sapiopycommons 2025.4.8a473__py3-none-any.whl → 2025.4.9a150__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Potentially problematic release.


This version of sapiopycommons might be problematic. Click here for more details.

Files changed (42) hide show
  1. sapiopycommons/callbacks/callback_util.py +392 -1262
  2. sapiopycommons/callbacks/field_builder.py +0 -2
  3. sapiopycommons/chem/Molecules.py +2 -0
  4. sapiopycommons/customreport/term_builder.py +1 -1
  5. sapiopycommons/datatype/attachment_util.py +2 -4
  6. sapiopycommons/datatype/data_fields.py +1 -23
  7. sapiopycommons/eln/experiment_handler.py +279 -933
  8. sapiopycommons/eln/experiment_report_util.py +10 -15
  9. sapiopycommons/eln/plate_designer.py +59 -159
  10. sapiopycommons/files/file_bridge.py +0 -76
  11. sapiopycommons/files/file_bridge_handler.py +110 -325
  12. sapiopycommons/files/file_data_handler.py +2 -2
  13. sapiopycommons/files/file_util.py +15 -40
  14. sapiopycommons/files/file_validator.py +5 -6
  15. sapiopycommons/files/file_writer.py +1 -1
  16. sapiopycommons/flowcyto/flow_cyto.py +1 -1
  17. sapiopycommons/general/accession_service.py +3 -3
  18. sapiopycommons/general/aliases.py +28 -51
  19. sapiopycommons/general/audit_log.py +2 -2
  20. sapiopycommons/general/custom_report_util.py +1 -24
  21. sapiopycommons/general/exceptions.py +2 -41
  22. sapiopycommons/general/popup_util.py +2 -2
  23. sapiopycommons/multimodal/multimodal.py +0 -1
  24. sapiopycommons/processtracking/custom_workflow_handler.py +30 -46
  25. sapiopycommons/recordmodel/record_handler.py +159 -547
  26. sapiopycommons/rules/eln_rule_handler.py +30 -41
  27. sapiopycommons/rules/on_save_rule_handler.py +30 -41
  28. sapiopycommons/webhook/webhook_handlers.py +55 -448
  29. sapiopycommons/webhook/webservice_handlers.py +2 -2
  30. {sapiopycommons-2025.4.8a473.dist-info → sapiopycommons-2025.4.9a150.dist-info}/METADATA +1 -1
  31. sapiopycommons-2025.4.9a150.dist-info/RECORD +59 -0
  32. sapiopycommons/customreport/auto_pagers.py +0 -281
  33. sapiopycommons/eln/experiment_cache.py +0 -173
  34. sapiopycommons/eln/experiment_step_factory.py +0 -474
  35. sapiopycommons/eln/experiment_tags.py +0 -7
  36. sapiopycommons/eln/step_creation.py +0 -235
  37. sapiopycommons/general/data_structure_util.py +0 -115
  38. sapiopycommons/general/directive_util.py +0 -86
  39. sapiopycommons/samples/aliquot.py +0 -48
  40. sapiopycommons-2025.4.8a473.dist-info/RECORD +0 -67
  41. {sapiopycommons-2025.4.8a473.dist-info → sapiopycommons-2025.4.9a150.dist-info}/WHEEL +0 -0
  42. {sapiopycommons-2025.4.8a473.dist-info → sapiopycommons-2025.4.9a150.dist-info}/licenses/LICENSE +0 -0
@@ -3,13 +3,12 @@ from typing import Iterable
3
3
  from sapiopylib.rest.User import SapioUser
4
4
  from sapiopylib.rest.pojo.CustomReport import CustomReportCriteria
5
5
  from sapiopylib.rest.pojo.webhook.WebhookContext import SapioWebhookContext
6
- from sapiopylib.rest.utils.recordmodel.PyRecordModel import PyRecordModel
7
6
  from sapiopylib.rest.utils.recordmodel.RecordModelWrapper import WrappedType
8
7
 
