Problem with User-created Annotations

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Problem with User-created Annotations

Henry
Hello,

I have a problem with my User-created Annotations.

When I zoom out, the User-created Annotations track has an error.

Before I zoom out, I can zoom in, view, and edit the User-created Annotations.

The Diagnostic message is "TypeError: cfg is undefined".

After reloading the page, the track shows up again.

Has anyone experienced this error before?


Thank you for your time,
Henry




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Re: Problem with User-created Annotations

nathandunn

I had run into this a while ago.    It disappears because it is probably loading the last non-failing version.  If you flush the cache (I like to open a new “incognito” window), you’ll probably see it again.  

If you had a stack-trace of the error, that might be helpful.   If you had modified any aspect of the trackList.json to specifically configure the annotations, that may also cause problems.

Most likely, though, doing a:

- ./apollo clean-all
- ./apollo deploy

will likely fix the problem as I seem to get this when not all of the jbrowse libraries downloaded when I did the initial build.

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


> On Feb 17, 2016, at 1:50 PM, Nathan Henry <[hidden email]> wrote:
>
> Hello,
>
> I have a problem with my User-created Annotations.
>
> When I zoom out, the User-created Annotations track has an error.
>
> Before I zoom out, I can zoom in, view, and edit the User-created Annotations.
>
> The Diagnostic message is "TypeError: cfg is undefined".
>
> After reloading the page, the track shows up again.
>
> Has anyone experienced this error before?
>
>
> Thank you for your time,
> Henry
>
>
>
> 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: Problem with User-created Annotations

Colin
Just to add to what Nathan said, it would be good to know which WA version you're using as it could be a real error. That error often crops up with corrupted annotations, specifically, orphaned features.

The basic idea behind the clue is that the "cfg" error that Henry mentions is probably caused by this line in AnnotTrack.js


var cfg = this.config.style.alternateClasses[clsName];

So if whatever feature appears doesn't have a corresponding style in the client/apollo/json/annot.json, then you get a null cfg there (often times, due to it being an orphan and not a transcript type) then it causes that error

The zoom level is probably a red herring as it would be showing up if you zoomed in on the specifically corrupted feature too


-Colin

On Wed, Feb 17, 2016 at 4:12 PM, Nathan Dunn <[hidden email]> wrote:

I had run into this a while ago.    It disappears because it is probably loading the last non-failing version.  If you flush the cache (I like to open a new “incognito” window), you’ll probably see it again.

If you had a stack-trace of the error, that might be helpful.   If you had modified any aspect of the trackList.json to specifically configure the annotations, that may also cause problems.

Most likely, though, doing a:

- ./apollo clean-all
- ./apollo deploy

will likely fix the problem as I seem to get this when not all of the jbrowse libraries downloaded when I did the initial build.

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


> On Feb 17, 2016, at 1:50 PM, Nathan Henry <[hidden email]> wrote:
>
> Hello,
>
> I have a problem with my User-created Annotations.
>
> When I zoom out, the User-created Annotations track has an error.
>
> Before I zoom out, I can zoom in, view, and edit the User-created Annotations.
>
> The Diagnostic message is "TypeError: cfg is undefined".
>
> After reloading the page, the track shows up again.
>
> Has anyone experienced this error before?
>
>
> Thank you for your time,
> Henry
>
>
>
> 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: Problem with User-created Annotations

Henry
I am using WA 2.0.0.

After looking at the stacktrace I think I found the problem. I had moved the organism data directory to a different location on my server. I then updated the filepath for the organism data file in WebApollo. From the stacktrace it appears that WebApollo was still looking for some files in the old (original) directory. To fix this, I simply created a new organism and pointed it to the new directory location.

Thanks Nathan and Collin for your help!

Henry



On Wed, Feb 17, 2016 at 5:38 PM, Colin <[hidden email]> wrote:
Just to add to what Nathan said, it would be good to know which WA version you're using as it could be a real error. That error often crops up with corrupted annotations, specifically, orphaned features.

