sapiopycommons 2024.11.7a354__py3-none-any.whl → 2024.11.8a359__py3-none-any.whl

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Files changed (47) hide show
  1. sapiopycommons/callbacks/callback_util.py +83 -532
  2. sapiopycommons/chem/IndigoMolecules.py +0 -2
  3. sapiopycommons/chem/Molecules.py +18 -77
  4. sapiopycommons/datatype/attachment_util.py +10 -11
  5. sapiopycommons/eln/experiment_handler.py +70 -272
  6. sapiopycommons/files/complex_data_loader.py +4 -5
  7. sapiopycommons/files/file_bridge.py +24 -31
  8. sapiopycommons/files/file_data_handler.py +5 -2
  9. sapiopycommons/files/file_util.py +9 -59
  10. sapiopycommons/files/file_validator.py +6 -92
  11. sapiopycommons/files/file_writer.py +15 -44
  12. sapiopycommons/general/aliases.py +6 -207
  13. sapiopycommons/general/custom_report_util.py +37 -212
  14. sapiopycommons/general/exceptions.py +8 -21
  15. sapiopycommons/general/popup_util.py +0 -21
  16. sapiopycommons/general/time_util.py +2 -8
  17. sapiopycommons/processtracking/endpoints.py +22 -22
  18. sapiopycommons/recordmodel/record_handler.py +97 -481
  19. sapiopycommons/rules/eln_rule_handler.py +25 -34
  20. sapiopycommons/rules/on_save_rule_handler.py +31 -34
  21. sapiopycommons/webhook/webhook_handlers.py +42 -201
  22. {sapiopycommons-2024.11.7a354.dist-info → sapiopycommons-2024.11.8a359.dist-info}/METADATA +2 -4
  23. sapiopycommons-2024.11.8a359.dist-info/RECORD +38 -0
  24. sapiopycommons/callbacks/field_builder.py +0 -537
  25. sapiopycommons/customreport/__init__.py +0 -0
  26. sapiopycommons/customreport/column_builder.py +0 -60
  27. sapiopycommons/customreport/custom_report_builder.py +0 -130
  28. sapiopycommons/customreport/term_builder.py +0 -299
  29. sapiopycommons/datatype/data_fields.py +0 -61
  30. sapiopycommons/datatype/pseudo_data_types.py +0 -440
  31. sapiopycommons/eln/experiment_report_util.py +0 -653
  32. sapiopycommons/files/file_bridge_handler.py +0 -340
  33. sapiopycommons/flowcyto/flow_cyto.py +0 -77
  34. sapiopycommons/flowcyto/flowcyto_data.py +0 -75
  35. sapiopycommons/general/accession_service.py +0 -375
  36. sapiopycommons/general/audit_log.py +0 -189
  37. sapiopycommons/general/sapio_links.py +0 -50
  38. sapiopycommons/multimodal/multimodal.py +0 -146
  39. sapiopycommons/multimodal/multimodal_data.py +0 -489
  40. sapiopycommons/processtracking/custom_workflow_handler.py +0 -406
  41. sapiopycommons/sftpconnect/__init__.py +0 -0
  42. sapiopycommons/sftpconnect/sftp_builder.py +0 -69
  43. sapiopycommons/webhook/webhook_context.py +0 -39
  44. sapiopycommons/webhook/webservice_handlers.py +0 -67
  45. sapiopycommons-2024.11.7a354.dist-info/RECORD +0 -59
  46. {sapiopycommons-2024.11.7a354.dist-info → sapiopycommons-2024.11.8a359.dist-info}/WHEEL +0 -0
  47. {sapiopycommons-2024.11.7a354.dist-info → sapiopycommons-2024.11.8a359.dist-info}/licenses/LICENSE +0 -0
@@ -1,375 +0,0 @@
1
- from __future__ import annotations
2
-
3
- from abc import ABC, abstractmethod
4
- from typing import Any
5
- from weakref import WeakValueDictionary
6
-
7
- from sapiopylib.rest.User import SapioUser
8
-
9
- _STR_JAVA_TYPE = "java.lang.String"
10
- _INT_JAVA_TYPE = "java.lang.Integer"
11
- _BOOL_JAVA_TYPE = "java.lang.Boolean"
12
-
13
-
14
- class AbstractAccessionServiceOperator(ABC):
15
- """
16
- Abstract class to define an accession service operator.
