Build server issues?

Suzanne has pointed out that the JalviewJS link

https://builds.jalview.org/userlogin!doDefault.action?os_destination=%2Fartifact%2FJB-JB47%2Fshared%2Fbuild-latest%2Fjalview-js-site%2Fjalview_bin_Jalview.html

is prompting for a login.

Also I cannot see any JalviewJS builds in the dashboard as I would expect:

https://builds.jalview.org/browse/JB

Is this possibly the out of space problem?

Mungo

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

···

Email signature

University of Dundee shield logo

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

University of Dundee FacebookUniversity of Dundee TwitterUniversity of Dundee LinkedInUniversity of Dundee YouTubeUniversity of Dundee InstagramUniversity of Dundee Snapchat
We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017

Not sure what the problem is but can confirm we seem to have lost all jalviewjs build plans. Will look at it in am.

J.

···

On Wed, 13 Mar 2019, 16:11 Mungo Carstairs (Staff), <g.m.carstairs@dundee.ac.uk> wrote:

Suzanne has pointed out that the JalviewJS link

https://builds.jalview.org/userlogin!doDefault.action?os_destination=%2Fartifact%2FJB-JB47%2Fshared%2Fbuild-latest%2Fjalview-js-site%2Fjalview_bin_Jalview.html

is prompting for a login.

Also I cannot see any JalviewJS builds in the dashboard as I would expect:

https://builds.jalview.org/browse/JB

Is this possibly the out of space problem?

Mungo

Email signature

University of Dundee shield logo

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

University of Dundee FacebookUniversity of Dundee TwitterUniversity of Dundee LinkedInUniversity of Dundee YouTubeUniversity of Dundee InstagramUniversity of Dundee Snapchat
We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017

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


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

I’m at least a little confused at how I managed this but I seem to have deleted the Jalview JS builds at 5 to 6 on Friday evening. I was trying to ‘clean up’ but I certainly didn’t intend to delete the whole plan.

I’ll get it back asap.

Jim

Not sure what the problem is but can confirm we seem to have lost all jalviewjs build plans. Will look at it in am.

J.

Suzanne has pointed out that the JalviewJS link

https://builds.jalview.org/userlogin!doDefault.action?os_destination=%2Fartifact%2FJB-JB47%2Fshared%2Fbuild-latest%2Fjalview-js-site%2Fjalview_bin_Jalview.html

is prompting for a login.

Also I cannot see any JalviewJS builds in the dashboard as I would expect:

https://builds.jalview.org/browse/JB

Is this possibly the out of space problem?

Mungo

Email signature

University of Dundee shield logo

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

University of Dundee FacebookUniversity of Dundee TwitterUniversity of Dundee LinkedInUniversity of Dundee YouTubeUniversity of Dundee InstagramUniversity of Dundee Snapchat
We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017

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


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

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

···

On 13/03/2019 23:06, Jim Procter wrote:

_______________________________________________
Jalview-dev mailing list
[Jalview-dev@jalview.org](mailto:Jalview-dev@jalview.org)
[http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev](http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev)

-- 
-------------------------------------------------------------------
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)

jalviewjs build plan is back in business - the original links that were posted aren’t going to work, however.

Now is as good a time as any to set up www.jalview.org/jalviewjs - I’ll look at that in a few hours - see you on gitter.

I’m at least a little confused at how I managed this but I seem to have deleted the Jalview JS builds at 5 to 6 on Friday evening. I was trying to ‘clean up’ but I certainly didn’t intend to delete the whole plan.

I’ll get it back asap.

Jim

Not sure what the problem is but can confirm we seem to have lost all jalviewjs build plans. Will look at it in am.

J.

Suzanne has pointed out that the JalviewJS link

https://builds.jalview.org/userlogin!doDefault.action?os_destination=%2Fartifact%2FJB-JB47%2Fshared%2Fbuild-latest%2Fjalview-js-site%2Fjalview_bin_Jalview.html

is prompting for a login.

Also I cannot see any JalviewJS builds in the dashboard as I would expect:

https://builds.jalview.org/browse/JB

Is this possibly the out of space problem?

Mungo

Email signature

University of Dundee shield logo

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

University of Dundee FacebookUniversity of Dundee TwitterUniversity of Dundee LinkedInUniversity of Dundee YouTubeUniversity of Dundee InstagramUniversity of Dundee Snapchat
We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017

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


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

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

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

···

On 14/03/2019 05:47, James Procter (Staff) wrote:

On 13/03/2019 23:06, Jim Procter wrote:

_______________________________________________
Jalview-dev mailing list
[Jalview-dev@jalview.org](mailto:Jalview-dev@jalview.org)
[http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev](http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev)

-- 
-------------------------------------------------------------------
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)

_______________________________________________
Jalview-dev mailing list
[Jalview-dev@jalview.org](mailto:Jalview-dev@jalview.org)
[http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev](http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev)

-- 
-------------------------------------------------------------------
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)

Thanks Jim.

Does the configuration run to being able to set up a redirect from the published url

https://builds.jalview.org/artifact/JB-JB83/shared/build-latest/jalview-js-site/jalview_bin_JalviewJS.html

and maybe also its encoded version

https://builds.jalview.org/userlogin!doDefault.action?os_destination=%2Fartifact%2FJB-JB83%2Fshared%2Fbuild-latest%2Fjalview-js-site%2Fjalview_bin_JalviewJS.html

to the latest JS-demo or JS-develop build?

I hope VIZBI is going well!

I should have a merged and tested Java/JS develop by the end of the week.

Mungo

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

···

Email signature

University of Dundee shield logo

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

University of Dundee FacebookUniversity of Dundee TwitterUniversity of Dundee LinkedInUniversity of Dundee YouTubeUniversity of Dundee InstagramUniversity of Dundee Snapchat
We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017


From: jalview-dev-bounces@jalview.org jalview-dev-bounces@jalview.org on behalf of James Procter (Staff) J.Procter@dundee.ac.uk
Sent: 14 March 2019 06:19:35
To: Jalview Development List
Subject: Re: [Jalview-dev] Build server issues?

jalviewjs build plan is back in business - the original links that were posted aren’t going to work, however.

