Qa fixes (#73)

* Removed the 'Exareme' restriction requiring all algorithm names to be in uppercase. * Fixed a bug in which we incorrectly expected the algorithm parameter to contain the variable "default" instead of "default_value." * Fixed a bug in which we incorrectly converted incoming str to int.
HBPMedical · Oct 31, 2023 · 95f246f · 95f246f
1 parent 24bae61
commit 95f246f
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Showing 6 changed files with 79 additions and 27 deletions.
diff --git a/src/main/java/hbp/mip/models/DTOs/AlgorithmSpecificationDTO.java b/src/main/java/hbp/mip/models/DTOs/AlgorithmSpecificationDTO.java
@@ -19,7 +19,7 @@ public record TransformerSpecificationDTO(String name, String label, String desc
                                               List<AlgorithmParameterSpecificationDTO> parameters) {
         public TransformerSpecificationDTO(Exareme2AlgorithmSpecificationDTO.Exareme2TransformerSpecificationDTO transformerDTO) {
             this(
-                    transformerDTO.name().toUpperCase(),
+                    transformerDTO.name(),
                     transformerDTO.label(),
                     transformerDTO.desc(),
                     getAlgorithmParameterSpecifications(transformerDTO.parameters())
@@ -128,7 +128,7 @@ private static String getParameterColumnValuesIsCategorical(String inputDataDeta
 
     public AlgorithmSpecificationDTO(Exareme2AlgorithmSpecificationDTO exareme2Algorithm){
         this(
-                exareme2Algorithm.name().toUpperCase(),
+                exareme2Algorithm.name(),
                 exareme2Algorithm.label(),
                 exareme2Algorithm.desc(),
                 getAlgorithmParameters(exareme2Algorithm),

diff --git a/src/main/java/hbp/mip/models/DTOs/exareme2/Exareme2AlgorithmRequestDTO.java b/src/main/java/hbp/mip/models/DTOs/exareme2/Exareme2AlgorithmRequestDTO.java
@@ -2,6 +2,7 @@
 
 import com.google.gson.JsonSyntaxException;
 import hbp.mip.models.DTOs.ExperimentExecutionDTO;
+import hbp.mip.utils.Exceptions.InternalServerError;
 import hbp.mip.utils.JsonConverters;
 
 import java.util.*;
@@ -16,13 +17,13 @@ public record Exareme2AlgorithmRequestDTO(
     public Exareme2AlgorithmRequestDTO(
             UUID experimentUUID,
             List<ExperimentExecutionDTO.AlgorithmExecutionDTO.AlgorithmParameterExecutionDTO> exaremeAlgorithmRequestParamDTOs,
-            List<ExperimentExecutionDTO.AlgorithmExecutionDTO.TransformerExecutionDTO> exaremeTransformers
-    ) {
+            List<ExperimentExecutionDTO.AlgorithmExecutionDTO.TransformerExecutionDTO> exaremeTransformers,
+            Exareme2AlgorithmSpecificationDTO exareme2AlgorithmSpecificationDTO) {
         this(
                 experimentUUID.toString(),
                 getInputData(exaremeAlgorithmRequestParamDTOs),
-                getParameters(exaremeAlgorithmRequestParamDTOs),
-                getPreprocessing(exaremeTransformers)
+                getParameters(exaremeAlgorithmRequestParamDTOs, exareme2AlgorithmSpecificationDTO),
+                getPreprocessing(exaremeTransformers, exareme2AlgorithmSpecificationDTO)
         );
     }
 
@@ -65,7 +66,7 @@ private static Exareme2InputDataRequestDTO getInputData(List<ExperimentExecution
         );
     }
 
-    private static Map<String, Object> getParameters(List<ExperimentExecutionDTO.AlgorithmExecutionDTO.AlgorithmParameterExecutionDTO> exaremeAlgorithmRequestParamDTOs) {
+    private static Map<String, Object> getParameters(List<ExperimentExecutionDTO.AlgorithmExecutionDTO.AlgorithmParameterExecutionDTO> exaremeAlgorithmRequestParamDTOs, Exareme2AlgorithmSpecificationDTO exareme2AlgorithmSpecificationDTO) {
         if (exaremeAlgorithmRequestParamDTOs == null) {
             return null;
         }
@@ -75,28 +76,46 @@ private static Map<String, Object> getParameters(List<ExperimentExecutionDTO.Alg
 