The basic idea behind the clue is that the "cfg" error that Henry mentions is probably caused by this line in AnnotTrack.js


var cfg = this.config.style.alternateClasses[clsName];

So if whatever feature appears doesn't have a corresponding style in the client/apollo/json/annot.json, then you get a null cfg there (often times, due to it being an orphan and not a transcript type) then it causes that error

The zoom level is probably a red herring as it would be showing up if you zoomed in on the specifically corrupted feature too


-Colin

On Wed, Feb 17, 2016 at 4:12 PM, Nathan Dunn <[hidden email]> wrote:

I had run into this a while ago.    It disappears because it is probably loading the last non-failing version.  If you flush the cache (I like to open a new “incognito” window), you’ll probably see it again.

If you had a stack-trace of the error, that might be helpful.   If you had modified any aspect of the trackList.json to specifically configure the annotations, that may also cause problems.

Most likely, though, doing a:

- ./apollo clean-all
- ./apollo deploy

will likely fix the problem as I seem to get this when not all of the jbrowse libraries downloaded when I did the initial build.

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


> On Feb 17, 2016, at 1:50 PM, Nathan Henry <[hidden email]> wrote:
>
> Hello,
>
> I have a problem with my User-created Annotations.
>
> When I zoom out, the User-created Annotations track has an error.
>
> Before I zoom out, I can zoom in, view, and edit the User-created Annotations.
>
> The Diagnostic message is "TypeError: cfg is undefined".
>
> After reloading the page, the track shows up again.
>
> Has anyone experienced this error before?
>
>
> Thank you for your time,
> Henry
>
>
>
> 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.

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Re: Problem with User-created Annotations

nathandunn

I think we *may* have fixed that in 2.0.1, but either way, glad you found a fix for it.  

If you need help migrating annotations between organisms let us know.  

Nathan

On Feb 18, 2016, at 1:07 PM, Nathan Henry <[hidden email]> wrote:

I am using WA 2.0.0.

After looking at the stacktrace I think I found the problem. I had moved the organism data directory to a different location on my server. I then updated the filepath for the organism data file in WebApollo. From the stacktrace it appears that WebApollo was still looking for some files in the old (original) directory. To fix this, I simply created a new organism and pointed it to the new directory location.

Thanks Nathan and Collin for your help!

Henry



On Wed, Feb 17, 2016 at 5:38 PM, Colin <[hidden email]> wrote:
Just to add to what Nathan said, it would be good to know which WA version you're using as it could be a real error. That error often crops up with corrupted annotations, specifically, orphaned features.

The basic idea behind the clue is that the "cfg" error that Henry mentions is probably caused by this line in AnnotTrack.js


var cfg = this.config.style.alternateClasses[clsName];

So if whatever feature appears doesn't have a corresponding style in the client/apollo/json/annot.json, then you get a null cfg there (often times, due to it being an orphan and not a transcript type) then it causes that error

The zoom level is probably a red herring as it would be showing up if you zoomed in on the specifically corrupted feature too


-Colin

On Wed, Feb 17, 2016 at 4:12 PM, Nathan Dunn <[hidden email]> wrote:

I had run into this a while ago.    It disappears because it is probably loading the last non-failing version.  If you flush the cache (I like to open a new “incognito” window), you’ll probably see it again.

If you had a stack-trace of the error, that might be helpful.   If you had modified any aspect of the trackList.json to specifically configure the annotations, that may also cause problems.

Most likely, though, doing a:

- ./apollo clean-all
- ./apollo deploy

will likely fix the problem as I seem to get this when not all of the jbrowse libraries downloaded when I did the initial build.

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


> On Feb 17, 2016, at 1:50 PM, Nathan Henry <[hidden email]> wrote:
>
> Hello,
>
> I have a problem with my User-created Annotations.
>
> When I zoom out, the User-created Annotations track has an error.
>
> Before I zoom out, I can zoom in, view, and edit the User-created Annotations.
>
> The Diagnostic message is "TypeError: cfg is undefined".
>
> After reloading the page, the track shows up again.
>
> Has anyone experienced this error before?
>
>
> Thank you for your time,
> Henry
>
>
>
> 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.






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: Problem with User-created Annotations

Henry
Thanks. We have so few annotations at this point that we can migrate manually.

Out of curiosity, do you have a method of moving annotations between WebApollo instances?

Thanks,

Henry

On Thu, Feb 18, 2016 at 4:34 PM, Nathan Dunn <[hidden email]> wrote:

I think we *may* have fixed that in 2.0.1, but either way, glad you found a fix for it.  

