From 3bf146ad4ee73f0f8ec5153c8937919ab6271f7c Mon Sep 17 00:00:00 2001
From: John Konecny <24961694+jfkonecn@users.noreply.github.com>
Date: Mon, 17 Feb 2025 18:29:06 -0500
Subject: [PATCH] a

---
 scripts/generate-news-sections.js             | 75 ++++++++++++++++++-
 .../code-generated/NewsContent01302025.tsx    | 45 +++++++++--
 2 files changed, 111 insertions(+), 9 deletions(-)

diff --git a/scripts/generate-news-sections.js b/scripts/generate-news-sections.js
index f023ba1b0..91d896572 100644
--- a/scripts/generate-news-sections.js
+++ b/scripts/generate-news-sections.js
@@ -9,10 +9,18 @@ const oncokbBaseUrls = [
   'http://www.oncokb.org',
 ];
 
+const autoLinkColumns = [
+  {
+    name: 'Gene',
+  },
+];
+
 const md = new MarkdownIt({
   html: true,
   linkify: true,
 }).use(md => {
+  // https://markdown-it.github.io/markdown-it
+  // https://github.com/markdown-it/markdown-it/blob/master/docs/examples/renderer_rules.md
   md.renderer.rules.table_open = function () {
     return '<div className="table-responsive">\n<table className="table">';
   };
@@ -20,6 +28,70 @@ const md = new MarkdownIt({
   md.renderer.rules.table_close = function () {
     return '</table>\n</div>';
   };
+
+  md.core.ruler.push('add-auto-table-links', state => {
+    let inTh = false;
+    let inTd = false;
+    let columnIdx = 0;
+    let geneIdx = -1;
+    let mutationIdx = -1;
+    let currentGene = '';
+    const columnIndexes = new Array(autoLinkColumns.length).fill(-1);
+    for (const token of state.tokens) {
+      if (token.type === 'table_open') {
+        for (let i = 0; i < columnIndexes.length; i++) {
+          columnIndexes[i] = -1;
+        }
+      } else if (token.type === 'th_open') {
+        inTh = true;
+      } else if (token.type === 'th_close') {
+        inTh = false;
+        columnIdx++;
+      } else if (token.type === 'td_open') {
+        inTd = true;
+      } else if (token.type === 'td_close') {
+        inTd = false;
+        columnIdx++;
+      } else if (token.type === 'tr_open') {
+        columnIdx = 0;
+        currentGene = '';
+      } else if (inTd && columnIdx === geneIdx && token.type === 'inline') {
+        const child = token.children[0];
+        // getAlternativeGenePageLinks();
+        //const children = md.parse(
+        //`[${child.content}](https://oncokb.org/gene/${child.content})`,
+        //{}
+        //)[1].children;
+        currentGene = child.content;
+        child.content = `{getAlternativeGenePageLinks('${child.content}')}`;
+
+        //token.children = children;
+      } else if (inTd && columnIdx === mutationIdx && token.type === 'inline') {
+        const child = token.children[0];
+        if (currentGene === '') {
+          throw new Error(
+            `No gene for this row and mutation "${child.content}"`
+          );
+        }
+        // can't figure out how to make a token on my own so I'm forcing
+        // markdown-it to make me one
+        const alterationPageLinkTags = md
+          .parse('[placeholder](placeholder)', {})[1]
+          .children.filter(x => x.type !== 'text');
+        alterationPageLinkTags[0].type = 'para';
+        alterationPageLinkTags[0].tag = 'AlterationPageLink';
+        alterationPageLinkTags[0].attrSet('hugoSymbol', currentGene);
+        alterationPageLinkTags[0].attrSet('alteration', child.content);
+        alterationPageLinkTags[1].tag = 'AlterationPageLink';
+        token.children = alterationPageLinkTags;
+      } else if (inTh && token.content === 'Gene') {
+        geneIdx = columnIdx;
+      } else if (inTh && token.content === 'Mutation') {
+        mutationIdx = columnIdx;
+      }
+    }
+  });
+
   md.core.ruler.push('fix-links', state => {
     for (const token of state.tokens) {
       if (token.type === 'inline') {
@@ -49,7 +121,6 @@ const md = new MarkdownIt({
             child.tag = 'Link';
             const attr = child.attrs[hrefIndex];
             attr[0] = 'to';
-            console.log(currentUrl);
             attr[1] = currentUrl.replace(replaceUrlString, '');
           }
         }
@@ -119,6 +190,8 @@ files.forEach(file => {
 
