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  • hbp-mip/portal-backend
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Dockerfile
View file @ 7a3dc737
####################################################### #######################################################
# Build the spring boot maven project # Build the spring boot maven project
####################################################### #######################################################
FROM maven:3.8.5-openjdk-11 as mvn-build-env FROM maven:3.9.3-amazoncorretto-17 as mvn-build-env
MAINTAINER Thanasis Karampatsis <tkarabatsis@athenarc.gr>
ENV CODE_PATH="/opt/code" ENV CODE_PATH="/opt/code"
WORKDIR $CODE_PATH WORKDIR $CODE_PATH
...@@ -17,8 +18,7 @@ RUN mvn clean package ...@@ -17,8 +18,7 @@ RUN mvn clean package
####################################################### #######################################################
# Setup the running container # Setup the running container
####################################################### #######################################################
FROM openjdk:11.0.15-jdk FROM amazoncorretto:17.0.8-alpine3.18
MAINTAINER Thanasis Karampatsis <tkarabatsis@athenarc.gr>
####################################################### #######################################################
# Setting up timezone # Setting up timezone
...@@ -27,7 +27,7 @@ ENV TZ=Etc/GMT ...@@ -27,7 +27,7 @@ ENV TZ=Etc/GMT
RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
####################################################### #######################################################
# Setting up env variables and workdir # Setting up environment
####################################################### #######################################################
ENV APP_CONFIG_TEMPLATE="/opt/config/application.tmpl" ENV APP_CONFIG_TEMPLATE="/opt/config/application.tmpl"
ENV APP_CONFIG_LOCATION="/opt/config/application.yml" ENV APP_CONFIG_LOCATION="/opt/config/application.yml"
...@@ -35,6 +35,7 @@ ENV SPRING_CONFIG_LOCATION="file:/opt/config/application.yml" ...@@ -35,6 +35,7 @@ ENV SPRING_CONFIG_LOCATION="file:/opt/config/application.yml"
WORKDIR /opt WORKDIR /opt
RUN apk add --no-cache curl
####################################################### #######################################################
# Install dockerize # Install dockerize
......
README.md
View file @ 7a3dc737
...@@ -7,7 +7,7 @@ ...@@ -7,7 +7,7 @@
To run the backend using an IDE for development, such as IntelliJ, you need a running instance of PostgreSQL. To run the backend using an IDE for development, such as IntelliJ, you need a running instance of PostgreSQL.
## Deployment (using a Docker image) ## Deployment (using a Docker image)
Build the image: ` docker build -t hbpmip/portal-backend:latest .` Build the image: `docker build -t hbpmip/portal-backend:testing .`
To use this image, you need a running instance of PostgreSQL and to configure the software using the following environment variables. To use this image, you need a running instance of PostgreSQL and to configure the software using the following environment variables.
...@@ -27,10 +27,6 @@ To use this image, you need a running instance of PostgreSQL and to configure th ...@@ -27,10 +27,6 @@ To use this image, you need a running instance of PostgreSQL and to configure th
#### EXTERNAL SERVICES ### #### EXTERNAL SERVICES ###
* EXAREME_URL: URL to Exareme server. Default is "http://localhost:9090" . * EXAREME_URL: URL to Exareme server. Default is "http://localhost:9090" .
* EXAREME2_URL: URL to Exareme2 server. Default is "http://localhost:5000" . * EXAREME2_URL: URL to Exareme2 server. Default is "http://localhost:5000" .
* 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.
#### KEYCLOAK ### #### KEYCLOAK ###
* KEYCLOAK_AUTH_URL: Keycloak authentication URL. * KEYCLOAK_AUTH_URL: Keycloak authentication URL.
......
config/application.tmpl
View file @ 7a3dc737
# Configuration template for the portal running inside a Docker container # Configuration template for the portal running inside a Docker container
### EMBEDDED SERVER CONFIGURATION ###
server:
servlet:
contextPath: "/services"
port: 8080
forward-headers-strategy: native
### LOG LEVELS ### ### LOG LEVELS ###
logging: logging:
level: level:
root: {{ default .Env.LOG_LEVEL_FRAMEWORK "ERROR" }} root: {{ default .Env.LOG_LEVEL_FRAMEWORK "ERROR" }}
org: {{ default .Env.LOG_LEVEL_FRAMEWORK "ERROR" }}
eu: eu:
hbp: {{ default .Env.LOG_LEVEL "INFO" }} hbp: {{ default .Env.LOG_LEVEL "INFO" }}
### AUTHENTICATION ###
authentication:
enabled: {{ default .Env.AUTHENTICATION "true" }}
### DATABASE CONFIGURATION ### ### DATABASE CONFIGURATION ###
spring: spring:
portal-datasource: datasource:
url: {{ default .Env.PORTAL_DB_URL "jdbc:postgresql://88.197.53.106:5432/portal" }} url: {{ default .Env.PORTAL_DB_URL "jdbc:postgresql://172.17.0.1:5433/portal" }}
schema: {{ default .Env.PORTAL_DB_SCHEMA "public" }} username: {{ default .Env.PORTAL_DB_USER "portal" }}
username: {{ default .Env.PORTAL_DB_USER "postgres" }} password: {{ default .Env.PORTAL_DB_PASSWORD "portalpwd" }}
password: {{ .Env.PORTAL_DB_PASSWORD }}
driver-class-name: org.postgresql.Driver driver-class-name: org.postgresql.Driver
data: data:
jpa: jpa:
...@@ -28,8 +30,35 @@ spring: ...@@ -28,8 +30,35 @@ spring:
bootstrap-mode: default bootstrap-mode: default
jpa: jpa:
hibernate: hibernate:
dialect: org.hibernate.dialect.PostgreSQL9Dialect
