Pre release mip 9.0.0

.github/workflows/ebrains.yml

@@ -2,9 +2,9 @@ name: Mirror to Ebrains
 
 on:
   push:
-    branches: [ master ]
+    branches: [master]
     tags:
-    - '*'
+      - "*"
 
 jobs:
   to_ebrains:
@@ -13,14 +13,14 @@ jobs:
       - name: syncmaster
         uses: wei/git-sync@v3
         with:
-          source_repo: "HBPMedical/portal-backend"
+          source_repo: "HBPMedical/platform-backend"
           source_branch: "master"
           destination_repo: "https://ghpusher:${{ secrets.EBRAINS_GITLAB_ACCESS_TOKEN }}@gitlab.ebrains.eu/hbp-mip/portal-backend.git"
           destination_branch: "master"
       - name: synctags
         uses: wei/git-sync@v3
         with:
-          source_repo: "HBPMedical/portal-backend"
+          source_repo: "HBPMedical/platform-backend"
           source_branch: "refs/tags/*"
           destination_repo: "https://ghpusher:${{ secrets.EBRAINS_GITLAB_ACCESS_TOKEN }}@gitlab.ebrains.eu/hbp-mip/portal-backend.git"
           destination_branch: "refs/tags/*"

.github/workflows/publish_images.yml

@@ -33,13 +33,13 @@ jobs:
         uses: docker/metadata-action@v4
         with:
           images: |
-            hbpmip/portal-backend
-            docker-registry.ebrains.eu/medical-informatics-platform/portal-backend
+            hbpmip/platform-backend
+            docker-registry.ebrains.eu/medical-informatics-platform/platform-backend
 
       - name: Load cached image
         uses: actions/cache@v3
         with:
-          path: /tmp/.buildx-cache/portal-backend
+          path: /tmp/.buildx-cache/platform-backend
           key: buildx-backend
           restore-keys: buildx-backend
 
@@ -50,8 +50,8 @@ jobs:
           file: ./Dockerfile
           push: true
           tags: ${{ steps.meta.outputs.tags }}
-          cache-from: type=local,src=/tmp/.buildx-cache/portal-backend
-          cache-to: type=local,dest=/tmp/.buildx-cache-new/portal-backend
+          cache-from: type=local,src=/tmp/.buildx-cache/platform-backend
+          cache-to: type=local,dest=/tmp/.buildx-cache-new/platform-backend
 
         # Temp fix
         # https://github.com/docker/build-push-action/issues/252
@@ -60,4 +60,3 @@ jobs:
         run: |
           rm -rf /tmp/.buildx-cache
           mv /tmp/.buildx-cache-new /tmp/.buildx-cache
-

Dockerfile

@@ -2,18 +2,19 @@
 # Build the spring boot maven project
 #######################################################
 FROM maven:3.9.3-amazoncorretto-17 AS mvn-build-env
-MAINTAINER Thanasis Karampatsis <[email protected]>
+LABEL maintainer="Thanasis Karampatsis <[email protected]>"
 
 ENV CODE_PATH="/opt/code"
 WORKDIR $CODE_PATH
 
-COPY pom.xml $CODE_PATH
+COPY pom.xml $CODE_PATH/
 
-RUN mvn clean compile test
+# Pre-fetch dependencies first to improve build cache efficiency.
+RUN mvn -B -ntp dependency:go-offline
 
 COPY src/ $CODE_PATH/src
 
-RUN mvn clean package
+RUN mvn -B -ntp clean package
 
 #######################################################
 # Setup the running container
@@ -33,7 +34,7 @@ ENV APP_CONFIG_TEMPLATE="/opt/config/application.tmpl"
 ENV APP_CONFIG_LOCATION="/opt/config/application.yml"
 ENV SPRING_CONFIG_LOCATION="file:/opt/config/application.yml"
 
-ENV SERVICE="portal-backend"
+ENV SERVICE="platform-backend"
 ENV FEDERATION="default"
 ENV LOG_LEVEL="INFO"
 ENV FRAMEWORK_LOG_LEVEL="INFO"
@@ -54,18 +55,18 @@ RUN wget https://github.com/jwilder/dockerize/releases/download/$DOCKERIZE_VERSI
 #######################################################
 # Prepare the spring boot application files
 #######################################################
-COPY /config/application.tmpl $APP_CONFIG_TEMPLATE
-COPY --from=mvn-build-env /opt/code/target/portal-backend.jar /usr/share/jars/
+COPY config/application.tmpl $APP_CONFIG_TEMPLATE
+COPY --from=mvn-build-env /opt/code/target/platform-backend.jar /usr/share/jars/
 
