Uppload and Download Images - Issiues

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Robin Kämpe

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Nov 24, 2015, 7:55:28 AM11/24/15
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Hi!

I think my previous post might have been too messy. Will try to make the problem more clear with a much shorter post.


Problem 1:

Independent of what OS or browser used, when I log in to xnat (1.6.4) and click on Download Images on the project level (session level gives a working popup) (and after fighting with the java security settings) the Applet is loaded but the "Select Local Directory:" edit field is grayed out and I can not use it. It never stops saying "Initializing". Loggin in with localhost (if succesfully battling the security settings) will also load the Applet but here the edit field is not gray and frozen.

My guess so far, based on other threads, is that it might have to do something with the url setting in the build.properties. But I have set that to be the ip of the xnat virtual machine (same as I put into the browser when I connect to the xnat webserver) so that should not be it... I have also swapped the applet files with new ones with updated certificated, as suggested in other posts.

Problem 2:


The uppload images is not working eihter. Here I do not get anyting, just white background. No flashing java window or anything. Same on remote computer as for lcoalhost.

Please let me know if I should post any logs.

Tried xnat-1.6.5 but with this build I get, with every OS, localhost/remote and every browser an instant errir saying: Unknown error...

Thanks

Robin

Robin Kämpe

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Nov 24, 2015, 9:25:16 AM11/24/15
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Minor update:

Problem 1:
The URL was correctly set in the build.properties file but under admin > Configure it still said http://xnatdev. Changed that to the ip.

Now it actually works on the windows machine. I can download the data via the applet. This is still not true on the Ubuntu machine, where the edit field is grayed out and stuck on initializing session. On other users Macs the applet is first of all not loading. Then, when you ad the ip as en exemption in the java settings it actually completley blocks it.

Problem 2:
Even on the windows machine this is still not working. One hint might be that on the bottom part of the firefox browser it says connecting to java.com. The servers do not have internet access. I can not imagine xnat was desinged with the need of an internet conenction but it might be a lead.

Herrick, Rick

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Nov 24, 2015, 11:18:58 AM11/24/15
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For problem 1: As you’ve now discovered, you can’t use different URLs for accessing XNAT from what’s set as the XNAT URL in the admin settings. This is because your authentication token is actually associated with the URL. That means going to http://192.168.100.5 is not the same as going to http://xnatdev which is also not the same as going to http://xnatdev.myschool.edu, and it’s DEFINITELY not the same as any of those with https. So what’s happening is you’re logging into XNAT with your IP but as far as the applet knows the URL is the configured site URL. They don’t play together well.

 

For the other issues, you’re just running into the wonderland that is managing the Java plugin on multiple browser platforms. We have a page that describes how to troubleshoot and understand a lot of these issues:

 

https://wiki.xnat.org/display/XNAT16/Troubleshooting+XNAT+Applet+Issues

 

We have wanted to replace the applet for a long time precisely because of problems like this, but the issue has been finding a cross-platform solution that can handle the DICOM anonymization features on the client side. To date, we still haven’t found anything that can do that other than Java and the easiest deployment is via applet. At least, until applets are no longer supported, which is already the case for the latest releases of Chrome.

 

As for the connecting to java.com message, that’s actually not XNAT, that’s Java. It’s trying to install or update the installed JRE and plugin. I would guess that either Java isn’t installed on those machines, Java is installed but something is wrong with either the plugin or the JRE itself, or perhaps you have Java 8 installed and you’re on an older version of XNAT (pre-1.6.4) which didn’t have 1.8 as a supported JRE version. If the latter, you can fix this by modifying the file xnat-templates/screens/UploadApplet.vm and changing this line:

 

var SUPPORTED_JRE_VERSIONS = ["1.6", "1.7"];

 

To this:

 

var SUPPORTED_JRE_VERSIONS = ["1.6", "1.7", "1.8"];

 

If the Java 8 thing isn’t the case, I’d suggest taking one of the machines, shutting down the browser, uninstalling everything Java (up to and including removing any folders left in the \Program Files or \Program Files (x86) folders, reinstalling Java to the desired version, then re-starting your browser. I’d guess it would work then.

 

You can get the offline installer from this URL:

 

https://www.java.com/en/download/manual.jsp

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Robin Kämpe

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Nov 24, 2015, 2:24:25 PM11/24/15
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Thanks for replying, don't really know where to turn.

Okay. I have basically looked at the steps in the troubleshooting+xnat+applet+issiues (now attatched the turbine log from my ubuntu machine).

But in that case it does not seem like I am putting in the URL wrong?

