v4.26

package.json

@@ -89,6 +89,7 @@
     "@types/classnames": "^2.2.9",
     "@types/enzyme": "3.10.5",
     "@types/jest": "25.2.1",
+    "@types/markdown-it": "^14.1.2",
     "@types/node": "13.13.4",
     "@types/pluralize": "0.0.29",
     "@types/react": "16.9.34",
@@ -143,6 +144,7 @@
     "lint-staged": "8.2.1",
     "mini-css-extract-plugin": "0.9.0",
     "moment-locales-webpack-plugin": "1.2.0",
+    "markdown-it": "^14.1.0",
     "node-sass": "^4.12.0",
     "optimize-css-assets-webpack-plugin": "5.0.3",
     "postcss-loader": "3.0.0",
@@ -190,6 +192,7 @@
     "updateAPI": "yarn run fetchAPI && yarn run buildAPI",
     "fetchAPI": "curl http://localhost:9095/v2/api-docs | json | grep -v basePath | grep -v termsOfService | grep -v host > src/main/webapp/app/shared/api/generated/API-docs.json",
     "buildAPI": "node scripts/generate-api.js src/main/webapp/app/shared/api/generated API",
+    "buildNewPages": "node scripts/generate-news-sections.js -f src/main/webapp/app/pages/newsPage/markdown -o src/main/webapp/app/pages/newsPage/code-generated && yarn run prettier --write \"{,src/main/webapp/app/pages/newsPage/code-generated/**/}*.{md,json,ts,tsx,css,scss,yml}\"",
     "updateOncoKbAPI": "yarn run fetchOncoKbAPI && yarn run buildOncoKbAPI",
     "fetchOncoKbAPI": "curl http://localhost:8080/oncokb-public/api/v1/v2/api-docs?group=Private%20APIs | json | grep -v basePath | grep -v termsOfService | grep -v host > src/main/webapp/app/shared/api/generated/OncoKbAPI-docs.json && curl http://localhost:8080/oncokb-public/api/private/v2/api-docs | json | grep -v basePath | grep -v termsOfService | grep -v host > src/main/webapp/app/shared/api/generated/OncoKbPrivateAPI-docs.json",
     "buildOncoKbAPI": "node scripts/generate-api.js src/main/webapp/app/shared/api/generated OncoKbAPI OncoKbPrivateAPI",

pom.xml

@@ -5,7 +5,7 @@
 
     <groupId>org.mskcc.cbio.oncokb</groupId>
     <artifactId>public-website</artifactId>
-    <version>3.18.0</version>
+    <version>3.19.0</version>
     <packaging>jar</packaging>
     <name>OncoKB Public Website</name>
 

