Apollo deploy issue

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Apollo deploy issue

Shane McCoy
Hello! I'm having an issue with deploying the production of an apollo.war. 
Apollo 2.0.4

Apollo will deploy fine before I run these scripts for Chado,

$ perl Makefile.PL
$ make 
$ sudo make install
$ Apollo/scripts/load_chado_schema.sh -u username -d apollo-db -h localhost -p 5432 -r -s Apollo/scripts/chado-schema-with-ontologies.sql.gz
$ gmod_add_organism.pl

When I redeploy it fails
$ Apollo/./apollo deploy

I have posted the last catalina.out file here - It seems like there is a lot of issues w/ the db. 
Should I not be using the 'load_chado_schema.sh' or is it missing an ontology? 

Thanks!
Shane M.

OpenJDK 64-Bit Server VM warning: ignoring option PermSize=256m; support was removed in 8.0
OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=256m; support was removed in 8.0
Please use CMSClassUnloadingEnabled in place of CMSPermGenSweepingEnabled in the future
OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=256m; support was removed in 8.0
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/common/classes], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/common], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/server/classes], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/server], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/shared/classes], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/shared], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server version:        Apache Tomcat/8.0.32 (Ubuntu)
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server built:          Sep 16 2016 13:11:41 UTC
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server number:         8.0.32.0
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Name:               Linux
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Version:            4.4.0-31-generic
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Architecture:          amd64
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Java Home:             /usr/lib/jvm/java-8-openjdk-amd64/jre
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Version:           1.8.0_91-8u91-b14-3ubuntu1~16.04.1-b14
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Vendor:            Oracle Corporation
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_BASE:         /var/lib/tomcat8
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_HOME:         /usr/share/tomcat8
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.config.file=/var/lib/tomcat8/conf/logging.properties
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xms512m
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xmx1g
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:PermSize=256m
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:MaxPermSize=256m
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xms512m
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xmx1g
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:+CMSClassUnloadingEnabled
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:+CMSPermGenSweepingEnabled
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:+UseConcMarkSweepGC
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.net.preferIPv4Stack=true
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:MaxPermSize=256m
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.endorsed.dirs=/usr/share/tomcat8/endorsed
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.base=/var/lib/tomcat8
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.home=/usr/share/tomcat8
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.io.tmpdir=/tmp/tomcat8-tomcat8-tmp
Oct 28, 2016 12:59:35 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-nio-8080"]
Oct 28, 2016 12:59:35 PM org.apache.tomcat.util.net.NioSelectorPool getSharedSelector
INFO: Using a shared selector for servlet write/read
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 784 ms
Oct 28, 2016 12:59:35 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Oct 28, 2016 12:59:35 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/8.0.32 (Ubuntu)
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat8/webapps/apollo.war
Oct 28, 2016 12:59:44 PM org.apache.jasper.servlet.TldScanner scanJars
INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
log4j:WARN No appenders could be found for logger (org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper).
log4j:WARN Please initialize the log4j system properly.

Configuring Shiro ...

Shiro Configured
2016-10-28 13:00:16,368 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column id int8 not null
2016-10-28 13:00:16,369 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,370 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column version int8 not null
2016-10-28 13:00:16,370 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,370 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column program_version varchar(255) not null
2016-10-28 13:00:16,370 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "program_version" contains null values
2016-10-28 13:00:16,371 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column source_name varchar(255) not null
2016-10-28 13:00:16,371 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "source_name" contains null values
2016-10-28 13:00:16,373 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column source_version varchar(255) not null
2016-10-28 13:00:16,373 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "source_version" contains null values
2016-10-28 13:00:16,373 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column time_executed timestamp not null
2016-10-28 13:00:16,373 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "time_executed" contains null values
2016-10-28 13:00:16,400 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cv add column id int8 not null
2016-10-28 13:00:16,400 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,407 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cv add column version int8 not null
2016-10-28 13:00:16,407 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,407 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column id int8 not null
2016-10-28 13:00:16,407 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,408 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column version int8 not null
2016-10-28 13:00:16,408 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,408 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column is_relationship_type int4 not null
2016-10-28 13:00:16,408 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "is_relationship_type" contains null values
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column id int8 not null
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column version int8 not null
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column objectcvterm_id int8 not null
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "objectcvterm_id" contains null values
2016-10-28 13:00:16,412 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column subjectcvterm_id int8 not null
2016-10-28 13:00:16,412 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "subjectcvterm_id" contains null values
2016-10-28 13:00:16,416 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table db add column id int8 not null
2016-10-28 13:00:16,416 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,416 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table db add column version int8 not null
2016-10-28 13:00:16,416 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,417 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref add column id int8 not null
2016-10-28 13:00:16,417 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,478 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column id int8 not null
2016-10-28 13:00:16,478 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,479 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column version int8 not null
2016-10-28 13:00:16,479 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,480 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column directory varchar(255) not null
2016-10-28 13:00:16,480 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "directory" contains null values
2016-10-28 13:00:16,699 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_r1o1rnfnsf7oipuv1h7h1fln7 foreign key (objectcvterm_id) references cvterm
2016-10-28 13:00:16,699 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "objectcvterm_id" referenced in foreign key constraint does not exist
2016-10-28 13:00:16,701 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_pwxrfyx6rqu5krq4nj5wa3u4f foreign key (subjectcvterm_id) references cvterm
2016-10-28 13:00:16,701 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "subjectcvterm_id" referenced in foreign key constraint does not exist
2016-10-28 13:00:24,657 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table chadoprop add column cvterm_id int8 not null
2016-10-28 13:00:24,657 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "cvterm_id" contains null values
2016-10-28 13:00:25,003 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table chadoprop add constraint FK_8twb5n8vjmldyy3eeyq7sppc3 foreign key (cvterm_id) references cvterm
2016-10-28 13:00:25,003 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "cvterm_id" referenced in foreign key constraint does not exist
2016-10-28 13:00:37,057 [localhost-startStop-1] ERROR liquibase  - Change Set changelog-2_0_1.groovy::1445460972540-4::nathandunn (generated) failed.  Error: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
at liquibase.Liquibase.update(Liquibase.java:114)
at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
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)
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
... 18 more
2016-10-28 13:00:37,101 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing the application: Migration failed for change set changelog-2_0_1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
liquibase.exception.MigrationFailedException: Migration failed for change set changelog-2_0_1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:347)
at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
at liquibase.Liquibase.update(Liquibase.java:114)
at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
... 14 more
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
... 18 more
2016-10-28 13:00:37,102 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing Grails: Migration failed for change set changelog-2_0_1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
liquibase.exception.MigrationFailedException: Migration failed for change set changelog-2_0_1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:347)
at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
at liquibase.Liquibase.update(Liquibase.java:114)
at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
... 14 more
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
... 18 more
Oct 28, 2016 1:00:37 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: One or more listeners failed to start. Full details will be found in the appropriate container log file
Oct 28, 2016 1:00:37 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/apollo] startup failed due to previous errors
Oct 28, 2016 1:00:37 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesJdbc
WARNING: The web application [apollo] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Oct 28, 2016 1:00:37 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
WARNING: The web application [apollo] appears to have started a thread named [Tomcat JDBC Pool Cleaner[1218195601:1477677600358]] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 java.util.TimerThread.mainLoop(Timer.java:552)
 java.util.TimerThread.run(Timer.java:505)
Oct 28, 2016 1:00:37 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
WARNING: The web application [apollo] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 java.util.TimerThread.mainLoop(Timer.java:552)
 java.util.TimerThread.run(Timer.java:505)
Oct 28, 2016 1:00:37 PM org.apache.catalina.loader.WebappClassLoaderBase checkThreadLocalMapForLeaks
SEVERE:The web application [apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@22ab40c]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Oct 28, 2016 1:00:37 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /var/lib/tomcat8/webapps/apollo.war has finished in 61,539 ms
Oct 28, 2016 1:00:37 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat8/webapps/ROOT
Oct 28, 2016 1:00:37 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat8/webapps/ROOT has finished in 404 ms
Oct 28, 2016 1:00:37 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-nio-8080"]
Oct 28, 2016 1:00:37 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 62069 ms





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Re: Apollo deploy issue

Deepak Unni
Hi Shane,

I think there is a bit of confusion so as to what Apollo can do with Chado.

