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pombase / pombase-config

Shared configuration for PomBase projects
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term1-minus-term2 for web page display config #2

Open mah11 opened 7 years ago

mah11 commented 7 years ago

We would like to have a way to specify "x-minus-y" sets of ontology terms when we specify extension relation display text for the website pages in chado-json-config.yaml.

For example, in the Canto GO BP extension configuration we have an entry for "GO:0034613-GO:0006886", meaning "apply this to anything that is a descendant of GO:0034613, unless it's a descendant of GO:0006886". We want to do the analogous thing in the config for the web pages.

Kim mentioned using something to the effect of "if_not_descendant_of"; I would find a sample yaml stanza very helpful indeed.

Not urgent, especially since the problem on legacy pombase that originally inspired this (https://github.com/pombase/curation/issues/1008) has magically gone away in pombase2. But we'll use it whenever it's available because it'll make the web display and Canto more mutually consistent.

mah11 commented 6 years ago

I think most of this is done, with the possible exception of this:

Kim mentioned using something to the effectt of "if_not_descendant_of"; I would find a sample yaml stanza very helpful indeed.

It looks like that would be useful if we need to say "display text1 if descendant of term1, but in all other cases display text2 for this relation".

kimrutherford commented 6 years ago

in the Canto GO BP extension configuration we have an entry for "GO:0034613-GO:0006886"

I think we should do something similar for the web config. Perhaps change the implementation of "if_descendent_of" to support the same syntax.

If this isn't urgent I'll leave it for now.

mah11 commented 6 years ago

I don't mind what the syntax is, although it would be convenient to have it the same in both configs. No rush, since it's just a display enhancement.

ValWood commented 4 years ago

Do we need this ticket still?

mah11 commented 4 years ago

Well, it requests a feature that we still don't have. But it is low priority.