Files
enviPy-bayer/epapi/v1/dal.py
Tobias O d06bd0d4fd [Feature] Minimal IUCLID export (#338)
This is an initial implementation that creates a working minimal .i6z document.
It passes schema validation and can be imported into IUCLID.

Caveat:
IUCLID files target individual compounds.
Pathway is not actually covered by the format.

It can be added in either soil or water and soil OECD endpoints.
**I currently only implemented the soil endpoint for all data.**

This sort of works, and I can report all degradation products in a pathway (not a nice view, but we can report many transformation products and add a diagram attachment in the future).

Adding additional information is an absolute pain, as we need to explicitly map each type of information to the relevant OECD field.
I use the XSD scheme for validation, but unfortunately the IUCLID parser is not fully compliant and requires a specific order, etc.

The workflow is: finding the AI structure from the XSD scheme -> make the scheme validation pass -> upload to IUCLID to get obscure error messages -> guess what could be wrong -> repeat 💣

New specifications get released once per year, so we will have to update accordingly.
I believe that this should be a more expensive feature, as it requires significant effort to uphold.

Currently implemented for root compound only in SOIL:

- Soil Texture 2
- Soil Texture 1
- pH value
- Half-life per soil sample / scenario (mapped to disappearance; not sure about that).
- CEC
- Organic Matter (only Carbon)
- Moisture content
- Humidity

<img width="2123" alt="image.png" src="attachments/d29830e1-65ef-4136-8939-1825e0959c62">
<img width="2124" alt="image.png" src="attachments/ac9de2ac-bf68-4ba4-b40b-82f810a9de93">
<img width="2139" alt="image.png" src="attachments/5674c7e6-865e-420e-974a-6b825b331e6c">

Reviewed-on: enviPath/enviPy#338
Co-authored-by: Tobias O <tobias.olenyi@envipath.com>
Co-committed-by: Tobias O <tobias.olenyi@envipath.com>
2026-04-07 19:46:12 +12:00

142 lines
5.1 KiB
Python

from uuid import UUID
from django.conf import settings as s
from django.db.models import Model
from epdb.logic import PackageManager
from epdb.models import CompoundStructure, User, Compound, Scenario
from .errors import EPAPINotFoundError, EPAPIPermissionDeniedError
Package = s.GET_PACKAGE_MODEL()
def get_compound_for_read(user, compound_uuid: UUID):
"""
Get compound by UUID with permission check.
"""
try:
compound = Compound.objects.get(uuid=compound_uuid)
package = compound.package
except Compound.DoesNotExist:
raise EPAPINotFoundError(f"Compound with UUID {compound_uuid} not found")
# FIXME: optimize package manager to exclusively work with UUIDs
if not user or user.is_anonymous or not PackageManager.readable(user, package):
raise EPAPIPermissionDeniedError("Insufficient permissions to access this compound.")
return compound
def get_package_for_read(user, package_uuid: UUID):
"""
Get package by UUID with permission check.
"""
# FIXME: update package manager with custom exceptions to avoid manual checks here
try:
package = Package.objects.get(uuid=package_uuid)
except Package.DoesNotExist:
raise EPAPINotFoundError(f"Package with UUID {package_uuid} not found")
# FIXME: optimize package manager to exclusively work with UUIDs
if not user or user.is_anonymous or not PackageManager.readable(user, package):
raise EPAPIPermissionDeniedError("Insufficient permissions to access this package.")
return package
def get_package_for_write(user, package_uuid: UUID):
"""
Get package by UUID with permission check.
"""
# FIXME: update package manager with custom exceptions to avoid manual checks here
try:
package = Package.objects.get(uuid=package_uuid)
except Package.DoesNotExist:
raise EPAPINotFoundError(f"Package with UUID {package_uuid} not found")
# FIXME: optimize package manager to exclusively work with UUIDs
if not user or user.is_anonymous or not PackageManager.writable(user, package):
raise EPAPIPermissionDeniedError("Insufficient permissions to access this package.")
return package
def get_scenario_for_read(user, scenario_uuid: UUID):
"""Get scenario by UUID with read permission check."""
try:
scenario = Scenario.objects.select_related("package").get(uuid=scenario_uuid)
except Scenario.DoesNotExist:
raise EPAPINotFoundError(f"Scenario with UUID {scenario_uuid} not found")
if not user or user.is_anonymous or not PackageManager.readable(user, scenario.package):
raise EPAPIPermissionDeniedError("Insufficient permissions to access this scenario.")
return scenario
def get_scenario_for_write(user, scenario_uuid: UUID):
"""Get scenario by UUID with write permission check."""
try:
scenario = Scenario.objects.select_related("package").get(uuid=scenario_uuid)
except Scenario.DoesNotExist:
raise EPAPINotFoundError(f"Scenario with UUID {scenario_uuid} not found")
if not user or user.is_anonymous or not PackageManager.writable(user, scenario.package):
raise EPAPIPermissionDeniedError("Insufficient permissions to modify this scenario.")
return scenario
def get_user_packages_for_read(user: User | None):
"""Get all packages readable by the user."""
if not user or user.is_anonymous:
return PackageManager.get_reviewed_packages()
return PackageManager.get_all_readable_packages(user, include_reviewed=True)
def get_user_entities_for_read(model_class: Model, user: User | None):
"""Build queryset for reviewed package entities."""
if not user or user.is_anonymous:
return model_class.objects.filter(package__reviewed=True).select_related("package")
qs = model_class.objects.filter(
package__in=PackageManager.get_all_readable_packages(user, include_reviewed=True)
).select_related("package")
return qs
def get_package_entities_for_read(model_class: Model, package_uuid: UUID, user: User | None = None):
"""Build queryset for specific package entities."""
package = get_package_for_read(user, package_uuid)
qs = model_class.objects.filter(package=package).select_related("package")
return qs
def get_user_structure_for_read(user: User | None):
"""Build queryset for structures accessible to the user (via compound->package)."""
if not user or user.is_anonymous:
return CompoundStructure.objects.filter(compound__package__reviewed=True).select_related(
"compound__package"
)
qs = CompoundStructure.objects.filter(
compound__package__in=PackageManager.get_all_readable_packages(user, include_reviewed=True)
).select_related("compound__package")
return qs
def get_package_compound_structure_for_read(
package_uuid: UUID, compound_uuid: UUID, user: User | None = None
):
"""Build queryset for specific package compound structures."""
get_package_for_read(user, package_uuid)
compound = get_compound_for_read(user, compound_uuid)
qs = CompoundStructure.objects.filter(compound=compound).select_related("compound__package")
return qs