   const tsxContent = `import React from 'react';
 import { Link } from 'react-router-dom';
+import { AlterationPageLink, getAlternativeGenePageLinks } from 'app/shared/utils/UrlUtils';
+
 export default function ${componentName}() {
   return (
     <>
diff --git a/src/main/webapp/app/pages/newsPage/code-generated/NewsContent01302025.tsx b/src/main/webapp/app/pages/newsPage/code-generated/NewsContent01302025.tsx
index 45e4af80d..68c4b81c8 100644
--- a/src/main/webapp/app/pages/newsPage/code-generated/NewsContent01302025.tsx
+++ b/src/main/webapp/app/pages/newsPage/code-generated/NewsContent01302025.tsx
@@ -1,5 +1,10 @@
 import React from 'react';
 import { Link } from 'react-router-dom';
+import {
+  AlterationPageLink,
+  getAlternativeGenePageLinks,
+} from 'app/shared/utils/UrlUtils';
+
 export default function NewsContent01302025() {
   return (
     <>
@@ -38,8 +43,14 @@ export default function NewsContent01302025() {
           <tbody>
             <tr>
               <td>2</td>
-              <td>ERBB2</td>
-              <td>Oncogenic Mutations</td>
+              <td>{getAlternativeGenePageLinks('ERBB2')}</td>
+              <td>
+                <AlterationPageLink
+                  href="placeholder"
+                  hugoSymbol="ERBB2"
+                  alteration="Oncogenic Mutations"
+                ></AlterationPageLink>
+              </td>
               <td>Cervical Cancer</td>
               <td>Neratinib</td>
               <td>
@@ -71,8 +82,14 @@ export default function NewsContent01302025() {
           </thead>
           <tbody>
             <tr>
-              <td>KRAS</td>
-              <td>G12C</td>
+              <td>{getAlternativeGenePageLinks('KRAS')}</td>
+              <td>
+                <AlterationPageLink
+                  href="placeholder"
+                  hugoSymbol="KRAS"
+                  alteration="G12C"
+                ></AlterationPageLink>
+              </td>
               <td>Small Bowel Cancer</td>
               <td>
                 <em>Drug(s) promoted in OncoKB™:</em> Adagrasib (Level 2,
@@ -119,8 +136,14 @@ export default function NewsContent01302025() {
           <tbody>
             <tr>
               <td>1</td>
-              <td>ALK</td>
-              <td>Fusions</td>
+              <td>{getAlternativeGenePageLinks('ALK')}</td>
+              <td>
+                <AlterationPageLink
+                  href="placeholder"
+                  hugoSymbol="ALK"
+                  alteration="Fusions"
+                ></AlterationPageLink>
+              </td>
               <td>Non-Small Cell Lung Cancer</td>
               <td>
                 Alectinib, Brigatinib, Certinib, Crizotinib, Lorlatinib (Level
@@ -137,8 +160,14 @@ export default function NewsContent01302025() {
             </tr>
             <tr>
               <td>1</td>
-              <td>KRAS</td>
-              <td>G12C</td>
+              <td>{getAlternativeGenePageLinks('KRAS')}</td>
+              <td>
+                <AlterationPageLink
+                  href="placeholder"
+                  hugoSymbol="KRAS"
+                  alteration="G12C"
+                ></AlterationPageLink>
+              </td>
               <td>Colorectal Cancer</td>
               <td>
                 Sensitivity Adagrasib + Cetuximab (Level 1) Adagrasib +