[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

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@ -5,10 +5,12 @@ repos:
rev: v3.2.0 rev: v3.2.0
hooks: hooks:
- id: trailing-whitespace - id: trailing-whitespace
exclude: epiuclid/schemas/
- id: end-of-file-fixer - id: end-of-file-fixer
exclude: epiuclid/schemas/
- id: check-yaml - id: check-yaml
- id: check-added-large-files - id: check-added-large-files
exclude: ^static/images/|fixtures/ exclude: ^static/images/|^epiuclid/schemas/|^fixtures/
- repo: https://github.com/astral-sh/ruff-pre-commit - repo: https://github.com/astral-sh/ruff-pre-commit
rev: v0.13.3 rev: v0.13.3

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@ -45,6 +45,7 @@ INSTALLED_APPS = [
"django.contrib.sessions", "django.contrib.sessions",
"django.contrib.messages", "django.contrib.messages",
"django.contrib.staticfiles", "django.contrib.staticfiles",
"django.contrib.postgres",
# 3rd party # 3rd party
"django_extensions", "django_extensions",
"oauth2_provider", "oauth2_provider",
@ -362,6 +363,10 @@ if SENTRY_ENABLED:
before_send=before_send, before_send=before_send,
) )
IUCLID_EXPORT_ENABLED = os.environ.get("IUCLID_EXPORT_ENABLED", "False") == "True"
if IUCLID_EXPORT_ENABLED:
INSTALLED_APPS.append("epiuclid")
# compile into digestible flags # compile into digestible flags
FLAGS = { FLAGS = {
"MODEL_BUILDING": MODEL_BUILDING_ENABLED, "MODEL_BUILDING": MODEL_BUILDING_ENABLED,
@ -370,6 +375,7 @@ FLAGS = {
"SENTRY": SENTRY_ENABLED, "SENTRY": SENTRY_ENABLED,
"ENVIFORMER": ENVIFORMER_PRESENT, "ENVIFORMER": ENVIFORMER_PRESENT,
"APPLICABILITY_DOMAIN": APPLICABILITY_DOMAIN_ENABLED, "APPLICABILITY_DOMAIN": APPLICABILITY_DOMAIN_ENABLED,
"IUCLID_EXPORT": IUCLID_EXPORT_ENABLED,
} }
# path of the URL are checked via "startswith" # path of the URL are checked via "startswith"

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@ -74,7 +74,6 @@ class TestSchemaGeneration:
assert all(isinstance(g, str) for g in groups), ( assert all(isinstance(g, str) for g in groups), (
f"{model_name}: all groups should be strings, got {groups}" f"{model_name}: all groups should be strings, got {groups}"
) )
assert len(groups) > 0, f"{model_name}: should have at least one group"
@pytest.mark.parametrize("model_name,model_cls", list(registry.list_models().items())) @pytest.mark.parametrize("model_name,model_cls", list(registry.list_models().items()))
def test_form_data_matches_schema(self, model_name: str, model_cls: Type[BaseModel]): def test_form_data_matches_schema(self, model_name: str, model_cls: Type[BaseModel]):

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@ -1,10 +1,14 @@
from django.db.models import Model
from epdb.logic import PackageManager
from epdb.models import CompoundStructure, User, Package, Compound, Scenario
from uuid import UUID 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 from .errors import EPAPINotFoundError, EPAPIPermissionDeniedError
Package = s.GET_PACKAGE_MODEL()
def get_compound_for_read(user, compound_uuid: UUID): def get_compound_for_read(user, compound_uuid: UUID):
""" """

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@ -0,0 +1,3 @@
"""
Service interfaces: each subdirectory defines the full boundary contract between enviPy and feature-flagged apps. DTOs and projections are shared concerns to avoid direct ORM access.
"""

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@ -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

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@ -0,0 +1,142 @@
from uuid import UUID
from epdb.logic import PackageManager
from epdb.models import Pathway
from epapi.v1.errors import EPAPINotFoundError, EPAPIPermissionDeniedError
from .dto import (
PathwayCompoundDTO,
PathwayEdgeDTO,
PathwayExportDTO,
PathwayModelInfoDTO,
PathwayNodeDTO,
PathwayScenarioDTO,
)
def get_pathway_for_iuclid_export(user, pathway_uuid: UUID) -> PathwayExportDTO:
"""Return pathway data projected into DTOs for the IUCLID export consumer."""
try:
pathway = (
Pathway.objects.select_related("package", "setting", "setting__model")
.prefetch_related(
"node_set__default_node_label__compound__external_identifiers__database",
"node_set__scenarios",
"edge_set__start_nodes__default_node_label__compound",
"edge_set__end_nodes__default_node_label__compound",
)
.get(uuid=pathway_uuid)
)
except Pathway.DoesNotExist:
raise EPAPINotFoundError(f"Pathway with UUID {pathway_uuid} not found")
if not user or user.is_anonymous or not PackageManager.readable(user, pathway.package):
raise EPAPIPermissionDeniedError("Insufficient permissions to access this pathway.")
nodes: list[PathwayNodeDTO] = []
edges: list[PathwayEdgeDTO] = []
compounds_by_pk: dict[int, PathwayCompoundDTO] = {}
root_compound_pks: list[int] = []
for node in pathway.node_set.all().order_by("depth", "pk"):
cs = node.default_node_label
if cs is None:
continue
compound = cs.compound
cas_number = None
ec_number = None
for ext_id in compound.external_identifiers.all():
db_name = ext_id.database.name if ext_id.database else None
if db_name == "CAS" and cas_number is None:
cas_number = ext_id.identifier_value
elif db_name == "EC" and ec_number is None:
ec_number = ext_id.identifier_value
ai_for_node = []
scenario_entries: list[PathwayScenarioDTO] = []
for scenario in sorted(node.scenarios.all(), key=lambda item: item.pk):
ai_for_scenario = list(scenario.get_additional_information(direct_only=True))
ai_for_node.extend(ai_for_scenario)
scenario_entries.append(
PathwayScenarioDTO(
scenario_uuid=scenario.uuid,
name=scenario.name,
additional_info=ai_for_scenario,
)
)
nodes.append(
PathwayNodeDTO(
node_uuid=node.uuid,
compound_pk=compound.pk,
name=compound.name,
depth=node.depth,
smiles=cs.smiles,
cas_number=cas_number,
ec_number=ec_number,
additional_info=ai_for_node,
scenarios=scenario_entries,
)
)
if node.depth == 0 and compound.pk not in root_compound_pks:
root_compound_pks.append(compound.pk)
if compound.pk not in compounds_by_pk:
compounds_by_pk[compound.pk] = PathwayCompoundDTO(
pk=compound.pk,
name=compound.name,
smiles=cs.smiles,
cas_number=cas_number,
ec_number=ec_number,
)
for edge in pathway.edge_set.all():
start_compounds = {
n.default_node_label.compound.pk
for n in edge.start_nodes.all()
if n.default_node_label is not None
}
end_compounds = {
n.default_node_label.compound.pk
for n in edge.end_nodes.all()
if n.default_node_label is not None
}
probability = None
if edge.kv and edge.kv.get("probability") is not None:
try:
probability = float(edge.kv.get("probability"))
except (TypeError, ValueError):
probability = None
edges.append(
PathwayEdgeDTO(
edge_uuid=edge.uuid,
start_compound_pks=sorted(start_compounds),
end_compound_pks=sorted(end_compounds),
probability=probability,
)
)
model_info = None
if pathway.setting and pathway.setting.model:
model = pathway.setting.model
model_info = PathwayModelInfoDTO(
model_name=model.get_name(),
model_uuid=model.uuid,
software_name="enviPath",
software_version=None,
)
return PathwayExportDTO(
pathway_uuid=pathway.uuid,
pathway_name=pathway.get_name(),
compounds=list(compounds_by_pk.values()),
nodes=nodes,
edges=edges,
root_compound_pks=root_compound_pks,
model_info=model_info,
)

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@ -14,6 +14,7 @@ from .endpoints import (
additional_information, additional_information,
settings, settings,
) )
from envipath import settings as s
# Main router with authentication # Main router with authentication
router = Router( router = Router(
@ -34,3 +35,8 @@ router.add_router("", models.router)
router.add_router("", structure.router) router.add_router("", structure.router)
router.add_router("", additional_information.router) router.add_router("", additional_information.router)
router.add_router("", settings.router) router.add_router("", settings.router)
if s.IUCLID_EXPORT_ENABLED:
from epiuclid.api import router as iuclid_router
router.add_router("", iuclid_router)

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@ -4251,7 +4251,7 @@ class AdditionalInformation(models.Model):
# Generic FK must be complete or empty # Generic FK must be complete or empty
models.CheckConstraint( models.CheckConstraint(
name="ck_addinfo_gfk_pair", name="ck_addinfo_gfk_pair",
check=( condition=(
(Q(content_type__isnull=True) & Q(object_id__isnull=True)) (Q(content_type__isnull=True) & Q(object_id__isnull=True))
| (Q(content_type__isnull=False) & Q(object_id__isnull=False)) | (Q(content_type__isnull=False) & Q(object_id__isnull=False))
), ),
@ -4259,7 +4259,7 @@ class AdditionalInformation(models.Model):
# Disallow "floating" info # Disallow "floating" info
models.CheckConstraint( models.CheckConstraint(
name="ck_addinfo_not_both_null", name="ck_addinfo_not_both_null",
check=Q(scenario__isnull=False) | Q(content_type__isnull=False), condition=Q(scenario__isnull=False) | Q(content_type__isnull=False),
), ),
] ]

0
epiuclid/__init__.py Normal file
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22
epiuclid/api.py Normal file
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@ -0,0 +1,22 @@
from uuid import UUID
from django.http import HttpResponse
from ninja import Router
from epapi.v1.interfaces.iuclid.projections import get_pathway_for_iuclid_export
from .serializers.i6z import I6ZSerializer
from .serializers.pathway_mapper import PathwayMapper
router = Router(tags=["iuclid"])
@router.get("/pathway/{uuid:pathway_uuid}/export/iuclid")
def export_pathway_iuclid(request, pathway_uuid: UUID):
export = get_pathway_for_iuclid_export(request.user, pathway_uuid)
bundle = PathwayMapper().map(export)
i6z_bytes = I6ZSerializer().serialize(bundle)
return HttpResponse(
i6z_bytes,
content_type="application/zip",
headers={"Content-Disposition": f'attachment; filename="pathway-{pathway_uuid}.i6z"'},
)

6
epiuclid/apps.py Normal file
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@ -0,0 +1,6 @@
from django.apps import AppConfig
class EpiuclidConfig(AppConfig):
default_auto_field = "django.db.models.BigAutoField"
name = "epiuclid"

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105
epiuclid/builders/base.py Normal file
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@ -0,0 +1,105 @@
import xml.etree.ElementTree as ET
from datetime import datetime, timezone
# IUCLID 6 XML namespaces
NS_PLATFORM_CONTAINER = "http://iuclid6.echa.europa.eu/namespaces/platform-container/v2"
NS_PLATFORM_METADATA = "http://iuclid6.echa.europa.eu/namespaces/platform-metadata/v1"
NS_PLATFORM_FIELDS = "http://iuclid6.echa.europa.eu/namespaces/platform-fields/v1"
NS_XLINK = "http://www.w3.org/1999/xlink"
# Register namespace prefixes for clean output
ET.register_namespace("i6c", NS_PLATFORM_CONTAINER)
ET.register_namespace("i6m", NS_PLATFORM_METADATA)
ET.register_namespace("i6", NS_PLATFORM_FIELDS)
ET.register_namespace("xlink", NS_XLINK)
IUCLID_VERSION = "6.0.0"
DEFINITION_VERSION = "10.0"
CREATION_TOOL = "enviPath"
def _tag(ns: str, local: str) -> str:
return f"{{{ns}}}{local}"
def _sub(parent: ET.Element, ns: str, local: str, text: str | None = None) -> ET.Element:
"""Create a sub-element under parent. Only sets text if not None."""
elem = ET.SubElement(parent, _tag(ns, local))
if text is not None:
elem.text = str(text)
return elem
def _sub_if(parent: ET.Element, ns: str, local: str, text: str | None = None) -> ET.Element | None:
"""Create a sub-element only when text is not None."""
if text is None:
return None
return _sub(parent, ns, local, text)
def build_platform_metadata(
document_key: str,
document_type: str,
name: str,
document_sub_type: str | None = None,
parent_document_key: str | None = None,
order_in_section_no: int | None = None,
) -> ET.Element:
"""Build the <i6c:PlatformMetadata> element for an i6d document."""
pm = ET.Element(_tag(NS_PLATFORM_CONTAINER, "PlatformMetadata"))
now = datetime.now(timezone.utc).strftime("%Y-%m-%dT%H:%M:%SZ")
_sub(pm, NS_PLATFORM_METADATA, "iuclidVersion", IUCLID_VERSION)
_sub(pm, NS_PLATFORM_METADATA, "documentKey", document_key)
_sub(pm, NS_PLATFORM_METADATA, "documentType", document_type)
_sub(pm, NS_PLATFORM_METADATA, "definitionVersion", DEFINITION_VERSION)
_sub(pm, NS_PLATFORM_METADATA, "creationDate", now)
_sub(pm, NS_PLATFORM_METADATA, "lastModificationDate", now)
_sub(pm, NS_PLATFORM_METADATA, "name", name)
if document_sub_type:
_sub(pm, NS_PLATFORM_METADATA, "documentSubType", document_sub_type)
if parent_document_key:
_sub(pm, NS_PLATFORM_METADATA, "parentDocumentKey", parent_document_key)
if order_in_section_no is not None:
_sub(pm, NS_PLATFORM_METADATA, "orderInSectionNo", str(order_in_section_no))
_sub(pm, NS_PLATFORM_METADATA, "i5Origin", "false")
_sub(pm, NS_PLATFORM_METADATA, "creationTool", CREATION_TOOL)
return pm
def build_document(
document_key: str,
document_type: str,
name: str,
content_element: ET.Element,
document_sub_type: str | None = None,
parent_document_key: str | None = None,
order_in_section_no: int | None = None,
) -> str:
"""Build a complete i6d document XML string."""
root = ET.Element(_tag(NS_PLATFORM_CONTAINER, "Document"))
pm = build_platform_metadata(
document_key=document_key,
document_type=document_type,
name=name,
document_sub_type=document_sub_type,
parent_document_key=parent_document_key,
order_in_section_no=order_in_section_no,
)
root.append(pm)
content_wrapper = _sub(root, NS_PLATFORM_CONTAINER, "Content")
content_wrapper.append(content_element)
_sub(root, NS_PLATFORM_CONTAINER, "Attachments")
_sub(root, NS_PLATFORM_CONTAINER, "ModificationHistory")
return ET.tostring(root, encoding="unicode", xml_declaration=True)
def document_key(uuid) -> str:
"""Format a UUID as an IUCLID document key (uuid/0 for raw data)."""
return f"{uuid}/0"

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@ -0,0 +1,259 @@
import xml.etree.ElementTree as ET
from uuid import uuid4
from epiuclid.serializers.pathway_mapper import IUCLIDEndpointStudyRecordData, SoilPropertiesData
from .base import (
NS_PLATFORM_FIELDS,
_sub,
_tag,
build_document,
document_key,
)
NS_ESR_BIODEG = (
"http://iuclid6.echa.europa.eu/namespaces/ENDPOINT_STUDY_RECORD-BiodegradationInSoil/10.0"
)
ET.register_namespace("", NS_ESR_BIODEG)
DOC_SUBTYPE = "BiodegradationInSoil"
PICKLIST_OTHER_CODE = "1342"
SOIL_TYPE_CODE_BY_KEY = {
"CLAY": "257",
"CLAY_LOAM": "258",
"LOAM": "1026",
"LOAMY_SAND": "1027",
"SAND": "1522",
"SANDY_CLAY_LOAM": "1523",
"SANDY_LOAM": "1524",
"SANDY_CLAY": "1525",
"SILT": "1549",
"SILT_LOAM": "1550",
"SILTY_CLAY": "1551",
"SILTY_CLAY_LOAM": "1552",
}
SOIL_CLASSIFICATION_CODE_BY_KEY = {
"USDA": "1649",
"DE": "314",
"INTERNATIONAL": "1658",
}
class EndpointStudyRecordBuilder:
def build(self, data: IUCLIDEndpointStudyRecordData) -> str:
esr = ET.Element(f"{{{NS_ESR_BIODEG}}}ENDPOINT_STUDY_RECORD.{DOC_SUBTYPE}")
soil_entries = list(data.soil_properties_entries)
if not soil_entries and data.soil_properties is not None:
soil_entries = [data.soil_properties]
has_materials = bool(
data.model_name_and_version
or data.software_name_and_version
or data.model_remarks
or soil_entries
)
if has_materials:
materials = _sub(esr, NS_ESR_BIODEG, "MaterialsAndMethods")
if soil_entries:
self._build_soil_structured_full(materials, soil_entries)
if data.model_name_and_version or data.software_name_and_version or data.model_remarks:
model_info = _sub(materials, NS_ESR_BIODEG, "ModelAndSoftware")
for model_name in data.model_name_and_version:
_sub(model_info, NS_ESR_BIODEG, "ModelNameAndVersion", model_name)
for software_name in data.software_name_and_version:
_sub(model_info, NS_ESR_BIODEG, "SoftwareNameAndVersion", software_name)
for remark in data.model_remarks:
_sub(model_info, NS_ESR_BIODEG, "Remarks", remark)
has_results = (
data.half_lives or data.transformation_products or data.temperature is not None
)
if has_results:
results = _sub(esr, NS_ESR_BIODEG, "ResultsAndDiscussion")
if data.half_lives or data.temperature is not None:
dt_parent = _sub(results, NS_ESR_BIODEG, "DTParentCompound")
if data.half_lives:
for hl in data.half_lives:
entry = ET.SubElement(dt_parent, _tag(NS_ESR_BIODEG, "entry"))
entry.set(_tag(NS_PLATFORM_FIELDS, "uuid"), str(uuid4()))
if hl.soil_no_code:
soil_no = _sub(entry, NS_ESR_BIODEG, "SoilNo")
_sub(soil_no, NS_ESR_BIODEG, "value", hl.soil_no_code)
value_range = _sub(entry, NS_ESR_BIODEG, "Value")
_sub(value_range, NS_ESR_BIODEG, "unitCode", "2329") # days
_sub(value_range, NS_ESR_BIODEG, "lowerValue", str(hl.dt50_start))
_sub(value_range, NS_ESR_BIODEG, "upperValue", str(hl.dt50_end))
temperature = (
hl.temperature if hl.temperature is not None else data.temperature
)
if temperature is not None:
temp_range = _sub(entry, NS_ESR_BIODEG, "Temp")
_sub(temp_range, NS_ESR_BIODEG, "unitCode", "2493") # degree Celsius
_sub(temp_range, NS_ESR_BIODEG, "lowerValue", str(temperature[0]))
_sub(temp_range, NS_ESR_BIODEG, "upperValue", str(temperature[1]))
_sub(entry, NS_ESR_BIODEG, "KineticParameters", hl.model)
else:
# Temperature without half-lives: single entry with only Temp
assert data.temperature is not None
entry = ET.SubElement(dt_parent, _tag(NS_ESR_BIODEG, "entry"))
entry.set(_tag(NS_PLATFORM_FIELDS, "uuid"), str(uuid4()))
temp_range = _sub(entry, NS_ESR_BIODEG, "Temp")
_sub(temp_range, NS_ESR_BIODEG, "unitCode", "2493") # degree Celsius
_sub(temp_range, NS_ESR_BIODEG, "lowerValue", str(data.temperature[0]))
_sub(temp_range, NS_ESR_BIODEG, "upperValue", str(data.temperature[1]))
if data.transformation_products:
tp_details = _sub(results, NS_ESR_BIODEG, "TransformationProductsDetails")
for tp in data.transformation_products:
entry = ET.SubElement(tp_details, _tag(NS_ESR_BIODEG, "entry"))
entry.set(_tag(NS_PLATFORM_FIELDS, "uuid"), str(tp.uuid))
_sub(
entry,
NS_ESR_BIODEG,
"IdentityOfCompound",
document_key(tp.product_reference_uuid),
)
if tp.parent_reference_uuids:
parents = _sub(entry, NS_ESR_BIODEG, "ParentCompoundS")
for parent_uuid in tp.parent_reference_uuids:
_sub(parents, NS_PLATFORM_FIELDS, "key", document_key(parent_uuid))
if tp.kinetic_formation_fraction is not None:
_sub(
entry,
NS_ESR_BIODEG,
"KineticFormationFraction",
str(tp.kinetic_formation_fraction),
)
doc_key = document_key(data.uuid)
return build_document(
document_key=doc_key,
document_type="ENDPOINT_STUDY_RECORD",
document_sub_type=DOC_SUBTYPE,
name=data.name,
content_element=esr,
parent_document_key=document_key(data.substance_uuid),
order_in_section_no=1,
)
@staticmethod
def _build_soil_structured_full(
materials: ET.Element,
props_entries: list[SoilPropertiesData],
) -> None:
study_design = _sub(materials, NS_ESR_BIODEG, "StudyDesign")
soil_classification = None
for props in props_entries:
soil_classification = EndpointStudyRecordBuilder._soil_classification(props)
if soil_classification:
break
if soil_classification:
soil_classification_el = _sub(study_design, NS_ESR_BIODEG, "SoilClassification")
value, other = EndpointStudyRecordBuilder._picklist_value_and_other(
soil_classification,
SOIL_CLASSIFICATION_CODE_BY_KEY,
)
if value:
_sub(soil_classification_el, NS_ESR_BIODEG, "value", value)
if other:
_sub(soil_classification_el, NS_ESR_BIODEG, "other", other)
soil_props = _sub(study_design, NS_ESR_BIODEG, "SoilProperties")
for props in props_entries:
entry = ET.SubElement(soil_props, _tag(NS_ESR_BIODEG, "entry"))
entry.set(_tag(NS_PLATFORM_FIELDS, "uuid"), str(uuid4()))
if props.soil_no_code:
soil_no = _sub(entry, NS_ESR_BIODEG, "SoilNo")
_sub(soil_no, NS_ESR_BIODEG, "value", props.soil_no_code)
soil_type = props.soil_type.strip() if props.soil_type else None
if soil_type:
soil_type_el = _sub(entry, NS_ESR_BIODEG, "SoilType")
value, other = EndpointStudyRecordBuilder._picklist_value_and_other(
soil_type,
SOIL_TYPE_CODE_BY_KEY,
)
if value:
_sub(soil_type_el, NS_ESR_BIODEG, "value", value)
if other:
_sub(soil_type_el, NS_ESR_BIODEG, "other", other)
if props.clay is not None:
clay_el = _sub(entry, NS_ESR_BIODEG, "Clay")
_sub(clay_el, NS_ESR_BIODEG, "lowerValue", str(props.clay))
if props.silt is not None:
silt_el = _sub(entry, NS_ESR_BIODEG, "Silt")
_sub(silt_el, NS_ESR_BIODEG, "lowerValue", str(props.silt))
if props.sand is not None:
sand_el = _sub(entry, NS_ESR_BIODEG, "Sand")
_sub(sand_el, NS_ESR_BIODEG, "lowerValue", str(props.sand))
if props.org_carbon is not None:
orgc_el = _sub(entry, NS_ESR_BIODEG, "OrgC")
_sub(orgc_el, NS_ESR_BIODEG, "lowerValue", str(props.org_carbon))
if props.ph_lower is not None or props.ph_upper is not None:
ph_el = _sub(entry, NS_ESR_BIODEG, "Ph")
if props.ph_lower is not None:
_sub(ph_el, NS_ESR_BIODEG, "lowerValue", str(props.ph_lower))
if props.ph_upper is not None:
_sub(ph_el, NS_ESR_BIODEG, "upperValue", str(props.ph_upper))
ph_method = props.ph_method.strip() if props.ph_method else None
if ph_method:
_sub(entry, NS_ESR_BIODEG, "PHMeasuredIn", ph_method)
if props.cec is not None:
cec_el = _sub(entry, NS_ESR_BIODEG, "CEC")
_sub(cec_el, NS_ESR_BIODEG, "lowerValue", str(props.cec))
if props.moisture_content is not None:
moisture_el = _sub(entry, NS_ESR_BIODEG, "MoistureContent")
_sub(moisture_el, NS_ESR_BIODEG, "lowerValue", str(props.moisture_content))
@staticmethod
def _soil_classification(props: SoilPropertiesData) -> str | None:
if props.soil_classification:
value = props.soil_classification.strip()
if value:
return value
if props.soil_type:
return "USDA"
return None
@staticmethod
def _picklist_value_and_other(
raw_value: str,
code_map: dict[str, str],
) -> tuple[str | None, str | None]:
value = raw_value.strip()
if not value:
return None, None
key = value.upper().replace("-", "_").replace(" ", "_")
code = code_map.get(key)
if code is not None:
return code, None
return PICKLIST_OTHER_CODE, value.replace("_", " ")

