To whom it may concern,
We have a site that has the jalviewApplet.jar applet installed that pulls a file from a page within the same domain.
The previous versions worked, but after we upgraded to the most recent version after the certificate expired last November, it was no longer able to load data, it just hangs on ‘Loading Data’ (screenshot attached).
I have attached the file that gets passed to the applet.
Thanks!
-Rob
clustal_output.rtf (9.3 KB)
···
Rob Wieck
Research Programmer
Center for Research Computing
University of Notre Dame
Hi Rob,
Just to eliminate one possible problem - I notice the data file is in RTF format and includes control characters. Jalview expects only plain text files.
Are you able to generate the file as plain text, and does that make a difference?
Though having said that, I can load your RTF file into Jalview (Desktop or applet), albeit with the control characters rendered as extra ‘nonsense’ sequences - so this may not be the root of your problem. Is there a public link to your site / applet?
Thanks,
Mungo
The University of Dundee is a registered Scottish Charity, No: SC015096
···
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
From: jalview-discuss-bounces@jalview.org jalview-discuss-bounces@jalview.org on behalf of Rob Wieck rwieck@nd.edu
Sent: 05 January 2016 20:47
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] New version Stuck on Loading Data
To whom it may concern,
We have a site that has the jalviewApplet.jar applet installed that pulls a file from a page within the same domain.
The previous versions worked, but after we upgraded to the most recent version after the certificate expired last November, it was no longer able to load data, it just hangs on ‘Loading Data’ (screenshot attached).
I have attached the file that gets passed to the applet.
Thanks!
-Rob
–
Rob Wieck
Research Programmer
Center for Research Computing
University of Notre Dame
Hi Mungo,
Thanks for the prompt reply. I only sent the file in rtf, so I can attach it to an email. We point the applet to a unique ur for the input and is just plain text, https://www.vectorbase.org/sites/all/modules/custom/clustalw/clustalwPrintResults.php?id=111045&type=align for example.
https://www.vectorbase.org/clustalw is the site where jalview is implemented. In order to see the applet, sequences must be ran through clustalw first, then under the results, the applet loads in the data.
Best,
Rob W
···
On Wed, Jan 6, 2016 at 4:00 AM, Mungo Carstairs (Staff) <g.m.carstairs@dundee.ac.uk> wrote:
Hi Rob,
Just to eliminate one possible problem - I notice the data file is in RTF format and includes control characters. Jalview expects only plain text files.
Are you able to generate the file as plain text, and does that make a difference?
Though having said that, I can load your RTF file into Jalview (Desktop or applet), albeit with the control characters rendered as extra ‘nonsense’ sequences - so this may not be the root of your problem. Is there a public link to your site / applet?
Thanks,
Mungo
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
From: jalview-discuss-bounces@jalview.org <jalview-discuss-bounces@jalview.org> on behalf of Rob Wieck <rwieck@nd.edu>
Sent: 05 January 2016 20:47
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] New version Stuck on Loading Data
To whom it may concern,
We have a site that has the jalviewApplet.jar applet installed that pulls a file from a page within the same domain.
The previous versions worked, but after we upgraded to the most recent version after the certificate expired last November, it was no longer able to load data, it just hangs on ‘Loading Data’ (screenshot attached).
I have attached the file that gets passed to the applet.
Thanks!
-Rob
–
Rob Wieck
Research Programmer
Center for Research Computing
University of Notre Dame
The University of Dundee is a registered Scottish Charity, No: SC015096
–
Rob Wieck
Research Programmer
Center for Research Computing
University of Notre Dame
Thanks Rob.
Running with Java console shows up the error as
ClassNotFoundException: org.jmol.api.JmolSelectionListener
Can you ensure your applet has been updated to include the updated Jmol library, available at http://www.jalview.org/examples/ at the link to
http://www.jalview.org/examples/JmolApplet-14.2.14_2015.06.11.jar
and let me know if that resolves the problem.
Our documentation for updating applet deployments could maybe be clearer. What steps did you follow to update after the certificate expired?
Thanks and regards,
Mungo
The University of Dundee is a registered Scottish Charity, No: SC015096
···
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
From: Rob Wieck rwieck@nd.edu
Sent: 06 January 2016 13:37
To: Mungo Carstairs (Staff)
Cc: jalview-discuss@jalview.org
Subject: Re: [Jalview-discuss] New version Stuck on Loading Data
Hi Mungo,
Thanks for the prompt reply. I only sent the file in rtf, so I can attach it to an email. We point the applet to a unique ur for the input and is just plain text, https://www.vectorbase.org/sites/all/modules/custom/clustalw/clustalwPrintResults.php?id=111045&type=align for example.
https://www.vectorbase.org/clustalw is the site where jalview is implemented. In order to see the applet, sequences must be ran through clustalw first, then under the results, the applet loads in the data.