9
- from sapiopycommons.customreport.auto_pagers import CustomReportDictAutoPager, CustomReportRecordAutoPager
10
8
  from sapiopycommons.customreport.custom_report_builder import CustomReportBuilder
11
9
  from sapiopycommons.datatype.data_fields import ProcessQueueItemFields, SystemFields, ProcessWorkflowTrackingFields
12
10
  from sapiopycommons.general.aliases import UserIdentifier, AliasUtil, SapioRecord
11
+ from sapiopycommons.general.custom_report_util import CustomReportUtil
13
12
  from sapiopycommons.general.exceptions import SapioException
14
13
  from sapiopycommons.general.time_util import TimeUtil
15
14
  from sapiopycommons.recordmodel.record_handler import RecordHandler
@@ -105,28 +104,24 @@ class QueueItemHandler:
105
104
  """
106
105
  self.user = AliasUtil.to_sapio_user(context)
107
106
  self.rec_handler = RecordHandler(self.user)
108
- # PR-47565: Only initialize a ProcessQueueContext if the given context object has context_data.
109
- if isinstance(context, SapioWebhookContext) and context.context_data:
107
+ if isinstance(context, SapioWebhookContext):
110
108
  self.context = ProcessQueueContext(context)
111
109
  else:
112
110
  self.context = None
113
111
 
114
- # CR-47491: Support providing a data type name string to receive PyRecordModels instead of requiring a WrapperType.
115
- def get_process_queue_items_from_context(self, wrapper: type[WrappedType] | str,
112
+ def get_process_queue_items_from_context(self, wrapper: type[WrappedType],
116
113
  context: SapioWebhookContext | ProcessQueueContext | None = None) \
117
- -> list[WrappedType] | list[PyRecordModel]:
114
+ -> list[WrappedType]:
118
115
  """
119
116
  When you launch records from a custom process queue, the process queue items related to the selected records
120
117
  are provided as record IDs to the process queue context. Using these record IDs, query for the queue item
121
118
  records and wrap them as record models.
122
119
 
123
- :param wrapper: The record model wrapper or data type name for the process queue items.
120
+ :param wrapper: The record model wrapper for the process queue items.
124
121
  :param context: If this handler was not initialized with a context object, or you wish to retrieve
125
122
  data from a different context object than the initializing context, then provide the context to retrieve the
126
123
  record IDs from.
127
124
  :return: The process queue items corresponding to the record IDs from the context wrapped as record models.
128
- If a data type name was used instead of a model wrapper, then the returned records will be PyRecordModels
129
- instead of WrappedRecordModels.
130
125
  """
131
126
  if context is None and self.context is not None:
132
127
  record_ids: list[int] = self.context.process_queue_item_record_ids
@@ -180,52 +175,46 @@ class QueueItemHandler:
180
175
  ret_val[queue_item] = record
181
176
  return ret_val
182
177
 
183
- def get_queue_items_from_report(self, wrapper: type[WrappedType] | None, criteria: QueueItemReportCriteria) \
184
- -> list[WrappedType] | list[PyRecordModel]:
178
+ def get_queue_items_from_report(self, wrapper: type[WrappedType], criteria: QueueItemReportCriteria) \
179
+ -> list[WrappedType]:
185
180
  """
186
181
  Run a custom report that retrieves every queue item in the system for the given search criteria.
187
182
 
188
- :param wrapper: The record model wrapper for the process queue items. If not provided, the returned records will
189
- be PyRecordModels instead of WrappedRecordModels.
183
+ :param wrapper: The record model wrapper for the process queue items.
190
184
  :param criteria: The search criteria to query for queue items with.
191
185
  :return: A list of every queue item in the system that matches the search criteria.
192
186
  """
193
187
  report = self.build_queue_item_report(criteria)
194
- dt: type[WrappedType] | str = wrapper if wrapper else ProcessQueueItemFields.DATA_TYPE_NAME
195
- return CustomReportRecordAutoPager(self.user, report, dt).get_all_at_once()
188
+ return self.rec_handler.query_models_by_report(wrapper, report)
196
189
 
197
- def get_records_from_item_report(self, wrapper: type[WrappedType] | str,
198
- criteria: QueueItemReportCriteria = QueueItemReportCriteria()) \
199
- -> list[WrappedType] | list[PyRecordModel]:
190
+ def get_records_from_item_report(self, wrapper: type[WrappedType],
191
+ criteria: QueueItemReportCriteria = QueueItemReportCriteria()) -> list[WrappedType]:
200
192
  """
201
193
  Run a custom report that retrieves for queue items that match the given search criteria, then query for the
202
194
  data records that those queue items refer to.
203
195
 