ddl-auto: validate ddl-auto: validate
mvc:
pathmatch:
matching-strategy: ant_path_matcher
jackson:
default-property-inclusion: non_null
security:
oauth2:
client:
registration:
keycloak:
authorization-grant-type: authorization_code
client-id: {{ .Env.KEYCLOAK_REALM }}
client-secret: {{ .Env.KEYCLOAK_CLIENT_SECRET }}
provider: keycloak
scope: openid
redirect-uri: http://172.17.0.1/${server.servlet.contextPath}/login/oauth2/code/{{ .Env.KEYCLOAK_REALM }}
provider:
keycloak:
issuer-uri: http://172.17.0.1/auth/realms/{{ .Env.KEYCLOAK_REALM }}
user-name-attribute: preferred_username
### AUTHENTICATION ###
authentication:
enabled: {{ default .Env.AUTHENTICATION "1" }}
all_datasets_allowed_claim: research_dataset_all
all_experiments_allowed_claim: research_experiment_all
dataset_claim_prefix: research_dataset_
### EXTERNAL SERVICES ### ### EXTERNAL SERVICES ###
...@@ -40,50 +69,9 @@ services: ...@@ -40,50 +69,9 @@ services:
attributesUrl: {{ .Env.EXAREME2_URL}}/data_models_attributes attributesUrl: {{ .Env.EXAREME2_URL}}/data_models_attributes
cdesMetadataUrl: {{ .Env.EXAREME2_URL}}/cdes_metadata cdesMetadataUrl: {{ .Env.EXAREME2_URL}}/cdes_metadata
exareme:
queryExaremeUrl: {{ default .Env.EXAREME_URL "http://localhost:9090" }}/mining/query
algorithmsUrl: {{ default .Env.EXAREME_URL "http://localhost:9090" }}/mining/algorithms.json
galaxy:
galaxyUrl: {{ default .Env.GALAXY_URL "http://localhost:8090/" }}
galaxyContext: "nativeGalaxy/workflows/list"
galaxyApiKey: {{ .Env.GALAXY_API_KEY }}
galaxyUsername: {{ default .Env.GALAXY_USERNAME "admin" }}
galaxyPassword: {{ default .Env.GALAXY_PASSWORD "password" }}
### KEYCLOAK ###
keycloak:
enabled: true
auth-server-url: {{ .Env.KEYCLOAK_AUTH_URL }}
realm: {{ .Env.KEYCLOAK_REALM }}
resource: {{ .Env.KEYCLOAK_CLIENT_ID }}
use-resource-role-mappings: true
enable-basic-auth: true
credentials:
secret: {{ .Env.KEYCLOAK_CLIENT_SECRET }}
principal-attribute: "preferred_username"
ssl-required: {{ .Env.KEYCLOAK_SSL_REQUIRED }}
### EXTERNAL FILES ### ### EXTERNAL FILES ###
# Files are imported when building the docker image # Files are imported when building the docker image
files: files:
pathologies_json: "file:/opt/portal/api/pathologies.json" pathologies_json: "file:/opt/portal/api/pathologies.json"
disabledAlgorithms_json: "file:{{ .Env.DISABLED_ALGORITHMS_CONFIG_PATH}}" disabledAlgorithms_json: "file:{{ .Env.DISABLED_ALGORITHMS_CONFIG_PATH}}"
### EMBEDDED SERVER CONFIGURATION ###
server:
servlet:
contextPath: "/services"
port: 8080
forward-headers-strategy: native
### ENDPOINTS ###
endpoints:
enabled: true
health:
enabled: true
endpoint: /health
sensitive: false
pom.xml
View file @ 7a3dc737
...@@ -3,65 +3,43 @@ ...@@ -3,65 +3,43 @@
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"> xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion> <modelVersion>4.0.0</modelVersion>
<groupId>eu.hbp.mip</groupId>
<artifactId>portal-backend</artifactId>
<version>4.0.0</version><!-- BUMP_VERSION -->
<packaging>jar</packaging>
<name>portal-backend</name> <name>portal-backend</name>
<description>Medical Informatics Platform - portal-backend</description> <description>Medical Informatics Platform - portal-backend</description>
<groupId>hbp.mip</groupId>
<artifactId>portal-backend</artifactId>
<version>1.0.0</version>
<packaging>jar</packaging>
<parent> <parent>
<groupId>org.springframework.boot</groupId> <groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId> <artifactId>spring-boot-starter-parent</artifactId>
<version>2.3.5.RELEASE</version> <version>3.1.2</version>
</parent> </parent>
<properties> <properties>
<java.version>1.8</java.version>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding> <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<keycloak-spring.version>11.0.2</keycloak-spring.version> <java.version>17</java.version>
<springfox-swagger.version>2.5.0</springfox-swagger.version> <spring-context.version>6.0.11</spring-context.version>
<spring-context.version>5.2.10.RELEASE</spring-context.version> <postgresql.version>42.6.0</postgresql.version>
<springfox-boot-starter.version>3.0.0</springfox-boot-starter.version> <jakarta.version>3.1.0</jakarta.version>
<asciidoctor.maven.plugin.version>1.5.5</asciidoctor.maven.plugin.version> <hibernate.version>6.2.7.Final</hibernate.version>
<asciidoctorj.pdf.version>1.5.0-alpha.15</asciidoctorj.pdf.version>
<asciidoctorj.version>1.5.5</asciidoctorj.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>2.2.220</h2.version>
<postgresql.version>42.3.8</postgresql.version>
<gson.version>2.8.9</gson.version>
<slugify.version>2.1.5</slugify.version>
<maven-resources-plugin.version>3.0.1</maven-resources-plugin.version>
<sonar-maven-plugin.version>3.0.2</sonar-maven-plugin.version>
<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> <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> <gson.version>2.10.1</gson.version>
<hibernate.version>5.4.24.Final</hibernate.version> <commons-dbcp.version>2.9.0</commons-dbcp.version>
<hibernate-validator.version>6.1.0.Final</hibernate-validator.version> <lombok.version>1.18.28</lombok.version>
<aspectjweaver.version>1.8.9</aspectjweaver.version>
<javax-inject.version>1</javax-inject.version>
<protobuf-java.version>3.16.3</protobuf-java.version>
</properties> </properties>
<repositories>
<repository>
<snapshots>
<enabled>false</enabled>
</snapshots>
<id>bintray-hbpmedical-maven</id>
<name>bintray</name>