Now is as good a time as any to set up www.jalview.org/jalviewjs - I’ll look at that in a few hours - see you on gitter.

On 14/03/2019 05:47, James Procter (Staff) wrote:

I’m at least a little confused at how I managed this but I seem to have deleted the Jalview JS builds at 5 to 6 on Friday evening. I was trying to ‘clean up’ but I certainly didn’t intend to delete the whole plan.

I’ll get it back asap.

Jim

On 13/03/2019 23:06, Jim Procter wrote:

Not sure what the problem is but can confirm we seem to have lost all jalviewjs build plans. Will look at it in am.

J.

On Wed, 13 Mar 2019, 16:11 Mungo Carstairs (Staff), <g.m.carstairs@dundee.ac.uk> wrote:

Suzanne has pointed out that the JalviewJS link

https://builds.jalview.org/userlogin!doDefault.action?os_destination=%2Fartifact%2FJB-JB47%2Fshared%2Fbuild-latest%2Fjalview-js-site%2Fjalview_bin_Jalview.html

is prompting for a login.

Also I cannot see any JalviewJS builds in the dashboard as I would expect:

https://builds.jalview.org/browse/JB

Is this possibly the out of space problem?

Mungo

Email signature

University of Dundee shield logo

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

University of Dundee FacebookUniversity of Dundee TwitterUniversity of Dundee LinkedInUniversity of Dundee YouTubeUniversity of Dundee InstagramUniversity of Dundee Snapchat
We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017

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


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

_______________________________________________
Jalview-dev mailing list
[Jalview-dev@jalview.org](mailto:Jalview-dev@jalview.org)
[http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev](http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev)

-- 
-------------------------------------------------------------------
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)

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

_______________________________________________
Jalview-dev mailing list
[Jalview-dev@jalview.org](mailto:Jalview-dev@jalview.org)
[http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev](http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev)

-- 
-------------------------------------------------------------------
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)

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

Current state is now:

Latest JS-develop:

https://builds.jalview.org/browse/JB-JB1-2/artifact/shared/jalviewjs/jalview_bin_Jalview.html?open examples/uniref50.fa features examples/exampleFeatures.txt

···

Latest JS-demo (as published with grant application):

https://builds.jalview.org/browse/JB-JB0-2/artifact/shared/jalviewjs/jalview_bin_JalviewJS.html

Mungo

University of Dundee shield logo

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

University of Dundee FacebookUniversity of Dundee TwitterUniversity of Dundee LinkedInUniversity of Dundee YouTubeUniversity of Dundee InstagramUniversity of Dundee Snapchat
We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017

Email signature


From: Mungo Carstairs (Staff)
Sent: 14 March 2019 07:44:09
To: Jalview Development List
Subject: Re: [Jalview-dev] Build server issues?

Thanks Jim.

Does the configuration run to being able to set up a redirect from the published url

https://builds.jalview.org/artifact/JB-JB83/shared/build-latest/jalview-js-site/jalview_bin_JalviewJS.html

and maybe also its encoded version

https://builds.jalview.org/userlogin!doDefault.action?os_destination=%2Fartifact%2FJB-JB83%2Fshared%2Fbuild-latest%2Fjalview-js-site%2Fjalview_bin_JalviewJS.html

to the latest JS-demo or JS-develop build?

I hope VIZBI is going well!

I should have a merged and tested Java/JS develop by the end of the week.

Mungo

Email signature

University of Dundee shield logo

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

University of Dundee FacebookUniversity of Dundee TwitterUniversity of Dundee LinkedInUniversity of Dundee YouTubeUniversity of Dundee InstagramUniversity of Dundee Snapchat
We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017

From: jalview-dev-bounces@jalview.org jalview-dev-bounces@jalview.org on behalf of James Procter (Staff) J.Procter@dundee.ac.uk
Sent: 14 March 2019 06:19:35
To: Jalview Development List
Subject: Re: [Jalview-dev] Build server issues?

jalviewjs build plan is back in business - the original links that were posted aren’t going to work, however.

Now is as good a time as any to set up www.jalview.org/jalviewjs - I’ll look at that in a few hours - see you on gitter.

On 14/03/2019 05:47, James Procter (Staff) wrote:

I’m at least a little confused at how I managed this but I seem to have deleted the Jalview JS builds at 5 to 6 on Friday evening. I was trying to ‘clean up’ but I certainly didn’t intend to delete the whole plan.

I’ll get it back asap.

Jim

On 13/03/2019 23:06, Jim Procter wrote:

Not sure what the problem is but can confirm we seem to have lost all jalviewjs build plans. Will look at it in am.

J.

On Wed, 13 Mar 2019, 16:11 Mungo Carstairs (Staff), <g.m.carstairs@dundee.ac.uk> wrote:

Suzanne has pointed out that the JalviewJS link

https://builds.jalview.org/userlogin!doDefault.action?os_destination=%2Fartifact%2FJB-JB47%2Fshared%2Fbuild-latest%2Fjalview-js-site%2Fjalview_bin_Jalview.html

is prompting for a login.

Also I cannot see any JalviewJS builds in the dashboard as I would expect:

https://builds.jalview.org/browse/JB

Is this possibly the out of space problem?

