sapiopycommons 2025.7.9a582__py3-none-any.whl → 2025.7.9a583__py3-none-any.whl
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- sapiopycommons/callbacks/callback_util.py +665 -332
- sapiopycommons/callbacks/field_builder.py +2 -0
- sapiopycommons/chem/IndigoMolecules.py +29 -1
- sapiopycommons/chem/Molecules.py +3 -3
- sapiopycommons/customreport/auto_pagers.py +26 -1
- sapiopycommons/customreport/term_builder.py +1 -1
- sapiopycommons/datatype/pseudo_data_types.py +349 -326
- sapiopycommons/eln/experiment_cache.py +188 -0
- sapiopycommons/eln/experiment_handler.py +408 -767
- sapiopycommons/eln/experiment_report_util.py +11 -6
- sapiopycommons/eln/experiment_step_factory.py +476 -0
- sapiopycommons/eln/plate_designer.py +7 -2
- sapiopycommons/eln/step_creation.py +236 -0
- sapiopycommons/files/file_util.py +7 -5
- sapiopycommons/general/accession_service.py +2 -2
- sapiopycommons/general/aliases.py +3 -1
- sapiopycommons/general/audit_log.py +7 -0
- sapiopycommons/general/custom_report_util.py +12 -0
- sapiopycommons/general/data_structure_util.py +115 -0
- sapiopycommons/processtracking/custom_workflow_handler.py +11 -1
- sapiopycommons/processtracking/endpoints.py +27 -0
- sapiopycommons/recordmodel/record_handler.py +783 -389
- sapiopycommons/rules/eln_rule_handler.py +8 -1
- sapiopycommons/rules/on_save_rule_handler.py +8 -1
- sapiopycommons/webhook/webhook_handlers.py +9 -4
- sapiopycommons/webhook/webservice_handlers.py +2 -2
- {sapiopycommons-2025.7.9a582.dist-info → sapiopycommons-2025.7.9a583.dist-info}/METADATA +2 -2
- sapiopycommons-2025.7.9a583.dist-info/RECORD +68 -0
- sapiopycommons/ai/__init__.py +0 -0
- sapiopycommons/ai/api/fielddefinitions/proto/fields_pb2.py +0 -43
- sapiopycommons/ai/api/fielddefinitions/proto/fields_pb2.pyi +0 -31
- sapiopycommons/ai/api/fielddefinitions/proto/fields_pb2_grpc.py +0 -24
- sapiopycommons/ai/api/fielddefinitions/proto/velox_field_def_pb2.py +0 -123
- sapiopycommons/ai/api/fielddefinitions/proto/velox_field_def_pb2.pyi +0 -598
- sapiopycommons/ai/api/fielddefinitions/proto/velox_field_def_pb2_grpc.py +0 -24
- sapiopycommons/ai/api/plan/proto/step_output_pb2.py +0 -45
- sapiopycommons/ai/api/plan/proto/step_output_pb2.pyi +0 -42
- sapiopycommons/ai/api/plan/proto/step_output_pb2_grpc.py +0 -24
- sapiopycommons/ai/api/plan/proto/step_pb2.py +0 -43
- sapiopycommons/ai/api/plan/proto/step_pb2.pyi +0 -43
- sapiopycommons/ai/api/plan/proto/step_pb2_grpc.py +0 -24
- sapiopycommons/ai/api/plan/script/proto/script_pb2.py +0 -55
- sapiopycommons/ai/api/plan/script/proto/script_pb2.pyi +0 -115
- sapiopycommons/ai/api/plan/script/proto/script_pb2_grpc.py +0 -153
- sapiopycommons/ai/api/plan/tool/proto/entry_pb2.py +0 -57
- sapiopycommons/ai/api/plan/tool/proto/entry_pb2.pyi +0 -96
- sapiopycommons/ai/api/plan/tool/proto/entry_pb2_grpc.py +0 -24
- sapiopycommons/ai/api/plan/tool/proto/tool_pb2.py +0 -67
- sapiopycommons/ai/api/plan/tool/proto/tool_pb2.pyi +0 -220
- sapiopycommons/ai/api/plan/tool/proto/tool_pb2_grpc.py +0 -154
- sapiopycommons/ai/api/session/proto/sapio_conn_info_pb2.py +0 -39
- sapiopycommons/ai/api/session/proto/sapio_conn_info_pb2.pyi +0 -32
- sapiopycommons/ai/api/session/proto/sapio_conn_info_pb2_grpc.py +0 -24
- sapiopycommons/ai/protobuf_utils.py +0 -508
- sapiopycommons/ai/test_client.py +0 -251
- sapiopycommons/ai/tool_service_base.py +0 -798
- sapiopycommons-2025.7.9a582.dist-info/RECORD +0 -92
- {sapiopycommons-2025.7.9a582.dist-info → sapiopycommons-2025.7.9a583.dist-info}/WHEEL +0 -0
- {sapiopycommons-2025.7.9a582.dist-info → sapiopycommons-2025.7.9a583.dist-info}/licenses/LICENSE +0 -0
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from typing import Iterable
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from sapiopycommons.general.aliases import DataTypeIdentifier, FieldIdentifier, ExperimentEntryIdentifier
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from sapiopylib.rest.pojo.TableColumn import TableColumn
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from sapiopylib.rest.pojo.datatype.FieldDefinition import AbstractVeloxFieldDefinition
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from sapiopylib.rest.pojo.eln.SapioELNEnums import ExperimentEntryStatus, ElnEntryType
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from sapiopylib.rest.pojo.eln.field_set import ElnFieldSetInfo
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# CR-47564: Created these classes to streamline entry creation using the ExperimentEntryFactory.
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class StepCreation:
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"""
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An object that contains the criteria for creating a new entry in the experiment.
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"""
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_entry_type: ElnEntryType
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"""The type of the entry to be created."""
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is_shown_in_template: bool | None
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"""Whether the entry will appear in the template if the experiment this entry is in is saved to a new template."""
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is_removable: bool | None
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"""Whether the entry can be removed by users."""
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is_renamable: bool | None
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"""Whether the entry can be renamed by users."""
