Test the diagram's elements against real pathways

[adamjohnwright]

DiagramService.getDiagram turns Reactome's layout and graph files into the elements cytoscape draws. That's about 700 lines, and no test covered it.

These tests run it on two real pathways, stored as fixtures exactly as the release serves them:

• R-HSA-9679191, Potential therapeutics for SARS: drugs, entity sets, links.
• R-HSA-2206292, MPS VII: a disease diagram, with normal entities faded out and affected ones crossed out.

What any drawn diagram must satisfy:

• every element has its own id;
• no line points at something that isn't drawn;
• every entity in the layout is drawn as its kind (the classes from nodeTypeMap) and keeps its reactomeId;
• every reaction becomes a node.

And for these pathways:

• each drug carries the drug class;
• each crossed-out entity carries crossed;
• each faded entity is isFadeOut, and whatever replaces it is drawn.

Shown to catch faults: I broke the service four ways, one at a time: dropped the drug class, dropped the crossed class, broke a link's source, and switched off the fade. Each made exactly one test fail; restored, all 18 pass.

avoidOverlap lays sub-pathway labels out in a rendered cytoscape graph, which measures text on a canvas that jsdom doesn't have. The spec stubs a 2D context that measures a character as 6px and draws nothing. The fixtures are minified (about 250 KB in all) and excluded from Prettier.

🤖 Generated with Claude Code