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tool_shed.webapp.model package

class tool_shed.webapp.model.APIKeys(**kwargs)[source]

Bases: tool_shed.webapp.model.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.

create_time
id
key
user
user_id
class tool_shed.webapp.model.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 tool_shed.webapp.model.Category(deleted=False, **kwd)[source]

Bases: tool_shed.webapp.model.Base, galaxy.util.dictifiable.Dictifiable, object

__init__(deleted=False, **kwd)
create_time
deleted
description
dict_collection_visible_keys = ['id', 'name', 'description', 'deleted']
dict_element_visible_keys = ['id', 'name', 'description', 'deleted']
id
name
repositories
update_time
class tool_shed.webapp.model.Component(**kwargs)[source]

Bases: tool_shed.webapp.model.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.

description
id
name
class tool_shed.webapp.model.ComponentReview(private=False, approved=False, deleted=False, **kwd)[source]

Bases: tool_shed.webapp.model.Base, galaxy.util.dictifiable.Dictifiable, object

__init__(private=False, approved=False, deleted=False, **kwd)
approved
approved_states = <galaxy.util.bunch.Bunch object>
comment
component
component_id
create_time
deleted
dict_collection_visible_keys = ['id', 'repository_review_id', 'component_id', 'private', 'approved', 'rating', 'deleted']
dict_element_visible_keys = ['id', 'repository_review_id', 'component_id', 'private', 'approved', 'rating', 'deleted']
id
private
rating
repository_review
repository_review_id
update_time
class tool_shed.webapp.model.GalaxySession(is_valid=False, **kwd)[source]

Bases: tool_shed.webapp.model.Base, object

__init__(is_valid=False, **kwd)
create_time
id
is_valid
last_action
prev_session_id
referer
remote_addr
remote_host
session_key
update_time
user
user_id
class tool_shed.webapp.model.Group(name=None)[source]

Bases: tool_shed.webapp.model.Base, galaxy.util.dictifiable.Dictifiable, object

__init__(name=None)
create_time
deleted
dict_collection_visible_keys = ['id', 'name']
dict_element_visible_keys = ['id', 'name']
id
name
roles
update_time
users
class tool_shed.webapp.model.GroupRoleAssociation(group, role)[source]

Bases: tool_shed.webapp.model.Base, object

__init__(group, role)
create_time
group
group_id
id
role
role_id
update_time
class tool_shed.webapp.model.ItemRatingAssociation(id=None, user=None, item=None, rating=0, comment='')[source]

Bases: object

__init__(id=None, user=None, item=None, rating=0, comment='')[source]
set_item(item)[source]

Set association’s item.

class tool_shed.webapp.model.PasswordResetToken(user, token=None)[source]

Bases: tool_shed.webapp.model.Base, object

__init__(user, token=None)
expiration_time
token
user
user_id
class tool_shed.webapp.model.Repository(private=False, times_downloaded=0, deprecated=False, **kwd)[source]

Bases: tool_shed.webapp.model.Base, galaxy.util.dictifiable.Dictifiable, object

__init__(private=False, times_downloaded=0, deprecated=False, **kwd)
admin_role
allow_push()[source]
can_change_type()[source]
can_change_type_to(app, new_type_label)[source]
categories
create_time
deleted
deprecated
description
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']
downloadable_revisions
email_alerts
file_states = <galaxy.util.bunch.Bunch object>
get_changesets_for_setting_metadata(app)[source]
get_repository_dependencies(app, changeset, toolshed_url)[source]
get_tool_dependencies(app, changeset_revision)[source]
get_type_class(app)[source]
hg_repo
homepage_url
id
installable_revisions(app, sort_revisions=True)[source]
is_new()[source]
long_description
metadata_revisions
name
private
ratings
remote_repository_url
repo_path(app=None)[source]
reviewers
reviews
revision()[source]
roles
set_allow_push(usernames, remove_auth='')[source]
times_downloaded
tip()[source]
to_dict(view='collection', value_mapper=None)[source]
type
update_time
user
user_id
class tool_shed.webapp.model.RepositoryCategoryAssociation(repository=None, category=None)[source]

