updated model to serialize Map as Object

cBioPortal · Apr 5, 2017 · c6b65a8 · c6b65a8
1 parent 2918ce7
commit c6b65a8
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Showing 5 changed files with 73 additions and 40 deletions.
diff --git a/model/src/main/java/org/cmo/cancerhotspots/model/Cluster.java b/model/src/main/java/org/cmo/cancerhotspots/model/Cluster.java
@@ -1,5 +1,6 @@
 package org.cmo.cancerhotspots.model;
 
+import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.univocity.parsers.annotations.Convert;
 import com.univocity.parsers.annotations.Parsed;
 import com.univocity.parsers.annotations.Trim;
@@ -26,20 +27,20 @@ public class Cluster
     @Trim
     @Convert(conversionClass = ChainMapConversion.class)
     @Parsed(field = "PDB_Chains")
-    private Map<String, Double> pdbChains;
+    private Map<String, Double> pdbChainMap;
 
     @Trim
     @Convert(conversionClass = CompositionMapConversion.class)
     @Parsed(field = "Residues")
-    private Map<String, Integer> residues;
+    private Map<String, Integer> residueMap;
 
     @Trim
     @Parsed(field = "P-Value")
     private String pValue;
 
     public Cluster()
     {
-        this.residues = new LinkedHashMap<>();
+        this.residueMap = new LinkedHashMap<>();
     }
 
     @ApiModelProperty(value = "Hugo gene symbol", required = true)
@@ -76,29 +77,41 @@ public void setClusterId(String clusterId)
     }
 
     @ApiModelProperty(value = "PDB chains (with p-value)", required = true)
-    public Map<String, Double> getPdbChains()
+    public Object getPdbChains()
     {
-        return pdbChains;
+        return getPdbChainMap();
     }
 
-    public void setPdbChains(Map<String, Double> pdbChains)
+    @JsonIgnore
+    public Map<String, Double> getPdbChainMap()
     {
-        this.pdbChains = pdbChains;
+        return pdbChainMap;
+    }
+
+    public void setPdbChainMap(Map<String, Double> pdbChainMap)
+    {
+        this.pdbChainMap = pdbChainMap;
     }
 
     @ApiModelProperty(value = "Residues within this cluster (with overall tumor count)", required = true)
-    public Map<String, Integer> getResidues()
+    public Object getResidues()
+    {
+        return getResidueMap();
+    }
+
+    @JsonIgnore
+    public Map<String, Integer> getResidueMap()
     {
-        return residues;
+        return residueMap;
     }
 
-    public void setResidues(Map<String, Integer> residues)
+    public void setResidueMap(Map<String, Integer> residueMap)
     {
-        this.residues = residues;
+        this.residueMap = residueMap;
     }
 
     public void addResidue(String residue, Integer tumorCount)
     {
-        this.residues.put(residue, tumorCount);
+        this.residueMap.put(residue, tumorCount);
     }
 }
diff --git a/model/src/main/java/org/cmo/cancerhotspots/model/HotspotMutation.java b/model/src/main/java/org/cmo/cancerhotspots/model/HotspotMutation.java
@@ -32,6 +32,7 @@
 
 package org.cmo.cancerhotspots.model;
 
+import com.fasterxml.jackson.annotation.JsonIgnore;
 import io.swagger.annotations.ApiModelProperty;
 import org.cmo.cancerhotspots.data.IntegerRange;
 
@@ -44,10 +45,10 @@ public class HotspotMutation
 {
     private String hugoSymbol;
     private String residue;
-    private Map<String, Integer> variantAminoAcid;
+    private Map<String, Integer> variantAminoAcidMap;
     private Integer tumorTypeCount;
     private Integer tumorCount;
-    private Map<String, Integer> tumorTypeComposition;
+    private Map<String, Integer> tumorTypeCompositionMap;
     private String transcriptId;
     private IntegerRange aminoAcidPosition;
 
