forked from enviPath/enviPy
[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:
0
epiuclid/builders/__init__.py
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0
epiuclid/builders/__init__.py
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105
epiuclid/builders/base.py
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105
epiuclid/builders/base.py
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import xml.etree.ElementTree as ET
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from datetime import datetime, timezone
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# IUCLID 6 XML namespaces
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NS_PLATFORM_CONTAINER = "http://iuclid6.echa.europa.eu/namespaces/platform-container/v2"
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NS_PLATFORM_METADATA = "http://iuclid6.echa.europa.eu/namespaces/platform-metadata/v1"
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NS_PLATFORM_FIELDS = "http://iuclid6.echa.europa.eu/namespaces/platform-fields/v1"
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NS_XLINK = "http://www.w3.org/1999/xlink"
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# Register namespace prefixes for clean output
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ET.register_namespace("i6c", NS_PLATFORM_CONTAINER)
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ET.register_namespace("i6m", NS_PLATFORM_METADATA)
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ET.register_namespace("i6", NS_PLATFORM_FIELDS)
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ET.register_namespace("xlink", NS_XLINK)
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IUCLID_VERSION = "6.0.0"
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DEFINITION_VERSION = "10.0"
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CREATION_TOOL = "enviPath"
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def _tag(ns: str, local: str) -> str:
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return f"{{{ns}}}{local}"
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def _sub(parent: ET.Element, ns: str, local: str, text: str | None = None) -> ET.Element:
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"""Create a sub-element under parent. Only sets text if not None."""
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elem = ET.SubElement(parent, _tag(ns, local))
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if text is not None:
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elem.text = str(text)
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return elem
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def _sub_if(parent: ET.Element, ns: str, local: str, text: str | None = None) -> ET.Element | None:
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"""Create a sub-element only when text is not None."""
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if text is None:
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return None
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return _sub(parent, ns, local, text)
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def build_platform_metadata(
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document_key: str,
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document_type: str,
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name: str,
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document_sub_type: str | None = None,
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parent_document_key: str | None = None,
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order_in_section_no: int | None = None,
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) -> ET.Element:
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"""Build the <i6c:PlatformMetadata> element for an i6d document."""
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pm = ET.Element(_tag(NS_PLATFORM_CONTAINER, "PlatformMetadata"))
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now = datetime.now(timezone.utc).strftime("%Y-%m-%dT%H:%M:%SZ")
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_sub(pm, NS_PLATFORM_METADATA, "iuclidVersion", IUCLID_VERSION)
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_sub(pm, NS_PLATFORM_METADATA, "documentKey", document_key)
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_sub(pm, NS_PLATFORM_METADATA, "documentType", document_type)
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_sub(pm, NS_PLATFORM_METADATA, "definitionVersion", DEFINITION_VERSION)
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_sub(pm, NS_PLATFORM_METADATA, "creationDate", now)
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_sub(pm, NS_PLATFORM_METADATA, "lastModificationDate", now)
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_sub(pm, NS_PLATFORM_METADATA, "name", name)
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if document_sub_type:
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_sub(pm, NS_PLATFORM_METADATA, "documentSubType", document_sub_type)
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if parent_document_key:
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_sub(pm, NS_PLATFORM_METADATA, "parentDocumentKey", parent_document_key)
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if order_in_section_no is not None:
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_sub(pm, NS_PLATFORM_METADATA, "orderInSectionNo", str(order_in_section_no))
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_sub(pm, NS_PLATFORM_METADATA, "i5Origin", "false")
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_sub(pm, NS_PLATFORM_METADATA, "creationTool", CREATION_TOOL)
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return pm
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def build_document(
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document_key: str,
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document_type: str,
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name: str,
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content_element: ET.Element,
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document_sub_type: str | None = None,
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parent_document_key: str | None = None,
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order_in_section_no: int | None = None,
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) -> str:
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"""Build a complete i6d document XML string."""
