sapiopycommons 2024.8.28a315__py3-none-any.whl → 2024.8.29a317__py3-none-any.whl

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Files changed (33) hide show
  1. sapiopycommons/callbacks/callback_util.py +37 -133
  2. sapiopycommons/datatype/attachment_util.py +10 -11
  3. sapiopycommons/eln/experiment_handler.py +48 -209
  4. sapiopycommons/eln/experiment_report_util.py +129 -33
  5. sapiopycommons/files/complex_data_loader.py +4 -5
  6. sapiopycommons/files/file_bridge.py +14 -15
  7. sapiopycommons/files/file_bridge_handler.py +5 -27
  8. sapiopycommons/files/file_data_handler.py +5 -2
  9. sapiopycommons/files/file_util.py +5 -38
  10. sapiopycommons/files/file_validator.py +11 -26
  11. sapiopycommons/files/file_writer.py +15 -44
  12. sapiopycommons/general/aliases.py +3 -147
  13. sapiopycommons/general/custom_report_util.py +32 -34
  14. sapiopycommons/general/popup_util.py +0 -17
  15. sapiopycommons/general/time_util.py +0 -40
  16. sapiopycommons/multimodal/multimodal_data.py +1 -0
  17. sapiopycommons/processtracking/endpoints.py +22 -22
  18. sapiopycommons/recordmodel/record_handler.py +77 -228
  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 +26 -90
  22. {sapiopycommons-2024.8.28a315.dist-info → sapiopycommons-2024.8.29a317.dist-info}/METADATA +1 -1
  23. sapiopycommons-2024.8.29a317.dist-info/RECORD +43 -0
  24. sapiopycommons/customreport/__init__.py +0 -0
  25. sapiopycommons/customreport/column_builder.py +0 -60
  26. sapiopycommons/customreport/custom_report_builder.py +0 -125
  27. sapiopycommons/customreport/term_builder.py +0 -299
  28. sapiopycommons/general/audit_log.py +0 -196
  29. sapiopycommons/general/sapio_links.py +0 -50
  30. sapiopycommons/webhook/webservice_handlers.py +0 -67
  31. sapiopycommons-2024.8.28a315.dist-info/RECORD +0 -50
  32. {sapiopycommons-2024.8.28a315.dist-info → sapiopycommons-2024.8.29a317.dist-info}/WHEEL +0 -0
  33. {sapiopycommons-2024.8.28a315.dist-info → sapiopycommons-2024.8.29a317.dist-info}/licenses/LICENSE +0 -0
sapiopycommons/processtracking/endpoints.py CHANGED
@@ -1,12 +1,12 @@
1
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  from sapiopylib.rest.User import SapioUser
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+ from sapiopylib.rest.pojo.webhook.WebhookContext import SapioWebhookContext
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3
 
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- from sapiopycommons.general.aliases import RecordIdentifier, AliasUtil, ExperimentIdentifier, DataTypeIdentifier, \
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- UserIdentifier
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+ from sapiopycommons.general.aliases import RecordIdentifier, AliasUtil, ExperimentIdentifier
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5
 
