Warning
This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.
galaxy.model package¶
Galaxy data model classes
Naming: try to use class names that have a distinct plural form so that the relationship cardinalities are obvious (e.g. prefer Dataset to Data)
-
class
galaxy.model.
HasTags
[source]¶ Bases:
object
-
dict_collection_visible_keys
= ['tags']¶
-
dict_element_visible_keys
= ['tags']¶
-
-
class
galaxy.model.
SerializationOptions
(for_edit, serialize_dataset_objects=None, serialize_files_handler=None, strip_metadata_files=None)[source]¶ Bases:
object
-
class
galaxy.model.
UsesCreateAndUpdateTime
[source]¶ Bases:
object
-
seconds_since_updated
¶
-
seconds_since_created
¶
-
-
class
galaxy.model.
WorkerProcess
(server_name, hostname)[source]¶ Bases:
galaxy.model.UsesCreateAndUpdateTime
-
__init__
(server_name, hostname)¶
-
server_name
¶
-
hostname
¶
-
pid
¶
-
id
¶
-
table
= Table('worker_process', MetaData(bind=None), Column('id', Integer(), table=<worker_process>, primary_key=True, nullable=False), Column('server_name', String(length=255), table=<worker_process>), Column('hostname', String(length=255), table=<worker_process>), Column('pid', Integer(), table=<worker_process>), Column('update_time', DateTime(), table=<worker_process>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)¶
-
update_time
¶
-
-
galaxy.model.
cached_id
(galaxy_model_object)[source]¶ Get model object id attribute without a firing a database query.
Useful to fetching the id of a typical Galaxy model object after a flush, where SA is going to mark the id attribute as unloaded but we know the id is immutable and so we can use the database identity to fetch.
With Galaxy’s default SA initialization - any flush marks all attributes as unloaded - even objects completely unrelated to the flushed changes and even attributes we know to be immutable like id. See test_galaxy_mapping.py for verification of this behavior. This method is a workaround that uses the fact that we know all Galaxy objects use the id attribute as identity and SA internals (_sa_instance_state) to infer the previously loaded ID value. I tried digging into the SA internals extensively and couldn’t find a way to get the previously loaded values after a flush to allow a generalization of this for other attributes.
-
class
galaxy.model.
JobLike
[source]¶ Bases:
object
-
MAX_NUMERIC
= 9999999999999999999¶
-
metrics
¶
-
stdout
¶
-
stderr
¶
-
-
class
galaxy.model.
User
(email=None, password=None, username=None)[source]¶ Bases:
galaxy.util.dictifiable.Dictifiable
,galaxy.model.RepresentById
-
use_pbkdf2
= True¶ Data for a Galaxy user or admin and relations to their histories, credentials, and roles.
-
dict_collection_visible_keys
= ['id', 'email', 'username', 'deleted', 'active', 'last_password_change']¶
-
dict_element_visible_keys
= ['id', 'email', 'username', 'total_disk_usage', 'nice_total_disk_usage', 'deleted', 'active', 'last_password_change']¶
-
__init__
(email=None, password=None, username=None)¶
-
email
¶
-
password
¶
-
external
¶
-
deleted
¶
-
purged
¶
-
active
¶
-
activation_token
¶
-
username
¶
-
last_password_change
¶
-
histories
¶
-
extra_preferences
¶
-
set_random_password
(length=16)[source]¶ Sets user password to a random string of the given length. :return: void
-
system_user_pwent
(real_system_username)[source]¶ Gives the system user pwent entry based on e-mail or username depending on the value in real_system_username
-
all_roles
()[source]¶ Return a unique list of Roles associated with this user or any of their groups.
-
get_disk_usage
(nice_size=False)[source]¶ Return byte count of disk space used by user or a human-readable string if nice_size is True.
-
total_disk_usage
¶ Return byte count of disk space used by user or a human-readable string if nice_size is True.
-
nice_total_disk_usage
¶ Return byte count of disk space used in a human-readable string.
-
calculate_disk_usage
()[source]¶ Return byte count total of disk space used by all non-purged, non-library HDAs in non-purged histories.
-
static
user_template_environment
(user)[source]¶ >>> env = User.user_template_environment(None) >>> env['__user_email__'] 'Anonymous' >>> env['__user_id__'] 'Anonymous' >>> user = User('foo@example.com') >>> user.id = 6 >>> user.username = 'foo2' >>> env = User.user_template_environment(user) >>> env['__user_id__'] '6' >>> env['__user_name__'] 'foo2'
-
active_histories
¶
-
addresses
¶
-
api_keys
¶
-
cloudauthz
¶
-
cloudauthzs
¶
-
create_time
¶
-
custos_auth
¶
-
data_manager_histories
¶
-
default_permissions
¶
-
disk_usage
¶
-
form_values_id
¶
-
galaxy_sessions
¶
-
groups
¶
-
id
¶
-
non_private_roles
¶
-
preferences
= ColumnAssociationProxyInstance(AssociationProxy('_preferences', 'value'))¶
-
quotas
¶
-
reset_tokens
¶
-
roles
¶
-
stored_workflows
¶
-
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 datetime.utcnow>)), Column('update_time', DateTime(), table=<galaxy_user>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('email', TrimmedString(length=255), table=<galaxy_user>, nullable=False), Column('username', TrimmedString(length=255), table=<galaxy_user>), Column('password', TrimmedString(length=255), table=<galaxy_user>, nullable=False), Column('last_password_change', DateTime(), table=<galaxy_user>, default=ColumnDefault(<function datetime.utcnow>)), Column('external', Boolean(), table=<galaxy_user>, default=ColumnDefault(False)), Column('form_values_id', Integer(), ForeignKey('form_values.id'), table=<galaxy_user>), Column('deleted', Boolean(), table=<galaxy_user>, default=ColumnDefault(False)), Column('purged', Boolean(), table=<galaxy_user>, default=ColumnDefault(False)), Column('disk_usage', Numeric(precision=15, scale=0), table=<galaxy_user>), Column('active', Boolean(), table=<galaxy_user>, nullable=False, default=ColumnDefault(True)), Column('activation_token', TrimmedString(length=64), table=<galaxy_user>), schema=None)¶
-
update_time
¶
-
values
¶
-
-
class
galaxy.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.model.
DynamicTool
(tool_format=None, tool_id=None, tool_version=None, tool_path=None, tool_directory=None, uuid=None, active=True, hidden=True, value=None)[source]¶ Bases:
galaxy.util.dictifiable.Dictifiable
-
dict_collection_visible_keys
= ('id', 'tool_id', 'tool_format', 'tool_version', 'uuid', 'active', 'hidden')¶
-
dict_element_visible_keys
= ('id', 'tool_id', 'tool_format', 'tool_version', 'uuid', 'active', 'hidden')¶
-
__init__
(tool_format=None, tool_id=None, tool_version=None, tool_path=None, tool_directory=None, uuid=None, active=True, hidden=True, value=None)¶
-
tool_format
¶
-
tool_id
¶
-
tool_version
¶
-
tool_path
¶
-
tool_directory
¶
-
active
¶
-
value
¶
-
uuid
¶
-
create_time
¶
-
id
¶
-
table
= Table('dynamic_tool', MetaData(bind=None), Column('id', Integer(), table=<dynamic_tool>, primary_key=True, nullable=False), Column('uuid', UUIDType(), table=<dynamic_tool>), Column('create_time', DateTime(), table=<dynamic_tool>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<dynamic_tool>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('tool_id', Unicode(length=255), table=<dynamic_tool>), Column('tool_version', Unicode(length=255), table=<dynamic_tool>), Column('tool_format', Unicode(length=255), table=<dynamic_tool>), Column('tool_path', Unicode(length=255), table=<dynamic_tool>), Column('tool_directory', Unicode(length=255), table=<dynamic_tool>), Column('hidden', Boolean(), table=<dynamic_tool>, default=ColumnDefault(True)), Column('active', Boolean(), table=<dynamic_tool>, default=ColumnDefault(True)), Column('value', JSONType(), table=<dynamic_tool>), schema=None)¶
-
update_time
¶
-
workflow_steps
¶
-
-
class
galaxy.model.
JobMetricText
(plugin, metric_name, metric_value)[source]¶ Bases:
galaxy.model.BaseJobMetric
,galaxy.model.RepresentById
-
__init__
(plugin, metric_name, metric_value)¶
-
id
¶
-
job
¶
-
job_id
¶
-
metric_name
¶
-
metric_value
¶
-
plugin
¶
-
table
= Table('job_metric_text', MetaData(bind=None), Column('id', Integer(), table=<job_metric_text>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_metric_text>), Column('plugin', Unicode(length=255), table=<job_metric_text>), Column('metric_name', Unicode(length=255), table=<job_metric_text>), Column('metric_value', Unicode(length=1023), table=<job_metric_text>), schema=None)¶
-
-
class
galaxy.model.
JobMetricNumeric
(plugin, metric_name, metric_value)[source]¶ Bases:
galaxy.model.BaseJobMetric
,galaxy.model.RepresentById
-
__init__
(plugin, metric_name, metric_value)¶
-
id
¶
-
job
¶
-
job_id
¶
-
metric_name
¶
-
metric_value
¶
-
plugin
¶
-
table
= Table('job_metric_numeric', MetaData(bind=None), Column('id', Integer(), table=<job_metric_numeric>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_metric_numeric>), Column('plugin', Unicode(length=255), table=<job_metric_numeric>), Column('metric_name', Unicode(length=255), table=<job_metric_numeric>), Column('metric_value', Numeric(precision=26, scale=7), table=<job_metric_numeric>), schema=None)¶
-
-
class
galaxy.model.
TaskMetricText
(plugin, metric_name, metric_value)[source]¶ Bases:
galaxy.model.BaseJobMetric
,galaxy.model.RepresentById
-
__init__
(plugin, metric_name, metric_value)¶
-
id
¶
-
metric_name
¶
-
metric_value
¶
-
plugin
¶
-
table
= Table('task_metric_text', MetaData(bind=None), Column('id', Integer(), table=<task_metric_text>, primary_key=True, nullable=False), Column('task_id', Integer(), ForeignKey('task.id'), table=<task_metric_text>), Column('plugin', Unicode(length=255), table=<task_metric_text>), Column('metric_name', Unicode(length=255), table=<task_metric_text>), Column('metric_value', Unicode(length=1023), table=<task_metric_text>), schema=None)¶
-
task
¶
-
task_id
¶
-
-
class
galaxy.model.
TaskMetricNumeric
(plugin, metric_name, metric_value)[source]¶ Bases:
galaxy.model.BaseJobMetric
,galaxy.model.RepresentById
-
__init__
(plugin, metric_name, metric_value)¶
-
id
¶
-
metric_name
¶
-
metric_value
¶
-
plugin
¶
-
table
= Table('task_metric_numeric', MetaData(bind=None), Column('id', Integer(), table=<task_metric_numeric>, primary_key=True, nullable=False), Column('task_id', Integer(), ForeignKey('task.id'), table=<task_metric_numeric>), Column('plugin', Unicode(length=255), table=<task_metric_numeric>), Column('metric_name', Unicode(length=255), table=<task_metric_numeric>), Column('metric_value', Numeric(precision=26, scale=7), table=<task_metric_numeric>), schema=None)¶
-
task
¶
-
task_id
¶
-
-
class
galaxy.model.
Job
[source]¶ Bases:
galaxy.model.JobLike
,galaxy.model.UsesCreateAndUpdateTime
,galaxy.util.dictifiable.Dictifiable
,galaxy.model.RepresentById
-
dict_collection_visible_keys
= ['id', 'state', 'exit_code', 'update_time', 'create_time', 'galaxy_version']¶
-
dict_element_visible_keys
= ['id', 'state', 'exit_code', 'update_time', 'create_time', 'galaxy_version', 'command_version']¶ A job represents a request to run a tool given input datasets, tool parameters, and output datasets.
-
states
= <galaxy.util.bunch.Bunch object>¶
-
terminal_states
= ['ok', 'error', 'deleted']¶
-
non_ready_states
= ['new', 'resubmitted', 'upload', 'waiting', 'queued', 'running']¶ job states where the job hasn’t finished and the model may still change
-
__init__
()¶
-
session_id
¶
-
user_id
¶
-
tool_id
¶
-
tool_version
¶
-
copied_from_job_id
¶
-
command_line
¶
-
dependencies
¶
-
param_filename
¶
-
parameters
¶
-
input_datasets
¶
-
output_datasets
¶
-
input_dataset_collections
¶
-
output_dataset_collection_instances
¶
-
output_dataset_collections
¶
-
input_library_datasets
¶
-
output_library_datasets
¶
-
state
¶
-
info
¶
-
job_runner_name
¶
-
job_runner_external_id
¶
-
destination_id
¶
-
destination_params
¶
-
post_job_actions
¶
-
state_history
¶
-
imported
¶
-
handler
¶
-
exit_code
¶
-
job_messages
¶
-
running
¶
-
finished
¶
-
get_external_output_metadata
()[source]¶ The external_output_metadata is currently a reference from Job to JobExternalOutputMetadata. It exists for a job but not a task.
-
get_id_tag
()[source]¶ Return a tag that can be useful in identifying a Job. This returns the Job’s get_id
-
all_entry_points_configured
¶
-
get_param_values
(app, ignore_errors=False)[source]¶ Read encoded parameter values from the database and turn back into a dict of tool parameter values.
-
check_if_output_datasets_deleted
()[source]¶ Return true if all of the output datasets associated with this job are in the deleted state
-
mark_deleted
(track_jobs_in_database=False)[source]¶ Mark this job as deleted, and mark any output datasets as discarded.
-
mark_failed
(info='Job execution failed', blurb=None, peek=None)[source]¶ Mark this job as failed, and mark any output datasets as errored.
-
get_destination_configuration
(dest_params, config, key, default=None)[source]¶ Get a destination parameter that can be defaulted back in specified config if it needs to be applied globally.
