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When running through robot diff, the generated string overflows the max size #55

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psiotwo opened this issue Apr 4, 2023 · 2 comments · Fixed by #90
Closed

When running through robot diff, the generated string overflows the max size #55

psiotwo opened this issue Apr 4, 2023 · 2 comments · Fixed by #90

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@psiotwo
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psiotwo commented Apr 4, 2023

For large diffs

java -Xmx600G -jar robot.jar diff -l ... -r ... > diff.txt

ends up with

Exception in thread "main" java.lang.OutOfMemoryError
	at java.base/java.lang.AbstractStringBuilder.hugeCapacity(AbstractStringBuilder.java:214)
	at java.base/java.lang.AbstractStringBuilder.newCapacity(AbstractStringBuilder.java:206)
	at java.base/java.lang.AbstractStringBuilder.ensureCapacityInternal(AbstractStringBuilder.java:173)
	at java.base/java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:538)
	at java.base/java.lang.StringBuilder.append(StringBuilder.java:178)
	at org.geneontology.owl.differ.render.BasicDiffRenderer$.format(BasicDiffRenderer.scala:52)
	at org.geneontology.owl.differ.render.BasicDiffRenderer$.renderPlain(BasicDiffRenderer.scala:16)
	at org.geneontology.owl.differ.render.BasicDiffRenderer.renderPlain(BasicDiffRenderer.scala)
	at org.obolibrary.robot.DiffOperation.compare(DiffOperation.java:126)
	at org.obolibrary.robot.DiffCommand.execute(DiffCommand.java:163)
	at org.obolibrary.robot.CommandManager.executeCommand(CommandManager.java:244)
	at org.obolibrary.robot.CommandManager.execute(CommandManager.java:188)
	at org.obolibrary.robot.CommandManager.main(CommandManager.java:135)
	at org.obolibrary.robot.CommandLineInterface.main(CommandLineInterface.java:62)
@psiotwo psiotwo changed the title When running through robot diff, the generated string overflows the maximum When running through robot diff, the generated string overflows the max size Apr 4, 2023
@balhoff
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balhoff commented Apr 5, 2023

I suppose we need some kind of streaming output. That probably would require some changes on the ROBOT side also.

@balhoff
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balhoff commented Nov 19, 2024

I've opened a PR at ROBOT with a new owl-diff version to address this: ontodev/robot#1227

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2 participants