sapiopycommons 2025.4.3a469__py3-none-any.whl → 2025.4.8a473__py3-none-any.whl

sapiopycommons/eln/step_creation.py

@@ -0,0 +1,235 @@
+from typing import Iterable
+
+from sapiopycommons.general.aliases import DataTypeIdentifier, FieldIdentifier, ExperimentEntryIdentifier
+from sapiopylib.rest.pojo.TableColumn import TableColumn
+from sapiopylib.rest.pojo.datatype.FieldDefinition import AbstractVeloxFieldDefinition
+from sapiopylib.rest.pojo.eln.SapioELNEnums import ExperimentEntryStatus, ElnEntryType
+from sapiopylib.rest.pojo.eln.field_set import ElnFieldSetInfo
+
+
+# CR-47564: Created these classes to streamline entry creation using the ExperimentEntryFactory.
+class StepCreation:
+    """
+    An object that contains the criteria for creating a new entry in the experiment.
+    """
+    _entry_type: ElnEntryType
+    """The type of the entry to be created."""
+    is_shown_in_template: bool | None
+    """Whether the entry will appear in the template if the experiment this entry is in is saved to a new template."""
+    is_removable: bool | None
+    """Whether the entry can be removed by users."""
+    is_renamable: bool | None
+    """Whether the entry can be renamed by users."""
+    is_static_view: bool | None
+    """Whether the entry's attachment is static. For attachment entries only. Static attachment entries will store
+    their attachment data in the template."""
+    related_entry_set: Iterable[ExperimentEntryIdentifier | str] | None
+    """The IDs of the entries this entry is implicitly dependent on. If any of the entries are deleted then this entry
+    is also deleted."""
+    dependency_set: Iterable[ExperimentEntryIdentifier | str] | None
+    """The IDs of the entries this entry is dependent on. Requires the entries to be completed before this entry will
+    be enabled."""
+    requires_grabber_plugin: bool
+    """Whether to run a grabber plugin when this entry is initialized."""
+    entry_singleton_id: str | None
+    """When this field is present (i.e. not null or blank) it will enforce that only one entry with this singleton
+    value is present in the experiment. If you attempt to create an entry with the singletonId of an entry already
+    present in the experiment it will return the existing entry instead of creating a new one. If an entry isn't
+    present in the Notebook Experiment with a matching singletonId it will create a new entry like normal."""
+    is_hidden: bool | None
+    """Whether the user is able to visibly see this entry within the experiment."""
+    entry_height: int | None
+    """The height of this entry in pixels. Setting the height to 0 will cause the entry to auto-size to its contents."""
+    description: str | None
+    """The description of the entry."""
+    is_initialization_required: bool | None
+    """Whether the user must manually initialize this entry by clicking on it."""
+    collapse_entry: bool | None
+    """Whether the entry should be collapsed by default."""
+    entry_status: ExperimentEntryStatus | None
+    """The current status of the entry."""
+    template_item_fulfilled_timestamp: int | None
+    """The time in milliseconds since the epoch that this entry became initialized."""
+    entry_options: dict[str, str] | None
+    """The entry options of the entry."""
+
+    def __init__(self, entry_type: ElnEntryType):
+        self._entry_type = entry_type
+        self.is_shown_in_template = None
+        self.is_removable = None
+        self.is_renamable = None
+        self.is_static_view = None
+        self._related_entry_set = None
+        self._dependency_set = None
+        self.requires_grabber_plugin = False
+        self.entry_singleton_id = None
+        self.is_hidden = None
+        self.entry_height = None
+        self.description = None
+        self.is_initialization_required = None
+        self.collapse_entry = None
+        self.entry_status = None
+        self.template_item_fulfilled_timestamp = None
+        self.entry_options = None
+
+    @property
+    def entry_type(self) -> ElnEntryType:
+        return self._entry_type
+
+class AttachmentStepCreation(StepCreation):
+    """
+    An object that contains criteria for creating a new attachment entry in an experiment.
+    """
+    def __init__(self):
+        super().__init__(ElnEntryType.Attachment)
+
+
+class DashboardStepCreation(StepCreation):
+    """
+    An object that contains criteria for creating a new dashboard entry in an experiment.
+    """
+    source_entry: ExperimentEntryIdentifier | str | None
+    """The entry that contains the source data for this entry's dashboard(s)."""
+    dashboard_guids: Iterable[str] | None
+    """The GUIDs of the dashboards to display in this entry."""
+
+    def __init__(self):
+        super().__init__(ElnEntryType.Dashboard)
+        self.source_entry = None
+        self.dashboard_guids = None
+
+
+class GlobalDtFormStepCreation(StepCreation):
+    """
+    An object that contains criteria for creating a new global data type form entry in an experiment.
+    """
+    layout_name: str | None
+    """The name of the data type layout to be displayed in this form. The layout must be for the data type for this
+    entry."""
+    form_names: Iterable[str] | None