17
- The default one in sapiopycommon only includes the out of box operators.
18
- More can be added via java plugins for global operators.
19
- """
20
-
21
- @property
22
- @abstractmethod
23
- def op_class_name(self) -> str:
24
- pass
25
-
26
- @property
27
- @abstractmethod
28
- def op_param_value_list(self) -> list[Any] | None:
29
- pass
30
-
31
- @property
32
- @abstractmethod
33
- def op_param_class_name_list(self) -> list[str] | None:
34
- pass
35
-
36
- @property
37
- @abstractmethod
38
- def default_accessor_name(self) -> str:
39
- pass
40
-
41
-
42
- class AccessionWithPrefixSuffix(AbstractAccessionServiceOperator):
43
- """
44
- Local operator for accessioning prefix and suffix format.
45
- """
46
- _prefix: str | None
47
- _suffix: str | None
48
- _num_of_digits: int | None
49
- _start_num: int
50
- _strict_mode: bool
51
-
52
- @property
53
- def prefix(self):
54
- return self._prefix
55
-
56
- @property
57
- def suffix(self):
58
- return self._suffix
59
-
60
- @property
61
- def num_of_digits(self):
62
- return self._num_of_digits
63
-
64
- @property
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- def start_num(self):
66
- return self._start_num
67
-
68
- @property
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- def strict_mode(self):
70
- return self._strict_mode
71
-
72
- def __init__(self, prefix: str | None, suffix: str | None, num_of_digits: int | None = None,
73
- start_num: int = 1, strict_mode: bool = False):
74
- if prefix is None:
75
- prefix = ""
76
- if suffix is None:
77
- suffix = ""
78
- self._prefix = prefix
79
- self._suffix = suffix
80
- self._num_of_digits = num_of_digits
81
- self._start_num = start_num
82
- self._strict_mode = strict_mode
83
-
84
- @property
85
- def op_param_value_list(self):
86
- return [self._prefix, self._suffix, self._num_of_digits, self._start_num, self._strict_mode]
87
-
88
- @property
89
- def op_param_class_name_list(self):
90
- return [_STR_JAVA_TYPE, _STR_JAVA_TYPE, _INT_JAVA_TYPE, _INT_JAVA_TYPE, _BOOL_JAVA_TYPE]
91
-
92
- @property
93
- def op_class_name(self):
94
- return "com.velox.accessionservice.operators.AccessionWithPrefixSuffix"
95
-
96
- @property
97
- def default_accessor_name(self):
98
- return "PREFIX_AND_SUFFIX" + "(" + self.prefix + "," + self.suffix + ")";
99
-
100
-
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- class AccessionGlobalPrefixSuffix(AbstractAccessionServiceOperator):
102
- """
103
- Global operator for accessioning prefix and suffix format.
