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tool_shed.webapp.model package¶
- tool_shed.webapp.model.now()¶
Return a new datetime representing UTC day and time.
- class tool_shed.webapp.model.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 tool_shed.webapp.model.APIKeys(**kwargs)[source]¶
Bases:
Base
- id¶
- create_time¶
- user_id¶
- key¶
- user¶
- deleted¶
- __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 tool_shed.webapp.model.User(email=None, password=None)[source]¶
Bases:
Base
,Dictifiable
- id¶
- create_time¶
- update_time¶
- username¶
- active_repositories¶
- galaxy_sessions¶
- api_keys¶
- reset_tokens¶
- groups¶
- dict_collection_visible_keys = ['id', 'username']¶
- dict_element_visible_keys = ['id', 'username']¶
- bootstrap_admin_user = False¶
- roles¶
- non_private_roles¶
- __init__(email=None, password=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.
- email¶
- password¶
- external¶
- deleted¶
- purged¶
- new_repo_alert¶
- property nice_total_disk_usage¶
- property total_disk_usage¶
- class tool_shed.webapp.model.PasswordResetToken(user, token=None)[source]¶
Bases:
Base
- user_id¶
- __init__(user, token=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.
- token¶
- user¶
- expiration_time¶
- class tool_shed.webapp.model.Group(name=None)[source]¶
Bases:
Base
,Dictifiable
- id¶
- create_time¶
- update_time¶
- roles¶
- users¶
- dict_collection_visible_keys = ['id', 'name']¶
- dict_element_visible_keys = ['id', 'name']¶
- __init__(name=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.
- name¶
- deleted¶
- class tool_shed.webapp.model.Role(name=None, description=None, type='system', deleted=False)[source]¶
Bases:
Base
,Dictifiable
- id¶
- create_time¶
- update_time¶
- repositories¶
- groups¶
- users¶
- dict_collection_visible_keys = ['id', 'name']¶
- dict_element_visible_keys = ['id', 'name', 'description', 'type']¶
- private_id = None¶
- types = <galaxy.util.bunch.Bunch object>¶
- __init__(name=None, description=None, type='system', deleted=False)¶
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.
- name¶
- description¶
- type¶
- deleted¶
- property is_repository_admin_role¶
- class tool_shed.webapp.model.UserGroupAssociation(user, group)[source]¶
Bases:
Base
- id¶
- user_id¶
- group_id¶
- create_time¶
- update_time¶
- __init__(user, group)¶
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.
- user¶
- group¶
- class tool_shed.webapp.model.UserRoleAssociation(user, role)[source]¶
Bases:
Base
- id¶
- user_id¶
- role_id¶
- create_time¶
- update_time¶
- __init__(user, role)¶
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.
- user¶
- role¶
- class tool_shed.webapp.model.GroupRoleAssociation(group, role)[source]¶
Bases:
Base
- id¶
- group_id¶
- role_id¶
- create_time¶
- update_time¶
- __init__(group, role)¶
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.
- group¶
- role¶
- class tool_shed.webapp.model.RepositoryRoleAssociation(repository, role)[source]¶
Bases:
Base
- id¶
- repository_id¶
- role_id¶
- create_time¶
- update_time¶
- __init__(repository, role)¶
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.
- repository¶
- role¶
- class tool_shed.webapp.model.GalaxySession(is_valid=False, **kwd)[source]¶
Bases:
Base
- id¶
- create_time¶
- update_time¶
- user_id¶
- remote_host¶
- remote_addr¶
- referer¶
- session_key¶
- prev_session_id¶
- user¶
- __init__(is_valid=False, **kwd)¶
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.
- is_valid¶
- last_action¶
- class tool_shed.webapp.model.Repository(private=False, times_downloaded=0, deprecated=False, **kwd)[source]¶
Bases:
Base
,Dictifiable
- id¶
- create_time¶
- update_time¶
- type¶
- remote_repository_url¶
- homepage_url¶
- description¶
- long_description¶
- user_id¶
- deleted¶
- email_alerts¶
- categories¶
- ratings¶
- user¶
- downloadable_revisions¶
- metadata_revisions¶
- roles¶
- dict_collection_visible_keys = ['id', 'name', 'type', 'remote_repository_url', 'homepage_url', 'description', 'user_id', 'private', 'deleted', 'times_downloaded', 'deprecated', 'create_time']¶
- dict_element_visible_keys = ['id', 'name', 'type', 'remote_repository_url', 'homepage_url', 'description', 'long_description', 'user_id', 'private', 'deleted', 'times_downloaded', 'deprecated', 'create_time']¶
- file_states = <galaxy.util.bunch.Bunch object>¶
- __init__(private=False, times_downloaded=0, deprecated=False, **kwd)¶
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.
