Fixed handling for SMIRKS/SMARTS, adjusted test values as they are now cleaned, refactored logic for object update

# Conflicts:
#	pyproject.toml
#	uv.lock

envipath/settings.py

@@ -92,6 +92,8 @@ TEMPLATES = [
     },
 ]
 
+ALLOWED_HTML_TAGS = {'b', 'i', 'u', 'br', 'em', 'mark', 'p', 's', 'strong'}
+
 WSGI_APPLICATION = "envipath.wsgi.application"
 
 # Database

epdb/logic.py

@@ -4,6 +4,7 @@ import json
 from typing import Union, List, Optional, Set, Dict, Any
 from uuid import UUID
 
+import nh3
 from django.contrib.auth import get_user_model
 from django.db import transaction
 from django.conf import settings as s
@@ -185,6 +186,12 @@ class UserManager(object):
     def create_user(
         username, email, password, set_setting=True, add_to_group=True, *args, **kwargs
     ):
+        # Clean for potential XSS
+        clean_username = nh3.clean(username).strip()
+        clean_email = nh3.clean(email).strip()
+        if clean_username != username or clean_email != email:
+            # This will be caught by the try in view.py/register
+            raise ValueError("Invalid username or password")
         # avoid circular import :S
         from .tasks import send_registration_mail
 
@@ -262,8 +269,9 @@ class GroupManager(object):
     @staticmethod
     def create_group(current_user, name, description):
         g = Group()
-        g.name = name
-        g.description = description
+        # Clean for potential XSS
+        g.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+        g.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
         g.owner = current_user
         g.save()
 
@@ -518,8 +526,13 @@ class PackageManager(object):
     @transaction.atomic
     def create_package(current_user, name: str, description: str = None):
         p = Package()
-        p.name = name
-        p.description = description
+
+        # Clean for potential XSS
+        p.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+
+        if description is not None and description.strip() != "":
+            p.description = nh3.clean(description.strip(), tags=s.ALLOWED_HTML_TAGS).strip()
+
         p.save()
 
         up = UserPackagePermission()
@@ -1094,28 +1107,29 @@ class SettingManager(object):
         model: EPModel = None,
         model_threshold: float = None,
     ):
-        s = Setting()
-        s.name = name
-        s.description = description
-        s.max_nodes = max_nodes
-        s.max_depth = max_depth
-        s.model = model
-        s.model_threshold = model_threshold
+        new_s = Setting()
+        # Clean for potential XSS
+        new_s.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+        new_s.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
+        new_s.max_nodes = max_nodes
+        new_s.max_depth = max_depth
+        new_s.model = model
+        new_s.model_threshold = model_threshold
 
-        s.save()
+        new_s.save()
 
         if rule_packages is not None:
             for r in rule_packages:
-                s.rule_packages.add(r)
-            s.save()
+                new_s.rule_packages.add(r)
+            new_s.save()
 
         usp = UserSettingPermission()
         usp.user = user
-        usp.setting = s
+        usp.setting = new_s
         usp.permission = Permission.ALL[0]
         usp.save()
 
-        return s
+        return new_s
 
     @staticmethod
     def get_default_setting(user: User):
@@ -1542,7 +1556,9 @@ class SPathway(object):
                 if sub.app_domain_assessment is None:
                     if self.prediction_setting.model:
                         if self.prediction_setting.model.app_domain:
-                            app_domain_assessment = self.prediction_setting.model.app_domain.assess(sub.smiles)
+                            app_domain_assessment = self.prediction_setting.model.app_domain.assess(
+                                sub.smiles
+                            )
 
                             if self.persist is not None:
                                 n = self.snode_persist_lookup[sub]
@@ -1574,7 +1590,9 @@ class SPathway(object):
                                     app_domain_assessment = None
                                     if self.prediction_setting.model:
                                         if self.prediction_setting.model.app_domain:
-                                            app_domain_assessment = (self.prediction_setting.model.app_domain.assess(c))
+                                            app_domain_assessment = (
+                                                self.prediction_setting.model.app_domain.assess(c)
+                                            )
 
                                     self.smiles_to_node[c] = SNode(
                                         c, sub.depth + 1, app_domain_assessment

epdb/models.py

@@ -11,6 +11,7 @@ from typing import Union, List, Optional, Dict, Tuple, Set, Any
 from uuid import uuid4
 import math
 import joblib
+import nh3
 import numpy as np
 from django.conf import settings as s
 from django.contrib.auth.models import AbstractUser
@@ -28,8 +29,14 @@ from sklearn.metrics import precision_score, recall_score, jaccard_score
 from sklearn.model_selection import ShuffleSplit
 
 from utilities.chem import FormatConverter, ProductSet, PredictionResult, IndigoUtils
-from utilities.ml import RuleBasedDataset, ApplicabilityDomainPCA, EnsembleClassifierChain, RelativeReasoning, \
-    EnviFormerDataset, Dataset
+from utilities.ml import (
+    RuleBasedDataset,
+    ApplicabilityDomainPCA,
+    EnsembleClassifierChain,
+    RelativeReasoning,
+    EnviFormerDataset,
+    Dataset,
+)
 
 logger = logging.getLogger(__name__)
 
@@ -803,14 +810,16 @@ class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin
         c = Compound()
         c.package = package
 
-        if name is None or name.strip() == "":
+        if name is not None:
+            # Clean for potential XSS
+            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+        if name is None or name == "":
             name = f"Compound {Compound.objects.filter(package=package).count() + 1}"
-
         c.name = name
 
         # We have a default here only set the value if it carries some payload
         if description is not None and description.strip() != "":
-            c.description = description.strip()
+            c.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
         c.save()
 
@@ -982,11 +991,11 @@ class CompoundStructure(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdenti
             raise ValueError("Unpersisted Compound! Persist compound first!")
 
         cs = CompoundStructure()
+        # Clean for potential XSS
         if name is not None:
-            cs.name = name
-
+            cs.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
         if description is not None:
-            cs.description = description
+            cs.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
         cs.smiles = smiles
         cs.compound = compound
@@ -1188,21 +1197,29 @@ class SimpleAmbitRule(SimpleRule):
         r = SimpleAmbitRule()
         r.package = package
 
-        if name is None or name.strip() == "":
+        if name is not None:
+            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+
+        if name is None or name == "":
             name = f"Rule {Rule.objects.filter(package=package).count() + 1}"
 
         r.name = name
-
         if description is not None and description.strip() != "":
-            r.description = description
+            r.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
         r.smirks = smirks
 
         if reactant_filter_smarts is not None and reactant_filter_smarts.strip() != "":
-            r.reactant_filter_smarts = reactant_filter_smarts
+            if not FormatConverter.is_valid_smarts(reactant_filter_smarts.strip()):
+                raise ValueError(f'Reactant Filter SMARTS "{reactant_filter_smarts}" is invalid!')
+            else:
+                r.reactant_filter_smarts = reactant_filter_smarts.strip()
 
         if product_filter_smarts is not None and product_filter_smarts.strip() != "":
-            r.product_filter_smarts = product_filter_smarts
+            if not FormatConverter.is_valid_smarts(product_filter_smarts.strip()):
+                raise ValueError(f'Product Filter SMARTS "{product_filter_smarts}" is invalid!')
+            else:
+                r.product_filter_smarts = product_filter_smarts.strip()
 
         r.save()
         return r
@@ -1403,12 +1420,11 @@ class Reaction(EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin
 
         r = Reaction()
         r.package = package
-
+        # Clean for potential XSS
         if name is not None and name.strip() != "":
-            r.name = name
-
+            r.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
         if description is not None and name.strip() != "":
-            r.description = description
+            r.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
         r.multi_step = multi_step
 
@@ -1716,14 +1732,15 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
     ):
         pw = Pathway()
         pw.package = package
-
-        if name is None or name.strip() == "":
+        if name is not None:
+            # Clean for potential XSS
+            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+        if name is None or name == "":
             name = f"Pathway {Pathway.objects.filter(package=package).count() + 1}"
 
         pw.name = name
-
         if description is not None and description.strip() != "":
-            pw.description = description
+            pw.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
         pw.save()
         try:
@@ -2018,11 +2035,16 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin):
         for node in end_nodes:
             e.end_nodes.add(node)
 
-        if name is None:
+        # Clean for potential XSS
+        # Cleaning technically not needed as it is also done in Reaction.create, including it here for consistency
+        if name is not None:
+            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+        if name is None or name == "":
             name = f"Reaction {pathway.package.reactions.count() + 1}"
 
         if description is None:
             description = s.DEFAULT_VALUES["description"]
+        description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
         r = Reaction.create(
             pathway.package,
@@ -2344,7 +2366,9 @@ class PackageBasedModel(EPModel):
             eval_reactions = list(
                 Reaction.objects.filter(package__in=self.eval_packages.all()).distinct()
             )
-            ds = RuleBasedDataset.generate_dataset(eval_reactions, self.applicable_rules, educts_only=True)
+            ds = RuleBasedDataset.generate_dataset(
+                eval_reactions, self.applicable_rules, educts_only=True
+            )
             if isinstance(self, RuleBasedRelativeReasoning):
                 X = ds.X(exclude_id_col=False, na_replacement=None).to_numpy()
                 y = ds.y(na_replacement=np.nan).to_numpy()
@@ -2542,14 +2566,15 @@ class RuleBasedRelativeReasoning(PackageBasedModel):
     ):
         rbrr = RuleBasedRelativeReasoning()
         rbrr.package = package
-
-        if name is None or name.strip() == "":
+        if name is not None:
+            # Clean for potential XSS
+            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+        if name is None or name == "":
             name = f"RuleBasedRelativeReasoning {RuleBasedRelativeReasoning.objects.filter(package=package).count() + 1}"
 
         rbrr.name = name
-
         if description is not None and description.strip() != "":
-            rbrr.description = description
+            rbrr.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
         if threshold is None or (threshold <= 0 or 1 <= threshold):
             raise ValueError("Threshold must be a float between 0 and 1.")
@@ -2646,14 +2671,15 @@ class MLRelativeReasoning(PackageBasedModel):
     ):
         mlrr = MLRelativeReasoning()
         mlrr.package = package
-
-        if name is None or name.strip() == "":
+        if name is not None:
+            # Clean for potential XSS
+            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+        if name is None or name == "":
             name = f"MLRelativeReasoning {MLRelativeReasoning.objects.filter(package=package).count() + 1}"
 
         mlrr.name = name
-
         if description is not None and description.strip() != "":
-            mlrr.description = description
+            mlrr.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
         if threshold is None or (threshold <= 0 or 1 <= threshold):
             raise ValueError("Threshold must be a float between 0 and 1.")
@@ -2807,7 +2833,9 @@ class ApplicabilityDomain(EnviPathModel):
             else:
                 smiles.append(structures)
 
