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galaxy.schema package

class galaxy.schema.BootstrapAdminUser[source]

Bases: pydantic.main.BaseModel

all_roles(*args) → list[source]
class galaxy.schema.FilterQueryParams[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.PdfDocumentType[source]

Bases: str, enum.Enum

An enumeration.

invocation_report = 'invocation_report'
page = 'page'
class galaxy.schema.SerializationParams[source]

Bases: pydantic.main.BaseModel

Contains common parameters for customizing model serialization.

Submodules

galaxy.schema.fields module

class galaxy.schema.fields.BaseDatabaseIdField[source]

Bases: object

Database ID validation.

classmethod validate(v)[source]
class galaxy.schema.fields.DecodedDatabaseIdField[source]

Bases: int, galaxy.schema.fields.BaseDatabaseIdField

classmethod validate(v)[source]
class galaxy.schema.fields.EncodedDatabaseIdField[source]

Bases: str, galaxy.schema.fields.BaseDatabaseIdField

classmethod validate(v)[source]
galaxy.schema.fields.ModelClassField(class_name: str) → str[source]

Represents a database model class name annotated as a constant pydantic Field. :param class_name: The name of the database class. :return: A constant pydantic Field with default annotations for model classes.

galaxy.schema.fields.OrderParamField(default_order: str) → typing.Optional[str][source]

galaxy.schema.schema module

This module contains general pydantic models and common schema field annotations for them.

class galaxy.schema.schema.BasicRoleModel[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.CollectionElementIdentifier[source]

Bases: galaxy.schema.schema.Model

class galaxy.schema.schema.ColletionSourceType[source]

Bases: str, enum.Enum

An enumeration.

hda = 'hda'
hdca = 'hdca'
ldda = 'ldda'
new_collection = 'new_collection'
class galaxy.schema.schema.ContentsNearResult[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.ContentsNearStats[source]

Bases: pydantic.main.BaseModel

Stats used by the contents_near endpoint.

to_headers() → typing.Dict[str, str][source]

Converts all field values to json strings.

The headers values need to be json strings or updating the response headers will raise encoding errors.

class galaxy.schema.schema.CreateHistoryPayload[source]

Bases: galaxy.schema.schema.Model

class galaxy.schema.schema.CreateLibraryFolderPayload[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.CreateLibraryPayload[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.CreateNewCollectionPayload[source]

Bases: galaxy.schema.schema.Model

class galaxy.schema.schema.CreatePagePayload[source]

Bases: galaxy.schema.schema.PageSummaryBase

class Config[source]

Bases: object

extra = 'allow'
use_enum_values = True
class galaxy.schema.schema.Creator[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.CustomBuildsMetadataResponse[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.CustomHistoryItem[source]

Bases: galaxy.schema.schema.Model

Can contain any serializable property of the item.

Allows arbitrary custom keys to be specified in the serialization parameters without a particular view (predefined set of keys).

class Config[source]

Bases: object

extra = 'allow'
class galaxy.schema.schema.DCDetailed[source]

Bases: galaxy.schema.schema.DCSummary

Dataset Collection detailed information.

class galaxy.schema.schema.DCESummary[source]

Bases: galaxy.schema.schema.Model

Dataset Collection Element summary information.

class galaxy.schema.schema.DCEType[source]

Bases: str, enum.Enum

Available types of dataset collection elements.

dataset_collection = 'dataset_collection'
hda = 'hda'
class galaxy.schema.schema.DCObject[source]

Bases: galaxy.schema.schema.Model

Dataset Collection Object

class galaxy.schema.schema.DCSummary[source]

Bases: galaxy.schema.schema.Model

Dataset Collection summary information.

class galaxy.schema.schema.DatasetAssociationRoles[source]

Bases: galaxy.schema.schema.Model

class galaxy.schema.schema.DatasetCollectionInstanceType[source]

Bases: str, enum.Enum

An enumeration.

history = 'history'
library = 'library'
class galaxy.schema.schema.DatasetJobInfo[source]

Bases: galaxy.schema.schema.Model

class galaxy.schema.schema.DatasetPermissionAction[source]

Bases: str, enum.Enum

An enumeration.

make_private = 'make_private'
remove_restrictions = 'remove_restrictions'
set_permissions = 'set_permissions'
class galaxy.schema.schema.DatasetPermissions[source]

Bases: galaxy.schema.schema.Model

Role-based permissions for accessing and managing a dataset.

class galaxy.schema.schema.DatasetSourceType[source]

Bases: str, enum.Enum

An enumeration.

hda = 'hda'
ldda = 'ldda'
class galaxy.schema.schema.DeleteHistoryContentPayload[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.DeleteHistoryContentResult[source]

Bases: galaxy.schema.schema.CustomHistoryItem

Contains minimum information about the deletion state of a history item.

