CoreMS 4.0.0__py3-none-any.whl

corems/encapsulation/input/parameter_from_json.py

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+from pathlib import Path
+import json
+import toml
+
+from corems.encapsulation.factory.parameters import MSParameters, LCMSParameters
+from corems.encapsulation.factory.processingSetting import (
+    MolecularFormulaSearchSettings,
+    TransientSetting,
+)
+from corems.encapsulation.factory.processingSetting import (
+    MassSpectrumSetting,
+    DataInputSetting,
+)
+from corems.encapsulation.factory.processingSetting import MassSpecPeakSetting, GasChromatographSetting, CompoundSearchSettings, LCMSCollectionSettings
+
+
+def load_and_set_toml_parameters_ms(mass_spec_obj, parameters_path=False):
+    """Load parameters from a toml file and set the parameters in the mass_spec_obj
+
+    Parameters
+    ----------
+    mass_spec_obj : MassSpectrum
+        corems MassSpectrum object
+
+    parameters_path : str, optional
+        path to the parameters file, by default False
+
+    Raises
+    ------
+    FileNotFoundError
+        if the file is not found
+    """
+
+    if parameters_path:
+        file_path = Path(parameters_path)
+
+    else:
+        filename = "SettingsCoreMS.toml"
+        file_path = Path.cwd() / filename
+
+    if file_path.exists():
+        with open(
+            file_path,
+            "r",
+            encoding="utf8",
+        ) as stream:
+            data_loaded = toml.load(stream)
+            _set_dict_data_ms(data_loaded, mass_spec_obj)
+    else:
+        raise FileNotFoundError("Could not locate %s", file_path)
+
+
+def load_and_set_parameters_ms(mass_spec_obj, parameters_path=False):
+    """Load parameters from a json file and set the parameters in the mass_spec_obj
+
+    Parameters
+    ----------
+    mass_spec_obj : MassSpectrum
+        corems MassSpectrum object
+    parameters_path : str, optional
+        path to the parameters file, by default False
+
+    Raises
+    ------
+    FileNotFoundError
+        if the file is not found
+    """
+
+    if parameters_path:
+        file_path = Path(parameters_path)
+
+    else:
+        filename = "SettingsCoreMS.json"
+        file_path = Path.cwd() / filename
+
+    if file_path.exists():
+        with open(
+            file_path,
+            "r",
+            encoding="utf8",
+        ) as stream:
+            data_loaded = json.load(stream)
+            _set_dict_data_ms(data_loaded, mass_spec_obj)
+    else:
+        raise FileNotFoundError("Could not locate %s", file_path)
+
+
+def load_and_set_toml_parameters_gcms(gcms_obj, parameters_path=False):
+    """Load parameters from a toml file and set the parameters in the GCMS object
+
+    Parameters
+    ----------
+    gcms_obj : GCMSBase
+        corems GCMSBase object
+    parameters_path : str, optional
+        path to the parameters file, by default False
+
+    Raises
+    ------
+    FileNotFoundError
+        if the file is not found
+    """
+
+    if parameters_path:
+        file_path = Path(parameters_path)
+
+    else:
+        filename = "SettingsCoreMS.toml"
+        file_path = Path.cwd() / filename
+
+    if file_path.exists():
+        with open(
+            file_path,
+            "r",
+            encoding="utf8",
+        ) as stream:
+            data_loaded = toml.load(stream)
+            _set_dict_data_gcms(data_loaded, gcms_obj)
+    else:
+        raise FileNotFoundError("Could not locate %s", file_path)
+
+
+def load_and_set_parameters_gcms(gcms_obj, parameters_path=False):
+    """Load parameters from a json file and set the parameters in the GCMS object
+
+    Parameters
+    ----------
+    gcms_obj : GCMSBase
+        corems GCMSBase object
+    parameters_path : str, optional
+        path to the parameters file, by default False
+
+    Raises
+    ------
+    FileNotFoundError
+        if the file is not found
+    """
+
+    if parameters_path:
+        file_path = Path(parameters_path)
+
+    else:
+        filename = "SettingsCoreMS.json"
+        file_path = Path.cwd() / filename
+
+    if file_path.exists():
+        with open(
+            file_path,
+            "r",
+            encoding="utf8",
+        ) as stream:
+            data_loaded = json.load(stream)
+            _set_dict_data_gcms(data_loaded, gcms_obj)
+    else:
+        raise FileNotFoundError("Could not locate %s", file_path)
+
+
+def load_and_set_json_parameters_lcms(lcms_obj, parameters_path=False):
+    """Load parameters from a json file and set the parameters in the LCMS object
+
+    Parameters
+    ----------
+    lcms_obj : LCMSBase
+        corems LCMSBase object
+    parameters_path : str
+        path to the parameters file saved as a .json, by default False
+
+    Raises
+    ------
+    FileNotFoundError
+        if the file is not found
+    """
+
+    if parameters_path:
+        file_path = Path(parameters_path)
+
+    if file_path.exists():
+        with open(
+            file_path,
+            "r",
+            encoding="utf8",
+        ) as stream:
+            data_loaded = json.load(stream)
+            _set_dict_data_lcms(data_loaded, lcms_obj)
+    else:
+        raise FileNotFoundError("Could not locate %s", file_path)
+
+
+def load_and_set_toml_parameters_lcms(lcms_obj, parameters_path=False):
+    """Load parameters from a toml file and set the parameters in the LCMS object
+
+    Parameters
+    ----------
+    lcms_obj : LCMSBase
+        corems LCMSBase object
+    parameters_path : str
+        path to the parameters file saved as a .toml, by default False
+
+    Raises
+    ------
+    FileNotFoundError
+        if the file is not found
+    """
+
+    if parameters_path:
+        file_path = Path(parameters_path)
+
+    if file_path.exists():
+        with open(
+            file_path,
+            "r",
+            encoding="utf8",
+        ) as stream:
+            data_loaded = toml.load(stream)
+            _set_dict_data_lcms(data_loaded, lcms_obj)
+    else:
+        raise FileNotFoundError("Could not locate %s", file_path)
+
+
+def _set_dict_data_gcms(data_loaded, gcms_obj):
+    """Set the parameters in the GCMS object from a dict
+
+    This function is called by load_and_set_parameters_gcms and load_and_set_toml_parameters_gcms and should not be called directly.
+
+    Parameters
+    ----------
+    data_loaded : dict
+        dict with the parameters
+    gcms_obj : GCMSBase
+        corems GCMSBase object
+    """
+
+    classes = [
+        GasChromatographSetting(),
+        CompoundSearchSettings(),
+    ]
+
+    labels = ["GasChromatograph", "MolecularSearch"]
+
+    label_class = zip(labels, classes)
+
+    if data_loaded:
+        for label, classe in label_class:
+            class_data = data_loaded.get(label)
+            # not always we will not all the settings
+            # this allow a class data to be none and continue
+            # to import the other classes
+            if class_data:
+                for item, value in class_data.items():
+                    setattr(classe, item, value)
+
+    gcms_obj.chromatogram_settings = classes[0]
+    gcms_obj.molecular_search_settings = classes[1]
+
+
+def _set_dict_data_lcms(data_loaded, lcms_obj):
+    """Set the parameters on a LCMS object from a dict
+
+    This function is called by load_and_set_parameters_lcms and load_and_set_toml_parameters_lcms and should not be called directly.
+
+    Parameters
+    ----------
+    data_loaded : dict
+        dict with the parameters
+    lcms_obj : LCMSBase
+        corems LCMSBase object
+    """
+
+    # Load the lcms parameters
+    default_params = LCMSParameters(use_defaults=True)
+    lcms_params = data_loaded.get("LiquidChromatograph")
+    for item, value in lcms_params.items():
+        # If the original value is a tuple but the new one is a list we need to convert the list to a tuple
+        if isinstance(value, list) and isinstance(
+            getattr(default_params.lc_ms, item), tuple
+        ):
+            setattr(lcms_obj.parameters.lc_ms, item, tuple(value))
+        else:
+            setattr(lcms_obj.parameters.lc_ms, item, value)
+
+    def set_ms_params_by_key(ms_key):
+        classes = [
+            MassSpectrumSetting,
+            MassSpecPeakSetting,
+            MolecularFormulaSearchSettings,
+            DataInputSetting,
+            TransientSetting,
+        ]
+
+        labels = [
+            "mass_spectrum",
+            "ms_peak",
+            "molecular_search",
+            "data_input",
+            "transient",
+        ]
+
+        label_class = zip(labels, classes)
+
+        for label, classe in label_class:
+            class_data = data_loaded.get("mass_spectrum").get(ms_key).get(label)
+            param_instance = classe()
+            if class_data is not None:
+                # Set the attributes of the nested class
+                for item, value in class_data.items():
+                    if item == "usedAtoms":
+                        # Convert the lists to tuples
+                        for atom, atom_value in value.items():
+                            value[atom] = tuple(atom_value)
+                    if isinstance(value, list) and isinstance(
+                        getattr(param_instance, item), tuple
+                    ):
+                        setattr(param_instance, item, tuple(value))
+                    else:
+                        setattr(param_instance, item, value)
+            setattr(lcms_obj.parameters.mass_spectrum[ms_key], label, param_instance)
+
+    # Load the mass spectrum parameters
+    ms_keys = data_loaded["mass_spectrum"].keys()
+    for ms_key in ms_keys:
+        lcms_obj.parameters.mass_spectrum[ms_key] = MSParameters()
+        set_ms_params_by_key(ms_key)
+
+
+def _set_dict_data_ms(data_loaded, mass_spec_obj):
+    """Set the parameters in the MassSpectrum object from a dict
+
+    This function is called by load_and_set_parameters_ms and load_and_set_toml_parameters_ms and should not be called directly.
+
+    Parameters
+    ----------
+    data_loaded : dict
+        dict with the parameters
+    mass_spec_obj : MassSpectrum
+        corems MassSpectrum object
+    """
+
+    from copy import deepcopy
+
+    classes = [
+        MolecularFormulaSearchSettings(),
+        TransientSetting(),
+        MassSpectrumSetting(),
+        MassSpecPeakSetting(),
+    ]
+
+    labels = ["MolecularFormulaSearch", "Transient", "MassSpectrum", "MassSpecPeak"]
+
+    label_class = zip(labels, classes)
+
+    if data_loaded:
+        for label, classe in label_class:
+            class_data = data_loaded.get(label)
+            # not always we will have all the settings classes
+            # this allow a class data to be none and continue
+            # to import the other classes
+            if class_data:
+                for item, value in class_data.items():
+                    setattr(classe, item, value)
+
+    mass_spec_obj.molecular_search_settings = classes[0]
+    mass_spec_obj.transient_settings = classes[1]
+    mass_spec_obj.settings = classes[2]
+    mass_spec_obj.mspeaks_settings = classes[3]
+
+
+def load_and_set_toml_parameters_class(
+    parameter_label, instance_parameters_class, parameters_path=False
+):
+    """Load parameters from a toml file and set the parameters in the instance_parameters_class
+
+    Parameters
+    ----------
+    parameter_label : str
+        label of the parameters in the toml file
+    instance_parameters_class : object
+        instance of the parameters class
+    parameters_path : str, optional
+        path to the parameters file, by default False
+
+    Raises
+    ------
+    FileNotFoundError
+        if the file is not found
+
+    Returns
+    -------
+    object
+        instance of the parameters class
+    """
+
+    if parameters_path:
+        file_path = Path(parameters_path)
+
+    else:
+        file_path = Path.cwd() / "SettingsCoreMS.toml"
+
+    if file_path.exists():
+        with open(
+            file_path,
+            "r",
+            encoding="utf8",
+        ) as stream:
+            data_loaded = toml.load(stream)
+            parameter_class = _set_dict_data(
+                data_loaded, parameter_label, instance_parameters_class
+            )
+
+            return parameter_class
+    else:
+        raise FileNotFoundError("Could not locate %s", file_path)
+
+
+def load_and_set_parameters_class(
+    parameter_label, instance_parameters_class, parameters_path=False
+):
+    """Load parameters from a json file and set the parameters in the instance_parameters_class
+
+    Parameters
+    ----------
+    parameter_label : str
+        label of the parameters in the json file
+    instance_parameters_class : object
+        instance of the parameters class
+    parameters_path : str, optional
+        path to the parameters file, by default False
+
+    Raises
+    ------
+    FileNotFoundError
+        if the file is not found
+
+    Returns
+    -------
+    object
+        instance of the parameters class
+    """
+
+    if parameters_path:
+        file_path = Path(parameters_path)
+
+    else:
+        file_path = Path.cwd() / "SettingsCoreMS.json"
+
+    if file_path.exists():
+        with open(
+            file_path,
+            "r",
+            encoding="utf8",
+        ) as stream:
+            data_loaded = json.load(stream)
+            parameter_class = _set_dict_data(
+                data_loaded, parameter_label, instance_parameters_class
+            )
+
+            return parameter_class
+    else:
+        raise FileNotFoundError("Could not locate %s", file_path)
+
+
+def _set_dict_data(data_loaded, parameter_label, instance_ParameterClass):
+    """Set the parameters in an instance of a parameter class from a dict
+
+    This function is called by load_and_set_parameters_class and load_and_set_toml_parameters_class and should not be called directly.
