diff --git a/Dockerfile b/Dockerfile
index 458fbc8a353233f0bda3dbff9be8b421d7fbaf5b..866c01bf47a4cff2589e9298b166d5b374fbe62b 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -43,17 +43,16 @@ WORKDIR /home/portal
ENTRYPOINT ["/run.sh"]
# 8080: Web service API, health checks on http://host:8080$CONTEXT_PATH/health
-# 4089: Akka cluster
-EXPOSE 4089 8080
+EXPOSE 8080
HEALTHCHECK --start-period=60s CMD curl -v --silent http://localhost:8080$CONTEXT_PATH/health 2>&1 | grep UP
LABEL org.label-schema.build-date=$BUILD_DATE \
org.label-schema.name="hbpmip/portal-backend" \
- org.label-schema.description="Java backend for the MIP portal" \
+ org.label-schema.description="Spring backend for the MIP portal" \
org.label-schema.url="https://mip.humanbrainproject.eu" \
org.label-schema.vcs-type="git" \
- org.label-schema.vcs-url="https://github.com/LREN-CHUV/portal-backend" \
+ org.label-schema.vcs-url="https://github.com/HBPMedical/portal-backend" \
org.label-schema.vcs-ref=$VCS_REF \
org.label-schema.version="$VERSION" \
org.label-schema.vendor="LREN CHUV" \
diff --git a/build.sh b/build.sh
index ef4f10565705b3eb3d0fae54b60de23671f356bf..6a18d98ecec05885651675049490ca44c990ec7f 100755
--- a/build.sh
+++ b/build.sh
@@ -26,7 +26,7 @@ else
DOCKER="sudo docker"
fi
-IMAGE="hbpmip/portal-backend"
+IMAGE="kfilippopolitis/portal-backend"
VCS_REF=$(git describe --tags --dirty)
VERSION=$(git describe --tags --dirty)
diff --git a/docker/README.md b/docker/README.md
index 3f3437aec65ab4cc28b6236bf31a305b79572ea5..9636ff324e43b29c67fa367165370bbbf5c3a5f7 100644
--- a/docker/README.md
+++ b/docker/README.md
@@ -7,69 +7,33 @@
To use this image, you need a running instance of PostgreSQL and to configure the software using the following environment variables.
-### DATABASES
-
-* PORTAL_DB_URL: JDBC URL to connect to the portal database, default value is "jdbc:postgresql://172.22.0.1:5432/portal".
-* PORTAL_DB_SCHEMA: Database schema, default value is "public".
-* PORTAL_DB_USER: User to use when connecting to the portal database, default value is "postgres".
-* PORTAL_DB_PASSWORD: Password to use when connecting to the portal database.
-
-* META_DB_URL: JDBC URL to connect to the metadata database, default value is "jdbc:postgresql://172.22.0.1:5432/meta".
-* META_DB_SCHEMA: Database schema, default value is "public".
-* 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 science database, default value is "jdbc:postgresql://172.22.0.1:5433/features".
-* FEATURES_DB_SCHEMA: Database schema, default value is "public".
-* FEATURES_DB_USER: User to use when connecting to the science database, default value is "postgres".
-* FEATURES_DB_PASSWORD: Password to use when connecting to the science database.
-* FEATURES_DB_MAIN_TABLE: Table that contains the scientific data to use, default value is "features".
-
-
-### OAUTH2 LOGIN
-
-* AUTHENTICATION: "0" to disable authentication or "1" to enable authentication, default value is "1".
-* 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".
-* REVOKE_TOKEN_URI "https://services.humanbrainproject.eu/oidc/slo".
-
-
-### WEB FRONTEND
-
-* 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".
-
-
-### LOGGING
-
+### LOG LEVELS ###
* LOG_LEVEL: log level for the developer added logs. Default is "ERROR".
* LOG_LEVEL_FRAMEWORK: log level for all the framework logs. Default is "ERROR".
-### ENDPOINTS
+### AUTHENTICATION ###
+* AUTHENTICATION: true for production, false for development.
-* EXAREME_URL: URL to Exareme server, default value is "http://hbps2.chuv.ch:9090".
-* WORKFLOW_URL: URL to Workflow server
-* JWT_SECRET: "secret"
-### EMBEDDED SERVER CONFIGURATION
+### DATABASE CONFIGURATION ###
+* PORTAL_DB_URL: JDBC URL to connect to the portal database, default value is "jdbc:postgresql://127.0.0.1:5432/portal".
+* PORTAL_DB_SCHEMA: Database schema, default value is "public".
+* PORTAL_DB_USER: User to use when connecting to the portal database, default value is "postgres".
+* PORTAL_DB_PASSWORD: Password to use when connecting to the portal database.
-* CONTEXT_PATH: context path appended to all services running in this container. Default to "/services".
-* SESSION_TIMEOUT: Timeout in milliseconds for session expiration. Default to 2592000.
-### PROXY
+### EXTERNAL SERVICES ###
+* EXAREME_URL: URL to Exareme server. Default is "http://localhost:9090" .
-* HTTP_PROXY_HOST: HTTP proxy host
-* HTTP_PROXY_PORT: HTTP proxy port
-* HTTPS_PROXY_HOST: HTTPS proxy host
-* HTTPS_PROXY_PORT: HTTPS proxy port
+* GALAXY_URL: URL to Workflow server. Default is "http://localhost:8090/" .
+* GALAXY_API_KEY: The api key to authorize galaxy requests.
+* GALAXY_USERNAME: The username of galaxy user to be able to embed the frame.
+* GALAXY_PASSWORD: The password of galaxy user.
-## ERROR REPORTING
-* RELEASE_STAGE: Release stage used when reporting errors to Bugsnag. Values are dev, staging, production
-* DATA_CENTER_LOCATION: Location of the datacenter, used when reporting errors to Bugsnag
-* CONTAINER_ORCHESTRATION: Container orchestration system used to execute the Docker containers. Values are mesos, docker-compose, kubernetes
+### KEYCLOAK ###
+* KEYCLOAK_AUTH_URL: Keycloak authentication URL.
+* KEYCLOAK_REALM: Keycloak realm user for authentication.
+* KEYCLOAK_CLIENT_ID: The keycloak client id.
+* KEYCLOAK_CLIENT_SECRET: The keycloak secret to be able to authenticate.
\ No newline at end of file
diff --git a/docker/config/application.tmpl b/docker/config/application.tmpl
index 13fc6577970ede925089895265e8a3f6b0a409ae..ae10744aa2424e7421da83da173d6e662608e843 100644
--- a/docker/config/application.tmpl
+++ b/docker/config/application.tmpl
@@ -1,14 +1,27 @@
# 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
diff --git a/pom.xml b/pom.xml
index 20a6f066122779eab771ca0d012dbcc4a8e8a208..d92ff1f2dd22cd477f702ec2486f675c117c39c6 100644
--- a/pom.xml
+++ b/pom.xml
@@ -14,27 +14,25 @@
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
- <version>1.3.8.RELEASE</version>
- <relativePath/>
-
+ <version>2.3.5.RELEASE</version>
</parent>
<properties>
- <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
- <sonar.host.url>https://hbps1.chuv.ch/sonarqube/</sonar.host.url>
- <sonar.projectName>MIP portal-backend</sonar.projectName>
- <sonar.sources>src/main/java/</sonar.sources>
<java.version>1.8</java.version>
+ <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+ <keycloak-spring.version>11.0.2</keycloak-spring.version>
+ <springfox-swagger.version>2.5.0</springfox-swagger.version>
+ <spring-context.version>5.2.10.RELEASE</spring-context.version>
+ <springfox-boot-starter.version>3.0.0</springfox-boot-starter.version>
<asciidoctor.maven.plugin.version>1.5.5</asciidoctor.maven.plugin.version>
<asciidoctorj.pdf.version>1.5.0-alpha.15</asciidoctorj.pdf.version>
<asciidoctorj.version>1.5.5</asciidoctorj.version>
- <spring-data-commons.version>1.12.3.RELEASE</spring-data-commons.version>
<angularjs.version>1.5.7</angularjs.version>
<jquery.version>3.0.0</jquery.version>
<bootstrap.version>3.3.7</bootstrap.version>
+ <webjars-locator.version>0.36</webjars-locator.version>
<h2.version>1.4.192</h2.version>
<postgresql.version>42.2.1</postgresql.version>
- <springfox-swagger.version>2.5.0</springfox-swagger.version>
<gson.version>2.7</gson.version>
<slugify.version>2.1.5</slugify.version>
<maven-resources-plugin.version>3.0.1</maven-resources-plugin.version>
@@ -42,15 +40,13 @@
<swagger2markup-maven-plugin.version>1.0.0</swagger2markup-maven-plugin.version>
<maven-compiler-plugin.version>3.5.1</maven-compiler-plugin.version>
<hibernate4-maven-plugin.version>1.1.1</hibernate4-maven-plugin.version>
+ <commons-dbcp.version>2.7.0</commons-dbcp.version>
<flyway-core.version>4.2.0</flyway-core.version>
<hibernate-jpa-2.1-api.version>1.0.0.Final</hibernate-jpa-2.1-api.version>
- <hibernate.version>4.3.11.Final</hibernate.version>
- <spring-data-jpa.version>1.10.11.RELEASE</spring-data-jpa.version>
- <spring-boot-starter-actuator.version>1.4.7.RELEASE</spring-boot-starter-actuator.version>
+ <hibernate.version>5.4.10.Final</hibernate.version>
+ <hibernate-validator.version>6.1.0.Final</hibernate-validator.version>
<aspectjweaver.version>1.8.9</aspectjweaver.version>
<javax-inject.version>1</javax-inject.version>
- <akka.version>2.5.22</akka.version>
- <spring-context.version>4.3.4.RELEASE</spring-context.version>
<protobuf-java.version>3.1.0</protobuf-java.version>
</properties>
@@ -66,32 +62,39 @@
</repositories>
<dependencies>
-
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter</artifactId>
</dependency>
<dependency>
- <groupId>org.springframework.boot</groupId>
- <artifactId>spring-boot-starter-actuator</artifactId>
- <version>${spring-boot-starter-actuator.version}</version>
+ <groupId>org.springframework.boot</groupId>
+ <artifactId>spring-boot-starter-data-rest</artifactId>
</dependency>
<dependency>
- <groupId>org.springframework.data</groupId>
- <artifactId>spring-data-commons</artifactId>
- <version>${spring-data-commons.version}</version>
+ <groupId>org.springframework.boot</groupId>
+ <artifactId>spring-boot-starter-security</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
- <artifactId>spring-boot-starter-security</artifactId>
+ <artifactId>spring-boot-starter-actuator</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-web</artifactId>
</dependency>
<dependency>
- <groupId>org.springframework.security.oauth</groupId>
- <artifactId>spring-security-oauth2</artifactId>
+ <groupId>org.springframework.data</groupId>
+ <artifactId>spring-data-commons</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.keycloak</groupId>
+ <artifactId>keycloak-spring-boot-starter</artifactId>
+ <version>${keycloak-spring.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.keycloak</groupId>
+ <artifactId>keycloak-spring-security-adapter</artifactId>
+ <version>${keycloak-spring.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
@@ -115,6 +118,7 @@
<dependency>
<groupId>org.webjars</groupId>
<artifactId>webjars-locator</artifactId>
+ <version>${webjars-locator.version}</version>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
@@ -131,6 +135,11 @@
<artifactId>hibernate-core</artifactId>
<version>${hibernate.version}</version>
</dependency>
+ <dependency>
+ <groupId>org.hibernate</groupId>
+ <artifactId>hibernate-validator</artifactId>
+ <version>${hibernate-validator.version}</version>
+ </dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-entitymanager</artifactId>
@@ -148,13 +157,8 @@
</dependency>
<dependency>
<groupId>io.springfox</groupId>
- <artifactId>springfox-swagger2</artifactId>
- <version>${springfox-swagger.version}</version>
- </dependency>
- <dependency>
- <groupId>io.springfox</groupId>
- <artifactId>springfox-swagger-ui</artifactId>
- <version>${springfox-swagger.version}</version>
+ <artifactId>springfox-boot-starter</artifactId>
+ <version>${springfox-boot-starter.version}</version>
</dependency>
<dependency>
<groupId>com.google.code.gson</groupId>
@@ -169,11 +173,11 @@
<dependency>
<groupId>org.springframework.data</groupId>
<artifactId>spring-data-jpa</artifactId>
- <version>${spring-data-jpa.version}</version>
</dependency>
<dependency>
- <groupId>commons-dbcp</groupId>
- <artifactId>commons-dbcp</artifactId>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>commons-dbcp2</artifactId>
+ <version>${commons-dbcp.version}</version>
</dependency>
<dependency>
<groupId>org.flywaydb</groupId>
@@ -185,16 +189,15 @@
<artifactId>aspectjweaver</artifactId>
<version>${aspectjweaver.version}</version>
</dependency>
-
<dependency>
<groupId>javax.inject</groupId>
<artifactId>javax.inject</artifactId>
<version>${javax-inject.version}</version>
</dependency>
<dependency>
- <groupId>org.springframework</groupId>
- <artifactId>spring-context</artifactId>
- <version>${spring.version}</version>
+ <groupId>org.springframework</groupId>
+ <artifactId>spring-context</artifactId>
+ <version>${spring-context.version}</version>
</dependency>
<dependency>
<groupId>com.google.protobuf</groupId>
@@ -209,60 +212,70 @@
<dependency>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
- <version>2.4.0-b180830.0438</version>
- </dependency>
-
- <dependency>
- <groupId>com.auth0</groupId>
- <artifactId>java-jwt</artifactId>
- <version>3.8.3</version>
+ <version>3.0.0-M4</version>
</dependency>
-
<!-- https://mvnrepository.com/artifact/com.github.jmchilton.blend4j/blend4j -->
<dependency>
<groupId>com.github.jmchilton.blend4j</groupId>
<artifactId>blend4j</artifactId>
<version>0.2.0</version>
</dependency>
-
<dependency>
<groupId>com.squareup.retrofit2</groupId>
<artifactId>retrofit</artifactId>
- <version>2.5.0</version>
+ <version>2.9.0</version>
</dependency>
-
<!-- https://mvnrepository.com/artifact/com.squareup.retrofit2/converter-gson -->
<dependency>
<groupId>com.squareup.retrofit2</groupId>
<artifactId>converter-gson</artifactId>
- <version>2.4.0</version>
+ <version>2.9.0</version>
</dependency>
-
<!-- https://mvnrepository.com/artifact/com.squareup.okhttp3/logging-interceptor -->
<dependency>
<groupId>com.squareup.okhttp3</groupId>
<artifactId>logging-interceptor</artifactId>
- <version>3.12.1</version>
</dependency>
-
<dependency>
<groupId>com.auth0</groupId>
<artifactId>java-jwt</artifactId>
- <version>3.8.3</version>
+ <version>3.11.0</version>
+ </dependency>
+ <dependency>
+ <groupId>com.google.code.svenson</groupId>
+ <artifactId>svenson</artifactId>
+ <version>1.5.8</version>
+ </dependency>
+ <dependency>
+ <groupId>org.projectlombok</groupId>
+ <artifactId>lombok</artifactId>
+ <version>1.18.16</version>
+ <scope>provided</scope>
</dependency>
+
</dependencies>
- <build>
- <finalName>portal-backend</finalName>
- <resources>
+ <build>
+ <finalName>portal-backend</finalName>
+ <resources>
+ <resource>
+ <directory>src/main/resources</directory>
+ <includes>
+ <include>**/*.xml</include>
+ <include>**/*.json</include>
+ <include>**/*.csv</include>
+ <include>**/*.sql</include>
+ <include>**/*.conf</include>
+ <include>**/*.yml</include> <!-- Only for development -->
+ </includes>
+ <filtering>true</filtering>
+ </resource>
+
+ <!-- Used for development. Docker/config folder files added as resources -->
<resource>
- <directory>src/main/resources</directory>
+ <directory>config</directory>
<includes>
- <include>**/*.xml</include>
- <include>**/*.json</include>
- <include>**/*.csv</include>
- <include>**/*.sql</include>
- <include>**/*.conf</include>
+ <include>*.json</include>
</includes>
<filtering>true</filtering>
</resource>
diff --git a/src/main/java/eu/hbp/mip/MIPApplication.java b/src/main/java/eu/hbp/mip/MIPApplication.java
index 9af69bdd9cdc04e555a24f8a0ca4e7b3882206ed..f4001f93c477307cf0d464f76e8b22b2905af198 100644
--- a/src/main/java/eu/hbp/mip/MIPApplication.java
+++ b/src/main/java/eu/hbp/mip/MIPApplication.java
@@ -7,17 +7,12 @@ package eu.hbp.mip;
import org.springframework.boot.SpringApplication;
import org.springframework.boot.autoconfigure.SpringBootApplication;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
@SpringBootApplication
public class MIPApplication {
- private static final Logger LOGGER = LoggerFactory.getLogger(MIPApplication.class);
-
public static void main(String[] args) {
SpringApplication.run(MIPApplication.class, args);
}
-
}
diff --git a/src/main/java/eu/hbp/mip/configuration/CacheConfiguration.java b/src/main/java/eu/hbp/mip/configuration/CacheConfiguration.java
deleted file mode 100644
index b7300fc257fcef4afd29421d8ccef64aeb0a11dd..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/configuration/CacheConfiguration.java
+++ /dev/null
@@ -1,13 +0,0 @@
-package eu.hbp.mip.configuration;
-
-import org.springframework.cache.annotation.EnableCaching;
-import org.springframework.context.annotation.Configuration;
-
-/**
- * Created by mirco on 07.11.16.
- */
-
-@Configuration
-@EnableCaching
-public class CacheConfiguration {
-}
diff --git a/src/main/java/eu/hbp/mip/configuration/PortalErrorAttributes.java b/src/main/java/eu/hbp/mip/configuration/PortalErrorAttributes.java
deleted file mode 100644
index 352b1d156558ef42b9862b644ed5668070899708..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/configuration/PortalErrorAttributes.java
+++ /dev/null
@@ -1,43 +0,0 @@
-package eu.hbp.mip.configuration;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.boot.autoconfigure.web.DefaultErrorAttributes;
-import org.springframework.stereotype.Component;
-import org.springframework.web.context.request.RequestAttributes;
-
-import java.util.HashMap;
-import java.util.Map;
-
-@Component
-public class PortalErrorAttributes extends DefaultErrorAttributes {
-
- private static final Logger LOGGER = LoggerFactory.getLogger(PortalErrorAttributes.class);
-
- @Override
- public Map<String, Object> getErrorAttributes(RequestAttributes requestAttributes, boolean includeStackTrace) {
- Map<String, Object> errorAttributes = super.getErrorAttributes(requestAttributes, includeStackTrace);
-
- Throwable throwable = getError(requestAttributes);
- StringBuilder sb = new StringBuilder("[");
- for (String attr : requestAttributes.getAttributeNames(RequestAttributes.SCOPE_REQUEST)) {
- Object v = requestAttributes.getAttribute(attr, RequestAttributes.SCOPE_REQUEST);
- sb.append(attr).append(" = ").append(v).append('\n');
- }
- sb.append("]");
- LOGGER.error("Reporting server error on request with attributes " + sb.toString(), throwable);
-
- if (throwable != null) {
-
- Throwable cause = throwable.getCause();
- if (cause != null) {
- Map<String, Object> causeErrorAttributes = new HashMap<>();
- causeErrorAttributes.put("exception", cause.getClass().getName());
- causeErrorAttributes.put("message", cause.getMessage());
- errorAttributes.put("cause", causeErrorAttributes);
- }
- }
-
- return errorAttributes;
- }
-}
diff --git a/src/main/java/eu/hbp/mip/configuration/SecurityConfiguration.java b/src/main/java/eu/hbp/mip/configuration/SecurityConfiguration.java
deleted file mode 100644
index 4ea52570fd3bde8c8b21253fe202aa3fc61363d4..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/configuration/SecurityConfiguration.java
+++ /dev/null
@@ -1,343 +0,0 @@
-package eu.hbp.mip.configuration;
-
-import eu.hbp.mip.model.UserInfo;
-import eu.hbp.mip.utils.*;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Value;
-import org.springframework.boot.autoconfigure.security.oauth2.resource.AuthoritiesExtractor;
-import org.springframework.boot.autoconfigure.security.oauth2.resource.ResourceServerProperties;
-import org.springframework.boot.autoconfigure.security.oauth2.resource.UserInfoTokenServices;
-import org.springframework.boot.context.embedded.FilterRegistrationBean;
-import org.springframework.boot.context.properties.ConfigurationProperties;
-import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.Configuration;
-import org.springframework.http.*;
-import org.springframework.security.config.annotation.web.builders.HttpSecurity;
-import org.springframework.security.config.annotation.web.configuration.WebSecurityConfigurerAdapter;
-import org.springframework.security.core.Authentication;
-import org.springframework.security.core.GrantedAuthority;
-import org.springframework.security.core.authority.AuthorityUtils;
-import org.springframework.security.oauth2.client.OAuth2ClientContext;
-import org.springframework.security.oauth2.client.OAuth2RestTemplate;
-import org.springframework.security.oauth2.client.filter.OAuth2ClientAuthenticationProcessingFilter;
-import org.springframework.security.oauth2.client.filter.OAuth2ClientContextFilter;
-import org.springframework.security.oauth2.client.resource.BaseOAuth2ProtectedResourceDetails;
-import org.springframework.security.oauth2.client.token.grant.code.AuthorizationCodeResourceDetails;
-import org.springframework.security.oauth2.config.annotation.web.configuration.EnableOAuth2Client;
-import org.springframework.security.web.access.channel.ChannelProcessingFilter;
-import org.springframework.security.web.authentication.SimpleUrlAuthenticationSuccessHandler;
-import org.springframework.security.web.authentication.logout.LogoutHandler;
-import org.springframework.security.web.authentication.www.BasicAuthenticationFilter;
-import org.springframework.security.web.csrf.CsrfFilter;
-import org.springframework.security.web.csrf.CsrfToken;
-import org.springframework.security.web.csrf.CsrfTokenRepository;
-import org.springframework.security.web.csrf.HttpSessionCsrfTokenRepository;
-import org.springframework.util.LinkedMultiValueMap;
-import org.springframework.util.MultiValueMap;
-import org.springframework.web.client.RestTemplate;
-import org.springframework.web.filter.OncePerRequestFilter;
-import org.springframework.web.util.WebUtils;
-
-import javax.net.ssl.*;
-import javax.servlet.Filter;
-import javax.servlet.FilterChain;
-import javax.servlet.ServletException;
-import javax.servlet.http.Cookie;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-import java.io.IOException;
-import java.net.URI;
-import java.security.SecureRandom;
-import java.security.cert.X509Certificate;
-import java.util.ArrayList;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-
-
-// See https://spring.io/guides/tutorials/spring-boot-oauth2/ for reference about configuring OAuth2 login
-// also http://cscarioni.blogspot.ch/2013/04/pro-spring-security-and-oauth-2.html
-
-@Configuration
-@EnableOAuth2Client
-public class SecurityConfiguration extends WebSecurityConfigurerAdapter {
-
- private static final Logger LOGGER = LoggerFactory.getLogger(SecurityConfiguration.class);
-
- @Autowired
- private OAuth2ClientContext oauth2ClientContext;
-
- /**
- * Enable HBP collab authentication (1) or disable it (0). Default is 1
- */
- @Value("#{'${hbp.authentication.enabled:1}'}")
- private boolean authentication;
-
- /**
- * Absolute URL to redirect to when login is required
- */
- @Value("#{'${frontend.loginUrl:/login/hbp}'}")
- private String loginUrl;
-
- /**
- * Absolute URL to redirect to when logout is required
- */
- @Value("#{'${hbp.client.logoutUri}'}")
- private String logoutUri;
-
- /**
- * Absolute URL to redirect to after successful login
- */
- @Value("#{'${frontend.redirectAfterLoginUrl:http://frontend/home}'}")
- private String frontendRedirectAfterLogin;
-
- /**
- * Absolute URL to redirect to after logout has occurred
- */
- @Value("#{'${frontend.redirectAfterLogoutUrl:/login/hbp}'}")
- private String redirectAfterLogoutUrl;
-
- /**
- * URL to revoke auth token
- */
- @Value("#{'${hbp.resource.revokeTokenUri:https://services.humanbrainproject.eu/oidc/revoke}'}")
- private String revokeTokenURI;
-
- @Override
- protected void configure(HttpSecurity http) throws Exception {
- disableCertificateValidation();
- // @formatter:off
- http.addFilterBefore(new CORSFilter(), ChannelProcessingFilter.class);
-
- if (authentication) {
- http.antMatcher("/**")
- .authorizeRequests()
- .antMatchers(
- "/", "/login/**", "/health/**", "/info/**", "/metrics/**", "/trace/**", "/frontend/**", "/webjars/**", "/v2/api-docs", "/swagger-ui.html", "/swagger-resources/**"
- )
- .permitAll()
- .antMatchers("/galaxy*", "/galaxy/*").hasRole("Data Manager")
- //.anyRequest().authenticated()
- .anyRequest().hasRole("Researcher")
- .and().exceptionHandling().authenticationEntryPoint(new CustomLoginUrlAuthenticationEntryPoint(loginUrl))
- .accessDeniedHandler(new CustomAccessDeniedHandler())
- .and().logout().addLogoutHandler(authLogoutHandler()).logoutSuccessUrl(redirectAfterLogoutUrl)
- .and().logout().permitAll()
- .and().csrf().ignoringAntMatchers("/logout").csrfTokenRepository(csrfTokenRepository())
- .and().addFilterAfter(csrfHeaderFilter(), CsrfFilter.class)
- .addFilterBefore(ssoFilter(), BasicAuthenticationFilter.class);
- } else {
- http.antMatcher("/**")
- .authorizeRequests()
- .antMatchers("/**").permitAll().and().csrf().disable();
- }
- }
-
- private Filter ssoFilter() {
- OAuth2ClientAuthenticationProcessingFilter hbpFilter = new OAuth2ClientAuthenticationProcessingFilter("/login/hbp");
- OAuth2RestTemplate hbpTemplate = new OAuth2RestTemplate(hbp(), oauth2ClientContext);
- hbpFilter.setAuthenticationSuccessHandler(new SimpleUrlAuthenticationSuccessHandler(frontendRedirectAfterLogin));
- hbpFilter.setRestTemplate(hbpTemplate);
- hbpFilter.setTokenServices(new UserInfoTokenServices(hbpResource().getUserInfoUri(), hbp().getClientId()));
- return hbpFilter;
- }
-
- @Bean
- public FilterRegistrationBean oauth2ClientFilterRegistration(
- OAuth2ClientContextFilter filter) {
- FilterRegistrationBean registration = new FilterRegistrationBean();
- registration.setFilter(filter);
- registration.setOrder(-100);
- return registration;
- }
-
- @Bean(name = "hbp")
- @ConfigurationProperties("hbp.client")
- public BaseOAuth2ProtectedResourceDetails hbp() {
- return new AuthorizationCodeResourceDetails();
- }
-
- @Bean(name = "hbpResource")
- @ConfigurationProperties("hbp.resource")
- public ResourceServerProperties hbpResource() {
- return new ResourceServerProperties();
- }
-
- public boolean isAuthentication() {
- return authentication;
- }
-
- public String getFrontendRedirectAfterLogin() {
- return frontendRedirectAfterLogin;
- }
-
- private Filter csrfHeaderFilter() {
- return new OncePerRequestFilter() {
- @Override
- protected void doFilterInternal(HttpServletRequest request, HttpServletResponse response,
- FilterChain filterChain) throws ServletException, IOException {
- CsrfToken csrf = (CsrfToken) request.getAttribute(CsrfToken.class.getName());
- if (csrf != null) {
- Cookie cookie = WebUtils.getCookie(request, "XSRF-TOKEN");
- String token = csrf.getToken();
- if (cookie == null || token != null && !token.equals(cookie.getValue())) {
- cookie = new Cookie("XSRF-TOKEN", token);
- cookie.setPath("/");
- response.addCookie(cookie);
- }
- }
- filterChain.doFilter(request, response);
- }
- };
- }
-
- private CsrfTokenRepository csrfTokenRepository() {
- HttpSessionCsrfTokenRepository repository = new HttpSessionCsrfTokenRepository();
- repository.setHeaderName("X-XSRF-TOKEN");
- return repository;
- }
-
- private class CustomLogoutHandler implements LogoutHandler {
- @Override
- public void logout(HttpServletRequest httpServletRequest, HttpServletResponse httpServletResponse, Authentication authentication) {
-
- // Hackish way of accessing to this information...
- final UserInfo userInfo = (UserInfo) httpServletRequest.getSession().getAttribute("userInfo");
- if (userInfo != null) {
- userInfo.setFakeAuth(false);
- }
-
- if (oauth2ClientContext == null || oauth2ClientContext.getAccessToken() == null) {
- return;
- }
-
- String idToken = oauth2ClientContext.getAccessToken().getAdditionalInformation().get("id_token").toString();
-
- StringBuilder query = new StringBuilder();
- query.append("{");
- query.append("\"token\":");
- query.append("\"").append(idToken).append("\"");
- query.append("}");
-
- try {
- int responseCode = HTTPUtil.sendPost(revokeTokenURI, query.toString(), new StringBuilder());
- if (responseCode != 200) {
- LOGGER.warn("Cannot send request to OIDC server for revocation ! ");
- } else {
- LOGGER.info("Should be logged out");
- }
- } catch (IOException e) {
- LOGGER.warn("Cannot notify logout to OIDC server !");
- LOGGER.trace("Cannot notify logout", e);
- }
-
- }
- }
-
- @Bean
- public AuthoritiesExtractor keycloakAuthoritiesExtractor() {
- return new KeycloakAuthoritiesExtractor();
- }
-
-
- public class KeycloakAuthoritiesExtractor
- implements AuthoritiesExtractor {
-
- @Override
- public List<GrantedAuthority> extractAuthorities
- (Map<String, Object> map) {
- return AuthorityUtils
- .commaSeparatedStringToAuthorityList(asAuthorities(map));
- }
-
- private String asAuthorities(Map<String, Object> map) {
- List<String> authorities = new ArrayList<>();
-// authorities.add("BAELDUNG_USER");
- List<LinkedHashMap<String, String>> authz;
- authz = (List<LinkedHashMap<String, String>>) map.get("authorities");
- for (LinkedHashMap<String, String> entry : authz) {
- authorities.add(entry.get("authority"));
- }
- return String.join(",", authorities);
- }
- }
-
-
- private LogoutHandler authLogoutHandler() {
- return (request, response, authentication) -> {
- logout();
- };
- }
-
-
- public void logout() {
- // POSTã™ã‚‹ãƒªã‚¯ã‚¨ã‚¹ãƒˆãƒ‘ラメーターを作æˆ
- RestTemplate restTemplate = new RestTemplate();
- MultiValueMap<String, String> formParams = new LinkedMultiValueMap<>();
- formParams.add("client_id", hbp().getClientId());
- formParams.add("client_secret", hbp().getClientSecret());
- formParams.add("refresh_token", this.oauth2ClientContext.getAccessToken().getRefreshToken().getValue());
- // リクエストヘッダーを作æˆ
- HttpHeaders httpHeaders = new HttpHeaders();
- httpHeaders.add(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_FORM_URLENCODED_VALUE);
- // リクエストを作æˆ
- RequestEntity<MultiValueMap<String, String>> requestEntity =
- new RequestEntity<>(formParams, httpHeaders, HttpMethod.POST,
- URI.create(logoutUri));
- // POSTリクエストé€ä¿¡ï¼ˆãƒã‚°ã‚¢ã‚¦ãƒˆå®Ÿè¡Œï¼‰
-
- ResponseEntity<String> responseEntity = restTemplate.exchange(requestEntity, String.class);
- }
-
- @Value("#{'${services.keycloak.keycloakUrl}'}")
- private String keycloakUrl;
-
- // static {
- // disableCertificateValidation();
- // }
-
- public void disableCertificateValidation() {
- LOGGER.info("disabling certificate validation host : " + keycloakUrl);
- // Create a trust manager that does not validate certificate chains
- TrustManager[] trustAllCerts = new TrustManager[]{
- new X509TrustManager() {
- public X509Certificate[] getAcceptedIssuers() {
- return new X509Certificate[0];
- }
-
- public void checkClientTrusted(X509Certificate[] certs, String authType) {
- }
-
- public void checkServerTrusted(X509Certificate[] certs, String authType) {
- }
- }};
-
-
- // Ignore differences between given hostname and certificate hostname
- HostnameVerifier hv = new HostnameVerifier() {
- public boolean verify(String hostname, SSLSession session) {
-
- // System.out.println("Warning: URL Host: " + hostname + " vs. "
- // + session.getPeerHost());
- if (hostname.equals(keycloakUrl) && session.getPeerHost().equals(keycloakUrl)) {
- return true;
- } else {
- return false;
- }
- }
- };
-
- // Install the all-trusting trust manager
- try {
- SSLContext sc = SSLContext.getInstance("SSL");
- sc.init(null, trustAllCerts, new SecureRandom());
- HttpsURLConnection.setDefaultSSLSocketFactory(sc.getSocketFactory());
- HttpsURLConnection.setDefaultHostnameVerifier(hv);
- } catch (Exception e) {
- }
-
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/configuration/WebConfiguration.java b/src/main/java/eu/hbp/mip/configurations/APIMetadataConfiguration.java
similarity index 61%
rename from src/main/java/eu/hbp/mip/configuration/WebConfiguration.java
rename to src/main/java/eu/hbp/mip/configurations/APIMetadataConfiguration.java
index a5b514dfb815c9df88c0475b7c3ce24df1f06803..7b9eab4563d9c71af0a0eac7d6bae42d798df93b 100644
--- a/src/main/java/eu/hbp/mip/configuration/WebConfiguration.java
+++ b/src/main/java/eu/hbp/mip/configurations/APIMetadataConfiguration.java
@@ -1,31 +1,18 @@
-package eu.hbp.mip.configuration;
+package eu.hbp.mip.configurations;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
-import org.springframework.context.annotation.DependsOn;
-import org.springframework.data.web.config.EnableSpringDataWebSupport;
import springfox.documentation.builders.ApiInfoBuilder;
import springfox.documentation.builders.RequestHandlerSelectors;
import springfox.documentation.service.ApiInfo;
import springfox.documentation.service.Contact;
import springfox.documentation.spi.DocumentationType;
import springfox.documentation.spring.web.plugins.Docket;
-import springfox.documentation.swagger.web.UiConfiguration;
import springfox.documentation.swagger2.annotations.EnableSwagger2;
-/**
- * Created by mirco on 11.07.16.
