From 7128f32f9bd5d05c9bb75bdf7645b36437c4505b Mon Sep 17 00:00:00 2001
From: kfilippopolitis <kostasfilippop@gmail.com>
Date: Wed, 16 Nov 2022 19:06:49 +0200
Subject: [PATCH] Now the dataset enumeration will be updated even if it not
present in the first level variables.
---
.../hbp/mip/controllers/PathologiesAPI.java | 12 ++++++-
.../mip/models/DTOs/MetadataHierarchyDTO.java | 33 +++++++++++++++++++
.../eu/hbp/mip/models/DTOs/PathologyDTO.java | 7 ++--
.../hbp/mip/services/ExperimentService.java | 6 ++--
4 files changed, 51 insertions(+), 7 deletions(-)
diff --git a/src/main/java/eu/hbp/mip/controllers/PathologiesAPI.java b/src/main/java/eu/hbp/mip/controllers/PathologiesAPI.java
index e6a2de685..8949e9c5d 100644
--- a/src/main/java/eu/hbp/mip/controllers/PathologiesAPI.java
+++ b/src/main/java/eu/hbp/mip/controllers/PathologiesAPI.java
@@ -7,6 +7,7 @@ import eu.hbp.mip.models.DTOs.MetadataHierarchyDTO;
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;
@@ -53,7 +54,16 @@ public class PathologiesAPI {
List<PathologyDTO> pathologyDTOS = new ArrayList<>();
for (String pathology : mipEnginePathologyAttributes.keySet()) {
- pathologyDTOS.add(new PathologyDTO(pathology, mipEnginePathologyAttributes.get(pathology), datasetsPerPathology.get(pathology)));
+ PathologyDTO newPathology;
+ try {
+ newPathology = new PathologyDTO(pathology, mipEnginePathologyAttributes.get(pathology), datasetsPerPathology.get(pathology));
+ }
+ catch(InternalServerError e) {
+ logger.LogUserAction(e.getMessage());
+ continue;
+ }
+
+ pathologyDTOS.add(newPathology);
}
// If authentication is disabled return everything
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/MetadataHierarchyDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/MetadataHierarchyDTO.java
index 200523a91..fbfd8bd34 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/MetadataHierarchyDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/MetadataHierarchyDTO.java
@@ -95,4 +95,37 @@ public class MetadataHierarchyDTO {
}
this.groups = updated_groups;
}
+
+ public boolean isDatasetCDEPresent(){
+ if (this.variables != null) {
+ for (CommonDataElement variable : this.variables) {
+ if (variable.code.equals("dataset")){
+ return true;
+ }
+ }
+
+ }
+ if (this.groups != null) {
+ for (MetadataHierarchyDTO group: this.groups){
+ if (group.isDatasetCDEPresent()){
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+
+ public void updateDatasetCde(List<PathologyDTO.EnumerationDTO> pathologyDatasetDTOS){
+ if (this.variables != null) {
+ List<MetadataHierarchyDTO.CommonDataElement> variables = this.variables;
+ variables.stream().filter(cde -> cde.getCode().equals("dataset")).
+ findAny().ifPresent(cde -> cde.setEnumerations(pathologyDatasetDTOS));
+ }
+
+ if (this.groups != null) {
+ for (MetadataHierarchyDTO group: this.groups){
+ group.updateDatasetCde(pathologyDatasetDTOS);
+ }
+ }
+ }
}
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java
index e47a27a9f..de85a0fa2 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java
@@ -1,6 +1,7 @@
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;
@@ -34,10 +35,8 @@ public class PathologyDTO {
public PathologyDTO(String pathology, MIPEngineAttributesDTO mipEngineAttributesDTO, List<EnumerationDTO> pathologyDatasetDTOS) {
MetadataHierarchyDTO metadataHierarchyDTO = mipEngineAttributesDTO.getProperties().get("cdes").get(0);
- List<MetadataHierarchyDTO.CommonDataElement> variables = metadataHierarchyDTO.getVariables();
- variables.stream().filter(cde -> cde.getCode().equals("dataset")).
- findAny().ifPresent(cde -> cde.setEnumerations(pathologyDatasetDTOS));
- metadataHierarchyDTO.setVariables(variables);
+ if (!metadataHierarchyDTO.isDatasetCDEPresent()) throw new InternalServerError("CommonDataElement Dataset was not present in the pathology:" + pathology);
+ metadataHierarchyDTO.updateDatasetCde(pathologyDatasetDTOS);
List<String> pathology_info = Arrays.asList(pathology.split(":", 2));
this.code = pathology_info.get(0);
diff --git a/src/main/java/eu/hbp/mip/services/ExperimentService.java b/src/main/java/eu/hbp/mip/services/ExperimentService.java
index de27f46fe..a1c16a546 100644
--- a/src/main/java/eu/hbp/mip/services/ExperimentService.java
+++ b/src/main/java/eu/hbp/mip/services/ExperimentService.java
@@ -152,7 +152,7 @@ public class ExperimentService {
//Checking if check (POST) /experiments has proper input.
checkPostExperimentProperInput(experimentDTO, logger);
- // Get the type and name of algorithm
+ // Get the type of algorithm
String algorithmType = experimentDTO.getAlgorithm().getType();
if (algorithmType == null) {
@@ -190,9 +190,11 @@ public class ExperimentService {
//Checking if check (POST) /experiments has proper input.
checkPostExperimentProperInput(experimentDTO, logger);
- // Get the type and name of algorithm
+ // Get the type of algorithm
String algorithmType = experimentDTO.getAlgorithm().getType();
+ experimentDTO.setUuid(UUID.randomUUID());
+
if (algorithmType.equals("workflow")) {
logger.LogUserAction("You can not run workflow algorithms transiently.");
throw new BadRequestException("You can not run workflow algorithms transiently.");
--
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