galaxy.model.store package

class galaxy.model.store.StoreAppProtocol(*args, **kwargs)

Bases: Protocol

Define the parts of a Galaxy-like app consumed by model store.

datatypes_registry: Registry

object_store: BaseObjectStore

security: IdEncodingHelper

tag_handler: GalaxyTagHandler

model: GalaxyModelMapping

file_sources: ConfiguredFileSources

workflow_contents_manager: WorkflowContentsManager

__init__(*args, **kwargs)

class galaxy.model.store.ImportDiscardedDataType(value)

Bases: Enum

An enumeration.

FORBID = 'forbid'

ALLOW = 'allow'

FORCE = 'force'

class galaxy.model.store.DatasetAttributeImportModel(*, state: DatasetState[DatasetState] | None = None, external_filename: str | None = None, file_size: int | None = None, object_store_id: str | None = None, total_size: int | None = None, created_from_basename: str | None = None, uuid: str | None = None)

Bases: BaseModel

state: DatasetState[DatasetState] | None

external_filename: str | None

file_size: int | None

object_store_id: str | None

total_size: int | None

created_from_basename: str | None

uuid: str | None

model_config: ClassVar[ConfigDict] = {'extra': 'ignore'}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

model_fields: ClassVar[dict[str, FieldInfo]] = {'created_from_basename': FieldInfo(annotation=Union[str, NoneType], required=False, default=None), 'external_filename': FieldInfo(annotation=Union[str, NoneType], required=False, default=None), 'file_size': FieldInfo(annotation=Union[int, NoneType], required=False, default=None), 'object_store_id': FieldInfo(annotation=Union[str, NoneType], required=False, default=None), 'state': FieldInfo(annotation=Union[Annotated[galaxy.schema.schema.DatasetState, BeforeValidator(func=<function <lambda>>), FieldInfo(annotation=NoneType, required=True, title='State', description='The current state of this dataset.')], NoneType], required=False, default=None), 'total_size': FieldInfo(annotation=Union[int, NoneType], required=False, default=None), 'uuid': FieldInfo(annotation=Union[str, NoneType], required=False, default=None)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

model_post_init(__context: Any) → None

This function is meant to behave like a BaseModel method to initialise private attributes.

It takes context as an argument since that’s what pydantic-core passes when calling it.

Args:

self: The BaseModel instance. __context: The context.

class galaxy.model.store.ImportOptions(allow_edit: bool = False, allow_library_creation: bool = False, allow_dataset_object_edit: bool | None = None, discarded_data: ImportDiscardedDataType = ImportDiscardedDataType.FORBID)

Bases: object

__init__(allow_edit: bool = False, allow_library_creation: bool = False, allow_dataset_object_edit: bool | None = None, discarded_data: ImportDiscardedDataType = ImportDiscardedDataType.FORBID) → None

allow_edit: bool

allow_library_creation: bool

allow_dataset_object_edit: bool

discarded_data: ImportDiscardedDataType

class galaxy.model.store.SessionlessContext

Bases: object

__init__() → None

commit() → None

flush() → None

add(obj: RepresentById) → None

query(model_class: RepresentById) → Bunch

get(model_class: RepresentById, primary_key: Any)

galaxy.model.store.replace_metadata_file(metadata: Dict[str, Any], dataset_instance: DatasetInstance, sa_session: SessionlessContext | scoped_session) → Dict[str, Any]

class galaxy.model.store.ModelImportStore(import_options: ImportOptions | None = None, app: StoreAppProtocol | None = None, user: User | None = None, object_store: ObjectStore | None = None, tag_handler: GalaxyTagHandlerSession | None = None)

Bases: object

archive_dir: str

__init__(import_options: ImportOptions | None = None, app: StoreAppProtocol | None = None, user: User | None = None, object_store: ObjectStore | None = None, tag_handler: GalaxyTagHandlerSession | None = None) → None

app: StoreAppProtocol | None

abstract workflow_paths() → Iterator[Tuple[str, str]]

abstract defines_new_history() → bool

Does this store define a new history to create.

abstract new_history_properties() → Dict[str, Any]

Dict of history properties if defines_new_history() is truthy.

abstract datasets_properties() → List[Dict[str, Any]]

Return a list of HDA properties.

library_properties() → List[Dict[str, Any]]

Return a list of library properties.

abstract invocations_properties() → List[Dict[str, Any]]

abstract collections_properties() → List[Dict[str, Any]]

Return a list of HDCA properties.

abstract implicit_dataset_conversion_properties() → List[Dict[str, Any]]

Return a list of ImplicitlyConvertedDatasetAssociation properties.

abstract jobs_properties() → List[Dict[str, Any]]

Return a list of jobs properties.

abstract implicit_collection_jobs_properties() → List[Dict[str, Any]]

abstract property object_key: str

Key used to connect objects in metadata.

