Merge pull request #40 from KPMP/KPMP-5365_replace_tissue_type

KPMP-5365: replace tissueType
KPMP · Nov 4, 2024 · f5f652d · f5f652d
2 parents 153f9c1 + 67f3733
commit f5f652d
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Showing 7 changed files with 32 additions and 32 deletions.
diff --git a/src/main/java/org/kpmp/repositoryDataset/RepositoryDatasetDisplay.java b/src/main/java/org/kpmp/repositoryDataset/RepositoryDatasetDisplay.java
@@ -10,7 +10,7 @@ public class RepositoryDatasetDisplay {
     private String dlFileId;
     private Set<String> redcapId;
     private Set<String> sampleType;
-    private Set<String> tissueType;
+    private Set<String> enrollmentCategory;
     private Set<String> ageBinned;
     private Set<String> sex;
     private Set<String> doi;
@@ -33,7 +33,7 @@ public RepositoryDatasetDisplay(RepositoryFileDataset repositoryFile) {
         dlFileId = repositoryFile.getId().getDlFileId();
         redcapId = new HashSet<String>();
         sampleType = new HashSet<String>();
-        tissueType = new HashSet<String>();
+        enrollmentCategory = new HashSet<String>();
         ageBinned = new HashSet<String>();
         sex = new HashSet<String>();
         doi = new TreeSet<String>();
@@ -45,8 +45,8 @@ public RepositoryDatasetDisplay(RepositoryFileDataset repositoryFile) {
         if (shouldAdd(repositoryFile.getSampleType())) {
             sampleType.add(repositoryFile.getSampleType());
         }
-        if (shouldAdd(repositoryFile.getTissueType())) {
-            tissueType.add(repositoryFile.getTissueType());
+        if (shouldAdd(repositoryFile.getEnrollmentCategory())) {
+            enrollmentCategory.add(repositoryFile.getEnrollmentCategory());
         }
         if(shouldAdd(repositoryFile.getAgeBinned())){
             ageBinned.add(repositoryFile.getAgeBinned());
@@ -133,24 +133,24 @@ public void setSampleType(Set<String> sampleType) {
         this.sampleType = sampleType;
     }
 
-    public void addTissueType(String tissueType) {
-        if(tissueType != null && !tissueType.isEmpty()){
-            this.tissueType.add(tissueType);
+    public void addEnrollmentCategory(String enrollmentCategory) {
+        if(enrollmentCategory != null && !enrollmentCategory.isEmpty()){
+            this.enrollmentCategory.add(enrollmentCategory);
         }
     }
 
-    @JsonProperty("tissue_type")
-    public Set<String> getTissueType() {
-        if(tissueType.isEmpty()){
+    @JsonProperty("enrollment_category")
+    public Set<String> getEnrollmentCategory() {
+        if(enrollmentCategory.isEmpty()){
             return null;
         }else{
-            return this.tissueType;
+            return this.enrollmentCategory;
         }
 
     }
 
-    public void setTissueType(Set<String> tissueType) {
-        this.tissueType = tissueType;
+    public void setEnrollmentCategory(Set<String> enrollmentCategory) {
+        this.enrollmentCategory = enrollmentCategory;
     }
 
     public void addAgeBinned(String ageBinned) {

diff --git a/src/main/java/org/kpmp/repositoryDataset/RepositoryDatasetService.java b/src/main/java/org/kpmp/repositoryDataset/RepositoryDatasetService.java
@@ -72,7 +72,7 @@ public List<RepositoryDatasetDisplay> getRepositoryDataset() throws Exception {
             displayFile.addAgeBinned(repositoryDataset.getAgeBinned());
             displayFile.addRedCapId(repositoryDataset.getId().getRedcapId());
             displayFile.addSampleType(repositoryDataset.getSampleType());
-            displayFile.addTissueType(repositoryDataset.getTissueType());
+            displayFile.addEnrollmentCategory(repositoryDataset.getEnrollmentCategory());
             displayFile.addSex(repositoryDataset.getSex());
             displayFile.addProtocol(repositoryDataset.getProtocol());
             displayFile.addTissueSource(repositoryDataset.getTissueSource());

diff --git a/src/main/java/org/kpmp/repositoryDataset/RepositoryFileDataset.java b/src/main/java/org/kpmp/repositoryDataset/RepositoryFileDataset.java
@@ -9,7 +9,7 @@ public class RepositoryFileDataset {
     @EmbeddedId
     private RepositoryFileDatasetId id;
     private String sampleType;
-    private String tissueType;
+    private String enrollmentCategory;
     private String ageBinned;
     private String sex;
     private String access;
@@ -41,12 +41,12 @@ public void setSampleType(String sampleType) {
         this.sampleType = sampleType;
     }
 
