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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)[source]

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)[source]

Bases: Base, object

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)[source]

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)[source]

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=None)[source]
property can_install
property can_reset_metadata
property can_uninstall
property can_deactivate
property can_reinstall_or_activate
get_sharable_url(app)[source]
property shed_config_filename
get_shed_config_dict(app)[source]

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)[source]
guess_shed_config(app)[source]
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)[source]
repo_path(app)[source]
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=None)[source]
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)[source]

Bases: Base, object

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)[source]

Bases: Base, object

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)[source]

Bases: Base, object

id
create_time
update_time
tool_shed_repository
installation_status = <galaxy.util.bunch.Bunch object>
class states(value)[source]

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)[source]
property is_installed
class galaxy.model.tool_shed_install.ToolVersion(**kwargs)[source]

Bases: Base, Dictifiable, object

__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')[source]

Return item dictionary.

class galaxy.model.tool_shed_install.ToolVersionAssociation(**kwargs)[source]

Bases: Base, object

__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)[source]
galaxy.model.tool_shed_install.mapping.create_database_objects(engine)[source]
galaxy.model.tool_shed_install.mapping.configure_model_mapping(engine)[source]