Best,
Rob W
On Wed, Jan 6, 2016 at 4:00 AM, Mungo Carstairs (Staff) <g.m.carstairs@dundee.ac.uk> wrote:
Hi Rob,
Just to eliminate one possible problem - I notice the data file is in RTF format and includes control characters. Jalview expects only plain text files.
Are you able to generate the file as plain text, and does that make a difference?
Though having said that, I can load your RTF file into Jalview (Desktop or applet), albeit with the control characters rendered as extra ‘nonsense’ sequences - so this may not be the root of your problem. Is there a public link to your site / applet?
Thanks,
Mungo
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
From: jalview-discuss-bounces@jalview.org <jalview-discuss-bounces@jalview.org> on behalf of Rob Wieck <rwieck@nd.edu>
Sent: 05 January 2016 20:47
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] New version Stuck on Loading Data
To whom it may concern,
We have a site that has the jalviewApplet.jar applet installed that pulls a file from a page within the same domain.
The previous versions worked, but after we upgraded to the most recent version after the certificate expired last November, it was no longer able to load data, it just hangs on ‘Loading Data’ (screenshot attached).
I have attached the file that gets passed to the applet.
Thanks!
-Rob
–
Rob Wieck
Research Programmer
Center for Research Computing
University of Notre Dame
The University of Dundee is a registered Scottish Charity, No: SC015096
–
Rob Wieck
Research Programmer
Center for Research Computing
University of Notre Dame
Thanks Mungo,
Adding in that JmolApplet allowed it to run without errors. Just so you know, we haven’t needed that applet before and haven’t changed anything else with the output of that feature.
Thanks for your help!
-Rob W
···
On Wed, Jan 6, 2016 at 9:08 AM, Mungo Carstairs (Staff) <g.m.carstairs@dundee.ac.uk> wrote:
Thanks Rob.
Running with Java console shows up the error as
ClassNotFoundException: org.jmol.api.JmolSelectionListener
Can you ensure your applet has been updated to include the updated Jmol library, available at http://www.jalview.org/examples/ at the link to
http://www.jalview.org/examples/JmolApplet-14.2.14_2015.06.11.jar
and let me know if that resolves the problem.
Our documentation for updating applet deployments could maybe be clearer. What steps did you follow to update after the certificate expired?
Thanks and regards,
Mungo
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
From: Rob Wieck <rwieck@nd.edu>
Sent: 06 January 2016 13:37
To: Mungo Carstairs (Staff)
Cc: jalview-discuss@jalview.org
Subject: Re: [Jalview-discuss] New version Stuck on Loading Data
Hi Mungo,
Thanks for the prompt reply. I only sent the file in rtf, so I can attach it to an email. We point the applet to a unique ur for the input and is just plain text, https://www.vectorbase.org/sites/all/modules/custom/clustalw/clustalwPrintResults.php?id=111045&type=align for example.
https://www.vectorbase.org/clustalw is the site where jalview is implemented. In order to see the applet, sequences must be ran through clustalw first, then under the results, the applet loads in the data.
Best,
Rob W
The University of Dundee is a registered Scottish Charity, No: SC015096
–
On Wed, Jan 6, 2016 at 4:00 AM, Mungo Carstairs (Staff) <g.m.carstairs@dundee.ac.uk> wrote:
Hi Rob,
Just to eliminate one possible problem - I notice the data file is in RTF format and includes control characters. Jalview expects only plain text files.
Are you able to generate the file as plain text, and does that make a difference?
Though having said that, I can load your RTF file into Jalview (Desktop or applet), albeit with the control characters rendered as extra ‘nonsense’ sequences - so this may not be the root of your problem. Is there a public link to your site / applet?
Thanks,
Mungo
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
From: jalview-discuss-bounces@jalview.org <jalview-discuss-bounces@jalview.org> on behalf of Rob Wieck <rwieck@nd.edu>
Sent: 05 January 2016 20:47
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] New version Stuck on Loading Data
To whom it may concern,
We have a site that has the jalviewApplet.jar applet installed that pulls a file from a page within the same domain.
The previous versions worked, but after we upgraded to the most recent version after the certificate expired last November, it was no longer able to load data, it just hangs on ‘Loading Data’ (screenshot attached).
I have attached the file that gets passed to the applet.
Thanks!
-Rob
–
Rob Wieck
Research Programmer
Center for Research Computing
University of Notre Dame
The University of Dundee is a registered Scottish Charity, No: SC015096
–
Rob Wieck
Research Programmer
Center for Research Computing
University of Notre Dame
Rob Wieck
Research Programmer
Center for Research Computing
University of Notre Dame