diff --git a/docker/runner/config/application.tmpl b/docker/runner/config/application.tmpl
index f47a73a31fd43bb5e7fe71cfe5390588109328bf..c3e6883f6482acba55379749c75b9a69957fdb17 100644
--- a/docker/runner/config/application.tmpl
+++ b/docker/runner/config/application.tmpl
@@ -4,17 +4,17 @@
spring:
portalDatasource:
url: {{ default .Env.PORTAL_DB_URL "jdbc:postgresql://172.22.0.1:5432/portal" }}
- username: {{ default .Env.PORTAL_DB_USER "portal" }}
+ username: {{ default .Env.PORTAL_DB_USER "postgres" }}
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" }}
+ url: {{ default .Env.META_DB_URL "jdbc:postgresql://172.22.0.1:5432/meta" }}
+ username: {{ default .Env.META_DB_USER "postgres" }}
password: {{ .Env.META_DB_PASSWORD }}
driver-class-name: org.postgresql.Driver
scienceDatasource:
url: {{ default .Env.SCIENCE_DB_URL "jdbc:postgresql://172.22.0.1:5433/science" }}
- username: {{ default .Env.SCIENCE_DB_USER "science" }}
+ username: {{ default .Env.SCIENCE_DB_USER "postgres" }}
password: {{ .Env.SCIENCE_DB_PASSWORD }}
driver-class-name: org.postgresql.Driver
jpa:
diff --git a/src/main/java/eu/hbp/mip/controllers/GroupsApi.java b/src/main/java/eu/hbp/mip/controllers/GroupsApi.java
index a253391c28d70304ec671d9139d574c83ab5c98a..07f19aa0187313592ea2635ecd43f702d6da1378 100644
--- a/src/main/java/eu/hbp/mip/controllers/GroupsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/GroupsApi.java
@@ -54,7 +54,7 @@ public class GroupsApi {
private void loadGroups() {
if(groups == null)
{
- String sqlQuery = "SELECT * FROM meta.meta_variables";
+ String sqlQuery = "SELECT * FROM meta_variables";
SqlRowSet data = metaJdbcTemplate.queryForRowSet(sqlQuery);
data.next();
String json = ((PGobject) data.getObject("hierarchy")).getValue();
diff --git a/src/main/java/eu/hbp/mip/controllers/VariablesApi.java b/src/main/java/eu/hbp/mip/controllers/VariablesApi.java
index 0a1785eb012b63a41c3a728f05fd6e7e9a7bab38..bad8c4e055218bd82b24292f71e864aaa3219709 100644
--- a/src/main/java/eu/hbp/mip/controllers/VariablesApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/VariablesApi.java
@@ -125,7 +125,7 @@ public class VariablesApi {
) {
LOGGER.info("Get groups and variables hierarchy");
- String sqlQuery = "SELECT * FROM meta.meta_variables";
+ String sqlQuery = "SELECT * FROM meta_variables";
SqlRowSet data = metaJdbcTemplate.queryForRowSet(sqlQuery);
data.next();
String json = ((PGobject) data.getObject("hierarchy")).getValue();
@@ -139,7 +139,7 @@ public class VariablesApi {
private void loadVariables() {
if(variables == null)
{
- String sqlQuery = "SELECT * FROM meta.meta_variables";
+ String sqlQuery = "SELECT * FROM meta_variables";
SqlRowSet data = metaJdbcTemplate.queryForRowSet(sqlQuery);
data.next();
String json = ((PGobject) data.getObject("hierarchy")).getValue();
diff --git a/src/main/java/eu/hbp/mip/utils/DataUtil.java b/src/main/java/eu/hbp/mip/utils/DataUtil.java
index 2f4758dfafbe1204ef0123e1813c7b4061bcf761..e4f004ab7934045c1f91ea612bd55f1df8d955ec 100644
--- a/src/main/java/eu/hbp/mip/utils/DataUtil.java
+++ b/src/main/java/eu/hbp/mip/utils/DataUtil.java
@@ -32,7 +32,7 @@ public class DataUtil {
JsonArray currentVarData = new JsonArray();
int samplingPercentage = (int) countAdniRows()/NB_ROWS_SAMPLING;
List<Object> queryResult = jdbcTemplate.queryForList(
- "SELECT " + var + " FROM science.adni_merge " +
+ "SELECT " + var + " FROM adni_merge " +
"TABLESAMPLE SYSTEM ("+ samplingPercentage +") REPEATABLE ( "+ TABLESAMPLE_SEED +" )", Object.class);
for (Object value : queryResult)
{
@@ -55,7 +55,7 @@ public class DataUtil {
{
long count = jdbcTemplate.queryForObject(
"SELECT COUNT(*) FROM INFORMATION_SCHEMA.COLUMNS " +
- "WHERE table_schema = 'science' AND table_name = 'adni_merge'", Long.class);
+ "WHERE table_name = 'adni_merge'", Long.class);
return count;
}
@@ -63,7 +63,7 @@ public class DataUtil {
public long countAdniRows()
{
long count = jdbcTemplate.queryForObject(
- "SELECT COUNT(*) FROM science.adni_merge", Long.class);
+ "SELECT COUNT(*) FROM adni_merge", Long.class);
return count;
}
diff --git a/tests/meta-db/sql/create.sql b/tests/meta-db/sql/create.sql
index 2fa8f5a3461513bc8bd9159d38e2ccec02645201..13d3f6bf7f9dea40294473949a46e79a0baa0354 100644
--- a/tests/meta-db/sql/create.sql
+++ b/tests/meta-db/sql/create.sql
@@ -1,11 +1,14 @@
-CREATE SCHEMA IF NOT EXISTS meta;
+CREATE DATABASE meta;
+\c meta
-CREATE TABLE IF NOT EXISTS meta.meta_variables (
+SET datestyle to 'European';
+
+CREATE TABLE IF NOT EXISTS meta_variables (
ID serial NOT NULL PRIMARY KEY,
source varchar(256) UNIQUE NOT NULL,
hierarchy json NOT NULL
);
-INSERT INTO meta.meta_variables (source, hierarchy) VALUES (
+INSERT INTO meta_variables (source, hierarchy) VALUES (
'adni',
'
{
diff --git a/tests/pre-test-run.sh b/tests/pre-test-run.sh
index 80194a1de121d25a004cdf3279c73f114b7aef42..e323d19c3eb71fbe1690809a8bcf9c812f67d039 100755
--- a/tests/pre-test-run.sh
+++ b/tests/pre-test-run.sh
@@ -32,8 +32,8 @@ fi
# Run databases containers
echo "Running databases containers..."
