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Automate deployment of postgres database schema #3

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bakhansen opened this issue Apr 5, 2018 · 0 comments
Open

Automate deployment of postgres database schema #3

bakhansen opened this issue Apr 5, 2018 · 0 comments
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@bakhansen
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bakhansen commented Apr 5, 2018 •
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Steps to reproduce:

(...)
web-ds_1  | Apr 5, 2018 4:14:11 PM org.hibernate.cfg.annotations.Version <clinit>
web-ds_1  | INFO: Hibernate Annotations 3.3.0.GA
web-ds_1  | Apr 5, 2018 4:14:11 PM org.hibernate.cfg.Environment <clinit>
web-ds_1  | INFO: Hibernate 3.2.1
web-ds_1  | Apr 5, 2018 4:14:11 PM org.hibernate.cfg.Environment <clinit>
web-ds_1  | INFO: hibernate.properties not found
web-ds_1  | Apr 5, 2018 4:14:11 PM org.hibernate.cfg.Environment buildBytecodeProvider
web-ds_1  | INFO: Bytecode provider name : cglib
web-ds_1  | Apr 5, 2018 4:14:11 PM org.hibernate.cfg.Environment <clinit>
web-ds_1  | INFO: using JDK 1.4 java.sql.Timestamp handling
web-ds_1  | Apr 5, 2018 4:14:11 PM org.hibernate.cfg.Configuration configure
web-ds_1  | INFO: configuring from resource: /hibernate.cfg.xml
web-ds_1  | Apr 5, 2018 4:14:11 PM org.hibernate.cfg.Configuration getConfigurationInputStream
web-ds_1  | INFO: Configuration resource: /hibernate.cfg.xml
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.Configuration addResource
web-ds_1  | INFO: Reading mappings from resource : Access.hbm.xml
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.Configuration doConfigure
web-ds_1  | INFO: Configured SessionFactory: null
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.HbmBinder bindRootPersistentClassCommonValues
web-ds_1  | INFO: Mapping class: org.b3mn.poem.Access -> access
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.AnnotationBinder bindClass
web-ds_1  | INFO: Binding entity from annotated class: org.b3mn.poem.Identity
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.annotations.EntityBinder bindTable
web-ds_1  | INFO: Bind entity org.b3mn.poem.Identity on table Identity
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.AnnotationBinder bindClass
web-ds_1  | INFO: Binding entity from annotated class: org.b3mn.poem.Representation
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.annotations.EntityBinder bindTable
web-ds_1  | INFO: Bind entity org.b3mn.poem.Representation on table Representation
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.AnnotationBinder bindClass
web-ds_1  | INFO: Binding entity from annotated class: org.b3mn.poem.Plugin
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.annotations.EntityBinder bindTable
web-ds_1  | INFO: Bind entity org.b3mn.poem.Plugin on table Plugin
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.AnnotationBinder bindClass
web-ds_1  | INFO: Binding entity from annotated class: org.b3mn.poem.Interaction
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.annotations.EntityBinder bindTable
web-ds_1  | INFO: Bind entity org.b3mn.poem.Interaction on table Interaction
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.AnnotationBinder bindClass
web-ds_1  | INFO: Binding entity from annotated class: org.b3mn.poem.Structure
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.annotations.EntityBinder bindTable
web-ds_1  | INFO: Bind entity org.b3mn.poem.Structure on table Structure
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.AnnotationBinder bindClass
web-ds_1  | INFO: Binding entity from annotated class: org.b3mn.poem.Subject
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.annotations.EntityBinder bindTable
web-ds_1  | INFO: Bind entity org.b3mn.poem.Subject on table subject
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.AnnotationBinder bindClass
web-ds_1  | INFO: Binding entity from annotated class: org.b3mn.poem.Setting
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.annotations.EntityBinder bindTable
web-ds_1  | INFO: Bind entity org.b3mn.poem.Setting on table Setting
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.AnnotationBinder bindClass
web-ds_1  | INFO: Binding entity from annotated class: org.b3mn.poem.TagDefinition
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.annotations.EntityBinder bindTable
web-ds_1  | INFO: Bind entity org.b3mn.poem.TagDefinition on table tag_definition
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.AnnotationBinder bindClass
web-ds_1  | INFO: Binding entity from annotated class: org.b3mn.poem.TagRelation
