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Jon Belyeu
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include tests
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‎tests/__init__.py‎

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# Tests package

‎tests/conftest.py‎

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"""
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Pytest configuration and common fixtures
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"""
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import tempfile
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from pathlib import Path
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import pytest
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@pytest.fixture
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def temp_dir():
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"""Create a temporary directory for testing"""
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with tempfile.TemporaryDirectory() as tmp_dir:
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yield Path(tmp_dir)
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@pytest.fixture
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def sample_data():
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"""Sample data for testing"""
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return {
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"samples": ["sample1", "sample2", "sample3"],
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"include_list": ["sample1", "sample2"],
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"exclude_list": ["sample3"],
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"file_paths": [
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"/path/to/file1.txt",
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"/path/to/file2.txt",
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"/path/to/dir/file3.txt",
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],
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}
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@pytest.fixture(autouse=True)
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def setup_test_environment(monkeypatch):
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"""Setup test environment variables and paths"""
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# Set up test-specific environment
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monkeypatch.setenv("TESTING", "true")

‎tests/data/expected_outputs/paraviewer/HG002.paraphase.small/cfc1/chr2_130592001_130605000_bokeh.html‎

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<!DOCTYPE html>
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<html lang="en">
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<head>
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<meta charset="utf-8">
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<title>Orographer Plot</title>
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<style>
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html, body {
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box-sizing: border-box;
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display: flow-root;
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height: 100%;
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margin: 0;
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padding: 0;
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}
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</style>
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<script src="https://cdn.bokeh.org/bokeh/release/bokeh-3.9.0.min.js"></script>
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<script src="https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.9.0.min.js"></script>
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<script>
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Bokeh.set_log_level("info");
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</script>
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</head>
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<body>
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<div id="dbc693e8-6d13-4a46-8f1f-88fdc58db67e" data-root-id="p1249" style="display: contents;"></div>
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<script>
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(function() {
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const fn = function() {
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Bokeh.safely(function() {
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(function(root) {
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function embed_document(root) {
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// Load JSON data from external .json.gz file and decompress in browser
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const jsonFile = "chr2_130592001_130605000_bokeh.json.gz?v=1774040304";
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const headerBreakpoint = 825;
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const centerOffsetWide = 20;
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const centerOffsetNarrow = 0;
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const centerOffsetFullWidthAt = 1500;
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function getScaledCenterOffset(windowWidth) {
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if (windowWidth <= headerBreakpoint) return centerOffsetNarrow;
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if (windowWidth >= centerOffsetFullWidthAt) return centerOffsetWide;
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const span = centerOffsetFullWidthAt - headerBreakpoint;
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const ratio = (windowWidth - headerBreakpoint) / span;
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return Math.round(centerOffsetNarrow + ratio * (centerOffsetWide - centerOffsetNarrow));
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}
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function updateResponsiveHeaderByModel() {
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if (!root || !root.Bokeh || !root.Bokeh.documents) return false;
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const docs = root.Bokeh.documents;
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const useWide = window.innerWidth > headerBreakpoint;
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for (let i = 0; i < docs.length; i++) {
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const doc = docs[i];
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const wide = doc.get_model_by_name("orographer_original_region_wide");
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const narrow = doc.get_model_by_name("orographer_original_region_narrow_row");
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const centerOffsetSpacer = doc.get_model_by_name("orographer_center_offset_spacer");
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if (wide && narrow && centerOffsetSpacer) {
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wide.visible = useWide;
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narrow.visible = !useWide;
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centerOffsetSpacer.width = getScaledCenterOffset(window.innerWidth);
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wide.change.emit();
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narrow.change.emit();
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centerOffsetSpacer.change.emit();
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return true;
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}
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}
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return false;
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}
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(async function () {
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try {
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const response = await fetch(jsonFile);
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if (!response.ok) {
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throw new Error(
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"Failed to load JSON file: " + response.status + " " + response.statusText
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);
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}
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const stream = response.body.pipeThrough(new DecompressionStream("gzip"));
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const streamResponse = await new Response(stream);
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const data = await streamResponse.json();
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const docs_json = data.docs_json;
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const render_items = data.render_items;
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root.Bokeh.embed.embed_items(docs_json, render_items);
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let tries = 0;
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const maxTries = 80;
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function tryUpdateHeader() {
