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[Chore] Package Export, Blanks for fields, Styling (#421)

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Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#421
This commit is contained in:
jebus
2026-07-02 20:12:26 +12:00
parent a092d4a558
commit dba6514013
21 changed files with 647 additions and 450 deletions
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2
epdb/exceptions.py Normal file
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@ -0,0 +1,2 @@
class InvalidSMILESException(Exception):
pass

6
epdb/legacy_api.py
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@ -1610,13 +1610,13 @@ class PathwayNode(Schema):
dt50s: List[Dict[str, str]] = Field([], alias="dt50s")
engineeredIntermediate: bool = Field(None, alias="engineered_intermediate")
id: str = Field(None, alias="url")
idcomp: str = Field(None, alias="default_node_label.url")
idreact: str = Field(None, alias="default_node_label.url")
idcomp: str = Field(None, alias="node_label_id")
idreact: str = Field(None, alias="node_label_id")
image: str = Field(None, alias="image")
imageSize: int = Field(None, alias="image_size")
name: str = Field(None, alias="name")
proposed: List[Dict[str, str]] = Field([], alias="proposed_intermediate")
smiles: str = Field(None, alias="default_node_label.smiles")
smiles: str = Field(None, alias="smiles")
pseudo: bool = Field(False, alias="pseudo")
@staticmethod

10
epdb/management/commands/bootstrap.py
View File

@ -99,11 +99,15 @@ class Command(BaseCommand):
new_license.image_link = f"https://licensebuttons.net/l/{cc_string}/4.0/88x31.png"
new_license.save()
def import_package(self, data, owner):
return PackageManager.import_legacy_package(
def import_package(self, data, owner, all_envipath_user_group):
p = PackageManager.import_legacy_package(
data, owner, keep_ids=True, add_import_timestamp=False, trust_reviewed=True
)
PackageManager.grant_read(owner, p, all_envipath_user_group)
return p
def create_default_setting(self, owner, packages):
s = SettingManager.create_setting(
owner,
@ -198,7 +202,7 @@ class Command(BaseCommand):
s.BASE_DIR / "fixtures" / "packages" / "2025-07-18" / p, encoding="utf-8"
).read()
)
imported_package = self.import_package(package_data, admin)
imported_package = self.import_package(package_data, admin, g)
mapping[p.replace(".json", "")] = imported_package
setting = self.create_default_setting(admin, [mapping["EAWAG-BBD"]])

150
epdb/migrations/0027_alter_compound_aliases_and_more.py Normal file
View File

@ -0,0 +1,150 @@
# Generated by Django 6.0.3 on 2026-07-01 20:59
import django.contrib.postgres.fields
import django.db.models.deletion
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
("epdb", "0026_auto_20260602_1718"),
]
operations = [
migrations.AlterField(
model_name="compound",
name="aliases",
field=django.contrib.postgres.fields.ArrayField(
base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
),
),
migrations.AlterField(
model_name="compound",
name="default_structure",
field=models.ForeignKey(
null=True,
on_delete=django.db.models.deletion.SET_NULL,
related_name="compound_default_structure",
to="epdb.compoundstructure",
verbose_name="Default Structure",
),
),
migrations.AlterField(
model_name="compound",
name="scenarios",
field=models.ManyToManyField(
blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
),
),
migrations.AlterField(
model_name="compoundstructure",
name="aliases",
field=django.contrib.postgres.fields.ArrayField(
base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
),
),
migrations.AlterField(
model_name="compoundstructure",
name="scenarios",
field=models.ManyToManyField(
blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
),
),
migrations.AlterField(
model_name="edge",
name="aliases",
field=django.contrib.postgres.fields.ArrayField(
base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
),
),
migrations.AlterField(
model_name="edge",
name="edge_label",
field=models.ForeignKey(
null=True,
on_delete=django.db.models.deletion.CASCADE,
to="epdb.reaction",
verbose_name="Edge label",
),
),
migrations.AlterField(
model_name="edge",
name="scenarios",
field=models.ManyToManyField(
blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
),
),
migrations.AlterField(
model_name="node",
name="aliases",
field=django.contrib.postgres.fields.ArrayField(
base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
),
),
migrations.AlterField(
model_name="node",
name="scenarios",
field=models.ManyToManyField(
blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
),
),
migrations.AlterField(
model_name="pathway",
name="aliases",
field=django.contrib.postgres.fields.ArrayField(
base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
),
),
migrations.AlterField(
model_name="pathway",
name="scenarios",
field=models.ManyToManyField(
blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
),
),
migrations.AlterField(
model_name="reaction",
name="aliases",
field=django.contrib.postgres.fields.ArrayField(
base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
),
),
migrations.AlterField(
model_name="reaction",
name="medline_references",
field=django.contrib.postgres.fields.ArrayField(
base_field=models.TextField(),
blank=True,
null=True,
verbose_name="Medline References",
),
),
migrations.AlterField(
model_name="reaction",
name="rules",
field=models.ManyToManyField(
blank=True, related_name="reaction_rule", to="epdb.rule", verbose_name="Rule"
),
),
migrations.AlterField(
model_name="reaction",
name="scenarios",
field=models.ManyToManyField(
blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
),
),
migrations.AlterField(
model_name="rule",
name="aliases",
field=django.contrib.postgres.fields.ArrayField(
base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
),
),
migrations.AlterField(
model_name="rule",
name="scenarios",
field=models.ManyToManyField(
blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
),
),
]