         HashMap<String, Object> exareme2Parameters = new HashMap<>();
         exaremeAlgorithmRequestParamDTOs.forEach(parameter -> {
-            if (!inputDataFields.contains(parameter.name()))
-                exareme2Parameters.put(parameter.name(), convertStringToProperExareme2ParameterType(parameter.value()));
+            if (!inputDataFields.contains(parameter.name())){
+                Exareme2AlgorithmSpecificationDTO.Exareme2AlgorithmParameterSpecificationDTO paramSpecDto = exareme2AlgorithmSpecificationDTO.parameters().get(parameter.name());
+                exareme2Parameters.put(parameter.name(), convertStringToProperExareme2ParameterTypeAccordingToSpecs(parameter.value(), paramSpecDto));
+            }
         });
         return exareme2Parameters;
     }
 
-    private static Map<String, Object> getPreprocessing(List<ExperimentExecutionDTO.AlgorithmExecutionDTO.TransformerExecutionDTO> exaremeTransformers) {
+    private static Map<String, Object> getPreprocessing(List<ExperimentExecutionDTO.AlgorithmExecutionDTO.TransformerExecutionDTO> exaremeTransformers, Exareme2AlgorithmSpecificationDTO exareme2AlgorithmSpecificationDTO) {
         if (exaremeTransformers == null) {
             return null;
         }
 
         HashMap<String, Object> exareme2Preprocessing = new HashMap<>();
         exaremeTransformers.forEach(transformer -> {
+            String transformer_name = transformer.name();
             HashMap<String, Object> transformerParameterDTOs = new HashMap<>();
-            for (ExperimentExecutionDTO.AlgorithmExecutionDTO.AlgorithmParameterExecutionDTO parameter : transformer.parameters())
-                transformerParameterDTOs.put(parameter.name(), convertStringToProperExareme2ParameterType(parameter.value()));
-            exareme2Preprocessing.put(transformer.name(), transformerParameterDTOs);
+            for (ExperimentExecutionDTO.AlgorithmExecutionDTO.AlgorithmParameterExecutionDTO parameter : transformer.parameters()){
+                String param_name = parameter.name();
+                Optional<Exareme2AlgorithmSpecificationDTO.Exareme2TransformerSpecificationDTO> transformerSpecificationDTO = exareme2AlgorithmSpecificationDTO.preprocessing().stream()
+                        .filter(transformerSpec-> transformerSpec.name().equals(transformer_name))
+                        .findFirst();
+                if (transformerSpecificationDTO.isEmpty()) throw new InternalServerError("Missing the transformer: " + transformer_name);
+
+                Exareme2AlgorithmSpecificationDTO.Exareme2AlgorithmParameterSpecificationDTO paramSpecDto = transformerSpecificationDTO.get().parameters().get(param_name);
+                transformerParameterDTOs.put(param_name, convertStringToProperExareme2ParameterTypeAccordingToSpecs(parameter.value(), paramSpecDto));
+            }
+            exareme2Preprocessing.put(transformer_name, transformerParameterDTOs);
         });
 
         return exareme2Preprocessing;
     }
 
+    private static Object convertStringToProperExareme2ParameterTypeAccordingToSpecs(String value, Exareme2AlgorithmSpecificationDTO.Exareme2AlgorithmParameterSpecificationDTO paramSpecDto) {
+        if (paramSpecDto.enums() != null){
+            return value;
+        }
+        return convertStringToProperExareme2ParameterType(value);
+    }
+
     private static Object convertStringToProperExareme2ParameterType(String str) {
         if (isMap(str))
             return JsonConverters.convertJsonStringToObject(str, Map.class);

diff --git a/src/main/java/hbp/mip/models/DTOs/exareme2/Exareme2AlgorithmSpecificationDTO.java b/src/main/java/hbp/mip/models/DTOs/exareme2/Exareme2AlgorithmSpecificationDTO.java
@@ -1,5 +1,7 @@
 package hbp.mip.models.DTOs.exareme2;
 