- */
-
@Configuration
@EnableSwagger2
-@EnableSpringDataWebSupport
-public class WebConfiguration {
-
- @Bean
- public UiConfiguration swaggerUiConfig() {
- return UiConfiguration.DEFAULT;
- }
+public class APIMetadataConfiguration {
@Bean
public Docket swaggerDocumentation() {
@@ -40,10 +27,8 @@ public class WebConfiguration {
private ApiInfo metadata() {
return new ApiInfoBuilder()
.title("Medical Informatics Platform API")
- .description("Serve the MIP Frontend")
- .version("1.0")
- .contact(new Contact("Mirco Nasuti", "https://www.unil.ch/lren/en/home.html", "mirco.nasuti@chuv.ch"))
+ .description("Serving the MIP Frontend")
+ .contact(new Contact("Kostas Filippopolitis", "https://github.com/KFilippopolitis", "kostasfilippop@gmail.com"))
.build();
}
-
}
diff --git a/src/main/java/eu/hbp/mip/configurations/GalaxyAuthentication.java b/src/main/java/eu/hbp/mip/configurations/GalaxyAuthentication.java
new file mode 100644
index 0000000000000000000000000000000000000000..e8a5df4bc7311cc86683c546f27de0208a850d20
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/configurations/GalaxyAuthentication.java
@@ -0,0 +1,54 @@
+package eu.hbp.mip.configurations;
+
+import com.google.gson.Gson;
+import com.google.gson.JsonObject;
+import eu.hbp.mip.services.ActiveUserService;
+import eu.hbp.mip.utils.Logger;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.ResponseEntity;
+import org.springframework.security.access.prepost.PreAuthorize;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.ResponseStatus;
+import org.springframework.web.bind.annotation.RestController;
+
+import java.util.Base64;
+
+@RestController
+public class GalaxyAuthentication {
+
+ private final ActiveUserService activeUserService;
+
+ @Value("#{'${services.galaxy.galaxyUsername:admin}'}")
+ private String galaxyUsername;
+
+ @Value("#{'${services.galaxy.galaxyPassword:password}'}")
+ private String galaxyPassword;
+
+ @Value("#{'${services.galaxy.galaxpathoyContext:nativeGalaxy}'}")
+ private String galaxyContext;
+
+ public GalaxyAuthentication(ActiveUserService activeUserService) {
+ this.activeUserService = activeUserService;
+ }
+
+ /**
+ * Get Galaxy Reverse Proxy basic access token.
+ *
+ * @return Return a @{@link ResponseEntity} with the token.
+ */
+ @RequestMapping(path = "/galaxy", method = RequestMethod.GET, produces = "application/json")
+ @PreAuthorize("hasRole('WORKFLOW_ADMIN')")
+ @ResponseStatus(value = HttpStatus.OK)
+ public ResponseEntity getGalaxyConfiguration() {
+ Logger logger = new Logger(activeUserService.getActiveUser().getUsername(), "(GET) /user/galaxy");
+ String stringEncoded = Base64.getEncoder().encodeToString((galaxyUsername + ":" + galaxyPassword).getBytes());
+ JsonObject object = new JsonObject();
+ object.addProperty("authorization", stringEncoded);
+ object.addProperty("context", galaxyContext);
+ logger.LogUserAction("Successfully Loaded galaxy information.");
+
+ return ResponseEntity.ok(new Gson().toJson(object));
+ }
+}
diff --git a/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java b/src/main/java/eu/hbp/mip/configurations/PersistenceConfiguration.java
similarity index 62%
rename from src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java
rename to src/main/java/eu/hbp/mip/configurations/PersistenceConfiguration.java
index c8024e1bffa90604da6d13712bc07cbac815b3d7..181bc639c05ea4b3987459cf36a62664db6812cb 100644
--- a/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java
+++ b/src/main/java/eu/hbp/mip/configurations/PersistenceConfiguration.java
@@ -1,10 +1,12 @@
-package eu.hbp.mip.configuration;
+package eu.hbp.mip.configurations;
import org.flywaydb.core.Flyway;
-import org.springframework.boot.autoconfigure.jdbc.DataSourceBuilder;
import org.springframework.boot.context.properties.ConfigurationProperties;
-import org.springframework.boot.orm.jpa.EntityScan;
-import org.springframework.context.annotation.*;
+import org.springframework.boot.jdbc.DataSourceBuilder;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.DependsOn;
+import org.springframework.context.annotation.Primary;
import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
import org.springframework.orm.jpa.JpaVendorAdapter;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
@@ -18,25 +20,24 @@ import javax.sql.DataSource;
@Configuration
@EnableJpaRepositories("eu.hbp.mip.repositories")
-@EntityScan(basePackages = "eu.hbp.mip.model")
public class PersistenceConfiguration {
@Primary
- @Bean(name = "portalDatasource")
- @ConfigurationProperties(prefix = "spring.portalDatasource")
+ @Bean(name = "portal-datasource")
+ @ConfigurationProperties(prefix = "spring.portal-datasource")
public DataSource portalDataSource() {
return DataSourceBuilder.create().build();
}
-
@Bean(name = "entityManagerFactory")
@DependsOn("flyway")
public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
- LocalContainerEntityManagerFactoryBean em = new LocalContainerEntityManagerFactoryBean();
- em.setDataSource(portalDataSource());
+ LocalContainerEntityManagerFactoryBean emfb = new LocalContainerEntityManagerFactoryBean();
+ emfb.setDataSource(portalDataSource());
JpaVendorAdapter vendorAdapter = new HibernateJpaVendorAdapter();
- em.setJpaVendorAdapter(vendorAdapter);
- return em;
+ emfb.setJpaVendorAdapter(vendorAdapter);
+ emfb.setPackagesToScan("eu.hbp.mip.models.DAOs");
+ return emfb;
}
@Bean(name = "flyway", initMethod = "migrate")
diff --git a/src/main/java/eu/hbp/mip/configurations/SecurityConfiguration.java b/src/main/java/eu/hbp/mip/configurations/SecurityConfiguration.java
new file mode 100644
index 0000000000000000000000000000000000000000..9f583da4ef31205007e7467c63cfaf95645a5f28
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/configurations/SecurityConfiguration.java
@@ -0,0 +1,126 @@
+package eu.hbp.mip.configurations;
+
+import eu.hbp.mip.utils.CORSFilter;
+import org.keycloak.adapters.KeycloakConfigResolver;
+import org.keycloak.adapters.springboot.KeycloakSpringBootConfigResolver;
+import org.keycloak.adapters.springsecurity.KeycloakConfiguration;
+import org.keycloak.adapters.springsecurity.authentication.KeycloakAuthenticationProvider;
+import org.keycloak.adapters.springsecurity.config.KeycloakWebSecurityConfigurerAdapter;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.context.annotation.Bean;
+import org.springframework.security.config.annotation.authentication.builders.AuthenticationManagerBuilder;
+import org.springframework.security.config.annotation.web.builders.HttpSecurity;
+import org.springframework.security.core.authority.mapping.SimpleAuthorityMapper;
+import org.springframework.security.core.session.SessionRegistryImpl;
+import org.springframework.security.web.access.channel.ChannelProcessingFilter;
+import org.springframework.security.web.authentication.session.RegisterSessionAuthenticationStrategy;
+import org.springframework.security.web.authentication.session.SessionAuthenticationStrategy;
+import org.springframework.security.web.csrf.CsrfFilter;
+import org.springframework.security.web.csrf.CsrfToken;
+import org.springframework.security.web.csrf.CsrfTokenRepository;
+import org.springframework.security.web.csrf.HttpSessionCsrfTokenRepository;
+import org.springframework.stereotype.Controller;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.filter.OncePerRequestFilter;
+import org.springframework.web.util.WebUtils;
+
+import javax.servlet.*;
+import javax.servlet.http.Cookie;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+import java.io.IOException;
+
+
+@Controller
+@KeycloakConfiguration
+public class SecurityConfiguration extends KeycloakWebSecurityConfigurerAdapter {
+
+ // Upon logout, redirect to login page url
+ private static final String logoutRedirectURL = "/sso/login";
+
+ @Value("#{'${authentication.enabled}'}")
+ private boolean authenticationEnabled;
+
+ public SecurityConfiguration(HttpServletRequest request) {
+ this.request = request;
+ }
+
+ @Override
+ protected void configure(HttpSecurity http) throws Exception {
+ super.configure(http);
+
+ if (authenticationEnabled) {
+ http.authorizeRequests()
+ .antMatchers(
+ "/sso/login",
+ "/v2/api-docs", "/swagger-ui/**", "/swagger-resources/**" // Swagger URLs
+ ).permitAll()
+ .antMatchers("/galaxy*", "/galaxy/*").hasRole("WORKFLOW_ADMIN")
+ .antMatchers("/**").authenticated()
+ .and().csrf().ignoringAntMatchers("/logout").csrfTokenRepository(csrfTokenRepository())
+ .and().addFilterAfter(csrfHeaderFilter(), CsrfFilter.class);
+ } else {
+ http.addFilterBefore(new CORSFilter(), ChannelProcessingFilter.class);
+ http.antMatcher("/**")
+ .authorizeRequests()
+ .antMatchers("/**").permitAll()
+ .and().csrf().disable();
+ }
+ }
+
+ private Filter csrfHeaderFilter() {
+ return new OncePerRequestFilter() {
+ @Override
+ protected void doFilterInternal(HttpServletRequest request, HttpServletResponse response,
+ FilterChain filterChain) throws ServletException, IOException {
+ CsrfToken csrf = (CsrfToken) request.getAttribute(CsrfToken.class.getName());
+ if (csrf != null) {
+ Cookie cookie = WebUtils.getCookie(request, "XSRF-TOKEN");
+ String token = csrf.getToken();
+ if (cookie == null || token != null && !token.equals(cookie.getValue())) {
+ cookie = new Cookie("XSRF-TOKEN", token);
+ cookie.setPath("/");
+ response.addCookie(cookie);
+ }
+ }
+ filterChain.doFilter(request, response);
+ }
+ };
+ }
+
+ private CsrfTokenRepository csrfTokenRepository() {
+ HttpSessionCsrfTokenRepository repository = new HttpSessionCsrfTokenRepository();
+ repository.setHeaderName("X-XSRF-TOKEN");
+ return repository;
+ }
+
+ private final HttpServletRequest request;
+
+ @GetMapping(value = "/logout")
+ public String logout() throws ServletException {
+ request.logout();
+ return String.format("redirect:%s", logoutRedirectURL);
+ }
+
+ @Bean
+ public KeycloakConfigResolver KeycloakConfigResolver() {
+ return new KeycloakSpringBootConfigResolver();
+ }
+
+ @Override
+ protected SessionAuthenticationStrategy sessionAuthenticationStrategy() {
+ return new RegisterSessionAuthenticationStrategy(new SessionRegistryImpl());
+ }
+
+ @Autowired
+ public void configureGlobal(AuthenticationManagerBuilder auth) {
+ SimpleAuthorityMapper grantedAuthorityMapper = new SimpleAuthorityMapper();
+ grantedAuthorityMapper.setConvertToUpperCase(true);
+
+ KeycloakAuthenticationProvider keycloakAuthenticationProvider = keycloakAuthenticationProvider();
+ keycloakAuthenticationProvider.setGrantedAuthoritiesMapper(grantedAuthorityMapper);
+ auth.authenticationProvider(keycloakAuthenticationProvider);
+ }
+
+}
diff --git a/src/main/java/eu/hbp/mip/controllers/ActiveUserAPI.java b/src/main/java/eu/hbp/mip/controllers/ActiveUserAPI.java
new file mode 100644
index 0000000000000000000000000000000000000000..aca62c4b6c2771e45ffa60a9cbc09040b1a3248a
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/controllers/ActiveUserAPI.java
@@ -0,0 +1,46 @@
+package eu.hbp.mip.controllers;
+
+import eu.hbp.mip.models.DAOs.UserDAO;
+import eu.hbp.mip.services.ActiveUserService;
+import eu.hbp.mip.utils.Logger;
+import io.swagger.annotations.Api;
+import io.swagger.annotations.ApiOperation;
+import org.springframework.http.ResponseEntity;
+import org.springframework.web.bind.annotation.RequestBody;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RestController;
+
+import javax.servlet.http.HttpServletResponse;
+
+import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
+
+@RestController
+@RequestMapping(value = "/activeUser", produces = {APPLICATION_JSON_VALUE})
+@Api(value = "/activeUser")
+public class ActiveUserAPI {
+
+ private final ActiveUserService activeUserService;
+
+ public ActiveUserAPI(ActiveUserService activeUserService) {
+ this.activeUserService = activeUserService;
+ }
+
+ @ApiOperation(value = "Get the active user", response = UserDAO.class)
+ @RequestMapping(method = RequestMethod.GET)
+ public ResponseEntity<UserDAO> getTheActiveUser(HttpServletResponse response) {
+ Logger logger = new Logger(activeUserService.getActiveUser().getUsername(), "(GET) /activeUser");
+ logger.LogUserAction("Loading the details of the activeUser");
+
+ return ResponseEntity.ok(activeUserService.getActiveUser());
+ }
+
+ @ApiOperation(value = "The active user agrees to the NDA", response = UserDAO.class)
+ @RequestMapping(value = "/agreeNDA", method = RequestMethod.POST)
+ public ResponseEntity<UserDAO> activeUserServiceAgreesToNDA(@RequestBody(required = false) UserDAO userDAO) {
+ Logger logger = new Logger(activeUserService.getActiveUser().getUsername(), "(GET) /activeUser/agreeNDA");
+ logger.LogUserAction("The user agreed to the NDA");
+
+ return ResponseEntity.ok(activeUserService.agreeToNDA());
+ }
+}
diff --git a/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java b/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
similarity index 64%
rename from src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java
rename to src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
index 8310973a308ec810853519552dc48855f494e4d7..48500bb10470059f1fe7d37079dfb391ef395b31 100644
--- a/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java
@@ -8,15 +8,14 @@ import com.google.gson.Gson;
import com.google.gson.reflect.TypeToken;
import eu.hbp.mip.controllers.galaxy.retrofit.RetroFitGalaxyClients;
import eu.hbp.mip.controllers.galaxy.retrofit.RetrofitClientInstance;
-import eu.hbp.mip.model.AlgorithmDTO;
-import eu.hbp.mip.model.UserInfo;
-import eu.hbp.mip.model.galaxy.WorkflowDTO;
+import eu.hbp.mip.models.DTOs.AlgorithmDTO;
+import eu.hbp.mip.models.galaxy.WorkflowDTO;
+import eu.hbp.mip.services.ActiveUserService;
import eu.hbp.mip.utils.CustomResourceLoader;
import eu.hbp.mip.utils.HTTPUtil;
-import eu.hbp.mip.utils.Logging;
+import eu.hbp.mip.utils.Logger;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
-import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.core.io.Resource;
import org.springframework.http.ResponseEntity;
@@ -31,19 +30,17 @@ import java.util.ArrayList;
import java.util.LinkedList;
import java.util.List;
-import static eu.hbp.mip.utils.ErrorMessages.disabledAlgorithmsCouldNotBeLoaded;
import static eu.hbp.mip.utils.InputStreamConverter.convertInputStreamToString;
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@RestController
@RequestMapping(value = "/algorithms", produces = {APPLICATION_JSON_VALUE})
@Api(value = "/algorithms")
-public class AlgorithmsApi {
+public class AlgorithmsAPI {
private static final Gson gson = new Gson();
- @Autowired
- private UserInfo userInfo;
+ private final ActiveUserService activeUserService;
@Value("#{'${services.exareme.algorithmsUrl}'}")
private String exaremeAlgorithmsUrl;
@@ -54,36 +51,43 @@ public class AlgorithmsApi {
@Value("#{'${services.galaxy.galaxyApiKey}'}")
private String galaxyApiKey;
+ @Value("#{'${files.disabledAlgorithms_json}'}")
+ private String disabledAlgorithmsFilePath;
+
+ public AlgorithmsAPI(ActiveUserService activeUserService, CustomResourceLoader resourceLoader) {
+ this.activeUserService = activeUserService;
+ this.resourceLoader = resourceLoader;
+ }
+
@ApiOperation(value = "List all algorithms", response = String.class)
@RequestMapping(method = RequestMethod.GET)
public ResponseEntity<List<AlgorithmDTO>> getAlgorithms() {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Executing...");
+ Logger logger = new Logger(activeUserService.getActiveUser().getUsername(), "(GET) /algorithms");
+
+ logger.LogUserAction("Executing...");
- LinkedList<AlgorithmDTO> exaremeAlgorithms = getExaremeAlgorithms();
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Loaded " + exaremeAlgorithms.size() + " exareme algorithms");
- LinkedList<AlgorithmDTO> galaxyAlgorithms = getGalaxyWorkflows();
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Loaded " + galaxyAlgorithms.size() + " galaxy algorithms");
+ LinkedList<AlgorithmDTO> exaremeAlgorithms = getExaremeAlgorithms(logger);
+ logger.LogUserAction("Loaded " + exaremeAlgorithms.size() + " exareme algorithms");
+ LinkedList<AlgorithmDTO> galaxyAlgorithms = getGalaxyWorkflows(logger);
+ logger.LogUserAction("Loaded " + galaxyAlgorithms.size() + " galaxy algorithms");
LinkedList<AlgorithmDTO> algorithms = new LinkedList<>();
if (exaremeAlgorithms != null) {
algorithms.addAll(exaremeAlgorithms);
} else {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms",
- "Getting exareme algorithms failed and returned null");
+ logger.LogUserAction("Getting exareme algorithms failed and returned null");
}
if (galaxyAlgorithms != null) {
algorithms.addAll(galaxyAlgorithms);
} else {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms",
- "Getting galaxy workflows failed and returned null");
+ logger.LogUserAction("Getting galaxy workflows failed and returned null");
}
List<String> disabledAlgorithms = new ArrayList<>();
try {
disabledAlgorithms = getDisabledAlgorithms();
} catch (IOException e) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms",
- disabledAlgorithmsCouldNotBeLoaded);
+ logger.LogUserAction("The disabled algorithms could not be loaded.");
}
// Remove any disabled algorithm
@@ -93,8 +97,7 @@ public class AlgorithmsApi {
allowedAlgorithms.add(algorithm);
}
}
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms",
- "Successfully listed " + allowedAlgorithms.size() + " algorithms");
+ logger.LogUserAction("Successfully listed " + allowedAlgorithms.size() + " algorithms");
return ResponseEntity.ok(allowedAlgorithms);
}
@@ -103,8 +106,8 @@ public class AlgorithmsApi {
*
* @return a list of AlgorithmDTOs or null if something fails
*/
- public LinkedList<AlgorithmDTO> getExaremeAlgorithms() {
- LinkedList<AlgorithmDTO> algorithms = new LinkedList<>();
+ public LinkedList<AlgorithmDTO> getExaremeAlgorithms(Logger logger) {
+ LinkedList<AlgorithmDTO> algorithms;
// Get exareme algorithms
try {
StringBuilder response = new StringBuilder();
@@ -116,12 +119,11 @@ public class AlgorithmsApi {
}.getType()
);
} catch (IOException e) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "An exception occurred: " + e.getMessage());
+ logger.LogUserAction("An exception occurred: " + e.getMessage());
return null;
}
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms",
- "Completed, returned " + algorithms.size() + " algorithms.");
+ logger.LogUserAction("Completed, returned " + algorithms.size() + " algorithms.");
return algorithms;
}
@@ -130,8 +132,7 @@ public class AlgorithmsApi {
*
* @return a list of AlgorithmDTOs or null if something fails
*/
- public LinkedList<AlgorithmDTO> getGalaxyWorkflows() {
-
+ public LinkedList<AlgorithmDTO> getGalaxyWorkflows(Logger logger) {
List<Workflow> workflowList;
try {
// Get all the workflows with the galaxy client
@@ -140,8 +141,7 @@ public class AlgorithmsApi {
workflowList = new ArrayList<>(workflowsClient.getWorkflows());
} catch (Exception e) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Error when calling list galaxy workflows: " + e.getMessage());
-
+ logger.LogUserAction("Error when calling list galaxy workflows: " + e.getMessage());
return null;
}
@@ -160,33 +160,31 @@ public class AlgorithmsApi {
} else { // Something unexpected happened
String msgErr = gson.toJson(response.errorBody());
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Error Response: " + msgErr);
+ logger.LogUserAction("Error Response: " + msgErr);
return null;
}
} catch (Exception e) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "An exception occurred: " + e.getMessage());
+ logger.LogUserAction("An exception occurred: " + e.getMessage());
return null;
}
}
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Workflows fetched: " + workflows.size());
+ logger.LogUserAction("Workflows fetched: " + workflows.size());
// Convert the workflows to algorithms
LinkedList<AlgorithmDTO> algorithms = new LinkedList<>();
for (WorkflowDTO workflow : workflows) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Converting workflow: " + workflow);
+ logger.LogUserAction("Converting workflow: " + workflow);
algorithms.add(workflow.convertToAlgorithmDTO());
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms",
- "Converted algorithm: " + algorithms.get(algorithms.size() - 1));
+ logger.LogUserAction("Converted algorithm: " + algorithms.get(algorithms.size() - 1));
}
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /algorithms", "Completed!");
+ logger.LogUserAction("Completed!");
return algorithms;
}
- @Autowired
- private CustomResourceLoader resourceLoader;
+ private final CustomResourceLoader resourceLoader;
/**
* Fetches the disabled algorithms from a .json file
@@ -196,13 +194,12 @@ public class AlgorithmsApi {
*/
List<String> getDisabledAlgorithms() throws IOException {
- Resource resource = resourceLoader.getResource("file:/opt/portal/api/disabledAlgorithms.json");
+ Resource resource = resourceLoader.getResource(disabledAlgorithmsFilePath);
- List<String> response = gson.fromJson(convertInputStreamToString(
+ return gson.fromJson(convertInputStreamToString(
resource.getInputStream()),
new TypeToken<List<String>>() {
}.getType()
);
- return response;
}
}
diff --git a/src/main/java/eu/hbp/mip/controllers/ArticlesApi.java b/src/main/java/eu/hbp/mip/controllers/ArticlesApi.java
deleted file mode 100644
index d4eb46e9f3d072255e23be8a37a4e956add16873..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/controllers/ArticlesApi.java
+++ /dev/null
@@ -1,193 +0,0 @@
-/*
- * Created by mirco on 04.12.15.
- */
-
-package eu.hbp.mip.controllers;
-
-
-import com.github.slugify.Slugify;
-import eu.hbp.mip.model.Article;
-import eu.hbp.mip.model.User;
-import eu.hbp.mip.model.UserInfo;
-import eu.hbp.mip.repositories.ArticleRepository;
-import eu.hbp.mip.utils.Logging;
-import io.swagger.annotations.*;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.HttpStatus;
-import org.springframework.http.ResponseEntity;
-import org.springframework.web.bind.annotation.*;
-
-import javax.validation.Valid;
-import java.io.IOException;
-import java.util.Date;
-import java.util.Iterator;
-
-import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
-
-@RestController
-@RequestMapping(value = "/articles", produces = {APPLICATION_JSON_VALUE})
-@Api(value = "/articles", description = "the articles API")
-public class ArticlesApi {
-
- @Autowired
- private UserInfo userInfo;
-
- @Autowired
- private ArticleRepository articleRepository;
-
- @ApiOperation(value = "Get articles", response = Article.class, responseContainer = "List")
- @RequestMapping(method = RequestMethod.GET)
- public ResponseEntity<Iterable> getArticles(
- @ApiParam(value = "Only ask own articles") @RequestParam(value = "own", required = false) Boolean own,
- @ApiParam(value = "Only ask results matching status", allowableValues = "draft, published") @RequestParam(value = "status", required = false) String status
- ) {
- User user = userInfo.getUser();
- Iterable<Article> articles;
- Logging.LogUserAction(user.getUsername(), "(GET) /articles", "Loading articles...");
-
- if (own != null && own) {
- articles = articleRepository.findByCreatedBy(user);
- } else {
- articles = articleRepository.findByStatusOrCreatedBy("published", user);
- }
- int articlesSize = 0;
- if (status != null) {
- for (Iterator<Article> i = articles.iterator(); i.hasNext(); ) {
- Article a = i.next();
- if (!status.equals(a.getStatus())) {
- i.remove();
- }
- articlesSize++;
- }
- }
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /articles", "Successfully Loaded " + articlesSize + " articles");
-
- return ResponseEntity.ok(articles);
- }
-
-
- @ApiOperation(value = "Create an article")
- @ApiResponses(value = {@ApiResponse(code = 201, message = "Article created")})
- @RequestMapping(method = RequestMethod.POST)
- public ResponseEntity<Void> addAnArticle(
- @RequestBody @ApiParam(value = "Article to create", required = true) @Valid Article article
- ) {
-
- User user = userInfo.getUser();
- Logging.LogUserAction(user.getUsername(), "(POST) /articles", "Creating article...");
-
- article.setCreatedAt(new Date());
- if ("published".equals(article.getStatus())) {
- article.setPublishedAt(new Date());
- }
- article.setCreatedBy(user);
-
- long count = 1;
- for (int i = 1; count > 0; i++) {
- count = articleRepository.countByTitle(article.getTitle());
-
- if (count > 0) {
- String title = article.getTitle();
- if (i > 1) {
- title = title.substring(0, title.length() - 4);
- }
- article.setTitle(title + " (" + i + ")");
- }
- }
-
- String slug;
- try {
- slug = new Slugify().slugify(article.getTitle());
- } catch (IOException e) {
- slug = "";
- //LOGGER.trace("Cannot slugify title", e);
- }
-
- boolean alreadyExists = true;
- for (int i = 1; alreadyExists; i++) {
- alreadyExists = articleRepository.exists(slug);
- if (alreadyExists) {
- if (i > 1) {
- slug = slug.substring(0, slug.length() - 2);
- }
- slug += "-" + i;
- }
- article.setSlug(slug);
- }
- articleRepository.save(article);
-
- Logging.LogUserAction(user.getUsername(), "(POST) /articles", "Successfully created article with id : " + article.getSlug());
- return new ResponseEntity<>(HttpStatus.CREATED);
- }
-
-
- @ApiOperation(value = "Get an article", response = Article.class)
- @RequestMapping(value = "/{slug}", method = RequestMethod.GET)
- public ResponseEntity<Article> getAnArticle(
- @ApiParam(value = "slug", required = true) @PathVariable("slug") String slug
- ) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /articles/{slug}", "Loading article with id : " + slug);
-
- User user = userInfo.getUser();
- Article article;
- article = articleRepository.findOne(slug);
-
- if (article == null) {
- //LOGGER.warn("Cannot find article : " + slug);
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /articles/{slug}", "Article not found");
- return ResponseEntity.badRequest().body(null);
- }
-
- if (!"published".equals(article.getStatus()) && !article.getCreatedBy().getUsername().equals(user.getUsername())) {
- return new ResponseEntity<>(HttpStatus.FORBIDDEN);
- }
-
- Logging.LogUserAction(user.getUsername(), "(GET) /articles/{slug}", "Successfully Loaded article with id : " + slug);
-
- return ResponseEntity.ok(article);
- }
-
-
- @ApiOperation(value = "Update an article")
- @ApiResponses(value = {@ApiResponse(code = 204, message = "Article updated")})
- @RequestMapping(value = "/{slug}", method = RequestMethod.PUT)
- public ResponseEntity<Void> updateAnArticle(
- @ApiParam(value = "slug", required = true) @PathVariable("slug") String slug,
- @RequestBody @ApiParam(value = "Article to update", required = true) @Valid Article article
- ) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(PUT) /articles/{slug}", "Updating article with id : " + slug);
-
- User user = userInfo.getUser();
-
- String author = articleRepository.findOne(slug).getCreatedBy().getUsername();
-
- if (!user.getUsername().equals(author)) {
- return new ResponseEntity<>(HttpStatus.FORBIDDEN);
- }
-
- String oldTitle = articleRepository.findOne(slug).getTitle();
-
- String newTitle = article.getTitle();
-
- if (!newTitle.equals(oldTitle)) {
- long count = 1;
- for (int i = 1; count > 0 && !newTitle.equals(oldTitle); i++) {
- newTitle = article.getTitle();
- count = articleRepository.countByTitle(newTitle);
- if (count > 0 && !newTitle.equals(oldTitle)) {
- if (i > 1) {
- newTitle = newTitle.substring(0, newTitle.length() - 4);
- }
- article.setTitle(newTitle + " (" + i + ")");
- }
- }
- }
-
- articleRepository.save(article);
-
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(PUT) /articles/{slug}", "Successfully pdated article with id : " + slug);
-
- return new ResponseEntity<>(HttpStatus.NO_CONTENT);
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/controllers/ExperimentAPI.java b/src/main/java/eu/hbp/mip/controllers/ExperimentAPI.java
new file mode 100644
index 0000000000000000000000000000000000000000..e5d0b04c54b0fd8652f5d284cb8690eaf14d3acf
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/controllers/ExperimentAPI.java
@@ -0,0 +1,109 @@
+package eu.hbp.mip.controllers;
+
+
+import eu.hbp.mip.models.DTOs.ExperimentDTO;
+import eu.hbp.mip.services.ActiveUserService;
+import eu.hbp.mip.services.ExperimentService;
+import eu.hbp.mip.utils.JsonConverters;
+import eu.hbp.mip.utils.Logger;
+import io.swagger.annotations.Api;
+import io.swagger.annotations.ApiOperation;
+import io.swagger.annotations.ApiParam;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.ResponseEntity;
+import org.springframework.security.core.Authentication;
+import org.springframework.web.bind.annotation.*;
+
+import java.util.Map;
+
+import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
+
+/*
+ This api is creating experiments and running it's algorithm on the
+ exareme or galaxy clients.
+ */
+
+@RestController
+@RequestMapping(value = "/experiments", produces = {APPLICATION_JSON_VALUE})
+@Api(value = "/experiments")
+public class ExperimentAPI {
+
+ private final ExperimentService experimentService;
+ private final ActiveUserService activeUserService;
+ public ExperimentAPI(
+ ExperimentService experimentService,
+ ActiveUserService activeUserService
+ ) {
+ this.experimentService = experimentService;
+ this.activeUserService = activeUserService;
+ }
+
+ @ApiOperation(value = "Get experiments", response = Map.class, responseContainer = "List")
+ @RequestMapping(method = RequestMethod.GET)
+ public ResponseEntity<String> getExperiments(Authentication authentication,
+ @RequestParam(name = "name", required = false) String name,
+ @RequestParam(name = "algorithm", required = false) String algorithm,
+ @RequestParam(name = "shared", required = false) Boolean shared,
+ @RequestParam(name = "viewed", required = false) Boolean viewed,
+ @RequestParam(name = "includeShared", required = false, defaultValue = "true") boolean includeShared,
+ @RequestParam(name = "orderBy", required = false, defaultValue = "created") String orderBy,
+ @RequestParam(name = "descending", required = false, defaultValue = "true") Boolean descending,
+ @RequestParam(defaultValue = "0") int page,
+ @RequestParam(defaultValue = "10") int size
+ ) {
+ Map experiments = experimentService.getExperiments(authentication,
+ name,
+ algorithm,
+ shared,
+ viewed,
+ includeShared,
+ page,
+ size,
+ orderBy,
+ descending,
+ new Logger(activeUserService.getActiveUser().getUsername(),"(GET) /experiments"));
+ return new ResponseEntity(experiments, HttpStatus.OK);
+ }
+
+
+ @ApiOperation(value = "Get an experiment", response = ExperimentDTO.class)
+ @RequestMapping(value = "/{uuid}", method = RequestMethod.GET)
+ public ResponseEntity<String> getExperiment(Authentication authentication,
+ @ApiParam(value = "uuid", required = true) @PathVariable("uuid") String uuid) {
+ ExperimentDTO experimentDTO = experimentService.getExperiment(authentication, uuid, new Logger(activeUserService.getActiveUser().getUsername(),"(GET) /experiments/{uuid}"));
+ return new ResponseEntity<>(JsonConverters.convertObjectToJsonString(experimentDTO), HttpStatus.OK);
+ }
+
+
+ @ApiOperation(value = "Create an experiment", response = ExperimentDTO.class)
+ @RequestMapping(method = RequestMethod.POST)
+ public ResponseEntity<String> createExperiment(Authentication authentication, @RequestBody ExperimentDTO experimentDTO) {
+ experimentDTO = experimentService.createExperiment(authentication, experimentDTO, new Logger(activeUserService.getActiveUser().getUsername(),"(POST) /experiments"));
+ return new ResponseEntity<>(JsonConverters.convertObjectToJsonString(experimentDTO), HttpStatus.CREATED);
+ }
+
+
+ @ApiOperation(value = "Update an experiment", response = ExperimentDTO.class)
+ @RequestMapping(value = "/{uuid}", method = RequestMethod.PATCH)
+ public ResponseEntity<String> updateExperiment(@RequestBody ExperimentDTO experimentDTO, @ApiParam(value = "uuid", required = true) @PathVariable("uuid") String uuid) {
+ experimentDTO = experimentService.updateExperiment(uuid, experimentDTO, new Logger(activeUserService.getActiveUser().getUsername(),"(PATCH) /experiments/{uuid}"));
+ return new ResponseEntity<>(JsonConverters.convertObjectToJsonString(experimentDTO), HttpStatus.OK);
+ }
+
+
+ @ApiOperation(value = "Delete an experiment", response = boolean.class)
+ @RequestMapping(value = "/{uuid}", method = RequestMethod.DELETE)
+ public ResponseEntity<String> deleteExperiment(
+ @ApiParam(value = "uuid", required = true) @PathVariable("uuid") String uuid) {
+ experimentService.deleteExperiment(uuid, new Logger(activeUserService.getActiveUser().getUsername(), "(DELETE) /experiments/{uuid}"));
+ return new ResponseEntity<>(HttpStatus.OK);
+ }
+
+
+ @ApiOperation(value = "Create a transient experiment", response = ExperimentDTO.class)
+ @RequestMapping(value = "/transient", method = RequestMethod.POST)
+ public ResponseEntity<String> createTransientExperiment(Authentication authentication, @RequestBody ExperimentDTO experimentDTO) {
+ experimentDTO = experimentService.createTransientExperiment(authentication, experimentDTO, new Logger(activeUserService.getActiveUser().getUsername(), "(POST) /experiments/transient"));
+ return new ResponseEntity<>(JsonConverters.convertObjectToJsonString(experimentDTO), HttpStatus.OK);
+ }
+}
\ No newline at end of file
diff --git a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
deleted file mode 100644
index a54b93df5facaeaa98c7ad35eef44793ad91e899..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
+++ /dev/null
@@ -1,833 +0,0 @@
-package eu.hbp.mip.controllers;
-
-import com.github.jmchilton.blend4j.galaxy.GalaxyInstance;
-import com.github.jmchilton.blend4j.galaxy.GalaxyInstanceFactory;
-import com.github.jmchilton.blend4j.galaxy.WorkflowsClient;
-import com.github.jmchilton.blend4j.galaxy.beans.Workflow;
-import com.github.jmchilton.blend4j.galaxy.beans.WorkflowDetails;
-import com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputDefinition;
-import com.google.common.collect.Lists;
-import com.google.gson.*;
-import eu.hbp.mip.controllers.galaxy.retrofit.RetroFitGalaxyClients;
-import eu.hbp.mip.controllers.galaxy.retrofit.RetrofitClientInstance;
-import eu.hbp.mip.model.*;
-import eu.hbp.mip.model.ExperimentExecutionDTO.AlgorithmExecutionDTO.AlgorithmExecutionParamDTO;
-import eu.hbp.mip.model.galaxy.ErrorResponse;
-import eu.hbp.mip.model.galaxy.GalaxyWorkflowResult;
-import eu.hbp.mip.model.galaxy.PostWorkflowToGalaxyDtoResponse;
-import eu.hbp.mip.repositories.ExperimentRepository;
-import eu.hbp.mip.repositories.ModelRepository;
-import eu.hbp.mip.utils.ClaimUtils;
-import eu.hbp.mip.utils.HTTPUtil;
-import eu.hbp.mip.utils.Logging;
-import io.swagger.annotations.Api;
-import io.swagger.annotations.ApiOperation;
-import io.swagger.annotations.ApiParam;
-import org.codehaus.jettison.json.JSONException;
-import org.codehaus.jettison.json.JSONObject;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Value;
-import org.springframework.http.HttpStatus;
-import org.springframework.http.ResponseEntity;
-import org.springframework.security.core.Authentication;
-import org.springframework.web.bind.annotation.*;
-import retrofit2.Call;
-import retrofit2.Response;
-
-import java.io.IOException;
-import java.util.*;
-
-import static java.lang.Thread.sleep;
-import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
-
-/*
- This api is creating experiments and running it's algorithm on the
- exareme or galaxy clients.
