Codex/make table column order user configurable

main.py

@@ -7,6 +7,7 @@
 from typing import List
 from pathlib import Path
 import random
+import asyncio
 
 import csv
 import os
@@ -122,6 +123,10 @@ def setup_logging():
 from auth.supabase.connection import create_supabase_client
 
 
+# Lock to serialize backup and restore operations
+db_lock = asyncio.Lock()
+
+
 # local udata prefernces
 UDAT_FILE = "./etc/udat.json"
 # Create if not exists
@@ -255,6 +260,14 @@ def highlight_json_changes(old_json_str, new_json_str):
     return '\n'.join(old_json_highlighted), '\n'.join(new_json_highlighted)
 
 
+def apply_column_order(columns, order_pref):
+    """Reorder columns based on user preference."""
+    if isinstance(order_pref, list):
+        ordered = [c for c in order_pref if c in columns]
+        remaining = [c for c in columns if c not in ordered]
+        return ordered + remaining
+    return columns
+
 async def get_relationship_data(obj):
     relationship_data = {}
     for relationship in obj.__mapper__.relationships:
@@ -311,6 +324,47 @@ async def get_relationship_data(obj):
     return relationship_data
 
 
+def _pg_env():
+    env = os.environ.copy()
+    env.setdefault("PGHOST", "localhost")
+    env.setdefault("PGPORT", "5445")
+    env.setdefault("PGUSER", env.get("USER", "bloom"))
+    env.setdefault("PGPASSWORD", env.get("PGPASSWORD", "passw0rd"))
+    env.setdefault("PGDBNAME", env.get("PGDBNAME", "bloom"))
+    return env
+
+
+def pg_dump_file(out_path: Path):
+    env = _pg_env()
+    cmd = ["pg_dump", "-Fp", env["PGDBNAME"]]
+    with open(out_path, "w") as fh:
+        subprocess.run(cmd, stdout=fh, check=True, env=env)
+
+
+def pg_restore_file(sql_path: Path):
+    env = _pg_env()
+    # Drop existing objects to ensure the restore can proceed
+    drop_cmd = ["psql", env["PGDBNAME"], "-c", "DROP SCHEMA IF EXISTS public CASCADE; CREATE SCHEMA public;"]
+    subprocess.run(drop_cmd, check=True, env=env)
+
+    cmd = ["psql", env["PGDBNAME"], "-v", "ON_ERROR_STOP=1"]
+
+    with open(sql_path, "r") as fh:
+        try:
+            subprocess.run(
+                cmd,
+                stdin=fh,
+                check=True,
+                env=env,
+                capture_output=True,
+                text=True,
+            )
+        except subprocess.CalledProcessError as e:
+            raise RuntimeError(
+                f"Database restore failed: {e.stderr.strip()}"
+            ) from e
+
+
 class RequireAuthException(HTTPException):
     def __init__(self, detail: str):
         super().__init__(status_code=403, detail=detail)
@@ -729,6 +783,8 @@ async def query_by_euids(request: Request, file_euids: str = Form(...)):
             table_data.append(row)
 
         user_data = request.session.get("user_data", {})
+        order_pref = user_data.get("search_columns_order")
+        columns = apply_column_order(columns, order_pref)
         style = {"skin_css": user_data.get("style_css", "static/skins/bloom.css")}
 
         content = templates.get_template("search_results.html").render(
@@ -804,6 +860,13 @@ async def admin(request: Request, _auth=Depends(require_auth), dest="na"):
     ]  # Get just the file names
 
     printer_info["style_css"] = csss
+
+    backup_path = user_data.get("db_backup_path", "./db_backups")
+    if os.path.isdir(backup_path):
+        backup_files = sorted([p.name for p in Path(backup_path).glob("*.sql")], reverse=True)
+    else:
+        backup_files = []
+
     style = {"skin_css": user_data.get("style_css", "static/skins/bloom.css")}
 
     # Rendering the template with the dynamic content
@@ -813,6 +876,8 @@ async def admin(request: Request, _auth=Depends(require_auth), dest="na"):
         user_data=user_data,
         printer_info=printer_info,
         dest_section=dest_section,
+        backup_path=backup_path,
+        backups=backup_files,
         udat=request.session["user_data"],
     )
 
@@ -851,6 +916,33 @@ async def update_preference(request: Request, auth: dict = Depends(require_auth)
         return {"status": "error", "message": "User not found in user data"}
 
