Dev

.gitignore

@@ -70,6 +70,7 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+.DS_Store
 
 # PyBuilder
 .pybuilder/

README.md

@@ -1,5 +1,11 @@
 biosimdb-interface
 ==================
+
+<p align="center">
+    <img src="docs/source/_static/logos/biosimdb-logo-white.png#gh-dark-mode-only" alt="biosimdb logo" width="300"/>
+    <img src="docs/source/_static/logos/biosimdb-logo-black.png#gh-light-mode-only" alt="biosimdb logo" width="300"/>
+</p>
+
 A repository for extracting and uploading simulation data via a web interface to the PSDI hosted BioSimDB community data-collection.
 
 ## Project Status

biosimdb_interface/form/extract.py

@@ -33,6 +33,7 @@ def extract_files_validate(top_file, traj_file):
         schema_path=os.getenv("ENGINE_MAPPING_SCHEMA_PATH", ""),
         top_file=top_file,
         traj_file=traj_file,
+        store_file_metadata=False,  # not on webform so exclude
     )
 
     result = populator.populate()

biosimdb_interface/form/upload.py

@@ -3,15 +3,68 @@
 import glob
 import json
 import os
+import shutil
 import tempfile
 
+from biosim_extractor.metadata.filemetadata import files_metadata
 from flask import current_app, request, session
 from werkzeug.utils import secure_filename
 
 from .invenio import run_record_upload
 from .utils import fill_invenio_metadata, form_to_json
 
 
+def _save_request_files(tmpdir):
+    """Save uploaded request files into a temporary directory grouped by role.
+
+    Maps the trajectory[] field to trajectory and keeps other field names as roles.
+
+    Args:
+        tmpdir: Path to the temporary directory where uploaded files are written.
+
+    Returns:
+        Dictionary mapping file roles to lists of saved file paths.
+    """
+    saved_files = {"topology": [], "trajectory": []}
+    for field in request.files:
+        role = "trajectory" if field == "trajectory[]" else field
+        for file in request.files.getlist(field):
+            if file.filename:
+                path = os.path.join(tmpdir, secure_filename(file.filename))
+                file.save(path)
+                saved_files.setdefault(role, []).append(path)
+    return saved_files
+
+
+def _save_files_and_extract_metadata(tmpdir):
+    """Save uploaded request files and compute file metadata in one step.
+
+    Args:
+        tmpdir: Path to the temporary directory where uploaded files are written.
+
+    Returns:
+        Tuple of:
+        - saved_files: Dictionary of role to saved file paths.
+        - file_meta: List of extracted file metadata dictionaries.
+    """
+    saved_files = _save_request_files(tmpdir)
+    file_meta = files_metadata(saved_files)
+    return saved_files, file_meta
+
+
+def extract_uploaded_file_metadata():
+    """Extract file metadata from the current request's uploaded files."""
+    tmpdir = tempfile.mkdtemp(prefix="biosimdb_file_metadata_")
+    try:
+        _, file_meta = _save_files_and_extract_metadata(tmpdir)
+        return file_meta
+    finally:
+        for field in request.files:
+            for file in request.files.getlist(field):
+                file.stream.seek(0)
+        shutil.rmtree(tmpdir, ignore_errors=True)
+
+
 def _data_collections_upload(metadata_path, files_path):
     """Upload metadata as a draft PSDI data-collections record.
 
@@ -35,6 +88,40 @@ def _data_collections_upload(metadata_path, files_path):
     return repository, draft_id
 
 
+def save_pending_submission(json_form=None):
+    """Save uploaded files and form data for deferred post-login submission.
+
+    Writes uploaded request files to a new temporary directory, computes file
+    metadata from those saved files, and stores pending submission state in the
+    Flask session so submission can resume after OAuth login.
+
+    If ``json_form`` is provided, this function attaches the computed file
+    metadata under ``json_form["files"]`` and writes the result to
+    ``simulation_metadata.json`` in the temporary directory.
+
+    Args:
+        json_form: Optional converted/validated BioSim metadata dictionary to
+            persist alongside uploaded files. When provided, file metadata is
+            added before writing.
+
+    Side effects:
+        session["pending_form_data"]: Set to submitted form data (dict of lists).
+        session["pending_files_dir"]: Set to temporary directory path containing
+            uploaded files and optional ``simulation_metadata.json``.
+    """
+    tmpdir = tempfile.mkdtemp(prefix="biosimdb_pending_")
+    _, file_meta = _save_files_and_extract_metadata(tmpdir)
+
+    if json_form is not None:
+        json_form["files"] = file_meta
+        json_path = os.path.join(tmpdir, "simulation_metadata.json")
+        with open(json_path, "w") as f:
+            json.dump(json_form, f, indent=2)
+
+    session["pending_form_data"] = request.form.to_dict(flat=False)
+    session["pending_files_dir"] = tmpdir
+
+
 def prepare_for_invenio(form_data, tmpdir):
     """Convert form data and upload files from tmpdir to Invenio. Cleans up tmpdir.
 
