(GSoC) Generic Assay Categorical/Binary data implementation Backend (c…

…BioPortal#10303) * update backend * finish tests * modify controller file structure * modify import * update backend * finish tests * modify controller file structure * refactor some variables * modify enrichment compare and validate issue * refactor the controllers and services * refactor test * Update GenericAssayEnrichmentServiceImpl.java * fixed simplification issues * add inline comments * modify import * solve core test issue * test check * modify expressionenrichment * modify imports * update backend * finish tests * modify controller file structure * modify import * update backend * finish tests * modify controller file structure * refactor some variables * modify enrichment compare and validate issue * refactor the controllers and services * refactor test * Update GenericAssayEnrichmentServiceImpl.java * fixed simplification issues * add inline comments * modify import * solve core test issue * test check * modify expressionenrichment * modify imports * update imports * Update GenericAssayEnrichment.java
pughlab · Nov 8, 2023 · 446f6ce · 446f6ce
1 parent 76c7f0a
commit 446f6ce
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Showing 14 changed files with 1,096 additions and 273 deletions.
diff --git a/model/src/main/java/org/cbioportal/model/GenericAssayBinaryEnrichment.java b/model/src/main/java/org/cbioportal/model/GenericAssayBinaryEnrichment.java
@@ -0,0 +1,19 @@
+package org.cbioportal.model;
+
+import javax.validation.constraints.NotNull;
+import java.math.BigDecimal;
+import java.util.List;
+
+public class GenericAssayBinaryEnrichment extends GenericAssayEnrichment {
+    @NotNull
+    private List<GenericAssayCountSummary> counts;
+
+    public List<GenericAssayCountSummary> getCounts() {
+        return counts;
+    }
+
+    public void setCounts(List<GenericAssayCountSummary> counts) {
+        this.counts = counts;
+    }
+
+}
diff --git a/model/src/main/java/org/cbioportal/model/GenericAssayCategoricalEnrichment.java b/model/src/main/java/org/cbioportal/model/GenericAssayCategoricalEnrichment.java
@@ -0,0 +1,18 @@
+package org.cbioportal.model;
+
+import javax.validation.constraints.NotNull;
+import java.math.BigDecimal;
+
+public class GenericAssayCategoricalEnrichment extends GenericAssayEnrichment {
+    @NotNull
+    private BigDecimal qValue;
+
+    public BigDecimal getqValue() {
+        return qValue;
+    }
+
+    public void setqValue(BigDecimal qValue) {
+        this.qValue = qValue;
+    }
+
+}
diff --git a/model/src/main/java/org/cbioportal/model/GenericAssayCountSummary.java b/model/src/main/java/org/cbioportal/model/GenericAssayCountSummary.java
@@ -0,0 +1,38 @@
+package org.cbioportal.model;
+
+import javax.validation.constraints.NotNull;
+import java.io.Serializable;
+
+public class GenericAssayCountSummary implements Serializable {
+
+    @NotNull
+    private String name;
+    @NotNull
+    private Integer count;
+    @NotNull
+    private Integer totalCount;
+
+    public Integer getCount() {
+        return count;
+    }
+
+    public void setCount(Integer count) {
+        this.count = count;
+    }
+
+    public String getName() {
+        return name;
+    }
+
+    public void setName(String name) {
+        this.name = name;
+    }
+
+    public Integer getTotalCount() {
+        return totalCount;
+    }
+
+    public void setTotalCount(Integer totalCount) {
+        this.totalCount = totalCount;
+    }
+}
diff --git a/model/src/main/java/org/cbioportal/model/GenericAssayEnrichment.java b/model/src/main/java/org/cbioportal/model/GenericAssayEnrichment.java
@@ -1,6 +1,7 @@
 package org.cbioportal.model;
 
 import java.io.Serializable;
+import java.math.BigDecimal;
 import java.util.HashMap;
 
 import javax.validation.constraints.NotNull;
@@ -11,6 +12,8 @@ public class GenericAssayEnrichment extends ExpressionEnrichment implements Seri
 	private String stableId;
 	@NotNull
 	private String name;
+    @NotNull
+    private BigDecimal qValue;
 	@NotNull
 	private HashMap<String, String> genericEntityMetaProperties;
 
@@ -37,5 +40,16 @@ public HashMap<String, String> getGenericEntityMetaProperties() {
 	public void setGenericEntityMetaProperties(HashMap<String, String> genericEntityMetaProperties) {
 		this.genericEntityMetaProperties = genericEntityMetaProperties;
 	}
-
+
+    public BigDecimal getqValue() {
+        return qValue;
+    }
+
+    public void setqValue(BigDecimal qValue) {
+        this.qValue = qValue;
+    }
+
+    public static int compare(GenericAssayEnrichment c1, GenericAssayEnrichment c2) {
+        return c1.getpValue().compareTo(c2.getpValue());
+    }
 }
diff --git a/service/src/main/java/org/cbioportal/service/ExpressionEnrichmentService.java b/service/src/main/java/org/cbioportal/service/ExpressionEnrichmentService.java
@@ -7,6 +7,8 @@
 import org.cbioportal.model.GenericAssayEnrichment;
 import org.cbioportal.model.GenomicEnrichment;
 import org.cbioportal.model.MolecularProfileCaseIdentifier;
+import org.cbioportal.model.GenericAssayBinaryEnrichment;
+import org.cbioportal.model.GenericAssayCategoricalEnrichment;
 import org.cbioportal.service.exception.MolecularProfileNotFoundException;
 
 public interface ExpressionEnrichmentService {
@@ -15,8 +17,18 @@ List<GenomicEnrichment> getGenomicEnrichments(String molecularProfileId,
             Map<String, List<MolecularProfileCaseIdentifier>> molecularProfileCaseSets, EnrichmentType enrichmentType)
             throws MolecularProfileNotFoundException;
 
-    List<GenericAssayEnrichment> getGenericAssayEnrichments(String molecularProfileId,
+    List<GenericAssayEnrichment> getGenericAssayNumericalEnrichments(String molecularProfileId,
             Map<String, List<MolecularProfileCaseIdentifier>> molecularProfileCaseSets, EnrichmentType enrichmentType)
             throws MolecularProfileNotFoundException;
+    List<GenericAssayBinaryEnrichment> getGenericAssayBinaryEnrichments(
+        String molecularProfileId,
+        Map<String, List<MolecularProfileCaseIdentifier>> molecularProfileCaseSets,
+        EnrichmentType enrichmentType)
+        throws MolecularProfileNotFoundException;
+
+    List<GenericAssayCategoricalEnrichment> getGenericAssayCategoricalEnrichments(String molecularProfileId,
+                                                                                  Map<String, List<MolecularProfileCaseIdentifier>> molecularProfileCaseSets,
+                                                                                  EnrichmentType enrichmentType)
+        throws MolecularProfileNotFoundException;
 
 }