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barclay fails to set collection arguments initialized with an immutable collection #4702

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droazen opened this issue Apr 24, 2018 · 3 comments
Open

barclay fails to set collection arguments initialized with an immutable collection #4702

droazen opened this issue Apr 24, 2018 · 3 comments
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@cmnbroad
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Barclay bug

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@droazen
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droazen commented Apr 24, 2018 •
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If you have a barclay @Argument field of type List, barclay will fail to set the field value properly when the argument is specified if the List is initialized using an immutable Collection, such as that returned by Collections.emptyList(). Example error:

java.lang.UnsupportedOperationException
	at java.util.AbstractList.add(AbstractList.java:148)
	at java.util.AbstractList.add(AbstractList.java:108)
	at org.broadinstitute.barclay.argparser.CommandLineArgumentParser.setArgument(CommandLineArgumentParser.java:706)
	at org.broadinstitute.barclay.argparser.CommandLineArgumentParser.parseArguments(CommandLineArgumentParser.java:427)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.parseArgs(CommandLineProgram.java:220)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:194)
	at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
	at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
	at org.broadinstitute.hellbender.Main.main(Main.java:289)

Ideally, barclay should detect immutable collections and replace them with mutable ones when necessary.
@droazen droazen added this to the Engine-2Q2018 milestone Apr 24, 2018
@droazen
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droazen commented Apr 24, 2018

For @cmnbroad

@magicDGS
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There's a solution here: broadinstitute/barclay#102

droazen added a commit that referenced this issue Apr 24, 2018
@droazen
Fix two instances of immutable collections being used to initialize L…
bf20ae5 
…ist arguments

Barclay can't currently handle immutable collections in @argument values due to
#4702

Tests for these arguments are coming in a separate, larger branch, but I
wanted to get the fixes in first since it's such a simple fix.
@droazen droazen mentioned this issue Apr 24, 2018
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@magicDGS
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Also, some discussion about what to do with immutable collections in barclay is here: broadinstitute/barclay#100

droazen added a commit that referenced this issue Apr 25, 2018
@droazen
Fix two instances of immutable collections being used to initialize L…
bc640b9 
…ist arguments (#4703)

Barclay can't currently handle immutable collections in @argument values due to
#4702

Tests for these arguments are coming in a separate, larger branch, but I
wanted to get the fixes in first since it's such a simple fix.
cwhelan pushed a commit to cwhelan/gatk-linked-reads that referenced this issue May 25, 2018
@droazen @cwhelan
Fix two instances of immutable collections being used to initialize L…
fc80547 
…ist arguments (broadinstitute#4703)

Barclay can't currently handle immutable collections in @argument values due to
broadinstitute#4702

Tests for these arguments are coming in a separate, larger branch, but I
wanted to get the fixes in first since it's such a simple fix.
@droazen droazen removed this from the Engine-2Q2018 milestone Oct 4, 2018
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@droazen @magicDGS @cmnbroad