37 feature streamline serverside data management

biosimdb_interface/__init__.py

@@ -86,4 +86,8 @@ def inject_base_url():
 
     app.register_blueprint(login_bp, url_prefix=app.config["APPLICATION_BASE"])
 
+    from .home import home_bp
+
+    app.register_blueprint(home_bp, url_prefix=app.config["APPLICATION_BASE"])
+
     return app

biosimdb_interface/form/__init__.py

@@ -3,4 +3,4 @@
 
 form_bp = Blueprint("form", __name__)
 
-from . import extract, home, webform  # noqa: E402, F401
+from . import extract, webform  # noqa: E402, F401

biosimdb_interface/form/extract.py

@@ -8,12 +8,13 @@
 """
 
 import os
-import shutil
 
 from biosim_extractor.metadata.populatemetadata import MetadataPopulator
-from flask import jsonify, request
+from flask import jsonify, request, session
+from werkzeug.utils import secure_filename
 
 from . import form_bp
+from .upload import cache_extracted_files, cleanup_tmpdir
 from .utils import make_upload_tmpdir
 
 
@@ -51,6 +52,7 @@ def extract_files_validate(top_file, traj_file):
 @form_bp.route("/extract_metadata", methods=["POST"])
 def extract_metadata():
     """Extract simulation metadata from uploaded topology and trajectory files.
+    This is where the tmpdir for the files is created.
 
     Expects a multipart POST with:
         - ``topology``: a single topology file.
@@ -65,49 +67,65 @@ def extract_metadata():
         - ``{"simulation_metadata": ..., "validation_errors": [...]}`` if schema validation fails.
         - ``{"error": "..."}`` with status 400 if files are missing, or 500 on unexpected error.
     """
+    # clear the existing tmpdir from previous extraction
+    tmpdir = session.get("submission_tmpdir")
+    if tmpdir:
+        cleanup_tmpdir(tmpdir)
+        session.pop("submission_tmpdir", None)
+    tmpdir = make_upload_tmpdir("biosimdb_submission_")
+    session["submission_tmpdir"] = tmpdir
+
     try:
         topology = request.files.get("topology")
         trajectories = request.files.getlist("trajectory[]")
 
         if not topology or not trajectories:
             return jsonify({"error": "Simulation files are missing."}), 400
 
-        temp_dir = make_upload_tmpdir("biosimdb_extract_")
-        try:
-            topo_path = os.path.join(temp_dir, topology.filename)
-            topology.save(topo_path)
-            traj_files = []
-
-            for traj in trajectories:
-                traj_path = os.path.join(temp_dir, traj.filename)
-                traj.save(traj_path)
-                traj_files.append(traj_path)
-
-            result, validation_errors = extract_files_validate(topo_path, traj_files)
-
-            # Keep authoritative extracted payload on the server
-            # session["extracted_metadata"] = result
-
-            if len(validation_errors) > 0:
-                return jsonify(
-                    {
-                        "simulation_metadata": result,
-                        "validation_errors": validation_errors,
-                    }
-                )
-            else:
-                return jsonify(
-                    {
-                        "simulation_metadata": result,
-                        "message": "Metadata extracted successfully.",
-                    }
-                )
-        finally:
-            shutil.rmtree(temp_dir, ignore_errors=True)
+        topo_path = os.path.join(tmpdir, secure_filename(topology.filename))
+        topology.save(topo_path, buffer_size=16 * 1024 * 1024)  # 16 MB chunks
+
+        traj_files = []
+        for traj in trajectories:
+            traj_path = os.path.join(tmpdir, secure_filename(traj.filename))
+            traj.save(traj_path, buffer_size=16 * 1024 * 1024)
+            traj_files.append(traj_path)
+
+        saved_files = {"topology": [topo_path], "trajectory": traj_files}
+        cache_extracted_files(tmpdir, saved_files)
+
+        result, validation_errors = extract_files_validate(topo_path, traj_files)
+
+        if len(validation_errors) > 0:
+            cleanup_tmpdir(tmpdir)
+            session.pop("submission_tmpdir", None)
+            return jsonify(
+                {
+                    "simulation_metadata": result,
+                    "validation_errors": validation_errors,
+                }
+            )
+        else:
+            return jsonify(
+                {
+                    "simulation_metadata": result,
+                    "message": "Metadata extracted successfully.",
+                }
+            )
 
     except Exception as e:
         print(f"ERROR: {e}")
         import traceback
 
         traceback.print_exc()
         return jsonify({"error": str(e)}), 500
+
+
+@form_bp.route("/clear_extraction", methods=["POST"])
+def clear_extraction():
+    """Discard extracted files and reset the pending submission tmpdir."""
+    tmpdir = session.get("submission_tmpdir")
+    cleanup_tmpdir(tmpdir)
+    for key in ("submission_tmpdir", "topo_path", "traj_files"):
+        session.pop(key, None)
+    return jsonify({"success": True})