<url>https://dl.bintray.com/hbpmedical/maven</url>
</repository>
</repositories>
<dependencies> <dependencies>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-orm</artifactId>
<version>${spring-context.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
<version>${spring-context.version}</version>
</dependency>
<dependency> <dependency>
<groupId>org.springframework.boot</groupId> <groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter</artifactId> <artifactId>spring-boot-starter</artifactId>
...@@ -72,187 +50,59 @@ ...@@ -72,187 +50,59 @@
</dependency> </dependency>
<dependency> <dependency>
<groupId>org.springframework.boot</groupId> <groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-security</artifactId> <artifactId>spring-boot-starter-actuator</artifactId>
</dependency> </dependency>
<dependency> <dependency>
<groupId>org.springframework.boot</groupId> <groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-actuator</artifactId> <artifactId>spring-boot-starter-security</artifactId>
</dependency> </dependency>
<dependency> <dependency>
<groupId>org.springframework.boot</groupId> <groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-web</artifactId> <artifactId>spring-boot-starter-oauth2-client</artifactId>
</dependency> </dependency>
<dependency> <dependency>
<groupId>org.springframework.data</groupId> <groupId>org.springframework.data</groupId>
<artifactId>spring-data-commons</artifactId> <artifactId>spring-data-commons</artifactId>
</dependency> </dependency>
<dependency> <dependency>
<groupId>org.keycloak</groupId> <groupId>org.springframework.data</groupId>
<artifactId>keycloak-spring-boot-starter</artifactId> <artifactId>spring-data-jpa</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>
<artifactId>spring-orm</artifactId>
</dependency>
<dependency>
<groupId>org.webjars</groupId>
<artifactId>angularjs</artifactId>
<version>${angularjs.version}</version>
</dependency>
<dependency>
<groupId>org.webjars</groupId>
<artifactId>jquery</artifactId>
<version>${jquery.version}</version>
</dependency>
<dependency>
<groupId>org.webjars</groupId>
<artifactId>bootstrap</artifactId>
<version>${bootstrap.version}</version>
</dependency>
<dependency>
<groupId>org.webjars</groupId>
<artifactId>webjars-locator</artifactId>
<version>${webjars-locator.version}</version>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-test</artifactId>
<scope>test</scope>
</dependency> </dependency>
<dependency> <dependency>
<groupId>org.hibernate.javax.persistence</groupId> <groupId>jakarta.persistence</groupId>
<artifactId>hibernate-jpa-2.1-api</artifactId> <artifactId>jakarta.persistence-api</artifactId>
<version>${hibernate-jpa-2.1-api.version}</version> <version>${jakarta.version}</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>org.hibernate</groupId> <groupId>org.hibernate.orm</groupId>
<artifactId>hibernate-core</artifactId> <artifactId>hibernate-core</artifactId>
<version>${hibernate.version}</version> <version>${hibernate.version}</version>
</dependency> </dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-validator</artifactId>
<version>${hibernate-validator.version}</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-entitymanager</artifactId>
<version>${hibernate.version}</version>
</dependency>
<dependency>
<groupId>com.h2database</groupId>
<artifactId>h2</artifactId>
<version>${h2.version}</version>
</dependency>
<dependency> <dependency>
<groupId>org.postgresql</groupId> <groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId> <artifactId>postgresql</artifactId>
<version>${postgresql.version}</version> <version>${postgresql.version}</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>io.springfox</groupId> <groupId>org.flywaydb</groupId>
<artifactId>springfox-boot-starter</artifactId> <artifactId>flyway-core</artifactId>
<version>${springfox-boot-starter.version}</version> <version>${flyway-core.version}</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>com.google.code.gson</groupId> <groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId> <artifactId>gson</artifactId>
<version>${gson.version}</version> <version>${gson.version}</version>
</dependency> </dependency>
<dependency>
<groupId>com.github.slugify</groupId>
<artifactId>slugify</artifactId>
<version>${slugify.version}</version>
</dependency>
<dependency>
<groupId>org.springframework.data</groupId>
<artifactId>spring-data-jpa</artifactId>
</dependency>
<dependency> <dependency>
<groupId>org.apache.commons</groupId> <groupId>org.apache.commons</groupId>
<artifactId>commons-dbcp2</artifactId> <artifactId>commons-dbcp2</artifactId>
<version>${commons-dbcp.version}</version> <version>${commons-dbcp.version}</version>
</dependency> </dependency>
<dependency>
<groupId>org.flywaydb</groupId>
<artifactId>flyway-core</artifactId>
<version>${flyway-core.version}</version>
</dependency>
<dependency>
<groupId>org.aspectj</groupId>
<artifactId>aspectjweaver</artifactId>
<version>${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-context.version}</version>
</dependency>
<dependency>
<groupId>com.google.protobuf</groupId>
<artifactId>protobuf-java</artifactId>
<version>${protobuf-java.version}</version>
</dependency>
<dependency>
<groupId>javax.validation</groupId>
<artifactId>validation-api</artifactId>
<version>2.0.1.Final</version>
</dependency>
<dependency>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
<version>3.0.0-M4</version>
