Shane McCoy
2016-10-28 18:32:17 UTC
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
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.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for
more info.
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$2]
(value
[org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$***@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
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$ 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
$ Apollo/./apollo deploy
I have posted the last catalina.out file here - It seems like there is alot 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.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for
more info.
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$2]
(value
[org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$***@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