+import com.google.gson.annotations.SerializedName;
+
 import java.util.Collections;
 import java.util.List;
 import java.util.Map;
@@ -9,7 +11,6 @@ public record Exareme2AlgorithmSpecificationDTO(
         String name,
         String label,
         String desc,
-        String type,
         Exareme2AlgorithmInputdataSpecificationDTO inputdata,
         Map<String, Exareme2AlgorithmParameterSpecificationDTO> parameters,
         List<Exareme2TransformerSpecificationDTO> preprocessing
@@ -24,7 +25,6 @@ public List<Exareme2TransformerSpecificationDTO> preprocessing() {
         return Objects.requireNonNullElse(preprocessing, Collections.EMPTY_LIST);
     }
 
-
     public record Exareme2AlgorithmParameterSpecificationDTO(
             String label,
             String desc,
@@ -33,8 +33,9 @@ public record Exareme2AlgorithmParameterSpecificationDTO(
             String multiple,
             String min,
             String max,
+            @SerializedName("default")
             String default_value,
-            Exareme2AlgorithmParameterSpecificationDTO.Exareme2AlgorithmEnumDTO enums,
+            Exareme2AlgorithmEnumDTO enums,
             Exareme2AlgorithmEnumDTO dict_keys_enums,
             Exareme2AlgorithmEnumDTO dict_values_enums
 

diff --git a/src/main/java/hbp/mip/services/AlgorithmService.java b/src/main/java/hbp/mip/services/AlgorithmService.java
@@ -5,6 +5,7 @@
 import hbp.mip.models.DTOs.AlgorithmSpecificationDTO;
 import hbp.mip.models.DTOs.exareme2.Exareme2AlgorithmSpecificationDTO;
 import hbp.mip.utils.CustomResourceLoader;
+import hbp.mip.utils.Exareme2AlgorithmsSpecs;
 import hbp.mip.utils.HTTPUtil;
 import hbp.mip.utils.Logger;
 import org.springframework.beans.factory.annotation.Value;
@@ -23,6 +24,7 @@ public class AlgorithmService {
 
     private static final Gson gson = new Gson();
 
+    private final Exareme2AlgorithmsSpecs exareme2AlgorithmsSpecs;
     private final CustomResourceLoader resourceLoader;
 
     @Value("${files.disabledAlgorithms_json}")
@@ -31,7 +33,8 @@ public class AlgorithmService {
     @Value("${services.exareme2.algorithmsUrl}")
     private String exareme2AlgorithmsUrl;
 
-    public AlgorithmService(CustomResourceLoader resourceLoader) {
+    public AlgorithmService(Exareme2AlgorithmsSpecs exareme2AlgorithmsSpecs, CustomResourceLoader resourceLoader) {
+        this.exareme2AlgorithmsSpecs = exareme2AlgorithmsSpecs;
         this.resourceLoader = resourceLoader;
     }
 
@@ -77,6 +80,7 @@ private List<Exareme2AlgorithmSpecificationDTO> getExareme2Algorithms(Logger log
         }
 
         logger.debug("Fetched " + algorithms.size() + " exareme2 algorithms.");
+        exareme2AlgorithmsSpecs.setAlgorithms(algorithms);
         return algorithms;
     }
 

diff --git a/src/main/java/hbp/mip/services/ExperimentService.java b/src/main/java/hbp/mip/services/ExperimentService.java
@@ -1,21 +1,16 @@
 package hbp.mip.services;
 
 import hbp.mip.models.DAOs.ExperimentDAO;
-import hbp.mip.models.DTOs.ExperimentDTO;
-import hbp.mip.models.DTOs.ExperimentExecutionDTO;
-import hbp.mip.models.DTOs.ExperimentsDTO;
-import hbp.mip.models.DTOs.UserDTO;
+import hbp.mip.models.DTOs.*;
 import hbp.mip.models.DTOs.exareme2.Exareme2AlgorithmRequestDTO;
+import hbp.mip.models.DTOs.exareme2.Exareme2AlgorithmSpecificationDTO;
 import hbp.mip.repositories.ExperimentRepository;
 import hbp.mip.repositories.ExperimentSpecifications;
-import hbp.mip.utils.ClaimUtils;
+import hbp.mip.utils.*;
 import hbp.mip.utils.Exceptions.BadRequestException;
 import hbp.mip.utils.Exceptions.InternalServerError;
 import hbp.mip.utils.Exceptions.NoContent;
 import hbp.mip.utils.Exceptions.UnauthorizedException;
-import hbp.mip.utils.HTTPUtil;
-import hbp.mip.utils.JsonConverters;
-import hbp.mip.utils.Logger;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.PageRequest;
@@ -36,6 +31,7 @@ public class ExperimentService {
     private final ActiveUserService activeUserService;
 
