galaxy.webapps.tool_shed.model package

class galaxy.webapps.tool_shed.model.APIKeys[source]

Bases: object

__init__()

x.__init__(…) initializes x; see help(type(x)) for signature

create_time
id
key
table = Table('api_keys', MetaData(bind=None), Column('id', Integer(), table=<api_keys>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<api_keys>, default=ColumnDefault(<function utcnow>)), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<api_keys>), Column('key', TrimmedString(length=32), table=<api_keys>), schema=None)
user_id
class galaxy.webapps.tool_shed.model.User(email=None, password=None)[source]

Bases: galaxy.util.dictifiable.Dictifiable

dict_collection_visible_keys = ['id', 'username']
dict_element_visible_keys = ['id', 'username']
__init__(email=None, password=None)
email
password
external
deleted
purged
username
new_repo_alert
all_roles()[source]
check_password(cleartext)[source]

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

get_disk_usage(nice_size=False)[source]
nice_total_disk_usage
set_disk_usage(bytes)[source]
total_disk_usage
set_password_cleartext(cleartext)[source]

Set ‘self.password’ to the digest of ‘cleartext’.

active_repositories
api_keys
create_time
galaxy_sessions
id
table = Table('galaxy_user', MetaData(bind=None), Column('id', Integer(), table=<galaxy_user>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<galaxy_user>, default=ColumnDefault(<function utcnow>)), Column('update_time', DateTime(), table=<galaxy_user>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function utcnow>)), Column('email', TrimmedString(length=255), table=<galaxy_user>, nullable=False), Column('username', String(length=255), table=<galaxy_user>), Column('password', TrimmedString(length=40), table=<galaxy_user>, nullable=False), Column('external', Boolean(), table=<galaxy_user>, default=ColumnDefault(False)), Column('new_repo_alert', Boolean(), table=<galaxy_user>, default=ColumnDefault(False)), Column('deleted', Boolean(), table=<galaxy_user>, default=ColumnDefault(False)), Column('purged', Boolean(), table=<galaxy_user>, default=ColumnDefault(False)), schema=None)
update_time
class galaxy.webapps.tool_shed.model.PasswordResetToken(user, token=None)[source]

Bases: object

__init__(user, token=None)
token
user
expiration_time
table = Table('password_reset_token', MetaData(bind=None), Column('token', String(length=32), table=<password_reset_token>, primary_key=True, nullable=False), Column('expiration_time', DateTime(), table=<password_reset_token>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<password_reset_token>), schema=None)
user_id
class galaxy.webapps.tool_shed.model.Group(name=None)[source]

Bases: galaxy.util.dictifiable.Dictifiable

dict_collection_visible_keys = ['id', 'name']
dict_element_visible_keys = ['id', 'name']
__init__(name=None)
name
deleted
create_time
id
table = Table('galaxy_group', MetaData(bind=None), Column('id', Integer(), table=<galaxy_group>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<galaxy_group>, default=ColumnDefault(<function utcnow>)), Column('update_time', DateTime(), table=<galaxy_group>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function utcnow>)), Column('name', String(length=255), table=<galaxy_group>), Column('deleted', Boolean(), table=<galaxy_group>, default=ColumnDefault(False)), schema=None)
update_time
users
class galaxy.webapps.tool_shed.model.Role(name='', description='', type='system', deleted=False)[source]

Bases: galaxy.util.dictifiable.Dictifiable

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='', description='', type='system', deleted=False)
name
description
type
deleted
is_repository_admin_role
create_time
groups
id
repositories
table = Table('role', MetaData(bind=None), Column('id', Integer(), table=<role>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<role>, default=ColumnDefault(<function utcnow>)), Column('update_time', DateTime(), table=<role>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function utcnow>)), Column('name', String(length=255), table=<role>), Column('description', TEXT(), table=<role>), Column('type', String(length=40), table=<role>), Column('deleted', Boolean(), table=<role>, default=ColumnDefault(False)), schema=None)
update_time
users
class galaxy.webapps.tool_shed.model.UserGroupAssociation(user, group)[source]

Bases: object

__init__(user, group)
user
group
create_time
group_id
id
table = Table('user_group_association', MetaData(bind=None), Column('id', Integer(), table=<user_group_association>, primary_key=True, nullable=False), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<user_group_association>), Column('group_id', Integer(), ForeignKey('galaxy_group.id'), table=<user_group_association>), Column('create_time', DateTime(), table=<user_group_association>, default=ColumnDefault(<function utcnow>)), Column('update_time', DateTime(), table=<user_group_association>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function utcnow>)), schema=None)
update_time
user_id
class galaxy.webapps.tool_shed.model.UserRoleAssociation(user, role)[source]

