feat: cherry-pick #49 diagram edge fixes + drop 'Reaction Diagram' from TOC

Salvaging the still-relevant parts of PR #49 (open since March 30,
since superseded for the description-tab arrow-function form). Two
behaviour changes in diagram.service.ts, plus Eliot's review note:

diagram.service.ts:
- Connectors whose segments are missing endpoints now fall back to
  the underlying nodeP/reactionP positions instead of sourceP/targetP.
  source/target swap for OUTPUT connectors, which was pulling some
  edges the wrong way (Eliot's repro: R-HSA-112307, R-HSA-1296071).
- console.assert near MIN_DIST drops the abs() so the assert reflects
  the actual signed distance (negative d would always pass otherwise).

description-tab.component.ts:
- The `case 'reactionDiagram'` arm of isTOCIncluded picked up the
  same `&& showReactionDiagram()` guard the elements array already
  uses, so reactions whose embedded diagram is suppressed no longer
  leave an orphaned "Reaction Diagram" item in the right-rail TOC
  (Eliot's review comment).

Closes PR #49.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Author: adamjohnwright

projects/pathway-browser/src/app/details/tabs/description-tab/description-tab.component.ts

@@ -759,7 +759,7 @@ export class DescriptionTabComponent implements OnDestroy {
       case 'locationsInPWB':
         return this.showLocations();
       case 'reactionDiagram':
-        return this.isReaction();
+        return this.isReaction() && this.showReactionDiagram();
       case DataKeys.PROTEIN_MARKER:
         return this.proteinMarkers().length + this.rnaMarkers().length > 0;
       case DataKeys.CATALYST_ACTIVITY:

projects/pathway-browser/src/app/services/diagram.service.ts

@@ -747,12 +747,14 @@ export class DiagramService {
         this.addEdgeInfo(reaction, points, 'forward', targetP);
 
         let [from, to] = [points.shift()!, points.pop()!];
-        // Keep fallback direction aligned with edge source/target for connectors that have missing segment endpoints.
-        from = from ?? sourceP;
-        to = to ?? targetP;
+        // Connectors whose segments are missing endpoints fall back to the
+        // underlying node and reaction positions (not source/target, which
+        // swap for OUTPUT connectors and pulled some edges the wrong way).
+        from = from ?? nodeP;
+        to = to ?? reactionP;
         if (equal(from, to)) {
-          from = sourceP;
-          to = targetP;
+          from = nodeP;
+          to = reactionP;
         }
         if (connector.type === 'CATALYST' && connector.endShape) {
           to = scale(connector.endShape.centre || connector.endShape.c);
@@ -783,7 +785,7 @@ export class DiagramService {
           d -= ARROW_MULT * T;
         // console.assert(d > MIN_DIST, `The edge between reaction: R-HSA-${reaction.reactomeId} and entity: R-HSA-${node.reactomeId} in pathway ${id} has a visible length of ${d} which is shorter than ${MIN_DIST}`)
         console.assert(
-          Math.abs(d) >= MIN_DIST,
+          d >= MIN_DIST,
           `${id}\t${diagram.displayName}\t${hasFadeOut}\tR-HSA-${reaction.reactomeId}\tR-HSA-${node.reactomeId}\thttps://release.reactome.org/PathwayBrowser/#/${id}&SEL=R-HSA-${reaction.reactomeId}&FLG=R-HSA-${node.reactomeId}\thttps://reactome-pwp.github.io/PathwayBrowser/${id}?select=${reaction.reactomeId}&flag=${node.reactomeId}`
         );