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import xml.etree.ElementTree as ET
from epiuclid.serializers.pathway_mapper import IUCLIDReferenceSubstanceData
from .base import (
_sub,
_sub_if,
build_document,
document_key,
)
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,
)

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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,
)

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"""Load and cache IUCLID XSD schemas with cross-reference resolution.
The bundled XSD schemas use bare ``schemaLocation`` filenames (e.g.
``platform-fields.xsd``, ``commonTypesDomainV10.xsd``) that don't match the
actual directory layout. This module builds an explicit namespace → file-path
mapping so that ``xmlschema`` can resolve every import.
"""
from __future__ import annotations
from functools import lru_cache
from pathlib import Path
import xmlschema
_SCHEMA_ROOT = Path(__file__).resolve().parent / "v10"
# Namespace → relative file-path (from _SCHEMA_ROOT) for schemas that are
# referenced by bare filename from subdirectories that don't contain them.
_NS_LOCATIONS: dict[str, str] = {
"http://iuclid6.echa.europa.eu/namespaces/platform-fields/v1": "platform-fields.xsd",
"http://iuclid6.echa.europa.eu/namespaces/platform-metadata/v1": "platform-metadata.xsd",
"http://iuclid6.echa.europa.eu/namespaces/platform-container/v2": "platform-container-v2.xsd",
"http://iuclid6.echa.europa.eu/namespaces/platform-attachment/v1": "platform-attachment.xsd",
"http://iuclid6.echa.europa.eu/namespaces/platform-modification-history/v1": (
"platform-modification-history.xsd"
),
"http://www.w3.org/1999/xlink": "xlink.xsd",
"http://www.w3.org/XML/1998/namespace": "xml.xsd",
"http://iuclid6.echa.europa.eu/namespaces/domain/v10": ("domain/v10/commonTypesDomainV10.xsd"),
"http://iuclid6.echa.europa.eu/namespaces/oecd/v10": ("oecd/v10/commonTypesOecdV10.xsd"),
}
# doc_type → (subdir, filename-pattern)
_DOC_TYPE_PATHS: dict[str, tuple[str, str]] = {
"SUBSTANCE": ("domain/v10", "SUBSTANCE-10.0.xsd"),
"REFERENCE_SUBSTANCE": ("domain/v10", "REFERENCE_SUBSTANCE-10.0.xsd"),
}
def _absolute_locations() -> list[tuple[str, str]]:
"""Return (namespace, absolute-file-URI) pairs for all known schemas."""
return [(ns, (_SCHEMA_ROOT / rel).as_uri()) for ns, rel in _NS_LOCATIONS.items()]
def _esr_path(subtype: str) -> Path:
"""Return the path to an Endpoint Study Record schema."""
return _SCHEMA_ROOT / "oecd" / "v10" / f"ENDPOINT_STUDY_RECORD-{subtype}-10.0.xsd"
def _doc_type_path(doc_type: str, subtype: str | None = None) -> Path:
if doc_type == "ENDPOINT_STUDY_RECORD":
if not subtype:
raise ValueError("subtype is required for ENDPOINT_STUDY_RECORD schemas")
return _esr_path(subtype)
info = _DOC_TYPE_PATHS.get(doc_type)
if info is None:
raise ValueError(f"Unknown document type: {doc_type}")
subdir, filename = info
return _SCHEMA_ROOT / subdir / filename
@lru_cache(maxsize=32)
def get_content_schema(doc_type: str, subtype: str | None = None) -> xmlschema.XMLSchema:
"""Return a compiled XSD schema for validating content elements.
Parameters
----------
doc_type:
IUCLID document type (``SUBSTANCE``, ``REFERENCE_SUBSTANCE``,
``ENDPOINT_STUDY_RECORD``).
subtype:
Required for ``ENDPOINT_STUDY_RECORD`` (e.g. ``BiodegradationInSoil``).
"""
path = _doc_type_path(doc_type, subtype)
return xmlschema.XMLSchema(str(path), locations=_absolute_locations())
@lru_cache(maxsize=1)
def get_document_schema() -> xmlschema.XMLSchema:
"""Return a compiled XSD schema for the ``platform-container-v2`` wrapper.
This validates the full ``<Document>`` element (PlatformMetadata + Content +
Attachments + ModificationHistory). Content is validated with
``processContents="strict"`` via ``xs:any``, but only if the content
namespace has been loaded. For full content validation, use
:func:`get_content_schema` separately.
"""
path = _SCHEMA_ROOT / "platform-container-v2.xsd"
return xmlschema.XMLSchema(str(path), locations=_absolute_locations())

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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns="http://iuclid6.echa.europa.eu/namespaces/REFERENCE_SUBSTANCE/10.0" xmlns:ct="http://iuclid6.echa.europa.eu/namespaces/domain/v10" xmlns:i6="http://iuclid6.echa.europa.eu/namespaces/platform-fields/v1" attributeFormDefault="qualified" elementFormDefault="qualified" targetNamespace="http://iuclid6.echa.europa.eu/namespaces/REFERENCE_SUBSTANCE/10.0">
<xs:import namespace="http://iuclid6.echa.europa.eu/namespaces/platform-fields/v1" schemaLocation="platform-fields.xsd"/>
<xs:import namespace="http://iuclid6.echa.europa.eu/namespaces/domain/v10" schemaLocation="commonTypesDomainV10.xsd"/>
<xs:element name="REFERENCE_SUBSTANCE">
<xs:complexType>
<xs:sequence>
<xs:element minOccurs="0" name="DataProtection">
<xs:complexType>
<xs:complexContent>
<xs:extension base="i6:baseDataProtectionField">
<xs:sequence>
<xs:element minOccurs="0" name="confidentiality" type="ct:N64"/>
<xs:element minOccurs="0" name="justification" type="i6:textField"/>
<xs:element maxOccurs="unbounded" minOccurs="0" name="legislation">
<xs:complexType>
<xs:sequence>
<xs:element minOccurs="0" name="value" type="ct:N78"/>
<xs:element minOccurs="0" name="other" type="i6:textFieldSmall"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element name="ReferenceSubstanceName">
<xs:simpleType>
<xs:restriction base="i6:textFieldMultiLine">
<xs:minLength value="1"/>
</xs:restriction>
</xs:simpleType>
</xs:element>
<xs:element minOccurs="0" name="IupacName" type="i6:textFieldMultiLine"/>
<xs:element maxOccurs="unbounded" minOccurs="0" name="Description" type="i6:multilingualTextFieldLarge"/>
<xs:element minOccurs="0" name="Inventory">
<xs:complexType>
<xs:sequence>
<xs:element minOccurs="0" name="InventoryEntry">
<xs:complexType>
<xs:sequence>
<xs:element maxOccurs="unbounded" minOccurs="0" name="entry" type="i6:inventoryEntry"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element minOccurs="0" name="InventoryEntryJustification">
<xs:complexType>
<xs:complexContent>
<xs:extension base="i6:basePicklistField">
<xs:sequence>
<xs:element minOccurs="0" name="value" type="ct:N95"/>
<xs:element maxOccurs="unbounded" minOccurs="0" name="other" type="i6:multilingualTextFieldSmall"/>
<xs:element maxOccurs="unbounded" minOccurs="0" name="remarks" type="i6:multilingualTextField"/>
</xs:sequence>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element minOccurs="0" name="CASNumber" type="i6:textFieldSmall"/>
<xs:element minOccurs="0" name="CASName" type="i6:textFieldMultiLine"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element minOccurs="0" name="Synonyms">
<xs:complexType>
<xs:sequence>
<xs:element minOccurs="0" name="Synonyms">
<xs:complexType>
<xs:sequence>
<xs:element maxOccurs="unbounded" minOccurs="0" name="entry">
<xs:complexType>
<xs:complexContent>
<xs:extension base="i6:repeatableEntryType">
<xs:sequence>
<xs:element minOccurs="0" name="DataProtection">
<xs:complexType>
<xs:complexContent>
<xs:extension base="i6:baseDataProtectionField">
<xs:sequence>
<xs:element minOccurs="0" name="confidentiality" type="ct:N64"/>
<xs:element minOccurs="0" name="justification" type="i6:textField"/>
<xs:element maxOccurs="unbounded" minOccurs="0" name="legislation">
<xs:complexType>
<xs:sequence>
<xs:element minOccurs="0" name="value" type="ct:N78"/>
<xs:element minOccurs="0" name="other" type="i6:textFieldSmall"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element minOccurs="0" name="Identifier">
<xs:complexType>
<xs:complexContent>
<xs:extension base="i6:basePicklistField">
<xs:sequence>
<xs:element minOccurs="0" name="value" type="ct:PG6_60192"/>
<xs:element maxOccurs="unbounded" minOccurs="0" name="other" type="i6:multilingualTextFieldSmall"/>
</xs:sequence>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element minOccurs="0" name="Name" type="i6:textFieldMultiLine"/>
<xs:element maxOccurs="unbounded" minOccurs="0" name="Remarks" type="i6:multilingualTextFieldSmall"/>
</xs:sequence>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element minOccurs="0" name="MolecularStructuralInfo">
<xs:complexType>
<xs:sequence>
<xs:element minOccurs="0" name="DataProtection">
<xs:complexType>
<xs:complexContent>
<xs:extension base="i6:baseDataProtectionField">
<xs:sequence>
<xs:element minOccurs="0" name="confidentiality" type="ct:N64"/>
<xs:element minOccurs="0" name="justification" type="i6:textField"/>
<xs:element maxOccurs="unbounded" minOccurs="0" name="legislation">
<xs:complexType>
<xs:sequence>
<xs:element minOccurs="0" name="value" type="ct:N78"/>
<xs:element minOccurs="0" name="other" type="i6:textFieldSmall"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element minOccurs="0" name="MolecularFormula" type="i6:textFieldMultiLine"/>
<xs:element minOccurs="0" name="MolecularWeightRange">
<xs:complexType>
<xs:complexContent>
<xs:extension base="i6:basePhysicalQuantityRangeField">
<xs:sequence>
<xs:element minOccurs="0" name="lowerQualifier" type="i6:lowerQualifier"/>
<xs:element minOccurs="0" name="upperQualifier" type="i6:upperQualifier"/>
<xs:element minOccurs="0" name="lowerValue" type="xs:decimal"/>
<xs:element minOccurs="0" name="upperValue" type="xs:decimal"/>
</xs:sequence>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element minOccurs="0" name="SmilesNotation" type="i6:textFieldMultiLine"/>
<xs:element minOccurs="0" name="InChl" type="i6:textFieldMultiLine"/>
<xs:element maxOccurs="unbounded" minOccurs="0" name="InChIKey" type="i6:multilingualTextFieldSmall"/>
<xs:element minOccurs="0" name="StructuralFormula" type="i6:attachmentField"/>
<xs:element maxOccurs="unbounded" minOccurs="0" name="Remarks" type="i6:multilingualTextFieldLarge"/>
<xs:element minOccurs="0" name="ChemicalStructureFiles">
<xs:complexType>
<xs:sequence>
<xs:element maxOccurs="unbounded" minOccurs="0" name="entry">
<xs:complexType>
<xs:complexContent>
<xs:extension base="i6:repeatableEntryType">
<xs:sequence>
<xs:element minOccurs="0" name="StructureFile" type="i6:attachmentField"/>
<xs:element maxOccurs="unbounded" minOccurs="0" name="RemarksChemStruct" type="i6:multilingualTextFieldSmall"/>
</xs:sequence>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element minOccurs="0" name="RelatedSubstances">
<xs:complexType>
<xs:sequence>
<xs:element minOccurs="0" name="RelatedSubstances">
<xs:complexType>
<xs:sequence>
<xs:element maxOccurs="unbounded" minOccurs="0" name="entry">
<xs:complexType>
<xs:complexContent>
<xs:extension base="i6:repeatableEntryType">
<xs:sequence>
<xs:element minOccurs="0" name="Identifier">
<xs:complexType>
<xs:complexContent>
<xs:extension base="i6:basePicklistField">
<xs:sequence>
<xs:element minOccurs="0" name="value" type="ct:PG6_60192"/>
<xs:element maxOccurs="unbounded" minOccurs="0" name="other" type="i6:multilingualTextFieldSmall"/>
</xs:sequence>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element minOccurs="0" name="Identity" type="i6:textFieldLarge"/>
<xs:element maxOccurs="unbounded" minOccurs="0" name="Remarks" type="i6:multilingualTextFieldSmall"/>
<xs:element minOccurs="0" name="Relation">
<xs:complexType>
<xs:complexContent>
<xs:extension base="i6:basePicklistField">
<xs:sequence>
<xs:element minOccurs="0" name="value" type="ct:N05"/>
<xs:element maxOccurs="unbounded" minOccurs="0" name="other" type="i6:multilingualTextFieldSmall"/>
</xs:sequence>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element maxOccurs="unbounded" minOccurs="0" name="GroupCategoryInfo" type="i6:multilingualTextFieldMultiLine"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:schema>

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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns="http://iuclid6.echa.europa.eu/namespaces/SUBSTANCE/10.0" xmlns:ct="http://iuclid6.echa.europa.eu/namespaces/domain/v10" xmlns:i6="http://iuclid6.echa.europa.eu/namespaces/platform-fields/v1" attributeFormDefault="qualified" elementFormDefault="qualified" targetNamespace="http://iuclid6.echa.europa.eu/namespaces/SUBSTANCE/10.0">
<xs:import namespace="http://iuclid6.echa.europa.eu/namespaces/platform-fields/v1" schemaLocation="platform-fields.xsd"/>
<xs:import namespace="http://iuclid6.echa.europa.eu/namespaces/domain/v10" schemaLocation="commonTypesDomainV10.xsd"/>
<xs:element name="SUBSTANCE">
<xs:complexType>
<xs:sequence>
<xs:element name="Templates">
<xs:complexType>
<xs:sequence>
<xs:element maxOccurs="unbounded" minOccurs="0" name="Template" type="xs:string"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="ChemicalName">
<xs:simpleType>
<xs:restriction base="i6:textFieldMultiLine">
<xs:minLength value="1"/>
</xs:restriction>
</xs:simpleType>
</xs:element>
<xs:element minOccurs="0" name="PublicName" type="i6:textFieldMultiLine"/>
<xs:element minOccurs="0" name="OtherNames">
<xs:complexType>
<xs:sequence>
<xs:element maxOccurs="unbounded" minOccurs="0" name="entry">
<xs:complexType>
<xs:complexContent>
<xs:extension base="i6:repeatableEntryType">
<xs:sequence>
<xs:element minOccurs="0" name="DataProtection">
<xs:complexType>
<xs:complexContent>
<xs:extension base="i6:baseDataProtectionField">
<xs:sequence>
<xs:element minOccurs="0" name="confidentiality" type="ct:N64"/>
<xs:element minOccurs="0" name="justification" type="i6:textField"/>
<xs:element maxOccurs="unbounded" minOccurs="0" name="legislation">
<xs:complexType>
<xs:sequence>
<xs:element minOccurs="0" name="value" type="ct:N78"/>
<xs:element minOccurs="0" name="other" type="i6:textFieldSmall"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element minOccurs="0" name="NameType">
<xs:complexType>
<xs:complexContent>
<xs:extension base="i6:basePicklistField">
<xs:sequence>
<xs:element minOccurs="0" name="value" type="ct:N97"/>
<xs:element maxOccurs="unbounded" minOccurs="0" name="other" type="i6:multilingualTextFieldSmall"/>
</xs:sequence>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element minOccurs="0" name="Name" type="i6:textFieldMultiLine"/>
<xs:element maxOccurs="unbounded" minOccurs="0" name="Country">
<xs:complexType>
<xs:complexContent>
<xs:extension base="i6:basePicklistField">
<xs:sequence>
<xs:element minOccurs="0" name="value" type="ct:A31"/>
<xs:element maxOccurs="unbounded" minOccurs="0" name="other" type="i6:multilingualTextFieldSmall"/>
</xs:sequence>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element minOccurs="0" name="Relation">
<xs:complexType>
<xs:complexContent>
<xs:extension base="i6:basePicklistField">
<xs:sequence>
<xs:element minOccurs="0" name="value" type="ct:PG6_60200"/>
<xs:element maxOccurs="unbounded" minOccurs="0" name="other" type="i6:multilingualTextFieldSmall"/>
</xs:sequence>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element maxOccurs="unbounded" minOccurs="0" name="Remarks" type="i6:multilingualTextFieldLarge"/>
</xs:sequence>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element minOccurs="0" name="OwnerLegalEntityProtection">
<xs:complexType>
<xs:complexContent>
<xs:extension base="i6:baseDataProtectionField">
<xs:sequence>
<xs:element minOccurs="0" name="confidentiality" type="ct:N64"/>
<xs:element minOccurs="0" name="justification" type="i6:textField"/>
<xs:element maxOccurs="unbounded" minOccurs="0" name="legislation">
<xs:complexType>
<xs:sequence>
<xs:element minOccurs="0" name="value" type="ct:N78"/>
<xs:element minOccurs="0" name="other" type="i6:textFieldSmall"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element minOccurs="0" name="OwnerLegalEntity" type="i6:documentReferenceField"/>
<xs:element minOccurs="0" name="ThirdPartyProtection">
<xs:complexType>
<xs:complexContent>
<xs:extension base="i6:baseDataProtectionField">
<xs:sequence>
<xs:element minOccurs="0" name="confidentiality" type="ct:N64"/>
<xs:element minOccurs="0" name="justification" type="i6:textField"/>
<xs:element maxOccurs="unbounded" minOccurs="0" name="legislation">
<xs:complexType>
<xs:sequence>
<xs:element minOccurs="0" name="value" type="ct:N78"/>
<xs:element minOccurs="0" name="other" type="i6:textFieldSmall"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element minOccurs="0" name="ThirdParty" type="i6:documentReferenceField"/>
<xs:element minOccurs="0" name="ContactPersons">
<xs:complexType>
<xs:sequence>
<xs:element maxOccurs="unbounded" minOccurs="0" name="entry">
<xs:complexType>
<xs:complexContent>
<xs:extension base="i6:repeatableEntryType">
<xs:sequence>
<xs:element minOccurs="0" name="DataProtection">
<xs:complexType>
<xs:complexContent>
<xs:extension base="i6:baseDataProtectionField">
<xs:sequence>
<xs:element minOccurs="0" name="confidentiality" type="ct:N64"/>
<xs:element minOccurs="0" name="justification" type="i6:textField"/>
<xs:element maxOccurs="unbounded" minOccurs="0" name="legislation">
<xs:complexType>
<xs:sequence>
<xs:element minOccurs="0" name="value" type="ct:N78"/>
<xs:element minOccurs="0" name="other" type="i6:textFieldSmall"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element minOccurs="0" name="ContactPerson" type="i6:documentReferenceField"/>
</xs:sequence>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element minOccurs="0" name="ReferenceSubstance">
<xs:complexType>
<xs:sequence>
<xs:element minOccurs="0" name="Protection">
<xs:complexType>
<xs:complexContent>
<xs:extension base="i6:baseDataProtectionField">
<xs:sequence>
<xs:element minOccurs="0" name="confidentiality" type="ct:N64"/>
<xs:element minOccurs="0" name="justification" type="i6:textField"/>
<xs:element maxOccurs="unbounded" minOccurs="0" name="legislation">
<xs:complexType>
<xs:sequence>
<xs:element minOccurs="0" name="value" type="ct:N78"/>
<xs:element minOccurs="0" name="other" type="i6:textFieldSmall"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element minOccurs="0" name="ReferenceSubstance" type="i6:documentReferenceField"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element minOccurs="0" name="TypeOfSubstance">
<xs:complexType>
<xs:sequence>
<xs:element minOccurs="0" name="Composition">
<xs:complexType>
<xs:complexContent>
<xs:extension base="i6:basePicklistField">
<xs:sequence>
<xs:element minOccurs="0" name="value" type="ct:N08"/>
<xs:element maxOccurs="unbounded" minOccurs="0" name="other" type="i6:multilingualTextFieldSmall"/>
</xs:sequence>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element minOccurs="0" name="Origin">
<xs:complexType>
<xs:complexContent>
<xs:extension base="i6:basePicklistField">
<xs:sequence>
<xs:element minOccurs="0" name="value" type="ct:N58"/>
<xs:element maxOccurs="unbounded" minOccurs="0" name="other" type="i6:multilingualTextFieldSmall"/>
</xs:sequence>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element minOccurs="0" name="RoleInSupplyChain">
<xs:complexType>
<xs:sequence>
<xs:element minOccurs="0" name="RoleProtection">
<xs:complexType>
<xs:complexContent>
<xs:extension base="i6:baseDataProtectionField">
<xs:sequence>
<xs:element minOccurs="0" name="confidentiality" type="ct:N64"/>
<xs:element minOccurs="0" name="justification" type="i6:textField"/>
<xs:element maxOccurs="unbounded" minOccurs="0" name="legislation">
<xs:complexType>
<xs:sequence>
<xs:element minOccurs="0" name="value" type="ct:N78"/>
<xs:element minOccurs="0" name="other" type="i6:textFieldSmall"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element minOccurs="0" name="Manufacturer" nillable="true" type="i6:booleanField"/>
<xs:element minOccurs="0" name="Importer" nillable="true" type="i6:booleanField"/>
<xs:element minOccurs="0" name="OnlyRepresentative" nillable="true" type="i6:booleanField"/>
<xs:element minOccurs="0" name="DownstreamUser" nillable="true" type="i6:booleanField"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:schema>