scripts/generate-news-sections.js

@@ -0,0 +1,361 @@
+const fs = require('fs');
+const path = require('path');
+const MarkdownIt = require('markdown-it');
+
+const oncokbBaseUrls = [
+  'https://oncokb.org',
+  'http://oncokb.org',
+  'https://www.oncokb.org',
+  'http://www.oncokb.org',
+  'https://beta.oncokb.org',
+  'http://beta.oncokb.org',
+];
+
+const objectPropertyMark = '-------------------';
+const objectPropertyMarkRegex = new RegExp(
+  `"${objectPropertyMark}(.*)${objectPropertyMark}"`,
+  'gm'
+);
+
+/**
+ * Escapes special characters in a string to be used in a regular expression.
+ *
+ * This ensures that characters such as `.*+?^${}()|[]\` are treated as literals.
+ *
+ * @param {string} string - The input string to escape.
+ * @returns {string} - The escaped string safe for use in a regex.
+ *
+ * @example
+ * const escaped = escapeRegExp("Hello (world)!");
+ * console.log(escaped); // "Hello \\(world\\)!"
+ */
+function escapeRegExp(string) {
+  return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string
+}
+
+/**
+ * Replaces all occurrences of a substring in a given string.
+ *
+ * Since `String.prototype.replaceAll()` is not available in older Node.js versions,
+ * this function uses `RegExp` with the global flag.
+ *
+ * @param {string} str - The original string.
+ * @param {string} match - The substring to be replaced.
+ * @param {string} replacement - The replacement string.
+ * @returns {string} - The modified string with all occurrences replaced.
+ *
+ * @example
+ * const result = replaceAll("Hello world, world!", "world", "Earth");
+ * console.log(result); // "Hello Earth, Earth!"
+ */
+function replaceAll(str, match, replacement) {
+  return str.replace(new RegExp(escapeRegExp(match), 'g'), () => replacement);
+}
+
+/**
+ * Decodes specific HTML entities in a given string.
+ *
+ * This function currently only replaces `"` with `"`.
+ * Extend this function if more entities need to be decoded.
+ *
+ * @param {string} text - The input string containing HTML entities.
+ * @returns {string} - The decoded string.
+ *
+ * @example
+ * const decoded = decodeHtmlEntities("This is "quoted" text.");
+ * console.log(decoded); // 'This is "quoted" text.'
+ */
+function decodeHtmlEntities(text) {
+  return replaceAll(text, '"', '"');
+}
+
+/**
+ * Fixes HTML-escaped entities in a specific pattern within a string.
+ *
+ * This function finds occurrences matching `objectPropertyMarkRegex`,
+ * extracts the inner content, decodes HTML entities, and wraps it in `{}`.
+ *
+ * @param {string} htmlString - The input HTML string to process.
+ * @returns {string} - The fixed string with decoded entities.
+ *
+ * @example
+ * const fixed = fixHtmlString('"----["Example"]----"');
+ * console.log(fixed); // '{["Example]"}'
+ */
+function fixHtmlString(htmlString) {
+  return htmlString.replace(objectPropertyMarkRegex, (_, group) => {
+    return `{${decodeHtmlEntities(group)}}`;
+  });
+}
+
+/**
+ * @param {import('markdown-it')} md - The markdown-it instance used for parsing.
+ * @param {import('markdown-it').StateCore} state - The state object containing Markdown parsing tokens.
+ * @returns {boolean | undefined} - The modified string with all occurrences replaced.
+ *
+ * @throws {Error} If a mutation is found in a row without an associated gene.
+ */
+function newlyAddedGenes(md, state) {
+  let foundNewlyAddedGenes = false;
+  let index = 0;
+  let toRemoveStart = -1;
+  let toRemoveEnd = -1;
+  const genes = [];
+  for (const token of state.tokens) {
+    if (token.content.toLowerCase().includes('new gene')) {
+      foundNewlyAddedGenes = true;
+      toRemoveStart = index;
+    } else if (foundNewlyAddedGenes && token.type === 'bullet_list_close') {
+      toRemoveEnd = index;
+      break;
+    } else if (foundNewlyAddedGenes && token.type === 'inline') {
+      genes.push(token.content);
+    }
+    index++;
+  }
+  if (toRemoveStart < 0 && toRemoveEnd < 0) {
+    return true;
+  } else if (toRemoveStart < 0 || toRemoveEnd < 0) {
+    throw new Error(
+      `Found one remove gene index, but not the other (${toRemoveStart}, ${toRemoveEnd})`
+    );
+  }
+
+  const alterationPageLinkTags = createMarkdownToken(
+    md,
+    'NewlyAddedGenesListItem'
+  );
+  alterationPageLinkTags[0].attrSet(
+    'genes',
+    `${objectPropertyMark}${JSON.stringify(genes)}${objectPropertyMark}`
+  );
+  alterationPageLinkTags[1].tag = 'NewlyAddedGenesListItem';
+
+  state.tokens = state.tokens.filter(
+    (_, idx) => idx < toRemoveStart || idx > toRemoveEnd
+  );
+  state.tokens.splice(toRemoveStart, 0, ...alterationPageLinkTags);
+
+  return true;
+}
+
+/**
+ * @param {import('markdown-it').StateCore} state - The state object containing Markdown parsing tokens.
+ * @returns {boolean | undefined} - The modified string with all occurrences replaced.
+ *
+ * @throws {Error} If a mutation is found in a row without an associated gene.
+ */
+function fixLinks(state) {
+  for (const token of state.tokens) {
+    if (token.type === 'inline') {
+      let foundLocalLink = false;
+      for (const child of token.children) {
+        if (child.type === 'link_close' && foundLocalLink) {
+          foundLocalLink = false;
+          child.tag = 'Link';
+          continue;
+        } else if (child.type !== 'link_open') {
+          continue;
+        }
+        const hrefIndex = child.attrIndex('href');
+        if (hrefIndex < 0) {
+          continue;
+        }
+        const currentUrl = child.attrs[hrefIndex][1];