@@ -74,14 +75,20 @@ public void setResidue(String residue)
     }
 
     @ApiModelProperty(value = "Variant Amino Acid", required = true)
-    public Map<String, Integer> getVariantAminoAcid()
+    public Object getVariantAminoAcid()
     {
-        return variantAminoAcid;
+        return getVariantAminoAcidMap();
     }
 
-    public void setVariantAminoAcid(Map<String, Integer> variantAminoAcid)
+    @JsonIgnore
+    public Map<String, Integer> getVariantAminoAcidMap()
     {
-        this.variantAminoAcid = variantAminoAcid;
+        return variantAminoAcidMap;
+    }
+
+    public void setVariantAminoAcidMap(Map<String, Integer> variantAminoAcidMap)
+    {
+        this.variantAminoAcidMap = variantAminoAcidMap;
     }
 
     @ApiModelProperty(value = "Number of Tumors", required = true)
@@ -96,14 +103,20 @@ public void setTumorCount(Integer tumorCount)
     }
 
     @ApiModelProperty(value = "Tumor Type Composition", required = true)
-    public Map<String, Integer> getTumorTypeComposition()
+    public Object getTumorTypeComposition()
+    {
+        return getTumorTypeCompositionMap();
+    }
+
+    @JsonIgnore
+    public Map<String, Integer> getTumorTypeCompositionMap()
     {
-        return tumorTypeComposition;
+        return tumorTypeCompositionMap;
     }
 
-    public void setTumorTypeComposition(Map<String, Integer> tumorTypeComposition)
+    public void setTumorTypeCompositionMap(Map<String, Integer> tumorTypeCompositionMap)
     {
-        this.tumorTypeComposition = tumorTypeComposition;
+        this.tumorTypeCompositionMap = tumorTypeCompositionMap;
     }
 
     @ApiModelProperty(value = "Number of Distinct Tumor Types", required = false)
@@ -142,10 +155,10 @@ public void init(Mutation mutation)
     {
         setHugoSymbol(mutation.getHugoSymbol());
         setTumorCount(mutation.getTumorCount());
-        setTumorTypeComposition(mutation.getTumorTypeComposition());
+        setTumorTypeCompositionMap(mutation.getTumorTypeComposition());
         setTumorTypeCount(mutation.getTumorTypeCount());
         setResidue(mutation.getResidue());
-        setVariantAminoAcid(mutation.getVariantAminoAcid());
+        setVariantAminoAcidMap(mutation.getVariantAminoAcid());
         setTranscriptId(mutation.getTranscriptId());
         setAminoAcidPosition(mutation.getAminoAcidPosition());
     }

diff --git a/model/src/main/java/org/cmo/cancerhotspots/model/TumorTypeComposition.java b/model/src/main/java/org/cmo/cancerhotspots/model/TumorTypeComposition.java
@@ -1,5 +1,6 @@
 package org.cmo.cancerhotspots.model;
 
+import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.univocity.parsers.annotations.Convert;
 import com.univocity.parsers.annotations.Parsed;
 import com.univocity.parsers.annotations.Trim;
@@ -41,11 +42,11 @@ public class TumorTypeComposition
     @Trim
     @Convert(conversionClass = CompositionMapConversion.class)
     @Parsed(field = "Tumor_Type_Composition")
-    private Map<String, Integer> tumorTypeComposition;
+    private Map<String, Integer> tumorTypeCompositionMap;
 
     public TumorTypeComposition()
     {
-        this.tumorTypeComposition = new LinkedHashMap<>();
+        this.tumorTypeCompositionMap = new LinkedHashMap<>();
     }
 
     public String getHugoSymbol()
@@ -68,9 +69,9 @@ public void setResidue(String residue)
         this.residue = residue;
     }
 
-    public void setTumorTypeComposition(Map<String, Integer> tumorTypeComposition)
+    public void setTumorTypeCompositionMap(Map<String, Integer> tumorTypeCompositionMap)
     {
-        this.tumorTypeComposition = tumorTypeComposition;
+        this.tumorTypeCompositionMap = tumorTypeCompositionMap;
     }
 
     public String getReferenceAminoAcid()
@@ -103,35 +104,41 @@ public void setAminoAcidPosition(IntegerRange aminoAcidPosition)
         this.aminoAcidPosition = aminoAcidPosition;
     }
 
