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[Chore] Leftovers (#426)

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Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#426
This commit is contained in:
jebus
2026-07-16 21:33:12 +12:00
parent 72a63b4876
commit 3566571b42
6 changed files with 109 additions and 46 deletions
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115
epdb/models.py
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@ -894,34 +894,46 @@ class Compound(
if parsed is None:
raise InvalidSMILESException("Given SMILES is invalid")
if name is not None:
# Clean for potential XSS
name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
standardized_smiles = FormatConverter.standardize(smiles, remove_stereo=True)
qs = CompoundStructure.objects.filter(smiles=smiles, compound__package=package)
# Check if we find a direct match for a given SMILES
if CompoundStructure.objects.filter(smiles=smiles, compound__package=package).exists():
return CompoundStructure.objects.get(smiles=smiles, compound__package=package).compound
if qs.exists():
found_structure = qs.first()
found_compound = found_structure.compound
if name:
found_structure.add_alias(name)
found_compound.add_alias(name)
return found_compound
qs = CompoundStructure.objects.filter(smiles=standardized_smiles, compound__package=package)
# Check if we can find the standardized one
if CompoundStructure.objects.filter(
smiles=standardized_smiles, compound__package=package
).exists():
found_c = CompoundStructure.objects.get(
smiles=standardized_smiles, compound__package=package
).compound
if qs.exists():
found_structure = qs.first()
found_compound = found_structure.compound
# As a direct match wasn't found add a new structure
# TODO return newly created structure
_ = found_c.add_structure(smiles, molfile=molfile, name=name, description=description)
# We've only found the standardized one, create the very structure
_ = found_compound.add_structure(
smiles, molfile=molfile, name=name, description=description
)
return found_c
if name:
found_compound.add_alias(name)
return found_compound
# Generate Compound
c = Compound()
c.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"Compound {Compound.objects.filter(package=package).count() + 1}"
@ -1218,8 +1230,15 @@ class CompoundStructure(
# Overwrite SMILES from molfile
smiles = FormatConverter.to_smiles(mol)
# Clean for potential XSS
if name is not None:
name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
if CompoundStructure.objects.filter(compound=compound, smiles=smiles).exists():
found_cs = CompoundStructure.objects.get(smiles=smiles, compound=compound)
found_cs = CompoundStructure.objects.get(compound=compound, smiles=smiles)
if name:
found_cs.add_alias(name)
if found_cs.molfile is None and (molfile is not None and molfile.strip() != ""):
logger.info(
@ -1236,16 +1255,17 @@ class CompoundStructure(
cs = CompoundStructure()
# Clean for potential XSS
if name is not None:
cs.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
cs.name = name
if description is not None:
# We have a default here only set the value if it carries some payload
if description is not None and description.strip() != "":
cs.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
cs.compound = compound
cs.smiles = smiles
# Check if molfile is present and valid
if molfile is not None and molfile.strip() != "":
# If molfile is not None, it hase to be a valid Molfile as we've survived the parsing check
if molfile is not None:
cs.molfile = molfile
if "normalized_structure" in kwargs:
@ -1464,6 +1484,9 @@ class SimpleAmbitRule(SimpleRule):
if not FormatConverter.is_valid_smirks(smirks):
raise ValueError(f'SMIRKS "{smirks}" is invalid!')
if name is not None:
name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
query = SimpleAmbitRule.objects.filter(package=package, smirks=smirks)
if reactant_filter_smarts is not None and reactant_filter_smarts.strip() != "":
@ -1475,14 +1498,17 @@ class SimpleAmbitRule(SimpleRule):
if query.exists():
if query.count() > 1:
logger.error(f"More than one rule matched this one! {query}")
return query.first()
found_rule = query.first()
if name:
found_rule.add_alias(name)
return found_rule
r = SimpleAmbitRule()
r.package = package
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}"
@ -1615,6 +1641,9 @@ class ParallelRule(Rule):
f"Simple rule {sr.uuid} does not belong to package {package.uuid}!"
)
if name is not None:
name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
# Deduplication check
query = ParallelRule.objects.annotate(
srs_count=Count("simple_rules", filter=Q(simple_rules__in=simple_rules), distinct=True)
@ -1626,15 +1655,19 @@ class ParallelRule(Rule):
if existing_rule_qs.exists():
if existing_rule_qs.count() > 1:
logger.error(f"Found more than one reaction for given input! {existing_rule_qs}")
return existing_rule_qs.first()
logger.error(
f"Found more than one ParallelRule for given input! {existing_rule_qs}"
)
found_rule = existing_rule_qs.first()
if name:
found_rule.add_alias(name)
return found_rule
r = ParallelRule()
r.package = package
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}"
@ -1730,6 +1763,10 @@ class Reaction(
rules: Union[Rule | List[Rule]] = None,
multi_step: bool = False,
):
# Clean for potential XSS
if name is not None and name.strip() != "":
name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
_educts = []
_products = []
@ -1784,14 +1821,21 @@ class Reaction(
logger.error(
f"Found more than one reaction for given input! {existing_reaction_qs}"
)
return existing_reaction_qs.first()
found_reaction = existing_reaction_qs.first()
if name:
found_reaction.add_alias(name)
return found_reaction
r = Reaction()
r.package = package
# Clean for potential XSS
if name is not None and name.strip() != "":
r.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
if name is None or name == "":
name = f"Reaction {Reaction.objects.filter(package=package).count() + 1}"
r.name = name
if description is not None and description.strip() != "":
r.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
@ -2420,6 +2464,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
},
"predicted_properties": predicted_properties,
"is_engineered_intermediate": self.kv.get("is_engineered_intermediate", False),
"proposed": self.get_proposed_info(),
"timeseries": self.get_timeseries_data(),
**structure_data,
}
@ -2516,7 +2561,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
return res
def is_proposed_intermediate(self):
def get_proposed_info(self):
collected = defaultdict(dict)
for ai in self.additional_information.filter(
type__in=["ProposedIntermediate", "TransformationProductImportance", "Confidence"],