[Feature] Show Multi Gen Eval + Batch Prediction (#267)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#267

epdb/legacy_api.py

@@ -1451,7 +1451,7 @@ def create_pathway(
 
             from .tasks import dispatch, predict
 
-            dispatch(request.user, predict, new_pw.pk, setting.pk, limit=-1)
+            dispatch(request.user, predict, new_pw.pk, setting.pk, limit=None)
 
         return redirect(new_pw.url)
     except ValueError as e:

epdb/logic.py

@@ -1,7 +1,7 @@
 import json
 import logging
 import re
-from typing import Any, Dict, List, Optional, Set, Union
+from typing import Any, Dict, List, Optional, Set, Union, Tuple
 from uuid import UUID
 
 import nh3
@@ -16,6 +16,7 @@ from epdb.models import (
     Edge,
     EnzymeLink,
     EPModel,
+    ExpansionSchemeChoice,
     Group,
     GroupPackagePermission,
     Node,
@@ -1116,6 +1117,7 @@ class SettingManager(object):
         rule_packages: List[Package] = None,
         model: EPModel = None,
         model_threshold: float = None,
+        expansion_scheme: ExpansionSchemeChoice = ExpansionSchemeChoice.BFS,
     ):
         new_s = Setting()
         # Clean for potential XSS
@@ -1550,22 +1552,32 @@ class SPathway(object):
 
         return sorted(res, key=lambda x: hash(x))
 
-    def predict_step(self, from_depth: int = None, from_node: "Node" = None):
-        substrates: List[SNode] = []
+    def _expand(self, substrates: List[SNode]) -> Tuple[List[SNode], List[SEdge]]:
+        """
+        Expands the given substrates by generating new nodes and edges based on prediction settings.
 
-        if from_depth is not None:
-            substrates = self._get_nodes_for_depth(from_depth)
-        elif from_node is not None:
-            for k, v in self.snode_persist_lookup.items():
-                if from_node == v:
-                    substrates = [k]
-                    break
-        else:
-            raise ValueError("Neither from_depth nor from_node_url specified")
+        This method processes a list of substrates and expands them into new nodes and edges using defined
+        rules and settings. It evaluates each substrate to determine its applicability domain, persists
+        domain assessments, and generates candidates for further processing. Newly created nodes and edges
+        are returned, and any applicable information is stored or updated internally during the process.
+
+        Parameters:
+            substrates (List[SNode]): A list of substrate nodes to be expanded.
+
+        Returns:
+            Tuple[List[SNode], List[SEdge]]:
+                A tuple containing:
+                - A list of new nodes generated during the expansion.
+                - A list of new edges representing connections between nodes based on candidate reactions.
+
+        Raises:
+            ValueError: If a node does not have an ID when it should have been saved already.
+        """
+        new_nodes: List[SNode] = []
+        new_edges: List[SEdge] = []
 
-        new_tp = False
-        if substrates:
         for sub in substrates:
+            # For App Domain we have to ensure that each Node is evaluated
             if sub.app_domain_assessment is None:
                 if self.prediction_setting.model:
                     if self.prediction_setting.model.app_domain:
@@ -1576,9 +1588,9 @@ class SPathway(object):
                         if self.persist is not None:
                             n = self.snode_persist_lookup[sub]
 
-                                assert n.id is not None, (
-                                    "Node has no id! Should have been saved already... aborting!"
-                                )
+                            if n.id is None:
+                                raise ValueError(f"Node {n} has no ID... aborting!")
+
                             node_data = n.simple_json()
                             node_data["image"] = f"{n.url}?image=svg"
                             app_domain_assessment["assessment"]["node"] = node_data
@@ -1592,7 +1604,6 @@ class SPathway(object):
             # candidates is a List of PredictionResult. The length of the List is equal to the number of rules
             for cand_set in candidates:
                 if cand_set:
-                        new_tp = True
                     # cand_set is a PredictionResult object that can consist of multiple candidate reactions
                     for cand in cand_set:
                         cand_nodes = []
@@ -1606,10 +1617,9 @@ class SPathway(object):
                                         app_domain_assessment = (
                                             self.prediction_setting.model.app_domain.assess(c)
                                         )
-
-                                    self.smiles_to_node[c] = SNode(
-                                        c, sub.depth + 1, app_domain_assessment
-                                    )
+                                snode = SNode(c, sub.depth + 1, app_domain_assessment)
+                                self.smiles_to_node[c] = snode
+                                new_nodes.append(snode)
 
