From 695ba10e9b495c6570d480ada9a5568dd3fd3939 Mon Sep 17 00:00:00 2001
From: JacobsonMT <JacobsonMT+github@gmail.com>
Date: Fri, 25 May 2018 14:34:15 -0700
Subject: [PATCH 1/4] update for next development version

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 9290b021..b76b51ae 100644
--- 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-SNAPSHOT</version>
 
     <parent>
         <groupId>org.springframework.boot</groupId>

From ed91785935f2825765d42337f3bdd3458ac78f2f Mon Sep 17 00:00:00 2001
From: JacobsonMT <JacobsonMT+github@gmail.com>
Date: Tue, 26 Jun 2018 16:25:32 -0700
Subject: [PATCH 2/4] Increase default UserGene cache local heap size

---
 src/main/resources/ehcache.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/resources/ehcache.xml b/src/main/resources/ehcache.xml
index 1c3d38e8..c0b024e1 100644
--- 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"

From 6437e06467bae779e78015cefbdf6a1f8a7fb70e Mon Sep 17 00:00:00 2001
From: JacobsonMT <JacobsonMT+github@gmail.com>
Date: Tue, 26 Jun 2018 16:26:38 -0700
Subject: [PATCH 3/4] Fix bug where Gene2GoParser was using null genes

Genes were being added to the direct geneset of terms
even when the gene was not found in memory (null).
---
 .../java/ubc/pavlab/rdp/util/Gene2GoParser.java | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/src/main/java/ubc/pavlab/rdp/util/Gene2GoParser.java b/src/main/java/ubc/pavlab/rdp/util/Gene2GoParser.java
index fb2fe7a1..5a1aa638 100644
--- 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 );

From bc9e63418afa8972b22c0476a5aba4f4dc793348 Mon Sep 17 00:00:00 2001
From: JacobsonMT <JacobsonMT+github@gmail.com>
Date: Tue, 26 Jun 2018 16:30:30 -0700
Subject: [PATCH 4/4] update versions for release

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index b76b51ae..992bda95 100644
--- a/pom.xml
+++ b/pom.xml
@@ -5,7 +5,7 @@
 
     <groupId>ubc.pavlab</groupId>
     <artifactId>rdp</artifactId>
-    <version>1.1.4-SNAPSHOT</version>
+    <version>1.1.4</version>
 
     <parent>
         <groupId>org.springframework.boot</groupId>