</dependency>
<!-- https://mvnrepository.com/artifact/com.github.jmchilton.blend4j/blend4j -->
<dependency>
<groupId>com.github.jmchilton.blend4j</groupId>
<artifactId>blend4j</artifactId>
<version>0.2.0</version>
</dependency>
<dependency>
<groupId>com.squareup.retrofit2</groupId>
<artifactId>retrofit</artifactId>
<version>2.9.0</version>
</dependency>
<!-- https://mvnrepository.com/artifact/com.squareup.retrofit2/converter-gson -->
<dependency>
<groupId>com.squareup.retrofit2</groupId>
<artifactId>converter-gson</artifactId>
<version>2.9.0</version>
</dependency>
<!-- https://mvnrepository.com/artifact/com.squareup.okhttp3/logging-interceptor -->
<dependency>
<groupId>com.squareup.okhttp3</groupId>
<artifactId>logging-interceptor</artifactId>
</dependency>
<dependency>
<groupId>com.auth0</groupId>
<artifactId>java-jwt</artifactId>
<version>3.11.0</version>
</dependency>
<dependency>
<groupId>com.google.code.svenson</groupId>
<artifactId>svenson</artifactId>
<version>1.5.8</version>
</dependency>
<dependency> <dependency>
<groupId>org.projectlombok</groupId> <groupId>org.projectlombok</groupId>
<artifactId>lombok</artifactId> <artifactId>lombok</artifactId>
<version>1.18.16</version> <version>${lombok.version}</version>
<scope>provided</scope>
</dependency> </dependency>
</dependencies> </dependencies>
<build> <build>
...@@ -270,90 +120,12 @@ ...@@ -270,90 +120,12 @@
</includes> </includes>
<filtering>true</filtering> <filtering>true</filtering>
</resource> </resource>
<!-- Used for development. Docker/config folder files added as resources -->
<resource>
<directory>config</directory>
<includes>
<include>*.json</include>
</includes>
<filtering>true</filtering>
</resource>
</resources> </resources>
<plugins>
<plugins> <plugin>
<plugin> <groupId>org.springframework.boot</groupId>
<groupId>org.apache.maven.plugins</groupId> <artifactId>spring-boot-maven-plugin</artifactId>
<artifactId>maven-resources-plugin</artifactId> </plugin>
<version>${maven-resources-plugin.version}</version> </plugins>
<configuration>
<!-- specify UTF-8, ISO-8859-1 or any other file encoding -->
<encoding>UTF-8</encoding>
</configuration>
</plugin>
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
</plugin>
<plugin>
<groupId>de.juplo</groupId>
<artifactId>hibernate4-maven-plugin</artifactId>
<version>${hibernate4-maven-plugin.version}</version>
<executions>
<execution>
<phase>compile</phase>
</execution>
</executions>
</plugin>
<!-- Disable default compiler. -->
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>${maven-compiler-plugin.version}</version>
<configuration>
<source>${java.version}</source>
<target>${java.version}</target>
</configuration>
</plugin>
<plugin>
<groupId>io.github.swagger2markup</groupId>
<artifactId>swagger2markup-maven-plugin</artifactId>
<version>${swagger2markup-maven-plugin.version}</version>
<configuration>
<swaggerInput>http://localhost:8080/services/v2/api-docs</swaggerInput>
<outputFile>${project.build.directory}/asciidoc/api</outputFile>
<config>
<swagger2markup.markupLanguage>ASCIIDOC</swagger2markup.markupLanguage>
</config>
</configuration>
</plugin>
<plugin>
<groupId>org.asciidoctor</groupId>
<artifactId>asciidoctor-maven-plugin</artifactId>
<version>${asciidoctor.maven.plugin.version}</version>
<dependencies>
<dependency>
<groupId>org.asciidoctor</groupId>
<artifactId>asciidoctorj-pdf</artifactId>
<version>${asciidoctorj.pdf.version}</version>
</dependency>
</dependencies>
<configuration>
<sourceDirectory>${project.build.directory}/asciidoc</sourceDirectory>
<backend>pdf</backend>
<attributes>
<toc/>
<idseparator>-</idseparator>
</attributes>
</configuration>
</plugin>
<plugin>
<groupId>org.sonarsource.scanner.maven</groupId>
<artifactId>sonar-maven-plugin</artifactId>
<version>${sonar-maven-plugin.version}</version>
</plugin>
</plugins>
</build> </build>
</project> </project>
src/main/java/eu/hbp/mip/configurations/APIMetadataConfiguration.java deleted 100644 → 0
View file @ 2e6de1ad
package eu.hbp.mip.configurations;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
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.swagger2.annotations.EnableSwagger2;
@Configuration
@EnableSwagger2
public class APIMetadataConfiguration {
@Bean
public Docket swaggerDocumentation() {
return new Docket(DocumentationType.SWAGGER_2)
.select()
.apis(RequestHandlerSelectors.basePackage("eu.hbp.mip.controllers"))
.build()
.pathMapping("/")
.apiInfo(metadata());
}
private ApiInfo metadata() {
return new ApiInfoBuilder()
.title("Medical Informatics Platform API")
.description("Serving the MIP Frontend")
.contact(new Contact("Kostas Filippopolitis", "https://github.com/KFilippopolitis", "kostasfilippop@gmail.com"))
.build();
}
}
src/main/java/eu/hbp/mip/configurations/GalaxyAuthentication.java deleted 100644 → 0
View file @ 2e6de1ad
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));
}
}
src/main/java/eu/hbp/mip/configurations/SecurityConfiguration.java deleted 100644 → 0
View file @ 2e6de1ad
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", "/actuator/**",
"/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);
}
}
src/main/java/eu/hbp/mip/controllers/ActiveUserAPI.java deleted 100644 → 0
View file @ 2e6de1ad
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());
}
}
src/main/java/eu/hbp/mip/controllers/ExperimentAPI.java deleted 100644 → 0
View file @ 2e6de1ad
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.
