corems.encapsulation.output.parameter_to_json

  1import json
  2
  3import tomlkit
  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 _toml_array_item(item):
 11    """Prepare one array element for TOML.
 12
 13    The previous encoder wrote a null array element as the string ``None``.
 14    """
 15    if item is None:
 16        return "None"
 17    return _toml_value(item)
 18
 19
 20def _toml_value(value):
 21    """Prepare ``value`` for TOML.
 22
 23    TOML has no null. Table entries whose value is ``None`` are omitted, which
 24    matches the encoder previously used for settings files.
 25    """
 26    if isinstance(value, dict):
 27        return {
 28            key: _toml_value(item) for key, item in value.items() if item is not None
 29        }
 30    if isinstance(value, tuple):
 31        return tuple(_toml_array_item(item) for item in value)
 32    if isinstance(value, list):
 33        return [_toml_array_item(item) for item in value]
 34    return value
 35
 36
 37def _dumps_toml(data):
 38    """Serialize ``data`` to a TOML string."""
 39    return tomlkit.dumps(_toml_value(data))
 40
 41
 42def dump_all_settings_json(filename="SettingsCoreMS.json", file_path=None):
 43    """
 44    Write JSON file into current directory with all the default settings for the CoreMS package.
 45
 46    Parameters:
 47    ----------
 48    filename : str, optional
 49        The name of the JSON file to be created. Default is 'SettingsCoreMS.json'.
 50    file_path : str or Path, optional
 51        The path where the JSON file will be saved. If not provided, the file will be saved in the current working directory.
 52    """
 53
 54    data_dict_all = parameter_to_dict.get_dict_all_default_data()
 55
 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_all, sort_keys=False, indent=4, separators=(",", ": ")
 69        )
 70        output = re.sub(r'",\s+', '", ', output)
 71
 72        outfile.write(output)
 73
 74
 75def dump_ms_settings_json(filename="SettingsCoreMS.json", file_path=None):
 76    """
 77    Write JSON file into current directory with all the mass spectrum default settings for the CoreMS package.
 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, 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    data_dict = parameter_to_dict.get_dict_ms_default_data()
 88    if not file_path:
 89        file_path = Path.cwd() / filename
 90
 91    with open(
 92        file_path,
 93        "w",
 94        encoding="utf8",
 95    ) as outfile:
 96        import re
 97
 98        # pretty print
 99        output = json.dumps(
100            data_dict, sort_keys=False, indent=4, separators=(",", ": ")
101        )
102        output = re.sub(r'",\s+', '", ', output)
103
104        outfile.write(output)
105
106
107def dump_gcms_settings_json(filename="SettingsCoreMS.json", file_path=None):
108    """
109    Write JSON file into current directory containing the default GCMS settings data.
110
111    Parameters
112    ----------
113    filename : str, optional
114        The name of the JSON file to be created. Default is 'SettingsCoreMS.json'.
115    file_path : str or Path-like object, optional
116        The path where the JSON file will be saved. If not provided, the file will be saved in the current working directory.
117    """
118
119    from pathlib import Path
120    import json
121
122    data_dict = parameter_to_dict.get_dict_gcms_default_data()
123
124    if not file_path:
125        file_path = Path.cwd() / filename
126
127    with open(
128        file_path,
129        "w",
130        encoding="utf8",
131    ) as outfile:
132        import re
133
134        # pretty print
135        output = json.dumps(
136            data_dict, sort_keys=False, indent=4, separators=(",", ": ")
137        )
138        output = re.sub(r'",\s+', '", ', output)
139
140        outfile.write(output)
141
142
143def dump_all_settings_toml(filename="SettingsCoreMS.toml", file_path=None):
144    """
145    Write TOML file into the specified file path or the current directory with all the default settings for the CoreMS package.
146
147    Parameters
148    ----------
149    filename : str, optional
150        The name of the TOML file. Defaults to 'SettingsCoreMS.toml'.
151    file_path : str or Path, optional
152        The path where the TOML file will be saved. If not provided, the file will be saved in the current directory.
153
154    """
155    from pathlib import Path
156
157    data_dict_all = parameter_to_dict.get_dict_all_default_data()
158
159    if not file_path:
160        file_path = Path.cwd() / filename
161
162    with open(
163        file_path,
164        "w",
165        encoding="utf8",
166    ) as outfile:
167
168        output = _dumps_toml(data_dict_all)
169        outfile.write(output)
170
171
172def dump_ms_settings_toml(filename="SettingsCoreMS.toml", file_path=None):
173    """
174    Write TOML file into the current directory with all the mass spectrum default settings for the CoreMS package.
175
176    Parameters
177    ----------
178    filename : str, optional
179        The name of the TOML file to be created. Default is 'SettingsCoreMS.toml'.
180    file_path : str or Path, optional
181        The path where the TOML file should be saved. If not provided, the file will be saved in the current working directory.
182
183    """
184    data_dict = parameter_to_dict.get_dict_ms_default_data()
185
186    if not file_path:
187        file_path = Path.cwd() / filename
188
189    with open(
190        file_path,
191        "w",
192        encoding="utf8",
193    ) as outfile:
194
195        # pretty print
196        output = _dumps_toml(data_dict)
197        outfile.write(output)
198
199
200def dump_gcms_settings_toml(filename="SettingsCoreMS.toml", file_path=None):
201    """
202    Write TOML file into current directory containing the default GCMS settings data.
203
204    Parameters
205    ----------
206    filename : str, optional
207        The name of the TOML file. Defaults to 'SettingsCoreMS.toml'.
208    file_path : str or Path, optional
209        The path where the TOML file will be saved. If not provided, the file will be saved in the current working directory.
