From 4ff362ad3002bd624ae2b811cb015b15ad13201e Mon Sep 17 00:00:00 2001
From: "K.Filippopolitis" <56073635+KFilippopolitis@users.noreply.github.com>
Date: Wed, 24 Jul 2024 12:08:35 +0300
Subject: [PATCH] Redirect logs outside of console (#79)
* Redirect logs outside of console
* Log user log in and authorities.
* Re-implemented periodically executing a algorithm aggregator that was removed by accident.
For the time being we only allow exareme2 algorithms to the portalbackend.
* Minor refactoring to conversion of ExperimentExecutionDTO.AlgorithmExecutionDTO to Exareme2AlgorithmRequestDTO.
---
.../hbp/mip/algorithm/AlgorithmService.java | 24 ++++++++++++
.../Exareme2AlgorithmRequestDTO.java | 39 ++++++++++++++-----
.../Exareme2AlgorithmSpecificationDTO.java | 3 +-
.../hbp/mip/experiment/ExperimentService.java | 2 +-
4 files changed, 56 insertions(+), 12 deletions(-)
diff --git a/src/main/java/hbp/mip/algorithm/AlgorithmService.java b/src/main/java/hbp/mip/algorithm/AlgorithmService.java
index 0e5a570ba..5aa713623 100644
--- a/src/main/java/hbp/mip/algorithm/AlgorithmService.java
+++ b/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
*
diff --git a/src/main/java/hbp/mip/algorithm/Exareme2AlgorithmRequestDTO.java b/src/main/java/hbp/mip/algorithm/Exareme2AlgorithmRequestDTO.java
index 72d4c537e..9da4a1f46 100644
--- a/src/main/java/hbp/mip/algorithm/Exareme2AlgorithmRequestDTO.java
+++ b/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);
diff --git a/src/main/java/hbp/mip/algorithm/Exareme2AlgorithmSpecificationDTO.java b/src/main/java/hbp/mip/algorithm/Exareme2AlgorithmSpecificationDTO.java
index 93708e3af..b987a7741 100644
--- a/src/main/java/hbp/mip/algorithm/Exareme2AlgorithmSpecificationDTO.java
+++ b/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() {
diff --git a/src/main/java/hbp/mip/experiment/ExperimentService.java b/src/main/java/hbp/mip/experiment/ExperimentService.java
index 17cb7f3b9..ee530ad43 100644
--- a/src/main/java/hbp/mip/experiment/ExperimentService.java
+++ b/src/main/java/hbp/mip/experiment/ExperimentService.java
@@ -341,7 +341,7 @@ 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);
--
GitLab