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Tim Lorsbach
2025-10-29 19:46:20 +01:00
parent 13ed86a780
commit 138846d84d
35 changed files with 477 additions and 108 deletions
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45
epdb/models.py
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@ -7,7 +7,7 @@ import secrets
from abc import abstractmethod
from collections import defaultdict
from datetime import datetime
from typing import Union, List, Optional, Dict, Tuple, Set, Any
from typing import Union, List, Optional, Dict, Tuple, Set, Any, TYPE_CHECKING
from uuid import uuid4
import math
import joblib
@ -32,6 +32,8 @@ from utilities.ml import Dataset, ApplicabilityDomainPCA, EnsembleClassifierChai
logger = logging.getLogger(__name__)
if TYPE_CHECKING:
Package = s.GET_PACKAGE_MODEL()
##########################
# User/Groups/Permission #
@ -45,7 +47,10 @@ class User(AbstractUser):
)
url = models.TextField(blank=False, null=True, verbose_name="URL", unique=True)
default_package = models.ForeignKey(
"epdb.Package", verbose_name="Default Package", null=True, on_delete=models.SET_NULL
s.PACKAGE_IMPLEMENTATION,
verbose_name="Default Package",
null=True,
on_delete=models.SET_NULL,
)
default_group = models.ForeignKey(
"Group",
@ -235,7 +240,7 @@ class UserPackagePermission(Permission):
)
user = models.ForeignKey("User", verbose_name="Permission to", on_delete=models.CASCADE)
package = models.ForeignKey(
"epdb.Package", verbose_name="Permission on", on_delete=models.CASCADE
s.PACKAGE_IMPLEMENTATION, verbose_name="Permission on", on_delete=models.CASCADE
)
class Meta:
@ -251,7 +256,7 @@ class GroupPackagePermission(Permission):
)
group = models.ForeignKey("Group", verbose_name="Permission to", on_delete=models.CASCADE)
package = models.ForeignKey(
"epdb.Package", verbose_name="Permission on", on_delete=models.CASCADE
s.PACKAGE_IMPLEMENTATION, verbose_name="Permission on", on_delete=models.CASCADE
)
class Meta:
@ -651,7 +656,7 @@ class License(models.Model):
image_link = models.URLField(blank=False, null=False, verbose_name="Image link")
class Package(EnviPathModel):
class AbstractPackage(EnviPathModel):
reviewed = models.BooleanField(verbose_name="Reviewstatus", default=False)
license = models.ForeignKey(
"epdb.License", on_delete=models.SET_NULL, blank=True, null=True, verbose_name="License"
@ -719,10 +724,13 @@ class Package(EnviPathModel):
rules = sorted(rules, key=lambda x: x.url)
return rules
class Meta:
abstract = True
class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin):
package = models.ForeignKey(
"epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
s.PACKAGE_IMPLEMENTATION, verbose_name="Package", on_delete=models.CASCADE, db_index=True
)
default_structure = models.ForeignKey(
"CompoundStructure",
@ -772,7 +780,7 @@ class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin
@staticmethod
@transaction.atomic
def create(
package: Package, smiles: str, name: str = None, description: str = None, *args, **kwargs
package: "Package", smiles: str, name: str = None, description: str = None, *args, **kwargs
) -> "Compound":
if smiles is None or smiles.strip() == "":
raise ValueError("SMILES is required")
@ -1050,7 +1058,7 @@ class EnzymeLink(EnviPathModel, KEGGIdentifierMixin):
class Rule(PolymorphicModel, EnviPathModel, AliasMixin, ScenarioMixin):
package = models.ForeignKey(
"epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
s.PACKAGE_IMPLEMENTATION, verbose_name="Package", on_delete=models.CASCADE, db_index=True
)
# # https://github.com/django-polymorphic/django-polymorphic/issues/229
@ -1156,7 +1164,7 @@ class SimpleAmbitRule(SimpleRule):
@staticmethod
@transaction.atomic
def create(
package: Package,
package: "Package",
name: str = None,
description: str = None,
smirks: str = None,
@ -1222,6 +1230,7 @@ class SimpleAmbitRule(SimpleRule):
@property
def related_reactions(self):
Package = s.GET_PACKAGE_MODEL()
qs = Package.objects.filter(reviewed=True)
return self.reaction_rule.filter(package__in=qs).order_by("name")
@ -1314,7 +1323,7 @@ class SequentialRuleOrdering(models.Model):
class Reaction(EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin):
package = models.ForeignKey(
"epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
s.PACKAGE_IMPLEMENTATION, verbose_name="Package", on_delete=models.CASCADE, db_index=True
)
educts = models.ManyToManyField(
"epdb.CompoundStructure", verbose_name="Educts", related_name="reaction_educts"
@ -1336,7 +1345,7 @@ class Reaction(EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin
@staticmethod
@transaction.atomic
def create(
package: Package,
package: "Package",
name: str = None,
description: str = None,
educts: Union[List[str], List[CompoundStructure]] = None,
@ -1496,7 +1505,7 @@ class Reaction(EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin
class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
package = models.ForeignKey(
"epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
s.PACKAGE_IMPLEMENTATION, verbose_name="Package", on_delete=models.CASCADE, db_index=True
)
setting = models.ForeignKey(
"epdb.Setting", verbose_name="Setting", on_delete=models.CASCADE, null=True, blank=True
@ -2052,7 +2061,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin):
class EPModel(PolymorphicModel, EnviPathModel):
package = models.ForeignKey(
"epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
s.PACKAGE_IMPLEMENTATION, verbose_name="Package", on_delete=models.CASCADE, db_index=True
)
def _url(self):
@ -2061,17 +2070,17 @@ class EPModel(PolymorphicModel, EnviPathModel):
class PackageBasedModel(EPModel):
rule_packages = models.ManyToManyField(
"Package",
s.PACKAGE_IMPLEMENTATION,
verbose_name="Rule Packages",
related_name="%(app_label)s_%(class)s_rule_packages",
)
data_packages = models.ManyToManyField(
"Package",
s.PACKAGE_IMPLEMENTATION,
verbose_name="Data Packages",
related_name="%(app_label)s_%(class)s_data_packages",
)
eval_packages = models.ManyToManyField(
"Package",
s.PACKAGE_IMPLEMENTATION,
verbose_name="Evaluation Packages",
related_name="%(app_label)s_%(class)s_eval_packages",
)
@ -3439,7 +3448,7 @@ class PluginModel(EPModel):
class Scenario(EnviPathModel):
package = models.ForeignKey(
"epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
s.PACKAGE_IMPLEMENTATION, verbose_name="Package", on_delete=models.CASCADE, db_index=True
)
scenario_date = models.CharField(max_length=256, null=False, blank=False, default="No date")
scenario_type = models.CharField(
@ -3590,7 +3599,7 @@ class Setting(EnviPathModel):
)
rule_packages = models.ManyToManyField(
"Package",
s.PACKAGE_IMPLEMENTATION,
verbose_name="Setting Rule Packages",
related_name="setting_rule_packages",
blank=True,