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<?xml version="1.0" encoding="UTF-8"?>
<xs:schema xmlns="http://iuclid6.echa.europa.eu/namespaces/platform-attachment/v1"
xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xlink="http://www.w3.org/1999/xlink"
targetNamespace="http://iuclid6.echa.europa.eu/namespaces/platform-attachment/v1"
elementFormDefault="qualified" attributeFormDefault="qualified">
<xs:annotation>
<xs:appinfo>XML Schema Definition of the IUCLID6 Attachment entity</xs:appinfo>
</xs:annotation>
<xs:import namespace="http://www.w3.org/1999/xlink" schemaLocation="xlink.xsd"/>
<xs:element name="Attachment">
<xs:annotation>
<xs:documentation>Defines the attachment metadata information</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:all>
<xs:element name="documentKey" type="xs:string">
<xs:annotation>
<xs:documentation>The unique identifier of the attachment</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="name" type="xs:string">
<xs:annotation>
<xs:documentation>The name of the uploaded attachment</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="creationDate" type="xs:dateTime">
<xs:annotation>
<xs:documentation>The date that the attachment was created</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="lastModificationDate" type="xs:dateTime">
<xs:annotation>
<xs:documentation>The last modification date of the attachment</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="remarks" type="xs:string" minOccurs="0">
<xs:annotation>
<xs:documentation>The remarks provided by the user during the attachment uploading</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="md5" type="xs:string">
<xs:annotation>
<xs:documentation>The MD5 hash of the uploaded attachment content</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="mimetype" type="xs:string" minOccurs="0">
<xs:annotation>
<xs:documentation>The media type of the attachment content</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element type="xs:boolean" name="symbolic" minOccurs="0">
<xs:annotation>
<xs:documentation>Indicates that the actual attachment file is not included in the i6z file</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="content" minOccurs="0">
<xs:annotation>
<xs:documentation>The name/location of the attachment binary under the "attachments" directory inside the i6z archive file</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:attribute ref="xlink:type"/>
<xs:attribute ref="xlink:href"/>
</xs:complexType>
</xs:element>
</xs:all>
</xs:complexType>
</xs:element>
<xs:element name="AttachmentRef" type="xs:string">
<xs:annotation>
<xs:documentation>Specifies the unique identifier of an attachment that is directly linked to a IUCLID6 document</xs:documentation>
</xs:annotation>
</xs:element>
</xs:schema>

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<?xml version="1.0" encoding="UTF-8"?>
<xs:schema xmlns="http://iuclid6.echa.europa.eu/namespaces/platform-container/v2"
xmlns:xs="http://www.w3.org/2001/XMLSchema"
xmlns:pm="http://iuclid6.echa.europa.eu/namespaces/platform-metadata/v1"
xmlns:att="http://iuclid6.echa.europa.eu/namespaces/platform-attachment/v1"
xmlns:mh="http://iuclid6.echa.europa.eu/namespaces/platform-modification-history/v1"
targetNamespace="http://iuclid6.echa.europa.eu/namespaces/platform-container/v2"
elementFormDefault="qualified" attributeFormDefault="qualified">
<xs:import namespace="http://iuclid6.echa.europa.eu/namespaces/platform-metadata/v1" schemaLocation="platform-metadata.xsd"/>
<xs:import namespace="http://iuclid6.echa.europa.eu/namespaces/platform-attachment/v1" schemaLocation="platform-attachment.xsd"/>
<xs:import namespace="http://iuclid6.echa.europa.eu/namespaces/platform-modification-history/v1" schemaLocation="platform-modification-history.xsd"/>
<xs:annotation>
<xs:appinfo>XML Schema Definition of the IUCLID6 Document entity</xs:appinfo>
</xs:annotation>
<xs:element name="Document">
<xs:annotation>
<xs:documentation>Contains top-level information concerning the IUCLID6 document along with the document's actual chemical information content</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:sequence>
<xs:element name="PlatformMetadata">
<xs:annotation>
<xs:documentation>Contains the top-level information of a IUCLID6 document such as document identifier, name, type and subtype, etc.
<br/><br/>
The elements are included in the platform-metadata.xsd</xs:documentation>
</xs:annotation>
<xs:complexType >
<xs:all minOccurs="0">
<xs:element ref="pm:iuclidVersion" minOccurs="0" />
<xs:element ref="pm:documentKey" minOccurs="0" />
<xs:element ref="pm:documentType" />
<xs:element ref="pm:definitionVersion" minOccurs="0" />
<xs:element ref="pm:creationDate" />
<xs:element ref="pm:lastModificationDate" />
<xs:element ref="pm:name" minOccurs="0" />
<xs:element ref="pm:documentSubType" minOccurs="0" />
<xs:element ref="pm:parentDocumentKey" minOccurs="0" />
<xs:element ref="pm:orderInSectionNo" minOccurs="0" />
<xs:element ref="pm:submissionType" minOccurs="0" />
<xs:element ref="pm:submissionTypeVersion" minOccurs="0" />
<xs:element ref="pm:submittingLegalEntity" minOccurs="0" />
<xs:element ref="pm:dossierSubject" minOccurs="0" />
<xs:element ref="pm:i5Origin" minOccurs="0" />
<xs:element ref="pm:creationTool" minOccurs="0" />
<xs:element ref="pm:snapshotCreationTool" minOccurs="0" />
</xs:all>
</xs:complexType>
</xs:element>
<xs:element name="Content">
<xs:annotation>
<xs:documentation>Contains the chemical information of the specific IUCLID6 document.
<br/><br/>
The content is dynamic and is defined in the corresponding .xsd per document definition identifier.
in the form of "document_type"-"document_subtype"-"version".xsd.
Example: ENDPOINT_STUDY_RECORD-Density-4.0.xsd</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:sequence>
<xs:any namespace="##other" processContents="strict" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="Attachments" nillable="true">
<xs:annotation>
<xs:documentation>Lists the attachments that are directly linked to the document. The content of this section is an unbounded list of references to attachment identifiers that this document is linked to.
<br/><br/>
The elements are included in the platform-attachment.xsd</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:sequence minOccurs="0" maxOccurs="unbounded" >
<xs:element ref="att:Attachment" minOccurs="0" />
<xs:element ref="att:AttachmentRef" minOccurs="0" />
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="ModificationHistory" nillable="true">
<xs:annotation>
<xs:documentation>Lists the entries of the document's modification history. Every entry is a single operation that took place on the specific document and specifies the date of the action, the user that run the action, the submitting legal entity of the user and the modification remarks if any.
<br/><br/>
The elements are included in the platform-modification-history.xsd</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:sequence minOccurs="0" maxOccurs="unbounded">
<xs:element ref="mh:Modification" minOccurs="0" />
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:schema>

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<?xml version="1.0" encoding="UTF-8"?>
<xs:schema xmlns="http://iuclid6.echa.europa.eu/namespaces/platform-fields/v1"
xmlns:xs="http://www.w3.org/2001/XMLSchema"
targetNamespace="http://iuclid6.echa.europa.eu/namespaces/platform-fields/v1"
elementFormDefault="qualified" attributeFormDefault="qualified">
<xs:annotation>
<xs:appinfo>XML Schema Definition of the main IUCLID6 data types</xs:appinfo>
</xs:annotation>
<xs:import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="xml.xsd"/>
<xs:complexType name="sectionTypesField">
<xs:annotation>
<xs:documentation>Specifies the content of the section types field under Category document</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="documentDefinitionIdentifier" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
<xs:element name="documentType" type="xs:string"/>
<xs:element name="documentSubType" type="xs:string"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
<xs:complexType name="inventoryEntry">
<xs:annotation>
<xs:documentation>Specifies the content of the chemical inventory field</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="inventoryCode" type="xs:string"/>
<xs:element name="numberInInventory" type="xs:string"/>
</xs:sequence>
</xs:complexType>
<xs:complexType name="addressField">
<xs:annotation>
<xs:documentation>Contains the elements constituting the AddressField type</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="city" type="xs:string"/>
<xs:element name="country" type="picklistField"/>
<xs:element name="email" type="xs:string"/>
<xs:element name="fax" type="xs:string"/>
<xs:element name="phone" type="xs:string"/>
<xs:element name="state" type="xs:string"/>
<xs:element name="street1" type="xs:string"/>
<xs:element name="street2" type="xs:string"/>
<xs:element name="website" type="xs:string"/>
<xs:element name="zipcode" type="xs:string"/>
</xs:sequence>
</xs:complexType>
<xs:simpleType name="attachmentField">
<xs:annotation>
<xs:documentation>Holds the key of the attachment content attached to the specific field</xs:documentation>
</xs:annotation>
<xs:restriction base="xs:string"/>
</xs:simpleType>
<xs:complexType name="attachmentListField">
<xs:annotation>
<xs:documentation>Holds the list of the attachment content identifiers/keys attached to the specific field</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="key" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
<xs:simpleType name="booleanField">
<xs:annotation>
<xs:documentation>The value of IUCLID6 boolean fields</xs:documentation>
</xs:annotation>
<xs:restriction base="xs:boolean"/>
</xs:simpleType>
<xs:complexType name="legislation">
<xs:annotation>
<xs:documentation>Elements that constitute the regulatory programme legislation information of a data protection field</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="value" type="xs:string"/>
<xs:element name="other" minOccurs="0" maxOccurs="1" type="textFieldSmall"/>
</xs:sequence>
</xs:complexType>
<xs:complexType name="multilingualLegislation">
<xs:annotation>
<xs:documentation>The multilingual version of the legislation type</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="value" type="xs:string"/>
<xs:element name="other" minOccurs="0" maxOccurs="unbounded"
type="multilingualTextFieldSmall"/>
</xs:sequence>
</xs:complexType>
<xs:complexType name="dataProtectionField">
<xs:annotation>
<xs:documentation>The elements constituting the data protection field type</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="confidentiality" type="xs:string"/>
<xs:element name="justification" type="textField"/>
<xs:element name="legislation" minOccurs="0" maxOccurs="unbounded" type="legislation"/>
</xs:sequence>
</xs:complexType>
<xs:complexType name="multilingualDataProtectionField">
<xs:annotation>
<xs:documentation>The multilingual version of the data protection field type</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="confidentiality" type="xs:string"/>
<xs:element name="justification" maxOccurs="unbounded" type="multilingualTextField"/>
<xs:element name="legislation" minOccurs="0" maxOccurs="unbounded"
type="multilingualLegislation"/>
</xs:sequence>
</xs:complexType>
<xs:simpleType name="dateField">
<xs:annotation>
<xs:documentation>The value of IUCLID6 date/timestamp fields</xs:documentation>
</xs:annotation>
<xs:restriction base="xs:dateTime"/>
</xs:simpleType>
<xs:simpleType name="documentReferenceField">
<xs:annotation>
<xs:documentation>Holds the key of the IUCLID6 document that is referenced by the specific field</xs:documentation>
</xs:annotation>
<xs:restriction base="xs:string"/>
</xs:simpleType>
<xs:complexType name="documentReferenceMultipleField">
<xs:annotation>
<xs:documentation>Multilingual version of the document reference field</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="key" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
<xs:simpleType name="numericField">
<xs:annotation>
<xs:documentation>The value of IUCLID6 numeric fields</xs:documentation>
</xs:annotation>
<xs:restriction base="xs:decimal"/>
</xs:simpleType>
<xs:complexType name="physicalQuantityField">
<xs:annotation>
<xs:documentation>Specifies the elements constituting the IUCLID6 physical quantity fields</xs:documentation>
</xs:annotation>
<xs:sequence/>
</xs:complexType>
<xs:simpleType name="lowerQualifier">
<xs:annotation>
<xs:documentation>Restricts the eligible values of the "lowerQualifier" element</xs:documentation>
</xs:annotation>
<xs:restriction base="xs:string">
<xs:enumeration value="&gt;"/>
<xs:enumeration value="&gt;="/>
<xs:enumeration value="ca."/>
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="upperQualifier">
<xs:annotation>
<xs:documentation>Restricts the eligible values of the "upperQualifier" element</xs:documentation>
</xs:annotation>
<xs:restriction base="xs:string">
<xs:enumeration value="&lt;"/>
<xs:enumeration value="&lt;="/>
<xs:enumeration value="ca."/>
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="halfBoundedQualifier">
<xs:annotation>
<xs:documentation>Restricts the eligible values of the "halfBoundedQualifier" element</xs:documentation>
</xs:annotation>
<xs:restriction base="xs:string">
<xs:enumeration value="&gt;"/>
<xs:enumeration value="&gt;="/>
<xs:enumeration value="&lt;"/>
<xs:enumeration value="&lt;="/>
<xs:enumeration value="ca."/>
</xs:restriction>
</xs:simpleType>
<xs:group name="rangeQualifierDecimalGroup">
<xs:annotation>
<xs:documentation>Groups the qualifiers along with the decimal values of the physical quantity range field</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="lowerQualifier" minOccurs="0" type="lowerQualifier"/>
<xs:element name="upperQualifier" minOccurs="0" type="upperQualifier"/>
<xs:element name="lowerValue" type="xs:decimal" minOccurs="0"/>
<xs:element name="upperValue" type="xs:decimal" minOccurs="0"/>
</xs:sequence>
</xs:group>
<xs:group name="rangeQualifierIntegerGroup">
<xs:annotation>
<xs:documentation>Groups the qualifiers along with the integer values of the physical quantity range field</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="lowerQualifier" minOccurs="0" type="lowerQualifier"/>
<xs:element name="upperQualifier" minOccurs="0" type="upperQualifier"/>
<xs:element name="lowerValue" type="xs:integer" minOccurs="0"/>
<xs:element name="upperValue" type="xs:integer" minOccurs="0"/>
</xs:sequence>
</xs:group>
<xs:group name="halfBoundedRangeQualifierDecimalGroup">
<xs:annotation>
<xs:documentation>Groups the qualifier along with the decimal value of the half bounded physical quantity range field</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="qualifier" minOccurs="0" type="halfBoundedQualifier"/>
<xs:element name="value" type="xs:decimal" minOccurs="0"/>
</xs:sequence>
</xs:group>
<xs:group name="halfBoundedRangeQualifierIntegerGroup">
<xs:annotation>
<xs:documentation>Groups the qualifier along with the integer value of the half bounded physical quantity range field</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="qualifier" minOccurs="0" type="halfBoundedQualifier"/>
<xs:element name="value" type="xs:integer" minOccurs="0"/>
</xs:sequence>
</xs:group>
<xs:complexType name="physicalQuantityRangeField">
<xs:annotation>
<xs:documentation>Lists the elements constituting the decimal physical quantity range field</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="unitCode" minOccurs="0" type="textFieldSmall"/>
<xs:element name="unitOther" minOccurs="0" type="textFieldSmall"/>
<xs:group ref="rangeQualifierDecimalGroup"/>
</xs:sequence>
</xs:complexType>
<xs:complexType name="multilingualPhysicalQuantityRangeField">
<xs:annotation>
<xs:documentation>The multilingual version of the physical quantity range field</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="unitCode" minOccurs="0" type="textFieldSmall"/>
<xs:element name="unitOther" minOccurs="0" maxOccurs="unbounded"
type="multilingualTextFieldSmall"/>
<xs:group ref="rangeQualifierDecimalGroup"/>
</xs:sequence>
</xs:complexType>
<xs:complexType name="physicalQuantityIntegerRangeField">
<xs:annotation>
<xs:documentation>Lists the elements constituting the integer physical quantity range field</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="unitCode" minOccurs="0" type="textFieldSmall"/>
<xs:element name="unitOther" minOccurs="0" type="textFieldSmall"/>
<xs:group ref="rangeQualifierIntegerGroup"/>
</xs:sequence>
</xs:complexType>
<xs:complexType name="multilingualPhysicalQuantityIntegerRangeField">
<xs:annotation>
<xs:documentation>The multilingual version of the physical quantity range field with integer value</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="unitCode" minOccurs="0" type="textFieldSmall"/>
<xs:element name="unitOther" minOccurs="0" maxOccurs="unbounded"
type="multilingualTextFieldSmall"/>
<xs:group ref="rangeQualifierIntegerGroup"/>
</xs:sequence>
</xs:complexType>
<xs:complexType name="physicalQuantityHalfBoundedField">
<xs:annotation>
<xs:documentation>Lists the elements constituting the decimal, hald-bounded physical quantity range field</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="unitCode" minOccurs="0" type="textFieldSmall"/>
<xs:element name="unitOther" minOccurs="0" type="textFieldSmall"/>
<xs:group ref="halfBoundedRangeQualifierDecimalGroup"/>
</xs:sequence>
</xs:complexType>
<xs:complexType name="multilingualPhysicalQuantityHalfBoundedField">
<xs:annotation>
<xs:documentation>The multilingual version of the half bounded physical quantity range field</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="unitCode" minOccurs="0" type="textFieldSmall"/>
<xs:element name="unitOther" minOccurs="0" maxOccurs="unbounded"
type="multilingualTextFieldSmall"/>
<xs:group ref="halfBoundedRangeQualifierDecimalGroup"/>
</xs:sequence>
</xs:complexType>
<xs:complexType name="physicalQuantityIntegerHalfBoundedField">
<xs:annotation>
<xs:documentation>Lists the elements constituting the integer, half bounded physical quantity range field</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="unitCode" minOccurs="0" type="textFieldSmall"/>
<xs:element name="unitOther" minOccurs="0" type="textFieldSmall"/>
<xs:group ref="halfBoundedRangeQualifierIntegerGroup"/>
</xs:sequence>
</xs:complexType>
<xs:complexType name="multilingualPhysicalQuantityIntegerHalfBoundedField">
<xs:annotation>
<xs:documentation>The multilingual version of the half bounded physical quantity range field with integer value</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="unitCode" minOccurs="0" type="textFieldSmall"/>
<xs:element name="unitOther" minOccurs="0" maxOccurs="unbounded"
type="multilingualTextFieldSmall"/>
<xs:group ref="halfBoundedRangeQualifierIntegerGroup"/>
</xs:sequence>
</xs:complexType>
<xs:simpleType name="textField">
<xs:annotation>
<xs:documentation>Indicates that a field holds textual content</xs:documentation>
</xs:annotation>
<xs:restriction base="xs:string"/>
</xs:simpleType>
<xs:complexType name="multilingualTextField">
<xs:annotation>
<xs:documentation>Indicates that a field holds multilingual textual content</xs:documentation>
</xs:annotation>
<xs:simpleContent>
<xs:extension base="textField">
<xs:attribute ref="xml:lang" use="optional"/>
</xs:extension>
</xs:simpleContent>
</xs:complexType>
<xs:simpleType name="textFieldSmall">
<xs:annotation>
<xs:documentation>Indicates that a field holds textual content with a maximum of 255 characters</xs:documentation>
</xs:annotation>
<xs:restriction base="xs:string">
<xs:maxLength value="255"/>
</xs:restriction>
</xs:simpleType>
<xs:complexType name="multilingualTextFieldSmall">
<xs:annotation>
<xs:documentation>Indicates that a field holds multilingual textual content with a maximum of 255 characters</xs:documentation>
</xs:annotation>
<xs:simpleContent>
<xs:extension base="textFieldSmall">
<xs:attribute ref="xml:lang" use="optional"/>
</xs:extension>
</xs:simpleContent>
</xs:complexType>
<xs:simpleType name="textFieldLarge">
<xs:annotation>
<xs:documentation>Indicates that a field holds textual content with a maximum of 32768 characters</xs:documentation>
</xs:annotation>
<xs:restriction base="xs:string">
<xs:maxLength value="32768"/>
</xs:restriction>
</xs:simpleType>
<xs:complexType name="multilingualTextFieldLarge">
<xs:annotation>
<xs:documentation>Indicates that a field holds multilingual textual content with a maximum of 32768 characters</xs:documentation>
</xs:annotation>
<xs:simpleContent>
<xs:extension base="textFieldLarge">
<xs:attribute ref="xml:lang" use="optional"/>
</xs:extension>
</xs:simpleContent>
</xs:complexType>
<xs:simpleType name="textFieldMultiLine">
<xs:annotation>
<xs:documentation>Indicates that a field holds textual content with a maximum of 2000 characters</xs:documentation>
</xs:annotation>
<xs:restriction base="xs:string">
<xs:maxLength value="2000"/>
</xs:restriction>
</xs:simpleType>
<xs:complexType name="multilingualTextFieldMultiLine">
<xs:annotation>
<xs:documentation>Indicates that a field holds multilingual textual content with a maximum of 2000 characters</xs:documentation>
</xs:annotation>
<xs:simpleContent>
<xs:extension base="textFieldMultiLine">
<xs:attribute ref="xml:lang" use="optional"/>
</xs:extension>
</xs:simpleContent>
</xs:complexType>
<xs:complexType name="picklistField">
<xs:annotation>
<xs:documentation>Lists the elements (phrase code and other text) constituting the IUCLID6 picklist field</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="value" minOccurs="0" type="textFieldSmall"/>
<xs:element name="other" minOccurs="0" type="textFieldSmall"/>
</xs:sequence>
</xs:complexType>
<xs:complexType name="multilingualPicklistField">
<xs:annotation>
<xs:documentation>The multilingual version of the picklist field</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="value" minOccurs="0" type="textFieldSmall"/>
<xs:element name="other" minOccurs="0" maxOccurs="unbounded"
type="multilingualTextFieldSmall"/>
</xs:sequence>
</xs:complexType>
<xs:complexType name="picklistFieldWithSmallTextRemarks">
<xs:annotation>
<xs:documentation>Lists the elements (phrase code, other text and remarks) constituting the IUCLID6 picklist field - remarks information can be up to 255 characters</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="value" minOccurs="0" type="textFieldSmall"/>
<xs:element name="other" minOccurs="0" type="textFieldSmall"/>
<xs:element name="remarks" minOccurs="0" type="textFieldSmall"/>
</xs:sequence>
</xs:complexType>
<xs:complexType name="multilingualPicklistFieldWithSmallTextRemarks">
<xs:annotation>
<xs:documentation>The multilingual version of the picklist field including remarks information up to 255 characters</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="value" minOccurs="0" type="textFieldSmall"/>
<xs:element name="other" minOccurs="0" maxOccurs="unbounded"
type="multilingualTextFieldSmall"/>
<xs:element name="remarks" minOccurs="0" maxOccurs="unbounded"
type="multilingualTextFieldSmall"/>
</xs:sequence>
</xs:complexType>
<xs:complexType name="picklistFieldWithLargeTextRemarks">
<xs:annotation>
<xs:documentation>Lists the elements (phrase code, other text and remarks) constituting the IUCLID6 picklist field - remarks information can be up to 32768 characters</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="value" minOccurs="0" type="textFieldSmall"/>
<xs:element name="other" minOccurs="0" type="textFieldSmall"/>
<xs:element name="remarks" minOccurs="0" type="textFieldLarge"/>
</xs:sequence>
</xs:complexType>
<xs:complexType name="multilingualPicklistFieldWithLargeTextRemarks">
<xs:annotation>
<xs:documentation>The multilingual version of the picklist field including remarks information up to 32768 characters</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="value" minOccurs="0" type="textFieldSmall"/>
<xs:element name="other" minOccurs="0" maxOccurs="unbounded"
type="multilingualTextFieldSmall"/>
<xs:element name="remarks" minOccurs="0" maxOccurs="unbounded"
type="multilingualTextFieldLarge"/>
</xs:sequence>
</xs:complexType>
<xs:complexType name="picklistFieldWithMultiLineTextRemarks">
<xs:annotation>
<xs:documentation>Lists the elements (phrase code, other text and remarks) constituting the IUCLID6 picklist field - remarks information can be up to 2000 characters</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="value" minOccurs="0" type="textFieldSmall"/>
<xs:element name="other" minOccurs="0" type="textFieldSmall"/>
<xs:element name="remarks" minOccurs="0" type="textFieldMultiLine"/>
</xs:sequence>
</xs:complexType>
<xs:complexType name="multilingualPicklistFieldWithMultiLineTextRemarks">
<xs:annotation>
<xs:documentation>The multilingual version of the picklist field including remarks information up to 2000 characters</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="value" minOccurs="0" type="textFieldSmall"/>
<xs:element name="other" minOccurs="0" maxOccurs="unbounded"
type="multilingualTextFieldSmall"/>
<xs:element name="remarks" minOccurs="0" maxOccurs="unbounded"
type="multilingualTextFieldMultiLine"/>
</xs:sequence>
</xs:complexType>
<xs:complexType name="repeatableEntryType">
<xs:annotation>
<xs:documentation>Specifies the multiplicity and attribute of a repeatable block</xs:documentation>
</xs:annotation>
<xs:sequence/>
<xs:attribute name="uuid" type="uuidAttribute" use="required"/>
</xs:complexType>
<xs:simpleType name="uuidAttribute">
<xs:annotation>
<xs:documentation>Attribute used to hold unique identifier information</xs:documentation>
</xs:annotation>
<xs:restriction base="xs:string"/>
</xs:simpleType>
<xs:complexType name="basePicklistField">
<xs:annotation>
<xs:documentation>An empty complex type that is extended by the picklist fields which are defined inline in the auto-generated document xsds.
<br/><br/>
The picklist fields contain the following elements:
<ul>
<li>value</li>
<li>other</li>
<li>remarks</li>
</ul>
<br/><br/>
The inline definition of the fields take place in order to:
<ul>
<li>restrict the eligible phrase codes per picklist field</li>
<li>conditionally define or omit the "other" element based on the configured phrasegroup (open, close)</li>
<li>based on the picklist definition, properly define the multilingual behavior of the textual elements "other" and "remarks" elements </li>
<li>based on the picklist definition, properly define the length restriction of the "remarks" elements </li>
</ul></xs:documentation>
</xs:annotation>
<xs:sequence/>
</xs:complexType>
<xs:complexType name="basePhysicalQuantityField">
<xs:annotation>
<xs:documentation>An empty complex type that is extended by the physical quantity fields which are defined inline in the auto-generated document xsds.
<br/><br/>
The physical quantity fields contain the following elements:
<ul>
<li>unitCode</li>
<li>unitOther</li>
<li>value</li>
</ul>
<br/><br/>
The inline definition of the fields take place in order to:
<ul>
<li>restrict the eligible phrase codes for the "unitCode" element</li>
<li>conditionally define or omit the "unitOther" element based on the configured phrasegroup (open, close)</li>
<li>based on the field definition, properly define the multilingual behavior of the textual "unitOther" element</li>
</ul></xs:documentation>
</xs:annotation>
<xs:sequence/>
</xs:complexType>
<xs:complexType name="basePhysicalQuantityRangeField">
<xs:annotation>
<xs:documentation>An empty complex type that is extended by the physical quantity range fields which are defined inline in the auto-generated document xsds.
<br/><br/>
The physical quantity range fields contain the following elements:
<ul>
<li>unitCode</li>
<li>unitOther</li>
<li>lowerQualifier</li>
<li>upperQualifier</li>
<li>lowerValue</li>
<li>upperValue</li>
<li>qualifier: in case of half-bounded</li>
<li>value: in case of half-bounded</li>
</ul>
<br/><br/>
The inline definition of the fields take place in order to:
<ul>
<li>restrict the eligible phrase codes for the "unitCode" element</li>
<li>conditionally define or omit the "unitOther" element based on the configured phrasegroup (open, close)</li>
<li>based on the field definition, properly define the multilingual behavior of the textual "unitOther" element</li>
<li>based on the field definition, dynamically setup the bounded- or half-boudnded-related elements</li>
</ul></xs:documentation>
</xs:annotation>
<xs:sequence/>
</xs:complexType>
<xs:complexType name="baseDataProtectionField">
<xs:annotation>
<xs:documentation>An empty complex type that is extended by the data protection fields which are defined inline in the auto-generated document xsds.
<br/><br/>
The data protection fields contain the following elements:
<ul>
<li>confidentiality</li>
<li>justification</li>
<li>legislation</li>
<ul>
<li>value</li>
<li>other</li>
</ul>
</ul>
<br/><br/>
The inline definition of the fields take place in order to:
<ul>
<li>restrict the eligible phrase codes for the "confidentiality" and "value" element</li>
<li>based on the field definition, properly define the multilingual behavior of the textual "justification" and "other" elements</li>
</ul> </xs:documentation>
</xs:annotation>
<xs:sequence/>
</xs:complexType>
</xs:schema>