 
 #######################################################
 # Configuration for the backend config files
 #######################################################
-ENV DISABLED_ALGORITHMS_CONFIG_PATH="/opt/portal/algorithms/disabledAlgorithms.json"
-COPY /config/disabledAlgorithms.json $DISABLED_ALGORITHMS_CONFIG_PATH
-VOLUME /opt/portal/api
+ENV DISABLED_ALGORITHMS_CONFIG_PATH="/opt/platform/algorithms/disabledAlgorithms.json"
+COPY config/disabledAlgorithms.json $DISABLED_ALGORITHMS_CONFIG_PATH
+VOLUME /opt/platform/api
 
 
-ENTRYPOINT ["sh", "-c", "dockerize -template $APP_CONFIG_TEMPLATE:$APP_CONFIG_LOCATION java -Daeron.term.buffer.length -jar /usr/share/jars/portal-backend.jar"]
+ENTRYPOINT ["sh", "-ec", "exec dockerize -template ${APP_CONFIG_TEMPLATE}:${APP_CONFIG_LOCATION} java -Daeron.term.buffer.length -jar /usr/share/jars/platform-backend.jar"]
 EXPOSE 8080
-HEALTHCHECK --start-period=60s CMD curl -v --silent http://localhost:8080/services/actuator/health 2>&1 | grep UP
+HEALTHCHECK --start-period=60s CMD curl --fail --silent --show-error http://localhost:8080/services/actuator/health | grep -q '"status":"UP"'

README.md

@@ -1,13 +1,13 @@
 [![CHUV](https://img.shields.io/badge/CHUV-LREN-AF4C64.svg)](https://www.unil.ch/lren/en/home.html) [![License](https://img.shields.io/badge/license-AGPL--3.0-blue.svg)](https://www.gnu.org/licenses/agpl-3.0.html)
-[![DockerHub](https://img.shields.io/badge/docker-hbpmip%2Fportal--backend-008bb8.svg)](https://hub.docker.com/r/hbpmip/portal-backend/)
+[![DockerHub](https://img.shields.io/badge/docker-hbpmip%2Fplatform--backend-008bb8.svg)](https://hub.docker.com/r/hbpmip/platform-backend/)
 
-# Backend for the MIP portal
+# Backend for the MIP platform
 
 ## DEV Deployment
 To run the backend using an IDE for development, such as IntelliJ, you need a running instance of PostgreSQL.
 
 ## Deployment (using a Docker image)
-Build the image: `docker build -t hbpmip/portal-backend:testing .`
+Build the image: `docker build -t hbpmip/platform-backend:testing .`
 
 To use this image, you need a running instance of PostgreSQL and to configure the software using the following environment variables.
 
@@ -19,14 +19,13 @@ To use this image, you need a running instance of PostgreSQL and to configure th
 * AUTHENTICATION: true for production, false for development.
 
 #### 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.
+* PLATFORM_DB_URL: JDBC URL to connect to the platform database, default value is "jdbc:postgresql://127.0.0.1:5432/platform".
+* PLATFORM_DB_SCHEMA: Database schema, default value is "public".
+* PLATFORM_DB_USER: User to use when connecting to the platform database, default value is "postgres".
+* PLATFORM_DB_PASSWORD: Password to use when connecting to the platform database.
 
 #### EXTERNAL SERVICES ###
-* EXAREME_URL: URL to Exareme server. Default is "http://localhost:9090" .
-* EXAREME2_URL: URL to Exareme2 server. Default is "http://localhost:5000" .
+* EXAFLOW_URL: URL to Exaflow server. Default is "http://localhost:5000" .
 
 #### KEYCLOAK ###
 * KEYCLOAK_AUTH_URL: Keycloak authentication URL.

config/application.tmpl

@@ -1,4 +1,4 @@
-# Configuration template for the portal running inside a Docker container
+# Configuration template for the platform running inside a Docker container
 
 
 ### EMBEDDED SERVER CONFIGURATION ###
@@ -12,9 +12,9 @@ server:
 ### DATABASE CONFIGURATION ###
 spring:
   datasource:
-    url: {{ default .Env.PORTAL_DB_URL "jdbc:postgresql://172.17.0.1:5433/portal" }}
-    username: {{ default .Env.PORTAL_DB_USER "portal" }}
-    password: {{ default .Env.PORTAL_DB_PASSWORD "portalpwd" }}
+    url: {{ default .Env.PLATFORM_DB_URL "jdbc:postgresql://172.17.0.1:5433/portal" }}
+    username: {{ default .Env.PLATFORM_DB_USER "portal" }}
+    password: {{ default .Env.PLATFORM_DB_PASSWORD "portalpwd" }}
     driver-class-name: org.postgresql.Driver
   data:
     jpa:
@@ -42,6 +42,10 @@ spring:
           keycloak:
             issuer-uri: {{ .Env.KEYCLOAK_AUTH_URL }}realms/{{ .Env.KEYCLOAK_REALM }}
             user-name-attribute: preferred_username
+      # Allow API clients (e.g. notebooks) to authenticate with Bearer JWTs.
+      resourceserver:
+        jwt:
+          issuer-uri: {{ .Env.KEYCLOAK_AUTH_URL }}realms/{{ .Env.KEYCLOAK_REALM }}
 