-    public String getTissueType() {
-        return tissueType;
+    public String getEnrollmentCategory() {
+        return enrollmentCategory;
     }
 
-    public void setTissueType(String tissueType) {
-        this.tissueType = tissueType;
+    public void setEnrollmentCategory(String enrollmentCategory) {
+        this.enrollmentCategory = enrollmentCategory;
     }
 
     @Nullable

diff --git a/src/main/resources/knowledge_environment.graphqls b/src/main/resources/knowledge_environment.graphqls
@@ -6,7 +6,7 @@ type RepositoryDatasetDisplay {
     dlFileId: String
     redcapId: [String]
     sampleType: [String]
-    tissueType: [String]
+    enrollmentCategory: [String]
     ageBinned: [String]
     sex: [String]
     doi: [String]

diff --git a/src/test/java/org/kpmp/QueryTest.java b/src/test/java/org/kpmp/QueryTest.java
@@ -54,7 +54,7 @@ public void testGetRepositoryDataset() throws Exception {
         repositoryFileDataset.setSampleType("SampleType");
         repositoryFileDataset.setSex("Male");
         repositoryFileDataset.setTissueSource("Kidneys");
-        repositoryFileDataset.setTissueType("organic");
+        repositoryFileDataset.setEnrollmentCategory("organic");
         repositoryFileDataset.setWorkflowType("workflowType");
         repositoryFileDatasetId.setDlFileId("dlFileId");
         repositoryFileDataset.setId(repositoryFileDatasetId);

diff --git a/src/test/java/org/kpmp/repositoryDataset/RepositoryDatasetDisplayTest.java b/src/test/java/org/kpmp/repositoryDataset/RepositoryDatasetDisplayTest.java
@@ -82,20 +82,20 @@ public void setSampleType() {
   }
 
   @Test
-  public void testAddTissueType() {
+  public void testAddEnrollmentCategory() {
 
     RepositoryDatasetDisplay repositoryDatasetDisplay = new RepositoryDatasetDisplay(repositoryFile);
-    repositoryDatasetDisplay.addTissueType("tissue_type");
+    repositoryDatasetDisplay.addEnrollmentCategory("enrollment_category");
 
-    assertEquals(1, repositoryDatasetDisplay.getTissueType().size());
-    assertEquals(true, repositoryDatasetDisplay.getTissueType().contains("tissue_type"));
+    assertEquals(1, repositoryDatasetDisplay.getEnrollmentCategory().size());
+    assertEquals(true, repositoryDatasetDisplay.getEnrollmentCategory().contains("enrollment_category"));
   }
 
   @Test
-  public void setTissueType() {
-    Set<String> expected = new HashSet<String>(Arrays.asList("tissue_type"));
-    repositoryDatasetDisplay.setTissueType(expected);
-    Set<String> actual = repositoryDatasetDisplay.getTissueType();
+  public void setEnrollmentCategory() {
+    Set<String> expected = new HashSet<String>(Arrays.asList("enrollment_category"));
+    repositoryDatasetDisplay.setEnrollmentCategory(expected);
+    Set<String> actual = repositoryDatasetDisplay.getEnrollmentCategory();
     assertEquals(expected, actual);
   }
 

diff --git a/src/test/java/org/kpmp/repositoryDataset/RepositoryFileDatasetTest.java b/src/test/java/org/kpmp/repositoryDataset/RepositoryFileDatasetTest.java
@@ -27,9 +27,9 @@ public void setSampleType() {
     }
 
     @Test
-    public void setTissueType() {
-        repositoryDataset.setTissueType("ttype");
-        assertEquals("ttype", repositoryDataset.getTissueType());
+    public void setEnrollmentCategory() {
+        repositoryDataset.setEnrollmentCategory("ttype");
+        assertEquals("ttype", repositoryDataset.getEnrollmentCategory());
     }
 
     @Test