TypeError:

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TypeError:

Juhana Kammonen

Dear all,

The user-created annotations area of a single scaffold (length ca. 650 kbp) in
our annotation effort started showing the following erratic symptoms:

-A red box in the User-created annotations area with the text: "Error. An
error was encountered when displaying this track. Diagnostic message.
TypeError: cfg is undefined"

-Box only comes visible when having an area from 0 bp to around 10 kbp in the
JBrowse view in this scaffold. Other scaffolds on our production server
unaffected at this point.

-Box stays there even when scrolling away from the location where it comes
visible.

-After a user reported this I suspected a corrupt annotation in the PSQL
database, so I manually removed it from the PSQL database.

-Tried "apollo clean-all" and "apollo run-local". The annotation in the
location was removed but error box and message persist.

~$ uname -a
Linux dna-marker 3.13.0-107-generic #154-Ubuntu SMP Tue Dec 20 09:57:27 UTC
2016 x86_64 x86_64 x86_64 GNU/Linux


application.properties:

app.grails.version=2.5.5
app.name=apollo
app.servlet.version=3.0
app.version=2.0.4

Kind regards,
Juhana K
University of Helsinki
Finland




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Re: TypeError:

nathandunn

Could you past any information from the javascript web console (in developer information) and tomcat server (typically catalina.out) logs associated with the error? 

Also, if you have the outline of the command used to remove the annotation, that might help as well.  

Thanks,

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


On Mar 6, 2017, at 12:38 AM, Juhana Kammonen <[hidden email]> wrote:


Dear all,

The user-created annotations area of a single scaffold (length ca. 650 kbp) in
our annotation effort started showing the following erratic symptoms:

-A red box in the User-created annotations area with the text: "Error. An
error was encountered when displaying this track. Diagnostic message.
TypeError: cfg is undefined"

-Box only comes visible when having an area from 0 bp to around 10 kbp in the
JBrowse view in this scaffold. Other scaffolds on our production server
unaffected at this point.

-Box stays there even when scrolling away from the location where it comes
visible.

-After a user reported this I suspected a corrupt annotation in the PSQL
database, so I manually removed it from the PSQL database.

-Tried "apollo clean-all" and "apollo run-local". The annotation in the
location was removed but error box and message persist.

~$ uname -a
Linux dna-marker 3.13.0-107-generic #154-Ubuntu SMP Tue Dec 20 09:57:27 UTC
2016 x86_64 x86_64 x86_64 GNU/Linux


application.properties:

app.grails.version=2.5.5
app.name=apollo
app.servlet.version=3.0
app.version=2.0.4

Kind regards,
Juhana K
University of Helsinki
Finland



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: TypeError:

Juhana Kammonen

Dear Nathan,

Thanks for your answer. The responses are the following

* Nothing unusual shows up at catalina.out (will not post contents here)

* I removed the annotation from PSQL database using the following in psql console (the Error box was there before these commands so they did remove the annotation but the error box remained):

"
\c production_db;
select * from feature where name like '%scaffold1140%';
delete from feature where name like '%scaffold1140%';
select * from feature_relationship where parent_feature_id = 474170;
delete from feature_relationship where parent_feature_id = 474170;
delete from feature where name like '%scaffold1140%';
select * from feature_location where feature_id = 474170;
delete from feature_location where feature_id = 474170;
delete from feature where name like '%scaffold1140%';
select * from feature_relationship where parent_feature_id = 474172;
select * from feature_relationship where child_feature_id = 474172;
delete from feature where name like '%scaffold1140%';
select * from feature_location where feature_id = 474172;
select * from feature_relationship where child_feature_id = 474172;
select * from feature_relationship where parent_feature_id = 474172;
delete from feature_relationship where parent_feature_id = 474172;
delete from feature where name like '%scaffold1140%';
select * from feature_location where feature_id = 474172;
delete from feature_location where feature_id = 474172;
delete from feature where name like '%scaffold1140%';
\q
"


* I will blow up the developer tools javascript console (Firefox, and sorry for flooding):