-
command_version
¶
-
any_output_dataset_collection_instances_deleted
¶
-
any_output_dataset_deleted
¶
-
container
¶
-
create_time
¶
-
data_manager_association
¶
-
dynamic_tool_id
¶
-
external_output_metadata
¶
-
galaxy_session
¶
-
galaxy_version
¶
-
history
¶
-
history_dataset_collection_associations
¶
-
history_id
¶
-
id
¶
-
implicit_collection_jobs_association
¶
-
interactivetool_entry_points
¶
-
job
¶
-
job_stderr
¶
-
job_stdout
¶
-
library_folder
¶
-
library_folder_id
¶
-
numeric_metrics
¶
-
object_store_id
¶
-
params
¶
-
runner_name
¶
-
table
= Table('job', MetaData(bind=None), Column('id', Integer(), table=<job>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<job>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<job>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('history_id', Integer(), ForeignKey('history.id'), table=<job>), Column('library_folder_id', Integer(), ForeignKey('library_folder.id'), table=<job>), Column('tool_id', String(length=255), table=<job>), Column('tool_version', TEXT(), table=<job>, default=ColumnDefault('1.0.0')), Column('galaxy_version', String(length=64), table=<job>), Column('dynamic_tool_id', Integer(), ForeignKey('dynamic_tool.id'), table=<job>), Column('state', String(length=64), table=<job>), Column('info', TrimmedString(length=255), table=<job>), Column('copied_from_job_id', Integer(), table=<job>), Column('command_line', TEXT(), table=<job>), Column('dependencies', JSONType(), table=<job>), Column('job_messages', JSONType(), table=<job>), Column('param_filename', String(length=1024), table=<job>), Column('runner_name', String(length=255), table=<job>), Column('job_stdout', TEXT(), table=<job>), Column('job_stderr', TEXT(), table=<job>), Column('tool_stdout', TEXT(), table=<job>), Column('tool_stderr', TEXT(), table=<job>), Column('exit_code', Integer(), table=<job>), Column('traceback', TEXT(), table=<job>), Column('session_id', Integer(), ForeignKey('galaxy_session.id'), table=<job>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<job>), Column('job_runner_name', String(length=255), table=<job>), Column('job_runner_external_id', String(length=255), table=<job>), Column('destination_id', String(length=255), table=<job>), Column('destination_params', JSONType(), table=<job>), Column('object_store_id', TrimmedString(length=255), table=<job>), Column('imported', Boolean(), table=<job>, default=ColumnDefault(False)), Column('params', TrimmedString(length=255), table=<job>), Column('handler', TrimmedString(length=255), table=<job>), schema=None)¶
-
tasks
¶
-
text_metrics
¶
-
tool_stderr
¶
-
tool_stdout
¶
-
traceback
¶
-
update_time
¶
-
user
¶
-
workflow_invocation_step
¶
-
-
class
galaxy.model.
Task
(job, working_directory, prepare_files_cmd)[source]¶ Bases:
galaxy.model.JobLike
,galaxy.model.RepresentById
A task represents a single component of a job.
-
states
= <galaxy.util.bunch.Bunch object>¶
-
__init__
(job, working_directory, prepare_files_cmd)¶
-
command_line
¶
-
state
¶
-
info
¶
-
working_directory
¶
-
task_runner_name
¶
-
task_runner_external_id
¶
-
job
¶
-
exit_code
¶
-
prepare_input_files_cmd
¶
-
get_param_values
(app)[source]¶ Read encoded parameter values from the database and turn back into a dict of tool parameter values.
-
get_id_tag
()[source]¶ Return an id tag suitable for identifying the task. This combines the task’s job id and the task’s own id.
-
get_external_output_metadata
()[source]¶ The external_output_metadata is currently a backref to JobExternalOutputMetadata. It exists for a job but not a task, and when a task is cancelled its corresponding parent Job will be cancelled. So None is returned now, but that could be changed to self.get_job().get_external_output_metadata().
-
get_job_runner_name
()[source]¶ Since runners currently access Tasks the same way they access Jobs, this method just refers to this instance’s runner.
-
get_job_runner_external_id
()[source]¶ Runners will use the same methods to get information about the Task class as they will about the Job class, so this method just returns the task’s external id.
-
create_time
¶
-
execution_time
¶
-
id
¶
-
job_id
¶
-
job_messages
¶
-
job_stderr
¶
-
job_stdout
¶
-
numeric_metrics
¶
-
param_filename
¶
-
runner_name
¶
-
table
= Table('task', MetaData(bind=None), Column('id', Integer(), table=<task>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<task>, default=ColumnDefault(<function datetime.utcnow>)), Column('execution_time', DateTime(), table=<task>), Column('update_time', DateTime(), table=<task>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('state', String(length=64), table=<task>), Column('command_line', TEXT(), table=<task>), Column('param_filename', String(length=1024), table=<task>), Column('runner_name', String(length=255), table=<task>), Column('job_stdout', TEXT(), table=<task>), Column('job_stderr', TEXT(), table=<task>), Column('tool_stdout', TEXT(), table=<task>), Column('tool_stderr', TEXT(), table=<task>), Column('exit_code', Integer(), table=<task>), Column('job_messages', JSONType(), table=<task>), Column('info', TrimmedString(length=255), table=<task>), Column('traceback', TEXT(), table=<task>), Column('job_id', Integer(), ForeignKey('job.id'), table=<task>, nullable=False), Column('working_directory', String(length=1024), table=<task>), Column('task_runner_name', String(length=255), table=<task>), Column('task_runner_external_id', String(length=255), table=<task>), Column('prepare_input_files_cmd', TEXT(), table=<task>), schema=None)¶
-
text_metrics
¶
-
tool_stderr
¶
-
tool_stdout
¶
-
traceback
¶
-
update_time
¶
-
-
class
galaxy.model.
JobParameter
(name, value)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(name, value)¶
-
name
¶
-
value
¶
-
id
¶
-
job_id
¶
-
table
= Table('job_parameter', MetaData(bind=None), Column('id', Integer(), table=<job_parameter>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_parameter>), Column('name', String(length=255), table=<job_parameter>), Column('value', TEXT(), table=<job_parameter>), schema=None)¶
-
-
class
galaxy.model.
JobToInputDatasetAssociation
(name, dataset)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(name, dataset)¶
-
name
¶
-
dataset
¶
-
dataset_version
¶
-
dataset_id
¶
-
id
¶
-
job
¶
-
job_id
¶
-
table
= Table('job_to_input_dataset', MetaData(bind=None), Column('id', Integer(), table=<job_to_input_dataset>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_to_input_dataset>), Column('dataset_id', Integer(), ForeignKey('history_dataset_association.id'), table=<job_to_input_dataset>), Column('dataset_version', Integer(), table=<job_to_input_dataset>), Column('name', String(length=255), table=<job_to_input_dataset>), schema=None)¶
-
-
class
galaxy.model.
JobToOutputDatasetAssociation
(name, dataset)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(name, dataset)¶
-
name
¶
-
dataset
¶
-
dataset_id
¶
-
id
¶
-
job
¶
-
job_id
¶
-
table
= Table('job_to_output_dataset', MetaData(bind=None), Column('id', Integer(), table=<job_to_output_dataset>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_to_output_dataset>), Column('dataset_id', Integer(), ForeignKey('history_dataset_association.id'), table=<job_to_output_dataset>), Column('name', String(length=255), table=<job_to_output_dataset>), schema=None)¶
-
-
class
galaxy.model.
JobToInputDatasetCollectionAssociation
(name, dataset_collection)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(name, dataset_collection)¶
-
name
¶
-
dataset_collection
¶
-
dataset_collection_id
¶
-
id
¶
-
job
¶
-
job_id
¶
-
table
= Table('job_to_input_dataset_collection', MetaData(bind=None), Column('id', Integer(), table=<job_to_input_dataset_collection>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_to_input_dataset_collection>), Column('dataset_collection_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<job_to_input_dataset_collection>), Column('name', Unicode(length=255), table=<job_to_input_dataset_collection>), schema=None)¶
-
-
class
galaxy.model.
JobToOutputDatasetCollectionAssociation
(name, dataset_collection_instance)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(name, dataset_collection_instance)¶
-
name
¶
-
dataset_collection_instance
¶
-
dataset_collection_id
¶
-
id
¶
-
job
¶
-
job_id
¶
-
table
= Table('job_to_output_dataset_collection', MetaData(bind=None), Column('id', Integer(), table=<job_to_output_dataset_collection>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_to_output_dataset_collection>), Column('dataset_collection_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<job_to_output_dataset_collection>), Column('name', Unicode(length=255), table=<job_to_output_dataset_collection>), schema=None)¶
-
-
class
galaxy.model.
JobToImplicitOutputDatasetCollectionAssociation
(name, dataset_collection)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(name, dataset_collection)¶
-
name
¶
-
dataset_collection
¶
-
dataset_collection_id
¶
-
id
¶
-
job
¶
-
job_id
¶
-
table
= Table('job_to_implicit_output_dataset_collection', MetaData(bind=None), Column('id', Integer(), table=<job_to_implicit_output_dataset_collection>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_to_implicit_output_dataset_collection>), Column('dataset_collection_id', Integer(), ForeignKey('dataset_collection.id'), table=<job_to_implicit_output_dataset_collection>), Column('name', Unicode(length=255), table=<job_to_implicit_output_dataset_collection>), schema=None)¶
-
-
class
galaxy.model.
JobToInputLibraryDatasetAssociation
(name, dataset)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(name, dataset)¶
-
name
¶
-
dataset
¶
-
id
¶
-
job
¶
-
job_id
¶
-
ldda_id
¶
-
table
= Table('job_to_input_library_dataset', MetaData(bind=None), Column('id', Integer(), table=<job_to_input_library_dataset>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_to_input_library_dataset>), Column('ldda_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<job_to_input_library_dataset>), Column('name', String(length=255), table=<job_to_input_library_dataset>), schema=None)¶
-
-
class
galaxy.model.
JobToOutputLibraryDatasetAssociation
(name, dataset)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(name, dataset)¶
-
name
¶
-
dataset
¶
-
id
¶
-
job
¶
-
job_id
¶
-
ldda_id
¶
-
table
= Table('job_to_output_library_dataset', MetaData(bind=None), Column('id', Integer(), table=<job_to_output_library_dataset>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_to_output_library_dataset>), Column('ldda_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<job_to_output_library_dataset>), Column('name', String(length=255), table=<job_to_output_library_dataset>), schema=None)¶
-
-
class
galaxy.model.
JobStateHistory
(job)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(job)¶
-
job
¶
-
state
¶
-
info
¶
-
create_time
¶
-
id
¶
-
job_id
¶
-
table
= Table('job_state_history', MetaData(bind=None), Column('id', Integer(), table=<job_state_history>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<job_state_history>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<job_state_history>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_state_history>), Column('state', String(length=64), table=<job_state_history>), Column('info', TrimmedString(length=255), table=<job_state_history>), schema=None)¶
-
update_time
¶
-
-
class
galaxy.model.
ImplicitlyCreatedDatasetCollectionInput
(name, input_dataset_collection)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(name, input_dataset_collection)¶
-
name
¶
-
input_dataset_collection
¶
-
dataset_collection
¶
-
dataset_collection_id
¶
-
id
¶
-
input_dataset_collection_id
¶
-
table
= Table('implicitly_created_dataset_collection_inputs', MetaData(bind=None), Column('id', Integer(), table=<implicitly_created_dataset_collection_inputs>, primary_key=True, nullable=False), Column('dataset_collection_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<implicitly_created_dataset_collection_inputs>), Column('input_dataset_collection_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<implicitly_created_dataset_collection_inputs>), Column('name', Unicode(length=255), table=<implicitly_created_dataset_collection_inputs>), schema=None)¶
-
-
class
galaxy.model.
ImplicitCollectionJobs
(id=None, populated_state=None)[source]¶ Bases:
galaxy.model.RepresentById
-
populated_states
= <galaxy.util.bunch.Bunch object>¶
-
__init__
(id=None, populated_state=None)¶
-
id
¶
-
populated_state
¶
-
job_list
¶
-
history_dataset_collection_associations
¶
-
jobs
¶
-
table
= Table('implicit_collection_jobs', MetaData(bind=None), Column('id', Integer(), table=<implicit_collection_jobs>, primary_key=True, nullable=False), Column('populated_state', TrimmedString(length=64), table=<implicit_collection_jobs>, nullable=False, default=ColumnDefault('new')), schema=None)¶
-
workflow_invocation_step
¶
-
-
class
galaxy.model.
ImplicitCollectionJobsJobAssociation
[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
()¶
-
id
¶
-
implicit_collection_jobs
¶
-
implicit_collection_jobs_id
¶
-
job
¶
-
job_id
¶
-
order_index
¶
-
table
= Table('implicit_collection_jobs_job_association', MetaData(bind=None), Column('id', Integer(), table=<implicit_collection_jobs_job_association>, primary_key=True, nullable=False), Column('implicit_collection_jobs_id', Integer(), ForeignKey('implicit_collection_jobs.id'), table=<implicit_collection_jobs_job_association>), Column('job_id', Integer(), ForeignKey('job.id'), table=<implicit_collection_jobs_job_association>), Column('order_index', Integer(), table=<implicit_collection_jobs_job_association>, nullable=False), schema=None)¶
-
-
class
galaxy.model.
PostJobAction
(action_type, workflow_step=None, output_name=None, action_arguments=None)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(action_type, workflow_step=None, output_name=None, action_arguments=None)¶
-
action_type
¶
-
output_name
¶
-
action_arguments
¶
-
workflow_step
¶
-
id
¶
-
table
= Table('post_job_action', MetaData(bind=None), Column('id', Integer(), table=<post_job_action>, primary_key=True, nullable=False), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<post_job_action>), Column('action_type', String(length=255), table=<post_job_action>, nullable=False), Column('output_name', String(length=255), table=<post_job_action>), Column('action_arguments', JSONType(), table=<post_job_action>), schema=None)¶
-
workflow_step_id
¶
-
-
class
galaxy.model.
PostJobActionAssociation
(pja, job=None, job_id=None)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(pja, job=None, job_id=None)¶
-
job
¶
-
job_id
¶
-
post_job_action
¶
-
id
¶
-
post_job_action_id
¶
-
table
= Table('post_job_action_association', MetaData(bind=None), Column('id', Integer(), table=<post_job_action_association>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<post_job_action_association>, nullable=False), Column('post_job_action_id', Integer(), ForeignKey('post_job_action.id'), table=<post_job_action_association>, nullable=False), schema=None)¶
-
-
class
galaxy.model.