If you need help migrating annotations between organisms let us know.  

Nathan

On Feb 18, 2016, at 1:07 PM, Nathan Henry <[hidden email]> wrote:

I am using WA 2.0.0.

After looking at the stacktrace I think I found the problem. I had moved the organism data directory to a different location on my server. I then updated the filepath for the organism data file in WebApollo. From the stacktrace it appears that WebApollo was still looking for some files in the old (original) directory. To fix this, I simply created a new organism and pointed it to the new directory location.

Thanks Nathan and Collin for your help!

Henry



On Wed, Feb 17, 2016 at 5:38 PM, Colin <[hidden email]> wrote:
Just to add to what Nathan said, it would be good to know which WA version you're using as it could be a real error. That error often crops up with corrupted annotations, specifically, orphaned features.

The basic idea behind the clue is that the "cfg" error that Henry mentions is probably caused by this line in AnnotTrack.js


var cfg = this.config.style.alternateClasses[clsName];

So if whatever feature appears doesn't have a corresponding style in the client/apollo/json/annot.json, then you get a null cfg there (often times, due to it being an orphan and not a transcript type) then it causes that error

The zoom level is probably a red herring as it would be showing up if you zoomed in on the specifically corrupted feature too


-Colin

On Wed, Feb 17, 2016 at 4:12 PM, Nathan Dunn <[hidden email]> wrote:

I had run into this a while ago.    It disappears because it is probably loading the last non-failing version.  If you flush the cache (I like to open a new “incognito” window), you’ll probably see it again.

If you had a stack-trace of the error, that might be helpful.   If you had modified any aspect of the trackList.json to specifically configure the annotations, that may also cause problems.

Most likely, though, doing a:

- ./apollo clean-all
- ./apollo deploy

will likely fix the problem as I seem to get this when not all of the jbrowse libraries downloaded when I did the initial build.

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


> On Feb 17, 2016, at 1:50 PM, Nathan Henry <[hidden email]> wrote:
>
> Hello,
>
> I have a problem with my User-created Annotations.
>
> When I zoom out, the User-created Annotations track has an error.
>
> Before I zoom out, I can zoom in, view, and edit the User-created Annotations.
>
> The Diagnostic message is "TypeError: cfg is undefined".
>
> After reloading the page, the track shows up again.
>
> Has anyone experienced this error before?
>
>
> Thank you for your time,
> Henry
>
>
>
> 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.






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: Problem with User-created Annotations

nathandunn

Why yes we do ;)

Deepak wrote a couple of scripts for this.   You have to install groovy to run them.  I would recommend sdkman http://sdkman.io/install.html , but any version should work. 

This is WA2 to WA2:


This is WA1 to WA2:


Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


On Feb 18, 2016, at 1:44 PM, Nathan Henry <[hidden email]> wrote:

Thanks. We have so few annotations at this point that we can migrate manually.

Out of curiosity, do you have a method of moving annotations between WebApollo instances?

Thanks,

Henry

On Thu, Feb 18, 2016 at 4:34 PM, Nathan Dunn <[hidden email]> wrote:

I think we *may* have fixed that in 2.0.1, but either way, glad you found a fix for it.  

If you need help migrating annotations between organisms let us know.  

Nathan

On Feb 18, 2016, at 1:07 PM, Nathan Henry <[hidden email]> wrote:

I am using WA 2.0.0.

After looking at the stacktrace I think I found the problem. I had moved the organism data directory to a different location on my server. I then updated the filepath for the organism data file in WebApollo. From the stacktrace it appears that WebApollo was still looking for some files in the old (original) directory. To fix this, I simply created a new organism and pointed it to the new directory location.

Thanks Nathan and Collin for your help!

Henry



On Wed, Feb 17, 2016 at 5:38 PM, Colin <[hidden email]> wrote:
Just to add to what Nathan said, it would be good to know which WA version you're using as it could be a real error. That error often crops up with corrupted annotations, specifically, orphaned features.

