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galaxy.model.tool_shed_install package

galaxy.model.tool_shed_install.now()

Return a new datetime representing UTC day and time.

class galaxy.model.tool_shed_install.Base(**kwargs)

Bases: object

registry = <sqlalchemy.orm.decl_api.registry object>

metadata = MetaData()

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class galaxy.model.tool_shed_install.ToolShedRepository(id=None, create_time=None, tool_shed=None, name=None, description=None, owner=None, installed_changeset_revision=None, changeset_revision=None, ctx_rev=None, metadata_=None, tool_shed_status=None, deleted=False, uninstalled=False, dist_to_shed=False, status=None, error_message=None)

Bases: Base

update_time

includes_datatypes

tool_versions

tool_dependencies

required_repositories

dict_collection_visible_keys = ['id', 'tool_shed', 'name', 'owner', 'installed_changeset_revision', 'changeset_revision', 'ctx_rev', 'includes_datatypes', 'tool_shed_status', 'deleted', 'uninstalled', 'dist_to_shed', 'status', 'error_message', 'description']

dict_element_visible_keys = ['id', 'tool_shed', 'name', 'owner', 'installed_changeset_revision', 'changeset_revision', 'ctx_rev', 'includes_datatypes', 'tool_shed_status', 'deleted', 'uninstalled', 'dist_to_shed', 'status', 'error_message', 'description']

class installation_status(value)

Bases: str, Enum

An enumeration.

NEW = 'New'

CLONING = 'Cloning'

SETTING_TOOL_VERSIONS = 'Setting tool versions'

INSTALLING_REPOSITORY_DEPENDENCIES = 'Installing repository dependencies'

INSTALLING_TOOL_DEPENDENCIES = 'Installing tool dependencies'

LOADING_PROPRIETARY_DATATYPES = 'Loading proprietary datatypes'

INSTALLED = 'Installed'

DEACTIVATED = 'Deactivated'

ERROR = 'Error'

UNINSTALLED = 'Uninstalled'

class states(value)

Bases: str, Enum

An enumeration.

INSTALLING = 'running'

OK = 'ok'

WARNING = 'queued'

ERROR = 'error'

UNINSTALLED = 'deleted_new'

__init__(id=None, create_time=None, tool_shed=None, name=None, description=None, owner=None, installed_changeset_revision=None, changeset_revision=None, ctx_rev=None, metadata_=None, tool_shed_status=None, deleted=False, uninstalled=False, dist_to_shed=False, status=None, error_message=None)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

id

create_time

tool_shed

name

description

owner

installed_changeset_revision

changeset_revision

ctx_rev

metadata_

tool_shed_status

deleted

uninstalled

dist_to_shed

status

error_message

as_dict(value_mapper: Optional[Dict[str, Callable]] = None) → Dict[str, Any]

property can_install

property can_reset_metadata

property can_uninstall

property can_deactivate

property can_reinstall_or_activate

get_sharable_url(app)

property shed_config_filename

get_shed_config_dict(app)

Return the in-memory version of the shed_tool_conf file, which is stored in the config_elems entry in the shed_tool_conf_dict.

get_tool_relative_path(app)

guess_shed_config(app)

property has_readme_files

property has_repository_dependencies

property has_repository_dependencies_only_if_compiling_contained_td

property in_error_state

property includes_data_managers

property includes_tools

property includes_tools_for_display_in_tool_panel

property includes_tool_dependencies

property installed_repository_dependencies

Return the repository’s repository dependencies that are currently installed.

property installed_tool_dependencies

Return the repository’s tool dependencies that are currently installed, but possibly in an error state.

property is_deprecated_in_tool_shed

property is_deactivated_or_installed

property is_installed

property is_latest_installable_revision

property is_new

property missing_repository_dependencies

Return the repository’s repository dependencies that are not currently installed, and may not ever have been installed.

property missing_tool_dependencies

Return the repository’s tool dependencies that are not currently installed, and may not ever have been installed.

repo_files_directory(app)

repo_path(app)

property repository_dependencies

Return all of this repository’s repository dependencies, ignoring their attributes like prior_installation_required and only_if_compiling_contained_td.

property repository_dependencies_being_installed

Return the repository’s repository dependencies that are currently being installed.

property repository_dependencies_missing_or_being_installed

Return the repository’s repository dependencies that are either missing or currently being installed.

property repository_dependencies_with_installation_errors

Return the repository’s repository dependencies that have installation errors.

property requires_prior_installation_of

Return a list of repository dependency tuples like (tool_shed, name, owner, changeset_revision, prior_installation_required) for this repository’s repository dependencies where prior_installation_required is True. By definition, repository dependencies are required to be installed in order for this repository to function correctly. However, those repository dependencies that are defined for this repository with prior_installation_required set to True place them in a special category in that the required repositories must be installed before this repository is installed. Among other things, this enables these “special” repository dependencies to include information that enables the successful installation of this repository. This method is not used during the initial installation of this repository, but only after it has been installed (metadata must be set for this repository in order for this method to be useful).

property revision_update_available

to_dict(view='collection', value_mapper: Optional[Dict[str, Callable]] = None) → Dict[str, Any]

property tool_dependencies_being_installed

property tool_dependencies_installed_or_in_error

Return the repository’s tool dependencies that are currently installed, but possibly in an error state.

property tool_dependencies_missing_or_being_installed

property tool_dependencies_with_installation_errors

property tool_shed_path_name

property tuples_of_repository_dependencies_needed_for_compiling_td

Return tuples defining this repository’s repository dependencies that are necessary only for compiling this repository’s tool dependencies.

property uninstalled_repository_dependencies

Return the repository’s repository dependencies that have been uninstalled.