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@ -0,0 +1,138 @@
<xs:schema xmlns="http://iuclid6.echa.europa.eu/namespaces/platform-metadata/v1"
xmlns:xs="http://www.w3.org/2001/XMLSchema"
targetNamespace="http://iuclid6.echa.europa.eu/namespaces/platform-metadata/v1"
elementFormDefault="qualified" attributeFormDefault="qualified">
<xs:annotation>
<xs:appinfo>XML Schema Definition of the "PlatformMetadata" section</xs:appinfo>
</xs:annotation>
<xs:element name="iuclidVersion" type="xs:string">
<xs:annotation>
<xs:documentation>The current iuclid version used for exporting the .i6z archive</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="documentKey" type="xs:string">
<xs:annotation>
<xs:documentation>The unique identifier of the document</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="documentType" type="xs:string">
<xs:annotation>
<xs:documentation>The type of the document. Eligible values are:
<ul>
<li>ANNOTATION</li>
<li>ARTICLE</li>
<li>CATEGORY</li>
<li>DOSSIER</li>
<li>FIXED_RECORD</li>
<li>FLEXIBLE_RECORD</li>
<li>ENDPOINT_STUDY_RECORD</li>
<li>FLEXIBLE_SUMMARY</li>
<li>ENDPOINT_SUMMARY</li>
<li>ASSESSMENT_ENTITY</li>
<li>LEGAL_ENTITY</li>
<li>MIXTURE</li>
<li>REFERENCE_SUBSTANCE</li>
<li>SITE</li>
<li>CONTACT</li>
<li>LITERATURE</li>
<li>SUBSTANCE</li>
<li>TEMPLATE</li>
<li>TEST_MATERIAL_INFORMATION</li>
<li>INVENTORY</li>
<li>CUSTOM_ENTITY</li>
<li>CUSTOM_SECTION</li>
</ul></xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="definitionVersion" type="xs:string">
<xs:annotation>
<xs:documentation>The definition version of the exported document. This value is used:
<ul>
<li>indicates that the content section follows the document format of the specified version</li>
<li>during import operation, this value drives the resolution of the proper document's .xsd to run the validation with</li>
</ul></xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="creationDate" type="xs:dateTime">
<xs:annotation>
<xs:documentation>The date that the document was created</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="lastModificationDate" type="xs:dateTime">
<xs:annotation>
<xs:documentation>The last modification date of the document</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="name" type="xs:string">
<xs:annotation>
<xs:documentation>It is the name of the document as specified by the user.</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="documentSubType" type="xs:string">
<xs:annotation>
<xs:documentation>The subtype in case of section document. This information is not applicable to entity documents. "type"."subtype" uniquely identify the section document type and represent the document definition identifier</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="parentDocumentKey" type="xs:string">
<xs:annotation>
<xs:documentation>In case this document is a section document, this element keeps the unique identifier of its parent document</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="orderInSectionNo">
<xs:annotation>
<xs:documentation>In case this is a section document, the order of the document with the specific definition identifier (type, subtype) under the provided parent entity</xs:documentation>
</xs:annotation>
<xs:simpleType>
<xs:union>
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:length value="0"/>
</xs:restriction>
</xs:simpleType>
<xs:simpleType>
<xs:restriction base="xs:nonNegativeInteger"/>
</xs:simpleType>
</xs:union>
</xs:simpleType>
</xs:element>
<xs:element name="submissionType" type="xs:string">
<xs:annotation>
<xs:documentation>Applicable only to dossier archives. Indicates the submission type used during dossier generation. The value is specified in case the XML concerns:
<ul>
<li>the dossier document</li>
<li>the composite documents (SUBSTANCE/MIXTURE) under the dossier with a submission type different than the one of the dossier document</li>
</ul></xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="submissionTypeVersion" type="xs:string">
<xs:annotation>
<xs:documentation>The version of the submission type used to generate the dossier for</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="submittingLegalEntity" type="xs:string">
<xs:annotation>
<xs:documentation>The legal entity document identifier that originated toe dossier creation</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="dossierSubject" type="xs:string">
<xs:annotation>
<xs:documentation>In case this is the dossier document, it contains the document key (unique identifier)
of the dossier subject document (SUBSTANCE, MIXTURE, CATEGORY, ARTICLE) which is the document the dossier was created from</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="i5Origin" type="xs:boolean">
<xs:annotation>
<xs:documentation>Flag indicating whether this document originated from a IUCLID5 instance and migrated to the current IUCLID6 format or not</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="creationTool" type="xs:string">
<xs:annotation>
<xs:documentation>Element that specifies the application this document was first created with. Default value "IUC6" should be provided for IUCLID6-documents</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="snapshotCreationTool" type="xs:string">
<xs:annotation>
<xs:documentation>In case of dossier archive, element that specifies the application this dossier was created from. Upon dossier creation this is filled in with "IUC6"</xs:documentation>
</xs:annotation>
</xs:element>
</xs:schema>

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@ -0,0 +1,39 @@
<?xml version="1.0" encoding="UTF-8"?>
<xs:schema xmlns="http://iuclid6.echa.europa.eu/namespaces/platform-modification-history/v1"
xmlns:xs="http://www.w3.org/2001/XMLSchema"
targetNamespace="http://iuclid6.echa.europa.eu/namespaces/platform-modification-history/v1"
elementFormDefault="qualified" attributeFormDefault="qualified">
<xs:annotation>
<xs:appinfo>XML Schema Definition of the "ModificationHistory" section</xs:appinfo>
<xs:documentation>This section lists the entries of the document's modification history. Every entry is a single operation that took place on the specific document and specifies the date of the action, the user that run the action, the submitting legal entity of the user and the modification remarks if any</xs:documentation>
</xs:annotation>
<xs:element name="Modification">
<xs:annotation>
<xs:documentation>Holds the information concerning the document's modification. Every entry is a single operation that took place on the specific document and specifies the date of the action, the user that run the action, the submitting legal entity of the user and the modification remarks if any</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:all>
<xs:element name="Date" type="xs:dateTime">
<xs:annotation>
<xs:documentation>The date the action was performed on the document</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="Author" type="xs:string">
<xs:annotation>
<xs:documentation>The userName of the user that performed the modification</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="LegalEntity" type="xs:string" minOccurs="0">
<xs:annotation>
<xs:documentation>The description of the submitting legal entity of the user. This information contains the concatenated value of the LE name, city and localized country information</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="Remarks" type="xs:string" minOccurs="0">
<xs:annotation>
<xs:documentation>The modification comment</xs:documentation>
</xs:annotation>
</xs:element>
</xs:all>
</xs:complexType>
</xs:element>
</xs:schema>

View File

@ -0,0 +1,231 @@
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
xmlns:xlink="http://www.w3.org/1999/xlink" targetNamespace="http://www.w3.org/1999/xlink">
<xs:annotation>
<xs:documentation>
This schema document provides attribute declarations and attribute
group, complex type and simple type definitions which can be used in
the construction of user schemas to define the structure of
particular linking constructs, e.g.
<![CDATA[
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
xmlns:xl="http://www.w3.org/1999/xlink">
<xs:import namespace="http://www.w3.org/1999/xlink"
location="http://www.w3.org/1999/xlink.xsd">
<xs:element name="mySimple">
<xs:complexType>
...
<xs:attributeGroup ref="xl:simpleAttrs"/>
...
</xs:complexType>
</xs:element>
...
</xs:schema>
]]>
</xs:documentation>
</xs:annotation>
<xs:import namespace="http://www.w3.org/XML/1998/namespace"
schemaLocation="xml.xsd" />
<xs:attribute name="type" type="xlink:typeType" />
<xs:simpleType name="typeType">
<xs:restriction base="xs:token">
<xs:enumeration value="simple" />
<xs:enumeration value="extended" />
<xs:enumeration value="title" />
<xs:enumeration value="resource" />
<xs:enumeration value="locator" />
<xs:enumeration value="arc" />
</xs:restriction>
</xs:simpleType>
<xs:attribute name="href" type="xlink:hrefType" />
<xs:simpleType name="hrefType">
<xs:restriction base="xs:anyURI" />
</xs:simpleType>
<xs:attribute name="role" type="xlink:roleType" />
<xs:simpleType name="roleType">
<xs:restriction base="xs:anyURI">
<xs:minLength value="1" />
</xs:restriction>
</xs:simpleType>
<xs:attribute name="arcrole" type="xlink:arcroleType" />
<xs:simpleType name="arcroleType">
<xs:restriction base="xs:anyURI">
<xs:minLength value="1" />
</xs:restriction>
</xs:simpleType>
<xs:attribute name="title" type="xlink:titleAttrType" />
<xs:simpleType name="titleAttrType">
<xs:restriction base="xs:string" />
</xs:simpleType>
<xs:attribute name="show" type="xlink:showType" />
<xs:simpleType name="showType">
<xs:restriction base="xs:token">
<xs:enumeration value="new" />
<xs:enumeration value="replace" />
<xs:enumeration value="embed" />
<xs:enumeration value="other" />
<xs:enumeration value="none" />
</xs:restriction>
</xs:simpleType>
<xs:attribute name="actuate" type="xlink:actuateType" />
<xs:simpleType name="actuateType">
<xs:restriction base="xs:token">
<xs:enumeration value="onLoad" />
<xs:enumeration value="onRequest" />
<xs:enumeration value="other" />
<xs:enumeration value="none" />
</xs:restriction>
</xs:simpleType>
<xs:attribute name="label" type="xlink:labelType" />
<xs:simpleType name="labelType">
<xs:restriction base="xs:NCName" />
</xs:simpleType>
<xs:attribute name="from" type="xlink:fromType" />
<xs:simpleType name="fromType">
<xs:restriction base="xs:NCName" />
</xs:simpleType>
<xs:attribute name="to" type="xlink:toType" />
<xs:simpleType name="toType">
<xs:restriction base="xs:NCName" />
</xs:simpleType>
<xs:attributeGroup name="simpleAttrs">
<xs:attribute ref="xlink:type" fixed="simple" />
<xs:attribute ref="xlink:href" />
<xs:attribute ref="xlink:role" />
<xs:attribute ref="xlink:arcrole" />
<xs:attribute ref="xlink:title" />
<xs:attribute ref="xlink:show" />
<xs:attribute ref="xlink:actuate" />
</xs:attributeGroup>
<xs:group name="simpleModel">
<xs:sequence>
<xs:any processContents="lax" minOccurs="0" maxOccurs="unbounded" />
</xs:sequence>
</xs:group>
<xs:complexType mixed="true" name="simple">
<xs:annotation>
<xs:documentation>
Intended for use as the type of user-declared elements to make them simple
links.
</xs:documentation>
</xs:annotation>
<xs:group ref="xlink:simpleModel" />
<xs:attributeGroup ref="xlink:simpleAttrs" />
</xs:complexType>
<xs:attributeGroup name="extendedAttrs">
<xs:attribute ref="xlink:type" fixed="extended" use="required" />
<xs:attribute ref="xlink:role" />
<xs:attribute ref="xlink:title" />
</xs:attributeGroup>
<xs:group name="extendedModel">
<xs:choice>
<xs:element ref="xlink:title" />
<xs:element ref="xlink:resource" />
<xs:element ref="xlink:locator" />
<xs:element ref="xlink:arc" />
</xs:choice>
</xs:group>
<xs:complexType name="extended">
<xs:annotation>
<xs:documentation>
Intended for use as the type of user-declared elements to make them extended
links. Note that the elements referenced in the content model are
all abstract. The intention is that by simply declaring elements
with these as their substitutionGroup, all the right things will
happen.
</xs:documentation>
</xs:annotation>
<xs:group ref="xlink:extendedModel" minOccurs="0" maxOccurs="unbounded" />
<xs:attributeGroup ref="xlink:extendedAttrs" />
</xs:complexType>
<xs:element name="title" type="xlink:titleEltType" abstract="true" />
<xs:attributeGroup name="titleAttrs">
<xs:attribute ref="xlink:type" fixed="title" use="required" />
<xs:attribute ref="xml:lang">
<xs:annotation>
<xs:documentation>
xml:lang is not required, but provides much of the motivation for title
elements in addition to attributes, and so is provided here for
convenience.
</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:attributeGroup>
<xs:group name="titleModel">
<xs:sequence>
<xs:any processContents="lax" minOccurs="0" maxOccurs="unbounded" />
</xs:sequence>
</xs:group>
<xs:complexType mixed="true" name="titleEltType">
<xs:group ref="xlink:titleModel" />
<xs:attributeGroup ref="xlink:titleAttrs" />
</xs:complexType>
<xs:element name="resource" type="xlink:resourceType"
abstract="true" />
<xs:attributeGroup name="resourceAttrs">
<xs:attribute ref="xlink:type" fixed="resource" use="required" />
<xs:attribute ref="xlink:role" />
<xs:attribute ref="xlink:title" />
<xs:attribute ref="xlink:label" />
</xs:attributeGroup>
<xs:group name="resourceModel">
<xs:sequence>
<xs:any processContents="lax" minOccurs="0" maxOccurs="unbounded" />
</xs:sequence>
</xs:group>
<xs:complexType mixed="true" name="resourceType">
<xs:group ref="xlink:resourceModel" />
<xs:attributeGroup ref="xlink:resourceAttrs" />
</xs:complexType>
<xs:element name="locator" type="xlink:locatorType"
abstract="true" />
<xs:attributeGroup name="locatorAttrs">
<xs:attribute ref="xlink:type" fixed="locator" use="required" />
<xs:attribute ref="xlink:href" use="required" />
<xs:attribute ref="xlink:role" />
<xs:attribute ref="xlink:title" />
<xs:attribute ref="xlink:label">
<xs:annotation>
<xs:documentation>
label is not required, but locators have no particular XLink function if
they are not labeled.
</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:attributeGroup>
<xs:group name="locatorModel">
<xs:sequence>
<xs:element ref="xlink:title" minOccurs="0" maxOccurs="unbounded" />
</xs:sequence>
</xs:group>
<xs:complexType name="locatorType">
<xs:group ref="xlink:locatorModel" />
<xs:attributeGroup ref="xlink:locatorAttrs" />
</xs:complexType>
<xs:element name="arc" type="xlink:arcType" abstract="true" />
<xs:attributeGroup name="arcAttrs">
<xs:attribute ref="xlink:type" fixed="arc" use="required" />
<xs:attribute ref="xlink:arcrole" />
<xs:attribute ref="xlink:title" />
<xs:attribute ref="xlink:show" />
<xs:attribute ref="xlink:actuate" />
<xs:attribute ref="xlink:from" />
<xs:attribute ref="xlink:to">
<xs:annotation>
<xs:documentation>
from and to have default behavior when values are missing
</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:attributeGroup>
<xs:group name="arcModel">
<xs:sequence>
<xs:element ref="xlink:title" minOccurs="0" maxOccurs="unbounded" />
</xs:sequence>
</xs:group>
<xs:complexType name="arcType">
<xs:group ref="xlink:arcModel" />
<xs:attributeGroup ref="xlink:arcAttrs" />
</xs:complexType>
</xs:schema>

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<?xml version='1.0'?>
<xs:schema targetNamespace="http://www.w3.org/XML/1998/namespace" xmlns:xs="http://www.w3.org/2001/XMLSchema" xml:lang="en">
<xs:annotation>
<xs:documentation>
See http://www.w3.org/XML/1998/namespace.html and
http://www.w3.org/TR/REC-xml for information about this namespace.
This schema document describes the XML namespace, in a form
suitable for import by other schema documents.
Note that local names in this namespace are intended to be defined
only by the World Wide Web Consortium or its subgroups. The
following names are currently defined in this namespace and should
not be used with conflicting semantics by any Working Group,
specification, or document instance:
base (as an attribute name): denotes an attribute whose value
provides a URI to be used as the base for interpreting any
relative URIs in the scope of the element on which it
appears; its value is inherited. This name is reserved
by virtue of its definition in the XML Base specification.
id (as an attribute name): denotes an attribute whose value
should be interpreted as if declared to be of type ID.
This name is reserved by virtue of its definition in the
xml:id specification.
lang (as an attribute name): denotes an attribute whose value
is a language code for the natural language of the content of
any element; its value is inherited. This name is reserved
by virtue of its definition in the XML specification.
space (as an attribute name): denotes an attribute whose
value is a keyword indicating what whitespace processing
discipline is intended for the content of the element; its
value is inherited. This name is reserved by virtue of its
definition in the XML specification.
Father (in any context at all): denotes Jon Bosak, the chair of
the original XML Working Group. This name is reserved by
the following decision of the W3C XML Plenary and
XML Coordination groups:
In appreciation for his vision, leadership and dedication
the W3C XML Plenary on this 10th day of February, 2000
reserves for Jon Bosak in perpetuity the XML name
xml:Father
</xs:documentation>
</xs:annotation>
<xs:annotation>
<xs:documentation>This schema defines attributes and an attribute group
suitable for use by
schemas wishing to allow xml:base, xml:lang, xml:space or xml:id
attributes on elements they define.
To enable this, such a schema must import this schema
for the XML namespace, e.g. as follows:
&lt;schema . . .>
. . .
&lt;import namespace="http://www.w3.org/XML/1998/namespace"
schemaLocation="http://www.w3.org/2001/xml.xsd"/>
Subsequently, qualified reference to any of the attributes
or the group defined below will have the desired effect, e.g.
&lt;type . . .>
. . .
&lt;attributeGroup ref="xml:specialAttrs"/>
will define a type which will schema-validate an instance
element with any of those attributes</xs:documentation>
</xs:annotation>
<xs:annotation>
<xs:documentation>In keeping with the XML Schema WG's standard versioning
policy, this schema document will persist at
http://www.w3.org/2007/08/xml.xsd.
At the date of issue it can also be found at
http://www.w3.org/2001/xml.xsd.
The schema document at that URI may however change in the future,
in order to remain compatible with the latest version of XML Schema
itself, or with the XML namespace itself. In other words, if the XML
Schema or XML namespaces change, the version of this document at
http://www.w3.org/2001/xml.xsd will change
accordingly; the version at
http://www.w3.org/2007/08/xml.xsd will not change.
</xs:documentation>
</xs:annotation>
<xs:attribute name="lang">
<xs:annotation>
<xs:documentation>Attempting to install the relevant ISO 2- and 3-letter
codes as the enumerated possible values is probably never
going to be a realistic possibility. See
RFC 3066 at http://www.ietf.org/rfc/rfc3066.txt and the IANA registry
at http://www.iana.org/assignments/lang-tag-apps.htm for
further information.
The union allows for the 'un-declaration' of xml:lang with
the empty string.</xs:documentation>
</xs:annotation>
<xs:simpleType>
<xs:union memberTypes="xs:language">
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value=""/>
</xs:restriction>
</xs:simpleType>
</xs:union>
</xs:simpleType>
</xs:attribute>
<xs:attribute name="space">
<xs:simpleType>
<xs:restriction base="xs:NCName">
<xs:enumeration value="default"/>
<xs:enumeration value="preserve"/>
</xs:restriction>
</xs:simpleType>
</xs:attribute>
<xs:attribute name="base" type="xs:anyURI">
<xs:annotation>
<xs:documentation>See http://www.w3.org/TR/xmlbase/ for
information about this attribute.</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="id" type="xs:ID">
<xs:annotation>
<xs:documentation>See http://www.w3.org/TR/xml-id/ for
information about this attribute.</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attributeGroup name="specialAttrs">
<xs:attribute ref="xml:base"/>
<xs:attribute ref="xml:lang"/>
<xs:attribute ref="xml:space"/>
<xs:attribute ref="xml:id"/>
</xs:attributeGroup>
</xs:schema>