Bases: object

__init__(user, role)
user
role
create_time
id
non_private_roles
role_id
table = Table('user_role_association', MetaData(bind=None), Column('id', Integer(), table=<user_role_association>, primary_key=True, nullable=False), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<user_role_association>), Column('role_id', Integer(), ForeignKey('role.id'), table=<user_role_association>), Column('create_time', DateTime(), table=<user_role_association>, default=ColumnDefault(<function utcnow>)), Column('update_time', DateTime(), table=<user_role_association>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function utcnow>)), schema=None)
update_time
user_id
class galaxy.webapps.tool_shed.model.GroupRoleAssociation(group, role)[source]

Bases: object

__init__(group, role)
group
role
create_time
group_id
id
role_id
table = Table('group_role_association', MetaData(bind=None), Column('id', Integer(), table=<group_role_association>, primary_key=True, nullable=False), Column('group_id', Integer(), ForeignKey('galaxy_group.id'), table=<group_role_association>), Column('role_id', Integer(), ForeignKey('role.id'), table=<group_role_association>), Column('create_time', DateTime(), table=<group_role_association>, default=ColumnDefault(<function utcnow>)), Column('update_time', DateTime(), table=<group_role_association>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function utcnow>)), schema=None)
update_time
class galaxy.webapps.tool_shed.model.RepositoryRoleAssociation(repository, role)[source]

Bases: object

__init__(repository, role)
repository
role
create_time
id
repository_id
role_id
table = Table('repository_role_association', MetaData(bind=None), Column('id', Integer(), table=<repository_role_association>, primary_key=True, nullable=False), Column('repository_id', Integer(), ForeignKey('repository.id'), table=<repository_role_association>), Column('role_id', Integer(), ForeignKey('role.id'), table=<repository_role_association>), Column('create_time', DateTime(), table=<repository_role_association>, default=ColumnDefault(<function utcnow>)), Column('update_time', DateTime(), table=<repository_role_association>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function utcnow>)), schema=None)
update_time
class galaxy.webapps.tool_shed.model.GalaxySession(id=None, user=None, remote_host=None, remote_addr=None, referer=None, current_history=None, session_key=None, is_valid=False, prev_session_id=None, last_action=None)[source]

Bases: object

__init__(id=None, user=None, remote_host=None, remote_addr=None, referer=None, current_history=None, session_key=None, is_valid=False, prev_session_id=None, last_action=None)
id
user
remote_host
remote_addr
referer
session_key
is_valid
prev_session_id
last_action
create_time
table = Table('galaxy_session', MetaData(bind=None), Column('id', Integer(), table=<galaxy_session>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<galaxy_session>, default=ColumnDefault(<function utcnow>)), Column('update_time', DateTime(), table=<galaxy_session>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function utcnow>)), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<galaxy_session>), Column('remote_host', String(length=255), table=<galaxy_session>), Column('remote_addr', String(length=255), table=<galaxy_session>), Column('referer', TEXT(), table=<galaxy_session>), Column('session_key', TrimmedString(length=255), table=<galaxy_session>), Column('is_valid', Boolean(), table=<galaxy_session>, default=ColumnDefault(False)), Column('prev_session_id', Integer(), table=<galaxy_session>), Column('last_action', DateTime(), table=<galaxy_session>), schema=None)
update_time
user_id
class galaxy.webapps.tool_shed.model.Repository(id=None, name=None, type=None, remote_repository_url=None, homepage_url=None, description=None, long_description=None, user_id=None, private=False, deleted=None, email_alerts=None, times_downloaded=0, deprecated=False)[source]