104
- """
105
- _prefix: str | None
106
- _suffix: str | None
107
- _num_of_digits: int | None
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- _start_num: int
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- _strict_mode: bool
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-
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- @property
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- def prefix(self):
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- return self._prefix
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-
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- @property
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- def suffix(self):
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- return self._suffix
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-
119
- @property
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- def num_of_digits(self):
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- return self._num_of_digits
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-
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- @property
124
- def start_num(self):
125
- return self._start_num
126
-
127
- @property
128
- def strict_mode(self):
129
- return self._strict_mode
130
-
131
- def __init__(self, prefix: str | None, suffix: str | None, num_of_digits: int | None = None,
132
- start_num: int = 1, strict_mode: bool = False):
133
- if prefix is None:
134
- prefix = ""
135
- if suffix is None:
136
- suffix = ""
137
- self._prefix = prefix
138
- self._suffix = suffix
139
- self._num_of_digits = num_of_digits
140
- self._start_num = start_num
141
- self._strict_mode = strict_mode
142
-
143
- @property
144
- def op_param_value_list(self):
145
- return [self._prefix, self._suffix, self._num_of_digits, self._start_num, self._strict_mode]
146
-
147
- @property
148
- def op_param_class_name_list(self):
149
- return [_STR_JAVA_TYPE, _STR_JAVA_TYPE, _INT_JAVA_TYPE, _INT_JAVA_TYPE, _BOOL_JAVA_TYPE]
150
-
151
- @property
152
- def op_class_name(self):
153
- return "com.velox.accessionservice.operators.sapio.AccessionGlobalPrefixSuffix"
154
-
155
- @property
156
- def default_accessor_name(self):
157
- return "PREFIX_AND_SUFFIX" + "(" + self._prefix + "," + self._suffix + ")"
158
-
159
-
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- class AccessionNextBarcode(AbstractAccessionServiceOperator):
161
- """
162
- From Java description:
163
- This will start accessioning at the getNextBarcode() when there's no system preference to be backward compatible.
164
- However, once it completes setting the first ID, it will start increment by its own preference and disregards getNextBarcode().
165
-
166
- Recommend using AccessionServiceBasicManager to accession next barcode.
167
- To avoid ambiguity in preference cache.
168
-
169
- This should not be used unless we are using something legacy such as plate mapping template record creation
170
- (Note: not 3D plating, I'm talking about the older aliquoter).
171
- """
172
-
173
- @property
174
- def op_param_value_list(self):
175
- return []
176
-
177
- @property
178
- def op_param_class_name_list(self):
179
- return []
180
-
181
- @property
182
- def op_class_name(self):
183
- return "com.velox.accessionservice.operators.sapio.AccessionNextBarcode"
184
-
185
- @property
186
- def default_accessor_name(self):
187
- return "Barcode"
188
-
189
-
190
- class AccessionRequestId(AbstractAccessionServiceOperator):
191
- """
192
- This class implements the accessioning operator for com.velox.sapioutils.shared.managers.DataRecordUtilManager.getNextRequestId()
193
- and getNextRequestId(int numberOfCharacters).
194
-
195
- Operation: For 4 characters start with A001, increment by 1 until A999. Then We use B001.
196
- After Z999 we start with AA01 until we get to AA99, etc.
197
-
198
- Exception: Skips I and O to prevent confusions with 1 and 0 when incrementing letters.
199
-
200
- Properties:
201
- numberOfCharacters: Number of characters maximum in the request ID.
202
- accessorName: This is a legacy variable from drum.getNextIdListByMapName(), which allows setting different "accessorName" from old system. We need this for compability patch for converting these to the new preference format.
203
- """
204
- _num_of_characters: int
205
- _accessor_name: str
206
-
207
- @property
208
- def num_of_characters(self):
209
- return self._num_of_characters
210
-
211
- @property
212
- def accessor_name(self):
213
- return self._accessor_name
214
-
215
- def __init__(self, num_of_characters: int = 4, accessor_name: str = None):
216
- self._num_of_characters = num_of_characters
217
- if not accessor_name:
218
- accessor_name = self.default_accessor_name
219
- self._accessor_name = accessor_name
220
-
221
- @property
222
- def op_class_name(self):
223
- return "com.velox.accessionservice.operators.sapio.AccessionRequestId"
224
-
225
- @property
226
- def op_param_value_list(self):
227
- return [self._num_of_characters, self._accessor_name]
228
-
229
- @property
230
- def op_param_class_name_list(self):
231
- return [_INT_JAVA_TYPE, _STR_JAVA_TYPE]
232
-
233
- @property
234
- def default_accessor_name(self):
235
- return "SapioNextRequestIdMap"
236
-
237
-
238
- class AccessionServiceDescriptor:
239
- """
240
- Describes a single accession service's accessioning request
241
-
242
- Attributes:
243
- opClassName: The accession service operator class name as in Java
244
- opParamValueList: Ordered list of parameter values to construct the accession service operator.
245
- opParamClassNameList: Ordered list of FQCN of java classes in order of parameter value list.
246
- dataTypeName: The data type to accession. Should be blank if opClassName resolves to a global operator.
247
- dataFieldName: The data field to accession. Should be blank if opClassName resolves to a global operator.
248
- accessorName: The accessor cache name to be used for accessioning.
249
- numIds: The number of IDs to accession.
250
- """
251
- op: AbstractAccessionServiceOperator
252
- dataTypeName: str | None
253
- dataFieldName: str | None
254
- accessorName: str
255
- numIds: int
256
-
257
- def __init__(self, accessor_name: str, op: AbstractAccessionServiceOperator, num_ids: int,
258
- data_type_name: str | None, data_field_name: str | None):
259
- self.accessorName = accessor_name
260
- self.op = op
261
- self.dataTypeName = data_type_name
262
- self.dataFieldName = data_field_name
263
- self.numIds = num_ids
264
-
265
- def to_json(self):
266
- return {
267
- "opClassName": self.op.op_class_name,
268
- "opParamValueList": self.op.op_param_value_list,
269
- "opParamClassNameList": self.op.op_param_class_name_list,
270
- "accessorName": self.accessorName,
271
- "numIds": self.numIds,
272
- "dataTypeName": self.dataTypeName,
273
- "dataFieldName": self.dataFieldName
274
- }
275
-
276
-
277
- class AccessionService:
278
- """
279
- Provides Sapio Foundations Accession Service functionalities.
280
- """
281
- _user: SapioUser
282
-
283
- __instances: WeakValueDictionary[SapioUser, AccessionService] = WeakValueDictionary()
284
- __initialized: bool
285
-
286
- @property
287
- def user(self) -> SapioUser:
288
- return self._user
289
-
290
- def __new__(cls, user: SapioUser):
291
- """
292
- Observes singleton pattern per record model manager object.
293
-
294
- :param user: The user that will make the webservice request to the application.
295
- """
296
- obj = cls.__instances.get(user)
297
- if not obj:
298
- obj = object.__new__(cls)
299
- obj.__initialized = False
300
- cls.__instances[user] = obj
301
- return obj
302
-
303
- def __init__(self, user: SapioUser):
304
- if self.__initialized:
305
- return
306
- self._user = user
307
- self.__initialized = True
308
-
309
- def accession_with_config(self, data_type_name: str, data_field_name: str, num_ids: int) -> list[str]:
310
- """
311
- Accession with Configuration Manager => Accession Service configuration (This is not visible to regular users in SaaS)
312
- """
313
- payload = {
314
- "dataTypeName": data_type_name,
315
- "dataFieldName": data_field_name,
316
- "numIds": num_ids
317
- }
318
- response = self.user.plugin_post("accessionservice/accession_with_config", payload=payload)
319
- self.user.raise_for_status(response)
320
- return list(response.json())
321
-
322
- def accession_in_batch(self, descriptor: AccessionServiceDescriptor) -> list[str]:
323
- """
324
- This is the most flexible way to make use of accession service: directly via a descriptor object.
325
- """
326
- payload = descriptor.to_json()
327
- response = self.user.plugin_post("accessionservice/accession", payload=payload)
328
- self.user.raise_for_status(response)
329
- return list(response.json())
330
-
331
- def accession_next_request_id_list(self, num_of_characters: int, num_ids: int) -> list[str]:
332
- """
333
- Accession Request ID by old LIMS format. This is usually deprecated today.
