Literature reference marks are not displaying on some pathways

[khanspers]

This pathway has a lot of literature references for many of the data nodes, but none of them display in the viewer: http://wikipathways.org/index.php/Pathway:WP722

They are visible in PathVisio. See attached for comparison.

This pathway has one lit ref (for the PDIA2/MTTP complex) that is visible in the viewer: http://wikipathways.org/index.php/Pathway:WP430

However, a second pathway-level lit ref is not visible next to the pathway information box as expected.

Observed in Chrome, FF and Safari.

[ariutta]

It looks as if the lit refs that fail to display are all for interactions,
right?

On Fri, Dec 4, 2015 at 9:50 AM, khanspers [email protected] wrote:

This pathway has a lot of literature references for many of the data
nodes, but none of them display in the viewer:
http://wikipathways.org/index.php/Pathway:WP722

They are visible in PathVisio. See attached for comparison.

This pathway has one lit ref (for the PDIA2/MTTP complex) that is visible
in the viewer: http://wikipathways.org/index.php/Pathway:WP430

However, a second pathway-level lit ref is not visible next to the pathway
information box as expected.

Observed in Chrome, FF and Safari.
[image: screen shot 2015-12-04 at 9 50 02 am]
https://cloud.githubusercontent.com/assets/1442197/11596836/77fc596c-9a6c-11e5-9ce1-0c4563fc9041.png
[image: screen shot 2015-12-04 at 9 49 51 am]
https://cloud.githubusercontent.com/assets/1442197/11596835/77fc38c4-9a6c-11e5-88cf-6838d96b5ead.png

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[ariutta]

Oh, "pathway-level" meaning not on any specific node. @AlexanderPico, didn't you say you didn't want those to show up?

So two issues:

1. Lits refs on interactions
2. Pathway-level lit refs

[AlexanderPico]

Re: 2... I don't consider the viewing of numbers on the info box to be all that useful. It's just as easy to deduce that all the references that aren't on a specific node or interaction are for the whole pathway.

I wouldn't be against it if it was a byproduct of other fixes, but I wouldn't want to take time to implement it as a special case.

[khanspers]

Re interactions: yes, it appears the missing references are for interactions. Did we decide against displaying these? If so, please close this.

[ariutta]

@AlexanderPico, you would prefer that:

• references for interactions ARE shown
• pathway-level references ARE NOT shown

right? If so, we need to leave this open for the interaction references.

[AlexanderPico]

Right

[khanspers]

Literature references are still not showing on interactions on some pathways:

Not visible on this pathway: http://www.wikipathways.org/index.php/Pathway:WP4018

But visible on this one: http://www.wikipathways.org/index.php/Pathway:WP554

[AlexanderPico]

Ok. This bug is now focused on displaying literature refs on the interactions. I don't see these on WP4018 nor on WP554, for example. Refs on the infobox are not an issue, we are going to ditch that box entirely anyways.

[AlexanderPico]

@hasanbalci Here's another feature that we used to have and might be easy to turn on again (or provide GUI toggle to hide/show?)