-        assessment_ds, assessment_prods = ds.classification_dataset(structures, self.model.applicable_rules)
+        assessment_ds, assessment_prods = ds.classification_dataset(
+            structures, self.model.applicable_rules
+        )
 
         # qualified_neighbours_per_rule is a nested dictionary structured as:
         #   {
@@ -2823,12 +2851,16 @@ class ApplicabilityDomain(EnviPathModel):
         qualified_neighbours_per_rule: Dict = {}
 
         import polars as pl
+
         # Select only the triggered columns
         for i, row in enumerate(assessment_ds[:, assessment_ds.triggered()].iter_rows(named=True)):
             # Find the rules the structure triggers. For each rule, filter the training dataset to rows that also
             # trigger that rule.
-            train_trig = {trig_uuid.split("_")[-1]: ds.filter(pl.col(trig_uuid).eq(1))
-                          for trig_uuid, value in row.items() if value == 1}
+            train_trig = {
+                trig_uuid.split("_")[-1]: ds.filter(pl.col(trig_uuid).eq(1))
+                for trig_uuid, value in row.items()
+                if value == 1
+            }
             qualified_neighbours_per_rule[i] = train_trig
         rule_to_i = {str(r.uuid): i for i, r in enumerate(self.model.applicable_rules)}
         preds = self.model.combine_products_and_probs(
@@ -2848,18 +2880,28 @@ class ApplicabilityDomain(EnviPathModel):
             # loop through rule indices together with the collected neighbours indices from train dataset
             for rule_uuid, train_instances in qualified_neighbours_per_rule[i].items():
                 # compute tanimoto distance for all neighbours and add to dataset
-                dists = self._compute_distances(assessment_ds[i, assessment_ds.struct_features()].to_numpy()[0],
-                                                train_instances[:, train_instances.struct_features()].to_numpy())
+                dists = self._compute_distances(
+                    assessment_ds[i, assessment_ds.struct_features()].to_numpy()[0],
+                    train_instances[:, train_instances.struct_features()].to_numpy(),
+                )
                 train_instances = train_instances.with_columns(dist=pl.Series(dists))
 
                 #  sort them in a descending way and take at most `self.num_neighbours`
                 # TODO: Should this be descending? If we want the most similar then we want values close to zero (ascending)
-                train_instances = train_instances.sort("dist", descending=True)[:self.num_neighbours]
+                train_instances = train_instances.sort("dist", descending=True)[
+                    : self.num_neighbours
+                ]
                 # compute average distance
-                rule_reliabilities[rule_uuid] = train_instances.select(pl.mean("dist")).fill_nan(0.0).item()
+                rule_reliabilities[rule_uuid] = (
+                    train_instances.select(pl.mean("dist")).fill_nan(0.0).item()
+                )
                 # for local_compatibility we'll need the datasets for the indices having the highest similarity
-                local_compatibilities[rule_uuid] = self._compute_compatibility(rule_uuid, train_instances)
-                neighbours_per_rule[rule_uuid] = list(CompoundStructure.objects.filter(uuid__in=train_instances["structure_id"]))
+                local_compatibilities[rule_uuid] = self._compute_compatibility(
+                    rule_uuid, train_instances
+                )
+                neighbours_per_rule[rule_uuid] = list(
+                    CompoundStructure.objects.filter(uuid__in=train_instances["structure_id"])
+                )
                 neighbor_probs_per_rule[rule_uuid] = train_instances[f"prob_{rule_uuid}"].to_list()
 
             ad_res = {
@@ -2933,8 +2975,11 @@ class ApplicabilityDomain(EnviPathModel):
     def _compute_compatibility(self, rule_idx: int, neighbours: "RuleBasedDataset"):
         accuracy = 0.0
         import polars as pl
-        obs_pred = neighbours.select(obs=pl.col(f"obs_{rule_idx}").cast(pl.Boolean),
-                                     pred=pl.col(f"prob_{rule_idx}") >= self.model.threshold)
+
+        obs_pred = neighbours.select(
+            obs=pl.col(f"obs_{rule_idx}").cast(pl.Boolean),
+            pred=pl.col(f"prob_{rule_idx}") >= self.model.threshold,
+        )
         # Compute tp, tn, fp, fn using polars expressions
         tp = obs_pred.filter((pl.col("obs")) & (pl.col("pred"))).height
         tn = obs_pred.filter((~pl.col("obs")) & (~pl.col("pred"))).height
@@ -2961,14 +3006,15 @@ class EnviFormer(PackageBasedModel):
     ):
         mod = EnviFormer()
         mod.package = package
-
-        if name is None or name.strip() == "":
+        if name is not None:
+            # Clean for potential XSS
+            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+        if name is None or name == "":
             name = f"EnviFormer {EnviFormer.objects.filter(package=package).count() + 1}"
 
         mod.name = name
-
         if description is not None and description.strip() != "":
-            mod.description = description
+            mod.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
         if threshold is None or (threshold <= 0 or 1 <= threshold):
             raise ValueError("Threshold must be a float between 0 and 1.")
@@ -3103,7 +3149,7 @@ class EnviFormer(PackageBasedModel):
             pred_dict = {}
             for k, pred in enumerate(predictions):
                 pred_smiles, pred_proba = zip(*pred.items())
-                reactant, true_product = test_ds[k, "educts"], test_ds[k, "products"]
+                reactant, _ = test_ds[k, "educts"], test_ds[k, "products"]
                 pred_dict.setdefault(reactant, {"predict": [], "scores": []})
                 for smiles, proba in zip(pred_smiles, pred_proba):
                     smiles = set(smiles.split("."))
@@ -3217,8 +3263,9 @@ class EnviFormer(PackageBasedModel):
 
         # If there are eval packages perform single generation evaluation on them instead of random splits
         if self.eval_packages.count() > 0:
-            ds = EnviFormerDataset.generate_dataset(Reaction.objects.filter(
-                package__in=self.eval_packages.all()).distinct())
+            ds = EnviFormerDataset.generate_dataset(
+                Reaction.objects.filter(package__in=self.eval_packages.all()).distinct()
+            )
             test_result = self.model.predict_batch(ds.X())
             single_gen_result = evaluate_sg(ds, test_result, self.threshold)
             self.eval_results = self.compute_averages([single_gen_result])
@@ -3236,7 +3283,9 @@ class EnviFormer(PackageBasedModel):
                 train = ds[train_index]
                 test = ds[test_index]
                 start = datetime.now()
-                model = fine_tune(train.X(), train.y(), s.MODEL_DIR, str(split_id), device=s.ENVIFORMER_DEVICE)
+                model = fine_tune(
+                    train.X(), train.y(), s.MODEL_DIR, str(split_id), device=s.ENVIFORMER_DEVICE
+                )
                 end = datetime.now()
                 logger.debug(
                     f"EnviFormer finetuning took {(end - start).total_seconds():.2f} seconds"
@@ -3313,7 +3362,12 @@ class EnviFormer(PackageBasedModel):
                     for pathway in train_pathways:
                         for reaction in pathway.edges:
                             reaction = reaction.edge_label
-                            if any([educt in test_educts for educt in reaction_to_educts[str(reaction.uuid)]]):
+                            if any(
+                                [
+                                    educt in test_educts
+                                    for educt in reaction_to_educts[str(reaction.uuid)]
+                                ]
+                            ):
                                 overlap += 1
                                 continue
                             train_reactions.append(reaction)
@@ -3370,41 +3424,44 @@ class Scenario(EnviPathModel):
         scenario_type: str,
         additional_information: List["EnviPyModel"],
     ):
-        s = Scenario()
-        s.package = package
-
-        if name is None or name.strip() == "":
+        new_s = Scenario()
+        new_s.package = package
+        if name is not None:
+            # Clean for potential XSS
+            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+        if name is None or name == "":
             name = f"Scenario {Scenario.objects.filter(package=package).count() + 1}"
-
-        s.name = name
+        new_s.name = name
 
         if description is not None and description.strip() != "":
-            s.description = description
+            new_s.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
         if scenario_date is not None and scenario_date.strip() != "":
-            s.scenario_date = scenario_date
+            new_s.scenario_date = nh3.clean(scenario_date).strip()
 
         if scenario_type is not None and scenario_type.strip() != "":
-            s.scenario_type = scenario_type
+            new_s.scenario_type = scenario_type
 
         add_inf = defaultdict(list)
 
         for info in additional_information:
             cls_name = info.__class__.__name__
-            ai_data = json.loads(info.model_dump_json())
+            # Clean for potential XSS hidden in the additional information fields.
+            ai_data = json.loads(nh3.clean(info.model_dump_json()).strip())
             ai_data["uuid"] = f"{uuid4()}"
             add_inf[cls_name].append(ai_data)
 
-        s.additional_information = add_inf
+        new_s.additional_information = add_inf
 
-        s.save()
+        new_s.save()
 
-        return s
+        return new_s
 
     @transaction.atomic
     def add_additional_information(self, data: "EnviPyModel"):
         cls_name = data.__class__.__name__
-        ai_data = json.loads(data.model_dump_json())
+        # Clean for potential XSS hidden in the additional information fields.
+        ai_data = json.loads(nh3.clean(data.model_dump_json()).strip())
         ai_data["uuid"] = f"{uuid4()}"
 
         if cls_name not in self.additional_information:
@@ -3439,7 +3496,8 @@ class Scenario(EnviPathModel):
         new_ais = defaultdict(list)
         for k, vals in data.items():
             for v in vals:
-                ai_data = json.loads(v.model_dump_json())
+                # Clean for potential XSS hidden in the additional information fields.
+                ai_data = json.loads(nh3.clean(v.model_dump_json()).strip())
                 if hasattr(v, "uuid"):
                     ai_data["uuid"] = str(v.uuid)
                 else:

epdb/views.py

@@ -10,6 +10,7 @@ from django.urls import reverse
 from django.views.decorators.csrf import csrf_exempt
 from envipy_additional_information import NAME_MAPPING
 from oauth2_provider.decorators import protected_resource
+import nh3
 
 from utilities.chem import FormatConverter, IndigoUtils
 from utilities.decorators import package_permission_required
@@ -85,7 +86,10 @@ def login(request):
         from django.contrib.auth import authenticate
         from django.contrib.auth import login
 