runTransientExperiment(authentication, experimentDTO, new Logger(activeUserService.getActiveUser().getUsername(), "(POST) /experiments/transient"));
return new ResponseEntity<>(JsonConverters.convertObjectToJsonString(experimentDTO), HttpStatus.OK);
}
}
\ No newline at end of file
src/main/java/eu/hbp/mip/controllers/PathologiesAPI.java deleted 100644 → 0
View file @ 2e6de1ad
package eu.hbp.mip.controllers;
import com.google.gson.Gson;
import com.google.gson.reflect.TypeToken;
import eu.hbp.mip.models.DTOs.Exareme2AttributesDTO;
import eu.hbp.mip.models.DTOs.Exareme2CommonDataElement;
import eu.hbp.mip.models.DTOs.PathologyDTO;
import eu.hbp.mip.services.ActiveUserService;
import eu.hbp.mip.utils.*;
import eu.hbp.mip.utils.Exceptions.InternalServerError;
import io.swagger.annotations.Api;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.http.ResponseEntity;
import org.springframework.security.core.Authentication;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RestController;
import java.util.*;
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@RestController
@RequestMapping(value = "/pathologies", produces = {APPLICATION_JSON_VALUE})
@Api(value = "/pathologies")
public class PathologiesAPI {
private static final Gson gson = new Gson();
// Enable HBP collab authentication (1) or disable it (0). Default is 1
@Value("#{'${authentication.enabled}'}")
private boolean authenticationIsEnabled;
@Value("#{'${services.exareme2.attributesUrl}'}")
private String exareme2AttributesUrl;
@Value("#{'${services.exareme2.cdesMetadataUrl}'}")
private String exareme2CDEsMetadataUrl;
private final ActiveUserService activeUserService;
public PathologiesAPI(ActiveUserService activeUserService) {
this.activeUserService = activeUserService;
}
@RequestMapping(name = "/pathologies", method = RequestMethod.GET)
public ResponseEntity<String> getPathologies(Authentication authentication) {
Logger logger = new Logger(activeUserService.getActiveUser().getUsername(), "(GET) /pathologies");
logger.LogUserAction("Loading pathologies ...");
Map<String, List<PathologyDTO.EnumerationDTO>> datasetsPerPathology = getExareme2DatasetsPerPathology(logger);
Map<String, Exareme2AttributesDTO> exareme2PathologyAttributes = getExareme2PathologyAttributes(logger);
List<PathologyDTO> pathologyDTOS = new ArrayList<>();
for (String pathology : exareme2PathologyAttributes.keySet()) {
PathologyDTO newPathology;
try {
newPathology = new PathologyDTO(pathology, exareme2PathologyAttributes.get(pathology), datasetsPerPathology.get(pathology));
}
catch(InternalServerError e) {
logger.LogUserAction(e.getMessage());
continue;
}
pathologyDTOS.add(newPathology);
}
// If authentication is disabled return everything
if (!authenticationIsEnabled) {
logger.LogUserAction("Successfully loaded " + pathologyDTOS.size() + " pathologies");
return ResponseEntity.ok().body(gson.toJson(pathologyDTOS));
}
logger.LogUserAction("Successfully loaded all authorized pathologies");
return ResponseEntity.ok().body(gson.toJson(ClaimUtils.getAuthorizedPathologies(logger, authentication, pathologyDTOS)));
}
public Map<String, List<PathologyDTO.EnumerationDTO>> getExareme2DatasetsPerPathology(Logger logger) {
Map<String, Map<String, Exareme2CommonDataElement>> exareme2CDEsMetadata;
// Get Exareme2 algorithms
try {
StringBuilder response = new StringBuilder();
HTTPUtil.sendGet(exareme2CDEsMetadataUrl, response);
exareme2CDEsMetadata = gson.fromJson(
response.toString(),
new TypeToken<HashMap<String, Map<String, Exareme2CommonDataElement>>>() {
}.getType()
);
} catch (Exception e) {
logger.LogUserAction("An exception occurred: " + e.getMessage());
return null;
}
Map<String, List<PathologyDTO.EnumerationDTO>> datasetsPerPathology = new HashMap<>();
exareme2CDEsMetadata.forEach( (pathology, cdePerDataset) -> {
List<PathologyDTO.EnumerationDTO> pathologyDatasetDTOS = new ArrayList<>();
Map datasetEnumerations = (Map) cdePerDataset.get("dataset").getEnumerations();
datasetEnumerations.forEach((code, label) -> pathologyDatasetDTOS.add(new PathologyDTO.EnumerationDTO((String) code, (String) label)));
datasetsPerPathology.put(pathology, pathologyDatasetDTOS);
});
return datasetsPerPathology;
}
public Map<String, Exareme2AttributesDTO> getExareme2PathologyAttributes(Logger logger) {
Map<String, Exareme2AttributesDTO> exareme2PathologyAttributes;
// Get Exareme2 algorithms
try {
StringBuilder response = new StringBuilder();
HTTPUtil.sendGet(exareme2AttributesUrl, response);
exareme2PathologyAttributes = gson.fromJson(
response.toString(),
new TypeToken<HashMap<String, Exareme2AttributesDTO>>() {
}.getType()
);
} catch (Exception e) {
logger.LogUserAction("An exception occurred: " + e.getMessage());
return null;
}
return exareme2PathologyAttributes;
}
}
src/main/java/eu/hbp/mip/controllers/galaxy/retrofit/RetroFitGalaxyClients.java deleted 100644 → 0
View file @ 2e6de1ad
package eu.hbp.mip.controllers.galaxy.retrofit;
import com.google.gson.JsonObject;
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.*;
import java.util.List;
public interface RetroFitGalaxyClients {
@GET("workflows/{workflowId}")
Call<WorkflowDTO> getWorkflowFromGalaxy(@Path("workflowId") String workflowId, @Query("key") String key);
@POST("workflows/{workflowId}/invocations")
Call<PostWorkflowToGalaxyDtoResponse> postWorkflowToGalaxy(@Path("workflowId") String workflowId, @Query("key") String key, @Body JsonObject body);
@GET("histories/{historyId}")
Call<Object> getWorkflowStatusFromGalaxy(@Path("historyId") String historyId, @Query("key") String key);
@GET("histories/{historyId}/contents")
Call<List<GalaxyWorkflowResult>> getWorkflowResultsFromGalaxy(@Path("historyId") String historyId, @Query("key") String key);
@GET("histories/{historyId}/contents/{contentId}/display")
Call<Object> getWorkflowResultsBodyFromGalaxy(@Path("historyId") String historyId, @Path("contentId") String contentId, @Query("key") String key);
@GET("jobs/{jobId}?full=true")
Call<Object> getErrorMessageOfWorkflowFromGalaxy(@Path("jobId") String jobId, @Query("key") String key);
}
\ No newline at end of file
src/main/java/eu/hbp/mip/controllers/galaxy/retrofit/RetrofitClientInstance.java deleted 100644 → 0
View file @ 2e6de1ad
package eu.hbp.mip.controllers.galaxy.retrofit;
import okhttp3.OkHttpClient;
import okhttp3.logging.HttpLoggingInterceptor;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.stereotype.Component;
import retrofit2.Retrofit;
import retrofit2.converter.gson.GsonConverterFactory;
import javax.annotation.PostConstruct;
@Component
public class RetrofitClientInstance {
private static Retrofit retrofit;
@Value("#{'${services.galaxy.galaxyUrl}'}")
private String galaxyUrl;
private static String BASE_URL;
@PostConstruct