"
loaded WebApollo plugin  main.js:79:9
plugin HideTracksButton constructor  main.js:40:9
plugin: NeatHTMLFeatures  main.js:29:9
plugin: NeatCanvasFeatures  main.js:29:9
Use of getAttributeNode() is deprecated. Use getAttribute() instead.  dom-attr.js:36:38
Synchronous XMLHttpRequest on the main thread is deprecated because of its detrimental effects to the end user’s experience. For more help http://xhr.spec.whatwg.org/  xhr.js:176:3
Registering embedded system with ApolloGwt-2.0.  AnnotTrack.js:315:21
connection established  AnnotTrack.js:383:21
AnnotTrack<.renderExonSegments@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:169:21
draggableTrack<.handleSubFeatures@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/DraggableHTMLFeatures.js:565:34
HTMLFeatures<.renderFeature@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/HTMLFeatures.js:1116:13
inherited@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/_base/declare.js:189:28
draggableTrack<.renderFeature@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/DraggableHTMLFeatures.js:313:23
AnnotTrack<.renderFeature@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:559:31
HTMLFeatures<.addFeatureToBlock@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/HTMLFeatures.js:674:23
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lang.hitch/<@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/_base/lang.js:375:48
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HTMLFeatures<.fillBlock@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/HTMLFeatures.js:369:9
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inherited@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/_base/declare.js:189:28
draggableTrack<.showRange@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/DraggableHTMLFeatures.js:1087:9
.showVisibleBlocks/<@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/GenomeView.js:2016:27
.trackIterate@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/GenomeView.js:2265:9
.showVisibleBlocks@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/GenomeView.js:2015:5
lang._hitchArgs/<@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/_base/lang.js:327:17
.changed@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/BlockBased.js:401:13
inherited@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/_base/declare.js:189:28
HTMLFeatures<.changed@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/HTMLFeatures.js:1346:9
AnnotTrack<.setViewInfo/<@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:242:25
signalListener@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:37:21
signalWaiting@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:28:4
Deferred/this.resolve@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:192:5
signalDeferred@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:81:6
signalListener@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:52:6
signalWaiting@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:28:4
Deferred/this.resolve@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:192:5
signalDeferred@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:81:6
signalListener@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:58:4
signalWaiting@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:28:4
Deferred/this.resolve@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:192:5
signalDeferred@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:81:6
signalListener@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:52:6
signalWaiting@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:28:4
Deferred/this.resolve@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:192:5
handleResponse@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/request/xhr.js:50:4
onLoad@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/request/xhr.js:76:5
 TypeError: cfg is undefined
Stack trace:
AnnotTrack<.renderExonSegments@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:169:21
draggableTrack<.handleSubFeatures@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/DraggableHTMLFeatures.js:565:34
HTMLFeatures<.renderFeature@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/HTMLFeatures.js:1116:13
inherited@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/_base/declare.js:189:28
draggableTrack<.renderFeature@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/DraggableHTMLFeatures.js:313:23
AnnotTrack<.renderFeature@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:559:31
HTMLFeatures<.addFeatureToBlock@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/HTMLFeatures.js:674:23
HTMLFeatures<.fillFeatures/featCallback<@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/HTMLFeatures.js:624:21
lang.hitch/<@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/_base/lang.js:375:48
.getFeatures@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/Store/SeqFeature/ScratchPad.js:69:17
HTMLFeatures<.fillFeatures@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/HTMLFeatures.js:630:9
HTMLFeatures<.fillBlock/<@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/HTMLFeatures.js:410:21
lang.hitch/<@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/_base/lang.js:375:48
.getGlobalStats@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/Store/SeqFeature.js:41:9
HTMLFeatures<.fillBlock@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/HTMLFeatures.js:369:9
._showBlock@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/BlockBased.js:573:13
.showRange@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/BlockBased.js:298:13
inherited@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/_base/declare.js:189:28
draggableTrack<.showRange@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/DraggableHTMLFeatures.js:1087:9
.showVisibleBlocks/<@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/GenomeView.js:2016:27
.trackIterate@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/GenomeView.js:2265:9
.showVisibleBlocks@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/GenomeView.js:2015:5
lang._hitchArgs/<@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/_base/lang.js:327:17
.changed@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/BlockBased.js:401:13
inherited@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/_base/declare.js:189:28
HTMLFeatures<.changed@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/HTMLFeatures.js:1346:9
AnnotTrack<.setViewInfo/<@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:242:25
signalListener@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:37:21
signalWaiting@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:28:4
Deferred/this.resolve@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:192:5
signalDeferred@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:81:6
signalListener@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:52:6
signalWaiting@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:28:4
Deferred/this.resolve@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:192:5
signalDeferred@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:81:6
signalListener@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:58:4
signalWaiting@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:28:4
Deferred/this.resolve@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:192:5
signalDeferred@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:81:6
signalListener@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:52:6
signalWaiting@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:28:4
Deferred/this.resolve@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:192:5
handleResponse@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/request/xhr.js:50:4
onLoad@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/request/xhr.js:76:5
  BlockBased.js:448:13
        ._handleError http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/BlockBased.js:448:13
        ._showBlock http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/BlockBased.js:575:13
        .showRange http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/BlockBased.js:298:13
        inherited http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/_base/declare.js:189:28
        draggableTrack<.showRange http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/DraggableHTMLFeatures.js:1087:9
        .showVisibleBlocks/< http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/GenomeView.js:2016:27
        .trackIterate http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/GenomeView.js:2265:9
        .showVisibleBlocks http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/GenomeView.js:2015:5
        lang._hitchArgs/< http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/_base/lang.js:327:17
        .changed http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/BlockBased.js:401:13
        inherited http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/_base/declare.js:189:28
        HTMLFeatures<.changed http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/HTMLFeatures.js:1346:9
        AnnotTrack<.setViewInfo/< http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:242:25
        signalListener http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:37:21
        signalWaiting http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:28:4
        Deferred/this.resolve http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:192:5
        signalDeferred http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:81:6
        signalListener http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:52:6
        signalWaiting http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:28:4
        Deferred/this.resolve http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:192:5
        signalDeferred http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:81:6
        signalListener http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:58:4
        signalWaiting http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:28:4
        Deferred/this.resolve http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:192:5
        signalDeferred http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:81:6
        signalListener http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:52:6
        signalWaiting http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:28:4
        Deferred/this.resolve http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:192:5
        handleResponse http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/request/xhr.js:50:4
        onLoad http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/request/xhr.js:76:5
"

