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galaxy.model.tool_shed_install package¶

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: object

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.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.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, includes_datatypes=False, tool_shed_status=None, deleted=False, uninstalled=False, dist_to_shed=False, status=None, error_message=None)¶: Initialize self. See help(type(self)) for accurate signature.

id¶

create_time¶

tool_shed¶

name¶

description¶

owner¶

installed_changeset_revision¶

changeset_revision¶

ctx_rev¶

metadata¶

includes_datatypes¶

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 includes_workflows¶

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¶

required_repositories¶

table = Table('tool_shed_repository', MetaData(bind=None), 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', JSONType(), table=<tool_shed_repository>), Column('includes_datatypes', Boolean(), table=<tool_shed_repository>, default=ColumnDefault(False)), Column('tool_shed_status', JSONType(), 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)¶

tool_dependencies¶

tool_versions¶

update_time¶

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

Bases: object

__init__(tool_shed_repository_id=None, repository_dependency_id=None)¶: Initialize self. See help(type(self)) for accurate signature.

tool_shed_repository_id¶

repository_dependency_id¶

create_time¶

id¶

repository¶

repository_dependency¶

table = Table('repository_repository_dependency_association', MetaData(bind=None), 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)¶

update_time¶

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

Bases: object

__init__(tool_shed_repository_id=None)¶: Initialize self. See help(type(self)) for accurate signature.

tool_shed_repository_id¶

create_time¶

id¶

repository¶

table = Table('repository_dependency', MetaData(bind=None), 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)¶

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: object

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

class states(value)[source]¶

Bases: str, enum.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)¶: Initialize self. See help(type(self)) for accurate signature.

tool_shed_repository_id¶

name¶

version¶

type¶

status¶

error_message¶

property can_install¶

property can_uninstall¶

property can_update¶

get_env_shell_file_path(app)[source]¶

property in_error_state¶

installation_directory(app)[source]¶

property is_installed¶

create_time¶

id¶

table = Table('tool_dependency', MetaData(bind=None), 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¶

update_time¶

class galaxy.model.tool_shed_install.ToolVersion(id=None, create_time=None, tool_id=None, tool_shed_repository=None)[source]¶

Bases: galaxy.util.dictifiable.Dictifiable, object

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

__init__(id=None, create_time=None, tool_id=None, tool_shed_repository=None)¶: Initialize self. See help(type(self)) for accurate signature.

id¶

create_time¶

tool_id¶

tool_shed_repository¶

to_dict(view='element')[source]¶: Return item dictionary.

child_tool_association¶

parent_tool_association¶

table = Table('tool_version', MetaData(bind=None), 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)¶

tool_shed_repository_id¶

update_time¶

class galaxy.model.tool_shed_install.ToolVersionAssociation(id=None, tool_id=None, parent_id=None)[source]¶

Bases: object

__init__(id=None, tool_id=None, parent_id=None)¶: Initialize self. See help(type(self)) for accurate signature.

id¶

tool_id¶

parent_id¶

table = Table('tool_version_association', MetaData(bind=None), 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)¶

class galaxy.model.tool_shed_install.MigrateTools(repository_id=None, repository_path=None, version=None)[source]¶

Bases: object

__init__(repository_id=None, repository_path=None, version=None)[source]¶: Initialize self. See help(type(self)) for accurate signature.

table = Table('migrate_tools', MetaData(bind=None), Column('repository_id', TrimmedString(length=255), table=<migrate_tools>), Column('repository_path', TEXT(), table=<migrate_tools>), Column('version', Integer(), table=<migrate_tools>), schema=None)¶

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

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