                             node = self.smiles_to_node[c]
                             cand_nodes.append(node)
@@ -1621,6 +1631,136 @@ class SPathway(object):
                             probability=cand_set.probability,
                         )
                         self.edges.add(edge)
+                        new_edges.append(edge)
+
+        return new_nodes, new_edges
+
+    def predict(self):
+        """
+        Predicts outcomes based on a graph traversal algorithm using the specified expansion schema.
+
+        This method iteratively explores the nodes of a graph starting from the root nodes, propagating
+        probabilities through edges, and updating the probabilities of the connected nodes. The traversal
+        can follow one of three predefined expansion schemas: Depth-First Search (DFS), Breadth-First Search
+        (BFS), or a Greedy approach based on node probabilities. The methodology ensures that all reachable
+        nodes are processed systematically according to the specified schema.
+
+        Errors will be raised if the expansion schema is undefined or invalid. Additionally, this method
+        supports persisting changes by writing back data to the database when configured to do so.
+
+        Attributes
+        ----------
+        done : bool
+            A flag indicating whether the prediction process is completed.
+        persist : Any
+            An optional object that manages persistence operations for saving modifications.
+        root_nodes : List[SNode]
+            A collection of initial nodes in the graph from which traversal begins.
+        prediction_setting : Any
+            Configuration object specifying settings for graph traversal, such as the choice of
+            expansion schema.
+
+        Raises
+        ------
+        ValueError
+            If an invalid or unknown expansion schema is provided in `prediction_setting`.
+        """
+        # populate initial queue
+        queue = list(self.root_nodes)
+        processed = set()
+
+        # initial nodes have prob 1.0
+        node_probs: Dict[SNode, float] = {}
+        node_probs.update({n: 1.0 for n in queue})
+
+        while queue:
+            current = queue.pop(0)
+
+            if current in processed:
+                continue
+
+            processed.add(current)
+
+            new_nodes, new_edges = self._expand([current])
+
+            if new_nodes or new_edges:
+                # Check if we need to write back data to the database
+                if self.persist:
+                    self._sync_to_pathway()
+                    # call save to update the internal modified field
+                    self.persist.save()
+
+                if new_nodes:
+                    for edge in new_edges:
+                        # All edge have `current` as educt
+                        # Use `current` and adjust probs
+                        current_prob = node_probs[current]
+
+                        for prod in edge.products:
+                            # Either is a new product or a product and we found a path with a higher prob
+                            if (
+                                prod not in node_probs
+                                or current_prob * edge.probability > node_probs[prod]
+                            ):
+                                node_probs[prod] = current_prob * edge.probability
+
+                    # Update Queue to proceed
+                    if self.prediction_setting.expansion_scheme == "DFS":
+                        for n in new_nodes:
+                            if n not in processed:
+                                # We want to follow this path -> prepend queue
+                                queue.insert(0, n)
+                    elif self.prediction_setting.expansion_scheme == "BFS":
+                        for n in new_nodes:
+                            if n not in processed:
+                                # Add at the end, everything queued before will be processed
+                                # before new_nodese
+                                queue.append(n)
+                    elif self.prediction_setting.expansion_scheme == "GREEDY":
+                        # Simply add them, as we will re-order the queue later
+                        for n in new_nodes:
+                            if n not in processed:
+                                queue.append(n)
+
+                        node_and_probs = []
+                        for queued_val in queue:
+                            node_and_probs.append((queued_val, node_probs[queued_val]))
+
+                        from pprint import pprint
+
+                        pprint(node_and_probs)
+
+                        # re-order the queue and only pick smiles
+                        queue = [
+                            n[0] for n in sorted(node_and_probs, key=lambda x: x[1], reverse=True)
+                        ]
+                    else:
+                        raise ValueError(
+                            f"Unknown expansion schema: {self.prediction_setting.expansion_scheme}"
+                        )
+
+        # Queue exhausted, we're done
+        self.done = True
+
+    def predict_step(self, from_depth: int = None, from_node: "Node" = None):
+        substrates: List[SNode] = []
+
+        if from_depth is not None:
+            substrates = self._get_nodes_for_depth(from_depth)
+        elif from_node is not None:
+            for k, v in self.snode_persist_lookup.items():
+                if from_node == v:
+                    substrates = [k]
+                    break
+            else:
+                raise ValueError(f"Node {from_node} not found in SPathway!")
+        else:
+            raise ValueError("Neither from_depth nor from_node_url specified")
+
+        new_tp = False
+        if substrates:
+            new_nodes, _ = self._expand(substrates)
+            new_tp = len(new_nodes) > 0
 
         # In case no substrates are found, we're done.
         # For "predict from node" we're always done
@@ -1704,11 +1844,6 @@ class SPathway(object):
                 "to": to_indices,
             }
 
-            # if edge.rule:
-            #     e['rule'] = {
-            #         'name': edge.rule.name,
-            #         'id': edge.rule.url,
-            #     }
             edges.append(e)
 
         return {

epdb/migrations/0013_setting_expansion_schema.py

@@ -0,0 +1,25 @@
+# Generated by Django 5.2.7 on 2025-12-14 11:30
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0012_node_stereo_removed_pathway_predicted"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="setting",
+            name="expansion_schema",
+            field=models.CharField(
+                choices=[
+                    ("BFS", "Breadth First Search"),
+                    ("DFS", "Depth First Search"),
+                    ("GREEDY", "Greedy"),
+                ],
+                default="BFS",
+                max_length=20,
+            ),
+        ),
+    ]

epdb/migrations/0014_rename_expansion_schema_setting_expansion_scheme.py

@@ -0,0 +1,17 @@
+# Generated by Django 5.2.7 on 2025-12-14 16:02
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0013_setting_expansion_schema"),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name="setting",
+            old_name="expansion_schema",
+            new_name="expansion_scheme",
+        ),
+    ]

epdb/models.py

@@ -1744,6 +1744,16 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
         # potentially prefetched edge_set
         return self.edge_set.all()
 
+    @property
+    def setting_with_overrides(self):
+        mem_copy = Setting.objects.get(pk=self.setting.pk)
+
+        if "setting_overrides" in self.kv:
+            for k, v in self.kv["setting_overrides"].items():
+                setattr(mem_copy, k, f"{v} (this is an override for this particular pathway)")
+
+        return mem_copy
+
     def _url(self):
         return "{}/pathway/{}".format(self.package.url, self.uuid)
 
@@ -1879,13 +1889,16 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
 
         return json.dumps(res)
 
-    def to_csv(self) -> str:
+    def to_csv(self, include_header=True, include_pathway_url=False) -> str:
         import csv
         import io
 
-        rows = []
-        rows.append(
-            [
+        header = []
+
+        if include_pathway_url:
+            header += ["Pathway URL"]
+
+        header += [
             "SMILES",
             "name",
             "depth",
@@ -1894,10 +1907,20 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
             "rule_ids",
             "parent_smiles",
         ]
-        )
+
+        rows = []
+
+        if include_header:
+            rows.append(header)
+
         for n in self.nodes.order_by("depth"):
             cs = n.default_node_label
-            row = [cs.smiles, cs.name, n.depth]
+            row = []
+
+            if include_pathway_url:
+                row.append(n.pathway.url)
+
+            row += [cs.smiles, cs.name, n.depth]
 
             edges = self.edges.filter(end_nodes__in=[n])
             if len(edges):
@@ -2362,6 +2385,29 @@ class PackageBasedModel(EPModel):
 
         return res
 
+    @property
+    def mg_pr_curve(self):
+        if self.model_status != self.FINISHED:
+            raise ValueError(f"Expected {self.FINISHED} but model is in status {self.model_status}")
+
+        if not self.multigen_eval:
+            raise ValueError("MG PR Curve is only available for multigen models")
+
+        res = []
+
+        thresholds = self.eval_results["multigen_average_precision_per_threshold"].keys()
+
+        for t in thresholds:
+            res.append(
+                {
+                    "precision": self.eval_results["multigen_average_precision_per_threshold"][t],
+                    "recall": self.eval_results["multigen_average_recall_per_threshold"][t],
+                    "threshold": float(t),
+                }
+            )
+
+        return res
+
     @cached_property
     def applicable_rules(self) -> List["Rule"]:
         """
@@ -2565,7 +2611,7 @@ class PackageBasedModel(EPModel):
             for i, root in enumerate(root_compounds):
                 logger.debug(f"Evaluating pathway {i + 1} of {len(root_compounds)}...")
 