The basic idea behind the clue is that the "cfg" error that Henry mentions is probably caused by this line in AnnotTrack.js


var cfg = this.config.style.alternateClasses[clsName];

So if whatever feature appears doesn't have a corresponding style in the client/apollo/json/annot.json, then you get a null cfg there (often times, due to it being an orphan and not a transcript type) then it causes that error

The zoom level is probably a red herring as it would be showing up if you zoomed in on the specifically corrupted feature too


-Colin

On Wed, Feb 17, 2016 at 4:12 PM, Nathan Dunn <[hidden email]> wrote:

I had run into this a while ago.    It disappears because it is probably loading the last non-failing version.  If you flush the cache (I like to open a new “incognito” window), you’ll probably see it again.

If you had a stack-trace of the error, that might be helpful.   If you had modified any aspect of the trackList.json to specifically configure the annotations, that may also cause problems.

Most likely, though, doing a:

- ./apollo clean-all
- ./apollo deploy

will likely fix the problem as I seem to get this when not all of the jbrowse libraries downloaded when I did the initial build.

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


> On Feb 17, 2016, at 1:50 PM, Nathan Henry <[hidden email]> wrote:
>
> Hello,
>
> I have a problem with my User-created Annotations.
>
> When I zoom out, the User-created Annotations track has an error.
>
> Before I zoom out, I can zoom in, view, and edit the User-created Annotations.
>
> The Diagnostic message is "TypeError: cfg is undefined".
>
> After reloading the page, the track shows up again.
>
> Has anyone experienced this error before?
>
>
> Thank you for your time,
> Henry
>
>
>
> 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.






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: Problem with User-created Annotations

Henry
Great!

Thanks again for your help!

Henry

On Thu, Feb 18, 2016 at 4:48 PM, Nathan Dunn <[hidden email]> wrote:

Why yes we do ;)

Deepak wrote a couple of scripts for this.   You have to install groovy to run them.  I would recommend sdkman http://sdkman.io/install.html , but any version should work. 

This is WA2 to WA2:


This is WA1 to WA2:


Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


On Feb 18, 2016, at 1:44 PM, Nathan Henry <[hidden email]> wrote:

Thanks. We have so few annotations at this point that we can migrate manually.

Out of curiosity, do you have a method of moving annotations between WebApollo instances?

Thanks,

Henry

On Thu, Feb 18, 2016 at 4:34 PM, Nathan Dunn <[hidden email]> wrote:

I think we *may* have fixed that in 2.0.1, but either way, glad you found a fix for it.  

If you need help migrating annotations between organisms let us know.  

Nathan

On Feb 18, 2016, at 1:07 PM, Nathan Henry <[hidden email]> wrote:

I am using WA 2.0.0.

After looking at the stacktrace I think I found the problem. I had moved the organism data directory to a different location on my server. I then updated the filepath for the organism data file in WebApollo. From the stacktrace it appears that WebApollo was still looking for some files in the old (original) directory. To fix this, I simply created a new organism and pointed it to the new directory location.

Thanks Nathan and Collin for your help!

Henry



On Wed, Feb 17, 2016 at 5:38 PM, Colin <[hidden email]> wrote:
Just to add to what Nathan said, it would be good to know which WA version you're using as it could be a real error. That error often crops up with corrupted annotations, specifically, orphaned features.

The basic idea behind the clue is that the "cfg" error that Henry mentions is probably caused by this line in AnnotTrack.js


var cfg = this.config.style.alternateClasses[clsName];

So if whatever feature appears doesn't have a corresponding style in the client/apollo/json/annot.json, then you get a null cfg there (often times, due to it being an orphan and not a transcript type) then it causes that error

The zoom level is probably a red herring as it would be showing up if you zoomed in on the specifically corrupted feature too


-Colin

On Wed, Feb 17, 2016 at 4:12 PM, Nathan Dunn <[hidden email]> wrote:

I had run into this a while ago.    It disappears because it is probably loading the last non-failing version.  If you flush the cache (I like to open a new “incognito” window), you’ll probably see it again.

If you had a stack-trace of the error, that might be helpful.   If you had modified any aspect of the trackList.json to specifically configure the annotations, that may also cause problems.

Most likely, though, doing a:

- ./apollo clean-all
- ./apollo deploy

will likely fix the problem as I seem to get this when not all of the jbrowse libraries downloaded when I did the initial build.