-        username = request.POST.get("username")
+        username = request.POST.get("username").strip()
+        if username != request.POST.get("username"):
+            context["message"] = "Login failed!"
+            return render(request, "static/login.html", context)
         password = request.POST.get("password")
 
         # Get email for username and check if the account is active
@@ -670,7 +674,8 @@ def search(request):
 
     if request.method == "GET":
         package_urls = request.GET.getlist("packages")
-        searchterm = request.GET.get("search")
+        searchterm = request.GET.get("search").strip()
+
         mode = request.GET.get("mode")
 
         # add HTTP_ACCEPT check to differentiate between index and ajax call
@@ -771,7 +776,6 @@ def package_models(request, package_uuid):
 
     elif request.method == "POST":
         log_post_params(request)
-
         name = request.POST.get("model-name")
         description = request.POST.get("model-description")
 
@@ -936,8 +940,14 @@ def package_model(request, package_uuid, model_uuid):
             else:
                 return HttpResponseBadRequest()
         else:
-            name = request.POST.get("model-name", "").strip()
-            description = request.POST.get("model-description", "").strip()
+            # TODO: Move cleaning to property updater
+            name = request.POST.get("model-name")
+            if name is not None:
+                name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+
+            description = request.POST.get("model-description")
+            if description is not None:
+                description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
             if any([name, description]):
                 if name:
@@ -1039,8 +1049,16 @@ def package(request, package_uuid):
             else:
                 return HttpResponseBadRequest()
 
+        # TODO: Move cleaning to property updater
         new_package_name = request.POST.get("package-name")
+        if new_package_name is not None:
+            new_package_name = nh3.clean(new_package_name, tags=s.ALLOWED_HTML_TAGS).strip()
+
         new_package_description = request.POST.get("package-description")
+        if new_package_description is not None:
+            new_package_description = nh3.clean(
+                new_package_description, tags=s.ALLOWED_HTML_TAGS
+            ).strip()
 
         grantee_url = request.POST.get("grantee")
         read = request.POST.get("read") == "on"
@@ -1149,7 +1167,7 @@ def package_compounds(request, package_uuid):
 
     elif request.method == "POST":
         compound_name = request.POST.get("compound-name")
-        compound_smiles = request.POST.get("compound-smiles")
+        compound_smiles = request.POST.get("compound-smiles").strip()
         compound_description = request.POST.get("compound-description")
 
         c = Compound.create(current_package, compound_smiles, compound_name, compound_description)
@@ -1202,8 +1220,16 @@ def package_compound(request, package_uuid, compound_uuid):
 
             return JsonResponse({"success": current_compound.url})
 
-        new_compound_name = request.POST.get("compound-name", "").strip()
-        new_compound_description = request.POST.get("compound-description", "").strip()
+        # TODO: Move cleaning to property updater
+        new_compound_name = request.POST.get("compound-name")
+        if new_compound_name is not None:
+            new_compound_name = nh3.clean(new_compound_name, tags=s.ALLOWED_HTML_TAGS).strip()
+
+        new_compound_description = request.POST.get("compound-description")
+        if new_compound_description is not None:
+            new_compound_description = nh3.clean(
+                new_compound_description, tags=s.ALLOWED_HTML_TAGS
+            ).strip()
 
         if new_compound_name:
             current_compound.name = new_compound_name
@@ -1268,7 +1294,7 @@ def package_compound_structures(request, package_uuid, compound_uuid):
 
     elif request.method == "POST":
         structure_name = request.POST.get("structure-name")
-        structure_smiles = request.POST.get("structure-smiles")
+        structure_smiles = request.POST.get("structure-smiles").strip()
         structure_description = request.POST.get("structure-description")
 
         try:
@@ -1339,8 +1365,16 @@ def package_compound_structure(request, package_uuid, compound_uuid, structure_u
             else:
                 return HttpResponseBadRequest()
 
-        new_structure_name = request.POST.get("compound-structure-name", "").strip()
-        new_structure_description = request.POST.get("compound-structure-description", "").strip()
+        # TODO: Move cleaning to property updater
+        new_structure_name = request.POST.get("compound-structure-name")
+        if new_structure_name is not None:
+            new_structure_name = nh3.clean(new_structure_name, tags=s.ALLOWED_HTML_TAGS).strip()
+
+        new_structure_description = request.POST.get("compound-structure-description")
+        if new_structure_description is not None:
+            new_structure_description = nh3.clean(
+                new_structure_description, tags=s.ALLOWED_HTML_TAGS
+            ).strip()
 
         if new_structure_name:
             current_structure.name = new_structure_name
@@ -1442,11 +1476,11 @@ def package_rules(request, package_uuid):
 
         # Obtain parameters as required by rule type
         if rule_type == "SimpleAmbitRule":
-            params["smirks"] = request.POST.get("rule-smirks")
+            params["smirks"] = request.POST.get("rule-smirks").strip()
             params["reactant_filter_smarts"] = request.POST.get("rule-reactant-smarts")
             params["product_filter_smarts"] = request.POST.get("rule-product-smarts")
         elif rule_type == "SimpleRDKitRule":
-            params["reaction_smarts"] = request.POST.get("rule-reaction-smarts")
+            params["reaction_smarts"] = request.POST.get("rule-reaction-smarts").strip()
         elif rule_type == "ParallelRule":
             pass
         elif rule_type == "SequentialRule":
@@ -1547,8 +1581,14 @@ def package_rule(request, package_uuid, rule_uuid):
 
             return JsonResponse({"success": current_rule.url})
 
-        rule_name = request.POST.get("rule-name", "").strip()
-        rule_description = request.POST.get("rule-description", "").strip()
+        # TODO: Move cleaning to property updater
+        rule_name = request.POST.get("rule-name")
+        if rule_name is not None:
+            rule_name = nh3.clean(rule_name, tags=s.ALLOWED_HTML_TAGS).strip()
+
+        rule_description = request.POST.get("rule-description")
+        if rule_description is not None:
+            rule_description = nh3.clean(rule_description, tags=s.ALLOWED_HTML_TAGS).strip()
 
         if rule_name:
             current_rule.name = rule_name
@@ -1637,8 +1677,8 @@ def package_reactions(request, package_uuid):
     elif request.method == "POST":
         reaction_name = request.POST.get("reaction-name")
         reaction_description = request.POST.get("reaction-description")
-        reactions_smirks = request.POST.get("reaction-smirks")
 
+        reactions_smirks = request.POST.get("reaction-smirks").strip()
         educts = reactions_smirks.split(">>")[0].split(".")
         products = reactions_smirks.split(">>")[1].split(".")
 
@@ -1699,8 +1739,16 @@ def package_reaction(request, package_uuid, reaction_uuid):
 
             return JsonResponse({"success": current_reaction.url})
 
-        new_reaction_name = request.POST.get("reaction-name", "").strip()
-        new_reaction_description = request.POST.get("reaction-description", "").strip()
+        # TODO: Move cleaning to property updater
+        new_reaction_name = request.POST.get("reaction-name")
+        if new_reaction_name is not None:
+            new_reaction_name = nh3.clean(new_reaction_name, tags=s.ALLOWED_HTML_TAGS).strip()
+
+        new_reaction_description = request.POST.get("reaction-description")
+        if new_reaction_description is not None:
+            new_reaction_description = nh3.clean(
+                new_reaction_description, tags=s.ALLOWED_HTML_TAGS
+            ).strip()
 
         if new_reaction_name:
             current_reaction.name = new_reaction_name
@@ -1777,8 +1825,9 @@ def package_pathways(request, package_uuid):
 
         name = request.POST.get("name")
         description = request.POST.get("description")
-        pw_mode = request.POST.get("predict", "predict").strip()
+
         smiles = request.POST.get("smiles", "").strip()
+        pw_mode = request.POST.get("predict", "predict").strip()
 
         if "smiles" in request.POST and smiles == "":
             return error(
@@ -1787,8 +1836,6 @@ def package_pathways(request, package_uuid):
                 "Pathway prediction failed due to missing or empty SMILES",
             )
 
-        smiles = smiles.strip()
-
         try:
             stand_smiles = FormatConverter.standardize(smiles)
         except ValueError:
@@ -1947,8 +1994,14 @@ def package_pathway(request, package_uuid, pathway_uuid):
 
             return JsonResponse({"success": current_pathway.url})
 
+        # TODO: Move cleaning to property updater
         pathway_name = request.POST.get("pathway-name")
+        if pathway_name is not None:
+            pathway_name = nh3.clean(pathway_name, tags=s.ALLOWED_HTML_TAGS).strip()
+
         pathway_description = request.POST.get("pathway-description")
+        if pathway_description is not None:
+            pathway_description = nh3.clean(pathway_description, tags=s.ALLOWED_HTML_TAGS).strip()
 
         if any([pathway_name, pathway_description]):
             if pathway_name is not None and pathway_name.strip() != "":
@@ -2036,8 +2089,8 @@ def package_pathway_nodes(request, package_uuid, pathway_uuid):
     elif request.method == "POST":
         node_name = request.POST.get("node-name")
         node_description = request.POST.get("node-description")
-        node_smiles = request.POST.get("node-smiles")
 
+        node_smiles = request.POST.get("node-smiles").strip()
         current_pathway.add_node(node_smiles, name=node_name, description=node_description)
 
         return redirect(current_pathway.url)
@@ -2199,9 +2252,9 @@ def package_pathway_edges(request, package_uuid, pathway_uuid):
 
     elif request.method == "POST":
         log_post_params(request)
-
         edge_name = request.POST.get("edge-name")
         edge_description = request.POST.get("edge-description")
+
         edge_substrates = request.POST.getlist("edge-substrates")
         edge_products = request.POST.getlist("edge-products")
 
