:whale::bar_chart::books: Galaxy + Apollo + Chado + Tripal + JBrowse + JBrowse REST API + PostGraphQL + JBrowse GraphQL Experiment all as a docker-compose.yml
License: GNU General Public License v3.0
The way the NGINX proxy of this project is configured, the "landing" page of the URL is the Galaxy instance, and the Tripal site is on the path "/tripal". Although the Proxy NGINX default.conf can be superficial reconfigured to show Tripal as the landing page, putting Galaxy at the end of the path "/galaxy" breaks Galaxy and Apollo. It would be good to know how to make this swap work.
Another mildly related issue is how to best secure the /galaxy and /apollo (and possibly other) system paths as accessible only to users with specific designated "roles" such as "administrator" and "curator". This is a more restricted model of access than the system currently supports, I think.
I am wondering if I'm doing something wrong, but each invocation of the dockerized-gmod-deployment (DGD) project build seems to completely overwrite user session changes to the state of the system, state items such as user accounts, Tripal customization, etc.
I am going to take a close look at the construction of the system to see whether we can build in two build/run modes: "Initialise" and "Reboot", the latter mode preserving the user data and core (external) configuration from the previous startup phase. If I get something working, I'll submit pull requests for review and consideration.
I suspect that some of the changes needed may need to be applied to the Docker builds of component images which form part of the aggregate system, components such as docker-tripal. There may be affiliated issues (and pull requests) posted to those component projects. Other changes may simply involve changes local to the DGD.
This behaviour of the DGD may also be related to the apparent fragility of the system to selective restart of containers.
Aside from perhaps overriding the docker image (through an extra Dockerfile), it is unclear how one applies Apollo configuration options. One gets the impression that this is normally done using the apollo-config.groovy file.
Beyond that, the simple question arises as to what exactly are the default Apollo admin credentials for this system?
Sorry for my relative ignorance about this.
I'm feeling a little lost in the way to handle authentication on my setup, so maybe you can help me a little @erasche @nathandunn ?
So here's the situation:
Now if I go directly to the apollo url, I get connected with ldap with no problem, but of course, no organism is available
I can use the galaxy tools to:
Now 2 questions:
(I also have some proxying problems, but I'll fix that later)
Another example of deficient idempotency in the system?
postgraphql_1 | chado:5432 - accepting connections
postgraphql_1 |
postgraphql_1 | PostGraphQL server listening on port 5000 🚀
postgraphql_1 |
postgraphql_1 | ‣ Connected to Postgres instance postgres://chado:5432/postgres
postgraphql_1 | ‣ Introspected Postgres schema(s) public, chado
postgraphql_1 | ‣ GraphQL endpoint served at http://0.0.0.0:5000/graphql
postgraphql_1 | ‣ GraphiQL endpoint served at http://0.0.0.0:5000/graphiql
postgraphql_1 |
postgraphql_1 | * * *
postgraphql_1 |
postgraphql_1 | Error: Collection of name 'analysis_organisms' already exists in the inventory.
postgraphql_1 | at Inventory.addCollection (/app/build/interface/Inventory.js:28:19)
postgraphql_1 | at Object.addPgCatalogToInventory (/app/build/postgres/inventory/addPgCatalogToInventory.js:26:23)
postgraphql_1 | at Object.<anonymous> (/app/build/postgraphql/schema/createPostGraphQLSchema.js:55:32)
postgraphql_1 | at step (/app/node_modules/tslib/tslib.js:121:27)
postgraphql_1 | at Object.next (/app/node_modules/tslib/tslib.js:102:57)
postgraphql_1 | at fulfilled (/app/node_modules/tslib/tslib.js:92:62)
postgraphql_1 | at process._tickCallback (internal/process/next_tick.js:109:7)
postgraphql_1 |
divseek-canada-portal_postgraphql_1 exited with code 1
In working with the project, one notices a fair number of errors reported in the docker-compose build log. It is hard to say which are worth worrying about. A survey of the error messages can be crudely extracted by:
docker-compose logs |grep -i error
I wonder if we may wish to do a more careful audit of the build process to see what can be cleaned up.
It is unclear how best to robust reboot the system. Even after a (relatively) successful power up sequence, attempting restarting of the Tripal container (alone), i.e.
docker-compose restart tripal
goes partway then hits fails with an exit code of 1.
Bring the whole system "down" first, then rebooting it in sequence is a bit time consuming.
Some things to be done for tripal:
By applying the proposed pull request patch inspired by Issue #10 , the docker-compose build can be made to complete to running a swarm of containers, but one strongly suspects that the docker-compose.yml container ports are not yet properly set to access each of the resulting web components. If I figure out what is going on, I'll update this issue report...but hopefully, somebody else more on top of this complex project will sort things out.
The only component that properly works is the pgadmin docker web container. I notice that this the pgadmin container is the only one for which proper explicit port mappings are really specified inside the docker-compose.yml file.
Here's what docker ps reports:
$ docker ps
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
b62a4a779413 quay.io/erasche/gx-cookie-proxy:latest "/usr/bin/gx-cookie-…" 3 hours ago Up 3 hours 5000/tcp dockerized-gmod-deployment_remoteuser_1
6e3690e97e6e quay.io/erasche/apollo:remote_user "/bin/sh -c \"/launch…" 3 hours ago Up 3 hours 8080/tcp dockerized-gmod-deployment_apollo_1
ad7ad5ec8aaa quay.io/galaxy-genome-annotation/jbrowse:v1.12.5 "/docker-entrypoint.…" 3 hours ago Up 3 hours 80/tcp dockerized-gmod-deployment_jbrowse_1
07741da2ecac thajeztah/pgadmin4 "python ./usr/local/…" 3 hours ago Up 3 hours 0.0.0.0:8201->5050/tcp dockerized-gmod-deployment_pgadmin4_1
4b1d06df6370 quay.io/erasche/postgrest:latest "/bin/sh -c /run.sh" 3 hours ago Up 3 hours 3000/tcp dockerized-gmod-deployment_postgrest_1
781c7d3144dd quay.io/erasche/chado-jbrowse-connector:latest "bash /go/src/github…" 3 hours ago Up 3 hours dockerized-gmod-deployment_chado_jb_1
32259a8f98df erasche/postgraphql:gmod-hacks "/run.sh" 3 hours ago Up 3 hours 5000/tcp dockerized-gmod-deployment_postgraphql_1
bc70bbf95a03 quay.io/galaxy-genome-annotation/docker-galaxy-annotation:master "/usr/bin/startup" 3 hours ago Up 3 hours 21/tcp, 80/tcp, 443/tcp, 8800/tcp, 9002/tcp dockerized-gmod-deployment_galaxy_1
0ca845a1a3dd quay.io/galaxy-genome-annotation/jbrowse:v1.12.5 "/docker-entrypoint.…" 3 hours ago Up 3 hours 80/tcp dockerized-gmod-deployment_jbrowse-graphql_1
2db572cc32ec quay.io/galaxy-genome-annotation/tripal:latest "/usr/local/bin/tini…" 3 hours ago Up 3 hours 80/tcp dockerized-gmod-deployment_tripal_1
39269fa808e1 docker.elastic.co/elasticsearch/elasticsearch:6.4.2 "/usr/local/bin/dock…" 3 hours ago Up 3 hours 9200/tcp, 9300/tcp dockerized-gmod-deployment_elasticsearch_1
a5d86f7aeda0 quay.io/galaxy-genome-annotation/chado:1.31-jenkins97-pg9.5 "docker-entrypoint.s…" 3 hours ago Up 3 hours 5432/tcp dockerized-gmod-deployment_tripal_db_1
e3ddcf29c594 postgres:9.5 "docker-entrypoint.s…" 3 hours ago Up 3 hours 5432/tcp dockerized-gmod-deployment_apollo_db_1
Hmm.. and some key containers exited prematurely: docker ps -A also reports:
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
5786313b0729 nginx:latest "nginx -g 'daemon of…" 3 hours ago Exited (1) 3 hours ago dockerized-gmod-deployment_proxy_1
...
