Dockerfile

 #######################################################
 # Build the spring boot maven project
 #######################################################
-FROM maven:3.9.3-amazoncorretto-17 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"
@@ -33,6 +33,11 @@ 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 FEDERATION="default"
+ENV LOG_LEVEL="INFO"
+ENV FRAMEWORK_LOG_LEVEL="INFO"
+
 WORKDIR /opt
 
 RUN apk add --no-cache curl
@@ -40,7 +45,7 @@ RUN apk add --no-cache curl
 #######################################################
 # Install dockerize
 #######################################################
-ENV DOCKERIZE_VERSION v0.6.1
+ENV DOCKERIZE_VERSION=v0.6.1
 RUN wget https://github.com/jwilder/dockerize/releases/download/$DOCKERIZE_VERSION/dockerize-alpine-linux-amd64-$DOCKERIZE_VERSION.tar.gz \
     && tar -C /usr/local/bin -xzvf dockerize-alpine-linux-amd64-$DOCKERIZE_VERSION.tar.gz \
     && rm dockerize-alpine-linux-amd64-$DOCKERIZE_VERSION.tar.gz

config/application.tmpl

@@ -9,14 +9,6 @@ server:
   forward-headers-strategy: native
 
 
-### LOG LEVELS ###
-logging:
-  level:
-    root: {{ default .Env.LOG_LEVEL_FRAMEWORK "ERROR" }}
-    eu:
-      hbp: {{ default .Env.LOG_LEVEL "INFO" }}
-
-
 ### DATABASE CONFIGURATION ###
 spring:
   datasource:

pom.xml

@@ -44,6 +44,16 @@
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter</artifactId>
+            <exclusions>
+                <exclusion>
+                    <groupId>org.springframework.boot</groupId>
+                    <artifactId>spring-boot-starter-logging</artifactId>
+                </exclusion>
+            </exclusions>
+        </dependency>
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-log4j2</artifactId>
         </dependency>
         <dependency>
         <groupId>org.springframework.boot</groupId>

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

@@ -7,16 +7,22 @@ import hbp.mip.utils.HTTPUtil;
 import hbp.mip.utils.Logger;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.core.io.Resource;
+import org.springframework.scheduling.annotation.Async;
+import org.springframework.scheduling.annotation.EnableAsync;
+import org.springframework.scheduling.annotation.EnableScheduling;
+import org.springframework.scheduling.annotation.Scheduled;
 import org.springframework.stereotype.Service;
 
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
+import java.util.stream.Collectors;
 
 import static hbp.mip.utils.InputStreamConverter.convertInputStreamToString;
 
 @Service
+@EnableScheduling
 public class AlgorithmService {
 
     private static final Gson gson = new Gson();
@@ -76,11 +82,29 @@ public class AlgorithmService {
             return Collections.emptyList();
         }
 
+        // Filter out algorithms with type "flower"
+        algorithms = algorithms.stream()
+                .filter(algorithm -> "exareme2".equals(algorithm.type()))
+                .collect(Collectors.toList());
         logger.debug("Fetched " + algorithms.size() + " exareme2 algorithms.");
         exareme2AlgorithmsSpecs.setAlgorithms(algorithms);
         return algorithms;
     }
 
+    @EnableAsync
+    public static class AlgorithmAggregator {
+
+        private final AlgorithmService algorithmService;
+
+        public AlgorithmAggregator(AlgorithmService algorithmService){
+            this.algorithmService = algorithmService;
+        }
+        @Async
+        @Scheduled(fixedDelayString = "${services.algorithmsUpdateInterval}000")
+        public void scheduleFixedRateTaskAsync() {
+            algorithmService.getExareme2Algorithms(new Logger("AlgorithmAggregator","(GET) /algorithms"));
+        }
+    }
     /**
      * Fetches the disabled algorithms from a .json file
      *

src/main/java/hbp/mip/algorithm/Exareme2AlgorithmRequestDTO.java

@@ -15,15 +15,33 @@ public record Exareme2AlgorithmRequestDTO(
         String type
 ) {
 
