[apollo] Canned Comments not available (css display:none)

[Rob Syme]

Hi all (again)

When editing the annotation information, the "comments" section is not
available (hidden by css), and when I un-hide it, the "add" button does not
add a comment. Is there some configuration to enable adding comments to
annotations?

Here is an example:

-r

[Nathan Dunn]

I’m not seeing this behavior, even after I add the canned comments that you have. You can go to the demo site (which also has the identical canned comment) and observe that it is working:

http://genomearchitect.org/demo/ <http://genomearchitect.org/demo/>

Some possibilities:

1 - you are loading other css / javascript that is interfering
2 - plugins loaded in your trackList.json conf are causing problems (try removing all plugins and see what you get)
3 - there is garbage in the cache that is leading to #1 (I would try another browser and see if you can’t see the same result)
4 - there was a problem with the build (typically the effects are much more severe)

Questions:

- You are running 2.0.4-RC2, right?
- Do you see anything in the javascript console when you load the page?
- Do you have any customizations in the apollo-config.groovy other than the database?

Nathan

Post by Rob Syme
Hi all (again)
When editing the annotation information, the "comments" section is not available (hidden by css), and when I un-hide it, the "add" button does not add a comment. Is there some configuration to enable adding comments to annotations?
Here is an example: http://youtu.be/Dc8z4CoGUyc http://youtu.be/Dc8z4CoGUyc
-r
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/

[Rob Syme]

Hi Nathan

Thanks for your quick response and for the suggestions.

To try and remove the effect of any extensions or side-loaded js, I loaded
apollo in Chrome's private mode and also in Firefox, but the effect is the
same.
I don't *think* my trackList.json has anything unusual in it (screenshot
below), and I'm running:

- Version: 2.0.4-RC2
<https://github.com/GMOD/Apollo/releases/tag/2.0.4-RC2>
- Grails version: 2.5.5
- Groovy version: 2.4.4
- JVM version: 1.7.0_101

On the gmod/apollo:latest docker image (Image ID: 6453d434c1e3). Is the
demo site running from the Docker image?

I do get an error printed to the js console when loading
.../apollo/annotator/index:

WebSocket connection to 'ws://
apollo.ppglab.org/apollo/stomp/448/i9jt2zj9/websocket' failed: Error during
WebSocket handshake: Unexpected response code: 400

[image: Screenshot from 2016-07-29 08-44-23.png]
I'm not sure that this is the cause of the problem though. No js errors are
printed when opening up the "Edit information" dialog.

Here is my trackList.json. Any help appreciated.

[image: Screenshot from 2016-07-29 08-34-17.png]

Post by Nathan Dunn
I’m not seeing this behavior, even after I add the canned comments that
you have. You can go to the demo site (which also has the identical canned
http://genomearchitect.org/demo/
1 - you are loading other css / javascript that is interfering
2 - plugins loaded in your trackList.json conf are causing problems (try
removing all plugins and see what you get)
3 - there is garbage in the cache that is leading to #1 (I would try
another browser and see if you can’t see the same result)
4 - there was a problem with the build (typically the effects are much more severe)
- You are running 2.0.4-RC2, right?
- Do you see anything in the javascript console when you load the page?
- Do you have any customizations in the apollo-config.groovy other than the database?
Nathan
Hi all (again)
When editing the annotation information, the "comments" section is not
available (hidden by css), and when I un-hide it, the "add" button does not
add a comment. Is there some configuration to enable adding comments to
annotations?
Here is an example: http://youtu.be/Dc8z4CoGUyc
-r
This list is for the Apollo Annotation Editing Tool. Info at
http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with
2. In the subject line of your email type: unsubscribe apollo | 3. Leave
the message body blank.

[Nathan Dunn]

The web sockets error is probably due to bad tunneling through a proxy:

http://genomearchitect.readthedocs.io/en/stable/Configure.html?highlight=nginx#apache-nginx-configuration <http://genomearchitect.readthedocs.io/en/stable/Configure.html?highlight=nginx#apache-nginx-configuration>

Probably not catastrophic (especially if you are able to add transcripts!), as it should fall-back gracefully, but better to get that fixed.

We aren’t running the demo site from the Docker image. However, I just finished updating the docker image, as well.

Try running from the github source directly and see if that helps if the updated docker image doesn’t work.

