TSUMUGI 1.0.1__py3-none-any.whl

TSUMUGI/web/js/top.js

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+// Track which search mode is active (defaults to 'phenotype')
+let searchMode = "phenotype";
+
+const geneListPlaceHolder = "Trappc11\r\nRab10\r\nInts8\r\nVrk1\r\nSox4"; // Example content for the placeholder
+
+// ====================================================================
+// Handle tab switching and keep searchMode in sync
+// ====================================================================
+function setSearchMode(mode) {
+    searchMode = mode;
+
+    document.getElementById("phenotypeSection").style.display = mode === "phenotype" ? "block" : "none";
+    document.getElementById("geneSection").style.display = mode === "gene" ? "block" : "none";
+    document.getElementById("geneListSection").style.display = mode === "geneList" ? "block" : "none";
+
+    // Update tab button styles
+    document.querySelectorAll(".Tab").forEach((tabButton) => {
+        tabButton.classList.remove("active-tab");
+    });
+    document.querySelectorAll(`button[data-tab="${mode}"]`).forEach((tabButton) => {
+        tabButton.classList.add("active-tab");
+    });
+
+    // Reset all input fields
+    document.querySelectorAll('input[type="text"], textarea').forEach((input) => {
+        input.value = "";
+    });
+    document.querySelectorAll("ul.suggestions").forEach((ul) => {
+        ul.innerHTML = "";
+    });
+
+    // Prefill the textarea when the Gene List tab is selected
+    const geneListTextarea = document.getElementById("geneList");
+    if (mode === "geneList") {
+        geneListTextarea.value = geneListPlaceHolder;
+    }
+
+    // Toggle the correct submit button
+    const submitBtn = document.getElementById("submitBtn");
+    const submitBtnList = document.getElementById("submitBtn_List");
+
+    submitBtn.style.display = mode === "geneList" ? "none" : "inline-block";
+    submitBtnList.style.display = mode === "geneList" ? "inline-block" : "none";
+
+    // Reset the submit buttons according to the active mode
+    if (mode === "geneList") {
+        submitBtnList.disabled = true;
+    } else {
+        submitBtn.disabled = true;
+    }
+
+    if (mode === "geneList") {
+        checkGeneListInput();
+    } else {
+        checkValidInput();
+    }
+}
+
+// Disable the submit button when the Gene List textarea is empty
+function checkGeneListInput() {
+    const geneListTextarea = document.getElementById("geneList");
+    const submitBtnList = document.getElementById("submitBtn_List");
+
+    if (geneListTextarea.value.trim() === "") {
+        submitBtnList.disabled = true;
+    } else {
+        submitBtnList.disabled = false;
+    }
+}
+
+// ====================================================================
+// Fetch JSON data from the URL and assign to phenotypes
+// ====================================================================
+
+const URL_MP_TERMS = "./data/available_mp_terms.json";
+const URL_GENE_SYMBOLS = "./data/available_gene_symbols.txt";
+
+// Track when loading the supporting data completes
+let phenotypesLoaded = fetch(URL_MP_TERMS)
+    .then((response) => response.json())
+    .then((data) => {
+        phenotypes = data;
+    })
+    .catch((error) => console.error("Error fetching phenotypes:", error));
+
+let geneSymbolsLoaded = fetch(URL_GENE_SYMBOLS)
+    .then((response) => response.text())
+    .then((data) => {
+        geneSymbols = data.split("\n").reduce((acc, symbol) => {
+            acc[symbol.trim()] = null;
+            return acc;
+        }, {});
+    })
+    .catch((error) => console.error("Error fetching gene symbols:", error));
+
+// Initialize with the phenotype search mode
+setSearchMode("phenotype");
+
+// Attach click handlers to the tab buttons
+document.querySelectorAll(".Tab").forEach((button) => {
+    button.addEventListener("click", () => setSearchMode(button.dataset.tab));
+});
+
+// Update the button whenever the Gene List textarea changes
+document.getElementById("geneList").addEventListener("input", checkGeneListInput);
+
+// Helper that waits for all prerequisite data to load
+async function ensureDataLoaded() {
+    await Promise.all([phenotypesLoaded, geneSymbolsLoaded]);
+}
+
+// ====================================================================
+// Input handling
+// ====================================================================
+
+// --------------------------------------------------------------------
+// Display search suggestions based on the user's input
+// --------------------------------------------------------------------
+
+async function handleInput(event) {
+    await ensureDataLoaded(); // Ensure reference data has finished loading
+
+    const userInput = event.target.value.toLowerCase();
+    const suggestionList =
+        searchMode === "phenotype"
+            ? document.getElementById("phenotypeSuggestions")
+            : document.getElementById("geneSuggestions");
+
+    const submitButton = document.getElementById("submitBtn");
+
+    if (!submitButton) {
+        console.error(`submitButton not found`);
+        return;
+    }
+
+    suggestionList.innerHTML = "";
+
+    let isValidSelection = false;
+    if (userInput) {
+        const dataDictionary = searchMode === "phenotype" ? phenotypes : geneSymbols;
+        let matchingCandidates = Object.keys(dataDictionary)
+            .map((candidate) => ({
+                text: candidate,
+                score: wordMatchScore(userInput, candidate),
+            }))
+            .sort((a, b) => b.score - a.score)
+            .filter((candidate) => candidate.score > 0)
+            .slice(0, 10);
+
+        matchingCandidates.forEach((candidate) => {
+            const listItem = document.createElement("li");
+            listItem.textContent = candidate.text;
+            listItem.addEventListener("click", function () {
+                event.target.value = candidate.text;
+                suggestionList.innerHTML = "";
+                checkValidInput();
+            });
+            suggestionList.appendChild(listItem);
+        });
+
+        isValidSelection = matchingCandidates.some((candidate) => candidate.text.toLowerCase() === userInput);