-    public Exareme2AlgorithmRequestDTO(
+    public static Exareme2AlgorithmRequestDTO create(
             UUID experimentUUID,
             List<ExperimentExecutionDTO.AlgorithmExecutionDTO.AlgorithmParameterExecutionDTO> exaremeAlgorithmRequestParamDTOs,
             List<ExperimentExecutionDTO.AlgorithmExecutionDTO.TransformerExecutionDTO> exaremeTransformers,
             Exareme2AlgorithmSpecificationDTO exareme2AlgorithmSpecificationDTO) {
-        this(
+
+        // List of inputDataFields
+        List<String> inputDataFields = Arrays.asList("pathology", "dataset", "x", "y", "filter");
+
+        // Create lists to hold the separated DTOs
+        List<ExperimentExecutionDTO.AlgorithmExecutionDTO.AlgorithmParameterExecutionDTO> inputDataDTOs = new ArrayList<>();
+        List<ExperimentExecutionDTO.AlgorithmExecutionDTO.AlgorithmParameterExecutionDTO> parametersDTOs = new ArrayList<>();
+
+        // Split the DTOs into the respective lists
+        for (ExperimentExecutionDTO.AlgorithmExecutionDTO.AlgorithmParameterExecutionDTO dto : exaremeAlgorithmRequestParamDTOs) {
+            if (inputDataFields.contains(dto.name())) {
+                inputDataDTOs.add(dto);
+            } else {
+                parametersDTOs.add(dto);
+            }
+        }
+
+        // Call the constructor with the separated lists
+        return new Exareme2AlgorithmRequestDTO(
                 experimentUUID.toString(),
-                getInputData(exaremeAlgorithmRequestParamDTOs),
-                getParameters(exaremeAlgorithmRequestParamDTOs, exareme2AlgorithmSpecificationDTO),
+                getInputData(inputDataDTOs),
+                getParameters(parametersDTOs, exareme2AlgorithmSpecificationDTO),
                 getPreprocessing(exaremeTransformers, exareme2AlgorithmSpecificationDTO),
                 "exareme2"
         );
@@ -73,15 +91,13 @@ public record Exareme2AlgorithmRequestDTO(
             return null;
         }
 
-        // The input_data fields should be ignored and shouldn't be added in the parameters.
-        List<String> inputDataFields = Arrays.asList("pathology", "dataset", "x", "y", "filter");
-
         HashMap<String, Object> exareme2Parameters = new HashMap<>();
         exaremeAlgorithmRequestParamDTOs.forEach(parameter -> {
-            if (!inputDataFields.contains(parameter.name())){
-                Exareme2AlgorithmSpecificationDTO.Exareme2AlgorithmParameterSpecificationDTO paramSpecDto = exareme2AlgorithmSpecificationDTO.parameters().get(parameter.name());
-                exareme2Parameters.put(parameter.name(), convertStringToProperExareme2ParameterTypeAccordingToSpecs(parameter.value(), paramSpecDto));
+            Exareme2AlgorithmSpecificationDTO.Exareme2AlgorithmParameterSpecificationDTO paramSpecDto = exareme2AlgorithmSpecificationDTO.parameters().get(parameter.name());
+            if (paramSpecDto == null){
+                throw new InternalServerError("Parameter " + parameter.name() + " not found in algorithm:" + exareme2AlgorithmSpecificationDTO.name());
             }
+            exareme2Parameters.put(parameter.name(), convertStringToProperExareme2ParameterTypeAccordingToSpecs(parameter.value(), paramSpecDto));
         });
         return exareme2Parameters;
     }
@@ -103,6 +119,9 @@ public record Exareme2AlgorithmRequestDTO(
                 if (transformerSpecificationDTO.isEmpty()) throw new InternalServerError("Missing the transformer: " + transformer_name);
 
