Launching Jalview via JNLP

Dear list,

Our platform (https://www.genoscope.cns.fr/agc/microscope/home/index.php) uses JNLP to launch Jalview.

We have realized yesterday that it doesn't work anymore (we don't know since when it has been the case). The JNLP error is:

#### Java Web Start Error:
#### JAR resources in JNLP file are not signed by same certificate

If I'm correct, we can't do anything on our side: it's up to you to sign all the JAR files with the same certificate. Is it right ?

Thanks in advance,
Mathieu

···

--
Mathieu Dubois - IR - UMR 8030 équipe LABGeM
CEA - Genoscope. 2 rue Gaston Crémieux. 91057 Evry Cedex France.
Bureau B07
+33 1 60 87 53 35

Hi Mathieu,

Please could you try the steps described at

http://www.jalview.org/faq#jar

(if you haven’t already done so), and let us know if that resolves the problems.

Best regards,

Mungo

···

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Mungo Carstairs
Jalview Computational Scientist

The Barton Group
Division of Computational Biology

School of Life Sciences

University of Dundee, Dundee, Scotland, UK

www.jalview.org

www.compbio.dundee.ac.uk
g.m.carstairs@dundee.ac.uk

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From: jalview-discuss-bounces@jalview.org jalview-discuss-bounces@jalview.org on behalf of Mathieu Dubois mdubois@genoscope.cns.fr
Sent: 20 November 2018 08:15:30
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] Launching Jalview via JNLP

Dear list,

Our platform
(https://www.genoscope.cns.fr/agc/microscope/home/index.php) uses JNLP
to launch Jalview.

We have realized yesterday that it doesn’t work anymore (we don’t know
since when it has been the case). The JNLP error is:

Java Web Start Error:

JAR resources in JNLP file are not signed by same certificate

If I’m correct, we can’t do anything on our side: it’s up to you to sign
all the JAR files with the same certificate. Is it right ?

Thanks in advance,
Mathieu


Mathieu Dubois - IR - UMR 8030 équipe LABGeM
CEA - Genoscope. 2 rue Gaston Crémieux. 91057 Evry Cedex France.
Bureau B07
+33 1 60 87 53 35


Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

The University of Dundee is a registered Scottish Charity, No: SC015096

Hi Mathieu.

Just as a follow on from Mungo’s email - we recommend that web applications use our launchApp servlet at www.jalview.org/services/launchApp, which always offers the latest version of the JNLP file.

Our platform 
([https://www.genoscope.cns.fr/agc/microscope/home/index.php](https://www.genoscope.cns.fr/agc/microscope/home/index.php)) uses JNLP 
to launch Jalview.

I’ve also added MicroScope to our ‘Links’ section of our Jalview community pages (http://www.jalview.org/community/links - should appear there shortly).

···

On 20/11/2018 08:15, Mathieu Dubois wrote:

-------------------------------------------------------------------
Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | [www.jalview.org](http://www.jalview.org) | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk)

Hi Jim and Mongo,

Thank you very much for your help. I was able to generate a correct JNLP file.

We generate the JNLP file ourselves because we pass a parameter to JalView (-open URL). I'm not sure if we can do that with the launchApp servlet.

And thanks for mentioning MicroScope on your site. Of course, we mention JalView in our doc but we should probably give it more credits. I will think about that, too.

Mathieu

···

--
Mathieu Dubois - IR - UMR 8030 équipe LABGeM
CEA - Genoscope. 2 rue Gaston Crémieux. 91057 Evry Cedex France.
Bureau B07
+33 1 60 87 53 35

Hi Mathieu

Hi Jim and Mongo,

Thank you very much for your help. I was able to generate a correct JNLP 
file.

very welcome :slight_smile:

We generate the JNLP file ourselves because we pass a parameter to 
JalView (-open URL). I'm not sure if we can do that with the launchApp 
servlet.

That’s actually the reason we set up the service:

http://www.jalview.org/services/launchApp?open=http%3A%2F%2Fwww.jalview.org%2Fexamples%2Funiref50.fa&annotations=http%3A%2F%2Fwww.jalview.org%2Fexamples%2Funiref50.score_ascii&treeFile=http%3A%2F%2Fwww.jalview.org%2Fexamples%2Fferredoxin.nw

Documentation for supported parameters is given as a comment in the JNLP file:

<?xml version="1.0" encoding="UTF-8"?><!--

Jalview Launch Desktop service
If you have downloaded this file after pressing “Launch Full Application” from Jalview on a web page and you don’t know what to do with this file, you must install Java from http://www.java.sun.com then try opening this file again.

JNLP generated by /jalviewServlet/services/launchApp
JNLP generated from http://www.jalview.org/webstart/jalview.jnlp
Available servlet parameters (please URLEncode):
open=
version= (default is latest patched release, other available versions are ‘stable’, ‘release’, ‘next’, ‘test’, ‘develop’)
jvm-max-heap=heap size in M or G
features maps to ‘-features’
treeFile maps to ‘-tree’
tree maps to ‘-tree’
annotations maps to ‘-annotations’
colour maps to ‘-colour’

If there’s anything else you’d like to be able to do with this then do let us know. As you might be aware, Java Webstart is not going to be widely available on many systems in the future and we are exploring ways to replace the web launch functionality.

Jim.

···

On 20/11/2018 14:46, Mathieu Dubois wrote:

-- 
-------------------------------------------------------------------
Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | [www.jalview.org](http://www.jalview.org) | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk)

Jim, Mungo,

We generate the JNLP file ourselves because we pass a parameter to 
JalView (-open URL). I'm not sure if we can do that with the launchApp 
servlet.

That’s actually the reason we set up the service:

http://www.jalview.org/services/launchApp?open=http%3A%2F%2Fwww.jalview.org%2Fexamples%2Funiref50.fa&annotations=http%3A%2F%2Fwww.jalview.org%2Fexamples%2Funiref50.score_ascii&treeFile=http%3A%2F%2Fwww.jalview.org%2Fexamples%2Fferredoxin.nw

Documentation for supported parameters is given as a comment in the JNLP file:

<?xml version="1.0" encoding="UTF-8"?><!--

Jalview Launch Desktop service
If you have downloaded this file after pressing “Launch Full Application” from Jalview on a web page and you don’t know what to do with this file, you must install Java from http://www.java.sun.com then try opening this file again.

JNLP generated by /jalviewServlet/services/launchApp
JNLP generated from http://www.jalview.org/webstart/jalview.jnlp
Available servlet parameters (please URLEncode):
open=
version= (default is latest patched release, other available versions are ‘stable’, ‘release’, ‘next’, ‘test’, ‘develop’)
jvm-max-heap=heap size in M or G
features maps to ‘-features’
treeFile maps to ‘-tree’
tree maps to ‘-tree’
annotations maps to ‘-annotations’
colour maps to ‘-colour’

Thanks for the explanation. We will probably use the launch service in the next version as it’s very convenient and simple to use.

If there’s anything else you’d like to be able to do with this then do let us know. As you might be aware, Java Webstart is not going to be widely available on many systems in the future and we are exploring ways to replace the web launch functionality.

As for the future of JNLP, if I’m correct, it will disappear soon so I guess the only option is JS.

Mathieu

···

Le 21/11/2018 à 12:57, Jim Procter a écrit :