Feat/186 experiment refactor

Created by: KFilippopolitis

Changelog:

1. Major cleanup on the database objects/DAOs/DTOs.
2. Upgraded all the dependencies.
3. New Keycloak handling with integrated library.
4. Refactored the experiments.
5. Added CRUD on the experiments.
6. Service layer added.
7. Improved exception handling.
8. Added non-dockerised way of developing
9. Env Variables cleanup.
10. Backwards Compatibility.

docker/config/application.tmpl

 # Configuration template for the portal running inside a Docker container
 
-# See http://docs.spring.io/spring-boot/docs/current/reference/html/common-application-properties.html
+### LOG LEVELS ###
+logging:
+  level:
+    root: {{ default .Env.LOG_LEVEL_FRAMEWORK "ERROR" }}
+    org: {{ default .Env.LOG_LEVEL_FRAMEWORK "ERROR" }}
+    eu:
+      hbp: {{ default .Env.LOG_LEVEL "INFO" }}
+
+
+### AUTHENTICATION ###
+authentication:
+  enabled: {{ default .Env.AUTHENTICATION "true" }}
+
+
+### DATABASE CONFIGURATION ###
 spring:
-  portalDatasource:
-    url: {{ default .Env.PORTAL_DB_URL "jdbc:postgresql://172.22.0.1:5432/portal" }}
+  portal-datasource:
+    url: {{ default .Env.PORTAL_DB_URL "jdbc:postgresql://88.197.53.106:5432/portal" }}
     schema: {{ default .Env.PORTAL_DB_SCHEMA "public" }}
     username: {{ default .Env.PORTAL_DB_USER "postgres" }}
     password: {{ .Env.PORTAL_DB_PASSWORD }}
     driver-class-name: org.postgresql.Driver
-
   data:
     jpa:
       repositories:
@@ -16,60 +29,10 @@ spring:
   jpa:
     hibernate:
       dialect: org.hibernate.dialect.PostgreSQL9Dialect
-  # SPRING RESOURCES HANDLING
-  resources:
-    chain:
-      enabled: true # TODO: why is that enabled? Do we serve any resources from the backend?
+      ddl-auto: validate
 
-# HBP OAUTH2 LOGIN
-hbp:
-  authentication:
-    enabled: {{ default .Env.AUTHENTICATION "1" }}
-  client:
-    clientId: {{ default .Env.CLIENT_ID "996f97c5-a3ca-460e-b18b-00df3e2be89a" }}
-    clientSecret: {{ .Env.CLIENT_SECRET }}
-    accessTokenUri: {{ default .Env.TOKEN_URI "https://services.humanbrainproject.eu/oidc/token" }}
-    userAuthorizationUri: {{ default .Env.AUTH_URI "https://services.humanbrainproject.eu/oidc/authorize" }}
-    logoutUri: {{ .Env.LOGOUT_URI }}
-    tokenName: access_token
-    authenticationScheme: query
-    clientAuthenticationScheme: form
-    useCurrentUri: false
-    preEstablishedRedirectUri: {{ default .Env.FRONTEND_LOGIN_URL "http://frontend/services/login/hbp" }}
-  resource:
-    userInfoUri: {{ default .Env.USER_INFO_URI "https://services.humanbrainproject.eu/oidc/userinfo" }}
-    revokeTokenUri: {{ default .Env.REVOKE_TOKEN_URI "https://services.humanbrainproject.eu/oidc/slo" }}
-  sso:
-    login-path:
-
-# WEB FRONTEND
-frontend:
-  loginUrl: {{ default .Env.FRONTEND_LOGIN_URL "http://frontend/services/login/hbp" }}
-  redirectAfterLogoutUrl: {{ default .Env.FRONTEND_AFTER_LOGOUT_URL (default .Env.LOGIN_URI "http://frontend/services/login/hbp") }}
-  redirectAfterLoginUrl: {{ default .Env.FRONTEND_AFTER_LOGIN_URL "http://frontend/home" }}
-  
-logging:
-  level:
-    root: {{ default .Env.LOG_LEVEL_FRAMEWORK "ERROR" }}
-    eu:
-      hbp: {{ default .Env.LOG_LEVEL "INFO" }}
-
-# EMBEDDED SERVER CONFIGURATION
-server:
-  contextPath: {{ default .Env.CONTEXT_PATH "/services" }}
-  port: 8080
-  use-forward-headers: true
-  session:
-    timeout: {{ default .Env.SESSION_TIMEOUT "2592000" }}
-
-# ENDPOINTS
-endpoints:
-  enabled: true
-  health:
-    enabled: true
-    endpoint: /health
-    sensitive: false
 
+### EXTERNAL SERVICES ###
 services:
   exareme:
     queryExaremeUrl: {{ default .Env.EXAREME_URL "http://localhost:9090" }}/mining/query
@@ -77,10 +40,43 @@ services:
 
   galaxy:
     galaxyUrl:      {{ default .Env.GALAXY_URL "http://localhost:8090/" }}
-    galaxyContext:  {{ default .Env.GALAXY_CONTEXT "nativeGalaxy/workflows/list" }}
+    galaxyContext:  "nativeGalaxy/workflows/list"
     galaxyApiKey:   {{ .Env.GALAXY_API_KEY }}
     galaxyUsername:  {{ default .Env.GALAXY_USERNAME "admin" }}
     galaxyPassword:  {{ default .Env.GALAXY_PASSWORD "password" }}
 
-  keycloak:
-    keycloakUrl: {{ .Env.KEYCLOAK_URL }}
+
+### KEYCLOAK ###
+keycloak:
+  enabled: true
+  auth-server-url: {{ .Env.KEYCLOAK_AUTH_URL }}
+  realm: {{ .Env.KEYCLOAK_REALM }}
+  resource: {{ .Env.KEYCLOAK_CLIENT_ID }}
+  enable-basic-auth: true
+  credentials:
+    secret: {{ .Env.KEYCLOAK_CLIENT_SECRET }}
+  principal-attribute: "preferred_username"
+  ssl-required: none
+
+### EXTERNAL FILES ###
+# Files are imported when building the docker image
+files:
+  pathologies_json: "file:/opt/portal/api/pathologies.json"
+  disabledAlgorithms_json: "file:/opt/portal/api/disabledAlgorithms.json"
+
+
+### EMBEDDED SERVER CONFIGURATION ###
+server:
+  servlet:
+    contextPath: "/services"
+  port: 8080
+  forward-headers-strategy: native
+
+
+### ENDPOINTS ###
+endpoints:
+  enabled: true
+  health:
+    enabled: true
+    endpoint: /health
+    sensitive: false
\ No newline at end of file