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Merge remote-tracking branch 'origin/master' into searchengine_container_data_url
2 parents 55e75bb + 72294b3 commit cef6db5

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Lines changed: 540 additions & 11 deletions

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‎.bumpversion.cfg‎

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[bumpversion]
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current_version = 3.14.1.dev0
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current_version = 3.15.1.dev0
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commit = True
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tag = True
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sign_tags = True

‎idr_gallery/data/tabs.py‎

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"text": "Find a specific IDR study from a publication. View images and Regions of Interest (ROIs) in IDR. Explore study metadata.",
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},
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{
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"id": "JboK6Kds28U",
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"id": "sxgfFXgpJ7U",
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"title": "From gene to phenotypes",
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"text": "Query images by gene. Explore retrieved images and metadata, including associated phenotypes. View images in context of a plate.",
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"text": "Query images by gene. Explore retrieved images and metadata, including associated phenotypes. View images in BioFile Finder.",
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},
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{
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"id": "stF4Q4m5GZg",

‎idr_gallery/templates/idr_gallery/archived_image.html‎

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{% extends "idr_gallery/base.html" %} {% block content %}
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<style>
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article {
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max-width: 800px;
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margin: 0 auto;
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padding: 20px;
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}
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.download_list {
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list-style: none;
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background: white;
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margin: 0;
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padding: 15px;
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margin-bottom: 20px;
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border-radius: 5px;
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box-shadow: 0 2px 5px rgba(0,0,0,0.1);
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border: solid 1px lightgrey;
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}
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a.file_download {
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color: #03A9F4;
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text-decoration: none;
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font-weight: normal;
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font-size: 14px;
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}
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a.file_download:hover {
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text-decoration: underline;
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}
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</style>
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<article>
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<div style="display: flex; gap: 20px; flex-direction: row;">
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<div style="flex: 0 0 96px;">
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<img src="{% url 'render_thumbnail' image.id %}" alt="Thumbnail for {{ image.name }}" border: 1px solid #ccc; border-radius: 5px;">
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</div>
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<div style="flex: 1 1 auto">
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<h2>Image Name: {{ image.name }}</h2>
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<strong>ID: {{ image.id }}</strong><br />
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<strong>Study: {{ idr_study }}</strong>
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<p>
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This image is not viewable online. <br/>
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The IDR only supports the viewing of OME-Zarr images.
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</p>
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</div>
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</div>
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{% if fileset %}
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<h3>Download Image Files</h3>
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{% if data_location == "Github" %}
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<p>
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This image is defined by a {% if is_pattern %}.pattern{% else %}companion.ome{% endif %} file
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and sibling .tiff files which are on GitHub (links below).
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Each .tiff file is a symbolic link to the actual image file in
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<!-- link is updated from download_urls.tsv info -->
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<a id="download_url_tsv" target="_blank" class="file_download" href="{{ download_url }}">{{ download_url }}</a>.
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</p>
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{% elif fileset.file_urls|length == 1 %}
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<p>There is 1 file associated with this image. Click to download:</p>
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{% else %}
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<p>
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There are {{ fileset.file_urls|length }} files associated with this image
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which can be downloaded from the links below. For more download options,
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including bulk download using Globus or FTP clients, see the
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<a href="/about/download.html">IDR Data download page</a>.
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</p>
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{% endif %}
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<ul class="download_list">
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{% for file in fileset.file_urls %}
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<li>
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{% if file.url %}
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<a class="file_download" target="_blank" href="{{ file.url }}">{{ file.path }}</a>
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{% else %} {{ file.path }} {% endif %}
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</li>
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{% endfor %}
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</ul>
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{% else %}
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<!-- Only expected for some OME-Zarr images (this page won't show for them) -->
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<p>No associated fileset.</p>
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{% endif %}
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<!-- <details><summary>Extra info (debug)</summary>
