update default value for main_table in config + clean and fix tests

docker/runner/README.md

@@ -9,42 +9,42 @@ You need to configure a few things using some environment variables.
 
 Environment variables:
 
-* PORTAL_DB_URL: JDBC URL to connect to the portal database, for example "jdbc:postgresql://db:5432/portal"
-* PORTAL_DB_SCHEMA: Database schema, default value is "public"
+* PORTAL_DB_URL: JDBC URL to connect to the portal database, for example "jdbc:postgresql://db:5432/portal".
+* PORTAL_DB_SCHEMA: Database schema, default value is "public".
 * 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
+* 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_SCHEMA: Database schema, default value is "public"
+* META_DB_URL: JDBC URL to connect to the metadata database.
+* META_DB_SCHEMA: Database schema, default value is "public".
 * 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
+* META_DB_USER: User to use when connecting to the metadata database.
+* META_DB_PASSWORD: Password to use when connecting to the metadata database.
 
-* FEATURES_DB_URL: JDBC URL to connect to the features database
-* FEATURES_DB_SCHEMA: Database schema, default value is "public"
+* FEATURES_DB_URL: JDBC URL to connect to the features database.
+* FEATURES_DB_SCHEMA: Database schema, default value is "public".
 * FEATURES_DB_SERVER: optional, address of the features database server. Used to wait for the database to be up and running.
-* FEATURES_DB_USER: User to use when connecting to the features database
-* FEATURES_DB_PASSWORD: Password to use when connecting to the features database
-* FEATURES_DB_MAIN_TABLE: Table that contains the scientific data to use, default value is adni_merge
+* FEATURES_DB_USER: User to use when connecting to the features database.
+* FEATURES_DB_PASSWORD: Password to use when connecting to the features database.
+* FEATURES_DB_MAIN_TABLE: Table that contains the scientific data to use, default value is "features".
 
-* CONTEXT_PATH:  context path appended to all services running in this container. Default to "/services"
+* CONTEXT_PATH:  context path appended to all services running in this container. Default to "/services".
 
 * AUTHENTICATION: 0 to disable authentication or 1 to enable authentication.
-* CLIENT_ID: required when authentication is turned on, client ID for the [OpenID server of HBP](https://services.humanbrainproject.eu/oidc/)
-* CLIENT_SECRET: required when authentication is turned on, client secret for the [OpenID server of HBP](https://services.humanbrainproject.eu/oidc/)
-* TOKEN_URI: default to "https://services.humanbrainproject.eu/oidc/token"
-* AUTH_URI: default to "https://services.humanbrainproject.eu/oidc/authorize"
-* USER_INFO_URI: default to "https://services.humanbrainproject.eu/oidc/userinfo"
+* CLIENT_ID: required when authentication is turned on, client ID for the [OpenID server of HBP](https://services.humanbrainproject.eu/oidc/).
+* CLIENT_SECRET: required when authentication is turned on, client secret for the [OpenID server of HBP](https://services.humanbrainproject.eu/oidc/).
+* TOKEN_URI: default to "https://services.humanbrainproject.eu/oidc/token".
+* AUTH_URI: default to "https://services.humanbrainproject.eu/oidc/authorize".
+* USER_INFO_URI: default to "https://services.humanbrainproject.eu/oidc/userinfo".
 
-* FRONTEND_LOGIN_URL: URL to redirect to when login is required. Default to "http://frontend/services/login/hbp"
-* FRONTEND_AFTER_LOGIN_URL: URL to redirect after login. Default to "http://frontend/home"
-* FRONTEND_AFTER_LOGOUT_URL: URL to redirect to after logout. Default to "http://frontend/services/login/hbp"
+* FRONTEND_LOGIN_URL: URL to redirect to when login is required. Default to "http://frontend/services/login/hbp".
+* FRONTEND_AFTER_LOGIN_URL: URL to redirect after login. Default to "http://frontend/home".
+* FRONTEND_AFTER_LOGOUT_URL: URL to redirect to after logout. Default to "http://frontend/services/login/hbp".
 
 * WOKEN_URL: URL to woken machine learning server.
 * EXAREME_URL: URL to Exareme server.
 
-* LOGGING_LEVEL_WEB: log level for the web layer of the application. Default to "DEBUG"
-* LOGGING_LEVEL_HIBERNATE: log level for the Hibernate layer of the application. Default to "DEBUG"
+* LOGGING_LEVEL_WEB: log level for the web layer of the application. Default to "DEBUG".
+* LOGGING_LEVEL_HIBERNATE: log level for the Hibernate layer of the application. Default to "DEBUG".
 
-* SESSION_TIMEOUT: Timeout in milliseconds for session expiration. Default to 2592000
+* SESSION_TIMEOUT: Timeout in milliseconds for session expiration. Default to 2592000.

docker/runner/config/application.tmpl

@@ -17,7 +17,7 @@ spring:
   featuresDatasource:
       url: {{ default .Env.FEATURES_DB_URL "jdbc:postgresql://172.22.0.1:5433/features" }}
       schema: {{ default .Env.FEATURES_DB_SCHEMA "public" }}
-      main-table: {{ default .Env.FEATURES_DB_MAIN_TABLE "adni_merge" }}
+      main-table: {{ default .Env.FEATURES_DB_MAIN_TABLE "features" }}
       username: {{ default .Env.FEATURES_DB_USER "postgres" }}
       password: {{ .Env.FEATURES_DB_PASSWORD }}
       driver-class-name: org.postgresql.Driver

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

@@ -26,7 +26,7 @@ import javax.sql.DataSource;
 @EntityScan(basePackages = "eu.hbp.mip.model")
 public class PersistenceConfiguration {
 
-    @Value("#{'${spring.featuresDatasource.main-table:adni_merge}'}")
+    @Value("#{'${spring.featuresDatasource.main-table:features}'}")
     private String featuresMainTable;
 
     @Primary

tests/science-db/sql/create.sql → tests/features-db/sql/create.sql

 SET datestyle to 'European';
 
-CREATE TABLE IF NOT EXISTS ADNI_MERGE
+CREATE TABLE IF NOT EXISTS FEATURES
 (
   tv1 char(256),
   tv2 numeric,
   tv3 numeric,
 
-  CONSTRAINT pk_adni_merge PRIMARY KEY (tv2)
+  CONSTRAINT pk_features PRIMARY KEY (tv2)
 )
 WITH (
   OIDS=FALSE
 );
 
-COPY ADNI_MERGE FROM '/docker-entrypoint-initdb.d/values.csv' CSV HEADER;
+COPY FEATURES FROM '/docker-entrypoint-initdb.d/values.csv' CSV HEADER;

tests/meta-db/sql/create.sql

@@ -6,7 +6,7 @@ CREATE TABLE IF NOT EXISTS meta_variables (
   hierarchy json NOT NULL
 );
 INSERT INTO meta_variables (source, hierarchy) VALUES (
-  'adni',
+  'features',
   '
   {
     "code": "root",