From 2792e210a64e1dd44c860094fd6c17ec087147b8 Mon Sep 17 00:00:00 2001
From: kfilippopolitis <kostasfilippop@gmail.com>
Date: Thu, 10 Nov 2022 18:09:04 +0200
Subject: [PATCH 1/2] Properly formatted the enumerations on the
CommonDataElements.
---
.../hbp/mip/controllers/PathologiesAPI.java | 27 ++++++----
.../models/DTOs/MIPEngineAttributesDTO.java | 18 ++++++-
.../mip/models/DTOs/MetadataHierarchyDTO.java | 51 +++++++++++++++++--
.../eu/hbp/mip/models/DTOs/PathologyDTO.java | 7 ++-
.../java/eu/hbp/mip/utils/ClaimUtils.java | 4 +-
5 files changed, 84 insertions(+), 23 deletions(-)
diff --git a/src/main/java/eu/hbp/mip/controllers/PathologiesAPI.java b/src/main/java/eu/hbp/mip/controllers/PathologiesAPI.java
index e53d8d354..e6a2de685 100644
--- a/src/main/java/eu/hbp/mip/controllers/PathologiesAPI.java
+++ b/src/main/java/eu/hbp/mip/controllers/PathologiesAPI.java
@@ -15,8 +15,6 @@ import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RestController;
-import java.io.IOException;
-import java.net.ConnectException;
import java.util.*;
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@@ -49,17 +47,14 @@ public class PathologiesAPI {
Logger logger = new Logger(activeUserService.getActiveUser().getUsername(), "(GET) /pathologies");
logger.LogUserAction("Loading pathologies ...");
- Map<String, List<PathologyDTO.PathologyDatasetDTO>> datasetsPerPathology = getMIPEngineDatasetsPerPathology(logger);
- System.out.println(datasetsPerPathology);
+ Map<String, List<PathologyDTO.EnumerationDTO>> datasetsPerPathology = getMIPEngineDatasetsPerPathology(logger);
Map<String, MIPEngineAttributesDTO> mipEnginePathologyAttributes = getMIPEnginePathologyAttributes(logger);
- System.out.println(mipEnginePathologyAttributes);
List<PathologyDTO> pathologyDTOS = new ArrayList<>();
for (String pathology : mipEnginePathologyAttributes.keySet()) {
pathologyDTOS.add(new PathologyDTO(pathology, mipEnginePathologyAttributes.get(pathology), datasetsPerPathology.get(pathology)));
}
- System.out.println(pathologyDTOS);
// If authentication is disabled return everything
if (!authenticationIsEnabled) {
@@ -71,7 +66,7 @@ public class PathologiesAPI {
return ResponseEntity.ok().body(gson.toJson(ClaimUtils.getAuthorizedPathologies(logger, authentication, pathologyDTOS)));
}
- public Map<String, List<PathologyDTO.PathologyDatasetDTO>> getMIPEngineDatasetsPerPathology(Logger logger) {
+ public Map<String, List<PathologyDTO.EnumerationDTO>> getMIPEngineDatasetsPerPathology(Logger logger) {
Map<String, Map<String, MetadataHierarchyDTO.CommonDataElement>> mipEngineCDEsMetadata;
// Get MIPEngine algorithms
try {
@@ -87,15 +82,17 @@ public class PathologiesAPI {
return null;
}
- Map<String, List<PathologyDTO.PathologyDatasetDTO>> datasetsPerPathology = new HashMap<>();
+ Map<String, List<PathologyDTO.EnumerationDTO>> datasetsPerPathology = new HashMap<>();
mipEngineCDEsMetadata.forEach( (pathology, cdePerDataset) -> {
- List<PathologyDTO.PathologyDatasetDTO> pathologyDatasetDTOS = new ArrayList<>();
- cdePerDataset.forEach((dataset, cde) -> pathologyDatasetDTOS.add(new PathologyDTO.PathologyDatasetDTO(dataset, cde.getLabel())));
+ List<PathologyDTO.EnumerationDTO> pathologyDatasetDTOS = new ArrayList<>();
+ Map datasetEnumerations = (Map) cdePerDataset.get("dataset").getEnumerations();