8466b42aab83 dockerized-gmod-deployment_postgraphql-refseqs "/usr/local/bin/guni…" 3 hours ago Exited (3) 3 hours ago
dockerized-gmod-deployment_postgraphql-refseqs_1
Interesting, trying to start the nginx up again (using docker-compose) generates the following error:
proxy_1 | 2018/12/03 01:04:06 [emerg] 1#1: host not found in upstream "postgraphql-refseqs" in /etc/nginx/conf.d/default.conf:133
proxy_1 | nginx: [emerg] host not found in upstream "postgraphql-refseqs" in /etc/nginx/conf.d/default.conf:133
dockerized-gmod-deployment_proxy_1 exited with code 1
hmm.... Digging a bit deeper by attempting to restart "postgraphql-refseqs" gives:
$ docker-compose -f docker-compose-fixed.yml up postgraphql-refseqs
dockerized-gmod-deployment_tripal_db_1 is up-to-date
Starting dockerized-gmod-deployment_postgraphql-refseqs_1 ... done
Attaching to dockerized-gmod-deployment_postgraphql-refseqs_1
postgraphql-refseqs_1 | [2018-12-03 01:05:47 +0000] [1] [INFO] Starting gunicorn 19.9.0
postgraphql-refseqs_1 | [2018-12-03 01:05:47 +0000] [1] [INFO] Listening at: http://0.0.0.0:5000 (1)
postgraphql-refseqs_1 | [2018-12-03 01:05:47 +0000] [1] [INFO] Using worker: sync
postgraphql-refseqs_1 | [2018-12-03 01:05:47 +0000] [14] [INFO] Booting worker with pid: 14
postgraphql-refseqs_1 | [2018-12-03 01:05:48 +0000] [14] [ERROR] Exception in worker process
postgraphql-refseqs_1 | Traceback (most recent call last):
postgraphql-refseqs_1 | File "/usr/local/lib/python2.7/site-packages/gunicorn/arbiter.py", line 583, in spawn_worker
postgraphql-refseqs_1 | worker.init_process()
postgraphql-refseqs_1 | File "/usr/local/lib/python2.7/site-packages/gunicorn/workers/base.py", line 129, in init_process
postgraphql-refseqs_1 | self.load_wsgi()
postgraphql-refseqs_1 | File "/usr/local/lib/python2.7/site-packages/gunicorn/workers/base.py", line 138, in load_wsgi
postgraphql-refseqs_1 | self.wsgi = self.app.wsgi()
postgraphql-refseqs_1 | File "/usr/local/lib/python2.7/site-packages/gunicorn/app/base.py", line 67, in wsgi
postgraphql-refseqs_1 | self.callable = self.load()
postgraphql-refseqs_1 | File "/usr/local/lib/python2.7/site-packages/gunicorn/app/wsgiapp.py", line 52, in load
postgraphql-refseqs_1 | return self.load_wsgiapp()
postgraphql-refseqs_1 | File "/usr/local/lib/python2.7/site-packages/gunicorn/app/wsgiapp.py", line 41, in load_wsgiapp
postgraphql-refseqs_1 | return util.import_app(self.app_uri)
postgraphql-refseqs_1 | File "/usr/local/lib/python2.7/site-packages/gunicorn/util.py", line 350, in import_app
postgraphql-refseqs_1 | __import__(module)
postgraphql-refseqs_1 | File "/deploy/app/hello.py", line 3, in <module>
postgraphql-refseqs_1 | from flask.ext.sqlalchemy import SQLAlchemy
**postgraphql-refseqs_1 | ImportError: No module named ext.sqlalchemy**
postgraphql-refseqs_1 | [2018-12-03 01:05:48 +0000] [14] [INFO] Worker exiting (pid: 14)
postgraphql-refseqs_1 | [2018-12-03 01:05:48 +0000] [1] [INFO] Shutting down: Master
postgraphql-refseqs_1 | [2018-12-03 01:05:48 +0000] [1] [INFO] Reason: Worker failed to boot.
dockerized-gmod-deployment_postgraphql-refseqs_1 exited with code 3
Missing python module pip requirement somewhere in postgraphql-refseqs?
Hi @erasche and @nathandunn ,
I have got the following docker-compose.yml file:
apollo:
image: quay.io/gmod/docker-apollo:apollo-only
restart: always
links:
- apollo_db
- chado
ports:
- "8888:8080"
environment:
- WEBAPOLLO_DB_USERNAME=postgres
- WEBAPOLLO_DB_PASSWORD=password
- WEBAPOLLO_DB_DRIVER="org.postgresql.Driver"
- WEBAPOLLO_DB_DIALECT="org.hibernate.dialect.PostgresPlusDialect"
- WEBAPOLLO_DB_URI="jdbc:postgresql://db/postgres"
- WEBAPOLLO_CHADO_DB_USERNAME=postgres
- WEBAPOLLO_CHADO_DB_PASSWORD=password
- WEBAPOLLO_CHADO_DB_DRIVER="org.postgresql.Driver"
- WEBAPOLLO_CHADO_DB_DIALECT="org.hibernate.dialect.PostgresPlusDialect"
- WEBAPOLLO_CHADO_DB_URI="jdbc:postgresql://chado/postgres"
volumes:
- ./data/jbrowse:/data
- ./data/postgres-data:/var/lib/postgresql
chado:
image: erasche/chado:latest
environment:
- POSTGRES_PASSWORD=password
volumes:
- ./data/postgres-data:/var/lib/postgresql
apollo_db:
image: postgres:latest
environment:
- POSTGRES_PASSWORD=postgres
However, I got many Errors and Execptions :
apollo_1 | Jul 13, 2018 8:04:00 AM org.apache.catalina.startup.Catalina stopServer
apollo_1 | SEVERE: Could not contact [localhost:[8005]]. Tomcat may not be running.
