From e6644d43d9704ca944a7b8b086656540153ecbeb Mon Sep 17 00:00:00 2001
From: kfilippopolitis <kostasfilippop@gmail.com>
Date: Wed, 30 Nov 2022 21:39:08 +0200
Subject: [PATCH] Fix on pathologies
---
.../hbp/mip/controllers/PathologiesAPI.java | 15 ++-----
.../models/DTOs/MIPEngineAttributesDTO.java | 15 -------
.../DTOs/MIPEngineCommonDataElement.java | 43 +++++++++++++++++++
.../mip/models/DTOs/MetadataHierarchyDTO.java | 39 +----------------
4 files changed, 48 insertions(+), 64 deletions(-)
create mode 100644 src/main/java/eu/hbp/mip/models/DTOs/MIPEngineCommonDataElement.java
diff --git a/src/main/java/eu/hbp/mip/controllers/PathologiesAPI.java b/src/main/java/eu/hbp/mip/controllers/PathologiesAPI.java
index 8949e9c5d..4320f90c7 100644
--- a/src/main/java/eu/hbp/mip/controllers/PathologiesAPI.java
+++ b/src/main/java/eu/hbp/mip/controllers/PathologiesAPI.java
@@ -3,7 +3,7 @@ package eu.hbp.mip.controllers;
import com.google.gson.Gson;
import com.google.gson.reflect.TypeToken;
import eu.hbp.mip.models.DTOs.MIPEngineAttributesDTO;
-import eu.hbp.mip.models.DTOs.MetadataHierarchyDTO;
+import eu.hbp.mip.models.DTOs.MIPEngineCommonDataElement;
import eu.hbp.mip.models.DTOs.PathologyDTO;
import eu.hbp.mip.services.ActiveUserService;
import eu.hbp.mip.utils.*;
@@ -77,14 +77,14 @@ public class PathologiesAPI {
}
public Map<String, List<PathologyDTO.EnumerationDTO>> getMIPEngineDatasetsPerPathology(Logger logger) {
- Map<String, Map<String, MetadataHierarchyDTO.CommonDataElement>> mipEngineCDEsMetadata;
+ Map<String, Map<String, MIPEngineCommonDataElement>> mipEngineCDEsMetadata;
// Get MIPEngine algorithms
try {
StringBuilder response = new StringBuilder();
HTTPUtil.sendGet(mipengineCDEsMetadataUrl, response);
mipEngineCDEsMetadata = gson.fromJson(
response.toString(),
- new TypeToken<HashMap<String, Map<String, MetadataHierarchyDTO.CommonDataElement>>>() {
+ new TypeToken<HashMap<String, Map<String, MIPEngineCommonDataElement>>>() {
}.getType()
);
} catch (Exception e) {
@@ -122,14 +122,7 @@ public class PathologiesAPI {
return null;
}
- 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;
+ return mipEnginePathologyAttributes;
}
}
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 2c4794d7e..1da25fe91 100644
--- a/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAttributesDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineAttributesDTO.java
@@ -18,19 +18,4 @@ 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/MIPEngineCommonDataElement.java b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineCommonDataElement.java
new file mode 100644
index 000000000..9d81a3c77
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/models/DTOs/MIPEngineCommonDataElement.java
@@ -0,0 +1,43 @@
+package eu.hbp.mip.models.DTOs;
+
+
+import com.google.gson.annotations.SerializedName;
+import lombok.AllArgsConstructor;
+import lombok.Data;
+
+@Data
+@AllArgsConstructor
+public class MIPEngineCommonDataElement {
+ @SerializedName("is_categorical")
+ private Boolean is_categorical;
+
+ @SerializedName("code")
+ private String code;
+
+ @SerializedName("sql_type")
+ private String sql_type;
+
+ @SerializedName("description")
+ private String description;
+
+ @SerializedName("enumerations")
+ private Object enumerations;
+
+ @SerializedName("label")
+ private String label;
+
+ @SerializedName("units")
+ private String units;
+
+ @SerializedName("type")
+ private String type;
+
+ @SerializedName("methodology")
+ private String methodology;
+
+ @SerializedName("min")
+ private String min;
+
+ @SerializedName("max")
+ private String max;
+}
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 fbfd8bd34..ff73005c4 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 +4,7 @@ import com.google.gson.annotations.SerializedName;
import lombok.AllArgsConstructor;
import lombok.Data;
-import java.util.ArrayList;
import java.util.List;
-import java.util.Map;
@Data
@AllArgsConstructor
@@ -39,7 +37,7 @@ public class MetadataHierarchyDTO {
private String description;
@SerializedName("enumerations")
- private Object enumerations;
+ private List<PathologyDTO.EnumerationDTO> enumerations;
@SerializedName("label")
private String label;
@@ -58,43 +56,8 @@ public class MetadataHierarchyDTO {
@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;
- }
public boolean isDatasetCDEPresent(){
if (this.variables != null) {
--
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