-docker run --name science-db-test -p 65432:5432 -v $(pwd)/tests/science-db/sql:/docker-entrypoint-initdb.d/ -e POSTGRES_USER=science -d postgres:9.5.3
-docker run --name portal-db-test -p 65433:5432 -v $(pwd)/tests/meta-db/sql:/docker-entrypoint-initdb.d/ -e POSTGRES_USER=portal -d postgres:9.5.3
+docker run --name science-db-test -p 65432:5432 -v $(pwd)/tests/science-db/sql:/docker-entrypoint-initdb.d/ -e POSTGRES_USER=postgres -d postgres:9.5.3
+docker run --name portal-db-test -p 65433:5432 -v $(pwd)/tests/meta-db/sql:/docker-entrypoint-initdb.d/ -e POSTGRES_USER=postgres -d postgres:9.5.3
# Get gateway IP
@@ -46,6 +46,7 @@ echo "Gateway IP: $GATEWAY_IP"
# Wait for databases to be ready
echo "Waiting for science-db to start..."
+sleep 3
until [ $(docker exec science-db-test psql -U postgres -c "\q" 2>&1 | wc -l) -eq 0 ]; do
printf '.'
sleep 1
@@ -53,6 +54,7 @@ done
echo ""
echo "Waiting for portal-db to start..."
+sleep 3
until [ $(docker exec portal-db-test psql -U postgres -c "\q" 2>&1 | wc -l) -eq 0 ]; do
printf '.'
sleep 1
@@ -66,13 +68,13 @@ echo "Running backend container..."
docker run --name backend-test -p 65434:8080 \
-e "PORTAL_DB_URL=jdbc:postgresql://$GATEWAY_IP:65433/portal" \
-e "PORTAL_DB_SERVER=$GATEWAY_IP:65433/portal" \
--e "PORTAL_DB_USER=portal" \
--e "META_DB_URL=jdbc:postgresql://$GATEWAY_IP:65433/portal" \
--e "META_DB_SERVER=$GATEWAY_IP:65433/portal" \
--e "META_DB_USER=portal" \
+-e "PORTAL_DB_USER=postgres" \
+-e "META_DB_URL=jdbc:postgresql://$GATEWAY_IP:65433/meta" \
+-e "META_DB_SERVER=$GATEWAY_IP:65433/meta" \
+-e "META_DB_USER=postgres" \
-e "SCIENCE_DB_URL=jdbc:postgresql://$GATEWAY_IP:65432/science" \
-e "SCIENCE_DB_SERVER=$GATEWAY_IP:65432/science" \
--e "SCIENCE_DB_USER=science" \
+-e "SCIENCE_DB_USER=postgres" \
-e "CONTEXT_PATH=/services" \
-e "AUTHENTICATION=0" \
-d hbpmip/portal-backend:latest
diff --git a/tests/science-db/sql/create.sql b/tests/science-db/sql/create.sql
index c41f732daf8a7861d9382d2ff1a5919f1e4ab08f..648bec0a8925f08bf03bc20303f2aba3ce30ba89 100644
--- a/tests/science-db/sql/create.sql
+++ b/tests/science-db/sql/create.sql
@@ -1,8 +1,9 @@
-SET datestyle to 'European';
+CREATE DATABASE science;
+\c science
-CREATE SCHEMA IF NOT EXISTS science;
+SET datestyle to 'European';
-CREATE TABLE science.ADNI_MERGE
+CREATE TABLE IF NOT EXISTS ADNI_MERGE
(
tv1 char(256),
tv2 numeric,
@@ -14,4 +15,4 @@ WITH (
OIDS=FALSE
);
-COPY science.ADNI_MERGE FROM '/docker-entrypoint-initdb.d/values.csv' CSV HEADER;
+COPY ADNI_MERGE FROM '/docker-entrypoint-initdb.d/values.csv' CSV HEADER;