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is_static_view: bool | None
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"""Whether the entry's attachment is static. For attachment entries only. Static attachment entries will store
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their attachment data in the template."""
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related_entry_set: Iterable[ExperimentEntryIdentifier | str] | None
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"""The IDs of the entries this entry is implicitly dependent on. If any of the entries are deleted then this entry
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is also deleted."""
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dependency_set: Iterable[ExperimentEntryIdentifier | str] | None
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"""The IDs of the entries this entry is dependent on. Requires the entries to be completed before this entry will
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be enabled."""
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requires_grabber_plugin: bool
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"""Whether to run a grabber plugin when this entry is initialized."""
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entry_singleton_id: str | None
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"""When this field is present (i.e. not null or blank) it will enforce that only one entry with this singleton
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value is present in the experiment. If you attempt to create an entry with the singletonId of an entry already
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present in the experiment it will return the existing entry instead of creating a new one. If an entry isn't
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present in the Notebook Experiment with a matching singletonId it will create a new entry like normal."""
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is_hidden: bool | None
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"""Whether the user is able to visibly see this entry within the experiment."""
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entry_height: int | None
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"""The height of this entry in pixels. Setting the height to 0 will cause the entry to auto-size to its contents."""
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description: str | None
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"""The description of the entry."""
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is_initialization_required: bool | None
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"""Whether the user must manually initialize this entry by clicking on it."""
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collapse_entry: bool | None
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"""Whether the entry should be collapsed by default."""
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entry_status: ExperimentEntryStatus | None
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"""The current status of the entry."""
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template_item_fulfilled_timestamp: int | None
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"""The time in milliseconds since the epoch that this entry became initialized."""
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entry_options: dict[str, str] | None
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"""The entry options of the entry."""
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def __init__(self, entry_type: ElnEntryType):
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self._entry_type = entry_type
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self.is_shown_in_template = None
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self.is_removable = None
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self.is_renamable = None
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self.is_static_view = None
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self.related_entry_set = None
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self.dependency_set = None
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self.requires_grabber_plugin = False
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self.entry_singleton_id = None
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self.is_hidden = None
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self.entry_height = None
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self.description = None
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self.is_initialization_required = None
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self.collapse_entry = None
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self.entry_status = None
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self.template_item_fulfilled_timestamp = None
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self.entry_options = None
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@property
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def entry_type(self) -> ElnEntryType:
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return self._entry_type
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class AttachmentStepCreation(StepCreation):
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"""
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An object that contains criteria for creating a new attachment entry in an experiment.
