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GMOD / Apollo

Genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin.
http://genomearchitect.readthedocs.io/
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User-created annotations area locked by red error box "TypeError: Cannot read property 'ClassName' of undefined" #1933

Closed kammoji closed 6 years ago

kammoji commented 6 years ago

Hi,

We have a situation where 2 out of ca. 2,000 contigs in Apollo have jammed User-created annotation areas due to the error message in the attached screenshot. By "jammed" I mean that the annotations in the area cannot be viewed and no new annotations can be added.

This screenshot shows other of these two contigs. The other contigs open properly - for now.

What can cause this and what would be the steps to fix this issue aside from resetting the whole Apollo?

apollo_error_09_2018

kammoji commented 6 years ago

Oh, and here's the JavaScript console, please remove if determined unnecessary:

loaded WebApollo plugin
main.js:29 plugin: NeatHTMLFeatures
main.js:29 plugin: NeatCanvasFeatures
xhr.js:267 GET http://dna-marker.biocenter.helsinki.fi:8085/apollo/2221618391274443105171153093/jbrowse/data/names/root.json 404 (Not Found)
xhr @ xhr.js:267
dojo.xhr @ xhr.js:615
dojo.xhrGet @ xhr.js:643
constructor @ LazyTrie.js:66
(anonymous) @ declare.js:473
(anonymous) @ Browser.js:620
_milestoneFunction @ Browser.js:1988
loadNames @ Browser.js:594
(anonymous) @ Browser.js:167
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
(anonymous) @ Browser.js:323
notify @ Deferred.js:187
complete @ Deferred.js:168
resolve.callback @ Deferred.js:248
addResult @ DeferredList.js:54
(anonymous) @ DeferredList.js:37
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
(anonymous) @ Browser.js:356
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
(anonymous) @ Browser.js:585
finish @ lazyload.js:111
pollWebKit @ lazyload.js:326
setTimeout (async)
pollWebKit @ lazyload.js:335
setTimeout (async)
pollWebKit @ lazyload.js:335
setTimeout (async)
pollWebKit @ lazyload.js:335
load @ lazyload.js:247
finish @ lazyload.js:113
pollWebKit @ lazyload.js:326
setTimeout (async)
pollWebKit @ lazyload.js:335
load @ lazyload.js:247
css @ lazyload.js:365
_loadCSS @ Browser.js:585
(anonymous) @ Browser.js:352
forEach @ array.js:247
(anonymous) @ Browser.js:335
(anonymous) @ lang.js:385
runFactory @ dojo.js:1164
execModule @ dojo.js:1292
(anonymous) @ dojo.js:1330
guardCheckComplete @ dojo.js:1307
checkComplete @ dojo.js:1325
onLoadCallback @ dojo.js:1492
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
(anonymous) @ dojo.js:1655
forEach @ dojo.js:112
runDefQ @ dojo.js:1654
onLoadCallback @ dojo.js:1471
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
contextRequire @ dojo.js:849
result @ dojo.js:876
loadRenderer @ renderer.js:81
load @ renderer.js:92
injectPlugin @ dojo.js:1385
(anonymous) @ dojo.js:1196
forEach @ dojo.js:112
resolvePluginLoadQ @ dojo.js:1189
finishExec @ dojo.js:1230
execModule @ dojo.js:1293
(anonymous) @ dojo.js:1330
guardCheckComplete @ dojo.js:1307
checkComplete @ dojo.js:1325
onLoadCallback @ dojo.js:1492
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
injectPlugin @ dojo.js:1395
injectModule @ dojo.js:1465
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
(anonymous) @ dojo.js:1655
forEach @ dojo.js:112
runDefQ @ dojo.js:1654
onLoadCallback @ dojo.js:1471
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
(anonymous) @ dojo.js:1655
forEach @ dojo.js:112
runDefQ @ dojo.js:1654
onLoadCallback @ dojo.js:1471
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
(anonymous) @ dojo.js:1655
forEach @ dojo.js:112
runDefQ @ dojo.js:1654
onLoadCallback @ dojo.js:1471
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
(anonymous) @ dojo.js:1655
forEach @ dojo.js:112
runDefQ @ dojo.js:1654
onLoadCallback @ dojo.js:1471
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