334
- :param num_of_characters: Number of characters minimum in request ID.
335
- :param num_ids: Number of request IDs to accession.
336
- """
337
- op = AccessionRequestId(num_of_characters)
338
- descriptor = AccessionServiceDescriptor(op.default_accessor_name, op, num_ids, None, None)
339
- return self.accession_in_batch(descriptor)
340
-
341
- def get_affixed_id_in_batch(self, data_type_name: str, data_field_name: str, num_ids: int, prefix: str | None,
342
- suffix: str | None, num_digits: int | None, start_num: int = 1) -> list[str]:
343
- """
344
- Get the batch affixed IDs that are maximal in cache and contiguious for a particular datatype.datafield under a given format.
345
- :param data_type_name: The datatype name to look for max ID
346
- :param data_field_name: The datafield name to look for max ID
347
- :param num_ids: The number of IDs to accession.
348
- :param prefix: leave it empty string "" if no prefix. Otherwise, specifies the prefix of ID.
349
- :param suffix: leave it empty string "" if no suffix. Otherwise, specifies the suffix of ID.
350
- :param num_digits: None if unlimited with no leading zeros.
351
- :param start_num The number to begin accessioning if this is the first time.
352
- :return:
353
- """
354
- op = AccessionWithPrefixSuffix(prefix, suffix, num_digits, start_num)
355
- descriptor = AccessionServiceDescriptor(op.default_accessor_name, op, num_ids, data_type_name, data_field_name)
356
- return self.accession_in_batch(descriptor)
357
-
358
- def get_global_affixed_id_in_batch(
359
- self, num_ids: int, prefix: str | None, suffix: str | None, num_digits: int | None, start_num: int = 1) -> list[str]:
360
- """
361
- Get the next numOfIds affixed IDs using system preference cache that's maximum across all datatype and datafields and maximal for the format.
362
- This method allows users to customize a start number instead of always starting at 1.
363
- :param num_ids: The number of IDs to accession.
364
- :param prefix: leave it empty string "" if no prefix. Otherwise, specifies the prefix of ID.
365
- :param suffix: leave it empty string "" if no suffix. Otherwise, specifies the suffix of ID.
366
- :param num_digits: None if unlimited with no leading zeros.
367
- :param start_num The number to begin accessioning if this is the first time.
368
- """
369
- op: AbstractAccessionServiceOperator
370
- if not prefix and not suffix:
371
- op = AccessionNextBarcode()
372
- else:
373
- op = AccessionGlobalPrefixSuffix(prefix, suffix, num_digits, start_num)
374
- descriptor = AccessionServiceDescriptor(op.default_accessor_name, op, num_ids, None, None)
375
- return self.accession_in_batch(descriptor)
@@ -1,189 +0,0 @@
1
- from enum import Enum
2
-
3
- from sapiopylib.rest.User import SapioUser
4
- from sapiopylib.rest.pojo.CustomReport import ReportColumn, CustomReportCriteria
5
-
6
- from sapiopycommons.customreport.column_builder import ColumnBuilder
7
- from sapiopycommons.customreport.term_builder import TermBuilder
8
- from sapiopycommons.datatype.pseudo_data_types import AuditLogPseudoDef
9
- from sapiopycommons.general.aliases import RecordIdentifier, AliasUtil, UserIdentifier, FieldIdentifier, FieldValue
10
- from sapiopycommons.general.custom_report_util import CustomReportUtil
11
-
12
-
13
- class EventType(Enum):
14
- """An enum to represent the possible event type values with the event type column in the audit log table."""