- private¶
- times_downloaded¶
- deprecated¶
- name¶
- property hg_repo¶
- property admin_role¶
- class tool_shed.webapp.model.ItemRatingAssociation(id=None, user=None, item=None, rating=0, comment='')[source]¶
Bases:
object
- class tool_shed.webapp.model.RepositoryRatingAssociation(**kwargs)[source]¶
Bases:
Base
,ItemRatingAssociation
- id¶
- create_time¶
- update_time¶
- repository_id¶
- user_id¶
- rating¶
- comment¶
- repository¶
- user¶
- __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 tool_shed.webapp.model.Category(deleted=False, **kwd)[source]¶
Bases:
Base
,Dictifiable
- id¶
- create_time¶
- update_time¶
- name¶
- description¶
- repositories¶
- dict_collection_visible_keys = ['id', 'name', 'description', 'deleted']¶
- dict_element_visible_keys = ['id', 'name', 'description', 'deleted']¶
- __init__(deleted=False, **kwd)¶
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.
- deleted¶
- class tool_shed.webapp.model.RepositoryCategoryAssociation(repository=None, category=None)[source]¶
Bases:
Base
- id¶
- repository_id¶
- category_id¶
- __init__(repository=None, category=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.
- repository¶
- category¶
- class tool_shed.webapp.model.Tag(**kwargs)[source]¶
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.
- id¶
- type¶
- parent_id¶
- name¶
- children¶
- parent¶
- class tool_shed.webapp.model.RepositoryMetadata(id=None, repository_id=None, numeric_revision=None, changeset_revision=None, metadata=None, tool_versions=None, malicious=False, downloadable=False, missing_test_components=None, tools_functionally_correct=False, test_install_error=False, has_repository_dependencies=False, includes_datatypes=False, includes_tools=False, includes_tool_dependencies=False, includes_workflows=False)[source]¶
Bases:
Dictifiable
- create_time¶
- repository¶
- update_time¶
- table = Table('repository_metadata', MetaData(), Column('id', Integer(), table=<repository_metadata>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<repository_metadata>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<repository_metadata>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('repository_id', Integer(), ForeignKey('repository.id'), table=<repository_metadata>), Column('changeset_revision', TrimmedString(length=255), table=<repository_metadata>), Column('numeric_revision', Integer(), table=<repository_metadata>), Column('metadata', MutableJSONType(), table=<repository_metadata>), Column('tool_versions', MutableJSONType(), table=<repository_metadata>), Column('malicious', Boolean(), table=<repository_metadata>, default=ColumnDefault(False)), Column('downloadable', Boolean(), table=<repository_metadata>, default=ColumnDefault(True)), Column('missing_test_components', Boolean(), table=<repository_metadata>, default=ColumnDefault(False)), Column('has_repository_dependencies', Boolean(), table=<repository_metadata>, default=ColumnDefault(False)), Column('includes_datatypes', Boolean(), table=<repository_metadata>, default=ColumnDefault(False)), Column('includes_tools', Boolean(), table=<repository_metadata>, default=ColumnDefault(False)), Column('includes_tool_dependencies', Boolean(), table=<repository_metadata>, default=ColumnDefault(False)), Column('includes_workflows', Boolean(), table=<repository_metadata>, default=ColumnDefault(False)), schema=None)¶
- dict_collection_visible_keys = ['id', 'repository_id', 'numeric_revision', 'changeset_revision', 'malicious', 'downloadable', 'missing_test_components', 'has_repository_dependencies', 'includes_datatypes', 'includes_tools', 'includes_tool_dependencies', 'includes_tools_for_display_in_tool_panel', 'includes_workflows']¶
- dict_element_visible_keys = ['id', 'repository_id', 'numeric_revision', 'changeset_revision', 'malicious', 'downloadable', 'missing_test_components', 'has_repository_dependencies', 'includes_datatypes', 'includes_tools', 'includes_tool_dependencies', 'includes_tools_for_display_in_tool_panel', 'includes_workflows', 'repository_dependencies']¶