@@ -2288,7 +2341,7 @@ def package_scenarios(request, package_uuid):
             "all", False
         ):
             scens = Scenario.objects.filter(package=current_package).order_by("name")
-            res = [{"name": s.name, "url": s.url, "uuid": s.uuid} for s in scens]
+            res = [{"name": s_.name, "url": s_.url, "uuid": s_.uuid} for s_ in scens]
             return JsonResponse(res, safe=False)
 
         context = get_base_context(request)
@@ -2336,21 +2389,21 @@ def package_scenarios(request, package_uuid):
                 "name": "soil",
                 "widgets": [
                     HTMLGenerator.generate_html(ai, prefix=f"soil_{0}")
-                    for ai in [x for s in SOIL_ADDITIONAL_INFORMATION.values() for x in s]
+                    for ai in [x for sv in SOIL_ADDITIONAL_INFORMATION.values() for x in sv]
                 ],
             },
             "Sludge Data": {
                 "name": "sludge",
                 "widgets": [
                     HTMLGenerator.generate_html(ai, prefix=f"sludge_{0}")
-                    for ai in [x for s in SLUDGE_ADDITIONAL_INFORMATION.values() for x in s]
+                    for ai in [x for sv in SLUDGE_ADDITIONAL_INFORMATION.values() for x in sv]
                 ],
             },
             "Water-Sediment System Data": {
                 "name": "sediment",
                 "widgets": [
                     HTMLGenerator.generate_html(ai, prefix=f"sediment_{0}")
-                    for ai in [x for s in SEDIMENT_ADDITIONAL_INFORMATION.values() for x in s]
+                    for ai in [x for sv in SEDIMENT_ADDITIONAL_INFORMATION.values() for x in sv]
                 ],
             },
         }
@@ -2365,6 +2418,7 @@ def package_scenarios(request, package_uuid):
 
         scenario_name = request.POST.get("scenario-name")
         scenario_description = request.POST.get("scenario-description")
+
         scenario_date_year = request.POST.get("scenario-date-year")
         scenario_date_month = request.POST.get("scenario-date-month")
         scenario_date_day = request.POST.get("scenario-date-day")
@@ -2378,9 +2432,9 @@ def package_scenarios(request, package_uuid):
         scenario_type = request.POST.get("scenario-type")
 
         additional_information = HTMLGenerator.build_models(request.POST.dict())
-        additional_information = [x for s in additional_information.values() for x in s]
+        additional_information = [x for sv in additional_information.values() for x in sv]
 
-        s = Scenario.create(
+        new_scen = Scenario.create(
             current_package,
             name=scenario_name,
             description=scenario_description,
@@ -2389,7 +2443,7 @@ def package_scenarios(request, package_uuid):
             additional_information=additional_information,
         )
 
-        return redirect(s.url)
+        return redirect(new_scen.url)
     else:
         return HttpResponseNotAllowed(
             [
@@ -2689,6 +2743,7 @@ def settings(request):
 
         name = request.POST.get("prediction-setting-name")
         description = request.POST.get("prediction-setting-description")
+
         new_default = request.POST.get("prediction-setting-new-default", "off") == "on"
 
         max_nodes = min(

pyproject.toml

@@ -27,6 +27,7 @@ dependencies = [
     "scikit-learn>=1.6.1",
     "sentry-sdk[django]>=2.32.0",
     "setuptools>=80.8.0",
+    "nh3==0.3.2",
     "polars==1.35.1",
 ]
 

templates/collections/joblog.html

@@ -1,6 +1,5 @@
 {% extends "framework.html" %}
 {% load static %}
-{% load envipytags %}
 {% block content %}
 
     <div class="panel-group" id="reviewListAccordion">

templates/collections/objects_list.html

@@ -192,7 +192,7 @@
             <div class="panel-body list-group-item" id="ReviewedContent">
                 {% if object_type == 'package' %}
                 {% for obj in reviewed_objects %}
-                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}
+                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}
                     <span class="glyphicon glyphicon-star" aria-hidden="true"
                           style="float:right" data-toggle="tooltip"
                           data-placement="top" title="" data-original-title="Reviewed">
@@ -201,7 +201,7 @@
                 {% endfor %}
                 {% else %}
                 {% for obj in reviewed_objects|slice:":50" %}
-                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}{# <i>({{ obj.package.name }})</i> #}
+                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}{# <i>({{ obj.package.name }})</i> #}
                     <span class="glyphicon glyphicon-star" aria-hidden="true"
                           style="float:right" data-toggle="tooltip"
                           data-placement="top" title="" data-original-title="Reviewed">
@@ -221,11 +221,11 @@
             <div class="panel-body list-group-item" id="UnreviewedContent">
                 {% if object_type == 'package' %}
                 {% for obj in unreviewed_objects %}
-                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}</a>
+                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}</a>
                 {% endfor %}
                 {% else %}
                 {% for obj in unreviewed_objects|slice:":50" %}
-                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}</a>
+                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}</a>
                 {% endfor %}
                 {% endif %}
             </div>
@@ -236,9 +236,9 @@
         <ul class='list-group'>
             {% for obj in objects %}
             {% if object_type == 'user' %}
-            <a class="list-group-item" href="{{ obj.url }}">{{ obj.username }}</a>
+            <a class="list-group-item" href="{{ obj.url }}">{{ obj.username|safe }}</a>
             {% else %}
-            <a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}</a>
+            <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}</a>
             {% endif %}
             {% endfor %}
         </ul>

templates/migration.html

@@ -26,12 +26,12 @@
             {% endif %}
             <h4 class="panel-title">
                 <a id="{{ obj.id }}-link" data-toggle="collapse" data-parent="#migration-detail"
-                   href="#{{ obj.id }}">{{ obj.name }}</a>
+                   href="#{{ obj.id }}">{{ obj.name|safe }}</a>
             </h4>
         </div>
         <div id="{{ obj.id }}" class="panel-collapse collapse {% if not obj.status %}in{% endif %}">
             <div class="panel-body list-group-item">
-                <a class="list-group-item" href="{{ obj.detail_url }}">{{ obj.name }} Migration Detail Page</a>
+                <a class="list-group-item" href="{{ obj.detail_url }}">{{ obj.name|safe }} Migration Detail Page</a>
             </div>
         </div>
         {% endfor %}

templates/migration_detail.html

@@ -27,7 +27,7 @@
                     {% endif %}
                     <h4 class="panel-title">
                         <a id="{{ obj.id }}-link" data-toggle="collapse" data-parent="#migration-detail"
-                           href="#{{ obj.id }}">{{ obj.name }}</a>
+                           href="#{{ obj.id }}">{{ obj.name|safe }}</a>
                     </h4>
                 </div>
                 <div id="{{ obj.id }}" class="panel-collapse collapse {% if not obj.status %}in{% endif %}">

templates/modals/collections/new_model_modal.html

@@ -1,3 +1,4 @@
+
 <div class="modal fade" tabindex="-1" id="new_model_modal" role="dialog" aria-labelledby="new_model_modal"
      aria-hidden="true">
     <div class="modal-dialog modal-lg">
@@ -47,14 +48,14 @@
                             <option disabled>Reviewed Packages</option>
                             {% for obj in meta.readable_packages %}
                                 {% if obj.reviewed %}
-                                    <option value="{{ obj.url }}">{{ obj.name }}</option>
+                                    <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
                                 {% endif %}
                             {% endfor %}
 
                             <option disabled>Unreviewed Packages</option>
                             {% for obj in meta.readable_packages %}
                                 {% if not obj.reviewed %}
-                                    <option value="{{ obj.url }}">{{ obj.name }}</option>
+                                    <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
                                 {% endif %}
                             {% endfor %}
                         </select>
@@ -68,14 +69,14 @@
                             <option disabled>Reviewed Packages</option>
                             {% for obj in meta.readable_packages %}
                                 {% if obj.reviewed %}
-                                    <option value="{{ obj.url }}">{{ obj.name }}</option>
+                                    <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
                                 {% endif %}
                             {% endfor %}
 
                             <option disabled>Unreviewed Packages</option>
                             {% for obj in meta.readable_packages %}
                                 {% if not obj.reviewed %}
-                                    <option value="{{ obj.url }}">{{ obj.name }}</option>
+                                    <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
                                 {% endif %}
                             {% endfor %}
                         </select>

templates/modals/collections/new_pathway_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 <div class="modal fade" tabindex="-1" id="new_pathway_modal" role="dialog" aria-labelledby="new_pathway_modal"
      aria-hidden="true" style="overflow-y: auto;">
@@ -111,7 +112,7 @@
 
                     <select id="settingSelect" name="settingSelect" class="form-control">
                         {% for setting in available_settings %}
-                        <option value="{{ setting.id }}">{{ setting.name }}</option>
+                        <option value="{{ setting.id }}">{{ setting.name|safe }}</option>
                         {% endfor %}
                     </select>
                     <p></p>

templates/modals/collections/new_prediction_setting_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 
 <div id="new_prediction_setting_modal" class="modal" tabindex="-1">
@@ -40,14 +41,14 @@
                             <option disabled>Reviewed Packages</option>
                             {% for obj in meta.readable_packages %}
                             {% if obj.reviewed %}
-                            <option value="{{ obj.url }}">{{ obj.name }}</option>
+                            <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
                             {% endif %}
                             {% endfor %}
 