- */
-
-@RestController
-@RequestMapping(value = "/experiments", produces = {APPLICATION_JSON_VALUE})
-@Api(value = "/experiments")
-public class ExperimentApi {
-
- private static final Gson gson = new Gson();
-
- @Autowired
- private UserInfo userInfo;
-
- private static final Gson gsonOnlyExposed = new GsonBuilder().serializeNulls()
- .setDateFormat("yyyy-MM-dd'T'HH:mm:ssZ").excludeFieldsWithoutExposeAnnotation().create();
-
- @Value("#{'${services.exareme.queryExaremeUrl}'}")
- private String queryExaremeUrl;
-
- @Value("#{'${services.workflows.workflowUrl}'}")
- private String workflowUrl;
-
- @Value("#{'${services.workflows.jwtSecret}'}")
- private String jwtSecret;
-
- @Value("#{'${services.galaxy.galaxyUrl}'}")
- private String galaxyUrl;
-
- @Value("#{'${services.galaxy.galaxyApiKey}'}")
- private String galaxyApiKey;
-
- // Enable HBP collab authentication (1) or disable it (0). Default is 1
- @Value("#{'${hbp.authentication.enabled:1}'}")
- private boolean authenticationIsEnabled;
-
- @Autowired
- private ModelRepository modelRepository;
-
- @Autowired
- private ExperimentRepository experimentRepository;
-
- @ApiOperation(value = "get an experiment", response = Experiment.class)
- @RequestMapping(value = "/{uuid}", method = RequestMethod.GET)
- public ResponseEntity<String> getExperiment(
- @ApiParam(value = "uuid", required = true) @PathVariable("uuid") String uuid) {
-
- Experiment experiment;
- UUID experimentUuid;
- User user = userInfo.getUser();
-
- Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}", "Loading Experiment with uuid : " + uuid);
-
- try {
- experimentUuid = UUID.fromString(uuid);
- } catch (IllegalArgumentException iae) {
- Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}", "Invalid Experiment UUID.");
- return ResponseEntity.badRequest().body("Invalid Experiment UUID");
- }
-
- experiment = experimentRepository.findOne(experimentUuid);
-
- if (experiment == null) {
- Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}", "Experiment Not found.");
- return new ResponseEntity<>("Not found", HttpStatus.NOT_FOUND);
- }
-
- if (!experiment.isShared() && !experiment.getCreatedBy().getUsername().equals(user.getUsername())) {
- Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}", "Accessing Experiment is unauthorized.");
- return new ResponseEntity<>("You don't have access to the experiment.", HttpStatus.UNAUTHORIZED);
- }
-
- Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}", "Experiment was Loaded with uuid : " + uuid + ".");
-
- return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
- }
-
-
- @ApiOperation(value = "Create an experiment", response = Experiment.class)
- @RequestMapping(value = "/runAlgorithm", method = RequestMethod.POST)
- public ResponseEntity<String> runExperiment(Authentication authentication, @RequestBody ExperimentExecutionDTO experimentExecutionDTO) {
- User user = userInfo.getUser();
- // Get the type and name of algorithm
- String algorithmType = experimentExecutionDTO.getAlgorithms().get(0).getType();
- String algorithmName = experimentExecutionDTO.getAlgorithms().get(0).getName();
-
- StringBuilder parametersLogMessage = new StringBuilder(", Parameters:\n");
- for (ExperimentExecutionDTO.AlgorithmExecutionDTO.AlgorithmExecutionParamDTO params : experimentExecutionDTO.getAlgorithms().get(0).getParameters()) {
- parametersLogMessage
- .append(" ")
- .append(params.getLabel())
- .append(" -> ")
- .append(params.getValue())
- .append("\n");
- }
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Executing " + algorithmName + parametersLogMessage);
-
- if (authenticationIsEnabled) {
- // Getting the dataset from the experiment parameters
- String experimentDatasets = null;
- for (ExperimentExecutionDTO.AlgorithmExecutionDTO.AlgorithmExecutionParamDTO parameter : experimentExecutionDTO.getAlgorithms().get(0).getParameters()) {
- if (parameter.getLabel().equals("dataset")) {
- experimentDatasets = parameter.getValue();
- break;
- }
- }
-
- if (experimentDatasets == null || experimentDatasets.equals("")) {
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm",
- "A dataset should be specified to run an algorithm.");
- return ResponseEntity.badRequest().body("Please provide at least one dataset to run the algorithm.");
- }
-
- // --- Validating proper access rights on the datasets ---
- if (!ClaimUtils.userHasDatasetsAuthorization(user.getUsername(), authentication.getAuthorities(), experimentDatasets)) {
- return ResponseEntity.badRequest().body("You are not authorized to use these datasets.");
- }
- }
-
- // Run with the appropriate engine
- if (algorithmType.equals("workflow")) {
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Algorithm runs on Galaxy.");
- return runGalaxyWorkflow(experimentExecutionDTO);
- } else {
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Algorithm runs on Exareme.");
- return runExaremeAlgorithm(experimentExecutionDTO);
- }
- }
-
- @ApiOperation(value = "Mark an experiment as viewed", response = Experiment.class)
- @RequestMapping(value = "/{uuid}/markAsViewed", method = RequestMethod.GET)
- public ResponseEntity<String> markExperimentAsViewed(
- @ApiParam(value = "uuid", required = true) @PathVariable("uuid") String uuid) {
-
- Experiment experiment;
- UUID experimentUuid;
- User user = userInfo.getUser();
-
- Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}/markAsViewed", "Marking as viewed the experiment with uuid : " + uuid + ".");
-
- try {
- experimentUuid = UUID.fromString(uuid);
- } catch (IllegalArgumentException iae) {
- Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}/markAsViewed", "Invalid Experiment UUID" + uuid + ".");
- return ResponseEntity.badRequest().body("Invalid Experiment UUID");
- }
-
- experiment = experimentRepository.findOne(experimentUuid);
- if (!experiment.getCreatedBy().getUsername().equals(user.getUsername())) {
- Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}/markAsViewed", "You're not the owner of this experiment");
- return new ResponseEntity<>("You're not the owner of this experiment", HttpStatus.UNAUTHORIZED);
- }
- experiment.setResultsViewed(true);
- experimentRepository.save(experiment);
-
- Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{uuid}/markAsViewed", "Experiment with uuid: " + uuid + " was marked as viewed.");
-
- return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
- }
-
- @ApiOperation(value = "Mark an experiment as shared", response = Experiment.class)
- @RequestMapping(value = "/{uuid}/markAsShared", method = RequestMethod.GET)
- public ResponseEntity<String> markExperimentAsShared(
- @ApiParam(value = "uuid", required = true) @PathVariable("uuid") String uuid) {
-
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /experiments/{uuid}/markAsShared", "Marking as shared the experiment with uuid : " + uuid + ".");
-
- return doMarkExperimentAsShared(uuid, true);
- }
-
- @ApiOperation(value = "Mark an experiment as unshared", response = Experiment.class)
- @RequestMapping(value = "/{uuid}/markAsUnshared", method = RequestMethod.GET)
- public ResponseEntity<String> markExperimentAsUnshared(
- @ApiParam(value = "uuid", required = true) @PathVariable("uuid") String uuid) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /experiments/{uuid}/markAs/Unshared", "Marking as unshared the experiment with uuid : " + uuid + ".");
-
- return doMarkExperimentAsShared(uuid, false);
- }
-
- @ApiOperation(value = "list experiments", response = Experiment.class, responseContainer = "List")
- @RequestMapping(method = RequestMethod.GET, params = {"maxResultCount"})
- public ResponseEntity<String> listExperiments(
- @ApiParam(value = "maxResultCount") @RequestParam int maxResultCount) {
- User user = userInfo.getUser();
- Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{maxResultCount}", "Listing experiments with a maximum amount of : " + maxResultCount + ".");
-
- List<Experiment> expList = doListExperiments(false, null);
- Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{maxResultCount}", "Successfully listed experiments.");
-
- return new ResponseEntity<>(gsonOnlyExposed.toJson(expList), HttpStatus.OK);
- }
-
- @ApiOperation(value = "list experiments", response = Experiment.class, responseContainer = "List")
- @RequestMapping(method = RequestMethod.GET, params = {"slug", "maxResultCount"})
- public ResponseEntity<String> listExperiments(@ApiParam(value = "slug") @RequestParam("slug") String modelSlug,
- @ApiParam(value = "maxResultCount") @RequestParam("maxResultCount") int maxResultCount) {
- User user = userInfo.getUser();
- Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{slug}/{maxResultCount}", "Listing experiments with a maximum amount of :" + maxResultCount + "with modelSlug : " + modelSlug + ".");
-
- if (maxResultCount <= 0 || modelSlug == null || "".equals(modelSlug)) {
- return new ResponseEntity<>("You must provide at least a slug or a limit of result",
- HttpStatus.BAD_REQUEST);
- }
-
- List<Experiment> expList = doListExperiments(false, null);
- Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{slug}/{maxResultCount}", "Successfully listed my experiments.");
- return new ResponseEntity<>(gsonOnlyExposed.toJson(expList), HttpStatus.OK);
- }
-
- @ApiOperation(value = "list my experiments", response = Experiment.class, responseContainer = "List")
- @RequestMapping(method = RequestMethod.GET, params = {"mine"})
- public ResponseEntity<String> listMyExperiments(Authentication authentication, @ApiParam(value = "mine") @RequestParam("mine") boolean mine) {
- User user = userInfo.getUser();
- Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{mine}", "Listing my experiments.");
- List<Experiment> expList = doListExperiments(true, null);
- Logging.LogUserAction(user.getUsername(), "(GET) /experiments/{mine}", "Successfully listed my experiments.");
- return new ResponseEntity<>(gsonOnlyExposed.toJson(expList), HttpStatus.OK);
- }
-
- private List<Experiment> doListExperiments(boolean mine, String modelSlug) {
- User user = userInfo.getUser();
-
- Iterable<Experiment> myExperiments = experimentRepository.findByCreatedBy(user);
- List<Experiment> expList = Lists.newLinkedList(myExperiments);
- if (!mine) {
- Iterable<Experiment> sharedExperiments = experimentRepository.findByShared(true);
- List<Experiment> sharedExpList = Lists.newLinkedList(sharedExperiments);
- expList.addAll(sharedExpList);
- }
-
- if (modelSlug != null && !"".equals(modelSlug)) {
- for (Iterator<Experiment> it = expList.iterator(); it.hasNext(); ) {
- Experiment e = it.next();
- e.setResult(null);
- e.setAlgorithms(null);
- e.setValidations(null);
- if (!e.getModel().getSlug().equals(modelSlug)) {
- it.remove();
- }
- }
- }
- return expList;
- }
-
- private ResponseEntity<String> doMarkExperimentAsShared(String uuid, boolean shared) {
- Experiment experiment;
- UUID experimentUuid;
- User user = userInfo.getUser();
-
- try {
- experimentUuid = UUID.fromString(uuid);
- } catch (IllegalArgumentException iae) {
- //LOGGER.trace("Invalid UUID", iae);
- //LOGGER.warn("An invalid Experiment UUID was received !");
- Logging.LogUserAction(user.getUsername(), "List my experiments", "Listing my experiments.");
- return ResponseEntity.badRequest().body("Invalid Experiment UUID");
- }
-
- experiment = experimentRepository.findOne(experimentUuid);
-
- if (!experiment.getCreatedBy().getUsername().equals(user.getUsername()))
- return new ResponseEntity<>("You're not the owner of this experiment", HttpStatus.UNAUTHORIZED);
-
- experiment.setShared(shared);
- experimentRepository.save(experiment);
-
- Logging.LogUserAction(user.getUsername(), "Experiment updated (marked as shared)", "");
-
- return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
- }
-
- /* ------------------------------- EXPERIMENT MODEL METHODS ----------------------------------------------------*/
-
- public Experiment createExperiment(ExperimentExecutionDTO experimentExecutionDTO) {
- User user = userInfo.getUser();
-
- Experiment experiment = new Experiment();
- experiment.setUuid(UUID.randomUUID());
- experiment.setCreatedBy(user);
- experiment.setAlgorithms(gson.toJson(experimentExecutionDTO.getAlgorithms()));
- Model model = modelRepository.findOne(experimentExecutionDTO.getModel());
- experiment.setModel(model);
- experiment.setName(experimentExecutionDTO.getName());
- experimentRepository.save(experiment);
-
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " id : " + experiment.getUuid());
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " algorithms : " + experiment.getAlgorithms());
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " model : " + experiment.getModel().getSlug());
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " name : " + experiment.getName());
- return experiment;
- }
-
- private void saveExperiment(Experiment experiment) {
- User user = userInfo.getUser();
-
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " id : " + experiment.getUuid());
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " algorithms : " + experiment.getAlgorithms());
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " model : " + experiment.getModel().getSlug());
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " name : " + experiment.getName());
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " historyId : " + experiment.getWorkflowHistoryId());
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", " status : " + experiment.getWorkflowStatus());
-
- experimentRepository.save(experiment);
-
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Saved experiment");
- }
-
- private void finishExperiment(Experiment experiment) {
- experiment.setFinished(new Date());
- experimentRepository.save(experiment);
- }
-
- /* -------------------------------------- EXAREME CALLS ---------------------------------------------------------*/
-
- /**
- * The runExaremeExperiment will POST the algorithm to the exareme client
- *
- * @param experimentExecutionDTO is the request with the experiment information
- * @return the response to be returned
- */
- public ResponseEntity<String> runExaremeAlgorithm(ExperimentExecutionDTO experimentExecutionDTO) {
- User user = userInfo.getUser();
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Running the algorithm...");
-
- Experiment experiment = createExperiment(experimentExecutionDTO);
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Created experiment with uuid :" + experiment.getUuid());
-
- // Run the 1st algorithm from the list
- String algorithmName = experimentExecutionDTO.getAlgorithms().get(0).getName();
-
- // Get the parameters
- List<ExperimentExecutionDTO.AlgorithmExecutionDTO.AlgorithmExecutionParamDTO> algorithmParameters
- = experimentExecutionDTO.getAlgorithms().get(0).getParameters();
-
- String body = gson.toJson(algorithmParameters);
- String url = queryExaremeUrl + "/" + algorithmName;
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "url: " + url + ", body: " + body);
-
- ResponseEntity<String> response = new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm",
- "Completed, returning: " + experiment.toString());
-
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm",
- "Starting exareme execution thread");
- new Thread(() -> {
- // ATTENTION: Inside the Thread only LogExperimentAction should be used, not LogUserAction!
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Thread named :" + Thread.currentThread().getName() + " with id :" + Thread.currentThread().getId() + " started!");
-
- try {
- StringBuilder results = new StringBuilder();
- int code = HTTPUtil.sendPost(url, body, results);
-
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Algorithm finished with code: " + code);
-
- // Results are stored in the experiment object
- experiment.setResult("[" + results.toString() + "]");
- experiment.setHasError(code >= 400);
- experiment.setHasServerError(code >= 500);
- } catch (Exception e) {
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "There was an exception: " + e.getMessage());
-
- experiment.setHasError(true);
- experiment.setHasServerError(true);
- experiment.setResult(e.getMessage());
- }
-
- finishExperiment(experiment);
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Finished the experiment: " + experiment.toString());
- }).start();
-
- return response;
- }
-
- /* --------------------------------------- GALAXY CALLS ---------------------------------------------------------*/
-
-
- /**
- * The runWorkflow will POST the algorithm to the galaxy client
- *
- * @param experimentExecutionDTO is the request with the experiment information
- * @return the response to be returned
- */
- public ResponseEntity<String> runGalaxyWorkflow(ExperimentExecutionDTO experimentExecutionDTO) {
- User user = userInfo.getUser();
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Running a workflow...");
-
- Experiment experiment = createExperiment(experimentExecutionDTO);
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Created experiment with uuid :" + experiment.getUuid());
-
-
- // Run the 1st algorithm from the list
- String workflowId = experimentExecutionDTO.getAlgorithms().get(0).getName();
-
- // Get the parameters
- List<AlgorithmExecutionParamDTO> algorithmParameters
- = experimentExecutionDTO.getAlgorithms().get(0).getParameters();
-
- // Convert the parameters to workflow parameters
- HashMap<String, String> algorithmParamsIncludingEmpty = new HashMap<>();
- if (algorithmParameters != null) {
- for (AlgorithmExecutionParamDTO param : algorithmParameters) {
- algorithmParamsIncludingEmpty.put(param.getName(), param.getValue());
- }
- }
-
- // Get all the algorithm parameters because the frontend provides only the non-null
- final GalaxyInstance instance = GalaxyInstanceFactory.get(galaxyUrl, galaxyApiKey);
- final WorkflowsClient workflowsClient = instance.getWorkflowsClient();
- Workflow workflow = null;
- for (Workflow curWorkflow : workflowsClient.getWorkflows()) {
- if (curWorkflow.getId().equals(workflowId)) {
- workflow = curWorkflow;
- break;
- }
- }
- if (workflow == null) {
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm",
- "Could not find algorithm code: " + workflowId);
- return ResponseEntity.status(HttpStatus.BAD_REQUEST)
- .body(new ErrorResponse("Could not find galaxy algorithm.").toString());
- }
- final WorkflowDetails workflowDetails = workflowsClient.showWorkflow(workflow.getId());
- for (Map.Entry<String, WorkflowInputDefinition> workflowParameter : workflowDetails.getInputs().entrySet()) {
- if (!(algorithmParamsIncludingEmpty.containsKey(workflowParameter.getValue().getUuid()))) {
- algorithmParamsIncludingEmpty.put(workflowParameter.getValue().getUuid(), "");
- }
- }
-
- // Create the body of the request
- HashMap<String, HashMap<String, String>> requestBody = new HashMap<>();
- requestBody.put("inputs", algorithmParamsIncludingEmpty);
- JsonObject requestBodyJson = new JsonParser().parse(gson.toJson(requestBody)).getAsJsonObject();
-
- // Create the request client
- RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Running Galaxy workflow with id: " + workflow.getId());
-
- // Call Galaxy to run the workflow
- Call<PostWorkflowToGalaxyDtoResponse> call = service.postWorkflowToGalaxy(workflow.getId(), galaxyApiKey, requestBodyJson);
- try {
- Response<PostWorkflowToGalaxyDtoResponse> response = call.execute();
-
- if (response.code() == 200) { // Call succeeded
- String responseBody = gson.toJson(response.body());
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Response: " + responseBody);
-
- String historyId = (String) new JSONObject(responseBody).get("history_id");
- experiment.setWorkflowHistoryId(historyId);
- experiment.setWorkflowStatus("running");
- experiment.setHasError(false);
- experiment.setHasServerError(response.code() >= 500);
-
- } else { // Something unexpected happened
- String msgErr = gson.toJson(response.errorBody());
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Error Response: " + msgErr);
-
- // Values are read from streams.
- JSONObject jObjectError = new JSONObject(msgErr);
- String errMsg = jObjectError.get("err_msg").toString();
-
- experiment.setResult("[" + new ErrorResponse(errMsg).toString() + "]");
- experiment.setHasError(response.code() >= 400);
- experiment.setHasServerError(response.code() >= 500);
- }
-
- } catch (Exception e) {
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "An exception occurred: " + e.getMessage());
- experiment.setHasError(true);
- experiment.setHasServerError(true);
- experiment.setResult(e.getMessage());
- }
- saveExperiment(experiment);
-
- // Start the process of fetching the status
- updateWorkflowExperiment(experiment);
-
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Run workflow completed!");
-
- return new ResponseEntity(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
- }
-
-
- /**
- * This method creates a thread that will fetch the workflow result when it is ready
- *
- * @param experiment will be used to fetch it's workflow status, it should have the workflowHistoryId initialized
- * and the result should not already be fetched
- * @return nothing, just updates the experiment
- */
- public void updateWorkflowExperiment(Experiment experiment) {
- User user = userInfo.getUser();
-
- if (experiment == null) {
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "The experiment does not exist.");
- return;
- }
-
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm",
- " Experiment id : " + experiment.getUuid());
- if (experiment.getWorkflowHistoryId() == null) {
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "History Id does not exist.");
- return;
- }
-
- Logging.LogUserAction(user.getUsername(), "(POST) /experiments/runAlgorithm", "Starting Thread...");
- new Thread(() -> {
- while (true) {
- // ATTENTION: Inside the Thread only LogExperimentAction should be used, not LogExperimentAction!
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Thread is running...");
-
- try {
- sleep(2000);
- } catch (InterruptedException e) {
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Sleep was disrupted: " + e.getMessage());
- }
-
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Fetching status for experiment Id: " + experiment.getUuid());
-
- String state = getWorkflowStatus(experiment);
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "State is: " + state);
-
- switch (state) {
- case "running":
- // Do nothing, when the experiment is created the status is set to running
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Workflow is still running.");
- break;
-
- case "completed":
- // Get only the job result that is visible
- List<GalaxyWorkflowResult> workflowJobsResults = getWorkflowResults(experiment);
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Results are: " + workflowJobsResults.toString());
-
- boolean resultFound = false;
- for (GalaxyWorkflowResult jobResult : workflowJobsResults) {
- if (jobResult.getVisible()) {
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Visible result are: " + jobResult.getId());
-
- String result = getWorkflowResultBody(experiment, jobResult.getId());
-
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Result: " + result);
- if (result == null) {
- experiment.setHasError(true);
- experiment.setHasServerError(true);
- }
- experiment.setResult(result);
- experiment.setWorkflowStatus("completed");
- resultFound = true;
- }
- }
-
- if (!resultFound) { // If there is no visible result
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "No visible result");
- experiment.setResult("[" + new ErrorResponse("The workflow has no visible result.").toString() + "]");
- experiment.setHasError(true);
- experiment.setHasServerError(true);
- }
-
- finishExperiment(experiment);
- break;
-
- case "error":
- // Get the job result that failed
- workflowJobsResults = getWorkflowResults(experiment);
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Error results are: " + workflowJobsResults.toString());
-
- boolean failedJobFound = false;
- for (GalaxyWorkflowResult jobResult : workflowJobsResults) {
- if (jobResult.getState().equals("error")) {
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Failed job is: " + jobResult.getId());
-
- String result = getWorkflowJobError(jobResult.getId(), experiment);
-
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Job result: " + result);
- if (result == null) {
- experiment.setHasError(true);
- experiment.setHasServerError(true);
- }
- experiment.setResult("[" + result + "]");
- experiment.setWorkflowStatus("error");
- failedJobFound = true;
- }
- }
-
- if (!failedJobFound) { // If there is no visible failed job
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "No failed result");
- experiment.setResult("[" + new ErrorResponse("The workflow has no failed result.").toString() + "]");
- experiment.setHasError(true);
- experiment.setHasServerError(true);
- }
- finishExperiment(experiment);
- break;
-
- default: // InternalError or unexpected result
- experiment.setResult("[" + new ErrorResponse("An unexpected error occurred.").toString() + "]");
- experiment.setHasError(true);
- experiment.setHasServerError(true);
- finishExperiment(experiment);
- break;
- }
-
- // If result exists return
- if (experiment.getResult() != null) {
- Logging.LogExperimentAction(experiment.getName(), experiment.getUuid(), "Result exists: " + experiment.getResult());
- return;
- }
- }
- }).start();
- }
-
-
- /**
- * @param experiment The experiment of the workflow
- * @return "running" -> When the workflow is still running
- * "internalError" -> When an exception or a bad request occurred
- * "error" -> When the workflow produced an error
- * "completed" -> When the workflow completed successfully
- */
- public String getWorkflowStatus(Experiment experiment) {
- String historyId = experiment.getWorkflowHistoryId();
- String experimentName = experiment.getName();
- UUID experimentId = experiment.getUuid();
-
- // ATTENTION: This function is used from a Thread. Only LogExperimentAction should be used, not LogUserAction!
- Logging.LogExperimentAction(experimentName, experimentId, " History Id : " + historyId);
-
- // Create the request client
- RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
- Call<Object> call = service.getWorkflowStatusFromGalaxy(historyId, galaxyApiKey);
-
- String result = null;
- try {
- Response<Object> response = call.execute();
- if (response.code() >= 400) {
- Logging.LogExperimentAction(experimentName, experimentId, " Response code: "
- + response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
- return "internalError";
- }
- result = new Gson().toJson(response.body());
- Logging.LogExperimentAction(experimentName, experimentId, " Result: " + result);
-
- } catch (IOException e) {
- Logging.LogExperimentAction(experimentName, experimentId, " An exception happened: " + e.getMessage());
- return "internalError";
- }
-
- String state = null;
- try {
- JSONObject resultJson = new JSONObject(result);
- state = resultJson.getString("state");
- } catch (JSONException e) {
- Logging.LogExperimentAction(experimentName, experimentId, " An exception happened: " + e.getMessage());
- return "internalError";
- }
-
- Logging.LogExperimentAction(experimentName, experimentId, " Completed!");
- switch (state) {
- case "ok":
- return "completed";
- case "error":
- return "error";
- case "running":
- case "new":
- case "waiting":
- case "queued":
- return "running";
- default:
- return "internalError";
- }
- }
-
- /**
- * @param experiment The experiment of the workflow
- * @return a List<GalaxyWorkflowResult> or null when an error occurred
- */
- public List<GalaxyWorkflowResult> getWorkflowResults(Experiment experiment) {
-
- String historyId = experiment.getWorkflowHistoryId();
- String experimentName = experiment.getName();
- UUID experimentId = experiment.getUuid();
- Logging.LogExperimentAction(experimentName, experimentId, " historyId : " + historyId);
-
- RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
- Call<List<GalaxyWorkflowResult>> call = service.getWorkflowResultsFromGalaxy(historyId, galaxyApiKey);
-
- List<GalaxyWorkflowResult> getGalaxyWorkflowResultList = null;
- try {
- Response<List<GalaxyWorkflowResult>> response = call.execute();
- if (response.code() >= 400) {
- Logging.LogExperimentAction(experimentName, experimentId, " Response code: "
- + response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
- return null;
- }
- getGalaxyWorkflowResultList = response.body();
- Logging.LogExperimentAction(experimentName, experimentId, " Result: " + response.body());
-
- } catch (IOException e) {
- Logging.LogExperimentAction(experimentName, experimentId, " An exception happened: " + e.getMessage());
- return null;
- }
-
- Logging.LogExperimentAction(experimentName, experimentId, " Completed!");
- return getGalaxyWorkflowResultList;
-
- }
-
- /**
- * @param experiment The experiment of the workflow
- * @param contentId the id of the job result that we want
- * @return the result of the specific workflow job, null if there was an error
- */
- public String getWorkflowResultBody(Experiment experiment, String contentId) {
-
- String historyId = experiment.getWorkflowHistoryId();
- String experimentName = experiment.getName();
- UUID experimentId = experiment.getUuid();
-
- Logging.LogExperimentAction(experimentName, experimentId, " historyId : " + historyId);
-
- RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
- Call<Object> call =
- service.getWorkflowResultsBodyFromGalaxy(historyId, contentId, galaxyApiKey);
-
- String resultJson = null;
- try {
- Response<Object> response = call.execute();
- if (response.code() >= 400) {
- Logging.LogExperimentAction(experimentName, experimentId, " Response code: "
- + response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
- return null;
- }
- resultJson = new Gson().toJson(response.body());
- Logging.LogExperimentAction(experimentName, experimentId, " Result: " + resultJson);
-
- } catch (IOException e) {
- Logging.LogExperimentAction(experimentName, experimentId,
- " An exception happened: " + e.getMessage());
- return null;
- }
-
- Logging.LogExperimentAction(experimentName, experimentId, " Completed!");
- return resultJson;
- }
-
-
- /**
- * @param jobId the id of the workflow job that failed
- * @return the error that was produced or null if an error occurred
- */
- public String getWorkflowJobError(String jobId, Experiment experiment) {
- String experimentName = experiment.getName();
- UUID experimentId = experiment.getUuid();
-
- Logging.LogExperimentAction(experimentName, experimentId, " jobId : " + jobId);
- RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
- Call<Object> callError = service.getErrorMessageOfWorkflowFromGalaxy(jobId, galaxyApiKey);
-
- String fullError = null;
- String returnError = null;
- try {
- Response<Object> response = callError.execute();
- if (response.code() >= 400) {
- Logging.LogExperimentAction(experimentName, experimentId, "Response code: "
- + response.code() + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
- return null;
- }
-
- // Parsing the stderr of the job that failed
- String jsonString = new Gson().toJson(response.body());
- JsonElement jsonElement = new JsonParser().parse(jsonString);
- JsonObject rootObject = jsonElement.getAsJsonObject();
- fullError = rootObject.get("stderr").getAsString();
- Logging.LogExperimentAction(experimentName, experimentId, "Error: " + fullError);
-
- String[] arrOfStr = fullError.split("ValueError", 0);
- String specError = arrOfStr[arrOfStr.length - 1];
- returnError = specError.substring(1);
- Logging.LogExperimentAction(experimentName, experimentId, "Parsed Error: " + returnError);
-
- } catch (IOException e) {
- Logging.LogExperimentAction(experimentName, experimentId, "Exception: " + e.getMessage());
- return null;
- }
-
- Logging.LogExperimentAction(experimentName, experimentId, "Completed successfully!");
-
- return returnError;
- }
-
-
-}
diff --git a/src/main/java/eu/hbp/mip/controllers/FilesAPI.java b/src/main/java/eu/hbp/mip/controllers/FilesAPI.java
deleted file mode 100644
index 69e7f3ba94702ee9b5465920d3234ca4dcac0248..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/controllers/FilesAPI.java
+++ /dev/null
@@ -1,47 +0,0 @@
-package eu.hbp.mip.controllers;
-
-import eu.hbp.mip.model.User;
-import eu.hbp.mip.model.UserInfo;
-import io.swagger.annotations.Api;
-import io.swagger.annotations.ApiOperation;
-import io.swagger.annotations.ApiParam;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.HttpHeaders;
-import org.springframework.http.HttpStatus;
-import org.springframework.http.ResponseEntity;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RestController;
-import eu.hbp.mip.utils.Logging;
-
-/**
- * Created by mirco on 08.05.17.
- */
-
-@RestController
-@RequestMapping(value = "/protected")
-@Api(value = "/protected", description = "the protected files API")
-public class FilesAPI {
-
-
- @Autowired
- private UserInfo userInfo;
-
- @ApiOperation(value = "Get protected files")
- @RequestMapping(value = "/{filename:.+}", method = RequestMethod.GET)
- public ResponseEntity<Void> getProtectedFile(
- @ApiParam(value = "filename", required = true) @PathVariable("filename") String filename
- ) {
- User user = userInfo.getUser();
- Logging.LogUserAction(user.getUsername(), "(GET) /protected/{filename:.+}", "Loading protected file with filename : " + filename);
-
- String filepath = "/protected/" + filename;
- Logging.LogUserAction(user.getUsername(), "(GET) /protected/{filename:.+}" + filepath, "Downloaded protected file");
-
- HttpHeaders headers = new HttpHeaders();
- headers.add("X-Accel-Redirect", filepath);
-
- return new ResponseEntity<>(headers, HttpStatus.OK);
- }
-}
diff --git a/src/main/java/eu/hbp/mip/controllers/MiningApi.java b/src/main/java/eu/hbp/mip/controllers/MiningApi.java
deleted file mode 100644
index 6a198cc0d4571c58b1ff424e590bc418893a39f1..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/controllers/MiningApi.java
+++ /dev/null
@@ -1,110 +0,0 @@
-package eu.hbp.mip.controllers;
-
-import eu.hbp.mip.utils.HTTPUtil;
-
-import com.google.gson.Gson;
-
-import eu.hbp.mip.model.UserInfo;
-import io.swagger.annotations.Api;
-import io.swagger.annotations.ApiOperation;
-
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Value;
-import org.springframework.http.HttpStatus;
-import org.springframework.http.ResponseEntity;
-import org.springframework.web.bind.annotation.RequestBody;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RestController;
-
-import eu.hbp.mip.utils.Logging;
-
-
-import java.util.*;
-import java.io.IOException;
-
-import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
-
-/**
- * Created by mirco on 06.01.17.
- */
-@RestController
-@RequestMapping(value = "/mining", produces = {APPLICATION_JSON_VALUE})
-@Api(value = "/mining", description = "the mining API")
-public class MiningApi {
-
- private static final Gson gson = new Gson();
-
- @Autowired
- private UserInfo userInfo;
-
- @Value("#{'${services.exareme.queryExaremeUrl:http://localhost:9090/mining/query}'}")
- public String queryExaremeUrl;
-
- @ApiOperation(value = "Create a histogram on Exareme", response = String.class)
- @RequestMapping(value = "/histograms", method = RequestMethod.POST)
- public ResponseEntity runExaremeHistograms(@RequestBody List<HashMap<String, String>> queryList) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /mining/histogram", "Executing histogram...");
-
- String query = gson.toJson(queryList);
- String url = queryExaremeUrl + "/" + "MULTIPLE_HISTOGRAMS";
-
- try {
- StringBuilder results = new StringBuilder();
- int code = HTTPUtil.sendPost(url, query, results);
-
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /mining/histogram", "Executed histogram with result :" + results.toString());
- return ResponseEntity.ok(gson.toJson(results.toString()));
- } catch (IOException e) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /mining/histogram", "Histogram algorithm was not found");
- return new ResponseEntity<>("Not found", HttpStatus.NOT_FOUND);
- }
- }
-
- @ApiOperation(value = "Create a descriptive statistic on Exareme", response = String.class)
- @RequestMapping(value = "/descriptive_stats", method = RequestMethod.POST)
- public ResponseEntity runExaremeDescriptiveStats(@RequestBody List<HashMap<String, String>> queryList) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/descriptive_stats", "Executing Exareme descriptive stats...");
-
- String query = gson.toJson(queryList);
- String url = queryExaremeUrl + "/" + "DESCRIPTIVE_STATS";
-
- try {
- StringBuilder results = new StringBuilder();
- int code = HTTPUtil.sendPost(url, query, results);
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/descriptive_stats", "Executed descriptive stats with result : " + results.toString());
- return ResponseEntity.ok(gson.toJson(results.toString()));
- } catch (IOException e) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/descriptive_stats", "Descriptive stats algorithm was not found");
- return new ResponseEntity<>("Not found", HttpStatus.NOT_FOUND);
- }
- }
-
- @ApiOperation(value = "Create a descriptive statistic on Exareme", response = String.class)
- @RequestMapping(value = "/descriptive_stats_v2", method = RequestMethod.POST)
- public ResponseEntity runExaremeDescriptiveStatsV2(@RequestBody List<HashMap<String, String>> queryList) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/descriptive_stats_v2", "Executing an Exareme descriptive stats v2");
-
- String query = gson.toJson(queryList);
- String url = queryExaremeUrl + "/" + "DESCRIPTIVE_STATS_v2";
-
- try {
- StringBuilder results = new StringBuilder();
- int code = HTTPUtil.sendPost(url, query, results);
-
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/descriptive_stats_v2", "Successfully executed descriptive stats v2 with results : " + results.toString());
- return ResponseEntity.ok(gson.toJson(results.toString()));
- } catch (IOException e) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/descriptive_stats_v2", "Descriptive stats v2 algorithm was not found");
- return new ResponseEntity<>("Not found", HttpStatus.NOT_FOUND);
- }
- }
-
- @ApiOperation(value = "Check if a formula is valid", response = String.class)
- @RequestMapping(value = "/checkFormula", method = RequestMethod.POST)
- public ResponseEntity checkFormulaValidity(String formula) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /experiments/checkFormula", "Executing checkFormula ...");
-
- return ResponseEntity.ok("");
- }
-}
diff --git a/src/main/java/eu/hbp/mip/controllers/ModelsApi.java b/src/main/java/eu/hbp/mip/controllers/ModelsApi.java
deleted file mode 100644
index 6f013ee336815bbb25514b37cdb764fe7710e8fd..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/controllers/ModelsApi.java
+++ /dev/null
@@ -1,259 +0,0 @@
-/*
- * Created by mirco on 04.12.15.
- */
-
-package eu.hbp.mip.controllers;
-
-import com.github.slugify.Slugify;
-import eu.hbp.mip.model.Model;
-import eu.hbp.mip.model.User;
-import eu.hbp.mip.model.UserInfo;
-import eu.hbp.mip.model.Variable;
-import eu.hbp.mip.repositories.*;
-import io.swagger.annotations.*;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.HttpStatus;
-import org.springframework.http.ResponseEntity;
-import org.springframework.web.bind.annotation.*;
-import eu.hbp.mip.utils.Logging;
-
-import java.io.IOException;
-import java.util.*;
-
-import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
-
-@RestController
-@RequestMapping(value = "/models", produces = {APPLICATION_JSON_VALUE})
-@Api(value = "/models", description = "the models API")
-public class ModelsApi {
-
-
- @Autowired
- private UserInfo userInfo;
-
- @Autowired
- private DatasetRepository datasetRepository;
-
- @Autowired
- private ModelRepository modelRepository;
-
- @Autowired
- private QueryRepository queryRepository;
-
- @Autowired
- private ConfigRepository configRepository;
-
- @Autowired
- private VariableRepository variableRepository;
-
- @ApiOperation(value = "get models", response = Model.class, responseContainer = "List")
- @RequestMapping(method = RequestMethod.GET)
- public ResponseEntity<List> getModels(
- @ApiParam(value = "Only ask own models") @RequestParam(value = "own", required = false) Boolean own,
- @ApiParam(value = "Only ask published models") @RequestParam(value = "valid", required = false) Boolean valid
- ) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /models", "Loading models ...");
-
- User user = userInfo.getUser();
-
- Iterable<Model> models;
- if (own != null && own) {
- models = modelRepository.findByCreatedByOrderByCreatedAt(user);
- } else {
- models = modelRepository.findByValidOrCreatedByOrderByCreatedAt(true, user);
- }
-
- if (valid != null && models != null) {
- for (Iterator<Model> i = models.iterator(); i.hasNext(); ) {
- Model m = i.next();
- if (valid != m.getValid()) {
- i.remove();
- }
- }
- }
-
- List<Object> modelsList = new LinkedList<>();
- models = models != null ? models : new LinkedList<>();
- for (Model m : models) {
- m.setDataset(datasetRepository.findOne(m.getDataset().getCode()));
- modelsList.add(m);
- }
-
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /models", "Successfully loaded " + modelsList.size() + " models.");
-
- return ResponseEntity.ok(modelsList);
- }
-
-
- @ApiOperation(value = "Create a model", response = Model.class)
- @ApiResponses(value = {@ApiResponse(code = 201, message = "Model created")})
- @RequestMapping(method = RequestMethod.POST)
- public ResponseEntity<Model> addAModel(
- @RequestBody @ApiParam(value = "Model to create", required = true) Model model
- ) {
- User user = userInfo.getUser();
- Logging.LogUserAction(user.getUsername(), "(POST) /models", "Creating a model");
-
- model.setTitle(model.getConfig().getTitle().get("text"));
- model.setCreatedBy(user);
- model.setCreatedAt(new Date());
- if (model.getValid() == null) {
- model.setValid(false);
- }
-
- ensureTitleUniqueness(model);
- ensureSlugUniqueness(model);
-
- Map<String, String> map = new HashMap<>(model.getConfig().getTitle());
- map.put("text", model.getTitle());
- model.getConfig().setTitle(map);
-
- saveVariables(model.getQuery().getVariables());
- saveVariables(model.getQuery().getCovariables());
- saveVariables(model.getQuery().getGrouping());
- saveVariables(model.getQuery().getTrainingDatasets());
-
- configRepository.save(model.getConfig());
- queryRepository.save(model.getQuery());
- if (model.getDataset() != null) {
- datasetRepository.save(model.getDataset());
- }
- modelRepository.save(model);
-
- Logging.LogUserAction(user.getUsername(), "(POST) /models", "Created model with id : " + model.getSlug() + ", model.config and model.query");
-
- return ResponseEntity.status(HttpStatus.CREATED).body(model);
- }
-
- private void saveVariables(@RequestBody @ApiParam(value = "Model to create", required = true) List<Variable> variables) {
- for (Variable var : variables) {
- variableRepository.save(var);
- }
- }
-
- private void ensureSlugUniqueness(@RequestBody @ApiParam(value = "Model to create", required = true) Model model) {
- String slug = createSlug(model.getTitle());
- boolean slugExists = true;
- for (int i = 1; slugExists; i++) {
- slugExists = modelRepository.exists(slug);
- if (slugExists) {
- if (i > 1) {
- slug = slug.substring(0, slug.length() - 2);
- }
- slug += "-" + i;
- }
- model.setSlug(slug);
- }
- }
-
- private String createSlug(@RequestBody @ApiParam(value = "Model to create", required = true) String title) {
- String slug;
- try {
- slug = new Slugify().slugify(title);
- } catch (IOException e) {
- slug = ""; // Should never happen
- //LOGGER.trace("Cannot slugify title", e);
- }
- return slug;
- }
-
- private void ensureTitleUniqueness(@RequestBody @ApiParam(value = "Model to create", required = true) Model model) {
- boolean titleExists = true;
- for (int i = 1; titleExists; i++) {
- String title = model.getTitle();
- titleExists = modelRepository.countByTitle(title) > 0;
- if (titleExists) {
- if (i > 1) {
- title = title.substring(0, title.length() - 4);
- }
- model.setTitle(title + " (" + i + ")");
- }
- }
- }
-
- @ApiOperation(value = "Get a model", response = Model.class)
- @RequestMapping(value = "/{slug}", method = RequestMethod.GET)
- public ResponseEntity<Model> getAModel(
- @ApiParam(value = "slug", required = true) @PathVariable("slug") String slug
- ) {
-
- User user = userInfo.getUser();
-
- Logging.LogUserAction(user.getUsername(), "(GET) /models/{slug}", "Loading model with id : " + slug);
-
- Model model = modelRepository.findOne(slug);
- if (model == null) {
- //LOGGER.warn("Cannot find model : " + slug);
- Logging.LogUserAction(user.getUsername(), "(GET) /models/{slug}", "Model was not found");
- return ResponseEntity.badRequest().body(null);
- }
-
- if (!model.getValid() && !model.getCreatedBy().getUsername().equals(user.getUsername())) {
- Logging.LogUserAction(user.getUsername(), "(GET) /models/{slug}", "You are not authorized to retrieve models. ");
- return new ResponseEntity<>(HttpStatus.FORBIDDEN);
- }
-
- List<String> yAxisVars = configRepository.findOne(model.getConfig().getId()).getyAxisVariables();
- Collection<String> yAxisVarsColl = new LinkedHashSet<>(yAxisVars);
- model.getConfig().setyAxisVariables(new LinkedList<>(yAxisVarsColl));
-
- Logging.LogUserAction(user.getUsername(), "(GET) /models/{slug}", "Loaded model with id : " + slug);
- return ResponseEntity.ok(model);
- }
-
-
- @ApiOperation(value = "Update a model", response = Void.class)
- @ApiResponses(value = {@ApiResponse(code = 204, message = "Model updated")})
- @RequestMapping(value = "/{slug}", method = RequestMethod.PUT)
- public ResponseEntity<Void> updateAModel(
- @ApiParam(value = "slug", required = true) @PathVariable("slug") String slug,
- @RequestBody @ApiParam(value = "Model to update", required = true) Model model
- ) {
- User user = userInfo.getUser();
- Logging.LogUserAction(user.getUsername(), "(PUT) /models/{slug}", "Updating model with id : " + slug);
- Model oldModel = modelRepository.findOne(slug);
-
- if (!user.getUsername().equals(oldModel.getCreatedBy().getUsername())) {
- return new ResponseEntity<>(HttpStatus.FORBIDDEN);
- }
-
- model.setTitle(model.getConfig().getTitle().get("text"));
-
- String oldTitle = oldModel.getTitle();
- String newTitle = model.getTitle();
-
- // If title has been updated, ensure it is unique
- if (!newTitle.equals(oldTitle)) {
- boolean newTitleExists = true;
- for (int i = 1; newTitleExists && !newTitle.equals(oldTitle); i++) {
- newTitle = model.getTitle();
- newTitleExists = modelRepository.countByTitle(newTitle) > 0;
- if (newTitleExists && !newTitle.equals(oldTitle)) {
- if (i > 1) {
- newTitle = newTitle.substring(0, newTitle.length() - 4);
- }
- model.setTitle(newTitle + " (" + i + ")");
- }
- }
- }
-
- Map<String, String> map = new HashMap<>(model.getConfig().getTitle());
- map.put("text", model.getTitle());
- model.getConfig().setTitle(map);
-
- saveVariables(model.getQuery().getVariables());
- saveVariables(model.getQuery().getCovariables());
- saveVariables(model.getQuery().getGrouping());
- saveVariables(model.getQuery().getTrainingDatasets());
-
- configRepository.save(model.getConfig());
- queryRepository.save(model.getQuery());
- datasetRepository.save(model.getDataset());
- modelRepository.save(model);
-
- Logging.LogUserAction(user.getUsername(), "(PUT) /models/{slug}", "Updated model and saved/updated model.config and model.query");
-
- return new ResponseEntity<>(HttpStatus.NO_CONTENT);
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/controllers/PathologiesApi.java b/src/main/java/eu/hbp/mip/controllers/PathologiesAPI.java
similarity index 58%
rename from src/main/java/eu/hbp/mip/controllers/PathologiesApi.java
rename to src/main/java/eu/hbp/mip/controllers/PathologiesAPI.java
index 77916981465827ae4e0806366663a16c7ad1e70b..5e9a9d34452f81ff5293bccaf3a5a5aca0624057 100644
--- a/src/main/java/eu/hbp/mip/controllers/PathologiesApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/PathologiesAPI.java
@@ -1,19 +1,15 @@
-/**
- * Created by mirco on 04.12.15.
- */
-
package eu.hbp.mip.controllers;
import com.google.gson.Gson;
import com.google.gson.reflect.TypeToken;
-import eu.hbp.mip.model.PathologyDTO;
-import eu.hbp.mip.model.UserInfo;
+import eu.hbp.mip.models.DTOs.PathologyDTO;
+import eu.hbp.mip.services.ActiveUserService;
import eu.hbp.mip.utils.ClaimUtils;
import eu.hbp.mip.utils.CustomResourceLoader;
+import eu.hbp.mip.utils.Exceptions.BadRequestException;
import eu.hbp.mip.utils.InputStreamConverter;
-import eu.hbp.mip.utils.Logging;
+import eu.hbp.mip.utils.Logger;
import io.swagger.annotations.Api;
-import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.core.io.Resource;
import org.springframework.http.ResponseEntity;
@@ -25,49 +21,55 @@ import org.springframework.web.bind.annotation.RestController;
import java.io.IOException;
import java.util.List;
-import static eu.hbp.mip.utils.ErrorMessages.pathologiesCouldNotBeLoaded;
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@RestController
@RequestMapping(value = "/pathologies", produces = {APPLICATION_JSON_VALUE})
@Api(value = "/pathologies")
-public class PathologiesApi {
+public class PathologiesAPI {
private static final Gson gson = new Gson();
- @Autowired
- private UserInfo userInfo;
// Enable HBP collab authentication (1) or disable it (0). Default is 1
- @Value("#{'${hbp.authentication.enabled:1}'}")
+ @Value("#{'${authentication.enabled}'}")
private boolean authenticationIsEnabled;
- @Autowired
- private CustomResourceLoader resourceLoader;
+ @Value("#{'${files.pathologies_json}'}")
+ private String pathologiesFilePath;
+
+ private final ActiveUserService activeUserService;
+
+ private final CustomResourceLoader resourceLoader;
+
+ public PathologiesAPI(ActiveUserService activeUserService, CustomResourceLoader resourceLoader) {
+ this.activeUserService = activeUserService;
+ this.resourceLoader = resourceLoader;
+ }
@RequestMapping(name = "/pathologies", method = RequestMethod.GET)
public ResponseEntity<String> getPathologies(Authentication authentication) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /pathologies", "Loading pathologies ...");
+ Logger logger = new Logger(activeUserService.getActiveUser().getUsername(), "(GET) /pathologies");
+ logger.LogUserAction("Loading pathologies ...");
// Load pathologies from file
- Resource resource = resourceLoader.getResource("file:/opt/portal/api/pathologies.json");
+ Resource resource = resourceLoader.getResource(pathologiesFilePath);
List<PathologyDTO> allPathologies;
try {
allPathologies = gson.fromJson(InputStreamConverter.convertInputStreamToString(resource.getInputStream()), new TypeToken<List<PathologyDTO>>() {
}.getType());
} catch (IOException e) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /pathologies", "Unable to load pathologies");
- return ResponseEntity.badRequest().body(pathologiesCouldNotBeLoaded);
+ logger.LogUserAction("Unable to load pathologies");
+ throw new BadRequestException("The pathologies could not be loaded.");
}
// If authentication is disabled return everything
if (!authenticationIsEnabled) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /pathologies", "Successfully loaded " + allPathologies.size() + " pathologies");
+ logger.LogUserAction("Successfully loaded " + allPathologies.size() + " pathologies");
return ResponseEntity.ok().body(gson.toJson(allPathologies));
}
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /pathologies", "Successfully loaded all authorized pathologies");
- return ResponseEntity.ok().body(ClaimUtils.getAuthorizedPathologies(
- userInfo.getUser().getUsername(), authentication.getAuthorities(), allPathologies));
+ logger.LogUserAction("Successfully loaded all authorized pathologies");
+ return ResponseEntity.ok().body(ClaimUtils.getAuthorizedPathologies(logger, authentication, allPathologies));
}
}
diff --git a/src/main/java/eu/hbp/mip/controllers/SecurityApi.java b/src/main/java/eu/hbp/mip/controllers/SecurityApi.java
deleted file mode 100644
index 4e412aea08da5612f47d60baafd4bac791f2fc6e..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/controllers/SecurityApi.java
+++ /dev/null
@@ -1,120 +0,0 @@
-package eu.hbp.mip.controllers;
-
-import com.fasterxml.jackson.core.JsonProcessingException;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.google.gson.Gson;
-import com.google.gson.JsonObject;
-import eu.hbp.mip.configuration.SecurityConfiguration;
-import eu.hbp.mip.model.User;
-import eu.hbp.mip.model.UserInfo;
-import eu.hbp.mip.repositories.UserRepository;
-import eu.hbp.mip.utils.Logging;
-import io.swagger.annotations.ApiParam;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Value;
-import org.springframework.boot.autoconfigure.condition.ConditionalOnExpression;
-import org.springframework.http.HttpStatus;
-import org.springframework.http.ResponseEntity;
-import org.springframework.security.access.prepost.PreAuthorize;
-import org.springframework.web.bind.annotation.*;
-
-import javax.servlet.http.Cookie;
-import javax.servlet.http.HttpServletResponse;
-import java.io.IOException;
-import java.io.UnsupportedEncodingException;
-import java.net.URLEncoder;
-import java.security.Principal;
-import java.util.Base64;
-
-@RestController
-public class SecurityApi {
-
- private static final Gson gson = new Gson();
-
- @Autowired
- private UserInfo userInfo;
-
- @Autowired
- private UserRepository userRepository;
-
- @Autowired
- private SecurityConfiguration securityConfiguration;
-
- @RequestMapping(path = "/user", method = RequestMethod.GET)
- public Object user(Principal principal, HttpServletResponse response) {
- ObjectMapper mapper = new ObjectMapper();
-
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /user", "Loading user : " + userInfo.getUser().getUsername());
- try {
- String userJSON = mapper.writeValueAsString(userInfo.getUser());
- Cookie cookie = new Cookie("user", URLEncoder.encode(userJSON, "UTF-8"));
- cookie.setSecure(true);
- cookie.setPath("/");
- response.addCookie(cookie);
- } catch (JsonProcessingException | UnsupportedEncodingException e) {
- //LOGGER.trace("Cannot read user json", e);
- }
-
- if (!securityConfiguration.isAuthentication()) {
- if (userInfo.isFakeAuth()) {
- response.setStatus(401);
- }
- String principalJson = "{\"principal\": \"anonymous\", \"name\": \"anonymous\", \"userAuthentication\": {"
- + "\"details\": {\"preferred_username\": \"anonymous\"}}}";
- return new Gson().fromJson(principalJson, Object.class);
- }
-
- return principal;
- }
-
- @RequestMapping(path = "/user", method = RequestMethod.POST)
- public ResponseEntity<Void> postUser(
- @ApiParam(value = "Has the user agreed on the NDA") @RequestParam(value = "agreeNDA") Boolean agreeNDA) {
- User user = userInfo.getUser();
- if (user != null) {
- user.setAgreeNDA(agreeNDA);
- userRepository.save(user);
- }
-
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(POST) /user", "User has agreed on the NDA");
-
- return new ResponseEntity<>(HttpStatus.NO_CONTENT);
- }
-
- @RequestMapping(path = "/login/hbp", method = RequestMethod.GET)
- @ConditionalOnExpression("${hbp.authentication.enabled:0}")
- public void noLogin(HttpServletResponse httpServletResponse) throws IOException {
- userInfo.setFakeAuth(true);
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /user/login/hbp", "Unathorized login.");
-
- httpServletResponse.sendRedirect(securityConfiguration.getFrontendRedirectAfterLogin());
- }
-
- @Value("#{'${services.galaxy.galaxyUsername:admin}'}")
- private String galaxyUsername;
-
- @Value("#{'${services.galaxy.galaxyPassword:password}'}")
- private String galaxyPassword;
-
- @Value("#{'${services.galaxy.galaxyContext:nativeGalaxy}'}")
- private String galaxyContext;
-
- /**
- * Get Galaxy Reverse Proxy basic access token.
- *
- * @return Return a @{@link ResponseEntity} with the token.
- */
-
- @RequestMapping(path = "/galaxy", method = RequestMethod.GET, produces = "application/json")
- @PreAuthorize("hasRole('Data Manager')")
- @ResponseStatus(value = HttpStatus.OK)
- public ResponseEntity getGalaxyConfiguration() {
- String stringEncoded = Base64.getEncoder().encodeToString((galaxyUsername + ":" + galaxyPassword).getBytes());
- JsonObject object = new JsonObject();
- object.addProperty("authorization", stringEncoded);
- object.addProperty("context", galaxyContext);
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /user/galaxy", "Successfully Loaded galaxy information.");
-
- return ResponseEntity.ok(gson.toJson(object));
- }
-}
diff --git a/src/main/java/eu/hbp/mip/controllers/StatsApi.java b/src/main/java/eu/hbp/mip/controllers/StatsApi.java
deleted file mode 100644
index 8bd109e535b7c29b5dac96b68b2ba59329ca6a59..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/controllers/StatsApi.java
+++ /dev/null
@@ -1,50 +0,0 @@
-/*
- * Created by mirco on 18.01.16.
- */
-
-package eu.hbp.mip.controllers;
-
-import eu.hbp.mip.model.GeneralStats;
-import eu.hbp.mip.model.UserInfo;
-import eu.hbp.mip.repositories.ArticleRepository;
-import eu.hbp.mip.repositories.UserRepository;
-import eu.hbp.mip.utils.Logging;
-import io.swagger.annotations.Api;
-import io.swagger.annotations.ApiOperation;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.ResponseEntity;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RestController;
-
-import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
-
-@RestController
-@RequestMapping(value = "/stats", produces = {APPLICATION_JSON_VALUE})
-@Api(value = "/stats", description = "the stats API")
-public class StatsApi {
- @Autowired
- private UserRepository userRepository;
-
- @Autowired
- private UserInfo userInfo;
-
- @Autowired
- private ArticleRepository articleRepository;
-
-
- @ApiOperation(value = "Get general statistics", response = GeneralStats.class)
- @RequestMapping(method = RequestMethod.GET)
- public ResponseEntity<GeneralStats> getGeneralStatistics() {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /stats", "Loading general statistics");
-
- GeneralStats stats = new GeneralStats();
-
- stats.setUsers(userRepository.count());
- stats.setArticles(articleRepository.count());
-
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /stats", "Loaded " + userRepository.count() + " user statistics and " + articleRepository.count() + " artcle statistics.");
- return ResponseEntity.ok(stats);
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/controllers/UsersApi.java b/src/main/java/eu/hbp/mip/controllers/UsersApi.java
deleted file mode 100644
index b791a7858e216d8ce0f8cd36610763c5c123e66a..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/controllers/UsersApi.java
+++ /dev/null
@@ -1,43 +0,0 @@
-/*
- * Created by mirco on 14.01.16.
- */
-
-package eu.hbp.mip.controllers;
-
-import eu.hbp.mip.model.User;
-import eu.hbp.mip.model.UserInfo;
-import eu.hbp.mip.repositories.UserRepository;
-import eu.hbp.mip.utils.Logging;
-import io.swagger.annotations.Api;
-import io.swagger.annotations.ApiOperation;
-import io.swagger.annotations.ApiParam;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.ResponseEntity;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RestController;
-
-import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
-
-@RestController
-@RequestMapping(value = "/users", produces = {APPLICATION_JSON_VALUE})
-@Api(value = "/users", description = "the users API")
-public class UsersApi {
-
- @Autowired
- private UserRepository userRepository;
-
- @Autowired
- private UserInfo userInfo;
-
- @ApiOperation(value = "Get a user", response = User.class)
- @RequestMapping(value = "/{username}", method = RequestMethod.GET)
- public ResponseEntity<User> getAUser(
- @ApiParam(value = "username", required = true) @PathVariable("username") String username
- ) {
- Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /users/{username}", "Loaded a user with username : " + userInfo.getUser().getUsername());
-
- return ResponseEntity.ok(userRepository.findOne(username));
- }
-}
diff --git a/src/main/java/eu/hbp/mip/controllers/galaxy/retrofit/RetroFitGalaxyClients.java b/src/main/java/eu/hbp/mip/controllers/galaxy/retrofit/RetroFitGalaxyClients.java
index 612dce6ca5b557f23deafdf873978c0f442eb1d9..609163e8920ad3443e908c36aea6143ba69533c1 100644
--- a/src/main/java/eu/hbp/mip/controllers/galaxy/retrofit/RetroFitGalaxyClients.java
+++ b/src/main/java/eu/hbp/mip/controllers/galaxy/retrofit/RetroFitGalaxyClients.java
@@ -1,9 +1,9 @@
package eu.hbp.mip.controllers.galaxy.retrofit;
import com.google.gson.JsonObject;
-import eu.hbp.mip.model.galaxy.GalaxyWorkflowResult;
-import eu.hbp.mip.model.galaxy.PostWorkflowToGalaxyDtoResponse;
-import eu.hbp.mip.model.galaxy.WorkflowDTO;
+import eu.hbp.mip.models.galaxy.GalaxyWorkflowResult;
+import eu.hbp.mip.models.galaxy.PostWorkflowToGalaxyDtoResponse;
+import eu.hbp.mip.models.galaxy.WorkflowDTO;
import retrofit2.Call;
import retrofit2.http.*;
diff --git a/src/main/java/eu/hbp/mip/model/AlgorithmDTO.java b/src/main/java/eu/hbp/mip/model/AlgorithmDTO.java
deleted file mode 100644
index ed0ef2a15606ef09f139bad65c90c3cf436c2474..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/AlgorithmDTO.java
+++ /dev/null
@@ -1,220 +0,0 @@
-package eu.hbp.mip.model;
-
-import com.google.gson.annotations.SerializedName;
-
-import java.util.List;
-
-public class AlgorithmDTO {
-
- public String getName() {
- return name;
- }
-
- public void setName(String name) {
- this.name = name;
- }
-
- public String getDesc() {
- return desc;
- }
-
- public void setDesc(String desc) {
- this.desc = desc;
- }
-
- public String getLabel() {
- return label;
- }
-
- public void setLabel(String label) {
- this.label = label;
- }
-
- public String getType() {
- return type;
- }
-
- public void setType(String type) {
- this.type = type;
- }
-
- public List<AlgorithmParamDTO> getParameters() {
- return parameters;
- }
-
- public void setParameters(List<AlgorithmParamDTO> parameters) {
- this.parameters = parameters;
- }
-
- @SerializedName("name")
- private String name;
-
- @SerializedName("desc")
- private String desc;
-
- @SerializedName("label")
- private String label;
-
- @SerializedName("type")
- private String type;
-
- @SerializedName("parameters")
- private List<AlgorithmParamDTO> parameters;
-
- public static class AlgorithmParamDTO {
- @SerializedName("name")
- private String name;
-
- @SerializedName("desc")
- private String desc;
-
- @SerializedName("label")
- private String label;
-
- @SerializedName("type")
- private String type;
-
- @SerializedName("columnValuesSQLType")
- private String columnValuesSQLType;
-
- @SerializedName("columnValuesIsCategorical")
- private String columnValuesIsCategorical;
-
- @SerializedName("value")
- private String value;
-
- @SerializedName("defaultValue")
- private String defaultValue;
-
- @SerializedName("valueType")
- private String valueType;
-
- @SerializedName("valueNotBlank")
- private String valueNotBlank;
-
- @SerializedName("valueMultiple")
- private String valueMultiple;
-
- @SerializedName("valueMin")
- private String valueMin;
-
- @SerializedName("valueMax")
- private String valueMax;
-
- @SerializedName("valueEnumerations")
- private List<String> valueEnumerations;
-
- public String getName() {
- return name;
- }
-
- public void setName(String name) {
- this.name = name;
- }
-
- public String getDesc() {
- return desc;
- }
-
- public void setDesc(String desc) {
- this.desc = desc;
- }
-
- public String getLabel() {
- return label;
- }
-
- public void setLabel(String label) {
- this.label = label;
- }
-
- public String getType() {
- return type;
- }
-
- public void setType(String type) {
- this.type = type;
- }
-
- public String getColumnValuesSQLType() {
- return columnValuesSQLType;
- }
-
- public void setColumnValuesSQLType(String columnValuesSQLType) {
- this.columnValuesSQLType = columnValuesSQLType;
- }
-
- public String getColumnValuesIsCategorical() {
- return columnValuesIsCategorical;
- }
-
- public void setColumnValuesIsCategorical(String columnValuesIsCategorical) {
- this.columnValuesIsCategorical = columnValuesIsCategorical;
- }
-
- public String getValue() {
- return value;
- }
-
- public void setValue(String value) {
- this.value = value;
- }
-
- public String getDefaultValue() {
- return defaultValue;
- }
-
- public void setDefaultValue(String defaultValue) {
- this.defaultValue = defaultValue;
- }
-
- public String getValueType() {
- return valueType;
- }
-
- public void setValueType(String valueType) {
- this.valueType = valueType;
- }
-
- public String getValueNotBlank() {
- return valueNotBlank;
- }
-
- public void setValueNotBlank(String valueNotBlank) {
- this.valueNotBlank = valueNotBlank;
- }
-
- public String getValueMultiple() {
- return valueMultiple;
- }
-
- public void setValueMultiple(String valueMultiple) {
- this.valueMultiple = valueMultiple;
- }
-
- public String getValueMin() {
- return valueMin;
- }
-
- public void setValueMin(String valueMin) {
- this.valueMin = valueMin;
- }
-
- public String getValueMax() {
- return valueMax;
- }
-
- public void setValueMax(String valueMax) {
- this.valueMax = valueMax;
- }
-
- public List<String> getValueEnumerations() {
- return valueEnumerations;
- }
-
- public void setValueEnumerations(List<String> valueEnumerations) {
- this.valueEnumerations = valueEnumerations;
- }
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/model/Article.java b/src/main/java/eu/hbp/mip/model/Article.java
deleted file mode 100644
index 95c7cbbae0701558b249dec7a5cf0b9a07bd3e92..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/Article.java
+++ /dev/null
@@ -1,166 +0,0 @@
-/*
- * Created by mirco on 04.12.15.
- */
-
-package eu.hbp.mip.model;
-
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.annotation.JsonProperty;
-import io.swagger.annotations.ApiModel;
-import org.springframework.validation.annotation.Validated;
-
-import javax.persistence.*;
-import javax.validation.constraints.NotNull;
-import javax.validation.constraints.Size;
-import java.util.Date;
-import java.util.LinkedList;
-import java.util.List;
-
-@Entity
-@Table(name = "`article`")
-@ApiModel
-@JsonInclude(JsonInclude.Include.NON_NULL)
-@Validated
-public class Article {
-
- @Id
- private String slug = null;
-
- @NotNull
- @Size(min = 1, max = 255)
- private String title;
-
- private String status = null;
-
- @Column(columnDefinition = "text", name = "abstract")
- private String abstractText = null;
-
- @Column(columnDefinition = "text")
- private String content = null;
-
- private Date publishedAt = null;
-
- private Date createdAt = null;
-
- private Date updatedAt = null;
-
- @ManyToOne
- @JoinColumn(name = "createdby_username")
- private User createdBy = null;
-
- @ManyToOne
- @JoinColumn(name = "updatedby_username")
- private User updatedBy = null;
-
- @ManyToMany(fetch = FetchType.EAGER, cascade = CascadeType.PERSIST)
- private List<Tag> tags = new LinkedList<>();
-
-
- public Article() {
- /*
- * Empty constructor is needed by Hibernate
- */
- title = "";
- }
-
-
- public String getStatus() {
- return status;
- }
-
- public void setStatus(String status) {
- this.status = status;
- }
-
-
- public String getTitle() {
- return title;
- }
-
- public void setTitle(String title) {
- this.title = title;
- }
-
-
- public String getSlug() {
- return slug;
- }
-
- public void setSlug(String slug) {
- this.slug = slug;
- }
-
-
- @JsonProperty("abstract")
- public String getAbstract() {
- return abstractText;
- }
-
- public void setAbstract(String abstractText) {
- this.abstractText = abstractText;
- }
-
-
- public String getContent() {
- return content;
- }
-
- public void setContent(String content) {
- this.content = content;
- }
-
-
- public Date getPublishedAt() {
- return publishedAt;
- }
-
- public void setPublishedAt(Date publishedAt) {
- this.publishedAt = publishedAt;
- }
-
-
- public Date getCreatedAt() {
- return createdAt;
- }
-
- public void setCreatedAt(Date createdAt) {
- this.createdAt = createdAt;
- }
-
-
- public Date getUpdatedAt() {
- return updatedAt;
- }
-
- public void setUpdatedAt(Date updatedAt) {
- this.updatedAt = updatedAt;
- }
-
-
- public User getCreatedBy() {
- return createdBy;
- }
-
- public void setCreatedBy(User createdBy) {
- this.createdBy = createdBy;
- }
-
-
- public User getUpdatedBy() {
- return updatedBy;
- }
-
- public void setUpdatedBy(User updatedBy) {
- this.updatedBy = updatedBy;
- }
-
-
- public List<Tag> getTags() {
- return tags;
- }
-
- public void setTags(List<Tag> tags) {
- this.tags = tags;
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/model/Config.java b/src/main/java/eu/hbp/mip/model/Config.java
deleted file mode 100644
index 2362194b2b8338d7ab7a0b781c7891e88acfd293..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/Config.java
+++ /dev/null
@@ -1,112 +0,0 @@
-/**
- * Created by mirco on 25.02.16.
- */
-
-package eu.hbp.mip.model;
-
-import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
-import io.swagger.annotations.ApiModel;
-
-import javax.persistence.*;
-import java.util.HashMap;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
-
-@Entity
-@Table(name = "`config`")
-@ApiModel
-@JsonIgnoreProperties(value = {"id"})
-public class Config {
-
- @Id
- @GeneratedValue(strategy = GenerationType.SEQUENCE)
- private Long id = null;
-
- private String type = null;
-
- private Integer height = null;
-
- @ElementCollection(fetch = FetchType.EAGER)
- @CollectionTable(name = "config_yAxisVariables", joinColumns = @JoinColumn(name = "config_id"))
- private List<String> yAxisVariables = new LinkedList<>();
-
- private String xAxisVariable = null;
-
- private Boolean hasXAxis = null;
-
- @ElementCollection(fetch = FetchType.EAGER)
- @CollectionTable(name = "config_title", joinColumns = @JoinColumn(name = "config_id"))
- private Map<String, String> title = new HashMap<>();
-
-
- public Config() {
- /*
- * Empty constructor is needed by Hibernate
- */
- }
-
-
- public Long getId() {
- return id;
- }
-
- public void setId(Long id) {
- this.id = id;
- }
-
-
- public String getType() {
- return type;
- }
-
- public void setType(String type) {
- this.type = type;
- }
-
-
- public Integer getHeight() {
- return height;
- }
-
- public void setHeight(Integer height) {
- this.height = height;
- }
-
-
- public List<String> getyAxisVariables() {
- return yAxisVariables;
- }
-
- public void setyAxisVariables(List<String> yAxisVariables) {
- this.yAxisVariables = yAxisVariables;
- }
-
-
- public String getxAxisVariable() {
- return xAxisVariable;
- }
-
- public void setxAxisVariable(String xAxisVariable) {
- this.xAxisVariable = xAxisVariable;
- }
-
-
- public Boolean getHasXAxis() {
- return hasXAxis;
- }
-
- public void setHasXAxis(Boolean hasXAxis) {
- this.hasXAxis = hasXAxis;
- }
-
-
- public Map<String, String> getTitle() {
- return title;
- }
-
- public void setTitle(Map<String, String> title) {
- this.title = title;
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/model/Dataset.java b/src/main/java/eu/hbp/mip/model/Dataset.java
deleted file mode 100644
index d920571d9526dca8d29316d8d56578dc3d0b3b9b..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/Dataset.java
+++ /dev/null
@@ -1,106 +0,0 @@
-/*
- * Created by mirco on 04.12.15.
