethodAccessor231.invoke(Unknown Source) ~[?:?]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:1.8.0_101]
	at java.lang.reflect.Method.invoke(Method.java:498) ~[?:1.8.0_101]
	at org.springframework.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler.invoke(SharedEntityManagerCreator.java:298) ~[spring-orm-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at com.sun.proxy.$Proxy108.persist(Unknown Source) ~[?:?]
	at org.springframework.data.jpa.repository.support.SimpleJpaRepository.save(SimpleJpaRepository.java:506) ~[spring-data-jpa-1.10.3.RELEASE.jar!/:?]
	at sun.reflect.GeneratedMethodAccessor227.invoke(Unknown Source) ~[?:?]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:1.8.0_101]
	at java.lang.reflect.Method.invoke(Method.java:498) ~[?:1.8.0_101]
	at org.springframework.data.repository.core.support.RepositoryFactorySupport$QueryExecutorMethodInterceptor.executeMethodOn(RepositoryFactorySupport.java:503) ~[spring-data-commons-1.12.3.RELEASE.jar!/:?]
	at org.springframework.data.repository.core.support.RepositoryFactorySupport$QueryExecutorMethodInterceptor.doInvoke(RepositoryFactorySupport.java:488) ~[spring-data-commons-1.12.3.RELEASE.jar!/:?]
	at org.springframework.data.repository.core.support.RepositoryFactorySupport$QueryExecutorMethodInterceptor.invoke(RepositoryFactorySupport.java:460) ~[spring-data-commons-1.12.3.RELEASE.jar!/:?]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) ~[spring-aop-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.data.projection.DefaultMethodInvokingMethodInterceptor.invoke(DefaultMethodInvokingMethodInterceptor.java:61) ~[spring-data-commons-1.12.3.RELEASE.jar!/:?]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) ~[spring-aop-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) ~[spring-tx-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281) ~[spring-tx-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) ~[spring-tx-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) ~[spring-aop-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(PersistenceExceptionTranslationInterceptor.java:136) ~[spring-tx-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	... 84 more
Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLIntegrityConstraintViolationException: Column 'first_name' cannot be null
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[?:1.8.0_101]
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) ~[?:1.8.0_101]
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[?:1.8.0_101]
	at java.lang.reflect.Constructor.newInstance(Constructor.java:423) ~[?:1.8.0_101]
	at com.mysql.jdbc.Util.handleNewInstance(Util.java:404) ~[mysql-connector-java-5.1.39.jar!/:5.1.39]
	at com.mysql.jdbc.Util.getInstance(Util.java:387) ~[mysql-connector-java-5.1.39.jar!/:5.1.39]
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:934) ~[mysql-connector-java-5.1.39.jar!/:5.1.39]
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3966) ~[mysql-connector-java-5.1.39.jar!/:5.1.39]
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3902) ~[mysql-connector-java-5.1.39.jar!/:5.1.39]
	at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2526) ~[mysql-connector-java-5.1.39.jar!/:5.1.39]
	at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2673) ~[mysql-connector-java-5.1.39.jar!/:5.1.39]
	at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2549) ~[mysql-connector-java-5.1.39.jar!/:5.1.39]
	at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1861) ~[mysql-connector-java-5.1.39.jar!/:5.1.39]
	at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(PreparedStatement.java:2073) ~[mysql-connector-java-5.1.39.jar!/:5.1.39]
	at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(PreparedStatement.java:2009) ~[mysql-connector-java-5.1.39.jar!/:5.1.39]
	at com.mysql.jdbc.PreparedStatement.executeLargeUpdate(PreparedStatement.java:5098) ~[mysql-connector-java-5.1.39.jar!/:5.1.39]
	at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1994) ~[mysql-connector-java-5.1.39.jar!/:5.1.39]
	at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.executeUpdate(ResultSetReturnImpl.java:204) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.dialect.identity.GetGeneratedKeysDelegate.executeAndExtract(GetGeneratedKeysDelegate.java:57) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.id.insert.AbstractReturningDelegate.performInsert(AbstractReturningDelegate.java:42) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2803) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:3374) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.action.internal.EntityIdentityInsertAction.execute(EntityIdentityInsertAction.java:81) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.engine.spi.ActionQueue.execute(ActionQueue.java:619) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.engine.spi.ActionQueue.addResolvedEntityInsertAction(ActionQueue.java:273) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.engine.spi.ActionQueue.addInsertAction(ActionQueue.java:254) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.engine.spi.ActionQueue.addAction(ActionQueue.java:299) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.event.internal.AbstractSaveEventListener.addInsertAction(AbstractSaveEventListener.java:317) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.event.internal.