Comments (16)
Do we know what version this is?
I think you are correct that it is definitely a session error that likely occurs at the first .substring call. Not sure when we should schedule this.
if (setTranslationEnd && translationTable != null) {
String mrna = getSession().getResiduesWithAlterationsAndFrameshifts(transcript);
if (mrna == null || mrna.equals("null")) {
return;
}
int stopCodonCount = 0;
for (int i = transcript.convertSourceCoordinateToLocalCoordinate(translationStart); i < transcript.getLength(); i += 3) {
if (i + 3 > mrna.length()) {
break;
}
String codon = mrna.substring(i, i + 3);
if (translationTable.getStopCodons().contains(codon)) {
if (readThroughStopCodon && ++stopCodonCount < 2) {
from apollo.
I don't have a better answer than "I'm pretty sure they are using the 2014-04-03 release.
And I also don't have a better option for when we should schedule this; not sure whether moving it to be done "earlier" would affect the rest of the process.
Apologies for the less-than-helpful answers.
from apollo.
I see behavior like that when there is an error on the back-end that causes the interface to get out of sync. We probably need more log files that occurred prior to this error.
If there is a way we could get more information on how to reliably get here, that would be great.
from apollo.
mmmm... I'll ask.
from apollo.
This is what the user was doing when he got the error log I pasted above:
"...the most obvious thing is that I simply cannot change the boundaries of an exon. It comes and goes, and sometimes reloading fixes it (I've already emptied the cache several times). Sometimes completely restarting the browser or WebApollo page does it, but soon I'll get stuck with an exon whose boundaries I cannot change. Strangely, sometimes when I restart it shows the boundary changed. Sometimes I can't elevate an exon or model into the user-generated level to edit, but again, if I restart sometimes it actually did elevate it, just did not show it. “
…"when I try it either does nothing, or when I just now tried to delete that exon to try to build it anew, I got the error message 'Feature with unique name 2D7459743AD9E6797BE82B6D2688536F not found'."
This happened using an instance from i5K@NAL (USDA). Waiting to hear the version they were using to be 100% sure.
from apollo.
This instance is using Web Apollo version: WebApollo-2013-11-22
from apollo.
I wonder if this is related to #27 ?
from apollo.
I don't think it is related.
Today I have been receiving this error quite regularly while attempting to delete features from the User-Created Annotation area (using the Demo instance). Steps taken:
- Select entire feature
- Delete
- The result is that the deleted feature stays visible on the screen. The error log follows:
SyntaxError: Unexpected token < {stack: (...), message: "Unexpected token <"} "SyntaxError: Unexpected token <
at declare.handleError (http://icebox.lbl.gov/WebApolloDemo/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:4132:54)
at http://icebox.lbl.gov/WebApolloDemo/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:5578:19
at signalListener (http://icebox.lbl.gov/WebApolloDemo/jbrowse/src/dojo/Deferred.js:37:21)
at signalWaiting (http://icebox.lbl.gov/WebApolloDemo/jbrowse/src/dojo/Deferred.js:28:4)
at reject.reject (http://icebox.lbl.gov/WebApolloDemo/jbrowse/src/dojo/Deferred.js:219:5)
at signalDeferred (http://icebox.lbl.gov/WebApolloDemo/jbrowse/src/dojo/Deferred.js:84:15)
at signalListener (http://icebox.lbl.gov/WebApolloDemo/jbrowse/src/dojo/Deferred.js:58:4)
at signalWaiting (http://icebox.lbl.gov/WebApolloDemo/jbrowse/src/dojo/Deferred.js:28:4)
at reject.reject (http://icebox.lbl.gov/WebApolloDemo/jbrowse/src/dojo/Deferred.js:219:5)
at signalDeferred (http://icebox.lbl.gov/WebApolloDemo/jbrowse/src/dojo/Deferred.js:84:15)
----------------------------------------
rejected at signalDeferred (http://icebox.lbl.gov/WebApolloDemo/jbrowse/src/dojo/Deferred.js:84:15)
at signalListener (http://icebox.lbl.gov/WebApolloDemo/jbrowse/src/dojo/Deferred.js:55:5)
at signalWaiting (http://icebox.lbl.gov/WebApolloDemo/jbrowse/src/dojo/Deferred.js:28:4)
at reject.reject (http://icebox.lbl.gov/WebApolloDemo/jbrowse/src/dojo/Deferred.js:219:5)
at signalDeferred (http://icebox.lbl.gov/WebApolloDemo/jbrowse/src/dojo/Deferred.js:84:15)
at signalListener (http://icebox.lbl.gov/WebApolloDemo/jbrowse/src/dojo/Deferred.js:58:4)
at signalWaiting (http://icebox.lbl.gov/WebApolloDemo/jbrowse/src/dojo/Deferred.js:28:4)
at reject.reject (http://icebox.lbl.gov/WebApolloDemo/jbrowse/src/dojo/Deferred.js:219:5)
at signalDeferred (http://icebox.lbl.gov/WebApolloDemo/jbrowse/src/dojo/Deferred.js:84:15)