                 Exareme2AlgorithmSpecificationDTO.Exareme2AlgorithmParameterSpecificationDTO paramSpecDto = transformerSpecificationDTO.get().parameters().get(param_name);
+                if (paramSpecDto == null){
+                    throw new InternalServerError("Parameter " + parameter.name() + " not found in transformer:" + transformerSpecificationDTO.get().name());
+                }
                 transformerParameterDTOs.put(param_name, convertStringToProperExareme2ParameterTypeAccordingToSpecs(parameter.value(), paramSpecDto));
             }
             exareme2Preprocessing.put(transformer_name, transformerParameterDTOs);

src/main/java/hbp/mip/algorithm/Exareme2AlgorithmSpecificationDTO.java

@@ -13,7 +13,8 @@ public record Exareme2AlgorithmSpecificationDTO(
         String desc,
         Exareme2AlgorithmInputdataSpecificationDTO inputdata,
         Map<String, Exareme2AlgorithmParameterSpecificationDTO> parameters,
-        List<Exareme2TransformerSpecificationDTO> preprocessing
+        List<Exareme2TransformerSpecificationDTO> preprocessing,
+        String type
 ) {
     @Override
     public Map<String, Exareme2AlgorithmParameterSpecificationDTO> parameters() {

src/main/java/hbp/mip/configurations/AuthenticationEventListener.java

+package hbp.mip.configurations;
+
+import hbp.mip.utils.Logger;
+import lombok.extern.slf4j.Slf4j;
+import org.springframework.context.event.EventListener;
+import org.springframework.security.authentication.event.AuthenticationSuccessEvent;
+import org.springframework.security.core.Authentication;
+import org.springframework.stereotype.Component;
+
+@Slf4j
+@Component
+public class AuthenticationEventListener {
+
+    @EventListener
+    public void handleAuthenticationSuccess(AuthenticationSuccessEvent event) {
+        Authentication authentication = event.getAuthentication();
+        String username = authentication.getName();
+        Logger logger = new Logger(username, "LOGGING IN");
+        logger.info("User " + username + " has logged in successfully");
+
+        // If you need to log additional details:
+        authentication.getAuthorities().forEach(authority ->
+                logger.info("User " + username + " has authority " + authority.getAuthority())
+        );
+    }
+}

src/main/java/hbp/mip/experiment/ExperimentAPI.java

@@ -42,15 +42,15 @@ public class ExperimentAPI {
         var logger = new Logger(activeUserService.getActiveUser(authentication).username(), "(GET) /experiments");
         logger.info(
                 "Request for experiments with parameters: " +
-                        "\n\tname -> " + name +
-                        "\n\talgorithm -> " + algorithm +
-                        "\n\tshared -> " + shared +
-                        "\n\tviewed -> " + viewed +
-                        "\n\tincludeShared -> " + includeShared +
-                        "\n\torderBy -> " + orderBy +
-                        "\n\tdescending -> " + descending +
-                        "\n\tpage -> " + page +
-                        "\n\tsize -> " + size
+                        "name -> " + name +
+                        " , algorithm -> " + algorithm +
+                        " , shared -> " + shared +
+                        " , viewed -> " + viewed +
+                        " , includeShared -> " + includeShared +
+                        " , orderBy -> " + orderBy +
+                        " , descending -> " + descending +
+                        " , page -> " + page +
+                        " , size -> " + size
         );
         var experimentsDTO = experimentService.getExperiments(authentication,
                 name,
@@ -71,7 +71,7 @@ public class ExperimentAPI {
 
     @GetMapping(value = "/{uuid}")
     public ResponseEntity<ExperimentDTO> getExperiment(Authentication authentication, @PathVariable("uuid") String uuid) {
-        var logger = new Logger(activeUserService.getActiveUser(authentication).username(), "(GET) /experiments/{uuid}");
+        var logger = new Logger(activeUserService.getActiveUser(authentication).username(), "(GET) /experiments/" + uuid);
         logger.info("Request for experiment with id: " + uuid);
         var experimentResponse = experimentService.getExperiment(authentication, uuid, logger);
         logger.info("Experiment returned.");
@@ -92,7 +92,7 @@ public class ExperimentAPI {
     @PatchMapping(value = "/{uuid}")
     public ResponseEntity<ExperimentDTO> updateExperiment(Authentication authentication, @RequestBody ExperimentDTO experimentRequest, @PathVariable("uuid") String uuid) {
         var user = activeUserService.getActiveUser(authentication);
-        var logger = new Logger(user.username(), "(PATCH) /experiments/{uuid}");
+        var logger = new Logger(user.username(), "(PATCH) /experiments/" + uuid);
         logger.info("Request for experiment update with id: " + uuid + ".  Request Body: " + JsonConverters.convertObjectToJsonString(experimentRequest));
         var experimentResponse = experimentService.updateExperiment(user, uuid, experimentRequest, logger);
         logger.info("Experiment updated. Id: " + uuid);
@@ -103,7 +103,7 @@ public class ExperimentAPI {
     @RequestMapping(value = "/{uuid}", method = RequestMethod.DELETE)
     public ResponseEntity<String> deleteExperiment(Authentication authentication, @PathVariable("uuid") String uuid) {
         var user = activeUserService.getActiveUser(authentication);
-        var logger = new Logger(user.username(), "(DELETE) /experiments/{uuid}");
+        var logger = new Logger(user.username(), "(DELETE) /experiments/" + uuid);
         logger.info("Request for experiment deletion with id: " + uuid);
         experimentService.deleteExperiment(user, uuid, logger);
         logger.info("Experiment deleted. Id: " + uuid);
@@ -124,8 +124,8 @@ public class ExperimentAPI {
 