Kind regards,
Juhana K
University of Helsinki
Finland

________________________________________
From: [hidden email] <[hidden email]> on behalf of Nathan Dunn <[hidden email]>
Sent: Monday, March 6, 2017 7:30 PM
To: [hidden email]
Subject: Re: [apollo] TypeError:

Could you past any information from the javascript web console (in developer information) and tomcat server (typically catalina.out) logs associated with the error?

Also, if you have the outline of the command used to remove the annotation, that might help as well.

Thanks,

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory
[hidden email]<mailto:[hidden email]>


On Mar 6, 2017, at 12:38 AM, Juhana Kammonen <[hidden email]<mailto:[hidden email]>> wrote:


Dear all,

The user-created annotations area of a single scaffold (length ca. 650 kbp) in
our annotation effort started showing the following erratic symptoms:

-A red box in the User-created annotations area with the text: "Error. An
error was encountered when displaying this track. Diagnostic message.
TypeError: cfg is undefined"

-Box only comes visible when having an area from 0 bp to around 10 kbp in the
JBrowse view in this scaffold. Other scaffolds on our production server
unaffected at this point.

-Box stays there even when scrolling away from the location where it comes
visible.

-After a user reported this I suspected a corrupt annotation in the PSQL
database, so I manually removed it from the PSQL database.

-Tried "apollo clean-all" and "apollo run-local". The annotation in the
location was removed but error box and message persist.

~$ uname -a
Linux dna-marker 3.13.0-107-generic #154-Ubuntu SMP Tue Dec 20 09:57:27 UTC
2016 x86_64 x86_64 x86_64 GNU/Linux


application.properties:

app.grails.version=2.5.5
app.name=apollo
app.servlet.version=3.0
app.version=2.0.4

Kind regards,
Juhana K
University of Helsinki
Finland



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Re: TypeError:

nathandunn

Juhana,

The error is here:


It is typically caused because when it pulls the features in and they are incomplete.   Most likely in your SQL-script you deleted part, but not all of it.    

I would typically advocate doing this from the command-line or using a web-service script to do this (we have one for deleting all features for an organism, but let us know if you want this done for a single sequence - should be pretty easy):


A couple of questions:

1 - were you trying to delete all of the features from a scaffold (and if so how many?)
2 - you can figure out which one is failing this way:

When you load your tracks, open the dev window to the network tabs and filter for: AnnotationEditorService.  

You should see a request like this:


and a response that looks like this:



If you post this response (or you can figure out how the JSON is incomplete), we can probably figure that out.  

In general, though, if you want to remove all of the references to a scaffold you would do something like:

delete from feature_location where sequence_id in (select id from sequence s where s.name like ‘%scaffold1140%’ ); 

This will disassociate them, though for completeness, doing what you did below is good practice.  

