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Issue converting wdl files with input{} in workflow {} #9

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Nitromon opened this issue Jul 3, 2020 · 2 comments
Open

Issue converting wdl files with input{} in workflow {} #9

Nitromon opened this issue Jul 3, 2020 · 2 comments

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@Nitromon
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Nitromon commented Jul 3, 2020

I have a wdl file from Bammetrics that is unable to convert to cwl and throws an error wdl.parser.SyntaxError: Unexpected symbol (line 26, col 5) when parsing parse__gen10. Expected rbrace, got <string:26:5 input "aW5wdXQ=">.

This occurs with any WDL file having a format:
workflow xyz { input {abc} }
Since $input is not considered a $wf_body_element. I want to make changes to the parser.py but am unable to generate it using Hermes Parser Generator since I don't have the original grammar file to modify and input into the tool. May I get assistance on where to find it?

@mr-c
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mr-c commented Jul 3, 2020

Hello @Nitromon , it looks like the parser is no longer supported: https://github.com/broadinstitute/pywdl which contains a dead link that I think is supposed to go to https://github.com/openwdl/wdl/tree/master/versions/draft-2/parsers/python (but that is obviously out of date as you have a version 1 and not a WDL draft-2 document)

Perhaps this project could be updated to use https://github.com/chanzuckerberg/miniwdl which is also written in Python

There appears to be a v1.0 Hermes Grammer at https://github.com/openwdl/wdl/blob/master/versions/1.0/parsers/hermes/grammar.hgr

@mr-c
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mr-c commented Jul 3, 2020

Here is the corresponding auto-generated WDL v1.0 parser for Python: https://github.com/openwdl/wdl/tree/master/versions/1.0/parsers/hermes/python

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