(anonymous) @ dojo.js:1655
forEach @ dojo.js:112
runDefQ @ dojo.js:1654
onLoadCallback @ dojo.js:1471
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
(anonymous) @ dojo.js:1655
forEach @ dojo.js:112
runDefQ @ dojo.js:1654
onLoadCallback @ dojo.js:1471
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
(anonymous) @ dojo.js:1655
forEach @ dojo.js:112
runDefQ @ dojo.js:1654
onLoadCallback @ dojo.js:1471
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
(anonymous) @ dojo.js:1655
forEach @ dojo.js:112
runDefQ @ dojo.js:1654
onLoadCallback @ dojo.js:1471
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
contextRequire @ dojo.js:849
req @ dojo.js:143
(anonymous) @ Browser.js:325
_milestoneFunction @ Browser.js:1988
initPlugins @ Browser.js:265
(anonymous) @ Browser.js:166
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
(anonymous) @ Browser.js:2070
(anonymous) @ lang.js:385
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
(anonymous) @ all.js:68
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
(anonymous) @ Deferred.js:70
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
(anonymous) @ all.js:68
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
(anonymous) @ Deferred.js:70
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
(anonymous) @ all.js:68
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
(anonymous) @ Deferred.js:70
signalListener @ Deferred.js:37
Deferred.then.promise.then @ Deferred.js:258
signalListener @ Deferred.js:45
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:58
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
(anonymous) @ Deferred.js:70
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:58
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
handleResponse @ xhr.js:88
onLoad @ xhr.js:123
load (async)
addListeners @ xhr.js:142
xhr @ xhr.js:223
load @ JB_json_v1.js:45
(anonymous) @ ConfigManager.js:178
signalListener @ Deferred.js:37
Deferred.then.promise.then @ Deferred.js:258
_loadInclude @ ConfigManager.js:170
(anonymous) @ ConfigManager.js:146
map @ array.js:289
_loadRecur @ ConfigManager.js:144
(anonymous) @ ConfigManager.js:148
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:58
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
(anonymous) @ Deferred.js:70
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:58
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
handleResponse @ xhr.js:88
onLoad @ xhr.js:123
load (async)
addListeners @ xhr.js:142
xhr @ xhr.js:223
load @ JB_json_v1.js:45
(anonymous) @ ConfigManager.js:178
signalListener @ Deferred.js:37
Deferred.then.promise.then @ Deferred.js:258
_loadInclude @ ConfigManager.js:170
(anonymous) @ ConfigManager.js:146
map @ array.js:289
_loadRecur @ ConfigManager.js:144
(anonymous) @ ConfigManager.js:148
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:58
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
(anonymous) @ Deferred.js:70
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:58
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
handleResponse @ xhr.js:88
onLoad @ xhr.js:123
load (async)
addListeners @ xhr.js:142
xhr @ xhr.js:223
load @ JB_json_v1.js:45
(anonymous) @ ConfigManager.js:178
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
(anonymous) @ Util.js:261
runFactory @ dojo.js:1164
execModule @ dojo.js:1292
(anonymous) @ dojo.js:1330
guardCheckComplete @ dojo.js:1307
checkComplete @ dojo.js:1325
onLoadCallback @ dojo.js:1492
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
contextRequire @ dojo.js:849
req @ dojo.js:143
loadJS @ Util.js:250
_getConfigAdaptor @ ConfigManager.js:95
_loadInclude @ ConfigManager.js:169
(anonymous) @ ConfigManager.js:146
map @ array.js:289
_loadRecur @ ConfigManager.js:144
_loadIncludes @ ConfigManager.js:163
(anonymous) @ ConfigManager.js:62
getFinalConfig @ ConfigManager.js:78
(anonymous) @ Browser.js:2047
_milestoneFunction @ Browser.js:1988