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"""
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def __init__(self):
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super().__init__(ElnEntryType.Attachment)
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class DashboardStepCreation(StepCreation):
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"""
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An object that contains criteria for creating a new dashboard entry in an experiment.
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"""
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source_entry: ExperimentEntryIdentifier | str | None
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"""The entry that contains the source data for this entry's dashboard(s)."""
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dashboard_guids: Iterable[str] | None
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"""The GUIDs of the dashboards to display in this entry."""
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def __init__(self):
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super().__init__(ElnEntryType.Dashboard)
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self.source_entry = None
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self.dashboard_guids = None
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class GlobalDtFormStepCreation(StepCreation):
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"""
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An object that contains criteria for creating a new global data type form entry in an experiment.
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"""
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layout_name: str | None
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"""The name of the data type layout to be displayed in this form. The layout must be for the data type for this
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entry."""
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form_names: Iterable[str] | None
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"""The names of the components in the chosen data type layout to display in this form."""
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extension_types: Iterable[DataTypeIdentifier] | None
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"""The names of the extension data types to display fields from within the form."""
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field_names: Iterable[FieldIdentifier] | None
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"""A list of data field names for the fields to be displayed in the form."""
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def __init__(self):
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super().__init__(ElnEntryType.Form)
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self.form_names = None
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self.layout_name = None
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self.extension_types = None
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self.field_names = None
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class ELnDtFormStepCreation(StepCreation):
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"""
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An object that contains criteria for creating a new ELN data type form entry in an experiment.
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"""
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is_field_addable: bool | None
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"""Whether new fields can be added to the entry by users."""
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is_existing_field_removable: bool | None
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"""Whether existing fields on the entry can be removed by users."""
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field_sets: Iterable[int | str | ElnFieldSetInfo] | None
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"""The predefined field sets to display in this form."""
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field_definitions: Iterable[AbstractVeloxFieldDefinition] | None
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"""New field definitions to be created for this entry."""
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predefined_field_names: Iterable[str] | None
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"""The names of the predefined fields to display in this form."""
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def __init__(self):
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super().__init__(ElnEntryType.Form)
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self.is_field_addable = None
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self.is_existing_field_removable = None
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self.field_sets = None
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self.field_definitions = None
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self.predefined_field_names = None
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self.table_columns = None
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class PluginStepCreation(StepCreation):
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"""
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An object that contains criteria for creating a new plugin entry in an experiment.
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"""
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plugin_name: str | None
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"""The client side plugin name to render this entry with."""
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using_template_data: bool | None
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"""Whether this entry will use the data from the template."""
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provides_template_data: bool | None
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"""Whether this entry can provide data to copy into a new template."""
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def __init__(self):
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super().__init__(ElnEntryType.Plugin)
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self.plugin_name = None
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self.using_template_data = None
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self.provides_template_data = None
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class GlobalDtTableStepCreation(StepCreation):
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"""
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An object that contains criteria for creating a new global data type table entry in an experiment.
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"""
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layout_name: str | None
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"""The name of the data type layout to display in this table."""
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extension_types: Iterable[str] | None
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"""The names of the extension data types to display fields from within the table."""
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table_columns: Iterable[TableColumn] | None
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"""The columns to display in the table. This can be used to change the sort order and direction of columns."""
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field_names: Iterable[FieldIdentifier] | None
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"""A list of data field names for the fields to be displayed in the table. These will be added as TableColumns and
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placed after any of the existing columns specified in the table_columns parameter without any sorting."""
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show_key_fields: bool | None
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"""Whether the key fields of the data type should be shown in the entry."""
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def __init__(self):
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super().__init__(ElnEntryType.Table)
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self.layout_name = None
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self.extension_types = None
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self.table_columns = None
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self.field_names = None
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self.show_key_fields = None
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class ELnDtTableStepCreation(StepCreation):
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"""
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An object that contains criteria for creating a new ELN data type table entry in an experiment.
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"""
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is_field_addable: bool | None
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"""Whether new fields can be added to the entry by users."""
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is_existing_field_removable: bool | None
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"""Whether existing fields on the entry can be removed by users."""