                             <option disabled>Unreviewed Packages</option>
                             {% for obj in meta.readable_packages %}
                             {% if not obj.reviewed %}
-                            <option value="{{ obj.url }}">{{ obj.name }}</option>
+                            <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
                             {% endif %}
                             {% endfor %}
                         </select>
@@ -57,7 +58,7 @@
                         <select id="model-based-prediction-setting-model" name="model-based-prediction-setting-model" class="form-control" data-width='100%'>
                         <option disabled selected>Select the model</option>
                         {% for m in models %}
-                        <option value="{{ m.url }}">{{ m.name }}</option>
+                        <option value="{{ m.url }}">{{ m.name|safe }}</option>
                         {% endfor %}
                         </select>
                         <label for="model-based-prediction-setting-threshold">Threshold</label>

templates/modals/objects/add_pathway_edge_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 <div class="modal fade bs-modal-lg" id="add_pathway_edge_modal" tabindex="-1" aria-labelledby="add_pathway_edge_modal"
      aria-modal="true"
@@ -36,7 +37,7 @@
                             <select id="add_pathway_edge_substrates" name="edge-substrates"
                                     data-actions-box='true' class="form-control" multiple data-width='100%'>
                                 {% for n in pathway.nodes %}
-                                    <option data-smiles="{{ n.default_node_label.smiles }}" value="{{ n.url }}">{{ n.default_node_label.name }}</option>
+                                    <option data-smiles="{{ n.default_node_label.smiles }}" value="{{ n.url }}">{{ n.default_node_label.name|safe }}</option>
                                 {% endfor %}
                             </select>
                         </div>
@@ -47,7 +48,7 @@
                             <select id="add_pathway_edge_products" name="edge-products"
                                     data-actions-box='true' class="form-control" multiple data-width='100%'>
                                 {% for n in pathway.nodes %}
-                                    <option data-smiles="{{ n.default_node_label.smiles }}" value="{{ n.url }}">{{ n.default_node_label.name }}</option>
+                                    <option data-smiles="{{ n.default_node_label.smiles }}" value="{{ n.url }}">{{ n.default_node_label.name|safe }}</option>
                                 {% endfor %}
                             </select>
                         </div>

templates/modals/objects/delete_pathway_edge_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 <!-- Delete Edge -->
 <div id="delete_pathway_edge_modal" class="modal" tabindex="-1">
@@ -19,7 +20,7 @@
                             data-actions-box='true' class="form-control" data-width='100%'>
                         <option value="" disabled selected>Select Reaction to delete</option>
                         {% for e in pathway.edges %}
-                            <option value="{{ e.url }}">{{ e.edge_label.name }}</option>
+                            <option value="{{ e.url }}">{{ e.edge_label.name|safe }}</option>
                         {% endfor %}
                     </select>
                     <input type="hidden" id="hidden" name="hidden" value="delete"/>

templates/modals/objects/delete_pathway_node_modal.html

@@ -1,4 +1,5 @@
 {% load static %}
+
 <!-- Delete Node -->
 <div id="delete_pathway_node_modal" class="modal" tabindex="-1">
     <div class="modal-dialog">
@@ -19,7 +20,7 @@
                             data-actions-box='true' class="form-control" data-width='100%'>
                         <option value="" disabled selected>Select Compound to delete</option>
                         {% for n in pathway.nodes %}
-                            <option value="{{ n.url }}">{{ n.default_node_label.name }}</option>
+                            <option value="{{ n.url }}">{{ n.default_node_label.name|safe }}</option>
                         {% endfor %}
                     </select>
                     <input type="hidden" id="hidden" name="hidden" value="delete"/>

templates/modals/objects/edit_compound_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 <!-- Edit Compound -->
 <div id="edit_compound_modal" class="modal" tabindex="-1">
@@ -15,12 +16,12 @@
                     {% csrf_token %}
                     <p>
                         <label for="compound-name">Name</label>
-                        <input id="compound-name" class="form-control" name="compound-name" value="{{ compound.name}}">
+                        <input id="compound-name" class="form-control" name="compound-name" value="{{ compound.name|safe}}">
                     </p>
                     <p>
                         <label for="compound-description">Description</label>
                         <input id="compound-description" type="text" class="form-control"
-                               value="{{ compound.description }}"
+                               value="{{ compound.description|safe }}"
                                name="compound-description">
                     </p>
                 </form>

templates/modals/objects/edit_compound_structure_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 <!-- Edit Compound -->
 <div id="edit_compound_structure_modal" class="modal" tabindex="-1">
@@ -15,12 +16,12 @@
                     {% csrf_token %}
                     <p>
                         <label for="compound-structure-name">Name</label>
-                        <input id="compound-structure-name" class="form-control" name="compound-structure-name" value="{{ compound_structure.name }}">
+                        <input id="compound-structure-name" class="form-control" name="compound-structure-name" value="{{ compound_structure.name|safe }}">
                     </p>
                     <p>
                         <label for="compound-structure-description">Description</label>
                         <input id="compound-structure-description" type="text" class="form-control"
-                               value="{{ compound_structure.description }}" name="compound-structure-description">
+                               value="{{ compound_structure.description|safe }}" name="compound-structure-description">
                     </p>
                 </form>
             </div>

templates/modals/objects/edit_group_member_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 <!-- Edit Package Permission -->
 <div id="edit_group_member_modal" class="modal" tabindex="-1">
@@ -39,7 +40,7 @@
                                 {% endfor %}
                                 <option disabled>Groups</option>
                                 {% for g in groups %}
-                                <option value="{{ g.url }}">{{ g.name }}</option>
+                                <option value="{{ g.url }}">{{ g.name|safe }}</option>
                                 {% endfor %}
                             </select>
                             <input type="hidden" name="action" value="add">
@@ -81,7 +82,7 @@
                           accept-charset="UTF-8" action="" data-remote="true" method="post">
                         {% csrf_token %}
                         <div class="col-xs-8">
-                            {{ g.name }}
+                            {{ g.name|safe }}
                             <input type="hidden" name="member" value="{{ g.url }}"/>
                             <input type="hidden" name="action" value="remove">
                         </div>

templates/modals/objects/edit_model_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 <!-- Edit Model -->
 <div id="edit_model_modal" class="modal" tabindex="-1">
@@ -16,12 +17,12 @@
                     <p>
                         <label for="model-name">Name</label>
                         <input id="model-name" type="text" class="form-control" name="model-name"
-                               value="{{ model.name }}">
+                               value="{{ model.name|safe }}">
                     </p>
                     <p>
                         <label for="model-description">Description</label>
                         <input id="model-description" type="text" class="form-control" name="model-description"
-                               value="{{ model.description }}">
+                               value="{{ model.description|safe }}">
                     </p>
                 </form>
             </div>

templates/modals/objects/edit_node_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 <!-- Edit Node -->
 <div id="edit_node_modal" class="modal" tabindex="-1">
@@ -15,12 +16,12 @@
                     {% csrf_token %}
                     <p>
                         <label for="node-name">Name</label>
-                        <input id="node-name" class="form-control" name="node-name" value="{{ node.name}}">
+                        <input id="node-name" class="form-control" name="node-name" value="{{ node.name|safe}}">
                     </p>
                     <p>
                         <label for="node-description">Description</label>
                         <input id="node-description" type="text" class="form-control"
-                               value="{{ node.description }}"
+                               value="{{ node.description|safe }}"
                                name="node-description">
                     </p>
                 </form>

templates/modals/objects/edit_package_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 <!-- Edit Package -->
 <div id="edit_package_modal" class="modal" tabindex="-1">
@@ -15,12 +16,12 @@
                     {% csrf_token %}
                     <p>
                         <label for="package-name">Name</label>
-                        <input id="package-name" class="form-control" name="package-name" value="{{ package.name}}">
+                        <input id="package-name" class="form-control" name="package-name" value="{{ package.name|safe}}">
                     </p>
                     <p>
                         <label for="package-description">Description</label>
                         <input id="package-description" type="text" class="form-control"
-                               value="{{ package.description }}"
+                               value="{{ package.description|safe }}"
                                name="package-description">
                     </p>
                 </form>

templates/modals/objects/edit_package_permissions_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 <!-- Edit Package Permission -->
 <div id="edit_package_permissions_modal" class="modal" tabindex="-1">
@@ -46,7 +47,7 @@
                                 {% endfor %}
                                 <option disabled>Groups</option>
                                 {% for g in groups %}
-                                <option value="{{ g.url }}">{{ g.name }}</option>
+                                <option value="{{ g.url }}">{{ g.name|safe }}</option>
                                 {% endfor %}
                             </select>
                         </div>
@@ -100,7 +101,7 @@
                           accept-charset="UTF-8" action="" data-remote="true" method="post">
                         {% csrf_token %}
                         <div class="col-xs-4">
-                            {{ gp.group.name }}
+                            {{ gp.group.name|safe }}
                             <input type="hidden" name="grantee" value="{{ gp.group.url }}"/>
                         </div>
                         <div class="col-xs-2">

templates/modals/objects/edit_pathway_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 <!-- Edit Pathway -->
 <div id="edit_pathway_modal" class="modal" tabindex="-1">
@@ -15,12 +16,12 @@
                     {% csrf_token %}
                     <p>
                         <label for="pathway-name">Name</label>
-                        <input id="pathway-name" class="form-control" name="pathway-name" value="{{ pathway.name }}">
+                        <input id="pathway-name" class="form-control" name="pathway-name" value="{{ pathway.name|safe }}">
                     </p>
                     <p>
                         <label for="pathway-description">Description</label>
                         <textarea id="pathway-description" type="text" class="form-control" name="pathway-description"
-                                  rows="10">{{ pathway.description }}</textarea>
+                                  rows="10">{{ pathway.description|safe }}</textarea>
                     </p>
                 </form>
             </div>

templates/modals/objects/edit_prediction_setting_modal.html

@@ -32,7 +32,7 @@
                                                 <td colspan="2">
                                                     <select id="model" name="model" class="form-control" data-width='100%'>
                                                     {% for m in models %}
-                                                    <option value="{{ m.id }}" {% if user.prediction_settings.model.url == m.url %}selected{% endif %}>{{ m.name }}</option>
+                                                    <option value="{{ m.id }}" {% if user.prediction_settings.model.url == m.url %}selected{% endif %}>{{ m.name|safe }}</option>
                                                     {% endfor %}
                                                     </select>
                                                 </td>

templates/modals/objects/edit_reaction_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 <!-- Edit Reaction -->
 <div id="edit_reaction_modal" class="modal" tabindex="-1">
@@ -14,12 +15,12 @@
                     {% csrf_token %}
                     <p>
                         <label for="reaction-name">Name</label>
-                        <input id="reaction-name" class="form-control" name="reaction-name" value="{{ reaction.name }}">
+                        <input id="reaction-name" class="form-control" name="reaction-name" value="{{ reaction.name|safe }}">
                     </p>
                     <p>
                         <label for="reaction-description">Description</label>
                         <input id="reaction-description" type="text" class="form-control"
-                               value="{{ reaction.description }}" name="reaction-description">
+                               value="{{ reaction.description|safe }}" name="reaction-description">
                     </p>
                 </form>
             </div>

