sapiopycommons 2025.7.17a612__py3-none-any.whl → 2025.7.18a614__py3-none-any.whl

sapiopycommons/eln/step_creation.py

@@ -1,236 +0,0 @@
-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.field_names = 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/data_structure_util.py

@@ -1,115 +0,0 @@
-from enum import Enum
-from typing import Iterable, Any, Collection
-
-from sapiopycommons.general.exceptions import SapioException
-
-
-class ArrayTransformation(Enum):
-    """
-    An enumeration of the different transformations that can be applied to a 2D array.
-    """
-    ROTATE_CLOCKWISE = 0
-    ROTATE_COUNTER_CLOCKWISE = 1
-    ROTATE_180_DEGREES = 2
-    MIRROR_HORIZONTAL = 3
-    MIRROR_VERTICAL = 4
-
-
-# FR-47524: Create a DataStructureUtils class that implements various collection utility functions from our Java
-# libraries.
-class DataStructureUtil:
-    """
-    Utility class for working with data structures. Copies from ListUtil, SetUtil, and various other classes in
-    our Java library.
-    """
-    @staticmethod
-    def find_first_or_none(values: Iterable[Any]) -> Any | None:
-        """
-        Get the first value from an iterable, or None if the iterable is empty.
-
-        :param values: An iterable of values.
-        :return: The first value from the input, or None if the input is empty.
-        """
-        return next(iter(values), None)
-
-    @staticmethod
-    def remove_null_values(values: Iterable[Any]) -> list[Any]:
-        """
-        Remove null values from a list.
-
-        :param values: An iterable of values.
-        :return: A list containing all the non-null values from the input.
-        """
-        return [value for value in values if value is not None]
-
-    @staticmethod
-    def transform_2d_array(values: Collection[Collection[Any]], transformation: ArrayTransformation) \
-            -> Collection[Collection[Any]]:
-        """
-        Perform a transformation on a 2D list.
-
-        :param values: An iterable of iterables. The iterables should all be of the same size.
-        :param transformation: The transformation to apply to the input.
-        :return: A new 2D list containing the input transformed according to the specified transformation.
-        """
-        x: int = len(values)
-        for row in values:
-            y = len(row)
-            if y != x:
-                raise SapioException(f"Input must be a square 2D array. The provided array has a length of {x} but "
-                                     f"at least one row has a length of {y}.")
-
-        match transformation:
-            case ArrayTransformation.ROTATE_CLOCKWISE:
-                return [list(row) for row in zip(*values[::-1])]
-            case ArrayTransformation.ROTATE_COUNTER_CLOCKWISE:
-                return [list(row) for row in zip(*values)][::-1]
-            case ArrayTransformation.ROTATE_180_DEGREES:
-                return [row[::-1] for row in values[::-1]]
-            case ArrayTransformation.MIRROR_HORIZONTAL:
-                return [list(row[::-1]) for row in values]
-            case ArrayTransformation.MIRROR_VERTICAL:
-                return values[::-1]
-
-        raise SapioException(f"Invalid transformation: {transformation}")
-
-    @staticmethod
-    def flatten_to_list(values: Iterable[Iterable[Any]]) -> list[Any]:
-        """
-        Flatten a list of lists into a single list.
-
-        :param values: An iterable of iterables.
-        :return: A single list containing all the values from the input. Elements are in the order they appear in the
-            input.
-        """
-        return [item for sublist in values for item in sublist]
-
-    @staticmethod
-    def flatten_to_set(values: Iterable[Iterable[Any]]) -> set[Any]:
-        """
-        Flatten a list of lists into a single set.
-
-        :param values: An iterable of iterables.
-        :return: A single set containing all the values from the input. Elements are in the order they appear in the
-            input.
-        """
-        return {item for subset in values for item in subset}
-
-    @staticmethod
-    def invert_dictionary(dictionary: dict[Any, Any], list_values: bool = False) \
-            -> dict[Any, Any] | dict[Any, list[Any]]:
-        """
-        Invert a dictionary, swapping keys and values. Note that the values of the input dictionary must be hashable.
-
-        :param dictionary: A dictionary to invert.
-        :param list_values: If false, keys that share the same value in the input dictionary will be overwritten in
-            the output dictionary so that only the last key remains. If true, the values of the output dictionary will
-            be lists where input keys that share the same value will be stored together.
-        :return: A new dictionary with the keys and values swapped.
-        """
-        if list_values:
-            inverted = {}
-            for key, value in dictionary.items():
-                inverted.setdefault(value, []).append(key)
-            return inverted
-        return {value: key for key, value in dictionary.items()}

sapiopycommons-2025.7.17a612.dist-info/RECORD

@@ -1,68 +0,0 @@
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