clean up code

Author: leexgh

component/src/main/java/org/cbioportal/genome_nexus/component/annotation/HugoGeneSymbolResolver.java

@@ -30,14 +30,13 @@ public String resolve(TranscriptConsequence transcriptConsequence)
         }
 
         String symbol = transcriptConsequence.getGeneSymbol();
-        if (symbol == null || symbol.trim().isEmpty()) {
+        if (symbol == null || symbol.isEmpty()) {
             return null;
         }
 
         String hgncId = transcriptConsequence.getHgncId();
-        if (hgncId != null && !hgncId.trim().isEmpty()) {
-            String mapped = ensemblRepository.getOfficialHugoSymbol(symbol, hgncId);
-            return mapped;
+        if (hgncId != null && !hgncId.isEmpty()) {
+            return ensemblRepository.getOfficialHugoSymbol(symbol, hgncId);
         }
         return ensemblRepository.getOfficialHugoSymbol(symbol);
     }

component/src/main/java/org/cbioportal/genome_nexus/component/annotation/IndexBuilder.java

@@ -32,7 +32,7 @@ public Index buildIndex(VariantAnnotation variantAnnotation)
     {
         Index index = new Index();
         index.setVariant(this.resolveVariant(variantAnnotation));
-          List<String> hugoSymbols;
+        List<String> hugoSymbols;
         if (Boolean.TRUE.equals(this.replaceOldGeneSymbol)) {
             hugoSymbols = this.hugoGeneSymbolResolver.resolveAllHugoGeneSymbols(variantAnnotation);
         } else {
@@ -74,7 +74,7 @@ private List<String> resolveAllOriginalGeneSymbols(VariantAnnotation variantAnno
         Set<String> hugoSymbolSet = new HashSet<>();
 
         for (TranscriptConsequence tc : variantAnnotation.getTranscriptConsequences()) {
-            if (tc.getGeneSymbol() != null && !tc.getGeneSymbol().trim().isEmpty()) {
+            if (tc.getGeneSymbol() != null && !tc.getGeneSymbol().isEmpty()) {
                 hugoSymbolSet.add(tc.getGeneSymbol());
             }
         }

persistence/src/main/java/org/cbioportal/genome_nexus/persistence/internal/EnsemblRepositoryImpl.java

@@ -215,21 +215,21 @@ public String findEntrezGeneIdByHugoSymbol(String hugoSymbol) {
 
     @Override
     public List<String> findEntrezGeneIdByHugoSymbol(String hugoSymbol, Boolean searchInAliases) {
-        List<String> results = new ArrayList<>();
-        String direct = hugoSymbolToEntrezGeneIdMap.get(hugoSymbol);
-        if (direct != null && !results.contains(direct)) {
-            results.add(direct);
+        List<String> entrezGeneIds = new ArrayList<>();
+        String entrezGeneId = hugoSymbolToEntrezGeneIdMap.get(hugoSymbol);
+        if (entrezGeneId != null && !entrezGeneIds.contains(entrezGeneId)) {
+            entrezGeneIds.add(entrezGeneId);
         }
 
         if (Boolean.TRUE.equals(searchInAliases)) {
             List<String> aliasMatches = geneAliasToEntrezGeneIdMap.get(hugoSymbol);
             if (aliasMatches != null) {
                 for (String id : aliasMatches) {
-                    if (id != null && !results.contains(id)) results.add(id);
+                    if (id != null && !entrezGeneIds.contains(id)) entrezGeneIds.add(id);
                 }
             }
         }
-        return results;
+        return entrezGeneIds;
     }
 
     @Override

web/src/main/resources/application.properties.EXAMPLE

@@ -74,4 +74,4 @@ prioritize_cancer_gene_transcripts=true
 cache.enabled=true
 
 # replace old HGNC gene symbol to the latest HGNC gene symbol in annotationSummary - transcriptConsequenceSummary
-replace_old_hgnc_gene_symbol=true
+replace_old_hgnc_gene_symbol=true

web/src/test/java/org/cbioportal/genome_nexus/web/NucleotideContextIntegrationTest.java

@@ -1,14 +1,13 @@
 package org.cbioportal.genome_nexus.web;
 
 import org.cbioportal.genome_nexus.model.NucleotideContext;
+import static org.junit.Assert.assertEquals;
 import org.junit.Test;
 import org.junit.runner.RunWith;
 import org.springframework.boot.test.context.SpringBootTest;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.web.client.RestTemplate;
 
-import static org.junit.Assert.assertEquals;
-
 @RunWith(SpringJUnit4ClassRunner.class)
 @SpringBootTest(
     webEnvironment = SpringBootTest.WebEnvironment.DEFINED_PORT,