loadConfig @ Browser.js:2045
(anonymous) @ Browser.js:157
callback @ ready.js:121
onEvent @ ready.js:47
processQ @ domReady.js:49
detectReady @ domReady.js:62
xhr.js:440 ErrorCtor {message: "Unable to load data/names/root.json status: 404", response: {…}, status: 404, responseText: "<!DOCTYPE html><html><head><title>Apache Tomcat/8.…line"><h3>Apache Tomcat/8.0.33</h3></body></html>", xhr: XMLHttpRequest, …}message: "Unable to load data/names/root.json status: 404"response: {url: "data/names/root.json", options: TMP, getHeader: ƒ, xhr: XMLHttpRequest, loaded: 1122, …}responseText: "<!DOCTYPE html><html><head><title>Apache Tomcat/8.0.33 - Error report</title><style type="text/css">H1 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;} H2 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;} H3 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:14px;} BODY {font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;} B {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;} P {font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A {color : black;}A.name {color : black;}.line {height: 1px; background-color: #525D76; border: none;}</style> </head><body><h1>HTTP Status 404 - &quot;/WEB-INF/grails-app/views/jbrowse/data.gsp&quot; not found.</h1><div class="line"></div><p><b>type</b> Status report</p><p><b>message</b> <u>&quot;/WEB-INF/grails-app/views/jbrowse/data.gsp&quot; not found.</u></p><p><b>description</b> <u>The requested resource is not available.</u></p><hr class="line"><h3>Apache Tomcat/8.0.33</h3></body></html>"status: 404xhr: XMLHttpRequest {onreadystatechange: null, readyState: 4, timeout: 0, withCredentials: false, upload: XMLHttpRequestUpload, …}stack: "Error: Unable to load data/names/root.json status: 404↵    at new ErrorCtor (http://dna-marker.biocenter.helsinki.fi:8085/apollo/2221618391274443105171153093/jbrowse/src/dojo/errors/create.js:13:21)↵    at Deferred.handleResponse (http://dna-marker.biocenter.helsinki.fi:8085/apollo/2221618391274443105171153093/jbrowse/src/dojo/request/xhr.js:94:14)↵    at XMLHttpRequest.onLoad (http://dna-marker.biocenter.helsinki.fi:8085/apollo/2221618391274443105171153093/jbrowse/src/dojo/request/xhr.js:123:9)"__proto__: Error
_deferError @ xhr.js:440
(anonymous) @ xhr.js:400
notify @ Deferred.js:187
complete @ Deferred.js:168
reject.errback @ Deferred.js:263
notify @ Deferred.js:202
complete @ Deferred.js:168
reject.errback @ Deferred.js:263
notify @ Deferred.js:202
complete @ Deferred.js:168
reject.errback @ Deferred.js:263
(anonymous) @ xhr.js:635
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.reject.reject @ Deferred.js:219
signalDeferred @ Deferred.js:84
signalListener @ Deferred.js:58
signalWaiting @ Deferred.js:28
Deferred.reject.reject @ Deferred.js:219
signalDeferred @ Deferred.js:84
signalListener @ Deferred.js:58
signalWaiting @ Deferred.js:28
Deferred.reject.reject @ Deferred.js:219
signalDeferred @ Deferred.js:84
signalListener @ Deferred.js:55
signalWaiting @ Deferred.js:28
Deferred.reject.reject @ Deferred.js:219
signalDeferred @ Deferred.js:84
signalListener @ Deferred.js:58
signalWaiting @ Deferred.js:28
Deferred.reject.reject @ Deferred.js:219
handleResponse @ xhr.js:95
onLoad @ xhr.js:123
load (async)
addListeners @ xhr.js:142
xhr @ xhr.js:223
dojo.xhr @ xhr.js:615
dojo.xhrGet @ xhr.js:643
constructor @ LazyTrie.js:66
(anonymous) @ declare.js:473
(anonymous) @ Browser.js:620
_milestoneFunction @ Browser.js:1988
loadNames @ Browser.js:594
(anonymous) @ Browser.js:167
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
(anonymous) @ Browser.js:323
notify @ Deferred.js:187
complete @ Deferred.js:168
resolve.callback @ Deferred.js:248
addResult @ DeferredList.js:54
(anonymous) @ DeferredList.js:37
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
(anonymous) @ Browser.js:356
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
(anonymous) @ Browser.js:585