+    }
+
+    submitButton.disabled = !isValidSelection;
+}
+
+// --------------------------------------------------------------------
+// Validate the current input field
+// --------------------------------------------------------------------
+async function checkValidInput() {
+    await ensureDataLoaded();
+
+    const userInput =
+        searchMode === "phenotype" ? document.getElementById("phenotype") : document.getElementById("gene");
+
+    let isEmptyInput = userInput.value.trim() === "";
+
+    let isValidSelection = false;
+    if (searchMode === "phenotype") {
+        isValidSelection = phenotypes.hasOwnProperty(userInput.value);
+    } else if (searchMode === "gene") {
+        isValidSelection = geneSymbols.hasOwnProperty(userInput.value);
+    }
+
+    const submitBtn = document.getElementById("submitBtn");
+    submitBtn.disabled = !isValidSelection || isEmptyInput;
+}
+
+// --------------------------------------------------------------------
+// Register input listeners once the datasets are ready
+// --------------------------------------------------------------------
+ensureDataLoaded().then(() => {
+    document.getElementById("phenotype").addEventListener("input", handleInput);
+    document.getElementById("gene").addEventListener("input", handleInput);
+    document.getElementById("phenotype").addEventListener("blur", checkValidInput);
+    document.getElementById("gene").addEventListener("blur", checkValidInput);
+});
+
+// ====================================================================
+// Open the detail page that corresponds to the form selection in a new tab
+// ====================================================================
+function handleFormSubmit(event) {
+    event.preventDefault();
+
+    const rawMode = searchMode;
+    const mode = rawMode === "gene" ? "genesymbol" : rawMode === "geneList" ? "genelist" : rawMode;
+
+    // Run the Gene List workflow directly
+    if (rawMode === "geneList") {
+        fetchGeneData(); // Trigger immediately for gene lists
+        return;
+    }
+
+    // For phenotype/gene searches, navigate to the dedicated page
+    const userInput = mode === "phenotype" ? document.getElementById("phenotype") : document.getElementById("gene");
+    const submitBtn = document.getElementById("submitBtn");
+    const selectedData = mode === "phenotype" ? phenotypes[userInput.value] : userInput.value;
+
+    if (!submitBtn.disabled) {
+        const query = new URLSearchParams({
+            mode,
+            name: selectedData,
+            title: userInput.value,
+        });
+        window.open(`app/viewer.html?${query.toString()}`, "_blank");
+    }
+}
+
+// Listen for the form's submit event
+document.getElementById("searchForm").addEventListener("submit", handleFormSubmit);
+
+// ====================================================================
+// Calculate similarity scores between the input strings
+// ====================================================================
+
+function jaroWinkler(s1, s2) {
+    const m = 0.1;
+    const scalingFactor = 0.1;
+    const s1Len = s1.length;
+    const s2Len = s2.length;
+
+    if (s1Len === 0 || s2Len === 0) return 0;
+
+    const matchWindow = Math.max(0, Math.floor(Math.max(s1Len, s2Len) / 2) - 1);
+    const s1Matches = new Array(s1Len).fill(false);
+    const s2Matches = new Array(s2Len).fill(false);
+    let matches = 0;
+
+    for (let i = 0; i < s1Len; i++) {
+        const start = Math.max(0, i - matchWindow);
+        const end = Math.min(i + matchWindow + 1, s2Len);
+
+        for (let j = start; j < end; j++) {
+            if (s2Matches[j]) continue;
+            if (s1[i] !== s2[j]) continue;
+            s1Matches[i] = true;
+            s2Matches[j] = true;
+            matches++;
+            break;
+        }
+    }
+
+    if (matches === 0) return 0;
+
+    let transpositions = 0;
+    let k = 0;
+
+    for (let i = 0; i < s1Len; i++) {
+        if (!s1Matches[i]) continue;
+        while (!s2Matches[k]) k++;
+        if (s1[i] !== s2[k]) transpositions++;
+        k++;
+    }
+
+    transpositions /= 2;
+
+    const jaroScore = (matches / s1Len + matches / s2Len + (matches - transpositions) / matches) / 3;
+
+    let prefixLength = 0;
+    for (let i = 0; i < Math.min(4, s1Len, s2Len); i++) {
+        if (s1[i] === s2[i]) prefixLength++;
+        else break;
+    }
+
+    return jaroScore + prefixLength * scalingFactor * (1 - jaroScore);
+}
+
+function wordMatchScore(term1, term2) {
+    const term1Words = term1.split(" ").filter(Boolean);
+    const term2Words = term2.split(" ").filter(Boolean);
+    let score = 0;
+
+    term1Words.forEach((word1) => {
+        let maxScore = 0;
+        term2Words.forEach((word2) => {
+            const similarity = jaroWinkler(word1.toLowerCase(), word2.toLowerCase());
+            maxScore = Math.max(maxScore, similarity);
+        });
+
+        score += maxScore;
+    });
+
+    return score;
+}
+
+// ====================================================================
+// Info Tooltip Functionality
+// ====================================================================
+
+// Initialize tooltips when DOM is loaded
+document.addEventListener("DOMContentLoaded", function () {
+    // Handle tooltip click interactions for mobile devices
+    const tooltipIcons = document.querySelectorAll(".info-tooltip-icon");
+
+    tooltipIcons.forEach((icon) => {
+        icon.addEventListener("click", function (e) {
+            e.preventDefault();
+            e.stopPropagation();
+
+            const container = this.parentElement;
+            container.classList.toggle("active");
+
+            // Close other active tooltips
+            document.querySelectorAll(".info-tooltip-container.active").forEach((el) => {
+                if (el !== container) {
+                    el.classList.remove("active");
+                }
+            });
+        });
+    });
+
+    // Close tooltips when clicking outside
+    document.addEventListener("click", function () {
+        document.querySelectorAll(".info-tooltip-container.active").forEach((el) => {
+            el.classList.remove("active");
+        });
+    });
+});