-                spw = SPathway(root_nodes=root, prediction_setting=s)
+                spw = SPathway(root_nodes=root.smiles, prediction_setting=s)
                 level = 0
 
                 while not spw.done:
@@ -3771,6 +3817,12 @@ class UserSettingPermission(Permission):
         return f"User: {self.user} has Permission: {self.permission} on Setting: {self.setting}"
 
 
+class ExpansionSchemeChoice(models.TextChoices):
+    BFS = "BFS", "Breadth First Search"
+    DFS = "DFS", "Depth First Search"
+    GREEDY = "GREEDY", "Greedy"
+
+
 class Setting(EnviPathModel):
     public = models.BooleanField(null=False, blank=False, default=False)
     global_default = models.BooleanField(null=False, blank=False, default=False)
@@ -3795,6 +3847,12 @@ class Setting(EnviPathModel):
         null=True, blank=True, verbose_name="Setting Model Threshold", default=0.25
     )
 
+    expansion_scheme = models.CharField(
+        max_length=20,
+        choices=ExpansionSchemeChoice.choices,
+        default=ExpansionSchemeChoice.BFS,
+    )
+
     def _url(self):
         return "{}/setting/{}".format(s.SERVER_URL, self.uuid)
 
@@ -3833,7 +3891,7 @@ class Setting(EnviPathModel):
         """Decision Method whether to expand on a certain Node or not"""
         if pathway.num_nodes() >= self.max_nodes:
             logger.info(
-                f"Pathway has {pathway.num_nodes()} which exceeds the limit of {self.max_nodes}"
+                f"Pathway has {pathway.num_nodes()} Nodes which exceeds the limit of {self.max_nodes}"
             )
             return []
 
@@ -3931,3 +3989,8 @@ class JobLog(TimeStampedModel):
         if self.job_name == "engineer_pathways":
             return ast.literal_eval(self.task_result)
         return self.task_result
+
+    def is_result_downloadable(self):
+        downloadable = ["batch_predict"]
+
+        return self.job_name in downloadable

epdb/tasks.py

@@ -11,6 +11,7 @@ from django.utils import timezone
 
 from epdb.logic import SPathway
 from epdb.models import Edge, EPModel, JobLog, Node, Pathway, Rule, Setting, User
+from utilities.chem import FormatConverter
 
 logger = logging.getLogger(__name__)
 ML_CACHE = LRUCache(3)  # Cache the three most recent ML models to reduce load times.
@@ -139,14 +140,25 @@ def predict(
     pred_setting_pk: int,
     limit: Optional[int] = None,
     node_pk: Optional[int] = None,
+    setting_overrides: Optional[dict] = None,
 ) -> Pathway:
     pw = Pathway.objects.get(id=pw_pk)
     setting = Setting.objects.get(id=pred_setting_pk)
+
+    if setting_overrides:
+        for k, v in setting_overrides.items():
+            setattr(setting, k, v)
+
     # If the setting has a model add/restore it from the cache
     if setting.model is not None:
         setting.model = get_ml_model(setting.model.pk)
 
-    pw.kv.update(**{"status": "running"})
+    kv = {"status": "running"}
+
+    if setting_overrides:
+        kv["setting_overrides"] = setting_overrides
+
+    pw.kv.update(**kv)
     pw.save()
 
     if JobLog.objects.filter(task_id=self.request.id).exists():
@@ -171,7 +183,8 @@ def predict(
             spw = SPathway.from_pathway(pw)
             spw.predict_step(from_node=n)
         else:
-            raise ValueError("Neither limit nor node_pk given!")
+            spw = SPathway(prediction_setting=setting, persist=pw)
+            spw.predict()
 
     except Exception as e:
         pw.kv.update({"status": "failed"})
@@ -353,3 +366,76 @@ def engineer_pathways(self, pw_pks: List[int], setting_pk: int, target_package_p
             predicted_pathways.append(pred_pw.url)
 
     return intermediate_pathways, predicted_pathways
+
+
+@shared_task(bind=True, queue="background")
+def batch_predict(
+    self,
+    substrates: List[str] | List[List[str]],
+    prediction_setting_pk: int,
+    target_package_pk: int,
+    num_tps: int = 50,
+):
+    target_package = Package.objects.get(pk=target_package_pk)
+    prediction_setting = Setting.objects.get(pk=prediction_setting_pk)
+
+    if len(substrates) == 0:
+        raise ValueError("No substrates given!")
+
+    is_pair = isinstance(substrates[0], list)
+
+    substrate_and_names = []
+    if not is_pair:
+        for sub in substrates:
+            substrate_and_names.append([sub, None])
+    else:
+        substrate_and_names = substrates
+
+    # Check prerequisite that we can standardize all substrates
+    standardized_substrates_and_smiles = []
+    for substrate in substrate_and_names:
+        try:
+            stand_smiles = FormatConverter.standardize(substrate[0])
+            standardized_substrates_and_smiles.append([stand_smiles, substrate[1]])
+        except ValueError:
+            raise ValueError(
+                f'Pathway prediction failed as standardization of SMILES "{substrate}" failed!'
+            )
+
+    pathways = []
+
+    for pair in standardized_substrates_and_smiles:
+        pw = Pathway.create(
+            target_package,
+            pair[0],
+            name=pair[1],
+            predicted=True,
+        )
+
+        # set mode and setting
+        pw.setting = prediction_setting
+        pw.kv.update({"mode": "predict"})
+        pw.save()
+
+        predict(
+            pw.pk,
+            prediction_setting.pk,
+            limit=None,
+            setting_overrides={
+                "max_nodes": num_tps,
+                "max_depth": num_tps,
+                "model_threshold": 0.001,
+            },
+        )
+
+        pathways.append(pw)
+
+    buffer = io.StringIO()
+
+    for idx, pw in enumerate(pathways):
+        # Carry out header only for the first pathway
+        buffer.write(pw.to_csv(include_header=idx == 0, include_pathway_url=True))
+
+    buffer.seek(0)
+
+    return buffer.getvalue()