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field_sets: Iterable[int | str | ElnFieldSetInfo] | None
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"""The predefined field sets to display in this form."""
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field_definitions: Iterable[AbstractVeloxFieldDefinition] | None
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"""New field definitions to be created for this entry."""
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predefined_field_names: Iterable[str] | None
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"""The names of the predefined fields to display in this form."""
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table_columns: Iterable[TableColumn] | None
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"""The columns to display in the table."""
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def __init__(self):
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super().__init__(ElnEntryType.Table)
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self.is_field_addable = None
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self.is_existing_field_removable = None
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self.field_sets = None
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self.field_definitions = None
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class TempDataStepCreation(StepCreation):
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"""
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An object that contains criteria for creating a new temp data entry in an experiment.
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"""
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plugin_path: str | None
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"""The temp data plugin path to run to populate the entry."""
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def __init__(self):
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super().__init__(ElnEntryType.TempData)
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self.plugin_path = None
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class TextStepCreation(StepCreation):
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"""
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An object that contains criteria for creating a new text entry in an experiment.
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"""
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def __init__(self):
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super().__init__(ElnEntryType.Text)
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:param files: A dictionary of file name to file data as a string or bytes.
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:return: The bytes for a zip file containing the input files.
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"""
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with io.BytesIO() as zip_buffer:
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with zipfile.ZipFile(zip_buffer, "w", zipfile.ZIP_DEFLATED) as zip_file:
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for file_name, file_data in files.items():
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zip_file.writestr(file_name, file_data)
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accessorName: This is a legacy variable from drum.getNextIdListByMapName(), which allows setting different "accessorName" from old system. We need this for compatibility patch for converting these to the new preference format.
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An enumeration of the different transformations that can be applied to a 2D array.
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Utility class for working with data structures. Copies from ListUtil, SetUtil, and various other classes in
|
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|
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|
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Remove null values from a list.
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|
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|
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|
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|
|
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+
-> Collection[Collection[Any]]:
|
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|
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Perform a transformation on a 2D list.
|
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|
|
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|
+
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|
|
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|
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|
|
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|
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|
|
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|
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|
|
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|
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|
|
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|
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|
|
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|
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|
|
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|
+
|
|
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|
+
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|
|
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|
+
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|
|
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|
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|
|
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|
+
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|
|
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|
+
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|
|
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|
+
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|
|
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|
+
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|
|
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|
+
case ArrayTransformation.MIRROR_HORIZONTAL:
|
|
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|
+
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|
|
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|
+
case ArrayTransformation.MIRROR_VERTICAL:
|
|
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|
+
return values[::-1]
|
|
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|
+
|
|
74
|
+
raise SapioException(f"Invalid transformation: {transformation}")
|
|
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|
+
|
|
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|
+
@staticmethod
|
|
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|
+
def flatten_to_list(values: Iterable[Iterable[Any]]) -> list[Any]:
|
|
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|
+
"""
|
|
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|
+
Flatten a list of lists into a single list.
|
|
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|
+
|
|
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|
+
:param values: An iterable of iterables.
|
|
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|
+
:return: A single list containing all the values from the input. Elements are in the order they appear in the
|
|
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|
+
input.
|
|
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|
+
"""
|
|
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|
+
return [item for sublist in values for item in sublist]
|
|
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|
+
|
|
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|
+
@staticmethod
|
|
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|
+
def flatten_to_set(values: Iterable[Iterable[Any]]) -> set[Any]:
|
|
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|
+
"""
|
|
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|
+
Flatten a list of lists into a single set.
|
|
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|
+
|
|
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|
+
:param values: An iterable of iterables.
|
|
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|
+
:return: A single set containing all the values from the input. Elements are in the order they appear in the
|
|
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|
+
input.
|
|
95
|
+
"""
|
|
96
|
+
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|
|
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|
+
|
|
98
|
+
@staticmethod
|
|
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|
+
def invert_dictionary(dictionary: dict[Any, Any], list_values: bool = False) \
|
|
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|
+
-> dict[Any, Any] | dict[Any, list[Any]]:
|
|
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|
+
"""
|
|
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|
+
Invert a dictionary, swapping keys and values. Note that the values of the input dictionary must be hashable.
