Fix incorrect error message on missing comma#4085
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pditommaso merged 3 commits intomasterfrom Jul 29, 2023
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Signed-off-by: Ben Sherman <[email protected]>
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What about adding a unit test for capture this behavior |
Signed-off-by: Ben Sherman <[email protected]>
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I added a unit test for process inputs. As for outputs, I modified the example to have a tuple output with missing comma: process foo {
debug true
output:
tuple val(x) val(y) // missing comma
script:
"""
echo "foo ${task.index} ${task.workDir}"
"""
}
workflow {
foo()
}Which produces this syntax: this._out_tuple(new nextflow.script.TokenValCall(new nextflow.script.TokenVar('x'))).val(y)And finally this error: Since outputs are not wrapped in a TokenVar, the Groovy shell encounters a missing variable before it reaches the |
Signed-off-by: Paolo Di Tommaso <[email protected]>
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…ast] Signed-off-by: Ben Sherman <[email protected]> Signed-off-by: Paolo Di Tommaso <[email protected]> Co-authored-by: Paolo Di Tommaso <[email protected]>
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Close #3185
This PR fixes a particularly nasty error message that occurs with missing commas in process inputs/outputs.
Consider the following example:
process foo { debug true input: tuple val(x) val(y) // missing comma script: """ echo "foo ${task.index} ${task.workDir}" """ } workflow { foo(['x', 'y']) }Currently, the script compiles despite the missing comma but then Nextflow reports that the process has been used twice:
The transpiled Groovy code looks like this:
So I just add a
methodMissing()implementation toBaseParamto catch the incorrect.val()call. With that change, the error now looks like this:The error message is correctly called a syntax error and it gives the exact line where it happened.
Note however that it doesn't catch all missing comma errors. For example if you forget a comma before
emit: ..., the script fails to compile so we can't catch the error.