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Store problem configuration in Problem #326

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merged 1 commit into from
Dec 9, 2024
Merged

Store problem configuration in Problem #326

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104 changes: 77 additions & 27 deletions petab/v1/problem.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@
from warnings import warn

import pandas as pd
from pydantic import AnyUrl, BaseModel, Field, RootModel

from . import (
conditions,
Expand Down Expand Up @@ -79,6 +80,7 @@ def __init__(
observable_df: pd.DataFrame = None,
mapping_df: pd.DataFrame = None,
extensions_config: dict = None,
config: ProblemConfig = None,
):
self.condition_df: pd.DataFrame | None = condition_df
self.measurement_df: pd.DataFrame | None = measurement_df
Expand Down Expand Up @@ -113,6 +115,7 @@ def __init__(

self.model: Model | None = model
self.extensions_config = extensions_config or {}
self.config = config

def __getattr__(self, name):
# For backward-compatibility, allow access to SBML model related
Expand Down Expand Up @@ -262,10 +265,14 @@ def from_yaml(
yaml_config: PEtab configuration as dictionary or YAML file name
base_path: Base directory or URL to resolve relative paths
"""
# path to the yaml file
filepath = None

if isinstance(yaml_config, Path):
yaml_config = str(yaml_config)

if isinstance(yaml_config, str):
filepath = yaml_config
if base_path is None:
base_path = get_path_prefix(yaml_config)
yaml_config = yaml.load_yaml(yaml_config)
Expand Down Expand Up @@ -297,59 +304,58 @@ def get_path(filename):
DeprecationWarning,
stacklevel=2,
)
config = ProblemConfig(
**yaml_config, base_path=base_path, filepath=filepath
)
problem0 = config.problems[0]
# currently required for handling PEtab v2 in here
problem0_ = yaml_config["problems"][0]

problem0 = yaml_config["problems"][0]

if isinstance(yaml_config[PARAMETER_FILE], list):
if isinstance(config.parameter_file, list):
parameter_df = parameters.get_parameter_df(
[get_path(f) for f in yaml_config[PARAMETER_FILE]]
[get_path(f) for f in config.parameter_file]
)
else:
parameter_df = (
parameters.get_parameter_df(
get_path(yaml_config[PARAMETER_FILE])
)
if yaml_config[PARAMETER_FILE]
parameters.get_parameter_df(get_path(config.parameter_file))
if config.parameter_file
else None
)

if yaml_config[FORMAT_VERSION] in [1, "1", "1.0.0"]:
if len(problem0[SBML_FILES]) > 1:
if config.format_version.root in [1, "1", "1.0.0"]:
if len(problem0.sbml_files) > 1:
# TODO https://github.com/PEtab-dev/libpetab-python/issues/6
raise NotImplementedError(
"Support for multiple models is not yet implemented."
)

model = (
model_factory(
get_path(problem0[SBML_FILES][0]),
get_path(problem0.sbml_files[0]),
MODEL_TYPE_SBML,
model_id=None,
)
if problem0[SBML_FILES]
if problem0.sbml_files
else None
)
else:
if len(problem0[MODEL_FILES]) > 1:
if len(problem0_[MODEL_FILES]) > 1:
# TODO https://github.com/PEtab-dev/libpetab-python/issues/6
raise NotImplementedError(
"Support for multiple models is not yet implemented."
)
if not problem0[MODEL_FILES]:
if not problem0_[MODEL_FILES]:
model = None
else:
model_id, model_info = next(
iter(problem0[MODEL_FILES].items())
iter(problem0_[MODEL_FILES].items())
)
model = model_factory(
get_path(model_info[MODEL_LOCATION]),
model_info[MODEL_LANGUAGE],
model_id=model_id,
)

measurement_files = [
get_path(f) for f in problem0.get(MEASUREMENT_FILES, [])
]
measurement_files = [get_path(f) for f in problem0.measurement_files]
# If there are multiple tables, we will merge them
measurement_df = (
core.concat_tables(
Expand All @@ -359,9 +365,7 @@ def get_path(filename):
else None
)

condition_files = [
get_path(f) for f in problem0.get(CONDITION_FILES, [])
]
condition_files = [get_path(f) for f in problem0.condition_files]
# If there are multiple tables, we will merge them
condition_df = (
core.concat_tables(condition_files, conditions.get_condition_df)
Expand All @@ -370,7 +374,7 @@ def get_path(filename):
)

visualization_files = [
get_path(f) for f in problem0.get(VISUALIZATION_FILES, [])
get_path(f) for f in problem0.visualization_files
]
# If there are multiple tables, we will merge them
visualization_df = (
Expand All @@ -379,17 +383,15 @@ def get_path(filename):
else None
)

observable_files = [
get_path(f) for f in problem0.get(OBSERVABLE_FILES, [])
]
observable_files = [get_path(f) for f in problem0.observable_files]
# If there are multiple tables, we will merge them
observable_df = (
core.concat_tables(observable_files, observables.get_observable_df)
if observable_files
else None
)

mapping_files = [get_path(f) for f in problem0.get(MAPPING_FILES, [])]
mapping_files = [get_path(f) for f in problem0_.get(MAPPING_FILES, [])]
# If there are multiple tables, we will merge them
mapping_df = (
core.concat_tables(mapping_files, mapping.get_mapping_df)
Expand All @@ -406,6 +408,7 @@ def get_path(filename):
visualization_df=visualization_df,
mapping_df=mapping_df,
extensions_config=yaml_config.get(EXTENSIONS, {}),
config=config,
)

@staticmethod
Expand Down Expand Up @@ -1184,3 +1187,50 @@ def add_measurement(
if self.measurement_df is not None
else tmp_df
)


class VersionNumber(RootModel):
root: str | int


class ListOfFiles(RootModel):
"""List of files."""

root: list[str | AnyUrl] = Field(..., description="List of files.")

def __iter__(self):
return iter(self.root)

def __len__(self):
return len(self.root)

def __getitem__(self, index):
return self.root[index]


class SubProblem(BaseModel):
"""A `problems` object in the PEtab problem configuration."""

sbml_files: ListOfFiles = []
measurement_files: ListOfFiles = []
condition_files: ListOfFiles = []
observable_files: ListOfFiles = []
visualization_files: ListOfFiles = []


class ProblemConfig(BaseModel):
"""The PEtab problem configuration."""

filepath: str | AnyUrl | None = Field(
None,
description="The path to the PEtab problem configuration.",
exclude=True,
)
base_path: str | AnyUrl | None = Field(
None,
description="The base path to resolve relative paths.",
exclude=True,
)
format_version: VersionNumber = 1
parameter_file: str | AnyUrl | None = None
problems: list[SubProblem] = []
1 change: 1 addition & 0 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@ dependencies = [
"pyyaml",
"jsonschema",
"antlr4-python3-runtime==4.13.1",
"pydantic>=2.10",
]
license = {text = "MIT License"}
authors = [
Expand Down
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