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  class ProcessTracking:
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  @staticmethod
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- def assign_to_process(context: UserIdentifier, data_type: DataTypeIdentifier, records: list[RecordIdentifier],
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+ def assign_to_process(context: SapioWebhookContext | SapioUser, data_type: str, records: list[RecordIdentifier],
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  process_name: str, step_number: int | None = None, branch_id: int | None = None,
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  request: RecordIdentifier | None = None) -> None:
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  """
@@ -27,19 +27,19 @@ class ProcessTracking:
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  """
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  sub_path = '/ext/process-tracking/assign-to-process'
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  payload = {
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- "data-type-name": AliasUtil.to_data_type_name(data_type),
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+ "data-type-name": data_type,
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  "record-ids": AliasUtil.to_record_ids(records),
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  "process-name": process_name,
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  "step-number": step_number,
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  "branch-id": branch_id,
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  "request-record-id": AliasUtil.to_record_ids([request])[0] if request is not None else None
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  }
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- user: SapioUser = AliasUtil.to_sapio_user(context)
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+ user: SapioUser = context if isinstance(context, SapioUser) else context.user
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  response = user.post(sub_path, payload=payload)
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  user.raise_for_status(response)
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  @staticmethod
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- def begin_protocol(context: UserIdentifier, data_type: DataTypeIdentifier, records: list[RecordIdentifier],
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+ def begin_protocol(context: SapioWebhookContext | SapioUser, data_type: str, records: list[RecordIdentifier],
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  experiment: ExperimentIdentifier) -> None:
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  """
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  Begin the assigned processes of the given tracked records as the given experiment. This sets the status of the
@@ -54,16 +54,16 @@ class ProcessTracking:
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  """
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  sub_path = '/ext/process-tracking/begin-protocol'
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  payload = {
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- "data-type-name": AliasUtil.to_data_type_name(data_type),
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+ "data-type-name": data_type,
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  "record-ids": AliasUtil.to_record_ids(records),
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  "experiment-id": AliasUtil.to_notebook_id(experiment),
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  }
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- user: SapioUser = AliasUtil.to_sapio_user(context)
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+ user: SapioUser = context if isinstance(context, SapioUser) else context.user
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  response = user.post(sub_path, payload=payload)
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  user.raise_for_status(response)
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  @staticmethod
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- def complete_protocol(context: UserIdentifier, data_type: DataTypeIdentifier, records: list[RecordIdentifier],
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+ def complete_protocol(context: SapioWebhookContext | SapioUser, data_type: str, records: list[RecordIdentifier],
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  experiment: ExperimentIdentifier) -> None:
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  """
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  Complete the current step that the given tracked records are at given the experiment.
@@ -80,16 +80,16 @@ class ProcessTracking:
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  """
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  sub_path = '/ext/process-tracking/complete-protocol'
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  payload = {
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- "data-type-name": AliasUtil.to_data_type_name(data_type),
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+ "data-type-name": data_type,
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  "record-ids": AliasUtil.to_record_ids(records),
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  "experiment-id": AliasUtil.to_notebook_id(experiment),
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  }
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- user: SapioUser = AliasUtil.to_sapio_user(context)
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+ user: SapioUser = context if isinstance(context, SapioUser) else context.user
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  response = user.post(sub_path, payload=payload)
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  user.raise_for_status(response)
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  @staticmethod
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- def fail(context: UserIdentifier, data_type: DataTypeIdentifier, records: list[RecordIdentifier],
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+ def fail(context: SapioWebhookContext | SapioUser, data_type: str, records: list[RecordIdentifier],
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  experiment: ExperimentIdentifier) -> None:
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  """
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  Fail the assigned processes of the given tracked records, changing their statuses to "Failed -". The tracked
@@ -103,16 +103,16 @@ class ProcessTracking:
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  """
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  sub_path = '/ext/process-tracking/fail'
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  payload = {
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- "data-type-name": AliasUtil.to_data_type_name(data_type),
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+ "data-type-name": data_type,
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  "record-ids": AliasUtil.to_record_ids(records),
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  "experiment-id": AliasUtil.to_notebook_id(experiment),
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  }
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- user: SapioUser = AliasUtil.to_sapio_user(context)
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+ user: SapioUser = context if isinstance(context, SapioUser) else context.user
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  response = user.post(sub_path, payload=payload)
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  user.raise_for_status(response)
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  @staticmethod
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- def promote_to_next_by_experiment(context: UserIdentifier, data_type: DataTypeIdentifier,
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+ def promote_to_next_by_experiment(context: SapioWebhookContext | SapioUser, data_type: str,
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  records: list[RecordIdentifier], experiment: ExperimentIdentifier) -> None:
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  """
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  Promote the status of the given tracked records to the next status in their process using an experiment.
@@ -129,16 +129,16 @@ class ProcessTracking:
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  """
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  sub_path = '/ext/process-tracking/promote-status-to-next'
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  payload = {
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- "data-type-name": AliasUtil.to_data_type_name(data_type),
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+ "data-type-name": data_type,
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  "record-ids": AliasUtil.to_record_ids(records),
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  "experiment-id": AliasUtil.to_notebook_id(experiment),
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  }
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- user: SapioUser = AliasUtil.to_sapio_user(context)
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+ user: SapioUser = context if isinstance(context, SapioUser) else context.user
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  response = user.post(sub_path, payload=payload)
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  user.raise_for_status(response)
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  @staticmethod
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- def promote_to_next_by_step(context: UserIdentifier, data_type: DataTypeIdentifier,
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+ def promote_to_next_by_step(context: SapioWebhookContext | SapioUser, data_type: str,
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  records: list[RecordIdentifier], process_name: str, step_number: int,
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  branch_id: int | None = None) -> None:
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  """
@@ -159,7 +159,7 @@ class ProcessTracking:
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  """
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  sub_path = '/ext/process-tracking/promote-status-to-next'
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  payload = {
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- "data-type-name": AliasUtil.to_data_type_name(data_type),
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+ "data-type-name": data_type,
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  "record-ids": AliasUtil.to_record_ids(records),
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  "current-process-status": {
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  "process-name": process_name,
@@ -167,12 +167,12 @@ class ProcessTracking:
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  "branch-id": branch_id
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  }
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  }
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- user: SapioUser = AliasUtil.to_sapio_user(context)
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+ user: SapioUser = context if isinstance(context, SapioUser) else context.user
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  response = user.post(sub_path, payload=payload)
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  user.raise_for_status(response)
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174
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  @staticmethod
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- def reprocess(context: UserIdentifier, records: list[RecordIdentifier]) -> None:
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+ def reprocess(context: SapioWebhookContext | SapioUser, records: list[RecordIdentifier]) -> None:
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  """
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  Reprocess tracked records to a previous step in their process. Reprocessing is controlled by ReturnPoint records
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  which are children of the AssignedProcess on the tracked records. Creates a new AssignedProcess record for the
@@ -187,6 +187,6 @@ class ProcessTracking:
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  payload = {
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  "record-ids": AliasUtil.to_record_ids(records)
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  }
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- user: SapioUser = AliasUtil.to_sapio_user(context)
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+ user: SapioUser = context if isinstance(context, SapioUser) else context.user
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  response = user.post(sub_path, payload=payload)
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  user.raise_for_status(response)