+
+    Parameters
+    ----------
+    data_loaded : dict
+        dict with the parameters
+    parameter_label : str
+        label of the parameters in the json file
+    instance_ParameterClass : object
+        instance of the parameters class
+
+    Returns
+    -------
+    object
+        instance of the parameters class
+    """
+
+    classes = [instance_ParameterClass]
+
+    labels = [parameter_label]
+
+    label_class = zip(labels, classes)
+
+    if data_loaded:
+        for label, classe in label_class:
+            class_data = data_loaded.get(label)
+            # not always we will have all the settings classes
+            # this allow a class data to be none and continue
+            # to import the other classes
+            if class_data:
+                for item, value in class_data.items():
+                    setattr(classe, item, value)
+
+    return classes[0]
+
+
+def load_and_set_json_parameters_lcms_collection(lcms_collection, parameters_path):
+    """Load parameters from a json file and set the parameters in the LCMS collection object
+
+    Parameters
+    ----------
+    lcms_collection : LCMSCollection
+        corems LCMSCollection object
+    parameters_path : str or Path
+        path to the parameters file saved as a .json
+
+    Raises
+    ------
+    FileNotFoundError
+        if the file is not found
+    """
+    file_path = Path(parameters_path)
+
+    if file_path.exists():
+        with open(file_path, "r", encoding="utf8") as stream:
+            data_loaded = json.load(stream)
+            _set_dict_data_lcms_collection(data_loaded, lcms_collection)
+    else:
+        raise FileNotFoundError(f"Could not locate {file_path}")
+
+
+def load_and_set_toml_parameters_lcms_collection(lcms_collection, parameters_path):
+    """Load parameters from a toml file and set the parameters in the LCMS collection object
+
+    Parameters
+    ----------
+    lcms_collection : LCMSCollection
+        corems LCMSCollection object
+    parameters_path : str or Path
+        path to the parameters file saved as a .toml
+
+    Raises
+    ------
+    FileNotFoundError
+        if the file is not found
+    """
+    file_path = Path(parameters_path)
+
+    if file_path.exists():
+        with open(file_path, "r", encoding="utf8") as stream:
+            data_loaded = toml.load(stream)
+            _set_dict_data_lcms_collection(data_loaded, lcms_collection)
+    else:
+        raise FileNotFoundError(f"Could not locate {file_path}")
+
+
+def _set_dict_data_lcms_collection(data_loaded, lcms_collection):
+    """Set the parameters in the LCMS collection object from a dict
+
+    This function is called by load_and_set_json_parameters_lcms_collection and 
+    load_and_set_toml_parameters_lcms_collection and should not be called directly.
+
+    Parameters
+    ----------
+    data_loaded : dict
+        dict with the parameters
+    lcms_collection : LCMSCollection
+        corems LCMSCollection object
+    """
+    classes = [LCMSCollectionSettings()]
+    labels = ["LCMSCollection"]
+
+    label_class = zip(labels, classes)
+
+    if data_loaded:
+        for label, classe in label_class:
+            class_data = data_loaded.get(label)
+            # not always we will have all the settings
+            # this allows a class data to be none and continue
+            # to import the other classes
+            if class_data:
+                for attr, value in class_data.items():
+                    if hasattr(classe, attr):
+                        setattr(classe, attr, value)
+        
+        lcms_collection.parameters.lcms_collection = classes[0]