The cure - Interactive decision tree

Karthik G

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Apr 14, 2013, 10:03:50 AM4/14/13

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Hey Ben and Max,

I made a small demo in d3.js to demonstrate an interactive tree that can be manipulated by dragging and dropping.

The Logic:

When a node is dragged around and left, it is added as a child element to the nearest node along with all its child elements. The tree dynamically rearranges itself.

Bugs:

1. If a parent element is dropped over a child element, the code fails to run. Working on rectifying this.

The demo is housed at http://gkarthik.net/thecureprototype/.

Am I on the right track here?

I set up the Java backend on my localhost but when I try to sign up as a new user, I encounter the following error that I'm copying from my logs.

Apr 14, 2013 7:29:49 PM org.apache.catalina.core.StandardWrapperValve invoke

SEVERE: Servlet.service() for servlet [jsp] in context with path [/thecure] threw exception [Unable to compile class for JSP:

An error occurred at line: 14 in the generated java file

Only a type can be imported. org.scripps.combo.model.Player resolves to a package

An error occurred at line: 14 in the jsp file: /WebContent/checkuser.jsp

Player cannot be resolved to a type

11: String degree = request.getParameter("degree");

12: String cancer = request.getParameter("cancer");

13: String biologist = request.getParameter("biologist");

14: Player player = new Player();

15: player.setName(username);

16: player.setPassword(password);

17: player.setIp(ip);

An error occurred at line: 14 in the jsp file: /WebContent/checkuser.jsp

Player cannot be resolved to a type

11: String degree = request.getParameter("degree");

12: String cancer = request.getParameter("cancer");

13: String biologist = request.getParameter("biologist");

14: Player player = new Player();

15: player.setName(username);

16: player.setPassword(password);

17: player.setIp(ip);

An error occurred at line: 32 in the jsp file: /WebContent/checkuser.jsp

Player cannot be resolved

29: boolean passwordfailed = false;

30: //try to create a new user

31: if(newuser!=null){

32: player = Player.create(username, ip, password, email, degree, cancer, biologist);

33: //returns null if the user name is taken

34: if(player==null){

35: nametaken = true;

Stacktrace:] with root cause

org.apache.jasper.JasperException: Unable to compile class for JSP:

An error occurred at line: 14 in the generated java file

Only a type can be imported. org.scripps.combo.model.Player resolves to a package

An error occurred at line: 14 in the jsp file: /WebContent/checkuser.jsp

Player cannot be resolved to a type

11: String degree = request.getParameter("degree");

12: String cancer = request.getParameter("cancer");

13: String biologist = request.getParameter("biologist");

14: Player player = new Player();

15: player.setName(username);

16: player.setPassword(password);

17: player.setIp(ip);

An error occurred at line: 14 in the jsp file: /WebContent/checkuser.jsp

Player cannot be resolved to a type

11: String degree = request.getParameter("degree");

12: String cancer = request.getParameter("cancer");

13: String biologist = request.getParameter("biologist");

14: Player player = new Player();

15: player.setName(username);

16: player.setPassword(password);

17: player.setIp(ip);

An error occurred at line: 32 in the jsp file: /WebContent/checkuser.jsp

Player cannot be resolved

29: boolean passwordfailed = false;

30: //try to create a new user

31: if(newuser!=null){

32: player = Player.create(username, ip, password, email, degree, cancer, biologist);

33: //returns null if the user name is taken

34: if(player==null){

35: nametaken = true;

Stacktrace:

at org.apache.jasper.compiler.DefaultErrorHandler.javacError(DefaultErrorHandler.java:102)

at org.apache.jasper.compiler.ErrorDispatcher.javacError(ErrorDispatcher.java:331)

at org.apache.jasper.compiler.JDTCompiler.generateClass(JDTCompiler.java:469)

at org.apache.jasper.compiler.Compiler.compile(Compiler.java:378)

at org.apache.jasper.compiler.Compiler.compile(Compiler.java:353)

at org.apache.jasper.compiler.Compiler.compile(Compiler.java:340)

at org.apache.jasper.JspCompilationContext.compile(JspCompilationContext.java:646)

at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:357)

at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:390)

at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:334)

at javax.servlet.http.HttpServlet.service(HttpServlet.java:722)

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)

at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)

at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)

at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)

at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:168)

at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:99)

at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:929)

at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)

at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)

at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1002)

at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:585)

at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:312)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)

at java.lang.Thread.run(Thread.java:722)

How do I resolve this?

--

Best Regards,

G.Karthik

Tune Patrol

+91-9660898828 | LinkedIn | Bitbucket | Twitter | http://gkarthik.net/

Birla Institute of Technology and Science, India

Benjamin Good

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Apr 15, 2013, 1:01:43 PM4/15/13

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Hi Karthik,

The d3 tree is a useful start, though there isn't really enough here to give a lot of feedback. I feel like it should move around a little less. It gets confusing trying to figure out where things went after you make a change. Let the user do the moving and then (maybe..) give them a button that says 'auto-layout').

As you think about this (and consider writing it up as a proposal), keep in mind that there are a few different elements to work with here:

1) selection of genes that will be used in the tree

2) arrangement of nodes in the tree (e.g. what you have started on)

3) selection of split points in each decision node. Each node internally amounts to a function that says if X > threshold go one way, else go the other. We would like to allow the user to set the threshold.