JobExternalOutputMetadata
(job=None, dataset=None)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(job=None, dataset=None)¶
-
job
¶
-
history_dataset_association
¶
-
library_dataset_dataset_association
¶
-
dataset
¶
-
filename_in
¶
-
filename_kwds
¶
-
filename_out
¶
-
filename_override_metadata
¶
-
filename_results_code
¶
-
history_dataset_association_id
¶
-
id
¶
-
is_valid
¶
-
job_id
¶
-
job_runner_external_pid
¶
-
library_dataset_dataset_association_id
¶
-
table
= Table('job_external_output_metadata', MetaData(bind=None), Column('id', Integer(), table=<job_external_output_metadata>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_external_output_metadata>), Column('history_dataset_association_id', Integer(), ForeignKey('history_dataset_association.id'), table=<job_external_output_metadata>), Column('library_dataset_dataset_association_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<job_external_output_metadata>), Column('is_valid', Boolean(), table=<job_external_output_metadata>, default=ColumnDefault(True)), Column('filename_in', String(length=255), table=<job_external_output_metadata>), Column('filename_out', String(length=255), table=<job_external_output_metadata>), Column('filename_results_code', String(length=255), table=<job_external_output_metadata>), Column('filename_kwds', String(length=255), table=<job_external_output_metadata>), Column('filename_override_metadata', String(length=255), table=<job_external_output_metadata>), Column('job_runner_external_pid', String(length=255), table=<job_external_output_metadata>), schema=None)¶
-
-
class
galaxy.model.
JobExportHistoryArchive
(job=None, history=None, dataset=None, compressed=False, history_attrs_filename=None)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(job=None, history=None, dataset=None, compressed=False, history_attrs_filename=None)¶
-
job
¶
-
history
¶
-
dataset
¶
-
compressed
¶
-
history_attrs_filename
¶
-
temp_directory
¶
-
up_to_date
¶ Return False, if a new export should be generated for corresponding history.
-
ready
¶
-
preparing
¶
-
export_name
¶
-
dataset_id
¶
-
history_id
¶
-
id
¶
-
job_id
¶
-
table
= Table('job_export_history_archive', MetaData(bind=None), Column('id', Integer(), table=<job_export_history_archive>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_export_history_archive>), Column('history_id', Integer(), ForeignKey('history.id'), table=<job_export_history_archive>), Column('dataset_id', Integer(), ForeignKey('dataset.id'), table=<job_export_history_archive>), Column('compressed', Boolean(), table=<job_export_history_archive>, default=ColumnDefault(False)), Column('history_attrs_filename', TEXT(), table=<job_export_history_archive>), schema=None)¶
-
-
class
galaxy.model.
JobImportHistoryArchive
(job=None, history=None, archive_dir=None)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(job=None, history=None, archive_dir=None)¶
-
job
¶
-
history
¶
-
archive_dir
¶
-
history_id
¶
-
id
¶
-
job_id
¶
-
table
= Table('job_import_history_archive', MetaData(bind=None), Column('id', Integer(), table=<job_import_history_archive>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_import_history_archive>), Column('history_id', Integer(), ForeignKey('history.id'), table=<job_import_history_archive>), Column('archive_dir', TEXT(), table=<job_import_history_archive>), schema=None)¶
-
-
class
galaxy.model.
JobContainerAssociation
(job=None, container_type=None, container_name=None, container_info=None)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(job=None, container_type=None, container_name=None, container_info=None)¶
-
job
¶
-
container_type
¶
-
container_name
¶
-
container_info
¶
-
created_time
¶
-
id
¶
-
job_id
¶
-
modified_time
¶
-
table
= Table('job_container_association', MetaData(bind=None), Column('id', Integer(), table=<job_container_association>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_container_association>), Column('container_type', TEXT(), table=<job_container_association>), Column('container_name', TEXT(), table=<job_container_association>), Column('container_info', JSONType(), table=<job_container_association>), Column('created_time', DateTime(), table=<job_container_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('modified_time', DateTime(), table=<job_container_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)¶
-
-
class
galaxy.model.
InteractiveToolEntryPoint
(job=None, name=None, token=None, tool_port=None, host=None, port=None, protocol=None, entry_url=None, info=None, configured=False, deleted=False)[source]¶ Bases:
galaxy.util.dictifiable.Dictifiable
,galaxy.model.RepresentById
-
dict_collection_visible_keys
= ['id', 'name', 'active']¶
-
dict_element_visible_keys
= ['id', 'name', 'active']¶
-
__init__
(job=None, name=None, token=None, tool_port=None, host=None, port=None, protocol=None, entry_url=None, info=None, configured=False, deleted=False)¶
-
job
¶
-
name
¶
-
token
¶
-
tool_port
¶
-
host
¶
-
port
¶
-
protocol
¶
-
entry_url
¶
-
info
¶
-
configured
¶
-
deleted
¶
-
active
¶
-
created_time
¶
-
id
¶
-
job_id
¶
-
modified_time
¶
-
table
= Table('interactivetool_entry_point', MetaData(bind=None), Column('id', Integer(), table=<interactivetool_entry_point>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<interactivetool_entry_point>), Column('name', TEXT(), table=<interactivetool_entry_point>), Column('token', TEXT(), table=<interactivetool_entry_point>), Column('tool_port', Integer(), table=<interactivetool_entry_point>), Column('host', TEXT(), table=<interactivetool_entry_point>), Column('port', Integer(), table=<interactivetool_entry_point>), Column('protocol', TEXT(), table=<interactivetool_entry_point>), Column('entry_url', TEXT(), table=<interactivetool_entry_point>), Column('info', JSONType(), table=<interactivetool_entry_point>), Column('configured', Boolean(), table=<interactivetool_entry_point>, default=ColumnDefault(False)), Column('deleted', Boolean(), table=<interactivetool_entry_point>, default=ColumnDefault(False)), Column('created_time', DateTime(), table=<interactivetool_entry_point>, default=ColumnDefault(<function datetime.utcnow>)), Column('modified_time', DateTime(), table=<interactivetool_entry_point>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)¶
-
-
class
galaxy.model.
GenomeIndexToolData
(job=None, params=None, dataset=None, deferred_job=None, transfer_job=None, fasta_path=None, created_time=None, modified_time=None, dbkey=None, user=None, indexer=None)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(job=None, params=None, dataset=None, deferred_job=None, transfer_job=None, fasta_path=None, created_time=None, modified_time=None, dbkey=None, user=None, indexer=None)¶
-
job
¶
-
dataset
¶
-
fasta_path
¶
-
user
¶
-
indexer
¶
-
created_time
¶
-
modified_time
¶
-
deferred
¶
-
transfer
¶
-
dataset_id
¶
-
deferred_job_id
¶
-
id
¶
-
job_id
¶
-
table
= Table('genome_index_tool_data', MetaData(bind=None), Column('id', Integer(), table=<genome_index_tool_data>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<genome_index_tool_data>), Column('deferred_job_id', Integer(), ForeignKey('deferred_job.id'), table=<genome_index_tool_data>), Column('transfer_job_id', Integer(), ForeignKey('transfer_job.id'), table=<genome_index_tool_data>), Column('dataset_id', Integer(), ForeignKey('dataset.id'), table=<genome_index_tool_data>), Column('fasta_path', String(length=255), table=<genome_index_tool_data>), Column('created_time', DateTime(), table=<genome_index_tool_data>, default=ColumnDefault(<function datetime.utcnow>)), Column('modified_time', DateTime(), table=<genome_index_tool_data>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('indexer', String(length=64), table=<genome_index_tool_data>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<genome_index_tool_data>), schema=None)¶
-
transfer_job_id
¶
-
user_id
¶
-
-
class
galaxy.model.
DeferredJob
(state=None, plugin=None, params=None)[source]¶ Bases:
galaxy.model.RepresentById
-
states
= <galaxy.util.bunch.Bunch object>¶
-
__init__
(state=None, plugin=None, params=None)¶
-
state
¶
-
plugin
¶
-
params
¶
-
check_interval
¶
-
last_check
¶
-
is_check_time
¶
-
create_time
¶
-
deferred_job
¶
-
id
¶
-
table
= Table('deferred_job', MetaData(bind=None), Column('id', Integer(), table=<deferred_job>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<deferred_job>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<deferred_job>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('state', String(length=64), table=<deferred_job>), Column('plugin', String(length=128), table=<deferred_job>), Column('params', JSONType(), table=<deferred_job>), schema=None)¶
-
update_time
¶
-
-
class
galaxy.model.
Group
(name=None)[source]¶ Bases:
galaxy.util.dictifiable.Dictifiable
,galaxy.model.RepresentById
-
dict_collection_visible_keys
= ['id', 'name']¶
-
dict_element_visible_keys
= ['id', 'name']¶
-
__init__
(name=None)¶
-
name
¶
-
deleted
¶
-
create_time
¶
-
id
¶
-
members
¶
-
quotas
¶
-
roles
¶
-
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 datetime.utcnow>)), Column('update_time', DateTime(), table=<galaxy_group>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.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.model.
UserGroupAssociation
(user, group)[source]¶ Bases:
galaxy.model.RepresentById
-
__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 datetime.utcnow>)), Column('update_time', DateTime(), table=<user_group_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)¶
-
update_time
¶
-
user_id
¶
-
-
class
galaxy.model.
History
(id=None, name=None, user=None)[source]¶ Bases:
galaxy.model.HasTags
,galaxy.util.dictifiable.Dictifiable
,galaxy.model.item_attrs.UsesAnnotations
,galaxy.model.HasName
,galaxy.model.RepresentById
-
dict_collection_visible_keys
= ['id', 'name', 'published', 'deleted']¶
-
dict_element_visible_keys
= ['id', 'name', 'genome_build', 'deleted', 'purged', 'update_time', 'published', 'importable', 'slug', 'empty']¶
-
default_name
= 'Unnamed history'¶
-
__init__
(id=None, name=None, user=None)¶
-
id
¶
-
name
¶
-
deleted
¶
-
purged
¶
-
importing
¶
-
genome_build
¶
-
published
¶
-
user
¶
-
datasets
¶
-
galaxy_sessions
¶
-
empty
¶
-
add_datasets
(sa_session, datasets, parent_id=None, genome_build=None, set_hid=True, quota=True, flush=False)[source]¶ Optimized version of add_dataset above that minimizes database interactions when adding many datasets to history at once.
-
copy
(name=None, target_user=None, activatable=False, all_datasets=False)[source]¶ Return a copy of this history using the given name and target_user. If activatable, copy only non-deleted datasets. If all_datasets, copy non-deleted, deleted, and purged datasets.
-
has_possible_members
¶
-
activatable_datasets
¶
-
latest_export
¶
-
paused_jobs
¶
-
disk_size
¶ Return a query scalar that will get any history’s size in bytes by summing the ‘total_size’s of all non-purged, unique datasets within it.
-
disk_nice_size
¶ Returns human readable size of history on disk.
-
active_dataset_and_roles_query
¶
-
active_datasets_and_roles
¶
-
active_visible_datasets_and_roles
¶
-
active_visible_dataset_collections
¶
-
active_contents
¶ Return all active contents ordered by hid.
-
active_dataset_collections
¶
-
active_datasets
¶
-
annotations
¶
-
average_rating
¶
-
create_time
¶
-
dataset_collections
¶
-
default_permissions
¶
-
exports
¶
-
hid_counter
¶
-
importable
¶
-
jobs
¶
-
ratings
¶
-
slug
¶
-
table
= Table('history', MetaData(bind=None), Column('id', Integer(), table=<history>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<history>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<history>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history>), Column('name', TrimmedString(length=255), table=<history>), Column('hid_counter', Integer(), table=<history>, default=ColumnDefault(1)), Column('deleted', Boolean(), table=<history>, default=ColumnDefault(False)), Column('purged', Boolean(), table=<history>, default=ColumnDefault(False)), Column('importing', Boolean(), table=<history>, default=ColumnDefault(False)), Column('genome_build', TrimmedString(length=40), table=<history>), Column('importable', Boolean(), table=<history>, default=ColumnDefault(False)), Column('slug', TEXT(), table=<history>), Column('published', Boolean(), table=<history>, default=ColumnDefault(False)), schema=None)¶
-
update_time
¶
-
user_id
¶
-
visible_dataset_collections
¶
-
visible_datasets
¶
-
workflow_invocations
¶
-
Bases:
galaxy.model.RepresentById
-
class
galaxy.model.
UserRoleAssociation
(user, role)[source]¶ Bases:
galaxy.model.RepresentById
-
__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 datetime.utcnow>)), Column('update_time', DateTime(), table=<user_role_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)¶
-
update_time
¶
-
user_id
¶
-
-
class
galaxy.model.
GroupRoleAssociation
(group, role)[source]¶ Bases:
galaxy.model.RepresentById
-
__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 datetime.utcnow>)), Column('update_time', DateTime(), table=<group_role_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)¶
-
update_time
¶
-
-
class
galaxy.model.
Role
(name='', description='', type='system', deleted=False)[source]¶ Bases:
galaxy.util.dictifiable.Dictifiable
,galaxy.model.RepresentById
-
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
¶
-
create_time
¶
-
dataset_actions
¶
-
groups
¶
-
id
¶
-
library_actions
¶
-
library_dataset_actions
¶
-
library_dataset_dataset_actions
¶
-
library_folder_actions
¶
-
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 datetime.utcnow>)), Column('update_time', DateTime(), table=<role>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.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.model.
UserQuotaAssociation
(user, quota)[source]¶ Bases:
galaxy.util.dictifiable.Dictifiable
,galaxy.model.RepresentById
-
dict_element_visible_keys
= ['user']¶
-
__init__
(user, quota)¶
-
user
¶
-
quota
¶
-
create_time
¶
-
id
¶
-
quota_id
¶
-
table
= Table('user_quota_association', MetaData(bind=None), Column('id', Integer(), table=<user_quota_association>, primary_key=True, nullable=False), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<user_quota_association>), Column('quota_id', Integer(), ForeignKey('quota.id'), table=<user_quota_association>), Column('create_time', DateTime(), table=<user_quota_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<user_quota_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)¶
-
update_time
¶
-
user_id
¶
-
-
class
galaxy.model.
GroupQuotaAssociation
(group, quota)[source]¶ Bases:
galaxy.util.dictifiable.Dictifiable
,galaxy.model.RepresentById
-
dict_element_visible_keys
= ['group']¶
-
__init__
(group, quota)¶
-
group
¶
-
quota
¶
-
create_time
¶
-
group_id
¶
-
id
¶
-
quota_id
¶
-
table
= Table('group_quota_association', MetaData(bind=None), Column('id', Integer(), table=<group_quota_association>, primary_key=True, nullable=False), Column('group_id', Integer(), ForeignKey('galaxy_group.id'), table=<group_quota_association>), Column('quota_id', Integer(), ForeignKey('quota.id'), table=<group_quota_association>), Column('create_time', DateTime(), table=<group_quota_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<group_quota_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)¶
-
update_time
¶
-
-
class
galaxy.model.