apollo_1 | Jul 13, 2018 8:04:00 AM org.apache.catalina.startup.Catalina stopServer
apollo_1 | SEVERE: Catalina.stop:
apollo_1 | java.net.ConnectException: Connection refused (Connection refused)
apollo_1 | at java.net.PlainSocketImpl.socketConnect(Native Method)
apollo_1 | at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
apollo_1 | at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
apollo_1 | at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
apollo_1 | at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
apollo_1 | at java.net.Socket.connect(Socket.java:589)
apollo_1 | at java.net.Socket.connect(Socket.java:538)
apollo_1 | at java.net.Socket.<init>(Socket.java:434)
apollo_1 | at java.net.Socket.<init>(Socket.java:211)
apollo_1 | at org.apache.catalina.startup.Catalina.stopServer(Catalina.java:497)
apollo_1 | at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
apollo_1 | at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
apollo_1 | at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
apollo_1 | at java.lang.reflect.Method.invoke(Method.java:498)
apollo_1 | at org.apache.catalina.startup.Bootstrap.stopServer(Bootstrap.java:406)
apollo_1 | at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:495)
apollo_1 |
apollo_1 | Starting tomcat with /usr/local/tomcat/
apollo_1 | Tomcat started.
...
chado_1 | /usr/local/bin/docker-entrypoint.sh: running /docker-entrypoint-initdb.d/00-load_schema.sh
chado_1 | ERROR: relation "chadoprop" does not exist at character 15
chado_1 | STATEMENT: select * from chadoprop
chado_1 | SET
chado_1 | SET
chado_1 | ERROR: unrecognized configuration parameter "idle_in_transaction_session_timeout"
chado_1 | STATEMENT: SET idle_in_transaction_session_timeout = 0;
chado_1 | ERROR: unrecognized configuration parameter "idle_in_transaction_session_timeout"
...
chado_1 | ERROR: function create_point(integer, bigint) does not exist at character 13
chado_1 | HINT: No function matches the given name and argument types. You might need to add explicit type casts.
chado_1 | QUERY: SELECT box (create_point(0, $1), create_point($2,500000000))
chado_1 | CONTEXT: SQL function "boxrange" during inlining
chado_1 | STATEMENT: CREATE INDEX bingroup_boxrange ON featuregroup USING gist (public.boxrange(fmin, fmax)) WHERE (is_root = 1);
chado_1 | ERROR: function create_point(integer, bigint) does not exist
chado_1 | LINE 1: SELECT box (create_point(0, $1), create_point($2,500000000))
chado_1 | ^
chado_1 | HINT: No function matches the given name and argument types. You might need to add explicit type casts.
chado_1 | QUERY: SELECT box (create_point(0, $1), create_point($2,500000000))
chado_1 | CONTEXT: SQL function "boxrange" during inlining
...
chado_1 | ERROR: canceling autovacuum task
chado_1 | CONTEXT: automatic analyze of table "postgres.public.cvtermpath"
...
apollo_1 | 13-Jul-2018 08:05:23.079 SEVERE [localhost-startStop-1] org.apache.tomcat.jdbc.pool.ConnectionPool.init Unable to create initial connections of pool.
apollo_1 | org.postgresql.util.PSQLException: Connection to 127.0.0.1:5432 refused. Check that the hostname and port are correct and that the postmaster is accepting TCP/IP connections.
apollo_1 | at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:262)
apollo_1 | at org.postgresql.core.ConnectionFactory.openConnection(ConnectionFactory.java:52)
apollo_1 | at org.postgresql.jdbc.PgConnection.<init>(PgConnection.java:216)
apollo_1 | at org.postgresql.Driver.makeConnection(Driver.java:404)
apollo_1 | at org.postgresql.Driver.connect(Driver.java:272)
apollo_1 | at org.apache.tomcat.jdbc.pool.PooledConnection.connectUsingDriver(PooledConnection.java:278)
apollo_1 | at org.apache.tomcat.jdbc.pool.PooledConnection.connect(PooledConnection.java:182)
apollo_1 | at org.apache.tomcat.jdbc.pool.ConnectionPool.createConnection(ConnectionPool.java:712)
apollo_1 | at org.apache.tomcat.jdbc.pool.ConnectionPool.borrowConnection(ConnectionPool.java:646)
apollo_1 | at org.apache.tomcat.jdbc.pool.ConnectionPool.init(ConnectionPool.java:468)
apollo_1 | at org.apache.tomcat.jdbc.pool.ConnectionPool.<init>(ConnectionPool.java:145)
apollo_1 | at org.apache.tomcat.jdbc.pool.DataSourceProxy.pCreatePool(DataSourceProxy.java:116)
apollo_1 | at org.apache.tomcat.jdbc.pool.DataSourceProxy.createPool(DataSourceProxy.java:103)
apollo_1 | at org.apache.tomcat.jdbc.pool.DataSourceProxy.getConnection(DataSourceProxy.java:127)
apollo_1 | at org.springframework.jdbc.datasource.LazyConnectionDataSourceProxy.afterPropertiesSet(LazyConnectionDataSourceProxy.java:162)
apollo_1 | at org.springframework.jdbc.datasource.LazyConnectionDataSourceProxy.<init>(LazyConnectionDataSourceProxy.java:106)
apollo_1 | at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
apollo_1 | at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
apollo_1 | at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
apollo_1 | at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
apollo_1 | at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:147)
apollo_1 | at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:122)
apollo_1 | at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:267)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1137)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1040)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:504)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303)
apollo_1 | at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:194)
apollo_1 | at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:351)
apollo_1 | at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:108)
apollo_1 | at org.springframework.beans.factory.support.ConstructorResolver.resolveConstructorArguments(ConstructorResolver.java:648)
apollo_1 | at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:140)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1137)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1040)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:504)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303)
apollo_1 | at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:194)
apollo_1 | at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:351)
apollo_1 | at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:108)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1475)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1220)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:537)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303)
apollo_1 | at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:194)
apollo_1 | at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:351)
apollo_1 | at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:108)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1475)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1220)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:537)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303)
apollo_1 | at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:194)
apollo_1 | at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:351)
apollo_1 | at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:108)
apollo_1 | at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveManagedList(BeanDefinitionValueResolver.java:382)
apollo_1 | at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:157)
apollo_1 | at org.springframework.beans.factory.support.ConstructorResolver.resolveConstructorArguments(ConstructorResolver.java:634)
apollo_1 | at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:140)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1137)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1040)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:504)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303)
apollo_1 | at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199)
apollo_1 | at org.codehaus.groovy.grails.orm.support.TransactionManagerPostProcessor.initialize(TransactionManagerPostProcessor.java:74)
apollo_1 | at org.codehaus.groovy.grails.orm.support.TransactionManagerPostProcessor.setBeanFactory(TransactionManagerPostProcessor.java:52)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeAwareMethods(AbstractAutowireCapableBeanFactory.java:1591)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1559)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:539)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303)