Mungo

Email signature

University of Dundee shield logo

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

University of Dundee FacebookUniversity of Dundee TwitterUniversity of Dundee LinkedInUniversity of Dundee YouTubeUniversity of Dundee InstagramUniversity of Dundee Snapchat
We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017

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


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

_______________________________________________
Jalview-dev mailing list
[Jalview-dev@jalview.org](mailto:Jalview-dev@jalview.org)
[http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev](http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev)

-- 
-------------------------------------------------------------------
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)

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

_______________________________________________
Jalview-dev mailing list
[Jalview-dev@jalview.org](mailto:Jalview-dev@jalview.org)
[http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev](http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev)

-- 
-------------------------------------------------------------------
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)

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

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


I was thinking of putting in a proxypass for that specific path dir in spacewalk to the jalviewjs I downloaded (which was JB83) a couple of weeks ago, hosted on combo~bsoares (though that URL wouldn’t appear). I can do that this morning some time if I get a chance (in Crieff).

Should I do this? (going to be on the road for the next hour)

Ben

···

From: jalview-dev-bounces@jalview.org jalview-dev-bounces@jalview.org on behalf of Mungo Carstairs (Staff) g.m.carstairs@dundee.ac.uk
Sent: 14 March 2019 08:01:20
To: Jalview Development List
Subject: Re: [Jalview-dev] Build server issues?

Current state is now:

Latest JS-develop:

https://builds.jalview.org/browse/JB-JB1-2/artifact/shared/jalviewjs/jalview_bin_Jalview.html?open examples/uniref50.fa features examples/exampleFeatures.txt

Latest JS-demo (as published with grant application):

https://builds.jalview.org/browse/JB-JB0-2/artifact/shared/jalviewjs/jalview_bin_JalviewJS.html

Email signatureMungo

University of Dundee shield logo

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

University of Dundee FacebookUniversity of Dundee TwitterUniversity of Dundee LinkedInUniversity of Dundee YouTubeUniversity of Dundee InstagramUniversity of Dundee Snapchat
We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017

From: Mungo Carstairs (Staff)
Sent: 14 March 2019 07:44:09
To: Jalview Development List
Subject: Re: [Jalview-dev] Build server issues?

Thanks Jim.

Does the configuration run to being able to set up a redirect from the published url

https://builds.jalview.org/artifact/JB-JB83/shared/build-latest/jalview-js-site/jalview_bin_JalviewJS.html

and maybe also its encoded version

https://builds.jalview.org/userlogin!doDefault.action?os_destination=%2Fartifact%2FJB-JB83%2Fshared%2Fbuild-latest%2Fjalview-js-site%2Fjalview_bin_JalviewJS.html

to the latest JS-demo or JS-develop build?

I hope VIZBI is going well!

I should have a merged and tested Java/JS develop by the end of the week.

Mungo

Email signature

University of Dundee shield logo

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

University of Dundee FacebookUniversity of Dundee TwitterUniversity of Dundee LinkedInUniversity of Dundee YouTubeUniversity of Dundee InstagramUniversity of Dundee Snapchat
We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017

From: jalview-dev-bounces@jalview.org jalview-dev-bounces@jalview.org on behalf of James Procter (Staff) J.Procter@dundee.ac.uk
Sent: 14 March 2019 06:19:35
To: Jalview Development List
Subject: Re: [Jalview-dev] Build server issues?

jalviewjs build plan is back in business - the original links that were posted aren’t going to work, however.

Now is as good a time as any to set up www.jalview.org/jalviewjs - I’ll look at that in a few hours - see you on gitter.

On 14/03/2019 05:47, James Procter (Staff) wrote:

I’m at least a little confused at how I managed this but I seem to have deleted the Jalview JS builds at 5 to 6 on Friday evening. I was trying to ‘clean up’ but I certainly didn’t intend to delete the whole plan.

I’ll get it back asap.

Jim

On 13/03/2019 23:06, Jim Procter wrote:

Not sure what the problem is but can confirm we seem to have lost all jalviewjs build plans. Will look at it in am.

J.

On Wed, 13 Mar 2019, 16:11 Mungo Carstairs (Staff), <g.m.carstairs@dundee.ac.uk> wrote:

Suzanne has pointed out that the JalviewJS link

https://builds.jalview.org/userlogin!doDefault.action?os_destination=%2Fartifact%2FJB-JB47%2Fshared%2Fbuild-latest%2Fjalview-js-site%2Fjalview_bin_Jalview.html

is prompting for a login.

Also I cannot see any JalviewJS builds in the dashboard as I would expect:

https://builds.jalview.org/browse/JB

Is this possibly the out of space problem?

Mungo

Email signature

University of Dundee shield logo

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

University of Dundee FacebookUniversity of Dundee TwitterUniversity of Dundee LinkedInUniversity of Dundee YouTubeUniversity of Dundee InstagramUniversity of Dundee Snapchat
We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017

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


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

_______________________________________________
Jalview-dev mailing list
[Jalview-dev@jalview.org](mailto:Jalview-dev@jalview.org)
[http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev](http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev)

-- 
-------------------------------------------------------------------
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)

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

_______________________________________________
Jalview-dev mailing list
[Jalview-dev@jalview.org](mailto:Jalview-dev@jalview.org)
[http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev](http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev)

-- 
-------------------------------------------------------------------
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)

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

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

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



which specific path ?

···

On 14/03/2019 08:04, Benedict Soares (Staff) wrote:

I was thinking of putting in a proxypass for that specific path dir in
spacewalk to the jalviewjs I downloaded (which was JB83) a couple of
weeks ago, hosted on combo~bsoares (though that URL wouldn't appear). I
can do that this morning some time if I get a chance (in Crieff).

Should I do this? (going to be on the road for the next hour)

Ben

------------------------------------------------------------------------
*From:* jalview-dev-bounces@jalview.org
<jalview-dev-bounces@jalview.org> on behalf of Mungo Carstairs (Staff)
<g.m.carstairs@dundee.ac.uk>
*Sent:* 14 March 2019 08:01:20
*To:* Jalview Development List
*Subject:* Re: [Jalview-dev] Build server issues?

