From 0f4e72e5902e309f082083068b17bffaf2a86565 Mon Sep 17 00:00:00 2001
From: Calla Chennault <51501715+callachennault@users.noreply.github.com>
Date: Wed, 11 Oct 2023 16:48:28 -0400
Subject: [PATCH] Java11 updates (#267)

* java11

* Check if gnResponse is null

* Try checking if gnresponse is null or not successfully annotated

* Try java 11 image

* use updated image name

---------

Co-authored-by: cbioportal import user <cbioportal_importer@pipelines.cbioportal.mskcc.org>
---
 .circleci/config.yml                                       | 2 +-
 .../org/cbioportal/annotator/internal/GenomeNexusImpl.java | 2 +-
 jitpack.yml                                                | 7 +++++++
 pom.xml                                                    | 4 ++--
 4 files changed, 11 insertions(+), 4 deletions(-)
 create mode 100644 jitpack.yml

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 1e551973..9902b2f0 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -7,7 +7,7 @@ jobs:
   build:
     docker:
       # specify the version you desire here
-      - image: circleci/openjdk:8-jdk-browsers
+      - image: cimg/openjdk:11.0.20-browsers
 
       # Specify service dependencies here if necessary
       # CircleCI maintains a library of pre-built images
diff --git a/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java b/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java
index 04587748..7fb9f3bd 100644
--- a/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java
+++ b/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java
@@ -656,7 +656,7 @@ public List<AnnotatedRecord> getAnnotatedRecordsUsingPOST(AnnotationSummaryStati
             AnnotatedRecord annotatedRecord = new AnnotatedRecord(record);
             // if not a failed annotation then convert/merge the response from gn with the maf record
             VariantAnnotation gnResponse = gnResponseVariantKeyMap.get(genomicLocation);
-            if (!gnResponse.isSuccessfullyAnnotated()) {
+            if (gnResponse == null || !gnResponse.isSuccessfullyAnnotated()) {
                 if(reannotate || annotationNeeded(record)) {
                     // only log if record actually attempted annotation
                     annotatedRecord.setANNOTATION_STATUS("FAILED");
diff --git a/jitpack.yml b/jitpack.yml
new file mode 100644
index 00000000..c37cf255
--- /dev/null
+++ b/jitpack.yml
@@ -0,0 +1,7 @@
+jdk:
+  - openjdk11
+before_install:
+  - sdk install java 11.0.20-tem
+  - sdk use java 11.0.20-tem
+  - sdk install maven
+  - mvn -v
diff --git a/pom.xml b/pom.xml
index 50e40675..10014040 100644
--- a/pom.xml
+++ b/pom.xml
@@ -25,7 +25,7 @@
   </parent>
 
   <properties>
-    <java.version>1.8</java.version>
+    <java.version>11</java.version>
     <slf4j.version>1.7.30</slf4j.version>
     <spring.version>5.2.6.RELEASE</spring.version>
     <jackson.version>2.11.2</jackson.version>
@@ -80,7 +80,7 @@
     <dependency>
       <groupId>com.github.cbioportal.cbioportal</groupId>
       <artifactId>maf</artifactId>
-      <version>0b2dfa674e</version>
+      <version>ee5802d836c05ed846d7d1ea3f584febdc07ffa8</version>
       <exclusions>
         <exclusion>
           <groupId>ch.qos.logback</groupId>