The script load_chado_schema.sh loads chado-schema-with-ontologies.sql.gz into a new (clean) database and Apollo expects the database to remain clean (i.e. no entries in organism, feature and featureloc tables) when Apollo is deployed. 

The main purpose of this empty Chado database is for Apollo to export annotations, created by Apollo itself.
This capability was made as an export strategy which supplements FASTA and GFF3 export.

There have been requests for Apollo to read and write to a Chado database (real-time) but we haven't gotten around that yet, although we have it on our radar :)


Please feel free to rectify if I misunderstood the issue you were facing.

Cheers,

Deepak



On Fri, Oct 28, 2016 at 1:32 PM, Shane McCoy <[hidden email]> wrote:
Hello! I'm having an issue with deploying the production of an apollo.war. 
Apollo 2.0.4

Apollo will deploy fine before I run these scripts for Chado,

$ perl Makefile.PL
$ make 
$ sudo make install
$ Apollo/scripts/load_chado_schema.sh -u username -d apollo-db -h localhost -p 5432 -r -s Apollo/scripts/chado-schema-with-ontologies.sql.gz
$ gmod_add_organism.pl

When I redeploy it fails
$ Apollo/./apollo deploy

I have posted the last catalina.out file here - It seems like there is a lot of issues w/ the db. 
Should I not be using the 'load_chado_schema.sh' or is it missing an ontology? 

Thanks!
Shane M.

OpenJDK 64-Bit Server VM warning: ignoring option PermSize=256m; support was removed in 8.0
OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=256m; support was removed in 8.0
Please use CMSClassUnloadingEnabled in place of CMSPermGenSweepingEnabled in the future
OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=256m; support was removed in 8.0
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/common/classes], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/common], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/server/classes], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/server], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/shared/classes], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/shared], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server version:        Apache Tomcat/8.0.32 (Ubuntu)
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server built:          Sep 16 2016 13:11:41 UTC
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server number:         8.0.32.0
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Name:               Linux
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Version:            4.4.0-31-generic
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Architecture:          amd64
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Java Home:             /usr/lib/jvm/java-8-openjdk-amd64/jre
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Version:           1.8.0_91-8u91-b14-3ubuntu1~16.04.1-b14
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Vendor:            Oracle Corporation
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_BASE:         /var/lib/tomcat8
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_HOME:         /usr/share/tomcat8
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.config.file=/var/lib/tomcat8/conf/logging.properties
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xms512m
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xmx1g
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:PermSize=256m
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:MaxPermSize=256m
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xms512m
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xmx1g
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:+CMSClassUnloadingEnabled
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:+CMSPermGenSweepingEnabled
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:+UseConcMarkSweepGC
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.net.preferIPv4Stack=true
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:MaxPermSize=256m
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.endorsed.dirs=/usr/share/tomcat8/endorsed
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.base=/var/lib/tomcat8
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.home=/usr/share/tomcat8
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.io.tmpdir=/tmp/tomcat8-tomcat8-tmp
Oct 28, 2016 12:59:35 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-nio-8080"]
Oct 28, 2016 12:59:35 PM org.apache.tomcat.util.net.NioSelectorPool getSharedSelector
INFO: Using a shared selector for servlet write/read
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 784 ms
Oct 28, 2016 12:59:35 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Oct 28, 2016 12:59:35 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/8.0.32 (Ubuntu)
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat8/webapps/apollo.war
Oct 28, 2016 12:59:44 PM org.apache.jasper.servlet.TldScanner scanJars
INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
log4j:WARN No appenders could be found for logger (org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper).
log4j:WARN Please initialize the log4j system properly.

Configuring Shiro ...