Bases: tool_shed.webapp.model.Base, object

__init__(repository=None, category=None)
category
category_id
id
repository
repository_id
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: galaxy.util.dictifiable.Dictifiable, object

__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)
changeset_revision
create_time
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']
downloadable
has_repository_dependencies
id
includes_datatypes
includes_tool_dependencies
includes_tools
includes_tools_for_display_in_tool_panel
includes_workflows
malicious
metadata
missing_test_components
numeric_revision
repository
repository_dependencies
repository_id
reviews
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)
tool_versions
update_time
class tool_shed.webapp.model.RepositoryRatingAssociation(**kwargs)[source]

Bases: tool_shed.webapp.model.Base, tool_shed.webapp.model.ItemRatingAssociation, 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.

comment
create_time
id
rating
repository
repository_id
set_item(repository)[source]
update_time
user
user_id
class tool_shed.webapp.model.RepositoryReview(deleted=False, **kwd)[source]

Bases: tool_shed.webapp.model.Base, galaxy.util.dictifiable.Dictifiable, object

__init__(deleted=False, **kwd)
approved
approved_states = <galaxy.util.bunch.Bunch object>
changeset_revision
component_reviews
create_time
deleted
dict_collection_visible_keys = ['id', 'repository_id', 'changeset_revision', 'user_id', 'rating', 'deleted']
dict_element_visible_keys = ['id', 'repository_id', 'changeset_revision', 'user_id', 'rating', 'deleted']
id
private_component_reviews
rating
repository
repository_id
repository_metadata
update_time
user
user_id
class tool_shed.webapp.model.RepositoryRoleAssociation(repository, role)[source]

Bases: tool_shed.webapp.model.Base, object

__init__(repository, role)
create_time
id
repository
repository_id
role
role_id
update_time
class tool_shed.webapp.model.Role(name=None, description=None, type='system', deleted=False)[source]

Bases: tool_shed.webapp.model.Base, galaxy.util.dictifiable.Dictifiable, object

__init__(name=None, description=None, type='system', deleted=False)
create_time
deleted
description
dict_collection_visible_keys = ['id', 'name']
dict_element_visible_keys = ['id', 'name', 'description', 'type']
groups
id
is_repository_admin_role
name
private_id = None
repositories
type
types = <galaxy.util.bunch.Bunch object>
update_time
users
class tool_shed.webapp.model.Tag(**kwargs)[source]

Bases: tool_shed.webapp.model.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.

children
id
name
parent
parent_id
type
class tool_shed.webapp.model.User(email=None, password=None)[source]

Bases: tool_shed.webapp.model.Base, galaxy.util.dictifiable.Dictifiable, object

__init__(email=None, password=None)
active_repositories
all_roles()[source]
api_keys
bootstrap_admin_user = False
check_password(cleartext)[source]

Check if ‘cleartext’ matches ‘self.password’ when hashed.

create_time
deleted
dict_collection_visible_keys = ['id', 'username']
dict_element_visible_keys = ['id', 'username']
email
external
galaxy_sessions
get_disk_usage(nice_size=False)[source]
groups
id
new_repo_alert
nice_total_disk_usage
non_private_roles
password
purged
repository_reviews
reset_tokens
roles
set_disk_usage(bytes)[source]
set_password_cleartext(cleartext)[source]
total_disk_usage
update_time
username
class tool_shed.webapp.model.UserGroupAssociation(user, group)[source]

Bases: tool_shed.webapp.model.Base, object

__init__(user, group)
create_time
group
group_id
id
update_time
user
user_id
class tool_shed.webapp.model.UserRoleAssociation(user, role)[source]

Bases: tool_shed.webapp.model.Base, object

__init__(user, role)
create_time
id
role
role_id
update_time
user
user_id
tool_shed.webapp.model.now()

Return a new datetime representing UTC day and time.

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

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: galaxy.model.base.SharedModelMapping

tool_shed.webapp.model.mapping.init(file_path, url, engine_options=None, create_tables=False) → tool_shed.webapp.model.mapping.ToolShedModelMapping[source]

Connect mappings to the database