15
- ADD = 0
16
- DELETE = 1
17
- MODIFY = 2
18
- INFO = 3
19
- ERROR = 4
20
- WARNING = 5
21
- IMPORT = 6
22
- GENERATE = 7
23
- EXPORT = 8
24
- ADDREF = 9
25
- REMOVEREF = 10
26
- ESIGNATURE = 11
27
- ROLEASSIGNMENT = 12
28
-
29
-
30
- class AuditLogEntry:
31
- __event_type: EventType
32
- __date: int
33
- __data_type_name: str
34
- __record_id: int
35
- __description: str
36
- __users_login_name: str
37
- __comment: str
38
- __data_record_name: str
39
- __data_field_name: str
40
- __original_value: str
41
- __new_value: str
42
-
43
- @property
44
- def event_type(self) -> EventType:
45
- return self.__event_type
46
-
47
- @property
48
- def date(self) -> int:
49
- return self.__date
50
-
51
- @property
52
- def data_type_name(self) -> str:
53
- return self.__data_type_name
54
-
55
- @property
56
- def record_id(self) -> int:
57
- return self.__record_id
58
-
59
- @property
60
- def description(self) -> str:
61
- return self.__description
62
-
63
- @property
64
- def users_login_name(self) -> str:
65
- return self.__users_login_name
66
-
67
- @property
68
- def comment(self) -> str:
69
- return self.__comment
70
-
71
- @property
72
- def data_record_name(self) -> str:
73
- return self.__data_record_name
74
-
75
- @property
76
- def data_field_name(self) -> str:
77
- return self.__data_field_name
78
-
79
- @property
80
- def original_value(self) -> str:
81
- return self.__original_value
82
-
83
- @property
84
- def new_value(self) -> str:
85
- return self.__new_value
86
-
87
- def __init__(self, report_row: dict[str, FieldValue]):
88
- self.__event_type = EventType((report_row[AuditLogPseudoDef.EVENT_TYPE__FIELD_NAME.field_name]))
89
- self.__date = report_row[AuditLogPseudoDef.TIME_STAMP__FIELD_NAME.field_name]
90
- self.__data_type_name = report_row[AuditLogPseudoDef.DATA_TYPE_NAME__FIELD_NAME.field_name]
91
- self.__record_id = report_row[AuditLogPseudoDef.RECORD_ID__FIELD_NAME.field_name]
92
- self.__description = report_row[AuditLogPseudoDef.DESCRIPTION__FIELD_NAME.field_name]
93
- self.__users_login_name = report_row[AuditLogPseudoDef.USER_NAME__FIELD_NAME.field_name]
94
- self.__comment = report_row[AuditLogPseudoDef.USER_COMMENT__FIELD_NAME.field_name]
95
- self.__data_record_name = report_row[AuditLogPseudoDef.RECORD_NAME__FIELD_NAME]
96
- self.__data_field_name = report_row[AuditLogPseudoDef.DATA_FIELD_NAME__FIELD_NAME.field_name]
97
- self.__original_value = report_row[AuditLogPseudoDef.ORIGINAL_VALUE__FIELD_NAME.field_name]
98
- self.__new_value = report_row[AuditLogPseudoDef.NEW_VALUE__FIELD_NAME.field_name]
99
-
100
-
101
- class AuditLogUtil:
102
- user: SapioUser
103
-
104
- def __init__(self, context: UserIdentifier):
105
- self.user = AliasUtil.to_sapio_user(context)
106
-
107
- @staticmethod
108
- def report_columns() -> list[ReportColumn]:
109
- return [
110
- ColumnBuilder.build_column(AuditLogPseudoDef.DATA_TYPE_NAME, AuditLogPseudoDef.EVENT_TYPE__FIELD_NAME),
111
- ColumnBuilder.build_column(AuditLogPseudoDef.DATA_TYPE_NAME, AuditLogPseudoDef.TIME_STAMP__FIELD_NAME),
112
- ColumnBuilder.build_column(AuditLogPseudoDef.DATA_TYPE_NAME, AuditLogPseudoDef.DATA_TYPE_NAME__FIELD_NAME),
113
- ColumnBuilder.build_column(AuditLogPseudoDef.DATA_TYPE_NAME, AuditLogPseudoDef.RECORD_ID__FIELD_NAME),
114
- ColumnBuilder.build_column(AuditLogPseudoDef.DATA_TYPE_NAME, AuditLogPseudoDef.DESCRIPTION__FIELD_NAME),