         logger.info(
                 "Experiment (transient) finished. " +
-                        "\n\tStatus: " + experimentResponse.status() +
-                        "\n\tResult: " + experimentResponse.result()
+                        " Status: " + experimentResponse.status() +
+                        " Result: " + experimentResponse.result()
         );
 
         return new ResponseEntity<>(experimentResponse, HttpStatus.OK);

src/main/java/hbp/mip/experiment/ExperimentService.java

@@ -172,7 +172,7 @@ public class ExperimentService {
                 experimentDAO.setStatus((exaremeExperimentAlgorithmResultDTO.code() >= 400)
                         ? ExperimentDAO.Status.error : ExperimentDAO.Status.success);
             } catch (Exception e) {
-                logger.error("Exareme2 algorithm execution failed: " + e.getMessage() + "\nStacktrace: " + Arrays.toString(e.getStackTrace()));
+                logger.error("Exareme2 algorithm execution failed: " + e.getMessage() + " Stacktrace: " + Arrays.toString(e.getStackTrace()));
                 experimentDAO.setStatus(ExperimentDAO.Status.error);
             }
 
@@ -289,36 +289,33 @@ public class ExperimentService {
         if (algorithm.parameters() != null) {
             algorithm.parameters().forEach(
                     params -> parametersLogMessage
-                            .append("  ")
+                            .append(" ")
                             .append(params.name())
                             .append(" -> ")
                             .append(params.value())
-                            .append("\n"));
+            );
         }
 
         if (algorithm.preprocessing() != null) {
             algorithm.preprocessing().forEach(transformer ->
             {
                 parametersLogMessage
-                        .append("  ")
+                        .append(" ")
                         .append(transformer.name())
-                        .append(" -> ")
-                        .append("\n");
+                        .append(" -> ");
 
                 if (transformer.parameters() != null) {
                     transformer.parameters().forEach(
                             transformerParams -> parametersLogMessage
-                                    .append("        ")
+                                    .append(" ")
                                     .append(transformerParams.name())
                                     .append(" -> ")
-                                    .append(transformerParams.value())
-                                    .append("\n"));
-                    parametersLogMessage.append("\n");
+                                    .append(transformerParams.value()));
                 }
             });
         }
 
-        logger.debug("Algorithm " + algorithmName + " execution starting with parameters: \n" + parametersLogMessage);
+        logger.debug("Algorithm " + algorithmName + " execution starting with parameters: " + parametersLogMessage);
     }
 
     private String getExperimentDatasets(ExperimentExecutionDTO experimentExecutionDTO, Logger logger) {
@@ -341,7 +338,7 @@ public class ExperimentService {
         String algorithmName = experimentExecutionDTO.algorithm().name();
         String algorithmEndpoint = exareme2AlgorithmsUrl + "/" + algorithmName;
         Exareme2AlgorithmSpecificationDTO exareme2AlgorithmSpecificationDTO = getAlgorithmSpec(algorithmName);
-        var exareme2AlgorithmRequestDTO = new Exareme2AlgorithmRequestDTO(uuid, experimentExecutionDTO.algorithm().parameters(), experimentExecutionDTO.algorithm().preprocessing(), exareme2AlgorithmSpecificationDTO);
+        var exareme2AlgorithmRequestDTO = Exareme2AlgorithmRequestDTO.create(uuid, experimentExecutionDTO.algorithm().parameters(), experimentExecutionDTO.algorithm().preprocessing(), exareme2AlgorithmSpecificationDTO);
         String algorithmBody = convertObjectToJsonString(exareme2AlgorithmRequestDTO);
         logger.debug("Exareme2 algorithm request, endpoint: " + algorithmEndpoint);
         logger.debug("Exareme2 algorithm request, body: " + algorithmBody);