Shiro Configured
2016-10-28 13:00:16,368 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column id int8 not null
2016-10-28 13:00:16,369 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,370 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column version int8 not null
2016-10-28 13:00:16,370 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,370 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column program_version varchar(255) not null
2016-10-28 13:00:16,370 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "program_version" contains null values
2016-10-28 13:00:16,371 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column source_name varchar(255) not null
2016-10-28 13:00:16,371 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "source_name" contains null values
2016-10-28 13:00:16,373 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column source_version varchar(255) not null
2016-10-28 13:00:16,373 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "source_version" contains null values
2016-10-28 13:00:16,373 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column time_executed timestamp not null
2016-10-28 13:00:16,373 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "time_executed" contains null values
2016-10-28 13:00:16,400 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cv add column id int8 not null
2016-10-28 13:00:16,400 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,407 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cv add column version int8 not null
2016-10-28 13:00:16,407 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,407 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column id int8 not null
2016-10-28 13:00:16,407 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,408 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column version int8 not null
2016-10-28 13:00:16,408 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,408 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column is_relationship_type int4 not null
2016-10-28 13:00:16,408 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "is_relationship_type" contains null values
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column id int8 not null
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column version int8 not null
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column objectcvterm_id int8 not null
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "objectcvterm_id" contains null values
2016-10-28 13:00:16,412 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column subjectcvterm_id int8 not null
2016-10-28 13:00:16,412 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "subjectcvterm_id" contains null values
2016-10-28 13:00:16,416 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table db add column id int8 not null
2016-10-28 13:00:16,416 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,416 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table db add column version int8 not null
2016-10-28 13:00:16,416 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,417 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref add column id int8 not null
2016-10-28 13:00:16,417 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,478 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column id int8 not null
2016-10-28 13:00:16,478 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,479 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column version int8 not null
2016-10-28 13:00:16,479 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,480 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column directory varchar(255) not null
2016-10-28 13:00:16,480 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "directory" contains null values
2016-10-28 13:00:16,699 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_r1o1rnfnsf7oipuv1h7h1fln7 foreign key (objectcvterm_id) references cvterm
2016-10-28 13:00:16,699 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "objectcvterm_id" referenced in foreign key constraint does not exist
2016-10-28 13:00:16,701 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_pwxrfyx6rqu5krq4nj5wa3u4f foreign key (subjectcvterm_id) references cvterm
2016-10-28 13:00:16,701 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "subjectcvterm_id" referenced in foreign key constraint does not exist
2016-10-28 13:00:24,657 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table chadoprop add column cvterm_id int8 not null
2016-10-28 13:00:24,657 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "cvterm_id" contains null values
2016-10-28 13:00:25,003 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table chadoprop add constraint FK_8twb5n8vjmldyy3eeyq7sppc3 foreign key (cvterm_id) references cvterm
2016-10-28 13:00:25,003 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "cvterm_id" referenced in foreign key constraint does not exist
2016-10-28 13:00:37,057 [localhost-startStop-1] ERROR liquibase  - Change Set changelog-2_0_1.groovy::1445460972540-4::nathandunn (generated) failed.  Error: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
at liquibase.Liquibase.update(Liquibase.java:114)
at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
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)
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
... 18 more
2016-10-28 13:00:37,101 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing the application: Migration failed for change set changelog-2_0_1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
liquibase.exception.MigrationFailedException: Migration failed for change set changelog-2_0_1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:347)
at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
at liquibase.Liquibase.update(Liquibase.java:114)
at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
... 14 more
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
... 18 more
2016-10-28 13:00:37,102 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing Grails: Migration failed for change set changelog-2_0_1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
liquibase.exception.MigrationFailedException: Migration failed for change set changelog-2_0_1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:347)
at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
at liquibase.Liquibase.update(Liquibase.java:114)
at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
... 14 more
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
... 18 more
Oct 28, 2016 1:00:37 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: One or more listeners failed to start. Full details will be found in the appropriate container log file
Oct 28, 2016 1:00:37 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/apollo] startup failed due to previous errors
Oct 28, 2016 1:00:37 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesJdbc
WARNING: The web application [apollo] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Oct 28, 2016 1:00:37 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
WARNING: The web application [apollo] appears to have started a thread named [Tomcat JDBC Pool Cleaner[1218195601:1477677600358]] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 java.util.TimerThread.mainLoop(Timer.java:552)
 java.util.TimerThread.run(Timer.java:505)
Oct 28, 2016 1:00:37 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
WARNING: The web application [apollo] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 java.util.TimerThread.mainLoop(Timer.java:552)
 java.util.TimerThread.run(Timer.java:505)
Oct 28, 2016 1:00:37 PM org.apache.catalina.loader.WebappClassLoaderBase checkThreadLocalMapForLeaks
SEVERE:The web application [apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@22ab40c]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Oct 28, 2016 1:00:37 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /var/lib/tomcat8/webapps/apollo.war has finished in 61,539 ms
Oct 28, 2016 1:00:37 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat8/webapps/ROOT
Oct 28, 2016 1:00:37 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat8/webapps/ROOT has finished in 404 ms
Oct 28, 2016 1:00:37 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-nio-8080"]
Oct 28, 2016 1:00:37 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 62069 ms





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--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia




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.

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Re: Apollo deploy issue

Shane McCoy
Thank you for responding. I would like to save annotations to a (clean/empty) chado database. I attempted a clean start with a newly created database. To make sure I understand - I do not need to run the load_chado script to utilize the export to chado option? 
Thanks,
Shane M.

On Fri, Oct 28, 2016 at 3:26 PM, Deepak Unni <[hidden email]> wrote:
Hi Shane,

I think there is a bit of confusion so as to what Apollo can do with Chado.

The script load_chado_schema.sh loads chado-schema-with-ontologies.sql.gz into a new (clean) database and Apollo expects the database to remain clean (i.e. no entries in organism, feature and featureloc tables) when Apollo is deployed. 

The main purpose of this empty Chado database is for Apollo to export annotations, created by Apollo itself.
This capability was made as an export strategy which supplements FASTA and GFF3 export.

There have been requests for Apollo to read and write to a Chado database (real-time) but we haven't gotten around that yet, although we have it on our radar :)


Please feel free to rectify if I misunderstood the issue you were facing.

Cheers,

Deepak



On Fri, Oct 28, 2016 at 1:32 PM, Shane McCoy <[hidden email]> wrote:
Hello! I'm having an issue with deploying the production of an apollo.war. 
Apollo 2.0.4

Apollo will deploy fine before I run these scripts for Chado,

$ perl Makefile.PL
$ make 
$ sudo make install
$ Apollo/scripts/load_chado_schema.sh -u username -d apollo-db -h localhost -p 5432 -r -s Apollo/scripts/chado-schema-with-ontologies.sql.gz
$ gmod_add_organism.pl

When I redeploy it fails
$ Apollo/./apollo deploy

I have posted the last catalina.out file here - It seems like there is a lot of issues w/ the db. 
Should I not be using the 'load_chado_schema.sh' or is it missing an ontology? 

Thanks!
Shane M.

OpenJDK 64-Bit Server VM warning: ignoring option PermSize=256m; support was removed in 8.0
OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=256m; support was removed in 8.0
Please use CMSClassUnloadingEnabled in place of CMSPermGenSweepingEnabled in the future
OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=256m; support was removed in 8.0
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/common/classes], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/common], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/server/classes], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/server], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/shared/classes], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/shared], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server version:        Apache Tomcat/8.0.32 (Ubuntu)
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server built:          Sep 16 2016 13:11:41 UTC
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server number:         8.0.32.0
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Name:               Linux
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Version:            4.4.0-31-generic
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Architecture:          amd64
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Java Home:             /usr/lib/jvm/java-8-openjdk-amd64/jre
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Version:           1.8.0_91-8u91-b14-3ubuntu1~16.04.1-b14
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Vendor:            Oracle Corporation
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_BASE:         /var/lib/tomcat8
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_HOME:         /usr/share/tomcat8
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.config.file=/var/lib/tomcat8/conf/logging.properties
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xms512m
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xmx1g
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:PermSize=256m
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:MaxPermSize=256m
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xms512m
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xmx1g
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:+CMSClassUnloadingEnabled
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:+CMSPermGenSweepingEnabled
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:+UseConcMarkSweepGC
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.net.preferIPv4Stack=true
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:MaxPermSize=256m
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.endorsed.dirs=/usr/share/tomcat8/endorsed
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.base=/var/lib/tomcat8
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.home=/usr/share/tomcat8
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.io.tmpdir=/tmp/tomcat8-tomcat8-tmp
Oct 28, 2016 12:59:35 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-nio-8080"]
Oct 28, 2016 12:59:35 PM org.apache.tomcat.util.net.NioSelectorPool getSharedSelector
INFO: Using a shared selector for servlet write/read
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 784 ms
Oct 28, 2016 12:59:35 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Oct 28, 2016 12:59:35 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/8.0.32 (Ubuntu)
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat8/webapps/apollo.war
Oct 28, 2016 12:59:44 PM org.apache.jasper.servlet.TldScanner scanJars
INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
log4j:WARN No appenders could be found for logger (org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper).
log4j:WARN Please initialize the log4j system properly.

Configuring Shiro ...