 
 ### AUTHENTICATION ###
@@ -55,15 +59,18 @@ authentication:
 ### EXTERNAL SERVICES ###
 services:
   algorithmsUpdateInterval: {{  .Env.ALGORITHM_UPDATE_INTERVAL}}
-  exareme2:
-    algorithmsUrl: {{ .Env.EXAREME2_URL}}/algorithms
-    attributesUrl: {{ .Env.EXAREME2_URL}}/data_models_attributes
-    cdesMetadataUrl: {{ .Env.EXAREME2_URL}}/cdes_metadata
-    datasets_variables: {{ .Env.EXAREME2_URL}}/datasets_variables
+  exaflow:
+    algorithmsUrl: {{ .Env.EXAFLOW_URL}}/algorithms
+    attributesUrl: {{ .Env.EXAFLOW_URL}}/data_models_attributes
+    cdesMetadataUrl: {{ .Env.EXAFLOW_URL}}/cdes_metadata
+    datasets_variables: {{ .Env.EXAFLOW_URL}}/datasets_variables
 
 
 ### EXTERNAL FILES ###
 # Files are imported when building the docker image
 files:
-  pathologies_json: "file:/opt/portal/api/pathologies.json"
   disabledAlgorithms_json: "file:{{ .Env.DISABLED_ALGORITHMS_CONFIG_PATH}}"
+
+
+frontend:
+  base-url: {{ .Env.FRONTEND_BASE_URL }}

pom.xml

@@ -3,10 +3,10 @@
          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>
 
-    <name>portal-backend</name>
-    <description>Medical Informatics Platform - portal-backend</description>
+    <name>platform-backend</name>
+    <description>Medical Informatics Platform - platform-backend</description>
     <groupId>hbp.mip</groupId>
-    <artifactId>portal-backend</artifactId>
+    <artifactId>platform-backend</artifactId>
     <version>1.0.0</version>
     <packaging>jar</packaging>
 
@@ -19,27 +19,24 @@
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <java.version>17</java.version>
-        <spring-context.version>6.1.20</spring-context.version>
         <postgresql.version>42.6.1</postgresql.version>
         <jakarta.version>3.1.0</jakarta.version>
         <hibernate.version>6.2.7.Final</hibernate.version>
         <flyway-core.version>4.2.0</flyway-core.version>
         <gson.version>2.10.1</gson.version>
         <commons-dbcp.version>2.9.0</commons-dbcp.version>
         <springdoc-openapi-starter-webmvc-ui.version>2.1.0</springdoc-openapi-starter-webmvc-ui.version>
-        <lombok.version>1.18.28</lombok.version>
+        <lombok.version>1.18.34</lombok.version>
     </properties>
 
     <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>
             <groupId>org.springframework.boot</groupId>
@@ -71,6 +68,10 @@
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-oauth2-client</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-oauth2-resource-server</artifactId>
+        </dependency>
         <dependency>
             <groupId>org.springframework.data</groupId>
             <artifactId>spring-data-commons</artifactId>
@@ -122,7 +123,7 @@
     </dependencies>
 
    <build>
-       <finalName>portal-backend</finalName>
+       <finalName>platform-backend</finalName>
        <resources>
            <resource>
                <directory>src/main/resources</directory>

src/main/java/hbp/mip/algorithm/AlgorithmRequestDTO.java

@@ -0,0 +1,31 @@
+package hbp.mip.algorithm;
+
+import hbp.mip.experiment.ExperimentExecutionDTO;
+import lombok.extern.slf4j.Slf4j;
+
+import java.util.*;
+
+@Slf4j
+public record AlgorithmRequestDTO(
+        String request_id,
+        InputDataRequestDTO inputdata,
+        Map<String, Object> parameters,
+        Map<String, Object> preprocessing
+) {
+
+    public static AlgorithmRequestDTO create(UUID experimentUUID,ExperimentExecutionDTO.AlgorithmExecutionDTO algorithmExecutionDTO){
+        return new AlgorithmRequestDTO(
+                experimentUUID.toString(),
+                algorithmExecutionDTO.inputdata(),
+                algorithmExecutionDTO.parameters(),
+                algorithmExecutionDTO.preprocessing()
+        );
+    }
+
+    public record InputDataRequestDTO(String data_model, List<String> datasets, List<String> x, List<String> y,
+                                      FilterRequestDTO filters) {
+    }
+
+    public record FilterRequestDTO(String condition, List<Object> rules) {
+    }
+}