epdb/urls.py

@@ -49,6 +49,7 @@ urlpatterns = [
     re_path(r"^group$", v.groups, name="groups"),
     re_path(r"^search$", v.search, name="search"),
     re_path(r"^predict$", v.predict_pathway, name="predict_pathway"),
+    re_path(r"^batch-predict$", v.batch_predict_pathway, name="batch_predict_pathway"),
     # User Detail
     re_path(rf"^user/(?P<user_uuid>{UUID})", v.user, name="user"),
     # Group Detail

epdb/views.py

@@ -1,11 +1,12 @@
 import json
 import logging
 from typing import Any, Dict, List
+from datetime import datetime
 
 import nh3
 from django.conf import settings as s
 from django.contrib.auth import get_user_model
-from django.core.exceptions import BadRequest
+from django.core.exceptions import BadRequest, PermissionDenied
 from django.http import HttpResponse, HttpResponseBadRequest, HttpResponseNotAllowed, JsonResponse
 from django.shortcuts import redirect, render
 from django.urls import reverse
@@ -50,6 +51,7 @@ from .models import (
     SimpleAmbitRule,
     User,
     UserPackagePermission,
+    ExpansionSchemeChoice,
 )
 
 logger = logging.getLogger(__name__)
@@ -438,6 +440,18 @@ def predict_pathway(request):
     return render(request, "predict_pathway.html", context)
 
 
+def batch_predict_pathway(request):
+    """Top-level predict pathway view using user's default package."""
+    if request.method != "GET":
+        return HttpResponseNotAllowed(["GET"])
+
+    context = get_base_context(request)
+    context["title"] = "enviPath - Batch Predict Pathway"
+    context["meta"]["current_package"] = context["meta"]["user"].default_package
+
+    return render(request, "batch_predict_pathway.html", context)
+
+
 @package_permission_required()
 def package_predict_pathway(request, package_uuid):
     """Package-specific predict pathway view."""
@@ -1967,7 +1981,7 @@ def package_pathways(request, package_uuid):
 
         if pw_mode == "predict" or pw_mode == "incremental":
             # unlimited pred (will be handled by setting)
-            limit = -1
+            limit = None
 
             # For incremental predict first level and return
             if pw_mode == "incremental":
@@ -2877,15 +2891,25 @@ def settings(request):
             )
 
             if not PackageManager.readable(current_user, params["model"].package):
-                raise ValueError("")
+                raise PermissionDenied("You're not allowed to access this model!")
+
+            expansion_scheme = request.POST.get(
+                "model-based-prediction-setting-expansion-scheme", "BFS"
+            )
+
+            if expansion_scheme not in ExpansionSchemeChoice.values:
+                raise BadRequest(f"Unknown expansion scheme: {expansion_scheme}")
+
+            params["expansion_scheme"] = ExpansionSchemeChoice(expansion_scheme)
 
         elif tp_gen_method == "rule-based-prediction-setting":
             rule_packages = request.POST.getlist("rule-based-prediction-setting-packages")
             params["rule_packages"] = [
                 PackageManager.get_package_by_url(current_user, p) for p in rule_packages
             ]
+
         else:
-            raise ValueError("")
+            raise BadRequest("Neither Model-Based nor Rule-Based as Method selected!")
 
         created_setting = SettingManager.create_setting(
             current_user,
@@ -2963,6 +2987,59 @@ def jobs(request):
             )
 
             return redirect(f"{s.SERVER_URL}/jobs/{res.task_id}")
+
+        elif job_name == "batch-predict":
+            substrates = request.POST.get("substrates")
+            prediction_setting_url = request.POST.get("prediction-setting")
+            num_tps = request.POST.get("num-tps")
+
+            if substrates is None or substrates.strip() == "":
+                raise BadRequest("No substrates provided.")
+
+            pred_data = []
+            for pair in substrates.split("\n"):
+                parts = pair.split(",")
+
+                try:
+                    smiles = FormatConverter.standardize(parts[0])
+                except ValueError:
+                    raise BadRequest(f"Couldn't standardize SMILES {parts[0]}!")
+
+                # name is optional
+                name = parts[1] if len(parts) > 1 else None
+                pred_data.append([smiles, name])
+
+            max_tps = 50
+            if num_tps is not None and num_tps.strip() != "":
+                try:
+                    num_tps = int(num_tps)
+                    max_tps = max(min(num_tps, 50), 1)
+                except ValueError:
+                    raise BadRequest(f"Parameter for num-tps {num_tps} is not a valid integer.")
+
+            batch_predict_setting = SettingManager.get_setting_by_url(
+                current_user, prediction_setting_url
+            )
+
+            target_package = PackageManager.create_package(
+                current_user,
+                f"Autogenerated Package for Batch Prediction {datetime.now()}",
+                "This Package was generated automatically for the batch prediction task.",
+            )
+
+            from .tasks import dispatch, batch_predict
+
+            res = dispatch(
+                current_user,
+                batch_predict,
+                pred_data,
+                batch_predict_setting.pk,
+                target_package.pk,
+                num_tps=max_tps,
+            )
+
+            return redirect(f"{s.SERVER_URL}/jobs/{res.task_id}")
+
         else:
             raise BadRequest(f"Job {job_name} is not supported!")
     else:
@@ -2982,6 +3059,21 @@ def job(request, job_uuid):
         # No op if status is already in a terminal state
         job.check_for_update()
 