Shiro Configured
2016-10-28 13:00:16,368 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column id int8 not null
2016-10-28 13:00:16,369 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,370 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column version int8 not null
2016-10-28 13:00:16,370 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,370 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column program_version varchar(255) not null
2016-10-28 13:00:16,370 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "program_version" contains null values
2016-10-28 13:00:16,371 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column source_name varchar(255) not null
2016-10-28 13:00:16,371 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "source_name" contains null values
2016-10-28 13:00:16,373 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column source_version varchar(255) not null
2016-10-28 13:00:16,373 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "source_version" contains null values
2016-10-28 13:00:16,373 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column time_executed timestamp not null
2016-10-28 13:00:16,373 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "time_executed" contains null values
2016-10-28 13:00:16,400 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cv add column id int8 not null
2016-10-28 13:00:16,400 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,407 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cv add column version int8 not null
2016-10-28 13:00:16,407 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,407 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column id int8 not null
2016-10-28 13:00:16,407 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,408 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column version int8 not null
2016-10-28 13:00:16,408 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,408 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column is_relationship_type int4 not null
2016-10-28 13:00:16,408 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "is_relationship_type" contains null values
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column id int8 not null
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column version int8 not null
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column objectcvterm_id int8 not null
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "objectcvterm_id" contains null values
2016-10-28 13:00:16,412 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column subjectcvterm_id int8 not null
2016-10-28 13:00:16,412 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "subjectcvterm_id" contains null values
2016-10-28 13:00:16,416 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table db add column id int8 not null
2016-10-28 13:00:16,416 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,416 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table db add column version int8 not null
2016-10-28 13:00:16,416 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,417 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref add column id int8 not null
2016-10-28 13:00:16,417 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,478 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column id int8 not null
2016-10-28 13:00:16,478 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,479 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column version int8 not null
2016-10-28 13:00:16,479 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,480 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column directory varchar(255) not null
2016-10-28 13:00:16,480 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "directory" contains null values
2016-10-28 13:00:16,699 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_r1o1rnfnsf7oipuv1h7h1fln7 foreign key (objectcvterm_id) references cvterm
2016-10-28 13:00:16,699 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "objectcvterm_id" referenced in foreign key constraint does not exist
2016-10-28 13:00:16,701 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_pwxrfyx6rqu5krq4nj5wa3u4f foreign key (subjectcvterm_id) references cvterm
2016-10-28 13:00:16,701 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "subjectcvterm_id" referenced in foreign key constraint does not exist
2016-10-28 13:00:24,657 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table chadoprop add column cvterm_id int8 not null
2016-10-28 13:00:24,657 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "cvterm_id" contains null values
2016-10-28 13:00:25,003 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table chadoprop add constraint FK_8twb5n8vjmldyy3eeyq7sppc3 foreign key (cvterm_id) references cvterm
2016-10-28 13:00:25,003 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "cvterm_id" referenced in foreign key constraint does not exist
2016-10-28 13:00:37,057 [localhost-startStop-1] ERROR liquibase  - Change Set changelog-2_0_1.groovy::1445460972540-4::nathandunn (generated) failed.  Error: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
at liquibase.Liquibase.update(Liquibase.java:114)
at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
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)
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
... 18 more
2016-10-28 13:00:37,101 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing the application: Migration failed for change set changelog-2_0_1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
liquibase.exception.MigrationFailedException: Migration failed for change set changelog-2_0_1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:347)
at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
at liquibase.Liquibase.update(Liquibase.java:114)
at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
... 14 more
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
... 18 more
2016-10-28 13:00:37,102 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing Grails: Migration failed for change set changelog-2_0_1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
liquibase.exception.MigrationFailedException: Migration failed for change set changelog-2_0_1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:347)
at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
at liquibase.Liquibase.update(Liquibase.java:114)
at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
... 14 more
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
... 18 more
Oct 28, 2016 1:00:37 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: One or more listeners failed to start. Full details will be found in the appropriate container log file
Oct 28, 2016 1:00:37 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/apollo] startup failed due to previous errors
Oct 28, 2016 1:00:37 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesJdbc
WARNING: The web application [apollo] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Oct 28, 2016 1:00:37 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
WARNING: The web application [apollo] appears to have started a thread named [Tomcat JDBC Pool Cleaner[1218195601:1477677600358]] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 java.util.TimerThread.mainLoop(Timer.java:552)
 java.util.TimerThread.run(Timer.java:505)
Oct 28, 2016 1:00:37 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
WARNING: The web application [apollo] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 java.util.TimerThread.mainLoop(Timer.java:552)
 java.util.TimerThread.run(Timer.java:505)
Oct 28, 2016 1:00:37 PM org.apache.catalina.loader.WebappClassLoaderBase checkThreadLocalMapForLeaks
SEVERE:The web application [apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@22ab40c]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Oct 28, 2016 1:00:37 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /var/lib/tomcat8/webapps/apollo.war has finished in 61,539 ms
Oct 28, 2016 1:00:37 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat8/webapps/ROOT
Oct 28, 2016 1:00:37 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat8/webapps/ROOT has finished in 404 ms
Oct 28, 2016 1:00:37 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-nio-8080"]
Oct 28, 2016 1:00:37 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 62069 ms





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--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia




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.

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Re: Apollo deploy issue

Deepak Unni
Hi Shane,


To export annotations from Apollo to a clean Chado database, you will have to run the script to load Chado schema. The script loads a prebuilt Chado schema with ontologies from Relations Ontology, Sequence Ontology and Gene Ontology.

Following are the steps to enable Chado export:

1. Run the load_chado_schema.sh script to load Chado schema and prebuilt ontologies into the clean Chado database.
2. Make sure that Chado data source is configured in your apollo-config.groovy with the proper database username and password.
3. Run apollo 

To check if it has configured properly, you can go to the Reference Sequences tab in Apollo's Annotator Panel and see if Chado is an option for your exports.

Here is a link to the documentation which describes more on running load_chado_schema.sh script: http://genomearchitect.readthedocs.io/en/latest/ChadoExport.html


Cheers,

Deepak


On Tue, Nov 1, 2016 at 8:59 AM, Shane McCoy <[hidden email]> wrote:
Thank you for responding. I would like to save annotations to a (clean/empty) chado database. I attempted a clean start with a newly created database. To make sure I understand - I do not need to run the load_chado script to utilize the export to chado option? 
Thanks,
Shane M.

On Fri, Oct 28, 2016 at 3:26 PM, Deepak Unni <[hidden email]> wrote:
Hi Shane,

I think there is a bit of confusion so as to what Apollo can do with Chado.

The script load_chado_schema.sh loads chado-schema-with-ontologies.sql.gz into a new (clean) database and Apollo expects the database to remain clean (i.e. no entries in organism, feature and featureloc tables) when Apollo is deployed. 

The main purpose of this empty Chado database is for Apollo to export annotations, created by Apollo itself.
This capability was made as an export strategy which supplements FASTA and GFF3 export.

There have been requests for Apollo to read and write to a Chado database (real-time) but we haven't gotten around that yet, although we have it on our radar :)


Please feel free to rectify if I misunderstood the issue you were facing.

Cheers,

Deepak



On Fri, Oct 28, 2016 at 1:32 PM, Shane McCoy <[hidden email]> wrote:
Hello! I'm having an issue with deploying the production of an apollo.war. 
Apollo 2.0.4

Apollo will deploy fine before I run these scripts for Chado,

$ perl Makefile.PL
$ make 
$ sudo make install
$ Apollo/scripts/load_chado_schema.sh -u username -d apollo-db -h localhost -p 5432 -r -s Apollo/scripts/chado-schema-with-ontologies.sql.gz
$ gmod_add_organism.pl

When I redeploy it fails
$ Apollo/./apollo deploy

I have posted the last catalina.out file here - It seems like there is a lot of issues w/ the db. 
Should I not be using the 'load_chado_schema.sh' or is it missing an ontology? 

