model Package

model Package

class galaxy.webapps.tool_shed.model.APIKeys

Bases: object

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 <lambda> at 0x7f92e159e8c0>)), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<api_keys>), Column('key', TrimmedString(), table=<api_keys>), schema=None)

user_id

class galaxy.webapps.tool_shed.model.Category(name=None, description=None, deleted=False)

Bases: object, galaxy.model.item_attrs.Dictifiable

create_time

deleted

description

dict_collection_visible_keys = ('id', 'name', 'description', 'deleted')

dict_element_visible_keys = ('id', 'name', 'description', 'deleted')

id

name

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 <lambda> at 0x7f92e14e0398>)), Column('update_time', DateTime(), table=<category>, onupdate=ColumnDefault(<function <lambda> at 0x7f92e14e0488>), default=ColumnDefault(<function <lambda> at 0x7f92e14e0410>)), Column('name', TrimmedString(), 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.Component(name=None, description=None)

Bases: object

description

id

name

table = Table('component', MetaData(bind=None), Column('id', Integer(), table=<component>, primary_key=True, nullable=False), Column('name', TrimmedString(), table=<component>), Column('description', TEXT(), table=<component>), schema=None)

class galaxy.webapps.tool_shed.model.ComponentReview(repository_review_id=None, component_id=None, comment=None, private=False, approved=False, rating=None, deleted=False)

Bases: object, galaxy.model.item_attrs.Dictifiable

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

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 <lambda> at 0x7f92e14e0050>)), Column('update_time', DateTime(), table=<component_review>, onupdate=ColumnDefault(<function <lambda> at 0x7f92e14e0230>), default=ColumnDefault(<function <lambda> at 0x7f92e14e01b8>)), 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(), 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.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)

Bases: object

create_time

id

is_valid

prev_session_id

referer

remote_addr

remote_host

session_key

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 <lambda> at 0x7f92e153d668>)), Column('update_time', DateTime(), table=<galaxy_session>, onupdate=ColumnDefault(<function <lambda> at 0x7f92e153d758>), default=ColumnDefault(<function <lambda> at 0x7f92e153d6e0>)), 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(), table=<galaxy_session>), Column('is_valid', Boolean(), table=<galaxy_session>, default=ColumnDefault(False)), Column('prev_session_id', Integer(), table=<galaxy_session>), schema=None)

update_time

user

user_id

class galaxy.webapps.tool_shed.model.Group(name=None)

Bases: object, galaxy.model.item_attrs.Dictifiable

create_time

deleted

dict_collection_visible_keys = ('id', 'name')

dict_element_visible_keys = ('id', 'name')

id

name

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 <lambda> at 0x7f92e159eaa0>)), Column('update_time', DateTime(), table=<galaxy_group>, onupdate=ColumnDefault(<function <lambda> at 0x7f92e159ec80>), default=ColumnDefault(<function <lambda> at 0x7f92e159ec08>)), 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.GroupRoleAssociation(group, role)

Bases: object

create_time

group

group_id

id

role

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 <lambda> at 0x7f92e153d2a8>)), Column('update_time', DateTime(), table=<group_role_association>, onupdate=ColumnDefault(<function <lambda> at 0x7f92e153d488>), default=ColumnDefault(<function <lambda> at 0x7f92e153d410>)), schema=None)

update_time

class galaxy.webapps.tool_shed.model.ItemRatingAssociation(id=None, user=None, item=None, rating=0, comment='')

Bases: object

set_item(item)

Set association’s item.

class galaxy.webapps.tool_shed.model.ItemTagAssociation(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)

Bases: object

class galaxy.webapps.tool_shed.model.PostJobAction(action_type, workflow_step, output_name=None, action_arguments=None)

Bases: object

class galaxy.webapps.tool_shed.model.Repository(id=None, name=None, type=None, description=None, long_description=None, user_id=None, private=False, deleted=None, email_alerts=None, times_downloaded=0, deprecated=False)

Bases: object, galaxy.model.item_attrs.Dictifiable

admin_role

allow_push(app)

can_change_type(app)

can_change_type_to(app, new_type_label)

categories

create_time

deleted

deprecated

description

dict_collection_visible_keys = ('id', 'name', 'type', 'description', 'user_id', 'private', 'deleted', 'times_downloaded', 'deprecated')

dict_element_visible_keys = ('id', 'name', 'type', 'description', 'long_description', 'user_id', 'private', 'deleted', 'times_downloaded', 'deprecated')

downloadable_revisions

email_alerts

file_states = <galaxy.util.bunch.Bunch object>

get_changesets_for_setting_metadata(app)

get_type_class(app)

id

is_new(app)

long_description

metadata_revisions

name

private

ratings

repo_path(app)

reviewers

reviews

revision(app)

roles

set_allow_push(app, usernames, remove_auth='')