finish @ lazyload.js:111
pollWebKit @ lazyload.js:326
setTimeout (async)
pollWebKit @ lazyload.js:335
setTimeout (async)
pollWebKit @ lazyload.js:335
setTimeout (async)
pollWebKit @ lazyload.js:335
load @ lazyload.js:247
finish @ lazyload.js:113
pollWebKit @ lazyload.js:326
setTimeout (async)
pollWebKit @ lazyload.js:335
load @ lazyload.js:247
css @ lazyload.js:365
_loadCSS @ Browser.js:585
(anonymous) @ Browser.js:352
forEach @ array.js:247
(anonymous) @ Browser.js:335
(anonymous) @ lang.js:385
runFactory @ dojo.js:1164
execModule @ dojo.js:1292
(anonymous) @ dojo.js:1330
guardCheckComplete @ dojo.js:1307
checkComplete @ dojo.js:1325
onLoadCallback @ dojo.js:1492
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
(anonymous) @ dojo.js:1655
forEach @ dojo.js:112
runDefQ @ dojo.js:1654
onLoadCallback @ dojo.js:1471
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
contextRequire @ dojo.js:849
result @ dojo.js:876
loadRenderer @ renderer.js:81
load @ renderer.js:92
injectPlugin @ dojo.js:1385
(anonymous) @ dojo.js:1196
forEach @ dojo.js:112
resolvePluginLoadQ @ dojo.js:1189
finishExec @ dojo.js:1230
execModule @ dojo.js:1293
(anonymous) @ dojo.js:1330
guardCheckComplete @ dojo.js:1307
checkComplete @ dojo.js:1325
onLoadCallback @ dojo.js:1492
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
injectPlugin @ dojo.js:1395
injectModule @ dojo.js:1465
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
(anonymous) @ dojo.js:1655
forEach @ dojo.js:112
runDefQ @ dojo.js:1654
onLoadCallback @ dojo.js:1471
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
(anonymous) @ dojo.js:1655
forEach @ dojo.js:112
runDefQ @ dojo.js:1654
onLoadCallback @ dojo.js:1471
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
(anonymous) @ dojo.js:1655
forEach @ dojo.js:112
runDefQ @ dojo.js:1654
onLoadCallback @ dojo.js:1471
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
(anonymous) @ dojo.js:1655
forEach @ dojo.js:112
runDefQ @ dojo.js:1654
onLoadCallback @ dojo.js:1471
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
(anonymous) @ dojo.js:1655
forEach @ dojo.js:112
runDefQ @ dojo.js:1654
onLoadCallback @ dojo.js:1471
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
(anonymous) @ dojo.js:1655
forEach @ dojo.js:112
runDefQ @ dojo.js:1654
onLoadCallback @ dojo.js:1471
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
(anonymous) @ dojo.js:1655
forEach @ dojo.js:112
runDefQ @ dojo.js:1654
onLoadCallback @ dojo.js:1471
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
(anonymous) @ dojo.js:1655
forEach @ dojo.js:112
runDefQ @ dojo.js:1654
onLoadCallback @ dojo.js:1471
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
contextRequire @ dojo.js:849
req @ dojo.js:143
(anonymous) @ Browser.js:325
_milestoneFunction @ Browser.js:1988
initPlugins @ Browser.js:265
(anonymous) @ Browser.js:166
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
(anonymous) @ Browser.js:2070
(anonymous) @ lang.js:385
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
(anonymous) @ all.js:68
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
(anonymous) @ Deferred.js:70
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
(anonymous) @ all.js:68
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
(anonymous) @ Deferred.js:70
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
(anonymous) @ all.js:68
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
(anonymous) @ Deferred.js:70
signalListener @ Deferred.js:37
Deferred.then.promise.then @ Deferred.js:258
signalListener @ Deferred.js:45
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:58
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
(anonymous) @ Deferred.js:70
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:58
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
handleResponse @ xhr.js:88
onLoad @ xhr.js:123
load (async)
addListeners @ xhr.js:142
xhr @ xhr.js:223
load @ JB_json_v1.js:45