204
- :param wrapper: The record model wrapper or data type name for the records being queried for.
196
+ :param wrapper: The record model wrapper for the records being queried for.
205
197
  :param criteria: Additional search criteria to filter the results. This function forces the data_type_names
206
198
  parameter of the criteria to match the data type of the given record model wrapper.
207
199
  :return: A list of all records related to the queue items in the system that match the search criteria.
208
- If a data type name was used instead of a model wrapper, then the returned records will be PyRecordModels
209
- instead of WrappedRecordModels.
210
200
  """
211
201
  # Don't try to query for process queue items that don't match the data type of this wrapper.
212
- criteria.data_type_names = [AliasUtil.to_data_type_name(wrapper)]
202
+ criteria.data_type_names = [wrapper.get_wrapper_data_type_name()]
213
203
  criteria.not_data_type_names = None
214
204
  report = self.build_queue_item_report(criteria)
215
205
  record_ids: list[int] = [x[ProcessQueueItemFields.DATA_RECORD_ID__FIELD.field_name]
216
- for x in CustomReportDictAutoPager(self.user, report)]
206
+ for x in CustomReportUtil.run_custom_report(self.user, report)]
217
207
  return self.rec_handler.query_models_by_id(wrapper, record_ids)
218
208
 
219
- def get_queue_items_for_records(self, records: Iterable[SapioRecord], wrapper: type[WrappedType] | None = None,
209
+ def get_queue_items_for_records(self, records: Iterable[SapioRecord], wrapper: type[WrappedType],
220
210
  criteria: QueueItemReportCriteria = QueueItemReportCriteria()) \
221
- -> dict[SapioRecord, list[WrappedType] | list[PyRecordModel]]:
211
+ -> dict[SapioRecord, list[WrappedType]]:
222
212
  """
223
213
  Given a list of records, query the system for every process queue item that refers to those records and matches
224
214
  the provided search criteria.
225
215
 
226
216
  :param records: The queued records to query for the process queue items of.
227
- :param wrapper: The record model wrapper for the returned process queue item records. If not provided, the
228
- returned records will be PyRecordModels instead of WrappedRecordModels.
217
+ :param wrapper: The record model wrapper for the returned process queue item records.
229
218
  :param criteria: Additional search criteria to filter the results. This function forces the data_record_ids and
230
219
  data_type_names parameters on the criteria to match the given records.
231
220
  :return: A dictionary mapping the input records to a list of the process queue items that refer to them. If a
@@ -237,43 +226,40 @@ class QueueItemHandler:
237
226
  criteria.not_data_record_ids = None
238
227
  criteria.data_type_names = AliasUtil.to_data_type_names(records)
239
228
  criteria.not_data_type_names = None
240
- items: list[WrappedType] | list[PyRecordModel] = self.get_queue_items_from_report(wrapper, criteria)
229
+ items: list[WrappedType] = self.get_queue_items_from_report(wrapper, criteria)
241
230
  return self.map_records_to_queue_items(records, items)
242
231
 
243
- def get_records_for_queue_items(self, queue_items: Iterable[SapioRecord], wrapper: type[WrappedType] | str) \
244
- -> dict[SapioRecord, WrappedType | PyRecordModel]:
232
+ def get_records_for_queue_items(self, queue_items: Iterable[SapioRecord], wrapper: type[WrappedType]) \
233
+ -> dict[SapioRecord, WrappedType]:
245
234
  """
246
235
  Given a list of process queue items, query the system for the records that those queue items refer to.
247
236
 
248
237
  :param queue_items: The process queue items to query for the referenced records of.
249
- :param wrapper: The record model wrapper or data type name for the records being queried.
250
- :return: A dictionary mapping the input process queue items to the record tht they refer to. If a data type
251
- name was used instead of a model wrapper, then the returned records will be PyRecordModels instead of
252
- WrappedRecordModels.
238
+ :param wrapper: The record model wrapper for the records being queried.
239
+ :return: A dictionary mapping the input process queue items to the record tht they refer to.
253
240
  """
254
241
  record_ids: set[int] = {x.get_field_value(ProcessQueueItemFields.DATA_RECORD_ID__FIELD) for x in queue_items}
255
- records: list[WrappedType] | list[PyRecordModel] = self.rec_handler.query_models_by_id(wrapper, record_ids)
242
+ records: list[WrappedType] = self.rec_handler.query_models_by_id(wrapper, record_ids)
256
243
  return self.map_queue_items_to_records(queue_items, records)
257
244
 
