Can't Annotate

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Can't Annotate

Sofia Robb
Hi,

I think I am missing something simple. My Apollo is up and running. I can see all my tracks, but I can't drag anything to the annotation box (or add from right click). I added admin, write, read, and export permissions to my user. I am the admin user. i do not see any errors.

Thank you!!
Sofia




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Re: Can't Annotate

nathandunn
Can you add any screenshots .. Catalina.out or Deb logs from the client?

Nathan

> On Nov 17, 2015, at 4:46 PM, Sofia Robb <[hidden email]> wrote:
>
> Hi,
>
> I think I am missing something simple. My Apollo is up and running. I can see all my tracks, but I can't drag anything to the annotation box (or add from right click). I added admin, write, read, and export permissions to my user. I am the admin user. i do not see any errors.
>
> Thank you!!
> Sofia
>
>
>
> 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 which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>




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 which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: Can't Annotate

nathandunn
In reply to this post by Sofia Robb
You might want to look here:

http://webapollo.readthedocs.org/en/latest/Troubleshooting.html

Most likely you are using a tomcat where the web sockets are misconfigured or are proxying through Apache without configuring the web socket.   Or the organism permissions are wrong for that user.  

Also the admin user should not need any additional permissions.  There was a bug in 2.0.0 that was fixed.  In the interim try removing the additional permissions and see that if that works.

Nathan

> On Nov 17, 2015, at 4:46 PM, Sofia Robb <[hidden email]> wrote:
>
> Hi,
>
> I think I am missing something simple. My Apollo is up and running. I can see all my tracks, but I can't drag anything to the annotation box (or add from right click). I added admin, write, read, and export permissions to my user. I am the admin user. i do not see any errors.
>
> Thank you!!
> Sofia
>
>
>
> 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 which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>




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 which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: Can't Annotate

Sofia Robb
In reply to this post by nathandunn
Hi Nathan,

I added the extra permissions when I first saw that I couldn't annotate. I do not see anything weird in my catalina.out.

Removing the permissions did not work. I looked in my httpd conf file and I don't see anything about proxys.

On Tue, Nov 17, 2015 at 6:07 PM, Lbl <[hidden email]> wrote:
Can you add any screenshots .. Catalina.out or Deb logs from the client?

Nathan

> On Nov 17, 2015, at 4:46 PM, Sofia Robb <[hidden email]> wrote:
>
> Hi,
>
> I think I am missing something simple. My Apollo is up and running. I can see all my tracks, but I can't drag anything to the annotation box (or add from right click). I added admin, write, read, and export permissions to my user. I am the admin user. i do not see any errors.
>
> Thank you!!
> Sofia
>
>
>
> 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 which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>





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 which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







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 which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.


cannotAnnotate.mov (9M) Download Attachment
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Re: Can't Annotate

nathandunn

I see.   You can’t annotate canvas features in 2.0.0.  

In 2.0.1 (currently in release candidate 5) you can annotate them with a drop-down. 

In the interim . . you’ll want to use HTMLFeatures instead of CanvasFeatures:


I *think* you can just change the "type" in the trackList.json to: Feature or FeatureTrack . . . 

then it should just work after refreshing the screen. 

Nathan

On Nov 17, 2015, at 6:10 PM, Sofia Robb <[hidden email]> wrote:

Hi Nathan,

I added the extra permissions when I first saw that I couldn't annotate. I do not see anything weird in my catalina.out.

Removing the permissions did not work. I looked in my httpd conf file and I don't see anything about proxys.

On Tue, Nov 17, 2015 at 6:07 PM, Lbl <[hidden email]> wrote:
Can you add any screenshots .. Catalina.out or Deb logs from the client?

Nathan

> On Nov 17, 2015, at 4:46 PM, Sofia Robb <[hidden email]> wrote:
>
> Hi,
>
> I think I am missing something simple. My Apollo is up and running. I can see all my tracks, but I can't drag anything to the annotation box (or add from right click). I added admin, write, read, and export permissions to my user. I am the admin user. i do not see any errors.
>
> Thank you!!
> Sofia
>
>
>
> 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 which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>





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 which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.