+    """The names of the components in the chosen data type layout to display in this form."""
+    extension_types: Iterable[DataTypeIdentifier] | None
+    """The names of the extension data types to display fields from within the form."""
+    field_names: Iterable[FieldIdentifier] | None
+    """A list of data field names for the fields to be displayed in the form."""
+
+    def __init__(self):
+        super().__init__(ElnEntryType.Form)
+        self.form_names = None
+        self.layout_name = None
+        self.extension_types = None
+        self.field_names = None
+
+
+class ELnDtFormStepCreation(StepCreation):
+    """
+    An object that contains criteria for creating a new ELN data type form entry in an experiment.
+    """
+    is_field_addable: bool | None
+    """Whether new fields can be added to the entry by users."""
+    is_existing_field_removable: bool | None
+    """Whether existing fields on the entry can be removed by users."""
+    field_sets: Iterable[int | str | ElnFieldSetInfo] | None
+    """The predefined field sets to display in this form."""
+    field_definitions: Iterable[AbstractVeloxFieldDefinition] | None
+    """New field definitions to be created for this entry."""
+    predefined_field_names: Iterable[str] | None
+    """The names of the predefined fields to display in this form."""
+
+    def __init__(self):
+        super().__init__(ElnEntryType.Form)
+        self.is_field_addable = None
+        self.is_existing_field_removable = None
+        self.field_sets = None
+        self.field_definitions = None
+        self.predefined_field_names = None
+        self.table_columns = None
+
+
+class PluginStepCreation(StepCreation):
+    """
+    An object that contains criteria for creating a new plugin entry in an experiment.
+    """
+    plugin_name: str | None
+    """The client side plugin name to render this entry with."""
+    using_template_data: bool | None
+    """Whether this entry will use the data from the template."""
+    provides_template_data: bool | None
+    """Whether this entry can provide data to copy into a new template."""
+
+    def __init__(self):
+        super().__init__(ElnEntryType.Plugin)
+        self.plugin_name = None
+        self.using_template_data = None
+        self.provides_template_data = None
+
+
+class GlobalDtTableStepCreation(StepCreation):
+    """
+    An object that contains criteria for creating a new global data type table entry in an experiment.
+    """
+    layout_name: str | None
+    """The name of the data type layout to display in this table."""
+    extension_types: Iterable[str] | None
+    """The names of the extension data types to display fields from within the table."""
+    table_columns: Iterable[TableColumn] | None
+    """The columns to display in the table. This can be used to change the sort order and direction of columns."""
+    field_names: Iterable[FieldIdentifier] | None
+    """A list of data field names for the fields to be displayed in the table. These will be added as TableColumns and
+    placed after any of the existing columns specified in the table_columns parameter without any sorting."""
+    show_key_fields: bool | None
+    """Whether the key fields of the data type should be shown in the entry."""
+
+    def __init__(self):
+        super().__init__(ElnEntryType.Table)
+        self.layout_name = None
+        self.extension_types = None
+        self.table_columns = None
+        self.show_key_fields = None
+
+
+class ELnDtTableStepCreation(StepCreation):
+    """
+    An object that contains criteria for creating a new ELN data type table entry in an experiment.
+    """
+    is_field_addable: bool | None
+    """Whether new fields can be added to the entry by users."""
+    is_existing_field_removable: bool | None
+    """Whether existing fields on the entry can be removed by users."""
+    field_sets: Iterable[int | str | ElnFieldSetInfo] | None
+    """The predefined field sets to display in this form."""
+    field_definitions: Iterable[AbstractVeloxFieldDefinition] | None
+    """New field definitions to be created for this entry."""
+    predefined_field_names: Iterable[str] | None
+    """The names of the predefined fields to display in this form."""
+    table_columns: Iterable[TableColumn] | None
+    """The columns to display in the table."""
+
+    def __init__(self):
+        super().__init__(ElnEntryType.Table)
+        self.is_field_addable = None
+        self.is_existing_field_removable = None
+        self.field_sets = None
+        self.field_definitions = None
+        self.predefined_field_names = None
+        self.table_columns = None
+
+
+class TempDataStepCreation(StepCreation):
+    """
+    An object that contains criteria for creating a new temp data entry in an experiment.
+    """
+    plugin_path: str | None
+    """The temp data plugin path to run to populate the entry."""
+
+    def __init__(self):
+        super().__init__(ElnEntryType.TempData)
+        self.plugin_path = None
+
+
+class TextStepCreation(StepCreation):
+    """
+    An object that contains criteria for creating a new text entry in an experiment.
+    """
+    def __init__(self):
+        super().__init__(ElnEntryType.Text)

sapiopycommons/general/aliases.py

@@ -7,6 +7,7 @@ from sapiopylib.rest.pojo.datatype.FieldDefinition import FieldType, AbstractVel
 from sapiopylib.rest.pojo.eln.ElnExperiment import ElnExperiment
 from sapiopylib.rest.pojo.eln.ExperimentEntry import ExperimentEntry
 from sapiopylib.rest.pojo.eln.SapioELNEnums import ElnBaseDataType
+from sapiopylib.rest.pojo.eln.eln_headings import ElnExperimentTab
 from sapiopylib.rest.pojo.webhook.WebhookContext import SapioWebhookContext
 from sapiopylib.rest.utils.Protocols import ElnExperimentProtocol, ElnEntryStep
 from sapiopylib.rest.utils.recordmodel.PyRecordModel import PyRecordModel, AbstractRecordModel
@@ -37,6 +38,8 @@ ExperimentIdentifier: TypeAlias = ElnExperimentProtocol | ElnExperiment | int
 ID."""
 ExperimentEntryIdentifier: TypeAlias = ElnEntryStep | ExperimentEntry | int
 """An ExperimentEntryIdentifier is either an ELN entry step, experiment entry, or an integer for the entry's ID."""
+TabIdentifier: TypeAlias = int | ElnExperimentTab
+"""A TabIdentifier is either an integer for the tab's ID or an ElnExperimentTab object."""
 FieldMap: TypeAlias = dict[str, FieldValue]
 """A field map is simply a dict of data field names to values. The purpose of aliasing this is to help distinguish
 any random dict in a webhook from one which is explicitly used for record fields."""

sapiopycommons/processtracking/custom_workflow_handler.py

@@ -105,7 +105,8 @@ class QueueItemHandler:
         """
         self.user = AliasUtil.to_sapio_user(context)
         self.rec_handler = RecordHandler(self.user)
-        if isinstance(context, SapioWebhookContext):
+        # PR-47565: Only initialize a ProcessQueueContext if the given context object has context_data.
+        if isinstance(context, SapioWebhookContext) and context.context_data:
             self.context = ProcessQueueContext(context)
         else:
             self.context = None