templates/modals/objects/edit_rule_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 <!-- Edit Rule -->
 <div id="edit_rule_modal" class="modal" tabindex="-1">
@@ -14,12 +15,12 @@
                     {% csrf_token %}
                     <p>
                         <label for="rule-name">Name</label>
-                        <input id="rule-name" class="form-control" name="rule-name" value="{{ rule.name }}">
+                        <input id="rule-name" class="form-control" name="rule-name" value="{{ rule.name|safe }}">
                     </p>
                     <p>
                         <label for="rule-description">Description</label>
                         <input id="rule-description" type="text" class="form-control"
-                               value="{{ rule.description }}" name="rule-description">
+                               value="{{ rule.description|safe }}" name="rule-description">
                     </p>
                 </form>
             </div>

templates/modals/objects/edit_user_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 <!-- Edit User -->
 <div id="edit_user_modal" class="modal" tabindex="-1">
@@ -18,7 +19,7 @@
                         <select id="default-package" name="default-package" class="form-control" data-width='100%'>
                             <option disabled>Select a Package</option>
                             {% for p in meta.writeable_packages %}
-                            <option value="{{ p.url }}" {% if p.id == meta.user.default_package.id %}selected{% endif %}>{{ p.name }}</option>
+                            <option value="{{ p.url }}" {% if p.id == meta.user.default_package.id %}selected{% endif %}>{{ p.name|safe }}</option>
                             {% endfor %}
                         </select>
                     </p>
@@ -27,7 +28,7 @@
                         <select id="default-group" name="default-group" class="form-control" data-width='100%'>
                             <option disabled>Select a Group</option>
                             {% for g in meta.available_groups %}
-                            <option value="{{ g.url }}" {% if g.id == meta.user.default_group.id %}selected{% endif %}>{{ g.name }}</option>
+                            <option value="{{ g.url }}" {% if g.id == meta.user.default_group.id %}selected{% endif %}>{{ g.name|safe }}</option>
                             {% endfor %}
                         </select>
                     </p>
@@ -36,7 +37,7 @@
                         <select id="default-prediction-setting" name="default-prediction-setting" class="form-control" data-width='100%'>
                             <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 }}</option>
+                            <option value="{{ s.url }}" {% if s.id == meta.user.default_setting.id %}selected{% endif %}>{{ s.name|safe }}</option>
                             {% endfor %}
                         </select>
                     </p>

templates/modals/objects/evaluate_model_modal.html

@@ -1,3 +1,4 @@
+
 <div class="modal fade" tabindex="-1" id="evaluate_model_modal" role="dialog" aria-labelledby="evaluate_model_modal"
      aria-hidden="true">
     <div class="modal-dialog modal-lg">
@@ -24,14 +25,14 @@
                         <option disabled>Reviewed Packages</option>
                         {% for obj in meta.readable_packages %}
                             {% if obj.reviewed %}
-                                <option value="{{ obj.url }}">{{ obj.name }}</option>
+                                <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
                             {% endif %}
                         {% endfor %}
 
                         <option disabled>Unreviewed Packages</option>
                         {% for obj in meta.readable_packages %}
                             {% if not obj.reviewed %}
-                                <option value="{{ obj.url }}">{{ obj.name }}</option>
+                                <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
                             {% endif %}
                         {% endfor %}
                     </select>

templates/modals/objects/generic_copy_object_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 <!-- Copy Object -->
 <div id="generic_copy_object_modal" class="modal" tabindex="-1">
@@ -18,7 +19,7 @@
                             data-width='100%'>
                         <option disabled selected>Select Target Package</option>
                         {% for p in meta.writeable_packages %}
-                            <option value="{{ p.url }}">{{ p.name }}</option>`
+                            <option value="{{ p.url }}">{{ p.name|safe }}</option>`
                         {% endfor %}
                     </select>
                     <input type="hidden" name="hidden" value="copy">

templates/modals/objects/generic_set_aliases_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 
 <style>
@@ -55,7 +56,7 @@
                 <button type="button" class="close" data-dismiss="modal" aria-label="Close">
                     <span aria-hidden="true">×</span>
                 </button>
-                <h4 class="modal-title">Set Aliases for {{ current_object.name }}</h4>
+                <h4 class="modal-title">Set Aliases for {{ current_object.name|safe }}</h4>
             </div>
             <div class="modal-body">
                 <form id="set_aliases_modal_form" accept-charset="UTF-8" action="{{ current_object.url }}"

templates/modals/objects/generic_set_external_reference_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 <!-- Delete Object -->
 <div id="generic_set_external_reference_modal" class="modal" tabindex="-1">
@@ -23,7 +24,7 @@
                             {% if entity == object_type %}
                                 {% for db in databases %}
                                     <option id="db-select-{{ db.database.pk }}" data-input-placeholder="{{ db.placeholder }}"
-                                            value="{{ db.database.id }}">{{ db.database.name }}</option>`
+                                            value="{{ db.database.id }}">{{ db.database.name|safe }}</option>`
                                 {% endfor %}
                             {% endif %}
                         {% endfor %}

templates/modals/objects/generic_set_scenario_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 <div class="modal fade bs-modal-lg" id="set_scenario_modal" tabindex="-1" aria-labelledby="set_scenario_modal"
      aria-modal="true" role="dialog">
@@ -7,7 +8,7 @@
                 <button type="button" class="close" data-dismiss="modal" aria-label="Close">
                     <span aria-hidden="true">×</span>
                 </button>
-                <h4 class="modal-title">Set Scenarios for {{ current_object.name }}</h4>
+                <h4 class="modal-title">Set Scenarios for {{ current_object.name|safe }}</h4>
             </div>
             <div class="modal-body">
                 <div id="loading_scenario_div" class="text-center"></div>

templates/modals/objects/manage_api_token_modal.html

@@ -1,3 +1,4 @@
+
 <div class="modal fade"
      tabindex="-1"
      id="manage_api_token_modal"
@@ -41,7 +42,7 @@
                         <div class="input-group">
                             <input type="hidden" name="hidden" value="delete">
                             <input type="hidden" name="token-id" value="{{ t.pk }}">
-                            <input type="text" class="form-control" value="{{ t.name }}" disabled>
+                            <input type="text" class="form-control" value="{{ t.name|safe }}" disabled>
                             <span class="input-group-btn">
                                 <button type="submit" class="btn btn-danger">Delete</button>
                             </span>

templates/modals/predict_modal.html

@@ -56,7 +56,7 @@
                         <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 %} <i>(User default)</i>{% endif %}
+                                {{ s.name|safe }}{% if s.id == meta.user.default_setting.id %} <i>(User default)</i>{% endif %}
                             </option>
                         {% endfor %}
                     </select>

templates/objects/composite_rule.html

@@ -13,7 +13,7 @@
 <div class="panel-group" id="rule-detail">
     <div class="panel panel-default">
         <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-            {{ rule.name }}
+            {{ rule.name|safe }}
             <div id="actionsButton"
                  style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
                  class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
@@ -60,7 +60,7 @@
         <div id="rule-reaction-patterns" class="panel-collapse collapse in">
             <div class="panel-body list-group-item">
                 {% for r in rule.srs %}
-                <a class="list-group-item" href="{{ r.url }}">{{ r.name }}</a>
+                <a class="list-group-item" href="{{ r.url }}">{{ r.name|safe }}</a>
                 <div align="center">
                     <p>
                         {{r.as_svg|safe}}
@@ -81,7 +81,7 @@
             <div id="rule-scenario" class="panel-collapse collapse in">
                 <div class="panel-body list-group-item">
                     {% for s in rule.scenarios.all %}
-                        <a class="list-group-item" href="{{ s.url }}">{{ s.name }} <i>({{ s.package.name }})</i></a>
+                        <a class="list-group-item" href="{{ s.url }}">{{ s.name|safe }} <i>({{ s.package.name|safe }})</i></a>
                     {% endfor %}
                 </div>
             </div>

templates/objects/compound.html

@@ -15,7 +15,7 @@
     <div class="panel-group" id="compound-detail">
         <div class="panel panel-default">
             <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-                {{ compound.name }}
+                {{ compound.name|safe }}
                 <div id="actionsButton"
                      style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
                      class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
@@ -64,7 +64,7 @@
             </div>
             <div id="compound-desc" class="panel-collapse collapse in">
                 <div class="panel-body list-group-item">
-                    {{ compound.description }}
+                    {{ compound.description|safe }}
                 </div>
             </div>
 
@@ -133,7 +133,7 @@
                 <div id="compound-reaction" class="panel-collapse collapse in">
                     <div class="panel-body list-group-item">
                         {% for r in compound.related_reactions %}
-                            <a class="list-group-item" href="{{ r.url }}">{{ r.name }} <i>({{ r.package.name }})</i></a>
+                            <a class="list-group-item" href="{{ r.url }}">{{ r.name|safe }} <i>({{ r.package.name|safe }})</i></a>
                         {% endfor %}
                     </div>
                 </div>
@@ -150,7 +150,7 @@
                 <div id="compound-pathway" class="panel-collapse collapse in">
                     <div class="panel-body list-group-item">
                         {% for r in compound.related_pathways %}
-                            <a class="list-group-item" href="{{ r.url }}">{{ r.name }} <i>({{ r.package.name }})</i></a>
+                            <a class="list-group-item" href="{{ r.url }}">{{ r.name|safe }} <i>({{ r.package.name|safe }})</i></a>
                         {% endfor %}
                     </div>
                 </div>
@@ -167,7 +167,7 @@
                 <div id="compound-scenario" class="panel-collapse collapse in">
                     <div class="panel-body list-group-item">
                         {% for s in compound.scenarios.all %}
-                            <a class="list-group-item" href="{{ s.url }}">{{ s.name }} <i>({{ s.package.name }})</i></a>
+                            <a class="list-group-item" href="{{ s.url }}">{{ s.name|safe }} <i>({{ s.package.name|safe }})</i></a>
                         {% endfor %}
                     </div>
                 </div>

templates/objects/compound_structure.html

@@ -13,7 +13,7 @@
 <div class="panel-group" id="compound-structure-detail">
     <div class="panel panel-default">
         <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-            {{ compound_structure.name }}
+            {{ compound_structure.name|safe }}
             <div id="actionsButton"
                  style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
                  class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
@@ -28,7 +28,7 @@
             </div>
         </div>
         <div class="panel-body">
-            <p> {{ compound_structure.description }} </p>
+            <p> {{ compound_structure.description|safe }} </p>
         </div>
 
