So, unfortunately we need to formally add Chado integration back to Apollo.
of the 2.0.3 release. Weâll be pinging the community specifically to make
sure the export / integration works.
from Apollo and import that GFF3 into your Chado schema.
I did as you said and it started up just fine. Thank you!
won't be the best guide to a new setup.
I want to be able to use the CHADO schema & use web apollo to edit the genome.
I had set up CHADO on a database and had already uploaded the GFF. Can I
small test file and i don't have an issue putting back through the script.
Shane M.
If you are using postgresql and you donât have anything in the database
you want (or you back it up first) I would drop and re-create the database
(with tomcat off). When it comes back up it will create the database
1 - stop tomcat
1a - backup database?
2 - dropdb your-apollo-database-name
3 - createdb your-apollo-database-name
4 - start tomcat
Its in a pretty weird state.
Nathan
* Stopping Tomcat servlet engine tomcat7
[ OK ]
* Starting Tomcat servlet engine tomcat7
[ OK ]
--------------------------$$:/var/log/tomcat7$ tail -f catalina.out
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml_rt is already
defined
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml is already defined
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/xml is already
defined
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deploying configuration descriptor
/etc/tomcat7/Catalina/localhost/host-manager.xml
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive
/var/lib/tomcat7/webapps/apollo.war
^[[AFeb 20, 2016 8:44:43 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already
defined
Feb 20, 2016 8:44:43 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is
already defined
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
2016-02-20 20:45:40,539 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table analysis add
column id int8 not null
2016-02-20 20:45:40,543 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "id" contains null values
2016-02-20 20:45:40,546 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table analysis add
column version int8 not null
2016-02-20 20:45:40,548 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "version" contains null values
2016-02-20 20:45:40,550 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table analysis add
column program_version varchar(255) not null
2016-02-20 20:45:40,552 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "program_version" contains null values
2016-02-20 20:45:40,554 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table analysis add
column source_name varchar(255) not null
2016-02-20 20:45:40,555 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "source_name" contains null values
2016-02-20 20:45:40,558 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table analysis add
column source_version varchar(255) not null
2016-02-20 20:45:40,559 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "source_version" contains null values
2016-02-20 20:45:40,562 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table analysis add
column time_executed timestamp not null
2016-02-20 20:45:40,563 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "time_executed" contains null values
2016-02-20 20:45:40,566 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table cv add column
id int8 not null
2016-02-20 20:45:40,567 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "id" contains null values
2016-02-20 20:45:40,569 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table cv add column
version int8 not null
2016-02-20 20:45:40,570 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "version" contains null values
2016-02-20 20:45:40,573 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table cvterm add
column id int8 not null
2016-02-20 20:45:40,574 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "id" contains null values
2016-02-20 20:45:40,577 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table cvterm add
column version int8 not null
2016-02-20 20:45:40,578 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "version" contains null values
2016-02-20 20:45:40,583 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table cvterm add
column is_relationship_type int4 not null
2016-02-20 20:45:40,584 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "is_relationship_type" contains null
values
2016-02-20 20:45:40,587 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
cvterm_relationship add column id int8 not null
2016-02-20 20:45:40,588 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "id" contains null values
2016-02-20 20:45:40,590 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
cvterm_relationship add column version int8 not null
2016-02-20 20:45:40,591 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "version" contains null values
2016-02-20 20:45:40,593 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
cvterm_relationship add column objectcvterm_id int8 not null
2016-02-20 20:45:40,594 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "objectcvterm_id" contains null values
2016-02-20 20:45:40,598 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
cvterm_relationship add column subjectcvterm_id int8 not null
2016-02-20 20:45:40,599 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "subjectcvterm_id" contains null
values
2016-02-20 20:45:40,602 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table db add column
id int8 not null
2016-02-20 20:45:40,602 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "id" contains null values
2016-02-20 20:45:40,606 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table db add column
version int8 not null
2016-02-20 20:45:40,607 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "version" contains null values