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


> On Feb 17, 2016, at 1:50 PM, Nathan Henry <[hidden email]> wrote:
>
> Hello,
>
> I have a problem with my User-created Annotations.
>
> When I zoom out, the User-created Annotations track has an error.
>
> Before I zoom out, I can zoom in, view, and edit the User-created Annotations.
>
> The Diagnostic message is "TypeError: cfg is undefined".
>
> After reloading the page, the track shows up again.
>
> Has anyone experienced this error before?
>
>
> Thank you for your time,
> Henry
>
>
>
> 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: Problem with User-created Annotations

Chris Childers
Hi Nathan(s),

Have you had success using these scripts?  It is not working for me. I see two potential issues here. 

(1) When I tried running the script, I get the output "0 found in Scaffold10" even though I've verified that that scaffold has annotations created by my example user. 

(2) I have some instances with many, many thousands of scaffolds, and could automate somel number of scaffolds at a time for each user, this could take a long time to go through all the scaffolds. 


Below is an example call, and some of the state responses.  I've verified that the user can log in and view annotations on Apollo1, and verified that the user has 'READ' permissions in the Apollo1 admin interface. When I try to go through https, it throws an error, and the -ignoressl option doesn't help.

$ ./migrate_annotations1to2.groovy -username1 demo -password1 demo -username2 [hidden email] -password2 demo  -sourceurl http://apollo-stage:8080/oncfas_training/ -organism "Oncopeltus fasciatus" -destinationurl http://localhost:8080/apollo/ -sequence_names Scaffold10,Scaffold1

login={sessionId=F2B76E04C0E3C9775BD4A95B0DC8ED4D, url=sequences}
response=[error:You do not have read permissions]
response=[error:You do not have read permissions]
0 found in Scaffold10
0 found in Scaffold1


Thanks,
Chris



On Thu, Feb 18, 2016 at 4:59 PM, Nathan Henry <[hidden email]> wrote:
Great!

Thanks again for your help!

Henry

On Thu, Feb 18, 2016 at 4:48 PM, Nathan Dunn <[hidden email]> wrote:

Why yes we do ;)

Deepak wrote a couple of scripts for this.   You have to install groovy to run them.  I would recommend sdkman http://sdkman.io/install.html , but any version should work. 

This is WA2 to WA2:


This is WA1 to WA2:


Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


On Feb 18, 2016, at 1:44 PM, Nathan Henry <[hidden email]> wrote:

Thanks. We have so few annotations at this point that we can migrate manually.

Out of curiosity, do you have a method of moving annotations between WebApollo instances?

Thanks,

Henry

On Thu, Feb 18, 2016 at 4:34 PM, Nathan Dunn <[hidden email]> wrote:

I think we *may* have fixed that in 2.0.1, but either way, glad you found a fix for it.  

If you need help migrating annotations between organisms let us know.  

Nathan

On Feb 18, 2016, at 1:07 PM, Nathan Henry <[hidden email]> wrote:

I am using WA 2.0.0.

After looking at the stacktrace I think I found the problem. I had moved the organism data directory to a different location on my server. I then updated the filepath for the organism data file in WebApollo. From the stacktrace it appears that WebApollo was still looking for some files in the old (original) directory. To fix this, I simply created a new organism and pointed it to the new directory location.

Thanks Nathan and Collin for your help!

Henry



On Wed, Feb 17, 2016 at 5:38 PM, Colin <[hidden email]> wrote:
Just to add to what Nathan said, it would be good to know which WA version you're using as it could be a real error. That error often crops up with corrupted annotations, specifically, orphaned features.

The basic idea behind the clue is that the "cfg" error that Henry mentions is probably caused by this line in AnnotTrack.js


var cfg = this.config.style.alternateClasses[clsName];

So if whatever feature appears doesn't have a corresponding style in the client/apollo/json/annot.json, then you get a null cfg there (often times, due to it being an orphan and not a transcript type) then it causes that error

The zoom level is probably a red herring as it would be showing up if you zoomed in on the specifically corrupted feature too


-Colin

On Wed, Feb 17, 2016 at 4:12 PM, Nathan Dunn <[hidden email]> wrote:

I had run into this a while ago.    It disappears because it is probably loading the last non-failing version.  If you flush the cache (I like to open a new “incognito” window), you’ll probably see it again.

If you had a stack-trace of the error, that might be helpful.   If you had modified any aspect of the trackList.json to specifically configure the annotations, that may also cause problems.

Most likely, though, doing a:

- ./apollo clean-all
- ./apollo deploy

will likely fix the problem as I seem to get this when not all of the jbrowse libraries downloaded when I did the initial build.

