Cant launch GSEA from web application using Ubuntu

Question

[izzy.yichao.cai]

Hi all,

I got a gene list and I want to do GSEA.

I came into problem that when I want to launch GSEA from the website(web application) using Chrome in Ubuntu, I will always get a file named "gsea.jnlp" downloaded. I tried install icedtea-netx and run this .jnlp file. But I came into fatal problem.

My java version is :

java version "1.7.0_95"

OpenJDK Runtime Environment (IcedTea 2.6.4) (7u95-2.6.4-0ubuntu0.14.04.2)

OpenJDK 64-Bit Server VM (build 24.95-b01, mixed mode)

net.sourceforge.jnlp.LaunchException: Fatal: Read Error: Could not read or parse the JNLP file. You can try to download this file manually and send it as bug report to IcedTea-Web team. at net.sourceforge.jnlp.Launcher.fromUrl(Launcher.java:483) at net.sourceforge.jnlp.Launcher.launch(Launcher.java:279) at net.sourceforge.jnlp.runtime.Boot.run(Boot.java:258) at net.sourceforge.jnlp.runtime.Boot.run(Boot.java:59) at java.security.AccessController.doPrivileged(Native Method) at net.sourceforge.jnlp.runtime.Boot.main(Boot.java:225) Caused by: net.sourceforge.jnlp.ParseException: Invalid XML document syntax. at net.sourceforge.jnlp.XMLParser.getRootNode(XmlParser.java:117) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at net.sourceforge.jnlp.Parser.getRootNode(Parser.java:1307) at net.sourceforge.jnlp.JNLPFile.parse(JNLPFile.java:751) at net.sourceforge.jnlp.JNLPFile.<init>(JNLPFile.java:231) at net.sourceforge.jnlp.JNLPFile.<init>(JNLPFile.java:213) at net.sourceforge.jnlp.JNLPFile.<init>(JNLPFile.java:198) at net.sourceforge.jnlp.JNLPFile.<init>(JNLPFile.java:184) at net.sourceforge.jnlp.Launcher.fromUrl(Launcher.java:447) ... 5 more Caused by: net.sourceforge.nanoxml.XMLParseException: XML Parse Exception during parsing of a jnlp element at line 33: Unexpected end of data reached at net.sourceforge.nanoxml.XMLElement.unexpectedEndOfData(XMLElement.java:1084) at net.sourceforge.nanoxml.XMLElement.readChar(XMLElement.java:867) at net.sourceforge.nanoxml.XMLElement.resolveEntity(XMLElement.java:1003) at net.sourceforge.nanoxml.XMLElement.scanString(XMLElement.java:647) at net.sourceforge.nanoxml.XMLElement.scanElement(XMLElement.java:905) at net.sourceforge.nanoxml.XMLElement.parseFromReader(XMLElement.java:502) at net.sourceforge.nanoxml.XMLElement.parseFromReader(XMLElement.java:454) at net.sourceforge.jnlp.XMLParser.getRootNode(XmlParser.java:113) ... 16 more

This is my first time trying GSEA and I found no relevant question on this. Can anybody help me out with this?

[Pierre Lindenbaum]

what's the url of the gsea.jnlp ? are you working behind a proxy ?

[izzy.yichao.cai]

http://software.broadinstitute.org/gsea/downloads.jsp This is where I launch GSEA.

No, I am not working behind a proxy.

Answer 1

[Pierre Lindenbaum]

there is a non escapted '&' in a text in the top XML :

    $ curl  "http://software.broadinstitute.org/gsea/software/gsea.jnlp?servletPath=http%3A%2F%2Fsoftware.broadinstitute.org%2Fgsea&heap=1024&x=36&y=13"  | xmllint -
      % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                     Dload  Upload   Total   Spent    Left  Speed
    100  1278  100  1278    0     0   5474      0 --:--:-- --:--:-- --:--:--  5835
    -:4: parser error : EntityRef: expecting ';'
    href="gsea.jnlp?servletPath=http%3A%2F%2Fsoftware.broadinstitute.org%2Fgsea&heap

$ curl  "http://software.broadinstitute.org/gsea/software/gsea.jnlp?servletPath=http%3A%2F%2Fsoftware.broadinstitute.org%2Fgsea&heap=1024&x=36&y=13" 

<jnlp spec="1.0+" codebase="&lt;a href=" http:="" software.broadinstitute.org="" gsea="" software="" "="" rel="nofollow">http://software.broadinstitute.org/gsea/software/" href="gsea.jnlp?servletPath=http%3A%2F%2Fsoftware.broadinstitute.org%2Fgsea&heap=1024">
  <information>

the problem is this "&heap=" , it should be '&heap='

But this problem is ignored with my version of java (oracle jre8)

javaws "http://software.broadinstitute.org/gsea/software/gsea.jnlp?servletPath=http%3A%2F%2Fsoftware.broadinstitute.org%2Fgsea&heap=1024&x=36&y=13"

(the application is opened)

[izzy.yichao.cai]

I tried but getting the same error still.

netx: Read Error: Could not read or parse the JNLP file. (Invalid XML document syntax. (XML Parse Exception during parsing of a jnlp element at line 33: Unexpected end of data reached))

But this time I am getting another additional error:

Server returned HTTP response code: 405 for URL: http://software.broadinstitute.org/gsea/software/gsea.jnlp?servletPath=http%3A%2F%2Fsoftware.broadinstitute.org%2Fgsea&heap=1024&x=36&y=13

Then I tried the curl command as you did, but I received a different xml header like this:

<jnlp spec="1.0+" codebase="&lt;a href=" http:="" software.broadinstitute.org="" gsea="" software="" "="" rel="nofollow">http://software.broadinstitute.org/gsea/software/" href="gsea.jnlp?servletPath=http%3A%2F%2Fsoftware.broadinstitute.org%2Fgsea&heap=1024">

What would be the problem?