2016-02-20 20:45:40,610 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table dbxref add
column id int8 not null
2016-02-20 20:45:40,612 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "id" contains null values
2016-02-20 20:45:40,616 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table feature add
column id int8 not null
2016-02-20 20:45:40,617 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "id" contains null values
2016-02-20 20:45:40,620 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table feature add
column version int8 not null
2016-02-20 20:45:40,621 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "version" contains null values
2016-02-20 20:45:40,632 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table feature add
column unique_name varchar(255) not null
2016-02-20 20:45:40,633 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "unique_name" contains null values
2016-02-20 20:45:40,636 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table feature add
column class varchar(255) not null
2016-02-20 20:45:40,637 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "class" contains null values
2016-02-20 20:45:40,641 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
feature_relationship add column id int8 not null
2016-02-20 20:45:40,642 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "id" contains null values
2016-02-20 20:45:40,645 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
feature_relationship add column version int8 not null
2016-02-20 20:45:40,646 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "version" contains null values
2016-02-20 20:45:40,652 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
feature_relationship add column child_feature_id int8 not null
2016-02-20 20:45:40,653 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "child_feature_id" contains null
values
2016-02-20 20:45:40,656 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
feature_relationship add column parent_feature_id int8 not null
2016-02-20 20:45:40,657 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "parent_feature_id" contains null
values
2016-02-20 20:45:40,660 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
feature_synonym add column id int8 not null
2016-02-20 20:45:40,661 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "id" contains null values
2016-02-20 20:45:40,668 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
feature_synonym add column version int8 not null
2016-02-20 20:45:40,670 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "version" contains null values
2016-02-20 20:45:40,672 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
feature_synonym add column publication_id int8 not null
2016-02-20 20:45:40,677 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "publication_id" contains null values
2016-02-20 20:45:40,679 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table genome add
column id int8 not null
2016-02-20 20:45:40,681 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: relation "genome" does not exist
2016-02-20 20:45:40,684 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table genome add
column version int8 not null
2016-02-20 20:45:40,685 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: relation "genome" does not exist
2016-02-20 20:45:40,687 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table genome add
column directory varchar(255)
2016-02-20 20:45:40,688 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: relation "genome" does not exist
2016-02-20 20:45:40,692 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table organism add
column id int8 not null
2016-02-20 20:45:40,693 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "id" contains null values
2016-02-20 20:45:40,701 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table organism add
column version int8 not null
2016-02-20 20:45:40,702 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "version" contains null values
2016-02-20 20:45:40,704 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table organism add
column directory varchar(255) not null
2016-02-20 20:45:40,706 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "directory" contains null values
2016-02-20 20:45:40,709 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table synonym add
column id int8 not null
2016-02-20 20:45:40,710 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "id" contains null values
2016-02-20 20:45:40,715 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table synonym add
column version int8 not null
2016-02-20 20:45:40,716 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "version" contains null values
2016-02-20 20:45:40,719 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table synonym add
column synonymsgml varchar(255) not null
2016-02-20 20:45:40,720 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "synonymsgml" contains null values
2016-02-20 20:45:40,724 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
analysis_feature add constraint FK_8m30ycwh545b4aoxor9sbk1oq foreign key
(analysis_id) references analysis
2016-02-20 20:45:40,725 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_8m30ycwh545b4aoxor9sbk1oq"
for relation "analysis_feature" already exists
2016-02-20 20:45:40,727 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
analysis_feature add constraint FK_l94xl424xp988f06gr2b3t5tw foreign key
(feature_id) references feature
2016-02-20 20:45:40,728 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_l94xl424xp988f06gr2b3t5tw"
for relation "analysis_feature" already exists
2016-02-20 20:45:40,730 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
analysis_property add constraint FK_38g8n4bitmdwkrcs217uexrwx foreign key
(analysis_id) references analysis