at signalListener (http://icebox.lbl.gov/WebApolloDemo/jbrowse/src/dojo/Deferred.js:55:5)
----------------------------------------
Error
at Promise.then.promise.then (http://icebox.lbl.gov/WebApolloDemo/jbrowse/src/dojo/Deferred.js:252:24)
at declare.executeUpdateOperation (http://icebox.lbl.gov/WebApolloDemo/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:5570:12)
at declare.deleteAnnotations (http://icebox.lbl.gov/WebApolloDemo/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:1487:15)
at declare.deleteSelectedFeatures (http://icebox.lbl.gov/WebApolloDemo/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:1413:14)
at annot_context_menu.addChild.dijit.MenuItem.onClick (http://icebox.lbl.gov/WebApolloDemo/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:4347:29)
at declare.onItemClick (http://icebox.lbl.gov/WebApolloDemo/jbrowse/src/dijit/_MenuBase.js:258:46)
at HTMLTableRowElement.<anonymous> (http://icebox.lbl.gov/WebApolloDemo/jbrowse/src/dijit/_MenuBase.js:65:10)
at HTMLTableSectionElement.<anonymous> (http://icebox.lbl.gov/WebApolloDemo/jbrowse/src/dojo/on.js:198:36)
at HTMLTableSectionElement.<anonymous> (http://icebox.lbl.gov/WebApolloDemo/jbrowse/src/dijit/a11yclick.js:84:15)"
Then, if trying to delete the "already deleted" feature, the following error appears (example):
ERROR:
AnnotTrack.js:4129 Object {responseText: "{"error":"Feature with unique name FB5DC18438C46884AD69E18D1C7027EB not found"}"}
AnnotTrack.js:4131 undefined
from apollo.
@nathandunn it appears we lost the ErrorReportValve class in the conversion to 1.x
it's not in our codebase anymore. that's at least causing part of the problem that moni refers to above
from apollo.
@cmdcolin Thanks.
from apollo.
@cmdcolin I think that this code is working correctly. I got rid of CustomLogValve as log4j should replace it and we should handle 500 errors properly. I think that this is related to incorrect deletion of features.
@monicacecilia I think that this goes away in 2.0, but if you have a specific use-case or it is blocking we should fix this.
This is the error string: handleError: function(response) {
console.log("ERROR: ");
// error on the next line
console.log(response); // in Firebug, allows retrieval of stack trace,
// jump to code, etc.
console.log(response.stack);
var error = eval('(' + response.responseText + ')');
// var error = response.error ? response : eval('(' +
// response.responseText + ')');
if (error && error.error) {
alert(error.error);
return false;
}
},
from apollo.
@nathandunn Thanks! Other than being greatly annoying - because the only way to fix it is to refresh the window - I don't think it is a show-stopper. May almighty 2.0 save us.
from apollo.
@nathandunn I think the handleError code is expecting JSON and it's getting something more like HTML which is why there is the "syntax error" from Moni's error log.
I never really checked it out before but the old ErrorValveReporter class was seemingly converting the normal HTML response object to org.apache.catalina.connector.Response which i guess is either plain text or json or similar
Maybe log4j has something like this?
Edit: in any case this error handling should probably be made into a new issue
from apollo.
@cmdcolin Grails handles these correctly. Conversely, the webappollo client should be checking for a 500 error.
from apollo.
ok. well I'll create a new issue for the error logging then.
from apollo.
should be a non-issue in 2.0.0
from apollo.
Related Issues (20)
- GUI allows to change tracks order
- Apollo Search tab to get a parameter box HOT 1
- Apollo Search tab shows alignment and picture
- Unable to create combination tracks HOT 2
- log4j vulnerability: afaict we're safe? HOT 6
- imported annotations not populating annotations tab HOT 12
- Get gene sequence HOT 2
- CDS features not appearing when written via annotations._check_write HOT 1
- Upgrade to more modern versions of dependencies? HOT 3
- Add pop up to Fmin and Fmax radial button area in annotator panel
- How to install Apollo in Windows?
- [Feature request] Update owner info from web services
- Download all the manual curation history from Apollo? HOT 1
- new install error? HOT 2
- High vulnerability caused by Apache Shiro HOT 7
- OpenID/Oath support HOT 1
- Web service calls for ShowStatus and Update status not working as expected HOT 1
- Request: Video Tutorial for configuring with H2 Apollo (and perhaps any of the other two too)
- Refactor to support Postgres greater than 11 HOT 3
- IT just sent us the latest vulnerability report. Two dependencies need updating. HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from apollo.