Merge pull request #52 from KPMP/develop

Release v2.6 (Q4 2024)
KPMP · Dec 13, 2024 · 8f6abf2 · 8f6abf2
2 parents 4e252a0 + fe7678e
commit 8f6abf2
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diff --git a/.classpath b/.classpath
diff --git a/.github/workflows/build-gradle-project.yml b/.github/workflows/build-gradle-project.yml
@@ -6,7 +6,7 @@ on:
 jobs:
   build-gradle-project:
     env:
-      IMAGE_TAG: 2.5
+      IMAGE_TAG: 2.6
     runs-on: ubuntu-latest
     steps:
       - name: Get branch names

diff --git a/.java-version b/.java-version
@@ -0,0 +1 @@
+21.0.4
diff --git a/build.gradle b/build.gradle
@@ -13,7 +13,7 @@ plugins {
 }
 
 group = 'kingstonduo'
-version = 2.5
+version = 2.6
 
 apply plugin: 'java'
 apply plugin: 'eclipse'
@@ -23,6 +23,10 @@ apply plugin: 'io.spring.dependency-management'
 apply plugin: 'com.palantir.docker'
 
 
+test{
+    useJUnitPlatform()
+}
+
 repositories {
     mavenCentral()
 }

diff --git a/changelog.md b/changelog.md
@@ -1,5 +1,17 @@
 # Changelog
 
+## Release 2.6 (unreleased)
+Brief summary of what's in this release:
+- Add code to uniquify the clinical data for filters
+- changes to get clinical data from the new table
+- change tissueType to enrollmentCategory
+
+### Breaking changes
+Breaking changes include any database updates needed, if we need to edit any files on system (like .env or certs, etc). Things that are outside of the code itself that need changed for the system to work.
+- This will not work with older versions of the web front-ends because of changes to tables
+
+----
+
 ## Release 2.5 (10/3/2024)
 Brief summary of what's in this release:
 - Java upgrade

diff --git a/src/main/java/org/kpmp/QueryController.java b/src/main/java/org/kpmp/QueryController.java
@@ -6,7 +6,6 @@
 import org.kpmp.spatialViewerDataset.SpatialViewerExternalLinkDataset;
 import org.kpmp.spatialViewerDataset.SpatialViewerFileDataset;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.stereotype.Component;
 import org.springframework.stereotype.Controller;
 import org.springframework.graphql.data.method.annotation.QueryMapping;
 

diff --git a/src/main/java/org/kpmp/spatialViewerDataset/SpatialViewerDataset.java b/src/main/java/org/kpmp/spatialViewerDataset/SpatialViewerDataset.java
@@ -11,7 +11,7 @@ public interface SpatialViewerDataset {
 
   String getSpectrackSampleId();
 
-  String getTissueType();
+  String getEnrollmentCategory();
 
   String getTissueSource();
 
@@ -53,5 +53,29 @@ public interface SpatialViewerDataset {
 
   Double getReleaseVersion();
 
+  String getPrimaryAdjudicatedCategory();
+
+  String getKdigoStage();
+
+  String getBaselineEgfr();
+
+  String getProteinuria();
+
+  String getA1c();
+
+  String getAlbuminuria();
+
+  String getDiabetesDuration();
+
+  String getDiabetesHistory();
+
+  String getHypertensionDuration();
+
+  String getHypertensionHistory();
+
+  String getOnRaasBlockade();
+
+  String getRace();
+
 }
 
diff --git a/src/main/java/org/kpmp/spatialViewerDataset/SpatialViewerExternalLinkDataset.java b/src/main/java/org/kpmp/spatialViewerDataset/SpatialViewerExternalLinkDataset.java
@@ -8,6 +8,7 @@
 
 import com.fasterxml.jackson.annotation.*;
 import org.springframework.lang.Nullable;
+import org.apache.commons.text.WordUtils;
 import org.kpmp.file.File;
 
 import java.util.ArrayList;
@@ -21,18 +22,33 @@ public class SpatialViewerExternalLinkDataset implements SpatialViewerDataset {
     @Column(name = "external_link")
     private String externalLink;
     private String configType;
-    private String imageType;
+    private String imageType = "";
     private String dataType;
-    private String spectrackSampleId;	
-    private String redcapId;
+    private String spectrackSampleId;
+    private String redcapId = "";
     private int participantId;
     private String age;
     private String protocol;
     private String sampleType;
     private String sex;
     private String tissueSource;
-    private String tissueType;
+    private String enrollmentCategory;
     private Double releaseVersion;
+    @Column(name = "primary_adjudicated_cat")
+    private String primaryAdjudicatedCategory;
+    private String kdigoStage = "";
+    private String baselineEgfr = "";
+    private String proteinuria = "";
+    private String a1c = "";
+    private String albuminuria = "";
+    private String diabetesHistory = "";
+    private String diabetesDuration = "";
+    private String hypertensionDuration = "";
+    private String hypertensionHistory = "";
+    private String onRaasBlockade = "";
+    private String race ="";
+
+
     @Transient
     private String releaseVersionDisplay;
 
@@ -71,7 +87,7 @@ public void setImageType(String imageType) {
 
     @JsonProperty("datatype")
     public String getDataType() {
-            return dataType;
+        return dataType;
     }
 
     public void setDataType(String dataType) {
@@ -158,21 +174,21 @@ public void setTissueSource(String tissueSource) {
     }
 
     @Nullable
-    @JsonProperty("tissuetype")
-    public String getTissueType(){
-        return tissueType;
+    @JsonProperty("enrollmentcategory")
+    public String getEnrollmentCategory() {
+        return enrollmentCategory;
     }
 