Current state is now:

Latest JS-develop:

https://builds.jalview.org/browse/JB-JB1-2/artifact/shared/jalviewjs/jalview_bin_Jalview.html?open
examples/uniref50.fa features examples/exampleFeatures.txt

Latest JS-demo (as published with grant application):

https://builds.jalview.org/browse/JB-JB0-2/artifact/shared/jalviewjs/jalview_bin_JalviewJS.html

Email signatureMungo

University of Dundee shield logo <http://uod.ac.uk/sig-home>

*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 <http://www.jalview.org>

www.compbio.dundee.ac.uk <http://www.compbio.dundee.ac.uk>
g.m.carstairs@dundee.ac.uk <mailto:g.m.carstairs@dundee.ac.uk>

University of Dundee Facebook <http://uod.ac.uk/sig-fb> University of
Dundee Twitter <http://uod.ac.uk/sig-tw> University of Dundee LinkedIn
<http://uod.ac.uk/sig-li> University of Dundee YouTube
<http://uod.ac.uk/sig-yt> University of Dundee Instagram
<http://uod.ac.uk/sig-ig> University of Dundee Snapchat
<http://uod.ac.uk/sig-sc>
*We're Scottish University of the Year again!*
<http://uod.ac.uk/sig-strapline>
The Times / Sunday Times Good University Guide 2016 and 2017

------------------------------------------------------------------------
*From:* Mungo Carstairs (Staff)
*Sent:* 14 March 2019 07:44:09
*To:* Jalview Development List
*Subject:* Re: [Jalview-dev] Build server issues?

Thanks Jim.

Does the configuration run to being able to set up a redirect from the
published url

https://builds.jalview.org/artifact/JB-JB83/shared/build-latest/jalview-js-site/jalview_bin_JalviewJS.html

and maybe also its encoded version

https://builds.jalview.org/userlogin!doDefault.action?os_destination=%2Fartifact%2FJB-JB83%2Fshared%2Fbuild-latest%2Fjalview-js-site%2Fjalview_bin_JalviewJS.html

to the latest JS-demo or JS-develop build?

I hope VIZBI is going well!

I should have a merged and tested Java/JS develop by the end of the week.

Mungo

Email signature

University of Dundee shield logo <http://uod.ac.uk/sig-home>

*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 <http://www.jalview.org>

www.compbio.dundee.ac.uk <http://www.compbio.dundee.ac.uk>
g.m.carstairs@dundee.ac.uk <mailto:g.m.carstairs@dundee.ac.uk>

University of Dundee Facebook <http://uod.ac.uk/sig-fb> University of
Dundee Twitter <http://uod.ac.uk/sig-tw> University of Dundee LinkedIn
<http://uod.ac.uk/sig-li> University of Dundee YouTube
<http://uod.ac.uk/sig-yt> University of Dundee Instagram
<http://uod.ac.uk/sig-ig> University of Dundee Snapchat
<http://uod.ac.uk/sig-sc>
*We're Scottish University of the Year again!*
<http://uod.ac.uk/sig-strapline>
The Times / Sunday Times Good University Guide 2016 and 2017

------------------------------------------------------------------------
*From:* jalview-dev-bounces@jalview.org
<jalview-dev-bounces@jalview.org> on behalf of James Procter (Staff)
<J.Procter@dundee.ac.uk>
*Sent:* 14 March 2019 06:19:35
*To:* Jalview Development List
*Subject:* Re: [Jalview-dev] Build server issues?

jalviewjs build plan is back in business - the original links that were
posted aren't going to work, however.

Now is as good a time as any to set up www.jalview.org/jalviewjs
<http://www.jalview.org/jalviewjs> - I'll look at that in a few hours -
see you on gitter.

On 14/03/2019 05:47, James Procter (Staff) wrote:

I'm at least a little confused at how I managed this but I seem to
have deleted the Jalview JS builds at 5 to 6 on Friday evening. I was
trying to 'clean up' but I certainly didn't intend to delete the whole
plan.

I'll get it back asap.

Jim

On 13/03/2019 23:06, Jim Procter wrote:

Not sure what the problem is but can confirm we seem to have lost
all jalviewjs build plans. Will look at it in am.

J.

On Wed, 13 Mar 2019, 16:11 Mungo Carstairs (Staff), >>> <g.m.carstairs@dundee.ac.uk <mailto:g.m.carstairs@dundee.ac.uk>> wrote:

    Suzanne has pointed out that the JalviewJS link

    https://builds.jalview.org/userlogin!doDefault.action?os_destination=%2Fartifact%2FJB-JB47%2Fshared%2Fbuild-latest%2Fjalview-js-site%2Fjalview_bin_Jalview.html

    is prompting for a login.

    Also I cannot see any JalviewJS builds in the dashboard as I
    would expect:

    https://builds.jalview.org/browse/JB

    Is this possibly the out of space problem?

    Mungo

    Email signature
    
    University of Dundee shield logo <http://uod.ac.uk/sig-home>

    *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 <http://www.jalview.org>

    www.compbio.dundee.ac.uk <http://www.compbio.dundee.ac.uk>
    g.m.carstairs@dundee.ac.uk <mailto:g.m.carstairs@dundee.ac.uk>

    University of Dundee Facebook
    <http://uod.ac.uk/sig-fb> University of Dundee Twitter
    <http://uod.ac.uk/sig-tw> University of Dundee LinkedIn
    <http://uod.ac.uk/sig-li> University of Dundee YouTube
    <http://uod.ac.uk/sig-yt> University of Dundee Instagram
    <http://uod.ac.uk/sig-ig> University of Dundee Snapchat
    <http://uod.ac.uk/sig-sc>
    *We're Scottish University of the Year again!*
    <http://uod.ac.uk/sig-strapline>
    The Times / Sunday Times Good University Guide 2016 and 2017

    The University of Dundee is a registered Scottish Charity, No:
    SC015096
    _______________________________________________
    Jalview-dev mailing list
    Jalview-dev@jalview.org <mailto:Jalview-dev@jalview.org>
    http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