Nathan

On Mar 7, 2017, at 4:18 AM, Kammonen, Juhana <[hidden email]> wrote:


Dear Nathan,

Thanks for your answer. The responses are the following

* Nothing unusual shows up at catalina.out (will not post contents here)

* I removed the annotation from PSQL database using the following in psql console (the Error box was there before these commands so they did remove the annotation but the error box remained):

"
\c production_db;
select * from feature where name like '%scaffold1140%';
delete from feature where name like '%scaffold1140%';
select * from feature_relationship where parent_feature_id = 474170;
delete from feature_relationship where parent_feature_id = 474170;
delete from feature where name like '%scaffold1140%';
select * from feature_location where feature_id = 474170;
delete from feature_location where feature_id = 474170;
delete from feature where name like '%scaffold1140%';
select * from feature_relationship where parent_feature_id = 474172;
select * from feature_relationship where child_feature_id = 474172;
delete from feature where name like '%scaffold1140%';
select * from feature_location where feature_id = 474172;
select * from feature_relationship where child_feature_id = 474172;
select * from feature_relationship where parent_feature_id = 474172;
delete from feature_relationship where parent_feature_id = 474172;
delete from feature where name like '%scaffold1140%';
select * from feature_location where feature_id = 474172;
delete from feature_location where feature_id = 474172;
delete from feature where name like '%scaffold1140%';
\q
"


* I will blow up the developer tools javascript console (Firefox, and sorry for flooding):

"
loaded WebApollo plugin  main.js:79:9
plugin HideTracksButton constructor  main.js:40:9
plugin: NeatHTMLFeatures  main.js:29:9
plugin: NeatCanvasFeatures  main.js:29:9
Use of getAttributeNode() is deprecated. Use getAttribute() instead.  dom-attr.js:36:38
Synchronous XMLHttpRequest on the main thread is deprecated because of its detrimental effects to the end user’s experience. For more help http://xhr.spec.whatwg.org/  xhr.js:176:3
Registering embedded system with ApolloGwt-2.0.  AnnotTrack.js:315:21
connection established  AnnotTrack.js:383:21
AnnotTrack<.renderExonSegments@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:169:21
draggableTrack<.handleSubFeatures@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/DraggableHTMLFeatures.js:565:34
HTMLFeatures<.renderFeature@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/HTMLFeatures.js:1116:13
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onLoad@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/request/xhr.js:76:5
TypeError: cfg is undefined
Stack trace:
AnnotTrack<.renderExonSegments@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:169:21
draggableTrack<.handleSubFeatures@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/DraggableHTMLFeatures.js:565:34
HTMLFeatures<.renderFeature@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/HTMLFeatures.js:1116:13
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draggableTrack<.renderFeature@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/DraggableHTMLFeatures.js:313:23
AnnotTrack<.renderFeature@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:559:31
HTMLFeatures<.addFeatureToBlock@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/HTMLFeatures.js:674:23
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 BlockBased.js:448:13
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._showBlock http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/BlockBased.js:575:13
.showRange http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/BlockBased.js:298:13
inherited http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/_base/declare.js:189:28
draggableTrack<.showRange http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/DraggableHTMLFeatures.js:1087:9
.showVisibleBlocks/< http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/GenomeView.js:2016:27
.trackIterate http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/GenomeView.js:2265:9
.showVisibleBlocks http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/GenomeView.js:2015:5
lang._hitchArgs/< http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/_base/lang.js:327:17
.changed http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/BlockBased.js:401:13
inherited http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/_base/declare.js:189:28
HTMLFeatures<.changed http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/HTMLFeatures.js:1346:9
AnnotTrack<.setViewInfo/< http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:242:25
signalListener http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:37:21
signalWaiting http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:28:4
Deferred/this.resolve http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:192:5
signalDeferred http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:81:6
signalListener http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:52:6
signalWaiting http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:28:4
Deferred/this.resolve http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:192:5
signalDeferred http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:81:6
signalListener http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:58:4
signalWaiting http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:28:4
Deferred/this.resolve http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:192:5
signalDeferred http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:81:6
signalListener http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:52:6
signalWaiting http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:28:4
Deferred/this.resolve http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:192:5
handleResponse http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/request/xhr.js:50:4
onLoad http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/request/xhr.js:76:5
"

Kind regards,
Juhana K
University of Helsinki
Finland

________________________________________
From: [hidden email] <[hidden email]> on behalf of Nathan Dunn <[hidden email]>
Sent: Monday, March 6, 2017 7:30 PM
To: [hidden email]
Subject: Re: [apollo] TypeError:

Could you past any information from the javascript web console (in developer information) and tomcat server (typically catalina.out) logs associated with the error?