Can also contain any other properties of the item.

class galaxy.schema.schema.DeleteLibraryPayload[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.DisplayApp[source]

Bases: galaxy.schema.schema.Model

Basic linked information about an application that can display certain datatypes.

class galaxy.schema.schema.ExportHistoryArchivePayload[source]

Bases: galaxy.schema.schema.Model

class galaxy.schema.schema.GroupModel[source]

Bases: pydantic.main.BaseModel

User group model

class galaxy.schema.schema.GroupRoleListModel[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.GroupRoleModel[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.HDABasicInfo[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.HDABeta[source]

Bases: galaxy.schema.schema.HDADetailed

History Dataset Association information used in the new Beta History.

class galaxy.schema.schema.HDADetailed[source]

Bases: galaxy.schema.schema.HDASummary

History Dataset Association detailed information.

class galaxy.schema.schema.HDAExtended[source]

Bases: galaxy.schema.schema.HDADetailed

History Dataset Association extended information.

class galaxy.schema.schema.HDAInaccessible[source]

Bases: galaxy.schema.schema.HistoryItemBase

History Dataset Association information when the user can not access it.

class galaxy.schema.schema.HDAObject[source]

Bases: galaxy.schema.schema.Model

History Dataset Association Object

class Config[source]

Bases: object

extra = 'allow'
class galaxy.schema.schema.HDASummary[source]

Bases: galaxy.schema.schema.HistoryItemCommon

History Dataset Association summary information.

class galaxy.schema.schema.HDCABeta[source]

Bases: galaxy.schema.schema.HDCADetailed

History Dataset Collection Association information used in the new Beta History.

class galaxy.schema.schema.HDCADetailed[source]

Bases: galaxy.schema.schema.HDCASummary

History Dataset Collection Association detailed information.

class galaxy.schema.schema.HDCASummary[source]

Bases: galaxy.schema.schema.HistoryItemCommon

History Dataset Collection Association summary information.

class galaxy.schema.schema.HDCJobStateSummary[source]

Bases: galaxy.schema.schema.Model

Overview of the job states working inside a dataset collection.

class galaxy.schema.schema.HistoryActiveContentCounts[source]

Bases: galaxy.schema.schema.Model

Contains the number of active, deleted or hidden items in a History.

class galaxy.schema.schema.HistoryBase[source]

Bases: pydantic.main.BaseModel

Provides basic configuration for all the History models.

class Config[source]

Bases: object

extra = 'allow'
use_enum_values = True
class galaxy.schema.schema.HistoryBeta[source]

Bases: galaxy.schema.schema.HistoryDetailed

History detailed information used in the new Beta History.

class galaxy.schema.schema.HistoryContentSource[source]

Bases: str, enum.Enum

An enumeration.

hda = 'hda'
hdca = 'hdca'
library = 'library'
library_folder = 'library_folder'
new_collection = 'new_collection'
class galaxy.schema.schema.HistoryContentType[source]

Bases: str, enum.Enum

Available types of History contents.

dataset = 'dataset'
dataset_collection = 'dataset_collection'
class galaxy.schema.schema.HistoryContentsArchiveDryRunResult[source]

Bases: pydantic.main.BaseModel

Contains a collection of filepath/filename entries that represent the contents that would have been included in the archive. This is returned when the dry_run flag is active when creating an archive with the contents of the history.

This is used for debugging purposes.

class galaxy.schema.schema.HistoryContentsResult[source]

Bases: galaxy.schema.schema.Model

Collection of history content items. Can contain different views and kinds of items.

class galaxy.schema.schema.HistoryDetailed[source]

Bases: galaxy.schema.schema.HistorySummary

History detailed information.

class galaxy.schema.schema.HistoryImportArchiveSourceType[source]

Bases: str, enum.Enum

Available types of History archive sources.

file = 'file'
url = 'url'
class galaxy.schema.schema.HistoryItemBase[source]

Bases: galaxy.schema.schema.Model

Basic information provided by items contained in a History.

class galaxy.schema.schema.HistoryItemCommon[source]

Bases: galaxy.schema.schema.HistoryItemBase

Common information provided by items contained in a History.

class Config[source]

Bases: object

extra = 'allow'
class galaxy.schema.schema.HistorySummary[source]

Bases: galaxy.schema.schema.HistoryBase

History summary information.