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<ul style="background: white">
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<li>Image Path: {{ img_path }}</li>
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<li>Data Location: {{ data_location }}</li>
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<li>Is Zarr?: {{ is_zarr }}</li>
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<li>Download URL from IDR: <a href="{{ download_url }}">{{ download_url }}</a></li>
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<li>BIA NGFF ID: {{ bia_ngff_id }}</li>
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</ul>
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</details> -->
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</article>
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<script>
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const IDR_ID_NAME = "{{ idr_study }}";
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let IDR_ID = IDR_ID_NAME.split("-")[0];
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let DOWNLOAD_URL = "{{ download_url }}";
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function checkLinks() {
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let links = Array.from(document.querySelectorAll("a"));
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// links = links.slice(0,50)
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links.forEach((link) => {
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// ignore image viewer links
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if (!link.href || link.href.includes("img_detail")) return;
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// no cors-origin check for now, just check if the link is valid
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fetch(link.href, { method: "HEAD" })
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.then((response) => {
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link.style.color = response.ok ? "green" : "orange";
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link.title = response.ok ? "Link is valid" : "Link is broken";
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})
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.catch((error) => {
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// show "pink" and re-try with server-side check, to avoid CORS issues
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console.error("Error checking link:", error);
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link.style.color = "pink";
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link.title = "Error checking link";
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fetch(`/link_check/?url=${encodeURIComponent(link.href)}`)
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.then((res) => res.json())
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.then((data) => {
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console.log("Link check data:", data);
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if (data.is_valid) {
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link.style.color = "green";
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link.title = "Link is valid (checked with server)";
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} else {
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link.style.color = "red";
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link.title = `Link is broken: ${data.error}`;
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}
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});
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});
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});
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}
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document.addEventListener("DOMContentLoaded", function () {
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// Load download URLs from TSV file in GitHub to fix the download URL for this image
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fetch(
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"https://raw.githubusercontent.com/IDR/idr.openmicroscopy.org/refs/heads/master/_data/download_urls.tsv",
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)
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.then((response) => response.text())
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.then((data) => {
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const lines = data.split("\n");
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// Use first line as header to find column names...
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const headers = lines[0].split("\t");
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const idrIndex = headers.indexOf("idrid");
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// Find the line for this IDR ID
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const studyLine = lines.find(
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(line) => line.split("\t")[idrIndex] === IDR_ID,
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);
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console.log(`Found line for ${IDR_ID}:`, studyLine);
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if (studyLine) {
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const cells = studyLine.split("\t");
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const downloadUrlIndex = headers.indexOf("download_url");
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// downloadUrl e.g. https://ftp.ebi.ac.uk/pub/databases/IDR/idr0047-neuert-yeastmrna/
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const downloadUrl = cells[downloadUrlIndex];
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let link = document.getElementById("download_url_tsv");
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if (link) {
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link.textContent = downloadUrl;
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link.href = downloadUrl;
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}
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const baseUrl = downloadUrl.split(IDR_ID)[0]; // e.g. https://ftp.ebi.ac.uk/pub/databases/IDR/
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console.log(`Download URL for ${IDR_ID}:`, downloadUrl);
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if (downloadUrl && downloadUrl !== DOWNLOAD_URL) {
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console.log(`Updating download URLs from ${DOWNLOAD_URL} to ${downloadUrl}`);
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// update all ".file_download" links to this download URL
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const fileDownloadLinks =
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document.querySelectorAll(".file_download");
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fileDownloadLinks.forEach((link) => {
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link.href = link.href.replace(DOWNLOAD_URL, downloadUrl);
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});
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}
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} else {
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console.warn(`No download URL found for ${IDR_ID} in TSV file`);
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}
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// After updating links, check them if ?check_links=1 is in the URL
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const urlParams = new URLSearchParams(window.location.search);
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if (urlParams.get("check_links")) {
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checkLinks();
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}
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});
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});
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</script>
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{% endblock %}