58
epdb/models.py
View File

@ -31,6 +31,7 @@ from sklearn.model_selection import ShuffleSplit
from bridge.contracts import Property
from bridge.dto import RunResult, PropertyPrediction
from epdb.exceptions import InvalidSMILESException
from utilities.chem import FormatConverter, IndigoUtils, PredictionResult, ProductSet
from utilities.ml import (
ApplicabilityDomainPCA,
@ -631,7 +632,7 @@ class EnviPathModel(TimeStampedModel):
class AliasMixin(models.Model):
aliases = ArrayField(
models.TextField(blank=False, null=False), verbose_name="Aliases", default=list
models.TextField(blank=False, null=False), verbose_name="Aliases", default=list, blank=True
)
@transaction.atomic
@ -654,7 +655,9 @@ class AliasMixin(models.Model):
class ScenarioMixin(models.Model):
scenarios = models.ManyToManyField("epdb.Scenario", verbose_name="Attached Scenarios")
scenarios = models.ManyToManyField(
"epdb.Scenario", verbose_name="Attached Scenarios", blank=True
)
@transaction.atomic
def set_scenarios(self, scenarios: List["Scenario"]):
@ -780,7 +783,7 @@ class Compound(
"CompoundStructure",
verbose_name="Default Structure",
related_name="compound_default_structure",
on_delete=models.CASCADE,
on_delete=models.SET_NULL,
null=True,
)
@ -857,13 +860,13 @@ class Compound(
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")
raise InvalidSMILESException("SMILES is required")
smiles = smiles.strip()
parsed = FormatConverter.from_smiles(smiles)
if parsed is None:
raise ValueError("Given SMILES is invalid")
raise InvalidSMILESException("Given SMILES is invalid")
standardized_smiles = FormatConverter.standardize(smiles, remove_stereo=True)
@ -1174,6 +1177,8 @@ class CompoundStructure(
@property
def as_svg(self, width: int = 800, height: int = 400):
if self.molfile is not None and self.molfile.strip() != "":
return IndigoUtils.mol_to_svg(self.molfile, width=width, height=height)
return IndigoUtils.mol_to_svg(self.smiles, width=width, height=height)
@property
@ -1610,10 +1615,15 @@ class Reaction(
products = models.ManyToManyField(
"epdb.CompoundStructure", verbose_name="Products", related_name="reaction_products"
)
rules = models.ManyToManyField("epdb.Rule", verbose_name="Rule", related_name="reaction_rule")
rules = models.ManyToManyField(
"epdb.Rule", verbose_name="Rule", related_name="reaction_rule", blank=True
)
multi_step = models.BooleanField(verbose_name="Multistep Reaction")
medline_references = ArrayField(
models.TextField(blank=False, null=False), null=True, verbose_name="Medline References"
models.TextField(blank=False, null=False),
null=True,
verbose_name="Medline References",
blank=True,
)
external_identifiers = GenericRelation("ExternalIdentifier")
@ -1630,7 +1640,7 @@ class Reaction(
educts: Union[List[str], List[CompoundStructure]] = None,
products: Union[List[str], List[CompoundStructure]] = None,
rules: Union[Rule | List[Rule]] = None,
multi_step: bool = True,
multi_step: bool = False,
):
_educts = []
_products = []
@ -2197,7 +2207,25 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
depth_map[0] = list()
processed = set()
for n in self.root_nodes:
data_driven_root_nodes = (
self.node_set.all()
.annotate(prod_cnt=Count("edge_products"), educt_cnt=Count("edge_educts"))
.filter(prod_cnt=0, educt_cnt__gt=0)
.distinct()
)
# Eval QuerySet
root_nodes_by_depth = list(self.root_nodes)
data_driven_root_nodes.update(depth=0)
root_nodes = [n for n in data_driven_root_nodes]
for n in root_nodes_by_depth:
if n not in root_nodes:
if len(n.edge_products.all()) == 0:
root_nodes.append(n)
for n in root_nodes:
depth_map[0].append(n)
# At most depth len(nodes) is possible
@ -2277,7 +2305,12 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
"node_label_id": self.default_node_label.url,
"image": f"{self.url}?image=svg",
"image_svg": IndigoUtils.mol_to_svg(
self.default_node_label.smiles, width=40, height=40
self.default_node_label.molfile
if self.default_node_label.molfile is not None
and self.default_node_label.molfile.strip()
else self.default_node_label.smiles,
width=40,
height=40,
),
"image_type": "svg",
"name": self.get_name(),
@ -2331,6 +2364,11 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
@property
def as_svg(self):
if (
self.default_node_label.molfile is not None
and self.default_node_label.molfile.strip() != ""
):
return IndigoUtils.mol_to_svg(self.default_node_label.molfile)
return IndigoUtils.mol_to_svg(self.default_node_label.smiles)
def get_timeseries_data(self):