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 <lambda> at 0x7f92e153d7d0>)), Column('update_time', DateTime(), table=<repository>, onupdate=ColumnDefault(<function <lambda> at 0x7f92e153da28>), default=ColumnDefault(<function <lambda> at 0x7f92e153d9b0>)), Column('name', TrimmedString(), table=<repository>), Column('type', TrimmedString(), 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)

times_downloaded

tip(app)

to_dict(view='collection', value_mapper=None)

type

update_time

user

user_id

class galaxy.webapps.tool_shed.model.RepositoryCategoryAssociation(repository=None, category=None)

Bases: object

category

category_id

id

repository

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.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, do_not_test=False, test_install_error=False, time_last_tested=None, tool_test_results=None, has_repository_dependencies=False, includes_datatypes=False, includes_tools=False, includes_tool_dependencies=False, includes_workflows=False)

Bases: object, galaxy.model.item_attrs.Dictifiable

changeset_revision

create_time

dict_collection_visible_keys = ('id', 'repository_id', 'changeset_revision', 'malicious', 'downloadable', 'missing_test_components', 'tools_functionally_correct', 'do_not_test', 'test_install_error', 'has_repository_dependencies', 'includes_datatypes', 'includes_tools', 'includes_tool_dependencies', 'includes_tools_for_display_in_tool_panel', 'includes_workflows', 'time_last_tested')

dict_element_visible_keys = ('id', 'repository_id', 'changeset_revision', 'malicious', 'downloadable', 'missing_test_components', 'tools_functionally_correct', 'do_not_test', 'test_install_error', 'time_last_tested', 'tool_test_results', 'has_repository_dependencies', 'includes_datatypes', 'includes_tools', 'includes_tool_dependencies', 'includes_tools_for_display_in_tool_panel', 'includes_workflows')

do_not_test

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

repository

repository_id

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 <lambda> at 0x7f92e153daa0>)), Column('update_time', DateTime(), table=<repository_metadata>, onupdate=ColumnDefault(<function <lambda> at 0x7f92e153db90>), default=ColumnDefault(<function <lambda> at 0x7f92e153db18>)), Column('repository_id', Integer(), ForeignKey('repository.id'), table=<repository_metadata>), Column('changeset_revision', TrimmedString(), 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('tools_functionally_correct', Boolean(), table=<repository_metadata>, default=ColumnDefault(False)), Column('do_not_test', Boolean(), table=<repository_metadata>, default=ColumnDefault(False)), Column('test_install_error', Boolean(), table=<repository_metadata>, default=ColumnDefault(False)), Column('time_last_tested', DateTime(), table=<repository_metadata>), Column('missing_test_components', Boolean(), table=<repository_metadata>, default=ColumnDefault(False)), Column('tool_test_results', JSONType(), table=<repository_metadata>), 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)

test_install_error

time_last_tested

tool_test_results

tool_versions

tools_functionally_correct

update_time

class galaxy.webapps.tool_shed.model.RepositoryRatingAssociation(id=None, user=None, item=None, rating=0, comment='')

Bases: galaxy.webapps.tool_shed.model.ItemRatingAssociation

comment

create_time

id

rating

repository

repository_id

set_item(repository)

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 <lambda> at 0x7f92e1578500>)), Column('update_time', DateTime(), table=<repository_rating_association>, onupdate=ColumnDefault(<function <lambda> at 0x7f92e14e02a8>), default=ColumnDefault(<function <lambda> at 0x7f92e1578488>)), 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.RepositoryReview(repository_id=None, changeset_revision=None, user_id=None, rating=None, deleted=False)

Bases: object, galaxy.model.item_attrs.Dictifiable

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

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 <lambda> at 0x7f92e153de60>)), Column('update_time', DateTime(), table=<repository_review>, onupdate=ColumnDefault(<function <lambda> at 0x7f92e153df50>), default=ColumnDefault(<function <lambda> at 0x7f92e153ded8>)), Column('repository_id', Integer(), ForeignKey('repository.id'), table=<repository_review>), Column('changeset_revision', TrimmedString(), table=<repository_review>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<repository_review>, nullable=False), Column('approved', TrimmedString(), table=<repository_review>), Column('rating', Integer(), table=<repository_review>), Column('deleted', Boolean(), table=<repository_review>, default=ColumnDefault(False)), schema=None)

update_time

user

user_id

class galaxy.webapps.tool_shed.model.RepositoryRoleAssociation(repository, role)

