Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

adding a null check to avoid NPE in picard #199

Open
wants to merge 1 commit into
base: master
Choose a base branch
from

Conversation

lbergelson
Copy link
Member

This seems to fix a bug in picard when running picard docs with java 21. The docs pass and look reasonable with it instead of exploding with an NPE.

java.lang.NullPointerException: Cannot invoke "com.sun.source.doctree.DocTree.getKind()" because "t" is null
        at org.broadinstitute.barclay.help.scanners.UnknownInlineTagScanner.scan(UnknownInlineTagScanner.java:44)
        at org.broadinstitute.barclay.help.scanners.UnknownInlineTagScanner.scan(UnknownInlineTagScanner.java:18)
        at jdk.compiler/com.sun.source.util.DocTreeScanner.visitValue(DocTreeScanner.java:680)
        at jdk.compiler/com.sun.tools.javac.tree.DCTree$DCValue.accept(DCTree.java:1402)
        at jdk.compiler/com.sun.source.util.DocTreeScanner.scan(DocTreeScanner.java:90)
        at org.broadinstitute.barclay.help.scanners.UnknownInlineTagScanner.scan(UnknownInlineTagScanner.java:50)
        at org.broadinstitute.barclay.help.scanners.UnknownInlineTagScanner.scan(UnknownInlineTagScanner.java:18)
        at jdk.compiler/com.sun.source.util.DocTreeScanner.scanAndReduce(DocTreeScanner.java:94)
        at jdk.compiler/com.sun.source.util.DocTreeScanner.scan(DocTreeScanner.java:109)
        at jdk.compiler/com.sun.source.util.DocTreeScanner.scanAndReduce(DocTreeScanner.java:117)
        at jdk.compiler/com.sun.source.util.DocTreeScanner.visitDocComment(DocTreeScanner.java:205)
        at jdk.compiler/com.sun.tools.javac.tree.DCTree$DCDocComment.accept(DCTree.java:358)
        at jdk.compiler/com.sun.source.util.DocTreeScanner.scan(DocTreeScanner.java:90)
        at org.broadinstitute.barclay.help.scanners.UnknownInlineTagScanner.scan(UnknownInlineTagScanner.java:50)
        at org.broadinstitute.barclay.help.scanners.JavaLanguageModelScanners.getUnknownInlineTags(JavaLanguageModelScanners.java:140)
        at org.broadinstitute.barclay.help.DefaultDocWorkUnitHandler.addCustomBindings(DefaultDocWorkUnitHandler.java:257)
        at picard.util.help.PicardHelpDocWorkUnitHandler.addCustomBindings(PicardHelpDocWorkUnitHandler.java:74)
        at org.broadinstitute.barclay.help.DefaultDocWorkUnitHandler.processWorkUnit(DefaultDocWorkUnitHandler.java:208)
        at org.broadinstitute.barclay.help.DocWorkUnit.processDoc(DocWorkUnit.java:168)
        at org.broadinstitute.barclay.help.HelpDoclet.lambda$processDocs$1(HelpDoclet.java:305)
        at java.base/java.util.TreeMap$KeySpliterator.forEachRemaining(TreeMap.java:3099)
        at java.base/java.util.stream.ReferencePipeline$Head.forEach(ReferencePipeline.java:762)
        at org.broadinstitute.barclay.help.HelpDoclet.processDocs(HelpDoclet.java:305)
        at org.broadinstitute.barclay.help.HelpDoclet.run(HelpDoclet.java:113)
        at jdk.javadoc/jdk.javadoc.internal.tool.Start.parseAndExecute(Start.java:575)
        at jdk.javadoc/jdk.javadoc.internal.tool.Start.begin(Start.java:398)
        at jdk.javadoc/jdk.javadoc.internal.tool.Start.begin(Start.java:347)
        at jdk.javadoc/jdk.javadoc.internal.tool.Main.execute(Main.java:57)
        at jdk.javadoc/jdk.javadoc.internal.tool.Main.main(Main.java:46)

I don't really understand what's going on though so this really needs more investigation / a test before it goes in I think.

@cmnbroad cmnbroad self-assigned this Dec 19, 2023
@cmnbroad
Copy link
Collaborator

I definitely want to look into this before we merge it.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants