"""SED-ML uniform-time-course subset."""
from __future__ import annotations
import xml.etree.ElementTree as ET
from collections.abc import Mapping
from pathlib import Path
from typing import Any
from .._contracts import CompatibilityIssue
from .base import CompatibilityReport, InterchangeResult
def _local(tag: str) -> str:
return tag.rsplit("}", 1)[-1]
[docs]
def import_sedml(path: str | Path) -> InterchangeResult[dict[str, Any]]:
"""Import uniform-time-course simulations from a SED-ML document.
The result captures output grids and KiSAO algorithm identifiers. One-step,
steady-state, repeated-task, and functional-range constructs are reported
as ``unsupported``; call :meth:`InterchangeResult.require_supported` to
reject a partial translation.
"""
source = Path(path)
root = ET.parse(source).getroot()
simulations: list[dict[str, Any]] = []
unsupported: set[str] = set()
for element in root.iter():
kind = _local(element.tag)
if kind == "uniformTimeCourse":
simulations.append(
{
"id": element.attrib.get("id"),
"initial_time": float(element.attrib.get("initialTime", 0)),
"output_start_time": float(element.attrib.get("outputStartTime", 0)),
"output_end_time": float(element.attrib["outputEndTime"]),
"number_of_points": int(element.attrib["numberOfPoints"]),
"algorithm": next(
(
child.attrib.get("kisaoID")
for child in element
if _local(child.tag) == "algorithm"
),
None,
),
}
)
elif kind in {
"oneStep",
"steadyState",
"repeatedTask",
"functionalRange",
}:
unsupported.add(kind)
found = [
CompatibilityIssue(
"uniformTimeCourse",
"transformed",
f"Imported {len(simulations)} uniform time-course simulation(s).",
)
]
found.extend(
CompatibilityIssue(
name,
"unsupported",
"This SED-ML experiment construct is outside the initial subset.",
)
for name in sorted(unsupported)
)
return InterchangeResult(
{"simulations": simulations, "source": str(source)},
CompatibilityReport("SED-ML", "PyMixEF simulation design", tuple(found)),
)
[docs]
def export_sedml(design: Mapping[str, Any], path: str | Path) -> InterchangeResult[Path]:
"""Export one uniform-time-course design as SED-ML Level 1 Version 4.
``output_end_time`` and ``number_of_points`` are required. The export
records the deterministic output grid and KiSAO identifier; richer SED-ML
tasks and ranges are outside this function's supported subset.
"""
namespace = "http://sed-ml.org/sed-ml/level1/version4"
ET.register_namespace("", namespace)
root = ET.Element(
f"{{{namespace}}}sedML",
{"level": "1", "version": "4"},
)
simulations = ET.SubElement(root, f"{{{namespace}}}listOfSimulations")
simulation = ET.SubElement(
simulations,
f"{{{namespace}}}uniformTimeCourse",
{
"id": str(design.get("id", "simulation")),
"initialTime": str(design.get("initial_time", 0.0)),
"outputStartTime": str(design.get("output_start_time", 0.0)),
"outputEndTime": str(design["output_end_time"]),
"numberOfPoints": str(design["number_of_points"]),
},
)
ET.SubElement(
simulation,
f"{{{namespace}}}algorithm",
{"kisaoID": str(design.get("algorithm", "KISAO:0000019"))},
)
destination = Path(path)
destination.parent.mkdir(parents=True, exist_ok=True)
ET.ElementTree(root).write(destination, encoding="utf-8", xml_declaration=True)
return InterchangeResult(
destination,
CompatibilityReport(
"PyMixEF simulation design",
"SED-ML",
(
CompatibilityIssue(
"uniformTimeCourse",
"exact",
"Exported deterministic output grid and KiSAO algorithm identifier.",
),
),
),
)