     private final ClaimUtils claimUtils;
+    private final Exareme2AlgorithmsSpecs exareme2AlgorithmsSpecs;
 
     private final ExperimentRepository experimentRepository;
 
@@ -48,10 +44,12 @@ public class ExperimentService {
     public ExperimentService(
             ActiveUserService activeUserService,
             ClaimUtils claimUtils,
+            Exareme2AlgorithmsSpecs exareme2AlgorithmsSpecs,
             ExperimentRepository experimentRepository
     ) {
         this.activeUserService = activeUserService;
         this.claimUtils = claimUtils;
+        this.exareme2AlgorithmsSpecs = exareme2AlgorithmsSpecs;
         this.experimentRepository = experimentRepository;
     }
 
@@ -342,8 +340,9 @@ private String getExperimentDatasets(ExperimentExecutionDTO experimentExecutionD
 
     private ExperimentAlgorithmResultDTO runExaremeAlgorithm(UUID uuid, ExperimentExecutionDTO experimentExecutionDTO, Logger logger) {
         String algorithmName = experimentExecutionDTO.algorithm().name();
-        String algorithmEndpoint = exareme2AlgorithmsUrl + "/" + algorithmName.toLowerCase();
-        var exareme2AlgorithmRequestDTO = new Exareme2AlgorithmRequestDTO(uuid, experimentExecutionDTO.algorithm().parameters(), experimentExecutionDTO.algorithm().preprocessing());
+        String algorithmEndpoint = exareme2AlgorithmsUrl + "/" + algorithmName;
+        Exareme2AlgorithmSpecificationDTO exareme2AlgorithmSpecificationDTO = getAlgorithmSpec(algorithmName);
+        var exareme2AlgorithmRequestDTO = new Exareme2AlgorithmRequestDTO(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);
@@ -362,6 +361,14 @@ private ExperimentAlgorithmResultDTO runExaremeAlgorithm(UUID uuid, ExperimentEx
         return new ExperimentAlgorithmResultDTO(requestResponseCode, result);
     }
 
+    private Exareme2AlgorithmSpecificationDTO getAlgorithmSpec(String algorithmName){
+        Optional<Exareme2AlgorithmSpecificationDTO> algorithmSpecification = exareme2AlgorithmsSpecs.getAlgorithms().stream()
+                .filter(algorithmSpec-> algorithmSpec.name().equals(algorithmName))
+                .findFirst();
+        if (algorithmSpecification.isEmpty()) throw new InternalServerError("Missing the algorithm: " + algorithmName);
+        return algorithmSpecification.get();
+    }
+
     record ExperimentAlgorithmResultDTO(int code, List<Object> result) {
     }
 }
diff --git a/src/main/java/hbp/mip/utils/Exareme2AlgorithmsSpecs.java b/src/main/java/hbp/mip/utils/Exareme2AlgorithmsSpecs.java
@@ -0,0 +1,21 @@
+package hbp.mip.utils;
+
+import hbp.mip.models.DTOs.exareme2.Exareme2AlgorithmSpecificationDTO;
+import org.springframework.stereotype.Component;
+
+import java.util.ArrayList;
+import java.util.List;
+
+@Component
+public class Exareme2AlgorithmsSpecs {
+    private List<Exareme2AlgorithmSpecificationDTO> algorithms = new ArrayList<>();
+
+
+    public List<Exareme2AlgorithmSpecificationDTO> getAlgorithms() {
+        return algorithms;
+    }
+
+    public void setAlgorithms(List<Exareme2AlgorithmSpecificationDTO> algorithms) {
+        this.algorithms = algorithms;
+    }
+}