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


> On Feb 17, 2016, at 1:50 PM, Nathan Henry <[hidden email]> wrote:
>
> Hello,
>
> I have a problem with my User-created Annotations.
>
> When I zoom out, the User-created Annotations track has an error.
>
> Before I zoom out, I can zoom in, view, and edit the User-created Annotations.
>
> The Diagnostic message is "TypeError: cfg is undefined".
>
> After reloading the page, the track shows up again.
>
> Has anyone experienced this error before?
>
>
> Thank you for your time,
> Henry
>
>
>
> 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: Problem with User-created Annotations

nathandunn

> On Mar 1, 2016, at 2:07 PM, Chris Childers <[hidden email]> wrote:
>
> Hi Nathan(s),
>
> Have you had success using these scripts?  It is not working for me. I see two potential issues here.  

We’ve definitely tested and used them, but as you can imagine, not for quite a few months.

> (1) When I tried running the script, I get the output "0 found in Scaffold10" even though I've verified that that scaffold has annotations created by my example user.  

My guess is that it is due to the read permissions error below.

> (2) I have some instances with many, many thousands of scaffolds, and could automate somel number of scaffolds at a time for each user, this could take a long time to go through all the scaffolds.  

Yeah, we don’t want to do that.

> Below is an example call, and some of the state responses.  I've verified that the user can log in and view annotations on Apollo1, and verified that the user has 'READ' permissions in the Apollo1 admin interface. When I try to go through https, it throws an error, and the -ignoressl option doesn't help.
>
> $ ./migrate_annotations1to2.groovy -username1 demo -password1 demo -username2 [hidden email] -password2 demo  -sourceurl http://apollo-stage:8080/oncfas_training/ -organism "Oncopeltus fasciatus" -destinationurl http://localhost:8080/apollo/ -sequence_names Scaffold10,Scaffold1
>
> login={sessionId=F2B76E04C0E3C9775BD4A95B0DC8ED4D, url=sequences}
> response=[error:You do not have read permissions]
> response=[error:You do not have read permissions]
> 0 found in Scaffold10
> 0 found in Scaffold1
>
>
> Thanks,
> Chris
>
If you have read permissions and the tracks are set it should just work as it did with the traditional web services.   I wonder if that user has weird permissions.  

You might want to try a simple curl operation (which the 1.0 side wraps).  There is from our “getFeatures.sh” script in our examples.  

curl -b demo_cookies.txt -c demo_cookies.txt -H "Content-Type:application/json" -d "{'username': 'demo', 'password': 'demo'}" http://apollo1.gov/WebApolloDemo/Login?operation=login
curl -b demo_cookies.txt -c demo_cookies.txt -e "http://apollo1.gov/WebApolloDemo/" --data "{ 'operation': 'get_features', 'track': 'Group1.10'}" http://apollo1.gov/WebApolloDemo/AnnotationEditorService

