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

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This commit is contained in:
Tim Lorsbach
2025-11-11 10:09:22 +01:00
parent db9036ce72
commit 35c342a3e3
5 changed files with 163 additions and 46 deletions
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81
epdb/views.py
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@ -397,7 +397,9 @@ def packages(request):
return HttpResponseBadRequest()
else:
package_name = request.POST.get("package-name")
package_description = request.POST.get("package-description", s.DEFAULT_VALUES["description"])
package_description = request.POST.get(
"package-description", s.DEFAULT_VALUES["description"]
)
created_package = PackageManager.create_package(
current_user, package_name, package_description
@ -939,8 +941,13 @@ def package_model(request, package_uuid, model_uuid):
return HttpResponseBadRequest()
else:
# TODO: Move cleaning to property updater
name = nh3.clean(request.POST.get("model-name", "").strip(), tags=s.ALLOWED_HTML_TAGS).strip()
description = nh3.clean(request.POST.get("model-description", "").strip(), tags=s.ALLOWED_HTML_TAGS).strip()
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:
@ -1043,8 +1050,15 @@ def package(request, package_uuid):
return HttpResponseBadRequest()
# TODO: Move cleaning to property updater
new_package_name = nh3.clean(request.POST.get("package-name"), tags=s.ALLOWED_HTML_TAGS).strip()
new_package_description = nh3.clean(request.POST.get("package-description"), tags=s.ALLOWED_HTML_TAGS).strip()
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"
@ -1205,10 +1219,17 @@ def package_compound(request, package_uuid, compound_uuid):
return JsonResponse({"error": str(e)}, status=400)
return JsonResponse({"success": current_compound.url})
# TODO: Move cleaning to property updater
new_compound_name = nh3.clean(request.POST.get("compound-name", ""), tags=s.ALLOWED_HTML_TAGS).strip()
new_compound_description = nh3.clean(request.POST.get("compound-description", ""),
tags=s.ALLOWED_HTML_TAGS).strip()
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
@ -1343,11 +1364,17 @@ def package_compound_structure(request, package_uuid, compound_uuid, structure_u
return redirect(current_compound.url + "/structure")
else:
return HttpResponseBadRequest()
# TODO: Move cleaning to property updater
new_structure_name = nh3.clean(request.POST.get("compound-structure-name", ""),
tags=s.ALLOWED_HTML_TAGS).strip()
new_structure_description = nh3.clean(request.POST.get("compound-structure-description", ""),
tags=s.ALLOWED_HTML_TAGS).strip()
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
@ -1555,8 +1582,13 @@ def package_rule(request, package_uuid, rule_uuid):
return JsonResponse({"success": current_rule.url})
# TODO: Move cleaning to property updater
rule_name = nh3.clean(request.POST.get("rule-name", ""), tags=s.ALLOWED_HTML_TAGS).strip()
rule_description = nh3.clean(request.POST.get("rule-description", "").strip(), tags=s.ALLOWED_HTML_TAGS).strip()
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
@ -1708,9 +1740,15 @@ def package_reaction(request, package_uuid, reaction_uuid):
return JsonResponse({"success": current_reaction.url})
# TODO: Move cleaning to property updater
new_reaction_name = nh3.clean(request.POST.get("reaction-name", ""), tags=s.ALLOWED_HTML_TAGS).strip()
new_reaction_description = nh3.clean(request.POST.get("reaction-description", ""),
tags=s.ALLOWED_HTML_TAGS).strip()
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
@ -1957,8 +1995,13 @@ def package_pathway(request, package_uuid, pathway_uuid):
return JsonResponse({"success": current_pathway.url})
# TODO: Move cleaning to property updater
pathway_name = nh3.clean(request.POST.get("pathway-name"), tags=s.ALLOWED_HTML_TAGS).strip()
pathway_description = nh3.clean(request.POST.get("pathway-description"), tags=s.ALLOWED_HTML_TAGS).strip()
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() != "":