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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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14
epdb/logic.py
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@ -526,9 +526,13 @@ class PackageManager(object):
@transaction.atomic
def create_package(current_user, name: str, description: str = None):
p = Package()
# Clean for potential XSS
p.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
p.description = nh3.clean(description, 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()
@ -1552,7 +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]
@ -1584,7 +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