removed envipytags.py and moved name cleaning to before default name assignment

epdb/models.py

@@ -804,10 +804,13 @@ 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}"
-        # Clean for potential XSS
+        c.name = name
-        c.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+
         # We have a default here only set the value if it carries some payload
         if description is not None and description.strip() != "":
             c.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
@@ -1187,12 +1190,13 @@ class SimpleAmbitRule(SimpleRule):
 
         r = SimpleAmbitRule()
         r.package = package
-
+        if name is not None:
-        if name is None or name.strip() == "":
+            # Clean for potential XSS
+            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}"
 
-        # Clean for potential XSS
+        r.name = name
-        r.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
         if description is not None and description.strip() != "":
             r.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
@@ -1715,12 +1719,13 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
     ):
         pw = Pathway()
         pw.package = package
-
+        if name is not None:
-        if name is None or name.strip() == "":
+            # 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}"
 
-        # Clean for potential XSS
+        pw.name = name
-        pw.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
         if description is not None and description.strip() != "":
             pw.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
@@ -2019,9 +2024,10 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin):
 
         # Clean for potential XSS
         # Cleaning technically not needed as it is also done in Reaction.create, including it here for consistency
-        if name is None:
+        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}"
-        name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
 
         if description is None:
             description = s.DEFAULT_VALUES["description"]
@@ -2545,12 +2551,13 @@ class RuleBasedRelativeReasoning(PackageBasedModel):
     ):
         rbrr = RuleBasedRelativeReasoning()
         rbrr.package = package
-
+        if name is not None:
-        if name is None or name.strip() == "":
+            # 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}"
 
-        # Clean for potential XSS
+        rbrr.name = name
-        rbrr.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
         if description is not None and description.strip() != "":
             rbrr.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
@@ -2649,12 +2656,13 @@ class MLRelativeReasoning(PackageBasedModel):
     ):
         mlrr = MLRelativeReasoning()
         mlrr.package = package
-
+        if name is not None:
-        if name is None or name.strip() == "":
+            # 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}"
 
-        # Clean for potential XSS
+        mlrr.name = name
-        mlrr.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
         if description is not None and description.strip() != "":
             mlrr.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
@@ -2964,12 +2972,13 @@ class EnviFormer(PackageBasedModel):
     ):
         mod = EnviFormer()
         mod.package = package
-
+        if name is not None:
-        if name is None or name.strip() == "":
+            # 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}"
 
-        # Clean for potential XSS
+        mod.name = name
-        mod.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
         if description is not None and description.strip() != "":
             mod.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
@@ -3375,11 +3384,12 @@ class Scenario(EnviPathModel):
     ):
         new_s = Scenario()
         new_s.package = package
-
+        if name is not None:
-        if name is None or name.strip() == "":
+            # 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}"
-
+        new_s.name = name
-        new_s.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
 
         if description is not None and description.strip() != "":
             new_s.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()

epdb/templatetags/envipytags.py

@@ -1,21 +0,0 @@
-from django import template
-from pydantic import AnyHttpUrl, ValidationError
-from pydantic.type_adapter import TypeAdapter
-
-register = template.Library()
-
-url_adapter = TypeAdapter(AnyHttpUrl)
-
-
-@register.filter
-def classname(obj):
-    return obj.__class__.__name__
-
-
-@register.filter
-def is_url(value):
-    try:
-        url_adapter.validate_python(value)
-        return True
-    except ValidationError:
-        return False

epdb/views.py

@@ -87,7 +87,7 @@ def login(request):
         from django.contrib.auth import login
 
         username = request.POST.get("username").strip()
-        if 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")

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

@@ -1,6 +1,5 @@
 {% extends "framework.html" %}
 {% load static %}
-{% load envipytags %}
 {% block content %}
 