_______________________________________________
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Jalview-dev@jalview.org <mailto:Jalview-dev@jalview.org>
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

--
-------------------------------------------------------------------
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>

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

_______________________________________________
Jalview-dev mailing list
Jalview-dev@jalview.org <mailto:Jalview-dev@jalview.org>
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

--
-------------------------------------------------------------------
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>

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

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

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

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

Suggest you use these URLs:

develop:
https://builds.jalview.org/artifact/JB-JB1/shared/build-latest/jalviewjs/JalviewJS_jalview.html

Once Mungo has merged Jalview-JS/develop onto Jalview-JS/demo this URL
will also work.

stable:
https://builds.jalview.org/artifact/JB-JB0/shared/build-latest/jalviewjs/JalviewJS_jalview.html

These will both have automatically built corefiles for JalviewJS:

So, e.g.

https://builds.jalview.org/artifact/JB-JB1/shared/build-latest/jalviewjs/JalviewJS_jalview.html?open%20examples/uniref50.fa%20features%20examples/exampleFeatures.txt

Once the corefile is cached I get a startup time of 4.5s from page load
to display of the example.

Jim.

···

On 14/03/2019 08:04, Benedict Soares (Staff) wrote:

I was thinking of putting in a proxypass for that specific path dir in
spacewalk to the jalviewjs I downloaded (which was JB83) a couple of
weeks ago, hosted on combo~bsoares (though that URL wouldn't appear). I
can do that this morning some time if I get a chance (in Crieff).

Should I do this? (going to be on the road for the next hour)

Ben

------------------------------------------------------------------------
*From:* jalview-dev-bounces@jalview.org
<jalview-dev-bounces@jalview.org> on behalf of Mungo Carstairs (Staff)
<g.m.carstairs@dundee.ac.uk>
*Sent:* 14 March 2019 08:01:20
*To:* Jalview Development List
*Subject:* Re: [Jalview-dev] Build server issues?

Current state is now:

Latest JS-develop:

https://builds.jalview.org/browse/JB-JB1-2/artifact/shared/jalviewjs/jalview_bin_Jalview.html?open
examples/uniref50.fa features examples/exampleFeatures.txt

Latest JS-demo (as published with grant application):

https://builds.jalview.org/browse/JB-JB0-2/artifact/shared/jalviewjs/jalview_bin_JalviewJS.html

Email signatureMungo

University of Dundee shield logo <http://uod.ac.uk/sig-home>

*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 <http://www.jalview.org>

www.compbio.dundee.ac.uk <http://www.compbio.dundee.ac.uk>
g.m.carstairs@dundee.ac.uk <mailto:g.m.carstairs@dundee.ac.uk>

University of Dundee Facebook <http://uod.ac.uk/sig-fb> University of
Dundee Twitter <http://uod.ac.uk/sig-tw> University of Dundee LinkedIn
<http://uod.ac.uk/sig-li> University of Dundee YouTube
<http://uod.ac.uk/sig-yt> University of Dundee Instagram
<http://uod.ac.uk/sig-ig> University of Dundee Snapchat
<http://uod.ac.uk/sig-sc>
*We're Scottish University of the Year again!*
<http://uod.ac.uk/sig-strapline>
The Times / Sunday Times Good University Guide 2016 and 2017

------------------------------------------------------------------------
*From:* Mungo Carstairs (Staff)
*Sent:* 14 March 2019 07:44:09
*To:* Jalview Development List
*Subject:* Re: [Jalview-dev] Build server issues?

Thanks Jim.

Does the configuration run to being able to set up a redirect from the
published url

https://builds.jalview.org/artifact/JB-JB83/shared/build-latest/jalview-js-site/jalview_bin_JalviewJS.html

and maybe also its encoded version

https://builds.jalview.org/userlogin!doDefault.action?os_destination=%2Fartifact%2FJB-JB83%2Fshared%2Fbuild-latest%2Fjalview-js-site%2Fjalview_bin_JalviewJS.html

to the latest JS-demo or JS-develop build?

I hope VIZBI is going well!

I should have a merged and tested Java/JS develop by the end of the week.

Mungo

Email signature

University of Dundee shield logo <http://uod.ac.uk/sig-home>

*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 <http://www.jalview.org>

www.compbio.dundee.ac.uk <http://www.compbio.dundee.ac.uk>
g.m.carstairs@dundee.ac.uk <mailto:g.m.carstairs@dundee.ac.uk>

University of Dundee Facebook <http://uod.ac.uk/sig-fb> University of
Dundee Twitter <http://uod.ac.uk/sig-tw> University of Dundee LinkedIn
<http://uod.ac.uk/sig-li> University of Dundee YouTube
<http://uod.ac.uk/sig-yt> University of Dundee Instagram
<http://uod.ac.uk/sig-ig> University of Dundee Snapchat
<http://uod.ac.uk/sig-sc>
*We're Scottish University of the Year again!*
<http://uod.ac.uk/sig-strapline>
The Times / Sunday Times Good University Guide 2016 and 2017

------------------------------------------------------------------------
*From:* jalview-dev-bounces@jalview.org
<jalview-dev-bounces@jalview.org> on behalf of James Procter (Staff)
<J.Procter@dundee.ac.uk>
*Sent:* 14 March 2019 06:19:35
*To:* Jalview Development List
*Subject:* Re: [Jalview-dev] Build server issues?

jalviewjs build plan is back in business - the original links that were
posted aren't going to work, however.

Now is as good a time as any to set up www.jalview.org/jalviewjs
<http://www.jalview.org/jalviewjs> - I'll look at that in a few hours -
see you on gitter.

On 14/03/2019 05:47, James Procter (Staff) wrote:

I'm at least a little confused at how I managed this but I seem to
have deleted the Jalview JS builds at 5 to 6 on Friday evening. I was
trying to 'clean up' but I certainly didn't intend to delete the whole
plan.