@@ -45,8 +132,6 @@ def prepare_for_invenio(form_data, tmpdir):
     Returns:
         draft_id: The Invenio draft record ID of the created upload.
     """
-    import shutil
-
     try:
         json_form = form_to_json(form_data)
         invenio_data = fill_invenio_metadata(json_form)
@@ -60,22 +145,3 @@ def prepare_for_invenio(form_data, tmpdir):
     finally:
         shutil.rmtree(tmpdir, ignore_errors=True)
     return draft_id
-
-
-def save_pending_submission():
-    """Save uploaded files and form data to a temp directory for post-login submission.
-
-    Stores uploaded files in a new temporary directory and saves the form data and
-    directory path in the Flask session so the submission can be resumed after OAuth login.
-
-    Side effects:
-        session["pending_form_data"]: Set to the submitted form data as a dict.
-        session["pending_files_dir"]: Set to the path of the temporary directory.
-    """
-    tmpdir = tempfile.mkdtemp(prefix="biosimdb_pending_")
-    for field in request.files:
-        for file in request.files.getlist(field):
-            if file.filename:
-                file.save(os.path.join(tmpdir, secure_filename(file.filename)))
-    session["pending_form_data"] = request.form.to_dict(flat=False)
-    session["pending_files_dir"] = tmpdir

biosimdb_interface/form/utils.py

@@ -3,7 +3,7 @@
 import copy
 import re
 
-from biosimdb_interface.schema.invenio import INVENIO_DSMD_TEMPLATE, INVENIO_FORM_EMPTY
+from biosimdb_interface.schema.invenio import INVENIO_FORM_EMPTY
 from biosimdb_interface.schema.webform import get_simulation_metadata
 
 
@@ -18,8 +18,8 @@ def fill_invenio_metadata(form_data):
     """
     invenio_data = copy.deepcopy(INVENIO_FORM_EMPTY)
     # invenio_data["custom_fields"]["dsmd"] = [form_data]
-    # temporarily use dsmd template for testing
-    invenio_data["custom_fields"]["dsmd"] = [INVENIO_DSMD_TEMPLATE]
+    # exclude dsmd template until updated to new schema
+    # invenio_data["custom_fields"]["dsmd"] = [INVENIO_DSMD_TEMPLATE]
     # add generated keywords
     # add generated subjects
 

biosimdb_interface/form/webform.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 import os
 
+import requests
 from biosim_extractor.metadata.convertpopulated import convert_populated_metadata_units
 from biosim_extractor.metadata.validatemetadata import validate_metadata
 from flask import (
@@ -13,22 +14,29 @@
     session,
     url_for,
 )
+from werkzeug.datastructures import ImmutableMultiDict
 
 from biosimdb_interface.schema.webform import WEBFORM_SCHEMA, get_simulation_metadata
 
 from . import form_bp
-from .upload import prepare_for_invenio, save_pending_submission
+from .upload import (
+    extract_uploaded_file_metadata,
+    prepare_for_invenio,
+    save_pending_submission,
+)
 from .utils import form_to_json, remove_empty_fields
 from .validation import validate_with_mdanalysis
 
 
 @form_bp.route("/webform", methods=["GET", "POST"])
 def webform():
-    """Render the metadata submission form and handle save/submit actions.
+    """Render the metadata form and handle save/submit actions.
 
-    On GET, renders the empty form. On POST, validates uploaded files with
-    MDAnalysis, then either downloads form data as JSON (save) or initiates
-    submission to BioSimDB (submit).
+    On POST, validates uploaded files, converts submitted metadata to standard
+    units, removes empty fields, and validates the result against the BioSim
+    schema. ``save`` returns the validated JSON to the browser. ``submit`` saves
+    uploaded files plus the validated JSON for deferred Invenio upload, then
+    starts login if needed.
     """
     token = session.get("access_token")
 
@@ -55,6 +63,9 @@ def webform():
             # convert to standard units
             json_form = convert_populated_metadata_units(json_form)
 
+            if action == "save":
+                json_form["files"] = extract_uploaded_file_metadata()
+
             # NOTE: note used yet, could be used to validate extracted fields are matching what is returned from json_form
             # extracted = session.get("extracted_metadata")
 