Bases: object

create_time

id

repository

repository_id

role

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 <lambda> at 0x7f92e153d500>)), Column('update_time', DateTime(), table=<repository_role_association>, onupdate=ColumnDefault(<function <lambda> at 0x7f92e153d5f0>), default=ColumnDefault(<function <lambda> at 0x7f92e153d578>)), schema=None)

update_time

class galaxy.webapps.tool_shed.model.Role(name='', description='', type='system', deleted=False)

Bases: object, galaxy.model.item_attrs.Dictifiable

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

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 <lambda> at 0x7f92e159ede8>)), Column('update_time', DateTime(), table=<role>, onupdate=ColumnDefault(<function <lambda> at 0x7f92e159eed8>), default=ColumnDefault(<function <lambda> at 0x7f92e159ee60>)), 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)

type

types = <galaxy.util.bunch.Bunch object>

update_time

users

class galaxy.webapps.tool_shed.model.SkipToolTest(id=None, repository_metadata_id=None, initial_changeset_revision=None, comment=None)

Bases: object, galaxy.model.item_attrs.Dictifiable

as_dict(value_mapper=None)

comment

create_time

dict_collection_visible_keys = ('id', 'repository_metadata_id', 'initial_changeset_revision')

dict_element_visible_keys = ('id', 'repository_metadata_id', 'initial_changeset_revision', 'comment')

id

initial_changeset_revision

repository_metadata_id

repository_revision

table = Table('skip_tool_test', MetaData(bind=None), Column('id', Integer(), table=<skip_tool_test>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<skip_tool_test>, default=ColumnDefault(<function <lambda> at 0x7f92e153dc08>)), Column('update_time', DateTime(), table=<skip_tool_test>, onupdate=ColumnDefault(<function <lambda> at 0x7f92e153dde8>), default=ColumnDefault(<function <lambda> at 0x7f92e153dd70>)), Column('repository_metadata_id', Integer(), ForeignKey('repository_metadata.id'), table=<skip_tool_test>), Column('initial_changeset_revision', TrimmedString(), table=<skip_tool_test>), Column('comment', TEXT(), table=<skip_tool_test>), schema=None)

update_time

class galaxy.webapps.tool_shed.model.StoredWorkflowAnnotationAssociation

Bases: object

class galaxy.webapps.tool_shed.model.Tag(id=None, type=None, parent_id=None, name=None)

Bases: object

children

id

name

parent_id

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(), table=<tag>), schema=None)

type

class galaxy.webapps.tool_shed.model.User(email=None, password=None)

Bases: object, galaxy.model.item_attrs.Dictifiable

active_repositories

all_roles()

api_keys

check_password(cleartext)

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)

id

new_repo_alert

nice_total_disk_usage

password

purged

set_disk_usage(bytes)

set_password_cleartext(cleartext)

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

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 <lambda> at 0x7f92e159e938>)), Column('update_time', DateTime(), table=<galaxy_user>, onupdate=ColumnDefault(<function <lambda> at 0x7f92e159ea28>), default=ColumnDefault(<function <lambda> at 0x7f92e159e9b0>)), Column('email', TrimmedString(), table=<galaxy_user>, nullable=False), Column('username', String(length=255), table=<galaxy_user>), Column('password', TrimmedString(), 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)

total_disk_usage

update_time

username

class galaxy.webapps.tool_shed.model.UserGroupAssociation(user, group)

Bases: object

create_time

group

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 <lambda> at 0x7f92e159ef50>)), Column('update_time', DateTime(), table=<user_group_association>, onupdate=ColumnDefault(<function <lambda> at 0x7f92e153d0c8>), default=ColumnDefault(<function <lambda> at 0x7f92e153d050>)), schema=None)

update_time

user

user_id

class galaxy.webapps.tool_shed.model.UserRoleAssociation(user, role)

Bases: object

create_time

id

non_private_roles

role

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 <lambda> at 0x7f92e153d140>)), Column('update_time', DateTime(), table=<user_role_association>, onupdate=ColumnDefault(<function <lambda> at 0x7f92e153d230>), default=ColumnDefault(<function <lambda> at 0x7f92e153d1b8>)), schema=None)

update_time

user

user_id

class galaxy.webapps.tool_shed.model.Workflow

Bases: object

class galaxy.webapps.tool_shed.model.WorkflowStep

Bases: object

class galaxy.webapps.tool_shed.model.WorkflowStepAnnotationAssociation

Bases: object

class galaxy.webapps.tool_shed.model.WorkflowStepConnection

Bases: object

galaxy.webapps.tool_shed.model.directory_hash_id(id)

galaxy.webapps.tool_shed.model.sort_by_attr(seq, attr)

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

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)

Connect mappings to the database

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

Return a new datetime representing UTC day and time.

Subpackages

• migrate Package
  • check Module