+ datasetEnumerations.forEach((code, label) -> pathologyDatasetDTOS.add(new PathologyDTO.EnumerationDTO((String) code, (String) label)));
datasetsPerPathology.put(pathology, pathologyDatasetDTOS);
});
+
return datasetsPerPathology;
}
@@ -115,6 +112,14 @@ public class PathologiesAPI {
return null;
}
- return mipEnginePathologyAttributes;
+ Map<String, MIPEngineAttributesDTO> mipEnginePathologyAttributesWithProperEnums = new HashMap<>();
+ for (Map.Entry<String, MIPEngineAttributesDTO> entry : mipEnginePathologyAttributes.entrySet()) {
+ String pathology = entry.getKey();
+ MIPEngineAttributesDTO attributes = entry.getValue();
+ attributes.updateAttributesWithProperEnums();
+ mipEnginePathologyAttributesWithProperEnums.put(pathology, attributes);
+ }
+
+ return mipEnginePathologyAttributesWithProperEnums;
}
}
diff --git a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAttributesDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAttributesDTO.java
index 2f81aee6a..2c4794d7e 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAttributesDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAttributesDTO.java
@@ -1,10 +1,11 @@
package eu.hbp.mip.models.DTOs;
import com.google.gson.annotations.SerializedName;
-import eu.hbp.mip.models.DTOs.MetadataHierarchyDTO;
import lombok.AllArgsConstructor;
import lombok.Data;
+import java.util.ArrayList;
+import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -17,4 +18,19 @@ public class MIPEngineAttributesDTO {
@SerializedName("tags")
private Object tags;
+ public void updateAttributesWithProperEnums(){
+ Map<String, List<MetadataHierarchyDTO>> updated_properties = new HashMap<>();
+ for (Map.Entry<String, List<MetadataHierarchyDTO>> entry : this.properties.entrySet()) {
+ String pathology = entry.getKey();
+ List<MetadataHierarchyDTO> hierarchyDTOS = entry.getValue();
+ List<MetadataHierarchyDTO> updatedHierarchyDTOS = new ArrayList<>();
+
+ for (MetadataHierarchyDTO hierarchyDTO : hierarchyDTOS) {
+ hierarchyDTO.updateGroupWithProperEnums();
+ updatedHierarchyDTOS.add(hierarchyDTO);
+ }
+ updated_properties.put(pathology,updatedHierarchyDTOS);
+ }
+ this.properties = updated_properties;
+ }
}
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 e0db0c70d..200523a91 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/MetadataHierarchyDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/MetadataHierarchyDTO.java
@@ -4,9 +4,9 @@ import com.google.gson.annotations.SerializedName;
import lombok.AllArgsConstructor;
import lombok.Data;
-import java.util.Hashtable;
+import java.util.ArrayList;
import java.util.List;
-import java.util.Optional;
+import java.util.Map;
@Data
@AllArgsConstructor
@@ -19,15 +19,15 @@ public class MetadataHierarchyDTO {
private String code;
@SerializedName("groups")
- private Object groups;
+ private List<MetadataHierarchyDTO> groups;
@SerializedName("label")
private String label;
@Data
@AllArgsConstructor
public static class CommonDataElement {
- @SerializedName("isCategorical")
- private Boolean isCategorical;
+ @SerializedName("is_categorical")
+ private Boolean is_categorical;
@SerializedName("code")
private String code;
@@ -53,5 +53,46 @@ public class MetadataHierarchyDTO {
@SerializedName("methodology")
private String methodology;