Legacy exports used ‘hid’ but associated objects may not be from the same history and a history may contain multiple objects with the same ‘hid’.

property file_source_root: str | None

Source of valid file data.

trust_hid(obj_attrs: Dict[str, Any]) → bool

Trust HID when importing objects into a new History.

target_history(default_history: History | None = None, legacy_history_naming: bool = True) → Iterator[History | None]

perform_import(history: History | None = None, new_history: bool = False, job: Job | None = None) → ObjectImportTracker

class galaxy.model.store.ObjectImportTracker

Bases: object

Keep track of new and existing imported objects.

Needed to re-establish connections and such in multiple passes.

__init__() → None

libraries_by_key: Dict[str | int, Library]

hdas_by_key: Dict[str | int, HistoryDatasetAssociation]

hdas_by_id: Dict[int, HistoryDatasetAssociation]

hdcas_by_key: Dict[str | int, HistoryDatasetCollectionAssociation]

hdcas_by_id: Dict[int, HistoryDatasetCollectionAssociation]

dces_by_key: Dict[str | int, DatasetCollectionElement]

dces_by_id: Dict[int, DatasetCollectionElement]

lddas_by_key: Dict[str | int, LibraryDatasetDatasetAssociation]

hda_copied_from_sinks: Dict[str | int, str | int]

hdca_copied_from_sinks: Dict[str | int, str | int]

jobs_by_key: Dict[str | int, Job]

requires_hid: List[HistoryItem]

copy_hid_for: List[Tuple[HistoryItem, HistoryItem]]

find_hda(input_key: str | int, hda_id: int | None = None) → HistoryDatasetAssociation | None

find_hdca(input_key: str | int) → HistoryDatasetCollectionAssociation | None

find_dce(input_key: str | int) → DatasetCollectionElement | None

exception galaxy.model.store.FileTracebackException(traceback: str, *args, **kwargs)

Bases: Exception

__init__(traceback: str, *args, **kwargs) → None

galaxy.model.store.get_import_model_store_for_directory(archive_dir: str, **kwd) → DirectoryImportModelStore1901 | DirectoryImportModelStoreLatest

class galaxy.model.store.DictImportModelStore(store_as_dict: Dict[str, Any], **kwd)

Bases: ModelImportStore

object_key = 'encoded_id'

__init__(store_as_dict: Dict[str, Any], **kwd) → None

archive_dir: str

defines_new_history() → bool

Does this store define a new history to create.

new_history_properties() → Dict[str, Any]

Dict of history properties if defines_new_history() is truthy.

datasets_properties() → List[Dict[str, Any]]

Return a list of HDA properties.

collections_properties() → List[Dict[str, Any]]

Return a list of HDCA properties.

implicit_dataset_conversion_properties() → List[Dict[str, Any]]

Return a list of ImplicitlyConvertedDatasetAssociation properties.

library_properties() → List[Dict[str, Any]]

Return a list of library properties.

jobs_properties() → List[Dict[str, Any]]

Return a list of jobs properties.

implicit_collection_jobs_properties() → List[Dict[str, Any]]

invocations_properties() → List[Dict[str, Any]]

workflow_paths() → Iterator[Tuple[str, str]]

app: StoreAppProtocol | None

galaxy.model.store.get_import_model_store_for_dict(as_dict: Dict[str, Any], **kwd) → DictImportModelStore

class galaxy.model.store.BaseDirectoryImportModelStore(import_options: ImportOptions | None = None, app: StoreAppProtocol | None = None, user: User | None = None, object_store: ObjectStore | None = None, tag_handler: GalaxyTagHandlerSession | None = None)

Bases: ModelImportStore

property file_source_root: str

Source of valid file data.

defines_new_history() → bool

Does this store define a new history to create.

new_history_properties() → Dict[str, Any]

Dict of history properties if defines_new_history() is truthy.

datasets_properties() → List[Dict[str, Any]]

Return a list of HDA properties.

collections_properties() → List[Dict[str, Any]]

