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Error exporting certain tables to Excel(R) #4000

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kazoompa opened this issue Feb 2, 2025 · 2 comments
Open

Error exporting certain tables to Excel(R) #4000

kazoompa opened this issue Feb 2, 2025 · 2 comments
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@kazoompa
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kazoompa commented Feb 2, 2025

Version information

master, vite

Expected behavior

Like the current opal-demo site, be able to axport a table from CLS (Wave1) or LBLS (1978).

Actual behavior

I get the following errors even when I installed the latest Rock image and re-installed all my related plugins:

org.obiba.magma.MagmaRuntimeException: java.lang.IndexOutOfBoundsException: Index 0 out of bounds for length 0
	at org.obiba.magma.support.Disposables.dispose(Disposables.java:51)
	at org.obiba.opal.r.datasource.RExportDatasource.onDispose(RExportDatasource.java:40)
	at org.obiba.magma.support.AbstractDatasource.dispose(AbstractDatasource.java:122)
	at org.obiba.magma.support.Disposables.dispose(Disposables.java:46)
	at org.obiba.opal.shell.commands.CopyCommand.execute(CopyCommand.java:191)
	at org.obiba.opal.shell.CommandJob.run(CommandJob.java:156)
	at org.apache.shiro.subject.support.SubjectRunnable.doRun(SubjectRunnable.java:120)
	at org.apache.shiro.subject.support.SubjectRunnable.run(SubjectRunnable.java:108)
	at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
	at java.base/java.lang.Thread.run(Thread.java:1583)
Caused by: java.lang.IndexOutOfBoundsException: Index 0 out of bounds for length 0
	at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:100)
	at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:106)
	at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:302)
	at java.base/java.util.Objects.checkIndex(Objects.java:385)
	at java.base/java.util.ArrayList.get(ArrayList.java:427)
	at org.obiba.datasource.opal.readxl.ReadXLDatasourceService$2$1.dispose(ReadXLDatasourceService.java:99)
	at org.obiba.magma.support.Disposables.dispose(Disposables.java:46)
	... 12 more

Reproduction steps

  • Clean build master / vite branch
  • Make sure all plugins are 2.0
  • Export CLS (Wave1) or LBLS (1978)

Browser

Google Chrome

@ymarcon
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ymarcon commented Feb 2, 2025

There are no values in these tables

@ymarcon ymarcon added improvement and removed bug labels Feb 2, 2025
@ymarcon
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ymarcon commented Feb 2, 2025

This is more an improvement: cleanly handle data export request of a table without data.

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