- */
-
-package eu.hbp.mip.model;
-
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.annotation.JsonProperty;
-import io.swagger.annotations.ApiModel;
-
-import javax.persistence.*;
-import java.util.Date;
-import java.util.LinkedList;
-import java.util.List;
-
-// TODO: deprecate
-
-@Entity
-@Table(name = "`dataset`")
-@ApiModel
-@JsonInclude(JsonInclude.Include.NON_NULL)
-public class Dataset {
-
- @Id
- private String code = null;
-
- private Date date = null;
-
- // Aka covariables
- @ElementCollection
- @CollectionTable(name = "dataset_header", joinColumns = @JoinColumn(name = "dataset_code"))
- private List<String> header = new LinkedList<>();
-
- @ElementCollection
- @CollectionTable(name = "dataset_grouping", joinColumns = @JoinColumn(name = "dataset_code"))
- private List<String> grouping = new LinkedList<>();
-
- @ElementCollection
- @CollectionTable(name = "dataset_variable", joinColumns = @JoinColumn(name = "dataset_code"))
- private List<String> variable = new LinkedList<>();
-
- // TODO:
- @Transient
- @JsonProperty(access = JsonProperty.Access.READ_ONLY)
- private Object data = null;
-
-
- public Dataset() {
- /*
- * Empty constructor is needed by Hibernate
- */
- }
-
-
- public String getCode() {
- return code;
- }
-
- public void setCode(String code) {
- this.code = code;
- }
-
-
- public Date getDate() {
- return date;
- }
-
- public void setDate(Date date) {
- this.date = date;
- }
-
-
- public List<String> getHeader() {
- return header;
- }
-
- public void setHeader(List<String> header) {
- this.header = header;
- }
-
-
- public List<String> getGrouping() {
- return grouping;
- }
-
- public void setGrouping(List<String> grouping) {
- this.grouping = grouping;
- }
-
-
- public List<String> getVariable() {
- return variable;
- }
-
- public void setVariable(List<String> variable) {
- this.variable = variable;
- }
-
- public Object getData() {
- return data;
- }
-
- public void setData(Object data) {
- this.data = data;
- }
-}
diff --git a/src/main/java/eu/hbp/mip/model/DatasetDescription.java b/src/main/java/eu/hbp/mip/model/DatasetDescription.java
deleted file mode 100644
index c77c50aeab3a4256ecadf78aa2f25f89a05a0b92..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/DatasetDescription.java
+++ /dev/null
@@ -1,46 +0,0 @@
-package eu.hbp.mip.model;
-
-import com.fasterxml.jackson.annotation.JsonInclude;
-import io.swagger.annotations.ApiModel;
-
-@ApiModel
-@JsonInclude(JsonInclude.Include.NON_NULL)
-public class DatasetDescription {
-
- private String code;
- private String label;
- private String description;
- private String anonymisationLevel;
-
- public String getCode() {
- return code;
- }
-
- public void setCode(String code) {
- this.code = code;
- }
-
- public String getLabel() {
- return label;
- }
-
- public void setLabel(String label) {
- this.label = label;
- }
-
- public String getDescription() {
- return description;
- }
-
- public void setDescription(String description) {
- this.description = description;
- }
-
- public String getAnonymisationLevel() {
- return anonymisationLevel;
- }
-
- public void setAnonymisationLevel(String anonymisationLevel) {
- this.anonymisationLevel = anonymisationLevel;
- }
-}
diff --git a/src/main/java/eu/hbp/mip/model/Experiment.java b/src/main/java/eu/hbp/mip/model/Experiment.java
deleted file mode 100644
index c40d91d3441ce131e45e5dbda0934c4a3ab0c30b..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/Experiment.java
+++ /dev/null
@@ -1,232 +0,0 @@
-package eu.hbp.mip.model;
-
-import com.google.gson.*;
-import com.google.gson.annotations.Expose;
-import org.hibernate.annotations.Cascade;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import javax.persistence.*;
-import java.util.*;
-
-/**
- * Created by habfast on 21/04/16.
- */
-@Entity
-@Table(name = "`experiment`")
-public class Experiment {
-
- private static final Gson gson = new Gson();
-
- @Id
- @Column(columnDefinition = "uuid")
- @org.hibernate.annotations.Type(type = "pg-uuid")
- @Expose
- private UUID uuid;
-
- @Column(columnDefinition = "TEXT")
- @Expose
- private String name;
-
- @Expose
- @ManyToOne
- @JoinColumn(name = "createdby_username")
- private User createdBy;
-
- @ManyToOne
- @Cascade(org.hibernate.annotations.CascadeType.SAVE_UPDATE)
- @Expose
- private Model model;
-
- @Column(columnDefinition = "TEXT")
- @Expose
- private String algorithms;
-
- @Column(columnDefinition = "TEXT")
- private String validations;
-
- @Column(columnDefinition = "TEXT")
- @Expose
- private String workflowHistoryId;
-
- @Column(columnDefinition = "TEXT")
- @Expose
- private String workflowStatus;
-
- @Column(columnDefinition = "TEXT")
- @Expose
- private String result;
-
- @Expose
- private Date created = new Date();
-
- @Expose
- private Date finished;
-
- @Expose
- private boolean hasError = false;
-
- @Expose
- private boolean hasServerError = false;
-
- @Expose
- private boolean shared = false;
-
- // whether or not the experiment's result have been resultsViewed by its owner
- @Expose
- private boolean resultsViewed = false;
-
- public Experiment() {
- /*
- * Empty constructor is needed by Hibernate
- */
- }
-
-
- public JsonObject jsonify() {
- JsonObject exp = gson.toJsonTree(this).getAsJsonObject();
- JsonParser parser = new JsonParser();
-
- if (this.algorithms != null) {
- exp.remove("algorithms");
- JsonArray jsonAlgorithms = parser.parse(this.algorithms).getAsJsonArray();
- exp.add("algorithms", jsonAlgorithms);
- }
-
- if (this.validations != null) {
- exp.remove("validations");
- JsonArray jsonValidations = parser.parse(this.validations).getAsJsonArray();
- exp.add("validations", jsonValidations);
- }
-
- if (this.result != null && !this.hasServerError) {
- exp.remove("result");
-
- JsonElement jsonResult = parser.parse(this.result);
- exp.add("result", jsonResult);
-
- }
-
- return exp;
- }
-
- public String getValidations() {
- return validations;
- }
-
- public void setValidations(String validations) {
- this.validations = validations;
- }
-
- public String getAlgorithms() {
- return algorithms;
- }
-
- public void setAlgorithms(String algorithms) {
- this.algorithms = algorithms;
- }
-
- public Model getModel() {
- return model;
- }
-
- public void setModel(Model model) {
- this.model = model;
- }
-
- public boolean isHasError() {
- return hasError;
- }
-
- public void setHasError(boolean hasError) {
- this.hasError = hasError;
- }
-
- public String getWorkflowHistoryId() {
- return workflowHistoryId;
- }
-
- public void setWorkflowHistoryId(String workflowHistoryId) {
- this.workflowHistoryId = workflowHistoryId;
- }
-
- public String getWorkflowStatus() {
- return workflowStatus;
- }
-
- public void setWorkflowStatus(String workflowStatus) {
- this.workflowStatus = workflowStatus;
- }
-
- public String getResult() {
- return result;
- }
-
- public void setResult(String result) {
- this.result = result;
- }
-
- public Date getFinished() {
- return finished;
- }
-
- public void setFinished(Date finished) {
- this.finished = finished;
- }
-
- public Date getCreated() {
- return created;
- }
-
- public void setCreated(Date created) {
- this.created = created;
- }
-
- public UUID getUuid() {
- return uuid;
- }
-
- public void setUuid(UUID uuid) {
- this.uuid = uuid;
- }
-
- public String getName() {
- return name;
- }
-
- public void setName(String name) {
- this.name = name;
- }
-
- public User getCreatedBy() {
- return createdBy;
- }
-
- public void setCreatedBy(User createdBy) {
- this.createdBy = createdBy;
- }
-
- public boolean isResultsViewed() {
- return resultsViewed;
- }
-
- public void setResultsViewed(boolean resultsViewed) {
- this.resultsViewed = resultsViewed;
- }
-
- public boolean isHasServerError() {
- return hasServerError;
- }
-
- public void setHasServerError(boolean hasServerError) {
- this.hasServerError = hasServerError;
- }
-
- public boolean isShared() {
- return shared;
- }
-
- public void setShared(boolean shared) {
- this.shared = shared;
- }
-}
diff --git a/src/main/java/eu/hbp/mip/model/ExperimentExecutionDTO.java b/src/main/java/eu/hbp/mip/model/ExperimentExecutionDTO.java
deleted file mode 100644
index a68cd9121d852503bc01eb6b2f0d23dd8af525dd..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/ExperimentExecutionDTO.java
+++ /dev/null
@@ -1,106 +0,0 @@
-package eu.hbp.mip.model;
-
-import java.util.List;
-
-public class ExperimentExecutionDTO {
-
- private String name;
- private String model;
- private List<AlgorithmExecutionDTO> algorithms;
-
- public String getModel() {
- return model;
- }
-
- public void setModel(String model) {
- this.model = model;
- }
-
- public List<AlgorithmExecutionDTO> getAlgorithms() {
- return algorithms;
- }
-
- public void setAlgorithms(List<AlgorithmExecutionDTO> algorithms) {
- this.algorithms = algorithms;
- }
-
- public String getName() {
- return name;
- }
-
- public void setName(String name) {
- this.name = name;
- }
-
- public static class AlgorithmExecutionDTO {
-
- private String name;
- private String label;
- private String type;
-
- private List<AlgorithmExecutionParamDTO> parameters;
-
- public String getName() {
- return name;
- }
-
- public void setName(String name) {
- this.name = name;
- }
-
- public String getType() {
- return type;
- }
-
- public void setType(String type) {
- this.type = type;
- }
-
- public List<AlgorithmExecutionDTO.AlgorithmExecutionParamDTO> getParameters() {
- return parameters;
- }
-
- public void setParameters(List<AlgorithmExecutionDTO.AlgorithmExecutionParamDTO> parameters) {
- this.parameters = parameters;
- }
-
- public String getLabel() {
- return label;
- }
-
- public void setLabel(String label) {
- this.label = label;
- }
-
- public static class AlgorithmExecutionParamDTO {
-
- private String name;
- private String label;
- private String value;
-
- public String getName() {
- return this.name;
- }
-
- public void setName(String name) {
- this.name = name;
- }
-
- public String getValue() {
- return value;
- }
-
- public void setValue(String value) {
- this.value = value;
- }
-
- public String getLabel() {
- return label;
- }
-
- public void setLabel(String label) {
- this.label = label;
- }
- }
- }
-}
diff --git a/src/main/java/eu/hbp/mip/model/GeneralStats.java b/src/main/java/eu/hbp/mip/model/GeneralStats.java
deleted file mode 100644
index 4253ae7dd859ed63a47ffba68a9bcafc5646302c..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/GeneralStats.java
+++ /dev/null
@@ -1,41 +0,0 @@
-/*
- * Created by mirco on 03.02.16.
- */
-
-package eu.hbp.mip.model;
-
-import com.fasterxml.jackson.annotation.JsonInclude;
-import io.swagger.annotations.ApiModel;
-
-@ApiModel
-@JsonInclude(JsonInclude.Include.NON_NULL)
-public class GeneralStats {
-
- private Long users = null;
- private Long articles = null;
-
-
- public GeneralStats() {
- /*
- * Empty constructor is needed by Hibernate
- */
- }
-
-
- public Long getUsers() {
- return users;
- }
-
- public void setUsers(Long users) {
- this.users = users;
- }
-
-
- public Long getArticles() {
- return articles;
- }
-
- public void setArticles(Long articles) {
- this.articles = articles;
- }
-}
diff --git a/src/main/java/eu/hbp/mip/model/Group.java b/src/main/java/eu/hbp/mip/model/Group.java
deleted file mode 100644
index abb195a932669d28785b407ad3738ab8087cffe7..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/Group.java
+++ /dev/null
@@ -1,37 +0,0 @@
-/*
- * Created by mirco on 04.12.15.
- */
-
-package eu.hbp.mip.model;
-
-import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
-import com.fasterxml.jackson.annotation.JsonInclude;
-import io.swagger.annotations.ApiModel;
-
-import javax.persistence.Entity;
-import javax.persistence.Id;
-import javax.persistence.Table;
-
-@Entity
-@Table(name = "`group`")
-@ApiModel
-@JsonIgnoreProperties(value = {"parent"})
-@JsonInclude(JsonInclude.Include.NON_NULL)
-public class Group {
-
- @Id
- private String code = null;
-
-
- public Group() {
- /*
- * Empty constructor is needed by Hibernate
- */
- }
-
-
- public String getCode() {
- return code;
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/model/Mining.java b/src/main/java/eu/hbp/mip/model/Mining.java
deleted file mode 100644
index 46cfd6c3ec64b0a7e552cd4f6e210a24a746fc1e..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/Mining.java
+++ /dev/null
@@ -1,64 +0,0 @@
-package eu.hbp.mip.model;
-
-import com.google.gson.*;
-
-import java.util.Date;
-
-public class Mining {
-
- private static final Gson gson = new Gson();
-
- private final String jobId;
- private final String node;
- private final String function;
- private final String shape;
- private final Date timestamp;
- private final String data;
-
- public Mining(String jobId, String node, String function, String shape, Date timestamp, String data) {
- this.jobId = jobId;
- this.node = node;
- this.function = function;
- this.shape = shape;
- this.timestamp = timestamp;
- this.data = data;
- }
-
- public String getJobId() {
- return jobId;
- }
-
- public String getNode() {
- return node;
- }
-
- public String getFunction() {
- return function;
- }
-
- public String getShape() {
- return shape;
- }
-
- public Date getTimestamp() {
- return timestamp;
- }
-
- public String getData() {
- return data;
- }
-
- public JsonObject jsonify() {
- JsonObject exp = gson.toJsonTree(this).getAsJsonObject();
- JsonParser parser = new JsonParser();
-
- if (this.data != null) {
- exp.remove("data");
- JsonElement jsonResult = parser.parse(this.data);
- exp.add("data", jsonResult);
- }
-
- return exp;
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/model/MiningQuery.java b/src/main/java/eu/hbp/mip/model/MiningQuery.java
deleted file mode 100644
index 171c55032eee4b3c5f63d636c137d6ae41bfe051..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/MiningQuery.java
+++ /dev/null
@@ -1,96 +0,0 @@
-package eu.hbp.mip.model;
-
-import com.google.gson.Gson;
-
-import java.util.LinkedList;
-import java.util.List;
-
-/**
- * Created by mirco on 06.01.17.
- */
-public class MiningQuery {
-
- private List<Variable> variables;
- private List<Variable> covariables;
- private List<Variable> grouping;
- private List<Variable> datasets;
- private String filters;
- private ExperimentExecutionDTO.AlgorithmExecutionDTO algorithm;
-
- public MiningQuery() {
- this.variables = new LinkedList<>();
- this.covariables = new LinkedList<>();
- this.grouping = new LinkedList<>();
- this.datasets = new LinkedList<>();
- this.filters = "";
- }
-
- public List<Variable> getVariables() {
- return variables;
- }
-
- public void setVariables(List<Variable> variables) {
- this.variables = variables;
- }
-
- public void addVariable(Variable variable) {
- this.variables.add(variable);
- }
-
- public List<Variable> getCovariables() {
- return covariables;
- }
-
- public void setCovariables(List<Variable> covariables) {
- this.covariables = covariables;
- }
-
- public void addCovariable(Variable variable) {
- this.covariables.add(variable);
- }
-
- public List<Variable> getGrouping() {
- return grouping;
- }
-
- public void setGrouping(List<Variable> grouping) {
- this.grouping = grouping;
- }
-
- public List<Variable> getDatasets() {
- return datasets;
- }
-
- public void setDataset(List<Variable> datasets) {
- this.datasets = datasets;
- }
-
- public void addDataset(Variable variable) {
- this.datasets.add(variable);
- }
-
- public void addGrouping(Variable variable) {
- this.grouping.add(variable);
- }
-
- public String getFilters() {
- return filters;
- }
-
- public void setFilters(String filters) {
- this.filters = filters;
- }
-
- public ExperimentExecutionDTO.AlgorithmExecutionDTO getAlgorithm() {
- return algorithm;
- }
-
- public void setAlgorithm(ExperimentExecutionDTO.AlgorithmExecutionDTO algorithm) {
- this.algorithm = algorithm;
- }
-
- @Override
- public String toString() {
- return new Gson().toJson(this);
- }
-}
diff --git a/src/main/java/eu/hbp/mip/model/Model.java b/src/main/java/eu/hbp/mip/model/Model.java
deleted file mode 100644
index b1590803720c5a0c38538667ef48c940d644399c..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/Model.java
+++ /dev/null
@@ -1,163 +0,0 @@
-/**
- * Created by mirco on 04.12.15.
- */
-
-package eu.hbp.mip.model;
-
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.google.gson.annotations.Expose;
-import io.swagger.annotations.ApiModel;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-
-import javax.persistence.*;
-import java.util.Date;
-
-@Entity
-@Table(name = "`model`")
-@ApiModel
-@JsonInclude(JsonInclude.Include.NON_NULL)
-public class Model {
-
- @Id
- @Expose
- private String slug = null;
-
- @Expose
- private String title = null;
-
- private String description = null;
-
- private Boolean valid = null;
-
- private Date createdAt = null;
-
- private Date updatedAt = null;
-
- @ManyToOne
- @Cascade(CascadeType.SAVE_UPDATE)
- private eu.hbp.mip.model.Query query = null;
-
- @ManyToOne
- @Cascade(CascadeType.SAVE_UPDATE)
- private Dataset dataset = null;
-
- @ManyToOne
- @Cascade(CascadeType.SAVE_UPDATE)
- private Config config = null;
-
- @ManyToOne
- @JoinColumn(name = "createdby_username")
- private User createdBy = null;
-
- @ManyToOne
- @JoinColumn(name = "updatedby_username")
- private User updatedBy = null;
-
-
- public Model() {
- /*
- * Empty constructor is needed by Hibernate
- */
- }
-
-
- public String getTitle() {
- return title;
- }
-
- public void setTitle(String title) {
- this.title = title;
- }
-
-
- public String getSlug() {
- return slug;
- }
-
- public void setSlug(String slug) {
- this.slug = slug;
- }
-
-
- public String getDescription() {
- return description;
- }
-
- public void setDescription(String description) {
- this.description = description;
- }
-
-
- public eu.hbp.mip.model.Query getQuery() {
- return query;
- }
-
- public void setQuery(eu.hbp.mip.model.Query query) {
- this.query = query;
- }
-
-
- public Dataset getDataset() {
- return dataset;
- }
-
- public void setDataset(Dataset dataset) {
- this.dataset = dataset;
- }
-
-
- public Boolean getValid() {
- return valid;
- }
-
- public void setValid(Boolean valid) {
- this.valid = valid;
- }
-
-
- public Config getConfig() {
- return config;
- }
-
- public void setConfig(Config config) {
- this.config = config;
- }
-
-
- public Date getCreatedAt() {
- return createdAt;
- }
-
- public void setCreatedAt(Date createdAt) {
- this.createdAt = createdAt;
- }
-
-
- public Date getUpdatedAt() {
- return updatedAt;
- }
-
- public void setUpdatedAt(Date updatedAt) {
- this.updatedAt = updatedAt;
- }
-
-
- public User getCreatedBy() {
- return createdBy;
- }
-
- public void setCreatedBy(User createdBy) {
- this.createdBy = createdBy;
- }
-
-
- public User getUpdatedBy() {
- return updatedBy;
- }
-
- public void setUpdatedBy(User updatedBy) {
- this.updatedBy = updatedBy;
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/model/PathologyDTO.java b/src/main/java/eu/hbp/mip/model/PathologyDTO.java
deleted file mode 100644
index c58238b623e18aa5f7942d9e4816f905ce48f3f8..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/PathologyDTO.java
+++ /dev/null
@@ -1,85 +0,0 @@
-package eu.hbp.mip.model;
-
-import com.google.gson.annotations.SerializedName;
-
-import java.util.List;
-
-public class PathologyDTO {
-
- public String getCode() {
- return code;
- }
-
- public void setCode(String code) {
- this.code = code;
- }
-
- public String getLabel() {
- return label;
- }
-
- public void setLabel(String label) {
- this.label = label;
- }
-
- public Object getMetadataHierarchy() {
- return metadataHierarchy;
- }
-
- public void setMetadataHierarchy(Object metadataHierarchy) {
- this.metadataHierarchy = metadataHierarchy;
- }
-
- public List<PathologyDatasetDTO> getDatasets() {
- return datasets;
- }
-
- public void setDatasets(List<PathologyDatasetDTO> datasets) {
- this.datasets = datasets;
- }
-
- @SerializedName("code")
- private String code;
-
- @SerializedName("label")
- private String label;
-
- @SerializedName("metadataHierarchy")
- private Object metadataHierarchy;
-
- @SerializedName("datasets")
- private List<PathologyDatasetDTO> datasets;
-
- public static class PathologyDatasetDTO {
- @SerializedName("code")
- private String code;
-
- @SerializedName("label")
- private String label;
-
- public String getCode() {
- return code;
- }
-
- public void setCode(String code) {
- this.code = code;
- }
-
- public String getLabel() {
- return label;
- }
-
- public void setLabel(String label) {
- this.label = label;
- }
-
- public String toString() {
- return code;
- }
- }
-
- public String toString() {
- return code;
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/model/Query.java b/src/main/java/eu/hbp/mip/model/Query.java
deleted file mode 100644
index 8e4d78dcbb1534052e9108aa9cf6d35be6ffa26e..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/Query.java
+++ /dev/null
@@ -1,164 +0,0 @@
-/*
- * Created by mirco on 04.12.15.
- */
-
-package eu.hbp.mip.model;
-
-import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.annotation.JsonProperty;
-import io.swagger.annotations.ApiModel;
-
-import javax.persistence.*;
-import java.util.LinkedList;
-import java.util.List;
-
-@Entity
-@ApiModel
-@Table(name = "`query`")
-@JsonIgnoreProperties(value = {"id"})
-@JsonInclude(JsonInclude.Include.NON_NULL)
-public class Query {
-
- @Id
- @GeneratedValue(strategy = GenerationType.SEQUENCE)
- private Long id = null;
-
- @ManyToMany
- @JoinTable(name = "query_variable", joinColumns = {
- @JoinColumn(name = "id", nullable = false, updatable = false)},
- inverseJoinColumns = {@JoinColumn(name = "code",
- nullable = false, updatable = false)})
- private List<Variable> variables = new LinkedList<>();
-
- @ManyToMany
- @JoinTable(name = "query_covariable", joinColumns = {
- @JoinColumn(name = "id", nullable = false, updatable = false)},
- inverseJoinColumns = {@JoinColumn(name = "code",
- nullable = false, updatable = false)})
- private List<Variable> covariables = new LinkedList<>();
-
- @ManyToMany
- @JoinTable(name = "query_grouping", joinColumns = {
- @JoinColumn(name = "id", nullable = false, updatable = false)},
- inverseJoinColumns = {@JoinColumn(name = "code",
- nullable = false, updatable = false)})
- private List<Variable> grouping = new LinkedList<>();
-
- @ManyToMany
- @JoinTable(name = "query_training_datasets", joinColumns = {
- @JoinColumn(name = "id", nullable = false, updatable = false)},
- inverseJoinColumns = {@JoinColumn(name = "code",
- nullable = false, updatable = false)})
- private List<Variable> trainingDatasets = new LinkedList<>();
-
- @ManyToMany
- @JoinTable(name = "query_testing_datasets", joinColumns = {
- @JoinColumn(name = "id", nullable = false, updatable = false)},
- inverseJoinColumns = {@JoinColumn(name = "code",
- nullable = false, updatable = false)})
- private List<Variable> testingDatasets = new LinkedList<>();
-
- @ManyToMany
- @JoinTable(name = "query_validation_datasets", joinColumns = {
- @JoinColumn(name = "id", nullable = false, updatable = false)},
- inverseJoinColumns = {@JoinColumn(name = "code",
- nullable = false, updatable = false)})
- private List<Variable> validationDatasets = new LinkedList<>();
-
- @Column(columnDefinition = "text")
- private String filters = "";
-
- @Column(columnDefinition = "text")
- private String pathology = "";
-
-
- public Query() {
- /*
- * Empty constructor is needed by Hibernate
- */
- }
-
-
- public Long getId() {
- return id;
- }
-
- public void setId(Long id) {
- this.id = id;
- }
-
-
- @JsonProperty("variables")
- public List<Variable> getVariables() {
- return variables;
- }
-
- public void setVariables(List<Variable> variables) {
- this.variables = variables;
- }
-
-
- @JsonProperty("coVariables")
- public List<Variable> getCovariables() {
- return covariables;
- }
-
- public void setCovariables(List<Variable> covariables) {
- this.covariables = covariables;
- }
-
-
- @JsonProperty("groupings")
- public List<Variable> getGrouping() {
- return grouping;
- }
-
- public void setGrouping(List<Variable> grouping) {
- this.grouping = grouping;
- }
-
- @JsonProperty("trainingDatasets")
- public List<Variable> getTrainingDatasets() {
- return trainingDatasets;
- }
-
- public void setTrainingDatasets(List<Variable> trainingDatasets) {
- this.trainingDatasets = trainingDatasets;
- }
-
- @JsonProperty("testingDatasets")
- public List<Variable> getTestingDatasets() {
- return testingDatasets;
- }
-
- public void setTestingDatasets(List<Variable> testingDatasets) {
- this.testingDatasets = testingDatasets;
- }
-
- @JsonProperty("validationDatasets")
- public List<Variable> getValidationDatasets() {
- return validationDatasets;
- }
-
- public void setValidationDatasets(List<Variable> validationDatasets) {
- this.validationDatasets = validationDatasets;
- }
-
- public String getFilters() {
- return filters;
- }
-
- public void setFilters(String filters) {
- this.filters = filters;
- }
-
- public String getPathology() {
- return pathology;
- }
-
- public void setPathology(String pathology) {
- this.pathology = pathology;
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/model/Tag.java b/src/main/java/eu/hbp/mip/model/Tag.java
deleted file mode 100644
index 693c9865602ace72de50d067e3dd5e3eaac97526..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/Tag.java
+++ /dev/null
@@ -1,39 +0,0 @@
-/*
- * Created by mirco on 04.12.15.
- */
-
-package eu.hbp.mip.model;
-
-import com.fasterxml.jackson.annotation.JsonInclude;
-import io.swagger.annotations.ApiModel;
-
-import javax.persistence.Entity;
-import javax.persistence.Id;
-import javax.persistence.Table;
-
-@Entity
-@Table(name = "`tag`")
-@ApiModel
-@JsonInclude(JsonInclude.Include.NON_NULL)
-public class Tag {
-
- @Id
- private String name = null;
-
-
- public Tag() {
- /*
- * Empty constructor is needed by Hibernate
- */
- }
-
-
- public String getName() {
- return name;
- }
-
- public void setName(String name) {
- this.name = name;
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/model/User.java b/src/main/java/eu/hbp/mip/model/User.java
deleted file mode 100644
index 64fee4b670e6285a0e06ada431975fd5c17cf50e..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/User.java
+++ /dev/null
@@ -1,332 +0,0 @@
-/*
- * Created by mirco on 04.12.15.
- */
-
-package eu.hbp.mip.model;
-
-import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.google.gson.annotations.Expose;
-import io.swagger.annotations.ApiModel;
-
-import javax.persistence.*;
-import java.util.*;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-import java.util.stream.Collectors;
-
-@Entity
-@Table(name = "`user`")
-@ApiModel
-@JsonInclude(JsonInclude.Include.NON_NULL)
-@JsonIgnoreProperties(value = {"appsVotes"})
-public class User {
-
- @Id
- @Expose
- private String username = null;
-
- @Expose
- private String fullname = null;
-
- @Expose
- private String firstname = null;
-
- @Expose
- private String lastname = null;
-
- @Expose
- private String picture = null;
-
- @Expose
- private String web = null;
-
- @Expose
- private String phone = null;
-
- @Expose
- private String birthday = null;
-
- @Expose
- private String gender = null;
-
- @Expose
- private String city = null;
-
- @Expose
- private String country = null;
-
- @Expose
- private String password = null;
-
- @Expose
- private String email = null;
-
- @Expose
- private String apikey = null;
-
- @Expose
- private String team = null;
-
- @Expose
- private Boolean isActive = null;
-
- @ElementCollection(fetch = FetchType.EAGER)
- @CollectionTable(name = "user_languages", joinColumns = @JoinColumn(name = "user_username"))
- @Expose
- private List<String> languages = new LinkedList<>();
-
- @ElementCollection(fetch = FetchType.EAGER)
- @CollectionTable(name = "user_roles", joinColumns = @JoinColumn(name = "user_username"))
- @Expose
- private List<String> roles = new LinkedList<>();
-
- private Boolean agreeNDA = null;
-
-
- public User() {
- /*
- * Empty constructor is needed by Hibernate
- */
- }
-
-
- /**
- * Create a user using OpenID user profile
- *
- * @param userInfo info from OpenID UserInfo endpoint
- */
- public User(String userInfo) {
-
- Pattern p;
- Matcher m;
-
- p = Pattern.compile("preferred_username=([\\w- ]+)");
- m = p.matcher(userInfo);
- if (m.find()) {
- this.username = m.group(1);
- }
-
- p = Pattern.compile("name=([\\w ]+)");
- m = p.matcher(userInfo);
- if (m.find()) {
- this.fullname = m.group(1);
- }
-
- p = Pattern.compile("given_name=([\\w ]+)");
- m = p.matcher(userInfo);
- if (m.find()) {
- this.firstname = m.group(1);
- }
-
- p = Pattern.compile("family_name=([\\w ]+)");
- m = p.matcher(userInfo);
- if (m.find()) {
- this.lastname = m.group(1);
- }
-
- p = Pattern.compile("email=([\\w.]+@[\\w.]+)");
- m = p.matcher(userInfo);
- if (m.find()) {
- this.email = m.group(1);
- }
-
- p = Pattern.compile("title=([\\w ]+)");
- m = p.matcher(userInfo);
- if (m.find()) {
- if ("Mr".equals(m.group(1))) {
- this.gender = "Male";
- } else {
- this.gender = "Female";
- }
- }
-
- p = Pattern.compile("contractor=([\\w ]+)");
- m = p.matcher(userInfo);
- if (m.find()) {
- this.team = m.group(1);
- }
-
- p = Pattern.compile("picture=([-a-zA-Z0-9+&@#/%=~_|.: ]+)");
- m = p.matcher(userInfo);
- if (m.find()) {
- this.picture = m.group(1);
- }
-
- if (this.picture == null || this.picture.isEmpty()) {
- this.picture = "images/users/default_user.png";
- }
-
- }
-
-
- public String getFullname() {
- return fullname;
- }
-
- public void setFullname(String fullname) {
- this.fullname = fullname;
- }
-
-
- public String getUsername() {
- return username;
- }
-
- public void setUsername(String username) {
- this.username = username;
- }
-
-
- public String getFirstname() {
- return firstname;
- }
-
- public void setFirstname(String firstname) {
- this.firstname = firstname;
- }
-
-
- public String getLastname() {
- return lastname;
- }
-
- public void setLastname(String lastname) {
- this.lastname = lastname;
- }
-
-
- public String getPicture() {
- return picture;
- }
-
- public void setPicture(String picture) {
- this.picture = picture;
- }
-
-
- public String getWeb() {
- return web;
- }
-
- public void setWeb(String web) {
- this.web = web;
- }
-
-
- public String getPhone() {
- return phone;
- }
-
- public void setPhone(String phone) {
- this.phone = phone;
- }
-
-
- public String getBirthday() {
- return birthday;
- }
-
- public void setBirthday(String birthday) {
- this.birthday = birthday;
- }
-
-
- public String getGender() {
- return gender;
- }
-
- public void setGender(String gender) {
- this.gender = gender;
- }
-
-
- public String getCity() {
- return city;
- }
-
- public void setCity(String city) {
- this.city = city;
- }
-
-
- public String getCountry() {
- return country;
- }
-
- public void setCountry(String country) {
- this.country = country;
- }
-
-
- public String getPassword() {
- return password;
- }
-
- public void setPassword(String password) {
- this.password = password;
- }
-
-
- public String getEmail() {
- return email;
- }
-
- public void setEmail(String email) {
- this.email = email;
- }
-
-
- public String getApikey() {
- return apikey;
- }
-
- public void setApikey(String apikey) {
- this.apikey = apikey;
- }
-
-
- public String getTeam() {
- return team;
- }
-
- public void setTeam(String team) {
- this.team = team;
- }
-
-
- public Boolean getIsActive() {
- return isActive;
- }
-
- public void setIsActive(Boolean isActive) {
- this.isActive = isActive;
- }
-
-
- public List<String> getLanguages() {
- return languages;
- }
-
- public void setLanguages(List<String> languages) {
- this.languages = languages;
- }
-
-
- public List<String> getRoles() {
- return roles;
- }
-
- public void setRoles(List<String> roles) {
- this.roles = roles;
- }
-
-
- public Boolean getAgreeNDA() {
- return agreeNDA;
- }
-
- public void setAgreeNDA(Boolean agreeNDA) {
- this.agreeNDA = agreeNDA;
- }
-}
diff --git a/src/main/java/eu/hbp/mip/model/UserInfo.java b/src/main/java/eu/hbp/mip/model/UserInfo.java
deleted file mode 100644
index 71eee3573b485d690c810b42c1344cc2170fb9f5..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/UserInfo.java
+++ /dev/null
@@ -1,84 +0,0 @@
-package eu.hbp.mip.model;
-
-import eu.hbp.mip.repositories.UserRepository;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Value;
-import org.springframework.context.annotation.Scope;
-import org.springframework.context.annotation.ScopedProxyMode;
-import org.springframework.security.core.Authentication;
-import org.springframework.security.core.context.SecurityContextHolder;
-import org.springframework.security.oauth2.provider.OAuth2Authentication;
-import org.springframework.stereotype.Component;
-
-import javax.inject.Named;
-
-@Component
-@Scope(value = "session", proxyMode = ScopedProxyMode.TARGET_CLASS)
-@Named("userInfo")
-public class UserInfo {
-
- @Autowired
- private UserRepository userRepository;
-
- /**
- * Enable HBP collab authentication (1) or disable it (0). Default is 1
- */
- @Value("#{'${hbp.authentication.enabled:1}'}")
- private boolean authentication;
-
- private User user;
-
- /**
- * Set to true if using no-auth mode and user has clicked on the login button
- */
- private boolean fakeAuth = false;
-
- /**
- * returns the user for the current session.
- * <p>
- * the "synchronized" keyword is there to avoid a bug that the transaction is supposed to protect me from.