+        if request.GET.get("download", False) == "true":
+            if not job.is_result_downloadable():
+                raise BadRequest("Result is not downloadable!")
+
+            if job.job_name == "batch_predict":
+                filename = f"{job.job_name.replace(' ', '_')}_{job.task_id}.csv"
+            else:
+                raise BadRequest("Result is not downloadable!")
+
+            res_str = job.task_result
+            response = HttpResponse(res_str, content_type="text/csv")
+            response["Content-Disposition"] = f'attachment; filename="{filename}"'
+
+            return response
+
         context["object_type"] = "joblog"
         context["breadcrumbs"] = [
             {"Home": s.SERVER_URL},

templates/actions/objects/joblog.html

@@ -0,0 +1,10 @@
+{% if job.is_result_downloadable %}
+  <li>
+    <a
+      class="button"
+      onclick="document.getElementById('download_job_result_modal').showModal(); return false;"
+    >
+      <i class="glyphicon glyphicon-floppy-save"></i> Download Result</a
+    >
+  </li>
+{% endif %}

templates/batch_predict_pathway.html

@@ -0,0 +1,168 @@
+{% extends "framework_modern.html" %}
+{% load static %}
+{% block content %}
+  <div class="mx-auto w-full p-8">
+    <h1 class="h1 mb-4 text-3xl font-bold">Batch Predict Pathways</h1>
+    <form id="smiles-form" method="POST" action="{% url "jobs" %}">
+      {% csrf_token %}
+      <input type="hidden" name="substrates" id="substrates" />
+      <input type="hidden" name="job-name" value="batch-predict" />
+
+      <fieldset class="flex flex-col gap-4 md:flex-3/4">
+        <table class="table table-zebra w-full">
+          <thead>
+            <tr>
+              <th>SMILES</th>
+              <th>Name</th>
+            </tr>
+          </thead>
+          <tbody id="smiles-table-body">
+            <tr>
+              <td>
+                <label>
+                  <input
+                    type="text"
+                    class="input input-bordered w-full smiles-input"
+                    placeholder="CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
+                    {% if meta.debug %}
+                      value="CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
+                    {% endif %}
+                  />
+                </label>
+              </td>
+              <td>
+                <label>
+                  <input
+                    type="text"
+                    class="input input-bordered w-full name-input"
+                    placeholder="Caffeine"
+                    {% if meta.debug %}
+                      value="Caffeine"
+                    {% endif %}
+                  />
+                </label>
+              </td>
+            </tr>
+            <tr>
+              <td>
+                <label>
+                  <input
+                    type="text"
+                    class="input input-bordered w-full smiles-input"
+                    placeholder="CC(C)CC1=CC=C(C=C1)C(C)C(=O)O"
+                    {% if meta.debug %}
+                      value="CC(C)CC1=CC=C(C=C1)C(C)C(=O)O"
+                    {% endif %}
+                  />
+                </label>
+              </td>
+              <td>
+                <label>
+                  <input
+                    type="text"
+                    class="input input-bordered w-full name-input"
+                    placeholder="Ibuprofen"
+                    {% if meta.debug %}
+                      value="Ibuprofen"
+                    {% endif %}
+                  />
+                </label>
+              </td>
+            </tr>
+          </tbody>
+        </table>
+        <label class="select mb-2 w-full">
+          <span class="label">Predictor</span>
+          <select id="prediction-setting" name="prediction-setting">
+            <option disabled>Select a Setting</option>
+            {% for s in meta.available_settings %}
+              <option
+                value="{{ s.url }}"
+                {% if s.id == meta.user.default_setting.id %}selected{% endif %}
+              >
+                {{ s.name }}{% if s.id == meta.user.default_setting.id %}
+                  (User default)
+                {% endif %}
+              </option>
+            {% endfor %}
+          </select>
+        </label>
+        <label class="floating-label" for="num-tps">
+          <input
+            type="number"
+            name="num-tps"
+            value="50"
+            step="1"
+            min="1"
+            max="100"
+            id="num-tps"
+            class="input input-md w-full"
+          />
+          <span>Max Transformation Products</span>
+        </label>
+        <div class="flex justify-end gap-2">
+          <button type="button" id="add-row-btn" class="btn btn-outline">
+            Add row
+          </button>
+          <button type="submit" class="btn btn-primary">Submit</button>
+        </div>
+      </fieldset>
+    </form>
+  </div>
+
+  <script>
+    const tableBody = document.getElementById("smiles-table-body");
+    const addRowBtn = document.getElementById("add-row-btn");
+    const form = document.getElementById("smiles-form");
+    const hiddenField = document.getElementById("substrates");
+
+    addRowBtn.addEventListener("click", () => {
+      const row = document.createElement("tr");
+
+      const tdSmiles = document.createElement("td");
+      const tdName = document.createElement("td");
+
+      const smilesInput = document.createElement("input");
+      smilesInput.type = "text";
+      smilesInput.className = "input input-bordered w-full smiles-input";
+      smilesInput.placeholder = "SMILES";
+
+      const nameInput = document.createElement("input");
+      nameInput.type = "text";
+      nameInput.className = "input input-bordered w-full name-input";
+      nameInput.placeholder = "Name";
+
+      tdSmiles.appendChild(smilesInput);
+      tdName.appendChild(nameInput);
+
+      row.appendChild(tdSmiles);
+      row.appendChild(tdName);
+
+      tableBody.appendChild(row);
+    });
+
+    // Before submit, gather table data into the hidden field
+    form.addEventListener("submit", (e) => {
+      const smilesInputs = Array.from(
+        document.querySelectorAll(".smiles-input"),
+      );
+      const nameInputs = Array.from(document.querySelectorAll(".name-input"));
+
+      const lines = [];
+
+      for (let i = 0; i < smilesInputs.length; i++) {
+        const smiles = smilesInputs[i].value.trim();
+        const name = nameInputs[i]?.value.trim() ?? "";
+
+        // Skip emtpy rows
+        if (!smiles && !name) {
+          continue;
+        }
+        lines.push(`${smiles},${name}`);
+      }
+      // Value looks like:
+      // "CN1C=NC2=C1C(=O)N(C(=O)N2C)C,Caffeine\nCC(C)CC1=CC=C(C=C1)C(C)C(=O)O,Ibuprofen"
+      hiddenField.value = lines.join("\n");
+    });
+  </script>
+{% endblock content %}

templates/modals/collections/new_prediction_setting_modal.html

@@ -210,6 +210,27 @@
               step="0.05"
             />
           </div>
+
+          <div class="form-control mb-3">
+            <label
+              class="label"
+              for="model-based-prediction-setting-expansion-scheme"
+            >
+              <span class="label-text">Select Expansion Scheme</span>
+            </label>
+            <select
+              id="model-based-prediction-setting-expansion-scheme"
+              name="model-based-prediction-setting-expansion-scheme"
+              class="select select-bordered w-full"
+            >
+              <option value="" disabled selected>
+                Select the Expansion Scheme
+              </option>
+              <option value="BFS">Breadth First Search</option>
+              <option value="DFS">Depth First Search</option>
+              <option value="GREEDY">Greedy</option>
+            </select>
+          </div>
         </div>
 