Also, if you have the outline of the command used to remove the annotation, that might help as well.

Thanks,

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory
[hidden email]<[hidden email]>


On Mar 6, 2017, at 12:38 AM, Juhana Kammonen <[hidden email]<[hidden email]>> wrote:


Dear all,

The user-created annotations area of a single scaffold (length ca. 650 kbp) in
our annotation effort started showing the following erratic symptoms:

-A red box in the User-created annotations area with the text: "Error. An
error was encountered when displaying this track. Diagnostic message.
TypeError: cfg is undefined"

-Box only comes visible when having an area from 0 bp to around 10 kbp in the
JBrowse view in this scaffold. Other scaffolds on our production server
unaffected at this point.

-Box stays there even when scrolling away from the location where it comes
visible.

-After a user reported this I suspected a corrupt annotation in the PSQL
database, so I manually removed it from the PSQL database.

-Tried "apollo clean-all" and "apollo run-local". The annotation in the
location was removed but error box and message persist.

~$ uname -a
Linux dna-marker 3.13.0-107-generic #154-Ubuntu SMP Tue Dec 20 09:57:27 UTC
2016 x86_64 x86_64 x86_64 GNU/Linux


application.properties:

app.grails.version=2.5.5
app.name=apollo
app.servlet.version=3.0
app.version=2.0.4

Kind regards,
Juhana K
University of Helsinki
Finland



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Re: TypeError:

Juhana Kammonen

Dear Nathan,

Thank you for your message. I was able to resolve the issue. Especially the SQL line:

delete from feature_location where sequence_id in (select id from sequence s where s.name like ‘%scaffold1140%’ );

was particularly useful here.

However, an issue remains. The problematic annotation that likely caused the error in the first place begins at location 0 (zero) of the scaffold in question. When I try to add it to the User-created annotation area, nothing happens at first. When I refresh the page, the annotation has showed up into the beginning of the scaffold but the owner of the annotation is reported as "None". If I add any other annotations in that scaffold, they show the owner (my name) properly.

In any case, this information was highly useful. I don't see a need for a separate script to do this at this point but it is good to know what to do next time this error message shows.

Thank you,
Juhana K



--
Juhana Kammonen
MSc, PhD student
---
DNA Sequencing and Genomics Lab
Institute of Biotechnology
Viikinkaari 5D (Biocenter 2, 4009b)
00014 University of Helsinki
FINLAND

________________________________________
From: [hidden email] <[hidden email]> on behalf of Nathan Dunn <[hidden email]>
Sent: Tuesday, March 7, 2017 7:02 PM
To: [hidden email]
Subject: Re: [apollo] TypeError:

Juhana,

The error is here:

https://github.com/GMOD/Apollo/blob/e0aa79bdc792cdda231b910800d2f90c48dac199/client/apollo/js/View/Track/AnnotTrack.js#L169

It is typically caused because when it pulls the features in and they are incomplete.   Most likely in your SQL-script you deleted part, but not all of it.

I would typically advocate doing this from the command-line or using a web-service script to do this (we have one for deleting all features for an organism, but let us know if you want this done for a single sequence - should be pretty easy):

https://github.com/GMOD/Apollo/blob/master/docs/web_services/examples/groovy/delete_annotations_from_organism.groovy

A couple of questions:

1 - were you trying to delete all of the features from a scaffold (and if so how many?)
2 - you can figure out which one is failing this way:

When you load your tracks, open the dev window to the network tabs and filter for: AnnotationEditorService.

You should see a request like this:

[cid:726ADD5F-B6F7-41E9-A8A8-BDCC7DE21634]

and a response that looks like this:

[cid:724988B3-CEB1-4788-880C-A4D10B228372]


If you post this response (or you can figure out how the JSON is incomplete), we can probably figure that out.

In general, though, if you want to remove all of the references to a scaffold you would do something like:

delete from feature_location where sequence_id in (select id from sequence s where s.name like ‘%scaffold1140%’ );

This will disassociate them, though for completeness, doing what you did below is good practice.

