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 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 @@ - 1.8 + 11 1.7.30 5.2.6.RELEASE 2.11.2 @@ -80,7 +80,7 @@ com.github.cbioportal.cbioportal maf - 0b2dfa674e + ee5802d836c05ed846d7d1ea3f584febdc07ffa8 ch.qos.logback