Nathan

Post by Rob Syme
Hi Nathan
Thanks for your quick response and for the suggestions.
To try and remove the effect of any extensions or side-loaded js, I loaded apollo in Chrome's private mode and also in Firefox, but the effect is the same.
Version: 2.0.4-RC2 <https://github.com/GMOD/Apollo/releases/tag/2.0.4-RC2>
Grails version: 2.5.5
Groovy version: 2.4.4
JVM version: 1.7.0_101
On the gmod/apollo:latest docker image (Image ID: 6453d434c1e3). Is the demo site running from the Docker image?
WebSocket connection to 'ws://apollo.ppglab.org/apollo/stomp/448/i9jt2zj9/websocket <http://apollo.ppglab.org/apollo/stomp/448/i9jt2zj9/websocket>' failed: Error during WebSocket handshake: Unexpected response code: 400
<Screenshot from 2016-07-29 08-44-23.png>
I'm not sure that this is the cause of the problem though. No js errors are printed when opening up the "Edit information" dialog.
Here is my trackList.json. Any help appreciated.
<Screenshot from 2016-07-29 08-34-17.png>
http://genomearchitect.org/demo/ <http://genomearchitect.org/demo/>
1 - you are loading other css / javascript that is interfering
2 - plugins loaded in your trackList.json conf are causing problems (try removing all plugins and see what you get)
3 - there is garbage in the cache that is leading to #1 (I would try another browser and see if you can’t see the same result)
4 - there was a problem with the build (typically the effects are much more severe)
- You are running 2.0.4-RC2, right?
- Do you see anything in the javascript console when you load the page?
- Do you have any customizations in the apollo-config.groovy other than the database?
Nathan

Post by Rob Syme
Hi all (again)
When editing the annotation information, the "comments" section is not available (hidden by css), and when I un-hide it, the "add" button does not add a comment. Is there some configuration to enable adding comments to annotations?
Here is an example: http://youtu.be/Dc8z4CoGUyc http://youtu.be/Dc8z4CoGUyc
-r
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>

<Screenshot 2016-07-28 05.39.19.png><Screenshot 2016-07-28 05.39.39.png><Screenshot 2016-07-28 05.39.49.png><Screenshot 2016-07-28 05.39.19.png><Screenshot 2016-07-28 05.39.39.png><Screenshot 2016-07-28 05.39.49.png>

[Rob Syme]

Thanks for the websockets pointer. That problem is now solved, thanks.

Just updated the docker image, but the same comments problem persists. I'll
try and get it running from source today. Thanks again for the help!

-r

Post by Nathan Dunn
http://genomearchitect.readthedocs.io/en/stable/Configure.html?highlight=nginx#apache-nginx-configuration
Probably not catastrophic (especially if you are able to add
transcripts!), as it should fall-back gracefully, but better to get that
fixed.
We aren’t running the demo site from the Docker image. However, I just
finished updating the docker image, as well.
Try running from the github source directly and see if that helps if the
updated docker image doesn’t work.
Nathan
Hi Nathan
Thanks for your quick response and for the suggestions.
To try and remove the effect of any extensions or side-loaded js, I loaded
apollo in Chrome's private mode and also in Firefox, but the effect is the
same.
I don't *think* my trackList.json has anything unusual in it (screenshot
- Version: 2.0.4-RC2
<https://github.com/GMOD/Apollo/releases/tag/2.0.4-RC2>
- Grails version: 2.5.5
- Groovy version: 2.4.4
- JVM version: 1.7.0_101
On the gmod/apollo:latest docker image (Image ID: 6453d434c1e3). Is the
demo site running from the Docker image?
I do get an error printed to the js console when loading
WebSocket connection to 'ws://
apollo.ppglab.org/apollo/stomp/448/i9jt2zj9/websocket' failed: Error
during WebSocket handshake: Unexpected response code: 400
<Screenshot from 2016-07-29 08-44-23.png>
I'm not sure that this is the cause of the problem though. No js errors
are printed when opening up the "Edit information" dialog.
Here is my trackList.json. Any help appreciated.
<Screenshot from 2016-07-29 08-34-17.png>

Post by Nathan Dunn
I’m not seeing this behavior, even after I add the canned comments that
you have. You can go to the demo site (which also has the identical canned
http://genomearchitect.org/demo/
1 - you are loading other css / javascript that is interfering
2 - plugins loaded in your trackList.json conf are causing problems (try
removing all plugins and see what you get)
3 - there is garbage in the cache that is leading to #1 (I would try
another browser and see if you can’t see the same result)
4 - there was a problem with the build (typically the effects are much more severe)
- You are running 2.0.4-RC2, right?
- Do you see anything in the javascript console when you load the page?
- Do you have any customizations in the apollo-config.groovy other than the database?
Nathan
Hi all (again)
When editing the annotation information, the "comments" section is not
available (hidden by css), and when I un-hide it, the "add" button does not
add a comment. Is there some configuration to enable adding comments to
annotations?
Here is an example: http://youtu.be/Dc8z4CoGUyc
-r
This list is for the Apollo Annotation Editing Tool. Info at
http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with
| 2. In the subject line of your email type: unsubscribe apollo | 3. Leave
the message body blank.
<Screenshot 2016-07-28 05.39.19.png><Screenshot 2016-07-28 05.39.39.png><Screenshot

2016-07-28 05.39.49.png><Screenshot 2016-07-28 05.39.19.png><Screenshot
2016-07-28 05.39.39.png><Screenshot 2016-07-28 05.39.49.png>