apollo_1 | at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199)
apollo_1 | at org.springframework.context.support.PostProcessorRegistrationDelegate.registerBeanPostProcessors(PostProcessorRegistrationDelegate.java:199)
apollo_1 | at org.springframework.context.support.AbstractApplicationContext.registerBeanPostProcessors(AbstractApplicationContext.java:616)
apollo_1 | at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:465)
apollo_1 | at org.codehaus.groovy.grails.commons.spring.DefaultRuntimeSpringConfiguration.getApplicationContext(DefaultRuntimeSpringConfiguration.java:156)
apollo_1 | at org.codehaus.groovy.grails.commons.spring.GrailsRuntimeConfigurator.initializeContext(GrailsRuntimeConfigurator.java:188)
apollo_1 | at org.codehaus.groovy.grails.commons.spring.GrailsRuntimeConfigurator.configure(GrailsRuntimeConfigurator.java:168)
apollo_1 | at org.codehaus.groovy.grails.commons.spring.GrailsRuntimeConfigurator.configure(GrailsRuntimeConfigurator.java:127)
apollo_1 | at org.codehaus.groovy.grails.web.context.GrailsConfigUtils.configureWebApplicationContext(GrailsConfigUtils.java:126)
apollo_1 | at org.codehaus.groovy.grails.web.context.GrailsContextLoaderListener.initWebApplicationContext(GrailsContextLoaderListener.java:109)
apollo_1 | at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:106)
apollo_1 | at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4792)
apollo_1 | at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5256)
apollo_1 | at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
apollo_1 | at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:754)
apollo_1 | at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:730)
apollo_1 | at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
apollo_1 | at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:985)
apollo_1 | at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1857)
apollo_1 | at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
apollo_1 | at java.util.concurrent.FutureTask.run(FutureTask.java:266)
apollo_1 | at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
apollo_1 | at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
apollo_1 | at java.lang.Thread.run(Thread.java:748)
apollo_1 | Caused by: java.net.ConnectException: Connection refused (Connection refused)
apollo_1 | at java.net.PlainSocketImpl.socketConnect(Native Method)
apollo_1 | at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
apollo_1 | at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
apollo_1 | at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
apollo_1 | at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
apollo_1 | at java.net.Socket.connect(Socket.java:589)
apollo_1 | at org.postgresql.core.PGStream.<init>(PGStream.java:61)
apollo_1 | at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:144)
apollo_1 | ... 109 more
apollo_1 |
apollo_1 | 13-Jul-2018 08:05:23.125 SEVERE [localhost-startStop-1] org.apache.tomcat.jdbc.pool.ConnectionPool.init Unable to create initial connections of pool.
apollo_1 | org.postgresql.util.PSQLException: Connection to 127.0.0.1:5432 refused. Check that the hostname and port are correct and that the postmaster is accepting TCP/IP connections.
apollo_1 | at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:262)
apollo_1 | at org.postgresql.core.ConnectionFactory.openConnection(ConnectionFactory.java:52)
apollo_1 | at org.postgresql.jdbc.PgConnection.<init>(PgConnection.java:216)
apollo_1 | at org.postgresql.Driver.makeConnection(Driver.java:404)
apollo_1 | at org.postgresql.Driver.connect(Driver.java:272)
apollo_1 | at org.apache.tomcat.jdbc.pool.PooledConnection.connectUsingDriver(PooledConnection.java:278)
apollo_1 | at org.apache.tomcat.jdbc.pool.PooledConnection.connect(PooledConnection.java:182)
apollo_1 | at org.apache.tomcat.jdbc.pool.ConnectionPool.createConnection(ConnectionPool.java:712)
apollo_1 | at org.apache.tomcat.jdbc.pool.ConnectionPool.borrowConnection(ConnectionPool.java:646)
apollo_1 | at org.apache.tomcat.jdbc.pool.ConnectionPool.init(ConnectionPool.java:468)
apollo_1 | at org.apache.tomcat.jdbc.pool.ConnectionPool.<init>(ConnectionPool.java:145)
apollo_1 | at org.apache.tomcat.jdbc.pool.DataSourceProxy.pCreatePool(DataSourceProxy.java:116)
apollo_1 | at org.apache.tomcat.jdbc.pool.DataSourceProxy.createPool(DataSourceProxy.java:103)
apollo_1 | at org.apache.tomcat.jdbc.pool.DataSourceProxy.getConnection(DataSourceProxy.java:127)
apollo_1 | at org.springframework.jdbc.datasource.LazyConnectionDataSourceProxy.afterPropertiesSet(LazyConnectionDataSourceProxy.java:162)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1631)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1568)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:539)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303)
apollo_1 | at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:194)
apollo_1 | at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:351)
apollo_1 | at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:108)
apollo_1 | at org.springframework.beans.factory.support.ConstructorResolver.resolveConstructorArguments(ConstructorResolver.java:648)
apollo_1 | at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:140)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1137)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1040)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:504)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303)
apollo_1 | at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:194)
apollo_1 | at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:351)
apollo_1 | at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:108)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1475)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1220)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:537)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303)
apollo_1 | at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:194)
apollo_1 | at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:351)
apollo_1 | at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:108)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1475)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1220)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:537)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303)
apollo_1 | at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:194)
apollo_1 | at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:351)
apollo_1 | at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:108)
apollo_1 | at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveManagedList(BeanDefinitionValueResolver.java:382)
apollo_1 | at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:157)
apollo_1 | at org.springframework.beans.factory.support.ConstructorResolver.resolveConstructorArguments(ConstructorResolver.java:634)
apollo_1 | at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:140)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1137)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1040)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:504)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303)
apollo_1 | at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199)
apollo_1 | at org.codehaus.groovy.grails.orm.support.TransactionManagerPostProcessor.initialize(TransactionManagerPostProcessor.java:74)
apollo_1 | at org.codehaus.groovy.grails.orm.support.TransactionManagerPostProcessor.setBeanFactory(TransactionManagerPostProcessor.java:52)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeAwareMethods(AbstractAutowireCapableBeanFactory.java:1591)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1559)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:539)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303)
apollo_1 | at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199)
apollo_1 | at org.springframework.context.support.PostProcessorRegistrationDelegate.registerBeanPostProcessors(PostProcessorRegistrationDelegate.java:199)