258
245
  def queue_records_for_process(self, records: Iterable[SapioRecord], process: str, step: str,
259
- wrapper: type[WrappedType] | None = None) -> dict[SapioRecord, WrappedType | PyRecordModel]:
246
+ wrapper: type[WrappedType]) -> dict[SapioRecord, WrappedType]:
260
247
  """
261
248
  Given a list of records, create process queue item records for them at the provided process and step names.
262
249
  You must store and commit using the record model manager in order for these changes to take effect.
263
250
 
264
251
  :param records: The records to create process queue items for.
252
+ :param wrapper: The record model wrapper for the process queue items being created.
265
253
  :param process: The name of the process to queue for.
266
254
  :param step: The name of the step in the above process to queue for. This is the "Workflow Name" field of the
267
255
  Process Workflow record corresponding to the step you want to assign these records to. For steps that
268
256
  launch an experiment, this is the name of the template that will be launched. For the other types of custom
269
257
  process steps, this is the "Workflow Name" as defined in the process manager config.
270
- :param wrapper: The record model wrapper for the process queue items being created. If not provided, the
271
- returned records will be PyRecordModels instead of WrappedRecordModels.
272
258
  :return: A dictionary mapping each input record to the newly created process queue item for that record.
273
259
  """
274
260
  ret_val: dict[SapioRecord, WrappedType] = {}
275
261
  for record in records:
276
- item = self.rec_handler.add_model(wrapper if wrapper else ProcessQueueItemFields.DATA_TYPE_NAME)
262
+ item = self.rec_handler.add_model(wrapper)
277
263
  item.set_field_values({
278
264
  ProcessQueueItemFields.PROCESS_HEADER_NAME__FIELD.field_name: process,
279
265
  ProcessQueueItemFields.WORKFLOW_HEADER_NAME__FIELD.field_name: step,
@@ -285,17 +271,16 @@ class QueueItemHandler:
285
271
  ret_val[record] = item
286
272
  return ret_val
287
273
 
288
- def dequeue_records_for_process(self, records: Iterable[SapioRecord], wrapper: type[WrappedType] | None = None,
274
+ def dequeue_records_for_process(self, records: Iterable[SapioRecord], wrapper: type[WrappedType],
289
275
  criteria: QueueItemReportCriteria = QueueItemReportCriteria()) \
290
- -> dict[SapioRecord, list[WrappedType] | list[PyRecordModel]]:
276
+ -> dict[SapioRecord, list[WrappedType]]:
291
277
  """
292
278
  Given a list of records, locate the process queue items that refer to them and that match the given search
293
279
  criteria and remove them from the queue by setting the ShowInQueue field on the process queue items to false.
294
280
  You must store and commit using the record model manager in order for these changes to take effect.
295
281
 
296
282
  :param records: The records to remove from the queue.
297
- :param wrapper: The record model wrapper for the process queue items being updated. If not provided, the
298
- returned records will be PyRecordModels instead of WrappedRecordModels.
283
+ :param wrapper: The record model wrapper for the process queue items being updated.
299
284
  :param criteria: Additional search criteria to filter the results. This function forces the show_in_queue
300
285
  parameter on the criteria to True.
301
286
  :return: A dictionary mapping each input record to the queue item records that refer to that record and were
@@ -304,8 +289,7 @@ class QueueItemHandler:
304
289
  """
305
290
  # Only locate queue items that are currently visible in the queue.
306
291
  criteria.shown_in_queue = True
307
- dequeue: dict[SapioRecord, list[WrappedType] | list[PyRecordModel]]
308
- dequeue = self.get_queue_items_for_records(records, wrapper, criteria)
292
+ dequeue: dict[SapioRecord, list[WrappedType]] = self.get_queue_items_for_records(records, wrapper, criteria)
309
293
  for record, items in dequeue.items():
310
294
  for item in items:
311
295
  item.set_field_value(ProcessQueueItemFields.SHOW_IN_QUEUE__FIELD.field_name, False)