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.annotations.EntityBinder bindTable
web-ds_1  | INFO: Bind entity org.b3mn.poem.TagRelation on table tag_relation
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.AnnotationBinder bindClass
web-ds_1  | INFO: Binding entity from annotated class: org.b3mn.poem.ModelRating
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.annotations.EntityBinder bindTable
web-ds_1  | INFO: Bind entity org.b3mn.poem.ModelRating on table model_rating
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.AnnotationBinder bindClass
web-ds_1  | INFO: Binding entity from annotated class: org.b3mn.poem.Friend
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.annotations.EntityBinder bindTable
web-ds_1  | INFO: Bind entity org.b3mn.poem.Friend on table Friend
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.AnnotationConfiguration secondPassCompile
web-ds_1  | INFO: Hibernate Validator not found: ignoring
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.connection.DriverManagerConnectionProvider configure
web-ds_1  | INFO: Using Hibernate built-in connection pool (not for production use!)
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.connection.DriverManagerConnectionProvider configure
web-ds_1  | INFO: Hibernate connection pool size: 20
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.connection.DriverManagerConnectionProvider configure
web-ds_1  | INFO: autocommit mode: false
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.connection.DriverManagerConnectionProvider configure
web-ds_1  | INFO: using driver: org.postgresql.Driver at URL: jdbc:postgresql://database/poem
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.connection.DriverManagerConnectionProvider configure
web-ds_1  | INFO: connection properties: {user=poem, password=****}
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.SettingsFactory buildSettings
web-ds_1  | INFO: RDBMS: PostgreSQL, version: 8.4.22
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.SettingsFactory buildSettings
web-ds_1  | INFO: JDBC driver: PostgreSQL Native Driver, version: PostgreSQL 8.3 JDBC3 with SSL (build 603)
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.dialect.Dialect <init>
web-ds_1  | INFO: Using dialect: org.hibernate.dialect.PostgreSQLDialect
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.transaction.TransactionFactoryFactory buildTransactionFactory
web-ds_1  | INFO: Using default transaction strategy (direct JDBC transactions)
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.transaction.TransactionManagerLookupFactory getTransactionManagerLookup
web-ds_1  | INFO: No TransactionManagerLookup configured (in JTA environment, use of read-write or transactional second-level cache is not recommended)
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.SettingsFactory buildSettings
web-ds_1  | INFO: Automatic flush during beforeCompletion(): disabled
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.SettingsFactory buildSettings
web-ds_1  | INFO: Automatic session close at end of transaction: disabled
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.SettingsFactory buildSettings
web-ds_1  | INFO: JDBC batch size: 15
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.SettingsFactory buildSettings
web-ds_1  | INFO: JDBC batch updates for versioned data: disabled
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.SettingsFactory buildSettings
web-ds_1  | INFO: Scrollable result sets: enabled
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.SettingsFactory buildSettings
web-ds_1  | INFO: JDBC3 getGeneratedKeys(): disabled
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.SettingsFactory buildSettings
web-ds_1  | INFO: Connection release mode: auto
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.SettingsFactory buildSettings
web-ds_1  | INFO: Default batch fetch size: 1
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.SettingsFactory buildSettings
web-ds_1  | INFO: Generate SQL with comments: disabled
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.SettingsFactory buildSettings
web-ds_1  | INFO: Order SQL updates by primary key: disabled
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.SettingsFactory createQueryTranslatorFactory
web-ds_1  | INFO: Query translator: org.hibernate.hql.ast.ASTQueryTranslatorFactory
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.hql.ast.ASTQueryTranslatorFactory <init>
web-ds_1  | INFO: Using ASTQueryTranslatorFactory
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.SettingsFactory buildSettings
web-ds_1  | INFO: Query language substitutions: {}
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.SettingsFactory buildSettings