         <!-- Image -->
@@ -86,7 +86,7 @@
             <div id="compound-structure-scenario" class="panel-collapse collapse in">
                 <div class="panel-body list-group-item">
                     {% for s in compound_structure.scenarios.all %}
-                        <a class="list-group-item" href="{{ s.url }}">{{ s.name }} <i>({{ s.package.name }})</i></a>
+                        <a class="list-group-item" href="{{ s.url }}">{{ s.name|safe }} <i>({{ s.package.name|safe }})</i></a>
                     {% endfor %}
                 </div>
             </div>

templates/objects/edge.html

@@ -12,7 +12,7 @@
     <div class="panel-group" id="edge-detail">
         <div class="panel panel-default">
             <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-                {{ edge.edge_label.name }}
+                {{ edge.edge_label.name|safe }}
                 <div id="actionsButton"
                      style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
                      class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
@@ -36,7 +36,7 @@
             </div>
             <div id="edge-desc" class="panel-collapse collapse in">
                 <div class="panel-body list-group-item">
-                    {{ edge.description }}
+                    {{ edge.description|safe }}
                 </div>
             </div>
 
@@ -82,12 +82,12 @@
             <div id="edge-description-smiles" class="panel-collapse collapse in">
                 <div class="panel-body list-group-item">
                     {% for educt in edge.start_nodes.all %}
-                        <a class="btn btn-default" href="{{ educt.url }}">{{ educt.name }}</a>
+                        <a class="btn btn-default" href="{{ educt.url }}">{{ educt.name|safe }}</a>
                     {% endfor %}
                     <span class="glyphicon glyphicon-arrow-right" style="margin-left:5em;margin-right:5em;"
                           aria-hidden="true"></span>
                     {% for product in edge.end_nodes.all %}
-                        <a class="btn btn-default" href="{{ product.url }}">{{ product.name }}</a>
+                        <a class="btn btn-default" href="{{ product.url }}">{{ product.name|safe }}</a>
                     {% endfor %}
                 </div>
             </div>
@@ -116,7 +116,7 @@
                 <div id="edge-rules" class="panel-collapse collapse in">
                     <div class="panel-body list-group-item">
                         {% for r in edge.edge_label.rules.all %}
-                            <a class="list-group-item" href="{{ r.url }}">{{ r.name }}</a>
+                            <a class="list-group-item" href="{{ r.url }}">{{ r.name|safe }}</a>
                         {% endfor %}
                     </div>
                 </div>
@@ -132,7 +132,7 @@
             <div id="edge-scenario" class="panel-collapse collapse in">
                 <div class="panel-body list-group-item">
                     {% for s in edge.scenarios.all %}
-                        <a class="list-group-item" href="{{ s.url }}">{{ s.name }} <i>({{ s.package.name }})</i></a>
+                        <a class="list-group-item" href="{{ s.url }}">{{ s.name|safe }} <i>({{ s.package.name|safe }})</i></a>
                     {% endfor %}
                 </div>
             </div>

templates/objects/group.html

@@ -11,7 +11,7 @@
 <div class="panel-group" id="package-detail">
     <div class="panel panel-default">
         <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-            {{ group.name }}
+            {{ group.name|safe }}
             <div id="actionsButton"
                  style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
                  class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
@@ -26,7 +26,7 @@
             </div>
         </div>
         <div class="panel-body">
-            <p> {{ group.description }} </p>
+            <p> {{ group.description|safe }} </p>
         </div>
     </div>
 
@@ -39,10 +39,10 @@
         </div>
         <ul class="list-group">
             {% for um in group.user_member.all %}
-            <a class="list-group-item" href="{{ um.url }}">{{ um.username }}</a>
+            <a class="list-group-item" href="{{ um.url }}">{{ um.username|safe }}</a>
             {% endfor %}
             {% for gm in group.group_member.all %}
-            <a class="list-group-item" href="{{ gm.url }}">{{ gm.name }}</a>
+            <a class="list-group-item" href="{{ gm.url }}">{{ gm.name|safe }}</a>
             {% endfor %}
         </ul>
     </div>
@@ -56,7 +56,7 @@
         </div>
         <ul class="list-group">
             {% for p in packages %}
-            <a class="list-group-item" href="{{ p.url }}">{{ p.name }}</a>
+            <a class="list-group-item" href="{{ p.url }}">{{ p.name|safe }}</a>
             {% endfor %}
         </ul>
     </div>

templates/objects/model.html

@@ -1,6 +1,5 @@
 {% extends "framework.html" %}
 {% load static %}
-{% load envipytags %}
 {% block content %}
 
     {% block action_modals %}
@@ -18,7 +17,7 @@
     <div class="panel-group" id="model-detail">
         <div class="panel panel-default">
             <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-                {{ model.name }}
+                {{ model.name|safe }}
                 <div id="actionsButton"
                      style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
                      class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
@@ -33,7 +32,7 @@
                 </div>
             </div>
             <div class="panel-body">
-                <p> {{ model.description }} </p>
+                <p> {{ model.description|safe }} </p>
             </div>
             {% if model|classname == 'MLRelativeReasoning' or model|classname == 'RuleBasedRelativeReasoning'%}
                 <!-- Rule Packages -->
@@ -46,7 +45,7 @@
                 <div id="rule-package" class="panel-collapse collapse in">
                     <div class="panel-body list-group-item">
                         {% for p in model.rule_packages.all %}
-                            <a class="list-group-item" href="{{ p.url }}">{{ p.name }}</a>
+                            <a class="list-group-item" href="{{ p.url }}">{{ p.name|safe }}</a>
                         {% endfor %}
                     </div>
                 </div>
@@ -60,7 +59,7 @@
                 <div id="reaction-package" class="panel-collapse collapse in">
                     <div class="panel-body list-group-item">
                         {% for p in model.data_packages.all %}
-                            <a class="list-group-item" href="{{ p.url }}">{{ p.name }}</a>
+                            <a class="list-group-item" href="{{ p.url }}">{{ p.name|safe }}</a>
                         {% endfor %}
                     </div>
                 </div>
@@ -75,7 +74,7 @@
                     <div id="eval-package" class="panel-collapse collapse in">
                         <div class="panel-body list-group-item">
                             {% for p in model.eval_packages.all %}
-                                <a class="list-group-item" href="{{ p.url }}">{{ p.name }}</a>
+                                <a class="list-group-item" href="{{ p.url }}">{{ p.name|safe }}</a>
                             {% endfor %}
                         </div>
                     </div>

templates/objects/node.html

@@ -12,7 +12,7 @@
     <div class="panel-group" id="node-detail">
         <div class="panel panel-default">
             <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-                {{ node.name }}
+                {{ node.name|safe }}
                 <div id="actionsButton"
                      style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
                      class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
@@ -39,7 +39,7 @@
             </div>
             <div id="node-desc" class="panel-collapse collapse in">
                 <div class="panel-body list-group-item">
-                    {{ node.description }}
+                    {{ node.description|safe }}
                 </div>
             </div>
 
@@ -98,7 +98,7 @@
                 <div id="node-scenario" class="panel-collapse collapse in">
                     <div class="panel-body list-group-item">
                         {% for s in node.scenarios.all %}
-                            <a class="list-group-item" href="{{ s.url }}">{{ s.name }} <i>({{ s.package.name }})</i></a>
+                            <a class="list-group-item" href="{{ s.url }}">{{ s.name|safe }} <i>({{ s.package.name|safe }})</i></a>
                         {% endfor %}
                     </div>
                 </div>

templates/objects/package.html

@@ -14,7 +14,7 @@
 <div class="panel-group" id="package-detail">
     <div class="panel panel-default">
         <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-            {{ package.name }}
+            {{ package.name|safe }}
             <div id="actionsButton"
                  style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
                  class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"

templates/objects/pathway.html

@@ -98,7 +98,7 @@
         <div class="panel-group" id="pwAccordion">
             <div class="panel panel-default">
                 <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-                    {{ pathway.name }}
+                    {{ pathway.name|safe }}
                 </div>
             </div>
             <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
@@ -236,7 +236,7 @@
                 <div id="pathway-scenario" class="panel-collapse collapse in">
                     <div class="panel-body list-group-item">
                         {% for s in pathway.scenarios.all %}
-                            <a class="list-group-item" href="{{ s.url }}">{{ s.name }} <i>({{ s.package.name }})</i></a>
+                            <a class="list-group-item" href="{{ s.url }}">{{ s.name|safe }} <i>({{ s.package.name|safe }})</i></a>
                         {% endfor %}
                     </div>
                 </div>
@@ -266,7 +266,7 @@
                                                 <td colspan="2">
                                                     <li class="list-group-item">
                                                         <a href="{{ pathway.setting.model.url }}">
-                                                            {{ pathway.setting.model.name }}
+                                                            {{ pathway.setting.model.name|safe }}
                                                         </a>
                                                     </li>
                                                 </td>
@@ -299,7 +299,7 @@
                                                     {% for p in pathway.setting.rule_packages.all %}
                                                         <li class="list-group-item">
                                                             <a href="{{ p.url }}">
-                                                                {{ p.name }}
+                                                                {{ p.name|safe }}
                                                             </a>
                                                         </li>
                                                     {% endfor %}

templates/objects/reaction.html

@@ -14,7 +14,7 @@
     <div class="panel-group" id="reaction-detail">
         <div class="panel panel-default">
             <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-                {{ reaction.name }}
+                {{ reaction.name|safe }}
                 <div id="actionsButton"
                      style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
                      class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
@@ -38,7 +38,7 @@
             </div>
             <div id="reaction-desc" class="panel-collapse collapse in">
                 <div class="panel-body list-group-item">
-                    {{ reaction.description }}
+                    {{ reaction.description|safe }}
                 </div>
             </div>
 