- __init__(id=None, repository_id=None, numeric_revision=None, changeset_revision=None, metadata=None, tool_versions=None, malicious=False, downloadable=False, missing_test_components=None, tools_functionally_correct=False, test_install_error=False, has_repository_dependencies=False, includes_datatypes=False, includes_tools=False, includes_tool_dependencies=False, includes_workflows=False)¶
- id¶
- repository_id¶
- numeric_revision¶
- changeset_revision¶
- metadata¶
- tool_versions¶
- malicious¶
- downloadable¶
- missing_test_components¶
- has_repository_dependencies¶
- includes_datatypes¶
- includes_tools¶
- includes_tool_dependencies¶
- includes_workflows¶
- property includes_tools_for_display_in_tool_panel¶
- property repository_dependencies¶
- tool_shed.webapp.model.sort_by_attr(seq, attr)[source]¶
Sort the sequence of objects by object’s attribute Arguments: seq - the list or any sequence (including immutable one) of objects to sort. attr - the name of attribute to sort by
Subpackages¶
- tool_shed.webapp.model.migrate package
- Subpackages
- tool_shed.webapp.model.migrate.versions package
- Submodules
- tool_shed.webapp.model.migrate.versions.0001_initial_tables module
- tool_shed.webapp.model.migrate.versions.0002_add_tool_suite_column module
- tool_shed.webapp.model.migrate.versions.0003_review_and_review_association_tables module
- tool_shed.webapp.model.migrate.versions.0004_repository_tables module
- tool_shed.webapp.model.migrate.versions.0005_drop_tool_related_tables module
- tool_shed.webapp.model.migrate.versions.0006_add_email_alerts_column module
- tool_shed.webapp.model.migrate.versions.0007_add_long_description_times_downloaded_columns module
- tool_shed.webapp.model.migrate.versions.0008_add_repository_metadata_table module
- tool_shed.webapp.model.migrate.versions.0009_add_malicious_column module
- tool_shed.webapp.model.migrate.versions.0010_add_new_repo_alert_column module
- tool_shed.webapp.model.migrate.versions.0011_add_tool_versions_column module
- tool_shed.webapp.model.migrate.versions.0012_add_downloadable_column module
- tool_shed.webapp.model.migrate.versions.0013_add_review_tables module
- tool_shed.webapp.model.migrate.versions.0014_add_deprecated_column module
- tool_shed.webapp.model.migrate.versions.0015_add_api_keys_table module
- tool_shed.webapp.model.migrate.versions.0016_add_do_not_test_tools_functionally_correct_errors_columns module
- tool_shed.webapp.model.migrate.versions.0017_add_galaxy_utility_columns_to_repository_metadata_table module
- tool_shed.webapp.model.migrate.versions.0018_add_repository_metadata_flag_columns module
- tool_shed.webapp.model.migrate.versions.0019_add_skip_tool_test_table_and_test_install_error_column module
- tool_shed.webapp.model.migrate.versions.0020_add_repository_type_column module
- tool_shed.webapp.model.migrate.versions.0021_change_repository_type_value module
- tool_shed.webapp.model.migrate.versions.0022_add_repository_admin_roles module
- tool_shed.webapp.model.migrate.versions.0023_add_repository_url_and_hompeage_url module
- tool_shed.webapp.model.migrate.versions.0024_password_reset module
- tool_shed.webapp.model.migrate.versions.0025_session_timeout module
- tool_shed.webapp.model.migrate.versions.0026_add_numeric_revision_column module
- tool_shed.webapp.model.migrate.versions package
- Submodules
- tool_shed.webapp.model.migrate.check module
- Subpackages
Submodules¶
tool_shed.webapp.model.mapping module¶
Details of how the data model objects are mapped onto the relational database are encapsulated here.
- class tool_shed.webapp.model.mapping.ToolShedModelMapping(model_modules, engine)[source]¶
Bases:
SharedModelMapping
- security_agent: CommunityRBACAgent¶
- shed_counter: ShedCounter¶