Quota
(name='', description='', amount=0, operation='=')[source]¶ Bases:
galaxy.util.dictifiable.Dictifiable
,galaxy.model.RepresentById
-
dict_collection_visible_keys
= ['id', 'name']¶
-
dict_element_visible_keys
= ['id', 'name', 'description', 'bytes', 'operation', 'display_amount', 'default', 'users', 'groups']¶
-
valid_operations
= ('+', '-', '=')¶
-
__init__
(name='', description='', amount=0, operation='=')¶
-
name
¶
-
description
¶
-
bytes
¶
-
operation
¶
-
amount
¶
-
display_amount
¶
-
create_time
¶
-
default
¶
-
deleted
¶
-
groups
¶
-
id
¶
-
table
= Table('quota', MetaData(bind=None), Column('id', Integer(), table=<quota>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<quota>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<quota>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('name', String(length=255), table=<quota>), Column('description', TEXT(), table=<quota>), Column('bytes', BigInteger(), table=<quota>), Column('operation', String(length=8), table=<quota>), Column('deleted', Boolean(), table=<quota>, default=ColumnDefault(False)), schema=None)¶
-
update_time
¶
-
users
¶
-
-
class
galaxy.model.
DefaultQuotaAssociation
(type, quota)[source]¶ Bases:
galaxy.model.Quota
,galaxy.util.dictifiable.Dictifiable
,galaxy.model.RepresentById
-
dict_element_visible_keys
= ['type']¶
-
types
= <galaxy.util.bunch.Bunch object>¶
-
__init__
(type, quota)¶
-
type
¶
-
quota
¶
-
create_time
¶
-
id
¶
-
quota_id
¶
-
table
= Table('default_quota_association', MetaData(bind=None), Column('id', Integer(), table=<default_quota_association>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<default_quota_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<default_quota_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('type', String(length=32), table=<default_quota_association>), Column('quota_id', Integer(), ForeignKey('quota.id'), table=<default_quota_association>), schema=None)¶
-
update_time
¶
-
-
class
galaxy.model.
DatasetPermissions
(action, dataset, role=None, role_id=None)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(action, dataset, role=None, role_id=None)¶
-
action
¶
-
dataset
¶
-
role
¶
-
role_id
¶
-
create_time
¶
-
dataset_id
¶
-
id
¶
-
table
= Table('dataset_permissions', MetaData(bind=None), Column('id', Integer(), table=<dataset_permissions>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<dataset_permissions>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<dataset_permissions>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('action', TEXT(), table=<dataset_permissions>), Column('dataset_id', Integer(), ForeignKey('dataset.id'), table=<dataset_permissions>), Column('role_id', Integer(), ForeignKey('role.id'), table=<dataset_permissions>), schema=None)¶
-
update_time
¶
-
-
class
galaxy.model.
LibraryPermissions
(action, library_item, role)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(action, library_item, role)¶
-
action
¶
-
library
¶
-
role
¶
-
create_time
¶
-
id
¶
-
library_id
¶
-
role_id
¶
-
table
= Table('library_permissions', MetaData(bind=None), Column('id', Integer(), table=<library_permissions>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<library_permissions>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<library_permissions>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('action', TEXT(), table=<library_permissions>), Column('library_id', Integer(), ForeignKey('library.id'), table=<library_permissions>), Column('role_id', Integer(), ForeignKey('role.id'), table=<library_permissions>), schema=None)¶
-
update_time
¶
-
-
class
galaxy.model.
LibraryFolderPermissions
(action, library_item, role)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(action, library_item, role)¶
-
action
¶
-
folder
¶
-
role
¶
-
create_time
¶
-
id
¶
-
library_folder_id
¶
-
role_id
¶
-
table
= Table('library_folder_permissions', MetaData(bind=None), Column('id', Integer(), table=<library_folder_permissions>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<library_folder_permissions>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<library_folder_permissions>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('action', TEXT(), table=<library_folder_permissions>), Column('library_folder_id', Integer(), ForeignKey('library_folder.id'), table=<library_folder_permissions>), Column('role_id', Integer(), ForeignKey('role.id'), table=<library_folder_permissions>), schema=None)¶
-
update_time
¶
-
-
class
galaxy.model.
LibraryDatasetPermissions
(action, library_item, role)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(action, library_item, role)¶
-
action
¶
-
library_dataset
¶
-
role
¶
-
create_time
¶
-
id
¶
-
library_dataset_id
¶
-
role_id
¶
-
table
= Table('library_dataset_permissions', MetaData(bind=None), Column('id', Integer(), table=<library_dataset_permissions>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<library_dataset_permissions>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<library_dataset_permissions>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('action', TEXT(), table=<library_dataset_permissions>), Column('library_dataset_id', Integer(), ForeignKey('library_dataset.id'), table=<library_dataset_permissions>), Column('role_id', Integer(), ForeignKey('role.id'), table=<library_dataset_permissions>), schema=None)¶
-
update_time
¶
-
-
class
galaxy.model.
LibraryDatasetDatasetAssociationPermissions
(action, library_item, role)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(action, library_item, role)¶
-
action
¶
-
library_dataset_dataset_association
¶
-
role
¶
-
create_time
¶
-
id
¶
-
library_dataset_dataset_association_id
¶
-
role_id
¶
-
table
= Table('library_dataset_dataset_association_permissions', MetaData(bind=None), Column('id', Integer(), table=<library_dataset_dataset_association_permissions>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<library_dataset_dataset_association_permissions>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<library_dataset_dataset_association_permissions>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('action', TEXT(), table=<library_dataset_dataset_association_permissions>), Column('library_dataset_dataset_association_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<library_dataset_dataset_association_permissions>), Column('role_id', Integer(), ForeignKey('role.id'), table=<library_dataset_dataset_association_permissions>), schema=None)¶
-
update_time
¶
-
-
class
galaxy.model.
DefaultUserPermissions
(user, action, role)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(user, action, role)¶
-
user
¶
-
action
¶
-
role
¶
-
id
¶
-
role_id
¶
-
table
= Table('default_user_permissions', MetaData(bind=None), Column('id', Integer(), table=<default_user_permissions>, primary_key=True, nullable=False), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<default_user_permissions>), Column('action', TEXT(), table=<default_user_permissions>), Column('role_id', Integer(), ForeignKey('role.id'), table=<default_user_permissions>), schema=None)¶
-
user_id
¶
-
-
class
galaxy.model.
DefaultHistoryPermissions
(history, action, role)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(history, action, role)¶
-
history
¶
-
action
¶
-
role
¶
-
history_id
¶
-
id
¶
-
role_id
¶
-
table
= Table('default_history_permissions', MetaData(bind=None), Column('id', Integer(), table=<default_history_permissions>, primary_key=True, nullable=False), Column('history_id', Integer(), ForeignKey('history.id'), table=<default_history_permissions>), Column('action', TEXT(), table=<default_history_permissions>), Column('role_id', Integer(), ForeignKey('role.id'), table=<default_history_permissions>), schema=None)¶
-
-
class
galaxy.model.
Dataset
(id=None, state=None, external_filename=None, extra_files_path=None, file_size=None, purgable=True, uuid=None)[source]¶ Bases:
galaxy.model.StorableObject
,galaxy.model.RepresentById
-
states
= <galaxy.util.bunch.Bunch object>¶
-
non_ready_states
= ('new', 'upload', 'queued', 'running', 'setting_metadata')¶
-
ready_states
= ('error', 'failed_metadata', 'discarded', 'empty', 'paused', 'ok')¶
-
valid_input_states
= ('new', 'upload', 'empty', 'queued', 'failed_metadata', 'running', 'setting_metadata', 'paused', 'ok')¶
-
terminal_states
= ('ok', 'empty', 'error', 'discarded', 'failed_metadata')¶
-
conversion_messages
= <galaxy.util.bunch.Bunch object>¶
-
permitted_actions
= <galaxy.util.bunch.Bunch object>¶
-
file_path
= '/tmp/'¶
-
object_store
= None¶
-
engine
= None¶
-
__init__
(id=None, state=None, external_filename=None, extra_files_path=None, file_size=None, purgable=True, uuid=None)¶
-
state
¶
-
deleted
¶
-
purged
¶
-
purgable
¶
-
external_filename
¶
-
file_size
¶
-
sources
¶
-
hashes
¶
-
file_name
¶
-
extra_files_path
¶
-
set_size
(no_extra_files=False)[source]¶ Sets the size of the data on disk.
If the caller is sure there are no extra files, pass no_extra_files as True to optimize subsequent calls to get_total_size or set_total_size - potentially avoiding both a database flush and check against the file system.
-
user_can_purge
¶
-
actions
¶
-
active_history_associations
¶
-
active_library_associations
¶
-
create_time
¶
-
created_from_basename
¶
-
genome_index_tool_data
¶
-
history_associations
¶
-
id
¶
-
job_export_history_archive
¶
-
library_associations
¶
-
object_store_id
¶
-
purged_history_associations
¶
-
table
= Table('dataset', MetaData(bind=None), Column('id', Integer(), table=<dataset>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<dataset>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<dataset>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('state', TrimmedString(length=64), table=<dataset>), Column('deleted', Boolean(), table=<dataset>, default=ColumnDefault(False)), Column('purged', Boolean(), table=<dataset>, default=ColumnDefault(False)), Column('purgable', Boolean(), table=<dataset>, default=ColumnDefault(True)), Column('object_store_id', TrimmedString(length=255), table=<dataset>), Column('external_filename', TEXT(), table=<dataset>), Column('_extra_files_path', TEXT(), table=<dataset>), Column('created_from_basename', TEXT(), table=<dataset>), Column('file_size', Numeric(precision=15, scale=0), table=<dataset>), Column('total_size', Numeric(precision=15, scale=0), table=<dataset>), Column('uuid', UUIDType(), table=<dataset>), schema=None)¶
-
total_size
¶
-
update_time
¶
-
uuid
¶
-
-
class
galaxy.model.
DatasetSource
[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
()¶ Initialize self. See help(type(self)) for accurate signature.
-
dataset
¶
-
dataset_id
¶
-
extra_files_path
¶
-
hashes
¶
-
id
¶
-
source_uri
¶
-
table
= Table('dataset_source', MetaData(bind=None), Column('id', Integer(), table=<dataset_source>, primary_key=True, nullable=False), Column('dataset_id', Integer(), ForeignKey('dataset.id'), table=<dataset_source>), Column('source_uri', TEXT(), table=<dataset_source>), Column('extra_files_path', TEXT(), table=<dataset_source>), Column('transform', JSONType(), table=<dataset_source>), schema=None)¶
-
transform
¶
-
-
class
galaxy.model.
DatasetSourceHash
[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
()¶ Initialize self. See help(type(self)) for accurate signature.
-
dataset_source_id
¶
-
hash_function
¶
-
hash_value
¶
-
id
¶
-
source
¶
-
table
= Table('dataset_source_hash', MetaData(bind=None), Column('id', Integer(), table=<dataset_source_hash>, primary_key=True, nullable=False), Column('dataset_source_id', Integer(), ForeignKey('dataset_source.id'), table=<dataset_source_hash>), Column('hash_function', TEXT(), table=<dataset_source_hash>), Column('hash_value', TEXT(), table=<dataset_source_hash>), schema=None)¶
-
-
class
galaxy.model.
DatasetHash
[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
()¶ Initialize self. See help(type(self)) for accurate signature.
-
dataset
¶
-
dataset_id
¶
-
extra_files_path
¶
-
hash_function
¶
-
hash_value
¶
-
id
¶
-
table
= Table('dataset_hash', MetaData(bind=None), Column('id', Integer(), table=<dataset_hash>, primary_key=True, nullable=False), Column('dataset_id', Integer(), ForeignKey('dataset.id'), table=<dataset_hash>), Column('hash_function', TEXT(), table=<dataset_hash>), Column('hash_value', TEXT(), table=<dataset_hash>), Column('extra_files_path', TEXT(), table=<dataset_hash>), schema=None)¶
-
-
class
galaxy.model.
DatasetInstance
(id=None, hid=None, name=None, info=None, blurb=None, peek=None, tool_version=None, extension=None, dbkey=None, metadata=None, history=None, dataset=None, deleted=False, designation=None, parent_id=None, validated_state='unknown', validated_state_message=None, visible=True, create_dataset=False, sa_session=None, extended_metadata=None, flush=True)[source]¶ Bases:
object
A base class for all ‘dataset instances’, HDAs, LDAs, etc
-
states
= <galaxy.util.bunch.Bunch object>¶
-
conversion_messages
= <galaxy.util.bunch.Bunch object>¶
-
permitted_actions
= <galaxy.util.bunch.Bunch object>¶
-
validated_states
= <galaxy.util.bunch.Bunch object>¶
-
__init__
(id=None, hid=None, name=None, info=None, blurb=None, peek=None, tool_version=None, extension=None, dbkey=None, metadata=None, history=None, dataset=None, deleted=False, designation=None, parent_id=None, validated_state='unknown', validated_state_message=None, visible=True, create_dataset=False, sa_session=None, extended_metadata=None, flush=True)[source]¶
-
peek
¶
-
ext
¶
-
state
¶
-
file_name
¶
-
extra_files_path
¶
-
datatype
¶
-
set_metadata_requires_flush
¶
-
metadata
¶
-
metadata_file_types
¶
-
dbkey
¶
-
created_from_basename
¶
-
get_raw_data
()[source]¶ Returns the full data. To stream it open the file_name and read/write as needed
-
get_converted_dataset
(trans, target_ext, target_context=None, history=None)[source]¶ Return converted dataset(s) if they exist, along with a dict of dependencies. If not converted yet, do so and return None (the first time). If unconvertible, raise exception.
-
copy_attributes
(new_dataset)[source]¶ Copies attributes to a new datasets, used for implicit conversions
-
get_metadata_dataset
(dataset_ext)[source]¶ Returns an HDA that points to a metadata file which contains a converted data with the requested extension.
-
find_conversion_destination
(accepted_formats, **kwd)[source]¶ Returns ( target_ext, existing converted dataset )
-
is_ok
¶
-
is_pending
¶ Return true if the dataset is neither ready nor in error
-
source_library_dataset
¶
-
source_dataset_chain
¶
-
creating_job
¶
-
get_datasources
(trans)[source]¶ Returns datasources for dataset; if datasources are not available due to indexing, indexing is started. Return value is a dictionary with entries of type (<datasource_type> : {<datasource_name>, <indexing_message>}).
-
-
class
galaxy.model.
HistoryDatasetAssociation
(hid=None, history=None, copied_from_history_dataset_association=None, copied_from_library_dataset_dataset_association=None, sa_session=None, **kwd)[source]¶ Bases:
galaxy.model.DatasetInstance
,galaxy.model.HasTags
,galaxy.util.dictifiable.Dictifiable
,galaxy.model.item_attrs.UsesAnnotations
,galaxy.model.HasName
,galaxy.model.RepresentById
Resource class that creates a relation between a dataset and a user history.
