no hard-coded db schema

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:

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();

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();

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;
     }
 

tests/meta-db/sql/create.sql

-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',
   '
   {

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

tests/science-db/sql/create.sql

-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;