- * To test if your solution to removing it works, do the following:
- * - clean DB from scratch
- * - restart DB and backend (no session or anything like that)
- * - log in using the front end
- * - check you have no 500 error in the network logs.
- *
- * @return the user for the current session
- */
- public User getUser() {
- if (user == null) {
-
- if (!authentication) {
- user = new User();
- user.setUsername("anonymous");
- user.setFullname("anonymous");
- user.setEmail("anonymous@anonymous.com");
- user.setPicture("images/users/default_user.png");
- } else {
- user = new User(getUserInfos());
- }
- User foundUser = userRepository.findOne(user.getUsername());
- if (foundUser != null) {
- user.setAgreeNDA(foundUser.getAgreeNDA());
- }
- userRepository.save(user);
- }
-
- return user;
- }
-
- public boolean isFakeAuth() {
- return fakeAuth;
- }
-
- public void setFakeAuth(boolean fakeAuth) {
- this.fakeAuth = fakeAuth;
- }
-
- private String getUserInfos() {
- OAuth2Authentication oAuth2Authentication = (OAuth2Authentication) SecurityContextHolder.getContext().getAuthentication();
- Authentication userAuthentication = oAuth2Authentication.getUserAuthentication();
- return userAuthentication.getDetails().toString();
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/model/Value.java b/src/main/java/eu/hbp/mip/model/Value.java
deleted file mode 100644
index 784452e591ffc8eb1f62ff5cc0c7f82694c78a3c..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/Value.java
+++ /dev/null
@@ -1,43 +0,0 @@
-/*
- * Created by mirco on 04.12.15.
- */
-
-package eu.hbp.mip.model;
-
-import com.fasterxml.jackson.annotation.JsonInclude;
-import io.swagger.annotations.ApiModel;
-
-import javax.persistence.Entity;
-import javax.persistence.Id;
-import javax.persistence.Table;
-
-@Entity
-@Table(name = "`value`")
-@ApiModel
-@JsonInclude(JsonInclude.Include.NON_NULL)
-public class Value {
-
- @Id
- private String code = null;
-
- private String label = null;
-
-
- public String getCode() {
- return code;
- }
-
- public void setCode(String code) {
- this.code = code;
- }
-
-
- public String getLabel() {
- return label;
- }
-
- public void setLabel(String label) {
- this.label = label;
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/model/Variable.java b/src/main/java/eu/hbp/mip/model/Variable.java
deleted file mode 100644
index 596be8d775673af068235dabed39323a4440de49..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/Variable.java
+++ /dev/null
@@ -1,59 +0,0 @@
-/*
- * Created by mirco on 04.12.15.
- */
-
-package eu.hbp.mip.model;
-
-import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.google.gson.annotations.Expose;
-import io.swagger.annotations.ApiModel;
-
-import javax.persistence.Entity;
-import javax.persistence.Id;
-import javax.persistence.Table;
-import java.util.List;
-
-@Entity
-@Table(name = "`variable`")
-@ApiModel
-@JsonIgnoreProperties(value = {"queries"})
-@JsonInclude(JsonInclude.Include.NON_NULL)
-public class Variable {
-
- @Id
- @Expose
- private String code = null;
-
- /**
- * Empty constructor is needed by Hibernate
- */
- public Variable() {
- }
-
- public Variable(String code) {
- this.code = code;
- }
-
- public String getCode() {
- return code;
- }
-
- public void setCode(String code) {
- this.code = code;
- }
-
- public static String stringFromVariables(List<Variable> variables, String operator) {
- StringBuilder sb = new StringBuilder();
- int i = 0;
- for (Variable s : variables) {
- i++;
- sb.append(s.getCode());
- if (i < variables.size()) {
- sb.append(operator);
- }
- }
- return sb.toString();
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/models/DAOs/ExperimentDAO.java b/src/main/java/eu/hbp/mip/models/DAOs/ExperimentDAO.java
new file mode 100644
index 0000000000000000000000000000000000000000..585bd8bd6694275d341fe1aea19f82f3105d97ea
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/models/DAOs/ExperimentDAO.java
@@ -0,0 +1,116 @@
+package eu.hbp.mip.models.DAOs;
+
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.google.gson.Gson;
+import com.google.gson.annotations.Expose;
+import eu.hbp.mip.models.DTOs.AlgorithmDTO;
+import eu.hbp.mip.models.DTOs.ExperimentDTO;
+import eu.hbp.mip.utils.JsonConverters;
+import io.swagger.annotations.ApiModel;
+import lombok.Getter;
+import lombok.Setter;
+
+import javax.persistence.*;
+import java.util.*;
+
+/**
+ * Created by habfast on 21/04/16.
+ */
+@Entity
+@Getter
+@Setter
+@Table(name = "`experiment`")
+@ApiModel
+@JsonInclude(JsonInclude.Include.NON_NULL)
+public class ExperimentDAO {
+
+ private static final Gson gson = new Gson();
+
+ @Expose
+ @Id
+ @Column(columnDefinition = "uuid", updatable = false)
+ @org.hibernate.annotations.Type(type = "pg-uuid")
+ private UUID uuid;
+
+ @Expose
+ @Column(columnDefinition = "TEXT")
+ private String name;
+
+ @Expose
+ @ManyToOne
+ @JoinColumn(name = "created_by_username",columnDefinition = "CHARACTER VARYING")
+ private UserDAO createdBy;
+
+ @Expose
+ @Column(name="workflow_history_id", columnDefinition = "TEXT")
+ private String workflowHistoryId;
+
+ @Expose
+ @Column(columnDefinition = "TEXT")
+ @Enumerated(EnumType.STRING)
+ private Status status;
+
+ @Expose
+ @Column(columnDefinition = "TEXT")
+ private String result;
+
+ @Expose
+ @Column(columnDefinition = "TIMESTAMP WITHOUT TIME ZONE")
+ private Date finished;
+
+ @Expose
+ @Column(columnDefinition = "TEXT")
+ private String algorithm;
+
+ @Expose
+ @Column(columnDefinition = "TEXT")
+ private String algorithmId;
+
+ @Expose
+ @Column(columnDefinition = "TIMESTAMP WITHOUT TIME ZONE")
+ private Date created = new Date();
+
+ @Expose
+ @Column(columnDefinition = "TIMESTAMP WITHOUT TIME ZONE")
+ private Date updated;
+
+ @Expose
+ @Column(columnDefinition = "BOOLEAN")
+ private boolean shared = false;
+
+ // whether or not the experiment's result have been viewed by its owner
+ @Expose
+ @Column(columnDefinition = "BOOLEAN")
+ private boolean viewed = false;
+
+ public enum Status {
+ error,
+ pending,
+ success
+ }
+
+ public ExperimentDAO() {
+ /*
+ * Empty constructor is needed by Hibernate
+ */
+ }
+
+ public ExperimentDTO convertToDTO(boolean includeResult)
+ {
+ ExperimentDTO experimentDTO = new ExperimentDTO();
+ experimentDTO.setAlgorithm(JsonConverters.convertJsonStringToObject(this.algorithm, AlgorithmDTO.class));
+ experimentDTO.setCreated(this.created);
+ experimentDTO.setUpdated(this.updated);
+ experimentDTO.setFinished(this.finished);
+ experimentDTO.setCreatedBy(this.createdBy.getUsername());
+ experimentDTO.setName(this.name);
+ if(includeResult){
+ experimentDTO.setResult(JsonConverters.convertJsonStringToObject(String.valueOf(this.result), new ArrayList<>().getClass()));
+ }
+ experimentDTO.setStatus(this.status);
+ experimentDTO.setShared(this.shared);
+ experimentDTO.setUuid(this.uuid);
+ experimentDTO.setViewed(this.viewed);
+ return experimentDTO;
+ }
+}
diff --git a/src/main/java/eu/hbp/mip/models/DAOs/UserDAO.java b/src/main/java/eu/hbp/mip/models/DAOs/UserDAO.java
new file mode 100644
index 0000000000000000000000000000000000000000..9279b3793c44c449302c083b823da674d7e4d46f
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/models/DAOs/UserDAO.java
@@ -0,0 +1,53 @@
+/*
+ * Created by mirco on 04.12.15.
+ */
+
+package eu.hbp.mip.models.DAOs;
+
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.google.gson.annotations.Expose;
+import io.swagger.annotations.ApiModel;
+import lombok.Getter;
+import lombok.Setter;
+
+import javax.persistence.Entity;
+import javax.persistence.Id;
+import javax.persistence.Table;
+
+@Entity
+@Getter
+@Setter
+@Table(name = "`user`")
+@ApiModel
+@JsonInclude(JsonInclude.Include.NON_NULL)
+public class UserDAO {
+
+ @Id
+ @Expose
+ private String username;
+
+ @Expose
+ private String subjectId;
+
+ @Expose
+ private String fullname;
+
+ @Expose
+ private String email;
+
+ @Expose
+ private Boolean agreeNDA;
+
+ public UserDAO() {
+ // Empty constructor is needed by Hibernate
+ }
+
+ public UserDAO(String username, String fullname, String email, String subjectId) {
+ this.username = username;
+ this.fullname = fullname;
+ this.email = email;
+ this.agreeNDA = false;
+ this.subjectId = subjectId;
+
+ }
+}
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/AlgorithmDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/AlgorithmDTO.java
new file mode 100644
index 0000000000000000000000000000000000000000..52db979d5ddd7b043572be8fc9255c45fa0e9c98
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/models/DTOs/AlgorithmDTO.java
@@ -0,0 +1,73 @@
+package eu.hbp.mip.models.DTOs;
+
+import com.google.gson.annotations.SerializedName;
+import lombok.Getter;
+import lombok.Setter;
+
+import java.util.List;
+
+@Getter
+@Setter
+public class AlgorithmDTO {
+
+ @SerializedName("name")
+ private String name;
+
+ @SerializedName("desc")
+ private String desc;
+
+ @SerializedName("label")
+ private String label;
+
+ @SerializedName("type")
+ private String type;
+
+ @SerializedName("parameters")
+ private List<AlgorithmParamDTO> parameters;
+
+ @Getter
+ @Setter
+ public static class AlgorithmParamDTO {
+ @SerializedName("name")
+ private String name;
+
+ @SerializedName("desc")
+ private String desc;
+
+ @SerializedName("label")
+ private String label;
+
+ @SerializedName("type")
+ private String type;
+
+ @SerializedName("columnValuesSQLType")
+ private String columnValuesSQLType;
+
+ @SerializedName("columnValuesIsCategorical")
+ private String columnValuesIsCategorical;
+
+ @SerializedName("value")
+ private String value;
+
+ @SerializedName("defaultValue")
+ private String defaultValue;
+
+ @SerializedName("valueType")
+ private String valueType;
+
+ @SerializedName("valueNotBlank")
+ private String valueNotBlank;
+
+ @SerializedName("valueMultiple")
+ private String valueMultiple;
+
+ @SerializedName("valueMin")
+ private String valueMin;
+
+ @SerializedName("valueMax")
+ private String valueMax;
+
+ @SerializedName("valueEnumerations")
+ private List<String> valueEnumerations;
+ }
+}
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/ExperimentDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/ExperimentDTO.java
new file mode 100644
index 0000000000000000000000000000000000000000..e64c6f75e7d7a4d7aafa8ba93d38f9d3edf6bf19
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/models/DTOs/ExperimentDTO.java
@@ -0,0 +1,31 @@
+package eu.hbp.mip.models.DTOs;
+
+import com.fasterxml.jackson.annotation.JsonInclude;
+import eu.hbp.mip.models.DAOs.ExperimentDAO;
+import lombok.Getter;
+import lombok.Setter;
+
+import java.util.Date;
+import java.util.List;
+import java.util.UUID;
+
+@Getter
+@Setter
+@JsonInclude(JsonInclude.Include.NON_NULL)
+public class ExperimentDTO {
+
+ private UUID uuid;
+ private String name;
+ private String createdBy;
+ private Date created;
+ private Date updated;
+ private Date finished;
+ private Boolean shared;
+ private Boolean viewed;
+ private List<Object> result;
+ private ExperimentDAO.Status status;
+ private AlgorithmDTO algorithm;
+
+ public ExperimentDTO() {
+ }
+}
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java
new file mode 100644
index 0000000000000000000000000000000000000000..aa78ef8b0e315a2f71261dc1fed480cb8617ccb2
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java
@@ -0,0 +1,42 @@
+package eu.hbp.mip.models.DTOs;
+
+import com.google.gson.annotations.SerializedName;
+import lombok.Getter;
+import lombok.Setter;
+
+import java.util.List;
+
+@Getter
+@Setter
+public class PathologyDTO {
+
+ @SerializedName("code")
+ private String code;
+
+ @SerializedName("label")
+ private String label;
+
+ @SerializedName("metadataHierarchy")
+ private Object metadataHierarchy;
+
+ @SerializedName("datasets")
+ private List<PathologyDatasetDTO> datasets;
+
+ @Getter
+ @Setter
+ public static class PathologyDatasetDTO {
+ @SerializedName("code")
+ private String code;
+
+ @SerializedName("label")
+ private String label;
+
+ public String toString() {
+ return code;
+ }
+ }
+
+ public String toString() {
+ return code;
+ }
+}
diff --git a/src/main/java/eu/hbp/mip/model/galaxy/ErrorResponse.java b/src/main/java/eu/hbp/mip/models/galaxy/ErrorResponse.java
similarity index 96%
rename from src/main/java/eu/hbp/mip/model/galaxy/ErrorResponse.java
rename to src/main/java/eu/hbp/mip/models/galaxy/ErrorResponse.java
index 77a171358b54561e3492dcb317acd835aeaa645f..2703e742541faf9f715ed19485076d397697059e 100644
--- a/src/main/java/eu/hbp/mip/model/galaxy/ErrorResponse.java
+++ b/src/main/java/eu/hbp/mip/models/galaxy/ErrorResponse.java
@@ -3,7 +3,7 @@
* Copyright (c) 2019. MIT License
*/
-package eu.hbp.mip.model.galaxy;
+package eu.hbp.mip.models.galaxy;
import com.google.gson.annotations.SerializedName;
diff --git a/src/main/java/eu/hbp/mip/model/galaxy/GalaxyWorkflowResult.java b/src/main/java/eu/hbp/mip/models/galaxy/GalaxyWorkflowResult.java
similarity index 99%
rename from src/main/java/eu/hbp/mip/model/galaxy/GalaxyWorkflowResult.java
rename to src/main/java/eu/hbp/mip/models/galaxy/GalaxyWorkflowResult.java
index 089a6a626ed1e0d38306c911b515edd3fa8fa5f0..ca7d98fe51e55cd60914893283f2c30b6fcf90be 100644
--- a/src/main/java/eu/hbp/mip/model/galaxy/GalaxyWorkflowResult.java
+++ b/src/main/java/eu/hbp/mip/models/galaxy/GalaxyWorkflowResult.java
@@ -3,7 +3,7 @@
* Copyright (c) 2019. MIT License
*/
-package eu.hbp.mip.model.galaxy;
+package eu.hbp.mip.models.galaxy;
import com.google.gson.annotations.SerializedName;
diff --git a/src/main/java/eu/hbp/mip/model/galaxy/PostWorkflowToGalaxyDtoResponse.java b/src/main/java/eu/hbp/mip/models/galaxy/PostWorkflowToGalaxyDtoResponse.java
similarity index 98%
rename from src/main/java/eu/hbp/mip/model/galaxy/PostWorkflowToGalaxyDtoResponse.java
rename to src/main/java/eu/hbp/mip/models/galaxy/PostWorkflowToGalaxyDtoResponse.java
index edefd63266a8d1678bf82d057882e4eccab112cc..96d8aa8efa089599093fed13ac8e0d0a4be81f42 100644
--- a/src/main/java/eu/hbp/mip/model/galaxy/PostWorkflowToGalaxyDtoResponse.java
+++ b/src/main/java/eu/hbp/mip/models/galaxy/PostWorkflowToGalaxyDtoResponse.java
@@ -3,7 +3,7 @@
* Copyright (c) 2019. MIT License
*/
-package eu.hbp.mip.model.galaxy;
+package eu.hbp.mip.models.galaxy;
import com.google.gson.annotations.SerializedName;
diff --git a/src/main/java/eu/hbp/mip/model/galaxy/WorkflowDTO.java b/src/main/java/eu/hbp/mip/models/galaxy/WorkflowDTO.java
similarity index 95%
rename from src/main/java/eu/hbp/mip/model/galaxy/WorkflowDTO.java
rename to src/main/java/eu/hbp/mip/models/galaxy/WorkflowDTO.java
index fa0cb4b336ef2f8276db39c1a03097f51a5c8ea7..496ee2dfebf50324b1443774cc48edd4e32c2de0 100644
--- a/src/main/java/eu/hbp/mip/model/galaxy/WorkflowDTO.java
+++ b/src/main/java/eu/hbp/mip/models/galaxy/WorkflowDTO.java
@@ -1,8 +1,8 @@
-package eu.hbp.mip.model.galaxy;
+package eu.hbp.mip.models.galaxy;
import com.google.gson.Gson;
import com.google.gson.annotations.SerializedName;
-import eu.hbp.mip.model.AlgorithmDTO;
+import eu.hbp.mip.models.DTOs.AlgorithmDTO;
import java.util.*;
diff --git a/src/main/java/eu/hbp/mip/repositories/ArticleRepository.java b/src/main/java/eu/hbp/mip/repositories/ArticleRepository.java
deleted file mode 100644
index 1a93186ff064bf5833246d82b2cb0d35bf838312..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/repositories/ArticleRepository.java
+++ /dev/null
@@ -1,17 +0,0 @@
-package eu.hbp.mip.repositories;
-
-import eu.hbp.mip.model.Article;
-import eu.hbp.mip.model.User;
-import org.springframework.data.repository.CrudRepository;
-
-/**
- * Created by mirco on 11.07.16.
- */
-
-public interface ArticleRepository extends CrudRepository<Article, String> {
- Long countByTitle(String title);
-
- Iterable<Article> findByCreatedBy(User user);
-
- Iterable<Article> findByStatusOrCreatedBy(String status, User user);
-}
diff --git a/src/main/java/eu/hbp/mip/repositories/ConfigRepository.java b/src/main/java/eu/hbp/mip/repositories/ConfigRepository.java
deleted file mode 100644
index deb286150c0ba9c7833b4dfa66a61d3890c011c4..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/repositories/ConfigRepository.java
+++ /dev/null
@@ -1,11 +0,0 @@
-package eu.hbp.mip.repositories;
-
-import eu.hbp.mip.model.Config;
-import org.springframework.data.repository.CrudRepository;
-
-/**
- * Created by mirco on 11.07.16.
- */
-
-public interface ConfigRepository extends CrudRepository<Config, Long> {
-}
diff --git a/src/main/java/eu/hbp/mip/repositories/DatasetRepository.java b/src/main/java/eu/hbp/mip/repositories/DatasetRepository.java
deleted file mode 100644
index 7c6da1e9745b8a144296d51a5d85434111213b96..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/repositories/DatasetRepository.java
+++ /dev/null
@@ -1,11 +0,0 @@
-package eu.hbp.mip.repositories;
-
-import eu.hbp.mip.model.Dataset;
-import org.springframework.data.repository.CrudRepository;
-
-/**
- * Created by mirco on 11.07.16.
- */
-
-public interface DatasetRepository extends CrudRepository<Dataset, String> {
-}
diff --git a/src/main/java/eu/hbp/mip/repositories/ExperimentRepository.java b/src/main/java/eu/hbp/mip/repositories/ExperimentRepository.java
index 2f6ae857d49018c5d9a3cb429f17cf3d2b80d313..9ac54cada906b78ad5ab5ac41d77d05562bedc4e 100644
--- a/src/main/java/eu/hbp/mip/repositories/ExperimentRepository.java
+++ b/src/main/java/eu/hbp/mip/repositories/ExperimentRepository.java
@@ -1,17 +1,17 @@
package eu.hbp.mip.repositories;
-import eu.hbp.mip.model.Experiment;
-import eu.hbp.mip.model.User;
+import eu.hbp.mip.models.DAOs.ExperimentDAO;
+import org.springframework.data.jpa.repository.JpaSpecificationExecutor;
import org.springframework.data.repository.CrudRepository;
+import java.util.Optional;
import java.util.UUID;
/**
* Created by mirco on 11.07.16.
*/
-public interface ExperimentRepository extends CrudRepository<Experiment, UUID> {
- Iterable<Experiment> findByCreatedBy(User user);
-
- Iterable<Experiment> findByShared(Boolean shared);
+public interface ExperimentRepository extends CrudRepository<ExperimentDAO, UUID>, JpaSpecificationExecutor<ExperimentDAO>
+{
+ ExperimentDAO findByUuid(UUID experimentUuid);
}
diff --git a/src/main/java/eu/hbp/mip/repositories/ModelRepository.java b/src/main/java/eu/hbp/mip/repositories/ModelRepository.java
deleted file mode 100644
index c25b1e5bb6c4a5e888851b08ae3f0a801d5a4553..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/repositories/ModelRepository.java
+++ /dev/null
@@ -1,17 +0,0 @@
-package eu.hbp.mip.repositories;
-
-import eu.hbp.mip.model.Model;
-import eu.hbp.mip.model.User;
-import org.springframework.data.repository.CrudRepository;
-
-/**
- * Created by mirco on 11.07.16.
- */
-
-public interface ModelRepository extends CrudRepository<Model, String> {
- Long countByTitle(String Title);
-
- Iterable<Model> findByCreatedByOrderByCreatedAt(User user);
-
- Iterable<Model> findByValidOrCreatedByOrderByCreatedAt(Boolean valid, User user);
-}
diff --git a/src/main/java/eu/hbp/mip/repositories/QueryRepository.java b/src/main/java/eu/hbp/mip/repositories/QueryRepository.java
deleted file mode 100644
index f0b95d39c4c3a480fe2bec20ce75e46361889e71..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/repositories/QueryRepository.java
+++ /dev/null
@@ -1,11 +0,0 @@
-package eu.hbp.mip.repositories;
-
-import eu.hbp.mip.model.Query;
-import org.springframework.data.repository.CrudRepository;
-
-/**
- * Created by mirco on 11.07.16.
- */
-
-public interface QueryRepository extends CrudRepository<Query, Long> {
-}
diff --git a/src/main/java/eu/hbp/mip/repositories/TagRepository.java b/src/main/java/eu/hbp/mip/repositories/TagRepository.java
deleted file mode 100644
index 4edb4090e0336ac034daf245d5ca3bb084a6f5ae..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/repositories/TagRepository.java
+++ /dev/null
@@ -1,11 +0,0 @@
-package eu.hbp.mip.repositories;
-
-import eu.hbp.mip.model.Tag;
-import org.springframework.data.repository.CrudRepository;
-
-/**
- * Created by mirco on 11.07.16.
- */
-
-public interface TagRepository extends CrudRepository<Tag, String> {
-}
diff --git a/src/main/java/eu/hbp/mip/repositories/UserRepository.java b/src/main/java/eu/hbp/mip/repositories/UserRepository.java
index 3a0db7ee31cf9c56cdd68397d641f4a71e8c37a2..99ae0b1dcfc237e875e7ba458175ae8441ec8c8e 100644
--- a/src/main/java/eu/hbp/mip/repositories/UserRepository.java
+++ b/src/main/java/eu/hbp/mip/repositories/UserRepository.java
@@ -1,12 +1,13 @@
package eu.hbp.mip.repositories;
-import eu.hbp.mip.model.User;
+import eu.hbp.mip.models.DAOs.UserDAO;
import org.springframework.data.repository.CrudRepository;
/**
* Created by mirco on 11.07.16.
*/
-public interface UserRepository extends CrudRepository<User, String> {
+public interface UserRepository extends CrudRepository<UserDAO, String> {
+ UserDAO findByUsername(String username);
}
diff --git a/src/main/java/eu/hbp/mip/repositories/ValueRepository.java b/src/main/java/eu/hbp/mip/repositories/ValueRepository.java
deleted file mode 100644
index b41574d6082542ec1539f8e14203e61eb27e0614..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/repositories/ValueRepository.java
+++ /dev/null
@@ -1,11 +0,0 @@
-package eu.hbp.mip.repositories;
-
-import eu.hbp.mip.model.Value;
-import org.springframework.data.repository.CrudRepository;
-
-/**
- * Created by mirco on 11.07.16.
- */
-
-public interface ValueRepository extends CrudRepository<Value, String> {
-}
diff --git a/src/main/java/eu/hbp/mip/repositories/VariableRepository.java b/src/main/java/eu/hbp/mip/repositories/VariableRepository.java
deleted file mode 100644
index 3ded949436f345143bb9e60a51bc0ee2ab20019b..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/repositories/VariableRepository.java
+++ /dev/null
@@ -1,10 +0,0 @@
-package eu.hbp.mip.repositories;
-
-import eu.hbp.mip.model.Variable;
-import org.springframework.data.repository.CrudRepository;
-
-/**
- * Created by mirco on 13.09.16.
- */
-public interface VariableRepository extends CrudRepository<Variable, String> {
-}
diff --git a/src/main/java/eu/hbp/mip/services/ActiveUserService.java b/src/main/java/eu/hbp/mip/services/ActiveUserService.java
new file mode 100644
index 0000000000000000000000000000000000000000..bc3c8ced7fc3a573a8fe67bd87abaf1dcf19246c
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/services/ActiveUserService.java
@@ -0,0 +1,85 @@
+package eu.hbp.mip.services;
+
+import eu.hbp.mip.models.DAOs.UserDAO;
+import eu.hbp.mip.repositories.UserRepository;
+import org.keycloak.KeycloakPrincipal;
+import org.keycloak.representations.IDToken;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.context.annotation.Scope;
+import org.springframework.context.annotation.ScopedProxyMode;
+import org.springframework.security.core.context.SecurityContextHolder;
+import org.springframework.stereotype.Component;
+
+import javax.inject.Named;
+import java.util.Objects;
+
+@Component
+@Named("ActiveUserService")
+@Scope(value = "session", proxyMode = ScopedProxyMode.TARGET_CLASS)
+public class ActiveUserService {
+
+ @Value("#{'${authentication.enabled}'}")
+ private boolean authenticationIsEnabled;
+
+ private UserDAO user;
+
+ private final UserRepository userRepository;
+
+ public ActiveUserService(UserRepository userRepository) {
+ this.userRepository = userRepository;
+ }
+
+ /**
+ * Fetches the details of the active user.
+ * If the user doesn't exist, it's created on the fly from the auth token.
+ *
+ * @return the userDAO
+ */
+ public UserDAO getActiveUser() {
+
+ // User already loaded
+ if (user != null)
+ return user;
+
+ // If Authentication is OFF, create anonymous user with accepted NDA
+ if (!authenticationIsEnabled) {
+ user = new UserDAO("anonymous", "anonymous", "anonymous@anonymous.com", "anonymousId");
+ user.setAgreeNDA(true);
+ userRepository.save(user);
+ return user;
+ }
+
+ // If authentication is ON get user info from Token
+ KeycloakPrincipal keycloakPrincipal =
+ (KeycloakPrincipal) SecurityContextHolder.getContext().getAuthentication().getPrincipal();
+ IDToken idToken = keycloakPrincipal.getKeycloakSecurityContext().getIdToken();
+ user = new UserDAO(idToken.getPreferredUsername(), idToken.getName(), idToken.getEmail(), idToken.getId());
+
+ UserDAO userInDatabase = userRepository.findByUsername(user.getUsername());
+ if (userInDatabase == null) {
+ userRepository.save(user);
+ return user;
+ }
+
+ if (!Objects.equals(user.getEmail(),userInDatabase.getEmail())
+ || !Objects.equals(user.getFullname(),userInDatabase.getFullname())
+ ) {
+ userInDatabase.setFullname(user.getFullname());
+ userInDatabase.setEmail(user.getEmail());
+ }
+
+ user = userInDatabase;
+ userRepository.save(user);
+ return user;
+ }
+
+ public UserDAO agreeToNDA() {
+ // Fetch the active user
+ getActiveUser();
+
+ user.setAgreeNDA(true);
+ userRepository.save(user);
+
+ return user;
+ }
+}
diff --git a/src/main/java/eu/hbp/mip/services/ExperimentService.java b/src/main/java/eu/hbp/mip/services/ExperimentService.java
new file mode 100644
index 0000000000000000000000000000000000000000..45345c8a5b33d5826c149cd384a5b17c0d3b7a78
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/services/ExperimentService.java
@@ -0,0 +1,1008 @@
+package eu.hbp.mip.services;
+
+import com.github.jmchilton.blend4j.galaxy.GalaxyInstance;
+import com.github.jmchilton.blend4j.galaxy.GalaxyInstanceFactory;
+import com.github.jmchilton.blend4j.galaxy.WorkflowsClient;
+import com.github.jmchilton.blend4j.galaxy.beans.Workflow;
+import com.github.jmchilton.blend4j.galaxy.beans.WorkflowDetails;
+import com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputDefinition;
+import com.google.gson.Gson;
+import com.google.gson.JsonElement;
+import com.google.gson.JsonObject;
+import com.google.gson.JsonParser;
+import com.google.gson.internal.LinkedTreeMap;
+import eu.hbp.mip.controllers.galaxy.retrofit.RetroFitGalaxyClients;
+import eu.hbp.mip.controllers.galaxy.retrofit.RetrofitClientInstance;
+import eu.hbp.mip.models.DAOs.ExperimentDAO;
+import eu.hbp.mip.models.DAOs.UserDAO;
+import eu.hbp.mip.models.DTOs.AlgorithmDTO;
+import eu.hbp.mip.models.DTOs.ExperimentDTO;
+import eu.hbp.mip.models.galaxy.GalaxyWorkflowResult;
+import eu.hbp.mip.models.galaxy.PostWorkflowToGalaxyDtoResponse;
+import eu.hbp.mip.repositories.ExperimentRepository;
+import eu.hbp.mip.services.Specifications.ExperimentSpecifications;
+import eu.hbp.mip.utils.ClaimUtils;
+import eu.hbp.mip.utils.Exceptions.*;
+import eu.hbp.mip.utils.HTTPUtil;
+import eu.hbp.mip.utils.JsonConverters;
+import eu.hbp.mip.utils.Logger;
+import org.codehaus.jettison.json.JSONException;
+import org.codehaus.jettison.json.JSONObject;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.data.domain.Page;
+import org.springframework.data.domain.PageRequest;
+import org.springframework.data.domain.Pageable;
+import org.springframework.data.jpa.domain.Specification;
+import org.springframework.security.core.Authentication;
+import org.springframework.stereotype.Service;
+import retrofit2.Call;
+import retrofit2.Response;
+
+import java.io.IOException;
+import java.util.*;
+
+import static java.lang.Thread.sleep;
+
+@Service
+public class ExperimentService {
+
+
+ @Value("#{'${services.exareme.queryExaremeUrl}'}")
+ private String queryExaremeUrl;
+
+ @Value("#{'${services.galaxy.galaxyUrl}'}")
+ private String galaxyUrl;
+
+ @Value("#{'${services.galaxy.galaxyApiKey}'}")
+ private String galaxyApiKey;
+
+ @Value("#{'${authentication.enabled}'}")
+ private boolean authenticationIsEnabled;
+
+ private static final Gson gson = new Gson();
+
+ private final ActiveUserService activeUserService;
+ private final ExperimentRepository experimentRepository;
+
+ public ExperimentService(ActiveUserService activeUserService, ExperimentRepository experimentRepository) {
+ this.activeUserService = activeUserService;
+ this.experimentRepository = experimentRepository;
+ }
+
+ /**
+ * The getExperiments will retrieve the experiments from database according to the filters.
+ *
+ * @param name is optional, in case it is required to filter the experiments by name
+ * @param algorithm is optional, in case it is required to filter the experiments by algorithm name
+ * @param shared is optional, in case it is required to filter the experiments by shared
+ * @param viewed is optional, in case it is required to filter the experiments by viewed
+ * @param includeShared is optional, in case it is required to retrieve the experiment that is shared
+ * @param page is the page that is required to be retrieve
+ * @param size is the size of each page
+ * @param orderBy is the column that is required to ordered by
+ * @param descending is a boolean to determine if the experiments will be order by descending or ascending
+ * @param logger contains username and the endpoint.
+ * @return a list of mapped experiments
+ */
+
+ public Map getExperiments(Authentication authentication, String name, String algorithm, Boolean shared, Boolean viewed, boolean includeShared, int page, int size, String orderBy, Boolean descending, Logger logger) {
+
+ UserDAO user = activeUserService.getActiveUser();
+ logger.LogUserAction("Listing my experiments.");
+ if (size > 50)
+ throw new BadRequestException("Invalid size input, max size is 50.");
+ Specification<ExperimentDAO> spec;
+ if(!authenticationIsEnabled || ClaimUtils.validateAccessRightsOnExperiments(authentication, logger))
+ {
+ spec = Specification
+ .where(new ExperimentSpecifications.ExperimentWithName(name))
+ .and(new ExperimentSpecifications.ExperimentWithAlgorithm(algorithm))
+ .and(new ExperimentSpecifications.ExperimentWithShared(shared))
+ .and(new ExperimentSpecifications.ExperimentWithViewed(viewed))
+ .and(new ExperimentSpecifications.ExperimentOrderBy(orderBy, descending));
+ }
+ else {
+ spec = Specification
+ .where(new ExperimentSpecifications.MyExperiment(user.getUsername()))
+ .or(new ExperimentSpecifications.SharedExperiment(includeShared))
+ .and(new ExperimentSpecifications.ExperimentWithAlgorithm(algorithm))
+ .and(new ExperimentSpecifications.ExperimentWithShared(shared))
+ .and(new ExperimentSpecifications.ExperimentWithViewed(viewed))
+ .and(new ExperimentSpecifications.ExperimentWithName(name))
+ .and(new ExperimentSpecifications.ExperimentOrderBy(orderBy, descending));
+ }
+ Pageable paging = PageRequest.of(page, size);
+ Page<ExperimentDAO> pageExperiments = experimentRepository.findAll(spec, paging);
+ List<ExperimentDAO> experimentDAOs = pageExperiments.getContent();
+
+ if (experimentDAOs.isEmpty())
+ throw new NoContent("No experiment found with the filters provided.");
+
+ List<ExperimentDTO> experimentDTOs = new ArrayList<>();
+ experimentDAOs.forEach(experimentDAO -> experimentDTOs.add(experimentDAO.convertToDTO(false)));
+
+ Map<String, Object> response = new HashMap<>();
+ response.put("experiments", experimentDTOs);
+ response.put("currentPage", pageExperiments.getNumber());
+ response.put("totalExperiments", pageExperiments.getTotalElements());
+ response.put("totalPages", pageExperiments.getTotalPages());
+
+ return response;
+ }
+
+ /**
+ * The getExperiment will retrieve the experiment from database according to the input uuid
+ *
+ * @param uuid is the id of the experiment to be retrieved
+ * @param logger contains username and the endpoint.
