For 'Github' repos, clientPathLink links to companion or pattern file on github

Author: will-moore

idr_gallery/templates/idr_gallery/download_urls.html

@@ -28,7 +28,6 @@ <h1>Download URLs</h1>
     let links = Array.from(document.querySelectorAll('a'));
     // links = links.slice(0,50)
     for (let link of links) {
-      console.log('Checking link:', link);
     // links.forEach(async link => {
       // ignore image viewer links
       if (!link.href || link.href.includes("img_detail")) {
@@ -53,7 +52,6 @@ <h1>Download URLs</h1>
         await fetch(`/link_check/?url=${encodeURIComponent(link.href)}`)
           .then(res => res.json())
           .then(data => {
-            console.log('Link check data:', data);
             if (data.is_valid) {
               link.style.color = 'green';
               link.title = 'Link is valid (checked with server)';
@@ -92,6 +90,7 @@ <h1>Download URLs</h1>
         let downloadUrlIndex = headers.indexOf('download_url');
         let idrIdIndex = headers.indexOf('idrid');
         let imageIdIndex = headers.indexOf('image_id');
+        let dataLocationIndex = headers.indexOf('data_location');
 
         // Create table body - update client_path to URL, based on the download_url column...
         const tbody = table.createTBody();
@@ -103,9 +102,28 @@ <h1>Download URLs</h1>
           let idrId = cells[idrIdIndex];
           let clientPath = cells[clientPathIndex];
           let downloadUrl = cells[downloadUrlIndex];
+          let dataLocation = cells[dataLocationIndex];
           let clientPathUrl;
-          // e.g. https://ftp.ebi.ac.uk/pub/databases/IDR/idr0001-graml-sysgro
-          if (downloadUrl.includes(idrId) && clientPath.includes(idrId)) {
+          if (dataLocation == "Github") {
+            let branch = "main";
+            // e.g. data/idr-metadata/idr0106-kubota-lunglightsheet/experimentA/companions/Mosaic_Image.companion.ome
+            // links to https://github.com/IDR/idr0106-kubota-lunglightsheet/blob/main/experimentA/companions/Mosaic_Image.companion.ome
+            // uod/idr/metadata/idr0052-walther-condensinmap/experimentA/companions/160719_NCAPD2gfpc272c78_MitoSys2/conc/cell0005_R0001.companion.ome
+            // links to https://github.com/IDR/idr0052-walther-condensinmap/blob/master/experimentA/companions/160719_NCAPD2gfpc272c78_MitoSys2/conc/cell0005_R0001.companion.ome
+            // uod/idr/metadata/idr0079-hartmann-lateralline/companions/experimentA/056F63395C/056F63395C.companion.ome
+            // https://github.com/IDR/idr0079-hartmann-lateralline/blob/master/companions/experimentA/056F63395C/056F63395C.companion.ome
+            let relativePath = clientPath.split("metadata/idr")[1];
+            let githubRepo = "idr" + relativePath.split("/")[0];
+            // some repos use "master" branch, so check for those...
+            if ("idr0079,idr0052,idr0065,idr0075,idr0100".includes(githubRepo.split("-")[0])) {
+              branch = "master";
+            }
+            relativePath = relativePath.split("/").slice(1).join("/");
+            clientPathUrl = `https://github.com/IDR/${githubRepo}/blob/${branch}/${relativePath}`;
+            console.log("Client path URL (Github):", clientPath, clientPathUrl);
+
+          } else if (downloadUrl.includes(idrId) && clientPath.includes(idrId)) {
+            // e.g. https://ftp.ebi.ac.uk/pub/databases/IDR/idr0001-graml-sysgro
             let urlBase = downloadUrl.split(idrId)[0];
             let urlPath = clientPath.split(idrId)[1];
             clientPathUrl = urlBase + idrId + urlPath;