<cannotAnnotate.mov>


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 which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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 which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: Can't Annotate

Sofia Robb
Hi Nathan,

Ok!! Got it. I knew it had to be something simple. I had no idea that you couldn't edit canvas features. When do you suggest updating? I am happy to give 2.0.1 a test drive if you like? I am good at finding/creating problems :)

Thank you!!!
Sofia

On Tue, Nov 17, 2015 at 8:55 PM, Nathan Dunn <[hidden email]> wrote:

I see.   You can’t annotate canvas features in 2.0.0.  

In 2.0.1 (currently in release candidate 5) you can annotate them with a drop-down. 

In the interim . . you’ll want to use HTMLFeatures instead of CanvasFeatures:


I *think* you can just change the "type" in the trackList.json to: Feature or FeatureTrack . . . 

then it should just work after refreshing the screen. 

Nathan

On Nov 17, 2015, at 6:10 PM, Sofia Robb <[hidden email]> wrote:

Hi Nathan,

I added the extra permissions when I first saw that I couldn't annotate. I do not see anything weird in my catalina.out.

Removing the permissions did not work. I looked in my httpd conf file and I don't see anything about proxys.

On Tue, Nov 17, 2015 at 6:07 PM, Lbl <[hidden email]> wrote:
Can you add any screenshots .. Catalina.out or Deb logs from the client?

Nathan

> On Nov 17, 2015, at 4:46 PM, Sofia Robb <[hidden email]> wrote:
>
> Hi,
>
> I think I am missing something simple. My Apollo is up and running. I can see all my tracks, but I can't drag anything to the annotation box (or add from right click). I added admin, write, read, and export permissions to my user. I am the admin user. i do not see any errors.
>
> Thank you!!
> Sofia
>
>
>
> 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 which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>





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 which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.



<cannotAnnotate.mov>


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 which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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 which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







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 which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: Can't Annotate

nathandunn

Anyone who wants to give our release-candidate a test-drive gets a gold star (and of course better software):


Of course, you are also welcome to wait until we’ve given it the official test as well.  

Nathan

On Nov 17, 2015, at 9:14 PM, Sofia Robb <[hidden email]> wrote:

Hi Nathan,

Ok!! Got it. I knew it had to be something simple. I had no idea that you couldn't edit canvas features. When do you suggest updating? I am happy to give 2.0.1 a test drive if you like? I am good at finding/creating problems :)

Thank you!!!
Sofia

On Tue, Nov 17, 2015 at 8:55 PM, Nathan Dunn <[hidden email]> wrote:

I see.   You can’t annotate canvas features in 2.0.0.  

In 2.0.1 (currently in release candidate 5) you can annotate them with a drop-down. 

In the interim . . you’ll want to use HTMLFeatures instead of CanvasFeatures:


I *think* you can just change the "type" in the trackList.json to: Feature or FeatureTrack . . . 

then it should just work after refreshing the screen. 

Nathan

On Nov 17, 2015, at 6:10 PM, Sofia Robb <[hidden email]> wrote:

Hi Nathan,

I added the extra permissions when I first saw that I couldn't annotate. I do not see anything weird in my catalina.out.

Removing the permissions did not work. I looked in my httpd conf file and I don't see anything about proxys.

On Tue, Nov 17, 2015 at 6:07 PM, Lbl <[hidden email]> wrote:
Can you add any screenshots .. Catalina.out or Deb logs from the client?

Nathan

> On Nov 17, 2015, at 4:46 PM, Sofia Robb <[hidden email]> wrote:
>
> Hi,
>
> I think I am missing something simple. My Apollo is up and running. I can see all my tracks, but I can't drag anything to the annotation box (or add from right click). I added admin, write, read, and export permissions to my user. I am the admin user. i do not see any errors.
>
> Thank you!!
> Sofia
>
>
>
> 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 which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>





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 which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.



<cannotAnnotate.mov>


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 which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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 which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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 which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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 which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.