+ * @return the experiment information that was retrieved from the database
+ */
+ public ExperimentDTO getExperiment(Authentication authentication, String uuid, Logger logger) {
+
+ ExperimentDAO experimentDAO;
+ UserDAO user = activeUserService.getActiveUser();
+
+ logger.LogUserAction("Loading Experiment with uuid : " + uuid);
+
+ experimentDAO = loadExperiment(uuid, logger);
+ if (
+ !experimentDAO.isShared()
+ && !experimentDAO.getCreatedBy().getUsername().equals(user.getUsername())
+ && authenticationIsEnabled
+ && ClaimUtils.validateAccessRightsOnExperiments(authentication, logger)
+ ) {
+ logger.LogUserAction("Accessing Experiment is unauthorized.");
+ throw new UnauthorizedException("You don't have access to the experiment.");
+ }
+ ExperimentDTO experimentDTO = experimentDAO.convertToDTO(true);
+ logger.LogUserAction("Experiment was Loaded with uuid : " + uuid + ".");
+
+ return experimentDTO;
+ }
+
+ /**
+ * The createExperiment will create and save an experiment in the database.
+ *
+ * @param authentication is the role of the user
+ * @param experimentDTO is the experiment information
+ * @param logger contains username and the endpoint.
+ * @return the experiment information which was created
+ */
+ public ExperimentDTO createExperiment(Authentication authentication, ExperimentDTO experimentDTO, Logger logger) {
+
+ //Checking if check (POST) /experiments has proper input.
+ checkPostExperimentProperInput(experimentDTO, logger);
+
+ // Get the type and name of algorithm
+ String algorithmType = experimentDTO.getAlgorithm().getType();
+
+ if(algorithmType == null){
+ logger.LogUserAction("Please provide algorithm type.");
+ throw new BadRequestException("Please provide algorithm type.");
+ }
+
+ algorithmParametersLogging(experimentDTO, logger);
+
+ if (authenticationIsEnabled) {
+ String experimentDatasets = getDatasetFromExperimentParameters(experimentDTO, logger);
+ ClaimUtils.validateAccessRightsOnDatasets(authentication, experimentDatasets, logger);
+ }
+
+ // Run with the appropriate engine
+ if (algorithmType.equals("workflow")) {
+ logger.LogUserAction("Algorithm runs on Galaxy.");
+ return runGalaxyWorkflow(experimentDTO, logger);
+ } else {
+ logger.LogUserAction("Algorithm runs on Exareme.");
+ return createExaremeExperiment(experimentDTO, logger);
+ }
+ }
+
+ /**
+ * The createTransientExperiment will run synchronous a transient experiment into exareme and provide results
+ *
+ * @param authentication is the role of the user
+ * @param experimentDTO is the experiment information
+ * @param logger contains username and the endpoint.
+ * @return the experiment information which was created
+ */
+ public ExperimentDTO createTransientExperiment(Authentication authentication, ExperimentDTO experimentDTO, Logger logger) {
+
+ //Checking if check (POST) /experiments has proper input.
+ checkPostExperimentProperInput(experimentDTO, logger);
+
+ // Get the type and name of algorithm
+ String algorithmType = experimentDTO.getAlgorithm().getType();
+
+ if(algorithmType.equals("workflow")){
+ logger.LogUserAction("You can not run workflow algorithms transiently.");
+ throw new BadRequestException("You can not run workflow algorithms transiently.");
+ }
+
+ // Get the parameters
+ List<AlgorithmDTO.AlgorithmParamDTO> algorithmParameters
+ = experimentDTO.getAlgorithm().getParameters();
+
+ // Get the type and name of algorithm
+ String algorithmName = experimentDTO.getAlgorithm().getName();
+
+ algorithmParametersLogging(experimentDTO, logger);
+
+ if (authenticationIsEnabled) {
+ String experimentDatasets = getDatasetFromExperimentParameters(experimentDTO, logger);
+ ClaimUtils.validateAccessRightsOnDatasets(authentication, experimentDatasets, logger);
+ }
+
+ String body = gson.toJson(algorithmParameters);
+ String url = queryExaremeUrl + "/" + algorithmName;
+ logger.LogUserAction("url: " + url + ", body: " + body);
+
+ logger.LogUserAction("Completed, returning: " + experimentDTO.toString());
+
+ // Results are stored in the experiment object
+ ExaremeResult exaremeResult = runExaremeExperiment(url, body, experimentDTO);
+
+ logger.LogUserAction("Experiment with uuid: " + experimentDTO.getUuid() + "gave response code: " + exaremeResult.getCode() + " and result: " + exaremeResult.getResults());
+
+ experimentDTO.setResult((exaremeResult.getCode() >= 400) ? null : exaremeResult.getResults());
+ experimentDTO.setStatus((exaremeResult.getCode() >= 400) ? ExperimentDAO.Status.error : ExperimentDAO.Status.success);
+
+ return experimentDTO;
+ }
+
+ /**
+ * The updateExperiment will update the experiment's properties
+ *
+ * @param uuid is the id of the experiment to be updated
+ * @param experimentDTO is the experiment information to be updated
+ * @param logger contains username and the endpoint.
+ */
+ public ExperimentDTO updateExperiment(String uuid, ExperimentDTO experimentDTO, Logger logger) {
+ ExperimentDAO experimentDAO;
+ UserDAO user = activeUserService.getActiveUser();
+ logger.LogUserAction("Updating experiment with uuid : " + uuid + ".");
+
+ experimentDAO = loadExperiment(uuid, logger);
+
+ //Verify (PATCH) /experiments non editable fields.
+ verifyPatchExperimentNonEditableFields(experimentDTO, logger);
+
+ if (!experimentDAO.getCreatedBy().getUsername().equals(user.getUsername()))
+ throw new UnauthorizedException("You don't have access to the experiment.");
+
+ if (experimentDTO.getName() != null && experimentDTO.getName().length() != 0)
+ experimentDAO.setName(experimentDTO.getName());
+
+ if (experimentDTO.getShared() != null)
+ experimentDAO.setShared(experimentDTO.getShared());
+
+ if (experimentDTO.getViewed() != null)
+ experimentDAO.setViewed(experimentDTO.getViewed());
+
+ experimentDAO.setUpdated(new Date());
+
+ try {
+ experimentRepository.save(experimentDAO);
+ } catch (Exception e) {
+ logger.LogUserAction("Attempted to save changes to database but an error ocurred : " + e.getMessage() + ".");
+ throw new InternalServerError(e.getMessage());
+ }
+
+ logger.LogUserAction("Updated experiment with uuid : " + uuid + ".");
+
+ experimentDTO = experimentDAO.convertToDTO(true);
+ return experimentDTO;
+ }
+
+ /**
+ * The deleteExperiment will delete an experiment from the database
+ *
+ * @param uuid is the id of the experiment to be deleted
+ * @param logger contains username and the endpoint.
+ */
+ public void deleteExperiment(String uuid, Logger logger) {
+ ExperimentDAO experimentDAO;
+ UserDAO user = activeUserService.getActiveUser();
+ logger.LogUserAction("Deleting experiment with uuid : " + uuid + ".");
+
+ experimentDAO = loadExperiment(uuid, logger);
+
+ if (!experimentDAO.getCreatedBy().getUsername().equals(user.getUsername()))
+ throw new UnauthorizedException("You don't have access to the experiment.");
+
+ try {
+ experimentRepository.delete(experimentDAO);
+ } catch (Exception e) {
+ logger.LogUserAction("Attempted to delete an experiment to database but an error ocurred : " + e.getMessage() + ".");
+ throw new InternalServerError(e.getMessage());
+ }
+
+ logger.LogUserAction("Deleted experiment with uuid : " + uuid + ".");
+ }
+
+ // /* ------------------------------- PRIVATE METHODS ----------------------------------------------------*/
+
+ private void checkPostExperimentProperInput(ExperimentDTO experimentDTO, Logger logger) {
+
+ boolean properInput =
+ experimentDTO.getShared() == null
+ && experimentDTO.getViewed() == null
+ && experimentDTO.getCreated() == null
+ && experimentDTO.getCreatedBy() == null
+ && experimentDTO.getResult() == null
+ && experimentDTO.getStatus() == null
+ && experimentDTO.getUuid() == null;
+
+ if (!properInput) {
+ logger.LogUserAction( "Invalid input.");
+ throw new BadRequestException("Please provide proper input.");
+ }
+ }
+
+ private void verifyPatchExperimentNonEditableFields(ExperimentDTO experimentDTO, Logger logger) {
+ if (experimentDTO.getUuid() != null ) {
+ logger.LogUserAction( "Uuid is not editable.");
+ throw new BadRequestException("Uuid is not editable.");
+ }
+
+ if (experimentDTO.getAlgorithm() != null ) {
+ logger.LogUserAction( "Algorithm is not editable.");
+ throw new BadRequestException("Algorithm is not editable.");
+ }
+
+ if (experimentDTO.getCreated() != null) {
+ logger.LogUserAction( "Created is not editable.");
+ throw new BadRequestException("Created is not editable.");
+ }
+
+ if (experimentDTO.getCreatedBy() != null) {
+ logger.LogUserAction( "CreatedBy is not editable.");
+ throw new BadRequestException("CreatedBy is not editable.");
+ }
+
+ if (experimentDTO.getUpdated() != null) {
+ logger.LogUserAction( "Updated is not editable.");
+ throw new BadRequestException("Updated is not editable.");
+ }
+
+ if (experimentDTO.getFinished() != null) {
+ logger.LogUserAction( "Finished is not editable.");
+ throw new BadRequestException("Finished is not editable.");
+ }
+
+ if (experimentDTO.getResult() != null) {
+ logger.LogUserAction( "Result is not editable.");
+ throw new BadRequestException("Result is not editable.");
+ }
+
+ if (experimentDTO.getStatus() != null) {
+ logger.LogUserAction( "Status is not editable.");
+ throw new BadRequestException("Status is not editable.");
+ }
+ }
+
+ private void algorithmParametersLogging(ExperimentDTO experimentDTO, Logger logger) {
+ String algorithmName = experimentDTO.getAlgorithm().getName();
+ StringBuilder parametersLogMessage = new StringBuilder(", Parameters:\n");
+ experimentDTO.getAlgorithm().getParameters().forEach(
+ params -> parametersLogMessage
+ .append(" ")
+ .append(params.getLabel())
+ .append(" -> ")
+ .append(params.getValue())
+ .append("\n"));
+ logger.LogUserAction("Executing " + algorithmName + parametersLogMessage);
+ }
+
+ /**
+ * The getDatasetFromExperimentParameters will retrieve the dataset from the experiment parameters
+ *
+ * @param experimentDTO is the experiment information
+ * @param logger contains username and the endpoint.
+ * @return the dataset from the experiment
+ */
+ private String getDatasetFromExperimentParameters(ExperimentDTO experimentDTO, Logger logger) {
+
+ String experimentDatasets = null;
+ for (AlgorithmDTO.AlgorithmParamDTO parameter : experimentDTO.getAlgorithm().getParameters()) {
+ if (parameter.getLabel().equals("dataset")) {
+ experimentDatasets = parameter.getValue();
+ break;
+ }
+ }
+
+ if (experimentDatasets == null || experimentDatasets.equals("")) {
+ logger.LogUserAction("A dataset should be specified to run an algorithm.");
+ throw new BadRequestException("Please provide at least one dataset to run the algorithm.");
+ }
+ return experimentDatasets;
+ }
+
+ /**
+ * The loadExperiment access the database and load the information of a specific experiment
+ *
+ * @param uuid is the id of the experiment to be retrieved
+ * @return the experiment information that was retrieved from database
+ */
+ private ExperimentDAO loadExperiment(String uuid, Logger logger) {
+ UUID experimentUuid;
+ ExperimentDAO experimentDAO;
+
+ try {
+ experimentUuid = UUID.fromString(uuid);
+ } catch (Exception e) {
+ logger.LogUserAction( e.getMessage());
+ throw new BadRequestException(e.getMessage());
+ }
+
+ experimentDAO = experimentRepository.findByUuid(experimentUuid);
+ if (experimentDAO == null) {
+ logger.LogUserAction( "Experiment with uuid : " + uuid + "was not found.");
+ throw new ExperimentNotFoundException("Experiment with uuid : " + uuid + " was not found.");
+ }
+
+ return experimentDAO;
+ }
+
+ /**
+ * The createExperimentInTheDatabase will insert a new experiment in the database according to the given experiment information
+ *
+ * @param experimentDTO is the experiment information to inserted in the database
+ * @return the experiment information that was inserted into the database
+ * @Note In the database there will be stored Algorithm Details that is the whole information about the algorithm
+ * and an Algorithm column that is required for the filtering with algorithm name in the GET /experiments.
+ */
+ private ExperimentDAO createExperimentInTheDatabase(ExperimentDTO experimentDTO, Logger logger) {
+ UserDAO user = activeUserService.getActiveUser();
+
+ ExperimentDAO experimentDAO = new ExperimentDAO();
+ experimentDAO.setUuid(UUID.randomUUID());
+ experimentDAO.setCreatedBy(user);
+ experimentDAO.setAlgorithm(JsonConverters.convertObjectToJsonString(experimentDTO.getAlgorithm()));
+ experimentDAO.setAlgorithmId(experimentDTO.getAlgorithm().getName());
+ experimentDAO.setName(experimentDTO.getName());
+ experimentDAO.setStatus(ExperimentDAO.Status.pending);
+
+ try {
+ experimentRepository.save(experimentDAO);
+ } catch (Exception e) {
+ logger.LogUserAction("Attempted to save changes to database but an error ocurred : " + e.getMessage() + ".");
+ throw new InternalServerError(e.getMessage());
+ }
+
+ logger.LogUserAction(" id : " + experimentDAO.getUuid());
+ logger.LogUserAction(" algorithm : " + experimentDAO.getAlgorithm());
+ logger.LogUserAction(" name : " + experimentDAO.getName());
+ return experimentDAO;
+ }
+
+ private void saveExperiment(ExperimentDAO experimentDAO, Logger logger) {
+
+ logger.LogUserAction(" id : " + experimentDAO.getUuid());
+ logger.LogUserAction(" algorithm : " + experimentDAO.getAlgorithm());
+ logger.LogUserAction(" name : " + experimentDAO.getName());
+ logger.LogUserAction(" historyId : " + experimentDAO.getWorkflowHistoryId());
+ logger.LogUserAction(" status : " + experimentDAO.getStatus());
+
+ try {
+ experimentRepository.save(experimentDAO);
+ } catch (Exception e) {
+ logger.LogUserAction("Attempted to save changes to database but an error ocurred : " + e.getMessage() + ".");
+ throw new InternalServerError(e.getMessage());
+ }
+
+ logger.LogUserAction("Saved experiment");
+ }
+
+ private void finishExperiment(ExperimentDAO experimentDAO, Logger logger) {
+ experimentDAO.setFinished(new Date());
+
+ try {
+ experimentRepository.save(experimentDAO);
+ } catch (Exception e) {
+ logger.LogUserAction( "Attempted to save changes to database but an error ocurred : " + e.getMessage() + ".");
+ throw new InternalServerError(e.getMessage());
+ }
+ }
+
+ private String formattingGalaxyResult(String result) {
+ List<LinkedTreeMap<String,Object>> jsonObject = JsonConverters.convertJsonStringToObject(result, new ArrayList<ArrayList<Object>>().getClass());
+ LinkedTreeMap<String,Object> firstResult = jsonObject.get(0);
+ jsonObject = (List<LinkedTreeMap<String, Object>>) firstResult.get("result");
+ List<LinkedTreeMap<String,Object>> finalJsonObject = new ArrayList<>();
+ finalJsonObject.add(jsonObject.get(0));
+ return JsonConverters.convertObjectToJsonString(finalJsonObject);
+ }
+
+ /**
+ * The runExaremeExperiment will run to exareme the experiment
+ *
+ * @param url is the url that contain the results of the experiment
+ * @param body is the parameters of the algorithm
+ * @param experimentDTO is the experiment information to be executed in the exareme
+ * @return the result of exareme as well as the http status that was retrieved
+ */
+ public ExaremeResult runExaremeExperiment(String url, String body, ExperimentDTO experimentDTO) {
+
+ StringBuilder results = new StringBuilder();
+ int code;
+ try {
+ code = HTTPUtil.sendPost(url, body, results);
+ } catch (Exception e) {
+ throw new InternalServerError("Error occurred : " + e.getMessage());
+ }
+
+ // Results are stored in the experiment object
+ ExperimentDTO experimentDTOWithOnlyResult = JsonConverters.convertJsonStringToObject(String.valueOf(results), ExperimentDTO.class);
+ List<Object> resultDTOS = experimentDTOWithOnlyResult.getResult();
+
+ return new ExaremeResult(code, resultDTOS);
+ }
+
+ /* -------------------------------------- EXAREME CALLS ---------------------------------------------------------*/
+
+ /**
+ * The createExaremeExperiment will POST the algorithm to the exareme client
+ *
+ * @param experimentDTO is the request with the experiment information
+ * @param logger contains username and the endpoint.
+ * @return the experiment information that was retrieved from exareme
+ */
+ public ExperimentDTO createExaremeExperiment(ExperimentDTO experimentDTO, Logger logger) {
+
+ logger.LogUserAction("Running the algorithm...");
+
+ ExperimentDAO experimentDAO = createExperimentInTheDatabase(experimentDTO, logger);
+ logger.LogUserAction("Created experiment with uuid :" + experimentDAO.getUuid());
+
+ // Run the 1st algorithm from the list
+ String algorithmName = experimentDTO.getAlgorithm().getName();
+
+ // Get the parameters
+ List<AlgorithmDTO.AlgorithmParamDTO> algorithmParameters
+ = experimentDTO.getAlgorithm().getParameters();
+
+ String body = gson.toJson(algorithmParameters);
+ String url = queryExaremeUrl + "/" + algorithmName;
+ logger.LogUserAction("url: " + url + ", body: " + body);
+
+ logger.LogUserAction("Completed, returning: " + experimentDTO.toString());
+
+ logger.LogUserAction("Starting exareme execution thread");
+ ExperimentDTO finalExperimentDTO = experimentDTO;
+ new Thread(() -> {
+
+ // ATTENTION: Inside the Thread only LogExperimentAction should be used, not LogUserAction!
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Thread named :" + Thread.currentThread().getName() + " with id :" + Thread.currentThread().getId() + " started!");
+
+ try {
+ // Results are stored in the experiment object
+ ExaremeResult exaremeResult = runExaremeExperiment(url, body, finalExperimentDTO);
+
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Experiment with uuid: " + experimentDAO.getUuid() + "gave response code: " + exaremeResult.getCode() + " and result: " + exaremeResult.getResults());
+
+ experimentDAO.setResult((exaremeResult.getCode() >= 400) ? null : JsonConverters.convertObjectToJsonString(exaremeResult.getResults()));
+ experimentDAO.setStatus((exaremeResult.getCode() >= 400) ? ExperimentDAO.Status.error : ExperimentDAO.Status.success);
+ } catch (Exception e) {
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "There was an exception: " + e.getMessage());
+
+ experimentDAO.setStatus(ExperimentDAO.Status.error);
+ }
+
+ finishExperiment(experimentDAO, logger);
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Finished the experiment: " + experimentDAO.toString());
+ }).start();
+ experimentDTO = experimentDAO.convertToDTO(true);
+ return experimentDTO;
+ }
+
+ /* --------------------------------------- GALAXY CALLS ---------------------------------------------------------*/
+
+
+ /**
+ * The runWorkflow will POST the algorithm to the galaxy client
+ *
+ * @param experimentDTO is the request with the experiment information
+ * @return the response to be returned
+ */
+ public ExperimentDTO runGalaxyWorkflow(ExperimentDTO experimentDTO, Logger logger) {
+ logger.LogUserAction("Running a workflow...");
+
+ ExperimentDAO experimentDAO = createExperimentInTheDatabase(experimentDTO, logger);
+ logger.LogUserAction("Created experiment with uuid :" + experimentDAO.getUuid());
+
+
+ // Run the 1st algorithm from the list
+ String workflowId = experimentDTO.getAlgorithm().getName();
+
+ // Get the parameters
+ List<AlgorithmDTO.AlgorithmParamDTO> algorithmParameters
+ = experimentDTO.getAlgorithm().getParameters();
+
+ // Convert the parameters to workflow parameters
+ HashMap<String, String> algorithmParamsIncludingEmpty = new HashMap<>();
+ if (algorithmParameters != null) {
+ for (AlgorithmDTO.AlgorithmParamDTO param : algorithmParameters) {
+ algorithmParamsIncludingEmpty.put(param.getName(), param.getValue());
+ }
+ }
+
+ // Get all the algorithm parameters because the frontend provides only the non-null
+ final GalaxyInstance instance = GalaxyInstanceFactory.get(galaxyUrl, galaxyApiKey);
+ final WorkflowsClient workflowsClient = instance.getWorkflowsClient();
+ Workflow workflow = null;
+ for (Workflow curWorkflow : workflowsClient.getWorkflows()) {
+ if (curWorkflow.getId().equals(workflowId)) {
+ workflow = curWorkflow;
+ break;
+ }
+ }
+ if (workflow == null) {
+ logger.LogUserAction("Could not find algorithm code: " + workflowId);
+ throw new BadRequestException("Could not find galaxy algorithm.");
+ }
+ final WorkflowDetails workflowDetails = workflowsClient.showWorkflow(workflow.getId());
+ for (Map.Entry<String, WorkflowInputDefinition> workflowParameter : workflowDetails.getInputs().entrySet()) {
+ if (!(algorithmParamsIncludingEmpty.containsKey(workflowParameter.getValue().getUuid()))) {
+ algorithmParamsIncludingEmpty.put(workflowParameter.getValue().getUuid(), "");
+ }
+ }
+
+ // Create the body of the request
+ HashMap<String, HashMap<String, String>> requestBody = new HashMap<>();
+ requestBody.put("inputs", algorithmParamsIncludingEmpty);
+ JsonObject requestBodyJson = new JsonParser().parse(gson.toJson(requestBody)).getAsJsonObject();
+
+ // Create the request client
+ RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+ logger.LogUserAction("Running Galaxy workflow with id: " + workflow.getId());
+
+ // Call Galaxy to run the workflow
+ Call<PostWorkflowToGalaxyDtoResponse> call = service.postWorkflowToGalaxy(workflow.getId(), galaxyApiKey, requestBodyJson);
+ try {
+ Response<PostWorkflowToGalaxyDtoResponse> response = call.execute();
+
+ if (response.code() == 200) { // Call succeeded
+ String responseBody = gson.toJson(response.body());
+ logger.LogUserAction("Response: " + responseBody);
+
+ String historyId = (String) new JSONObject(responseBody).get("history_id");
+ experimentDAO.setWorkflowHistoryId(historyId);
+ experimentDAO.setStatus(ExperimentDAO.Status.success);
+
+ } else { // Something unexpected happened
+ String msgErr = gson.toJson(response.errorBody());
+ logger.LogUserAction("Error Response: " + msgErr);
+ experimentDTO.setStatus((response.code() >= 400) ? ExperimentDAO.Status.error : ExperimentDAO.Status.success);
+ }
+
+ } catch (Exception e) {
+ logger.LogUserAction("An exception occurred: " + e.getMessage());
+ experimentDAO.setStatus(ExperimentDAO.Status.error);
+ }
+ saveExperiment(experimentDAO, logger);
+
+ // Start the process of fetching the status
+ updateWorkflowExperiment(experimentDAO, logger);
+
+ logger.LogUserAction("Run workflow completed!");
+
+ experimentDTO = experimentDAO.convertToDTO(true);
+ return experimentDTO;
+ }
+
+
+ /**
+ * This method creates a thread that will fetch the workflow result when it is ready
+ *
+ * @param experimentDAO will be used to fetch it's workflow status, it should have the workflowHistoryId initialized
+ * and the result should not already be fetched
+ */
+ public void updateWorkflowExperiment(ExperimentDAO experimentDAO, Logger logger) {
+
+ if (experimentDAO == null) {
+ logger.LogUserAction("The experiment does not exist.");
+ return;
+ }
+
+ logger.LogUserAction(" Experiment id : " + experimentDAO.getUuid());
+ if (experimentDAO.getWorkflowHistoryId() == null) {
+ logger.LogUserAction("History Id does not exist.");
+ return;
+ }
+
+ logger.LogUserAction("Starting Thread...");
+ new Thread(() -> {
+ while (true) {
+ // ATTENTION: Inside the Thread only LogExperimentAction should be used, not LogExperimentAction!
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Thread is running...");
+
+ try {
+ sleep(2000);
+ } catch (InterruptedException e) {
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Sleep was disrupted: " + e.getMessage());
+ }
+
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Fetching status for experiment Id: " + experimentDAO.getUuid());
+
+ String state = getWorkflowStatus(experimentDAO);
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "State is: " + state);
+
+ switch (state) {
+ case "pending":
+ // Do nothing, when the experiment is created the status is set to running
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Workflow is still running.");
+ break;
+
+ case "success":
+ // Get only the job result that is visible
+ List<GalaxyWorkflowResult> workflowJobsResults = getWorkflowResults(experimentDAO);
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Results are: " + workflowJobsResults.toString());
+
+ boolean resultFound = false;
+ for (GalaxyWorkflowResult jobResult : workflowJobsResults) {
+ if (jobResult.getVisible()) {
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Visible result are: " + jobResult.getId());
+
+ String result = getWorkflowResultBody(experimentDAO, jobResult.getId());
+
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "ResultDTO: " + result);
+ if (result == null) {
+ experimentDAO.setStatus(ExperimentDAO.Status.error);
+ } else {
+ experimentDAO.setResult(result);
+ experimentDAO.setStatus(ExperimentDAO.Status.success);
+ resultFound = true;
+ }
+ }
+ }
+
+ if (!resultFound) { // If there is no visible result
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "No visible result");
+ experimentDAO.setStatus(ExperimentDAO.Status.error);
+ }
+
+ finishExperiment(experimentDAO, logger);
+ break;
+
+ case "error":
+ // Get the job result that failed
+ workflowJobsResults = getWorkflowResults(experimentDAO);
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Error results are: " + workflowJobsResults.toString());
+
+ boolean failedJobFound = false;
+ for (GalaxyWorkflowResult jobResult : workflowJobsResults) {
+ if (jobResult.getState().equals("error")) {
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Failed job is: " + jobResult.getId());
+
+ String result = getWorkflowJobError(jobResult.getId(), experimentDAO);
+
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "Job result: " + result);
+ if (result == null) {
+ experimentDAO.setStatus(ExperimentDAO.Status.error);
+ }
+ experimentDAO.setStatus(ExperimentDAO.Status.error);
+ failedJobFound = true;
+ }
+ }
+
+ if (!failedJobFound) { // If there is no visible failed job
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "No failed result");
+ experimentDAO.setStatus(ExperimentDAO.Status.error);
+ }
+ finishExperiment(experimentDAO, logger);
+ break;
+
+ default: // InternalError or unexpected result
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "An unexpected error occurred.");
+ experimentDAO.setStatus(ExperimentDAO.Status.error);
+ finishExperiment(experimentDAO, logger);
+ break;
+ }
+
+ // If result exists return
+ if (experimentDAO.getResult() != null) {
+ Logger.LogExperimentAction(experimentDAO.getName(), experimentDAO.getUuid(), "ResultDTO exists: " + experimentDAO.getResult());
+ return;
+ }
+ }
+ }).start();
+ }
+
+
+ /**
+ * @param experimentDAO The experiment of the workflow
+ * @return "pending" -> When the workflow is still running
+ * "internalError" -> When an exception or a bad request occurred
+ * "error" -> When the workflow produced an error
+ * "success" -> When the workflow completed successfully
+ */
+ public String getWorkflowStatus(ExperimentDAO experimentDAO) {
+ String historyId = experimentDAO.getWorkflowHistoryId();
+ String experimentName = experimentDAO.getName();
+ UUID experimentId = experimentDAO.getUuid();
+
+ // ATTENTION: This function is used from a Thread. Only LogExperimentAction should be used, not LogUserAction!
+ Logger.LogExperimentAction(experimentName, experimentId, " History Id : " + historyId);
+
+ // Create the request client
+ RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+ Call<Object> call = service.getWorkflowStatusFromGalaxy(historyId, galaxyApiKey);
+
+ String result;
+ try {
+ Response<Object> response = call.execute();
+ if (response.code() >= 400) {
+ Logger.LogExperimentAction(experimentName, experimentId, " Response code: "
+ + response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
+ return "internalError";
+ }
+ result = new Gson().toJson(response.body());
+ Logger.LogExperimentAction(experimentName, experimentId, " ResultDTO: " + result);
+
+ } catch (IOException e) {
+ Logger.LogExperimentAction(experimentName, experimentId, " An exception happened: " + e.getMessage());
+ return "internalError";
+ }
+
+ String state;
+ try {
+ JSONObject resultJson = new JSONObject(result);
+ state = resultJson.getString("state");
+ } catch (JSONException e) {
+ Logger.LogExperimentAction(experimentName, experimentId, " An exception happened: " + e.getMessage());
+ return "internalError";
+ }
+
+ Logger.LogExperimentAction(experimentName, experimentId, " Completed!");
+ switch (state) {
+ case "ok":
+ return "success";
+ case "error":
+ return "error";
+ case "pending":
+ case "new":
+ case "waiting":
+ case "queued":
+ return "pending";
+ default:
+ return "internalError";
+ }
+ }
+
+ /**
+ * @param experimentDAO The experiment of the workflow
+ * @return a List<GalaxyWorkflowResult> or null when an error occurred
+ */
+ public List<GalaxyWorkflowResult> getWorkflowResults(ExperimentDAO experimentDAO) {
+
+ String historyId = experimentDAO.getWorkflowHistoryId();
+ String experimentName = experimentDAO.getName();
+ UUID experimentId = experimentDAO.getUuid();
+ Logger.LogExperimentAction(experimentName, experimentId, " historyId : " + historyId);
+
+ RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+ Call<List<GalaxyWorkflowResult>> call = service.getWorkflowResultsFromGalaxy(historyId, galaxyApiKey);
+
+ List<GalaxyWorkflowResult> getGalaxyWorkflowResultList;
+ try {
+ Response<List<GalaxyWorkflowResult>> response = call.execute();
+ if (response.code() >= 400) {
+ Logger.LogExperimentAction(experimentName, experimentId, " Response code: "
+ + response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
+ return null;
+ }
+ getGalaxyWorkflowResultList = response.body();
+ Logger.LogExperimentAction(experimentName, experimentId, " ResultDTO: " + response.body());
+
+ } catch (IOException e) {
+ Logger.LogExperimentAction(experimentName, experimentId, " An exception happened: " + e.getMessage());
+ return null;
+ }
+
+ Logger.LogExperimentAction(experimentName, experimentId, " Completed!");
+ return getGalaxyWorkflowResultList;
+
+ }
+
+ /**
+ * @param experimentDAO The experiment of the workflow
+ * @param contentId the id of the job result that we want
+ * @return the result of the specific workflow job, null if there was an error
+ */
+ public String getWorkflowResultBody(ExperimentDAO experimentDAO, String contentId) {
+
+ String historyId = experimentDAO.getWorkflowHistoryId();
+ String experimentName = experimentDAO.getName();
+ UUID experimentId = experimentDAO.getUuid();
+
+ Logger.LogExperimentAction(experimentName, experimentId, " historyId : " + historyId);
+
+ RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+ Call<Object> call =
+ service.getWorkflowResultsBodyFromGalaxy(historyId, contentId, galaxyApiKey);
+
+ String resultJson;
+ try {
+ Response<Object> response = call.execute();
+ if (response.code() >= 400) {
+ Logger.LogExperimentAction(experimentName, experimentId, " Response code: "
+ + response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
+ return null;
+ }
+ resultJson = new Gson().toJson(response.body());
+ Logger.LogExperimentAction(experimentName, experimentId, " ResultDTO: " + resultJson);
+
+ } catch (IOException e) {
+ Logger.LogExperimentAction(experimentName, experimentId,
+ " An exception happened: " + e.getMessage());
+ return null;
+ }
+
+ Logger.LogExperimentAction(experimentName, experimentId, " Completed!");
+ return formattingGalaxyResult(resultJson);
+ }
+
+
+ /**
+ * @param jobId the id of the workflow job that failed
+ * @return the error that was produced or null if an error occurred
+ */
+ public String getWorkflowJobError(String jobId, ExperimentDAO experimentDAO) {
+ String experimentName = experimentDAO.getName();
+ UUID experimentId = experimentDAO.getUuid();
+
+ Logger.LogExperimentAction(experimentName, experimentId, " jobId : " + jobId);
+ RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+ Call<Object> callError = service.getErrorMessageOfWorkflowFromGalaxy(jobId, galaxyApiKey);
+
+ String fullError;
+ String returnError;
+ try {
+ Response<Object> response = callError.execute();
+ if (response.code() >= 400) {
+ Logger.LogExperimentAction(experimentName, experimentId, "Response code: "
+ + response.code() + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
+ return null;
+ }
+
+ // Parsing the stderr of the job that failed
+ String jsonString = new Gson().toJson(response.body());
+ JsonElement jsonElement = new JsonParser().parse(jsonString);
+ JsonObject rootObject = jsonElement.getAsJsonObject();
+ fullError = rootObject.get("stderr").getAsString();
+ Logger.LogExperimentAction(experimentName, experimentId, "Error: " + fullError);
+
+ String[] arrOfStr = fullError.split("ValueError", 0);
+ String specError = arrOfStr[arrOfStr.length - 1];
+ returnError = specError.substring(1);
+ Logger.LogExperimentAction(experimentName, experimentId, "Parsed Error: " + returnError);
+
+ } catch (IOException e) {
+ Logger.LogExperimentAction(experimentName, experimentId, "Exception: " + e.getMessage());
+ return null;
+ }
+
+ Logger.LogExperimentAction(experimentName, experimentId, "Completed successfully!");
+
+ return returnError;
+ }
+
+ static class ExaremeResult {
+ private final int code;
+ private final List<Object> results;
+
+ public ExaremeResult(int code, List<Object> results) {
+ this.code = code;
+ this.results = results;
+ }
+
+ public int getCode() {
+ return code;
+ }
+
+ public List<Object> getResults() {
+ return results;
+ }
+ }
+}
diff --git a/src/main/java/eu/hbp/mip/services/Specifications/ExperimentSpecifications.java b/src/main/java/eu/hbp/mip/services/Specifications/ExperimentSpecifications.java
new file mode 100644
index 0000000000000000000000000000000000000000..c1e6a13acae08d9ac2c516884773b5bf9b4c71b2
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/services/Specifications/ExperimentSpecifications.java
@@ -0,0 +1,158 @@
+package eu.hbp.mip.services.Specifications;
+
+import eu.hbp.mip.models.DAOs.ExperimentDAO;
+import eu.hbp.mip.models.DAOs.UserDAO;
+import eu.hbp.mip.utils.Exceptions.BadRequestException;
+import org.springframework.data.jpa.domain.Specification;
+
+import javax.persistence.criteria.*;
+import java.util.ArrayList;
+import java.util.List;
+
+public class ExperimentSpecifications {
+ public static class ExperimentWithName implements Specification<ExperimentDAO> {
+
+ private String name;
+ private String regExp;
+
+ public ExperimentWithName(String name) {
+ this.name = name;
+ this.regExp = name;
+ }
+
+ public Predicate toPredicate(Root<ExperimentDAO> root, CriteriaQuery<?> criteriaQuery, CriteriaBuilder cb) {
+ if (name == null) {
+ return cb.isTrue(cb.literal(true));
+ } else {
+ regExp = (name.contains("%") ? name : name + "%");
+ }
+
+ return cb.like(cb.lower(root.get("name")), this.regExp.toLowerCase());
+ }
+ }
+
+ public static class ExperimentWithAlgorithm implements Specification<ExperimentDAO> {
+
+ private String algorithm;
+
+ public ExperimentWithAlgorithm(String algorithm) {
+ this.algorithm = algorithm;
+ }
+
+ public Predicate toPredicate(Root<ExperimentDAO> root, CriteriaQuery<?> criteriaQuery, CriteriaBuilder cb) {
+ if (algorithm == null) {
+ return cb.isTrue(cb.literal(true));
+ }
+
+ return cb.equal(cb.lower(root.get("algorithm")), this.algorithm.toLowerCase());
+ }
+ }
+
+ public static class ExperimentWithViewed implements Specification<ExperimentDAO> {
+
+ private Boolean viewed;
+
+ public ExperimentWithViewed(Boolean viewed) {
+ this.viewed = viewed;
+ }
+
+ public Predicate toPredicate(Root<ExperimentDAO> root, CriteriaQuery<?> query, CriteriaBuilder cb) {
+ if (viewed == null) {
+ return cb.isTrue(cb.literal(true)); // always true = no filtering
+ }
+ return cb.equal(root.get("viewed"), this.viewed);
+ }
+ }
+
+ public static class ExperimentWithShared implements Specification<ExperimentDAO> {
+
+ private Boolean shared;
+
+ public ExperimentWithShared(Boolean shared) {
+ this.shared = shared;
+ }
+
+ public Predicate toPredicate(Root<ExperimentDAO> root, CriteriaQuery<?> criteriaQuery, CriteriaBuilder cb) {
+ if (shared == null) {
+ return cb.isTrue(cb.literal(true));
+ }
+ return cb.equal(root.get("shared"), this.shared);
+ }
+ }
+
+ public static class MyExperiment implements Specification<ExperimentDAO> {
+
+ private String username;
+
+ public MyExperiment(String username) {
+ this.username = username;
+ }
+
+ public Predicate toPredicate(Root<ExperimentDAO> root, CriteriaQuery<?> criteriaQuery, CriteriaBuilder cb) {
+ if (username == null) {
+ return cb.isTrue(cb.literal(true));
+ }
+ Join<ExperimentDAO, UserDAO> experimentDAOUserDAOJoin = root.join("createdBy");
+ return cb.equal(experimentDAOUserDAOJoin.get("username"), username);
+ }
+ }
+
+ public static class SharedExperiment implements Specification<ExperimentDAO> {
+
+ private boolean shared;
+
+ public SharedExperiment(boolean shared) {
+ this.shared = shared;
+ }
+
+ public Predicate toPredicate(Root<ExperimentDAO> root, CriteriaQuery<?> criteriaQuery, CriteriaBuilder cb) {
+ if (shared == false) {
+ return cb.isTrue(cb.literal(false));
+ }
+ return cb.equal(root.get("shared"), shared);
+ }
+ }
+
+ public static class ExperimentOrderBy implements Specification<ExperimentDAO> {
+
+ private String orderBy;
+ private Boolean descending;
+
+ public ExperimentOrderBy(String orderBy, Boolean descending) {
+ if (properColumnToBeOrderedBy(orderBy))
+ this.orderBy = orderBy;
+ else
+ throw new BadRequestException("Please provide proper column to order by.");
+ if (descending == null)
+ this.descending = true;
+ else
+ this.descending = descending;
+ }
+
+ public Predicate toPredicate(Root<ExperimentDAO> root, CriteriaQuery<?> criteriaQuery, CriteriaBuilder cb) {
+ if (descending) {
+ criteriaQuery.orderBy(cb.desc(root.get(orderBy)));
+ } else {
+ criteriaQuery.orderBy(cb.asc(root.get(orderBy)));
+ }
+ return cb.isTrue(cb.literal(true));
+ }
+
+ }
+
+ public static boolean properColumnToBeOrderedBy(String column) {
+ {
+ List<String> properColumns = new ArrayList<>();
+ properColumns.add("uuid");
+ properColumns.add("name");
+ properColumns.add("created_by_username");
+ properColumns.add("algorithm");
+ properColumns.add("created");
+ properColumns.add("status");
+ properColumns.add("shared");
+ properColumns.add("viewed");
+ return properColumns.contains(column);
+ }
+ }
+}
+
diff --git a/src/main/java/eu/hbp/mip/utils/CORSFilter.java b/src/main/java/eu/hbp/mip/utils/CORSFilter.java
index 7ed1ecf38d84fedddb5acb4750db327fbb9e5079..7d77b9022ef0855f0f5d6decf84601d0a00f75b0 100644
--- a/src/main/java/eu/hbp/mip/utils/CORSFilter.java
+++ b/src/main/java/eu/hbp/mip/utils/CORSFilter.java
@@ -1,32 +1,25 @@
package eu.hbp.mip.utils;
+
import javax.servlet.*;
import javax.servlet.http.HttpServletResponse;
import java.io.IOException;
+
/**
- * Created by mirco on 12.02.16.
