JalviewJS demonstration build

g_m_carstairs · 23 January 2019 15:10

I have made a new branch, intended to be stable for demo purposes, which can be run from:

https://builds.jalview.org/artifact/JB-JB81/shared/build-latest/jalview-js-site/jalview_bin_JalviewJS.html

This is pre-configured to load our example alignment uniref50.fa with exampleFeatures.txt (for a blank canvas, omit the last JS).

It can be reached externally (I tested via my phone’s 4G).

(Jim: I unchecked ‘Clean up plan branch automatically’ to avoid it being deleted for inactivity. Delete manually when no longer required.)

I want to push one more update before ‘freezing’ this version: currently popup menus don’t work, and these are needed in various places (show structure, create feature on selection, etc etc). I’m hoping Bob will have this fixed and pushed shortly.

Meanwhile plenty of stuff should work: calculate tree or PCA, adjust colour scheme or feature colouring, colour by annotation, Fetch from Uniprot etc.

As a development build, this is not optimised for production: initial load of screens is slow (faster thereafter), and there is a lot of debug logging.

Any questions please ask!

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
g.m.carstairs@dundee.ac.uk

We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017

g_m_carstairs · 23 January 2019 15:29

In fact popup menus do work, but very slowly (on MAC at least).

e.g. hold down right mouse button on sequence id for c. 5 seconds to get the menu.

Keep the right button down to move to the menu option e.g. 3D Structure Data…

Left click the menu option to action it.

This used to behave ‘normally’ and will do again.

···

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

We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017

From: Mungo Carstairs (Staff)
Sent: 23 January 2019 15:10:00
To: Geoffrey Barton (Staff); Jalview Development List
Cc: Suzanne Duce (Staff)
Subject: JalviewJS demonstration build

I have made a new branch, intended to be stable for demo purposes, which can be run from:

https://builds.jalview.org/artifact/JB-JB81/shared/build-latest/jalview-js-site/jalview_bin_JalviewJS.html

This is pre-configured to load our example alignment uniref50.fa with exampleFeatures.txt (for a blank canvas, omit the last JS).

It can be reached externally (I tested via my phone’s 4G).

(Jim: I unchecked ‘Clean up plan branch automatically’ to avoid it being deleted for inactivity. Delete manually when no longer required.)

I want to push one more update before ‘freezing’ this version: currently popup menus don’t work, and these are needed in various places (show structure, create feature on selection, etc etc). I’m hoping Bob will have this fixed and pushed shortly.

Meanwhile plenty of stuff should work: calculate tree or PCA, adjust colour scheme or feature colouring, colour by annotation, Fetch from Uniprot etc.

As a development build, this is not optimised for production: initial load of screens is slow (faster thereafter), and there is a lot of debug logging.

Any questions please ask!

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
g.m.carstairs@dundee.ac.uk

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

hansonr · 27 January 2019 19:42

Forbidden

Unable to access this resource. The maximum number of failed login attempts may have been reached. Please log into the web application through the web interface to reset the number of failed login attempts.

Go to…- Site homepage

That was harsh. A single login error! Now what?

By the way, we need to ensure that the build server is listed in the set of “known” direct-serving servers. I wonder if I should be doing that automatically. Maybe try once at least and see if there is a problem? As I recall, though, the problem with that idea is that some servers just respond with “404 file not found” rather than a meaningful message like “Sorry, direct ajax connections are not allowed on this server.”

. It really slows things down to have my St. Olaf proxy serving everything. Also, let’s make sure we have a good core_Jalview.z.js for anything that goes to referees so that loading is not slowed down for them.

Or is it too late for that?

Bob

···

On Wed, Jan 23, 2019 at 9:10 AM Mungo Carstairs (Staff) <g.m.carstairs@dundee.ac.uk> wrote:

I have made a new branch, intended to be stable for demo purposes, which can be run from:

https://builds.jalview.org/artifact/JB-JB81/shared/build-latest/jalview-js-site/jalview_bin_JalviewJS.html

This is pre-configured to load our example alignment uniref50.fa with exampleFeatures.txt (for a blank canvas, omit the last JS).

