Merge pull request #230 from thewtex/contrib-updates

Author: phcerdan

public/assets/visiblehuman-small.nii.gz

@@ -118,14 +118,7 @@ async function generateArticleArchive(
           `  Downloading thumbnail from ${pageData.frontmatter.thumbnail}`
         );
 
-        const controller = new AbortController();
-        const timeoutId = setTimeout(() => controller.abort(), 30000);
-
-        const response = await fetch(pageData.frontmatter.thumbnail, {
-          signal: controller.signal,
-        });
-
-        clearTimeout(timeoutId);
+        const response = await fetchWithRetry(pageData.frontmatter.thumbnail);
 
         if (response.ok) {
           const buffer = await response.arrayBuffer();
@@ -158,14 +151,7 @@ async function generateArticleArchive(
               `  Downloading ${download.filename} from ${download.url}`
             );
 
-            const controller = new AbortController();
-            const timeoutId = setTimeout(() => controller.abort(), 30000);
-
-            const response = await fetch(download.url, {
-              signal: controller.signal,
-            });
-
-            clearTimeout(timeoutId);
+            const response = await fetchWithRetry(download.url);
 
             if (response.ok) {
               const buffer = await response.arrayBuffer();
@@ -261,6 +247,50 @@ function getArticlesFromConfig(
   }
 }
 
+/**
+ * Fetch with retry logic
+ */
+async function fetchWithRetry(
+  url: string,
+  options: RequestInit = {},
+  maxRetries: number = 3,
+  timeout: number = 60000
+): Promise<Response> {
+  let lastError: Error | null = null;
+
+  for (let attempt = 1; attempt <= maxRetries; attempt++) {
+    try {
+      const controller = new AbortController();
+      const timeoutId = setTimeout(() => controller.abort(), timeout);
+
+      const response = await fetch(url, {
+        ...options,
+        signal: controller.signal,
+      });
+
+      clearTimeout(timeoutId);
+      return response;
+    } catch (error) {
+      lastError = error as Error;
+      console.warn(
+        `Fetch attempt ${attempt}/${maxRetries} failed for ${url}:`,
+        error
+      );
+
+      if (attempt < maxRetries) {
+        const delay = Math.min(1000 * Math.pow(2, attempt - 1), 5000);
+        console.log(`Retrying in ${delay}ms...`);
+        await new Promise((resolve) => setTimeout(resolve, delay));
+      }
+    }
+  }
+
+  throw (
+    lastError ||
+    new Error(`Failed to fetch ${url} after ${maxRetries} attempts`)
+  );
+}
+
 /**
  * Fetch all article IDs from myst.xref.json
  */
@@ -269,14 +299,7 @@ async function getAllArticles(baseUrl: string): Promise<number[]> {
     const xrefUrl = `${baseUrl}/myst.xref.json`;
     console.log(`Fetching all articles from ${xrefUrl}`);
 
-    const controller = new AbortController();
-    const timeoutId = setTimeout(() => controller.abort(), 10000);
-
-    const response = await fetch(xrefUrl, {
-      signal: controller.signal,
-    });
-
-    clearTimeout(timeoutId);
+    const response = await fetchWithRetry(xrefUrl);
 
     if (!response.ok) {
       console.warn(`Failed to fetch myst.xref.json: ${response.status}`);
@@ -346,18 +369,10 @@ const createFilteredPagesLoader = (
           `Fetching article ${articleId} from https://dev-beta.dpid.org/${articleId}?format=myst`
         );
 
-        const controller = new AbortController();
-        const timeoutId = setTimeout(() => controller.abort(), 10000);
-
-        const response = await fetch(
-          `https://dev-beta.dpid.org/${articleId}?format=myst`,
-          {
-            signal: controller.signal,
-          }
+        const response = await fetchWithRetry(
+          `https://dev-beta.dpid.org/${articleId}?format=myst`
         );
 
-        clearTimeout(timeoutId);
-
         if (!response.ok) {
           console.warn(
             `Failed to fetch article ${articleId}: ${response.status}`
@@ -447,17 +462,7 @@ const createFilteredPagesLoader = (
                 `Downloading article.pdf for ${insightJournalId} from ${articlePdfDownload.url}`
               );
 
-              const pdfController = new AbortController();
-              const pdfTimeoutId = setTimeout(
-                () => pdfController.abort(),
-                30000
-              );
-
-              const pdfResponse = await fetch(articlePdfDownload.url, {
-                signal: pdfController.signal,
-              });
-
-              clearTimeout(pdfTimeoutId);
+              const pdfResponse = await fetchWithRetry(articlePdfDownload.url);
 
               if (pdfResponse.ok) {
                 const pdfBuffer = await pdfResponse.arrayBuffer();
@@ -497,56 +502,16 @@ const createFilteredPagesLoader = (
                 `Fetching insight-journal-metadata.json for ${insightJournalId} from ${metadataDownload.url}`
               );
 