2016-02-20 20:45:40,731 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_38g8n4bitmdwkrcs217uexrwx"
for relation "analysis_property" already exists
2016-02-20 20:45:40,733 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
analysis_property add constraint FK_9o7xs7saygim8y0sm4ostvpc1 foreign key
(type_id) references cvterm
2016-02-20 20:45:40,734 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_9o7xs7saygim8y0sm4ostvpc1"
for relation "analysis_property" already exists
2016-02-20 20:45:40,737 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table cvterm add
constraint FK_oksfqluv12ktmut9s6o9jla7a foreign key (cv_id) references cv
2016-02-20 20:45:40,739 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_oksfqluv12ktmut9s6o9jla7a"
for relation "cvterm" already exists
2016-02-20 20:45:40,741 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table cvterm add
constraint FK_6d097oy44230tuoo8lb8dkkcp foreign key (dbxref_id) references
dbxref
2016-02-20 20:45:40,742 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_6d097oy44230tuoo8lb8dkkcp"
for relation "cvterm" already exists
2016-02-20 20:45:40,744 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table cvterm_path
add constraint FK_ke2nrw91sxil8mv7osgv83pw1 foreign key (cv_id) references
cv
2016-02-20 20:45:40,745 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_ke2nrw91sxil8mv7osgv83pw1"
for relation "cvterm_path" already exists
2016-02-20 20:45:40,748 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table cvterm_path
add constraint FK_tlfh10092i00g6rlv589naqy5 foreign key (objectcvterm_id)
references cvterm
2016-02-20 20:45:40,749 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_tlfh10092i00g6rlv589naqy5"
for relation "cvterm_path" already exists
2016-02-20 20:45:40,751 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table cvterm_path
add constraint FK_nq02ir0qeydr5tj3071k9gl7b foreign key (subjectcvterm_id)
references cvterm
2016-02-20 20:45:40,752 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_nq02ir0qeydr5tj3071k9gl7b"
for relation "cvterm_path" already exists
2016-02-20 20:45:40,760 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table cvterm_path
add constraint FK_jaqi1bk3t2c0m3pybmparp856 foreign key (type_id)
references cvterm
2016-02-20 20:45:40,761 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_jaqi1bk3t2c0m3pybmparp856"
for relation "cvterm_path" already exists
2016-02-20 20:45:40,763 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
cvterm_relationship add constraint FK_r1o1rnfnsf7oipuv1h7h1fln7 foreign key
(objectcvterm_id) references cvterm
2016-02-20 20:45:40,766 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "objectcvterm_id" referenced in
foreign key constraint does not exist
2016-02-20 20:45:40,771 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
cvterm_relationship add constraint FK_pwxrfyx6rqu5krq4nj5wa3u4f foreign key
(subjectcvterm_id) references cvterm
2016-02-20 20:45:40,775 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "subjectcvterm_id" referenced in
foreign key constraint does not exist
2016-02-20 20:45:40,777 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
cvterm_relationship add constraint FK_ob1d0vrfaix8b28j4tvilqnyv foreign key
(type_id) references cvterm
2016-02-20 20:45:40,778 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_ob1d0vrfaix8b28j4tvilqnyv"
for relation "cvterm_relationship" already exists
2016-02-20 20:45:40,781 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table dbxref add
constraint FK_np3tfcu9g867to3qux6raf9y8 foreign key (db_id) references db
2016-02-20 20:45:40,782 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_np3tfcu9g867to3qux6raf9y8"
for relation "dbxref" already exists
2016-02-20 20:45:40,786 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
dbxref_property add constraint FK_3p1ssctww083s0tt65mmm64uo foreign key
(dbxref_id) references dbxref
2016-02-20 20:45:40,787 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_3p1ssctww083s0tt65mmm64uo"
for relation "dbxref_property" already exists
2016-02-20 20:45:40,792 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
dbxref_property add constraint FK_t6ojbvugx8kou45oklsie3rt5 foreign key
(type_id) references cvterm
2016-02-20 20:45:40,793 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_t6ojbvugx8kou45oklsie3rt5"
for relation "dbxref_property" already exists
2016-02-20 20:45:40,796 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
environmentcvterm add constraint FK_tql9djnqw1d7migfndoj3lrph foreign key
(cvterm_id) references cvterm
2016-02-20 20:45:40,803 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_tql9djnqw1d7migfndoj3lrph"
for relation "environmentcvterm" already exists
2016-02-20 20:45:40,805 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
environmentcvterm add constraint FK_rrwb96jjqgtg077yv8pbim3jj foreign key
(environment_id) references environment
2016-02-20 20:45:40,807 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_rrwb96jjqgtg077yv8pbim3jj"
for relation "environmentcvterm" already exists
2016-02-20 20:45:40,813 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table feature add
constraint FK_hc4vrafs0ws7ugdkp0n6u3xdo foreign key (dbxref_id) references
dbxref
2016-02-20 20:45:40,816 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_hc4vrafs0ws7ugdkp0n6u3xdo"
for relation "feature" already exists
2016-02-20 20:45:40,819 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table feature_dbxref
add constraint FK_n6n7lheb1qkmlde8u6gvvjxne foreign key (dbxref_id)
references dbxref
2016-02-20 20:45:40,821 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_n6n7lheb1qkmlde8u6gvvjxne"
for relation "feature_dbxref" already exists
2016-02-20 20:45:40,829 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table feature_dbxref
