From da06c41065ea3531efcb46597bec007a1d068f85 Mon Sep 17 00:00:00 2001
From: Mirco Nasuti <mirco.nasuti@chuv.ch>
Date: Wed, 7 Sep 2016 14:51:19 +0200
Subject: [PATCH] rename datasources
---
docker/runner/README.md | 16 ++++++-------
docker/runner/config/application.tmpl | 16 ++++++-------
docker/runner/run.sh | 4 ++--
.../PersistenceConfiguration.java | 24 +++++++++----------
.../eu/hbp/mip/controllers/RequestsApi.java | 6 ++---
.../java/eu/hbp/mip/controllers/StatsApi.java | 8 +++----
tests/pre-test-run.sh | 2 +-
7 files changed, 38 insertions(+), 38 deletions(-)
diff --git a/docker/runner/README.md b/docker/runner/README.md
index efac75f50..ce6728749 100644
--- a/docker/runner/README.md
+++ b/docker/runner/README.md
@@ -9,20 +9,20 @@ You need to configure a few things using some environment variables.
Environment variables:
-* DB_URL: JDBC URL to connect to the portal database, for example "jdbc:postgresql://db:5432/portal"
-* DB_SERVER: optional, address of the portal database server, for example DB_SERVER="db:5432". Used to wait for the database to be up and running.
-* DB_USER: User to use when connecting to the portal database
-* DB_PASSWORD: Password to use when connecting to the portal database
+* PORTAL_DB_URL: JDBC URL to connect to the portal database, for example "jdbc:postgresql://db:5432/portal"
+* PORTAL_DB_SERVER: optional, address of the portal database server, for example DB_SERVER="db:5432". Used to wait for the database to be up and running.
+* PORTAL_DB_USER: User to use when connecting to the portal database
+* PORTAL_DB_PASSWORD: Password to use when connecting to the portal database
* META_DB_URL: JDBC URL to connect to the metadata database
* META_DB_SERVER: optional, address of the metadata database server. Used to wait for the database to be up and running.
* META_DB_USER: User to use when connecting to the metadata database
* META_DB_PASSWORD: Password to use when connecting to the metadata database
-* ADNI_DB_URL: JDBC URL to connect to the adni database
-* ADNI_DB_SERVER: optional, address of the adni database server. Used to wait for the database to be up and running.
-* ADNI_DB_USER: User to use when connecting to the adni database
-* ADNI_DB_PASSWORD: Password to use when connecting to the adni database
+* SCIENCE_DB_URL: JDBC URL to connect to the science database
+* SCIENCE_DB_SERVER: optional, address of the science database server. Used to wait for the database to be up and running.
+* SCIENCE_DB_USER: User to use when connecting to the science database
+* SCIENCE_DB_PASSWORD: Password to use when connecting to the science database
* CONTEXT_PATH: context path appended to all services running in this container. Default to "/services"
diff --git a/docker/runner/config/application.tmpl b/docker/runner/config/application.tmpl
index 84ded7fc3..f47a73a31 100644
--- a/docker/runner/config/application.tmpl
+++ b/docker/runner/config/application.tmpl
@@ -2,20 +2,20 @@
# 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/portal" }}
- username: {{ default .Env.DB_USER "portal" }}
- password: {{ .Env.DB_PASSWORD }}
+ portalDatasource:
+ url: {{ default .Env.PORTAL_DB_URL "jdbc:postgresql://172.22.0.1:5432/portal" }}
+ username: {{ default .Env.PORTAL_DB_USER "portal" }}
+ password: {{ .Env.PORTAL_DB_PASSWORD }}
driver-class-name: org.postgresql.Driver
metaDatasource:
url: {{ default .Env.META_DB_URL "jdbc:postgresql://172.22.0.1:5432/portal" }}
username: {{ default .Env.META_DB_USER "portal" }}
password: {{ .Env.META_DB_PASSWORD }}
driver-class-name: org.postgresql.Driver
- adniDatasource:
- url: {{ default .Env.ADNI_DB_URL "jdbc:postgresql://172.22.0.1:5433/adni" }}
- username: {{ default .Env.ADNI_DB_USER "adni" }}
- password: {{ .Env.ADNI_DB_PASSWORD }}
+ scienceDatasource:
+ url: {{ default .Env.SCIENCE_DB_URL "jdbc:postgresql://172.22.0.1:5433/science" }}
+ username: {{ default .Env.SCIENCE_DB_USER "science" }}
+ password: {{ .Env.SCIENCE_DB_PASSWORD }}
driver-class-name: org.postgresql.Driver
jpa:
hibernate:
diff --git a/docker/runner/run.sh b/docker/runner/run.sh
index 547145dda..49d26d0b2 100755
--- a/docker/runner/run.sh
+++ b/docker/runner/run.sh
@@ -7,7 +7,7 @@ fi
if [ ! -z "$META_DB_SERVER" ]; then
OPTS="$OPTS -wait tcp://$META_DB_SERVER -timeout 60s"
fi
-if [ ! -z "$ADNI_DB_SERVER" ]; then
- OPTS="$OPTS -wait tcp://$ADNI_DB_SERVER -timeout 60s"
+if [ ! -z "$SCIENCE_DB_SERVER" ]; then
+ OPTS="$OPTS -wait tcp://$SCIENCE_DB_SERVER -timeout 60s"
fi
dockerize $OPTS java -jar backend.jar
diff --git a/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java b/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java
index 03edada1f..475fd93d3 100644
--- a/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java
+++ b/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java