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118
epiuclid/serializers/i6z.py Normal file
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import io
import xml.etree.ElementTree as ET
import zipfile
from epiuclid.builders.base import NS_PLATFORM_CONTAINER, document_key
from epiuclid.builders.endpoint_study import EndpointStudyRecordBuilder
from epiuclid.builders.reference_substance import ReferenceSubstanceBuilder
from epiuclid.builders.substance import SubstanceBuilder
from epiuclid.serializers.manifest import ManifestBuilder
from epiuclid.serializers.pathway_mapper import IUCLIDDocumentBundle
from epiuclid.schemas.loader import get_content_schema
def _i6d_filename(uuid) -> str:
return f"{uuid}_0.i6d"
class I6ZSerializer:
"""Serialize a IUCLIDDocumentBundle to a ZIP file containing the manifest.xml and the i6d files in memory."""
def serialize(self, bundle: IUCLIDDocumentBundle, *, validate: bool = False) -> bytes:
return self._assemble(bundle, validate=validate)
def _assemble(self, bundle: IUCLIDDocumentBundle, *, validate: bool = False) -> bytes:
sub_builder = SubstanceBuilder()
ref_builder = ReferenceSubstanceBuilder()
esr_builder = EndpointStudyRecordBuilder()
# (filename, xml_string, doc_type, uuid, subtype)
files: list[tuple[str, str, str, str, str | None]] = []
for sub in bundle.substances:
fname = _i6d_filename(sub.uuid)
xml = sub_builder.build(sub)
files.append((fname, xml, "SUBSTANCE", str(sub.uuid), None))
for ref in bundle.reference_substances:
fname = _i6d_filename(ref.uuid)
xml = ref_builder.build(ref)
files.append((fname, xml, "REFERENCE_SUBSTANCE", str(ref.uuid), None))
for esr in bundle.endpoint_study_records:
fname = _i6d_filename(esr.uuid)
xml = esr_builder.build(esr)
files.append(
(fname, xml, "ENDPOINT_STUDY_RECORD", str(esr.uuid), "BiodegradationInSoil")
)
if validate:
self._validate_documents(files)
# Build document relationship links for manifest
links = self._build_links(bundle)
# Build manifest
manifest_docs = [(f[0], f[2], f[3], f[4]) for f in files]
base_uuid = str(bundle.substances[0].uuid) if bundle.substances else ""
manifest_xml = ManifestBuilder().build(manifest_docs, base_uuid, links=links)
# Assemble ZIP
buf = io.BytesIO()
with zipfile.ZipFile(buf, "w", zipfile.ZIP_DEFLATED) as zf:
zf.writestr("manifest.xml", manifest_xml)
for fname, xml, _, _, _ in files:
zf.writestr(fname, xml)
return buf.getvalue()
@staticmethod
def _validate_documents(
files: list[tuple[str, str, str, str, str | None]],
) -> None:
"""Validate each i6d document against its XSD schema.
Raises ``xmlschema.XMLSchemaValidationError`` on the first failure.
"""
for fname, xml, doc_type, _uuid, subtype in files:
root = ET.fromstring(xml)
content = root.find(f"{{{NS_PLATFORM_CONTAINER}}}Content")
if content is None or len(content) == 0:
continue
content_el = list(content)[0]
schema = get_content_schema(doc_type, subtype)
schema.validate(content_el)
@staticmethod
def _build_links(bundle: IUCLIDDocumentBundle) -> dict[str, list[tuple[str, str]]]:
"""Build manifest link relationships between documents.
Returns a dict mapping document UUID (str) to list of (target_doc_key, ref_type).
"""
links: dict[str, list[tuple[str, str]]] = {}
def _add(uuid_str: str, target_key: str, ref_type: str) -> None:
doc_links = links.setdefault(uuid_str, [])
link = (target_key, ref_type)
if link not in doc_links:
doc_links.append(link)
# Substance -> REFERENCE link to its reference substance
for sub in bundle.substances:
if sub.reference_substance_uuid:
ref_key = document_key(sub.reference_substance_uuid)
_add(str(sub.uuid), ref_key, "REFERENCE")
# ESR -> PARENT link to its substance; substance -> CHILD link to ESR
for esr in bundle.endpoint_study_records:
sub_key = document_key(esr.substance_uuid)
esr_key = document_key(esr.uuid)
_add(str(esr.uuid), sub_key, "PARENT")
_add(str(esr.substance_uuid), esr_key, "CHILD")
for tp in esr.transformation_products:
_add(str(esr.uuid), document_key(tp.product_reference_uuid), "REFERENCE")
for parent_ref_uuid in tp.parent_reference_uuids:
_add(str(esr.uuid), document_key(parent_ref_uuid), "REFERENCE")
return links

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import xml.etree.ElementTree as ET
from datetime import datetime, timezone
from epiuclid.builders.base import document_key
NS_MANIFEST = "http://iuclid6.echa.europa.eu/namespaces/manifest/v1"
NS_XLINK = "http://www.w3.org/1999/xlink"
ET.register_namespace("", NS_MANIFEST)
ET.register_namespace("xlink", NS_XLINK)
def _i6d_filename(uuid) -> str:
"""Convert UUID to i6d filename (uuid_0.i6d for raw data)."""
return f"{uuid}_0.i6d"
def _tag(local: str) -> str:
return f"{{{NS_MANIFEST}}}{local}"
def _add_link(links_elem: ET.Element, ref_uuid: str, ref_type: str) -> None:
"""Add a <link> element with ref-uuid and ref-type."""
link = ET.SubElement(links_elem, _tag("link"))
ref_uuid_elem = ET.SubElement(link, _tag("ref-uuid"))
ref_uuid_elem.text = ref_uuid
ref_type_elem = ET.SubElement(link, _tag("ref-type"))
ref_type_elem.text = ref_type
class ManifestBuilder:
def build(
self,
documents: list[tuple[str, str, str, str | None]],
base_document_uuid: str,
links: dict[str, list[tuple[str, str]]] | None = None,
) -> str:
"""Build manifest.xml.
Args:
documents: List of (filename, doc_type, uuid, subtype) tuples.
base_document_uuid: UUID of the base document (the substance export started from).
links: Optional dict mapping document UUID to list of (target_doc_key, ref_type) tuples.
ref_type is one of: PARENT, CHILD, REFERENCE.
"""
if links is None:
links = {}
root = ET.Element(_tag("manifest"))
# general-information
gi = ET.SubElement(root, _tag("general-information"))
title = ET.SubElement(gi, _tag("title"))
title.text = "IUCLID 6 container manifest file"
created = ET.SubElement(gi, _tag("created"))
created.text = datetime.now(timezone.utc).strftime("%a %b %d %H:%M:%S %Z %Y")
author = ET.SubElement(gi, _tag("author"))
author.text = "enviPath"
application = ET.SubElement(gi, _tag("application"))
application.text = "enviPath IUCLID Export"
submission_type = ET.SubElement(gi, _tag("submission-type"))
submission_type.text = "R_INT_ONSITE"
archive_type = ET.SubElement(gi, _tag("archive-type"))
archive_type.text = "RAW_DATA"
legislations = ET.SubElement(gi, _tag("legislations-info"))
leg = ET.SubElement(legislations, _tag("legislation"))
leg_id = ET.SubElement(leg, _tag("id"))
leg_id.text = "core"
leg_ver = ET.SubElement(leg, _tag("version"))
leg_ver.text = "10.0"
# base-document-uuid
base_doc = ET.SubElement(root, _tag("base-document-uuid"))
base_doc.text = document_key(base_document_uuid)
# contained-documents
contained = ET.SubElement(root, _tag("contained-documents"))
now = datetime.now(timezone.utc).strftime("%Y-%m-%dT%H:%M:%SZ")
for filename, doc_type, uuid, subtype in documents:
doc_key = document_key(uuid)
doc_elem = ET.SubElement(contained, _tag("document"))
doc_elem.set("id", doc_key)
type_elem = ET.SubElement(doc_elem, _tag("type"))
type_elem.text = doc_type
if subtype:
subtype_elem = ET.SubElement(doc_elem, _tag("subtype"))
subtype_elem.text = subtype
name_elem = ET.SubElement(doc_elem, _tag("name"))
name_elem.set(f"{{{NS_XLINK}}}type", "simple")
name_elem.set(f"{{{NS_XLINK}}}href", filename)
name_elem.text = filename
first_mod = ET.SubElement(doc_elem, _tag("first-modification-date"))
first_mod.text = now
last_mod = ET.SubElement(doc_elem, _tag("last-modification-date"))
last_mod.text = now
uuid_elem = ET.SubElement(doc_elem, _tag("uuid"))
uuid_elem.text = doc_key
# Add links for this document if any
doc_links = links.get(uuid, [])
if doc_links:
links_elem = ET.SubElement(doc_elem, _tag("links"))
for target_key, ref_type in doc_links:
_add_link(links_elem, target_key, ref_type)
return ET.tostring(root, encoding="unicode", xml_declaration=True)

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from __future__ import annotations
import logging
from dataclasses import dataclass, field
from uuid import UUID, uuid4
from epapi.v1.interfaces.iuclid.dto import PathwayExportDTO
from utilities.chem import FormatConverter
logger = logging.getLogger(__name__)
@dataclass
class IUCLIDReferenceSubstanceData:
uuid: UUID
name: str
smiles: str | None = None
cas_number: str | None = None
ec_number: str | None = None
iupac_name: str | None = None
molecular_formula: str | None = None
molecular_weight: float | None = None
inchi: str | None = None
inchi_key: str | None = None
@dataclass
class IUCLIDSubstanceData:
uuid: UUID
name: str
reference_substance_uuid: UUID | None = None
@dataclass
class SoilPropertiesData:
soil_no_code: str | None = None
soil_type: str | None = None
sand: float | None = None
silt: float | None = None
clay: float | None = None
org_carbon: float | None = None
ph_lower: float | None = None
ph_upper: float | None = None
ph_method: str | None = None
cec: float | None = None
moisture_content: float | None = None
soil_classification: str | None = None
@dataclass
class IUCLIDEndpointStudyRecordData:
uuid: UUID
substance_uuid: UUID
name: str
half_lives: list[HalfLifeEntry] = field(default_factory=list)
temperature: tuple[float, float] | None = None
transformation_products: list[IUCLIDTransformationProductEntry] = field(default_factory=list)
model_name_and_version: list[str] = field(default_factory=list)
software_name_and_version: list[str] = field(default_factory=list)
model_remarks: list[str] = field(default_factory=list)
soil_properties: SoilPropertiesData | None = None
soil_properties_entries: list[SoilPropertiesData] = field(default_factory=list)
@dataclass
class HalfLifeEntry:
model: str
dt50_start: float
dt50_end: float
unit: str
source: str
soil_no_code: str | None = None
temperature: tuple[float, float] | None = None
@dataclass
class IUCLIDTransformationProductEntry:
uuid: UUID
product_reference_uuid: UUID
parent_reference_uuids: list[UUID] = field(default_factory=list)
kinetic_formation_fraction: float | None = None
source_edge_uuid: UUID | None = None
@dataclass
class IUCLIDDocumentBundle:
substances: list[IUCLIDSubstanceData] = field(default_factory=list)
reference_substances: list[IUCLIDReferenceSubstanceData] = field(default_factory=list)
endpoint_study_records: list[IUCLIDEndpointStudyRecordData] = field(default_factory=list)
class PathwayMapper:
def map(self, export: PathwayExportDTO) -> IUCLIDDocumentBundle:
bundle = IUCLIDDocumentBundle()
seen_compounds: dict[
int, tuple[UUID, UUID]
] = {} # compound PK -> (substance UUID, ref UUID)
compound_names: dict[int, str] = {}
for compound in export.compounds:
if compound.pk in seen_compounds:
continue
derived = self._compute_derived_properties(compound.smiles)
ref_sub_uuid = uuid4()
sub_uuid = uuid4()
seen_compounds[compound.pk] = (sub_uuid, ref_sub_uuid)
compound_names[compound.pk] = compound.name
ref_sub = IUCLIDReferenceSubstanceData(
uuid=ref_sub_uuid,
name=compound.name,
smiles=compound.smiles,
cas_number=compound.cas_number,
molecular_formula=derived["molecular_formula"],
molecular_weight=derived["molecular_weight"],
inchi=derived["inchi"],
inchi_key=derived["inchi_key"],
)
bundle.reference_substances.append(ref_sub)
sub = IUCLIDSubstanceData(
uuid=sub_uuid,
name=compound.name,
reference_substance_uuid=ref_sub_uuid,
)
bundle.substances.append(sub)
if not export.compounds:
return bundle
root_compound_pks: list[int] = []
seen_root_pks: set[int] = set()
for root_pk in export.root_compound_pks:
if root_pk in seen_compounds and root_pk not in seen_root_pks:
root_compound_pks.append(root_pk)
seen_root_pks.add(root_pk)
if not root_compound_pks:
fallback_root_pk = export.compounds[0].pk
if fallback_root_pk in seen_compounds:
root_compound_pks = [fallback_root_pk]
if not root_compound_pks:
return bundle
edge_templates: list[tuple[UUID, frozenset[int], tuple[int, ...], tuple[UUID, ...]]] = []
for edge in sorted(export.edges, key=lambda item: str(item.edge_uuid)):
parent_compound_pks = sorted(
{pk for pk in edge.start_compound_pks if pk in seen_compounds}
)
product_compound_pks = sorted(
{pk for pk in edge.end_compound_pks if pk in seen_compounds}
)
if not parent_compound_pks or not product_compound_pks:
continue
parent_ref_uuids = tuple(
sorted({seen_compounds[pk][1] for pk in parent_compound_pks}, key=str)
)
edge_templates.append(
(
edge.edge_uuid,
frozenset(parent_compound_pks),
tuple(product_compound_pks),
parent_ref_uuids,
)
)
model_names: list[str] = []
software_names: list[str] = []
model_remarks: list[str] = []
if export.model_info:
if export.model_info.model_name:
model_names.append(export.model_info.model_name)
if export.model_info.model_uuid:
model_remarks.append(f"Model UUID: {export.model_info.model_uuid}")
if export.model_info.software_name:
if export.model_info.software_version:
software_names.append(
f"{export.model_info.software_name} {export.model_info.software_version}"
)
else:
software_names.append(export.model_info.software_name)
# Aggregate scenario-aware AI from all root nodes for each root compound.
# Each entry is (scenario_uuid, scenario_name, effective_ai_list).
root_node_ai_by_scenario: dict[int, dict[str, tuple[UUID | None, str | None, list]]] = {}
for node in export.nodes:
if node.depth == 0 and node.compound_pk in seen_root_pks:
scenario_bucket = root_node_ai_by_scenario.setdefault(node.compound_pk, {})
if node.scenarios:
for scenario in node.scenarios:
scenario_key = str(scenario.scenario_uuid)
existing = scenario_bucket.get(scenario_key)
if existing is None:
scenario_bucket[scenario_key] = (
scenario.scenario_uuid,
scenario.name,
list(scenario.additional_info),
)
else:
existing[2].extend(scenario.additional_info)
else:
# Backward compatibility path for callers that only provide node.additional_info.
fallback_key = f"fallback:{node.node_uuid}"
scenario_bucket[fallback_key] = (None, None, list(node.additional_info))
has_multiple_roots = len(root_compound_pks) > 1
for root_pk in root_compound_pks:
substance_uuid, _ = seen_compounds[root_pk]
esr_name = f"Biodegradation in soil - {export.pathway_name}"
if has_multiple_roots:
root_name = compound_names.get(root_pk)
if root_name:
esr_name = f"{esr_name} ({root_name})"
transformation_entries: list[IUCLIDTransformationProductEntry] = []
reachable_compound_pks = self._reachable_compounds_from_root(root_pk, edge_templates)
seen_transformations: set[tuple[UUID, tuple[UUID, ...]]] = set()
for (
edge_uuid,
parent_compound_pks,
product_compound_pks,
parent_reference_uuids,
) in edge_templates:
if not parent_compound_pks.issubset(reachable_compound_pks):
continue
for product_compound_pk in product_compound_pks:
if product_compound_pk not in reachable_compound_pks:
continue
product_ref_uuid = seen_compounds[product_compound_pk][1]
dedupe_key = (product_ref_uuid, parent_reference_uuids)
if dedupe_key in seen_transformations:
continue
seen_transformations.add(dedupe_key)
transformation_entries.append(
IUCLIDTransformationProductEntry(
uuid=uuid4(),
product_reference_uuid=product_ref_uuid,
parent_reference_uuids=list(parent_reference_uuids),
source_edge_uuid=edge_uuid,
)
)
scenarios_for_root = list(root_node_ai_by_scenario.get(root_pk, {}).values())
if not scenarios_for_root:
scenarios_for_root = [(None, None, [])]
soil_entries: list[SoilPropertiesData] = []
soil_no_by_signature: dict[tuple, str] = {}
half_lives: list[HalfLifeEntry] = []
merged_ai_for_root: list = []
for _, _, ai_for_scenario in scenarios_for_root:
merged_ai_for_root.extend(ai_for_scenario)
soil = self._extract_soil_properties(ai_for_scenario)
temperature = self._extract_temperature(ai_for_scenario)
soil_no_code: str | None = None
if soil is not None:
soil_signature = self._soil_signature(soil)
soil_no_code = soil_no_by_signature.get(soil_signature)
if soil_no_code is None:
soil_no_code = self._soil_no_code_for_index(len(soil_entries))
if soil_no_code is not None:
soil.soil_no_code = soil_no_code
soil_entries.append(soil)
soil_no_by_signature[soil_signature] = soil_no_code
for hl in self._extract_half_lives(ai_for_scenario):
hl.soil_no_code = soil_no_code
hl.temperature = temperature
half_lives.append(hl)
esr = IUCLIDEndpointStudyRecordData(
uuid=uuid4(),
substance_uuid=substance_uuid,
name=esr_name,
half_lives=half_lives,
temperature=self._extract_temperature(merged_ai_for_root),
transformation_products=transformation_entries,
model_name_and_version=model_names,
software_name_and_version=software_names,
model_remarks=model_remarks,
soil_properties=soil_entries[0] if soil_entries else None,
soil_properties_entries=soil_entries,
)
bundle.endpoint_study_records.append(esr)
return bundle
@staticmethod
def _extract_half_lives(ai_list: list) -> list[HalfLifeEntry]:
from envipy_additional_information.information import HalfLife
entries = []
for ai in ai_list:
if not isinstance(ai, HalfLife):
continue
start = ai.dt50.start
end = ai.dt50.end
if start is None or end is None:
continue
entries.append(
HalfLifeEntry(
model=ai.model,
dt50_start=start,
dt50_end=end,
unit="d",
source=ai.source,
)
)
return entries
@staticmethod
def _extract_temperature(ai_list: list) -> tuple[float, float] | None:
from envipy_additional_information.information import Temperature
for ai in ai_list:
if not isinstance(ai, Temperature):
continue
lower = ai.interval.start
upper = ai.interval.end
if lower is None or upper is None:
continue
return (lower, upper)
return None
@staticmethod
def _extract_soil_properties(ai_list: list) -> SoilPropertiesData | None:
from envipy_additional_information.information import (
Acidity,
BulkDensity,
CEC,
Humidity,
OMContent,
SoilClassification,
SoilTexture1,
SoilTexture2,
)
props = SoilPropertiesData()
for ai in ai_list:
if isinstance(ai, SoilTexture1) and props.soil_type is None:
props.soil_type = ai.type.value
elif isinstance(ai, SoilTexture2):
if props.sand is None:
props.sand = ai.sand
if props.silt is None:
props.silt = ai.silt
if props.clay is None:
props.clay = ai.clay
elif isinstance(ai, OMContent) and props.org_carbon is None:
props.org_carbon = ai.in_oc
elif isinstance(ai, Acidity) and props.ph_lower is None:
props.ph_lower = ai.interval.start
props.ph_upper = ai.interval.end
if isinstance(ai.method, str):
props.ph_method = ai.method.strip() or None
else:
props.ph_method = ai.method
elif isinstance(ai, CEC) and props.cec is None:
props.cec = ai.capacity
elif isinstance(ai, Humidity) and props.moisture_content is None:
props.moisture_content = ai.humiditiy
elif isinstance(ai, SoilClassification) and props.soil_classification is None:
props.soil_classification = ai.system.value
elif isinstance(ai, BulkDensity):
pass # BulkDensity.data is a free-text string; not mapped to SoilPropertiesData
all_none = all(
v is None
for v in (
props.soil_type,
props.sand,
props.silt,
props.clay,
props.org_carbon,
props.ph_lower,
props.ph_upper,
props.ph_method,
props.cec,
props.moisture_content,
props.soil_classification,
)
)
return None if all_none else props
@staticmethod
def _reachable_compounds_from_root(
root_compound_pk: int,
edge_templates: list[tuple[UUID, frozenset[int], tuple[int, ...], tuple[UUID, ...]]],
) -> set[int]:
reachable: set[int] = {root_compound_pk}
changed = True
while changed:
changed = False
for _, parent_compound_pks, product_compound_pks, _ in edge_templates:
if not parent_compound_pks.issubset(reachable):
continue
for product_compound_pk in product_compound_pks:
if product_compound_pk in reachable:
continue
reachable.add(product_compound_pk)
changed = True
return reachable
@staticmethod
def _soil_signature(props: SoilPropertiesData) -> tuple:
return (
props.soil_type,
props.sand,
props.silt,
props.clay,
props.org_carbon,
props.ph_lower,
props.ph_upper,
props.ph_method,
props.cec,
props.moisture_content,
props.soil_classification,
)
@staticmethod
def _soil_no_code_for_index(index: int) -> str | None:
f137_codes = [
"2",
"4",
"5",
"6",
"7",
"8",
"9",
"10",
"11",
"3",
"4070",
"4071",
"4072",
"4073",
"4074",
"4075",
"4076",
"4077",
"4078",
"4079",
]
if 0 <= index < len(f137_codes):
return f137_codes[index]
return None
@staticmethod
def _compute_derived_properties(smiles: str | None) -> dict:
molecular_formula = None
molecular_weight = None
inchi = None
inchi_key = None
if smiles:
try:
molecular_formula = FormatConverter.formula(smiles)
except Exception:
logger.debug("Could not compute formula for %s", smiles)
try:
molecular_weight = FormatConverter.mass(smiles)
except Exception:
logger.debug("Could not compute mass for %s", smiles)
try:
inchi = FormatConverter.InChI(smiles)
except Exception:
logger.debug("Could not compute InChI for %s", smiles)
try:
inchi_key = FormatConverter.InChIKey(smiles)
except Exception:
logger.debug("Could not compute InChIKey for %s", smiles)
return {
"molecular_formula": molecular_formula,
"molecular_weight": molecular_weight,
"inchi": inchi,
"inchi_key": inchi_key,
}

