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cytoscape / RCy3

New version of RCy3, redesigned and collaboratively maintained by Cytoscape developer community
MIT License
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In addAnnotationText (and others), name check seems misplaced #171

Closed bdemchak closed 2 years ago

bdemchak commented 2 years ago

In addAnnotationText and other functions, there is a check to make sure the caller can't create two annotations of the same name. But it's pretty easy to get around the check, and Cytoscape seems to be fine with this. Try:

add_annotation_text(text='ann1') add_annotation_text(text='ann2')

In this situation, I get two annotations, both with name "text", which Cytoscape assigned. Should add_annotation_text (and other annotation functions) be checking for a duplicate name after all??

It seems like Cytoscape is OK with duplicate names, and users can easily create them via the Cytoscape UI.

AlexanderPico commented 2 years ago

Yeah, it's technically ok, but not a great idea. So, this encourages best practice without enforcing it.

bdemchak commented 2 years ago

I'm re-opening this pending the solution to CSD-678. It could well be that Cytoscape can't handle annotations with multiple names when the names are duplicated across multiple networks.

But for that, I think you're still arguing for keeping this check in, and you don't care about the case where the user uses the GUI to create duplicate names.

True?

AlexanderPico commented 2 years ago

True. Mixed use (GUI + automation) is fraught with peril for many reasons. This is just one very very minor one :)