[Jalview-discuss] Launching Jalview via JNLP

[Mathieu Dubois]

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

[Mungo Carstairs (Staff)]

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

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________________________________
From: jalview-discuss-***@jalview.org <jalview-discuss-***@jalview.org> on behalf of Mathieu Dubois <***@genoscope.cns.fr>
Sent: 20 November 2018 08:15:30
To: jalview-***@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
[phone]

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[Jim Procter]

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.

Post by Mathieu Dubois
Our platform
(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).

[Mathieu Dubois]

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

[Jim Procter]

Hi Mathieu

Post by Mathieu Dubois
Hi Jim and Mongo,
Thank you very much for your help. I was able to generate a correct JNLP
file.

very welcome :)

Post by Mathieu Dubois
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=<alignment file URL>
    version=<Valid Jalview Version string> (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.

[Mathieu Dubois]

Jim, Mungo,

Post by Jim Procter

Post by Mathieu Dubois
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.

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
<?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
    open=<alignment file URL>
    version=<Valid Jalview Version string> (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.

Post by Jim Procter
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