I'll get it back asap.

Jim

On 13/03/2019 23:06, Jim Procter wrote:

Not sure what the problem is but can confirm we seem to have lost
all jalviewjs build plans. Will look at it in am.

J.

On Wed, 13 Mar 2019, 16:11 Mungo Carstairs (Staff), >>> <g.m.carstairs@dundee.ac.uk <mailto:g.m.carstairs@dundee.ac.uk>> wrote:

    Suzanne has pointed out that the JalviewJS link

    https://builds.jalview.org/userlogin!doDefault.action?os_destination=%2Fartifact%2FJB-JB47%2Fshared%2Fbuild-latest%2Fjalview-js-site%2Fjalview_bin_Jalview.html

    is prompting for a login.

    Also I cannot see any JalviewJS builds in the dashboard as I
    would expect:

    https://builds.jalview.org/browse/JB

    Is this possibly the out of space problem?

    Mungo

    Email signature

    University of Dundee shield logo <http://uod.ac.uk/sig-home>

    *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 <http://www.jalview.org>

    www.compbio.dundee.ac.uk <http://www.compbio.dundee.ac.uk>
    g.m.carstairs@dundee.ac.uk <mailto:g.m.carstairs@dundee.ac.uk>

    University of Dundee Facebook
    <http://uod.ac.uk/sig-fb> University of Dundee Twitter
    <http://uod.ac.uk/sig-tw> University of Dundee LinkedIn
    <http://uod.ac.uk/sig-li> University of Dundee YouTube
    <http://uod.ac.uk/sig-yt> University of Dundee Instagram
    <http://uod.ac.uk/sig-ig> University of Dundee Snapchat
    <http://uod.ac.uk/sig-sc>
    *We're Scottish University of the Year again!*
    <http://uod.ac.uk/sig-strapline>
    The Times / Sunday Times Good University Guide 2016 and 2017

    The University of Dundee is a registered Scottish Charity, No:
    SC015096
    _______________________________________________
    Jalview-dev mailing list
    Jalview-dev@jalview.org <mailto:Jalview-dev@jalview.org>
    http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

_______________________________________________
Jalview-dev mailing list
Jalview-dev@jalview.org <mailto:Jalview-dev@jalview.org>
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

--
-------------------------------------------------------------------
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>

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

_______________________________________________
Jalview-dev mailing list
Jalview-dev@jalview.org <mailto:Jalview-dev@jalview.org>
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

--
-------------------------------------------------------------------
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>

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

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

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

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

--
-------------------------------------------------------------------
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 | www.compbio.dundee.ac.uk

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

Specifically reverse proxying anything that goes to host

https://builds.jalview.org/

with path

artifact/JB-JB83/shared/build-latest/jalview-js-site/(*)

could be ProxyPass’ing (and ProxyPassReverse’ing) to the stable build

https://builds.jalview.org/artifact/JB-JB0/shared/build-latest/jalviewjs/$1

or similar (I’ll have to remind myself of the exact syntax but used to do this a lot!)

This should at least make the advertised URL work okay.

Ben

···

On 14 Mar 2019, at 09:14, James Procter (Staff) <J.Procter@dundee.ac.uk> wrote:

Suggest you use these URLs:

develop:
https://builds.jalview.org/artifact/JB-JB1/shared/build-latest/jalviewjs/JalviewJS_jalview.html

Once Mungo has merged Jalview-JS/develop onto Jalview-JS/demo this URL
will also work.

stable:
https://builds.jalview.org/artifact/JB-JB0/shared/build-latest/jalviewjs/JalviewJS_jalview.html

These will both have automatically built corefiles for JalviewJS:

So, e.g.

https://builds.jalview.org/artifact/JB-JB1/shared/build-latest/jalviewjs/JalviewJS_jalview.html?open%20examples/uniref50.fa%20features%20examples/exampleFeatures.txt

Once the corefile is cached I get a startup time of 4.5s from page load
to display of the example.

Jim.

On 14/03/2019 08:04, Benedict Soares (Staff) wrote:

I was thinking of putting in a proxypass for that specific path dir in
spacewalk to the jalviewjs I downloaded (which was JB83) a couple of
weeks ago, hosted on combo~bsoares (though that URL wouldn’t appear). I
can do that this morning some time if I get a chance (in Crieff).

Should I do this? (going to be on the road for the next hour)

Ben


From: jalview-dev-bounces@jalview.org
<jalview-dev-bounces@jalview.org> on behalf of Mungo Carstairs (Staff)
<g.m.carstairs@dundee.ac.uk>
Sent: 14 March 2019 08:01:20
To: Jalview Development List
Subject: Re: [Jalview-dev] Build server issues?

Current state is now:

Latest JS-develop:

https://builds.jalview.org/browse/JB-JB1-2/artifact/shared/jalviewjs/jalview_bin_Jalview.html?open
examples/uniref50.fa features examples/exampleFeatures.txt

Latest JS-demo (as published with grant application):

https://builds.jalview.org/browse/JB-JB0-2/artifact/shared/jalviewjs/jalview_bin_JalviewJS.html

Email signatureMungo

University of Dundee shield logo <http://uod.ac.uk/sig-home>

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 <http://www.jalview.org>

www.compbio.dundee.ac.uk <http://www.compbio.dundee.ac.uk>
g.m.carstairs@dundee.ac.uk <mailto:g.m.carstairs@dundee.ac.uk>

University of Dundee Facebook <http://uod.ac.uk/sig-fb> University of
Dundee Twitter <http://uod.ac.uk/sig-tw> University of Dundee LinkedIn
<http://uod.ac.uk/sig-li> University of Dundee YouTube
<http://uod.ac.uk/sig-yt> University of Dundee Instagram
<http://uod.ac.uk/sig-ig> University of Dundee Snapchat
<http://uod.ac.uk/sig-sc>
We’re Scottish University of the Year again!
<http://uod.ac.uk/sig-strapline>
The Times / Sunday Times Good University Guide 2016 and 2017


From: Mungo Carstairs (Staff)
Sent: 14 March 2019 07:44:09
To: Jalview Development List
Subject: Re: [Jalview-dev] Build server issues?