@@ -84,12 +84,12 @@
             <div id="reaction-description-smiles" class="panel-collapse collapse in">
                 <div class="panel-body list-group-item">
                     {% for educt in reaction.educts.all %}
-                        <a class="btn btn-default" href="{{ educt.url }}">{{ educt.name }}</a>
+                        <a class="btn btn-default" href="{{ educt.url }}">{{ educt.name|safe }}</a>
                     {% endfor %}
                     <span class="glyphicon glyphicon-arrow-right" style="margin-left:5em;margin-right:5em;"
                           aria-hidden="true"></span>
                     {% for product in reaction.products.all %}
-                        <a class="btn btn-default" href="{{ product.url }}">{{ product.name }}</a>
+                        <a class="btn btn-default" href="{{ product.url }}">{{ product.name|safe }}</a>
                     {% endfor %}
                 </div>
             </div>
@@ -118,7 +118,7 @@
                 <div id="reaction-rules" class="panel-collapse collapse in">
                     <div class="panel-body list-group-item">
                         {% for r in reaction.rules.all %}
-                            <a class="list-group-item" href="{{ r.url }}">{{ r.name }}</a>
+                            <a class="list-group-item" href="{{ r.url }}">{{ r.name|safe }}</a>
                         {% endfor %}
                     </div>
                 </div>
@@ -152,7 +152,7 @@
                 <div id="reaction-pathway" class="panel-collapse collapse in">
                     <div class="panel-body list-group-item">
                         {% for r in reaction.related_pathways %}
-                            <a class="list-group-item" href="{{ r.url }}">{{ r.name }}</a>
+                            <a class="list-group-item" href="{{ r.url }}">{{ r.name|safe }}</a>
                         {% endfor %}
                     </div>
                 </div>
@@ -168,7 +168,7 @@
                 <div id="reaction-scenario" class="panel-collapse collapse in">
                     <div class="panel-body list-group-item">
                         {% for s in reaction.scenarios.all %}
-                            <a class="list-group-item" href="{{ s.url }}">{{ s.name }} <i>({{ s.package.name }})</i></a>
+                            <a class="list-group-item" href="{{ s.url }}">{{ s.name|safe }} <i>({{ s.package.name|safe }})</i></a>
                         {% endfor %}
                     </div>
                 </div>

templates/objects/scenario.html

@@ -10,7 +10,7 @@
     <div class="panel-group" id="scenario-detail">
         <div class="panel panel-default">
             <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-                {{ scenario.name }}
+                {{ scenario.name|safe }}
                 <div id="actionsButton"
                      style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
                      class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
@@ -30,7 +30,7 @@
     <div class="panel panel-default">
         <div class="panel-heading">Description</div>
         <div class="panel-body">
-            {{ scenario.description }}
+            {{ scenario.description|safe }}
             <br>
             {{ scenario.scenario_type }}
             <br>

templates/objects/simple_rule.html

@@ -13,7 +13,7 @@
     <div class="panel-group" id="rule-detail">
         <div class="panel panel-default">
             <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-                {{ rule.name }}
+                {{ rule.name|safe }}
                 <div id="actionsButton"
                      style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;display: none;"
                      class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
@@ -29,7 +29,7 @@
             </div>
             <div class="panel-body">
                 <p>
-                    {{ rule.description }}
+                    {{ rule.description|safe }}
                 </p>
             </div>
 
@@ -145,7 +145,7 @@
                 <div id="rule-composite-rule" class="panel-collapse collapse in">
                     <div class="panel-body list-group-item">
                         {% for cr in rule.parallelrule_set.all %}
-                            <a class="list-group-item" href="{{ cr.url }}">{{ cr.name }}</a>
+                            <a class="list-group-item" href="{{ cr.url }}">{{ cr.name|safe }}</a>
                         {% endfor %}
                     </div>
                 </div>
@@ -162,7 +162,7 @@
                 <div id="rule-scenario" class="panel-collapse collapse in">
                     <div class="panel-body list-group-item">
                         {% for s in rule.scenarios.all %}
-                            <a class="list-group-item" href="{{ s.url }}">{{ s.name }}</a>
+                            <a class="list-group-item" href="{{ s.url }}">{{ s.name|safe }}</a>
                         {% endfor %}
                     </div>
                 </div>
@@ -179,7 +179,7 @@
                 <div id="rule-reaction" class="panel-collapse collapse">
                     <div class="panel-body list-group-item">
                         {% for r in rule.related_reactions %}
-                            <a class="list-group-item" href="{{ r.url }}">{{ r.name }}</a>
+                            <a class="list-group-item" href="{{ r.url }}">{{ r.name|safe }}</a>
                         {% endfor %}
                     </div>
                 </div>
@@ -196,7 +196,7 @@
                 <div id="rule-pathway" class="panel-collapse collapse">
                     <div class="panel-body list-group-item">
                         {% for r in rule.related_pathways %}
-                            <a class="list-group-item" href="{{ r.url }}">{{ r.name }}</a>
+                            <a class="list-group-item" href="{{ r.url }}">{{ r.name|safe }}</a>
                         {% endfor %}
                     </div>
                 </div>

templates/objects/user.html

@@ -41,7 +41,7 @@
     <div id="default-package" class="panel-collapse collapse in">
         <div class="panel-body list-group-item">
             <li class="list-group-item">
-                <a href="{{ user.default_package.url }}"> {{ user.default_package.name }}</a>
+                <a href="{{ user.default_package.url }}"> {{ user.default_package.name|safe }}</a>
             </li>
         </div>
     </div>
@@ -58,7 +58,7 @@
         <div class="panel-body list-group-item">
             {% for g in meta.available_groups %}
             <li class="list-group-item">
-                <a href="{{ g.url }}"> {{ g.name }}</a>
+                <a href="{{ g.url }}"> {{ g.name|safe }}</a>
             </li>
             {% endfor %}
         </div>
@@ -90,7 +90,7 @@
                                 <td colspan="2">
                                     <li class="list-group-item">
                                         <a href="{{user.default_setting.model.url}}">
-                                            {{ user.default_setting.model.name }}
+                                            {{ user.default_setting.model.name|safe }}
                                         </a>
                                     </li>
                                 </td>
@@ -123,7 +123,7 @@
                                     {% for p in user.default_setting.rule_packages.all %}
                                     <li class="list-group-item">
                                         <a href="{{p.url}}">
-                                            {{ p.name }}
+                                            {{ p.name|safe }}
                                         </a>
                                     </li>
                                     {% endfor %}

templates/pathway_playground2.html

@@ -18,7 +18,7 @@
 </head>
 <body>
 <p></p>
-{{ pathway.name }}
+{{ pathway.name|safe }}
 <div id="viz">
     <svg width="2000" height="2000"> <!-- Sehr großes SVG für Zoom -->
         <defs>

templates/search.html

@@ -11,13 +11,13 @@
                     <option disabled>Reviewed Packages</option>
                 {% endif %}
                 {% for obj in reviewed_objects %}
-                    <option value="{{ obj.url }}" selected>{{ obj.name }}</option>
+                    <option value="{{ obj.url }}" selected>{{ obj.name|safe }}</option>
                 {% endfor %}
                 {% if unreviewed_objects %}
                     <option disabled>Unreviewed Packages</option>
                 {% endif %}
                 {% for obj in unreviewed_objects %}
-                    <option value="{{ obj.url }}">{{ obj.name }}</option>
+                    <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
                 {% endfor %}
             </select>
         </div>

tests/test_rule_model.py

@@ -29,7 +29,7 @@ class RuleTest(TestCase):
         self.assertEqual(r.name, "bt0022-2833")
         self.assertEqual(
             r.description,
-            "Dihalomethyl derivative + Halomethyl derivative > 1-Halo-1-methylalcohol derivative + 1-Methylalcohol derivative",
+            "Dihalomethyl derivative + Halomethyl derivative > 1-Halo-1-methylalcohol derivative + 1-Methylalcohol derivative",
         )
 
     def test_smirks_are_trimmed(self):

utilities/chem.py

@@ -255,6 +255,30 @@ class FormatConverter(object):
         except Exception:
             return False
 
+    @staticmethod
+    def is_valid_smarts(smarts: str) -> bool:
+        """
+        Checks whether a given string is a valid SMARTS pattern.
+
+        Parameters
+        ----------
+        smarts : str
+            The SMARTS string to validate.
+
+        Returns
+        -------
+        bool
+            True if the SMARTS string is valid, False otherwise.
+        """
+        if not isinstance(smarts, str) or not smarts.strip():
+            return False
+
+        try:
+            mol = Chem.MolFromSmarts(smarts)
+            return mol is not None
+        except Exception:
+            return False
+
     @staticmethod
     def apply(
         smiles: str,

uv.lock

@@ -571,6 +571,7 @@ dependencies = [
     { name = "epam-indigo" },
     { name = "gunicorn" },
     { name = "networkx" },
+    { name = "nh3" },
     { name = "polars" },
     { name = "psycopg2-binary" },
     { name = "python-dotenv" },
@@ -613,6 +614,7 @@ requires-dist = [
     { name = "gunicorn", specifier = ">=23.0.0" },
     { name = "msal", marker = "extra == 'ms-login'", specifier = ">=1.33.0" },
     { name = "networkx", specifier = ">=3.4.2" },
+    { name = "nh3", specifier = "==0.3.2" },
     { name = "poethepoet", marker = "extra == 'dev'", specifier = ">=0.37.0" },
     { name = "polars", specifier = "==1.35.1" },
     { name = "pre-commit", marker = "extra == 'dev'", specifier = ">=4.3.0" },
@@ -1147,6 +1149,39 @@ wheels = [
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 ]
 
+[[package]]
+name = "nh3"
+version = "0.3.2"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/ca/a5/34c26015d3a434409f4d2a1cd8821a06c05238703f49283ffeb937bef093/nh3-0.3.2.tar.gz", hash = "sha256:f394759a06df8b685a4ebfb1874fb67a9cbfd58c64fc5ed587a663c0e63ec376", size = 19288, upload-time = "2025-10-30T11:17:45.948Z" }
+wheels = [
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+    { url = "https://files.pythonhosted.org/packages/30/57/07826ff65d59e7e9cc789ef1dc405f660cabd7458a1864ab58aefa17411b/nh3-0.3.2-cp314-cp314t-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:45c953e57028c31d473d6b648552d9cab1efe20a42ad139d78e11d8f42a36130", size = 791183, upload-time = "2025-10-30T11:17:11.99Z" },
+    { url = "https://files.pythonhosted.org/packages/af/2f/e8a86f861ad83f3bb5455f596d5c802e34fcdb8c53a489083a70fd301333/nh3-0.3.2-cp314-cp314t-manylinux_2_5_i686.manylinux1_i686.whl", hash = "sha256:2c9850041b77a9147d6bbd6dbbf13eeec7009eb60b44e83f07fcb2910075bf9b", size = 829127, upload-time = "2025-10-30T11:17:13.192Z" },
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