-    public void setTissueType(String tissueType){
-        this.tissueType = tissueType;
+    public void setEnrollmentCategory(String enrollmentCategory) {
+        this.enrollmentCategory = enrollmentCategory;
     }
 
     @JsonIgnore
-    public Double getReleaseVersion(){
+    public Double getReleaseVersion() {
         return releaseVersion;
     }
 
-    public void setReleaseVersion(Double releaseVersion){
+    public void setReleaseVersion(Double releaseVersion) {
         this.releaseVersion = releaseVersion;
     }
 
@@ -185,23 +201,145 @@ public void setReleaseVersionDisplay(String releaseVersionDisplay) {
         this.releaseVersionDisplay = releaseVersionDisplay;
     }
 
+    @JsonProperty("primaryadjudicatedcategory")
+    public String getPrimaryAdjudicatedCategory() {
+        return this.primaryAdjudicatedCategory;
+    }
+
+    public void setPrimaryAdjudicatedCategory(String primaryAdjudicatedCategory) {
+        this.primaryAdjudicatedCategory = primaryAdjudicatedCategory;
+    }
+
+    @JsonProperty("kdigostage")
+    public String getKdigoStage() {
+        return this.kdigoStage.isBlank() ? null : this.kdigoStage + " (ks)";
+    }
+
+    public void setKdigoStage(String kdigoStage) {
+        this.kdigoStage = kdigoStage;
+    }
+
+    @JsonProperty("baselineegfr")
+    public String getBaselineEgfr() {
+        return this.baselineEgfr.isBlank() ? null : this.baselineEgfr + " (eGFR)";
+    }
+
+    public void setBaselineEgfr(String baselineEgfr) {
+        this.baselineEgfr = baselineEgfr;
+    }
+
+    @JsonProperty("proteinuria")
+    public String getProteinuria() {
+        return this.proteinuria.isBlank() ? null : this.proteinuria + " (prot)";
+    }
+
+    public void setProteinuria(String proteinuria) {
+        this.proteinuria = proteinuria;
+    }
+
+    @JsonProperty("a1c")
+    public String getA1c() {
+        return this.a1c.isBlank() ? null : this.a1c + " (a1c)";
+    }
+
+    public void setA1c(String a1c) {
+        this.a1c = a1c;
+    }
+
+    @JsonProperty("albuminuria")
+    public String getAlbuminuria() {
+        return this.albuminuria.isBlank() ? null : this.albuminuria + " (alb)";
+    }
+
+    public void setAlbuminuria(String albuminuria) {
+        this.albuminuria = albuminuria;
+    }
+
+    @JsonProperty("diabeteshistory")
+    public String getDiabetesHistory() {
+        return this.diabetesHistory.isBlank() ? null : this.diabetesHistory + " (dh)";
+    }
+
+    public void setDiabetesHistory(String diabetesHistory) {
+        this.diabetesHistory = diabetesHistory;
+    }
+
+    @JsonProperty("diabetesduration")
+    public String getDiabetesDuration() {
+        return this.diabetesDuration.isBlank() ? null : this.diabetesDuration + " (dd)";
+    }
+
+    public void setDiabetesDuration(String diabetesDuration) {
+        this.diabetesDuration = diabetesDuration;
+    }
+
+    @JsonProperty("hypertensionduration")
+    public String getHypertensionDuration() {
+        return this.hypertensionDuration.isBlank() ? null : this.hypertensionDuration + " (hd)";
+    }
+
+    public void setHypertensionDuration(String hypertensionDuration) {
+        this.hypertensionDuration = hypertensionDuration;
+    }
+
+    @JsonProperty("hypertensionhistory")
+    public String getHypertensionHistory() {
+        return this.hypertensionHistory.isBlank() ? null : this.hypertensionHistory + " (hh)";
+    }
+
+    public void setHypertensionHistory(String hypertensionHistory) {
+        this.hypertensionHistory = hypertensionHistory;
+    }
+
+    @JsonProperty("onraasblockade")
+    public String getOnRaasBlockade() {
+        return this.onRaasBlockade.isBlank() ? null : this.onRaasBlockade + " (rb)";
+    }
+
+    public void setOnRaasBlockade(String onRaasBlockade) {
+        this.onRaasBlockade = onRaasBlockade;
+    }
+
+    @JsonProperty("race")
+    public String getRace() {
+        if (this.race.isEmpty()) {
+            return null;
+        } else {
+            return this.race;
+        }
+    }
+
+    public void setRace(String race) {
+        this.race = race;
+    }
+
+    public void setParticipantIdSort(int participantIdSort) {
+        this.participantIdSort = participantIdSort;
+    }
+
+    public void setImageTypeSort(String imageTypeSort) {
+        this.imageTypeSort = imageTypeSort;
+    }
+
     @JsonProperty("dlfileid")
     public String getDlFileId() {
         return null;
     }
+
     @Nullable
     @JsonProperty("relatedfiles")
     public List<File> getRelatedFiles() {
         return new ArrayList<>();
     }
 
     @JsonIgnore
-    public String  getFileName() {
+    public String getFileName() {
         return null;
     }
+
     @JsonIgnore
 
-    public String  getFileNameSort() {
+    public String getFileNameSort() {
         return null;
     }
 
@@ -220,22 +358,28 @@ public int getParticipantIdSort() {
     public int getFileId() {
         return (Integer) null;
     }
+
     @JsonIgnore
 
     public Long getFileSize() {
         return null;
     }
+
     @JsonIgnore
 
     public String getPackageId() {
         return null;
     }
+
     @JsonIgnore
 
     public String getLevel() {
         return null;
     }
-
-
-
+
+    public String fixCapitalization(String input) {
+        String updatedInput = WordUtils.capitalizeFully(input);
+        return updatedInput;
+    }
+
 }