public void init() {
BASE_URL = galaxyUrl + "/api/";
}
public static Retrofit getRetrofitInstance() {
if (retrofit == null) {
HttpLoggingInterceptor interceptor = new HttpLoggingInterceptor();
interceptor.setLevel(HttpLoggingInterceptor.Level.BODY);
OkHttpClient client = new OkHttpClient.Builder().addInterceptor(interceptor).build();
retrofit = new retrofit2.Retrofit.Builder()
.baseUrl(BASE_URL)
.client(client)
.addConverterFactory(GsonConverterFactory.create())
.build();
}
return retrofit;
}
}
\ No newline at end of file
src/main/java/eu/hbp/mip/models/DTOs/Exareme2AlgorithmDTO.java deleted 100644 → 0
View file @ 2e6de1ad
package eu.hbp.mip.models.DTOs;
import com.google.gson.annotations.SerializedName;
import lombok.AllArgsConstructor;
import lombok.Data;
import java.util.Hashtable;
import java.util.List;
import java.util.Optional;
@Data
@AllArgsConstructor
public class Exareme2AlgorithmDTO {
@SerializedName("name")
private String name;
@SerializedName("desc")
private String desc;
@SerializedName("label")
private String label;
@SerializedName("type")
private String type;
@SerializedName("parameters")
private Hashtable<String, Exareme2AlgorithmParameterDTO> parameters;
@SerializedName("crossvalidation")
private String crossvalidation;
@SerializedName("inputdata")
private Exareme2AlgorithmInputdataDTO inputdata;
public Optional<Hashtable<String, Exareme2AlgorithmParameterDTO>> getParameters() {
return Optional.ofNullable(parameters);
}
@SerializedName("preprocessing")
private List<Exareme2TransformerDTO> preprocessing;
public Optional<List<Exareme2TransformerDTO>> getPreprocessing() {
return Optional.ofNullable(preprocessing);
}
@Data
@AllArgsConstructor
public static class Exareme2AlgorithmParameterDTO {
@SerializedName("label")
private String label;
@SerializedName("notblank")
private String notblank;
@SerializedName("multiple")
private String multiple;
@SerializedName("types")
private List<String> types;
@SerializedName("desc")
private String desc;
@SerializedName("min")
private String min;
@SerializedName("max")
private String max;
@SerializedName("default")
private String default_value;
@SerializedName("enums")
private Exareme2AlgorithmEnumDTO enums;
@SerializedName("dict_keys_enums")
private Exareme2AlgorithmEnumDTO dict_keys_enums;
@SerializedName("dict_values_enums")
private Exareme2AlgorithmEnumDTO dict_values_enums;
public Optional<Exareme2AlgorithmEnumDTO> getEnums() {
return Optional.ofNullable(enums);
}
@Data
@AllArgsConstructor
public static class Exareme2AlgorithmEnumDTO {
@SerializedName("type")
private String type;
@SerializedName("source")
private List<String> source;
}
}
@Data
@AllArgsConstructor
public static class Exareme2AlgorithmInputdataDTO {
@SerializedName("x")
private Exareme2AlgorithmInputDataDetailDTO x;
@SerializedName("y")
private Exareme2AlgorithmInputDataDetailDTO y;
@SerializedName("data_model")
private Exareme2AlgorithmInputDataDetailDTO data_model;
@SerializedName("datasets")
private Exareme2AlgorithmInputDataDetailDTO datasets;
@SerializedName("filter")
private Exareme2AlgorithmInputDataDetailDTO filter;
public Optional<Exareme2AlgorithmInputDataDetailDTO> getY() {
return Optional.ofNullable(y);
}
public Optional<Exareme2AlgorithmInputDataDetailDTO> getX() {
return Optional.ofNullable(x);
}
}
@Data
@AllArgsConstructor
public static class Exareme2AlgorithmInputDataDetailDTO {
@SerializedName("stattypes")
private List<String> stattypes;
@SerializedName("label")
private String label;
@SerializedName("notblank")
private String notblank;
@SerializedName("enumslen")
private Integer enumslen;
@SerializedName("multiple")
private String multiple;
@SerializedName("types")
private List<String> types;
@SerializedName("desc")
private String desc;
}
@Data
@AllArgsConstructor
public static class Exareme2TransformerDTO {
@SerializedName("name")
private String name;
@SerializedName("desc")
private String desc;
@SerializedName("label")
private String label;
@SerializedName("parameters")
private Hashtable<String, Exareme2AlgorithmParameterDTO> parameters;
}
}
src/main/java/eu/hbp/mip/models/DTOs/Exareme2AlgorithmRequestDTO.java deleted 100644 → 0
View file @ 2e6de1ad
package eu.hbp.mip.models.DTOs;
import com.google.gson.annotations.SerializedName;
import eu.hbp.mip.utils.JsonConverters;
import lombok.AllArgsConstructor;
import lombok.Data;
import java.util.*;
@Data
@AllArgsConstructor
public class Exareme2AlgorithmRequestDTO {
@SerializedName("request_id")
private String request_id;
@SerializedName("inputdata")
private InputData inputdata;
@SerializedName("parameters")
private HashMap<String, Object> parameters;
@SerializedName("preprocessing")
private HashMap<String, Object> preprocessing;
public Exareme2AlgorithmRequestDTO(UUID experimentUUID, List<ExaremeAlgorithmRequestParamDTO> exaremeAlgorithmRequestParamDTOs, List<ExaremeAlgorithmDTO.ExaremeTransformerDTO> exaremeTransformers) {
this.request_id = experimentUUID.toString();
Exareme2AlgorithmRequestDTO.InputData inputData = new Exareme2AlgorithmRequestDTO.InputData();
HashMap<String, Object> exareme2Parameters = new HashMap<>();
HashMap<String, Object> exareme2Preprocessing = new HashMap<>();
exaremeAlgorithmRequestParamDTOs.forEach(parameter -> {
switch (parameter.getName()) {
case "x":
List<String> x = Arrays.asList(parameter.getValue().split(","));
inputData.setX(x);
break;
case "y":
List<String> y = Arrays.asList(parameter.getValue().split(","));
inputData.setY(y);
break;
case "dataset":
List<String> datasets = Arrays.asList(parameter.getValue().split(","));
inputData.setDatasets(datasets);
break;
case "pathology":
inputData.setData_model(parameter.getValue());
break;
case "filter":
if (parameter.getValue() != null && !parameter.getValue().equals(""))
inputData.setFilters(JsonConverters.convertJsonStringToObject(parameter.getValue(), Exareme2AlgorithmRequestDTO.Filter.class));
break;
default:
exareme2Parameters.put(parameter.getName(), convertStringToMultipleValues(parameter.getValue()));
}
});
if (exaremeTransformers != null) {
exaremeTransformers.forEach(transformer -> {
HashMap<String, Object> transformerParameterDTOs = new HashMap<>();
for (ExaremeAlgorithmRequestParamDTO parameter : transformer.getParameters()) {
if (parameter.getName().equals("strategies")){
transformerParameterDTOs.put(parameter.getName(),
JsonConverters.convertJsonStringToObject(parameter.getValue(), HashMap.class)
);
}
else {
transformerParameterDTOs.put(parameter.getName(), convertStringToMultipleValues(parameter.getValue()));
}
}
exareme2Preprocessing.put(transformer.getName(), transformerParameterDTOs);
});
}
this.inputdata = inputData;
this.parameters = exareme2Parameters;
this.preprocessing = exareme2Preprocessing;
}