Thanks!
Shane M.

OpenJDK 64-Bit Server VM warning: ignoring option PermSize=256m; support was removed in 8.0
OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=256m; support was removed in 8.0
Please use CMSClassUnloadingEnabled in place of CMSPermGenSweepingEnabled in the future
OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=256m; support was removed in 8.0
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/common/classes], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/common], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/server/classes], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/server], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/shared/classes], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/shared], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server version:        Apache Tomcat/8.0.32 (Ubuntu)
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server built:          Sep 16 2016 13:11:41 UTC
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server number:         8.0.32.0
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Name:               Linux
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Version:            4.4.0-31-generic
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Architecture:          amd64
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Java Home:             /usr/lib/jvm/java-8-openjdk-amd64/jre
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Version:           1.8.0_91-8u91-b14-3ubuntu1~16.04.1-b14
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Vendor:            Oracle Corporation
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_BASE:         /var/lib/tomcat8
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_HOME:         /usr/share/tomcat8
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.config.file=/var/lib/tomcat8/conf/logging.properties
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xms512m
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xmx1g
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:PermSize=256m
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:MaxPermSize=256m
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xms512m
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xmx1g
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:+CMSClassUnloadingEnabled
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:+CMSPermGenSweepingEnabled
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:+UseConcMarkSweepGC
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.net.preferIPv4Stack=true
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:MaxPermSize=256m
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.endorsed.dirs=/usr/share/tomcat8/endorsed
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.base=/var/lib/tomcat8
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.home=/usr/share/tomcat8
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.io.tmpdir=/tmp/tomcat8-tomcat8-tmp
Oct 28, 2016 12:59:35 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-nio-8080"]
Oct 28, 2016 12:59:35 PM org.apache.tomcat.util.net.NioSelectorPool getSharedSelector
INFO: Using a shared selector for servlet write/read
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 784 ms
Oct 28, 2016 12:59:35 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Oct 28, 2016 12:59:35 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/8.0.32 (Ubuntu)
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat8/webapps/apollo.war
Oct 28, 2016 12:59:44 PM org.apache.jasper.servlet.TldScanner scanJars
INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
log4j:WARN No appenders could be found for logger (org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper).
log4j:WARN Please initialize the log4j system properly.

Configuring Shiro ...

Shiro Configured
2016-10-28 13:00:16,368 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column id int8 not null
2016-10-28 13:00:16,369 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,370 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column version int8 not null
2016-10-28 13:00:16,370 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,370 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column program_version varchar(255) not null
2016-10-28 13:00:16,370 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "program_version" contains null values
2016-10-28 13:00:16,371 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column source_name varchar(255) not null
2016-10-28 13:00:16,371 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "source_name" contains null values
2016-10-28 13:00:16,373 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column source_version varchar(255) not null
2016-10-28 13:00:16,373 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "source_version" contains null values
2016-10-28 13:00:16,373 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column time_executed timestamp not null
2016-10-28 13:00:16,373 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "time_executed" contains null values
2016-10-28 13:00:16,400 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cv add column id int8 not null
2016-10-28 13:00:16,400 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,407 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cv add column version int8 not null
2016-10-28 13:00:16,407 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,407 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column id int8 not null
2016-10-28 13:00:16,407 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,408 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column version int8 not null
2016-10-28 13:00:16,408 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,408 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column is_relationship_type int4 not null
2016-10-28 13:00:16,408 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "is_relationship_type" contains null values
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column id int8 not null
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column version int8 not null
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column objectcvterm_id int8 not null
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "objectcvterm_id" contains null values
2016-10-28 13:00:16,412 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column subjectcvterm_id int8 not null
2016-10-28 13:00:16,412 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "subjectcvterm_id" contains null values
2016-10-28 13:00:16,416 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table db add column id int8 not null
2016-10-28 13:00:16,416 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,416 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table db add column version int8 not null
2016-10-28 13:00:16,416 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,417 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref add column id int8 not null
2016-10-28 13:00:16,417 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,478 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column id int8 not null
2016-10-28 13:00:16,478 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,479 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column version int8 not null
2016-10-28 13:00:16,479 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,480 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column directory varchar(255) not null
2016-10-28 13:00:16,480 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "directory" contains null values
2016-10-28 13:00:16,699 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_r1o1rnfnsf7oipuv1h7h1fln7 foreign key (objectcvterm_id) references cvterm
2016-10-28 13:00:16,699 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "objectcvterm_id" referenced in foreign key constraint does not exist
2016-10-28 13:00:16,701 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_pwxrfyx6rqu5krq4nj5wa3u4f foreign key (subjectcvterm_id) references cvterm
2016-10-28 13:00:16,701 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "subjectcvterm_id" referenced in foreign key constraint does not exist
2016-10-28 13:00:24,657 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table chadoprop add column cvterm_id int8 not null
2016-10-28 13:00:24,657 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "cvterm_id" contains null values
2016-10-28 13:00:25,003 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table chadoprop add constraint FK_8twb5n8vjmldyy3eeyq7sppc3 foreign key (cvterm_id) references cvterm
2016-10-28 13:00:25,003 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "cvterm_id" referenced in foreign key constraint does not exist
2016-10-28 13:00:37,057 [localhost-startStop-1] ERROR liquibase  - Change Set changelog-2_0_1.groovy::1445460972540-4::nathandunn (generated) failed.  Error: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
at liquibase.Liquibase.update(Liquibase.java:114)
at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
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)
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
... 18 more
2016-10-28 13:00:37,101 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing the application: Migration failed for change set changelog-2_0_1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
liquibase.exception.MigrationFailedException: Migration failed for change set changelog-2_0_1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:347)
at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
at liquibase.Liquibase.update(Liquibase.java:114)
at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
... 14 more
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
... 18 more
2016-10-28 13:00:37,102 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing Grails: Migration failed for change set changelog-2_0_1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
liquibase.exception.MigrationFailedException: Migration failed for change set changelog-2_0_1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:347)
at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
at liquibase.Liquibase.update(Liquibase.java:114)
at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
... 14 more
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
... 18 more
Oct 28, 2016 1:00:37 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: One or more listeners failed to start. Full details will be found in the appropriate container log file
Oct 28, 2016 1:00:37 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/apollo] startup failed due to previous errors
Oct 28, 2016 1:00:37 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesJdbc
WARNING: The web application [apollo] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Oct 28, 2016 1:00:37 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
WARNING: The web application [apollo] appears to have started a thread named [Tomcat JDBC Pool Cleaner[1218195601:1477677600358]] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 java.util.TimerThread.mainLoop(Timer.java:552)
 java.util.TimerThread.run(Timer.java:505)
Oct 28, 2016 1:00:37 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
WARNING: The web application [apollo] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 java.util.TimerThread.mainLoop(Timer.java:552)
 java.util.TimerThread.run(Timer.java:505)
Oct 28, 2016 1:00:37 PM org.apache.catalina.loader.WebappClassLoaderBase checkThreadLocalMapForLeaks
SEVERE:The web application [apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@22ab40c]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Oct 28, 2016 1:00:37 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /var/lib/tomcat8/webapps/apollo.war has finished in 61,539 ms
Oct 28, 2016 1:00:37 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat8/webapps/ROOT
Oct 28, 2016 1:00:37 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat8/webapps/ROOT has finished in 404 ms
Oct 28, 2016 1:00:37 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-nio-8080"]
Oct 28, 2016 1:00:37 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 62069 ms





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--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia




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--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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Re: Apollo deploy issue

Shane McCoy
Hi Deepak, 
Thanks again for the feedback. I reset and everything appears to be working. Export successfully to chado db! 
Cheers!
Shane M.