{sapiopycommons-2025.4.3a469.dist-info → sapiopycommons-2025.4.8a473.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: sapiopycommons
-Version: 2025.4.3a469
+Version: 2025.4.8a473
 Summary: Official Sapio Python API Utilities Package
 Project-URL: Homepage, https://github.com/sapiosciences
 Author-email: Jonathan Steck <jsteck@sapiosciences.com>, Yechen Qiao <yqiao@sapiosciences.com>

{sapiopycommons-2025.4.3a469.dist-info → sapiopycommons-2025.4.8a473.dist-info}/RECORD

@@ -13,13 +13,15 @@ sapiopycommons/customreport/term_builder.py,sha256=1_PGjxNUy5YWim8WJ_HJfiTq6i0D3
 sapiopycommons/datatype/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/datatype/attachment_util.py,sha256=N-nhsJ0oxa_Ft6Y6VWeNFYLzfuQqsjhHA6_-yIt2wVw,3596
 sapiopycommons/datatype/data_fields.py,sha256=pczUlEcE0TeHEDU0Gkvu7voacSLPXCB7l9UbI1Tb6V0,5656
-sapiopycommons/datatype/experiment_cache.py,sha256=kiYZBZEAuQpv-rFviv8_6g7uvXdzH9BMUEprvAHT0Ds,8181
 sapiopycommons/datatype/pseudo_data_types.py,sha256=6TG7aJxgmUZ8FQkWBcgmbK5oy7AFFNtKOPpi1w1OOYA,27657
 sapiopycommons/eln/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-sapiopycommons/eln/experiment_handler.py,sha256=GQxvCFRd8Oa_w5Jxdyn1fU34vg78rO-IUZB_Genre1E,127393
+sapiopycommons/eln/experiment_cache.py,sha256=kiYZBZEAuQpv-rFviv8_6g7uvXdzH9BMUEprvAHT0Ds,8181
+sapiopycommons/eln/experiment_handler.py,sha256=7vYRlYAW_xT5LcZ5nLqL9dxEHGRAPEuUxX8d8TElWV8,105742
 sapiopycommons/eln/experiment_report_util.py,sha256=NNNNPVD3_2ZAjoOqCMOnlnmPD0SCjDcgYi453ATSJBs,37027
+sapiopycommons/eln/experiment_step_factory.py,sha256=6mUv2JXN5-MCM_aUblcv95v4NMTp9i1W42AqJ8sdUkM,26007
 sapiopycommons/eln/experiment_tags.py,sha256=7-fpOiSqrjbXmWIJhEhaxMgLsVCPAtKqH8xRzpDVKoE,356
 sapiopycommons/eln/plate_designer.py,sha256=ix2cflz13PAHyu4deS3d5Qd3kQXk0C7IQxBQ2Dm9fEM,13692
+sapiopycommons/eln/step_creation.py,sha256=DiniCKef2Nkpa2QeDiRvh_Q_QBu6J7o7vNlU28TaYRI,10141
 sapiopycommons/files/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/files/complex_data_loader.py,sha256=T39veNhvYl6j_uZjIIJ8Mk5Aa7otR5RB-g8XlAdkksA,1421
 sapiopycommons/files/file_bridge.py,sha256=vKbqxPexi15epr_-_qLrEfYoxNxB031mXN92iVtOMqE,9511
@@ -32,7 +34,7 @@ sapiopycommons/flowcyto/flow_cyto.py,sha256=vs9WhXXKz3urpjL8QKSk56B-NSmQR3O3x_WF
 sapiopycommons/flowcyto/flowcyto_data.py,sha256=mYKFuLbtpJ-EsQxLGtu4tNHVlygTxKixgJxJqD68F58,2596
 sapiopycommons/general/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/general/accession_service.py,sha256=3e__bVs7CYZ1CduLlGA9plnK7nCtdy7GXjCrNObPFgo,13484