(anonymous) @ ConfigManager.js:178
signalListener @ Deferred.js:37
Deferred.then.promise.then @ Deferred.js:258
_loadInclude @ ConfigManager.js:170
(anonymous) @ ConfigManager.js:146
map @ array.js:289
_loadRecur @ ConfigManager.js:144
(anonymous) @ ConfigManager.js:148
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:58
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
(anonymous) @ Deferred.js:70
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:58
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
handleResponse @ xhr.js:88
onLoad @ xhr.js:123
load (async)
addListeners @ xhr.js:142
xhr @ xhr.js:223
load @ JB_json_v1.js:45
(anonymous) @ ConfigManager.js:178
signalListener @ Deferred.js:37
Deferred.then.promise.then @ Deferred.js:258
_loadInclude @ ConfigManager.js:170
(anonymous) @ ConfigManager.js:146
map @ array.js:289
_loadRecur @ ConfigManager.js:144
(anonymous) @ ConfigManager.js:148
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:58
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
(anonymous) @ Deferred.js:70
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:58
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
handleResponse @ xhr.js:88
onLoad @ xhr.js:123
load (async)
addListeners @ xhr.js:142
xhr @ xhr.js:223
load @ JB_json_v1.js:45
(anonymous) @ ConfigManager.js:178
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
(anonymous) @ Util.js:261
runFactory @ dojo.js:1164
execModule @ dojo.js:1292
(anonymous) @ dojo.js:1330
guardCheckComplete @ dojo.js:1307
checkComplete @ dojo.js:1325
onLoadCallback @ dojo.js:1492
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
contextRequire @ dojo.js:849
req @ dojo.js:143
loadJS @ Util.js:250
_getConfigAdaptor @ ConfigManager.js:95
_loadInclude @ ConfigManager.js:169
(anonymous) @ ConfigManager.js:146
map @ array.js:289
_loadRecur @ ConfigManager.js:144
_loadIncludes @ ConfigManager.js:163
(anonymous) @ ConfigManager.js:62
getFinalConfig @ ConfigManager.js:78
(anonymous) @ Browser.js:2047
_milestoneFunction @ Browser.js:1988
loadConfig @ Browser.js:2045
(anonymous) @ Browser.js:157
callback @ ready.js:121
onEvent @ ready.js:47
processQ @ domReady.js:49
detectReady @ domReady.js:62
GenomeView.js:62 >>> view constructor
xhr.js:233 [Deprecation] Synchronous XMLHttpRequest on the main thread is deprecated because of its detrimental effects to the end user's experience. For more help, check https://xhr.spec.whatwg.org/.
xhr @ xhr.js:233
dojo.xhr @ xhr.js:615
dojo.rawXhrPost.dojo.xhrPost @ xhr.js:652
getPermission @ AnnotTrack.js:4972
setViewInfo @ AnnotTrack.js:192
(anonymous) @ GenomeView.js:2284
(anonymous) @ lang.js:385
(anonymous) @ GenomeView.js:2310
(anonymous) @ Browser.js:1803
(anonymous) @ lang.js:385
runFactory @ dojo.js:1164
execModule @ dojo.js:1292
(anonymous) @ dojo.js:1330
guardCheckComplete @ dojo.js:1307
checkComplete @ dojo.js:1325
onLoadCallback @ dojo.js:1492
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
contextRequire @ dojo.js:849
req @ dojo.js:143
getStore @ Browser.js:1786
renderTrack @ GenomeView.js:2307
browser.view.renderTrack @ main.js:62
(anonymous) @ GenomeView.js:229
(anonymous) @ lang.js:385
_normalizedCreator @ Container.js:343
_normalizedCreator @ Selector.js:155
insertNodes @ Container.js:192
insertNodes @ Selector.js:172
showTracks @ GenomeView.js:2092
(anonymous) @ lang.js:383
dispatcher @ aspect.js:101
on.emit @ on.js:344
on.emit @ on.js:385
emit @ Evented.js:32
publish @ topic.js:25
publish @ Browser.js:1914
(anonymous) @ Browser.js:2608
(anonymous) @ lang.js:385
(anonymous) @ Browser.js:2016
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
(anonymous) @ Browser.js:988
(anonymous) @ lang.js:385
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
(anonymous) @ Browser.js:2356
(anonymous) @ lang.js:385
runFactory @ dojo.js:1164
execModule @ dojo.js:1292
(anonymous) @ dojo.js:1330
guardCheckComplete @ dojo.js:1307
checkComplete @ dojo.js:1325