On Tue, Nov 1, 2016 at 12:32 PM, Deepak Unni <[hidden email]> wrote:
Hi Shane,


To export annotations from Apollo to a clean Chado database, you will have to run the script to load Chado schema. The script loads a prebuilt Chado schema with ontologies from Relations Ontology, Sequence Ontology and Gene Ontology.

Following are the steps to enable Chado export:

1. Run the load_chado_schema.sh script to load Chado schema and prebuilt ontologies into the clean Chado database.
2. Make sure that Chado data source is configured in your apollo-config.groovy with the proper database username and password.
3. Run apollo 

To check if it has configured properly, you can go to the Reference Sequences tab in Apollo's Annotator Panel and see if Chado is an option for your exports.

Here is a link to the documentation which describes more on running load_chado_schema.sh script: http://genomearchitect.readthedocs.io/en/latest/ChadoExport.html


Cheers,

Deepak


On Tue, Nov 1, 2016 at 8:59 AM, Shane McCoy <[hidden email]> wrote:
Thank you for responding. I would like to save annotations to a (clean/empty) chado database. I attempted a clean start with a newly created database. To make sure I understand - I do not need to run the load_chado script to utilize the export to chado option? 
Thanks,
Shane M.

On Fri, Oct 28, 2016 at 3:26 PM, Deepak Unni <[hidden email]> wrote:
Hi Shane,

I think there is a bit of confusion so as to what Apollo can do with Chado.

The script load_chado_schema.sh loads chado-schema-with-ontologies.sql.gz into a new (clean) database and Apollo expects the database to remain clean (i.e. no entries in organism, feature and featureloc tables) when Apollo is deployed. 

The main purpose of this empty Chado database is for Apollo to export annotations, created by Apollo itself.
This capability was made as an export strategy which supplements FASTA and GFF3 export.

There have been requests for Apollo to read and write to a Chado database (real-time) but we haven't gotten around that yet, although we have it on our radar :)


Please feel free to rectify if I misunderstood the issue you were facing.

Cheers,

Deepak



On Fri, Oct 28, 2016 at 1:32 PM, Shane McCoy <[hidden email]> wrote:
Hello! I'm having an issue with deploying the production of an apollo.war. 
Apollo 2.0.4

Apollo will deploy fine before I run these scripts for Chado,

$ perl Makefile.PL
$ make 
$ sudo make install
$ Apollo/scripts/load_chado_schema.sh -u username -d apollo-db -h localhost -p 5432 -r -s Apollo/scripts/chado-schema-with-ontologies.sql.gz
$ gmod_add_organism.pl

When I redeploy it fails
$ Apollo/./apollo deploy

I have posted the last catalina.out file here - It seems like there is a lot of issues w/ the db. 
Should I not be using the 'load_chado_schema.sh' or is it missing an ontology? 

Thanks!
Shane M.

OpenJDK 64-Bit Server VM warning: ignoring option PermSize=256m; support was removed in 8.0
OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=256m; support was removed in 8.0
Please use CMSClassUnloadingEnabled in place of CMSPermGenSweepingEnabled in the future
OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=256m; support was removed in 8.0
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/common/classes], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/common], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/server/classes], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/server], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/shared/classes], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/shared], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server version:        Apache Tomcat/8.0.32 (Ubuntu)
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server built:          Sep 16 2016 13:11:41 UTC
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server number:         8.0.32.0
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Name:               Linux
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Version:            4.4.0-31-generic
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Architecture:          amd64
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Java Home:             /usr/lib/jvm/java-8-openjdk-amd64/jre
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Version:           1.8.0_91-8u91-b14-3ubuntu1~16.04.1-b14
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Vendor:            Oracle Corporation
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_BASE:         /var/lib/tomcat8
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_HOME:         /usr/share/tomcat8
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.config.file=/var/lib/tomcat8/conf/logging.properties
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xms512m
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xmx1g
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:PermSize=256m
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:MaxPermSize=256m
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xms512m
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xmx1g
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:+CMSClassUnloadingEnabled
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:+CMSPermGenSweepingEnabled
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:+UseConcMarkSweepGC
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.net.preferIPv4Stack=true
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:MaxPermSize=256m
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.endorsed.dirs=/usr/share/tomcat8/endorsed
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.base=/var/lib/tomcat8
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.home=/usr/share/tomcat8
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.io.tmpdir=/tmp/tomcat8-tomcat8-tmp
Oct 28, 2016 12:59:35 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-nio-8080"]
Oct 28, 2016 12:59:35 PM org.apache.tomcat.util.net.NioSelectorPool getSharedSelector
INFO: Using a shared selector for servlet write/read
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 784 ms
Oct 28, 2016 12:59:35 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Oct 28, 2016 12:59:35 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/8.0.32 (Ubuntu)
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat8/webapps/apollo.war
Oct 28, 2016 12:59:44 PM org.apache.jasper.servlet.TldScanner scanJars
INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
log4j:WARN No appenders could be found for logger (org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper).
log4j:WARN Please initialize the log4j system properly.

Configuring Shiro ...