Return a list of HDCA properties.

implicit_dataset_conversion_properties() → List[Dict[str, Any]]

Return a list of ImplicitlyConvertedDatasetAssociation properties.

library_properties() → List[Dict[str, Any]]

Return a list of library properties.

jobs_properties() → List[Dict[str, Any]]

Return a list of jobs properties.

implicit_collection_jobs_properties() → List[Dict[str, Any]]

invocations_properties() → List[Dict[str, Any]]

workflow_paths() → Iterator[Tuple[str, str]]

app: StoreAppProtocol | None

archive_dir: str

galaxy.model.store.restore_times(model_object: Job | WorkflowInvocation | WorkflowInvocationStep, attrs: Dict[str, Any]) → None

class galaxy.model.store.DirectoryImportModelStore1901(archive_dir: str, **kwd)

Bases: BaseDirectoryImportModelStore

object_key = 'hid'

__init__(archive_dir: str, **kwd) → None

archive_dir: str

trust_hid(obj_attrs: Dict[str, Any]) → bool

Trust HID when importing objects into a new History.

app: StoreAppProtocol | None

class galaxy.model.store.DirectoryImportModelStoreLatest(archive_dir: str, **kwd)

Bases: BaseDirectoryImportModelStore

object_key = 'encoded_id'

__init__(archive_dir: str, **kwd) → None

archive_dir: str

app: StoreAppProtocol | None

class galaxy.model.store.BagArchiveImportModelStore(bag_archive: str, **kwd)

Bases: DirectoryImportModelStoreLatest

__init__(bag_archive: str, **kwd) → None

app: StoreAppProtocol | None

archive_dir: str

class galaxy.model.store.ModelExportStore

Bases: object

abstract export_history(history: History, include_hidden: bool = False, include_deleted: bool = False) → None

Export history to store.

abstract export_library(library: Library, include_hidden: bool = False, include_deleted: bool = False) → None

Export library to store.

abstract export_library_folder(library_folder: LibraryFolder, include_hidden: bool = False, include_deleted: bool = False) → None

Export library folder to store.

abstract export_workflow_invocation(workflow_invocation, include_hidden=False, include_deleted=False)

Export workflow invocation to store.

abstract add_dataset_collection(collection: DatasetCollection | HistoryDatasetCollectionAssociation)

Add Dataset Collection or HDCA to export store.

abstract add_dataset(dataset: DatasetInstance, include_files: bool = True)

Add HDA to export store.

include_files controls whether file contents are exported as well.

class galaxy.model.store.DirectoryModelExportStore(export_directory: str | PathLike, app: StoreAppProtocol | None = None, file_sources: ConfiguredFileSources | None = None, for_edit: bool = False, serialize_dataset_objects: bool | None = None, export_files: str | None = None, strip_metadata_files: bool = True, serialize_jobs: bool = True, user_context=None)

Bases: ModelExportStore

__init__(export_directory: str | PathLike, app: StoreAppProtocol | None = None, file_sources: ConfiguredFileSources | None = None, for_edit: bool = False, serialize_dataset_objects: bool | None = None, export_files: str | None = None, strip_metadata_files: bool = True, serialize_jobs: bool = True, user_context=None) → None

Parameters:

• export_directory – path to export directory. Will be created if it does not exist.

• app – Galaxy App or app-like object. Must be provided if for_edit and/or serialize_dataset_objects are True

• for_edit – Allow modifying existing HDA and dataset metadata during import.

• serialize_dataset_objects – If True will encode IDs using the host secret. Defaults for_edit.

• export_files – How files should be exported, can be ‘symlink’, ‘copy’ or None, in which case files will not be serialized.

• serialize_jobs – Include job data in model export. Not needed for set_metadata script.

app: StoreAppProtocol | None

file_sources: ConfiguredFileSources | None

property workflows_directory: str

serialize_files(dataset: DatasetInstance, as_dict: Dict[str, Any]) → None

exported_key(obj: RepresentById) → str | int

push_metadata_files()

export_job(job: Job, tool=None, include_job_data=True)

export_jobs(jobs: Iterable[Job], jobs_attrs: List[Dict[str, Any]] | None = None, include_job_data: bool = True) → List[Dict[str, Any]]

Export jobs.

include_job_data determines whether datasets associated with jobs should be exported as well. This should generally be True, except when re-exporting a job (to store the generated command line) when running the set_meta script.