Nathan

>
>
> On Thu, Feb 18, 2016 at 4:59 PM, Nathan Henry <[hidden email]> wrote:
> Great!
>
> Thanks again for your help!
>
> Henry
>
> On Thu, Feb 18, 2016 at 4:48 PM, Nathan Dunn <[hidden email]> wrote:
>
> Why yes we do ;)
>
> Deepak wrote a couple of scripts for this.   You have to install groovy to run them.  I would recommend sdkman http://sdkman.io/install.html , but any version should work.
>
> This is WA2 to WA2:
>
> https://github.com/GMOD/Apollo/blob/master/docs/web_services/examples/groovy/transfer_annotations2to2.groovy
>
> This is WA1 to WA2:
>
> https://github.com/GMOD/Apollo/blob/master/docs/web_services/examples/groovy/migrate_annotations1to2.groovy
>
> Nathan Dunn, PhD
> Berkeley Bioinformatics Open-source Projects (BBOP)
> Genomics Division, Lawrence Berkeley National Laboratory
> [hidden email]
>
>
>> On Feb 18, 2016, at 1:44 PM, Nathan Henry <[hidden email]> wrote:
>>
>> Thanks. We have so few annotations at this point that we can migrate manually.
>>
>> Out of curiosity, do you have a method of moving annotations between WebApollo instances?
>>
>> Thanks,
>>
>> Henry
>>
>> On Thu, Feb 18, 2016 at 4:34 PM, Nathan Dunn <[hidden email]> wrote:
>>
>> I think we *may* have fixed that in 2.0.1, but either way, glad you found a fix for it.  
>>
>> If you need help migrating annotations between organisms let us know.  
>>
>> Nathan
>>
>>> On Feb 18, 2016, at 1:07 PM, Nathan Henry <[hidden email]> wrote:
>>>
>>> I am using WA 2.0.0.
>>>
>>> After looking at the stacktrace I think I found the problem. I had moved the organism data directory to a different location on my server. I then updated the filepath for the organism data file in WebApollo. From the stacktrace it appears that WebApollo was still looking for some files in the old (original) directory. To fix this, I simply created a new organism and pointed it to the new directory location.
>>>
>>> Thanks Nathan and Collin for your help!
>>>
>>> Henry
>>>
>>>
>>>
>>> On Wed, Feb 17, 2016 at 5:38 PM, Colin <[hidden email]> wrote:
>>> Just to add to what Nathan said, it would be good to know which WA version you're using as it could be a real error. That error often crops up with corrupted annotations, specifically, orphaned features.
>>>
>>> The basic idea behind the clue is that the "cfg" error that Henry mentions is probably caused by this line in AnnotTrack.js
>>>
>>>
>>> var cfg = this.config.style.alternateClasses[clsName];
>>>
>>> So if whatever feature appears doesn't have a corresponding style in the client/apollo/json/annot.json, then you get a null cfg there (often times, due to it being an orphan and not a transcript type) then it causes that error
>>>
>>> The zoom level is probably a red herring as it would be showing up if you zoomed in on the specifically corrupted feature too
>>>
>>>
>>> -Colin
>>>
>>> On Wed, Feb 17, 2016 at 4:12 PM, Nathan Dunn <[hidden email]> wrote:
>>>
>>> I had run into this a while ago.    It disappears because it is probably loading the last non-failing version.  If you flush the cache (I like to open a new “incognito” window), you’ll probably see it again.
>>>
>>> If you had a stack-trace of the error, that might be helpful.   If you had modified any aspect of the trackList.json to specifically configure the annotations, that may also cause problems.
>>>
>>> Most likely, though, doing a:
>>>
>>> - ./apollo clean-all
>>> - ./apollo deploy
>>>
>>> will likely fix the problem as I seem to get this when not all of the jbrowse libraries downloaded when I did the initial build.
>>>
>>> Nathan Dunn, PhD
>>> Berkeley Bioinformatics Open-source Projects (BBOP)
>>> Genomics Division, Lawrence Berkeley National Laboratory
>>> [hidden email]
>>>
>>>
>>>> On Feb 17, 2016, at 1:50 PM, Nathan Henry <[hidden email]> wrote:
>>>>
>>>> Hello,
>>>>
>>>> I have a problem with my User-created Annotations.
>>>>
>>>> When I zoom out, the User-created Annotations track has an error.
>>>>
>>>> Before I zoom out, I can zoom in, view, and edit the User-created Annotations.
>>>>
>>>> The Diagnostic message is "TypeError: cfg is undefined".
>>>>
>>>> After reloading the page, the track shows up again.
>>>>
>>>> Has anyone experienced this error before?
>>>>
>>>>
>>>> Thank you for your time,
>>>> Henry
>>>>
>>>>
>>>>
>>>> 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.
>>>
>>
>>
>>
>>
>>
>> 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.
>
>
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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>





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Re: Problem with User-created Annotations

nathandunn
In reply to this post by Chris Childers

Just wanted to update.  The fix / problem was that WA1 stores scaffolds named as “Annotations-XYZ” and Apollo2.X stores them as XYZ.  

Added it there (and added ignoring it as an option).  In master and 2.0.2-RC4.


Nathan

On Mar 1, 2016, at 2:07 PM, Chris Childers <[hidden email]> wrote:

Hi Nathan(s),

Have you had success using these scripts?  It is not working for me. I see two potential issues here. 

(1) When I tried running the script, I get the output "0 found in Scaffold10" even though I've verified that that scaffold has annotations created by my example user. 

(2) I have some instances with many, many thousands of scaffolds, and could automate somel number of scaffolds at a time for each user, this could take a long time to go through all the scaffolds. 


