Impossible to delete exons

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Impossible to delete exons

Jacques Dainat-3
Hello,

Is the first time I’m doing manual curation using version 2.0.8 of Webapollo. I have problem deleting exons like this one:



Indeed I get this error:

Hibernate operation: could not execute statement; SQL [n/a]; ERROR: update or delete on table "feature" violates foreign key constraint "fk_jpvdxc57abfiridcr57x8130" on table "feature_property" Detail: Key (id)=(301330) is still referenced from table "feature_property".; nested exception is org.postgresql.util.PSQLException: ERROR: update or delete on table "feature" violates foreign key constraint "fk_jpvdxc57abfiridcr57x8130" on table "feature_property" Detail: Key (id)=(301330) is still referenced from table "feature_property”.

Here is my configuration:

Version: 2.0.8
Grails version: 2.5.5
Groovy version: 2.4.4
JVM version: 1.8.0_161
Servlet Container Version: Apache Tomcat/7.0.84

With old version of Webapollo it was something possible. Something has changed recently ?

Best regards,

/Jacques






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Re: Impossible to delete exons

nathandunn

Its definitely still possible in Apollo.  

You can see it on the demo screen:  http://genomearchitect.github.io/demo/

Somehow the data must have gotten into an unusual state.  

Some questions:
1 - if you drag up another feature and delete an exon does it work? 
2 - can you change the exon boundaries?
3 - can you (if you haven’t done a lot of work on it) delete the transcript itself?
4 - if you refresh the page, you can pick out the network tab and the “get_features” method under “operations" to find the appropriate return JSON so we can see what the structure is:


5.   What are the results of:

select * from feature_property fp join feature f on f.id=fp.feature_id where fp.id= 
301330  ;

And 

select * from feature_property where id = 301330 ; 


6. What properties have been set on the transcript itself? 

7. If you haven’t bounced the database since you upgraded, it might not be a bad idea, but I can’t imagine it would be an issue. 

Feel free to send any data SQL dumps, directly to me. 

Nathan

On Mar 16, 2018, at 3:19 AM, Jacques Dainat <[hidden email]> wrote:

Hello,

Is the first time I’m doing manual curation using version 2.0.8 of Webapollo. I have problem deleting exons like this one:

<Screen Shot 2018-03-16 at 11.07.54.png>

Indeed I get this error:

Hibernate operation: could not execute statement; SQL [n/a]; ERROR: update or delete on table "feature" violates foreign key constraint "fk_jpvdxc57abfiridcr57x8130" on table "feature_property" Detail: Key (id)=(301330) is still referenced from table "feature_property".; nested exception is org.postgresql.util.PSQLException: ERROR: update or delete on table "feature" violates foreign key constraint "fk_jpvdxc57abfiridcr57x8130" on table "feature_property" Detail: Key (id)=(301330) is still referenced from table "feature_property”.

Here is my configuration:

Version: 2.0.8
Grails version: 2.5.5
Groovy version: 2.4.4
JVM version: 1.8.0_161
Servlet Container Version: Apache Tomcat/7.0.84

With old version of Webapollo it was something possible. Something has changed recently ?

Best regards,

/Jacques





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.