Discussion:
[apollo] Problem with User-created Annotations
Nathan Henry
2016-02-17 21:50:28 UTC
Permalink
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
Nathan Dunn
2016-02-17 22:12:39 UTC
Permalink
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
Post by Nathan 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
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
Colin
2016-02-17 22:38:32 UTC
Permalink
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
Post by Nathan Dunn
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.
- ./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
Post by Nathan 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.
Post by Nathan Henry
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/
Post by Nathan Henry
If you wish to unsubscribe from the Apollo List: 1. From the address
with which you subscribed to the list, send a message to
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
2. In the subject line of your email type: unsubscribe apollo | 3. Leave
the message body blank.
Nathan Henry
2016-02-18 21:07:43 UTC
Permalink
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
Post by 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
Post by Nathan Dunn
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.
- ./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
Post by Nathan 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.
Post by Nathan Henry
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/
Post by Nathan Henry
If you wish to unsubscribe from the Apollo List: 1. From the address
with which you subscribed to the list, send a message to
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
| 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
2. In the subject line of your email type: unsubscribe apollo | 3. Leave
the message body blank.
Nathan Dunn
2016-02-18 21:34:46 UTC
Permalink
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
Post by Nathan 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
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
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.
- ./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
Post by Nathan 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
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
Nathan Henry
2016-02-18 21:44:49 UTC
Permalink
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
Post by Nathan Dunn
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
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
Post by 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
Post by Nathan Dunn
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.
- ./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
Post by Nathan 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.
Post by Nathan Henry
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/
Post by Nathan Henry
If you wish to unsubscribe from the Apollo List: 1. From the address
with which you subscribed to the list, send a message to
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
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
| 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
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
2. In the subject line of your email type: unsubscribe apollo | 3. Leave
the message body blank.
Nathan Henry
2016-02-18 21:59:57 UTC
Permalink
Great!

Thanks again for your help!

Henry
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.
https://github.com/GMOD/Apollo/blob/master/docs/web_services/examples/groovy/transfer_annotations2to2.groovy
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
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
Post by Nathan Dunn
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
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
Post by 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
Post by Nathan Dunn
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.
- ./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
Post by Nathan 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.
Post by Nathan Henry
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/
Post by Nathan Henry
If you wish to unsubscribe from the Apollo List: 1. From the address
with which you subscribed to the list, send a message to
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
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
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
| 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
| 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
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
2. In the subject line of your email type: unsubscribe apollo | 3. Leave
the message body blank.
Chris Childers
2016-03-01 22:07:36 UTC
Permalink
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 ***@my.server.org -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
Post by Nathan Henry
Great!
Thanks again for your help!
Henry
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.
https://github.com/GMOD/Apollo/blob/master/docs/web_services/examples/groovy/transfer_annotations2to2.groovy
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
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
Post by Nathan Dunn
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
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
Post by 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
Post by Nathan Dunn
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.
- ./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
Post by Nathan 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.
Post by Nathan Henry
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/
Post by Nathan Henry
If you wish to unsubscribe from the Apollo List: 1. From the address
with which you subscribed to the list, send a message to
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
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
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
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
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
| 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
| 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
2. In the subject line of your email type: unsubscribe apollo | 3. Leave
the message body blank.
Nathan Dunn
2016-03-02 01:48:28 UTC
Permalink
Post by Chris Childers
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.
Post by Chris Childers
(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.
Post by Chris Childers
(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.
Post by Chris Childers
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.
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
Post by Chris Childers
Great!
Thanks again for your help!
Henry
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.
https://github.com/GMOD/Apollo/blob/master/docs/web_services/examples/groovy/transfer_annotations2to2.groovy
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
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
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
Post by Nathan 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
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
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.
- ./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
Post by Nathan 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
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
Nathan Dunn
2016-03-03 01:42:22 UTC
Permalink
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.

https://github.com/GMOD/Apollo/pull/915/files <https://github.com/GMOD/Apollo/pull/915/files>
Nathan
Post by 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.
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
Great!
Thanks again for your help!
Henry
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 <http://sdkman.io/install.html> , but any version should work.
https://github.com/GMOD/Apollo/blob/master/docs/web_services/examples/groovy/transfer_annotations2to2.groovy <https://github.com/GMOD/Apollo/blob/master/docs/web_services/examples/groovy/transfer_annotations2to2.groovy>
https://github.com/GMOD/Apollo/blob/master/docs/web_services/examples/groovy/migrate_annotations1to2.groovy <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
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
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
Post by Nathan 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
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
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.
- ./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
Post by Nathan 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
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
Continue reading on narkive:
Loading...