Below is an example call, and some of the state responses.  I've verified that the user can log in and view annotations on Apollo1, and verified that the user has 'READ' permissions in the Apollo1 admin interface. When I try to go through https, it throws an error, and the -ignoressl option doesn't help.

$ ./migrate_annotations1to2.groovy -username1 demo -password1 demo -username2 [hidden email] -password2 demo  -sourceurl http://apollo-stage:8080/oncfas_training/ -organism "Oncopeltus fasciatus" -destinationurl http://localhost:8080/apollo/ -sequence_names Scaffold10,Scaffold1

login={sessionId=F2B76E04C0E3C9775BD4A95B0DC8ED4D, url=sequences}
response=[error:You do not have read permissions]
response=[error:You do not have read permissions]
0 found in Scaffold10
0 found in Scaffold1


Thanks,
Chris



On Thu, Feb 18, 2016 at 4:59 PM, Nathan Henry <[hidden email]> wrote:
Great!

Thanks again for your help!

Henry

On Thu, Feb 18, 2016 at 4:48 PM, Nathan Dunn <[hidden email]> wrote:

Why yes we do ;)

Deepak wrote a couple of scripts for this.   You have to install groovy to run them.  I would recommend sdkman http://sdkman.io/install.html , but any version should work. 

This is WA2 to WA2:


This is WA1 to WA2:


Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


On Feb 18, 2016, at 1:44 PM, Nathan Henry <[hidden email]> wrote:

Thanks. We have so few annotations at this point that we can migrate manually.

Out of curiosity, do you have a method of moving annotations between WebApollo instances?

Thanks,

Henry

On Thu, Feb 18, 2016 at 4:34 PM, Nathan Dunn <[hidden email]> wrote:

I think we *may* have fixed that in 2.0.1, but either way, glad you found a fix for it.  

If you need help migrating annotations between organisms let us know.  

Nathan

On Feb 18, 2016, at 1:07 PM, Nathan Henry <[hidden email]> wrote:

I am using WA 2.0.0.

After looking at the stacktrace I think I found the problem. I had moved the organism data directory to a different location on my server. I then updated the filepath for the organism data file in WebApollo. From the stacktrace it appears that WebApollo was still looking for some files in the old (original) directory. To fix this, I simply created a new organism and pointed it to the new directory location.

Thanks Nathan and Collin for your help!

Henry



On Wed, Feb 17, 2016 at 5:38 PM, Colin <[hidden email]> wrote:
Just to add to what Nathan said, it would be good to know which WA version you're using as it could be a real error. That error often crops up with corrupted annotations, specifically, orphaned features.

The basic idea behind the clue is that the "cfg" error that Henry mentions is probably caused by this line in AnnotTrack.js


var cfg = this.config.style.alternateClasses[clsName];

So if whatever feature appears doesn't have a corresponding style in the client/apollo/json/annot.json, then you get a null cfg there (often times, due to it being an orphan and not a transcript type) then it causes that error

The zoom level is probably a red herring as it would be showing up if you zoomed in on the specifically corrupted feature too


-Colin

On Wed, Feb 17, 2016 at 4:12 PM, Nathan Dunn <[hidden email]> wrote:

I had run into this a while ago.    It disappears because it is probably loading the last non-failing version.  If you flush the cache (I like to open a new “incognito” window), you’ll probably see it again.

If you had a stack-trace of the error, that might be helpful.   If you had modified any aspect of the trackList.json to specifically configure the annotations, that may also cause problems.

Most likely, though, doing a:

- ./apollo clean-all
- ./apollo deploy

will likely fix the problem as I seem to get this when not all of the jbrowse libraries downloaded when I did the initial build.

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


> On Feb 17, 2016, at 1:50 PM, Nathan Henry <[hidden email]> wrote:
>
> Hello,
>
> I have a problem with my User-created Annotations.
>
> When I zoom out, the User-created Annotations track has an error.
>
> Before I zoom out, I can zoom in, view, and edit the User-created Annotations.
>
> The Diagnostic message is "TypeError: cfg is undefined".
>
> After reloading the page, the track shows up again.
>
> Has anyone experienced this error before?
>
>
> Thank you for your time,
> Henry
>
>
>
> 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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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.