-
__init__
(hid=None, history=None, copied_from_history_dataset_association=None, copied_from_library_dataset_dataset_association=None, sa_session=None, **kwd)¶ Create a a new HDA and associate it with the given history.
-
hid
¶
-
history
¶
-
copied_from_history_dataset_association
¶
-
copied_from_library_dataset_dataset_association
¶
-
copy
(parent_id=None, copy_tags=None, force_flush=True, copy_hid=True, new_name=None)[source]¶ Create a copy of this HDA.
-
to_library_dataset_dataset_association
(trans, target_folder, replace_dataset=None, parent_id=None, user=None, roles=None, ldda_message='', element_identifier=None)[source]¶ Copy this HDA to a library optionally replacing an existing LDDA.
-
quota_amount
(user)[source]¶ Return the disk space used for this HDA relevant to user quotas.
If the user has multiple instances of this dataset, it will not affect their disk usage statistic.
-
to_dict
(view='collection', expose_dataset_path=False)[source]¶ Return attributes of this HDA that are exposed using the API.
-
history_content_type
¶
-
content_type
= 'dataset'¶
-
type_id
¶
-
annotations
¶
-
blurb
¶
-
copied_from_history_dataset_association_id
¶
-
copied_from_library_dataset_dataset_association_id
¶
-
copied_to_history_dataset_associations
¶
-
copied_to_library_dataset_dataset_associations
¶
-
create_time
¶
-
creating_job_associations
¶
-
dataset
¶
-
dataset_id
¶
-
deleted
¶
-
dependent_jobs
¶
-
designation
¶
-
extended_metadata
¶
-
extended_metadata_id
¶
-
extension
¶
-
history_id
¶
-
id
¶
-
implicitly_converted_datasets
¶
-
implicitly_converted_parent_datasets
¶
-
info
¶
-
name
¶
-
parent_id
¶
-
purged
¶
-
ratings
¶
-
table
= Table('history_dataset_association', MetaData(bind=None), Column('id', Integer(), table=<history_dataset_association>, primary_key=True, nullable=False), Column('history_id', Integer(), ForeignKey('history.id'), table=<history_dataset_association>), Column('dataset_id', Integer(), ForeignKey('dataset.id'), table=<history_dataset_association>), Column('create_time', DateTime(), table=<history_dataset_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<history_dataset_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('state', TrimmedString(length=64), table=<history_dataset_association>, key='_state'), Column('copied_from_history_dataset_association_id', Integer(), ForeignKey('history_dataset_association.id'), table=<history_dataset_association>), Column('copied_from_library_dataset_dataset_association_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<history_dataset_association>), Column('name', TrimmedString(length=255), table=<history_dataset_association>), Column('info', TrimmedString(length=255), table=<history_dataset_association>), Column('blurb', TrimmedString(length=255), table=<history_dataset_association>), Column('peek', TEXT(), table=<history_dataset_association>, key='_peek'), Column('tool_version', TEXT(), table=<history_dataset_association>), Column('extension', TrimmedString(length=64), table=<history_dataset_association>), Column('metadata', MetadataType(), table=<history_dataset_association>, key='_metadata'), Column('parent_id', Integer(), ForeignKey('history_dataset_association.id'), table=<history_dataset_association>), Column('designation', TrimmedString(length=255), table=<history_dataset_association>), Column('deleted', Boolean(), table=<history_dataset_association>, default=ColumnDefault(False)), Column('visible', Boolean(), table=<history_dataset_association>), Column('extended_metadata_id', Integer(), ForeignKey('extended_metadata.id'), table=<history_dataset_association>), Column('version', Integer(), table=<history_dataset_association>, default=ColumnDefault(1)), Column('hid', Integer(), table=<history_dataset_association>), Column('purged', Boolean(), table=<history_dataset_association>, default=ColumnDefault(False)), Column('validated_state', TrimmedString(length=64), table=<history_dataset_association>, nullable=False, default=ColumnDefault('unvalidated')), Column('validated_state_message', TEXT(), table=<history_dataset_association>), Column('hidden_beneath_collection_instance_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<history_dataset_association>), schema=None)¶
-
tool_version
¶
-
update_time
¶
-
validated_state
¶
-
validated_state_message
¶
-
version
¶
-
visible
¶
-
-
class
galaxy.model.
HistoryDatasetAssociationHistory
(history_dataset_association_id, name, dbkey, update_time, version, extension, extended_metadata_id, metadata)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(history_dataset_association_id, name, dbkey, update_time, version, extension, extended_metadata_id, metadata)¶
-
history_dataset_association_id
¶
-
name
¶
-
update_time
¶
-
version
¶
-
extension
¶
-
extended_metadata_id
¶
-
id
¶
-
table
= Table('history_dataset_association_history', MetaData(bind=None), Column('id', Integer(), table=<history_dataset_association_history>, primary_key=True, nullable=False), Column('history_dataset_association_id', Integer(), ForeignKey('history_dataset_association.id'), table=<history_dataset_association_history>), Column('update_time', DateTime(), table=<history_dataset_association_history>, default=ColumnDefault(<function datetime.utcnow>)), Column('version', Integer(), table=<history_dataset_association_history>), Column('name', TrimmedString(length=255), table=<history_dataset_association_history>), Column('extension', TrimmedString(length=64), table=<history_dataset_association_history>), Column('metadata', MetadataType(), table=<history_dataset_association_history>, key='_metadata'), Column('extended_metadata_id', Integer(), ForeignKey('extended_metadata.id'), table=<history_dataset_association_history>), schema=None)¶
-
-
class
galaxy.model.
HistoryDatasetAssociationDisplayAtAuthorization
(hda=None, user=None, site=None)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(hda=None, user=None, site=None)¶
-
history_dataset_association
¶
-
user
¶
-
site
¶
-
create_time
¶
-
history_dataset_association_id
¶
-
id
¶
-
table
= Table('history_dataset_association_display_at_authorization', MetaData(bind=None), Column('id', Integer(), table=<history_dataset_association_display_at_authorization>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<history_dataset_association_display_at_authorization>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<history_dataset_association_display_at_authorization>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('history_dataset_association_id', Integer(), ForeignKey('history_dataset_association.id'), table=<history_dataset_association_display_at_authorization>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history_dataset_association_display_at_authorization>), Column('site', TrimmedString(length=255), table=<history_dataset_association_display_at_authorization>), schema=None)¶
-
update_time
¶
-
user_id
¶
-
-
class
galaxy.model.
HistoryDatasetAssociationSubset
(hda, subset, location)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(hda, subset, location)¶
-
hda
¶
-
subset
¶
-
location
¶
-
history_dataset_association_id
¶
-
history_dataset_association_subset_id
¶
-
id
¶
-
table
= Table('history_dataset_association_subset', MetaData(bind=None), Column('id', Integer(), table=<history_dataset_association_subset>, primary_key=True, nullable=False), Column('history_dataset_association_id', Integer(), ForeignKey('history_dataset_association.id'), table=<history_dataset_association_subset>), Column('history_dataset_association_subset_id', Integer(), ForeignKey('history_dataset_association.id'), table=<history_dataset_association_subset>), Column('location', Unicode(length=255), table=<history_dataset_association_subset>), schema=None)¶
-
-
class
galaxy.model.
Library
(name=None, description=None, synopsis=None, root_folder=None)[source]¶ Bases:
galaxy.util.dictifiable.Dictifiable
,galaxy.model.HasName
,galaxy.model.RepresentById
-
permitted_actions
= <galaxy.util.bunch.Bunch object>¶
-
dict_collection_visible_keys
= ['id', 'name']¶
-
dict_element_visible_keys
= ['id', 'deleted', 'name', 'description', 'synopsis', 'root_folder_id', 'create_time']¶
-
__init__
(name=None, description=None, synopsis=None, root_folder=None)¶
-
name
¶
-
description
¶
-
synopsis
¶
-
root_folder
¶
-
actions
¶
-
create_time
¶
-
deleted
¶
-
id
¶
-
info_association
¶
-
purged
¶
-
root_folder_id
¶
-
table
= Table('library', MetaData(bind=None), Column('id', Integer(), table=<library>, primary_key=True, nullable=False), Column('root_folder_id', Integer(), ForeignKey('library_folder.id'), table=<library>), Column('create_time', DateTime(), table=<library>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<library>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('name', String(length=255), table=<library>), Column('deleted', Boolean(), table=<library>, default=ColumnDefault(False)), Column('purged', Boolean(), table=<library>, default=ColumnDefault(False)), Column('description', TEXT(), table=<library>), Column('synopsis', TEXT(), table=<library>), schema=None)¶
-
update_time
¶
-
-
class
galaxy.model.
LibraryFolder
(name=None, description=None, item_count=0, order_id=None, genome_build=None)[source]¶ Bases:
galaxy.util.dictifiable.Dictifiable
,galaxy.model.HasName
,galaxy.model.RepresentById
-
dict_element_visible_keys
= ['id', 'parent_id', 'name', 'description', 'item_count', 'genome_build', 'update_time', 'deleted']¶
-
__init__
(name=None, description=None, item_count=0, order_id=None, genome_build=None)¶
-
name
¶
-
description
¶
-
item_count
¶
-
order_id
¶
-
genome_build
¶
-
folders
¶
-
datasets
¶
-
activatable_library_datasets
¶
-
library_path
¶
-
parent_library
¶
-
actions
¶
-
active_datasets
¶
-
active_folders
¶
-
create_time
¶
-
dataset_collections
¶
-
deleted
¶
-
id
¶
-
info_association
¶
-
library_root
¶
-
parent
¶
-
parent_id
¶
-
purged
¶
-
table
= Table('library_folder', MetaData(bind=None), Column('id', Integer(), table=<library_folder>, primary_key=True, nullable=False), Column('parent_id', Integer(), ForeignKey('library_folder.id'), table=<library_folder>), Column('create_time', DateTime(), table=<library_folder>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<library_folder>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('name', TEXT(), table=<library_folder>), Column('description', TEXT(), table=<library_folder>), Column('order_id', Integer(), table=<library_folder>), Column('item_count', Integer(), table=<library_folder>), Column('deleted', Boolean(), table=<library_folder>, default=ColumnDefault(False)), Column('purged', Boolean(), table=<library_folder>, default=ColumnDefault(False)), Column('genome_build', TrimmedString(length=40), table=<library_folder>), schema=None)¶
-
update_time
¶
-
-
class
galaxy.model.
LibraryDataset
(folder=None, order_id=None, name=None, info=None, library_dataset_dataset_association=None, **kwd)[source]¶ Bases:
galaxy.model.RepresentById
-
upload_options
= [('upload_file', 'Upload files'), ('upload_directory', 'Upload directory of files'), ('upload_paths', 'Upload files from filesystem paths'), ('import_from_history', 'Import datasets from your current history')]¶
-
__init__
(folder=None, order_id=None, name=None, info=None, library_dataset_dataset_association=None, **kwd)¶
-
folder
¶
-
order_id
¶
-
library_dataset_dataset_association
¶
-
info
¶
-
name
¶
-
actions
¶
-
create_time
¶
-
deleted
¶
-
expired_datasets
¶
-
folder_id
¶
-
id
¶
-
library_dataset_dataset_association_id
¶
-
purged
¶
-
table
= Table('library_dataset', MetaData(bind=None), Column('id', Integer(), table=<library_dataset>, primary_key=True, nullable=False), Column('library_dataset_dataset_association_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<library_dataset>), Column('folder_id', Integer(), ForeignKey('library_folder.id'), table=<library_dataset>), Column('order_id', Integer(), table=<library_dataset>), Column('create_time', DateTime(), table=<library_dataset>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<library_dataset>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('name', TrimmedString(length=255), table=<library_dataset>, key='_name'), Column('info', TrimmedString(length=255), table=<library_dataset>, key='_info'), Column('deleted', Boolean(), table=<library_dataset>, default=ColumnDefault(False)), Column('purged', Boolean(), table=<library_dataset>, default=ColumnDefault(False)), schema=None)¶
-
update_time
¶
-
-
class
galaxy.model.
LibraryDatasetDatasetAssociation
(copied_from_history_dataset_association=None, copied_from_library_dataset_dataset_association=None, library_dataset=None, user=None, sa_session=None, **kwd)[source]¶ Bases:
galaxy.model.DatasetInstance
,galaxy.model.HasName
,galaxy.model.RepresentById
-
__init__
(copied_from_history_dataset_association=None, copied_from_library_dataset_dataset_association=None, library_dataset=None, user=None, sa_session=None, **kwd)¶
-
copied_from_history_dataset_association_id
¶
-
copied_from_library_dataset_dataset_association_id
¶
-
library_dataset
¶
-
user
¶
-
to_history_dataset_association
(target_history, parent_id=None, add_to_history=False, visible=None)[source]¶
-
actions
¶
-
blurb
¶
-
copied_from_history_dataset_association
¶
-
copied_from_library_dataset_dataset_association
¶
-
copied_to_history_dataset_associations
¶
-
copied_to_library_dataset_dataset_associations
¶
-
create_time
¶
-
creating_job_associations
¶
-
dataset
¶
-
dataset_id
¶
-
deleted
¶
-
dependent_jobs
¶
-
designation
¶
-
extended_metadata
¶
-
extended_metadata_id
¶
-
extension
¶
-
id
¶
-
implicitly_converted_datasets
¶
-
implicitly_converted_parent_datasets
¶
-
info
¶
-
info_association
¶
-
library_dataset_id
¶
-
message
¶
-
name
¶
-
parent_id
¶
-
table
= Table('library_dataset_dataset_association', MetaData(bind=None), Column('id', Integer(), table=<library_dataset_dataset_association>, primary_key=True, nullable=False), Column('library_dataset_id', Integer(), ForeignKey('library_dataset.id'), table=<library_dataset_dataset_association>), Column('dataset_id', Integer(), ForeignKey('dataset.id'), table=<library_dataset_dataset_association>), Column('create_time', DateTime(), table=<library_dataset_dataset_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<library_dataset_dataset_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('state', TrimmedString(length=64), table=<library_dataset_dataset_association>, key='_state'), Column('copied_from_history_dataset_association_id', Integer(), ForeignKey('history_dataset_association.id'), table=<library_dataset_dataset_association>), Column('copied_from_library_dataset_dataset_association_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<library_dataset_dataset_association>), Column('name', TrimmedString(length=255), table=<library_dataset_dataset_association>), Column('info', TrimmedString(length=255), table=<library_dataset_dataset_association>), Column('blurb', TrimmedString(length=255), table=<library_dataset_dataset_association>), Column('peek', TEXT(), table=<library_dataset_dataset_association>, key='_peek'), Column('tool_version', TEXT(), table=<library_dataset_dataset_association>), Column('extension', TrimmedString(length=64), table=<library_dataset_dataset_association>), Column('metadata', MetadataType(), table=<library_dataset_dataset_association>, key='_metadata'), Column('parent_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<library_dataset_dataset_association>), Column('designation', TrimmedString(length=255), table=<library_dataset_dataset_association>), Column('deleted', Boolean(), table=<library_dataset_dataset_association>, default=ColumnDefault(False)), Column('validated_state', TrimmedString(length=64), table=<library_dataset_dataset_association>, nullable=False, default=ColumnDefault('unvalidated')), Column('validated_state_message', TEXT(), table=<library_dataset_dataset_association>), Column('visible', Boolean(), table=<library_dataset_dataset_association>), Column('extended_metadata_id', Integer(), ForeignKey('extended_metadata.id'), table=<library_dataset_dataset_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<library_dataset_dataset_association>), Column('message', TrimmedString(length=255), table=<library_dataset_dataset_association>), schema=None)¶
-
tool_version
¶
-
update_time
¶
-
user_id
¶
-
validated_state
¶
-
validated_state_message
¶
-
visible
¶
-
-
class
galaxy.model.