         <div class="form-control">

templates/modals/objects/download_job_result_modal.html

@@ -0,0 +1,66 @@
+{% load static %}
+
+<dialog
+  id="download_job_result_modal"
+  class="modal"
+  x-data="modalForm()"
+  @close="reset()"
+>
+  <div class="modal-box">
+    <!-- Header -->
+    <h3 class="font-bold text-lg">Download Job Result</h3>
+
+    <!-- Close button (X) -->
+    <form method="dialog">
+      <button
+        class="btn btn-sm btn-circle btn-ghost absolute right-2 top-2"
+        :disabled="isSubmitting"
+      >
+        ✕
+      </button>
+    </form>
+
+    <!-- Body -->
+    <div class="py-4">
+      <p>By clicking on Download the Result of this Job will be saved.</p>
+
+      <form
+        id="download-job-result-modal-form"
+        accept-charset="UTF-8"
+        action="{{ job.url }}"
+        method="GET"
+      >
+        <input type="hidden" name="download" value="true" />
+      </form>
+    </div>
+
+    <!-- Footer -->
+    <div class="modal-action">
+      <button
+        type="button"
+        class="btn"
+        onclick="this.closest('dialog').close()"
+        :disabled="isSubmitting"
+      >
+        Close
+      </button>
+      <button
+        type="button"
+        class="btn btn-primary"
+        @click="submit('download-job-result-modal-form'); $el.closest('dialog').close();"
+        :disabled="isSubmitting"
+      >
+        <span x-show="!isSubmitting">Download</span>
+        <span
+          x-show="isSubmitting"
+          class="loading loading-spinner loading-sm"
+        ></span>
+      </button>
+    </div>
+  </div>
+
+  <!-- Backdrop -->
+  <form method="dialog" class="modal-backdrop">
+    <button :disabled="isSubmitting">close</button>
+  </form>
+</dialog>

templates/objects/joblog.html

@@ -3,7 +3,9 @@
 {% block content %}
 
   {% block action_modals %}
-    {#    {% include "modals/objects/refresh_job_log.html" %}#}
+    {% if job.is_result_downloadable %}
+      {% include "modals/objects/download_job_result_modal.html" %}
+    {% endif %}
   {% endblock action_modals %}
 
   <div class="space-y-2 p-4">
@@ -49,22 +51,20 @@
     <div class="collapse-arrow bg-base-200 collapse">
       <input type="checkbox" checked />
       <div class="collapse-title text-xl font-medium">Description</div>
-      <div class="collapse-content">
-        Status page for Task {{ job.job_name }}
-      </div>
+      <div class="collapse-content">Status page for Job {{ job.job_name }}</div>
     </div>
 
     <!-- Job Status -->
     <div class="collapse-arrow bg-base-200 collapse">
       <input type="checkbox" checked />
-      <div class="collapse-title text-xl font-medium">Task Status</div>
+      <div class="collapse-title text-xl font-medium">Job Status</div>
       <div class="collapse-content">{{ job.status }}</div>
     </div>
 
     <!-- Job ID -->
     <div class="collapse-arrow bg-base-200 collapse">
       <input type="checkbox" checked />
-      <div class="collapse-title text-xl font-medium">Task ID</div>
+      <div class="collapse-title text-xl font-medium">Job ID</div>
       <div class="collapse-content">{{ job.task_id }}</div>
     </div>
 
@@ -72,7 +72,7 @@
     {% if job.is_in_terminal_state %}
       <div class="collapse-arrow bg-base-200 collapse">
         <input type="checkbox" checked />
-        <div class="collapse-title text-xl font-medium">Task Result</div>
+        <div class="collapse-title text-xl font-medium">Job Result</div>
         <div class="collapse-content">
           {% if job.job_name == 'engineer_pathways' %}
             <div class="card bg-base-100">
@@ -103,6 +103,68 @@
                 </ul>
               </div>
             </div>
+          {% elif job.job_name == 'batch_predict' %}
+            <div
+              id="table-container"
+              class="overflow-x-auto overflow-y-auto max-h-96 border rounded-lg"
+            ></div>
+
+            <script>
+              const input = `{{ job.task_result }}`;
+
+              function renderCsvTable(str) {
+                const lines = str
+                  .split("\n")
+                  .map((l) => l.trim())
+                  .filter(Boolean);
+                const [headerLine, ...rows] = lines;
+
+                const headers = headerLine.split(",").map((h) => h.trim());
+
+                const table = document.createElement("table");
+                table.className = "table table-zebra w-full";
+
+                const thead = document.createElement("thead");
+                const headerRow = document.createElement("tr");
+
+                headers.forEach((h) => {
+                  const th = document.createElement("th");
+                  th.textContent = h;
+                  headerRow.appendChild(th);
+                });
+
+                thead.appendChild(headerRow);
+
+                const tbody = document.createElement("tbody");
+
+                rows.forEach((rowStr) => {
+                  console.log(rowStr.split(","));
+                  console.log(headers);
+                  const row = document.createElement("tr");
+                  const cells = rowStr.split(",").map((c) => c.trim());
+
+                  headers.forEach((_, i) => {
+                    const td = document.createElement("td");
+
+                    const value = cells[i] || "";
+
+                    td.textContent = value;
+
+                    row.appendChild(td);
+                  });
+                  console.log(row);
+                  tbody.appendChild(row);
+                });
+
+                table.appendChild(thead);
+                table.appendChild(tbody);
+                return table;
+              }
+
+              document
+                .getElementById("table-container")
+                .appendChild(renderCsvTable(input));
+            </script>
           {% else %}
             {{ job.parsed_result }}
           {% endif %}