apollo_1 | at org.springframework.context.support.AbstractApplicationContext.registerBeanPostProcessors(AbstractApplicationContext.java:616)
apollo_1 | at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:465)
apollo_1 | at org.codehaus.groovy.grails.commons.spring.DefaultRuntimeSpringConfiguration.getApplicationContext(DefaultRuntimeSpringConfiguration.java:156)
apollo_1 | at org.codehaus.groovy.grails.commons.spring.GrailsRuntimeConfigurator.initializeContext(GrailsRuntimeConfigurator.java:188)
apollo_1 | at org.codehaus.groovy.grails.commons.spring.GrailsRuntimeConfigurator.configure(GrailsRuntimeConfigurator.java:168)
apollo_1 | at org.codehaus.groovy.grails.commons.spring.GrailsRuntimeConfigurator.configure(GrailsRuntimeConfigurator.java:127)
apollo_1 | at org.codehaus.groovy.grails.web.context.GrailsConfigUtils.configureWebApplicationContext(GrailsConfigUtils.java:126)
apollo_1 | at org.codehaus.groovy.grails.web.context.GrailsContextLoaderListener.initWebApplicationContext(GrailsContextLoaderListener.java:109)
apollo_1 | at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:106)
apollo_1 | at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4792)
apollo_1 | at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5256)
apollo_1 | at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
apollo_1 | at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:754)
apollo_1 | at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:730)
apollo_1 | at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
apollo_1 | at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:985)
apollo_1 | at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1857)
apollo_1 | at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
apollo_1 | at java.util.concurrent.FutureTask.run(FutureTask.java:266)
apollo_1 | at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
apollo_1 | at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
apollo_1 | at java.lang.Thread.run(Thread.java:748)
apollo_1 | Caused by: java.net.ConnectException: Connection refused (Connection refused)
apollo_1 | at java.net.PlainSocketImpl.socketConnect(Native Method)
apollo_1 | at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
apollo_1 | at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
apollo_1 | at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
apollo_1 | at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
apollo_1 | at java.net.Socket.connect(Socket.java:589)
apollo_1 | at org.postgresql.core.PGStream.<init>(PGStream.java:61)
apollo_1 | at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:144)
apollo_1 | ... 101 more
apollo_1 |
chado_1 | ALTER TABLE
chado_1 | ALTER TABLE
apollo_1 | 13-Jul-2018 08:05:24.526 SEVERE [localhost-startStop-1] org.apache.tomcat.jdbc.pool.ConnectionPool.init Unable to create initial connections of pool.
apollo_1 | org.postgresql.util.PSQLException: Connection to 127.0.0.1:5432 refused. Check that the hostname and port are correct and that the postmaster is accepting TCP/IP connections.
apollo_1 | at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:262)
apollo_1 | at org.postgresql.core.ConnectionFactory.openConnection(ConnectionFactory.java:52)
apollo_1 | at org.postgresql.jdbc.PgConnection.<init>(PgConnection.java:216)
apollo_1 | at org.postgresql.Driver.makeConnection(Driver.java:404)
apollo_1 | at org.postgresql.Driver.connect(Driver.java:272)
apollo_1 | at org.apache.tomcat.jdbc.pool.PooledConnection.connectUsingDriver(PooledConnection.java:278)
apollo_1 | at org.apache.tomcat.jdbc.pool.PooledConnection.connect(PooledConnection.java:182)
apollo_1 | at org.apache.tomcat.jdbc.pool.ConnectionPool.createConnection(ConnectionPool.java:712)
apollo_1 | at org.apache.tomcat.jdbc.pool.ConnectionPool.borrowConnection(ConnectionPool.java:646)
apollo_1 | at org.apache.tomcat.jdbc.pool.ConnectionPool.init(ConnectionPool.java:468)
apollo_1 | at org.apache.tomcat.jdbc.pool.ConnectionPool.<init>(ConnectionPool.java:145)
apollo_1 | at org.apache.tomcat.jdbc.pool.DataSourceProxy.pCreatePool(DataSourceProxy.java:116)
apollo_1 | at org.apache.tomcat.jdbc.pool.DataSourceProxy.createPool(DataSourceProxy.java:103)
apollo_1 | at org.apache.tomcat.jdbc.pool.DataSourceProxy.getConnection(DataSourceProxy.java:127)
apollo_1 | at org.springframework.jdbc.datasource.LazyConnectionDataSourceProxy$LazyConnectionInvocationHandler.getTargetConnection(LazyConnectionDataSourceProxy.java:403)
apollo_1 | at org.springframework.jdbc.datasource.LazyConnectionDataSourceProxy$LazyConnectionInvocationHandler.invoke(LazyConnectionDataSourceProxy.java:376)
apollo_1 | at com.sun.proxy.$Proxy44.getMetaData(Unknown Source)
apollo_1 | at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
apollo_1 | at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
apollo_1 | at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
apollo_1 | at java.lang.reflect.Method.invoke(Method.java:498)
apollo_1 | at org.springframework.jdbc.datasource.TransactionAwareDataSourceProxy$TransactionAwareInvocationHandler.invoke(TransactionAwareDataSourceProxy.java:240)
apollo_1 | at com.sun.proxy.$Proxy44.getMetaData(Unknown Source)
apollo_1 | at org.hibernate.engine.jdbc.internal.JdbcServicesImpl.configure(JdbcServicesImpl.java:126)
apollo_1 | at org.hibernate.boot.registry.internal.StandardServiceRegistryImpl.configureService(StandardServiceRegistryImpl.java:111)
apollo_1 | at org.hibernate.service.internal.AbstractServiceRegistryImpl.initializeService(AbstractServiceRegistryImpl.java:234)
apollo_1 | at org.hibernate.service.internal.AbstractServiceRegistryImpl.getService(AbstractServiceRegistryImpl.java:206)
apollo_1 | at org.hibernate.cfg.Configuration.buildTypeRegistrations(Configuration.java:1887)
apollo_1 | at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1845)
apollo_1 | at org.codehaus.groovy.grails.orm.hibernate.cfg.GrailsAnnotationConfiguration.buildSessionFactory(GrailsAnnotationConfiguration.java:372)
apollo_1 | at org.codehaus.groovy.grails.orm.hibernate.ConfigurableLocalSessionFactoryBean.doBuildSessionFactory(ConfigurableLocalSessionFactoryBean.java:479)
apollo_1 | at org.codehaus.groovy.grails.orm.hibernate.ConfigurableLocalSessionFactoryBean.buildSessionFactory(ConfigurableLocalSessionFactoryBean.java:473)
apollo_1 | at org.codehaus.groovy.grails.orm.hibernate.ConfigurableLocalSessionFactoryBean.afterPropertiesSet(ConfigurableLocalSessionFactoryBean.java:387)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1631)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1568)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:539)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303)
apollo_1 | at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:194)
apollo_1 | at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:351)
apollo_1 | at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:108)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1475)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1220)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:537)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303)
apollo_1 | at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:194)
apollo_1 | at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:351)
apollo_1 | at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:108)
apollo_1 | at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveManagedList(BeanDefinitionValueResolver.java:382)
apollo_1 | at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:157)
apollo_1 | at org.springframework.beans.factory.support.ConstructorResolver.resolveConstructorArguments(ConstructorResolver.java:634)
apollo_1 | at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:140)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1137)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1040)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:504)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303)
apollo_1 | at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199)
apollo_1 | at org.codehaus.groovy.grails.orm.support.TransactionManagerPostProcessor.initialize(TransactionManagerPostProcessor.java:74)