Thanks Jim.

Does the configuration run to being able to set up a redirect from the
published url

https://builds.jalview.org/artifact/JB-JB83/shared/build-latest/jalview-js-site/jalview_bin_JalviewJS.html

and maybe also its encoded version

https://builds.jalview.org/userlogin!doDefault.action?os_destination=%2Fartifact%2FJB-JB83%2Fshared%2Fbuild-latest%2Fjalview-js-site%2Fjalview_bin_JalviewJS.html

to the latest JS-demo or JS-develop build?

I hope VIZBI is going well!

I should have a merged and tested Java/JS develop by the end of the week.

Mungo

Email signature

University of Dundee shield logo <http://uod.ac.uk/sig-home>

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 <http://www.jalview.org>

www.compbio.dundee.ac.uk <http://www.compbio.dundee.ac.uk>
g.m.carstairs@dundee.ac.uk <mailto:g.m.carstairs@dundee.ac.uk>

University of Dundee Facebook <http://uod.ac.uk/sig-fb> University of
Dundee Twitter <http://uod.ac.uk/sig-tw> University of Dundee LinkedIn
<http://uod.ac.uk/sig-li> University of Dundee YouTube
<http://uod.ac.uk/sig-yt> University of Dundee Instagram
<http://uod.ac.uk/sig-ig> University of Dundee Snapchat
<http://uod.ac.uk/sig-sc>
We’re Scottish University of the Year again!
<http://uod.ac.uk/sig-strapline>
The Times / Sunday Times Good University Guide 2016 and 2017


From: jalview-dev-bounces@jalview.org
<jalview-dev-bounces@jalview.org> on behalf of James Procter (Staff)
<J.Procter@dundee.ac.uk>
Sent: 14 March 2019 06:19:35
To: Jalview Development List
Subject: Re: [Jalview-dev] Build server issues?

jalviewjs build plan is back in business - the original links that were
posted aren’t going to work, however.

Now is as good a time as any to set up www.jalview.org/jalviewjs
<http://www.jalview.org/jalviewjs> - I’ll look at that in a few hours -
see you on gitter.

On 14/03/2019 05:47, James Procter (Staff) wrote:

I’m at least a little confused at how I managed this but I seem to
have deleted the Jalview JS builds at 5 to 6 on Friday evening. I was
trying to ‘clean up’ but I certainly didn’t intend to delete the whole
plan.

I’ll get it back asap.

Jim

On 13/03/2019 23:06, Jim Procter wrote:

Not sure what the problem is but can confirm we seem to have lost
all jalviewjs build plans. Will look at it in am.

J.

On Wed, 13 Mar 2019, 16:11 Mungo Carstairs (Staff), > > > > <g.m.carstairs@dundee.ac.uk <mailto:g.m.carstairs@dundee.ac.uk>> wrote:

Suzanne has pointed out that the JalviewJS link

https://builds.jalview.org/userlogin!doDefault.action?os_destination=%2Fartifact%2FJB-JB47%2Fshared%2Fbuild-latest%2Fjalview-js-site%2Fjalview_bin_Jalview.html

is prompting for a login.

Also I cannot see any JalviewJS builds in the dashboard as I
would expect:

https://builds.jalview.org/browse/JB

Is this possibly the out of space problem?

Mungo

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Okay, after having tried some rewriterules that didn’t seem to take effect (and waiting 30-60 minutes for each scheduled deploy, test, restart !!) I put in a redirect from the original JB83 URL to the new JB01 one which now at last does seem to have taken effect.
It is quite specifically for that URL only though (including the jalview_bin_JalviewJS.html).

Ben

···

On 14 Mar 2019, at 09:39, Benedict Soares (Staff) <b.soares@dundee.ac.uk> wrote:

Specifically reverse proxying anything that goes to host

https://builds.jalview.org/

with path

artifact/JB-JB83/shared/build-latest/jalview-js-site/(*)

could be ProxyPass’ing (and ProxyPassReverse’ing) to the stable build

https://builds.jalview.org/artifact/JB-JB0/shared/build-latest/jalviewjs/$1

or similar (I’ll have to remind myself of the exact syntax but used to do this a lot!)

This should at least make the advertised URL work okay.

Ben

On 14 Mar 2019, at 09:14, James Procter (Staff) <J.Procter@dundee.ac.uk> wrote:

Suggest you use these URLs:

develop:
https://builds.jalview.org/artifact/JB-JB1/shared/build-latest/jalviewjs/JalviewJS_jalview.html

Once Mungo has merged Jalview-JS/develop onto Jalview-JS/demo this URL
will also work.

stable:
https://builds.jalview.org/artifact/JB-JB0/shared/build-latest/jalviewjs/JalviewJS_jalview.html

These will both have automatically built corefiles for JalviewJS:

So, e.g.

https://builds.jalview.org/artifact/JB-JB1/shared/build-latest/jalviewjs/JalviewJS_jalview.html?open%20examples/uniref50.fa%20features%20examples/exampleFeatures.txt

Once the corefile is cached I get a startup time of 4.5s from page load
to display of the example.

Jim.

On 14/03/2019 08:04, Benedict Soares (Staff) wrote:

I was thinking of putting in a proxypass for that specific path dir in
spacewalk to the jalviewjs I downloaded (which was JB83) a couple of
weeks ago, hosted on combo~bsoares (though that URL wouldn’t appear). I
can do that this morning some time if I get a chance (in Crieff).