add constraint FK_1mrfkxbb3n7fhjxcrkxappdn8 foreign key
(feature_featuredbxrefs_id) references feature
2016-02-20 20:45:40,831 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_1mrfkxbb3n7fhjxcrkxappdn8"
for relation "feature_dbxref" already exists
2016-02-20 20:45:40,836 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
feature_feature_phenotypes add constraint FK_dy5g29heir5ic3d36okyuihho
foreign key (phenotype_id) references phenotype
2016-02-20 20:45:40,839 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_dy5g29heir5ic3d36okyuihho"
for relation "feature_feature_phenotypes" already exists
2016-02-20 20:45:40,842 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
feature_feature_phenotypes add constraint FK_aqr7eiyx6puju6elciwubbwmo
foreign key (feature_id) references feature
2016-02-20 20:45:40,843 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_aqr7eiyx6puju6elciwubbwmo"
for relation "feature_feature_phenotypes" already exists
2016-02-20 20:45:40,847 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
feature_genotype add constraint FK_hak8r429shmpho06rbyvwnmt0 foreign key
(chromosome_feature_id) references feature
2016-02-20 20:45:40,848 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_hak8r429shmpho06rbyvwnmt0"
for relation "feature_genotype" already exists
2016-02-20 20:45:40,856 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
feature_genotype add constraint FK_b42u9iq4kuqe5ay544do81n32 foreign key
(cvterm_id) references cvterm
2016-02-20 20:45:40,857 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_b42u9iq4kuqe5ay544do81n32"
for relation "feature_genotype" already exists
2016-02-20 20:45:40,859 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
feature_genotype add constraint FK_cm3gqs38fa2lpllgoum8n4kgn foreign key
(feature_id) references feature
2016-02-20 20:45:40,861 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_cm3gqs38fa2lpllgoum8n4kgn"
for relation "feature_genotype" already exists
2016-02-20 20:45:40,863 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
feature_genotype add constraint FK_736wxgjs6pip5212ash5i68p foreign key
(genotype_id) references genotype
2016-02-20 20:45:40,864 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_736wxgjs6pip5212ash5i68p" for
relation "feature_genotype" already exists
2016-02-20 20:45:40,867 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
feature_grails_user add constraint FK_4dgbhgiw0vb9hqy2k5fqg3neh foreign key
(feature_owners_id) references feature
2016-02-20 20:45:40,868 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_4dgbhgiw0vb9hqy2k5fqg3neh"
for relation "feature_grails_user" already exists
2016-02-20 20:45:40,872 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
feature_location add constraint FK_qml7xp9f5uojcw7jwdxcb35le foreign key
(feature_id) references feature
2016-02-20 20:45:40,873 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_qml7xp9f5uojcw7jwdxcb35le"
for relation "feature_location" already exists
2016-02-20 20:45:40,875 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
feature_property add constraint FK_jpvdxc57abfiridcr57x8130 foreign key
(feature_id) references feature
2016-02-20 20:45:40,879 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_jpvdxc57abfiridcr57x8130" for
relation "feature_property" already exists
2016-02-20 20:45:40,881 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
feature_property add constraint FK_36e638geg9tew42b1mp2ehff foreign key
(type_id) references cvterm
2016-02-20 20:45:40,882 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_36e638geg9tew42b1mp2ehff" for
relation "feature_property" already exists
2016-02-20 20:45:40,885 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
feature_publication add constraint FK_qolh5l4blkx8vfmwcl7f3woan foreign key
(feature_feature_publications_id) references feature
2016-02-20 20:45:40,891 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_qolh5l4blkx8vfmwcl7f3woan"
for relation "feature_publication" already exists
2016-02-20 20:45:40,893 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
feature_relationship add constraint FK_8jm56covt0m7m0m191bc5jseh foreign
key (child_feature_id) references feature
2016-02-20 20:45:40,894 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "child_feature_id" referenced in
foreign key constraint does not exist
2016-02-20 20:45:40,898 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
feature_relationship add constraint FK_72kmd92rdc6gne0nrh026o1j0 foreign
key (parent_feature_id) references feature
2016-02-20 20:45:40,899 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "parent_feature_id" referenced in
foreign key constraint does not exist
2016-02-20 20:45:40,907 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
feature_relationship_feature_property add constraint
FK_ebgnfbogf1lwdxd8jc17511o7 foreign key
(feature_relationship_feature_relationship_properties_id) references
feature_relationship
2016-02-20 20:45:40,908 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_ebgnfbogf1lwdxd8jc17511o7"
for relation "feature_relationship_feature_property" already exists
2016-02-20 20:45:40,911 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
feature_relationship_publication add constraint
FK_bdd324e5jb0lpuhs7biy2kacm foreign key
(feature_relationship_feature_relationship_publications_id) references
feature_relationship
2016-02-20 20:45:40,912 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_bdd324e5jb0lpuhs7biy2kacm"
for relation "feature_relationship_publication" already exists
2016-02-20 20:45:40,914 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
feature_synonym add constraint FK_nf9qbuay984ixqd2k1425rnyo foreign key
(feature_id) references feature
2016-02-20 20:45:40,916 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_nf9qbuay984ixqd2k1425rnyo"