     {% if object_type != 'package' %}

templates/migration.html

@@ -1,5 +1,4 @@
 {% extends "framework.html" %}
-{% load envipytags %}
 
 {% block content %}
 <div class="panel-group" id="migration-detail">

templates/migration_detail.html

@@ -1,5 +1,4 @@
 {% extends "framework.html" %}
-{% load envipytags %}
 
 {% block content %}
     <div class="panel-group" id="migration-detail">

templates/modals/collections/new_model_modal.html

@@ -1,4 +1,4 @@
-{% load envipytags %}
+
 <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">

templates/modals/collections/new_pathway_modal.html

@@ -1,4 +1,4 @@
-{% load envipytags %}
+
 {% 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;">

templates/modals/collections/new_prediction_setting_modal.html

@@ -1,4 +1,4 @@
-{% load envipytags %}
+
 {% load static %}
 
 <div id="new_prediction_setting_modal" class="modal" tabindex="-1">

templates/modals/objects/add_pathway_edge_modal.html

@@ -1,4 +1,4 @@
-{% load envipytags %}
+
 {% 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"

templates/modals/objects/delete_pathway_edge_modal.html

@@ -1,4 +1,4 @@
-{% load envipytags %}
+
 {% load static %}
 <!-- Delete Edge -->
 <div id="delete_pathway_edge_modal" class="modal" tabindex="-1">

templates/modals/objects/delete_pathway_node_modal.html

@@ -1,5 +1,5 @@
 {% load static %}
-{% load envipytags %}
+
 <!-- Delete Node -->
 <div id="delete_pathway_node_modal" class="modal" tabindex="-1">
     <div class="modal-dialog">

templates/modals/objects/edit_compound_modal.html

@@ -1,4 +1,4 @@
-{% load envipytags %}
+
 {% load static %}
 <!-- Edit Compound -->
 <div id="edit_compound_modal" class="modal" tabindex="-1">

templates/modals/objects/edit_compound_structure_modal.html

@@ -1,4 +1,4 @@
-{% load envipytags %}
+
 {% load static %}
 <!-- Edit Compound -->
 <div id="edit_compound_structure_modal" class="modal" tabindex="-1">

templates/modals/objects/edit_group_member_modal.html

@@ -1,4 +1,4 @@
-{% load envipytags %}
+
 {% load static %}
 <!-- Edit Package Permission -->
 <div id="edit_group_member_modal" class="modal" tabindex="-1">

templates/modals/objects/edit_model_modal.html

@@ -1,4 +1,4 @@
-{% load envipytags %}
+
 {% load static %}
 <!-- Edit Model -->
 <div id="edit_model_modal" class="modal" tabindex="-1">

templates/modals/objects/edit_node_modal.html

@@ -1,4 +1,4 @@
-{% load envipytags %}
+
 {% load static %}
 <!-- Edit Node -->
 <div id="edit_node_modal" class="modal" tabindex="-1">

templates/modals/objects/edit_package_modal.html

@@ -1,4 +1,4 @@
-{% load envipytags %}
+
 {% load static %}
 <!-- Edit Package -->
 <div id="edit_package_modal" class="modal" tabindex="-1">

templates/modals/objects/edit_package_permissions_modal.html

@@ -1,4 +1,4 @@
-{% load envipytags %}
+
 {% load static %}
 <!-- Edit Package Permission -->
 <div id="edit_package_permissions_modal" class="modal" tabindex="-1">

templates/modals/objects/edit_pathway_modal.html

@@ -1,4 +1,4 @@
-{% load envipytags %}
+
 {% load static %}
 <!-- Edit Pathway -->
 <div id="edit_pathway_modal" class="modal" tabindex="-1">

templates/modals/objects/edit_prediction_setting_modal.html

@@ -1,4 +1,3 @@
-{% load envipytags %}
 {% load static %}
 <!-- Edit Package -->
 <div id="update_prediction_settings_modal" class="modal" tabindex="-1">

templates/modals/objects/edit_reaction_modal.html

@@ -1,4 +1,4 @@
-{% load envipytags %}
+
 {% load static %}
 <!-- Edit Reaction -->
 <div id="edit_reaction_modal" class="modal" tabindex="-1">

templates/modals/objects/edit_rule_modal.html

@@ -1,4 +1,4 @@
-{% load envipytags %}
+
 {% load static %}
 <!-- Edit Rule -->
 <div id="edit_rule_modal" class="modal" tabindex="-1">