Bases: galaxy.util.dictifiable.Dictifiable

dict_collection_visible_keys = ['id', 'name', 'type', 'remote_repository_url', 'homepage_url', 'description', 'user_id', 'private', 'deleted', 'times_downloaded', 'deprecated']
dict_element_visible_keys = ['id', 'name', 'type', 'remote_repository_url', 'homepage_url', 'description', 'long_description', 'user_id', 'private', 'deleted', 'times_downloaded', 'deprecated']
file_states = <galaxy.util.bunch.Bunch object>
__init__(id=None, name=None, type=None, remote_repository_url=None, homepage_url=None, description=None, long_description=None, user_id=None, private=False, deleted=None, email_alerts=None, times_downloaded=0, deprecated=False)
id
name
type
remote_repository_url
homepage_url
description
long_description
user_id
private
deleted
email_alerts
times_downloaded
deprecated
admin_role
allow_push(app)[source]
can_change_type(app)[source]
can_change_type_to(app, new_type_label)[source]
get_changesets_for_setting_metadata(app)[source]
get_repository_dependencies(app, changeset, toolshed_url)[source]
get_type_class(app)[source]
get_tool_dependencies(app, changeset_revision)[source]
installable_revisions(app, sort_revisions=True)[source]
is_new(app)[source]
repo_path(app)[source]
revision(app)[source]
set_allow_push(app, usernames, remove_auth='')[source]
tip(app)[source]
to_dict(view='collection', value_mapper=None)[source]
categories
create_time
downloadable_revisions
metadata_revisions
ratings
reviewers
reviews
roles
table = Table('repository', MetaData(bind=None), Column('id', Integer(), table=<repository>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<repository>, default=ColumnDefault(<function utcnow>)), Column('update_time', DateTime(), table=<repository>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function utcnow>)), Column('name', TrimmedString(length=255), table=<repository>), Column('type', TrimmedString(length=255), table=<repository>), Column('remote_repository_url', TrimmedString(length=255), table=<repository>), Column('homepage_url', TrimmedString(length=255), table=<repository>), Column('description', TEXT(), table=<repository>), Column('long_description', TEXT(), table=<repository>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<repository>), Column('private', Boolean(), table=<repository>, default=ColumnDefault(False)), Column('deleted', Boolean(), table=<repository>, default=ColumnDefault(False)), Column('email_alerts', JSONType(), table=<repository>), Column('times_downloaded', Integer(), table=<repository>), Column('deprecated', Boolean(), table=<repository>, default=ColumnDefault(False)), schema=None)
update_time
user
class galaxy.webapps.tool_shed.model.RepositoryMetadata(id=None, repository_id=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

dict_collection_visible_keys = ['id', 'repository_id', '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', '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, 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
changeset_revision
metadata
tool_versions
malicious
downloadable
missing_test_components
has_repository_dependencies
includes_datatypes
includes_tools
includes_tool_dependencies
includes_workflows
includes_tools_for_display_in_tool_panel
repository_dependencies
create_time
repository
reviews
table = Table('repository_metadata', MetaData(bind=None), Column('id', Integer(), table=<repository_metadata>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<repository_metadata>, default=ColumnDefault(<function utcnow>)), Column('update_time', DateTime(), table=<repository_metadata>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function utcnow>)), Column('repository_id', Integer(), ForeignKey('repository.id'), table=<repository_metadata>), Column('changeset_revision', TrimmedString(length=255), table=<repository_metadata>), Column('metadata', JSONType(), table=<repository_metadata>), Column('tool_versions', JSONType(), 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)
update_time
class galaxy.webapps.tool_shed.model.RepositoryReview(repository_id=None, changeset_revision=None, user_id=None, rating=None, deleted=False)[source]

Bases: galaxy.util.dictifiable.Dictifiable

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']
approved_states = <galaxy.util.bunch.Bunch object>
__init__(repository_id=None, changeset_revision=None, user_id=None, rating=None, deleted=False)
repository_id
changeset_revision
user_id
rating
deleted
approved
component_reviews
create_time
id
private_component_reviews
repository
repository_metadata
table = Table('repository_review', MetaData(bind=None), Column('id', Integer(), table=<repository_review>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<repository_review>, default=ColumnDefault(<function utcnow>)), Column('update_time', DateTime(), table=<repository_review>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function utcnow>)), Column('repository_id', Integer(), ForeignKey('repository.id'), table=<repository_review>), Column('changeset_revision', TrimmedString(length=255), table=<repository_review>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<repository_review>, nullable=False), Column('approved', TrimmedString(length=255), table=<repository_review>), Column('rating', Integer(), table=<repository_review>), Column('deleted', Boolean(), table=<repository_review>, default=ColumnDefault(False)), schema=None)
update_time
user
class galaxy.webapps.tool_shed.model.ComponentReview(repository_review_id=None, component_id=None, comment=None, private=False, approved=False, rating=None, deleted=False)[source]

Bases: galaxy.util.dictifiable.Dictifiable

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']
approved_states = <galaxy.util.bunch.Bunch object>
__init__(repository_review_id=None, component_id=None, comment=None, private=False, approved=False, rating=None, deleted=False)
repository_review_id
component_id
comment
private
approved
rating
deleted
component
create_time
id
repository_review
table = Table('component_review', MetaData(bind=None), Column('id', Integer(), table=<component_review>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<component_review>, default=ColumnDefault(<function utcnow>)), Column('update_time', DateTime(), table=<component_review>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function utcnow>)), Column('repository_review_id', Integer(), ForeignKey('repository_review.id'), table=<component_review>), Column('component_id', Integer(), ForeignKey('component.id'), table=<component_review>), Column('comment', TEXT(), table=<component_review>), Column('private', Boolean(), table=<component_review>, default=ColumnDefault(False)), Column('approved', TrimmedString(length=255), table=<component_review>), Column('rating', Integer(), table=<component_review>), Column('deleted', Boolean(), table=<component_review>, default=ColumnDefault(False)), schema=None)
update_time
class galaxy.webapps.tool_shed.model.Component(name=None, description=None)[source]