Shiro Configured
2016-10-28 13:00:16,368 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column id int8 not null
2016-10-28 13:00:16,369 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,370 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column version int8 not null
2016-10-28 13:00:16,370 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,370 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column program_version varchar(255) not null
2016-10-28 13:00:16,370 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "program_version" contains null values
2016-10-28 13:00:16,371 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column source_name varchar(255) not null
2016-10-28 13:00:16,371 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "source_name" contains null values
2016-10-28 13:00:16,373 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column source_version varchar(255) not null
2016-10-28 13:00:16,373 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "source_version" contains null values
2016-10-28 13:00:16,373 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column time_executed timestamp not null
2016-10-28 13:00:16,373 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "time_executed" contains null values
2016-10-28 13:00:16,400 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cv add column id int8 not null
2016-10-28 13:00:16,400 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,407 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cv add column version int8 not null
2016-10-28 13:00:16,407 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,407 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column id int8 not null
2016-10-28 13:00:16,407 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,408 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column version int8 not null
2016-10-28 13:00:16,408 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,408 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column is_relationship_type int4 not null
2016-10-28 13:00:16,408 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "is_relationship_type" contains null values
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column id int8 not null
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column version int8 not null
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column objectcvterm_id int8 not null
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "objectcvterm_id" contains null values
2016-10-28 13:00:16,412 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column subjectcvterm_id int8 not null
2016-10-28 13:00:16,412 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "subjectcvterm_id" contains null values
2016-10-28 13:00:16,416 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table db add column id int8 not null
2016-10-28 13:00:16,416 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,416 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table db add column version int8 not null
2016-10-28 13:00:16,416 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,417 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref add column id int8 not null
2016-10-28 13:00:16,417 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,478 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column id int8 not null
2016-10-28 13:00:16,478 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,479 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column version int8 not null
2016-10-28 13:00:16,479 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,480 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column directory varchar(255) not null
2016-10-28 13:00:16,480 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "directory" contains null values
2016-10-28 13:00:16,699 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_r1o1rnfnsf7oipuv1h7h1fln7 foreign key (objectcvterm_id) references cvterm
2016-10-28 13:00:16,699 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "objectcvterm_id" referenced in foreign key constraint does not exist
2016-10-28 13:00:16,701 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_pwxrfyx6rqu5krq4nj5wa3u4f foreign key (subjectcvterm_id) references cvterm
2016-10-28 13:00:16,701 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "subjectcvterm_id" referenced in foreign key constraint does not exist
2016-10-28 13:00:24,657 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table chadoprop add column cvterm_id int8 not null
2016-10-28 13:00:24,657 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "cvterm_id" contains null values
2016-10-28 13:00:25,003 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table chadoprop add constraint FK_8twb5n8vjmldyy3eeyq7sppc3 foreign key (cvterm_id) references cvterm
2016-10-28 13:00:25,003 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "cvterm_id" referenced in foreign key constraint does not exist
2016-10-28 13:00:37,057 [localhost-startStop-1] ERROR liquibase  - Change Set changelog-2_0_1.groovy::1445460972540-4::nathandunn (generated) failed.  Error: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
at liquibase.Liquibase.update(Liquibase.java:114)
at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
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)
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
... 18 more
2016-10-28 13:00:37,101 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing the application: Migration failed for change set changelog-2_0_1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
liquibase.exception.MigrationFailedException: Migration failed for change set changelog-2_0_1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:347)
at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
at liquibase.Liquibase.update(Liquibase.java:114)
at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
... 14 more
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
... 18 more
2016-10-28 13:00:37,102 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing Grails: Migration failed for change set changelog-2_0_1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
liquibase.exception.MigrationFailedException: Migration failed for change set changelog-2_0_1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:347)
at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
at liquibase.Liquibase.update(Liquibase.java:114)
at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
... 14 more
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
... 18 more
Oct 28, 2016 1:00:37 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: One or more listeners failed to start. Full details will be found in the appropriate container log file
Oct 28, 2016 1:00:37 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/apollo] startup failed due to previous errors
Oct 28, 2016 1:00:37 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesJdbc
WARNING: The web application [apollo] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Oct 28, 2016 1:00:37 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
WARNING: The web application [apollo] appears to have started a thread named [Tomcat JDBC Pool Cleaner[1218195601:1477677600358]] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 java.util.TimerThread.mainLoop(Timer.java:552)
 java.util.TimerThread.run(Timer.java:505)
Oct 28, 2016 1:00:37 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
WARNING: The web application [apollo] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 java.util.TimerThread.mainLoop(Timer.java:552)
 java.util.TimerThread.run(Timer.java:505)
Oct 28, 2016 1:00:37 PM org.apache.catalina.loader.WebappClassLoaderBase checkThreadLocalMapForLeaks
SEVERE:The web application [apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@22ab40c]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Oct 28, 2016 1:00:37 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /var/lib/tomcat8/webapps/apollo.war has finished in 61,539 ms
Oct 28, 2016 1:00:37 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat8/webapps/ROOT
Oct 28, 2016 1:00:37 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat8/webapps/ROOT has finished in 404 ms
Oct 28, 2016 1:00:37 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-nio-8080"]
Oct 28, 2016 1:00:37 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 62069 ms





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--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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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.





--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia




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.







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Re: Apollo deploy issue

Deepak Unni
Awesome, glad to help!

On Tue, Nov 1, 2016 at 2:15 PM, Shane McCoy <[hidden email]> wrote:
Hi Deepak, 
Thanks again for the feedback. I reset and everything appears to be working. Export successfully to chado db! 
Cheers!
Shane M.

On Tue, Nov 1, 2016 at 12:32 PM, Deepak Unni <[hidden email]> wrote:
Hi Shane,


To export annotations from Apollo to a clean Chado database, you will have to run the script to load Chado schema. The script loads a prebuilt Chado schema with ontologies from Relations Ontology, Sequence Ontology and Gene Ontology.

Following are the steps to enable Chado export:

1. Run the load_chado_schema.sh script to load Chado schema and prebuilt ontologies into the clean Chado database.
2. Make sure that Chado data source is configured in your apollo-config.groovy with the proper database username and password.
3. Run apollo 

To check if it has configured properly, you can go to the Reference Sequences tab in Apollo's Annotator Panel and see if Chado is an option for your exports.

Here is a link to the documentation which describes more on running load_chado_schema.sh script: http://genomearchitect.readthedocs.io/en/latest/ChadoExport.html


Cheers,

Deepak


On Tue, Nov 1, 2016 at 8:59 AM, Shane McCoy <[hidden email]> wrote:
Thank you for responding. I would like to save annotations to a (clean/empty) chado database. I attempted a clean start with a newly created database. To make sure I understand - I do not need to run the load_chado script to utilize the export to chado option? 
Thanks,
Shane M.

On Fri, Oct 28, 2016 at 3:26 PM, Deepak Unni <[hidden email]> wrote:
Hi Shane,

I think there is a bit of confusion so as to what Apollo can do with Chado.

The script load_chado_schema.sh loads chado-schema-with-ontologies.sql.gz into a new (clean) database and Apollo expects the database to remain clean (i.e. no entries in organism, feature and featureloc tables) when Apollo is deployed. 

The main purpose of this empty Chado database is for Apollo to export annotations, created by Apollo itself.
This capability was made as an export strategy which supplements FASTA and GFF3 export.

There have been requests for Apollo to read and write to a Chado database (real-time) but we haven't gotten around that yet, although we have it on our radar :)


Please feel free to rectify if I misunderstood the issue you were facing.

Cheers,

Deepak



On Fri, Oct 28, 2016 at 1:32 PM, Shane McCoy <[hidden email]> wrote:
Hello! I'm having an issue with deploying the production of an apollo.war. 
Apollo 2.0.4

Apollo will deploy fine before I run these scripts for Chado,

$ perl Makefile.PL
$ make 
$ sudo make install
$ Apollo/scripts/load_chado_schema.sh -u username -d apollo-db -h localhost -p 5432 -r -s Apollo/scripts/chado-schema-with-ontologies.sql.gz
$ gmod_add_organism.pl

When I redeploy it fails
$ Apollo/./apollo deploy

I have posted the last catalina.out file here - It seems like there is a lot of issues w/ the db. 
Should I not be using the 'load_chado_schema.sh' or is it missing an ontology? 

Thanks!
Shane M.