for relation "feature_synonym" already exists
2016-02-20 20:45:40,923 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
feature_synonym add constraint FK_82wsc3bv9i01t9851xv4xekis foreign key
(publication_id) references publication
2016-02-20 20:45:40,926 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: column "publication_id" referenced in
foreign key constraint does not exist
2016-02-20 20:45:40,929 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
feature_synonym add constraint FK_ll4cqdh994s6x8n7vku1q7iwd foreign key
(synonym_id) references synonym
2016-02-20 20:45:40,930 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_ll4cqdh994s6x8n7vku1q7iwd"
for relation "feature_synonym" already exists
2016-02-20 20:45:40,932 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
feature_synonym add constraint FK_gsol4u8wrfwbkh1qrx18i3u6 foreign key
(feature_synonyms_id) references feature
2016-02-20 20:45:40,933 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_gsol4u8wrfwbkh1qrx18i3u6" for
relation "feature_synonym" already exists
2016-02-20 20:45:40,935 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table featurecvterm
add constraint FK_cuwo3ernssd0t0wjceb7lmm11 foreign key (cvterm_id)
references cvterm
2016-02-20 20:45:40,936 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_cuwo3ernssd0t0wjceb7lmm11"
for relation "featurecvterm" already exists
2016-02-20 20:45:40,943 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table featurecvterm
add constraint FK_iy7bbt67s7jaemiajsrqalv5o foreign key (feature_id)
references feature
2016-02-20 20:45:40,944 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_iy7bbt67s7jaemiajsrqalv5o"
for relation "featurecvterm" already exists
2016-02-20 20:45:40,948 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
featurecvterm_dbxref add constraint FK_r9xhefcekikp1od79ectkb22b foreign
key (dbxref_id) references dbxref
2016-02-20 20:45:40,949 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_r9xhefcekikp1od79ectkb22b"
for relation "featurecvterm_dbxref" already exists
2016-02-20 20:45:40,951 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
organism_organism_property add constraint FK_qyxdgqthtlgixvtdkkhc8g3pu
foreign key (organism_organism_properties_id) references organism
2016-02-20 20:45:40,959 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_qyxdgqthtlgixvtdkkhc8g3pu"
for relation "organism_organism_property" already exists
2016-02-20 20:45:40,961 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table organismdbxref
add constraint FK_s3vk7onqrk0n4c86xnvqmm3ho foreign key (dbxref_id)
references dbxref
2016-02-20 20:45:40,962 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_s3vk7onqrk0n4c86xnvqmm3ho"
for relation "organismdbxref" already exists
2016-02-20 20:45:40,965 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table organismdbxref
add constraint FK_l1jfi0wpnyooutd820p5gskr foreign key (organism_id)
references organism
2016-02-20 20:45:40,966 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_l1jfi0wpnyooutd820p5gskr" for
relation "organismdbxref" already exists
2016-02-20 20:45:40,969 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table permission add
constraint FK_4nvoxx3htem6jseb4rmu0aqfp foreign key (organism_id)
references organism
2016-02-20 20:45:40,970 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_4nvoxx3htem6jseb4rmu0aqfp"
for relation "permission" already exists
2016-02-20 20:45:40,972 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table phenotype add
constraint FK_cwgh6naf9gackae2ei11v6p41 foreign key (assay_id) references
cvterm
2016-02-20 20:45:40,979 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_cwgh6naf9gackae2ei11v6p41"
for relation "phenotype" already exists
2016-02-20 20:45:40,981 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table phenotype add
constraint FK_phmfgylejydjqyrvo3imc97go foreign key (attribute_id)
references cvterm
2016-02-20 20:45:40,982 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_phmfgylejydjqyrvo3imc97go"
for relation "phenotype" already exists
2016-02-20 20:45:40,985 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table phenotype add
constraint FK_jh0fc3orduigl8s7ymentbtrs foreign key (cvalue_id) references
cvterm
2016-02-20 20:45:40,986 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_jh0fc3orduigl8s7ymentbtrs"
for relation "phenotype" already exists
2016-02-20 20:45:40,988 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table phenotype add
constraint FK_gb4wy9qesx6vnekxekm18k9xa foreign key (observable_id)
references cvterm
2016-02-20 20:45:40,989 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_gb4wy9qesx6vnekxekm18k9xa"
for relation "phenotype" already exists
2016-02-20 20:45:40,993 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
phenotype_cvterm add constraint FK_9e2v7goj5w6nds5jo0x1va1nm foreign key
(cvterm_id) references cvterm
2016-02-20 20:45:40,999 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_9e2v7goj5w6nds5jo0x1va1nm"
for relation "phenotype_cvterm" already exists
2016-02-20 20:45:41,001 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
phenotype_cvterm add constraint FK_aicsmj1kn20ikm14292g9r2j9 foreign key
(phenotype_phenotypecvterms_id) references phenotype
2016-02-20 20:45:41,002 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_aicsmj1kn20ikm14292g9r2j9"
for relation "phenotype_cvterm" already exists
2016-02-20 20:45:41,004 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
phenotype_description add constraint FK_t52r166gd8710vffy3aompe7d foreign
key (environment_id) references environment
2016-02-20 20:45:41,006 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_t52r166gd8710vffy3aompe7d"
for relation "phenotype_description" already exists
2016-02-20 20:45:41,011 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
