forked from enviPath/enviPy
Tobias O
d06bd0d4fd
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>
103 lines
2.9 KiB
Python
103 lines
2.9 KiB
Python
from __future__ import annotations
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from uuid import uuid4
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from epiuclid.serializers.pathway_mapper import (
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HalfLifeEntry,
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IUCLIDEndpointStudyRecordData,
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IUCLIDReferenceSubstanceData,
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IUCLIDSubstanceData,
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IUCLIDTransformationProductEntry,
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SoilPropertiesData,
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)
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def make_substance_data(**overrides) -> IUCLIDSubstanceData:
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payload = {
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"uuid": uuid4(),
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"name": "Atrazine",
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"reference_substance_uuid": uuid4(),
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}
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payload.update(overrides)
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return IUCLIDSubstanceData(**payload)
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def make_reference_substance_data(**overrides) -> IUCLIDReferenceSubstanceData:
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payload = {
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"uuid": uuid4(),
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"name": "Atrazine",
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"smiles": "CCNc1nc(Cl)nc(NC(C)C)n1",
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"cas_number": "1912-24-9",
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"ec_number": "217-617-8",
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"iupac_name": "6-chloro-N2-ethyl-N4-isopropyl-1,3,5-triazine-2,4-diamine",
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"molecular_formula": "C8H14ClN5",
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"molecular_weight": 215.68,
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"inchi": (
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"InChI=1S/C8H14ClN5/c1-4-10-7-12-6(9)11-8(13-7)"
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"14-5(2)3/h5H,4H2,1-3H3,(H2,10,11,12,13,14)"
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),
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"inchi_key": "MXWJVTOOROXGIU-UHFFFAOYSA-N",
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}
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payload.update(overrides)
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return IUCLIDReferenceSubstanceData(**payload)
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def make_half_life_entry(**overrides) -> HalfLifeEntry:
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payload = {
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"model": "SFO",
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"dt50_start": 12.5,
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"dt50_end": 15.0,
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"unit": "d",
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"source": "Model prediction",
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"soil_no_code": None,
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"temperature": None,
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}
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payload.update(overrides)
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return HalfLifeEntry(**payload)
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def make_transformation_entry(**overrides) -> IUCLIDTransformationProductEntry:
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payload = {
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"uuid": uuid4(),
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"product_reference_uuid": uuid4(),
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"parent_reference_uuids": [uuid4()],
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"kinetic_formation_fraction": 0.42,
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}
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payload.update(overrides)
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return IUCLIDTransformationProductEntry(**payload)
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def make_soil_properties_data(**overrides) -> SoilPropertiesData:
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payload = {
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"soil_no_code": None,
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"clay": 20.0,
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"silt": 30.0,
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"sand": 50.0,
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"org_carbon": 1.5,
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"ph_lower": 6.0,
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"ph_upper": 7.0,
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"ph_method": "CaCl2",
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"cec": 12.0,
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"moisture_content": 40.0,
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"soil_type": "LOAM",
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"soil_classification": "USDA",
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}
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payload.update(overrides)
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return SoilPropertiesData(**payload)
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def make_endpoint_study_record_data(**overrides) -> IUCLIDEndpointStudyRecordData:
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payload = {
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"uuid": uuid4(),
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"substance_uuid": uuid4(),
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"name": "Biodegradation study",
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"half_lives": [],
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"temperature": None,
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"transformation_products": [],
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"model_name_and_version": [],
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"software_name_and_version": [],
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"model_remarks": [],
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}
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payload.update(overrides)
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return IUCLIDEndpointStudyRecordData(**payload)
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