In build.properties it is by default set to
#e.g.dat.url=http://localhost:8080/xnat
dat.url=http://xnatdev

This I changed to dat.url=http://<ip_to_virtual_machine_running_xnat> (omnitted :8080/xnat - is that needed?)
Then I rebuilded/updaded xnat. I then realized that is still said http://xnatdev under administer < configure. So I changed it also under administer < configure to http://<the_ip>
On the windoes machine you can access the java confiugre via the start menu. There I put the security level to low and it will ask me if I want to run the applet. After the above changes it worked.

On the ubuntu system there is no "ControlPanel". There is itweb-settings. By setting it to low I can get the applet to show itself but, as I said, I cannot interact with it - the field is grayed out and it never stops saying Initilizing. I have tried to add it to exemptions but it is not as simple as on Windoes, it has two fields: one is called document-based and the other code-based ( I don't know what that means, on windows you just put the adress in the field).


Regarding problem 2. The Download applet is working on the windowes machine, but not the uppload. I.e. Java is installed. It might be, as you said java 8. But I do run xnat-1.6.4 so it should support java 8 (right?). I can still check that line.

I have re-installed Java on the ubuntu machine (sudo apt-get purge openjdk-7-jdk and icedtea-webplugin) and updated with sudo apt-get update / upgrade. It still gives no uploader and a gray downloader field. On windows I hope the issiue is the java 8 thing. Otherwise I don't know. Scary to re-install it - I just got the downloader to work, haha. But I guess I have to.

Very messy for me this whole thing - especially since I'm quite new to the whole xnat-scene. Very greatful for your help!


(On a side note - tried to upadate to xnat-1.6.5 in hopes of that fixing everything. On that build I instantly - on all platforms - get Unknown error, unknown error id in text where the applet should be. I guess that is another problem, just letting you know).

Best,

Robin





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turbine.log

Robin Kämpe

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Nov 24, 2015, 5:00:18 PM11/24/15
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Couldn't take it so took the bike to work to be able to test :P.

1. The UploadApplet.vm file had support for all Java versions. So I (on the windows machine) removed Java and did a clean install. The DownloadApplet is still working for the windows machine, I guess due to me setting the URL with the admin account. The UploadApplet is not launching. Nothing happens after you submit which project and subject you want to upload to. Even with a brand new java.

2. Still grayed out DownloadApplet and no UploadApplet using the Ubuntu.


New info is that I turned on the Java debugging and Console. When running the DownloadApplet on windows, this is succesfull and the javaconsole is popping up, displaying what happens. But when I click on Upload then the consol does not come up. This, I think?, is indicating that is never gets so far that it tries to launch the applet?

Doing the same thing on Ubuntu:
The upploadapplet gives the same, nothing and no java console.
The downloadapplet gave a lot of output in the console. I attached it as a text-file. I guess it is only the ending of the file that is interesting. Can you have a short look?

I don't really know what my next move should be. We could have lived with a semi working xnat-system but we kind of need the Upload function (to get in scans we already made before we got xnat).

Thanks again Rick!!

java_console_grayed_out_field

Robin Kämpe

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Nov 25, 2015, 5:19:29 AM11/25/15
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Added the Java_working logg file (when DownloadApplet works on windows) and the Java_gray logg file (when the DowloadApplets local directory field is grayed out on all the ubuntu systems).

The sad thing is that the log-file from the windows machie has some Swedish elements... Hopefully you can see what is differing!

Thanks
java_gray.txt
java-working.txt

Robin Kämpe

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Nov 25, 2015, 7:24:08 AM11/25/15
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Also. On the ubuntu machine, I can successfully run some java test pages like:

http://source.coolsmile.net/test/

But when I go to https://www.java.com/en/download/installed.jsp (verify java) it loads something, shows the icedtea logo and then gives an animated red "Error". When I go to more info and see the log  it has stopped at the same line as when i do the DownloadApplet  ("startup arguments:").

When getting more info from the verify java page the error seems to be from:

Caused by : net.sourceforge.jnfl.LaunchException; Fatal: Application Error: The signed JNLP file did not match the launching JNLP file. Missing Recourse: Signed Application did not match launching JNVL File
...
...
...

Robin Kämpe

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Nov 25, 2015, 10:46:05 AM11/25/15
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Sorry for updating in segments.

The DownloaderApplet also works on the Ubuntu machine that xnat is running on (the virtual machine). I.e. Localhost. Still putting in the real URL though.

Trying to figure out the difference between my ubuntu and that ubuntu, more than that the WM ubuntu is running another Java.

My java =
java version 1.7.0_85
OpenJDK RUntime Enviroment (IncedTea 2.6.1) (7u85-2.6.1-Subuntu0.14.04.1)
OpenJDK 64-Bit Server VM (build 24.85-b03, mixed mode)

The xnat server java =
java version 1.7.0_72
Java(TM) SE Runtime Enviroment (build 1.7.0_71-b14)
Java HotSpot(TM) 64-BIt server VM (build 24.72.-b04, mixed mode).

