v1.1 spec regex parsing

[adthrasher]

We recently switched to v1.1 of the WDL spec for our WDL. We noticed that the following WDL definition in one of our tasks is considered valid by miniwdl check in a version 1.1 document.

        String prefix = sub(
            basename(fastq),
            "([_\.][rR][12])?(\.subsampled)?\.(fastq|fq)(\.gz)?$",
            ""
        )

We were expecting this to show a validation error as the 1.1 spec indicates that backslashes need to be double-escaped in these regular expressions (https://github.com/openwdl/wdl/blob/main/versions/1.1/SPEC.md#string-substring-string-string).

Is miniwdl being lenient in its checking in this case? Or is our understanding of the spec incorrect?

Both \\ and \ seem to be accepted by miniwdl check.

[claymcleod]

Just to build on what Andrew said, it appears that WDL v1.0 restricts the escaped characters that can be included within a string: https://github.com/openwdl/wdl/blob/main/versions/1.0/SPEC.md#whitespace-strings-identifiers-constants. The above string has an escaped \., which is not allowed in a string, but miniwdl check passes that.

[mlin]

Just looked into this a little and found a relevant check commented out,

https://github.com/chanzuckerberg/miniwdl/blob/7344a900f408c2703e4dc4504c42a4f1d1844984/WDL/_parser.py#L63-L67

Sooo, I need to figure out if that was an oversight or what... 😅