Bases: galaxy.schema.schema.Model

Represents some text with an Hyperlink.

class galaxy.schema.schema.ImplicitCollectionJobsStateSummary[source]

Bases: galaxy.schema.schema.JobStateSummary

class galaxy.schema.schema.Input[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.InputConnection[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.InputDataCollectionStep[source]

Bases: galaxy.schema.schema.ToolBasedWorkflowStep

class galaxy.schema.schema.InputDataStep[source]

Bases: galaxy.schema.schema.ToolBasedWorkflowStep

class galaxy.schema.schema.InputParameterStep[source]

Bases: galaxy.schema.schema.ToolBasedWorkflowStep

class galaxy.schema.schema.InputStep[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.InvocationIndexPayload[source]

Bases: galaxy.schema.schema.Model

class galaxy.schema.schema.JobBaseModel[source]

Bases: galaxy.schema.schema.Model

class galaxy.schema.schema.JobDetails[source]

Bases: galaxy.schema.schema.JobSummary

class galaxy.schema.schema.JobExportHistoryArchiveCollection[source]

Bases: galaxy.schema.schema.Model

class galaxy.schema.schema.JobExportHistoryArchiveModel[source]

Bases: galaxy.schema.schema.Model

class galaxy.schema.schema.JobFullDetails[source]

Bases: galaxy.schema.schema.JobDetails

class galaxy.schema.schema.JobIdResponse[source]

Bases: pydantic.main.BaseModel

Contains the ID of the job associated with a particular request.

class galaxy.schema.schema.JobImportHistoryResponse[source]

Bases: galaxy.schema.schema.JobBaseModel

class galaxy.schema.schema.JobMetric[source]

Bases: galaxy.schema.schema.Model

class Config[source]

Bases: object

schema_extra = {'example': {'title': 'Job Start Time', 'value': '2021-02-25 14:55:40', 'plugin': 'core', 'name': 'start_epoch', 'raw_value': '1614261340.0000000'}}
class galaxy.schema.schema.JobMetricCollection[source]

Bases: galaxy.schema.schema.Model

Represents a collection of metrics associated with a Job.

class galaxy.schema.schema.JobSourceType[source]

Bases: str, enum.Enum

Available types of job sources (model classes) that produce dataset collections.

ImplicitCollectionJobs = 'ImplicitCollectionJobs'
Job = 'Job'
WorkflowInvocation = 'WorkflowInvocation'
class galaxy.schema.schema.JobStateSummary[source]

Bases: galaxy.schema.schema.Model

class galaxy.schema.schema.JobSummary[source]

Bases: galaxy.schema.schema.JobBaseModel

Basic information about a job.

class galaxy.schema.schema.LabelValuePair[source]

Bases: pydantic.main.BaseModel

Generic Label/Value pair model.

class galaxy.schema.schema.LegacyLibraryPermissionsPayload[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.LibraryAvailablePermissions[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.LibraryCurrentPermissions[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.LibraryFolderCurrentPermissions[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.LibraryFolderDetails[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.LibraryFolderPermissionAction[source]

Bases: str, enum.Enum

An enumeration.

set_permissions = 'set_permissions'
class galaxy.schema.schema.LibraryFolderPermissionsPayload[source]

Bases: galaxy.schema.schema.LibraryPermissionsPayloadBase

class galaxy.schema.schema.LibraryLegacySummary[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.LibraryPermissionAction[source]

Bases: str, enum.Enum

An enumeration.

remove_restrictions = 'remove_restrictions'
set_permissions = 'set_permissions'
class galaxy.schema.schema.LibraryPermissionScope[source]

Bases: str, enum.Enum

An enumeration.

available = 'available'
current = 'current'
class galaxy.schema.schema.LibraryPermissionsPayload[source]

Bases: galaxy.schema.schema.LibraryPermissionsPayloadBase

class galaxy.schema.schema.LibraryPermissionsPayloadBase[source]

Bases: galaxy.schema.schema.Model

class galaxy.schema.schema.LibrarySummary[source]

Bases: galaxy.schema.schema.LibraryLegacySummary

class galaxy.schema.schema.LibrarySummaryList[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.MetadataFile[source]

Bases: galaxy.schema.schema.Model

Metadata file associated with a dataset.

class galaxy.schema.schema.Model[source]

Bases: pydantic.main.BaseModel

Base model definition with common configuration used by all derived models.

class Config[source]

Bases: object

allow_population_by_field_name = True
use_enum_values = True
class galaxy.schema.schema.Organization[source]

Bases: galaxy.schema.schema.Creator

class galaxy.schema.schema.Output[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.PageContentFormat[source]

Bases: str, enum.Enum

An enumeration.

html = 'html'
markdown = 'markdown'
class galaxy.schema.schema.PageDetails[source]

Bases: galaxy.schema.schema.PageSummary

class Config[source]

Bases: object

extra = 'allow'
class galaxy.schema.schema.PageSummary[source]

Bases: galaxy.schema.schema.PageSummaryBase

class galaxy.schema.schema.PageSummaryBase[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.PageSummaryList[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.PauseStep[source]

Bases: galaxy.schema.schema.WorkflowStepBase

class galaxy.schema.schema.Person[source]