export_history(history: History, include_hidden: bool = False, include_deleted: bool = False) → None

Export history to store.

export_library(library: Library, include_hidden: bool = False, include_deleted: bool = False) → None

Export library to store.

export_library_folder(library_folder: LibraryFolder, include_hidden=False, include_deleted=False)

Export library folder to store.

export_library_folder_contents(library_folder: LibraryFolder, include_hidden: bool = False, include_deleted: bool = False) → None

export_workflow_invocation(workflow_invocation: WorkflowInvocation, include_hidden: bool = False, include_deleted: bool = False) → None

Export workflow invocation to store.

add_job_output_dataset_associations(job_id: int, name: str, dataset_instance: DatasetInstance) → None

export_collection(collection: DatasetCollection | HistoryDatasetCollectionAssociation, include_deleted: bool = False, include_hidden: bool = False) → None

add_dataset_collection(collection: DatasetCollection | HistoryDatasetCollectionAssociation) → None

Add Dataset Collection or HDCA to export store.

add_implicit_conversion_dataset(dataset: DatasetInstance, include_files: bool, conversion: ImplicitlyConvertedDatasetAssociation) → None

add_dataset(dataset: DatasetInstance, include_files: bool = True) → None

Add HDA to export store.

include_files controls whether file contents are exported as well.

class galaxy.model.store.WriteCrates

Bases: object

included_invocations: List[WorkflowInvocation]

export_directory: str | PathLike

included_datasets: Dict[DatasetInstance, Tuple[DatasetInstance, bool]]

dataset_implicit_conversions: Dict[DatasetInstance, ImplicitlyConvertedDatasetAssociation]

dataset_id_to_path: Dict[int, Tuple[str | None, str | None]]

abstract property workflows_directory: str

class galaxy.model.store.WorkflowInvocationOnlyExportStore(export_directory: str | PathLike, app: StoreAppProtocol | None = None, file_sources: ConfiguredFileSources | None = None, for_edit: bool = False, serialize_dataset_objects: bool | None = None, export_files: str | None = None, strip_metadata_files: bool = True, serialize_jobs: bool = True, user_context=None)

Bases: DirectoryModelExportStore

export_history(history: History, include_hidden: bool = False, include_deleted: bool = False)

Export history to store.

export_library(history, include_hidden=False, include_deleted=False)

Export library to store.

property only_invocation: WorkflowInvocation

app: StoreAppProtocol | None

file_sources: ConfiguredFileSources | None

included_datasets: Dict[DatasetInstance, Tuple[DatasetInstance, bool]]

dataset_implicit_conversions: Dict[DatasetInstance, ImplicitlyConvertedDatasetAssociation]

included_collections: List[DatasetCollection | HistoryDatasetCollectionAssociation]

included_libraries: List[Library]

included_library_folders: List[LibraryFolder]

included_invocations: List[WorkflowInvocation]

collection_datasets: Set[int]

collections_attrs: List[DatasetCollection | HistoryDatasetCollectionAssociation]

dataset_id_to_path: Dict[int, Tuple[str | None, str | None]]

job_output_dataset_associations: Dict[int, Dict[str, DatasetInstance]]

class galaxy.model.store.BcoExportOptions(galaxy_url: str, galaxy_version: str, merge_history_metadata: bool = False, override_environment_variables: Dict[str, str] | NoneType = None, override_empirical_error: Dict[str, str] | NoneType = None, override_algorithmic_error: Dict[str, str] | NoneType = None, override_xref: List[galaxy.schema.bco.description_domain.XrefItem] | NoneType = None)

Bases: object

galaxy_url: str

galaxy_version: str

merge_history_metadata: bool = False

override_environment_variables: Dict[str, str] | None = None

override_empirical_error: Dict[str, str] | None = None

override_algorithmic_error: Dict[str, str] | None = None

override_xref: List[XrefItem] | None = None

__init__(galaxy_url: str, galaxy_version: str, merge_history_metadata: bool = False, override_environment_variables: Dict[str, str] | None = None, override_empirical_error: Dict[str, str] | None = None, override_algorithmic_error: Dict[str, str] | None = None, override_xref: List[XrefItem] | None = None) → None

class galaxy.model.store.BcoModelExportStore(uri, export_options: BcoExportOptions, **kwds)

Bases: WorkflowInvocationOnlyExportStore

__init__(uri, export_options: BcoExportOptions, **kwds)

Parameters:

• export_directory – path to export directory. Will be created if it does not exist.