Nathan

On Mar 7, 2017, at 4:18 AM, Kammonen, Juhana <[hidden email]<mailto:[hidden email]>> wrote:


Dear Nathan,

Thanks for your answer. The responses are the following

* Nothing unusual shows up at catalina.out (will not post contents here)

* I removed the annotation from PSQL database using the following in psql console (the Error box was there before these commands so they did remove the annotation but the error box remained):

"
\c production_db;
select * from feature where name like '%scaffold1140%';
delete from feature where name like '%scaffold1140%';
select * from feature_relationship where parent_feature_id = 474170;
delete from feature_relationship where parent_feature_id = 474170;
delete from feature where name like '%scaffold1140%';
select * from feature_location where feature_id = 474170;
delete from feature_location where feature_id = 474170;
delete from feature where name like '%scaffold1140%';
select * from feature_relationship where parent_feature_id = 474172;
select * from feature_relationship where child_feature_id = 474172;
delete from feature where name like '%scaffold1140%';
select * from feature_location where feature_id = 474172;
select * from feature_relationship where child_feature_id = 474172;
select * from feature_relationship where parent_feature_id = 474172;
delete from feature_relationship where parent_feature_id = 474172;
delete from feature where name like '%scaffold1140%';
select * from feature_location where feature_id = 474172;
delete from feature_location where feature_id = 474172;
delete from feature where name like '%scaffold1140%';
\q
"


* I will blow up the developer tools javascript console (Firefox, and sorry for flooding):

"
loaded WebApollo plugin  main.js:79:9
plugin HideTracksButton constructor  main.js:40:9
plugin: NeatHTMLFeatures  main.js:29:9
plugin: NeatCanvasFeatures  main.js:29:9
Use of getAttributeNode() is deprecated. Use getAttribute() instead.  dom-attr.js:36:38
Synchronous XMLHttpRequest on the main thread is deprecated because of its detrimental effects to the end user’s experience. For more help http://xhr.spec.whatwg.org/  xhr.js:176:3
Registering embedded system with ApolloGwt-2.0.  AnnotTrack.js:315:21
connection established  AnnotTrack.js:383:21
AnnotTrack<.renderExonSegments@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:169:21
draggableTrack<.handleSubFeatures@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/DraggableHTMLFeatures.js:565:34
HTMLFeatures<.renderFeature@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/HTMLFeatures.js:1116:13
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draggableTrack<.renderFeature@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/DraggableHTMLFeatures.js:313:23
AnnotTrack<.renderFeature@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:559:31
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TypeError: cfg is undefined
Stack trace:
AnnotTrack<.renderExonSegments@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:169:21
draggableTrack<.handleSubFeatures@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/DraggableHTMLFeatures.js:565:34
HTMLFeatures<.renderFeature@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/HTMLFeatures.js:1116:13
inherited@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/_base/declare.js:189:28
draggableTrack<.renderFeature@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/DraggableHTMLFeatures.js:313:23
AnnotTrack<.renderFeature@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:559:31
HTMLFeatures<.addFeatureToBlock@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/HTMLFeatures.js:674:23
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 BlockBased.js:448:13
._handleError http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/BlockBased.js:448:13
._showBlock http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/BlockBased.js:575:13
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.showVisibleBlocks/< http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/GenomeView.js:2016:27
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.showVisibleBlocks http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/GenomeView.js:2015:5
lang._hitchArgs/< http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/_base/lang.js:327:17
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signalWaiting http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:28:4
Deferred/this.resolve http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:192:5
signalDeferred http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:81:6
signalListener http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:58:4
signalWaiting http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:28:4
Deferred/this.resolve http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:192:5
signalDeferred http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:81:6
signalListener http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/Deferred.js:52:6
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onLoad http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/request/xhr.js:76:5
"

Kind regards,
Juhana K
University of Helsinki
Finland

________________________________________
From: [hidden email]<mailto:[hidden email]> <[hidden email]<mailto:[hidden email]>> on behalf of Nathan Dunn <[hidden email]<mailto:[hidden email]>>
Sent: Monday, March 6, 2017 7:30 PM
To: [hidden email]<mailto:[hidden email]>
Subject: Re: [apollo] TypeError:

Could you past any information from the javascript web console (in developer information) and tomcat server (typically catalina.out) logs associated with the error?

Also, if you have the outline of the command used to remove the annotation, that might help as well.

Thanks,

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory
[hidden email]<mailto:[hidden email]><mailto:[hidden email]>


On Mar 6, 2017, at 12:38 AM, Juhana Kammonen <[hidden email]<mailto:[hidden email]><mailto:[hidden email]>> wrote:


Dear all,

The user-created annotations area of a single scaffold (length ca. 650 kbp) in
our annotation effort started showing the following erratic symptoms:

-A red box in the User-created annotations area with the text: "Error. An
error was encountered when displaying this track. Diagnostic message.
TypeError: cfg is undefined"

-Box only comes visible when having an area from 0 bp to around 10 kbp in the
JBrowse view in this scaffold. Other scaffolds on our production server
unaffected at this point.