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:272) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.event.internal.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:178) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.event.internal.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:109) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.jpa.event.internal.core.JpaPersistEventListener.saveWithGeneratedId(JpaPersistEventListener.java:67) ~[hibernate-entitymanager-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.event.internal.DefaultPersistEventListener.entityIsTransient(DefaultPersistEventListener.java:189) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.event.internal.DefaultPersistEventListener.onPersist(DefaultPersistEventListener.java:132) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.event.internal.DefaultPersistEventListener.onPersist(DefaultPersistEventListener.java:58) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.internal.SessionImpl.firePersist(SessionImpl.java:775) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.internal.SessionImpl.persist(SessionImpl.java:748) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.internal.SessionImpl.persist(SessionImpl.java:753) ~[hibernate-core-5.0.11.Final.jar!/:5.0.11.Final]
	at org.hibernate.jpa.spi.AbstractEntityManagerImpl.persist(AbstractEntityManagerImpl.java:1146) ~[hibernate-entitymanager-5.0.11.Final.jar!/:5.0.11.Final]
	at sun.reflect.GeneratedMethodAccessor231.invoke(Unknown Source) ~[?:?]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:1.8.0_101]
	at java.lang.reflect.Method.invoke(Method.java:498) ~[?:1.8.0_101]
	at org.springframework.orm.jpa.ExtendedEntityManagerCreator$ExtendedEntityManagerInvocationHandler.invoke(ExtendedEntityManagerCreator.java:347) ~[spring-orm-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at com.sun.proxy.$Proxy108.persist(Unknown Source) ~[?:?]
	at sun.reflect.GeneratedMethodAccessor231.invoke(Unknown Source) ~[?:?]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:1.8.0_101]
	at java.lang.reflect.Method.invoke(Method.java:498) ~[?:1.8.0_101]
	at org.springframework.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler.invoke(SharedEntityManagerCreator.java:298) ~[spring-orm-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at com.sun.proxy.$Proxy108.persist(Unknown Source) ~[?:?]
	at org.springframework.data.jpa.repository.support.SimpleJpaRepository.save(SimpleJpaRepository.java:506) ~[spring-data-jpa-1.10.3.RELEASE.jar!/:?]
	at sun.reflect.GeneratedMethodAccessor227.invoke(Unknown Source) ~[?:?]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:1.8.0_101]
	at java.lang.reflect.Method.invoke(Method.java:498) ~[?:1.8.0_101]
	at org.springframework.data.repository.core.support.RepositoryFactorySupport$QueryExecutorMethodInterceptor.executeMethodOn(RepositoryFactorySupport.java:503) ~[spring-data-commons-1.12.3.RELEASE.jar!/:?]
	at org.springframework.data.repository.core.support.RepositoryFactorySupport$QueryExecutorMethodInterceptor.doInvoke(RepositoryFactorySupport.java:488) ~[spring-data-commons-1.12.3.RELEASE.jar!/:?]
	at org.springframework.data.repository.core.support.RepositoryFactorySupport$QueryExecutorMethodInterceptor.invoke(RepositoryFactorySupport.java:460) ~[spring-data-commons-1.12.3.RELEASE.jar!/:?]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) ~[spring-aop-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.data.projection.DefaultMethodInvokingMethodInterceptor.invoke(DefaultMethodInvokingMethodInterceptor.java:61) ~[spring-data-commons-1.12.3.RELEASE.jar!/:?]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) ~[spring-aop-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) ~[spring-tx-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281) ~[spring-tx-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) ~[spring-tx-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) ~[spring-aop-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(PersistenceExceptionTranslationInterceptor.java:136) ~[spring-tx-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	... 84 more