• app – Galaxy App or app-like object. Must be provided if for_edit and/or serialize_dataset_objects are True

• for_edit – Allow modifying existing HDA and dataset metadata during import.

• serialize_dataset_objects – If True will encode IDs using the host secret. Defaults for_edit.

• export_files – How files should be exported, can be ‘symlink’, ‘copy’ or None, in which case files will not be serialized.

• serialize_jobs – Include job data in model export. Not needed for set_metadata script.

app: StoreAppProtocol | None

file_sources: ConfiguredFileSources | None

included_datasets: Dict[DatasetInstance, Tuple[DatasetInstance, bool]]

dataset_implicit_conversions: Dict[DatasetInstance, ImplicitlyConvertedDatasetAssociation]

included_collections: List[DatasetCollection | HistoryDatasetCollectionAssociation]

included_libraries: List[Library]

included_library_folders: List[LibraryFolder]

included_invocations: List[WorkflowInvocation]

collection_datasets: Set[int]

collections_attrs: List[DatasetCollection | HistoryDatasetCollectionAssociation]

dataset_id_to_path: Dict[int, Tuple[str | None, str | None]]

job_output_dataset_associations: Dict[int, Dict[str, DatasetInstance]]

class galaxy.model.store.ROCrateModelExportStore(crate_directory: str | PathLike, **kwds)

Bases: DirectoryModelExportStore, WriteCrates

__init__(crate_directory: str | PathLike, **kwds) → None

Parameters:

• export_directory – path to export directory. Will be created if it does not exist.

• app – Galaxy App or app-like object. Must be provided if for_edit and/or serialize_dataset_objects are True

• for_edit – Allow modifying existing HDA and dataset metadata during import.

• serialize_dataset_objects – If True will encode IDs using the host secret. Defaults for_edit.

• export_files – How files should be exported, can be ‘symlink’, ‘copy’ or None, in which case files will not be serialized.

• serialize_jobs – Include job data in model export. Not needed for set_metadata script.

app: StoreAppProtocol | None

file_sources: ConfiguredFileSources | None

included_datasets: Dict[DatasetInstance, Tuple[DatasetInstance, bool]]

dataset_implicit_conversions: Dict[DatasetInstance, ImplicitlyConvertedDatasetAssociation]

included_collections: List[DatasetCollection | HistoryDatasetCollectionAssociation]

included_libraries: List[Library]

included_library_folders: List[LibraryFolder]

included_invocations: List[WorkflowInvocation]

collection_datasets: Set[int]

collections_attrs: List[DatasetCollection | HistoryDatasetCollectionAssociation]

dataset_id_to_path: Dict[int, Tuple[str | None, str | None]]

job_output_dataset_associations: Dict[int, Dict[str, DatasetInstance]]

class galaxy.model.store.ROCrateArchiveModelExportStore(uri: str | PathLike, **kwds)

Bases: DirectoryModelExportStore, WriteCrates

__init__(uri: str | PathLike, **kwds) → None

Parameters:

• export_directory – path to export directory. Will be created if it does not exist.

• app – Galaxy App or app-like object. Must be provided if for_edit and/or serialize_dataset_objects are True

• for_edit – Allow modifying existing HDA and dataset metadata during import.

• serialize_dataset_objects – If True will encode IDs using the host secret. Defaults for_edit.

• export_files – How files should be exported, can be ‘symlink’, ‘copy’ or None, in which case files will not be serialized.

• serialize_jobs – Include job data in model export. Not needed for set_metadata script.

out_file: str | PathLike

file_source_uri: str | PathLike | None

class galaxy.model.store.TarModelExportStore(uri: str | PathLike, gzip: bool = True, **kwds)

Bases: DirectoryModelExportStore

__init__(uri: str | PathLike, gzip: bool = True, **kwds) → None

Parameters:

• export_directory – path to export directory. Will be created if it does not exist.

• app – Galaxy App or app-like object. Must be provided if for_edit and/or serialize_dataset_objects are True

• for_edit – Allow modifying existing HDA and dataset metadata during import.

• serialize_dataset_objects – If True will encode IDs using the host secret. Defaults for_edit.

• export_files – How files should be exported, can be ‘symlink’, ‘copy’ or None, in which case files will not be serialized.