53
epdb/views.py
View File

@ -19,6 +19,7 @@ from sentry_sdk import capture_exception
from utilities.chem import FormatConverter, IndigoUtils
from utilities.decorators import package_permission_required
from .exceptions import InvalidSMILESException
from .logic import (
EPDBURLParser,
@ -754,6 +755,11 @@ def models(request):
{"Model": s.SERVER_URL + "/model"},
]
context["entity_type"] = "model"
context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/models/"
context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
context["list_title"] = "models"
# Keep model_types for potential modal/action use
context["model_types"] = {
"ML Relative Reasoning": {
@ -766,19 +772,26 @@ def models(request):
"requires_rule_packages": True,
"requires_data_packages": True,
},
"EnviFormer": {
"type": "enviformer",
"requires_rule_packages": False,
"requires_data_packages": True,
},
}
if s.ENVIFORMER_PRESENT:
context["model_types"]["EnviFormer"] = (
{
"type": "enviformer",
"requires_rule_packages": False,
"requires_data_packages": True,
},
)
if s.FLAGS.get("PLUGINS", False):
for k, v in s.CLASSIFIER_PLUGINS.items():
context["model_types"][v.display()] = {
"type": k,
"requires_rule_packages": v.requires_rule_packages(),
"requires_data_packages": v.requires_data_packages(),
"additional_parameters": v.Config.__name__.lower()
if v.Config.__name__ != ""
else None,
}
for k, v in s.PROPERTY_PLUGINS.items():
context["model_types"][v.display()] = {
@ -787,12 +800,6 @@ def models(request):
"requires_data_packages": v.requires_data_packages(),
}
# Context for paginated template
context["entity_type"] = "model"
context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/models/"
context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
context["list_title"] = "models"
return render(request, "collections/models_paginated.html", context)
elif request.method == "POST":
@ -906,12 +913,13 @@ def package_models(request, package_uuid):
"requires_rule_packages": True,
"requires_data_packages": True,
},
"EnviFormer": {
}
if s.ENVIFORMER_PRESENT:
context["model_types"]["EnviFormer"] = {
"type": "enviformer",
"requires_rule_packages": False,
"requires_data_packages": True,
},
}
}
if s.FLAGS.get("PLUGINS", False):
for k, v in s.CLASSIFIER_PLUGINS.items():
@ -1087,6 +1095,11 @@ def package_model(request, package_uuid, model_uuid):
}
)
# Sort data by prob desc
res["pred"] = sorted(
res["pred"], key=lambda x: x["probability"], reverse=True
)
return JsonResponse(res, safe=False)
elif half_life:
@ -1190,9 +1203,7 @@ def package(request, package_uuid):
if request.method == "GET":
if request.GET.get("export", False) == "true":
filename = f"{current_package.get_name().replace(' ', '_')}_{current_package.uuid}.json"
pack_json = PackageManager.export_package(
current_package, include_models=False, include_external_identifiers=False
)
pack_json = PackageManager.export_package(current_package)
response = JsonResponse(pack_json, content_type="application/json")
response["Content-Disposition"] = f'attachment; filename="{filename}"'
@ -2328,7 +2339,13 @@ def package_pathway_nodes(request, package_uuid, pathway_uuid):
node_description = request.POST.get("node-description")
node_smiles = request.POST.get("node-smiles").strip()
current_pathway.add_node(node_smiles, name=node_name, description=node_description)
try:
current_pathway.add_node(node_smiles, name=node_name, description=node_description)
except InvalidSMILESException:
return error(
request, "Node creation failed!", f"Given SMILES ({node_smiles}) is invalid"
)
return redirect(current_pathway.url)