-sapiopycommons/general/aliases.py,sha256=alc2R5TOSKbZif3pcGZ706y23Y9F4HQPC-Kj4xJZ_Us,14503
+sapiopycommons/general/aliases.py,sha256=wDNg0HSZm13O4lS8L8DT5mMBZ5GDwSbSHpDDwSFcZpc,14711
 sapiopycommons/general/audit_log.py,sha256=KQq0PsvukUoE3l6TQb3-vpu5-MbSINpWlnQ9e7jojPg,8743
 sapiopycommons/general/custom_report_util.py,sha256=NwwmejSQLwSbrndEk1gPyFNYk9GZoS7Wrp9ab9moFgw,18014
 sapiopycommons/general/data_structure_util.py,sha256=fbQR_Fh4Scg67IpFPbQW9wVLw1oxlYxqp4LjBRTpjgU,4702
@@ -45,7 +47,7 @@ sapiopycommons/general/time_util.py,sha256=jU1urPoZRv6evNucR0-288EyT4PrsDpCr-H1-
 sapiopycommons/multimodal/multimodal.py,sha256=PFaGJPbKvW__tnxb8KkgkJZOKjQdgxF_kGfD5chet1s,6779
 sapiopycommons/multimodal/multimodal_data.py,sha256=0BeVPr9HaC0hNTF1v1phTIKGruvNnwerHsD994qJKBg,15099
 sapiopycommons/processtracking/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-sapiopycommons/processtracking/custom_workflow_handler.py,sha256=QZVRDUXpHfYIKD9LtaOcOt0Sr3RGDaeGQb-LZYAgkCc,25117
+sapiopycommons/processtracking/custom_workflow_handler.py,sha256=wsDmJvl6pgrKEhxpTdh41B0CXAUCMli5JBkVDj-jbWw,25246
 sapiopycommons/processtracking/endpoints.py,sha256=w5bziI2xC7450M95rCF8JpRwkoni1kEDibyAux9B12Q,10848
 sapiopycommons/recordmodel/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/recordmodel/record_handler.py,sha256=jN158FR1fMYrwrcptcLkzxdKU40qrC-JMdTjgVoDrtE,90126
@@ -59,7 +61,7 @@ sapiopycommons/webhook/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3
 sapiopycommons/webhook/webhook_context.py,sha256=D793uLsb1691SalaPnBUk3rOSxn_hYLhdvkaIxjNXss,1909
 sapiopycommons/webhook/webhook_handlers.py,sha256=tUVNCw05CDGu1gFDm2g558hX_O203WVm_n__ojjoRRM,39841
 sapiopycommons/webhook/webservice_handlers.py,sha256=tyaYGG1-v_JJrJHZ6cy5mGCxX9z1foLw7pM4MDJlFxs,14297
-sapiopycommons-2025.4.3a469.dist-info/METADATA,sha256=yMKudOSZVmxq9MJjCW_tRHpnQGWLUwkKcV7rATvxZA4,3142
-sapiopycommons-2025.4.3a469.dist-info/WHEEL,sha256=C2FUgwZgiLbznR-k0b_5k3Ai_1aASOXDss3lzCUsUug,87
-sapiopycommons-2025.4.3a469.dist-info/licenses/LICENSE,sha256=HyVuytGSiAUQ6ErWBHTqt1iSGHhLmlC8fO7jTCuR8dU,16725
-sapiopycommons-2025.4.3a469.dist-info/RECORD,,
+sapiopycommons-2025.4.8a473.dist-info/METADATA,sha256=j7dB9Oy9qtcyLF6QYmAzL3yIQc5NYGaLRvgudYh0pxg,3142
+sapiopycommons-2025.4.8a473.dist-info/WHEEL,sha256=C2FUgwZgiLbznR-k0b_5k3Ai_1aASOXDss3lzCUsUug,87
+sapiopycommons-2025.4.8a473.dist-info/licenses/LICENSE,sha256=HyVuytGSiAUQ6ErWBHTqt1iSGHhLmlC8fO7jTCuR8dU,16725
+sapiopycommons-2025.4.8a473.dist-info/RECORD,,