ExtendedMetadata
(data)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(data)¶
-
data
¶
-
children
¶
-
id
¶
-
table
= Table('extended_metadata', MetaData(bind=None), Column('id', Integer(), table=<extended_metadata>, primary_key=True, nullable=False), Column('data', JSONType(), table=<extended_metadata>), schema=None)¶
-
-
class
galaxy.model.
ExtendedMetadataIndex
(extended_metadata, path, value)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(extended_metadata, path, value)¶
-
extended_metadata
¶
-
path
¶
-
value
¶
-
extended_metadata_id
¶
-
id
¶
-
parent
¶
-
table
= Table('extended_metadata_index', MetaData(bind=None), Column('id', Integer(), table=<extended_metadata_index>, primary_key=True, nullable=False), Column('extended_metadata_id', Integer(), ForeignKey('extended_metadata.id'), table=<extended_metadata_index>), Column('path', String(length=255), table=<extended_metadata_index>), Column('value', TEXT(), table=<extended_metadata_index>), schema=None)¶
-
-
class
galaxy.model.
LibraryInfoAssociation
(library, form_definition, info, inheritable=False)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(library, form_definition, info, inheritable=False)¶
-
library
¶
-
template
¶
-
info
¶
-
inheritable
¶
-
deleted
¶
-
form_definition_id
¶
-
form_values_id
¶
-
id
¶
-
library_id
¶
-
table
= Table('library_info_association', MetaData(bind=None), Column('id', Integer(), table=<library_info_association>, primary_key=True, nullable=False), Column('library_id', Integer(), ForeignKey('library.id'), table=<library_info_association>), Column('form_definition_id', Integer(), ForeignKey('form_definition.id'), table=<library_info_association>), Column('form_values_id', Integer(), ForeignKey('form_values.id'), table=<library_info_association>), Column('inheritable', Boolean(), table=<library_info_association>, default=ColumnDefault(False)), Column('deleted', Boolean(), table=<library_info_association>, default=ColumnDefault(False)), schema=None)¶
-
-
class
galaxy.model.
LibraryFolderInfoAssociation
(folder, form_definition, info, inheritable=False)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(folder, form_definition, info, inheritable=False)¶
-
folder
¶
-
template
¶
-
info
¶
-
inheritable
¶
-
deleted
¶
-
form_definition_id
¶
-
form_values_id
¶
-
id
¶
-
library_folder_id
¶
-
table
= Table('library_folder_info_association', MetaData(bind=None), Column('id', Integer(), table=<library_folder_info_association>, primary_key=True, nullable=False), Column('library_folder_id', Integer(), ForeignKey('library_folder.id'), table=<library_folder_info_association>), Column('form_definition_id', Integer(), ForeignKey('form_definition.id'), table=<library_folder_info_association>), Column('form_values_id', Integer(), ForeignKey('form_values.id'), table=<library_folder_info_association>), Column('inheritable', Boolean(), table=<library_folder_info_association>, default=ColumnDefault(False)), Column('deleted', Boolean(), table=<library_folder_info_association>, default=ColumnDefault(False)), schema=None)¶
-
-
class
galaxy.model.
LibraryDatasetDatasetInfoAssociation
(library_dataset_dataset_association, form_definition, info)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(library_dataset_dataset_association, form_definition, info)¶
-
library_dataset_dataset_association
¶
-
template
¶
-
info
¶
-
inheritable
¶
-
deleted
¶
-
form_definition_id
¶
-
form_values_id
¶
-
id
¶
-
library_dataset_dataset_association_id
¶
-
table
= Table('library_dataset_dataset_info_association', MetaData(bind=None), Column('id', Integer(), table=<library_dataset_dataset_info_association>, primary_key=True, nullable=False), Column('library_dataset_dataset_association_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<library_dataset_dataset_info_association>), Column('form_definition_id', Integer(), ForeignKey('form_definition.id'), table=<library_dataset_dataset_info_association>), Column('form_values_id', Integer(), ForeignKey('form_values.id'), table=<library_dataset_dataset_info_association>), Column('deleted', Boolean(), table=<library_dataset_dataset_info_association>, default=ColumnDefault(False)), schema=None)¶
-
-
class
galaxy.model.
ValidationError
(message=None, err_type=None, attributes=None)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(message=None, err_type=None, attributes=None)¶
-
message
¶
-
err_type
¶
-
attributes
¶
-
dataset_id
¶
-
id
¶
-
table
= Table('validation_error', MetaData(bind=None), Column('id', Integer(), table=<validation_error>, primary_key=True, nullable=False), Column('dataset_id', Integer(), ForeignKey('history_dataset_association.id'), table=<validation_error>), Column('message', TrimmedString(length=255), table=<validation_error>), Column('err_type', TrimmedString(length=64), table=<validation_error>), Column('attributes', TEXT(), table=<validation_error>), schema=None)¶
-
-
class
galaxy.model.
DatasetToValidationErrorAssociation
(dataset, validation_error)[source]¶ Bases:
object
-
class
galaxy.model.
ImplicitlyConvertedDatasetAssociation
(id=None, parent=None, dataset=None, file_type=None, deleted=False, purged=False, metadata_safe=True)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(id=None, parent=None, dataset=None, file_type=None, deleted=False, purged=False, metadata_safe=True)¶
-
id
¶
-
dataset
¶
-
dataset_ldda
¶
-
parent_hda
¶
-
parent_ldda
¶
-
type
¶
-
deleted
¶
-
metadata_safe
¶
-
create_time
¶
-
hda_id
¶
-
hda_parent_id
¶
-
ldda_id
¶
-
ldda_parent_id
¶
-
table
= Table('implicitly_converted_dataset_association', MetaData(bind=None), Column('id', Integer(), table=<implicitly_converted_dataset_association>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<implicitly_converted_dataset_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<implicitly_converted_dataset_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('hda_id', Integer(), ForeignKey('history_dataset_association.id'), table=<implicitly_converted_dataset_association>), Column('ldda_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<implicitly_converted_dataset_association>), Column('hda_parent_id', Integer(), ForeignKey('history_dataset_association.id'), table=<implicitly_converted_dataset_association>), Column('ldda_parent_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<implicitly_converted_dataset_association>), Column('deleted', Boolean(), table=<implicitly_converted_dataset_association>, default=ColumnDefault(False)), Column('metadata_safe', Boolean(), table=<implicitly_converted_dataset_association>, default=ColumnDefault(True)), Column('type', TrimmedString(length=255), table=<implicitly_converted_dataset_association>), schema=None)¶
-
update_time
¶
-
-
class
galaxy.model.
DatasetCollection
(id=None, collection_type=None, populated=True, element_count=None)[source]¶ Bases:
galaxy.util.dictifiable.Dictifiable
,galaxy.model.item_attrs.UsesAnnotations
,galaxy.model.RepresentById
-
dict_collection_visible_keys
= ['id', 'collection_type']¶
-
dict_element_visible_keys
= ['id', 'collection_type']¶
-
populated_states
= <galaxy.util.bunch.Bunch object>¶
-
__init__
(id=None, collection_type=None, populated=True, element_count=None)¶
-
id
¶
-
collection_type
¶
-
populated_state
¶
-
element_count
¶
-
dataset_states_and_extensions_summary
¶
-
populated_optimized
¶
-
populated
¶
-
dataset_action_tuples
¶
-
waiting_for_elements
¶
-
dataset_instances
¶
-
dataset_elements
¶
-
first_dataset_element
¶
-
state
¶
-
has_subcollections
¶
-
create_time
¶
-
elements
¶
-
output_dataset_collections
¶
-
populated_state_message
¶
-
table
= Table('dataset_collection', MetaData(bind=None), Column('id', Integer(), table=<dataset_collection>, primary_key=True, nullable=False), Column('collection_type', Unicode(length=255), table=<dataset_collection>, nullable=False), Column('populated_state', TrimmedString(length=64), table=<dataset_collection>, nullable=False, default=ColumnDefault('ok')), Column('populated_state_message', TEXT(), table=<dataset_collection>), Column('element_count', Integer(), table=<dataset_collection>), Column('create_time', DateTime(), table=<dataset_collection>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<dataset_collection>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)¶
-
update_time
¶
-
-
class
galaxy.model.
DatasetCollectionInstance
(collection=None, deleted=False)[source]¶ Bases:
galaxy.model.HasName
-
state
¶
-
populated
¶
-
dataset_instances
¶
-
-
class
galaxy.model.
HistoryDatasetCollectionAssociation
(id=None, hid=None, collection=None, history=None, name=None, deleted=False, visible=True, copied_from_history_dataset_collection_association=None, implicit_output_name=None, implicit_input_collections=[])[source]¶ Bases:
galaxy.model.DatasetCollectionInstance
,galaxy.model.HasTags
,galaxy.util.dictifiable.Dictifiable
,galaxy.model.item_attrs.UsesAnnotations
,galaxy.model.RepresentById
Associates a DatasetCollection with a History.
-
editable_keys
= ('name', 'deleted', 'visible')¶
-
__init__
(id=None, hid=None, collection=None, history=None, name=None, deleted=False, visible=True, copied_from_history_dataset_collection_association=None, implicit_output_name=None, implicit_input_collections=[])¶
-
id
¶
-
hid
¶
-
history
¶
-
name
¶
-
visible
¶
-
copied_from_history_dataset_collection_association
¶
-
implicit_output_name
¶
-
implicit_input_collections
¶
-
history_content_type
¶
-
content_type
= 'dataset_collection'¶
-
type_id
¶
-
job_source_type
¶
-
job_source_id
¶
-
copy
(element_destination=None)[source]¶ Create a copy of this history dataset collection association. Copy underlying collection.
-
annotations
¶
-
collection
¶
-
collection_id
¶
-
copied_from_history_dataset_collection_association_id
¶
-
copied_to_history_dataset_collection_associations
¶
-
creating_job_associations
¶
-
deleted
¶
-
history_id
¶
-
implicit_collection_jobs
¶
-
implicit_collection_jobs_id
¶
-
job
¶
-
job_id
¶
-
output_dataset_collection_instances
¶
-
ratings
¶
-
table
= Table('history_dataset_collection_association', MetaData(bind=None), Column('id', Integer(), table=<history_dataset_collection_association>, primary_key=True, nullable=False), Column('collection_id', Integer(), ForeignKey('dataset_collection.id'), table=<history_dataset_collection_association>), Column('history_id', Integer(), ForeignKey('history.id'), table=<history_dataset_collection_association>), Column('name', TrimmedString(length=255), table=<history_dataset_collection_association>), Column('hid', Integer(), table=<history_dataset_collection_association>), Column('visible', Boolean(), table=<history_dataset_collection_association>), Column('deleted', Boolean(), table=<history_dataset_collection_association>, default=ColumnDefault(False)), Column('copied_from_history_dataset_collection_association_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<history_dataset_collection_association>), Column('implicit_output_name', Unicode(length=255), table=<history_dataset_collection_association>), Column('job_id', Integer(), ForeignKey('job.id'), table=<history_dataset_collection_association>), Column('implicit_collection_jobs_id', Integer(), ForeignKey('implicit_collection_jobs.id'), table=<history_dataset_collection_association>), schema=None)¶
-
-
class
galaxy.model.
LibraryDatasetCollectionAssociation
(id=None, collection=None, name=None, deleted=False, folder=None)[source]¶ Bases:
galaxy.model.DatasetCollectionInstance
,galaxy.model.RepresentById
Associates a DatasetCollection with a library folder.
-
editable_keys
= ('name', 'deleted')¶
-
__init__
(id=None, collection=None, name=None, deleted=False, folder=None)¶
-
id
¶
-
folder
¶
-
name
¶
-
annotations
¶
-
collection
¶
-
collection_id
¶
-
deleted
¶
-
folder_id
¶
-
ratings
¶
-
table
= Table('library_dataset_collection_association', MetaData(bind=None), Column('id', Integer(), table=<library_dataset_collection_association>, primary_key=True, nullable=False), Column('collection_id', Integer(), ForeignKey('dataset_collection.id'), table=<library_dataset_collection_association>), Column('folder_id', Integer(), ForeignKey('library_folder.id'), table=<library_dataset_collection_association>), Column('name', TrimmedString(length=255), table=<library_dataset_collection_association>), Column('deleted', Boolean(), table=<library_dataset_collection_association>, default=ColumnDefault(False)), schema=None)¶
-
-
class
galaxy.model.
DatasetCollectionElement
(id=None, collection=None, element=None, element_index=None, element_identifier=None)[source]¶ Bases:
galaxy.util.dictifiable.Dictifiable
,galaxy.model.RepresentById
Associates a DatasetInstance (hda or ldda) with a DatasetCollection.
