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galaxy.model.tool_shed_install package¶

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

Bases: 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.

metadata = MetaData()¶

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

class galaxy.model.tool_shed_install.RepositoryDependency(tool_shed_repository_id=None)[source]¶

Bases: galaxy.model.tool_shed_install.Base, object

__init__(tool_shed_repository_id=None)¶

create_time¶

id¶

repository¶

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)¶

tool_shed_repository_id¶

update_time¶

class galaxy.model.tool_shed_install.RepositoryRepositoryDependencyAssociation(tool_shed_repository_id=None, repository_dependency_id=None)[source]¶

Bases: galaxy.model.tool_shed_install.Base, object

__init__(tool_shed_repository_id=None, repository_dependency_id=None)¶

create_time¶

id¶

repository¶

repository_dependency¶

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)¶

tool_shed_repository_id¶

update_time¶

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: galaxy.model.tool_shed_install.Base, object

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

can_install¶

can_uninstall¶

can_update¶

create_time¶

error_message¶

get_env_shell_file_path(app)[source]¶

id¶

in_error_state¶

installation_directory(app)[source]¶

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

is_installed¶

name¶

class states[source]¶

Bases: str, enum.Enum

An enumeration.

ERROR = 'error'¶

INSTALLING = 'running'¶

OK = 'ok'¶

UNINSTALLED = 'deleted_new'¶

WARNING = 'queued'¶

status¶

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)¶

tool_shed_repository¶

tool_shed_repository_id¶

type¶

update_time¶

version¶

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, includes_datatypes=False, tool_shed_status=None, deleted=False, uninstalled=False, dist_to_shed=False, status=None, error_message=None)[source]¶

Bases: galaxy.model.tool_shed_install.Base, object

__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, includes_datatypes=False, tool_shed_status=None, deleted=False, uninstalled=False, dist_to_shed=False, status=None, error_message=None)¶

as_dict(value_mapper=None)[source]¶

can_deactivate¶

can_install¶

can_reinstall_or_activate¶

can_reset_metadata¶

can_uninstall¶

changeset_revision¶

create_time¶

ctx_rev¶

deleted¶

description¶

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']¶

dist_to_shed¶

error_message¶

get_sharable_url(app)[source]¶

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]¶

has_readme_files¶

has_repository_dependencies¶

has_repository_dependencies_only_if_compiling_contained_td¶

id¶

in_error_state¶

includes_data_managers¶

includes_datatypes¶

includes_tool_dependencies¶

includes_tools¶

includes_tools_for_display_in_tool_panel¶

includes_workflows¶

class installation_status[source]¶

Bases: str, enum.Enum

An enumeration.

CLONING = 'Cloning'¶

DEACTIVATED = 'Deactivated'¶

ERROR = 'Error'¶

INSTALLED = 'Installed'¶

INSTALLING_REPOSITORY_DEPENDENCIES = 'Installing repository dependencies'¶

INSTALLING_TOOL_DEPENDENCIES = 'Installing tool dependencies'¶

LOADING_PROPRIETARY_DATATYPES = 'Loading proprietary datatypes'¶

NEW = 'New'¶

SETTING_TOOL_VERSIONS = 'Setting tool versions'¶

UNINSTALLED = 'Uninstalled'¶

installed_changeset_revision¶

installed_repository_dependencies¶: Return the repository’s repository dependencies that are currently installed.

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

is_deactivated_or_installed¶

is_deprecated_in_tool_shed¶

is_installed¶

is_latest_installable_revision¶

is_new¶

metadata_¶

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

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

name¶

owner¶

repo_files_directory(app)[source]¶

repo_path(app)[source]¶

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

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

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

repository_dependencies_with_installation_errors¶: Return the repository’s repository dependencies that have installation errors.

required_repositories¶

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).

revision_update_available¶

shed_config_filename¶

class states[source]¶

Bases: str, enum.Enum

An enumeration.

ERROR = 'error'¶

INSTALLING = 'running'¶

OK = 'ok'¶

UNINSTALLED = 'deleted_new'¶

WARNING = 'queued'¶

status¶

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)¶

to_dict(view='collection', value_mapper=None)[source]¶

tool_dependencies¶

tool_dependencies_being_installed¶

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

tool_dependencies_missing_or_being_installed¶

tool_dependencies_with_installation_errors¶

tool_shed¶

tool_shed_path_name¶

tool_shed_status¶

tool_versions¶

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.

uninstalled¶

uninstalled_repository_dependencies¶: Return the repository’s repository dependencies that have been uninstalled.

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

update_time¶

upgrade_available¶

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

Bases: galaxy.model.tool_shed_install.Base, galaxy.util.dictifiable.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.

child_tool_association¶

create_time¶

dict_element_visible_keys = ['id', 'tool_shed_repository']¶

id¶

parent_tool_association¶

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)¶

to_dict(view='element')[source]¶

tool_id¶

tool_shed_repository¶

tool_shed_repository_id¶

update_time¶

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

Bases: galaxy.model.tool_shed_install.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.

id¶

parent_id¶

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)¶

tool_id¶

galaxy.model.tool_shed_install.now()¶: Return a new datetime representing UTC day and time.

Subpackages¶

galaxy.model.tool_shed_install.migrate package
- Submodules
- galaxy.model.tool_shed_install.migrate.check module

Submodules¶

galaxy.model.tool_shed_install.mapping module¶

galaxy.model.tool_shed_install.mapping.init(url, engine_options=None, create_tables=False)[source]¶: Connect mappings to the database