115
- ColumnBuilder.build_column(AuditLogPseudoDef.DATA_TYPE_NAME, AuditLogPseudoDef.USER_NAME__FIELD_NAME),
116
- ColumnBuilder.build_column(AuditLogPseudoDef.DATA_TYPE_NAME, AuditLogPseudoDef.USER_COMMENT__FIELD_NAME),
117
- ColumnBuilder.build_column(AuditLogPseudoDef.DATA_TYPE_NAME, AuditLogPseudoDef.RECORD_NAME__FIELD_NAME),
118
- ColumnBuilder.build_column(AuditLogPseudoDef.DATA_TYPE_NAME, AuditLogPseudoDef.DATA_FIELD_NAME__FIELD_NAME),
119
- ColumnBuilder.build_column(AuditLogPseudoDef.DATA_TYPE_NAME, AuditLogPseudoDef.ORIGINAL_VALUE__FIELD_NAME),
120
- ColumnBuilder.build_column(AuditLogPseudoDef.DATA_TYPE_NAME, AuditLogPseudoDef.NEW_VALUE__FIELD_NAME)
121
- ]
122
-
123
- @staticmethod
124
- def create_data_record_audit_log_report(records: list[RecordIdentifier],
125
- fields: list[FieldIdentifier] | None = None) -> CustomReportCriteria:
126
- """
127
- This method creates a CustomReportCriteria object for running an audit log query based on data records.
128
-
129
- Creates a CustomReportCriteria object with a query term based on the record ids/records passed into the method.
130
- Optionally, the fields parameter can be populated to limit the search to particular fields. If the fields
131
- parameter is not populated, the search will include results for all field changes.
132
-
133
- :param records: The DataRecords, RecordModels, or record ids to base the search on.
134
- :param fields: The data field names to include changes for.
135
- :return: The constructed CustomReportCriteria object, which can be used to run a report on the audit log.
136
- """
137
- # Build the raw report term querying for any entry with a matching record ID value to the record ID's
138
- # passed in.
139
- record_ids = AliasUtil.to_record_ids(records)
140
- root_term = TermBuilder.is_term(AuditLogPseudoDef.DATA_TYPE_NAME,
141
- AuditLogPseudoDef.RECORD_ID__FIELD_NAME,
142
- record_ids)
143
-
144
- # If the user passed in any specific fields, then we should limit the query to those fields.
145
- if fields:
146
- fields: list[str] = AliasUtil.to_data_field_names(fields)
147
- field_term = TermBuilder.is_term(AuditLogPseudoDef.DATA_TYPE_NAME,
148
- AuditLogPseudoDef.DATA_FIELD_NAME__FIELD_NAME,
149
- fields)
150
- root_term = TermBuilder.and_terms(root_term, field_term)
151
-
152
- return CustomReportCriteria(AuditLogUtil.report_columns(), root_term)
153
-
154
- def run_data_record_audit_log_report(self, records: list[RecordIdentifier],
155
- fields: list[FieldIdentifier] | None = None) \
156
- -> dict[RecordIdentifier, list[AuditLogEntry]]:
157
- """
158
- This method runs a custom report for changes made to the given data records using the audit log.
159
- See "create_data_record_audit_log_report" for more details about the data record audit log report.
160
-
161
- :param records: The DataRecords, RecordModels, or record ids to base the search on.
162
- :param fields: The data field names to include changes for.
163
- :return: A dictionary where the keys are the record identifiers passed in, and the values are a list of
164
- AuditLogEntry objects which match the record id value of those records.
165
- """
166
- fields: list[str] = AliasUtil.to_data_field_names(fields)
167
- # First, we must build our report criteria for running the Custom Report.