onLoadCallback @ dojo.js:1492
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
contextRequire @ dojo.js:849
req @ dojo.js:143
(anonymous) @ Browser.js:2331
_milestoneFunction @ Browser.js:1988
createTrackList @ Browser.js:2322
(anonymous) @ Browser.js:976
(anonymous) @ lang.js:385
(anonymous) @ Browser.js:2016
signalListener @ Deferred.js:37
Deferred.then.promise.then @ Deferred.js:258
afterMilestone @ Browser.js:2014
(anonymous) @ Browser.js:975
(anonymous) @ lang.js:385
(anonymous) @ Browser.js:2016
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
(anonymous) @ Browser.js:540
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:58
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
handleResponse @ xhr.js:88
onLoad @ xhr.js:123
load (async)
addListeners @ xhr.js:142
xhr @ xhr.js:223
(anonymous) @ Browser.js:532
_milestoneFunction @ Browser.js:1988
loadRefSeqs @ Browser.js:516
(anonymous) @ Browser.js:171
signalListener @ Deferred.js:37
Deferred.then.promise.then @ Deferred.js:258
(anonymous) @ Browser.js:168
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
(anonymous) @ Browser.js:323
notify @ Deferred.js:187
complete @ Deferred.js:168
resolve.callback @ Deferred.js:248
addResult @ DeferredList.js:54
(anonymous) @ DeferredList.js:37
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
(anonymous) @ Browser.js:356
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
(anonymous) @ Browser.js:585
finish @ lazyload.js:111
pollWebKit @ lazyload.js:326
setTimeout (async)
pollWebKit @ lazyload.js:335
setTimeout (async)
pollWebKit @ lazyload.js:335
setTimeout (async)
pollWebKit @ lazyload.js:335
load @ lazyload.js:247
finish @ lazyload.js:113
pollWebKit @ lazyload.js:326
setTimeout (async)
pollWebKit @ lazyload.js:335
load @ lazyload.js:247
css @ lazyload.js:365
_loadCSS @ Browser.js:585
(anonymous) @ Browser.js:352
forEach @ array.js:247
(anonymous) @ Browser.js:335
(anonymous) @ lang.js:385
runFactory @ dojo.js:1164
execModule @ dojo.js:1292
(anonymous) @ dojo.js:1330
guardCheckComplete @ dojo.js:1307
checkComplete @ dojo.js:1325
onLoadCallback @ dojo.js:1492
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
(anonymous) @ dojo.js:1655
forEach @ dojo.js:112
runDefQ @ dojo.js:1654
onLoadCallback @ dojo.js:1471
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
contextRequire @ dojo.js:849
result @ dojo.js:876
loadRenderer @ renderer.js:81
load @ renderer.js:92
injectPlugin @ dojo.js:1385
(anonymous) @ dojo.js:1196
forEach @ dojo.js:112
resolvePluginLoadQ @ dojo.js:1189
finishExec @ dojo.js:1230
execModule @ dojo.js:1293
(anonymous) @ dojo.js:1330
guardCheckComplete @ dojo.js:1307
checkComplete @ dojo.js:1325
onLoadCallback @ dojo.js:1492
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
injectPlugin @ dojo.js:1395
injectModule @ dojo.js:1465
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
(anonymous) @ dojo.js:1655
forEach @ dojo.js:112
runDefQ @ dojo.js:1654
onLoadCallback @ dojo.js:1471
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
(anonymous) @ dojo.js:1655
forEach @ dojo.js:112
runDefQ @ dojo.js:1654
onLoadCallback @ dojo.js:1471
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
(anonymous) @ dojo.js:1655
forEach @ dojo.js:112
runDefQ @ dojo.js:1654
onLoadCallback @ dojo.js:1471
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
(anonymous) @ dojo.js:1655
forEach @ dojo.js:112
runDefQ @ dojo.js:1654
onLoadCallback @ dojo.js:1471
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
(anonymous) @ dojo.js:1655
forEach @ dojo.js:112
runDefQ @ dojo.js:1654
onLoadCallback @ dojo.js:1471
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
(anonymous) @ dojo.js:1655
forEach @ dojo.js:112
runDefQ @ dojo.js:1654
onLoadCallback @ dojo.js:1471
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
(anonymous) @ dojo.js:1655
forEach @ dojo.js:112
runDefQ @ dojo.js:1654
onLoadCallback @ dojo.js:1471