It can be reached externally (I tested via my phone’s 4G).

(Jim: I unchecked ‘Clean up plan branch automatically’ to avoid it being deleted for inactivity. Delete manually when no longer required.)

I want to push one more update before ‘freezing’ this version: currently popup menus don’t work, and these are needed in various places (show structure, create feature on selection, etc etc). I’m hoping Bob will have this fixed and pushed shortly.

Meanwhile plenty of stuff should work: calculate tree or PCA, adjust colour scheme or feature colouring, colour by annotation, Fetch from Uniprot etc.

As a development build, this is not optimised for production: initial load of screens is slow (faster thereafter), and there is a lot of debug logging.

Any questions please ask!

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
g.m.carstairs@dundee.ac.uk

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

–

Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr

If nature does not answer first what we want,
it is better to take what answer we get.

– Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

hansonr · 27 January 2019 19:47

I checked, and the build server is fine. I forgot that, of course, it’s not a cross-domain call to get files from the host server. Duh.

···

Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr

If nature does not answer first what we want,
it is better to take what answer we get.

– Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

g_m_carstairs · 28 January 2019 08:37

Please note all that the URL is now

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

(81 has changed to 83).

This should now be stable for demo purposes!

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
g.m.carstairs@dundee.ac.uk

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 Robert Hanson hansonr@stolaf.edu
Sent: 27 January 2019 19:47:31
To: Jalview Development List; Geoffrey Barton (Staff)
Subject: Re: [Jalview-dev] JalviewJS demonstration build

I checked, and the build server is fine. I forgot that, of course, it’s not a cross-domain call to get files from the host server. Duh.

On Sun, Jan 27, 2019 at 1:42 PM Robert Hanson <hansonr@stolaf.edu> wrote:

Forbidden

Unable to access this resource. The maximum number of failed login attempts may have been reached. Please log into the web application through the web interface to reset the number of failed login attempts.

Go to…- Site homepage

That was harsh. A single login error! Now what?

By the way, we need to ensure that the build server is listed in the set of “known” direct-serving servers. I wonder if I should be doing that automatically. Maybe try once at least and see if there is a problem? As I recall, though, the problem with that idea is that some servers just respond with “404 file not found” rather than a meaningful message like “Sorry, direct ajax connections are not allowed on this server.”

. It really slows things down to have my St. Olaf proxy serving everything. Also, let’s make sure we have a good core_Jalview.z.js for anything that goes to referees so that loading is not slowed down for them.

Or is it too late for that?

Bob

On Wed, Jan 23, 2019 at 9:10 AM Mungo Carstairs (Staff) <g.m.carstairs@dundee.ac.uk> wrote:

I have made a new branch, intended to be stable for demo purposes, which can be run from:

https://builds.jalview.org/artifact/JB-JB81/shared/build-latest/jalview-js-site/jalview_bin_JalviewJS.html

This is pre-configured to load our example alignment uniref50.fa with exampleFeatures.txt (for a blank canvas, omit the last JS).

It can be reached externally (I tested via my phone’s 4G).

(Jim: I unchecked ‘Clean up plan branch automatically’ to avoid it being deleted for inactivity. Delete manually when no longer required.)

I want to push one more update before ‘freezing’ this version: currently popup menus don’t work, and these are needed in various places (show structure, create feature on selection, etc etc). I’m hoping Bob will have this fixed and pushed shortly.

Meanwhile plenty of stuff should work: calculate tree or PCA, adjust colour scheme or feature colouring, colour by annotation, Fetch from Uniprot etc.

As a development build, this is not optimised for production: initial load of screens is slow (faster thereafter), and there is a lot of debug logging.

Any questions please ask!

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
g.m.carstairs@dundee.ac.uk

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

–

Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr

If nature does not answer first what we want,
it is better to take what answer we get.

– Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

–

Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr

If nature does not answer first what we want,
it is better to take what answer we get.

– Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

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

g_m_carstairs · 30 January 2019 11:14

For info: we have discovered that Colour Picker dialogs are broken (don’t appear) in the demo build (for example, to change a feature colour).

This has been fixed in development, along with other improvements (including save PCA in project).

But I am going to err on the side of caution and test as thoroughly as possible before merging these changes on to the demo version.

I’ll send an update once this has been done.

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

···

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
g.m.carstairs@dundee.ac.uk

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 Mungo Carstairs (Staff) g.m.carstairs@dundee.ac.uk
Sent: 28 January 2019 08:37:53
To: Jalview Development List; Geoffrey Barton (Staff)
Subject: Re: [Jalview-dev] JalviewJS demonstration build

Please note all that the URL is now

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

(81 has changed to 83).

This should now be stable for demo purposes!

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
g.m.carstairs@dundee.ac.uk

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 Robert Hanson hansonr@stolaf.edu
Sent: 27 January 2019 19:47:31
To: Jalview Development List; Geoffrey Barton (Staff)
Subject: Re: [Jalview-dev] JalviewJS demonstration build

I checked, and the build server is fine. I forgot that, of course, it’s not a cross-domain call to get files from the host server. Duh.

On Sun, Jan 27, 2019 at 1:42 PM Robert Hanson <hansonr@stolaf.edu> wrote:

Forbidden

Unable to access this resource. The maximum number of failed login attempts may have been reached. Please log into the web application through the web interface to reset the number of failed login attempts.

Go to…- Site homepage

That was harsh. A single login error! Now what?

By the way, we need to ensure that the build server is listed in the set of “known” direct-serving servers. I wonder if I should be doing that automatically. Maybe try once at least and see if there is a problem? As I recall, though, the problem with that idea is that some servers just respond with “404 file not found” rather than a meaningful message like “Sorry, direct ajax connections are not allowed on this server.”

. It really slows things down to have my St. Olaf proxy serving everything. Also, let’s make sure we have a good core_Jalview.z.js for anything that goes to referees so that loading is not slowed down for them.

Or is it too late for that?

Bob

On Wed, Jan 23, 2019 at 9:10 AM Mungo Carstairs (Staff) <g.m.carstairs@dundee.ac.uk> wrote:

I have made a new branch, intended to be stable for demo purposes, which can be run from:

https://builds.jalview.org/artifact/JB-JB81/shared/build-latest/jalview-js-site/jalview_bin_JalviewJS.html

This is pre-configured to load our example alignment uniref50.fa with exampleFeatures.txt (for a blank canvas, omit the last JS).

It can be reached externally (I tested via my phone’s 4G).

(Jim: I unchecked ‘Clean up plan branch automatically’ to avoid it being deleted for inactivity. Delete manually when no longer required.)

I want to push one more update before ‘freezing’ this version: currently popup menus don’t work, and these are needed in various places (show structure, create feature on selection, etc etc). I’m hoping Bob will have this fixed and pushed shortly.

Meanwhile plenty of stuff should work: calculate tree or PCA, adjust colour scheme or feature colouring, colour by annotation, Fetch from Uniprot etc.

As a development build, this is not optimised for production: initial load of screens is slow (faster thereafter), and there is a lot of debug logging.

Any questions please ask!

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
g.m.carstairs@dundee.ac.uk

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

–

Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr

If nature does not answer first what we want,
it is better to take what answer we get.

– Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

–

Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr

If nature does not answer first what we want,
it is better to take what answer we get.

– Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

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

hansonr · 30 January 2019 15:42

Just a reminder that you don’t have core_jalview.z.js set up for that yet.

···

Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr

If nature does not answer first what we want,
it is better to take what answer we get.

– Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

hansonr · 30 January 2019 15:43

(testing with https://builds.jalview.org/artifact/JB-JB83/shared/build-latest/jalview-js-site/jalview_bin_JalviewJS.html?j2sverbose )

···

Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr

If nature does not answer first what we want,
it is better to take what answer we get.

– Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900