Update views.py and archived_image.html

Author: will-moore

idr_gallery/templates/idr_gallery/archived_image.html

@@ -66,11 +66,9 @@ <h3>Download Image Files</h3>
     {% endif %}
 
     <ul class="download_list">
-      {% for file in fileset.file_urls %}
+      {% for path in fileset.client_paths %}
       <li>
-        {% if file.url %}
-        <a class="file_download" target="_blank" href="{{ file.url }}">{{ file.path }}</a>
-        {% else %} {{ file.path }} {% endif %}
+        <a class="file_download" target="_blank" href="#">{{ path }}</a>
       </li>
       {% endfor %}
     </ul>
@@ -131,9 +129,13 @@ <h3>Download Image Files</h3>
 
   document.addEventListener("DOMContentLoaded", function () {
     // Load download URLs from TSV file in GitHub to fix the download URL for this image
-    fetch(
-      "https://raw.githubusercontent.com/IDR/idr.openmicroscopy.org/refs/heads/master/_data/download_urls.tsv",
-    )
+    let TABLE_URL = 'https://raw.githubusercontent.com/IDR/idr.openmicroscopy.org/refs/heads/master/_data/download_urls.tsv';
+    // check query params for ?tsv= to allow testing with a different TSV file
+    const urlParams = new URLSearchParams(window.location.search);
+    if (urlParams.has('tsv')) {
+      TABLE_URL = urlParams.get('tsv');
+    }
+    fetch(TABLE_URL)
       .then((response) => response.text())
       .then((data) => {
         const lines = data.split("\n");
@@ -158,15 +160,20 @@ <h3>Download Image Files</h3>
             link.textContent = downloadUrl;
             link.href = downloadUrl;
           }
-          const baseUrl = downloadUrl.split(IDR_ID)[0];    // e.g. https://ftp.ebi.ac.uk/pub/databases/IDR/
-          console.log(`Download URL for ${IDR_ID}:`, downloadUrl);
-          if (downloadUrl && downloadUrl !== DOWNLOAD_URL) {
-            console.log(`Updating download URLs from ${DOWNLOAD_URL} to ${downloadUrl}`);
+          
+          // Load "replaceThis" and "withThis" from the TSV file to allow replacing the download URL in the links on this page
+          const replaceThisIndex = headers.indexOf("replace_this");
+          const withThisIndex = headers.indexOf("with_this");
+          const replaceThis = cells[replaceThisIndex];
+          const withThis = cells[withThisIndex] || "";
+          console.log(`replaceThis: ${replaceThis}, withThis: ${withThis}`);
+          if (replaceThis) {
+          // if (downloadUrl && downloadUrl !== DOWNLOAD_URL) {
             // update all ".file_download" links to this download URL
             const fileDownloadLinks =
               document.querySelectorAll(".file_download");
             fileDownloadLinks.forEach((link) => {
-              link.href = link.href.replace(DOWNLOAD_URL, downloadUrl);
+              link.href = link.textContent.replace(replaceThis, withThis);
             });
           }
         } else {

idr_gallery/templates/idr_gallery/download_urls.html

@@ -65,7 +65,13 @@ <h1>Download URLs</h1>
   }
 
   // Fetch the TSV file and display it in a table
-  fetch('https://raw.githubusercontent.com/IDR/idr.openmicroscopy.org/refs/heads/master/_data/download_urls.tsv')
+  let TABLE_URL = 'https://raw.githubusercontent.com/IDR/idr.openmicroscopy.org/refs/heads/master/_data/download_urls.tsv';
+  // check query params for ?tsv= to allow testing with a different TSV file
+  const urlParams = new URLSearchParams(window.location.search);
+  if (urlParams.has('tsv')) {
+    TABLE_URL = urlParams.get('tsv');
+  }
+  fetch(TABLE_URL)
     .then(response => response.text())
     .then(data => {
       const lines = data.split('\n');
@@ -91,6 +97,8 @@ <h1>Download URLs</h1>
         let idrIdIndex = headers.indexOf('idrid');
         let imageIdIndex = headers.indexOf('image_id');
         let dataLocationIndex = headers.indexOf('data_location');
+        let replaceThisIndex = headers.indexOf('replace_this');
+        let withThisIndex = headers.indexOf('with_this');
 
         // Create table body - update client_path to URL, based on the download_url column...
         const tbody = table.createTBody();
@@ -103,34 +111,12 @@ <h1>Download URLs</h1>
           let clientPath = cells[clientPathIndex];
           let downloadUrl = cells[downloadUrlIndex];
           let dataLocation = cells[dataLocationIndex];
+          let replaceThis = cells[replaceThisIndex];
+          let withThis = cells[withThisIndex];
           let clientPathUrl;
-          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}`;
-
-          } 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;
-          }
-          if (clientPathUrl) {
-            // client_path needs patching for /idr0045-reichmann-zygotespindle/
-            clientPathUrl = clientPathUrl.replace("/idr0045-reichmann/", "/idr0045-reichmann-zygotespindle/");
-          }
+          
+          // Simple replace one prefix with another. We rely on the TSV file for correct values...
+          clientPathUrl = clientPath.replace(replaceThis, withThis);
 
           cells.forEach((cellText, colIndex) => {
             const td = document.createElement('td');

idr_gallery/views.py

@@ -586,31 +586,10 @@ def image_viewer(request, iid, conn=None, **kwargs):
     }
     if image.fileset is not None:
         paths = image.getImportedImageFilePaths()
-        file_urls = []
-        for path in paths["client_paths"]:
-            if idrid in path:
-                # we want path *after* /idr0002-heriche-condensation/
-                # split on idrid handles mismatch like idr0047-neuert-yeastmrna with path idr0047-neuert-yeastmRNA
-                file_path = path.split(idrid, 1)[-1]
-                # remove before first "/" if present
-                file_path = file_path.split("/", 1)[-1] if "/" in file_path else file_path
-                if data_location == "Github":
-                    file_urls.append({"url": f"{github_url}/{urllib.parse.quote(file_path)}", "path": file_path})
-                else:
-                    file_urls.append({"url": f"{download_url}/{urllib.parse.quote(file_path)}", "path": file_path})
-            elif path.startswith("bia-idr/S-BIAD582/"):
-                # for idr0151 path is e.g. bia-idr/S-BIAD582/05_wt_wg488-opa546-cadintron594-OPAprotein647/overlays/6a_05_wt_wg488-opa546-cadintron594-OPAprotein647_014_closeup_overlay.tif
-                # Need to manually map to e.g...
-                # https://ftp.ebi.ac.uk/biostudies/fire/S-BIAD/582/S-BIAD582/Files/05_wt_wg488-opa546-cadintron594-OPAprotein647/overlays/6a_05_wt_wg488-opa546-cadintron594-OPAprotein647_014_closeup_overlay.tif
-                url = path.replace("bia-idr/S-BIAD582/", "https://ftp.ebi.ac.uk/biostudies/fire/S-BIAD/582/S-BIAD582/Files/")
-                file_urls.append({"url": url, "path": path})
-            else:
-                file_urls.append({"url": None, "path": path})
         fileset_id = image.fileset.id.val
         rsp_json["fileset"] = {
             "id": fileset_id,
             "client_paths": paths["client_paths"],
-            "file_urls": file_urls,
         }
         rsp_json["is_pattern"] = paths["client_paths"][0].endswith("pattern")