Bases: galaxy.schema.schema.Creator

class galaxy.schema.schema.PostJobAction[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.RoleDefinitionModel[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.RoleListModel[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.RoleModel[source]

Bases: galaxy.schema.schema.BasicRoleModel

class galaxy.schema.schema.SetSlugPayload[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.ShareHistoryExtra[source]

Bases: galaxy.schema.schema.ShareWithExtra

class galaxy.schema.schema.ShareWithExtra[source]

Bases: pydantic.main.BaseModel

class Config[source]

Bases: object

extra = 'allow'
class galaxy.schema.schema.ShareWithPayload[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.ShareWithStatus[source]

Bases: galaxy.schema.schema.SharingStatus

class galaxy.schema.schema.SharingOptions[source]

Bases: str, enum.Enum

Options for sharing resources that may have restricted access to all or part of their contents.

make_accessible_to_shared = 'make_accessible_to_shared'
make_public = 'make_public'
no_changes = 'no_changes'
class galaxy.schema.schema.SharingStatus[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.SortByEnum[source]

Bases: str, enum.Enum

An enumeration.

create_time = 'create_time'
none = 'None'
update_time = 'update_time'
class galaxy.schema.schema.StoredWorkflowDetailed[source]

Bases: galaxy.schema.schema.StoredWorkflowSummary

class galaxy.schema.schema.StoredWorkflowSummary[source]

Bases: galaxy.schema.schema.Model

class galaxy.schema.schema.SubworkflowStep[source]

Bases: galaxy.schema.schema.WorkflowStepBase

class galaxy.schema.schema.SubworkflowStepToExport[source]

Bases: galaxy.schema.schema.WorkflowStepToExportBase

class galaxy.schema.schema.TagCollection[source]

Bases: galaxy.schema.schema.Model

Represents the collection of tags associated with an item.

class galaxy.schema.schema.TagItem[source]

Bases: pydantic.types.ConstrainedStr

regex = re.compile('^([^\\s.:])+(.[^\\s.:]+)*(:[^\\s.:]+)?$')
class galaxy.schema.schema.ToolBasedWorkflowStep[source]

Bases: galaxy.schema.schema.WorkflowStepBase

class galaxy.schema.schema.ToolShedRepositorySummary[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.ToolStep[source]

Bases: galaxy.schema.schema.ToolBasedWorkflowStep

class galaxy.schema.schema.UpdateContentItem[source]

Bases: galaxy.schema.schema.HistoryBase

Used for updating a particular HDA. All fields are optional.

class galaxy.schema.schema.UpdateDatasetPermissionsPayload[source]

Bases: galaxy.schema.schema.Model

class galaxy.schema.schema.UpdateHistoryContentsBatchPayload[source]

Bases: galaxy.schema.schema.HistoryBase

Contains property values that will be updated for all the history items provided.

class Config[source]

Bases: object

schema_extra = {'example': {'items': [{'history_content_type': 'dataset', 'id': 'string'}], 'visible': False}}
class galaxy.schema.schema.UpdateHistoryContentsPayload[source]

Bases: galaxy.schema.schema.HistoryBase

Contains arbitrary property values that will be updated for a particular history item.

class Config[source]

Bases: object

schema_extra = {'example': {'visible': False, 'annotation': 'Test'}}
class galaxy.schema.schema.UpdateLibraryFolderPayload[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.UpdateLibraryPayload[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.UserEmail[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.UserModel[source]

Bases: galaxy.schema.schema.Model

User in a transaction context.

class galaxy.schema.schema.Visualization[source]

Bases: galaxy.schema.schema.Model

class Config[source]

Bases: object

extra = 'allow'
class galaxy.schema.schema.WorkflowInput[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.WorkflowInvocationStateSummary[source]

Bases: galaxy.schema.schema.JobStateSummary

class galaxy.schema.schema.WorkflowModuleType[source]

Bases: str, enum.Enum

Available types of modules that represent a step in a Workflow.

data_collection_input = 'data_collection_input'
data_input = 'data_input'
parameter_input = 'parameter_input'
pause = 'pause'
subworkflow = 'subworkflow'
tool = 'tool'
class galaxy.schema.schema.WorkflowOutput[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.WorkflowStepBase[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.WorkflowStepLayoutPosition[source]

Bases: pydantic.main.BaseModel

Position and dimensions of the workflow step represented by a box on the graph.

class galaxy.schema.schema.WorkflowStepToExport[source]

Bases: galaxy.schema.schema.WorkflowStepToExportBase

class galaxy.schema.schema.WorkflowStepToExportBase[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.WorkflowToExport[source]

Bases: pydantic.main.BaseModel

class galaxy.schema.schema.WorkflowToolStepToExport[source]

Bases: galaxy.schema.schema.WorkflowStepToExportBase