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root = ET.Element(_tag(NS_PLATFORM_CONTAINER, "Document"))
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pm = build_platform_metadata(
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document_key=document_key,
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document_type=document_type,
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name=name,
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document_sub_type=document_sub_type,
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parent_document_key=parent_document_key,
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order_in_section_no=order_in_section_no,
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)
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root.append(pm)
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content_wrapper = _sub(root, NS_PLATFORM_CONTAINER, "Content")
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content_wrapper.append(content_element)
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_sub(root, NS_PLATFORM_CONTAINER, "Attachments")
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_sub(root, NS_PLATFORM_CONTAINER, "ModificationHistory")
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return ET.tostring(root, encoding="unicode", xml_declaration=True)
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def document_key(uuid) -> str:
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"""Format a UUID as an IUCLID document key (uuid/0 for raw data)."""
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return f"{uuid}/0"
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259
epiuclid/builders/endpoint_study.py
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epiuclid/builders/endpoint_study.py
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import xml.etree.ElementTree as ET
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from uuid import uuid4
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from epiuclid.serializers.pathway_mapper import IUCLIDEndpointStudyRecordData, SoilPropertiesData
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from .base import (
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NS_PLATFORM_FIELDS,
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_sub,
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_tag,
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build_document,
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document_key,
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)
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NS_ESR_BIODEG = (
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"http://iuclid6.echa.europa.eu/namespaces/ENDPOINT_STUDY_RECORD-BiodegradationInSoil/10.0"
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)
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ET.register_namespace("", NS_ESR_BIODEG)
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DOC_SUBTYPE = "BiodegradationInSoil"
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PICKLIST_OTHER_CODE = "1342"
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SOIL_TYPE_CODE_BY_KEY = {
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"CLAY": "257",
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"CLAY_LOAM": "258",
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"LOAM": "1026",
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"LOAMY_SAND": "1027",
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"SAND": "1522",
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"SANDY_CLAY_LOAM": "1523",
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"SANDY_LOAM": "1524",
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"SANDY_CLAY": "1525",
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"SILT": "1549",
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"SILT_LOAM": "1550",
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"SILTY_CLAY": "1551",
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"SILTY_CLAY_LOAM": "1552",
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}
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SOIL_CLASSIFICATION_CODE_BY_KEY = {
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"USDA": "1649",
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"DE": "314",
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"INTERNATIONAL": "1658",
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}
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class EndpointStudyRecordBuilder:
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def build(self, data: IUCLIDEndpointStudyRecordData) -> str:
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esr = ET.Element(f"{{{NS_ESR_BIODEG}}}ENDPOINT_STUDY_RECORD.{DOC_SUBTYPE}")
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soil_entries = list(data.soil_properties_entries)
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if not soil_entries and data.soil_properties is not None:
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soil_entries = [data.soil_properties]
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has_materials = bool(
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data.model_name_and_version
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or data.software_name_and_version
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or data.model_remarks
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or soil_entries
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)
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if has_materials:
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materials = _sub(esr, NS_ESR_BIODEG, "MaterialsAndMethods")
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if soil_entries:
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self._build_soil_structured_full(materials, soil_entries)
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if data.model_name_and_version or data.software_name_and_version or data.model_remarks:
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model_info = _sub(materials, NS_ESR_BIODEG, "ModelAndSoftware")
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for model_name in data.model_name_and_version:
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_sub(model_info, NS_ESR_BIODEG, "ModelNameAndVersion", model_name)
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for software_name in data.software_name_and_version:
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_sub(model_info, NS_ESR_BIODEG, "SoftwareNameAndVersion", software_name)
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for remark in data.model_remarks:
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_sub(model_info, NS_ESR_BIODEG, "Remarks", remark)
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has_results = (
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data.half_lives or data.transformation_products or data.temperature is not None
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)
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if has_results:
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results = _sub(esr, NS_ESR_BIODEG, "ResultsAndDiscussion")
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if data.half_lives or data.temperature is not None:
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dt_parent = _sub(results, NS_ESR_BIODEG, "DTParentCompound")
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if data.half_lives:
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for hl in data.half_lives:
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entry = ET.SubElement(dt_parent, _tag(NS_ESR_BIODEG, "entry"))
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entry.set(_tag(NS_PLATFORM_FIELDS, "uuid"), str(uuid4()))
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if hl.soil_no_code:
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soil_no = _sub(entry, NS_ESR_BIODEG, "SoilNo")
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_sub(soil_no, NS_ESR_BIODEG, "value", hl.soil_no_code)
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value_range = _sub(entry, NS_ESR_BIODEG, "Value")
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_sub(value_range, NS_ESR_BIODEG, "unitCode", "2329") # days
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_sub(value_range, NS_ESR_BIODEG, "lowerValue", str(hl.dt50_start))
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_sub(value_range, NS_ESR_BIODEG, "upperValue", str(hl.dt50_end))
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temperature = (
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hl.temperature if hl.temperature is not None else data.temperature
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)
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if temperature is not None:
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temp_range = _sub(entry, NS_ESR_BIODEG, "Temp")
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_sub(temp_range, NS_ESR_BIODEG, "unitCode", "2493") # degree Celsius
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_sub(temp_range, NS_ESR_BIODEG, "lowerValue", str(temperature[0]))
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_sub(temp_range, NS_ESR_BIODEG, "upperValue", str(temperature[1]))
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_sub(entry, NS_ESR_BIODEG, "KineticParameters", hl.model)
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else:
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# Temperature without half-lives: single entry with only Temp
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assert data.temperature is not None
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entry = ET.SubElement(dt_parent, _tag(NS_ESR_BIODEG, "entry"))
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entry.set(_tag(NS_PLATFORM_FIELDS, "uuid"), str(uuid4()))
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temp_range = _sub(entry, NS_ESR_BIODEG, "Temp")
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_sub(temp_range, NS_ESR_BIODEG, "unitCode", "2493") # degree Celsius
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_sub(temp_range, NS_ESR_BIODEG, "lowerValue", str(data.temperature[0]))
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_sub(temp_range, NS_ESR_BIODEG, "upperValue", str(data.temperature[1]))
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if data.transformation_products:
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tp_details = _sub(results, NS_ESR_BIODEG, "TransformationProductsDetails")
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for tp in data.transformation_products:
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entry = ET.SubElement(tp_details, _tag(NS_ESR_BIODEG, "entry"))
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entry.set(_tag(NS_PLATFORM_FIELDS, "uuid"), str(tp.uuid))
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_sub(
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entry,
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NS_ESR_BIODEG,
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"IdentityOfCompound",
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document_key(tp.product_reference_uuid),
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)
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if tp.parent_reference_uuids:
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parents = _sub(entry, NS_ESR_BIODEG, "ParentCompoundS")
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for parent_uuid in tp.parent_reference_uuids:
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_sub(parents, NS_PLATFORM_FIELDS, "key", document_key(parent_uuid))
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if tp.kinetic_formation_fraction is not None:
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_sub(
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entry,
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NS_ESR_BIODEG,
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"KineticFormationFraction",
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str(tp.kinetic_formation_fraction),
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)
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doc_key = document_key(data.uuid)
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return build_document(
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document_key=doc_key,