• serialize_jobs – Include job data in model export. Not needed for set_metadata script.

out_file: str | PathLike

file_source_uri: str | PathLike | None

class galaxy.model.store.BagDirectoryModelExportStore(out_directory: str, **kwds)

Bases: DirectoryModelExportStore

app: StoreAppProtocol | None

file_sources: ConfiguredFileSources | None

included_datasets: Dict[DatasetInstance, Tuple[DatasetInstance, bool]]

dataset_implicit_conversions: Dict[DatasetInstance, ImplicitlyConvertedDatasetAssociation]

included_collections: List[DatasetCollection | HistoryDatasetCollectionAssociation]

included_libraries: List[Library]

included_library_folders: List[LibraryFolder]

included_invocations: List[WorkflowInvocation]

collection_datasets: Set[int]

collections_attrs: List[DatasetCollection | HistoryDatasetCollectionAssociation]

dataset_id_to_path: Dict[int, Tuple[str | None, str | None]]

job_output_dataset_associations: Dict[int, Dict[str, DatasetInstance]]

__init__(out_directory: str, **kwds) → None

Parameters:

• export_directory – path to export directory. Will be created if it does not exist.

• app – Galaxy App or app-like object. Must be provided if for_edit and/or serialize_dataset_objects are True

• for_edit – Allow modifying existing HDA and dataset metadata during import.

• serialize_dataset_objects – If True will encode IDs using the host secret. Defaults for_edit.

• export_files – How files should be exported, can be ‘symlink’, ‘copy’ or None, in which case files will not be serialized.

• serialize_jobs – Include job data in model export. Not needed for set_metadata script.

class galaxy.model.store.BagArchiveModelExportStore(uri: str | PathLike, bag_archiver: str = 'tgz', **kwds)

Bases: BagDirectoryModelExportStore

__init__(uri: str | PathLike, bag_archiver: str = 'tgz', **kwds) → None

Parameters:

• export_directory – path to export directory. Will be created if it does not exist.

• app – Galaxy App or app-like object. Must be provided if for_edit and/or serialize_dataset_objects are True

• for_edit – Allow modifying existing HDA and dataset metadata during import.

• serialize_dataset_objects – If True will encode IDs using the host secret. Defaults for_edit.

• export_files – How files should be exported, can be ‘symlink’, ‘copy’ or None, in which case files will not be serialized.

• serialize_jobs – Include job data in model export. Not needed for set_metadata script.

file_source_uri: str | PathLike | None

galaxy.model.store.get_export_store_factory(app, download_format: str, export_files=None, bco_export_options: BcoExportOptions | None = None, user_context=None) → Callable[[str | PathLike], ModelExportStore]

galaxy.model.store.tar_export_directory(export_directory: str | PathLike, out_file: str | PathLike, gzip: bool) → None

galaxy.model.store.get_export_dataset_filename(name: str, ext: str, encoded_id: str, conversion_key: str | None) → str

Builds a filename for a dataset using its name an extension.

galaxy.model.store.get_export_dataset_extra_files_dir_name(encoded_id: str, conversion_key: str | None) → str

galaxy.model.store.imported_store_for_metadata(directory: str, object_store: ObjectStore | None = None) → BaseDirectoryImportModelStore

galaxy.model.store.source_to_import_store(source: str | dict, app: StoreAppProtocol, import_options: ImportOptions | None, model_store_format: ModelStoreFormat | None = None, user_context=None) → ModelImportStore

galaxy.model.store.payload_to_source_uri(payload) → str

galaxy.model.store.copy_dataset_instance_metadata_attributes(source: DatasetInstance, target: DatasetInstance) → None

Submodules

galaxy.model.store.build_objects module

galaxy.model.store.build_objects.main(argv=None)

galaxy.model.store.discover module

Utilities for discovering files to add to a model store.

Working with input “JSON” format used for Fetch API, galaxy.json imports, etc… High-level utilities in this file can be used during job output discovery or for persisting Galaxy model objects corresponding to files in other contexts.

exception galaxy.model.store.discover.MaxDiscoveredFilesExceededError

Bases: ValueError

class galaxy.model.store.discover.ModelPersistenceContext

Bases: object

Class for creating datasets while finding files.