‎idr_gallery/templates/idr_gallery/download_urls.html‎

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{% extends "idr_gallery/base.html" %}
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{% block content %}
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<style>
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body {
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background-color: #f6f6f9;
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}
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table {
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width: 100%;
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border-collapse: collapse;
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font-size: 12px;
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}
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</style>
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<h1>Download URLs</h1>
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<div id="table-container">
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<p>Loading download URLs...</p>
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</div>
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<script>
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async function checkLinks() {
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let links = Array.from(document.querySelectorAll('a'));
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// links = links.slice(0,50)
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for (let link of links) {
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// links.forEach(async link => {
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// ignore image viewer links
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if (!link.href || link.href.includes("img_detail")) {
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continue;
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};
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// no cors-origin check for now, just check if the link is valid
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let ok = await fetch(link.href, { method: 'HEAD'})
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.then(response => {
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link.style.color = response.ok ? 'green' : 'orange';
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link.title = response.ok ? 'Link is valid' : 'Link is broken';
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return true;
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})
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.catch(error => {
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console.error('Error checking link:', error);
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return false;
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});
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if (!ok) {
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// show "pink" and re-try with server-side check, to avoid CORS issues
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link.style.color = 'pink';
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link.title = 'Error checking link';
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await fetch(`/link_check/?url=${encodeURIComponent(link.href)}`)
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.then(res => res.json())
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.then(data => {
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if (data.is_valid) {
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link.style.color = 'green';
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link.title = 'Link is valid (checked with server)';
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} else {
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link.style.color = 'red';
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link.title = `Link is broken: ${data.error}`;
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}
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});
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}
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};
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}
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// Fetch the TSV file and display it in a table
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fetch('https://raw.githubusercontent.com/IDR/idr.openmicroscopy.org/refs/heads/master/_data/download_urls.tsv')
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.then(response => response.text())
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.then(data => {
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const lines = data.split('\n');
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const table = document.createElement('table');
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table.style.width = '100%';
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table.style.borderCollapse = 'collapse';
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// Create table header
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const header = table.createTHead();
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const headerRow = header.insertRow();
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const headers = lines[0].split('\t');
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headers.forEach(headerText => {
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const th = document.createElement('th');
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th.textContent = headerText;
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th.style.border = '1px solid #ddd';
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th.style.padding = '2px';
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th.style.backgroundColor = '#f2f2f2';
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headerRow.appendChild(th);
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});
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let clientPathIndex = headers.indexOf('client_path');
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let downloadUrlIndex = headers.indexOf('download_url');
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let idrIdIndex = headers.indexOf('idrid');
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let imageIdIndex = headers.indexOf('image_id');
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let dataLocationIndex = headers.indexOf('data_location');
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// Create table body - update client_path to URL, based on the download_url column...
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const tbody = table.createTBody();
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lines.slice(1).forEach(line => {
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if (line.trim() === '') return; // Skip empty lines
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const row = tbody.insertRow();
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const cells = line.split('\t');
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let idrId = cells[idrIdIndex];
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let clientPath = cells[clientPathIndex];
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let downloadUrl = cells[downloadUrlIndex];
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let dataLocation = cells[dataLocationIndex];
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let clientPathUrl;
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if (dataLocation == "Github") {
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let branch = "main";
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// e.g. data/idr-metadata/idr0106-kubota-lunglightsheet/experimentA/companions/Mosaic_Image.companion.ome
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// links to https://github.com/IDR/idr0106-kubota-lunglightsheet/blob/main/experimentA/companions/Mosaic_Image.companion.ome
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// uod/idr/metadata/idr0052-walther-condensinmap/experimentA/companions/160719_NCAPD2gfpc272c78_MitoSys2/conc/cell0005_R0001.companion.ome
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// links to https://github.com/IDR/idr0052-walther-condensinmap/blob/master/experimentA/companions/160719_NCAPD2gfpc272c78_MitoSys2/conc/cell0005_R0001.companion.ome
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// uod/idr/metadata/idr0079-hartmann-lateralline/companions/experimentA/056F63395C/056F63395C.companion.ome
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// https://github.com/IDR/idr0079-hartmann-lateralline/blob/master/companions/experimentA/056F63395C/056F63395C.companion.ome
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let relativePath = clientPath.split("metadata/idr")[1];
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let githubRepo = "idr" + relativePath.split("/")[0];
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// some repos use "master" branch, so check for those...
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if ("idr0079,idr0052,idr0065,idr0075,idr0100".includes(githubRepo.split("-")[0])) {
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branch = "master";
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}
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relativePath = relativePath.split("/").slice(1).join("/");
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clientPathUrl = `https://github.com/IDR/${githubRepo}/blob/${branch}/${relativePath}`;
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} else if (downloadUrl.includes(idrId) && clientPath.includes(idrId)) {
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// e.g. https://ftp.ebi.ac.uk/pub/databases/IDR/idr0001-graml-sysgro
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let urlBase = downloadUrl.split(idrId)[0];
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let urlPath = clientPath.split(idrId)[1];
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clientPathUrl = urlBase + idrId + urlPath;
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}
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if (clientPathUrl) {
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// client_path needs patching for /idr0045-reichmann-zygotespindle/
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clientPathUrl = clientPathUrl.replace("/idr0045-reichmann/", "/idr0045-reichmann-zygotespindle/");
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}
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cells.forEach((cellText, colIndex) => {
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const td = document.createElement('td');
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td.style.border = '1px solid #ddd';
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td.style.padding = '2px';
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// handle links or 'client_path' column...
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if (cellText.startsWith('http') || (headers[colIndex] === 'client_path' && clientPathUrl)) {
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const link = document.createElement('a');
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// escape the URL to avoid issues with special characters in the client_path
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link.href = encodeURI(cellText.startsWith('http') ? cellText : clientPathUrl).replace("#", "%23");
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// fix idr0045 as above
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cellText = cellText.replace("/idr0045-reichmann/", "/idr0045-reichmann-zygotespindle/");
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link.textContent = cellText;
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link.target = '_blank';
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td.textContent = '';
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td.appendChild(link);
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} else if (colIndex == imageIdIndex) {
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// Add link to image viewer at /webclient/img_detail/1884807/
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const link = document.createElement('a');
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link.href = encodeURI(`/webclient/img_detail/${cellText}/?check_links=true`).replace("#", "%23");
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link.textContent = cellText;
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link.target = '_blank';
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td.textContent = '';
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td.appendChild(link);
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} else {
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td.textContent = cellText;
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}
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row.appendChild(td);
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});
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});
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const tableContainer = document.getElementById('table-container');
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tableContainer.innerHTML = '';
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tableContainer.appendChild(table);
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checkLinks();
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})
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.catch(error => {
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console.error('Error fetching TSV file:', error);
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const tableContainer = document.getElementById('table-container');
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tableContainer.innerHTML = '<p>Error loading download URLs.</p>';
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});
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</script>
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{% endblock %}

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