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
(anonymous) @ dojo.js:1655
forEach @ dojo.js:112
runDefQ @ dojo.js:1654
onLoadCallback @ dojo.js:1471
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
contextRequire @ dojo.js:849
req @ dojo.js:143
(anonymous) @ Browser.js:325
_milestoneFunction @ Browser.js:1988
initPlugins @ Browser.js:265
(anonymous) @ Browser.js:166
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
(anonymous) @ Browser.js:2070
(anonymous) @ lang.js:385
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
(anonymous) @ all.js:68
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
(anonymous) @ Deferred.js:70
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
(anonymous) @ all.js:68
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
(anonymous) @ Deferred.js:70
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
(anonymous) @ all.js:68
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
(anonymous) @ Deferred.js:70
signalListener @ Deferred.js:37
Deferred.then.promise.then @ Deferred.js:258
signalListener @ Deferred.js:45
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:58
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
(anonymous) @ Deferred.js:70
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:58
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
handleResponse @ xhr.js:88
onLoad @ xhr.js:123
load (async)
addListeners @ xhr.js:142
xhr @ xhr.js:223
load @ JB_json_v1.js:45
(anonymous) @ ConfigManager.js:178
signalListener @ Deferred.js:37
Deferred.then.promise.then @ Deferred.js:258
_loadInclude @ ConfigManager.js:170
(anonymous) @ ConfigManager.js:146
map @ array.js:289
_loadRecur @ ConfigManager.js:144
(anonymous) @ ConfigManager.js:148
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:58
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
(anonymous) @ Deferred.js:70
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:58
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
handleResponse @ xhr.js:88
onLoad @ xhr.js:123
load (async)
addListeners @ xhr.js:142
xhr @ xhr.js:223
load @ JB_json_v1.js:45
(anonymous) @ ConfigManager.js:178
signalListener @ Deferred.js:37
Deferred.then.promise.then @ Deferred.js:258
_loadInclude @ ConfigManager.js:170
(anonymous) @ ConfigManager.js:146
map @ array.js:289
_loadRecur @ ConfigManager.js:144
(anonymous) @ ConfigManager.js:148
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:58
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
(anonymous) @ Deferred.js:70
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:58
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
handleResponse @ xhr.js:88
onLoad @ xhr.js:123
load (async)
addListeners @ xhr.js:142
xhr @ xhr.js:223
load @ JB_json_v1.js:45
(anonymous) @ ConfigManager.js:178
signalListener @ Deferred.js:37
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
signalDeferred @ Deferred.js:81
signalListener @ Deferred.js:52
signalWaiting @ Deferred.js:28
Deferred.resolve @ Deferred.js:192
(anonymous) @ Util.js:261
runFactory @ dojo.js:1164
execModule @ dojo.js:1292
(anonymous) @ dojo.js:1330
guardCheckComplete @ dojo.js:1307
checkComplete @ dojo.js:1325
onLoadCallback @ dojo.js:1492
onLoad @ dojo.js:1745
load (async)
domOn @ dojo.js:1697
req.injectUrl @ dojo.js:1748
injectModule @ dojo.js:1580
forEach @ dojo.js:112
(anonymous) @ dojo.js:786
guardCheckComplete @ dojo.js:1307
injectDependencies @ dojo.js:785
contextRequire @ dojo.js:849
req @ dojo.js:143
loadJS @ Util.js:250
_getConfigAdaptor @ ConfigManager.js:95
_loadInclude @ ConfigManager.js:169
(anonymous) @ ConfigManager.js:146
map @ array.js:289
_loadRecur @ ConfigManager.js:144
_loadIncludes @ ConfigManager.js:163
(anonymous) @ ConfigManager.js:62
getFinalConfig @ ConfigManager.js:78
(anonymous) @ Browser.js:2047
_milestoneFunction @ Browser.js:1988
loadConfig @ Browser.js:2045
(anonymous) @ Browser.js:157
callback @ ready.js:121
onEvent @ ready.js:47