web-ds_1  | INFO: JPA-QL strict compliance: disabled
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.SettingsFactory buildSettings
web-ds_1  | INFO: Second-level cache: enabled
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.SettingsFactory buildSettings
web-ds_1  | INFO: Query cache: disabled
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.SettingsFactory createCacheProvider
web-ds_1  | INFO: Cache provider: org.hibernate.cache.HashtableCacheProvider
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.SettingsFactory buildSettings
web-ds_1  | INFO: Optimize cache for minimal puts: disabled
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.SettingsFactory buildSettings
web-ds_1  | INFO: Structured second-level cache entries: disabled
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.SettingsFactory buildSettings
web-ds_1  | INFO: Statistics: disabled
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.SettingsFactory buildSettings
web-ds_1  | INFO: Deleted entity synthetic identifier rollback: disabled
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.cfg.SettingsFactory buildSettings
web-ds_1  | INFO: Default entity-mode: pojo
web-ds_1  | Apr 5, 2018 4:14:12 PM org.hibernate.impl.SessionFactoryImpl <init>
web-ds_1  | INFO: building session factory
web-ds_1  | Apr 5, 2018 4:14:13 PM org.hibernate.impl.SessionFactoryObjectFactory addInstance
web-ds_1  | INFO: Not binding factory to JNDI, no JNDI name configured
db-ds_1   | ERROR:  relation "identity" does not exist at character 60
db-ds_1   | STATEMENT:  select identity.id as id1_0_, identity.uri as uri1_0_ FROM identity where uri=$1
web-ds_1  | Apr 5, 2018 4:14:13 PM org.hibernate.util.JDBCExceptionReporter logExceptions
web-ds_1  | WARNING: SQL Error: 0, SQLState: 42P01
web-ds_1  | Apr 5, 2018 4:14:13 PM org.hibernate.util.JDBCExceptionReporter logExceptions
web-ds_1  | SEVERE: ERROR: relation "identity" does not exist
web-ds_1  | java.lang.NullPointerException
web-ds_1  | 	at org.b3mn.poem.Dispatcher.dispatch(Dispatcher.java:374)
web-ds_1  | 	at org.b3mn.poem.Dispatcher.doGet(Dispatcher.java:404)
web-ds_1  | 	at javax.servlet.http.HttpServlet.service(HttpServlet.java:617)
web-ds_1  | 	at javax.servlet.http.HttpServlet.service(HttpServlet.java:723)
web-ds_1  | 	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
web-ds_1  | 	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
web-ds_1  | 	at org.b3mn.poem.security.filter.AuthenticationFilter.doFilter(AuthenticationFilter.java:155)
web-ds_1  | 	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
web-ds_1  | 	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
web-ds_1  | 	at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
web-ds_1  | 	at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
web-ds_1  | 	at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
web-ds_1  | 	at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
web-ds_1  | 	at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
web-ds_1  | 	at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:293)
web-ds_1  | 	at org.apache.coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java:876)
web-ds_1  | 	at org.apache.coyote.http11.Http11AprProtocol$Http11ConnectionHandler.process(Http11AprProtocol.java:618)
web-ds_1  | 	at org.apache.tomcat.util.net.AprEndpoint$Worker.run(AprEndpoint.java:1790)
web-ds_1  | 	at java.lang.Thread.run(Thread.java:662)

Development in branch: docker-setup

Currently the postgres database is deployed via the web container by executing ant create-schema. But it would probably be useful to deploy it as part of docker-compose.

Docker image postgres:8.4 can run sh files in /docker-entrypoint-initdb.d/ as a part of the first run of docker-compose, but not sql files for instance. sql files are supported in more recent postgres docker images, but that would require ./poem-jvm/data/database/db_schema.sql to be (made) compatible.

The current workaround is to copy in ./poem-jvm/Dockerfile:

COPY data/database/db_schema.sh /docker-entrypoint-initdb.d/
COPY data/database/db_schema.sql /docker-entrypoint-initdb.d/

Where ./poem-jvm/data/database/db_schema.sh executes the following:

#!/bin/bash

gosu postgres postgres --single -jE < /docker-entrypoint-initdb.d/db_schema.sql
echo

It appears to be executed correctly using $ docker-compose -f docker-compose.yml up but the schema is not accessible when visiting http://localhost:9090/backend/poem/repository and requires further investigation/correction.

Related material:
@bakhansen bakhansen changed the title Automate deployment of postgres database Automate deployment of postgres database schema Apr 5, 2018
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