-              const metadataController = new AbortController();
-              const metadataTimeoutId = setTimeout(
-                () => metadataController.abort(),
-                10000
+              const metadataResponse = await fetchWithRetry(
+                metadataDownload.url
               );
 
-              const metadataResponse = await fetch(metadataDownload.url, {
-                signal: metadataController.signal,
-              });
-
-              clearTimeout(metadataTimeoutId);
-
               if (metadataResponse.ok) {
                 const metadataJson = await metadataResponse.json();
                 console.log(
                   `✓ Fetched insight-journal-metadata.json for ${insightJournalId}`
                 );
 
-                // Merge tags into keywords
-                if (metadataJson.tags && Array.isArray(metadataJson.tags)) {
-                  // Initialize keywords array if it doesn't exist
-                  if (!pageData.frontmatter) {
-                    pageData.frontmatter = {};
-                  }
-                  if (!Array.isArray(pageData.frontmatter.keywords)) {
-                    pageData.frontmatter.keywords = [];
-                  }
-
-                  // Add tags to keywords if not already present
-                  const existingKeywords = new Set(
-                    pageData.frontmatter.keywords.map((k: string) =>
-                      k.toLowerCase()
-                    )
-                  );
-
-                  for (const tag of metadataJson.tags) {
-                    if (
-                      typeof tag === "string" &&
-                      !existingKeywords.has(tag.toLowerCase())
-                    ) {
-                      pageData.frontmatter.keywords.push(tag);
-                      existingKeywords.add(tag.toLowerCase());
-                    }
-                  }
-
-                  console.log(
-                    `✓ Added ${metadataJson.tags.length} tags to keywords (now ${pageData.frontmatter.keywords.length} total)`
-                  );
-                }
-
                 // Set github property from source_code_git_repo if it contains "github.com"
                 if (
                   metadataJson.source_code_git_repo &&
@@ -582,21 +547,10 @@ const createFilteredPagesLoader = (
                 `Downloading thumbnail for ${insightJournalId} from ${pageData.frontmatter.thumbnail}`
               );
 
-              const thumbnailController = new AbortController();
-              const thumbnailTimeoutId = setTimeout(
-                () => thumbnailController.abort(),
-                30000
+              const thumbnailResponse = await fetchWithRetry(
+                pageData.frontmatter.thumbnail
               );
 
-              const thumbnailResponse = await fetch(
-                pageData.frontmatter.thumbnail,
-                {
-                  signal: thumbnailController.signal,
-                }
-              );
-
-              clearTimeout(thumbnailTimeoutId);
-
               if (thumbnailResponse.ok) {
                 const thumbnailBuffer = await thumbnailResponse.arrayBuffer();
                 const thumbnailsDir = join(publicDir, "thumbnails");

src/assets/use-this-template.png

@@ -13,6 +13,7 @@ import { Image } from 'astro:assets';
 import { Code } from 'astro:components';
 import galileoPortrait from '../assets/GalileoPortraitBySustermans.jpg';
 import merkleTrees from '../assets/Merkle.png';
+import useThisTemplate from '../assets/use-this-template.png';
 
 const title = "About - The Insight Journal";
 const description = "Learn about the Insight Journal's mission, technology, and how to contribute to open, reproducible medical image analysis research.";
@@ -456,6 +457,9 @@ image = itk.imread('data/img1.png')
             <li>Guidelines for including code, data, and visualizations</li>
             <li>Cross-platform continuous integration testing with GitHub Actions</li>
           </ul>
+          <a href="https://github.com/InsightSoftwareConsortium/InsightJournalTemplate" target="_blank" rel="noopener noreferrer">
+            <Image src={useThisTemplate} alt="Use this template screenshot" />
+          </a>
           <p>
             To create a new article repository, click the <i>"Use this template"</i> button on the GitHub page.
             This will create a new repository in your GitHub account that you can clone and edit locally.

src/content.config.ts

@@ -221,7 +221,7 @@ const featuredArticle = {
       };
       const nv1 = new Niivue(defaults);
       await nv1.attachToCanvas(gl1);
-      await nv1.loadVolumes([{ url: "/assets/visiblehuman.nii.gz" }]);
+      await nv1.loadVolumes([{ url: "/assets/visiblehuman-small.nii.gz" }]);
 
       // Set only rendering mode (no slices)
       nv1.setSliceType(nv1.sliceTypeRender);