It would be worth having a look at standalone systems that do this. I suggest you look into the WEKA machine learning system.

http://www.cs.waikato.ac.nz/ml/weka/

That is where the code we use for inferring the trees automatically comes from. It comes with a GUI interface that will let you try out all the different algorithms. Under 'trees' there is an interactive builder that is worth looking at. I'm not sure we would want to copy it exactly, but it certainly shows the core functionality we are working towards here. (though in a very nineties look and feel ;). Related to that, have a look at this paper - it shows that interface and explains the underlying point

http://www.cs.waikato.ac.nz/pubs/wp/2000/uow-cs-wp-2000-04.pdf

With regard to your error messages. They mean that you don't have the classes from the project on the classpath for your webapp.

Are you building the project in Eclipse (I hope)?

Whatever dev environment you have set up, try to get a separate, simple webapp running (find a tutorial) and make sure that you get as far as using a java class compiled from source in the context of a jsp page. I suspect that will teach what you need to know to fix the problem you have with the cure. If not, let me know and I will try to help.

-Ben

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Karthik G

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Apr 21, 2013, 6:22:12 PM4/21/13

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Hey Ben,

I've worked on setting up the dev environment on Eclipse. I've setup the CLASSPATH like you had suggested. I get this error when I sign up as a new user and have been stuck here for a while.

type Exception report

message java.lang.NullPointerException

description The server encountered an internal error that prevented it from fulfilling this request.

exception

org.apache.jasper.JasperException: java.lang.NullPointerException
	org.apache.jasper.servlet.JspServletWrapper.handleJspException(JspServletWrapper.java:549)
	org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:470)
	org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:390)
	org.apache.jasper.servlet.JspServlet.service(JspServlet.java:334)
	javax.servlet.http.HttpServlet.service(HttpServlet.java:722)

root cause

java.lang.NullPointerException
	org.scripps.combo.model.Player.lookupPlayerByName(Player.java:126)
	org.scripps.combo.model.Player.create(Player.java:291)
	org.apache.jsp.checkuser_jsp._jspService(checkuser_jsp.java:97)
	org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
	javax.servlet.http.HttpServlet.service(HttpServlet.java:722)
	org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:432)
	org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:390)
	org.apache.jasper.servlet.JspServlet.service(JspServlet.java:334)
	javax.servlet.http.HttpServlet.service(HttpServlet.java:722)

Karthik G

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Apr 21, 2013, 7:16:14 PM4/21/13

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I have also setup WEKA and am attempting to visualize data from the SQL database I had downloaded from thecure repo. I'm exploring WEKA further from their online resources.

Also I hadn't understood what you had meant by your third point, "selection of split points in each decision node. Each node internally amounts to a function that says if X > threshold go one way, else go the other. We would like to allow the user to set the threshold."

Are you suggesting that I allow the user to select the split points as well?

In that case how would the game flow proceed? How would I present the nodes to the user as soon as he lands on the page? In the form of a tree or random nodes lying in an arbitrary manner?

Benjamin Good

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Apr 22, 2013, 12:36:15 PM4/22/13

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Hi Karthik,

It looks like you don't have the jdbc connection set up properly yet. That last number in the stacktrace is a line number. It leads back to:

line 126 in Player.java -> PreparedStatement p = conn.connection.prepareStatement(insert);

Its failing because conn is null. Looking back earlier in that method, you will see this attempt to create it.

(line 123)-> JdbcConnection conn = new JdbcConnection();

If you then open up the JdbcConnection class (org.util.JdbcConnection). You will see that its attempting to read connection parameters from a file in its constructor (Line 36). InputStream in = JdbcConnection.class.getResourceAsStream("/props/database.properties") ;

If you don't have that file in the right spot or have not adapted it to match your local db configuration, its likely the cause of the problem. You can try setting the parameters directly in the code to see if its just failing to find that file or what. This was mentioned here:

https://bitbucket.org/sulab/thecure/wiki/Home

but I guess its not obvious if you aren't used to debugging java. Eclipse also has a very handy debugger that it would be worthwhile to use. You just set breakpoints by double clicking on the line number and, instead of "run" you launch with "debug".

Hope that gets you going.

-Ben

Benjamin Good

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Apr 22, 2013, 12:52:03 PM4/22/13

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I bet this happened because the project comes from bitbucket with the props directory named exampleprops ... Sorry, you will want to rename that to props and set the relevant files in that directory. (Its a directory under the src dir..)

This was done to avoid committing all the database passwords etc..

You are close!

-Ben

Benjamin Good

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Apr 22, 2013, 12:52:45 PM4/22/13

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Now - regarding your other query I'm going to start a new thread..

Karthik G

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Apr 22, 2013, 5:09:58 PM4/22/13

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Hey Ben,

I had already setup the database properties at /props/database.properties.

I used the debugging console on Eclipse, which is brilliant!

On the same page - /checkuser.jsp/ I get this error on the console.

I even checked and the mysql-java-connector is in /WEB_INF/lib/. /WEB-INF/lib/ is on the classpath by default when running tomcat from eclipse so that shouldn't be an issue I guess.

java.lang.ClassNotFoundException: com/mysql/jdbc/Driver

at java.lang.Class.forName0(Native Method)

at java.lang.Class.forName(Class.java:188)

at org.scripps.util.JdbcConnection.createConnection(JdbcConnection.java:71)

at org.scripps.util.JdbcConnection.<init>(JdbcConnection.java:45)

at org.scripps.combo.model.Player.lookupPlayerByName(Player.java:123)

at org.scripps.combo.model.Player.create(Player.java:291)

at org.apache.jsp.checkuser_jsp._jspService(checkuser_jsp.java:97)

at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)

at javax.servlet.http.HttpServlet.service(HttpServlet.java:722)

at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:432)