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wikipathways / wikipathways-development

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mim-modification not correct in svg #125

Closed khanspers closed 1 year ago

khanspers commented 1 year ago

Looks like mim-modification arrow is not correct in svg. From Isabel:

"I used the mim-modification arrow to show the phosporylation in my pathway (WP5358), but there seems to be an error somewhere. In PathVisio, the arrow looks correct and I have checked to make sure it is the modification arrow: Schermafbeelding 2023-04-25 om 13 15 14

However, on WikiPathways (I checked both the classic and new website), the arrow looks like this, even after trying again in PathVisio: Schermafbeelding 2023-04-25 om 13 17 28 Is there a way I can resolve this issue?"

Originally posted by @IsabelWassink in https://github.com/wikipathways/wikipathways-help/discussions/32#discussioncomment-5718651

AlexanderPico commented 1 year ago

The fix would be somewhere in the pvjson code that runs in the json-svg job in the on_gpml_change.yml workflow. That code translates Java graphical objects (like arrowheads) into SVG graphical objects. I think @hasanbalci is looking into this code base, so assigning him for now.

hasanbalci commented 1 year ago

Is there a difference between the arrow heads of mim-modification and mim-binding? They look the same in PathVisio and if they really are, I can change its svg to make it the same as mim-binding.

khanspers commented 1 year ago

Yes, mim-modification and mim-binding use the same arrow head.

AlexanderPico commented 1 year ago

@hasanbalci Go ahead and close this ticket if done.