This class implement the create_dataset method that takes care of populating metadata required for datasets and other potential model objects.

job_working_directory: str

max_discovered_files = inf

discovered_file_count: int

get_job() → Job | None

create_dataset(ext, designation, visible, dbkey, name, filename=None, extra_files=None, metadata_source_name=None, info=None, library_folder=None, link_data=False, primary_data=None, init_from=None, dataset_attributes=None, tag_list=None, sources=None, hashes=None, created_from_basename=None, final_job_state='ok', creating_job_id=None, output_name=None, storage_callbacks=None, purged=False)

finalize_storage(primary_data, dataset_attributes, extra_files, filename, link_data, output_name, init_from)

static set_datasets_metadata(datasets, datasets_attributes=None)

populate_collection_elements(collection, root_collection_builder, discovered_files, name=None, metadata_source_name=None, final_job_state='ok', change_datatype_actions=None)

add_tags_to_datasets(datasets, tag_lists)

update_object_store_with_datasets(datasets, paths, extra_files, output_name)

abstract property tag_handler

Return a galaxy.model.tags.TagHandler-like object for persisting tags.

abstract property user

If bound to a database, return the user the datasets should be created for.

Return None otherwise.

abstract property sa_session: scoped_session | None

If bound to a database, return the SQL Alchemy session.

Return None otherwise.

abstract property permission_provider: PermissionProvider

If bound to a database, return the SQL Alchemy session.

Return None otherwise.

get_implicit_collection_jobs_association_id() → str | None

No-op, no job context.

abstract property job: Job | None

Return associated job object if bound to a job finish context connected to a database.

override_object_store_id(output_name: str | None = None) → str | None

Object store ID to assign to a dataset before populating its contents.

abstract property metadata_source_provider: MetadataSourceProvider

Return associated MetadataSourceProvider object.

abstract property object_store: ObjectStore

Return object store to use for populating discovered dataset contents.

abstract property flush_per_n_datasets: int | None

property input_dbkey: str

abstract add_library_dataset_to_folder(library_folder, ld)

Add library dataset to persisted library folder.

abstract create_library_folder(parent_folder, name, description)

Create a library folder ready from supplied attributes for supplied parent.

abstract add_output_dataset_association(name, dataset)

If discovering outputs for a job, persist output dataset association.

abstract add_datasets_to_history(datasets, for_output_dataset=None)

Add datasets to the history this context points at.

job_id()

abstract persist_object(obj)

Add the target to the persistence layer.

persist_library_folder(library_folder: LibraryFolder) → None

Add library folder to sessionless export. Noop for session export.

abstract flush()

If database bound, flush the persisted objects to ensure IDs.

increment_discovered_file_count()

class galaxy.model.store.discover.PermissionProvider

Bases: object

Interface for working with permissions while importing datasets with ModelPersistenceContext.

property permissions

set_default_hda_permissions(primary_data)

abstract copy_dataset_permissions(init_from, primary_data)

Copy dataset permissions from supplied input dataset.

class galaxy.model.store.discover.UnusedPermissionProvider

Bases: PermissionProvider

copy_dataset_permissions(init_from, primary_data)

Throws NotImplementedError.

This should only be called as part of job output collection where there should be a session available to initialize this from.

class galaxy.model.store.discover.MetadataSourceProvider

Bases: object

Interface for working with fetching input dataset metadata with ModelPersistenceContext.

abstract get_metadata_source(input_name)

Get metadata for supplied input_name.

class galaxy.model.store.discover.UnusedMetadataSourceProvider

Bases: MetadataSourceProvider

get_metadata_source(input_name)

Throws NotImplementedError.

This should only be called as part of job output collection where one can actually collect metadata from inputs, this is unused in the context of SessionlessModelPersistenceContext.

class galaxy.model.store.discover.SessionlessModelPersistenceContext(object_store, export_store: ModelExportStore, working_directory: str)

Bases: ModelPersistenceContext

A variant of ModelPersistenceContext that persists to an export store instead of database directly.

__init__(object_store, export_store: ModelExportStore, working_directory: str) → None

discovered_file_count: int

job_working_directory: str

property tag_handler

Return a galaxy.model.tags.TagHandler-like object for persisting tags.

property sa_session

If bound to a database, return the SQL Alchemy session.

Return None otherwise.

property user

If bound to a database, return the user the datasets should be created for.

Return None otherwise.

property job

Return associated job object if bound to a job finish context connected to a database.

property permission_provider: UnusedPermissionProvider

If bound to a database, return the SQL Alchemy session.

