work in progress

docker/runner/config/application.tmpl

@@ -3,14 +3,14 @@
 # See http://docs.spring.io/spring-boot/docs/current/reference/html/common-application-properties.html
 spring:
   datasource:
-    url: {{ default .Env.DB_URL "jdbc:postgresql://172.22.0.1:5432/postgres" }}
+    url: {{ default .Env.DB_URL "jdbc:postgresql://172.22.0.1:5433/postgres" }}
     username: {{ default .Env.DB_USER "postgres" }}
     password: {{ .Env.DB_PASSWORD }}
     driver-class-name: org.postgresql.Driver
-  variablesDatasource:
-    url: {{ default .Env.VARIABLES_DB_URL "jdbc:postgresql://172.22.0.1:5433/postgres" }}
-    username: {{ default .Env.VARIABLES_DB_USER "postgres" }}
-    password: {{ .Env.VARIABLES_DB_PASSWORD }}
+  metaDatasource:
+    url: {{ default .Env.META_DB_URL "jdbc:postgresql://172.22.0.1:5432/postgres" }}
+    username: {{ default .Env.META_DB_USER "postgres" }}
+    password: {{ .Env.META_DB_PASSWORD }}
     driver-class-name: org.postgresql.Driver
   jpa:
     hibernate:

src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java

@@ -2,11 +2,16 @@ package eu.hbp.mip.configuration;
 
 import org.flywaydb.core.Flyway;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.boot.autoconfigure.jdbc.DataSourceBuilder;
+import org.springframework.boot.context.properties.ConfigurationProperties;
 import org.springframework.boot.orm.jpa.EntityScan;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.DependsOn;
+import org.springframework.context.annotation.Primary;
 import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
+import org.springframework.jdbc.core.JdbcTemplate;
 import org.springframework.orm.jpa.JpaVendorAdapter;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 import org.springframework.orm.jpa.vendor.HibernateJpaVendorAdapter;
@@ -22,27 +27,41 @@ import javax.sql.DataSource;
 @EntityScan(basePackages = "eu.hbp.mip.model")
 public class PersistenceConfiguration {
 
-    @Autowired
-    DataSource dataSource;
+    @Bean(name = "datasource")
+    @Primary
+    @ConfigurationProperties(prefix="spring.datasource")
+    public DataSource dataSource() {
+        return DataSourceBuilder.create().build();
+    }
 
-    @Autowired
-    DataSource variablesDatasource;  //  TODO: Fix this problem
+    @Bean(name = "metaDatasource")
+    @ConfigurationProperties(prefix="spring.variablesDatasource")
+    public DataSource metaDataSource() {
+        return DataSourceBuilder.create().build();
+    }
 
     @Bean
+    @Autowired
+    @Qualifier("metaJDBC")
+    public JdbcTemplate metaJDBC() {
+        return new JdbcTemplate(metaDataSource());
+    }
+
+    @Bean(name = "metaEntityManagerFactory")
     @DependsOn("flyway")
-    public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
+    public LocalContainerEntityManagerFactoryBean metaEntityManagerFactory() {
         LocalContainerEntityManagerFactoryBean em = new LocalContainerEntityManagerFactoryBean();
-        em.setDataSource(dataSource);
+        em.setDataSource(dataSource());
         JpaVendorAdapter vendorAdapter = new HibernateJpaVendorAdapter();
         em.setJpaVendorAdapter(vendorAdapter);
         return em;
     }
 
-    @Bean(initMethod = "migrate")
-    public Flyway flyway() {
+    @Bean(name = "metaMigrations", initMethod = "migrate")
+    public Flyway metaMigrations() {
         Flyway flyway = new Flyway();
         flyway.setBaselineOnMigrate(true);
-        flyway.setDataSource(dataSource);
+        flyway.setDataSource(metaDataSource());
         return flyway;
     }
 

src/main/java/eu/hbp/mip/controllers/StatsApi.java

@@ -13,14 +13,13 @@ import io.swagger.annotations.ApiResponse;
 import io.swagger.annotations.ApiResponses;
 import org.apache.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.http.ResponseEntity;
 import org.springframework.jdbc.core.JdbcTemplate;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestMethod;
 import org.springframework.web.bind.annotation.RestController;
 
-import javax.sql.DataSource;
-
 import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
 
 @RestController
@@ -37,8 +36,8 @@ public class StatsApi {
     ArticleRepository articleRepository;
 
     @Autowired
-    DataSource variablesDatasource;
-
+    @Qualifier("metaJDBC")
+    private JdbcTemplate metaJDBC;
 
     @ApiOperation(value = "Get general statistics", response = GeneralStats.class)
     @ApiResponses(value = {@ApiResponse(code = 200, message = "Found"), @ApiResponse(code = 404, message = "Not found") })
@@ -57,9 +56,8 @@ public class StatsApi {
 
     private Long countVariables()
     {
-        JdbcTemplate db = new JdbcTemplate(variablesDatasource);
-        LOGGER.warn("TEST DB : " + db.queryForObject("select count(*) from information_schema.tables", Long.class));  // This is a test
-        Long count = db.queryForObject("select count(*) from adni_merge", Long.class);  // TODO: compute from adni_merge DB
+        LOGGER.warn("TEST DB : " + metaJDBC.queryForObject("select count(*) from information_schema.tables", Long.class));  // This is a test
+        Long count = metaJDBC.queryForObject("select count(*) from adni_merge", Long.class);  // TODO: compute from adni_merge DB
         return count;
     }