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document_type="ENDPOINT_STUDY_RECORD",
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document_sub_type=DOC_SUBTYPE,
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name=data.name,
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content_element=esr,
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parent_document_key=document_key(data.substance_uuid),
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order_in_section_no=1,
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)
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@staticmethod
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def _build_soil_structured_full(
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materials: ET.Element,
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props_entries: list[SoilPropertiesData],
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) -> None:
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study_design = _sub(materials, NS_ESR_BIODEG, "StudyDesign")
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soil_classification = None
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for props in props_entries:
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soil_classification = EndpointStudyRecordBuilder._soil_classification(props)
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if soil_classification:
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break
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if soil_classification:
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soil_classification_el = _sub(study_design, NS_ESR_BIODEG, "SoilClassification")
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value, other = EndpointStudyRecordBuilder._picklist_value_and_other(
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soil_classification,
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SOIL_CLASSIFICATION_CODE_BY_KEY,
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)
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if value:
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_sub(soil_classification_el, NS_ESR_BIODEG, "value", value)
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if other:
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_sub(soil_classification_el, NS_ESR_BIODEG, "other", other)
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soil_props = _sub(study_design, NS_ESR_BIODEG, "SoilProperties")
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for props in props_entries:
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entry = ET.SubElement(soil_props, _tag(NS_ESR_BIODEG, "entry"))
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entry.set(_tag(NS_PLATFORM_FIELDS, "uuid"), str(uuid4()))
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if props.soil_no_code:
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soil_no = _sub(entry, NS_ESR_BIODEG, "SoilNo")
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_sub(soil_no, NS_ESR_BIODEG, "value", props.soil_no_code)
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soil_type = props.soil_type.strip() if props.soil_type else None
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if soil_type:
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soil_type_el = _sub(entry, NS_ESR_BIODEG, "SoilType")
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value, other = EndpointStudyRecordBuilder._picklist_value_and_other(
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soil_type,
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SOIL_TYPE_CODE_BY_KEY,
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)
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if value:
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_sub(soil_type_el, NS_ESR_BIODEG, "value", value)
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if other:
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_sub(soil_type_el, NS_ESR_BIODEG, "other", other)
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if props.clay is not None:
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clay_el = _sub(entry, NS_ESR_BIODEG, "Clay")
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_sub(clay_el, NS_ESR_BIODEG, "lowerValue", str(props.clay))
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if props.silt is not None:
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silt_el = _sub(entry, NS_ESR_BIODEG, "Silt")
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_sub(silt_el, NS_ESR_BIODEG, "lowerValue", str(props.silt))
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if props.sand is not None:
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sand_el = _sub(entry, NS_ESR_BIODEG, "Sand")
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_sub(sand_el, NS_ESR_BIODEG, "lowerValue", str(props.sand))
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if props.org_carbon is not None:
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orgc_el = _sub(entry, NS_ESR_BIODEG, "OrgC")
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_sub(orgc_el, NS_ESR_BIODEG, "lowerValue", str(props.org_carbon))
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if props.ph_lower is not None or props.ph_upper is not None:
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ph_el = _sub(entry, NS_ESR_BIODEG, "Ph")
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if props.ph_lower is not None:
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_sub(ph_el, NS_ESR_BIODEG, "lowerValue", str(props.ph_lower))
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if props.ph_upper is not None:
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_sub(ph_el, NS_ESR_BIODEG, "upperValue", str(props.ph_upper))
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ph_method = props.ph_method.strip() if props.ph_method else None
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if ph_method:
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_sub(entry, NS_ESR_BIODEG, "PHMeasuredIn", ph_method)
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if props.cec is not None:
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cec_el = _sub(entry, NS_ESR_BIODEG, "CEC")