 
+@app.post("/db_backup")
+async def db_backup(request: Request, _auth=Depends(require_auth)):
+    backup_path = request.session["user_data"].get("db_backup_path", "./db_backups")
+    os.makedirs(backup_path, exist_ok=True)
+    outfile = Path(backup_path) / f"backup_{get_clean_timestamp()}.sql"
+    async with db_lock:
+        await asyncio.to_thread(pg_dump_file, outfile)
+    return RedirectResponse(url="/admin?dest=backup", status_code=303)
+
+
+@app.post("/db_restore")
+async def db_restore(request: Request, filename: str = Form(...), _auth=Depends(require_auth)):
+    backup_path = request.session["user_data"].get("db_backup_path", "./db_backups")
+    target = Path(backup_path) / filename
+    if not target.exists():
+        raise HTTPException(status_code=404, detail="Backup not found")
+    os.makedirs(backup_path, exist_ok=True)
+    new_backup = Path(backup_path) / f"pre_restore_{get_clean_timestamp()}.sql"
+    async with db_lock:
+        await asyncio.to_thread(pg_dump_file, new_backup)
+        try:
+            await asyncio.to_thread(pg_restore_file, target)
+        except Exception as e:
+            raise HTTPException(status_code=500, detail=str(e))
+    return RedirectResponse(url="/admin?dest=backup", status_code=303)
+
+
 @app.get("/queue_details", response_class=HTMLResponse)
 async def queue_details(
     request: Request, queue_euid, page=1, _auth=Depends(require_auth)
@@ -1940,10 +2032,12 @@ async def delete_edge(request: Request, _auth=Depends(require_auth)):
 
 
 def generate_unique_upload_key():
-    color = random.choice(BVARS.pantone_colors)
-    invertebrate = random.choice(BVARS.marine_invertebrates)
-    number = random.randint(0, 1000000)
-    return f"{color.replace(' ','_')}_{invertebrate.replace(' ','_')}_{number}"
+    """Return a datestamp for default file set names.
+
+    The datestamp format follows ``YYYYMMDDTHHMMSS`` as required when a
+    file set name isn't explicitly provided.
+    """
+    return datetime.utcnow().strftime("%Y%m%dT%H%M%S")
 
 
 
@@ -2276,7 +2370,12 @@ async def create_file(
         user_data = request.session.get("user_data", {})
         style = {"skin_css": user_data.get("style_css", "static/skins/bloom.css")}
         content = templates.get_template("create_file_report.html").render(
-            request=request, results=results, style=style, udat=user_data
+            request=request,
+            results=results,
+            style=style,
+            udat=user_data,
+            file_set_euid=new_file_set.euid,
+            file_set_name=file_set_name,
         )
 
         return HTMLResponse(content=content)
@@ -2505,6 +2604,8 @@ async def search_files(
             table_data.append(row)
 
         user_data = request.session.get("user_data", {})
+        order_pref = user_data.get("search_columns_order")
+        columns = apply_column_order(columns, order_pref)
         style = {"skin_css": user_data.get("style_css", "static/skins/bloom.css")}
         fset_templates = bobdb.query_template_by_component_v2("file","file_set","generic","1.0")
 
@@ -2714,6 +2815,8 @@ async def search_file_sets(
             table_data.append(row)
 
         user_data = request.session.get("user_data", {})
+        order_pref = user_data.get("file_set_search_columns_order")
+        columns = apply_column_order(columns, order_pref)
         style = {"skin_css": user_data.get("style_css", "static/skins/bloom.css")}
 
         num_results = len(table_data)
@@ -3115,11 +3218,11 @@ def directory_listing(directory: Path, file_path: str) -> HTMLResponse:
     for item in items:
         if item.is_dir():
             files.append(
-                f'<li><a href="/serve_endpoint/{file_path.lstrip('/')}/{item.name}/">{item.name}/</a></li>'
+                f"<li><a href='/serve_endpoint/{file_path.lstrip('/')}/{item.name}/'>{item.name}/</a></li>"
             )
         else:
             files.append(
-                f'<li><a href="/serve_endpoint/{file_path.lstrip('/')}/{item.name}">{item.name}</a></li>'
+                f"<li><a href='/serve_endpoint/{file_path.lstrip('/')}/{item.name}'>{item.name}</a></li>"
             )
     print('PPPPPP', str(parent_path))
     html_content = f"""

templates/admin.html

@@ -49,6 +49,41 @@ <h2>
         <a style="display: none;" href="/workflow_summary">Original Raw Workflow View (not intended for operational use)</a>
     </h2>
 
+    <div id="backup-section">
+        <h3>Database Backups</h3>
+        <table>
+            <tr>
+                <td>Backup Directory:</td>
+                <td>
+                    <input type="text" value="{{ user_data.get('db_backup_path', './db_backups') }}" onchange="updatePreferenceAndReload('db_backup_path', this.value)">
+                    <form method="post" action="/db_backup" style="display:inline;">
+                        <button type="submit">Dump Backup</button>
+                    </form>
+                </td>
+            </tr>
+        </table>
+
+        {% if backups %}
+        <table border="1">
+            <tr><th>Backup File</th><th>Action</th></tr>
+            {% for b in backups %}
+            <tr>
+                <td>{{ b }}</td>
+                <td>
+                    <form method="post" action="/db_restore" onsubmit="return confirm('Restore from {{ b }}? This will overwrite the current database.');">
+
+                        <input type="hidden" name="filename" value="{{ b }}">
+                        <button type="submit">Restore</button>
+                    </form>
+                </td>
+            </tr>
+            {% endfor %}
+        </table>
+        {% else %}
+        <p>No backups found in {{ backup_path }}</p>
+        {% endif %}
+    </div>
+
 
