[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>
This commit is contained in:
2026-04-07 19:46:12 +12:00
committed by jebus
parent f7c45b8015
commit d06bd0d4fd
49 changed files with 66402 additions and 1014 deletions

View File

@ -0,0 +1,58 @@
from dataclasses import dataclass, field
from uuid import UUID
@dataclass(frozen=True)
class PathwayCompoundDTO:
pk: int
name: str
smiles: str | None = None
cas_number: str | None = None
ec_number: str | None = None
@dataclass(frozen=True)
class PathwayScenarioDTO:
scenario_uuid: UUID
name: str
additional_info: list = field(default_factory=list) # EnviPyModel instances
@dataclass(frozen=True)
class PathwayNodeDTO:
node_uuid: UUID
compound_pk: int
name: str
depth: int
smiles: str | None = None
cas_number: str | None = None
ec_number: str | None = None
additional_info: list = field(default_factory=list) # EnviPyModel instances
scenarios: list[PathwayScenarioDTO] = field(default_factory=list)
@dataclass(frozen=True)
class PathwayEdgeDTO:
edge_uuid: UUID
start_compound_pks: list[int] = field(default_factory=list)
end_compound_pks: list[int] = field(default_factory=list)
probability: float | None = None
@dataclass(frozen=True)
class PathwayModelInfoDTO:
model_name: str | None = None
model_uuid: UUID | None = None
software_name: str | None = None
software_version: str | None = None
@dataclass(frozen=True)
class PathwayExportDTO:
pathway_uuid: UUID
pathway_name: str
compounds: list[PathwayCompoundDTO] = field(default_factory=list)
nodes: list[PathwayNodeDTO] = field(default_factory=list)
edges: list[PathwayEdgeDTO] = field(default_factory=list)
root_compound_pks: list[int] = field(default_factory=list)
model_info: PathwayModelInfoDTO | None = None