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102
epiuclid/tests/factories.py Normal file
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from __future__ import annotations
from uuid import uuid4
from epiuclid.serializers.pathway_mapper import (
HalfLifeEntry,
IUCLIDEndpointStudyRecordData,
IUCLIDReferenceSubstanceData,
IUCLIDSubstanceData,
IUCLIDTransformationProductEntry,
SoilPropertiesData,
)
def make_substance_data(**overrides) -> IUCLIDSubstanceData:
payload = {
"uuid": uuid4(),
"name": "Atrazine",
"reference_substance_uuid": uuid4(),
}
payload.update(overrides)
return IUCLIDSubstanceData(**payload)
def make_reference_substance_data(**overrides) -> IUCLIDReferenceSubstanceData:
payload = {
"uuid": uuid4(),
"name": "Atrazine",
"smiles": "CCNc1nc(Cl)nc(NC(C)C)n1",
"cas_number": "1912-24-9",
"ec_number": "217-617-8",
"iupac_name": "6-chloro-N2-ethyl-N4-isopropyl-1,3,5-triazine-2,4-diamine",
"molecular_formula": "C8H14ClN5",
"molecular_weight": 215.68,
"inchi": (
"InChI=1S/C8H14ClN5/c1-4-10-7-12-6(9)11-8(13-7)"
"14-5(2)3/h5H,4H2,1-3H3,(H2,10,11,12,13,14)"
),
"inchi_key": "MXWJVTOOROXGIU-UHFFFAOYSA-N",
}
payload.update(overrides)
return IUCLIDReferenceSubstanceData(**payload)
def make_half_life_entry(**overrides) -> HalfLifeEntry:
payload = {
"model": "SFO",
"dt50_start": 12.5,
"dt50_end": 15.0,
"unit": "d",
"source": "Model prediction",
"soil_no_code": None,
"temperature": None,
}
payload.update(overrides)
return HalfLifeEntry(**payload)
def make_transformation_entry(**overrides) -> IUCLIDTransformationProductEntry:
payload = {
"uuid": uuid4(),
"product_reference_uuid": uuid4(),
"parent_reference_uuids": [uuid4()],
"kinetic_formation_fraction": 0.42,
}
payload.update(overrides)
return IUCLIDTransformationProductEntry(**payload)
def make_soil_properties_data(**overrides) -> SoilPropertiesData:
payload = {
"soil_no_code": None,
"clay": 20.0,
"silt": 30.0,
"sand": 50.0,
"org_carbon": 1.5,
"ph_lower": 6.0,
"ph_upper": 7.0,
"ph_method": "CaCl2",
"cec": 12.0,
"moisture_content": 40.0,
"soil_type": "LOAM",
"soil_classification": "USDA",
}
payload.update(overrides)
return SoilPropertiesData(**payload)
def make_endpoint_study_record_data(**overrides) -> IUCLIDEndpointStudyRecordData:
payload = {
"uuid": uuid4(),
"substance_uuid": uuid4(),
"name": "Biodegradation study",
"half_lives": [],
"temperature": None,
"transformation_products": [],
"model_name_and_version": [],
"software_name_and_version": [],
"model_remarks": [],
}
payload.update(overrides)
return IUCLIDEndpointStudyRecordData(**payload)

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"""Integration tests for IUCLID export API endpoint."""
import io
import zipfile
from uuid import uuid4
from django.test import TestCase, tag
from epdb.logic import PackageManager, UserManager
from epdb.models import Node, Pathway
@tag("iuclid")
class IUCLIDExportAPITest(TestCase):
@classmethod
def setUpTestData(cls):
cls.user = UserManager.create_user(
"iuclid-api-user",
"iuclid-api@test.com",
"TestPass123",
set_setting=False,
add_to_group=False,
is_active=True,
)
default_pkg = cls.user.default_package
cls.user.default_package = None
cls.user.save()
default_pkg.delete()
cls.package = PackageManager.create_package(cls.user, "IUCLID API Test Package")
cls.pathway = Pathway.create(
cls.package,
"c1ccccc1",
name="Export Test Pathway",
)
Node.create(cls.pathway, "c1ccc(O)cc1", depth=1, name="Phenol")
# Unauthorized user
cls.other_user = UserManager.create_user(
"iuclid-other-user",
"other@test.com",
"TestPass123",
set_setting=False,
add_to_group=False,
is_active=True,
)
other_pkg = cls.other_user.default_package
cls.other_user.default_package = None
cls.other_user.save()
other_pkg.delete()
def test_export_returns_zip(self):
self.client.force_login(self.user)
url = f"/api/v1/pathway/{self.pathway.uuid}/export/iuclid"
response = self.client.get(url)
self.assertEqual(response.status_code, 200)
self.assertEqual(response["Content-Type"], "application/zip")
self.assertIn(".i6z", response["Content-Disposition"])
self.assertTrue(zipfile.is_zipfile(io.BytesIO(response.content)))
def test_export_contains_expected_files(self):
self.client.force_login(self.user)
url = f"/api/v1/pathway/{self.pathway.uuid}/export/iuclid"
response = self.client.get(url)
with zipfile.ZipFile(io.BytesIO(response.content)) as zf:
names = zf.namelist()
self.assertIn("manifest.xml", names)
i6d_files = [n for n in names if n.endswith(".i6d")]
# 2 substances + 2 ref substances + 1 ESR = 5 i6d files
self.assertEqual(len(i6d_files), 5)
def test_anonymous_returns_401(self):
self.client.logout()
url = f"/api/v1/pathway/{self.pathway.uuid}/export/iuclid"
response = self.client.get(url)
self.assertEqual(response.status_code, 401)
def test_unauthorized_user_returns_403(self):
self.client.force_login(self.other_user)
url = f"/api/v1/pathway/{self.pathway.uuid}/export/iuclid"
response = self.client.get(url)
self.assertEqual(response.status_code, 403)
def test_nonexistent_pathway_returns_404(self):
self.client.force_login(self.user)
url = f"/api/v1/pathway/{uuid4()}/export/iuclid"
response = self.client.get(url)
self.assertEqual(response.status_code, 404)

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"""Contract tests for IUCLID XML builders - no DB required."""
import xml.etree.ElementTree as ET
from uuid import uuid4
from django.test import SimpleTestCase, tag
from epiuclid.builders.base import (
NS_PLATFORM_CONTAINER,
NS_PLATFORM_FIELDS,
NS_PLATFORM_METADATA,
document_key,
)
from epiuclid.builders.endpoint_study import DOC_SUBTYPE, EndpointStudyRecordBuilder, NS_ESR_BIODEG
from epiuclid.builders.reference_substance import NS_REFERENCE_SUBSTANCE, ReferenceSubstanceBuilder
from epiuclid.builders.substance import NS_SUBSTANCE, SubstanceBuilder
from .factories import (
make_endpoint_study_record_data,
make_half_life_entry,
make_reference_substance_data,
make_soil_properties_data,
make_substance_data,
make_transformation_entry,
)
from .xml_assertions import assert_xpath_absent, assert_xpath_text
@tag("iuclid")
class SubstanceBuilderContractTest(SimpleTestCase):
def test_maps_name_and_reference_key(self):
reference_uuid = uuid4()
data = make_substance_data(name="Atrazine", reference_substance_uuid=reference_uuid)
root = ET.fromstring(SubstanceBuilder().build(data))
assert_xpath_text(self, root, f".//{{{NS_SUBSTANCE}}}ChemicalName", "Atrazine")
assert_xpath_text(
self,
root,
f".//{{{NS_SUBSTANCE}}}ReferenceSubstance/{{{NS_SUBSTANCE}}}ReferenceSubstance",
document_key(reference_uuid),
)
def test_omits_reference_substance_when_missing(self):
data = make_substance_data(reference_substance_uuid=None)
root = ET.fromstring(SubstanceBuilder().build(data))
assert_xpath_absent(self, root, f".//{{{NS_SUBSTANCE}}}ReferenceSubstance")
def test_sets_substance_document_type(self):
data = make_substance_data()
root = ET.fromstring(SubstanceBuilder().build(data))
assert_xpath_text(
self,
root,
f"{{{NS_PLATFORM_CONTAINER}}}PlatformMetadata/{{{NS_PLATFORM_METADATA}}}documentType",
"SUBSTANCE",
)
@tag("iuclid")
class ReferenceSubstanceBuilderContractTest(SimpleTestCase):
def test_maps_structural_identifiers_and_mass_precision(self):
data = make_reference_substance_data(molecular_weight=215.6)
root = ET.fromstring(ReferenceSubstanceBuilder().build(data))
assert_xpath_text(
self,
root,
f".//{{{NS_REFERENCE_SUBSTANCE}}}Inventory/{{{NS_REFERENCE_SUBSTANCE}}}CASNumber",
"1912-24-9",
)
assert_xpath_text(
self,
root,
f".//{{{NS_REFERENCE_SUBSTANCE}}}MolecularStructuralInfo/{{{NS_REFERENCE_SUBSTANCE}}}InChl",
(
"InChI=1S/C8H14ClN5/c1-4-10-7-12-6(9)11-8(13-7)"
"14-5(2)3/h5H,4H2,1-3H3,(H2,10,11,12,13,14)"
),
)
assert_xpath_text(
self,
root,
f".//{{{NS_REFERENCE_SUBSTANCE}}}MolecularStructuralInfo/{{{NS_REFERENCE_SUBSTANCE}}}InChIKey",
"MXWJVTOOROXGIU-UHFFFAOYSA-N",
)
assert_xpath_text(
self,
root,
f".//{{{NS_REFERENCE_SUBSTANCE}}}MolecularStructuralInfo"
f"/{{{NS_REFERENCE_SUBSTANCE}}}MolecularWeightRange"
f"/{{{NS_REFERENCE_SUBSTANCE}}}lowerValue",
"215.60",
)
def test_omits_inventory_and_weight_for_minimal_payload(self):
data = make_reference_substance_data(
cas_number=None,
molecular_formula=None,
molecular_weight=None,
inchi=None,
inchi_key=None,
smiles="CC",
)
root = ET.fromstring(ReferenceSubstanceBuilder().build(data))
assert_xpath_absent(self, root, f".//{{{NS_REFERENCE_SUBSTANCE}}}Inventory")
assert_xpath_absent(
self,
root,
f".//{{{NS_REFERENCE_SUBSTANCE}}}MolecularWeightRange",
)
assert_xpath_text(
self,
root,
f".//{{{NS_REFERENCE_SUBSTANCE}}}MolecularStructuralInfo/{{{NS_REFERENCE_SUBSTANCE}}}SmilesNotation",
"CC",
)
@tag("iuclid")
class EndpointStudyRecordBuilderContractTest(SimpleTestCase):
def test_sets_document_metadata_and_parent_link(self):
substance_uuid = uuid4()
data = make_endpoint_study_record_data(substance_uuid=substance_uuid)
root = ET.fromstring(EndpointStudyRecordBuilder().build(data))
metadata_root = f"{{{NS_PLATFORM_CONTAINER}}}PlatformMetadata"
assert_xpath_text(
self,
root,
f"{metadata_root}/{{{NS_PLATFORM_METADATA}}}documentType",
"ENDPOINT_STUDY_RECORD",
)
assert_xpath_text(
self,
root,
f"{metadata_root}/{{{NS_PLATFORM_METADATA}}}documentSubType",
DOC_SUBTYPE,
)
assert_xpath_text(
self,
root,
f"{metadata_root}/{{{NS_PLATFORM_METADATA}}}parentDocumentKey",
document_key(substance_uuid),
)
assert_xpath_text(
self,
root,
f"{metadata_root}/{{{NS_PLATFORM_METADATA}}}orderInSectionNo",
"1",
)
def test_esr_metadata_order_uses_stax_safe_layout(self):
data = make_endpoint_study_record_data()
root = ET.fromstring(EndpointStudyRecordBuilder().build(data))
metadata = root.find(f"{{{NS_PLATFORM_CONTAINER}}}PlatformMetadata")
self.assertIsNotNone(metadata)
assert metadata is not None
child_tags = [el.tag.split("}", 1)[1] for el in list(metadata)]
self.assertEqual(
child_tags,
[
"iuclidVersion",
"documentKey",
"documentType",
"definitionVersion",
"creationDate",
"lastModificationDate",
"name",
"documentSubType",
"parentDocumentKey",
"orderInSectionNo",
"i5Origin",
"creationTool",
],
)
def test_omits_results_for_skeleton_payload(self):
data = make_endpoint_study_record_data()
root = ET.fromstring(EndpointStudyRecordBuilder().build(data))
assert_xpath_absent(self, root, f".//{{{NS_ESR_BIODEG}}}ResultsAndDiscussion")
def test_maps_half_life_and_temperature_ranges(self):
data = make_endpoint_study_record_data(
half_lives=[make_half_life_entry(model="SFO", dt50_start=12.5, dt50_end=15.0)],
temperature=(20.0, 20.0),
)
root = ET.fromstring(EndpointStudyRecordBuilder().build(data))
base = (
f".//{{{NS_ESR_BIODEG}}}ResultsAndDiscussion"
f"/{{{NS_ESR_BIODEG}}}DTParentCompound"
f"/{{{NS_ESR_BIODEG}}}entry"
)
assert_xpath_text(self, root, f"{base}/{{{NS_ESR_BIODEG}}}KineticParameters", "SFO")
assert_xpath_text(
self, root, f"{base}/{{{NS_ESR_BIODEG}}}Value/{{{NS_ESR_BIODEG}}}lowerValue", "12.5"
)
assert_xpath_text(
self, root, f"{base}/{{{NS_ESR_BIODEG}}}Value/{{{NS_ESR_BIODEG}}}upperValue", "15.0"
)
assert_xpath_text(
self, root, f"{base}/{{{NS_ESR_BIODEG}}}Temp/{{{NS_ESR_BIODEG}}}lowerValue", "20.0"
)
assert_xpath_text(
self, root, f"{base}/{{{NS_ESR_BIODEG}}}Temp/{{{NS_ESR_BIODEG}}}upperValue", "20.0"
)
def test_maps_soil_no_on_dt_entries(self):
data = make_endpoint_study_record_data(
half_lives=[
make_half_life_entry(
model="SFO",
dt50_start=12.5,
dt50_end=15.0,
soil_no_code="2",
temperature=(22.0, 22.0),
)
],
temperature=None,
)
root = ET.fromstring(EndpointStudyRecordBuilder().build(data))
base = (
f".//{{{NS_ESR_BIODEG}}}ResultsAndDiscussion"
f"/{{{NS_ESR_BIODEG}}}DTParentCompound"
f"/{{{NS_ESR_BIODEG}}}entry"
)
assert_xpath_text(
self, root, f"{base}/{{{NS_ESR_BIODEG}}}SoilNo/{{{NS_ESR_BIODEG}}}value", "2"
)
assert_xpath_text(
self, root, f"{base}/{{{NS_ESR_BIODEG}}}Temp/{{{NS_ESR_BIODEG}}}lowerValue", "22.0"
)
def test_maps_transformation_entries_and_model_context(self):
parent_ref_uuid = uuid4()
product_ref_uuid = uuid4()
data = make_endpoint_study_record_data(
transformation_products=[
make_transformation_entry(
parent_reference_uuids=[parent_ref_uuid],
product_reference_uuid=product_ref_uuid,
kinetic_formation_fraction=0.42,
)
],
model_name_and_version=["Test model 1.0"],
software_name_and_version=["enviPath"],
model_remarks=["Model UUID: 00000000-0000-0000-0000-000000000000"],
)
root = ET.fromstring(EndpointStudyRecordBuilder().build(data))
assert_xpath_text(
self,
root,
f".//{{{NS_ESR_BIODEG}}}MaterialsAndMethods"
f"/{{{NS_ESR_BIODEG}}}ModelAndSoftware"
f"/{{{NS_ESR_BIODEG}}}ModelNameAndVersion",
"Test model 1.0",
)
entry_base = (
f".//{{{NS_ESR_BIODEG}}}ResultsAndDiscussion"
f"/{{{NS_ESR_BIODEG}}}TransformationProductsDetails"
f"/{{{NS_ESR_BIODEG}}}entry"
)
assert_xpath_text(
self,
root,
f"{entry_base}/{{{NS_ESR_BIODEG}}}IdentityOfCompound",
document_key(product_ref_uuid),
)
assert_xpath_text(
self,
root,
f"{entry_base}/{{{NS_ESR_BIODEG}}}ParentCompoundS/{{{NS_PLATFORM_FIELDS}}}key",
document_key(parent_ref_uuid),
)
assert_xpath_text(
self,
root,
f"{entry_base}/{{{NS_ESR_BIODEG}}}KineticFormationFraction",
"0.42",
)
def test_temperature_without_half_lives_in_xml(self):
"""Temperature with no half-lives still renders a DTParentCompound entry."""
data = make_endpoint_study_record_data(temperature=(21.0, 21.0))
root = ET.fromstring(EndpointStudyRecordBuilder().build(data))
base = (
f".//{{{NS_ESR_BIODEG}}}ResultsAndDiscussion"
f"/{{{NS_ESR_BIODEG}}}DTParentCompound"
f"/{{{NS_ESR_BIODEG}}}entry"
)
assert_xpath_text(
self, root, f"{base}/{{{NS_ESR_BIODEG}}}Temp/{{{NS_ESR_BIODEG}}}lowerValue", "21.0"
)
assert_xpath_text(
self, root, f"{base}/{{{NS_ESR_BIODEG}}}Temp/{{{NS_ESR_BIODEG}}}upperValue", "21.0"
)
def test_temperature_interval_in_xml(self):
"""Temperature tuple renders as lowerValue/upperValue in Temp element."""
hl = make_half_life_entry()
data = make_endpoint_study_record_data(half_lives=[hl], temperature=(20.0, 25.0))
root = ET.fromstring(EndpointStudyRecordBuilder().build(data))
base = (
f".//{{{NS_ESR_BIODEG}}}ResultsAndDiscussion"
f"/{{{NS_ESR_BIODEG}}}DTParentCompound"
f"/{{{NS_ESR_BIODEG}}}entry"
)
assert_xpath_text(
self, root, f"{base}/{{{NS_ESR_BIODEG}}}Temp/{{{NS_ESR_BIODEG}}}lowerValue", "20.0"
)
assert_xpath_text(
self, root, f"{base}/{{{NS_ESR_BIODEG}}}Temp/{{{NS_ESR_BIODEG}}}upperValue", "25.0"
)
def test_esr_with_soil_properties_emits_structured_soil_by_default(self):
props = make_soil_properties_data(clay=15.0, silt=35.0, sand=50.0)
data = make_endpoint_study_record_data(soil_properties=props)
root = ET.fromstring(EndpointStudyRecordBuilder().build(data))
entry_path = (
f".//{{{NS_ESR_BIODEG}}}StudyDesign"
f"/{{{NS_ESR_BIODEG}}}SoilProperties"
f"/{{{NS_ESR_BIODEG}}}entry"
)
assert_xpath_text(
self,
root,
f"{entry_path}/{{{NS_ESR_BIODEG}}}Clay/{{{NS_ESR_BIODEG}}}lowerValue",
"15.0",
)
assert_xpath_text(
self,
root,
f"{entry_path}/{{{NS_ESR_BIODEG}}}Silt/{{{NS_ESR_BIODEG}}}lowerValue",
"35.0",
)
assert_xpath_text(
self,
root,
f"{entry_path}/{{{NS_ESR_BIODEG}}}Sand/{{{NS_ESR_BIODEG}}}lowerValue",
"50.0",
)
assert_xpath_text(
self,
root,
f".//{{{NS_ESR_BIODEG}}}StudyDesign"
f"/{{{NS_ESR_BIODEG}}}SoilClassification"
f"/{{{NS_ESR_BIODEG}}}value",
"1649",
)
assert_xpath_absent(
self,
root,
f".//{{{NS_ESR_BIODEG}}}StudyDesign"
f"/{{{NS_ESR_BIODEG}}}SoilClassification"
f"/{{{NS_ESR_BIODEG}}}other",
)
assert_xpath_text(
self,
root,
f"{entry_path}/{{{NS_ESR_BIODEG}}}SoilType/{{{NS_ESR_BIODEG}}}value",
"1026",
)
assert_xpath_absent(
self,
root,
f"{entry_path}/{{{NS_ESR_BIODEG}}}SoilType/{{{NS_ESR_BIODEG}}}other",
)
assert_xpath_absent(
self,
root,
f".//{{{NS_ESR_BIODEG}}}AnyOtherInformationOnMaterialsAndMethodsInclTables",
)
assert_xpath_absent(self, root, f".//{{{NS_ESR_BIODEG}}}DetailsOnSoilCharacteristics")
def test_maps_multiple_soil_entries_with_soil_no(self):
data = make_endpoint_study_record_data(
soil_properties_entries=[
make_soil_properties_data(soil_no_code="2", soil_type="LOAMY_SAND", sand=83.1),
make_soil_properties_data(soil_no_code="4", soil_type="CLAY_LOAM", sand=23.7),
]
)
root = ET.fromstring(EndpointStudyRecordBuilder().build(data))
entries = root.findall(
f".//{{{NS_ESR_BIODEG}}}StudyDesign"
f"/{{{NS_ESR_BIODEG}}}SoilProperties"
f"/{{{NS_ESR_BIODEG}}}entry"
)
self.assertEqual(len(entries), 2)
soil_no_values = [
entry.findtext(f"{{{NS_ESR_BIODEG}}}SoilNo/{{{NS_ESR_BIODEG}}}value")
for entry in entries
]
self.assertEqual(soil_no_values, ["2", "4"])
def test_maps_soil_type_and_soil_classification_to_structured_fields(self):
props = make_soil_properties_data(soil_type="LOAMY_SAND", soil_classification="USDA")
data = make_endpoint_study_record_data(soil_properties=props)
root = ET.fromstring(EndpointStudyRecordBuilder().build(data))
entry_path = (
f".//{{{NS_ESR_BIODEG}}}StudyDesign"
f"/{{{NS_ESR_BIODEG}}}SoilProperties"
f"/{{{NS_ESR_BIODEG}}}entry"
)
assert_xpath_text(
self,
root,
f"{entry_path}/{{{NS_ESR_BIODEG}}}SoilType/{{{NS_ESR_BIODEG}}}value",
"1027",
)
assert_xpath_absent(
self, root, f"{entry_path}/{{{NS_ESR_BIODEG}}}SoilType/{{{NS_ESR_BIODEG}}}other"
)
assert_xpath_text(
self,
root,
f".//{{{NS_ESR_BIODEG}}}StudyDesign"
f"/{{{NS_ESR_BIODEG}}}SoilClassification"
f"/{{{NS_ESR_BIODEG}}}value",
"1649",
)
assert_xpath_absent(
self,
root,
f".//{{{NS_ESR_BIODEG}}}StudyDesign"
f"/{{{NS_ESR_BIODEG}}}SoilClassification"
f"/{{{NS_ESR_BIODEG}}}other",
)
def test_unknown_soil_type_and_classification_use_open_picklist(self):
props = make_soil_properties_data(soil_type="SILTY_SAND", soil_classification="UK_ADAS")
data = make_endpoint_study_record_data(soil_properties=props)
root = ET.fromstring(EndpointStudyRecordBuilder().build(data))
entry_path = (
f".//{{{NS_ESR_BIODEG}}}StudyDesign"
f"/{{{NS_ESR_BIODEG}}}SoilProperties"
f"/{{{NS_ESR_BIODEG}}}entry"
)
assert_xpath_text(
self,
root,
f"{entry_path}/{{{NS_ESR_BIODEG}}}SoilType/{{{NS_ESR_BIODEG}}}value",
"1342",
)
assert_xpath_text(
self,
root,
f"{entry_path}/{{{NS_ESR_BIODEG}}}SoilType/{{{NS_ESR_BIODEG}}}other",
"SILTY SAND",
)
assert_xpath_text(
self,
root,
f".//{{{NS_ESR_BIODEG}}}StudyDesign"
f"/{{{NS_ESR_BIODEG}}}SoilClassification"
f"/{{{NS_ESR_BIODEG}}}value",
"1342",
)
assert_xpath_text(
self,
root,
f".//{{{NS_ESR_BIODEG}}}StudyDesign"
f"/{{{NS_ESR_BIODEG}}}SoilClassification"
f"/{{{NS_ESR_BIODEG}}}other",
"UK ADAS",
)
def test_infers_usda_soil_classification_from_soil_type(self):
props = make_soil_properties_data(soil_type="LOAMY_SAND", soil_classification=None)
data = make_endpoint_study_record_data(soil_properties=props)
root = ET.fromstring(EndpointStudyRecordBuilder().build(data))
assert_xpath_text(
self,
root,
f".//{{{NS_ESR_BIODEG}}}StudyDesign"
f"/{{{NS_ESR_BIODEG}}}SoilClassification"
f"/{{{NS_ESR_BIODEG}}}value",
"1649",
)
assert_xpath_absent(
self,
root,
f".//{{{NS_ESR_BIODEG}}}StudyDesign/{{{NS_ESR_BIODEG}}}SoilClassification/{{{NS_ESR_BIODEG}}}other",
)
def test_esr_without_soil_properties_omits_study_design(self):
"""ESR with soil_properties=None → no <StudyDesign> in XML."""
data = make_endpoint_study_record_data(soil_properties=None)
root = ET.fromstring(EndpointStudyRecordBuilder().build(data))
assert_xpath_absent(self, root, f".//{{{NS_ESR_BIODEG}}}StudyDesign")
def test_omits_empty_ph_measured_in(self):
props = make_soil_properties_data(ph_method="")
data = make_endpoint_study_record_data(soil_properties=props)
root = ET.fromstring(EndpointStudyRecordBuilder().build(data))
self.assertNotIn("PHMeasuredIn", ET.tostring(root, encoding="unicode"))