      <script>    
     function updatePreferenceAndReload(key, value) {

templates/create_file_report.html

@@ -73,6 +73,13 @@
     {% include 'bloom_header.html' %}
 
     <h1>Create File Report</h1>
+    {% if file_set_euid %}
+    <p>File Set:
+        <a target="_blank" href="euid_details?euid={{ file_set_euid }}">
+            {{ file_set_name }}
+        </a>
+    </p>
+    {% endif %}
     <hr>
     <table>
         <thead>

templates/file_set_search_results.html

@@ -5,21 +5,34 @@
     {% set page_title = 'File Search Results' %}
     <title>{{ page_title }}</title>
     {% set bloom_mod = 'dewey' %}
+    <script src="https://code.jquery.com/jquery-3.6.0.min.js"></script>
+    <link rel="stylesheet" href="https://code.jquery.com/ui/1.13.2/themes/base/jquery-ui.css">
+    <script src="https://code.jquery.com/ui/1.13.2/jquery-ui.min.js"></script>
 
     <link rel="stylesheet" type="text/css" href="{{ style.skin_css }}">
     <link rel="stylesheet" type="text/css" href="static/style.css">
 </head>
 <body>
     {% include 'bloom_header.html' %}
 
-    <h1>{{ num_results }} Results</h1>
+    <div style="display:flex; justify-content:space-between; align-items:center;">
+        <h1 style="margin:0;">{{ num_results }} Results</h1>
+        <div>
+            <button onclick="openColumnModal()" type="button">Edit Column Order</button>
+            <button onclick="downloadTableAsTSV()" type="button">⬇️</button>
+        </div>
+    </div>
+    <div id="column-modal" title="Column Order" style="display:none;">
+        <ul id="column-list">{% for col in columns %}<li class="ui-state-default" data-col="{{ col }}">{{ col }}</li>{% endfor %}</ul>
+        <button onclick="saveColumnOrder()" type="button">Save</button>
+    </div>
 
     <table id="results-table" border="1">
         <thead>
             <tr>
                 <th>Link</th> <!-- New column header for the link -->
                 {% for column in columns %}
-                <th onclick="sortTable({{ loop.index0 }})">{{ column }}</th>
+                <th onclick="sortTableByHeader(this)">{{ column }}</th>
                 {% endfor %}
             </tr>
         </thead>
@@ -47,20 +60,20 @@ <h1>{{ num_results }} Results</h1>
 
     <a href="/dewey">Go Back</a>
 
-    <button class="floating-button" onclick="downloadTableAsTSV()">⬇️ Download TSV</button>
-
     <script>
         let sortDirections = Array({{ columns | length }}).fill(true); // Track sort direction for each column
 
-        function sortTable(columnIndex) {
+        function sortTableByHeader(header) {
             const table = document.getElementById('results-table');
+            const columnIndex = Array.from(header.parentNode.children).indexOf(header) - 1; // subtract 1 for the link column
+            if (columnIndex < 0) return;
             const tbody = table.tBodies[0];
             const rows = Array.from(tbody.rows);
 
             const direction = sortDirections[columnIndex] ? 1 : -1;
 
             const sortedRows = rows.sort((a, b) => {
-                const cellA = a.cells[columnIndex + 1].innerText.toLowerCase(); // +1 because of new first column
+                const cellA = a.cells[columnIndex + 1].innerText.toLowerCase();
                 const cellB = b.cells[columnIndex + 1].innerText.toLowerCase();
 
                 if (cellA < cellB) return -1 * direction;
@@ -69,7 +82,7 @@ <h1>{{ num_results }} Results</h1>
             });
 
             tbody.append(...sortedRows);
-            sortDirections[columnIndex] = !sortDirections[columnIndex]; // Toggle sort direction
+            sortDirections[columnIndex] = !sortDirections[columnIndex];
         }
 
         function downloadTableAsTSV() {
@@ -91,24 +104,21 @@ <h1>{{ num_results }} Results</h1>
             document.body.removeChild(downloadLink);
         }
     </script>
+<script>
+    $(function(){
+        $("#column-list").sortable();
+        $("#column-modal").dialog({ autoOpen: false, modal: true });
+    });
+    function openColumnModal(){
+        $("#column-modal").dialog("open");
+    }
+    function saveColumnOrder(){
+        const order = $("#column-list").sortable("toArray", { attribute: "data-col" });
+        $.ajax({url: "/update_preference", type: "POST", contentType: "application/json", data: JSON.stringify({key: "file_set_search_columns_order", value: order}), success: function(){ location.reload(); }});
+    }
+</script>
 
     <style>
-        .floating-button {
-            position: fixed;
-            bottom: 10px;
-            right: 10px;
-            padding: 10px;
-            background-color: #008CBA; /* Blue background */
-            color: white; /* White text */
-            border: none;
-            text-align: center;
-            text-decoration: none;
-            display: inline-block;
-            font-size: 16px;
-            cursor: pointer;
-            border-radius: 50%;
-        }
-
         th {
             cursor: pointer;
         }