TSUMUGI/web/open_webapp_linux.sh

@@ -0,0 +1,25 @@
+#!/usr/bin/env bash
+
+cd "$(dirname "$0")"
+echo "=== Current working directory ==="
+pwd
+echo
+
+echo "=== Checking for Python executables ==="
+for CMD in py python3 python; do
+    if command -v "$CMD" >/dev/null 2>&1; then
+        echo "Found $CMD: $(command -v "$CMD")"
+        echo
+        echo "=== Starting serve_index.py ==="
+        "$CMD" serve_index.py
+        echo
+        echo "=== Server stopped or exited ==="
+        read -rp "Press Enter to close this window..."
+        exit 0
+    fi
+done
+
+echo "[ERROR] Python not found."
+echo "Please install Python 3 (apt install python3 or yum install python3)."
+echo
+read -rp "Press Enter to close this window..."

TSUMUGI/web/open_webapp_mac.command

@@ -0,0 +1,25 @@
+#!/usr/bin/env bash
+
+cd "$(dirname "$0")"
+echo "=== Current working directory ==="
+pwd
+echo
+
+echo "=== Checking for Python executables ==="
+for CMD in py python3 python; do
+    if command -v "$CMD" >/dev/null 2>&1; then
+        echo "Found $CMD: $(command -v "$CMD")"
+        echo
+        echo "=== Starting serve_index.py ==="
+        "$CMD" serve_index.py
+        echo
+        echo "=== Server stopped or exited ==="
+        read -rp "Press Enter to close this window..."
+        exit 0
+    fi
+done
+
+echo "[ERROR] Python not found."
+echo "Please install Python 3 from https://www.python.org/downloads/ or use Homebrew (brew install python)."
+echo
+read -rp "Press Enter to close this window..."