2016-11-29 22:05:50.305 ERROR 8991 --- [qtp1313618488-13] e.p.d.c.w.c.a.UserRegistrationController : Unable to fetch annotations tokens

java.net.MalformedURLException: no protocol: oauth/token
	at java.net.URL.<init>(URL.java:593) ~[?:1.8.0_101]
	at java.net.URL.<init>(URL.java:490) ~[?:1.8.0_101]
	at java.net.URL.<init>(URL.java:439) ~[?:1.8.0_101]
	at edu.pitt.dbmi.ccd.web.ctrl.account.UserRegistrationController.getAnnotationsTokens(UserRegistrationController.java:85) ~[classes!/:1.3.1]
	at edu.pitt.dbmi.ccd.web.ctrl.account.UserRegistrationController.registerNewRegularUser(UserRegistrationController.java:138) [classes!/:1.3.1]
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:1.8.0_101]
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[?:1.8.0_101]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:1.8.0_101]
	at java.lang.reflect.Method.invoke(Method.java:498) ~[?:1.8.0_101]
	at org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:221) [spring-web-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:136) [spring-web-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:114) [spring-webmvc-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:827) [spring-webmvc-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:738) [spring-webmvc-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:85) [spring-webmvc-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:963) [spring-webmvc-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:897) [spring-webmvc-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:970) [spring-webmvc-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:872) [spring-webmvc-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:707) [javax.servlet-api-3.1.0.jar!/:3.1.0]
	at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:846) [spring-webmvc-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:790) [javax.servlet-api-3.1.0.jar!/:3.1.0]
	at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:845) [jetty-servlet-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1689) [jetty-servlet-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.websocket.server.WebSocketUpgradeFilter.doFilter(WebSocketUpgradeFilter.java:225) [websocket-server-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1676) [jetty-servlet-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.springframework.boot.web.filter.ApplicationContextHeaderFilter.doFilterInternal(ApplicationContextHeaderFilter.java:55) [spring-boot-1.4.1.RELEASE.jar!/:1.4.1.RELEASE]
	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1676) [jetty-servlet-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:449) [shiro-web-1.3.2.jar!/:1.3.2]
	at org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:365) [shiro-web-1.3.2.jar!/:1.3.2]
	at org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90) [shiro-core-1.3.2.jar!/:1.3.2]
	at org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83) [shiro-core-1.3.2.jar!/:1.3.2]
	at org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:383) [shiro-core-1.3.2.jar!/:1.3.2]
	at org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:362) [shiro-web-1.3.2.jar!/:1.3.2]
	at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125) [shiro-web-1.3.2.jar!/:1.3.2]
	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1676) [jetty-servlet-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.springframework.boot.actuate.trace.WebRequestTraceFilter.doFilterInternal(WebRequestTraceFilter.java:105) [spring-boot-actuator-1.4.1.RELEASE.jar!/:1.4.1.RELEASE]
	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1676) [jetty-servlet-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.springframework.web.filter.RequestContextFilter.doFilterInternal(RequestContextFilter.java:99) [spring-web-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1676) [jetty-servlet-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.springframework.web.filter.HttpPutFormContentFilter.doFilterInternal(HttpPutFormContentFilter.java:89) [spring-web-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1676) [jetty-servlet-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.springframework.web.filter.HiddenHttpMethodFilter.doFilterInternal(HiddenHttpMethodFilter.java:77) [spring-web-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1676) [jetty-servlet-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:197) [spring-web-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1676) [jetty-servlet-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.springframework.boot.actuate.autoconfigure.MetricsFilter.doFilterInternal(MetricsFilter.java:107) [spring-boot-actuator-1.4.1.RELEASE.jar!/:1.4.1.RELEASE]
	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.3.3.RELEASE.jar!/:4.3.3.RELEASE]
	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1676) [jetty-servlet-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:581) [jetty-servlet-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143) [jetty-server-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:548) [jetty-security-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:226) [jetty-server-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1180) [jetty-server-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:511) [jetty-servlet-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:185) [jetty-server-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1112) [jetty-server-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141) [jetty-server-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:134) [jetty-server-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.server.Server.handle(Server.java:524) [jetty-server-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:319) [jetty-server-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:253) [jetty-server-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:273) [jetty-io-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:95) [jetty-io-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.io.SelectChannelEndPoint$2.run(SelectChannelEndPoint.java:93) [jetty-io-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.util.thread.strategy.ExecuteProduceConsume.executeProduceConsume(ExecuteProduceConsume.java:303) [jetty-util-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.util.thread.strategy.ExecuteProduceConsume.produceConsume(ExecuteProduceConsume.java:148) [jetty-util-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.util.thread.strategy.ExecuteProduceConsume.run(ExecuteProduceConsume.java:136) [jetty-util-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:671) [jetty-util-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at org.eclipse.jetty.util.thread.QueuedThreadPool$2.run(QueuedThreadPool.java:589) [jetty-util-9.3.11.v20160721.jar!/:9.3.11.v20160721]
	at java.lang.Thread.run(Thread.java:745) [?:1.8.0_101]

