corems.encapsulation.output.parameter_to_json

  1import json
  2
  3import toml
  4from pathlib import Path
  5
  6from corems.encapsulation.output import parameter_to_dict
  7from corems.encapsulation.output.parameter_to_dict import get_dict_data_lcms
  8
  9
 10def dump_all_settings_json(filename="SettingsCoreMS.json", file_path=None):
 11    """
 12    Write JSON file into current directory with all the default settings for the CoreMS package.
 13
 14    Parameters:
 15    ----------
 16    filename : str, optional
 17        The name of the JSON file to be created. Default is 'SettingsCoreMS.json'.
 18    file_path : str or Path, optional
 19        The path where the JSON file will be saved. If not provided, the file will be saved in the current working directory.
 20    """
 21
 22    data_dict_all = parameter_to_dict.get_dict_all_default_data()
 23
 24    if not file_path:
 25        file_path = Path.cwd() / filename
 26
 27    with open(
 28        file_path,
 29        "w",
 30        encoding="utf8",
 31    ) as outfile:
 32        import re
 33
 34        # pretty print
 35        output = json.dumps(
 36            data_dict_all, sort_keys=False, indent=4, separators=(",", ": ")
 37        )
 38        output = re.sub(r'",\s+', '", ', output)
 39
 40        outfile.write(output)
 41
 42
 43def dump_ms_settings_json(filename="SettingsCoreMS.json", file_path=None):
 44    """
 45    Write JSON file into current directory with all the mass spectrum default settings for the CoreMS package.
 46
 47    Parameters
 48    ----------
 49    filename : str, optional
 50        The name of the JSON file to be created. Default is 'SettingsCoreMS.json'.
 51    file_path : str or Path, optional
 52        The path where the JSON file will be saved. If not provided, the file will be saved in the current working directory.
 53
 54    """
 55    data_dict = parameter_to_dict.get_dict_ms_default_data()
 56    if not file_path:
 57        file_path = Path.cwd() / filename
 58
 59    with open(
 60        file_path,
 61        "w",
 62        encoding="utf8",
 63    ) as outfile:
 64        import re
 65
 66        # pretty print
 67        output = json.dumps(
 68            data_dict, sort_keys=False, indent=4, separators=(",", ": ")
 69        )
 70        output = re.sub(r'",\s+', '", ', output)
 71
 72        outfile.write(output)
 73
 74
 75def dump_gcms_settings_json(filename="SettingsCoreMS.json", file_path=None):
 76    """
 77    Write JSON file into current directory containing the default GCMS settings data.
 78
 79    Parameters
 80    ----------
 81    filename : str, optional
 82        The name of the JSON file to be created. Default is 'SettingsCoreMS.json'.
 83    file_path : str or Path-like object, optional
 84        The path where the JSON file will be saved. If not provided, the file will be saved in the current working directory.
 85    """
 86
 87    from pathlib import Path
 88    import json
 89
 90    data_dict = parameter_to_dict.get_dict_gcms_default_data()
 91
 92    if not file_path:
 93        file_path = Path.cwd() / filename
 94
 95    with open(
 96        file_path,
 97        "w",
 98        encoding="utf8",
 99    ) as outfile:
100        import re
101
102        # pretty print
103        output = json.dumps(
104            data_dict, sort_keys=False, indent=4, separators=(",", ": ")
105        )
106        output = re.sub(r'",\s+', '", ', output)
107
108        outfile.write(output)
109
110
111def dump_all_settings_toml(filename="SettingsCoreMS.toml", file_path=None):
112    """
113    Write TOML file into the specified file path or the current directory with all the default settings for the CoreMS package.
114
115    Parameters
116    ----------
117    filename : str, optional
118        The name of the TOML file. Defaults to 'SettingsCoreMS.toml'.
119    file_path : str or Path, optional
120        The path where the TOML file will be saved. If not provided, the file will be saved in the current directory.
121
122    """
123    from pathlib import Path
124
125    data_dict_all = parameter_to_dict.get_dict_all_default_data()
126
127    if not file_path:
128        file_path = Path.cwd() / filename
129
130    with open(
131        file_path,
132        "w",
133        encoding="utf8",
134    ) as outfile:
135        import re
136
137        output = toml.dumps(data_dict_all)
138        outfile.write(output)
139
140
141def dump_ms_settings_toml(filename="SettingsCoreMS.toml", file_path=None):
142    """
143    Write TOML file into the current directory with all the mass spectrum default settings for the CoreMS package.
144
145    Parameters
146    ----------
147    filename : str, optional
148        The name of the TOML file to be created. Default is 'SettingsCoreMS.toml'.
149    file_path : str or Path, optional
150        The path where the TOML file should be saved. If not provided, the file will be saved in the current working directory.
151
152    """
153    data_dict = parameter_to_dict.get_dict_ms_default_data()
154
155    if not file_path:
156        file_path = Path.cwd() / filename
157
158    with open(
159        file_path,
160        "w",
161        encoding="utf8",
162    ) as outfile:
163        import re
164
165        # pretty print
166        output = toml.dumps(data_dict)
167        outfile.write(output)
168
169
170def dump_gcms_settings_toml(filename="SettingsCoreMS.toml", file_path=None):
171    """
172    Write TOML file into current directory containing the default GCMS settings data.
173
174    Parameters
175    ----------
176    filename : str, optional
177        The name of the TOML file. Defaults to 'SettingsCoreMS.toml'.
178    file_path : str or Path, optional
179        The path where the TOML file will be saved. If not provided, the file will be saved in the current working directory.
180
181    """
182
183    data_dict = parameter_to_dict.get_dict_gcms_default_data()
184
185    if not file_path:
186        file_path = Path.cwd() / filename
187
188    with open(
189        file_path,
190        "w",
191        encoding="utf8",
192    ) as outfile:
193        output = toml.dumps(data_dict)
194        outfile.write(output)
195
196
197def dump_lcms_settings_json(
198    filename="SettingsCoreMS.json", file_path=None, lcms_obj=None
199):
200    """
201    Write JSON file into current directory with all the LCMS settings data for the CoreMS package.
202
203    Parameters
204    ----------
205    filename : str, optional
206        The name of the JSON file. Defaults to 'SettingsCoreMS.json'.
207    file_path : str or Path, optional
208        The path where the JSON file will be saved. If not provided, the file will be saved in the current working directory.
209    lcms_obj : object, optional
210        The LCMS object containing the settings data. If not provided, the settings data will be retrieved from the default settings.
211
212    """
213
214    if lcms_obj is None:
215        data_dict = parameter_to_dict.get_dict_lcms_default_data()
216    else:
217        data_dict = get_dict_data_lcms(lcms_obj)
218
219    if not file_path:
220        file_path = Path.cwd() / filename
221
222    with open(
223        file_path,
224        "w",
225        encoding="utf8",
226    ) as outfile:
227        outfile.write(json.dumps(data_dict, indent=4))
228
229
230def dump_lcms_settings_toml(
231    filename="SettingsCoreMS.toml", file_path=None, lcms_obj=None
232):
233    """
234    Write TOML file into current directory with all the LCMS settings data for the CoreMS package.
235
236    Parameters
237    ----------
238    filename : str, optional
239        The name of the TOML file. Defaults to 'SettingsCoreMS.toml'.
240    file_path : str or Path, optional
241        The path where the TOML file will be saved. If not provided, the file will be saved in the current working directory.
242    lcms_obj : object, optional
243        The LCMS object containing the settings data. If not provided, the settings data will be retrieved from the default settings.
244
245    """
246
247    if lcms_obj is None:
248        data_dict = parameter_to_dict.get_dict_lcms_default_data()
249    else:
250        data_dict = get_dict_data_lcms(lcms_obj)
251
252    if not file_path:
253        file_path = Path.cwd() / filename
254
255    with open(
256        file_path,
257        "w",
258        encoding="utf8",
259    ) as outfile:
260        output = toml.dumps(data_dict)
261        outfile.write(output)