168
- criteria = AuditLogUtil.create_data_record_audit_log_report(records, fields)
169
-
170
- # Then we must run the custom report using that criteria.
171
- raw_report_data: list[dict[str, FieldValue]] = CustomReportUtil.run_custom_report(self.user, criteria)
172
-
173
- # This section will prepare a map matching the original RecordIdentifier by record id.
174
- # This is because the audit log entries will have record ids, but we want the keys in our result map
175
- # to match the record identifiers that the user passed in, for convenience.
176
- record_identifier_mapping: dict[int, RecordIdentifier] = dict()
177
- for record in records:
178
- record_id = AliasUtil.to_record_id(record)
179
- record_identifier_mapping[record_id] = record
180
-
181
- # Finally, we compile our audit data into a map where the keys are the record identifiers passed in,
182
- # and the value is a list of applicable audit log entries.
183
- final_audit_data: dict[RecordIdentifier, list[AuditLogEntry]] = dict()
184
- for audit_entry_data in raw_report_data:
185
- audit_entry: AuditLogEntry = AuditLogEntry(audit_entry_data)
186
- identifier: RecordIdentifier = record_identifier_mapping.get(audit_entry.record_id)
187
- final_audit_data.setdefault(identifier, []).append(audit_entry)
188
-
189
- return final_audit_data
@@ -1,50 +0,0 @@
1
- from sapiopylib.rest.User import SapioUser
2
- from sapiopylib.rest.pojo.webhook.WebhookContext import SapioWebhookContext
3
-
4
- from sapiopycommons.general.aliases import RecordIdentifier, ExperimentIdentifier, AliasUtil, DataTypeIdentifier
5
- from sapiopycommons.general.exceptions import SapioException
6
-
7
-
8
- class SapioNavigationLinker:
9
- """
10
- Given a URL to a system's webservice API (example: https://company.exemplareln.com/webservice/api), construct
11
- URLs for navigation links to various locations in the system.
12
- """
13
- base_url: str
14
-
15
- def __init__(self, url: str | SapioUser | SapioWebhookContext):
16
- """
17
- :param url: A user or context object that is being used to send requests to a Sapio system, or a URL to a
18
- system's webservice API.
19
- """
20
- if isinstance(url, SapioWebhookContext):
21
- url = url.user.url
22
- elif isinstance(url, SapioUser):
23
- url = url.url
24
- self.base_url = url.rstrip("/").replace('webservice/api', 'veloxClient')
25
-
26
- def data_record(self, record_identifier: RecordIdentifier, data_type_name: DataTypeIdentifier | None = None) -> str:
27
- """
28
- :param record_identifier: An object that can be used to identify a record in the system, be that a record ID,
29
- a data record, or a record model.
30
- :param data_type_name: If the provided record identifier is a record ID, then the data type name of the record
31
- must be provided in this parameter. Otherwise, this parameter is ignored.
32
- :return: A URL for navigating to the input record.
33
- """
34
- record_id: int = AliasUtil.to_record_id(record_identifier)
35
- if data_type_name:
36
- data_type_name = AliasUtil.to_data_type_name(data_type_name)
37
- if not isinstance(record_identifier, int):
38
- data_type_name = AliasUtil.to_data_type_name(record_identifier)
39
- if not data_type_name:
40
- raise SapioException("Unable to create a data record link without a data type name. "
41
- "Only a record ID was provided.")
42
- return self.base_url + f"/#dataType={data_type_name};recordId={record_id};view=dataRecord"
43
-
44
- def experiment(self, experiment: ExperimentIdentifier) -> str:
45
- """
46
- :param experiment: An object that can be used to identify an experiment in the system, be that an experiment
47
- object, experiment protocol, or a notebook ID.
48
- :return: A URL for navigating to the input experiment.
49
- """
50
- return self.base_url + f"/#notebookExperimentId={AliasUtil.to_notebook_id(experiment)};view=eln"