|
|
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|
+
|
|
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|
+
:param dictionary: A dictionary to invert.
|
|
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|
+
:param list_values: If false, keys that share the same value in the input dictionary will be overwritten in
|
|
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|
+
the output dictionary so that only the last key remains. If true, the values of the output dictionary will
|
|
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|
+
be lists where input keys that share the same value will be stored together.
|
|
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|
+
:return: A new dictionary with the keys and values swapped.
|
|
109
|
+
"""
|
|
110
|
+
if list_values:
|
|
111
|
+
inverted = {}
|
|
112
|
+
for key, value in dictionary.items():
|
|
113
|
+
inverted.setdefault(value, []).append(key)
|
|
114
|
+
return inverted
|
|
115
|
+
return {value: key for key, value in dictionary.items()}
|
|
@@ -94,6 +94,9 @@ class QueueItemHandler:
|
|
|
94
94
|
"""
|
|
95
95
|
A class used for handling the display of records in custom process queues, which are controlled in the system by
|
|
96
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|
ProcessQueueItem data types.
|
|
97
|
+
|
|
98
|
+
IMPORTANT NOTICE: This is only for custom processes that make use of ProcessQueueItem records. For experiment
|
|
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|
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processes that use AssignedProcess records, see the ProcessTracking class.
|
|
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|
"""
|
|
98
101
|
user: SapioUser
|
|
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102
|
context: ProcessQueueContext | None
|
|
@@ -105,7 +108,8 @@ class QueueItemHandler:
|
|
|
105
108
|
"""
|
|
106
109
|
self.user = AliasUtil.to_sapio_user(context)
|
|
107
110
|
self.rec_handler = RecordHandler(self.user)
|
|
108
|
-
if
|
|
111
|
+
# PR-47565: Only initialize a ProcessQueueContext if the given context object has context_data.
|
|
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|
+
if isinstance(context, SapioWebhookContext) and context.context_data:
|
|
109
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|
self.context = ProcessQueueContext(context)
|
|
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|
else:
|
|
111
115
|
self.context = None
|
|
@@ -260,6 +264,9 @@ class QueueItemHandler:
|
|
|
260
264
|
Given a list of records, create process queue item records for them at the provided process and step names.
|
|
261
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|
You must store and commit using the record model manager in order for these changes to take effect.
|
|
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266
|
|
|
267
|
+
IMPORTANT NOTICE: This is only for custom processes that make use of ProcessQueueItem records. For experiment
|
|
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|
+
processes that use AssignedProcess records, see the ProcessTracking class.
|
|
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|
+
|
|
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270
|
:param records: The records to create process queue items for.
|
|
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:param process: The name of the process to queue for.
|
|
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272
|
:param step: The name of the step in the above process to queue for. This is the "Workflow Name" field of the
|
|
@@ -292,6 +299,9 @@ class QueueItemHandler:
|
|
|
292
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|
criteria and remove them from the queue by setting the ShowInQueue field on the process queue items to false.
|
|
293
300
|
You must store and commit using the record model manager in order for these changes to take effect.
|
|
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301
|
|
|
302
|
+
IMPORTANT NOTICE: This is only for custom processes that make use of ProcessQueueItem records. For experiment
|
|
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|
+
processes that use AssignedProcess records, see the ProcessTracking class.
|
|
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|
+
|
|
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|
:param records: The records to remove from the queue.
|
|
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|
:param wrapper: The record model wrapper for the process queue items being updated. If not provided, the
|
|
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returned records will be PyRecordModels instead of WrappedRecordModels.
|
|
@@ -5,6 +5,12 @@ from sapiopycommons.general.aliases import RecordIdentifier, AliasUtil, Experime
|
|
|
5
5
|
|
|
6
6
|
|
|
7
7
|
class ProcessTracking:
|
|
8
|
+
"""
|
|
9
|
+
A class for calling the Foundations process tracking endpoints.
|
|
10
|
+
|
|
11
|
+
IMPORTANT NOTICE: This is only for experiment processes that make use of AssignedProcess records. For custom
|
|
12
|
+
processes that use ProcessQueueItem records, see the QueueItemHandler class.
|
|
13
|
+
"""
|
|
8
14
|
@staticmethod
|
|
9
15
|
def assign_to_process(context: UserIdentifier, data_type: DataTypeIdentifier, records: list[RecordIdentifier],
|
|
10
16
|
process_name: str, step_number: int | None = None, branch_id: int | None = None,
|
|
@@ -14,6 +20,9 @@ class ProcessTracking:
|
|
|
14
20
|
at that step.
|
|
15
21
|
Synonymous with what occurs during request creation or when using the assign to process button.
|
|
16
22
|
|
|
23
|
+
IMPORTANT NOTICE: This is only for experiment processes that make use of AssignedProcess records. For custom
|
|
24
|
+
processes that use ProcessQueueItem records, see the QueueItemHandler class.
|
|
25
|
+
|
|
17
26
|
:param context: The current webhook context or a user object to send requests from.
|
|
18
27
|
:param data_type: The data type of the tracked records.
|
|
19
28
|
:param records: A list of the tracked records.
|
|
@@ -46,6 +55,9 @@ class ProcessTracking:
|
|
|
46
55
|
tracked records from "Ready for -" to "In Process -" for their current step.
|
|
47
56
|
Synonymous with what occurs when starting a process step in the system.
|
|
48
57
|
|
|
58
|
+
IMPORTANT NOTICE: This is only for experiment processes that make use of AssignedProcess records. For custom
|
|
59
|
+
processes that use ProcessQueueItem records, see the QueueItemHandler class.
|
|
60
|
+
|
|
49
61
|
:param context: The current webhook context or a user object to send requests from.
|
|
50
62
|
:param data_type: The data type of the tracked records.
|
|
51
63
|
:param records: A list of the tracked records.
|
|
@@ -73,6 +85,9 @@ class ProcessTracking:
|
|
|
73
85
|
Moves the assigned process down to the descendant sample(s) if both samples are provided in the records list.
|
|
74
86
|
Synonymous with what occurs when completing an experiment in the system.
|
|
75
87
|
|
|
88
|
+
IMPORTANT NOTICE: This is only for experiment processes that make use of AssignedProcess records. For custom
|
|
89
|
+
processes that use ProcessQueueItem records, see the QueueItemHandler class.
|
|
90
|
+
|
|
76
91
|
:param context: The current webhook context or a user object to send requests from.
|
|
77
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|
:param data_type: The data type of the tracked records.
|
|
78
93
|
:param records: A list of the tracked records.
|
|
@@ -96,6 +111,9 @@ class ProcessTracking:
|
|
|
96
111
|
records must be "In Process -" for the given step.
|
|
97
112
|
Synonymous with what occurs when failing a sample due to a QC failure in a process in the system.
|
|
98
113
|
|
|
114
|
+
IMPORTANT NOTICE: This is only for experiment processes that make use of AssignedProcess records. For custom
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processes that use ProcessQueueItem records, see the QueueItemHandler class.
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:param context: The current webhook context or a user object to send requests from.
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:param data_type: The data type of the tracked records.
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:param records: A list of the tracked records.
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will move their status to "Ready for -" for the next step in the process, or "Completed -" if this was the
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last step.
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IMPORTANT NOTICE: This is only for experiment processes that make use of AssignedProcess records. For custom
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:param context: The current webhook context or a user object to send requests from.
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:param data_type: The data type of the tracked records.
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:param records: A list of the tracked records.
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@@ -149,6 +170,9 @@ class ProcessTracking:
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step will move their status to "Ready for -" for the next step in the process, or "Completed -" if this was the
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last step.
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IMPORTANT NOTICE: This is only for experiment processes that make use of AssignedProcess records. For custom
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processes that use ProcessQueueItem records, see the QueueItemHandler class.
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:param context: The current webhook context or a user object to send requests from.
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:param data_type: The data type of the tracked records.
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:param records: A list of the tracked records.
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@@ -180,6 +204,9 @@ class ProcessTracking:
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Synonymous with what occurs when reprocessing records to a previous step due to QC failures in a process in the
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system.
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IMPORTANT NOTICE: This is only for experiment processes that make use of AssignedProcess records. For custom
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processes that use ProcessQueueItem records, see the QueueItemHandler class.
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+
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:param context: The current webhook context or a user object to send requests from.
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:param records: A list of ReturnPoint records to reprocess to.
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"""
|