@@ -23,14 +23,14 @@ import javax.sql.DataSource;
*/
@Configuration
-@EnableJpaRepositories(value = "eu.hbp.mip.repositories", entityManagerFactoryRef = "entityManagerFactory")
+@EnableJpaRepositories(value = "eu.hbp.mip.repositories")
@EntityScan(basePackages = "eu.hbp.mip.model")
public class PersistenceConfiguration {
@Primary
- @Bean(name = "datasource")
- @ConfigurationProperties(prefix="spring.datasource")
- public DataSource dataSource() {
+ @Bean(name = "portalDatasource")
+ @ConfigurationProperties(prefix="spring.portalDatasource")
+ public DataSource portalDataSource() {
return DataSourceBuilder.create().build();
}
@@ -40,9 +40,9 @@ public class PersistenceConfiguration {
return DataSourceBuilder.create().build();
}
- @Bean(name = "adniDatasource")
- @ConfigurationProperties(prefix="spring.adniDatasource")
- public DataSource adniDataSource() {
+ @Bean(name = "scienceDatasource")
+ @ConfigurationProperties(prefix="spring.scienceDatasource")
+ public DataSource scienceDataSource() {
return DataSourceBuilder.create().build();
}
@@ -55,16 +55,16 @@ public class PersistenceConfiguration {
@Bean
@Autowired
- @Qualifier("adniJdbcTemplate")
- public JdbcTemplate adniJdbcTemplate() {
- return new JdbcTemplate(adniDataSource());
+ @Qualifier("scienceJdbcTemplate")
+ public JdbcTemplate scienceJdbcTemplate() {
+ return new JdbcTemplate(scienceDataSource());
}
@Bean(name = "entityManagerFactory")
@DependsOn("flyway")
public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
LocalContainerEntityManagerFactoryBean em = new LocalContainerEntityManagerFactoryBean();
- em.setDataSource(dataSource());
+ em.setDataSource(portalDataSource());
JpaVendorAdapter vendorAdapter = new HibernateJpaVendorAdapter();
em.setJpaVendorAdapter(vendorAdapter);
return em;
@@ -74,7 +74,7 @@ public class PersistenceConfiguration {
public Flyway migrations() {
Flyway flyway = new Flyway();
flyway.setBaselineOnMigrate(true);
- flyway.setDataSource(dataSource());
+ flyway.setDataSource(portalDataSource());
return flyway;
}
diff --git a/src/main/java/eu/hbp/mip/controllers/RequestsApi.java b/src/main/java/eu/hbp/mip/controllers/RequestsApi.java
index c47482e73..fd88fde95 100644
--- a/src/main/java/eu/hbp/mip/controllers/RequestsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/RequestsApi.java
@@ -35,8 +35,8 @@ public class RequestsApi {
private static final Logger LOGGER = Logger.getLogger(RequestsApi.class);
@Autowired
- @Qualifier("adniJdbcTemplate")
- private JdbcTemplate adniJdbcTemplate;
+ @Qualifier("scienceJdbcTemplate")
+ private JdbcTemplate scienceJdbcTemplate;
@ApiOperation(value = "Post a request", response = Dataset.class)
@ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
@@ -87,7 +87,7 @@ public class RequestsApi {
{
List<Object> currentVarData = new LinkedList<>();
String sqlQuery = "SELECT " + varCode + " FROM adni_merge";
- for (Map resultMap : adniJdbcTemplate.queryForList(sqlQuery))
+ for (Map resultMap : scienceJdbcTemplate.queryForList(sqlQuery))
{
String strValue = String.valueOf(resultMap.get(varCode));
try {
diff --git a/src/main/java/eu/hbp/mip/controllers/StatsApi.java b/src/main/java/eu/hbp/mip/controllers/StatsApi.java
index af57626da..6bbf648f1 100644
--- a/src/main/java/eu/hbp/mip/controllers/StatsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/StatsApi.java
@@ -36,8 +36,8 @@ public class StatsApi {
ArticleRepository articleRepository;
@Autowired
- @Qualifier("adniJdbcTemplate")
- private JdbcTemplate adniJdbcTemplate;
+ @Qualifier("scienceJdbcTemplate")
+ private JdbcTemplate scienceJdbcTemplate;
@ApiOperation(value = "Get general statistics", response = GeneralStats.class)
@ApiResponses(value = {@ApiResponse(code = 200, message = "Found"), @ApiResponse(code = 404, message = "Not found") })
@@ -56,9 +56,9 @@ public class StatsApi {
private Long countVariables()
{
- Long count = adniJdbcTemplate.queryForObject(
+ Long count = scienceJdbcTemplate.queryForObject(
"SELECT COUNT(*) FROM INFORMATION_SCHEMA.COLUMNS " +
- "WHERE table_schema = 'public' AND table_name = 'adni_merge'", Long.class); // TODO: compute from adni_merge DB
+ "WHERE table_schema = 'public' AND table_name = 'adni_merge'", Long.class);
return count;
}
diff --git a/tests/pre-test-run.sh b/tests/pre-test-run.sh
index 04bed8a70..b71c4bb82 100755
--- a/tests/pre-test-run.sh
+++ b/tests/pre-test-run.sh
@@ -26,7 +26,7 @@ GATEWAY_IP=$(docker inspect portal-db-test | grep \"Gateway\":\ \" | sed 's/.*Ga
docker run --name portal-backend-test -p 8080:8080 \
-e "AUTHENTICATION=0" \
--e "DB_URL=jdbc:postgresql://$GATEWAY_IP:5433/postgres" \
+-e "PORTAL_DB_URL=jdbc:postgresql://$GATEWAY_IP:5433/postgres" \
-e "META_DB_URL=jdbc:postgresql://$GATEWAY_IP:5432/postgres" \
-d hbpmip/portal-backend
--
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