def json_for_sbml(uid: str, source: Union[Path, str, bytes]) -> Dict:
"""Create JSON content for given SBML source.
Source is either path to SBML file or SBML string.
"""
if isinstance(source, bytes):
source = source.decode("utf-8")
time_start = time.time()
info = SBMLDocumentInfo.from_sbml(source=source)
time_elapsed = round(time.time() - time_start, 3)
debug = False
if debug:
console.rule("Creating JSON content")
console.print(info.info)
console.rule()
logger.info(f"JSON created for '{uid}' in '{time_elapsed}'")
return {
"report": info.info,
"debug": {
"jsonReportTime": f"{time_elapsed} [s]",
},
}
def annotate_sbml(
source: Union[Path, str], annotations_path: Path, filepath: Path
) -> libsbml.SBMLDocument:
"""
Annotate a given SBML file with the provided annotations.
:param source: SBML to annotation
:param annotations_path: external file with annotations
:param filepath: annotated SBML file
:return: annotated SBMLDocument
"""
doc: libsbml.SBMLDocument = read_sbml(source=source)
# annotate
if not os.path.exists(str(annotations_path)):
raise IOError(f"Annotation file does not exist: {annotations_path}")
external_annotations = ModelAnnotator.read_annotations(
annotations_path, file_format="*"
)
doc = annotate_sbml_doc(doc, external_annotations) # type: ignore
# write annotated sbml
write_sbml(doc, filepath=filepath)
console.print(f"Model annotated: file://{filepath}", style="success")
return doc
def _create_biomodels_testfiles(output_dir: Path) -> None:
"""Download all curated biomodels and create omex files."""
# query the
biomodel_ids = query_curated_biomodels()
console.print(biomodel_ids)
for biomodel_id in biomodel_ids:
# download SBML model as omex
try:
download_biomodel_sbml(biomodel_id,
output_dir,
output_format="omex")
except HTTPError as err:
logger.error(
f"Could not retrieve OMEX for biomodel: '{biomodel_id}'")
logger.error(err)
def create_omex(tmp: bool = False) -> None:
"""Create omex with models."""
with tempfile.TemporaryDirectory() as tmp_dir:
if tmp:
output_dir = Path(tmp_dir)
else:
output_dir = EXAMPLES_DIR
results_minimal_model = create_model(
models=model_minimal,
output_dir=output_dir,
units_consistency=False,
)
results_comp_model = create_model(
models=comp_model,
output_dir=output_dir,
units_consistency=False,
)
sbml_flat_path = (
results_comp_model.sbml_path.parent / f"{comp_model.sid}_flat.xml"
)
flatten_sbml(
sbml_path=results_comp_model.sbml_path, sbml_flat_path=sbml_flat_path
)
sbml_paths = [
results_minimal_model.sbml_path,
results_comp_model.sbml_path,
sbml_flat_path,
]
# Create COMBINE archive
omex = Omex()
for path in sbml_paths:
omex.add_entry(
entry_path=path,
entry=ManifestEntry(
format=EntryFormat.SBML_L3V1, location=f"./models/{path.name}"
),
)
omex_path = output_dir / f"{comp_model.sid}.omex"
omex.to_omex(omex_path)
console.print(f"OMEX created: {omex_path}")
console.print(omex.manifest.dict())
return ustr
if __name__ == "__main__":
import libsbml
from sbmlutils.factory import *
doc: libsbml.SBMLDocument = libsbml.SBMLDocument()
model: libsbml.Model = doc.createModel()
for (key, definition, _, _) in [
# ("mmole_per_min", "mmole/min", "str", "mmol/min"),
# ("m3", "meter^3", "str", "m^3"),
# ("m3", "meter^3/second", "str", "m^3/s"),
# ("mM", "mmole/liter", "str", "mmol/l"),
# ("ml_per_s_kg", "ml/s/kg", "str", "ml/s/kg"),
# ("dimensionless", "dimensionless", "str", "dimensionless"),
("item", "item", "str", "item"),
# ("mM", "mmole/min", "latex", "\\frac{mmol}/{min}"),
]:
ud = UnitDefinition(key, definition=definition)
# ud = UnitDefinition("item")
udef: libsbml.UnitDefinition = ud.create_sbml(model=model)
console.rule()
console.print(udef)
console.print(udef_to_string(udef, format="str"))
console.print(udef_to_string(udef, format="latex"))
if __name__ == "__main__":
from pathlib import Path
from sbmlutils.console import console
output_dir = Path(__file__).parent / "tests"
if not output_dir.exists():
output_dir.mkdir(parents=True, exist_ok=True)
from sbmlutils.resources import GLUCOSE_SBML, REPRESSILATOR_SBML
for source in [
# COMP_ICG_BODY,
# COMP_ICG_BODY_FLAT,
# COMP_ICG_LIVER,
# COMP_MODEL_DEFINITIONS_SBML,
# FBC_RECON3D_SBML,
# FBC_ECOLI_CORE_SBML,
# DISTRIB_DISTRIBUTIONS_SBML,
# DISTRIB_UNCERTAINTIES_SBML,
# output_dir / "icg_body_flat_v2.xml",
# GLUCOSE_SBML
REPRESSILATOR_SBML,
]:
info = SBMLDocumentInfo.from_sbml(source)
console.rule()
json_str = info.to_json()
console.print(json_str)
with open(output_dir / "tests.json", "w") as fout:
fout.write(json_str)