phenotype_description add constraint FK_bf1bstadamyw0gsarkb933l5b foreign
key (genotype_id) references genotype
2016-02-20 20:45:41,012 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_bf1bstadamyw0gsarkb933l5b"
for relation "phenotype_description" already exists
2016-02-20 20:45:41,014 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
phenotype_description add constraint FK_8pbyj05khavdl5a648c7pmcil foreign
key (type_id) references cvterm
2016-02-20 20:45:41,015 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_8pbyj05khavdl5a648c7pmcil"
for relation "phenotype_description" already exists
2016-02-20 20:45:41,020 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
phenotype_statement add constraint FK_q6jvhi3l7ty0m9tpbn09d8pxj foreign key
(environment_id) references environment
2016-02-20 20:45:41,021 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_q6jvhi3l7ty0m9tpbn09d8pxj"
for relation "phenotype_statement" already exists
2016-02-20 20:45:41,024 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
phenotype_statement add constraint FK_8rbhsxxdf669tyed8jrr747hv foreign key
(genotype_id) references genotype
2016-02-20 20:45:41,027 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_8rbhsxxdf669tyed8jrr747hv"
for relation "phenotype_statement" already exists
2016-02-20 20:45:41,029 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
phenotype_statement add constraint FK_gskh1e7b6qa2du48ayu49lr3s foreign key
(phenotype_id) references phenotype
2016-02-20 20:45:41,030 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_gskh1e7b6qa2du48ayu49lr3s"
for relation "phenotype_statement" already exists
2016-02-20 20:45:41,035 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
phenotype_statement add constraint FK_tk1pgifvuhurefn0y3myfyyt4 foreign key
(type_id) references cvterm
2016-02-20 20:45:41,036 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_tk1pgifvuhurefn0y3myfyyt4"
for relation "phenotype_statement" already exists
2016-02-20 20:45:41,039 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table preference add
constraint FK_42b0lk4rcfjcagw84jugd1sgj foreign key (organism_id)
references organism
2016-02-20 20:45:41,044 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_42b0lk4rcfjcagw84jugd1sgj"
for relation "preference" already exists
2016-02-20 20:45:41,047 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table publication
add constraint FK_h3g8f3q2krcnwmq2nasbanlay foreign key (type_id)
references cvterm
2016-02-20 20:45:41,049 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_h3g8f3q2krcnwmq2nasbanlay"
for relation "publication" already exists
2016-02-20 20:45:41,051 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
publication_relationship add constraint FK_q6hf14oiq9pomkjrhtndonmeh
foreign key (type_id) references cvterm
2016-02-20 20:45:41,052 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_q6hf14oiq9pomkjrhtndonmeh"
for relation "publication_relationship" already exists
2016-02-20 20:45:41,055 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table
publicationdbxref add constraint FK_oh81hma8qx88fhvcmfugx836b foreign key
(dbxref_id) references dbxref
2016-02-20 20:45:41,059 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_oh81hma8qx88fhvcmfugx836b"
for relation "publicationdbxref" already exists
2016-02-20 20:45:41,061 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table sequence add
constraint FK_rux0954nxr4lwvj2qgyjibua7 foreign key (organism_id)
references organism
2016-02-20 20:45:41,062 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_rux0954nxr4lwvj2qgyjibua7"
for relation "sequence" already exists
2016-02-20 20:45:41,065 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter table synonym add
constraint FK_4ylco1irefvydmsnedglqqdfu foreign key (type_id) references
cvterm
2016-02-20 20:45:41,066 [localhost-startStop-1] ERROR
hbm2ddl.SchemaUpdate - ERROR: constraint "fk_4ylco1irefvydmsnedglqqdfu"
for relation "synonym" already exists
2016-02-20 20:45:52,529 [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.population_specific_variant 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.population_specific_variant 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:471)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
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.population_specific_variant 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$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
... 18 more
2016-02-20 20:45:52,579 [localhost-startStop-1] ERROR
Migration failed for change set
Reason: liquibase.exception.DatabaseException: Error executing SQL
ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot
alter type of a column used by a view or rule
Detail: rule _RETURN on view so.population_specific_variant depends on
Caused By: Error executing SQL ALTER TABLE feature ALTER
COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used
by a view or rule
Detail: rule _RETURN on view so.population_specific_variant depends on
Caused By: ERROR: cannot alter type of a column used by a view or rule
Detail: rule _RETURN on view so.population_specific_variant depends on
column "is_analysis"
liquibase.exception.MigrationFailedException: Migration failed for
Reason: liquibase.exception.DatabaseException: Error executing SQL
ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot
alter type of a column used by a view or rule
Detail: rule _RETURN on view so.population_specific_variant depends on
Caused By: Error executing SQL ALTER TABLE feature ALTER
COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used
by a view or rule
Detail: rule _RETURN on view so.population_specific_variant depends on
Caused By: ERROR: cannot alter type of a column used by a view or rule
Detail: rule _RETURN on view so.population_specific_variant depends on