@kvb2univpitt @marksilvis please take a look at this issue. I noticed this issue couple weeks ago and I thought we got it fixed. I'm using the v1.3.1 branch with d3 improvements: https://github.com/bd2kccd/causal-web/tree/v1.3.1-d3-improvements. Except the d3 updates, everything else should be the latest code.

what to do with results of a job

Look at the job results, I see this at the bottom of the page:

none of those links work. How do I see the results or the errors?

implement knowledge file in command that runs causal-cmd

Startup failed while running jar file causal-web-1.3.7.jar

Hi I am trying to setup causal-web in an Ubuntu VM. I have followed guide from the github https://github.com/bd2kccd/causal-web but I am stuck at startup failed issues. below is the response I am getting in my console.

`2022-04-25 02:10:43.219 INFO 32962 --- [main] e.p.d.c.w.CcdWebApplication : Starting CcdWebApplication v1.3.7 on CausalML-Experiment with PID 32962 (/var/causalml/causal-web/causal-web-1.3.7/target/causal-web-1.3.7.jar started by root in /var/causalml/causal-web/causal-web-1.3.7/target)
2022-04-25 02:10:43.221 INFO 32962 --- [main] e.p.d.c.w.CcdWebApplication : The following profiles are active: scheduler,mysql
2022-04-25 02:10:43.465 INFO 32962 --- [main] ationConfigEmbeddedWebApplicationContext : Refreshing org.springframework.boot.context.embedded.AnnotationConfigEmbeddedWebApplicationContext@20ce78ec: startup date [Mon Apr 25 02:10:43 UTC 2022]; root of context hierarchy
2022-04-25 02:10:45.263 INFO 32962 --- [main] o.s.b.f.s.DefaultListableBeanFactory : Overriding bean definition for bean 'managementServletContext' with a different definition: replacing [Root bean: class [null]; scope=; abstract=false; lazyInit=false; autowireMode=3; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=org.springframework.boot.actuate.autoconfigure.EndpointWebMvcHypermediaManagementContextConfiguration; factoryMethodName=managementServletContext; initMethodName=null; destroyMethodName=(inferred); defined in class path resource [org/springframework/boot/actuate/autoconfigure/EndpointWebMvcHypermediaManagementContextConfiguration.class]] with [Root bean: class [null]; scope=; abstract=false; lazyInit=false; autowireMode=3; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=org.springframework.boot.actuate.autoconfigure.EndpointWebMvcAutoConfiguration; factoryMethodName=managementServletContext; initMethodName=null; destroyMethodName=(inferred); defined in class path resource [org/springframework/boot/actuate/autoconfigure/EndpointWebMvcAutoConfiguration.class]]
2022-04-25 02:10:45.811 ERROR 32962 --- [main] o.s.b.SpringApplication : Application startup failed

java.lang.IllegalStateException: Cannot load configuration class: edu.pitt.dbmi.ccd.web.CcdWebApplication`

could someone please point me out where I am doing wrong. and how should I get around to this isssue? Thankyou. :)

Test EBS nfs mount to cfncluster

Slurm Client for Causal Web

Relogin after session expired via popup modal window

Just noticed this today, when I was on the datasets section, and my computer was inactive for a while. After I came back, I clicked the file name and got a popup with the login form. I assume this is because my session was destroyed. After I typed my username and password I got logged in again but this time the web page is displaying inside that small modal window. Maybe a redirection can solve this.

Auth0 not working

Script the setup of causal web on EC2 machine

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