property uninstalled_tool_dependencies

Return the repository’s tool dependencies that have been uninstalled.

property upgrade_available

table = Table('tool_shed_repository', MetaData(), Column('id', Integer(), table=<tool_shed_repository>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<tool_shed_repository>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<tool_shed_repository>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('tool_shed', TrimmedString(length=255), table=<tool_shed_repository>), Column('name', TrimmedString(length=255), table=<tool_shed_repository>), Column('description', TEXT(), table=<tool_shed_repository>), Column('owner', TrimmedString(length=255), table=<tool_shed_repository>), Column('installed_changeset_revision', TrimmedString(length=255), table=<tool_shed_repository>), Column('changeset_revision', TrimmedString(length=255), table=<tool_shed_repository>), Column('ctx_rev', TrimmedString(length=10), table=<tool_shed_repository>), Column('metadata', MutableJSONType(), table=<tool_shed_repository>), Column('includes_datatypes', Boolean(), table=<tool_shed_repository>, default=ColumnDefault(False)), Column('tool_shed_status', MutableJSONType(), table=<tool_shed_repository>), Column('deleted', Boolean(), table=<tool_shed_repository>, default=ColumnDefault(False)), Column('uninstalled', Boolean(), table=<tool_shed_repository>, default=ColumnDefault(False)), Column('dist_to_shed', Boolean(), table=<tool_shed_repository>, default=ColumnDefault(False)), Column('status', TrimmedString(length=255), table=<tool_shed_repository>), Column('error_message', TEXT(), table=<tool_shed_repository>), schema=None)

class galaxy.model.tool_shed_install.RepositoryRepositoryDependencyAssociation(tool_shed_repository_id=None, repository_dependency_id=None)

Bases: Base

id

create_time

update_time

repository

repository_dependency

__init__(tool_shed_repository_id=None, repository_dependency_id=None)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

tool_shed_repository_id

repository_dependency_id

table = Table('repository_repository_dependency_association', MetaData(), Column('id', Integer(), table=<repository_repository_dependency_association>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<repository_repository_dependency_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<repository_repository_dependency_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('tool_shed_repository_id', Integer(), ForeignKey('tool_shed_repository.id'), table=<repository_repository_dependency_association>), Column('repository_dependency_id', Integer(), ForeignKey('repository_dependency.id'), table=<repository_repository_dependency_association>), schema=None)

class galaxy.model.tool_shed_install.RepositoryDependency(tool_shed_repository_id=None)

Bases: Base

id

create_time

update_time

repository

__init__(tool_shed_repository_id=None)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

tool_shed_repository_id

table = Table('repository_dependency', MetaData(), Column('id', Integer(), table=<repository_dependency>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<repository_dependency>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<repository_dependency>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('tool_shed_repository_id', Integer(), ForeignKey('tool_shed_repository.id'), table=<repository_dependency>, nullable=False), schema=None)

class galaxy.model.tool_shed_install.ToolDependency(tool_shed_repository_id=None, name=None, version=None, type=None, status=None, error_message=None)

Bases: Base

id

create_time

update_time

tool_shed_repository

installation_status = <galaxy.util.bunch.Bunch object>

class states(value)

Bases: str, Enum

An enumeration.

INSTALLING = 'running'

OK = 'ok'

WARNING = 'queued'

ERROR = 'error'

UNINSTALLED = 'deleted_new'

__init__(tool_shed_repository_id=None, name=None, version=None, type=None, status=None, error_message=None)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

tool_shed_repository_id

name

table = Table('tool_dependency', MetaData(), Column('id', Integer(), table=<tool_dependency>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<tool_dependency>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<tool_dependency>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('tool_shed_repository_id', Integer(), ForeignKey('tool_shed_repository.id'), table=<tool_dependency>, nullable=False), Column('name', TrimmedString(length=255), table=<tool_dependency>), Column('version', TEXT(), table=<tool_dependency>), Column('type', TrimmedString(length=40), table=<tool_dependency>), Column('status', TrimmedString(length=255), table=<tool_dependency>, nullable=False), Column('error_message', TEXT(), table=<tool_dependency>), schema=None)

version

type

status

error_message

property can_install

property can_uninstall

property can_update

property in_error_state

installation_directory(app)

property is_installed

class galaxy.model.tool_shed_install.ToolVersion(**kwargs)

Bases: Base, Dictifiable

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

table = Table('tool_version', MetaData(), Column('id', Integer(), table=<tool_version>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<tool_version>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<tool_version>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('tool_id', String(length=255), table=<tool_version>), Column('tool_shed_repository_id', Integer(), ForeignKey('tool_shed_repository.id'), table=<tool_version>), schema=None)

id

create_time

update_time

tool_id

tool_shed_repository_id

parent_tool_association

child_tool_association

tool_shed_repository

dict_element_visible_keys = ['id', 'tool_shed_repository']

to_dict(view='element')

Return item dictionary.

class galaxy.model.tool_shed_install.ToolVersionAssociation(**kwargs)

Bases: Base

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

table = Table('tool_version_association', MetaData(), Column('id', Integer(), table=<tool_version_association>, primary_key=True, nullable=False), Column('tool_id', Integer(), ForeignKey('tool_version.id'), table=<tool_version_association>, nullable=False), Column('parent_id', Integer(), ForeignKey('tool_version.id'), table=<tool_version_association>, nullable=False), schema=None)

id

tool_id

parent_id

Submodules

galaxy.model.tool_shed_install.mapping module

galaxy.model.tool_shed_install.mapping.init(url, engine_options=None, create_tables=False)

galaxy.model.tool_shed_install.mapping.create_database_objects(engine)

galaxy.model.tool_shed_install.mapping.configure_model_mapping(engine)