private static Object convertStringToMultipleValues(String str) {
String[] stringValues = str.split(",");
if (stringValues.length == 0)
return "";
if (stringValues.length == 1)
return convertStringToNumeric(stringValues[0]);
List<Object> values = new ArrayList<>();
for (String value : stringValues) {
values.add(convertStringToNumeric(value));
}
return values;
}
private static Object convertStringToNumeric(String str) {
if (isInteger(str))
return Integer.parseInt(str);
else if (isFloat(str))
return Double.parseDouble(str);
else
return str;
}
private static boolean isFloat(String strNum) {
if (strNum == null) {
return false;
}
try {
double d = Double.parseDouble(strNum);
} catch (NumberFormatException nfe) {
return false;
}
return true;
}
private static boolean isInteger(String strNum) {
if (strNum == null) {
return false;
}
try {
double d = Integer.parseInt(strNum);
} catch (NumberFormatException nfe) {
return false;
}
return true;
}
@Data
@AllArgsConstructor
public static class InputData {
@SerializedName("data_model")
private String data_model;
@SerializedName("datasets")
private List<String> datasets;
@SerializedName("filters")
private Filter filters;
@SerializedName("x")
private List<String> x;
@SerializedName("y")
private List<String> y;
public InputData() {
}
}
@Data
@AllArgsConstructor
public static class Filter {
@SerializedName("condition")
private String condition;
@SerializedName("rules")
private List<Object> rules;
}
}
src/main/java/eu/hbp/mip/models/DTOs/Exareme2AttributesDTO.java deleted 100644 → 0
View file @ 2e6de1ad
package eu.hbp.mip.models.DTOs;
import com.google.gson.annotations.SerializedName;
import lombok.AllArgsConstructor;
import lombok.Data;
import java.util.List;
import java.util.Map;
@Data
@AllArgsConstructor
public class Exareme2AttributesDTO {
@SerializedName("properties")
private Map<String, List<MetadataHierarchyDTO>> properties;
@SerializedName("tags")
private Object tags;
}
src/main/java/eu/hbp/mip/models/DTOs/Exareme2CommonDataElement.java deleted 100644 → 0
View file @ 2e6de1ad
package eu.hbp.mip.models.DTOs;
import com.google.gson.annotations.SerializedName;
import lombok.AllArgsConstructor;
import lombok.Data;
@Data
@AllArgsConstructor
public class Exareme2CommonDataElement {
@SerializedName("is_categorical")
private Boolean is_categorical;
@SerializedName("code")
private String code;
@SerializedName("sql_type")
private String sql_type;
@SerializedName("description")
private String description;
@SerializedName("enumerations")
private Object enumerations;
@SerializedName("label")
private String label;
@SerializedName("units")
private String units;
@SerializedName("type")
private String type;
@SerializedName("methodology")
private String methodology;
@SerializedName("min")
private String min;
@SerializedName("max")
private String max;
}
src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmDTO.java deleted 100644 → 0
View file @ 2e6de1ad
package eu.hbp.mip.models.DTOs;
import com.google.gson.annotations.SerializedName;
import lombok.AllArgsConstructor;
import lombok.Data;
import lombok.NoArgsConstructor;
import java.util.ArrayList;
import java.util.List;
@Data
@AllArgsConstructor
public class ExaremeAlgorithmDTO {
@SerializedName("name")
private String name;
@SerializedName("desc")
private String desc;
@SerializedName("label")
private String label;
@SerializedName("type")
private String type;
@SerializedName("parameters")
private List<ExaremeAlgorithmRequestParamDTO> parameters;
@SerializedName("preprocessing")
private List<ExaremeTransformerDTO> preprocessing;
public ExaremeAlgorithmDTO() {
}
public ExaremeAlgorithmDTO(Exareme2AlgorithmDTO exareme2Algorithm) {
this.name = exareme2Algorithm.getName().toUpperCase();
this.label = exareme2Algorithm.getLabel();
this.desc = exareme2Algorithm.getDesc();
this.type = "exareme2";
List<ExaremeAlgorithmRequestParamDTO> parameters = new ArrayList<>();
if (exareme2Algorithm.getInputdata().getY().isPresent()) {
parameters.add(new ExaremeAlgorithmRequestParamDTO("y", exareme2Algorithm.getInputdata().getY().get()));
}
if (exareme2Algorithm.getInputdata().getX().isPresent()) {
parameters.add(new ExaremeAlgorithmRequestParamDTO("x", exareme2Algorithm.getInputdata().getX().get()));
}
parameters.add(new ExaremeAlgorithmRequestParamDTO("pathology", exareme2Algorithm.getInputdata().getData_model()));
parameters.add(new ExaremeAlgorithmRequestParamDTO("dataset", exareme2Algorithm.getInputdata().getDatasets()));
parameters.add(new ExaremeAlgorithmRequestParamDTO("filter", exareme2Algorithm.getInputdata().getFilter()));
if (exareme2Algorithm.getParameters().isPresent()) {
exareme2Algorithm.getParameters().get().forEach((name, parameterDTO) -> {
ExaremeAlgorithmRequestParamDTO parameter = new ExaremeAlgorithmRequestParamDTO(name, parameterDTO);
parameters.add(parameter);
});
}
this.parameters = parameters;
List<ExaremeTransformerDTO> preprocessing = new ArrayList<>();
if (exareme2Algorithm.getPreprocessing().isPresent()) {
exareme2Algorithm.getPreprocessing().get().forEach(exareme2TransformerDTO -> {
ExaremeTransformerDTO transformer = new ExaremeTransformerDTO(exareme2TransformerDTO);
preprocessing.add(transformer);
});
this.preprocessing = preprocessing;
}
}
@Data
@NoArgsConstructor
@AllArgsConstructor
public static class ExaremeTransformerDTO {
@SerializedName("name")
private String name;
@SerializedName("desc")
private String desc;
@SerializedName("label")
private String label;
@SerializedName("parameters")
private List<ExaremeAlgorithmRequestParamDTO> parameters;
public ExaremeTransformerDTO(Exareme2AlgorithmDTO.Exareme2TransformerDTO transformerDTO) {
this.name = transformerDTO.getName().toUpperCase();
this.label = transformerDTO.getLabel();
this.desc = transformerDTO.getDesc();
List<ExaremeAlgorithmRequestParamDTO> parameters = new ArrayList<>();
transformerDTO.getParameters().forEach((name, parameterDTO) -> {
ExaremeAlgorithmRequestParamDTO parameter = new ExaremeAlgorithmRequestParamDTO(name, parameterDTO);
parameters.add(parameter);
});
this.parameters = parameters;
}
}
@Data
@AllArgsConstructor
static class Rule {
@SerializedName("id")
private String id;
@SerializedName("type")
private String type;
@SerializedName("operator")
private String operator;
@SerializedName("value")
private Object value;
}
}
src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmRequestParamDTO.java deleted 100644 → 0
View file @ 2e6de1ad
package eu.hbp.mip.models.DTOs;
import com.google.gson.annotations.SerializedName;
import eu.hbp.mip.utils.Exceptions.InternalServerError;
import lombok.AllArgsConstructor;
import lombok.Data;
import java.util.Arrays;
import java.util.List;
//The request of an exareme algorithm is a list of ExaremeAlgorithmRequestParamDTOs.