Bases: object

__init__(name=None, description=None)
name
description
id
table = Table('component', MetaData(bind=None), Column('id', Integer(), table=<component>, primary_key=True, nullable=False), Column('name', TrimmedString(length=255), table=<component>), Column('description', TEXT(), table=<component>), schema=None)
class galaxy.webapps.tool_shed.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 galaxy.webapps.tool_shed.model.RepositoryRatingAssociation(id=None, user=None, item=None, rating=0, comment='')[source]

Bases: galaxy.webapps.tool_shed.model.ItemRatingAssociation

set_item(repository)[source]
__init__(id=None, user=None, item=None, rating=0, comment='')
comment
create_time
id
rating
repository
repository_id
table = Table('repository_rating_association', MetaData(bind=None), Column('id', Integer(), table=<repository_rating_association>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<repository_rating_association>, default=ColumnDefault(<function utcnow>)), Column('update_time', DateTime(), table=<repository_rating_association>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function utcnow>)), Column('repository_id', Integer(), ForeignKey('repository.id'), table=<repository_rating_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<repository_rating_association>), Column('rating', Integer(), table=<repository_rating_association>), Column('comment', TEXT(), table=<repository_rating_association>), schema=None)
update_time
user
user_id
class galaxy.webapps.tool_shed.model.Category(name=None, description=None, deleted=False)[source]

Bases: galaxy.util.dictifiable.Dictifiable

dict_collection_visible_keys = ['id', 'name', 'description', 'deleted']
dict_element_visible_keys = ['id', 'name', 'description', 'deleted']
__init__(name=None, description=None, deleted=False)
name
description
deleted
create_time
id
repositories
table = Table('category', MetaData(bind=None), Column('id', Integer(), table=<category>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<category>, default=ColumnDefault(<function utcnow>)), Column('update_time', DateTime(), table=<category>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function utcnow>)), Column('name', TrimmedString(length=255), table=<category>), Column('description', TEXT(), table=<category>), Column('deleted', Boolean(), table=<category>, default=ColumnDefault(False)), schema=None)
update_time
class galaxy.webapps.tool_shed.model.RepositoryCategoryAssociation(repository=None, category=None)[source]

Bases: object

__init__(repository=None, category=None)
repository
category
category_id
id
repository_id
table = Table('repository_category_association', MetaData(bind=None), Column('id', Integer(), table=<repository_category_association>, primary_key=True, nullable=False), Column('repository_id', Integer(), ForeignKey('repository.id'), table=<repository_category_association>), Column('category_id', Integer(), ForeignKey('category.id'), table=<repository_category_association>), schema=None)
class galaxy.webapps.tool_shed.model.Tag(id=None, type=None, parent_id=None, name=None)[source]

Bases: object

__init__(id=None, type=None, parent_id=None, name=None)
id
type
parent_id
name
children
table = Table('tag', MetaData(bind=None), Column('id', Integer(), table=<tag>, primary_key=True, nullable=False), Column('type', Integer(), table=<tag>), Column('parent_id', Integer(), ForeignKey('tag.id'), table=<tag>), Column('name', TrimmedString(length=255), table=<tag>), schema=None)
class galaxy.webapps.tool_shed.model.ItemTagAssociation(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)[source]

Bases: object

__init__(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)[source]
class galaxy.webapps.tool_shed.model.PostJobAction(action_type, workflow_step, output_name=None, action_arguments=None)[source]

Bases: object

__init__(action_type, workflow_step, output_name=None, action_arguments=None)[source]
class galaxy.webapps.tool_shed.model.StoredWorkflowAnnotationAssociation[source]

Bases: object

class galaxy.webapps.tool_shed.model.WorkflowStepAnnotationAssociation[source]

Bases: object

class galaxy.webapps.tool_shed.model.Workflow[source]

Bases: object

__init__()[source]
class galaxy.webapps.tool_shed.model.WorkflowStep[source]

Bases: object

__init__()[source]
get_or_add_input(input_name)[source]
input_connections
class galaxy.webapps.tool_shed.model.WorkflowStepInput[source]

Bases: object

__init__()[source]
class galaxy.webapps.tool_shed.model.WorkflowStepConnection[source]

Bases: object

__init__()[source]
galaxy.webapps.tool_shed.model.now()

Return a new datetime representing UTC day and time.

galaxy.webapps.tool_shed.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

Submodules

galaxy.webapps.tool_shed.model.mapping module

Details of how the data model objects are mapped onto the relational database are encapsulated here.

galaxy.webapps.tool_shed.model.mapping.init(file_path, url, engine_options={}, create_tables=False)[source]

Connect mappings to the database

galaxy.webapps.tool_shed.model.mapping.now()

Return a new datetime representing UTC day and time.