processQ @ domReady.js:49
detectReady @ domReady.js:62
AnnotTrack.js:309 Registering Apollo listeners.
AnnotTrack.js:413 connection established
BlockBased.js:457 TypeError: Cannot read property 'className' of undefined
    at Object.renderExonSegments (http://dna-marker.biocenter.helsinki.fi:8085/apollo/2221618391274443105171153093/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:169:36)
    at Object.handleSubFeatures (http://dna-marker.biocenter.helsinki.fi:8085/apollo/2221618391274443105171153093/jbrowse/plugins/WebApollo/js/View/Track/DraggableHTMLFeatures.js:565:39)
    at Object.renderFeature (http://dna-marker.biocenter.helsinki.fi:8085/apollo/2221618391274443105171153093/jbrowse/src/JBrowse/View/Track/HTMLFeatures.js:1145:26)
    at Object.inherited (http://dna-marker.biocenter.helsinki.fi:8085/apollo/2221618391274443105171153093/jbrowse/src/dojo/_base/declare.js:214:30)
    at Object.renderFeature (http://dna-marker.biocenter.helsinki.fi:8085/apollo/2221618391274443105171153093/jbrowse/plugins/WebApollo/js/View/Track/DraggableHTMLFeatures.js:313:28)
    at Object.renderFeature (http://dna-marker.biocenter.helsinki.fi:8085/apollo/2221618391274443105171153093/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:613:77)
    at Object.addFeatureToBlock (http://dna-marker.biocenter.helsinki.fi:8085/apollo/2221618391274443105171153093/jbrowse/src/JBrowse/View/Track/HTMLFeatures.js:699:36)
    at Object.<anonymous> (http://dna-marker.biocenter.helsinki.fi:8085/apollo/2221618391274443105171153093/jbrowse/src/JBrowse/View/Track/HTMLFeatures.js:639:38)
    at http://dna-marker.biocenter.helsinki.fi:8085/apollo/2221618391274443105171153093/jbrowse/src/dojo/_base/lang.js:385:55
    at Object.getFeatures (http://dna-marker.biocenter.helsinki.fi:8085/apollo/2221618391274443105171153093/jbrowse/plugins/WebApollo/js/Store/SeqFeature/ScratchPad.js:69:17) TypeError: Cannot read property 'className' of undefined
    at Object.renderExonSegments (AnnotTrack.js:169)
    at Object.handleSubFeatures (DraggableHTMLFeatures.js:565)
    at Object.renderFeature (HTMLFeatures.js:1145)
    at Object.inherited (declare.js:214)
    at Object.renderFeature (DraggableHTMLFeatures.js:313)
    at Object.renderFeature (AnnotTrack.js:613)
    at Object.addFeatureToBlock (HTMLFeatures.js:699)
    at Object.<anonymous> (HTMLFeatures.js:639)
    at lang.js:385
    at Object.getFeatures (ScratchPad.js:69)
nathandunn commented 6 years ago

@kammoji Agreed that this is a pain. To clarify, only two of your sequences are problematic?

Usually its because you have imported ill-formed GFF3 (an exon missing a gene, etc.)

If so, you can delete features off of those individual scaffolds and re-import them (I've had to do this before).

I'll see if I can't put together a SQL script for this, or modify the web services.

kammoji commented 6 years ago

@nathandunn Thank you. Yes, only two of our reference sequences report this.

It is quite likely that we've had an ill-formed GFF3.

Both of the sequences showing the error were OK at first, but the error boxes started appearing in the middle of editing existing annotations.

A web-service to do what you describe would be highly useful if this starts happening in other sequences as well. At least I would feel more comfortable using your pipeline than trying to tamper with the existing scripts or the database myself.

nathandunn commented 6 years ago

@kammoji if you pull in master, you should be able to specify sequences now: 

./delete_annotations_from_organism.groovy -organismname Human -destinationurl http://localhost:8080/apollo -adminusername demo@demo.com -adminpassword demo -sequences chr1,chr2
kammoji commented 6 years ago

@nathandunn thank you for the swift replies and actions. Will pull in master and try this :)

This ticket can be closed now, as you did.

nathandunn commented 6 years ago

Sounds good. Please re-open if you have any problems.