apollo_1 | at org.codehaus.groovy.grails.orm.support.TransactionManagerPostProcessor.setBeanFactory(TransactionManagerPostProcessor.java:52)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeAwareMethods(AbstractAutowireCapableBeanFactory.java:1591)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1559)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:539)
apollo_1 | at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303)
apollo_1 | at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299)
apollo_1 | at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199)
apollo_1 | at org.springframework.context.support.PostProcessorRegistrationDelegate.registerBeanPostProcessors(PostProcessorRegistrationDelegate.java:199)
apollo_1 | at org.springframework.context.support.AbstractApplicationContext.registerBeanPostProcessors(AbstractApplicationContext.java:616)
apollo_1 | at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:465)
apollo_1 | at org.codehaus.groovy.grails.commons.spring.DefaultRuntimeSpringConfiguration.getApplicationContext(DefaultRuntimeSpringConfiguration.java:156)
apollo_1 | at org.codehaus.groovy.grails.commons.spring.GrailsRuntimeConfigurator.initializeContext(GrailsRuntimeConfigurator.java:188)
apollo_1 | at org.codehaus.groovy.grails.commons.spring.GrailsRuntimeConfigurator.configure(GrailsRuntimeConfigurator.java:168)
apollo_1 | at org.codehaus.groovy.grails.commons.spring.GrailsRuntimeConfigurator.configure(GrailsRuntimeConfigurator.java:127)
apollo_1 | at org.codehaus.groovy.grails.web.context.GrailsConfigUtils.configureWebApplicationContext(GrailsConfigUtils.java:126)
apollo_1 | at org.codehaus.groovy.grails.web.context.GrailsContextLoaderListener.initWebApplicationContext(GrailsContextLoaderListener.java:109)
apollo_1 | at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:106)
apollo_1 | at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4792)
apollo_1 | at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5256)
apollo_1 | at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
apollo_1 | at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:754)
apollo_1 | at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:730)
apollo_1 | at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
apollo_1 | at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:985)
apollo_1 | at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1857)
apollo_1 | at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
apollo_1 | at java.util.concurrent.FutureTask.run(FutureTask.java:266)
apollo_1 | at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
apollo_1 | at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
apollo_1 | at java.lang.Thread.run(Thread.java:748)
apollo_1 | Caused by: java.net.ConnectException: Connection refused (Connection refused)
apollo_1 | at java.net.PlainSocketImpl.socketConnect(Native Method)
apollo_1 | at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
apollo_1 | at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
apollo_1 | at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
apollo_1 | at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
apollo_1 | at java.net.Socket.connect(Socket.java:589)
apollo_1 | at org.postgresql.core.PGStream.<init>(PGStream.java:61)
apollo_1 | at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:144)
apollo_1 | ... 97 more
apollo_1 |
apollo_1 | 2018-07-13 08:05:24,571 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener - Error initializing the application: Error creating bean with name 'transactionManagerPostProcessor': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean '$primaryTransactionManager' while setting constructor argument with key [0]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '$primaryTransactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is java.lang.NullPointerException
apollo_1 | org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManagerPostProcessor': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean '$primaryTransactionManager' while setting constructor argument with key [0]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '$primaryTransactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is java.lang.NullPointerException
apollo_1 | at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
apollo_1 | at java.util.concurrent.FutureTask.run(FutureTask.java:266)
apollo_1 | at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
apollo_1 | at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
apollo_1 | at java.lang.Thread.run(Thread.java:748)
apollo_1 | Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean '$primaryTransactionManager' while setting constructor argument with key [0]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '$primaryTransactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is java.lang.NullPointerException
apollo_1 | ... 5 more
apollo_1 | Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name '$primaryTransactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is java.lang.NullPointerException
apollo_1 | ... 5 more
apollo_1 | Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is java.lang.NullPointerException
apollo_1 | ... 5 more
apollo_1 | Caused by: java.lang.NullPointerException
apollo_1 | ... 5 more
apollo_1 | 2018-07-13 08:05:24,572 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener - Error initializing Grails: Error creating bean with name 'transactionManagerPostProcessor': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean '$primaryTransactionManager' while setting constructor argument with key [0]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '$primaryTransactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is java.lang.NullPointerException
apollo_1 | org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManagerPostProcessor': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean '$primaryTransactionManager' while setting constructor argument with key [0]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '$primaryTransactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is java.lang.NullPointerException
apollo_1 | at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
apollo_1 | at java.util.concurrent.FutureTask.run(FutureTask.java:266)
apollo_1 | at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
apollo_1 | at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
apollo_1 | at java.lang.Thread.run(Thread.java:748)
apollo_1 | Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager': Cannot resolve reference to bean '$primaryTransactionManager' while setting constructor argument with key [0]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '$primaryTransactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is java.lang.NullPointerException
apollo_1 | ... 5 more
apollo_1 | Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name '$primaryTransactionManager': Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is java.lang.NullPointerException
apollo_1 | ... 5 more
apollo_1 | Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory': Invocation of init method failed; nested exception is java.lang.NullPointerException
apollo_1 | ... 5 more
apollo_1 | Caused by: java.lang.NullPointerException
apollo_1 | ... 5 more
apollo_1 | 13-Jul-2018 08:05:24.585 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.startInternal One or more listeners failed to start. Full details will be found in the appropriate container log file
apollo_1 | 13-Jul-2018 08:05:24.635 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.startInternal Context [] startup failed due to previous errors
apollo_1 | 13-Jul-2018 08:05:24.675 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesJdbc The web application [ROOT] 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.
apollo_1 | 13-Jul-2018 08:05:24.714 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployWAR Deployment of web application archive [/usr/local/tomcat/webapps/ROOT.war] has finished in [76,174] ms
apollo_1 | 13-Jul-2018 08:05:24.745 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-8080"]
What did I miss?
Thank you in advance,
Michal
https://github.com/pombase/canto/ it's neat stuff.
