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Add support for using phylorefs as specifiers #73

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@gaurav gaurav commented Feb 10, 2021

This PR adds an example of a phyloreference used as a specifier in another phyloreference. I had to modify the code somewhat to make it work. There is one caveat: given how the logical expression generation system works right now, using relative URIs may be tricky. Unless I can figure out a way to fix that, I'll write in the manuscript that the phyloreference being referenced must be referred to by an absolute URI only.

WIP My example uses a phyloref as the external specifier, but for completeness' sake, it would be nice to include an example of the phyloref as an internal specifier as well. Also, the syntax I've defined for this purpose could also be used to refer to a taxonomic unit by URI (i.e. as an opaque identifier) as a specifier, so it might be a good idea to test this as well.

Should be merged after #72.

gaurav added 21 commits February 9, 2021 01:14
I don't think it's worth creating a new term for this.
This is so that phylorefs with no successes or failures are treated as 
test successes.
@gaurav gaurav changed the base branch from master to add-apomorphy-phyloref February 10, 2021 06:11
@gaurav gaurav force-pushed the add-apomorphy-phyloref branch 2 times, most recently from 4b63d30 to f102381 Compare February 23, 2021 19:00
Base automatically changed from add-apomorphy-phyloref to master March 9, 2021 05:06
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