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epiuclid/tests/test_i6z.py Normal file
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"""Tests for i6z archive assembly."""
import io
import xml.etree.ElementTree as ET
import zipfile
from uuid import uuid4
from django.test import SimpleTestCase, tag
from epiuclid.serializers.i6z import I6ZSerializer
from epiuclid.serializers.pathway_mapper import (
IUCLIDDocumentBundle,
IUCLIDEndpointStudyRecordData,
IUCLIDReferenceSubstanceData,
IUCLIDSubstanceData,
IUCLIDTransformationProductEntry,
)
def _make_bundle() -> IUCLIDDocumentBundle:
ref_uuid = uuid4()
sub_uuid = uuid4()
return IUCLIDDocumentBundle(
substances=[
IUCLIDSubstanceData(
uuid=sub_uuid,
name="Benzene",
reference_substance_uuid=ref_uuid,
),
],
reference_substances=[
IUCLIDReferenceSubstanceData(
uuid=ref_uuid,
name="Benzene",
smiles="c1ccccc1",
cas_number="71-43-2",
molecular_formula="C6H6",
molecular_weight=78.11,
),
],
endpoint_study_records=[
IUCLIDEndpointStudyRecordData(
uuid=uuid4(),
substance_uuid=sub_uuid,
name="Endpoint study - Benzene",
),
],
)
def _make_bundle_with_transformation_links() -> tuple[IUCLIDDocumentBundle, str, str]:
parent_ref_uuid = uuid4()
product_ref_uuid = uuid4()
sub_uuid = uuid4()
bundle = IUCLIDDocumentBundle(
substances=[
IUCLIDSubstanceData(
uuid=sub_uuid,
name="Benzene",
reference_substance_uuid=parent_ref_uuid,
),
],
reference_substances=[
IUCLIDReferenceSubstanceData(uuid=parent_ref_uuid, name="Benzene", smiles="c1ccccc1"),
IUCLIDReferenceSubstanceData(
uuid=product_ref_uuid, name="Phenol", smiles="c1ccc(O)cc1"
),
],
endpoint_study_records=[
IUCLIDEndpointStudyRecordData(
uuid=uuid4(),
substance_uuid=sub_uuid,
name="Endpoint study - Benzene",
transformation_products=[
IUCLIDTransformationProductEntry(
uuid=uuid4(),
product_reference_uuid=product_ref_uuid,
parent_reference_uuids=[parent_ref_uuid],
)
],
),
],
)
return bundle, f"{parent_ref_uuid}/0", f"{product_ref_uuid}/0"
@tag("iuclid")
class I6ZSerializerTest(SimpleTestCase):
def test_output_is_valid_zip(self):
bundle = _make_bundle()
data = I6ZSerializer().serialize(bundle)
self.assertTrue(zipfile.is_zipfile(io.BytesIO(data)))
def test_contains_manifest(self):
bundle = _make_bundle()
data = I6ZSerializer().serialize(bundle)
with zipfile.ZipFile(io.BytesIO(data)) as zf:
self.assertIn("manifest.xml", zf.namelist())
def test_contains_i6d_files(self):
bundle = _make_bundle()
data = I6ZSerializer().serialize(bundle)
with zipfile.ZipFile(io.BytesIO(data)) as zf:
names = zf.namelist()
# manifest + 1 substance + 1 ref substance + 1 ESR = 4 files
self.assertEqual(len(names), 4)
i6d_files = [n for n in names if n.endswith(".i6d")]
self.assertEqual(len(i6d_files), 3)
def test_manifest_references_all_documents(self):
bundle = _make_bundle()
data = I6ZSerializer().serialize(bundle)
with zipfile.ZipFile(io.BytesIO(data)) as zf:
manifest_xml = zf.read("manifest.xml").decode("utf-8")
root = ET.fromstring(manifest_xml)
ns = "http://iuclid6.echa.europa.eu/namespaces/manifest/v1"
docs = root.findall(f".//{{{ns}}}document")
self.assertEqual(len(docs), 3)
types = set()
for doc in docs:
type_elem = doc.find(f"{{{ns}}}type")
self.assertIsNotNone(type_elem)
assert type_elem is not None
types.add(type_elem.text)
self.assertEqual(types, {"SUBSTANCE", "REFERENCE_SUBSTANCE", "ENDPOINT_STUDY_RECORD"})
def test_manifest_contains_expected_document_links(self):
bundle = _make_bundle()
data = I6ZSerializer().serialize(bundle)
with zipfile.ZipFile(io.BytesIO(data)) as zf:
manifest_xml = zf.read("manifest.xml").decode("utf-8")
root = ET.fromstring(manifest_xml)
ns = "http://iuclid6.echa.europa.eu/namespaces/manifest/v1"
docs = root.findall(f".//{{{ns}}}document")
links_by_type: dict[str, set[tuple[str | None, str | None]]] = {}
for doc in docs:
doc_type = doc.findtext(f"{{{ns}}}type")
links = set()
for link in doc.findall(f"{{{ns}}}links/{{{ns}}}link"):
links.add(
(
link.findtext(f"{{{ns}}}ref-type"),
link.findtext(f"{{{ns}}}ref-uuid"),
)
)
if doc_type:
links_by_type[doc_type] = links
self.assertIn("REFERENCE", {ref_type for ref_type, _ in links_by_type["SUBSTANCE"]})
self.assertIn("CHILD", {ref_type for ref_type, _ in links_by_type["SUBSTANCE"]})
self.assertIn(
"PARENT", {ref_type for ref_type, _ in links_by_type["ENDPOINT_STUDY_RECORD"]}
)
def test_i6d_files_are_valid_xml(self):
bundle = _make_bundle()
data = I6ZSerializer().serialize(bundle)
with zipfile.ZipFile(io.BytesIO(data)) as zf:
for name in zf.namelist():
if name.endswith(".i6d"):
content = zf.read(name).decode("utf-8")
# Should not raise
ET.fromstring(content)
def test_manifest_links_esr_to_transformation_reference_substances(self):
bundle, parent_ref_key, product_ref_key = _make_bundle_with_transformation_links()
data = I6ZSerializer().serialize(bundle)
with zipfile.ZipFile(io.BytesIO(data)) as zf:
manifest_xml = zf.read("manifest.xml").decode("utf-8")
root = ET.fromstring(manifest_xml)
ns = "http://iuclid6.echa.europa.eu/namespaces/manifest/v1"
esr_doc = None
for doc in root.findall(f".//{{{ns}}}document"):
if doc.findtext(f"{{{ns}}}type") == "ENDPOINT_STUDY_RECORD":
esr_doc = doc
break
self.assertIsNotNone(esr_doc)
assert esr_doc is not None
reference_links = {
link.findtext(f"{{{ns}}}ref-uuid")
for link in esr_doc.findall(f"{{{ns}}}links/{{{ns}}}link")
if link.findtext(f"{{{ns}}}ref-type") == "REFERENCE"
}
self.assertIn(parent_ref_key, reference_links)
self.assertIn(product_ref_key, reference_links)

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"""
Tests for the IUCLID projection layer.
"""
from django.test import TestCase, tag
from envipy_additional_information.information import Temperature
from epdb.logic import PackageManager, UserManager
from epdb.models import AdditionalInformation, Pathway, Scenario
from epapi.v1.interfaces.iuclid.projections import get_pathway_for_iuclid_export
@tag("api", "iuclid")
class IUCLIDExportScenarioAITests(TestCase):
"""Test that scenario additional information is correctly reflected in the IUCLID export."""
@classmethod
def setUpTestData(cls):
cls.user = UserManager.create_user(
"iuclid-test-user",
"iuclid-test@envipath.com",
"SuperSafe",
set_setting=False,
add_to_group=False,
is_active=True,
)
cls.package = PackageManager.create_package(
cls.user, "IUCLID Test Package", "Package for IUCLID export tests"
)
cls.pathway = Pathway.create(cls.package, "CCO", name="Test Pathway")
cls.root_node = cls.pathway.node_set.get(depth=0)
cls.compound = cls.root_node.default_node_label.compound
cls.scenario = Scenario.objects.create(
package=cls.package,
name="Test Scenario",
scenario_type="biodegradation",
scenario_date="2024-01-01",
)
cls.root_node.scenarios.add(cls.scenario)
def test_scenario_with_no_ai_exports_without_error(self):
"""Scenario attached to a node but with no AI must export cleanly with empty lists.
Regression: previously scenario.parent was accessed here, causing AttributeError.
"""
result = get_pathway_for_iuclid_export(self.user, self.pathway.uuid)
self.assertEqual(len(result.nodes), 1)
node = result.nodes[0]
self.assertEqual(len(node.scenarios), 1)
self.assertEqual(node.scenarios[0].scenario_uuid, self.scenario.uuid)
self.assertEqual(node.scenarios[0].additional_info, [])
self.assertEqual(node.additional_info, [])
def test_direct_scenario_ai_appears_in_export(self):
"""AI added directly to a scenario (no object binding) must appear in the export DTO."""
ai = Temperature(interval={"start": 20, "end": 25})
AdditionalInformation.create(self.package, ai, scenario=self.scenario)
result = get_pathway_for_iuclid_export(self.user, self.pathway.uuid)
node = result.nodes[0]
self.assertEqual(len(node.scenarios), 1)
scenario_dto = node.scenarios[0]
self.assertEqual(len(scenario_dto.additional_info), 1)
# The same AI must roll up to the node level
self.assertEqual(len(node.additional_info), 1)
self.assertEqual(node.additional_info[0], scenario_dto.additional_info[0])
def test_object_bound_ai_excluded_from_scenario_direct_info(self):
"""AI bound to a specific object (object_id set) must not appear in direct scenario info.
get_additional_information(direct_only=True) filters object_id__isnull=False.
"""
ai = Temperature(interval={"start": 10, "end": 15})
AdditionalInformation.create(
self.package, ai, scenario=self.scenario, content_object=self.compound
)
result = get_pathway_for_iuclid_export(self.user, self.pathway.uuid)
node = result.nodes[0]
scenario_dto = node.scenarios[0]
self.assertEqual(scenario_dto.additional_info, [])
self.assertEqual(node.additional_info, [])