Canto is an online tool that supports functional gene annotation by community researchers as well as by professional curators. It provides a simple interface to gather genetic and molecular data from publications for inclusion in public biological databases. Canto employs OBO ontologies to ensure a consistent vocabulary is used to describe gene and gene product functionality and location.
Hi @erasche,
I updated Apollo in your dockerfile (erasche/docker-apollo) ENV WEBAPOLLO_VERSION 6189ff9e2973e1523ddcdbeee9d258c435c42a54 but the build failed:
$ docker-compose up
Building apollo
Step 1/8 : FROM tomcat:8.5-jre8-alpine
8.5-jre8-alpine: Pulling from library/tomcat
8e3ba11ec2a2: Pull complete
311ad0da4533: Pull complete
391a6a6b3651: Pull complete
b019068f0374: Pull complete
4af2bc8629f4: Pull complete
47b50a450cc9: Pull complete
Digest: sha256:ff9b220a0e311c29e12a85163fce690d90c0d33bcc8bf532fd25a6a0d9b43ddb
Status: Downloaded newer image for tomcat:8.5-jre8-alpine
---> cb132aeae2f7
Step 2/8 : COPY build.sh /bin/build.sh
---> 4b705965d849
Step 3/8 : ADD apollo-config.groovy /apollo/apollo-config.groovy
---> 43a3c9513e95
Step 4/8 : ENV WEBAPOLLO_VERSION 6189ff9e2973e1523ddcdbeee9d258c435c42a54
---> Running in ac59929f09d4
Removing intermediate container ac59929f09d4
---> 35be0d106992
Step 5/8 : RUN apk update && apk add --update tar && apk add curl ca-certificates bash nodejs git postgresql-client maven libpng make g++ zlib-dev expat-dev nodejs-npm sudo openssh-client perl && npm install -g bower && adduser -s /bin/bash -D -h /apollo apollo && curl -L https://github.com/GMOD/Apollo/archive/${WEBAPOLLO_VERSION}.tar.gz | tar xzf - --strip-components=1 -C /apollo && chown -R apollo:apollo /apollo && apk add openjdk8 openjdk8-jre && cp /usr/lib/jvm/java-1.8-openjdk/lib/tools.jar /usr/lib/jvm/java-1.8-openjdk/jre/lib/ext/tools.jar && sudo -u apollo /bin/build.sh && apk del curl bash nodejs git libpng make g++ nodejs-npm openjdk8 sudo
---> Running in addef1f810b6
fetch http://dl-cdn.alpinelinux.org/alpine/v3.8/main/x86_64/APKINDEX.tar.gz
fetch http://dl-cdn.alpinelinux.org/alpine/v3.8/community/x86_64/APKINDEX.tar.gz
v3.8.0-28-g923d74cddf [http://dl-cdn.alpinelinux.org/alpine/v3.8/main]
v3.8.0-28-g923d74cddf [http://dl-cdn.alpinelinux.org/alpine/v3.8/community]
OK: 9539 distinct packages available
(1/1) Installing tar (1.30-r0)
Executing busybox-1.28.4-r0.trigger
OK: 94 MiB in 63 packages
(1/38) Installing nghttp2-libs (1.32.0-r0)
(2/38) Installing libssh2 (1.8.0-r3)
(3/38) Installing libcurl (7.61.0-r0)
(4/38) Installing curl (7.61.0-r0)
(5/38) Installing expat (2.2.5-r0)
(6/38) Installing pkgconf (1.5.1-r0)
(7/38) Installing expat-dev (2.2.5-r0)
(8/38) Installing binutils (2.30-r5)
(9/38) Installing gmp (6.1.2-r1)
(10/38) Installing isl (0.18-r0)
(11/38) Installing libgomp (6.4.0-r8)
(12/38) Installing libatomic (6.4.0-r8)
(13/38) Installing mpfr3 (3.1.5-r1)
(14/38) Installing mpc1 (1.0.3-r1)
(15/38) Installing gcc (6.4.0-r8)
(16/38) Installing musl-dev (1.1.19-r10)
(17/38) Installing libc-dev (0.7.1-r0)
(18/38) Installing g++ (6.4.0-r8)
(19/38) Installing pcre2 (10.31-r0)
(20/38) Installing git (2.18.0-r0)
(21/38) Installing make (4.2.1-r2)
(22/38) Installing maven (3.5.4-r1)
(23/38) Installing c-ares (1.14.0-r0)
(24/38) Installing http-parser (2.8.1-r0)
(25/38) Installing libuv (1.20.2-r0)
(26/38) Installing nodejs (8.11.3-r1)
(27/38) Installing npm (8.11.3-r1)
(28/38) Installing openssh-keygen (7.7_p1-r2)
(29/38) Installing openssh-client (7.7_p1-r2)
(30/38) Installing perl (5.26.2-r1)
(31/38) Installing libedit (20170329.3.1-r3)
(32/38) Installing db (5.3.28-r0)
(33/38) Installing libsasl (2.1.26-r13)
(34/38) Installing libldap (2.4.46-r0)
(35/38) Installing libpq (10.4-r0)
(36/38) Installing postgresql-client (10.4-r0)
(37/38) Installing sudo (1.8.23-r2)
(38/38) Installing zlib-dev (1.2.11-r1)
Executing busybox-1.28.4-r0.trigger
OK: 370 MiB in 101 packages
npm WARN deprecated [email protected]: We don't recommend using Bower for new projects. Please consider Yarn and Webpack or Parcel. You can read how to migrate legacy project here: https://bower.io/blog/2017/how-to-migrate-away-from-bower/
/usr/bin/bower -> /usr/lib/node_modules/bower/bin/bower
+ [email protected]
added 1 package in 4.418s
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 153 0 153 0 0 187 0 --:--:-- --:--:-- --:--:-- 187
100 84.3M 0 84.3M 0 0 4823k 0 --:--:-- 0:00:17 --:--:-- 5970k
(1/1) Installing openjdk8 (8.171.11-r0)
Executing java-common-0.1-r0.trigger
OK: 389 MiB in 102 packages
+ export JAVA_HOME=/usr/lib/jvm/java-1.8-openjdk/jre
+ JAVA_HOME=/usr/lib/jvm/java-1.8-openjdk/jre
+ cd /apollo/
+ ./apollo deploy
Grails not found using grailsw
Gradle not found using gradlew
Node Version: 8
Npm Version: 5
javac 1.8.0_171 found
javac installed
JDK 1.8 found: javac 1.8.0_171
Downloading https://services.gradle.org/distributions/gradle-2.11-all.zip
...