Robin Kämpe

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Dec 2, 2015, 11:09:03 AM12/2/15
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If someone is interested:

Everything works on a windows machine. If you let it have access to internet via a proxy the uppload applet will load and work. The download applet will work without internet proxy.

Why is a proxy needed? Like I said, JAVA tries to conenct to the internet when using the upploader.

On ubuntu the download applet still loads, but the field is grayed out. No luck with the proxy on the ubuntu firefox, did not work.

Herrick, Rick

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Dec 2, 2015, 12:32:20 PM12/2/15
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There are two solutions I can think of at this point:
  • Turn off automatic update checks in the Java control panel. There should be a tab in the control panel labeled Updates. There’s a checkbox there labeled Check For Updates Automatically. Try turning that off and clicking OK until you’ve completely closed the Java control panel.
  • Try using the Upload Assistant application that we just announced. We built this specifically to provide an alternate way to upload DICOM and ECAT data to XNAT without having to go through the applet.
I think the same thing for the update check would apply on Ubuntu.

Another thing you may want to try on Firefox (and I think this is true across platforms) is to check the Java plugin state:
  1. In the address bar of the browser, type about:config and hit Enter.
  2. In the search bar at the top, type plugin*java and hit Enter.
  3. You should see two entries, plugin.java.mime and plugin.state.java. Make sure that plugin.state.java is set to 2.
  4. You can also try disabling the browser blocklist (this is a fairly desperate measure). Search for extensions.blocklist.enabled and set that to false.
These solutions do pose some security risks, so use with caution. Machines that are behind a firewall and used only for work purposes should be OK, though.

-- 

Rick Herrick

Sr. Programmer/Analyst

Neuroinformatics Research Group

Washington University School of Medicine

(314) 740-5961

Robin Kämpe

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Dec 2, 2015, 4:09:02 PM12/2/15
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Thanks!

I tried turning off automatic updates but in the IcedTea control panel there is no update box to uncheck (there is on windows however).

The plugin.state.java was set to 2

but I changed the extionsions.blocklist.enabled to false. That was the only thing from your suggestions that I could apply.

On my ubuntu with IcedTea it still halts on the same place for the Downloader, at startup aguments:

java.lang.ClassNotFoundException: java/net/URLPermission     at java.lang.Class.forName0(Native Method)     at java.lang.Class.forName(Class.java:195)     at net.sourceforge.jnlp.SecurityDesc.<clinit>(SecurityDesc.java:164)     at net.sourceforge.jnlp.JNLPFile.<init>(JNLPFile.java:137)     at net.sourceforge.jnlp.PluginBridge.<init>(PluginBridge.java:90)     at net.sourceforge.jnlp.PluginBridge.<init>(PluginBridge.java:67)     at net.sourceforge.jnlp.NetxPanel.ourRunLoader(NetxPanel.java:101)     at sun.applet.AppletViewerPanelAccess.run(AppletViewerPanelAccess.java:86)     at java.lang.Thread.run(Thread.java:745)
Exception while reflectively finding URLPermission - host is probably not running Java 8+
JNLPRuntime already initialized
Using NetX panel
Read 111 entries from Firefox's preferences
Found preferences file: /home/robka95/.mozilla/firefox/adc7se45.default/prefs.js
Using firefox's profiles file: /home/robka95/.mozilla/firefox/profiles.ini
Starting security dialog thread
Started processing of plugin-debug-to-console /run/user/1000/icedteaplugin-robka95-MRUEbw/28614-icedteanp-plugin-debug-to-appletviewer
Starting processing of plugin-debug-to-console /run/user/1000/icedteaplugin-robka95-MRUEbw/28614-icedteanp-plugin-debug-to-appletviewer
WARNING: key deployment.system.cachedir has no value, setting to default value
Loading User level properties from: /home/robka95/.config/icedtea-web/deployment.properties
cache: /home/robka95/.cache/icedtea-web file exists:true
config: /home/robka95/.config/icedtea-web file exists: true
System is already following XDG .cache and .config specifications
2: /run/user/1000/icedteaplugin-robka95-MRUEbw/28614-icedteanp-plugin-debug-to-appletviewer
1: /run/user/1000/icedteaplugin-robka95-MRUEbw/28614-icedteanp-appletviewer-to-plugin
0: /run/user/1000/icedteaplugin-robka95-MRUEbw/28614-icedteanp-plugin-to-appletviewer
startup arguments:


The upploader gives another error. When I started using the proxy it now atleast start loading the applet and then sais:

Applet startup failed; please contact ad...@yourplace.org for help.
Error details:
java.io.IOException
    at org.nrg.net.RestServer.getUserAuthMessage(RestServer.java:213)
    at org.nrg.upload.ui.UploadAssistantApplet.start(UploadAssistantApplet.java:143)
    at sun.applet.AppletPanel.run(AppletPanel.java:476)
    at sun.applet.AppletViewerPanelAccess.run(AppletViewerPanelAccess.java:90)
    at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.NullPointerException
    at org.nrg.net.RestServer.makeBasicAuthorization(RestServer.java:333)
    at org.nrg.net.RestServer.addBasicAuthorizationToHeaderMap(RestServer.java:338)
    at org.nrg.net.RestServer.request(RestServer.java:443)
    at org.nrg.net.RestServer.getUserAuthMessage(RestServer.java:208)
    ... 4 more

The java console error is the same: startup arguments:

When I use firefox on the other ubuntu server (older version of icedtea- still not possible to uncheck update java) I get the same java console message and error for the download: startup arguments:
[admin][ITW-APPLET][MESSAGE_DEBUG][Wed Dec 02 22:05:07 CET 2015][sun.applet.PluginMain.main(PluginMain.java:127)] NETX Thread# 4e33c558, name main: 1: /run/user/1000/icedteaplugin-admin-1Ej2qZ/133154-icedteanp-appletviewer-to-plugin
[admin][ITW-APPLET][MESSAGE_DEBUG][Wed Dec 02 22:05:07 CET 2015][sun.applet.PluginMain.main(PluginMain.java:127)] NETX Thread# 4e33c558, name main: 0: /run/user/1000/icedteaplugin-admin-1Ej2qZ/133154-icedteanp-plugin-to-appletviewer
[admin][ITW-APPLET][MESSAGE_DEBUG][Wed Dec 02 22:05:07 CET 2015][sun.applet.PluginMain.main(PluginMain.java:124)] NETX Thread# 4e33c558, name main: startup arguments:

And the uploader:

Pretty much the same thing! Promtps me for some kind of password and then fails and goes to: Startup argumetns:

Sorry this did not help but thanks!

Robin Kämpe

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Dec 2, 2015, 4:17:22 PM12/2/15
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and, localhost who also run ubuntu and firefox have a working downloader... (the uploader does not work however)

Herrick, Rick

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Dec 2, 2015, 4:50:14 PM12/2/15
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I think the java/net/URLPermission message is the key to your problem. Something’s going weird with the plugin:

java.lang.ClassNotFoundException: java/net/URLPermission
     at java.lang.Class.forName0(Native Method)
     at java.lang.Class.forName(Class.java:195)
     at net.sourceforge.jnlp.SecurityDesc.<clinit>(SecurityDesc.java:164)
     at net.sourceforge.jnlp.JNLPFile.<init>(JNLPFile.java:137)
     at net.sourceforge.jnlp.PluginBridge.<init>(PluginBridge.java:90)
     at net.sourceforge.jnlp.PluginBridge.<init>(PluginBridge.java:67)
     at net.sourceforge.jnlp.NetxPanel.ourRunLoader(NetxPanel.java:101)
     at sun.applet.AppletViewerPanelAccess.run(AppletViewerPanelAccess.java:86)
     at java.lang.Thread.run(Thread.java:745) 

Note that none of that code has yet gotten into the XNAT applet code. Somehow the plugin is starting up and getting Java 8 libraries, while running on top of non-Java 8. All of the XNAT applet code is compiled for 1.7, but that’s really irrelevant, since the loader is never even getting that far. I don’t know if this is an issue with the IcedTea plugin or just its integration with OpenJDK or what the deal is. But that’s definitely the issue in this particular case. Is it possible you have a 1.8-compatible version of IcedTea but a 1.7 version of OpenJDK installed?

Robin Kämpe

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Dec 2, 2015, 4:57:00 PM12/2/15
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Thanks!  I know very little about java!

I can check on monday but if I remember correctly I installed icedtea-7-plugin and openjdk-7-jdk.

Both my computer and our analysis server run Ubuntu, Firefox and icedtea and face the same problems. Is there another Web plugin I can test?

The xnat server (localhost) is also Ubuntu but with another java plugin I think and there atleast the download applet works. The upload  problem might be proxy related there

Robin Kämpe

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Dec 10, 2015, 6:53:30 AM12/10/15
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Update.

I got the downloader to work on mac. That was just a matter of setting the ip to xnat as an exception.


Uploader does not work - might be an issue with the  proxy (since it works on windows).

Issue is still ubuntu. Might be icedtea that is the bad guy. Is there another I can trY?
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