Merge branch 'release-1.1.4'

PavlidisLab · Jun 26, 2018 · 9034633 · 9034633
2 parents 0c1c7de + bc9e634
commit 9034633
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Showing 3 changed files with 14 additions and 7 deletions.
diff --git a/pom.xml b/pom.xml
@@ -5,7 +5,7 @@
 
     <groupId>ubc.pavlab</groupId>
     <artifactId>rdp</artifactId>
-    <version>1.1.3</version>
+    <version>1.1.4</version>
 
     <parent>
         <groupId>org.springframework.boot</groupId>

diff --git a/src/main/java/ubc/pavlab/rdp/util/Gene2GoParser.java b/src/main/java/ubc/pavlab/rdp/util/Gene2GoParser.java
@@ -95,15 +95,22 @@ private static void populateAnnotations( InputStream input, Collection<Taxon> ac
             br.lines().map( line -> line.split( "\t" ) ).filter( values -> fastMap.containsKey( Integer.valueOf( values[0] ) ) ).forEach( values -> {
 
                 GeneOntologyTerm term = goService.getTerm( values[2] );
+
+                if ( term == null ) {
+                    log.warn( "Problem finding data for term (" + values[2] + ")" );
+                    return;
+                }
+
                 Gene gene = geneService.load( Integer.valueOf( values[1] ) );
 
-                try {
-                    term.getDirectGenes().add( gene );
-                    gene.getTerms().add( term );
-                } catch (NullPointerException nullE) {
-                    log.warn( "Problem finding data for gene (" + values[1] + ") and term (" + values[2] + ")" );
+                if ( gene == null ) {
+                    log.warn( "Problem finding data for gene (" + values[1] + ")" );
+                    return;
                 }
 
+                term.getDirectGenes().add( gene );
+                gene.getTerms().add( term );
+
             } );
         } catch (IOException e) {
             throw new ParseException( e.getMessage(), 0 );

diff --git a/src/main/resources/ehcache.xml b/src/main/resources/ehcache.xml
@@ -73,7 +73,7 @@
     </cache>
 
     <cache name="ubc.pavlab.rdp.model.UserGene"
-           maxEntriesLocalHeap="200"
+           maxEntriesLocalHeap="500"
            eternal="false"
            overflowToDisk="false"
            timeToLiveSeconds="600"