@Data
@AllArgsConstructor
public class ExaremeAlgorithmRequestParamDTO {
@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 ExaremeAlgorithmRequestParamDTO (){}
public ExaremeAlgorithmRequestParamDTO (String name, Exareme2AlgorithmDTO.Exareme2AlgorithmParameterDTO parameter){
this.name = name;
this.desc = parameter.getDesc();
this.valueType = parameter.getTypes().get(0);
this.type = "other";
this.defaultValue = parameter.getDefault_value();
this.valueNotBlank = parameter.getNotblank();
this.label = parameter.getLabel();
this.valueEnumerations = parameter.getEnums().isPresent()? parameter.getEnums().get().getSource():null;
this.valueMultiple = parameter.getMultiple();
this.valueMax = parameter.getMax();
this.valueMin = parameter.getMin();
}
public ExaremeAlgorithmRequestParamDTO (String name, Exareme2AlgorithmDTO.Exareme2AlgorithmInputDataDetailDTO inputDataDetail){
this.name = name;
this.desc = inputDataDetail.getDesc();
this.value = "";
this.valueNotBlank = inputDataDetail.getNotblank();
this.valueMultiple = inputDataDetail.getMultiple();
String[] hidden = {"x","y","dataset", "filter","pathology","centers","formula"};
this.label = (Arrays.asList(hidden).contains(this.name) ? this.name : inputDataDetail.getLabel());
if(name.equals("dataset") || name.equals("filter") || name.equals("pathology")){
this.valueType = inputDataDetail.getTypes().get(0);
this.type = this.name;
}
else{
this.type = "column";
this.columnValuesSQLType = String.join(", ", inputDataDetail.getTypes());
this.columnValuesIsCategorical = getColumnValuesIsCategorical(inputDataDetail.getStattypes());
}
}
private String getColumnValuesIsCategorical(List<String> stattypes){
if (stattypes.contains("nominal") && stattypes.contains("numerical")){
return "";
}
else if (stattypes.contains("nominal")){
return "true";
}
else if (stattypes.contains("numerical")){
return "false";
}
else{
throw new InternalServerError("Invalid stattypes");
}
}
}
src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmResultDTO.java deleted 100644 → 0
View file @ 2e6de1ad
package eu.hbp.mip.models.DTOs;
import lombok.AllArgsConstructor;
import lombok.Data;
import java.util.List;
@Data
@AllArgsConstructor
public class ExaremeAlgorithmResultDTO {
private int code;
private List<Object> result;
}
src/main/java/eu/hbp/mip/models/DTOs/ExperimentDTO.java deleted 100644 → 0
View file @ 2e6de1ad
package eu.hbp.mip.models.DTOs;
import com.fasterxml.jackson.annotation.JsonInclude;
import eu.hbp.mip.models.DAOs.ExperimentDAO;
import eu.hbp.mip.utils.JsonConverters;
import lombok.AllArgsConstructor;
import lombok.Data;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.UUID;
@Data
@AllArgsConstructor
@JsonInclude(JsonInclude.Include.NON_NULL)
public class ExperimentDTO {
private UUID uuid;
private String name;
private UserDTO createdBy;
private Date created;
private Date updated;
private Date finished;
private Boolean shared;
private Boolean viewed;
// Result is a list of objects because there is a limitation that java has in types.
// Exareme has result in the type of List<HashMap<String, Object>>
// Galaxy has result in the type of List<HashMap<String, List<Object>>>
//And there is no generic type that describes either an object or a list of objects
private List<Object> result;
private ExperimentDAO.Status status;
private ExaremeAlgorithmDTO algorithm;
public ExperimentDTO(){
}
public ExperimentDTO(boolean includeResult, ExperimentDAO experimentDAO)
{
this.algorithm = JsonConverters.convertJsonStringToObject(experimentDAO.getAlgorithm(), ExaremeAlgorithmDTO.class);
this.created = experimentDAO.getCreated();
this.updated = experimentDAO.getUpdated();
this.finished = experimentDAO.getFinished();
this.createdBy = new UserDTO(experimentDAO.getCreatedBy());
this.name = experimentDAO.getName();
if(includeResult){
this.result = JsonConverters.convertJsonStringToObject(String.valueOf(experimentDAO.getResult()), new ArrayList<>().getClass());
}
this.status = experimentDAO.getStatus();
this.uuid = experimentDAO.getUuid();
this.shared = experimentDAO.isShared();
this.viewed = experimentDAO.isViewed();
}
}