+        let replaceUrlString = '';
+        for (const url of oncokbBaseUrls) {
+          if (currentUrl.startsWith(url)) {
+            replaceUrlString = url;
+            foundLocalLink = true;
+            break;
+          }
+        }
+        if (foundLocalLink) {
+          child.tag = 'Link';
+          const attr = child.attrs[hrefIndex];
+          attr[0] = 'to';
+          attr[1] = currentUrl.replace(replaceUrlString, '');
+        }
+      }
+    }
+  }
+}
+
+/**
+ * @param {import('markdown-it')} md - The markdown-it instance used for token processing.
+ * @param {import('markdown-it').StateCore} state - The state object containing Markdown parsing tokens.
+ * @returns {boolean | undefined} - The modified string with all occurrences replaced.
+ *
+ * @throws {Error} If a mutation is found in a row without an associated gene.
+ */
+function addAutoTableLinks(md, state) {
+  let inTh = false;
+  let inTd = false;
+  let columnIdx = 0;
+  let geneIdx = -1;
+  let mutationIdx = -1;
+  let currentGene = '';
+  for (const token of state.tokens) {
+    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];
+      currentGene = child.content;
+      child.content = `{getAlternativeGenePageLinks('${child.content}')}`;
+    } else if (inTd && columnIdx === mutationIdx && token.type === 'inline') {
+      const child = token.children[0];
+      if (currentGene === '') {
+        throw new Error(`No gene for this row and mutation "${child.content}"`);
+      }
+      const alterationPageLinkTags = createMarkdownToken(
+        md,
+        'AlterationPageLink'
+      );
+      alterationPageLinkTags[0].attrSet('hugoSymbol', currentGene);
+      alterationPageLinkTags[0].attrSet('alteration', child.content);
+      token.children = alterationPageLinkTags;
+    } else if (inTh && token.content === 'Gene') {
+      geneIdx = columnIdx;
+    } else if (inTh && token.content === 'Mutation') {
+      mutationIdx = columnIdx;
+    }
+  }
+}
+
+/**
+ * Creates a Markdown token with a specified tag.
+ *
+ * @param {import('markdown-it')} md - The markdown-it instance used for parsing.
+ * @param {string} tag - The tag to set on the first non-text token.
+ * @returns {import('markdown-it').Token[]} - An array of markdown-it token objects with the modified tag.
+ *
+ * @example
+ * const md = require('markdown-it')();
+ * const tokens = createMarkdownToken(md, 'custom-tag');
+ * console.log(tokens);
+ */
+function createMarkdownToken(md, tag) {
+  // 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 = tag;
+  alterationPageLinkTags[0].attrs = [];
+  alterationPageLinkTags[1].tag = tag;
+  return alterationPageLinkTags;
+}
+
+const md = new MarkdownIt({
+  html: true,
+  linkify: true,
+  breaks: 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">';
+  };
+
+  md.renderer.rules.table_close = function () {
+    return '</table>\n</div>';
+  };
+
+  md.core.ruler.push('add-auto-table-links', state => {
+    addAutoTableLinks(md, state);
+  });
+
+  md.core.ruler.push('fix-links', state => fixLinks(state));
+  md.core.ruler.push('fix-styles', state => {
+    for (const token of state.tokens) {
+      if (token.attrs != null && token.attrs.length > 0) {
+        token.attrs = token.attrs.filter(([name]) => name !== 'style');
+      }
+      if (token.type === 'table_open') {
+        token.attrSet('className', 'table');
+      }
+    }
+    return true;
+  });
+  md.core.ruler.push('newly-added-genes', state => {
+    newlyAddedGenes(md, state);
+  });
+});
+
+const args = process.argv.slice(2);
+let inputFolder = null;
+let outputFolder = null;
+
+for (let i = 0; i < args.length; i++) {
+  if (args[i] === '-f' && args[i + 1]) {
+    inputFolder = path.resolve(args[i + 1]);
+  } else if (args[i] === '-o' && args[i + 1]) {
+    outputFolder = path.resolve(args[i + 1]);
+  }
+}
+
+if (!inputFolder || !outputFolder) {
+  console.error(
+    'Error: Both -f (input folder) and -o (output folder) arguments are required.'
+  );
+  process.exit(1);
+}
+
+// Ensure input folder exists
+if (!fs.existsSync(inputFolder) || !fs.statSync(inputFolder).isDirectory()) {
+  console.error(
+    `Error: Input folder "${inputFolder}" does not exist or is not a directory.`
+  );
+  process.exit(1);
+}
+
+// Ensure output folder exists, or create it
+if (!fs.existsSync(outputFolder)) {
+  fs.mkdirSync(outputFolder, { recursive: true });
+}
+
+// Read all Markdown files in the input folder
+const files = fs.readdirSync(inputFolder).filter(file => file.endsWith('.md'));
+
+if (files.length === 0) {
+  console.warn(`Warning: No markdown files found in "${inputFolder}".`);
+}
+
+files.forEach(file => {
+  const filePath = path.join(inputFolder, file);
+  const content = fs.readFileSync(filePath, 'utf-8');
+  const htmlContent = fixHtmlString(md.render(content));
+
+  const componentName = path
+    .basename(file, '.md')
+    .replace(/[^a-zA-Z0-9]/g, '_');
+
+  const tsxContent = `import React from 'react';
+import { Link } from 'react-router-dom';
+import { AlterationPageLink, getAlternativeGenePageLinks } from 'app/shared/utils/UrlUtils';
+import { NewlyAddedGenesListItem } from 'app/pages/newsPage/NewlyAddedGenesListItem';
+
+export default function ${componentName}() {
+  return (
+    <>
+      ${htmlContent}
+    </>
+  );
+}`;
+
+  const outputFilePath = path.join(outputFolder, `${componentName}.tsx`);
+  fs.writeFileSync(outputFilePath, tsxContent, 'utf-8');
+  console.log(`Generated: ${outputFilePath}`);
+});