-Box stays there even when scrolling away from the location where it comes
visible.

-After a user reported this I suspected a corrupt annotation in the PSQL
database, so I manually removed it from the PSQL database.

-Tried "apollo clean-all" and "apollo run-local". The annotation in the
location was removed but error box and message persist.

~$ uname -a
Linux dna-marker 3.13.0-107-generic #154-Ubuntu SMP Tue Dec 20 09:57:27 UTC
2016 x86_64 x86_64 x86_64 GNU/Linux


application.properties:

app.grails.version=2.5.5
app.name=apollo
app.servlet.version=3.0
app.version=2.0.4

Kind regards,
Juhana K
University of Helsinki
Finland



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Re: TypeError:

nathandunn

Juhana,

It is a bit confusing, but JBrowse (what Apollo uses), uses 1-based externally and 0-based internally, so it would expect a 1-based GFF3 import.  My guess is that in the feature_location table you probably have an fmin of -1 somewhere, which is causing problems.  


I would recommend cleaning out the portions of the database affected and fixing the GFF3 to 1-based and re-adding, since it will effect the calculation of all of the CDS added.   

Nathan

On Mar 9, 2017, at 7:58 AM, Kammonen, Juhana <[hidden email]> wrote:


Dear Nathan,

Thank you for your message. I was able to resolve the issue. Especially the SQL line:

delete from feature_location where sequence_id in (select id from sequence s where s.name like ‘%scaffold1140%’ );

was particularly useful here.

However, an issue remains. The problematic annotation that likely caused the error in the first place begins at location 0 (zero) of the scaffold in question. When I try to add it to the User-created annotation area, nothing happens at first. When I refresh the page, the annotation has showed up into the beginning of the scaffold but the owner of the annotation is reported as "None". If I add any other annotations in that scaffold, they show the owner (my name) properly.

In any case, this information was highly useful. I don't see a need for a separate script to do this at this point but it is good to know what to do next time this error message shows.

Thank you,
Juhana K



--
Juhana Kammonen
MSc, PhD student
---
DNA Sequencing and Genomics Lab
Institute of Biotechnology
Viikinkaari 5D (Biocenter 2, 4009b)
00014 University of Helsinki
FINLAND

________________________________________
From: [hidden email] <[hidden email]> on behalf of Nathan Dunn <[hidden email]>
Sent: Tuesday, March 7, 2017 7:02 PM
To: [hidden email]
Subject: Re: [apollo] TypeError:

Juhana,

The error is here:

https://github.com/GMOD/Apollo/blob/e0aa79bdc792cdda231b910800d2f90c48dac199/client/apollo/js/View/Track/AnnotTrack.js#L169

It is typically caused because when it pulls the features in and they are incomplete.   Most likely in your SQL-script you deleted part, but not all of it.

I would typically advocate doing this from the command-line or using a web-service script to do this (we have one for deleting all features for an organism, but let us know if you want this done for a single sequence - should be pretty easy):

https://github.com/GMOD/Apollo/blob/master/docs/web_services/examples/groovy/delete_annotations_from_organism.groovy

A couple of questions:

1 - were you trying to delete all of the features from a scaffold (and if so how many?)
2 - you can figure out which one is failing this way:

When you load your tracks, open the dev window to the network tabs and filter for: AnnotationEditorService.

You should see a request like this:

[cid:726ADD5F-B6F7-41E9-A8A8-BDCC7DE21634]

and a response that looks like this:

[cid:724988B3-CEB1-4788-880C-A4D10B228372]


If you post this response (or you can figure out how the JSON is incomplete), we can probably figure that out.

In general, though, if you want to remove all of the references to a scaffold you would do something like:

delete from feature_location where sequence_id in (select id from sequence s where s.name like ‘%scaffold1140%’ );

This will disassociate them, though for completeness, doing what you did below is good practice.