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"""Tests for PathwayMapper - no DB needed, uses DTO fixtures."""
from django.test import SimpleTestCase, tag
from uuid import uuid4
from epapi.v1.interfaces.iuclid.dto import (
PathwayCompoundDTO,
PathwayEdgeDTO,
PathwayExportDTO,
PathwayNodeDTO,
PathwayScenarioDTO,
)
from epiuclid.serializers.pathway_mapper import PathwayMapper
@tag("iuclid")
class PathwayMapperTest(SimpleTestCase):
def setUp(self):
self.compounds = [
PathwayCompoundDTO(pk=1, name="Benzene", smiles="c1ccccc1"),
PathwayCompoundDTO(pk=2, name="Phenol", smiles="c1ccc(O)cc1"),
]
def test_mapper_produces_bundle(self):
export = PathwayExportDTO(
pathway_uuid=uuid4(),
pathway_name="Test Pathway",
compounds=self.compounds,
root_compound_pks=[1],
)
bundle = PathwayMapper().map(export)
self.assertEqual(len(bundle.substances), 2)
self.assertEqual(len(bundle.reference_substances), 2)
self.assertEqual(len(bundle.endpoint_study_records), 1)
def test_mapper_deduplicates_compounds(self):
compounds_with_dup = [
PathwayCompoundDTO(pk=1, name="Benzene", smiles="c1ccccc1"),
PathwayCompoundDTO(pk=2, name="Phenol", smiles="c1ccc(O)cc1"),
PathwayCompoundDTO(pk=1, name="Benzene", smiles="c1ccccc1"),
]
export = PathwayExportDTO(
pathway_uuid=uuid4(),
pathway_name="Test Pathway",
compounds=compounds_with_dup,
root_compound_pks=[1],
)
bundle = PathwayMapper().map(export)
# 2 unique compounds -> 2 substances, 2 ref substances
self.assertEqual(len(bundle.substances), 2)
self.assertEqual(len(bundle.reference_substances), 2)
# One endpoint study record per pathway
self.assertEqual(len(bundle.endpoint_study_records), 1)
def test_mapper_extracts_smiles(self):
export = PathwayExportDTO(
pathway_uuid=uuid4(),
pathway_name="Test Pathway",
compounds=self.compounds,
root_compound_pks=[1],
)
bundle = PathwayMapper().map(export)
smiles_values = [s.smiles for s in bundle.reference_substances]
self.assertTrue(all(s is not None for s in smiles_values))
def test_mapper_extracts_cas_when_present(self):
compounds = [
PathwayCompoundDTO(pk=1, name="Benzene", smiles="c1ccccc1", cas_number="71-43-2"),
PathwayCompoundDTO(pk=2, name="Phenol", smiles="c1ccc(O)cc1"),
]
export = PathwayExportDTO(
pathway_uuid=uuid4(),
pathway_name="Test Pathway",
compounds=compounds,
root_compound_pks=[1],
)
bundle = PathwayMapper().map(export)
cas_values = [r.cas_number for r in bundle.reference_substances]
self.assertIn("71-43-2", cas_values)
def test_mapper_builds_transformation_entries(self):
export = PathwayExportDTO(
pathway_uuid=uuid4(),
pathway_name="Test Pathway",
compounds=self.compounds,
edges=[
PathwayEdgeDTO(
edge_uuid=uuid4(),
start_compound_pks=[1],
end_compound_pks=[2],
probability=0.73,
)
],
root_compound_pks=[1],
)
bundle = PathwayMapper().map(export)
self.assertEqual(len(bundle.endpoint_study_records), 1)
esr = bundle.endpoint_study_records[0]
self.assertEqual(len(esr.transformation_products), 1)
self.assertIsNone(esr.transformation_products[0].kinetic_formation_fraction)
def test_mapper_deduplicates_transformation_entries(self):
export = PathwayExportDTO(
pathway_uuid=uuid4(),
pathway_name="Test Pathway",
compounds=self.compounds,
edges=[
PathwayEdgeDTO(edge_uuid=uuid4(), start_compound_pks=[1], end_compound_pks=[2]),
PathwayEdgeDTO(edge_uuid=uuid4(), start_compound_pks=[1], end_compound_pks=[2]),
],
root_compound_pks=[1],
)
bundle = PathwayMapper().map(export)
esr = bundle.endpoint_study_records[0]
self.assertEqual(len(esr.transformation_products), 1)
def test_mapper_creates_endpoint_record_for_each_root_compound(self):
export = PathwayExportDTO(
pathway_uuid=uuid4(),
pathway_name="Test Pathway",
compounds=self.compounds,
root_compound_pks=[1, 2],
)
bundle = PathwayMapper().map(export)
self.assertEqual(len(bundle.endpoint_study_records), 2)
esr_names = {record.name for record in bundle.endpoint_study_records}
self.assertIn("Biodegradation in soil - Test Pathway (Benzene)", esr_names)
self.assertIn("Biodegradation in soil - Test Pathway (Phenol)", esr_names)
def test_mapper_builds_root_specific_transformations_for_disjoint_subgraphs(self):
compounds = [
PathwayCompoundDTO(pk=1, name="Root A", smiles="CC"),
PathwayCompoundDTO(pk=2, name="Root B", smiles="CCC"),
PathwayCompoundDTO(pk=3, name="A Child", smiles="CCCC"),
PathwayCompoundDTO(pk=4, name="B Child", smiles="CCCCC"),
]
export = PathwayExportDTO(
pathway_uuid=uuid4(),
pathway_name="Disjoint Pathway",
compounds=compounds,
edges=[
PathwayEdgeDTO(edge_uuid=uuid4(), start_compound_pks=[1], end_compound_pks=[3]),
PathwayEdgeDTO(edge_uuid=uuid4(), start_compound_pks=[2], end_compound_pks=[4]),
],
root_compound_pks=[1, 2],
)
bundle = PathwayMapper().map(export)
substance_name_by_uuid = {sub.uuid: sub.name for sub in bundle.substances}
reference_name_by_uuid = {ref.uuid: ref.name for ref in bundle.reference_substances}
products_by_root: dict[str, set[str]] = {}
for esr in bundle.endpoint_study_records:
root_name = substance_name_by_uuid[esr.substance_uuid]
products_by_root[root_name] = {
reference_name_by_uuid[tp.product_reference_uuid]
for tp in esr.transformation_products
}
self.assertEqual(products_by_root["Root A"], {"A Child"})
self.assertEqual(products_by_root["Root B"], {"B Child"})
def test_mapper_requires_all_edge_parents_to_be_reachable(self):
compounds = [
PathwayCompoundDTO(pk=1, name="Root", smiles="CC"),
PathwayCompoundDTO(pk=2, name="Co-reactant", smiles="CCC"),
PathwayCompoundDTO(pk=3, name="Product", smiles="CCCC"),
]
export = PathwayExportDTO(
pathway_uuid=uuid4(),
pathway_name="Multi Parent Pathway",
compounds=compounds,
edges=[
PathwayEdgeDTO(edge_uuid=uuid4(), start_compound_pks=[1, 2], end_compound_pks=[3]),
],
root_compound_pks=[1],
)
bundle = PathwayMapper().map(export)
esr = bundle.endpoint_study_records[0]
self.assertEqual(len(esr.transformation_products), 0)
def test_mapper_resolves_multi_parent_transformations_after_intermediate_is_reachable(self):
compounds = [
PathwayCompoundDTO(pk=1, name="Root", smiles="CC"),
PathwayCompoundDTO(pk=2, name="Intermediate", smiles="CCC"),
PathwayCompoundDTO(pk=3, name="Product", smiles="CCCC"),
]
export = PathwayExportDTO(
pathway_uuid=uuid4(),
pathway_name="Closure Pathway",
compounds=compounds,
edges=[
PathwayEdgeDTO(edge_uuid=uuid4(), start_compound_pks=[1], end_compound_pks=[2]),
PathwayEdgeDTO(edge_uuid=uuid4(), start_compound_pks=[1, 2], end_compound_pks=[3]),
],
root_compound_pks=[1],
)
bundle = PathwayMapper().map(export)
esr = bundle.endpoint_study_records[0]
reference_name_by_uuid = {ref.uuid: ref.name for ref in bundle.reference_substances}
product_names = {
reference_name_by_uuid[tp.product_reference_uuid] for tp in esr.transformation_products
}
self.assertEqual(product_names, {"Intermediate", "Product"})
def test_mapper_populates_half_lives_from_root_node_ai(self):
"""HalfLife AI on root node → ESR.half_lives."""
from envipy_additional_information.information import HalfLife, Interval
hl = HalfLife(
model="SFO", fit="ok", comment="", dt50=Interval(start=5.0, end=10.0), source="test"
)
root_node = PathwayNodeDTO(
node_uuid=uuid4(),
compound_pk=1,
name="Root",
depth=0,
smiles="CC",
additional_info=[hl],
)
export = PathwayExportDTO(
pathway_uuid=uuid4(),
pathway_name="P",
compounds=[PathwayCompoundDTO(pk=1, name="Root", smiles="CC")],
nodes=[root_node],
root_compound_pks=[1],
)
bundle = PathwayMapper().map(export)
esr = bundle.endpoint_study_records[0]
self.assertEqual(len(esr.half_lives), 1)
self.assertEqual(esr.half_lives[0].dt50_start, 5.0)
self.assertEqual(esr.half_lives[0].dt50_end, 10.0)
def test_mapper_populates_temperature_from_root_node_ai(self):
"""Temperature AI on root node → ESR.temperature as tuple."""
from envipy_additional_information.information import Temperature, Interval
temp = Temperature(interval=Interval(start=20.0, end=25.0))
root_node = PathwayNodeDTO(
node_uuid=uuid4(),
compound_pk=1,
name="Root",
depth=0,
smiles="CC",
additional_info=[temp],
)
export = PathwayExportDTO(
pathway_uuid=uuid4(),
pathway_name="P",
compounds=[PathwayCompoundDTO(pk=1, name="Root", smiles="CC")],
nodes=[root_node],
root_compound_pks=[1],
)
bundle = PathwayMapper().map(export)
esr = bundle.endpoint_study_records[0]
self.assertEqual(esr.temperature, (20.0, 25.0))
def test_mapper_ignores_ai_on_non_root_nodes(self):
"""AI from non-root nodes (depth > 0) should not appear in ESR."""
from envipy_additional_information.information import HalfLife, Interval
hl = HalfLife(
model="SFO", fit="ok", comment="", dt50=Interval(start=5.0, end=10.0), source="test"
)
non_root_node = PathwayNodeDTO(
node_uuid=uuid4(),
compound_pk=2,
name="Product",
depth=1,
smiles="CCC",
additional_info=[hl],
)
export = PathwayExportDTO(
pathway_uuid=uuid4(),
pathway_name="P",
compounds=[
PathwayCompoundDTO(pk=1, name="Root", smiles="CC"),
PathwayCompoundDTO(pk=2, name="Product", smiles="CCC"),
],
nodes=[non_root_node],
root_compound_pks=[1],
)
bundle = PathwayMapper().map(export)
esr = bundle.endpoint_study_records[0]
self.assertEqual(len(esr.half_lives), 0)
def test_extracts_soil_texture2_from_root_node_ai(self):
"""SoilTexture2 AI on root node → ESR.soil_properties.sand/silt/clay."""
from envipy_additional_information.information import SoilTexture2
texture = SoilTexture2(sand=65.0, silt=25.0, clay=10.0)
root_node = PathwayNodeDTO(
node_uuid=uuid4(),
compound_pk=1,
name="Root",
depth=0,
smiles="CC",
additional_info=[texture],
)
export = PathwayExportDTO(
pathway_uuid=uuid4(),
pathway_name="P",
compounds=[PathwayCompoundDTO(pk=1, name="Root", smiles="CC")],
nodes=[root_node],
root_compound_pks=[1],
)
bundle = PathwayMapper().map(export)
esr = bundle.endpoint_study_records[0]
self.assertIsNotNone(esr.soil_properties)
self.assertEqual(esr.soil_properties.sand, 65.0)
self.assertEqual(esr.soil_properties.silt, 25.0)
self.assertEqual(esr.soil_properties.clay, 10.0)
def test_extracts_ph_from_root_node_ai(self):
"""Acidity AI on root node → ESR.soil_properties.ph_lower/ph_upper/ph_method."""
from envipy_additional_information.information import Acidity, Interval
acidity = Acidity(interval=Interval(start=6.5, end=7.2), method="CaCl2")
root_node = PathwayNodeDTO(
node_uuid=uuid4(),
compound_pk=1,
name="Root",
depth=0,
smiles="CC",
additional_info=[acidity],
)
export = PathwayExportDTO(
pathway_uuid=uuid4(),
pathway_name="P",
compounds=[PathwayCompoundDTO(pk=1, name="Root", smiles="CC")],
nodes=[root_node],
root_compound_pks=[1],
)
bundle = PathwayMapper().map(export)
esr = bundle.endpoint_study_records[0]
self.assertIsNotNone(esr.soil_properties)
self.assertEqual(esr.soil_properties.ph_lower, 6.5)
self.assertEqual(esr.soil_properties.ph_upper, 7.2)
self.assertEqual(esr.soil_properties.ph_method, "CaCl2")
def test_normalizes_blank_ph_method_to_none(self):
"""Blank Acidity method should not produce an empty PHMeasuredIn XML node."""
from envipy_additional_information.information import Acidity, Interval
acidity = Acidity(interval=Interval(start=6.5, end=7.2), method=" ")
root_node = PathwayNodeDTO(
node_uuid=uuid4(),
compound_pk=1,
name="Root",
depth=0,
smiles="CC",
additional_info=[acidity],
)
export = PathwayExportDTO(
pathway_uuid=uuid4(),
pathway_name="P",
compounds=[PathwayCompoundDTO(pk=1, name="Root", smiles="CC")],
nodes=[root_node],
root_compound_pks=[1],
)
bundle = PathwayMapper().map(export)
esr = bundle.endpoint_study_records[0]
self.assertIsNotNone(esr.soil_properties)
self.assertIsNone(esr.soil_properties.ph_method)
def test_extracts_cec_and_org_carbon(self):
"""CEC and OMContent AI on root node → ESR.soil_properties.cec/org_carbon."""
from envipy_additional_information.information import CEC, OMContent
cec = CEC(capacity=15.3)
om = OMContent(in_oc=2.1)
root_node = PathwayNodeDTO(
node_uuid=uuid4(),
compound_pk=1,
name="Root",
depth=0,
smiles="CC",
additional_info=[cec, om],
)
export = PathwayExportDTO(
pathway_uuid=uuid4(),
pathway_name="P",
compounds=[PathwayCompoundDTO(pk=1, name="Root", smiles="CC")],
nodes=[root_node],
root_compound_pks=[1],
)
bundle = PathwayMapper().map(export)
esr = bundle.endpoint_study_records[0]
self.assertIsNotNone(esr.soil_properties)
self.assertEqual(esr.soil_properties.cec, 15.3)
self.assertEqual(esr.soil_properties.org_carbon, 2.1)
def test_soil_properties_none_when_no_soil_ai(self):
"""No soil AI → soil_properties is None."""
export = PathwayExportDTO(
pathway_uuid=uuid4(),
pathway_name="P",
compounds=[PathwayCompoundDTO(pk=1, name="Root", smiles="CC")],
root_compound_pks=[1],
)
bundle = PathwayMapper().map(export)
esr = bundle.endpoint_study_records[0]
self.assertIsNone(esr.soil_properties)
def test_ignores_soil_ai_on_non_root_nodes(self):
"""Soil AI on non-root nodes (depth > 0) is not extracted."""
from envipy_additional_information.information import SoilTexture2
texture = SoilTexture2(sand=60.0, silt=30.0, clay=10.0)
non_root_node = PathwayNodeDTO(
node_uuid=uuid4(),
compound_pk=2,
name="Product",
depth=1,
smiles="CCC",
additional_info=[texture],
)
export = PathwayExportDTO(
pathway_uuid=uuid4(),
pathway_name="P",
compounds=[
PathwayCompoundDTO(pk=1, name="Root", smiles="CC"),
PathwayCompoundDTO(pk=2, name="Product", smiles="CCC"),
],
nodes=[non_root_node],
root_compound_pks=[1],
)
bundle = PathwayMapper().map(export)
esr = bundle.endpoint_study_records[0]
self.assertIsNone(esr.soil_properties)
def test_mapper_merges_root_scenarios_into_single_esr_with_soil_numbers(self):
"""Scenario-aware root export should merge scenarios into one ESR linked by SoilNo."""
from envipy_additional_information.information import HalfLife, Interval, SoilTexture2
scenario_a = PathwayScenarioDTO(
scenario_uuid=uuid4(),
name="Scenario A",
additional_info=[
HalfLife(
model="SFO",
fit="ok",
comment="",
dt50=Interval(start=2.0, end=2.0),
source="A",
),
SoilTexture2(sand=70.0, silt=20.0, clay=10.0),
],
)
scenario_b = PathwayScenarioDTO(
scenario_uuid=uuid4(),
name="Scenario B",
additional_info=[
HalfLife(
model="SFO",
fit="ok",
comment="",
dt50=Interval(start=5.0, end=5.0),
source="B",
),
SoilTexture2(sand=40.0, silt=40.0, clay=20.0),
],
)
root_node = PathwayNodeDTO(
node_uuid=uuid4(),
compound_pk=1,
name="Root",
depth=0,
smiles="CC",
scenarios=[scenario_a, scenario_b],
)
export = PathwayExportDTO(
pathway_uuid=uuid4(),
pathway_name="P",
compounds=[PathwayCompoundDTO(pk=1, name="Root", smiles="CC")],
nodes=[root_node],
root_compound_pks=[1],
)
bundle = PathwayMapper().map(export)
self.assertEqual(len(bundle.endpoint_study_records), 1)
esr = bundle.endpoint_study_records[0]
self.assertEqual(esr.name, "Biodegradation in soil - P")
self.assertEqual(len(esr.half_lives), 2)
self.assertEqual(len(esr.soil_properties_entries), 2)
by_dt50 = {hl.dt50_start: hl for hl in esr.half_lives}
self.assertEqual(by_dt50[2.0].soil_no_code, "2")
self.assertEqual(by_dt50[5.0].soil_no_code, "4")
self.assertEqual(by_dt50[2.0].temperature, None)
by_soil_no = {soil.soil_no_code: soil for soil in esr.soil_properties_entries}
self.assertEqual(by_soil_no["2"].sand, 70.0)
self.assertEqual(by_soil_no["4"].sand, 40.0)

View File

@ -0,0 +1,148 @@
"""XSD validation tests for IUCLID XML builders — no DB required."""
import xml.etree.ElementTree as ET
from django.test import SimpleTestCase, tag
from epiuclid.builders.base import NS_PLATFORM_CONTAINER
from epiuclid.builders.endpoint_study import EndpointStudyRecordBuilder
from epiuclid.builders.reference_substance import ReferenceSubstanceBuilder
from epiuclid.builders.substance import SubstanceBuilder
from epiuclid.schemas.loader import get_content_schema, get_document_schema
from .factories import (
make_endpoint_study_record_data,
make_half_life_entry,
make_reference_substance_data,
make_soil_properties_data,
make_substance_data,
make_transformation_entry,
)
def _content_element(xml_str: str) -> ET.Element:
"""Extract the first child of <Content> from a full i6d XML string."""
root = ET.fromstring(xml_str)
content = root.find(f"{{{NS_PLATFORM_CONTAINER}}}Content")
assert content is not None and len(content) > 0
return list(content)[0]
def _assert_content_valid(xml_str: str, doc_type: str, subtype: str | None = None) -> None:
schema = get_content_schema(doc_type, subtype)
schema.validate(_content_element(xml_str))
@tag("iuclid")
class SubstanceXSDValidationTest(SimpleTestCase):
def test_substance_validates_against_xsd(self):
data = make_substance_data()
xml_str = SubstanceBuilder().build(data)
_assert_content_valid(xml_str, "SUBSTANCE")
def test_minimal_substance_validates_against_xsd(self):
data = make_substance_data(name="Unknown compound", reference_substance_uuid=None)
xml_str = SubstanceBuilder().build(data)
_assert_content_valid(xml_str, "SUBSTANCE")
@tag("iuclid")
class ReferenceSubstanceXSDValidationTest(SimpleTestCase):
def test_reference_substance_validates_against_xsd(self):
data = make_reference_substance_data()
xml_str = ReferenceSubstanceBuilder().build(data)
_assert_content_valid(xml_str, "REFERENCE_SUBSTANCE")
def test_reference_substance_minimal_validates_against_xsd(self):
data = make_reference_substance_data(
name="Minimal compound",
smiles="CC",
cas_number=None,
molecular_formula=None,
molecular_weight=None,
inchi=None,
inchi_key=None,
)
xml_str = ReferenceSubstanceBuilder().build(data)
_assert_content_valid(xml_str, "REFERENCE_SUBSTANCE")
@tag("iuclid")
class EndpointStudyRecordXSDValidationTest(SimpleTestCase):
def test_endpoint_study_record_validates_against_xsd(self):
data = make_endpoint_study_record_data(
name="Biodegradation study with data",
half_lives=[
make_half_life_entry(),
],
temperature=(20.0, 20.0),
transformation_products=[
make_transformation_entry(),
],
model_name_and_version=["Test model 1.0"],
software_name_and_version=["enviPath"],
model_remarks=["Model UUID: 00000000-0000-0000-0000-000000000000"],
)
xml_str = EndpointStudyRecordBuilder().build(data)
_assert_content_valid(xml_str, "ENDPOINT_STUDY_RECORD", "BiodegradationInSoil")
def test_temperature_only_esr_validates_against_xsd(self):
data = make_endpoint_study_record_data(
name="Biodegradation study with temperature only", temperature=(21.0, 21.0)
)
xml_str = EndpointStudyRecordBuilder().build(data)
_assert_content_valid(xml_str, "ENDPOINT_STUDY_RECORD", "BiodegradationInSoil")
def test_skeleton_esr_validates_against_xsd(self):
data = make_endpoint_study_record_data(name="Biodegradation study")
xml_str = EndpointStudyRecordBuilder().build(data)
_assert_content_valid(xml_str, "ENDPOINT_STUDY_RECORD", "BiodegradationInSoil")
def test_esr_with_soil_properties_validates_against_xsd(self):
"""ESR with full soil properties validates against BiodegradationInSoil XSD."""
data = make_endpoint_study_record_data(
name="Biodegradation study with soil properties",
soil_properties=make_soil_properties_data(),
)
xml_str = EndpointStudyRecordBuilder().build(data)
_assert_content_valid(xml_str, "ENDPOINT_STUDY_RECORD", "BiodegradationInSoil")
def test_esr_with_multiple_soils_and_linked_dt_validates_against_xsd(self):
data = make_endpoint_study_record_data(
name="Biodegradation study with multiple soils",
soil_properties_entries=[
make_soil_properties_data(soil_no_code="2", soil_type="LOAMY_SAND"),
make_soil_properties_data(soil_no_code="4", soil_type="CLAY_LOAM"),
],
half_lives=[
make_half_life_entry(dt50_start=1.0, dt50_end=1.0, soil_no_code="2"),
make_half_life_entry(dt50_start=2.0, dt50_end=2.0, soil_no_code="4"),
],
)
xml_str = EndpointStudyRecordBuilder().build(data)
_assert_content_valid(xml_str, "ENDPOINT_STUDY_RECORD", "BiodegradationInSoil")
@tag("iuclid")
class DocumentWrapperXSDValidationTest(SimpleTestCase):
def test_full_i6d_document_validates_against_container_xsd(self):
"""Validate the Document wrapper (PlatformMetadata + Content + Attachments + ModificationHistory).
The container schema uses processContents="strict" for xs:any in Content,
so we need the content schema loaded into the validator too.
"""
data = make_substance_data()
xml_str = SubstanceBuilder().build(data)
root = ET.fromstring(xml_str)
doc_schema = get_document_schema()
content_schema = get_content_schema("SUBSTANCE")
# This is a xmlschema quirk and happens because there are children of the Content element not defined in the Content schema.
errors = [
e for e in doc_schema.iter_errors(root) if "unavailable namespace" not in str(e.reason)
]
self.assertEqual(errors, [], msg=f"Document wrapper errors: {errors}")
content_el = _content_element(xml_str)
content_schema.validate(content_el)

View File

@ -0,0 +1,22 @@
from __future__ import annotations
import xml.etree.ElementTree as ET
from django.test import SimpleTestCase
def assert_xpath_text(
case: SimpleTestCase,
root: ET.Element,
path: str,
expected: str,
) -> ET.Element:
element = root.find(path)
case.assertIsNotNone(element, msg=f"Missing element at xpath: {path}")
assert element is not None
case.assertEqual(element.text, expected)
return element
def assert_xpath_absent(case: SimpleTestCase, root: ET.Element, path: str) -> None:
case.assertIsNone(root.find(path), msg=f"Element should be absent at xpath: {path}")

View File

@ -31,6 +31,8 @@ dependencies = [
"setuptools>=80.8.0", "setuptools>=80.8.0",
"nh3==0.3.2", "nh3==0.3.2",
"polars==1.35.1", "polars==1.35.1",
"xmlschema>=3.0.0",
] ]
[tool.uv.sources] [tool.uv.sources]
@ -139,6 +141,7 @@ collectstatic = { cmd = "uv run python manage.py collectstatic --noinput", help
frontend-test-setup = { cmd = "playwright install", help = "Install the browsers required for frontend testing" } frontend-test-setup = { cmd = "playwright install", help = "Install the browsers required for frontend testing" }
[tool.pytest.ini_options] [tool.pytest.ini_options]
DJANGO_SETTINGS_MODULE = "envipath.settings"
addopts = "--verbose --capture=no --durations=10" addopts = "--verbose --capture=no --durations=10"
testpaths = ["tests", "*/tests"] testpaths = ["tests", "*/tests"]
pythonpath = ["."] pythonpath = ["."]
@ -155,4 +158,5 @@ markers = [
"frontend: Frontend tests", "frontend: Frontend tests",
"end2end: End-to-end tests", "end2end: End-to-end tests",
"slow: Slow tests", "slow: Slow tests",
"iuclid: IUCLID i6z export tests",
] ]

View File

@ -41,6 +41,14 @@
<i class="glyphicon glyphicon-floppy-save"></i> Download Pathway as Image</a <i class="glyphicon glyphicon-floppy-save"></i> Download Pathway as Image</a
> >
</li> </li>
{% if meta.enabled_features.IUCLID_EXPORT and meta.user.username != 'anonymous' %}
<li>
<a class="button" href="/api/v1/pathway/{{ pathway.uuid }}/export/iuclid">
<i class="glyphicon glyphicon-floppy-save"></i> Download Pathway as IUCLID
(.i6z)</a
>
</li>
{% endif %}
<li> <li>
<a <a
role="button" role="button"

View File

@ -38,7 +38,7 @@ class PathwayViewTest(TestCase):
}, },
) )
self.assertEqual(response.status_code, 302) self.assertEqual(response.status_code, 302)
pathway_url = response.url pathway_url = response["Location"]
pw = Pathway.objects.get(url=pathway_url) pw = Pathway.objects.get(url=pathway_url)
self.assertEqual(self.user1_default_package, pw.package) self.assertEqual(self.user1_default_package, pw.package)
@ -81,7 +81,7 @@ class PathwayViewTest(TestCase):
}, },
) )
self.assertEqual(response.status_code, 302) self.assertEqual(response.status_code, 302)
pathway_url = response.url pathway_url = response["Location"]
pw = Pathway.objects.get(url=pathway_url) pw = Pathway.objects.get(url=pathway_url)
self.assertEqual(self.package, pw.package) self.assertEqual(self.package, pw.package)
@ -128,7 +128,7 @@ class PathwayViewTest(TestCase):
) )
self.assertEqual(response.status_code, 302) self.assertEqual(response.status_code, 302)
pathway_url = response.url pathway_url = response["Location"]
pw = Pathway.objects.get(url=pathway_url) pw = Pathway.objects.get(url=pathway_url)
response = self.client.post( response = self.client.post(
@ -166,3 +166,37 @@ class PathwayViewTest(TestCase):
pw = Pathway.objects.get(url=pathway_url) pw = Pathway.objects.get(url=pathway_url)
self.assertEqual(len(pw.aliases), 0) self.assertEqual(len(pw.aliases), 0)
@override_settings(FLAGS={**s.FLAGS, "IUCLID_EXPORT": True})
def test_pathway_detail_shows_iuclid_export_action_when_enabled(self):
pathway = Pathway.create(self.package, "CCO", name="IUCLID Export Pathway")
response = self.client.get(
reverse(
"package pathway detail",
kwargs={
"package_uuid": str(pathway.package.uuid),
"pathway_uuid": str(pathway.uuid),
},
)
)
self.assertEqual(response.status_code, 200)
self.assertContains(response, f"/api/v1/pathway/{pathway.uuid}/export/iuclid")
@override_settings(FLAGS={**s.FLAGS, "IUCLID_EXPORT": False})
def test_pathway_detail_hides_iuclid_export_action_when_disabled(self):
pathway = Pathway.create(self.package, "CCO", name="IUCLID Export Pathway")
response = self.client.get(
reverse(
"package pathway detail",
kwargs={
"package_uuid": str(pathway.package.uuid),
"pathway_uuid": str(pathway.uuid),
},
)
)
self.assertEqual(response.status_code, 200)
self.assertNotContains(response, f"/api/v1/pathway/{pathway.uuid}/export/iuclid")

View File

@ -1,3 +1,5 @@
from urllib.parse import quote
from django.conf import settings as s from django.conf import settings as s
from django.test import TestCase, override_settings from django.test import TestCase, override_settings
from django.urls import reverse from django.urls import reverse
@ -5,6 +7,13 @@ from django.urls import reverse
from epdb.logic import PackageManager from epdb.logic import PackageManager
from epdb.models import Package, User from epdb.models import Package, User
_LOGIN_REQUIRED_MW = "epdb.middleware.login_required_middleware.LoginRequiredMiddleware"
def _middleware_with_login_required():
mw = list(s.MIDDLEWARE)
return mw if _LOGIN_REQUIRED_MW in mw else [*mw, _LOGIN_REQUIRED_MW]
@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True) @override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
class UserViewTest(TestCase): class UserViewTest(TestCase):
@ -39,6 +48,7 @@ class UserViewTest(TestCase):
self.assertEqual(response.status_code, 200) self.assertEqual(response.status_code, 200)
self.assertFalse(response.wsgi_request.user.is_authenticated) self.assertFalse(response.wsgi_request.user.is_authenticated)
@override_settings(ADMIN_APPROVAL_REQUIRED=True)
def test_register(self): def test_register(self):
response = self.client.post( response = self.client.post(
reverse("register"), reverse("register"),
@ -51,7 +61,8 @@ class UserViewTest(TestCase):
) )
self.assertEqual(response.status_code, 200) self.assertEqual(response.status_code, 200)
self.assertContains( self.assertContains(
response, "Your account has been created! An admin will activate it soon!" response,
"Your account has been created! An admin will activate it soon!",
) )
def test_register_password_mismatch(self): def test_register_password_mismatch(self):
@ -81,14 +92,19 @@ class UserViewTest(TestCase):
) )
self.assertFalse(response.wsgi_request.user.is_authenticated) self.assertFalse(response.wsgi_request.user.is_authenticated)
@override_settings(MIDDLEWARE=_middleware_with_login_required())
def test_next_param_properly_handled(self): def test_next_param_properly_handled(self):
response = self.client.get(reverse("packages")) packages_url = reverse("packages")
response = self.client.get(packages_url)
self.assertRedirects(response, f"{reverse('login')}/?next=/package") self.assertRedirects(
response,
f"{s.LOGIN_URL}?next={quote(packages_url)}",
fetch_redirect_response=False,
)
response = self.client.post( response = self.client.post(
reverse("login"), reverse("login"),
{"username": "user0", "password": "SuperSafe", "login": "true", "next": "/package"}, {"username": "user0", "password": "SuperSafe", "login": "true", "next": packages_url},
) )
self.assertRedirects(response, reverse("packages")) self.assertRedirects(response, packages_url)

2188
uv.lock generated

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