templates/objects/model.html

@@ -73,6 +73,7 @@
           </ul>
         </div>
       </div>
+    {% endif %}
     <!-- Reaction Packages -->
     <div class="collapse-arrow bg-base-200 collapse">
       <input type="checkbox" checked />
@@ -96,9 +97,7 @@
           <ul class="menu bg-base-100 rounded-box w-full">
             {% for p in model.eval_packages.all %}
               <li>
-                  <a href="{{ p.url }}" class="hover:bg-base-200"
-                    >{{ p.name }}</a
-                  >
+                <a href="{{ p.url }}" class="hover:bg-base-200">{{ p.name }}</a>
               </li>
             {% endfor %}
           </ul>
@@ -111,7 +110,6 @@
       <div class="collapse-title text-xl font-medium">Model Status</div>
       <div class="collapse-content">{{ model.status }}</div>
     </div>
-    {% endif %}
 
     {% if model.ready_for_prediction %}
       <!-- Predict Panel -->
@@ -174,7 +172,6 @@
         </div>
       </div>
     {% endif %}
-
     {% if model.model_status == 'FINISHED' %}
       <!-- Single Gen Curve Panel -->
       <div class="collapse-arrow bg-base-200 collapse">
@@ -188,6 +185,19 @@
           </div>
         </div>
       </div>
+      {% if model.multigen_eval %}
+        <div class="collapse-arrow bg-base-200 collapse">
+          <input type="checkbox" checked />
+          <div class="collapse-title text-xl font-medium">
+            Multi Gen Precision Recall Curve
+          </div>
+          <div class="collapse-content">
+            <div class="flex justify-center">
+              <div id="mg-chart"></div>
+            </div>
+          </div>
+        </div>
+      {% endif %}
     {% endif %}
   </div>
 
@@ -244,25 +254,7 @@
             }
         }
 
-        function makeLoadingGif(selector, gifPath) {
-            const element = document.querySelector(selector);
-            if (element) {
-                element.innerHTML = '<img src="' + gifPath + '" alt="Loading...">';
-            }
-        }
-
-        document.addEventListener('DOMContentLoaded', function() {
-            // Show actions button if there are actions
-            const actionsButton = document.getElementById('actionsButton');
-            const actionsList = actionsButton?.querySelector('ul');
-            if (actionsList && actionsList.children.length > 0) {
-                actionsButton?.classList.remove('hidden');
-            }
-
-            {% if model.model_status == 'FINISHED' %}
-            // Precision Recall Curve
-            const sgChart = document.getElementById('sg-chart');
-            if (sgChart) {
+        function makeChart(selector, data) {
             const x = ['Recall'];
             const y = ['Precision'];
             const thres = ['threshold'];
@@ -285,7 +277,6 @@
                 return -1;
             }
 
-                var data = {{ model.pr_curve|safe }};
             if (!data || data.length === 0) {
                 console.warn('PR curve data is empty');
                 return;
@@ -300,7 +291,7 @@
                 thres.push(d.threshold);
             }
             const chart = c3.generate({
-                    bindto: '#sg-chart',
+                bindto: selector,
                 data: {
                     onclick: function (d, e) {
                         const idx = d.index;
@@ -361,6 +352,29 @@
                 }
             });
         }
+
+        function makeLoadingGif(selector, gifPath) {
+            const element = document.querySelector(selector);
+            if (element) {
+                element.innerHTML = '<img src="' + gifPath + '" alt="Loading...">';
+            }
+        }
+
+        document.addEventListener('DOMContentLoaded', function() {
+            // Show actions button if there are actions
+            const actionsButton = document.getElementById('actionsButton');
+            const actionsList = actionsButton?.querySelector('ul');
+            if (actionsList && actionsList.children.length > 0) {
+                actionsButton?.classList.remove('hidden');
+            }
+
+            {% if model.model_status == 'FINISHED' %}
+                // Precision Recall Curve
+                makeChart('#sg-chart', {{ model.pr_curve|safe }});
+                {% if model.multigen_eval %}
+                    // Multi Gen Precision Recall Curve
+                    makeChart('#mg-chart', {{ model.mg_pr_curve|safe }});
+                {% endif %}
             {% endif %}
 
             // Predict button handler

templates/objects/pathway.html

@@ -393,7 +393,9 @@
                             <tbody>
                               <tr>
                                 <td>Threshold</td>
-                                <td>{{ pathway.setting.model_threshold }}</td>
+                                <td>
+                                  {{ pathway.setting_with_overrides.model_threshold }}
+                                </td>
                               </tr>
                             </tbody>
                           </table>
@@ -420,11 +422,15 @@
                 {% endif %}
                 <tr>
                   <td>Max Nodes</td>
-                  <td>{{ pathway.setting.max_nodes }}</td>
+                  <td>{{ pathway.setting_with_overrides.max_nodes }}</td>
                 </tr>
                 <tr>
                   <td>Max Depth</td>
-                  <td>{{ pathway.setting.max_depth }}</td>
+                  <td>{{ pathway.setting_with_overrides.max_depth }}</td>
+                </tr>
+                <tr>
+                  <td>Expansion Scheme</td>
+                  <td>{{ user.default_setting.expansion_scheme }}</td>
                 </tr>
               </tbody>
             </table>

templates/objects/user.html

@@ -150,6 +150,10 @@
                 <td>Max Depth</td>
                 <td>{{ user.default_setting.max_depth }}</td>
               </tr>
+              <tr>
+                <td>Expansion Scheme</td>
+                <td>{{ user.default_setting.expansion_scheme }}</td>
+              </tr>
             </tbody>
           </table>
         </div>

tests/test_jobs.py

@@ -1,3 +1,5 @@
+from datetime import datetime
+
 from django.conf import settings as s
 from django.test import TestCase, override_settings
 