Nathan

On Mar 7, 2017, at 4:18 AM, Kammonen, Juhana <[hidden email]<mailto:[hidden email]>> wrote:


Dear Nathan,

Thanks for your answer. The responses are the following

* Nothing unusual shows up at catalina.out (will not post contents here)

* I removed the annotation from PSQL database using the following in psql console (the Error box was there before these commands so they did remove the annotation but the error box remained):

"
\c production_db;
select * from feature where name like '%scaffold1140%';
delete from feature where name like '%scaffold1140%';
select * from feature_relationship where parent_feature_id = 474170;
delete from feature_relationship where parent_feature_id = 474170;
delete from feature where name like '%scaffold1140%';
select * from feature_location where feature_id = 474170;
delete from feature_location where feature_id = 474170;
delete from feature where name like '%scaffold1140%';
select * from feature_relationship where parent_feature_id = 474172;
select * from feature_relationship where child_feature_id = 474172;
delete from feature where name like '%scaffold1140%';
select * from feature_location where feature_id = 474172;
select * from feature_relationship where child_feature_id = 474172;
select * from feature_relationship where parent_feature_id = 474172;
delete from feature_relationship where parent_feature_id = 474172;
delete from feature where name like '%scaffold1140%';
select * from feature_location where feature_id = 474172;
delete from feature_location where feature_id = 474172;
delete from feature where name like '%scaffold1140%';
\q
"


* I will blow up the developer tools javascript console (Firefox, and sorry for flooding):

"
loaded WebApollo plugin  main.js:79:9
plugin HideTracksButton constructor  main.js:40:9
plugin: NeatHTMLFeatures  main.js:29:9
plugin: NeatCanvasFeatures  main.js:29:9
Use of getAttributeNode() is deprecated. Use getAttribute() instead.  dom-attr.js:36:38
Synchronous XMLHttpRequest on the main thread is deprecated because of its detrimental effects to the end user’s experience. For more help http://xhr.spec.whatwg.org/  xhr.js:176:3
Registering embedded system with ApolloGwt-2.0.  AnnotTrack.js:315:21
connection established  AnnotTrack.js:383:21
AnnotTrack<.renderExonSegments@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:169:21
draggableTrack<.handleSubFeatures@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/DraggableHTMLFeatures.js:565:34
HTMLFeatures<.renderFeature@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/HTMLFeatures.js:1116:13
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draggableTrack<.renderFeature@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/DraggableHTMLFeatures.js:313:23
AnnotTrack<.renderFeature@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:559:31
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TypeError: cfg is undefined
Stack trace:
AnnotTrack<.renderExonSegments@http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:169:21
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BlockBased.js:448:13
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._showBlock http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/BlockBased.js:575:13
.showRange http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/JBrowse/View/Track/BlockBased.js:298:13
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draggableTrack<.showRange http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/plugins/WebApollo/js/View/Track/DraggableHTMLFeatures.js:1087:9
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onLoad http://dna-marker.biocenter.helsinki.fi/apollo/21196275655859894231082821098/jbrowse/src/dojo/request/xhr.js:76:5
"

Kind regards,
Juhana K
University of Helsinki
Finland

________________________________________
From: [hidden email]<mailto:[hidden email]> <[hidden email]<mailto:[hidden email]>> on behalf of Nathan Dunn <[hidden email]<mailto:[hidden email]>>
Sent: Monday, March 6, 2017 7:30 PM
To: [hidden email]<mailto:[hidden email]>
Subject: Re: [apollo] TypeError:

Could you past any information from the javascript web console (in developer information) and tomcat server (typically catalina.out) logs associated with the error?

Also, if you have the outline of the command used to remove the annotation, that might help as well.

Thanks,

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory
[hidden email]<mailto:[hidden email]><mailto:[hidden email]>


On Mar 6, 2017, at 12:38 AM, Juhana Kammonen <[hidden email]<mailto:[hidden email]><mailto:[hidden email]>> wrote:


Dear all,

The user-created annotations area of a single scaffold (length ca. 650 kbp) in
our annotation effort started showing the following erratic symptoms:

-A red box in the User-created annotations area with the text: "Error. An
error was encountered when displaying this track. Diagnostic message.
TypeError: cfg is undefined"

-Box only comes visible when having an area from 0 bp to around 10 kbp in the
JBrowse view in this scaffold. Other scaffolds on our production server
unaffected at this point.

-Box stays there even when scrolling away from the location where it comes
visible.

-After a user reported this I suspected a corrupt annotation in the PSQL
database, so I manually removed it from the PSQL database.

-Tried "apollo clean-all" and "apollo run-local". The annotation in the
location was removed but error box and message persist.

~$ uname -a
Linux dna-marker 3.13.0-107-generic #154-Ubuntu SMP Tue Dec 20 09:57:27 UTC
2016 x86_64 x86_64 x86_64 GNU/Linux


application.properties:

app.grails.version=2.5.5
app.name=apollo
app.servlet.version=3.0
app.version=2.0.4

Kind regards,
Juhana K
University of Helsinki
Finland



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