@@ -74,7 +85,7 @@ def webform():
                 )
 
             if action == "submit":
-                save_pending_submission()
+                save_pending_submission(json_form)
                 if not token:
                     session["post_login_redirect"] = url_for("form.resume_submit")
                     return redirect(url_for("login.login"))
@@ -117,14 +128,42 @@ def do_submit():
     Called automatically by the loading page after login. Clears pending
     session data after upload and renders the success page with the record URL.
     """
-    from werkzeug.datastructures import ImmutableMultiDict
-
     form_data = session.pop("pending_form_data", None)
     tmpdir = session.pop("pending_files_dir", None)
+
+    if not form_data or not tmpdir:
+        flash("No pending submission found. Please submit again.", "warning")
+        return redirect(url_for("form.webform"))
+
     flat_form = ImmutableMultiDict(
         [(k, v) for k, vals in form_data.items() for v in vals]
     )
-    draft_id = prepare_for_invenio(flat_form, tmpdir)
+
+    try:
+        draft_id = prepare_for_invenio(flat_form, tmpdir)
+    except requests.HTTPError as exc:
+        status = exc.response.status_code if exc.response is not None else None
+
+        if status in (401, 403):
+            session.pop("access_token", None)  # force fresh login
+            session["post_login_redirect"] = url_for("form.resume_submit")
+            flash(
+                "Your login session is no longer valid for upload. "
+                "Please sign in again and the submission will resume automatically.",
+                "warning",
+            )
+            return redirect(url_for("login.login"))
+        else:
+            session.pop("access_token", None)  # force fresh login
+            flash("Upload failed unexpectedly. Please try again.", "danger")
+
+        # keep pending_form_data and pending_files_dir for retry
+        return redirect(url_for("form.webform"))
+
+    # success: now clear pending state
+    session.pop("pending_form_data", None)
+    session.pop("pending_files_dir", None)
+
     BASE_URL = current_app.config["BASE_URL"]
     record_url = f"{BASE_URL}/uploads/{draft_id}"
     return render_template("form/submit_success.html", record_url=record_url)

biosimdb_interface/schema/invenio.py

@@ -42,21 +42,21 @@
 
 
 INVENIO_DSMD_TEMPLATE = {
-    "software": "GROMACS",
+    "software": "",
     "software_version": "",
     "molecular_model": "",
     "simulation_method": "",
-    "timestep": "2",
-    "framestep": "2",
+    "timestep": "",
+    "framestep": "",
     "length": "",
-    "temperature": "298",
+    "temperature": "",
     "pressure": "",
     "ensemble": "",
     "box_type": "",
     "trajectories": "",
     "force_fields": "",
     "experimental_structures": "",
-    "pH": "7",
+    "pH": "",
     "membrane": "",
     "ligands": "",
     "sequences": "",
@@ -65,6 +65,6 @@
     "long_range_cutoff": "",
     "thermostat": "",
     "barostat": "",
-    "atom_count": "100",
+    "atom_count": "",
     "wall_time": "",
 }

biosimdb_interface/schema/webform.py

@@ -51,10 +51,10 @@ def get_simulation_metadata():
         "guidance": {
             "label": "Please Note:",
             "options": [
-                "To extract simulation metadata, please upload a topology and corresponding trajectory file/s. Optionally, upload the aiida archive file containing the simulation provenance to extract further information about the simulation protocol.",
+                "To extract simulation metadata, please upload a topology and corresponding trajectory file/s. Optionally, upload a aiida archive file containing the simulation provenance to extract further information about the simulation protocol.",
                 "Multiple trajectory files can be uploaded with a single associated topology file, both file types are required.",
                 'Various simulation file formats are accepted and read using <a href="https://www.mdanalysis.org/" target="_blank" class="text-reset"> MDAnalysis</a>, please ensure your files are compatible.',
-                "This form uses the following schema to define and group BioSim metadata: XXXX. Missing terms or units? Please considering raising an issue or contributing to the schema.",
+                'This form uses the <a href="https://biosim-schema.readthedocs.io/en/latest/index.html" target="_blank" class="text-reset"> biosim-schema</a> to define and group BioSim metadata. Missing terms or units? Please considering raising an issue or contributing to the schema.',
                 'Automatically add metadata associated with each entry using the "Extract metadata" button. Please fill in any missing metadata fields manually where applicable, click on each field name for further information about data field requirements.',
                 "Two options are available for your extracted simulation metadata: <ol> <li> Download the simulation metadata as a json file and share alongside simulation files. </li> <li> Submit your simulation files and metadata in one step to BioSimDB, you will be directed to a login page and asked to authorize this application. Please continue and complete the data submission process in BioSimDB. </li> </ol>",
             ],

docs/source/conf.py

@@ -40,6 +40,10 @@
 
 html_theme = 'furo'
 html_static_path = ['_static']
+html_theme_options = {
+    "dark_logo": "logos/biosimdb-logo-white.png",
+    "light_logo": "logos/biosimdb-logo-black.png",
+}
 
 import warnings
 warnings.filterwarnings("ignore", message="netCDF4 is not available")