@@ -23,6 +25,46 @@ class MultiGenTest(TestCase):
         cls.PW_WITH_INTERMEDIATE_NAME = "1,1,1-Trichloroethane (an/aerobic)"
         cls.PW_WITHOUT_INTERMEDIATE_NAME = "Caffeine"
 
+    def test_batch_predict(self):
+        from epdb.tasks import batch_predict
+
+        pred_data = [
+            ["CN1C=NC2=C1C(=O)N(C(=O)N2C)C", "Caffeine"],
+            ["CC(C)CC1=CC=C(C=C1)C(C)C(=O)O", "Ibuprofen"],
+        ]
+
+        batch_predict_setting = self.user.prediction_settings()
+
+        target_package = PackageManager.create_package(
+            self.user,
+            f"Autogenerated Package for Batch Prediction {datetime.now()}",
+            "This Package was generated automatically for the batch prediction task.",
+        )
+
+        num_tps = 50
+        res = batch_predict(
+            pred_data,
+            batch_predict_setting.pk,
+            target_package.pk,
+            num_tps=num_tps,
+        )
+
+        self.assertTrue(res.startswith("Pathway URL,"))
+        # Min 3 lines (1 header, 2 root nodes)
+        self.assertGreaterEqual(len(res.split("\n")), 3)
+        self.assertEqual(target_package.pathways.count(), 2)
+
+        pw = target_package.pathways.first()
+
+        self.assertEqual(
+            pw.setting_with_overrides.max_depth,
+            f"{num_tps} (this is an override for this particular pathway)",
+        )
+        self.assertEqual(
+            pw.setting_with_overrides.max_nodes,
+            f"{num_tps} (this is an override for this particular pathway)",
+        )
+
     def test_engineer_pathway(self):
         from epdb.tasks import engineer_pathways
 

tests/test_sobjects.py

@@ -1,20 +1,20 @@
+from unittest.mock import Mock, patch
+
 from django.test import TestCase
 
-from epdb.logic import SNode, SEdge
+from epdb.logic import SEdge, SNode, SPathway
+from epdb.models import Pathway, Setting
+from utilities.chem import PredictionResult, ProductSet
 
 
-class SObjectTest(TestCase):
-    def setUp(self):
-        pass
-
+class SNodeTest(TestCase):
     def test_snode_eq(self):
         snode1 = SNode("CN1C2C(N(C(N(C)C=2N=C1)=O)C)=O", 0)
         snode2 = SNode("CN1C2C(N(C(N(C)C=2N=C1)=O)C)=O", 0)
-        assert snode1 == snode2
+        self.assertEqual(snode1, snode2)
 
-    def test_snode_hash(self):
-        pass
 
+class SEdgeTest(TestCase):
     def test_sedge_eq(self):
         sedge1 = SEdge(
             [SNode("CN1C2C(N(C(N(C)C=2N=C1)=O)C)=O", 0)],
@@ -26,4 +26,62 @@ class SObjectTest(TestCase):
             [SNode("CN1C(=O)NC2=C(C1=O)N(C)C=N2", 1), SNode("C=O", 1)],
             rule=None,
         )
-        assert sedge1 == sedge2
+        self.assertEqual(sedge1, sedge2)
+
+
+class SPathwayTest(TestCase):
+    def setUp(self):
+        """Set up test data for SPathway tests."""
+        self.test_smiles = "CCN(CC)C(=O)C1=CC(=CC=C1)CO"
+        self.mock_setting = Mock(spec=Setting)
+        self.mock_pathway = Mock(spec=Pathway)
+
+    def test_predict_step_basic(self):
+        """Test basic predict_step functionality."""
+        spw = SPathway(root_nodes=self.test_smiles, prediction_setting=self.mock_setting)
+
+        # e.g. bt0002
+        pr = PredictionResult(
+            [
+                ProductSet(["CC1=CC=C(C2OC(CO)C(=O)C(O)C2O)C=C1CC1=CC=C(C2=CC=C(F)C=C2)S1"]),
+                ProductSet(["CC1=CC=C(C2OC(CO)C(O)C(O)C2=O)C=C1CC1=CC=C(C2=CC=C(F)C=C2)S1"]),
+                ProductSet(["CC1=CC=C(C2OC(CO)C(O)C(=O)C2O)C=C1CC1=CC=C(C2=CC=C(F)C=C2)S1"]),
+            ],
+            0.17,
+            None,
+        )
+
+        with patch.object(self.mock_setting, "expand", return_value=[pr]):
+            spw.predict_step(from_depth=0)
+
+        self.assertEqual(len(spw.smiles_to_node.keys()), 4)
+        self.assertEqual(len(spw.edges), 3)
+
+    def test_to_json(self):
+        """Test basic predict_step functionality."""
+        spw = SPathway(root_nodes=self.test_smiles, prediction_setting=self.mock_setting)
+
+        # e.g. bt0002
+        pr = PredictionResult(
+            [
+                ProductSet(["CC1=CC=C(C2OC(CO)C(=O)C(O)C2O)C=C1CC1=CC=C(C2=CC=C(F)C=C2)S1"]),
+                ProductSet(["CC1=CC=C(C2OC(CO)C(O)C(O)C2=O)C=C1CC1=CC=C(C2=CC=C(F)C=C2)S1"]),
+                ProductSet(["CC1=CC=C(C2OC(CO)C(O)C(=O)C2O)C=C1CC1=CC=C(C2=CC=C(F)C=C2)S1"]),
+            ],
+            0.17,
+            None,
+        )
+
+        with patch.object(self.mock_setting, "expand", return_value=[pr]):
+            spw.predict_step(from_depth=0)
+
+        self.assertEqual(len(spw.smiles_to_node.keys()), 4)
+        self.assertEqual(len(spw.edges), 3)
+
+        json_result = spw.to_json()
+
+        self.assertIsInstance(json_result, dict)
+        self.assertIn("nodes", json_result)
+        self.assertIn("edges", json_result)
+        self.assertEqual(len(json_result["nodes"]), 4)
+        self.assertEqual(len(json_result["edges"]), 3)