TSUMUGI/web/open_webapp_windows.bat

@@ -0,0 +1,37 @@
+:: File name: start_server_debug.bat
+@echo off
+setlocal
+pushd %~dp0
+
+echo === Current working directory ===
+cd
+echo.
+
+echo === Trying to launch with Python launcher (py) ===
+where py 2>nul
+if %errorlevel%==0 (
+  echo Found py launcher: & where py
+  echo.
+  py -3 serve_index.py
+  goto :PAUSE_AND_END
+)
+
+echo === Trying python / pythonw ===
+for %%P in (python.exe pythonw.exe) do (
+  where %%P >nul 2>nul
+  if not errorlevel 1 (
+    echo Found %%P: & where %%P
+    echo.
+    %%P serve_index.py
+    goto :PAUSE_AND_END
+  )
+)
+
+echo [ERROR] Python was not found.
+echo Please install Python from https://www.python.org/downloads/
+echo or check your PATH / py launcher settings.
+
+:PAUSE_AND_END
+echo.
+echo === Script finished. Check any error messages above. ===
+pause

TSUMUGI/web/serve_index.py

@@ -0,0 +1,110 @@
+# serve_index.py (WSL/mac/Linux/Windows aware; English-only messages)
+import contextlib
+import http.server
+import os
+import shlex
+import socket
+import socketserver
+import subprocess
+import sys
+import threading
+import webbrowser
+from pathlib import Path
+
+ROOT = Path(__file__).resolve().parent
+INDEX = ROOT / "index.html"
+
+
+def is_wsl() -> bool:
+    try:
+        with open("/proc/sys/kernel/osrelease", encoding="utf-8") as f:
+            return "microsoft" in f.read().lower()
+    except Exception:
+        return False
+
+
+def _popen(cmdlist):
+    subprocess.Popen(cmdlist, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
+
+
+def safe_open_url(url: str) -> None:
+    """Try multiple platform-specific openers; fall back to printing the URL."""
+    tried = []
+
+    # 0) WSL FIRST (because webbrowser may mistakenly pick gio)
+    if is_wsl():
+        for cmd in (["wslview", url], ["explorer.exe", url], ["powershell.exe", "/c", "start", url]):
+            try:
+                _popen(cmd)
+                return
+            except Exception as e:
+                tried.append(f"{' '.join(cmd)}: {e}")
+
+    # 1) Respect $BROWSER (allow commands with args)
+    browser_env = os.environ.get("BROWSER")
+    if browser_env:
+        try:
+            cmd = shlex.split(browser_env) + [url]
+            _popen(cmd)
+            return
+        except Exception as e:
+            tried.append(f"$BROWSER({browser_env}): {e}")
+
+    # 2) Python's webbrowser (may choose gio/xdg-open/open)
+    try:
+        # webbrowser may return True even if the underlying tool fails later; still worth trying.
+        if webbrowser.open_new_tab(url):
+            return
+    except Exception as e:
+        tried.append(f"webbrowser: {e}")
+
+    # 3) macOS
+    if sys.platform == "darwin":
+        try:
+            _popen(["open", url])
+            return
+        except Exception as e:
+            tried.append(f"open: {e}")
+
+    # 4) Linux/Unix (desktop)
+    for cmd in (["xdg-open", url], ["gio", "open", url]):
+        try:
+            _popen(cmd)
+            return
+        except Exception as e:
+            tried.append(f"{' '.join(cmd)}: {e}")
+
+    print("Could not auto-open the browser.")
+    print("Open this URL manually:", url)
+    if tried:
+        print("Tried:", *tried, sep="\n - ")
+
+
+def find_free_port() -> int:
+    with contextlib.closing(socket.socket(socket.AF_INET, socket.SOCK_STREAM)) as s:
+        s.bind(("127.0.0.1", 0))
+        return s.getsockname()[1]
+
+
+class Handler(http.server.SimpleHTTPRequestHandler):
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, directory=str(ROOT), **kwargs)
+
+
+def main():
+    if not INDEX.exists():
+        raise SystemExit("index.html not found. Place this script next to index.html.")
+    port = find_free_port()
+    with socketserver.ThreadingTCPServer(("127.0.0.1", port), Handler) as httpd:
+        url = f"http://127.0.0.1:{port}/index.html"
+        print(f"Serving {ROOT} at {url}")
+        threading.Thread(target=httpd.serve_forever, daemon=True).start()
+        safe_open_url(url)
+        try:
+            threading.Event().wait()
+        finally:
+            httpd.shutdown()
+
+
+if __name__ == "__main__":
+    main()