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tries += 1;
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if (updateResponsiveHeaderByModel()) return;
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if (tries < maxTries) setTimeout(tryUpdateHeader, 100);
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}
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setTimeout(tryUpdateHeader, 200);
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window.addEventListener("resize", function () {
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updateResponsiveHeaderByModel();
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});
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} catch (error) {
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const errorDiv = document.createElement("div");
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errorDiv.style.cssText =
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"position: fixed; top: 50%; left: 50%; transform: translate(-50%, -50%); " +
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"background: #f44336; color: white; padding: 20px; border-radius: 5px; " +
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"z-index: 10000; font-family: Arial, sans-serif; max-width: 500px;";
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errorDiv.innerHTML =
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"<h3 style=\"margin-top: 0;\">Error Loading Plot Data</h3>" +
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"<p style=\"margin: 10px 0;\">" + error.message + "</p>" +
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"<p style=\"font-size: 12px; margin-top: 10px;\">" +
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"Make sure you are serving files from a web server (not opening file:// directly).</p>" +
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"<p style=\"font-size: 12px;\">Try: <code>orographer deploy --output-dir ./output</code> " +
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"or any static file server.</p>" +
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"<p style=\"font-size: 12px; margin-top: 10px;\">" +
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"Then open: <code>http://localhost:8000/chr2_130592001_130605000_bokeh.html</code></p>";
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document.body.appendChild(errorDiv);
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console.error("Error loading JSON:", error);
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}
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})();
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}
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if (root.Bokeh !== undefined) {
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embed_document(root);
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} else {
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let attempts = 0;
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const timer = setInterval(function(root) {
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if (root.Bokeh !== undefined) {
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clearInterval(timer);
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embed_document(root);
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} else {
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attempts++;
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if (attempts > 100) {
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clearInterval(timer);
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console.log("Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing");
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}
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}
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}, 10, root)
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}
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})(window);
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});
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};
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if (document.readyState != "loading") fn();
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else document.addEventListener("DOMContentLoaded", fn);
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})();
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</script>
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<!-- Modal for details (alignments and variants) -->
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<div id="alignmentModal" style="display:none;position:fixed;z-index:1000;left:0;top:0;width:100%;height:100%;overflow:auto;background-color:rgba(0,0,0,0.4);align-items:center;justify-content:center;">
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<div id="alignmentModalWrapper" style="display:flex;align-items:center;justify-content:center;max-height:90vh;">
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<div id="alignmentModalDialog" style="background:#fefefe;padding:20px;border:1px solid #888;width:400px;">
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<span id="closeModal" style="color:#aaa;float:right;font-size:28px;font-weight:bold;cursor:pointer;">&times;</span>
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<h2 style="margin-top: 0; color: #333;">Details</h2>
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<div id="modalContent" style="font-size: 14px; line-height: 1.8;"></div>
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</div>
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</div>
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</div>
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<script>
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// Modal close handlers and fitAlignmentModalToPlot
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const modal = document.getElementById("alignmentModal");
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const closeBtn = document.getElementById("closeModal");
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window.fitAlignmentModalToPlot = function () {
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const wrapper = document.getElementById("alignmentModalWrapper");
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const dialog = document.getElementById("alignmentModalDialog");
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const root = document.querySelector(".bk-root");
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if (!wrapper || !dialog) return;
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const maxH = root
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? Math.max(120, 0.9 * root.getBoundingClientRect().height)
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: 0.9 * window.innerHeight;
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dialog.style.maxHeight = "";
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dialog.style.transform = "";
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const naturalH = dialog.scrollHeight;
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const naturalW = dialog.offsetWidth || 400;
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if (naturalH > maxH) {
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if (maxH > 0) {
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const scale = maxH / naturalH;
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dialog.style.transform = "scale(" + scale + ")";
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dialog.style.transformOrigin = "top left";
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wrapper.style.width = naturalW * scale + "px";
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wrapper.style.height = naturalH * scale + "px";
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wrapper.style.overflow = "hidden";
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}
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} else {
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dialog.style.transformOrigin = "";
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wrapper.style.width = "";
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wrapper.style.height = "";
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wrapper.style.overflow = "";
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}
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};
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if (closeBtn) closeBtn.onclick = function () { modal.style.display = "none"; };
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window.onclick = function (e) {
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if (e.target === modal) modal.style.display = "none";
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};
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document.addEventListener("keydown", function (e) {
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if (e.key === "Escape") modal.style.display = "none";
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});
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</script>
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</body>
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</html>

‎tests/data/expected_outputs/paraviewer/HG002.paraphase.small/cfc1/chr2_130592001_130605000_bokeh.json.gz‎

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