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_sub(cec_el, NS_ESR_BIODEG, "lowerValue", str(props.cec))
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if props.moisture_content is not None:
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moisture_el = _sub(entry, NS_ESR_BIODEG, "MoistureContent")
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_sub(moisture_el, NS_ESR_BIODEG, "lowerValue", str(props.moisture_content))
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@staticmethod
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def _soil_classification(props: SoilPropertiesData) -> str | None:
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if props.soil_classification:
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value = props.soil_classification.strip()
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if value:
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return value
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if props.soil_type:
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return "USDA"
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return None
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@staticmethod
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def _picklist_value_and_other(
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raw_value: str,
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code_map: dict[str, str],
|
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) -> tuple[str | None, str | None]:
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value = raw_value.strip()
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if not value:
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return None, None
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key = value.upper().replace("-", "_").replace(" ", "_")
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code = code_map.get(key)
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if code is not None:
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return code, None
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return PICKLIST_OTHER_CODE, value.replace("_", " ")
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54
epiuclid/builders/reference_substance.py
Normal file
54
epiuclid/builders/reference_substance.py
Normal file
@ -0,0 +1,54 @@
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import xml.etree.ElementTree as ET
|
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|
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from epiuclid.serializers.pathway_mapper import IUCLIDReferenceSubstanceData
|
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|
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from .base import (
|
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_sub,
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_sub_if,
|
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build_document,
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document_key,
|
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)
|
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|
||||
NS_REFERENCE_SUBSTANCE = "http://iuclid6.echa.europa.eu/namespaces/REFERENCE_SUBSTANCE/10.0"
|
||||
ET.register_namespace("", NS_REFERENCE_SUBSTANCE)
|
||||
|
||||
|
||||
class ReferenceSubstanceBuilder:
|
||||
def build(self, data: IUCLIDReferenceSubstanceData) -> str:
|
||||
ref = ET.Element(f"{{{NS_REFERENCE_SUBSTANCE}}}REFERENCE_SUBSTANCE")
|
||||
|
||||
_sub(ref, NS_REFERENCE_SUBSTANCE, "ReferenceSubstanceName", data.name)
|
||||
_sub_if(ref, NS_REFERENCE_SUBSTANCE, "IupacName", data.iupac_name)
|
||||
if data.cas_number:
|
||||
inventory = _sub(ref, NS_REFERENCE_SUBSTANCE, "Inventory")
|
||||
_sub(inventory, NS_REFERENCE_SUBSTANCE, "CASNumber", data.cas_number)
|
||||
|
||||
has_structural_info = any(
|
||||
[
|
||||
data.molecular_formula,
|
||||
data.molecular_weight is not None,
|
||||
data.smiles,
|
||||
data.inchi,
|
||||
data.inchi_key,
|
||||
]
|
||||
)
|
||||
if has_structural_info:
|
||||
structural = _sub(ref, NS_REFERENCE_SUBSTANCE, "MolecularStructuralInfo")
|
||||
_sub_if(structural, NS_REFERENCE_SUBSTANCE, "MolecularFormula", data.molecular_formula)
|
||||
|
||||
if data.molecular_weight is not None:
|
||||
mw = _sub(structural, NS_REFERENCE_SUBSTANCE, "MolecularWeightRange")
|
||||
_sub(mw, NS_REFERENCE_SUBSTANCE, "lowerValue", f"{data.molecular_weight:.2f}")
|
||||
_sub(mw, NS_REFERENCE_SUBSTANCE, "upperValue", f"{data.molecular_weight:.2f}")
|
||||
|
||||
_sub_if(structural, NS_REFERENCE_SUBSTANCE, "SmilesNotation", data.smiles)
|
||||
_sub_if(structural, NS_REFERENCE_SUBSTANCE, "InChl", data.inchi)
|
||||
_sub_if(structural, NS_REFERENCE_SUBSTANCE, "InChIKey", data.inchi_key)
|
||||
|
||||
doc_key = document_key(data.uuid)
|
||||
return build_document(
|
||||
document_key=doc_key,
|
||||
document_type="REFERENCE_SUBSTANCE",
|
||||
name=data.name,
|
||||
content_element=ref,
|
||||
)
|
||||
37
epiuclid/builders/substance.py
Normal file
37
epiuclid/builders/substance.py
Normal file
@ -0,0 +1,37 @@
|
||||
import xml.etree.ElementTree as ET
|
||||
|
||||
from epiuclid.serializers.pathway_mapper import IUCLIDSubstanceData
|
||||
|
||||
from .base import (
|
||||
_sub,
|
||||
build_document,
|
||||
document_key,
|
||||
)
|
||||
|
||||
NS_SUBSTANCE = "http://iuclid6.echa.europa.eu/namespaces/SUBSTANCE/10.0"
|
||||
ET.register_namespace("", NS_SUBSTANCE)
|
||||
|
||||
|
||||
class SubstanceBuilder:
|
||||
def build(self, data: IUCLIDSubstanceData) -> str:
|
||||
substance = ET.Element(f"{{{NS_SUBSTANCE}}}SUBSTANCE")
|
||||
|
||||
_sub(substance, NS_SUBSTANCE, "Templates")
|
||||
_sub(substance, NS_SUBSTANCE, "ChemicalName", data.name)
|
||||
|
||||
if data.reference_substance_uuid:
|
||||
ref_sub = _sub(substance, NS_SUBSTANCE, "ReferenceSubstance")
|
||||
_sub(
|
||||
ref_sub,
|
||||
NS_SUBSTANCE,
|
||||
"ReferenceSubstance",
|
||||
document_key(data.reference_substance_uuid),
|
||||
)
|
||||
|
||||
doc_key = document_key(data.uuid)
|
||||
return build_document(
|
||||
document_key=doc_key,
|
||||
document_type="SUBSTANCE",
|
||||
name=data.name,
|
||||
content_element=substance,
|
||||
)
|
||||
Reference in New Issue
Block a user