column "is_analysis"
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:347)
at
liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
at
liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
at liquibase.Liquibase.update(Liquibase.java:114)
at
grails.plugin.databasemigration.MigrationRunner$_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$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
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.population_specific_variant 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.population_specific_variant 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
2016-02-20 20:45:52,584 [localhost-startStop-1] ERROR
context.GrailsContextLoaderListener - Error initializing Grails: Migration
failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn
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.population_specific_variant depends on
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.population_specific_variant depends on
Caused By: ERROR: cannot alter type of a column used by a view or rule
Detail: rule _RETURN on view so.population_specific_variant depends on
column "is_analysis"
liquibase.exception.MigrationFailedException: Migration failed for
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.population_specific_variant depends on
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.population_specific_variant depends on
Caused By: ERROR: cannot alter type of a column used by a view or rule
Detail: rule _RETURN on view so.population_specific_variant 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$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
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.population_specific_variant 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.population_specific_variant 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
Feb 20, 2016 8:45:52 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Feb 20, 2016 8:45:52 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/apollo] startup failed due to previous errors
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader
clearReferencesJdbc
SEVERE: 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.
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader
clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread
named [PoolCleaner[25416670:1456022700075]] but has failed to stop it. This
is very likely to create a memory leak.
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader
clearReferencesThreads
SEVERE: 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.
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader
checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of
type
[org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2]
(value
and a value of type [java.util.HashMap] (value [{}]) but failed to remove
it when the web application was stopped. Threads are going to be renewed
over time to try and avoid a probable memory leak.
Feb 20, 2016 8:45:52 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 20, 2016 8:45:52 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 80376 ms
Try opening in an incognito or another browser of doing a shift reload
to flush the cache.
That being said .. This stack trace looks a bit terse. Typically
shiro (the security plugin) will reload but I don't see that here. Maybe
further up?
Nathan
Hey! I made the changes but I am still getting a blank screen.
/var/log/tomcat7$ tail -f catalina.out
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader
clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread
named [PoolCleaner[25416670:1456019437960]] but has failed to stop it. This
is very likely to create a memory leak.
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader
clearReferencesThreads
SEVERE: 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.
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader
checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of
type
[org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2]
(value
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.
Feb 20, 2016 7:51:28 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 20, 2016 7:51:28 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 77106 ms
Is this still a memory issue then?
I have updated tomcat memory to your doc specs already.
Thanks!
shane
Ok, that makes more sense now! thank you very much.
I'll will try with correct settings,
cheers!
Hi Shaun
url: jdbc:postgresql://myipaddress/apollo (it should be the
ipaddress and name of WAR correct?)
Just wanted to comment on this, actually, it would not be your IP and
war here. It is kind of confusing that this "setting" is called a url,
because it is actually a JDBC connector string, which actually references
your local database, so it would not be using the war file name or even the
IP address.
For example, if your database is named "apollodb", then your "url" would be
jdbc:postgresql://localhost/apollodb
It would generally just be localhost unless you have a separate
database server. I think it might be worth adding some more comments about
that in our setup guide, but I hope that helps!
-Colin
Hey!
So a lot has changed in a year! I'm currently still stuck at 2g but
wanted to ask about an issue i have w/ /.apollo deploy
I am getting a blank screen at the URL. I have not added any data
for generation yet. I assume i would still get a webapollo ui.
I am using postgresql. I edited apollo-config.groovy
Added (in *production* only)
*datasource.dbCreate* = "update" // one of... ( where does the
database name go? I don't understand this line, it seems i'm limited to the
options given?)
*username: *chado database username
*password: *chado database pw
url: jdbc:postgresql://myipaddress/apollo (it should be the
ipaddress and name of WAR correct?)
