Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

properly handle BAD track additions #28

Closed
nathandunn opened this issue Sep 23, 2014 · 3 comments
Closed

properly handle BAD track additions #28

nathandunn opened this issue Sep 23, 2014 · 3 comments
Milestone

Comments

@nathandunn
Copy link
Contributor

e.g., when importing a GFF3 file with both gene and mRNA on the same region into jbrowse, when the imported track is annotated, it causes an error, but still "adds" the annotation and leaves the database in an inconsistent state. It also is unclear what would be annotated, as well. We should disallow this type of annotation explicitly.

@nathandunn
Copy link
Contributor Author

This is the error we get:

15:13:25.506 [http-bio-8080-exec-1] DEBUG  - range: null
java.lang.NullPointerException
    at org.bbop.apollo.editor.AnnotationEditor.findNonCanonicalAcceptorDonorSpliceSites(AnnotationEditor.java:1150)
    at org.bbop.apollo.web.AnnotationEditorService.findNonCanonicalAcceptorDonorSpliceSites(AnnotationEditorService.java:2153)
    at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:4255)
    at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:1218)
    at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:1202)
    at org.bbop.apollo.web.AnnotationEditorService.doPost(AnnotationEditorService.java:367)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:647)

And the client says: "Error writing transcript: null"

@nathandunn nathandunn added this to the December 2014 Release milestone Sep 29, 2014
@nathandunn nathandunn modified the milestones: 3.0 Release - Early 2015, December 2014 Release Oct 17, 2014
@nathandunn nathandunn modified the milestones: 2.0.0, 2.0 Apr 6, 2015
@nathandunn
Copy link
Contributor Author

@deepakunni3 Feel free to kick this down the road (2.1) if it looks tough. Basically, should issue an error of some type. It might be that this is more appropriate for @cmdcolin as well.

@nathandunn nathandunn modified the milestones: 2.0.1, 2.0.0 Apr 6, 2015
@nathandunn nathandunn modified the milestones: 2.0.2, 2.1 Aug 7, 2015
@nathandunn nathandunn modified the milestones: 2.0.2, 2.0.3 Sep 10, 2015
@monicacecilia
Copy link
Member

We have not ran into this again -

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

3 participants