+ @SerializedName("min")
+ private String min;
+
+ @SerializedName("max")
+ private String max;
+
+ private void updateEnumerations(){
+ if (this.enumerations != null){
+ Map old_enumeration = (Map) this.enumerations;
+ List<PathologyDTO.EnumerationDTO> enumerationDTOS = new ArrayList<>();
+ old_enumeration.forEach((cdeCode, cdeLabel) -> {
+ enumerationDTOS.add(new PathologyDTO.EnumerationDTO((String) cdeCode, (String) cdeLabel));
+ });
+ setEnumerations(enumerationDTOS);
+ }
+ }
+ }
+
+ public void updateVariableWithProperEnums(){
+ List<CommonDataElement> updated_variables = new ArrayList<>();
+ this.variables.forEach(commonDataElement -> {
+ commonDataElement.updateEnumerations();
+ updated_variables.add(commonDataElement);
+ });
+ setVariables(updated_variables);
+ }
+
+ public void updateGroupWithProperEnums(){
+ List<MetadataHierarchyDTO> updated_groups = new ArrayList<>();
+ for (MetadataHierarchyDTO hierarchyDTO : this.groups) {
+
+ if (hierarchyDTO.getVariables() != null) {
+ hierarchyDTO.updateVariableWithProperEnums();
+ }
+
+ if (hierarchyDTO.getGroups() != null) {
+ hierarchyDTO.updateGroupWithProperEnums();
+ }
+ updated_groups.add(hierarchyDTO);
+ }
+ this.groups = updated_groups;
}
}
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 8771aefd1..e47a27a9f 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java
@@ -6,7 +6,6 @@ import lombok.Data;
import java.util.Arrays;
import java.util.List;
-import java.util.Optional;
@Data
@AllArgsConstructor
@@ -26,14 +25,14 @@ public class PathologyDTO {
private MetadataHierarchyDTO metadataHierarchyDTO;
@SerializedName("datasets")
- private List<PathologyDatasetDTO> datasets;
+ private List<EnumerationDTO> datasets;
public PathologyDTO(){
}
- public PathologyDTO(String pathology, MIPEngineAttributesDTO mipEngineAttributesDTO, List<PathologyDatasetDTO> pathologyDatasetDTOS) {
+ 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")).
@@ -50,7 +49,7 @@ public class PathologyDTO {
@Data
@AllArgsConstructor
- public static class PathologyDatasetDTO {
+ public static class EnumerationDTO {
@SerializedName("code")
private String code;
diff --git a/src/main/java/eu/hbp/mip/utils/ClaimUtils.java b/src/main/java/eu/hbp/mip/utils/ClaimUtils.java
index df2a75abf..650ac9c65 100644
--- a/src/main/java/eu/hbp/mip/utils/ClaimUtils.java
+++ b/src/main/java/eu/hbp/mip/utils/ClaimUtils.java
@@ -68,8 +68,8 @@ public class ClaimUtils {
List<PathologyDTO> userPathologies = new ArrayList<>();
for (PathologyDTO curPathology : allPathologies) {
- List<PathologyDTO.PathologyDatasetDTO> userPathologyDatasets = new ArrayList<>();
- for (PathologyDTO.PathologyDatasetDTO dataset : curPathology.getDatasets()) {
+ List<PathologyDTO.EnumerationDTO> userPathologyDatasets = new ArrayList<>();
+ for (PathologyDTO.EnumerationDTO dataset : curPathology.getDatasets()) {
if (hasRoleAccess(authorities, ClaimUtils.getDatasetClaim(dataset.getCode()), logger)) {
logger.LogUserAction("Added dataset: " + dataset.getCode());
userPathologyDatasets.add(dataset);
--
GitLab
From ac6d020311bc10019f4da385e187121fe33b4ce3 Mon Sep 17 00:00:00 2001
From: kfilippopolitis <kostasfilippop@gmail.com>
Date: Wed, 16 Nov 2022 19:06:49 +0200
Subject: [PATCH 2/2] 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.");
--
GitLab