src/main/java/hbp/mip/utils/ControllerExceptionHandler.java

@@ -64,8 +64,8 @@ public class ControllerExceptionHandler extends ResponseEntityExceptionHandler {
     @ExceptionHandler({InternalServerError.class, Exception.class})
     public ResponseEntity<ErrorMessage> globalExceptionHandler(Exception ex, WebRequest request) {
         logger.error("An unexpected exception occurred: " + ex.getClass() +
-                "\nMessage: " + ex.getMessage() +
-                "\nStacktrace: " + Arrays.toString(ex.getStackTrace()).replaceAll(", ", "\n")
+                " Message: " + ex.getMessage() +
+                " Stacktrace: " + Arrays.toString(ex.getStackTrace())
         );
         ErrorMessage message = new ErrorMessage(
                 HttpStatus.INTERNAL_SERVER_ERROR.value(),

src/main/java/hbp/mip/utils/Logger.java

@@ -16,7 +16,7 @@ public class Logger {
     }
 
     private void logUserAction(String message, String logLevel){
-        String logMessage = " User -> " + username + " , " + "Endpoint -> " + endpoint + " , " + "Info ->  " + message;
+        String logMessage = "User -> " + username + " , Endpoint -> " + endpoint + " , Info -> " + message;
 
         switch (logLevel) {
             case "ERROR" -> logger.error(logMessage);

src/main/resources/application.yml

 # Configuration for development purposes
 
-
 ### EMBEDDED SERVER CONFIGURATION ###
 server:
   servlet:
@@ -8,15 +7,6 @@ server:
   port: 8080
   forward-headers-strategy: native
 
-
-### LOG LEVELS ###
-logging:
-  level:
-    root: "INFO"
-    eu:
-      hbp: "DEBUG"
-
-
 ### DATABASE CONFIGURATION ###
 spring:
   datasource:
@@ -51,7 +41,6 @@ spring:
             user-name-attribute: preferred_username
             issuer-uri: http://172.17.0.1/auth/realms/MIP
 
-
 ### AUTHENTICATION ###
 authentication:
   enabled: 0
@@ -59,7 +48,6 @@ authentication:
   all_experiments_allowed_claim: research_experiment_all
   dataset_claim_prefix: research_dataset_
 
-
 ### EXTERNAL SERVICES ###
 services:
   algorithmsUpdateInterval: 100
@@ -68,7 +56,6 @@ services:
     attributesUrl: "http://127.0.0.1:5000/data_models_attributes"
     cdesMetadataUrl: "http://127.0.0.1:5000/cdes_metadata"
 
-
 ### EXTERNAL FILES ###
 # Files are loaded from the resources
 files:

src/main/resources/log4j2.yml

+Configuration:
+  name: Default
+
+  Properties:
+    Property:
+      name: log-path
+      value: "logs"
+
+  Appenders:
+    Console:
+      name: ConsoleAppender
+      target: SYSTEM_OUT
+      PatternLayout:
+        pattern: "%d{yyyy-MM-dd HH:mm:ss,SSS} - %-5level - %logger{36} - [${env:FEDERATION:-default}] - [${env:SERVICE:-portal-backend}] - %msg%n"
+
+  Loggers:
+    logger:
+      - name: hbp.mip
+        level: ${env:LOG_LEVEL:-INFO}
+        additivity: false  # Prevent log propagation to parent loggers
+        AppenderRef:
+          - ref: ConsoleAppender
+
+    Root:
+      level: ${env:LOG_LEVEL_FRAMEWORK:-INFO}
+      AppenderRef:
+        - ref: ConsoleAppender