Unzipping /apollo/.gradle/wrapper/dists/gradle-2.11-all/ace7yl0a7udokebb27mt9s3qr/gradle-2.11-all.zip to /apollo/.gradle/wrapper/dists/gradle-2.11-all/ace7yl0a7udokebb27mt9s3qr
Set executable permissions for: /apollo/.gradle/wrapper/dists/gradle-2.11-all/ace7yl0a7udokebb27mt9s3qr/gradle-2.11/bin/gradle
Final JBrowse settings [git:[url:https://github.com/GMOD/jbrowse, tag:9d765aecaee02a41844fed11a241fdb4c35fc9f8, alwaysPull:true, alwaysRecheck:true], plugins:[NeatHTMLFeatures:[included:true], NeatCanvasFeatures:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true], GCContent:[git:https://github.com/elsiklab/gccontent, branch:master, alwaysRecheck:true, alwaysPull:true], MyVariantInfo:[git:https://github.com/GMOD/myvariantviewer, branch:master, alwaysRecheck:true, alwaysPull:true], SashimiPlot:[git:https://github.com/cmdcolin/sashimiplot, branch:master, alwaysPull:true]]]
Final plugins [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true], NeatHTMLFeatures:[included:true], NeatCanvasFeatures:[included:true], GCContent:[git:https://github.com/elsiklab/gccontent, branch:master, alwaysRecheck:true, alwaysPull:true], MyVariantInfo:[git:https://github.com/GMOD/myvariantviewer, branch:master, alwaysRecheck:true, alwaysPull:true], SashimiPlot:[git:https://github.com/cmdcolin/sashimiplot, branch:master, alwaysPull:true]]
Copying apollo plugin
Handling JBrowse release [git:[url:https://github.com/GMOD/jbrowse, tag:9d765aecaee02a41844fed11a241fdb4c35fc9f8, alwaysPull:true, alwaysRecheck:true], plugins:[NeatHTMLFeatures:[included:true], NeatCanvasFeatures:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true], GCContent:[git:https://github.com/elsiklab/gccontent, branch:master, alwaysRecheck:true, alwaysPull:true], MyVariantInfo:[git:https://github.com/GMOD/myvariantviewer, branch:master, alwaysRecheck:true, alwaysPull:true], SashimiPlot:[git:https://github.com/cmdcolin/sashimiplot, branch:master, alwaysPull:true]]]
Handling JBrowse [git:[url:https://github.com/GMOD/jbrowse, tag:9d765aecaee02a41844fed11a241fdb4c35fc9f8, alwaysPull:true, alwaysRecheck:true], plugins:[NeatHTMLFeatures:[included:true], NeatCanvasFeatures:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true], GCContent:[git:https://github.com/elsiklab/gccontent, branch:master, alwaysRecheck:true, alwaysPull:true], MyVariantInfo:[git:https://github.com/GMOD/myvariantviewer, branch:master, alwaysRecheck:true, alwaysPull:true], SashimiPlot:[git:https://github.com/cmdcolin/sashimiplot, branch:master, alwaysPull:true]]]
Setting up JBrowse...
:evaluateJBrowseConfigs UP-TO-DATE
:installJBrowse
Installing JBrowse [git:[url:https://github.com/GMOD/jbrowse, tag:9d765aecaee02a41844fed11a241fdb4c35fc9f8, alwaysPull:true, alwaysRecheck:true], plugins:[NeatHTMLFeatures:[included:true], NeatCanvasFeatures:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true], GCContent:[git:https://github.com/elsiklab/gccontent, branch:master, alwaysRecheck:true, alwaysPull:true], MyVariantInfo:[git:https://github.com/GMOD/myvariantviewer, branch:master, alwaysRecheck:true, alwaysPull:true], SashimiPlot:[git:https://github.com/cmdcolin/sashimiplot, branch:master, alwaysPull:true]]]
Cloning: https://github.com/GMOD/jbrowse into jbrowse-download
Cloning repo with https://github.com/GMOD/jbrowse,jbrowse-download,tags/9d765aecaee02a41844fed11a241fdb4c35fc9f8
Final github URL: GMOD/jbrowse#9d765aecaee02a41844fed11a241fdb4c35fc9f8
Using npm to install: GMOD/jbrowse#9d765aecaee02a41844fed11a241fdb4c35fc9f8
npm WARN deprecated [email protected]: Unmaintained namespace. Please use the file-saver package: https://www.npmjs.com/package/file-saver
npm notice created a lockfile as package-lock.json. You should commit this file.
+ [email protected]
added 86 packages in 55.924s
Moving JBrowse into position GMOD/jbrowse#9d765aecaee02a41844fed11a241fdb4c35fc9f8
:installJBrowse FAILED
FAILURE: Build failed with an exception.
* Where:
Build file '/apollo/build.gradle' line: 321
* What went wrong:
Execution failed for task ':installJBrowseScript'.
> A problem occurred starting process 'command './setup.sh''
* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.
BUILD FAILED
What did I miss?
Thank you in advance,
Michal
I'm strongly suspecting that this project is in transition towards full implementation.. cutting and pasting its way to fulfillment! That would perhaps explain the following error?
ubuntu@divseek-canada-docker-gmod:/opt/divseekcanada/dockerized-gmod-deployment$ docker-compose pull
Pulling galaxy ... done
Pulling apollo_db ... done
Pulling tripal_db ... done
Pulling chado_jb ... done
Pulling pgadmin4 ... done
Pulling postgraphql-refseqs ... done
Pulling postgraphql ... done
Pulling postgrest ... done
Pulling apollo ... done
Pulling remoteuser ... done
Pulling elasticsearch ... **error**
Pulling tripal ... done
Pulling jbrowse ... **error**
Pulling jbrowse-graphql ... **error**
Pulling proxy ... done
**ERROR: for jbrowse b'manifest for quay.io/galaxy-genome-annotation/jbrowse:1.12.5 not found'**
**ERROR: for jbrowse-graphql b'manifest for quay.io/galaxy-genome-annotation/jbrowse:1.12.5 not found'**
**ERROR: for elasticsearch b'manifest for elasticsearch:latest not found'**
**ERROR: manifest for quay.io/galaxy-genome-annotation/jbrowse:1.12.5 not found**
**manifest for quay.io/galaxy-genome-annotation/jbrowse:1.12.5 not found**
**manifest for elasticsearch:latest not found**
maybe the following will fix (in the docker-compose.yml file?):
elasticsearch:
# I don't see a 'latest' tag in the elasticsearch repo; maybe need to explicitly tag an available release?
image: **docker.elastic.co/elasticsearch/elasticsearch:6.51** # latest seems to be 6.5.1?
jbrowse:
image: quay.io/galaxy-genome-annotation/jbrowse:**v**1.12.5
volumes_from:
- "galaxy:ro"
jbrowse-graphql:
image: quay.io/galaxy-genome-annotation/jbrowse:**v**1.12.5
volumes:
- "./jbgraphql:/data"Not too sure about the jbrowse-graphql... doesn't seem to have its own image yet?
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