[Feature] Integrate DOI Links, Handle Cycles in Pathway Viz (#407)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#407

static/js/alpine/components/widgets.js

@@ -293,6 +293,34 @@ document.addEventListener("alpine:init", () => {
     }),
   );
 
+    // PubMed link widget
+  Alpine.data(
+    "doiWidget",
+    (fieldName, data, schema, uiSchema, mode, debugErrors, context = null) => ({
+      ...baseWidget(
+        fieldName,
+        data,
+        schema,
+        uiSchema,
+        mode,
+        debugErrors,
+        context,
+      ),
+
+      get value() {
+        return this.data[this.fieldName] || "";
+      },
+      set value(v) {
+        this.data[this.fieldName] = v;
+      },
+      get doiUrl() {
+        return this.value
+          ? `https://dx.doi.org/${this.value}`
+          : null;
+      },
+    }),
+  );
+
   // Compound link widget
   Alpine.data(
     "compoundWidget",

static/js/pw.js

@@ -581,11 +581,11 @@ function draw(pathway, elem) {
         for (idx in parents) {
             p = nodes[parents[idx]]
             // console.log(p.depth)
-            if (p.depth >= n.depth) {
-                // keep the .5 steps for pseudo nodes
-                n.depth = n.pseudo ? p.depth + 1 : Math.floor(p.depth + 1);
-                // console.log("Adjusting", orig_depth, Math.floor(p.depth + 1));
-            }
+            // if (p.depth >= n.depth) {
+            //     // keep the .5 steps for pseudo nodes
+            //     n.depth = n.pseudo ? p.depth + 1 : Math.floor(p.depth + 1);
+            //     // console.log("Adjusting", orig_depth, Math.floor(p.depth + 1));
+            // }
         }
     });