-
dict_collection_visible_keys
= ['id', 'element_type', 'element_index', 'element_identifier']¶
-
dict_element_visible_keys
= ['id', 'element_type', 'element_index', 'element_identifier']¶
-
UNINITIALIZED_ELEMENT
= <object object>¶
-
__init__
(id=None, collection=None, element=None, element_index=None, element_identifier=None)¶
-
hda
¶
-
ldda
¶
-
child_collection
¶
-
id
¶
-
collection
¶
-
element_index
¶
-
element_identifier
¶
-
element_type
¶
-
is_collection
¶
-
element_object
¶
-
dataset_instance
¶
-
dataset
¶
-
dataset_instances
¶
-
child_collection_id
¶
-
dataset_collection_id
¶
-
hda_id
¶
-
ldda_id
¶
-
table
= Table('dataset_collection_element', MetaData(bind=None), Column('id', Integer(), table=<dataset_collection_element>, primary_key=True, nullable=False), Column('dataset_collection_id', Integer(), ForeignKey('dataset_collection.id'), table=<dataset_collection_element>, nullable=False), Column('hda_id', Integer(), ForeignKey('history_dataset_association.id'), table=<dataset_collection_element>), Column('ldda_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<dataset_collection_element>), Column('child_collection_id', Integer(), ForeignKey('dataset_collection.id'), table=<dataset_collection_element>), Column('element_index', Integer(), table=<dataset_collection_element>), Column('element_identifier', Unicode(length=255), table=<dataset_collection_element>), schema=None)¶
-
-
class
galaxy.model.
Event
(message=None, history=None, user=None, galaxy_session=None)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(message=None, history=None, user=None, galaxy_session=None)¶
-
history
¶
-
galaxy_session
¶
-
user
¶
-
tool_id
¶
-
message
¶
-
create_time
¶
-
history_id
¶
-
id
¶
-
session_id
¶
-
table
= Table('event', MetaData(bind=None), Column('id', Integer(), table=<event>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<event>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<event>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('history_id', Integer(), ForeignKey('history.id'), table=<event>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<event>), Column('message', TrimmedString(length=1024), table=<event>), Column('session_id', Integer(), ForeignKey('galaxy_session.id'), table=<event>), Column('tool_id', String(length=255), table=<event>), schema=None)¶
-
update_time
¶
-
user_id
¶
-
-
class
galaxy.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:
galaxy.model.RepresentById
-
__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
¶
-
current_history
¶
-
session_key
¶
-
is_valid
¶
-
prev_session_id
¶
-
histories
¶
-
last_action
¶
-
total_disk_usage
¶
-
create_time
¶
-
current_history_id
¶
-
disk_usage
¶
-
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 datetime.utcnow>)), Column('update_time', DateTime(), table=<galaxy_session>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.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('current_history_id', Integer(), ForeignKey('history.id'), 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('disk_usage', Numeric(precision=15, scale=0), table=<galaxy_session>), Column('last_action', DateTime(), table=<galaxy_session>), schema=None)¶
-
update_time
¶
-
user_id
¶
-
-
class
galaxy.model.
GalaxySessionToHistoryAssociation
(galaxy_session, history)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(galaxy_session, history)¶
-
galaxy_session
¶
-
history
¶
-
create_time
¶
-
history_id
¶
-
id
¶
-
session_id
¶
-
table
= Table('galaxy_session_to_history', MetaData(bind=None), Column('id', Integer(), table=<galaxy_session_to_history>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<galaxy_session_to_history>, default=ColumnDefault(<function datetime.utcnow>)), Column('session_id', Integer(), ForeignKey('galaxy_session.id'), table=<galaxy_session_to_history>), Column('history_id', Integer(), ForeignKey('history.id'), table=<galaxy_session_to_history>), schema=None)¶
-
-
class
galaxy.model.
StoredWorkflow
[source]¶ Bases:
galaxy.model.HasTags
,galaxy.util.dictifiable.Dictifiable
,galaxy.model.RepresentById
-
dict_collection_visible_keys
= ['id', 'name', 'create_time', 'published', 'deleted']¶
-
dict_element_visible_keys
= ['id', 'name', 'create_time', 'published', 'deleted']¶
-
__init__
()¶
-
id
¶
-
user
¶
-
name
¶
-
slug
¶
-
create_time
¶
-
published
¶
-
latest_workflow_id
¶
-
workflows
¶
-
annotations
¶
-
average_rating
¶
-
deleted
¶
-
from_path
¶
-
importable
¶
-
latest_workflow
¶
-
ratings
¶
-
table
= Table('stored_workflow', MetaData(bind=None), Column('id', Integer(), table=<stored_workflow>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<stored_workflow>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<stored_workflow>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<stored_workflow>, nullable=False), Column('latest_workflow_id', Integer(), ForeignKey('workflow.id'), table=<stored_workflow>), Column('name', TEXT(), table=<stored_workflow>), Column('deleted', Boolean(), table=<stored_workflow>, default=ColumnDefault(False)), Column('importable', Boolean(), table=<stored_workflow>, default=ColumnDefault(False)), Column('slug', TEXT(), table=<stored_workflow>), Column('from_path', TEXT(), table=<stored_workflow>), Column('published', Boolean(), table=<stored_workflow>, default=ColumnDefault(False)), schema=None)¶
-
update_time
¶
-
user_id
¶
-
-
class
galaxy.model.
Workflow
(uuid=None)[source]¶ Bases:
galaxy.util.dictifiable.Dictifiable
,galaxy.model.RepresentById
-
dict_collection_visible_keys
= ['name', 'has_cycles', 'has_errors']¶
-
dict_element_visible_keys
= ['name', 'has_cycles', 'has_errors']¶
-
input_step_types
= ['data_input', 'data_collection_input', 'parameter_input']¶
-
__init__
(uuid=None)¶
-
name
¶
-
has_cycles
¶
-
has_errors
¶
-
steps
¶
-
uuid
¶
-
has_outputs_defined
()[source]¶ Returns true or false indicating whether or not a workflow has outputs defined.
-
steps_by_id
¶
-
input_steps
¶
-
workflow_outputs
¶
-
workflow_output_labels
¶
-
top_level_workflow
¶ If this workflow is not attached to stored workflow directly, recursively grab its parents until it is the top level workflow which must have a stored workflow associated with it.
-
top_level_stored_workflow
¶ If this workflow is not attached to stored workflow directly, recursively grab its parents until it is the top level workflow which must have a stored workflow associated with it and then grab that stored workflow.
-
create_time
¶
-
id
¶
-
parent_workflow_id
¶
-
parent_workflow_steps
¶
-
reports_config
¶
-
step_count
¶
-
stored_workflow
¶
-
stored_workflow_id
¶
-
table
= Table('workflow', MetaData(bind=None), Column('id', Integer(), table=<workflow>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<workflow>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<workflow>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('stored_workflow_id', Integer(), ForeignKey('stored_workflow.id'), table=<workflow>), Column('parent_workflow_id', Integer(), ForeignKey('workflow.id'), table=<workflow>), Column('name', TEXT(), table=<workflow>), Column('has_cycles', Boolean(), table=<workflow>), Column('has_errors', Boolean(), table=<workflow>), Column('reports_config', JSONType(), table=<workflow>), Column('uuid', UUIDType(), table=<workflow>), schema=None)¶
-
update_time
¶
-
-
class
galaxy.model.
WorkflowStep
[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
()¶
-
id
¶
-
type
¶
-
tool_id
¶
-
tool_inputs
¶
-
tool_errors
¶
-
dynamic_tool
¶
-
position
¶
-
inputs
¶
-
config
¶
-
label
¶
-
uuid
¶
-
workflow_outputs
¶
-
tool_uuid
¶
-
input_default_value
¶
-
input_connections
¶
-
unique_workflow_outputs
¶
-
content_id
¶
-
input_connections_by_name
¶
-
annotations
¶
-
create_time
¶
-
dynamic_tool_id
¶
-
order_index
¶
-
output_connections
¶
-
parent_workflow_input_connections
¶
-
post_job_actions
¶
-
subworkflow
¶
-
subworkflow_id
¶
-
table
= Table('workflow_step', MetaData(bind=None), Column('id', Integer(), table=<workflow_step>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<workflow_step>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<workflow_step>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('workflow_id', Integer(), ForeignKey('workflow.id'), table=<workflow_step>, nullable=False), Column('subworkflow_id', Integer(), ForeignKey('workflow.id'), table=<workflow_step>), Column('dynamic_tool_id', Integer(), ForeignKey('dynamic_tool.id'), table=<workflow_step>), Column('type', String(length=64), table=<workflow_step>), Column('tool_id', TEXT(), table=<workflow_step>), Column('tool_version', TEXT(), table=<workflow_step>), Column('tool_inputs', JSONType(), table=<workflow_step>), Column('tool_errors', JSONType(), table=<workflow_step>), Column('position', JSONType(), table=<workflow_step>), Column('config', JSONType(), table=<workflow_step>), Column('order_index', Integer(), table=<workflow_step>), Column('uuid', UUIDType(), table=<workflow_step>), Column('label', Unicode(length=255), table=<workflow_step>), schema=None)¶
-
tool_version
¶
-
update_time
¶
-
workflow
¶
-
workflow_id
¶
-
-
class
galaxy.model.
WorkflowStepInput
(workflow_step)[source]¶ Bases:
galaxy.model.RepresentById
-
default_merge_type
= None¶
-
default_scatter_type
= None¶
-
__init__
(workflow_step)¶
-
workflow_step
¶
-
name
¶
-
default_value
¶
-
default_value_set
¶
-
merge_type
¶
-
scatter_type
¶
-
connections
¶
-
id
¶
-
runtime_value
¶
-
table
= Table('workflow_step_input', MetaData(bind=None), Column('id', Integer(), table=<workflow_step_input>, primary_key=True, nullable=False), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_step_input>), Column('name', TEXT(), table=<workflow_step_input>), Column('merge_type', TEXT(), table=<workflow_step_input>), Column('scatter_type', TEXT(), table=<workflow_step_input>), Column('value_from', JSONType(), table=<workflow_step_input>), Column('value_from_type', TEXT(), table=<workflow_step_input>), Column('default_value', JSONType(), table=<workflow_step_input>), Column('default_value_set', Boolean(), table=<workflow_step_input>, default=ColumnDefault(False)), Column('runtime_value', Boolean(), table=<workflow_step_input>, default=ColumnDefault(False)), schema=None)¶
-
value_from
¶
-
value_from_type
¶
-
workflow_step_id
¶
-
-
class
galaxy.model.
WorkflowStepConnection
[source]¶ Bases:
galaxy.model.RepresentById
-
NON_DATA_CONNECTION
= '__NO_INPUT_OUTPUT_NAME__'¶
-
__init__
()¶
-
output_step_id
¶
-
output_name
¶
-
input_step_input_id
¶
-
non_data_connection
¶
-
input_name
¶
-
input_step
¶
-
input_step_id
¶
-
id
¶
-
input_step_input
¶
-
input_subworkflow_step
¶
-
input_subworkflow_step_id
¶
-
output_step
¶
-
table
= Table('workflow_step_connection', MetaData(bind=None), Column('id', Integer(), table=<workflow_step_connection>, primary_key=True, nullable=False), Column('output_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_step_connection>), Column('input_step_input_id', Integer(), ForeignKey('workflow_step_input.id'), table=<workflow_step_connection>), Column('output_name', TEXT(), table=<workflow_step_connection>), Column('input_subworkflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_step_connection>), schema=None)¶
-
-
class
galaxy.model.
WorkflowOutput
(workflow_step, output_name=None, label=None, uuid=None)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(workflow_step, output_name=None, label=None, uuid=None)¶
-
workflow_step
¶
-
output_name
¶
-
label
¶
-
uuid
¶
-
id
¶
-
table
= Table('workflow_output', MetaData(bind=None), Column('id', Integer(), table=<workflow_output>, primary_key=True, nullable=False), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_output>, nullable=False), Column('output_name', String(length=255), table=<workflow_output>), Column('label', Unicode(length=255), table=<workflow_output>), Column('uuid', UUIDType(), table=<workflow_output>), schema=None)¶
-
workflow_step_id
¶
-
Bases:
galaxy.model.RepresentById
-
class
galaxy.model.
StoredWorkflowMenuEntry
[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
()¶
-
stored_workflow
¶
-
user
¶
-
order_index
¶
-
id
¶
-
stored_workflow_id
¶
-
table
= Table('stored_workflow_menu_entry', MetaData(bind=None), Column('id', Integer(), table=<stored_workflow_menu_entry>, primary_key=True, nullable=False), Column('stored_workflow_id', Integer(), ForeignKey('stored_workflow.id'), table=<stored_workflow_menu_entry>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<stored_workflow_menu_entry>), Column('order_index', Integer(), table=<stored_workflow_menu_entry>), schema=None)¶
-
user_id
¶
-
-
class
galaxy.model.
WorkflowInvocation
[source]¶ Bases:
galaxy.model.UsesCreateAndUpdateTime
,galaxy.util.dictifiable.Dictifiable
,galaxy.model.RepresentById
-
dict_collection_visible_keys
= ['id', 'update_time', 'create_time', 'workflow_id', 'history_id', 'uuid', 'state']¶
-
dict_element_visible_keys
= ['id', 'update_time', 'create_time', 'workflow_id', 'history_id', 'uuid', 'state']¶
-
states
= <galaxy.util.bunch.Bunch object>¶
-
non_terminal_states
= ['new', 'ready']¶
-
__init__
()¶
-
subworkflow_invocations
¶
-
step_states
¶
-
steps
¶
-
active
¶ Indicates the workflow invocation is somehow active - and in particular valid actions may be performed on its WorkflowInvocationSteps.
-
output_associations
¶
-
input_associations
¶
-
update
()¶
-
resource_parameters
¶
-
create_time
¶
-
handler
¶
-
history
¶
-
history_id
¶
-
id
¶
-
input_dataset_collections
¶
-
input_datasets
¶
-
input_parameters
¶
-
input_step_parameters
¶
-
output_dataset_collections
¶
-
output_datasets
¶
-
output_values
¶
-
parent_workflow_invocation_association
¶
-
scheduler
¶
-
state
¶
-
table
= Table('workflow_invocation', MetaData(bind=None), Column('id', Integer(), table=<workflow_invocation>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<workflow_invocation>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<workflow_invocation>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('workflow_id', Integer(), ForeignKey('workflow.id'), table=<workflow_invocation>, nullable=False), Column('state', TrimmedString(length=64), table=<workflow_invocation>), Column('scheduler', TrimmedString(length=255), table=<workflow_invocation>), Column('handler', TrimmedString(length=255), table=<workflow_invocation>), Column('uuid', UUIDType(), table=<workflow_invocation>), Column('history_id', Integer(), ForeignKey('history.id'), table=<workflow_invocation>), schema=None)¶
-
update_time
¶
-
uuid
¶
-
workflow
¶
-
workflow_id
¶
-
-
class
galaxy.model.
