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Entity View Schema

synapseclient.table.EntityViewSchema

Bases: ViewBase

A EntityViewSchema is a Entity that displays all files/projects (depending on user choice) within a given set of scopes.

ATTRIBUTE DESCRIPTION
name

The name of the Entity View Table object

columns

(Optional) A list of Column objects or their IDs.

parent

The project in Synapse to which this table belongs

scopes

A list of Projects/Folders or their ids

type

This field is deprecated. Please use includeEntityTypes

includeEntityTypes

A list of entity types to include in the view. Supported entity types are:

  • EntityViewType.FILE
  • EntityViewType.PROJECT
  • EntityViewType.TABLE
  • EntityViewType.FOLDER
  • EntityViewType.VIEW
  • EntityViewType.DOCKER

If none is provided, the view will default to include EntityViewType.FILE.

addDefaultViewColumns

If true, adds all default columns (e.g. name, createdOn, modifiedBy etc.) Defaults to True. The default columns will be added after a call to store.

addAnnotationColumns

If true, adds columns for all annotation keys defined across all Entities in the EntityViewSchema's scope. Defaults to True. The annotation columns will be added after a call to store.

ignoredAnnotationColumnNames

A list of strings representing annotation names. When addAnnotationColumns is True, the names in this list will not be automatically added as columns to the EntityViewSchema if they exist in any of the defined scopes.

properties

A map of Synapse properties

annotations

A map of user defined annotations

local_state

Internal use only

Example:

from synapseclient import EntityViewType

project_or_folder = syn.get("syn123")
schema = syn.store(EntityViewSchema(name='MyTable', parent=project, scopes=[project_or_folder_id, 'syn123'],
 includeEntityTypes=[EntityViewType.FILE]))
Source code in synapseclient/table.py
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class EntityViewSchema(ViewBase):
    """
    A EntityViewSchema is a [Entity][synapseclient.entity.Entity] that displays all files/projects
    (depending on user choice) within a given set of scopes.

    Attributes:
        name:                         The name of the Entity View Table object
        columns:                      (Optional) A list of [Column][synapseclient.table.Column] objects or their IDs.
        parent:                       The project in Synapse to which this table belongs
        scopes:                       A list of Projects/Folders or their ids
        type:                         This field is deprecated. Please use `includeEntityTypes`
        includeEntityTypes:           A list of entity types to include in the view. Supported entity types are:

            - `EntityViewType.FILE`
            - `EntityViewType.PROJECT`
            - `EntityViewType.TABLE`
            - `EntityViewType.FOLDER`
            - `EntityViewType.VIEW`
            - `EntityViewType.DOCKER`

            If none is provided, the view will default to include `EntityViewType.FILE`.
        addDefaultViewColumns:        If true, adds all default columns (e.g. name, createdOn, modifiedBy etc.)
                                      Defaults to True.
                                      The default columns will be added after a call to
                                      [store][synapseclient.Synapse.store].
        addAnnotationColumns:         If true, adds columns for all annotation keys defined across all Entities in
                                      the EntityViewSchema's scope. Defaults to True.
                                      The annotation columns will be added after a call to
                                      [store][synapseclient.Synapse.store].
        ignoredAnnotationColumnNames: A list of strings representing annotation names.
                                      When addAnnotationColumns is True, the names in this list will not be
                                      automatically added as columns to the EntityViewSchema if they exist in any
                                      of the defined scopes.
        properties:                   A map of Synapse properties
        annotations:                  A map of user defined annotations
        local_state:                  Internal use only

    Example:

        from synapseclient import EntityViewType

        project_or_folder = syn.get("syn123")
        schema = syn.store(EntityViewSchema(name='MyTable', parent=project, scopes=[project_or_folder_id, 'syn123'],
         includeEntityTypes=[EntityViewType.FILE]))
    """

    _synapse_entity_type = "org.sagebionetworks.repo.model.table.EntityView"

    def __init__(
        self,
        name=None,
        columns=None,
        parent=None,
        scopes=None,
        type=None,
        includeEntityTypes=None,
        addDefaultViewColumns=True,
        addAnnotationColumns=True,
        ignoredAnnotationColumnNames=[],
        properties=None,
        annotations=None,
        local_state=None,
        **kwargs,
    ):
        if includeEntityTypes:
            kwargs["viewTypeMask"] = _get_view_type_mask(includeEntityTypes)
        elif type:
            kwargs["viewTypeMask"] = _get_view_type_mask_for_deprecated_type(type)
        elif properties and "type" in properties:
            kwargs["viewTypeMask"] = _get_view_type_mask_for_deprecated_type(
                properties["type"]
            )
            properties["type"] = None

        self.ignoredAnnotationColumnNames = set(ignoredAnnotationColumnNames)
        super(EntityViewSchema, self).__init__(
            name=name,
            columns=columns,
            properties=properties,
            annotations=annotations,
            local_state=local_state,
            parent=parent,
            **kwargs,
        )

        # This is a hacky solution to make sure we don't try to add columns to schemas that we retrieve from synapse
        is_from_normal_constructor = not (properties or local_state)
        # allowing annotations because user might want to update annotations all at once
        self.addDefaultViewColumns = (
            addDefaultViewColumns and is_from_normal_constructor
        )
        self.addAnnotationColumns = addAnnotationColumns and is_from_normal_constructor

        # set default values after constructor so we don't overwrite the values defined in properties using .get()
        # because properties, unlike local_state, do not have nonexistent keys assigned with a value of None
        if self.get("viewTypeMask") is None:
            self.viewTypeMask = EntityViewType.FILE.value
        if self.get("scopeIds") is None:
            self.scopeIds = []

        # add the scopes last so that we can append the passed in scopes to those defined in properties
        if scopes is not None:
            self.add_scope(scopes)

    def set_entity_types(self, includeEntityTypes):
        """
        Set entity types

        Arguments:
            includeEntityTypes: A list of entity types to include in the view. This list will replace the previous
                                settings. Supported entity types are:

                - `EntityViewType.FILE`
                - `EntityViewType.PROJECT`
                - `EntityViewType.TABLE`
                - `EntityViewType.FOLDER`
                - `EntityViewType.VIEW`
                - `EntityViewType.DOCKER`
        """
        self.viewTypeMask = _get_view_type_mask(includeEntityTypes)

Functions

set_entity_types(includeEntityTypes)

Set entity types

PARAMETER DESCRIPTION
includeEntityTypes

A list of entity types to include in the view. This list will replace the previous settings. Supported entity types are:

  • EntityViewType.FILE
  • EntityViewType.PROJECT
  • EntityViewType.TABLE
  • EntityViewType.FOLDER
  • EntityViewType.VIEW
  • EntityViewType.DOCKER

Source code in synapseclient/table.py
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def set_entity_types(self, includeEntityTypes):
    """
    Set entity types

    Arguments:
        includeEntityTypes: A list of entity types to include in the view. This list will replace the previous
                            settings. Supported entity types are:

            - `EntityViewType.FILE`
            - `EntityViewType.PROJECT`
            - `EntityViewType.TABLE`
            - `EntityViewType.FOLDER`
            - `EntityViewType.VIEW`
            - `EntityViewType.DOCKER`
    """
    self.viewTypeMask = _get_view_type_mask(includeEntityTypes)