Fix custom annotation link (#741)

* - Fix link adding logic

* - Add clarity comment

frontend/src/pages/ontologies/entities/entityPageSections/addLinksToText.tsx

@@ -4,7 +4,6 @@ import { randomString } from "../../../../app/util";
 import EntityLink from "../../../../components/EntityLink";
 import Entity from "../../../../model/Entity";
 import LinkedEntities from "../../../../model/LinkedEntities";
-import Image3D from "../../../../components/Image3D";
 
 export default function addLinksToText(
   text: string,
@@ -13,15 +12,53 @@ export default function addLinksToText(
   currentEntity: Entity | undefined,
   entityType: "ontologies" | "classes" | "properties" | "individuals"
 ) {
-  let linksToSplice: Array<{ start: number; end: number; link: JSX.Element }> =
-    [];
 
+  let linksToSplice: Array<{ start: number; end: number; link: JSX.Element }> = [];
+  let urlMatches: Array<{ start: number; end: number }> = []; // To store the ranges of URLs
+
+  // First, find all URLs and record their ranges
+  const urlRe = /[A-z]+:\/\/[^\s]+/g;
+  for (let match = urlRe.exec(text); match; match = urlRe.exec(text)) {
+    const url = match[0];
+    linksToSplice.push({
+      start: match.index,
+      end: match.index + url.length,
+      link: (
+          <span key={url + randomString()}>
+          <Link
+              to={url}
+              className="link-default pr-1"
+              target="_blank"
+              rel="noopener noreferrer"
+          >
+            {url}
+          </Link>
+        </span>
+      ),
+    });
+    urlMatches.push({ start: match.index, end: match.index + url.length });
+  }
+
+  // Then, process entity IDs
   for (let entityId of Object.keys(linkedEntities.linkedEntities)) {
     for (
       let n = text.indexOf(entityId, 0);
       n !== -1;
       n = text.indexOf(entityId, n)
     ) {
+      // We need to handle this case when entity ID is part of a URL and it then gets linked to an entity but
+      // resulting url is broken. So, we need to keep the URL as is if the entity ID is part of a URL.
+      // Check if the entity ID is within any URL range
+      let isWithinURL = urlMatches.some(
+          (urlRange) =>
+              n >= urlRange.start && n + entityId.length <= urlRange.end
+      );
+      if (isWithinURL) {
+        // Skip this entity ID because it's part of a URL
+        n += entityId.length;
+        continue;
+      }
+
       linksToSplice.push({
         start: n,
         end: n + entityId.length,
@@ -41,65 +78,45 @@ export default function addLinksToText(
     }
   }
 
-  const urlRe = /[A-z]+:\/\/[^\s]+/g;
-  for (let match = urlRe.exec(text); match; match = urlRe.exec(text)) {
-    const url = match[0];
-    // console.log("found match " + url);
-    linksToSplice.push({
-      start: match.index,
-      end: match.index + url.length,
-      link: (
-        <span>
-            <Link
-              key={url + randomString()}
-              to={url}
-              className="link-default pr-1"
-              target="_blank"
-              rel="noopener noreferrer"
-            >
-              {url}
-            </Link>
-        </span>
-      ),
-    });
-  }
-
-  removeOverlapping: for (let n = 0; n < linksToSplice.length; ) {
-    for (let n2 = 0; n2 < linksToSplice.length; ++n2) {
-      let spliceA = linksToSplice[n];
-      let spliceB = linksToSplice[n2];
+  // Remove overlapping links by sorting and keeping the first one
+  linksToSplice.sort((a, b) => a.start - b.start);
 
-      if (spliceA === spliceB) continue;
-
-      // The splices overlap if neither ends before the other starts
-      if (spliceA.end >= spliceB.start && spliceB.end >= spliceA.start) {
-        // console.log("Removing overlapping");
-        linksToSplice.splice(n2, 1);
-        continue removeOverlapping;
-      }
+  // Remove overlaps
+  for (let i = 0; i < linksToSplice.length - 1; i++) {
+    const current = linksToSplice[i];
+    const next = linksToSplice[i + 1];
+    if (current.end > next.start) {
+      // Overlap detected, remove the next link
+      linksToSplice.splice(i + 1, 1);
+      i--; // Adjust index after removal
     }
-    ++n;
   }
 
   if (linksToSplice.length === 0) return text;
 
-  // linksToSplice.sort((a, b) => a.start - b.start);
-  // console.dir(linksToSplice);
+  // Build the final result
   let res: JSX.Element[] = [];
-  let n = 0;
+  let lastIndex = 0;
 
   for (let link of linksToSplice) {
+    if (lastIndex < link.start) {
+      res.push(
+          <Fragment key={randomString()}>
+            {text.substring(lastIndex, link.start)}
+          </Fragment>
+      );
+    }
+    res.push(link.link);
+    lastIndex = link.end;
+  }
+
+  if (lastIndex < text.length) {
     res.push(
-      <Fragment key={text.substring(n, link.start) + randomString()}>
-        {text.substring(n, link.start)}
-      </Fragment>
+        <Fragment key={text.substring(lastIndex) + randomString()}>
+          {text.substring(lastIndex)}
+        </Fragment>
     );
-    res.push(link.link);
-    n = link.end;
   }
-  res.push(
-    <Fragment key={text.slice(n) + randomString()}>{text.slice(n)}</Fragment>
-  );
 
   return res;
 }