210
211    """
212
213    data_dict = parameter_to_dict.get_dict_gcms_default_data()
214
215    if not file_path:
216        file_path = Path.cwd() / filename
217
218    with open(
219        file_path,
220        "w",
221        encoding="utf8",
222    ) as outfile:
223        output = _dumps_toml(data_dict)
224        outfile.write(output)
225
226
227def dump_lcms_settings_json(
228    filename="SettingsCoreMS.json", file_path=None, lcms_obj=None
229):
230    """
231    Write JSON file into current directory with all the LCMS settings data for the CoreMS package.
232
233    Parameters
234    ----------
235    filename : str, optional
236        The name of the JSON file. Defaults to 'SettingsCoreMS.json'.
237    file_path : str or Path, optional
238        The path where the JSON file will be saved. If not provided, the file will be saved in the current working directory.
239    lcms_obj : object, optional
240        The LCMS object containing the settings data. If not provided, the settings data will be retrieved from the default settings.
241
242    """
243
244    if lcms_obj is None:
245        data_dict = parameter_to_dict.get_dict_lcms_default_data()
246    else:
247        data_dict = get_dict_data_lcms(lcms_obj)
248
249    if not file_path:
250        file_path = Path.cwd() / filename
251
252    with open(
253        file_path,
254        "w",
255        encoding="utf8",
256    ) as outfile:
257        outfile.write(json.dumps(data_dict, indent=4))
258
259
260def dump_lcms_settings_toml(
261    filename="SettingsCoreMS.toml", file_path=None, lcms_obj=None
262):
263    """
264    Write TOML file into current directory with all the LCMS settings data for the CoreMS package.
265
266    Parameters
267    ----------
268    filename : str, optional
269        The name of the TOML file. Defaults to 'SettingsCoreMS.toml'.
270    file_path : str or Path, optional
271        The path where the TOML file will be saved. If not provided, the file will be saved in the current working directory.
272    lcms_obj : object, optional
273        The LCMS object containing the settings data. If not provided, the settings data will be retrieved from the default settings.
274
275    """
276
277    if lcms_obj is None:
278        data_dict = parameter_to_dict.get_dict_lcms_default_data()
279    else:
280        data_dict = get_dict_data_lcms(lcms_obj)
281
282    if not file_path:
283        file_path = Path.cwd() / filename
284
285    with open(
286        file_path,
287        "w",
288        encoding="utf8",
289    ) as outfile:
290        output = _dumps_toml(data_dict)
291        outfile.write(output)
292
293
294def dump_lcms_collection_settings_json(
295    filename="SettingsCoreMS.json", file_path=None, lcms_collection=None
296):
297    """Write JSON file with LCMS collection settings data.
298
299    Parameters
300    ----------
301    filename : str, optional
302        The name of the JSON file. Defaults to 'SettingsCoreMS.json'.
303    file_path : str or Path, optional
304        The path where the JSON file will be saved. If not provided, the file will be saved in the current working directory.
305    lcms_collection : LCMSCollection, optional
306        The LCMS collection object containing the settings data. If not provided, the settings data will be retrieved from the default settings.
307    """
308    from corems.encapsulation.output.parameter_to_dict import (
309        get_dict_data_lcms_collection,
310        get_dict_lcms_collection_default_data,
311    )
312
313    if lcms_collection is None:
314        data_dict = get_dict_lcms_collection_default_data()
315    else:
316        data_dict = get_dict_data_lcms_collection(lcms_collection)
317
318    if not file_path:
319        file_path = Path.cwd() / filename
320
321    with open(
322        file_path,
323        "w",
324        encoding="utf8",
325    ) as outfile:
326        outfile.write(json.dumps(data_dict, indent=4))
327
328
329def dump_lcms_collection_settings_toml(
330    filename="SettingsCoreMS.toml", file_path=None, lcms_collection=None
331):
332    """Write TOML file with LCMS collection settings data.
333
334    Parameters
335    ----------
336    filename : str, optional
337        The name of the TOML file. Defaults to 'SettingsCoreMS.toml'.
338    file_path : str or Path, optional
339        The path where the TOML file will be saved. If not provided, the file will be saved in the current working directory.
340    lcms_collection : LCMSCollection, optional
341        The LCMS collection object containing the settings data. If not provided, the settings data will be retrieved from the default settings.
342    """
343    from corems.encapsulation.output.parameter_to_dict import (
344        get_dict_data_lcms_collection,
345        get_dict_lcms_collection_default_data,
346    )
347
348    if lcms_collection is None:
349        data_dict = get_dict_lcms_collection_default_data()
350    else:
351        data_dict = get_dict_data_lcms_collection(lcms_collection)
352
353    if not file_path:
354        file_path = Path.cwd() / filename
355
356    with open(
357        file_path,
358        "w",
359        encoding="utf8",
360    ) as outfile:
361        output = _dumps_toml(data_dict)
362        outfile.write(output)