added synonymSgml nullable: true

[srobb1]

I was having issues adding aliases. I was getting the following error

2022-02-18 17:41:22,272 [http-bio-8080-exec-83] ERROR StackTrace  - Full Stack Trace:
org.postgresql.util.PSQLException: ERROR: null value in column "synonymsgml" violates not-null constraint
  Detail: Failing row contains (166049, 0, test, null, null).
	at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2455)
	at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2155)
	at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:288)
	at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:430)
	at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:356)
	at org.postgresql.jdbc.PgPreparedStatement.executeWithFlags(PgPreparedStatement.java:168)
	at org.postgresql.jdbc.PgPreparedStatement.executeUpdate(PgPreparedStatement.java:135)
	at org.bbop.apollo.AnnotatorController.$tt__updateFeature(AnnotatorController.groovy:268)
	at grails.plugin.cache.web.filter.PageFragmentCachingFilter.doFilter(PageFragmentCachingFilter.java:198)
	at grails.plugin.cache.web.filter.AbstractFilter.doFilter(AbstractFilter.java:63)
	at org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:449)
	at org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:365)
	at org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90)
	at org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83)
	at org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:383)
	at org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:362)
	at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125)
	at com.brandseye.cors.CorsFilter.doFilter(CorsFilter.java:82)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)

I then made the addition to the synonyms file and ran this sql alter statement

alter table synonym alter column synonymsgml drop not null;

then I got this error after restarting and trying again:

org.postgresql.util.PSQLException: ERROR: null value in column "type_id" violates not-null constraint
  Detail: Failing row contains (166058, 0, test, null, null).
        at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2455)
        at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2155)
        at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:288)
        at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:430)
        at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:356)
        at org.postgresql.jdbc.PgPreparedStatement.executeWithFlags(PgPreparedStatement.java:168)
        at org.postgresql.jdbc.PgPreparedStatement.executeUpdate(PgPreparedStatement.java:135)
        at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.executeUpdate(ResultSetReturnImpl.java:208)
        at org.hibernate.id.SequenceIdentityGenerator$Delegate.executeAndExtract(SequenceIdentityGenerator.java:111)
        at org.hibernate.id.insert.AbstractReturningDelegate.performInsert(AbstractReturningDelegate.java:58)
        at org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:3032)
        at org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:3558)
        at org.hibernate.action.internal.EntityIdentityInsertAction.execute(EntityIdentityInsertAction.java:98)
        at org.hibernate.engine.spi.ActionQueue.execute(ActionQueue.java:492)
        at org.hibernate.engine.spi.ActionQueue.addResolvedEntityInsertAction(ActionQueue.java:197)
        at org.hibernate.engine.spi.ActionQueue.addInsertAction(ActionQueue.java:181)
        at org.hibernate.engine.spi.ActionQueue.addAction(ActionQueue.java:216)
        at org.hibernate.event.internal.AbstractSaveEventListener.addInsertAction(AbstractSaveEventListener.java:324)
        at org.hibernate.event.internal.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:288)
        at org.hibernate.event.internal.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:194)
        at org.hibernate.event.internal.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:125)
        at org.hibernate.event.internal.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventListener.java:209)
        at org.hibernate.event.internal.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:194)
        at org.hibernate.event.internal.DefaultSaveOrUpdateEventListener.performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:114)
        at org.hibernate.event.internal.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:90)
        at org.hibernate.internal.SessionImpl.fireSaveOrUpdate(SessionImpl.java:684)
        at org.hibernate.internal.SessionImpl.saveOrUpdate(SessionImpl.java:676)
        at org.hibernate.internal.SessionImpl.saveOrUpdate(SessionImpl.java:671)
        at org.codehaus.groovy.grails.orm.hibernate.metaclass.SavePersistentMethod$1.doInHibernate(SavePersistentMethod.java:58)
        at org.codehaus.groovy.grails.orm.hibernate.GrailsHibernateTemplate.doExecute(GrailsHibernateTemplate.java:188)
        at org.codehaus.groovy.grails.orm.hibernate.GrailsHibernateTemplate.execute(GrailsHibernateTemplate.java:132)
        at org.codehaus.groovy.grails.orm.hibernate.metaclass.SavePersistentMethod.performSave(SavePersistentMethod.java:56)
        at org.codehaus.groovy.grails.orm.hibernate.metaclass.AbstractSavePersistentMethod.doInvokeInternal(AbstractSavePersistentMethod.java:215)
        at org.codehaus.groovy.grails.orm.hibernate.metaclass.AbstractDynamicPersistentMethod.invoke(AbstractDynamicPersistentMethod.java:69)
        at org.codehaus.groovy.grails.orm.hibernate.HibernateGormInstanceApi.save(HibernateGormInstanceApi.groovy:196)
        at org.bbop.apollo.Synonym.save(Synonym.groovy)
        at org.bbop.apollo.Synonym$save.call(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
        at org.bbop.apollo.AnnotatorController.$tt__updateFeature(AnnotatorController.groovy:268)
        at org.bbop.apollo.AnnotatorController$_updateFeature_closure3.doCall(AnnotatorController.groovy)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)

Then I ran this alter:

alter table synonym alter column type_id drop not null;

I can now add aliases.

Sofia

[garrettjstevens]

Thanks for this. I will try to review this PR this week.

[garrettjstevens]

I've been trying to replicate the original problem, but I can't seem to. Does the problem adding aliases happen with every organism and annotation you've tried, or just some of them?

[srobb1]

That stinks. I only tried with one. And now I have implemented the changes. I could undo everything and try in another organism.

[garrettjstevens]

Maybe you could try replicating it on one of the organisms on our demo instance? Don't worry about messing anything up, it's a sandbox for testing stuff out. https://genomearchitect.readthedocs.io/en/latest/Demo.html

[srobb1]

I do not get any errors in the demo. I do know why I get this on my install of the same version. Thanks.

[garrettjstevens]

I'm going to close this for now since I can't replicate the problem, and I don't know enough about this change to know if it would have other side effects. If anyone else can reproduce this, let me know.