Return None otherwise.

property metadata_source_provider: UnusedMetadataSourceProvider

Return associated MetadataSourceProvider object.

property object_store: ObjectStore

Return object store to use for populating discovered dataset contents.

property flush_per_n_datasets: int | None

add_tags_to_datasets(datasets, tag_lists)

add_library_dataset_to_folder(library_folder, ld)

Add library dataset to persisted library folder.

get_library_folder(destination)

get_hdca(object_id)

create_hdca(name, structure)

create_library_folder(parent_folder, name, description)

Create a library folder ready from supplied attributes for supplied parent.

persist_library_folder(library_folder: LibraryFolder) → None

Add library folder to sessionless export. Noop for session export.

add_datasets_to_history(datasets, for_output_dataset=None)

Add datasets to the history this context points at.

persist_object(obj)

No-op right now for the sessionless variant of this.

This works currently because either things are added to a target history with add_datasets_to_history or the parent LibraryFolder was added to the export store in persist_target_to_export_store.

flush()

No-op for the sessionless variant of this, no database to flush.

add_output_dataset_association(name, dataset)

No-op, no job context to persist this association for.

get_implicit_collection_jobs_association_id()

No-op, no job context.

galaxy.model.store.discover.persist_target_to_export_store(target_dict, export_store, object_store, work_directory)

galaxy.model.store.discover.persist_elements_to_hdca(model_persistence_context: ModelPersistenceContext, elements, hdca, collector=None)

galaxy.model.store.discover.persist_elements_to_folder(model_persistence_context, elements, library_folder)

galaxy.model.store.discover.persist_hdas(elements, model_persistence_context, final_job_state='ok')

galaxy.model.store.discover.get_required_item(from_dict, key, message)

galaxy.model.store.discover.validate_and_normalize_target(obj)

galaxy.model.store.discover.replace_request_syntax_sugar(obj)

class galaxy.model.store.discover.DiscoveredFile(path, collector, match)

Bases: tuple

path: str

Alias for field number 0

collector: DatasetCollector | ToolMetadataDatasetCollector | None

Alias for field number 1

match: JsonCollectedDatasetMatch

Alias for field number 2

discovered_state(element: Dict[str, Any], final_job_state='ok') → DiscoveredResultState

class galaxy.model.store.discover.DiscoveredResultState(info, state)

Bases: tuple

info: str | None

Alias for field number 0

state: str

Alias for field number 1

class galaxy.model.store.discover.DiscoveredDeferredFile(collector, match)

Bases: tuple

collector: DatasetCollector | ToolMetadataDatasetCollector | None

Alias for field number 0

match: JsonCollectedDatasetMatch

Alias for field number 1

discovered_state(element: Dict[str, Any], final_job_state='ok') → DiscoveredResultState

property path

galaxy.model.store.discover.discovered_file_for_element(dataset, model_persistence_context: ModelPersistenceContext, parent_identifiers=None, collector=None) → DiscoveredFile | DiscoveredDeferredFile | DiscoveredFileError

galaxy.model.store.discover.discover_target_directory(dir_name, job_working_directory)

class galaxy.model.store.discover.JsonCollectedDatasetMatch(as_dict, collector: DatasetCollector | ToolMetadataDatasetCollector | None, filename, path=None, parent_identifiers=None)

Bases: object

__init__(as_dict, collector: DatasetCollector | ToolMetadataDatasetCollector | None, filename, path=None, parent_identifiers=None)

property designation

property element_identifiers

property raw_element_identifiers

property name

Return name or None if not defined by the discovery pattern.

property dbkey: str

property ext: str

property visible: bool

property link_data

property tag_list

property object_id

property sources

property hashes

property created_from_basename

property extra_files

property effective_state

class galaxy.model.store.discover.RegexCollectedDatasetMatch(re_match, collector: DatasetCollector | ToolMetadataDatasetCollector | None, filename, path=None)

Bases: JsonCollectedDatasetMatch

__init__(re_match, collector: DatasetCollector | ToolMetadataDatasetCollector | None, filename, path=None)

class galaxy.model.store.discover.DiscoveredFileError(error_message, collector, match, path)

Bases: tuple

error_message: str

Alias for field number 0

collector: DatasetCollector | ToolMetadataDatasetCollector | None

Alias for field number 1

match: JsonCollectedDatasetMatch

Alias for field number 2

path: str | None

Alias for field number 3

discovered_state(element: Dict[str, Any], final_job_state='ok') → DiscoveredResultState

galaxy.model.store.load_objects module

galaxy.model.store.load_objects.main(argv=None)