templates/modals/objects/edit_user_modal.html

@@ -1,4 +1,4 @@
-{% load envipytags %}
+
 {% load static %}
 <!-- Edit User -->
 <div id="edit_user_modal" class="modal" tabindex="-1">

templates/modals/objects/evaluate_model_modal.html

@@ -1,4 +1,4 @@
-{% load envipytags %}
+
 <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">

templates/modals/objects/generic_copy_object_modal.html

@@ -1,4 +1,4 @@
-{% load envipytags %}
+
 {% load static %}
 <!-- Copy Object -->
 <div id="generic_copy_object_modal" class="modal" tabindex="-1">

templates/modals/objects/generic_set_aliases_modal.html

@@ -1,4 +1,4 @@
-{% load envipytags %}
+
 {% load static %}
 
 <style>

templates/modals/objects/generic_set_external_reference_modal.html

@@ -1,4 +1,4 @@
-{% load envipytags %}
+
 {% load static %}
 <!-- Delete Object -->
 <div id="generic_set_external_reference_modal" class="modal" tabindex="-1">

templates/modals/objects/generic_set_scenario_modal.html

@@ -1,4 +1,4 @@
-{% load envipytags %}
+
 {% 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">

templates/modals/objects/manage_api_token_modal.html

@@ -1,4 +1,4 @@
-{% load envipytags %}
+
 <div class="modal fade"
      tabindex="-1"
      id="manage_api_token_modal"

templates/modals/predict_modal.html

@@ -1,4 +1,3 @@
-{% load envipytags %}
 {% load static %}
 <div class="modal fade bs-modal-lg" id="predict_modal" tabindex="-1" aria-labelledby="predict_modal" aria-modal="true"
      role="dialog">

templates/objects/composite_rule.html

@@ -1,5 +1,4 @@
 {% extends "framework.html" %}
-{% load envipytags %}
 
 {% block content %}
 

templates/objects/compound.html

@@ -1,5 +1,4 @@
 {% extends "framework.html" %}
-{% load envipytags %}
 
 {% block content %}
 

templates/objects/compound_structure.html

@@ -1,5 +1,4 @@
 {% extends "framework.html" %}
-{% load envipytags %}
 
 {% block content %}
 

templates/objects/edge.html

@@ -1,5 +1,4 @@
 {% extends "framework.html" %}
-{% load envipytags %}
 
 {% block content %}
 

templates/objects/group.html

@@ -1,5 +1,4 @@
 {% extends "framework.html" %}
-{% load envipytags %}
 
 {% block content %}
 

templates/objects/model.html

@@ -1,6 +1,5 @@
 {% extends "framework.html" %}
 {% load static %}
-{% load envipytags %}
 {% block content %}
 
     {% block action_modals %}

templates/objects/node.html

@@ -1,5 +1,4 @@
 {% extends "framework.html" %}
-{% load envipytags %}
 
 {% block content %}
 

templates/objects/package.html

@@ -1,5 +1,4 @@
 {% extends "framework.html" %}
-{% load envipytags %}
 
 {% block content %}
 

templates/objects/pathway.html

@@ -1,5 +1,4 @@
 {% extends "framework.html" %}
-{% load envipytags %}
 {% load static %}
 {% block content %}
 

templates/objects/reaction.html

@@ -1,5 +1,4 @@
 {% extends "framework.html" %}
-{% load envipytags %}
 
 {% block content %}
 

templates/objects/scenario.html

@@ -1,5 +1,4 @@
 {% extends "framework.html" %}
-{% load envipytags %}
 
 {% block content %}
 

templates/objects/simple_rule.html

@@ -1,5 +1,4 @@
 {% extends "framework.html" %}
-{% load envipytags %}
 
 {% block content %}
 

templates/objects/user.html

@@ -1,5 +1,4 @@
 {% extends "framework.html" %}
-{% load envipytags %}
 
 {% block content %}
 

templates/pathway_playground2.html

@@ -1,4 +1,3 @@
-{% load envipytags %}
 <!DOCTYPE html>
 <html lang="en">
 <head>

templates/search.html

@@ -1,5 +1,4 @@
 {% extends "framework.html" %}
-{% load envipytags %}
 {% load static %}
 {% block content %}