+ * CORS Filter used only for development.
+ *
+ * Allows requests from all possible origins.
*/
public class CORSFilter implements Filter {
-
@Override
public void doFilter(ServletRequest req, ServletResponse res, FilterChain chain) throws IOException, ServletException {
HttpServletResponse response = (HttpServletResponse) res;
response.setHeader("Access-Control-Allow-Origin", "*");
- response.setHeader("Access-Control-Allow-Methods", "POST, GET, OPTIONS, DELETE, PUT");
+ response.setHeader("Access-Control-Allow-Methods", "GET,POST,PATCH,DELETE");
response.setHeader("Access-Control-Max-Age", "3600");
response.setHeader("Access-Control-Allow-Headers", "*");
response.setHeader("Access-Control-Request-Headers", "*");
chain.doFilter(req, res);
}
-
- @Override
- public void init(FilterConfig filterConfig) {
- /* Nothing to do */
- }
-
- @Override
- public void destroy() {
- /* Nothing to do */
- }
-}
+}
\ No newline at end of file
diff --git a/src/main/java/eu/hbp/mip/utils/ClaimUtils.java b/src/main/java/eu/hbp/mip/utils/ClaimUtils.java
index e71d3f19083d03ae0067176b2fccfe4f06175915..f5676b52c130f0b4be1c79d939567f74b752c0db 100644
--- a/src/main/java/eu/hbp/mip/utils/ClaimUtils.java
+++ b/src/main/java/eu/hbp/mip/utils/ClaimUtils.java
@@ -1,13 +1,14 @@
package eu.hbp.mip.utils;
import com.google.gson.Gson;
-import eu.hbp.mip.model.PathologyDTO;
-import org.springframework.security.core.GrantedAuthority;
+import eu.hbp.mip.models.DTOs.PathologyDTO;
+import eu.hbp.mip.utils.Exceptions.InternalServerError;
+import eu.hbp.mip.utils.Exceptions.UnauthorizedException;
+import org.keycloak.KeycloakPrincipal;
+import org.keycloak.adapters.springsecurity.token.KeycloakAuthenticationToken;
+import org.springframework.security.core.Authentication;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.List;
+import java.util.*;
public class ClaimUtils {
@@ -15,68 +16,68 @@ public class ClaimUtils {
private static final Gson gson = new Gson();
public static String allDatasetsAllowedClaim() {
- return "dataset_all";
+ return "research_dataset_all";
+ }
+
+ public static String allExperimentsAllowedClaim() {
+ return "research_experiment_all";
}
public static String getDatasetClaim(String datasetCode) {
- return "dataset_" + datasetCode.toLowerCase();
+ return "research_dataset_" + datasetCode.toLowerCase();
}
- public static boolean userHasDatasetsAuthorization(String username, Collection<? extends GrantedAuthority> authorities,
- String experimentDatasets) {
+ public static void validateAccessRightsOnDatasets(Authentication authentication,
+ String experimentDatasets, Logger logger) {
- List<String> userClaims = Arrays.asList(authorities.toString().toLowerCase()
- .replaceAll("[\\s+\\]\\[]", "").split(","));
- Logging.LogUserAction(username, "(POST) /experiments/runAlgorithm", userClaims.toString());
+ ArrayList<String> authorities = getKeycloakAuthorities(authentication, logger);
// Don't check for dataset claims if "super" claim exists allowing everything
- if (!userClaims.contains(ClaimUtils.allDatasetsAllowedClaim())) {
+ if (!hasRoleAccess(authorities, ClaimUtils.allDatasetsAllowedClaim(), logger)) {
for (String dataset : experimentDatasets.split(",")) {
String datasetRole = ClaimUtils.getDatasetClaim(dataset);
- if (!userClaims.contains(datasetRole.toLowerCase())) {
- Logging.LogUserAction(username, "(POST) /experiments/runAlgorithm",
- "You are not allowed to use dataset: " + dataset);
- return false;
+ if (!hasRoleAccess(authorities, datasetRole, logger)) {
+ logger.LogUserAction("You are not allowed to use dataset: " + dataset);
+ throw new UnauthorizedException("You are not authorized to use these datasets.");
}
}
- Logging.LogUserAction(username, "(POST) /experiments/runAlgorithm",
- "User is authorized to use the datasets: " + experimentDatasets);
+ logger.LogUserAction("User is authorized to use the datasets: " + experimentDatasets);
}
- return true;
}
- public static String getAuthorizedPathologies(String username, Collection<? extends GrantedAuthority> authorities,
+ public static boolean validateAccessRightsOnExperiments(Authentication authentication, Logger logger) {
+
+ ArrayList<String> authorities = getKeycloakAuthorities(authentication, logger);
+
+ // Check for experiment_all claims
+ return hasRoleAccess(authorities, ClaimUtils.allExperimentsAllowedClaim(), logger);
+ }
+
+ public static String getAuthorizedPathologies(Logger logger, Authentication authentication,
List<PathologyDTO> allPathologies) {
// --- Providing only the allowed pathologies/datasets to the user ---
- Logging.LogUserAction(username,
- "(GET) /pathologies", "Filter out the unauthorised datasets.");
+ logger.LogUserAction("Filter out the unauthorised datasets.");
- List<String> userClaims = Arrays.asList(authorities.toString().toLowerCase()
- .replaceAll("[\\s+\\]\\[]", "").split(","));
-
- Logging.LogUserAction(username,
- "(GET) /pathologies", "User Claims: " + userClaims);
+ ArrayList<String> authorities = getKeycloakAuthorities(authentication, logger);
// If the "dataset_all" claim exists then return everything
- if (userClaims.contains(ClaimUtils.allDatasetsAllowedClaim())) {
+ if (hasRoleAccess(authorities, ClaimUtils.allDatasetsAllowedClaim(), logger)) {
return gson.toJson(allPathologies);
}
List<PathologyDTO> userPathologies = new ArrayList<>();
for (PathologyDTO curPathology : allPathologies) {
- List<PathologyDTO.PathologyDatasetDTO> userPathologyDatasets = new ArrayList<PathologyDTO.PathologyDatasetDTO>();
+ List<PathologyDTO.PathologyDatasetDTO> userPathologyDatasets = new ArrayList<>();
for (PathologyDTO.PathologyDatasetDTO dataset : curPathology.getDatasets()) {
- if (userClaims.contains(ClaimUtils.getDatasetClaim(dataset.getCode()))) {
- Logging.LogUserAction(username, "(GET) /pathologies",
- "Added dataset: " + dataset.getCode());
+ if (hasRoleAccess(authorities, ClaimUtils.getDatasetClaim(dataset.getCode()), logger)) {
+ logger.LogUserAction("Added dataset: " + dataset.getCode());
userPathologyDatasets.add(dataset);
}
}
if (userPathologyDatasets.size() > 0) {
- Logging.LogUserAction(username, "(GET) /pathologies",
- "Added pathology '" + curPathology.getLabel()
+ logger.LogUserAction("Added pathology '" + curPathology.getLabel()
+ "' with datasets: '" + userPathologyDatasets + "'");
PathologyDTO userPathology = new PathologyDTO();
@@ -91,4 +92,24 @@ public class ClaimUtils {
return gson.toJson(userPathologies);
}
+ private static boolean hasRoleAccess(ArrayList<String> authorities, String role, Logger logger)
+ {
+ List<String> userClaims = Arrays.asList(authorities.toString().toLowerCase()
+ .replaceAll("[\\s+\\]\\[]", "").split(","));
+
+ logger.LogUserAction("User Claims: " + userClaims);
+ return userClaims.contains(role.toLowerCase());
+ }
+
+ private static ArrayList<String> getKeycloakAuthorities(Authentication authentication, Logger logger){
+ KeycloakAuthenticationToken token = (KeycloakAuthenticationToken) authentication;
+ KeycloakPrincipal keycloakPrincipal = (KeycloakPrincipal) token.getPrincipal();
+ if(keycloakPrincipal.getKeycloakSecurityContext().getIdToken().getOtherClaims().get("authorities") == null)
+ {
+ logger.LogUserAction("Your user has no roles.");
+ throw new InternalServerError("Your user has no roles.");
+ }
+
+ return (ArrayList<String>)keycloakPrincipal.getKeycloakSecurityContext().getIdToken().getOtherClaims().get("authorities");
+ }
}
diff --git a/src/main/java/eu/hbp/mip/utils/ControllerExceptionHandler.java b/src/main/java/eu/hbp/mip/utils/ControllerExceptionHandler.java
new file mode 100644
index 0000000000000000000000000000000000000000..7f644fb7fec4eec89a653236da29be79e3a2f80c
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/utils/ControllerExceptionHandler.java
@@ -0,0 +1,89 @@
+package eu.hbp.mip.utils;
+
+import eu.hbp.mip.utils.Exceptions.*;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.ResponseEntity;
+import org.springframework.web.bind.annotation.ControllerAdvice;
+import org.springframework.web.bind.annotation.ExceptionHandler;
+import org.springframework.web.context.request.WebRequest;
+import org.springframework.web.servlet.mvc.method.annotation.ResponseEntityExceptionHandler;
+
+import java.util.Date;
+
+@ControllerAdvice
+public class ControllerExceptionHandler extends ResponseEntityExceptionHandler {
+
+ @ExceptionHandler(ExperimentNotFoundException.class)
+ public ResponseEntity<Object> handleExperimentNotFoundException(ExperimentNotFoundException ex, WebRequest request) {
+
+ ErrorMessage message = new ErrorMessage(
+ HttpStatus.NOT_FOUND.value(),
+ new Date(),
+ ex.getMessage(),
+ request.getDescription(false));
+
+ return new ResponseEntity<>(message, HttpStatus.NOT_FOUND);
+ }
+
+ @ExceptionHandler(BadRequestException.class)
+ public ResponseEntity<Object> handleBadRequestException(BadRequestException ex, WebRequest request) {
+
+ ErrorMessage message = new ErrorMessage(
+ HttpStatus.BAD_REQUEST.value(),
+ new Date(),
+ ex.getMessage(),
+ request.getDescription(false));
+
+ return new ResponseEntity<>(message, HttpStatus.BAD_REQUEST);
+ }
+
+ @ExceptionHandler(UnauthorizedException.class)
+ public ResponseEntity<Object> handleUnauthorizedException(UnauthorizedException ex, WebRequest request) {
+
+ ErrorMessage message = new ErrorMessage(
+ HttpStatus.UNAUTHORIZED.value(),
+ new Date(),
+ ex.getMessage(),
+ request.getDescription(false));
+
+ return new ResponseEntity<>(message, HttpStatus.UNAUTHORIZED);
+ }
+
+ @ExceptionHandler(IllegalArgumentException.class)
+ public Object handleIllegalArgumentException(IllegalArgumentException ex, WebRequest request) {
+ return null;
+ }
+
+ @ExceptionHandler(InternalServerError.class)
+ public ResponseEntity<ErrorMessage> handleInternalServerError(InternalServerError er, WebRequest request) {
+ ErrorMessage message = new ErrorMessage(
+ HttpStatus.INTERNAL_SERVER_ERROR.value(),
+ new Date(),
+ er.getMessage(),
+ request.getDescription(false));
+
+ return new ResponseEntity<>(message, HttpStatus.INTERNAL_SERVER_ERROR);
+ }
+
+ @ExceptionHandler(NoContent.class)
+ public ResponseEntity<ErrorMessage> handleNoContent(NoContent nc, WebRequest request) {
+ ErrorMessage message = new ErrorMessage(
+ HttpStatus.NO_CONTENT.value(),
+ new Date(),
+ nc.getMessage(),
+ request.getDescription(false));
+
+ return new ResponseEntity<>(message, HttpStatus.NO_CONTENT);
+ }
+
+ @ExceptionHandler(Exception.class)
+ public ResponseEntity<ErrorMessage> globalExceptionHandler(Exception ex, WebRequest request) {
+ ErrorMessage message = new ErrorMessage(
+ HttpStatus.INTERNAL_SERVER_ERROR.value(),
+ new Date(),
+ ex.getMessage(),
+ request.getDescription(false));
+
+ return new ResponseEntity<>(message, HttpStatus.INTERNAL_SERVER_ERROR);
+ }
+}
diff --git a/src/main/java/eu/hbp/mip/utils/CustomAccessDeniedHandler.java b/src/main/java/eu/hbp/mip/utils/CustomAccessDeniedHandler.java
deleted file mode 100644
index 783e4a3ff68ab3384a798d9fc70f68f29c114bd6..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/utils/CustomAccessDeniedHandler.java
+++ /dev/null
@@ -1,33 +0,0 @@
-package eu.hbp.mip.utils;
-
-import org.codehaus.jettison.json.JSONException;
-import org.codehaus.jettison.json.JSONObject;
-import org.springframework.security.access.AccessDeniedException;
-import org.springframework.security.web.access.AccessDeniedHandler;
-
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-import java.io.IOException;
-import java.sql.Timestamp;
-
-public class CustomAccessDeniedHandler implements AccessDeniedHandler {
- @Override
- public void handle(HttpServletRequest request, HttpServletResponse response,
- AccessDeniedException accessDeniedException) throws IOException, ServletException {
- response.setContentType("application/json;charset=UTF-8");
- response.setStatus(403);
- try {
- response.getWriter().write(new JSONObject()
- .put("timestamp", new Timestamp(System.currentTimeMillis()))
- .put("status", 403)
- .put("error", "Forbidden")
- .put("message", "Access Denied. Please contact the system administrator to request access.")
- .put("path", request.getServletPath())
- .toString());
- } catch (JSONException e) {
- response.getWriter().write("");
- e.printStackTrace();
- }
- }
-}
diff --git a/src/main/java/eu/hbp/mip/utils/CustomLoginUrlAuthenticationEntryPoint.java b/src/main/java/eu/hbp/mip/utils/CustomLoginUrlAuthenticationEntryPoint.java
deleted file mode 100644
index 45870c7778280ff60c8ccca2908105ee677a6f7a..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/utils/CustomLoginUrlAuthenticationEntryPoint.java
+++ /dev/null
@@ -1,21 +0,0 @@
-package eu.hbp.mip.utils;
-
-import org.springframework.security.core.AuthenticationException;
-import org.springframework.security.web.authentication.LoginUrlAuthenticationEntryPoint;
-
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-import java.io.IOException;
-
-public class CustomLoginUrlAuthenticationEntryPoint extends LoginUrlAuthenticationEntryPoint {
-
- public CustomLoginUrlAuthenticationEntryPoint(String url) {
- super(url);
- }
-
- @Override
- public void commence(HttpServletRequest request, HttpServletResponse response, AuthenticationException authException) throws IOException, ServletException {
- response.sendError(HttpServletResponse.SC_UNAUTHORIZED);
- }
-}
diff --git a/src/main/java/eu/hbp/mip/utils/ErrorMessage.java b/src/main/java/eu/hbp/mip/utils/ErrorMessage.java
new file mode 100644
index 0000000000000000000000000000000000000000..ef15c71ae041b277e51c487afb03d17d11556aa8
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/utils/ErrorMessage.java
@@ -0,0 +1,34 @@
+package eu.hbp.mip.utils;
+
+
+import java.util.Date;
+
+public class ErrorMessage {
+ private int statusCode;
+ private Date timestamp;
+ private String message;
+ private String description;
+
+ public ErrorMessage(int statusCode, Date timestamp, String message, String description) {
+ this.statusCode = statusCode;
+ this.timestamp = timestamp;
+ this.message = message;
+ this.description = description;
+ }
+
+ public int getStatusCode() {
+ return statusCode;
+ }
+
+ public Date getTimestamp() {
+ return timestamp;
+ }
+
+ public String getMessage() {
+ return message;
+ }
+
+ public String getDescription() {
+ return description;
+ }
+}
diff --git a/src/main/java/eu/hbp/mip/utils/ErrorMessages.java b/src/main/java/eu/hbp/mip/utils/ErrorMessages.java
deleted file mode 100644
index 9f672f81b8bb57c559015a52bc65e44a0da7bd72..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/utils/ErrorMessages.java
+++ /dev/null
@@ -1,7 +0,0 @@
-package eu.hbp.mip.utils;
-
-public class ErrorMessages {
-
- public static String pathologiesCouldNotBeLoaded = "The pathologies could not be loaded.";
- public static String disabledAlgorithmsCouldNotBeLoaded = "The disabled algorithms could not be loaded.";
-}
diff --git a/src/main/java/eu/hbp/mip/utils/Exceptions/BadRequestException.java b/src/main/java/eu/hbp/mip/utils/Exceptions/BadRequestException.java
new file mode 100644
index 0000000000000000000000000000000000000000..6684cae281a0487aa5d39e78693b6c9f5bd04098
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/utils/Exceptions/BadRequestException.java
@@ -0,0 +1,8 @@
+package eu.hbp.mip.utils.Exceptions;
+
+public class BadRequestException extends RuntimeException {
+
+ public BadRequestException(String msg) {
+ super(msg);
+ }
+}
\ No newline at end of file
diff --git a/src/main/java/eu/hbp/mip/utils/Exceptions/ExperimentNotFoundException.java b/src/main/java/eu/hbp/mip/utils/Exceptions/ExperimentNotFoundException.java
new file mode 100644
index 0000000000000000000000000000000000000000..b8e05d7e667769537de9d540f436902dca6edc4e
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/utils/Exceptions/ExperimentNotFoundException.java
@@ -0,0 +1,8 @@
+package eu.hbp.mip.utils.Exceptions;
+
+public class ExperimentNotFoundException extends RuntimeException {
+
+ public ExperimentNotFoundException(String msg) {
+ super(msg);
+ }
+}
\ No newline at end of file
diff --git a/src/main/java/eu/hbp/mip/utils/Exceptions/InternalServerError.java b/src/main/java/eu/hbp/mip/utils/Exceptions/InternalServerError.java
new file mode 100644
index 0000000000000000000000000000000000000000..19bc88eed27b6e0e4ab36a05136f043be65725ec
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/utils/Exceptions/InternalServerError.java
@@ -0,0 +1,8 @@
+package eu.hbp.mip.utils.Exceptions;
+
+public class InternalServerError extends RuntimeException {
+
+ public InternalServerError(String msg) {
+ super(msg);
+ }
+}
\ No newline at end of file
diff --git a/src/main/java/eu/hbp/mip/utils/Exceptions/NoContent.java b/src/main/java/eu/hbp/mip/utils/Exceptions/NoContent.java
new file mode 100644
index 0000000000000000000000000000000000000000..9bb67d8114e71545b8a00a8eb0bcdb0f7285b714
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/utils/Exceptions/NoContent.java
@@ -0,0 +1,8 @@
+package eu.hbp.mip.utils.Exceptions;
+
+public class NoContent extends RuntimeException {
+
+ public NoContent(String msg) {
+ super(msg);
+ }
+}
\ No newline at end of file
diff --git a/src/main/java/eu/hbp/mip/utils/Exceptions/UnauthorizedException.java b/src/main/java/eu/hbp/mip/utils/Exceptions/UnauthorizedException.java
new file mode 100644
index 0000000000000000000000000000000000000000..379911daeabe7227497f3d5bb622e54f6ccffb87
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/utils/Exceptions/UnauthorizedException.java
@@ -0,0 +1,8 @@
+package eu.hbp.mip.utils.Exceptions;
+
+public class UnauthorizedException extends RuntimeException {
+
+ public UnauthorizedException(String msg) {
+ super(msg);
+ }
+}
\ No newline at end of file
diff --git a/src/main/java/eu/hbp/mip/utils/JsonConverters.java b/src/main/java/eu/hbp/mip/utils/JsonConverters.java
new file mode 100644
index 0000000000000000000000000000000000000000..74d01b851f44877fffe0e146d8f678ee3fb95dfb
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/utils/JsonConverters.java
@@ -0,0 +1,27 @@
+package eu.hbp.mip.utils;
+
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.gson.Gson;
+
+import java.lang.reflect.Type;
+
+public class JsonConverters {
+ private static final Gson gson = new Gson();
+
+ public static String convertObjectToJsonString(Object object) {
+ ObjectMapper mapper = new ObjectMapper();
+ //Converting the Object to JSONString
+ try {
+ return mapper.writeValueAsString(object);
+ } catch (JsonProcessingException e) {
+ return e.getMessage();
+ }
+ }
+
+ public static <T> T convertJsonStringToObject(String jsonString, Type typeOfT) {
+ if(jsonString == null || jsonString.isEmpty())
+ return null;
+ return gson.fromJson(jsonString, typeOfT);
+ }
+}
diff --git a/src/main/java/eu/hbp/mip/utils/Logging.java b/src/main/java/eu/hbp/mip/utils/Logger.java
similarity index 53%
rename from src/main/java/eu/hbp/mip/utils/Logging.java
rename to src/main/java/eu/hbp/mip/utils/Logger.java
index 9b75de636fc7c1721fca6dba59e2ce38cced1a7d..1e25d2c921f0338235bed01c2f2fcd55ab4cf94a 100644
--- a/src/main/java/eu/hbp/mip/utils/Logging.java
+++ b/src/main/java/eu/hbp/mip/utils/Logger.java
@@ -1,16 +1,23 @@
package eu.hbp.mip.utils;
-import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.UUID;
-public class Logging {
- private static final Logger LOGGER = LoggerFactory.getLogger(Logging.class);
+public class Logger {
- public static void LogUserAction(String userName, String endpoint, String actionInfo) {
- LOGGER.info(" User -> " + userName + " ,"
+ private static final org.slf4j.Logger LOGGER = LoggerFactory.getLogger(Logger.class);
+ private String username;
+ private String endpoint;
+
+ public Logger(String username, String endpoint){
+ this.username = username;
+ this.endpoint = endpoint;
+ }
+
+ public void LogUserAction(String actionInfo) {
+ LOGGER.info(" User -> " + username + " ,"
+ "Endpoint -> " + endpoint + " ,"
+ "Info -> " + actionInfo);
}
diff --git a/src/main/resources/application.conf b/src/main/resources/application.conf
deleted file mode 100644
index e2abfd5ae7f2a4e0e3ceb4abc888cdb065dbc79f..0000000000000000000000000000000000000000
--- a/src/main/resources/application.conf
+++ /dev/null
@@ -1,20 +0,0 @@
-app {
- # Name of the application
- name = "Portal backend"
- # Type of the application
- type = "Spring"
- clusterSystemName = ${clustering.cluster.name}
-}
-
-clustering {
- ip = "127.0.0.1"
- ip = ${?CLUSTER_IP}
- port = 4489
- port = ${?CLUSTER_PORT}
-}
-
-akka {
- cluster {
- roles = ["portal"]
- }
-}
diff --git a/src/main/resources/application.yml b/src/main/resources/application.yml
new file mode 100644
index 0000000000000000000000000000000000000000..345fc4bfa1955560e8cc33b2fb7cf62bb3698f12
--- /dev/null
+++ b/src/main/resources/application.yml
@@ -0,0 +1,81 @@
+# Configuration for development purposes
+
+### LOG LEVELS ###
+logging:
+ level:
+ root: "ERROR"
+ org: "ERROR"
+ eu:
+ hbp: "DEBUG"
+
+
+### AUTHENTICATION ###
+authentication:
+ enabled: false
+
+
+### DATABASE CONFIGURATION ###
+spring:
+ portal-datasource:
+ url: "jdbc:postgresql://127.0.0.1:5433/portal"
+ schema: "public"
+ username: "portal"
+ password: "portalpwd"
+ driver-class-name: org.postgresql.Driver
+ data:
+ jpa:
+ repositories:
+ bootstrap-mode: default
+ jpa:
+ hibernate:
+ dialect: org.hibernate.dialect.PostgreSQL9Dialect
+ ddl-auto: validate
+
+
+### EXTERNAL SERVICES ###
+services:
+ exareme:
+ queryExaremeUrl: "http://127.0.0.1:9090/mining/query"
+ algorithmsUrl: "http://127.0.0.1:9090/mining/algorithms.json"
+ galaxy:
+ galaxyUrl: "http://127.0.0.1:8090"
+ galaxyContext: "nativeGalaxy/workflows/list"
+ galaxyApiKey: "d14a4cc5eebf805eb2ff261374ed08a2"
+ galaxyUsername: "admin"
+ galaxyPassword: "password"
+
+
+### KEYCLOAK ###
+keycloak:
+ enabled: true
+ auth-server-url: "https://iam.humanbrainproject.eu/auth"
+ realm: "MIP"
+ resource: "mipfedqa"
+ enable-basic-auth: true
+ credentials:
+ secret: "dae83a6b-c769-4186-8383-f0984c6edf05"
+ principal-attribute: "preferred_username"
+
+
+### EXTERNAL FILES ###
+# Files are loaded from the resources
+files:
+ pathologies_json: "classPath:/pathologies.json"
+ disabledAlgorithms_json: "classPath:/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
diff --git a/src/main/resources/db/migration/V7_0__NewDatabaseStructure.sql b/src/main/resources/db/migration/V7_0__NewDatabaseStructure.sql
new file mode 100644
index 0000000000000000000000000000000000000000..c1732c9e94860337218e6af917b1b523980a3d63
--- /dev/null
+++ b/src/main/resources/db/migration/V7_0__NewDatabaseStructure.sql
@@ -0,0 +1,84 @@
+UPDATE experiment
+SET algorithms =
+ (
+ SELECT SUBSTR(algorithms, 2, LENGTH(algorithms) - 2)
+ );
+
+UPDATE experiment
+SET workflowstatus = 'error'
+WHERE workflowstatus IS NULL AND haserror;
+
+UPDATE experiment
+SET workflowstatus = 'success'
+WHERE workflowstatus IS NULL AND NOT haserror;
+
+UPDATE experiment
+SET workflowstatus = 'success'
+WHERE workflowstatus = 'completed';
+
+UPDATE experiment
+SET workflowstatus = 'pending'
+WHERE workflowstatus = 'running';
+
+ALTER TABLE experiment
+DROP COLUMN haserror,
+DROP COLUMN hasservererror,
+DROP COLUMN validations,
+DROP COLUMN model_slug;
+
+ALTER TABLE experiment
+RENAME algorithms TO algorithm;
+ALTER TABLE experiment
+ALTER COLUMN algorithm TYPE json USING algorithm::json;
+ALTER TABLE experiment
+RENAME createdby_username TO created_by_username;
+ALTER TABLE experiment
+RENAME workflowhistoryid TO workflow_history_id;
+ALTER TABLE experiment
+RENAME resultsviewed TO viewed;
+ALTER TABLE experiment
+RENAME workflowstatus TO status;
+
+ALTER TABLE experiment
+ADD COLUMN algorithmId text;
+
+UPDATE experiment
+SET algorithmId = (algorithm ->> 'name');
+
+ALTER TABLE experiment
+ALTER COLUMN algorithm TYPE text;
+ALTER TABLE experiment
+ADD COLUMN updated timestamp without time zone;
+
+ALTER TABLE "user"
+DROP COLUMN birthday,
+DROP COLUMN city,
+DROP COLUMN country,
+DROP COLUMN firstname,
+DROP COLUMN gender,
+DROP COLUMN isactive,
+DROP COLUMN lastname,
+DROP COLUMN password,
+DROP COLUMN phone,
+DROP COLUMN picture,
+DROP COLUMN team,
+DROP COLUMN web,
+DROP COLUMN apikey;
+
+ALTER TABLE "user"
+ADD COLUMN subjectID text;
+
+DROP TABLE "config_title", "config_yaxisvariables";
+DROP TABLE "dataset_variable", "dataset_grouping", "dataset_data", "dataset_header";
+DROP TABLE "query_variable", "query_grouping", "query_filter", "query_covariable";
+DROP TABLE "article_tag", "tag","article";
+DROP TABLE "variable_value";
+DROP TABLE "query_training_datasets", "query_validation_datasets", "query_testing_datasets";
+DROP TABLE "variable", "value";
+DROP TABLE "group_group", "group";
+DROP TABLE "model";
+DROP TABLE "query";
+DROP TABLE "dataset";
+DROP TABLE "config";
+DROP TABLE "vote", "app";
+DROP TABLE "user_roles", "user_languages";
diff --git a/src/main/resources/kamon.conf b/src/main/resources/kamon.conf
deleted file mode 100644
index face394cba2325ea855db49c88219256c610a333..0000000000000000000000000000000000000000
--- a/src/main/resources/kamon.conf
+++ /dev/null
@@ -1,75 +0,0 @@
-kamon {
- enabled = no
- enabled = ${?KAMON_ENABLED}
-
- environment {
- service = "portal-backend"
- service = ${?KAMON_SERVICE_NAME}
- }
-
- zipkin = {
- enabled = no
- enabled = ${?ZIPKIN_ENABLED}
- host = "zipkin"
- host = ${?ZIPKIN_IP}
- port = 9411
- port = ${?ZIPKIN_PORT}
- }
-
- prometheus = {
- enabled = no
- enabled = ${?PROMETHEUS_ENABLED}
- host = "prometheus"
- host = ${?PROMETHEUS_IP}
- port = 9090
- port = ${?PROMETHEUS_PORT}
- }
-
- util.filters {
- "akka.tracked-actor" {
- includes = ["**"]
- }
-
- "akka.tracked-dispatcher" {
- includes = ["**"]
- }
-
- "akka.traced-actor" {
- includes = ["**"]
- excludes = [
- ${clustering.cluster.name}"/system/IO**",
- ${clustering.cluster.name}"/user/Stream**",
- ${clustering.cluster.name}"/system/transports**",
- ${clustering.cluster.name}"/system/cluster**",
- ${clustering.cluster.name}"/system/remote**",
- ${clustering.cluster.name}"/system/endpointmanager/**",
- ${clustering.cluster.name}"/system/sharding/UserActor/**"]
- }
-
- }
-
- akka-http {
- add-http-status-code-as-metric-tag = true
- }
-
- akka {
- ask-pattern-timeout-warning = lightweight
- }
-
- trace {
- join-remote-parents-with-same-span-id = yes
- sampler = "always"
- }
-
- system-metrics {
- host {
- enabled = no
- enabled = ${?SIGAR_SYSTEM_METRICS}
- }
- jvm {
- enabled = no
- enabled = ${?JVM_SYSTEM_METRICS}
- }
- }
-
-}