Should I do this? (going to be on the road for the next hour)

Ben


From: jalview-dev-bounces@jalview.org
<jalview-dev-bounces@jalview.org> on behalf of Mungo Carstairs (Staff)
<g.m.carstairs@dundee.ac.uk>
Sent: 14 March 2019 08:01:20
To: Jalview Development List
Subject: Re: [Jalview-dev] Build server issues?

Current state is now:

Latest JS-develop:

https://builds.jalview.org/browse/JB-JB1-2/artifact/shared/jalviewjs/jalview_bin_Jalview.html?open
examples/uniref50.fa features examples/exampleFeatures.txt

Latest JS-demo (as published with grant application):

https://builds.jalview.org/browse/JB-JB0-2/artifact/shared/jalviewjs/jalview_bin_JalviewJS.html

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From: Mungo Carstairs (Staff)
Sent: 14 March 2019 07:44:09
To: Jalview Development List
Subject: Re: [Jalview-dev] Build server issues?

Thanks Jim.

Does the configuration run to being able to set up a redirect from the
published url

https://builds.jalview.org/artifact/JB-JB83/shared/build-latest/jalview-js-site/jalview_bin_JalviewJS.html

and maybe also its encoded version

https://builds.jalview.org/userlogin!doDefault.action?os_destination=%2Fartifact%2FJB-JB83%2Fshared%2Fbuild-latest%2Fjalview-js-site%2Fjalview_bin_JalviewJS.html

to the latest JS-demo or JS-develop build?

I hope VIZBI is going well!

I should have a merged and tested Java/JS develop by the end of the week.

Mungo

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From: jalview-dev-bounces@jalview.org
<jalview-dev-bounces@jalview.org> on behalf of James Procter (Staff)
<J.Procter@dundee.ac.uk>
Sent: 14 March 2019 06:19:35
To: Jalview Development List
Subject: Re: [Jalview-dev] Build server issues?

jalviewjs build plan is back in business - the original links that were
posted aren’t going to work, however.

Now is as good a time as any to set up www.jalview.org/jalviewjs
<http://www.jalview.org/jalviewjs> - I’ll look at that in a few hours -
see you on gitter.

On 14/03/2019 05:47, James Procter (Staff) wrote:

I’m at least a little confused at how I managed this but I seem to
have deleted the Jalview JS builds at 5 to 6 on Friday evening. I was
trying to ‘clean up’ but I certainly didn’t intend to delete the whole
plan.

I’ll get it back asap.

Jim

On 13/03/2019 23:06, Jim Procter wrote:

Not sure what the problem is but can confirm we seem to have lost
all jalviewjs build plans. Will look at it in am.

J.

On Wed, 13 Mar 2019, 16:11 Mungo Carstairs (Staff), > > > > > <g.m.carstairs@dundee.ac.uk <mailto:g.m.carstairs@dundee.ac.uk>> wrote:

Suzanne has pointed out that the JalviewJS link

https://builds.jalview.org/userlogin!doDefault.action?os_destination=%2Fartifact%2FJB-JB47%2Fshared%2Fbuild-latest%2Fjalview-js-site%2Fjalview_bin_Jalview.html

is prompting for a login.

Also I cannot see any JalviewJS builds in the dashboard as I
would expect:

https://builds.jalview.org/browse/JB

Is this possibly the out of space problem?

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 <http://www.jalview.org>

www.compbio.dundee.ac.uk <http://www.compbio.dundee.ac.uk>
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University of Dundee, Dundee DD1 5EH, UK.
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Not sure the JalviewJS build is quite right yet. Logs are showing errors including

java.lang.IllegalStateException: Workbench has not been created yet.
build	14-Mar-2019 17:51:01	     [exec] 	at org.eclipse.ui.PlatformUI.getWorkbench(PlatformUI.java:93)

https://builds.jalview.org/download/JB-JB1-JOB1/build_logs/JB-JB1-JOB1-3.log

Mungo

···

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Mungo Carstairs
Jalview Computational Scientist

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www.jalview.org

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

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From: jalview-dev-bounces@jalview.org jalview-dev-bounces@jalview.org on behalf of James Procter (Staff) J.Procter@dundee.ac.uk
Sent: 14 March 2019 06:19:35
To: Jalview Development List
Subject: Re: [Jalview-dev] Build server issues?

jalviewjs build plan is back in business - the original links that were posted aren’t going to work, however.

Now is as good a time as any to set up www.jalview.org/jalviewjs - I’ll look at that in a few hours - see you on gitter.

On 14/03/2019 05:47, James Procter (Staff) wrote:

I’m at least a little confused at how I managed this but I seem to have deleted the Jalview JS builds at 5 to 6 on Friday evening. I was trying to ‘clean up’ but I certainly didn’t intend to delete the whole plan.

I’ll get it back asap.

Jim

On 13/03/2019 23:06, Jim Procter wrote:

Not sure what the problem is but can confirm we seem to have lost all jalviewjs build plans. Will look at it in am.

J.

On Wed, 13 Mar 2019, 16:11 Mungo Carstairs (Staff), <g.m.carstairs@dundee.ac.uk> wrote:

Suzanne has pointed out that the JalviewJS link

https://builds.jalview.org/userlogin!doDefault.action?os_destination=%2Fartifact%2FJB-JB47%2Fshared%2Fbuild-latest%2Fjalview-js-site%2Fjalview_bin_Jalview.html

is prompting for a login.

Also I cannot see any JalviewJS builds in the dashboard as I would expect:

https://builds.jalview.org/browse/JB

Is this possibly the out of space problem?

Mungo

Email signature

University of Dundee shield logo

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

University of Dundee FacebookUniversity of Dundee TwitterUniversity of Dundee LinkedInUniversity of Dundee YouTubeUniversity of Dundee InstagramUniversity of Dundee Snapchat
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The University of Dundee is a registered Scottish Charity, No: SC015096


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-------------------------------------------------------------------
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)

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

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