I haven't changed any other settings and going to
http://myipaddress/apollo is a blank page.
I want to use this w/ a already setup postgresql chado database.
http://webapollo.readthedocs.org/en/latest/Setup.html
Thanks!
On Thu, Feb 11, 2016 at 2:29 PM, Shane McCoy <
Post by Shane McCoyThanks for the quick reply!
I will see what options I can take -
Shane M.
Post by Shane McCoyHey
I am getting this error running* ./apollo run-local 8085*
..........
BUILD SUCCESSFUL
| Compiling 5 source files
| Compiling 5 source files.....
***
Metrics servlet injected into web.xml
Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
***
| Running Grails application
Error occurred during initialization of VM
Could not reserve enough space for object heap
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.
| Error Forked Grails VM exited with error
Iâm guessing that Java is requesting more memory then you have to
allocate, and so exiting.
So, when running it with run-local (for dev purposes), it actually
has preset memory, of a max of up to 2 GB, though obviously this is high.
https://github.com/GMOD/Apollo/blob/master/grails-app/conf/BuildConfig.groovy#L23
run : [maxMemory: 2048, minMemory: 64, debug: false , maxPerm: 1024, forkReserve: false],
My guess is that your machine doesnât have sufficient memory to
run this, or there is another process.
1 - get a machine with at least 4 GBâs of memory, especially if
you are going to host to multiple users. This will enable better caching
and performance.
2 - if (1) is not an immediate option (or to test, or if you are
just running locally) your can edit your apollo-config.groovy create a line
grails.project.fork = [
// configure settings for compilation JVM, note that if you alter the Groovy version forked compilation is required
// compile: [maxMemory: 256, minMemory: 64, debug: false, maxPerm: 256, daemon:true],
test : false,
//run : false,
// configure settings for the test-app JVM, uses the daemon by default
//test: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
// configure settings for the run-app JVM
run : [maxMemory: 1024, minMemory: 64, debug: false , maxPerm: 512, forkReserve: false],
// configure settings for the run-war JVM
war : [maxMemory: 1024, minMemory: 64, debug: false, maxPerm: 512, forkReserve: false],
// configure settings for the Console UI JVM
console: [maxMemory: 1024, minMemory: 64, debug: false, maxPerm: 512]
]
Setting the java size as done below works for tomcat, but not for
the development mode (run-local).
Nathan
I looked over the same errors on Stack and made adjustments to the
memory but I am still getting this error. I am new to Grails but I believe
everything is setup correct and i can run a sample app (helloworld).
* -Xms512m -Xmx1g -XX:PermSize=256m*
This is the memory
* free -m*
total used free shared
buffers cached
Mem: 2015 1297 718 56
169 859
-/+ buffers/cache: 267 1748
Checking if parameters are being read
* $ ps -ef | grep java*
tomcat7 32158 1 1 11:02 ? 00:00:10
/usr/lib/jvm/default-java/bin/java
-Djava.util.logging.config.file=/var/lib/tomcat7/conf/logging.properties
-Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager *-Xms512m
-Xmx1g -XX:PermSize=256m* -XX:MaxPermSize=256m -Xms512m -Xmx1g
-XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled
-XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m
-Djava.endorsed.dirs=/usr/share/tomcat7/endorsed -classpath
/usr/share/tomcat7/bin/bootstrap.jar:/usr/share/tomcat7/bin/tomcat-juli.jar
-Dcatalina.base=/var/lib/tomcat7 -Dcatalina.home=/usr/share/tomcat7
-Djava.io.tmpdir=/tmp/tomcat7-tomcat7-tmp
org.apache.catalina.startup.Bootstrap start
I have this in my *$HOME/.profile*
export JAVA_OPTS="-Xms512m -Xmx1g -XX:MaxPermSize=256m"
in my *setenv.sh for Tomcat7*
export CATALINA_OPTS="-Xms512m -Xmx1g \
-XX:+CMSClassUnloadingEnabled \
-XX:+CMSPermGenSweepingEnabled \
-XX:+UseConcMarkSweepGC \
-XX:MaxPermSize=256m"
*Versions: *(i went w/ 2.4.5 per Apollo guide)
$ grails -version
* Grails version: 2.4.5*
$ java -version
* java version "1.7.0_95"*
OpenJDK Runtime Environment (IcedTea 2.6.4)
(7u95-2.6.4-0ubuntu0.14.04.1)
OpenJDK Client VM (build 24.95-b01, mixed mode, sharing)
I am not sure what to change now - it seems the memory would be
adequate? I know this isn't Apollo specific but maybe someone here has had
the same problem? Please any thoughts would be great. thank you
Shane M.
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