OpenJDK 64-Bit Server VM warning: ignoring option PermSize=256m; support was removed in 8.0
OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=256m; support was removed in 8.0
Please use CMSClassUnloadingEnabled in place of CMSPermGenSweepingEnabled in the future
OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=256m; support was removed in 8.0
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/common/classes], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/common], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/server/classes], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/server], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/shared/classes], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:34 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/shared], exists: [false], isDirectory: [false], canRead: [false]
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server version:        Apache Tomcat/8.0.32 (Ubuntu)
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server built:          Sep 16 2016 13:11:41 UTC
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server number:         8.0.32.0
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Name:               Linux
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Version:            4.4.0-31-generic
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Architecture:          amd64
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Java Home:             /usr/lib/jvm/java-8-openjdk-amd64/jre
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Version:           1.8.0_91-8u91-b14-3ubuntu1~16.04.1-b14
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Vendor:            Oracle Corporation
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_BASE:         /var/lib/tomcat8
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_HOME:         /usr/share/tomcat8
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.config.file=/var/lib/tomcat8/conf/logging.properties
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xms512m
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xmx1g
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:PermSize=256m
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:MaxPermSize=256m
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xms512m
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xmx1g
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:+CMSClassUnloadingEnabled
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:+CMSPermGenSweepingEnabled
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:+UseConcMarkSweepGC
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.net.preferIPv4Stack=true
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:MaxPermSize=256m
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.endorsed.dirs=/usr/share/tomcat8/endorsed
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.base=/var/lib/tomcat8
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.home=/usr/share/tomcat8
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.io.tmpdir=/tmp/tomcat8-tomcat8-tmp
Oct 28, 2016 12:59:35 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-nio-8080"]
Oct 28, 2016 12:59:35 PM org.apache.tomcat.util.net.NioSelectorPool getSharedSelector
INFO: Using a shared selector for servlet write/read
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 784 ms
Oct 28, 2016 12:59:35 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Oct 28, 2016 12:59:35 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/8.0.32 (Ubuntu)
Oct 28, 2016 12:59:35 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat8/webapps/apollo.war
Oct 28, 2016 12:59:44 PM org.apache.jasper.servlet.TldScanner scanJars
INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
log4j:WARN No appenders could be found for logger (org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper).
log4j:WARN Please initialize the log4j system properly.

Configuring Shiro ...

Shiro Configured
2016-10-28 13:00:16,368 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column id int8 not null
2016-10-28 13:00:16,369 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,370 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column version int8 not null
2016-10-28 13:00:16,370 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,370 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column program_version varchar(255) not null
2016-10-28 13:00:16,370 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "program_version" contains null values
2016-10-28 13:00:16,371 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column source_name varchar(255) not null
2016-10-28 13:00:16,371 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "source_name" contains null values
2016-10-28 13:00:16,373 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column source_version varchar(255) not null
2016-10-28 13:00:16,373 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "source_version" contains null values
2016-10-28 13:00:16,373 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column time_executed timestamp not null
2016-10-28 13:00:16,373 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "time_executed" contains null values
2016-10-28 13:00:16,400 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cv add column id int8 not null
2016-10-28 13:00:16,400 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,407 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cv add column version int8 not null
2016-10-28 13:00:16,407 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,407 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column id int8 not null
2016-10-28 13:00:16,407 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,408 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column version int8 not null
2016-10-28 13:00:16,408 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,408 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column is_relationship_type int4 not null
2016-10-28 13:00:16,408 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "is_relationship_type" contains null values
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column id int8 not null
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column version int8 not null
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column objectcvterm_id int8 not null
2016-10-28 13:00:16,411 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "objectcvterm_id" contains null values
2016-10-28 13:00:16,412 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column subjectcvterm_id int8 not null
2016-10-28 13:00:16,412 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "subjectcvterm_id" contains null values
2016-10-28 13:00:16,416 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table db add column id int8 not null
2016-10-28 13:00:16,416 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,416 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table db add column version int8 not null
2016-10-28 13:00:16,416 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,417 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref add column id int8 not null
2016-10-28 13:00:16,417 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,478 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column id int8 not null
2016-10-28 13:00:16,478 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-10-28 13:00:16,479 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column version int8 not null
2016-10-28 13:00:16,479 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-10-28 13:00:16,480 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column directory varchar(255) not null
2016-10-28 13:00:16,480 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "directory" contains null values
2016-10-28 13:00:16,699 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_r1o1rnfnsf7oipuv1h7h1fln7 foreign key (objectcvterm_id) references cvterm
2016-10-28 13:00:16,699 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "objectcvterm_id" referenced in foreign key constraint does not exist
2016-10-28 13:00:16,701 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_pwxrfyx6rqu5krq4nj5wa3u4f foreign key (subjectcvterm_id) references cvterm
2016-10-28 13:00:16,701 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "subjectcvterm_id" referenced in foreign key constraint does not exist
2016-10-28 13:00:24,657 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table chadoprop add column cvterm_id int8 not null
2016-10-28 13:00:24,657 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "cvterm_id" contains null values
2016-10-28 13:00:25,003 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table chadoprop add constraint FK_8twb5n8vjmldyy3eeyq7sppc3 foreign key (cvterm_id) references cvterm
2016-10-28 13:00:25,003 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "cvterm_id" referenced in foreign key constraint does not exist
2016-10-28 13:00:37,057 [localhost-startStop-1] ERROR liquibase  - Change Set changelog-2_0_1.groovy::1445460972540-4::nathandunn (generated) failed.  Error: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
at liquibase.Liquibase.update(Liquibase.java:114)
at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
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)
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
... 18 more
2016-10-28 13:00:37,101 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing the application: Migration failed for change set changelog-2_0_1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
liquibase.exception.MigrationFailedException: Migration failed for change set changelog-2_0_1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:347)
at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
at liquibase.Liquibase.update(Liquibase.java:114)
at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
... 14 more
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
... 18 more
2016-10-28 13:00:37,102 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing Grails: Migration failed for change set changelog-2_0_1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
liquibase.exception.MigrationFailedException: Migration failed for change set changelog-2_0_1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:347)
at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
at liquibase.Liquibase.update(Liquibase.java:114)
at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
... 14 more
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.v_dj_j_c_cluster depends on column "is_analysis"
at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
... 18 more
Oct 28, 2016 1:00:37 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: One or more listeners failed to start. Full details will be found in the appropriate container log file
Oct 28, 2016 1:00:37 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/apollo] startup failed due to previous errors
Oct 28, 2016 1:00:37 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesJdbc
WARNING: The web application [apollo] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Oct 28, 2016 1:00:37 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
WARNING: The web application [apollo] appears to have started a thread named [Tomcat JDBC Pool Cleaner[1218195601:1477677600358]] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 java.util.TimerThread.mainLoop(Timer.java:552)
 java.util.TimerThread.run(Timer.java:505)
Oct 28, 2016 1:00:37 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
WARNING: The web application [apollo] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Object.wait(Native Method)
 java.util.TimerThread.mainLoop(Timer.java:552)
 java.util.TimerThread.run(Timer.java:505)
Oct 28, 2016 1:00:37 PM org.apache.catalina.loader.WebappClassLoaderBase checkThreadLocalMapForLeaks
SEVERE:The web application [apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@22ab40c]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Oct 28, 2016 1:00:37 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /var/lib/tomcat8/webapps/apollo.war has finished in 61,539 ms
Oct 28, 2016 1:00:37 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat8/webapps/ROOT
Oct 28, 2016 1:00:37 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat8/webapps/ROOT has finished in 404 ms
Oct 28, 2016 1:00:37 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-nio-8080"]
Oct 28, 2016 1:00:37 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 62069 ms





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia




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.





--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia




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.





--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia




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.

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