-    public Map<String, Integer> getTumorTypeComposition()
+    public Object getTumorTypeComposition()
     {
-        return tumorTypeComposition;
+        return getTumorTypeCompositionMap();
+    }
+
+    @JsonIgnore
+    public Map<String, Integer> getTumorTypeCompositionMap()
+    {
+        return tumorTypeCompositionMap;
     }
 
     public void updateTumorTypeComposition(String tumorType)
     {
         String key = tumorType.toLowerCase();
-        Integer count = tumorTypeComposition.get(key);
+        Integer count = tumorTypeCompositionMap.get(key);
 
         if (count == null)
         {
             count = 0;
         }
 
-        tumorTypeComposition.put(key, count + 1);
+        tumorTypeCompositionMap.put(key, count + 1);
     }
 
     public void merge(TumorTypeComposition composition)
     {
-        DataUtils.mergeCompositions(this.getTumorTypeComposition(),
-                                    composition.getTumorTypeComposition());
+        DataUtils.mergeCompositions(this.getTumorTypeCompositionMap(),
+                                    composition.getTumorTypeCompositionMap());
     }
 
     public Integer tumorCount()
     {
         Integer total = 0;
 
-        for (Integer value: getTumorTypeComposition().values())
+        for (Integer value: getTumorTypeCompositionMap().values())
         {
             total += value;
         }
@@ -141,6 +148,6 @@ public Integer tumorCount()
 
     public Integer tumorTypeCount()
     {
-        return getTumorTypeComposition().keySet().size();
+        return getTumorTypeCompositionMap().keySet().size();
     }
 }
diff --git a/...ence/src/main/java/org/cmo/cancerhotspots/persistence/internal/ClusterRepositoryImpl.java b/...ence/src/main/java/org/cmo/cancerhotspots/persistence/internal/ClusterRepositoryImpl.java
@@ -124,7 +124,7 @@ private Map<String, List<Cluster>> cacheByGeneAndResidue(Iterable<Cluster> clust
         for (Cluster cluster : clusters)
         {
             // populate cache by gene and residue
-            for (String residue : cluster.getResidues().keySet())
+            for (String residue : cluster.getResidueMap().keySet())
             {
                 String key = (cluster.getHugoSymbol() + "_" + residue).toLowerCase();
 

diff --git a/service/src/main/java/org/cmo/cancerhotspots/service/internal/HotspotDataImportService.java b/service/src/main/java/org/cmo/cancerhotspots/service/internal/HotspotDataImportService.java
@@ -76,7 +76,7 @@ public TumorTypeComposition getTumorTypeComposition(Mutation mutation)
         composition.setAminoAcidPosition(mutation.getAminoAcidPosition());
         composition.setReferenceAminoAcid(mutation.mostFrequentReference());
         composition.setVariantAminoAcid(variant);
-        composition.setTumorTypeComposition(mutation.getTumorTypeComposition());
+        composition.setTumorTypeCompositionMap(mutation.getTumorTypeComposition());
         composition.setResidue(residue);
 
         return composition;
@@ -248,7 +248,7 @@ public void generateTumorTypeComposition(Iterable<Mutation> mutations)
                           composition.tumorCount());
             }
 
-            mutation.setTumorTypeComposition(composition.getTumorTypeComposition());
+            mutation.setTumorTypeComposition(composition.getTumorTypeCompositionMap());
             mutation.setTumorTypeCount(composition.tumorTypeCount());
             mutation.setTumorCount(composition.tumorCount());
         }
@@ -403,7 +403,7 @@ private Map<String, Cluster> constructClusterCache(Iterable<Mutation> mutations)
                 cluster = new Cluster();
 
                 cluster.setClusterId(key);
-                cluster.setPdbChains(mutation.getPdbChains());
+                cluster.setPdbChainMap(mutation.getPdbChains());
                 cluster.setpValue(mutation.getpValue());
                 cluster.setHugoSymbol(mutation.getHugoSymbol());