WorkflowInvocationToSubworkflowInvocationAssociation
[source]¶ Bases:
galaxy.util.dictifiable.Dictifiable
,galaxy.model.RepresentById
-
dict_collection_visible_keys
= ['id', 'workflow_step_id', 'workflow_invocation_id', 'subworkflow_invocation_id']¶
-
dict_element_visible_keys
= ['id', 'workflow_step_id', 'workflow_invocation_id', 'subworkflow_invocation_id']¶
-
__init__
()¶ Initialize self. See help(type(self)) for accurate signature.
-
id
¶
-
parent_workflow_invocation
¶
-
subworkflow_invocation
¶
-
subworkflow_invocation_id
¶
-
table
= Table('workflow_invocation_to_subworkflow_invocation_association', MetaData(bind=None), Column('id', Integer(), table=<workflow_invocation_to_subworkflow_invocation_association>, primary_key=True, nullable=False), Column('workflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_invocation_to_subworkflow_invocation_association>), Column('subworkflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_invocation_to_subworkflow_invocation_association>), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_invocation_to_subworkflow_invocation_association>), schema=None)¶
-
workflow_invocation_id
¶
-
workflow_step
¶
-
workflow_step_id
¶
-
-
class
galaxy.model.
WorkflowInvocationStep
[source]¶ Bases:
galaxy.util.dictifiable.Dictifiable
,galaxy.model.RepresentById
-
dict_collection_visible_keys
= ['id', 'update_time', 'job_id', 'workflow_step_id', 'state', 'action']¶
-
dict_element_visible_keys
= ['id', 'update_time', 'job_id', 'workflow_step_id', 'state', 'action']¶
-
states
= <galaxy.util.bunch.Bunch object>¶
-
is_new
¶
-
jobs
¶
-
__init__
()¶ Initialize self. See help(type(self)) for accurate signature.
-
action
¶
-
create_time
¶
-
id
¶
-
implicit_collection_jobs
¶
-
implicit_collection_jobs_id
¶
-
job
¶
-
job_id
¶
-
output_dataset_collections
¶
-
output_datasets
¶
-
output_value
¶
-
state
¶
-
table
= Table('workflow_invocation_step', MetaData(bind=None), Column('id', Integer(), table=<workflow_invocation_step>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<workflow_invocation_step>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<workflow_invocation_step>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('workflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_invocation_step>, nullable=False), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_invocation_step>, nullable=False), Column('state', TrimmedString(length=64), table=<workflow_invocation_step>), Column('job_id', Integer(), ForeignKey('job.id'), table=<workflow_invocation_step>), Column('implicit_collection_jobs_id', Integer(), ForeignKey('implicit_collection_jobs.id'), table=<workflow_invocation_step>), Column('action', JSONType(), table=<workflow_invocation_step>), schema=None)¶
-
update_time
¶
-
workflow_invocation
¶
-
workflow_invocation_id
¶
-
workflow_step
¶
-
workflow_step_id
¶
-
-
class
galaxy.model.
WorkflowRequestInputParameter
(name=None, value=None, type=None)[source]¶ Bases:
galaxy.util.dictifiable.Dictifiable
,galaxy.model.RepresentById
Workflow-related parameters not tied to steps or inputs.
-
dict_collection_visible_keys
= ['id', 'name', 'value', 'type']¶
-
types
= <galaxy.util.bunch.Bunch object>¶
-
__init__
(name=None, value=None, type=None)¶
-
name
¶
-
value
¶
-
type
¶
-
id
¶
-
table
= Table('workflow_request_input_parameters', MetaData(bind=None), Column('id', Integer(), table=<workflow_request_input_parameters>, primary_key=True, nullable=False), Column('workflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_request_input_parameters>), Column('name', Unicode(length=255), table=<workflow_request_input_parameters>), Column('value', TEXT(), table=<workflow_request_input_parameters>), Column('type', Unicode(length=255), table=<workflow_request_input_parameters>), schema=None)¶
-
workflow_invocation
¶
-
workflow_invocation_id
¶
-
-
class
galaxy.model.
WorkflowRequestStepState
(workflow_step=None, name=None, value=None)[source]¶ Bases:
galaxy.util.dictifiable.Dictifiable
,galaxy.model.RepresentById
Workflow step value parameters.
-
dict_collection_visible_keys
= ['id', 'name', 'value', 'workflow_step_id']¶
-
__init__
(workflow_step=None, name=None, value=None)¶
-
workflow_step
¶
-
value
¶
-
id
¶
-
table
= Table('workflow_request_step_states', MetaData(bind=None), Column('id', Integer(), table=<workflow_request_step_states>, primary_key=True, nullable=False), Column('workflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_request_step_states>), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_request_step_states>), Column('value', JSONType(), table=<workflow_request_step_states>), schema=None)¶
-
workflow_invocation
¶
-
workflow_invocation_id
¶
-
workflow_step_id
¶
-
-
class
galaxy.model.
WorkflowRequestToInputDatasetAssociation
[source]¶ Bases:
galaxy.util.dictifiable.Dictifiable
,galaxy.model.RepresentById
Workflow step input dataset parameters.
-
history_content_type
= 'dataset'¶
-
dict_collection_visible_keys
= ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_id', 'name']¶
-
__init__
()¶ Initialize self. See help(type(self)) for accurate signature.
-
dataset
¶
-
dataset_id
¶
-
id
¶
-
name
¶
-
table
= Table('workflow_request_to_input_dataset', MetaData(bind=None), Column('id', Integer(), table=<workflow_request_to_input_dataset>, primary_key=True, nullable=False), Column('name', String(length=255), table=<workflow_request_to_input_dataset>), Column('workflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_request_to_input_dataset>), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_request_to_input_dataset>), Column('dataset_id', Integer(), ForeignKey('history_dataset_association.id'), table=<workflow_request_to_input_dataset>), schema=None)¶
-
workflow_invocation
¶
-
workflow_invocation_id
¶
-
workflow_step
¶
-
workflow_step_id
¶
-
-
class
galaxy.model.
WorkflowRequestToInputDatasetCollectionAssociation
[source]¶ Bases:
galaxy.util.dictifiable.Dictifiable
,galaxy.model.RepresentById
Workflow step input dataset collection parameters.
-
history_content_type
= 'dataset_collection'¶
-
dict_collection_visible_keys
= ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_collection_id', 'name']¶
-
__init__
()¶ Initialize self. See help(type(self)) for accurate signature.
-
dataset_collection
¶
-
dataset_collection_id
¶
-
id
¶
-
name
¶
-
table
= Table('workflow_request_to_input_collection_dataset', MetaData(bind=None), Column('id', Integer(), table=<workflow_request_to_input_collection_dataset>, primary_key=True, nullable=False), Column('name', String(length=255), table=<workflow_request_to_input_collection_dataset>), Column('workflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_request_to_input_collection_dataset>), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_request_to_input_collection_dataset>), Column('dataset_collection_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<workflow_request_to_input_collection_dataset>), schema=None)¶
-
workflow_invocation
¶
-
workflow_invocation_id
¶
-
workflow_step
¶
-
workflow_step_id
¶
-
-
class
galaxy.model.
WorkflowRequestInputStepParameter
[source]¶ Bases:
galaxy.util.dictifiable.Dictifiable
,galaxy.model.RepresentById
Workflow step parameter inputs.
-
dict_collection_visible_keys
= ['id', 'workflow_invocation_id', 'workflow_step_id', 'parameter_value']¶
-
__init__
()¶ Initialize self. See help(type(self)) for accurate signature.
-
id
¶
-
parameter_value
¶
-
table
= Table('workflow_request_input_step_parameter', MetaData(bind=None), Column('id', Integer(), table=<workflow_request_input_step_parameter>, primary_key=True, nullable=False), Column('workflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_request_input_step_parameter>), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_request_input_step_parameter>), Column('parameter_value', JSONType(), table=<workflow_request_input_step_parameter>), schema=None)¶
-
workflow_invocation
¶
-
workflow_invocation_id
¶
-
workflow_step
¶
-
workflow_step_id
¶
-
-
class
galaxy.model.
WorkflowInvocationOutputDatasetAssociation
[source]¶ Bases:
galaxy.util.dictifiable.Dictifiable
,galaxy.model.RepresentById
Represents links to output datasets for the workflow.
-
history_content_type
= 'dataset'¶
-
dict_collection_visible_keys
= ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_id', 'name']¶
-
__init__
()¶ Initialize self. See help(type(self)) for accurate signature.
-
dataset
¶
-
dataset_id
¶
-
id
¶
-
table
= Table('workflow_invocation_output_dataset_association', MetaData(bind=None), Column('id', Integer(), table=<workflow_invocation_output_dataset_association>, primary_key=True, nullable=False), Column('workflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_invocation_output_dataset_association>), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_invocation_output_dataset_association>), Column('dataset_id', Integer(), ForeignKey('history_dataset_association.id'), table=<workflow_invocation_output_dataset_association>), Column('workflow_output_id', Integer(), ForeignKey('workflow_output.id'), table=<workflow_invocation_output_dataset_association>), schema=None)¶
-
workflow_invocation
¶
-
workflow_invocation_id
¶
-
workflow_output
¶
-
workflow_output_id
¶
-
workflow_step
¶
-
workflow_step_id
¶
-
-
class
galaxy.model.
WorkflowInvocationOutputDatasetCollectionAssociation
[source]¶ Bases:
galaxy.util.dictifiable.Dictifiable
,galaxy.model.RepresentById
Represents links to output dataset collections for the workflow.
-
history_content_type
= 'dataset_collection'¶
-
dict_collection_visible_keys
= ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_collection_id', 'name']¶
-
__init__
()¶ Initialize self. See help(type(self)) for accurate signature.
-
dataset_collection
¶
-
dataset_collection_id
¶
-
id
¶
-
table
= Table('workflow_invocation_output_dataset_collection_association', MetaData(bind=None), Column('id', Integer(), table=<workflow_invocation_output_dataset_collection_association>, primary_key=True, nullable=False), Column('workflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_invocation_output_dataset_collection_association>), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_invocation_output_dataset_collection_association>), Column('dataset_collection_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<workflow_invocation_output_dataset_collection_association>), Column('workflow_output_id', Integer(), ForeignKey('workflow_output.id'), table=<workflow_invocation_output_dataset_collection_association>), schema=None)¶
-
workflow_invocation
¶
-
workflow_invocation_id
¶
-
workflow_output
¶
-
workflow_output_id
¶
-
workflow_step
¶
-
workflow_step_id
¶
-
-
class
galaxy.model.
WorkflowInvocationOutputValue
[source]¶ Bases:
galaxy.util.dictifiable.Dictifiable
,galaxy.model.RepresentById
Represents a link to a specified or computed workflow parameter.
-
dict_collection_visible_keys
= ['id', 'workflow_invocation_id', 'workflow_step_id', 'value']¶
-
__init__
()¶ Initialize self. See help(type(self)) for accurate signature.
-
id
¶
-
table
= Table('workflow_invocation_output_value', MetaData(bind=None), Column('id', Integer(), table=<workflow_invocation_output_value>, primary_key=True, nullable=False), Column('workflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_invocation_output_value>), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_invocation_output_value>), Column('workflow_output_id', Integer(), ForeignKey('workflow_output.id'), table=<workflow_invocation_output_value>), Column('value', JSONType(), table=<workflow_invocation_output_value>), schema=None)¶
-
value
¶
-
workflow_invocation
¶
-
workflow_invocation_id
¶
-
workflow_invocation_step
¶
-
workflow_output
¶
-
workflow_output_id
¶
-
workflow_step
¶
-
workflow_step_id
¶
-
-
class
galaxy.model.
WorkflowInvocationStepOutputDatasetAssociation
[source]¶ Bases:
galaxy.util.dictifiable.Dictifiable
,galaxy.model.RepresentById
Represents links to output datasets for the workflow.
-
dict_collection_visible_keys
= ['id', 'workflow_invocation_step_id', 'dataset_id', 'output_name']¶
-
__init__
()¶ Initialize self. See help(type(self)) for accurate signature.
-
dataset
¶
-
dataset_id
¶
-
id
¶
-
output_name
¶
-
table
= Table('workflow_invocation_step_output_dataset_association', MetaData(bind=None), Column('id', Integer(), table=<workflow_invocation_step_output_dataset_association>, primary_key=True, nullable=False), Column('workflow_invocation_step_id', Integer(), ForeignKey('workflow_invocation_step.id'), table=<workflow_invocation_step_output_dataset_association>), Column('dataset_id', Integer(), ForeignKey('history_dataset_association.id'), table=<workflow_invocation_step_output_dataset_association>), Column('output_name', String(length=255), table=<workflow_invocation_step_output_dataset_association>), schema=None)¶
-
workflow_invocation_step
¶
-
workflow_invocation_step_id
¶
-
-
class
galaxy.model.
WorkflowInvocationStepOutputDatasetCollectionAssociation
[source]¶ Bases:
galaxy.util.dictifiable.Dictifiable
,galaxy.model.RepresentById
Represents links to output dataset collections for the workflow.
-
dict_collection_visible_keys
= ['id', 'workflow_invocation_step_id', 'dataset_collection_id', 'output_name']¶
-
__init__
()¶ Initialize self. See help(type(self)) for accurate signature.
-
dataset_collection
¶
-
dataset_collection_id
¶
-
id
¶
-
output_name
¶
-
table
= Table('workflow_invocation_step_output_dataset_collection_association', MetaData(bind=None), Column('id', Integer(), table=<workflow_invocation_step_output_dataset_collection_association>, primary_key=True, nullable=False), Column('workflow_invocation_step_id', Integer(), ForeignKey('workflow_invocation_step.id'), table=<workflow_invocation_step_output_dataset_collection_association>), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_invocation_step_output_dataset_collection_association>), Column('dataset_collection_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<workflow_invocation_step_output_dataset_collection_association>), Column('output_name', String(length=255), table=<workflow_invocation_step_output_dataset_collection_association>), schema=None)¶
-
workflow_invocation_step
¶
-
workflow_invocation_step_id
¶
-
workflow_step_id
¶
-
-
class
galaxy.model.
MetadataFile
(dataset=None, name=None, uuid=None)[source]¶ Bases:
galaxy.model.StorableObject
,galaxy.model.RepresentById
-
__init__
(dataset=None, name=None, uuid=None)¶
-
history_dataset
¶
-
library_dataset
¶
-
name
¶
-
file_name
¶
-
create_time
¶
-
deleted
¶
-
hda_id
¶
-
id
¶
-
lda_id
¶
-
object_store_id
¶
-
purged
¶
-
table
= Table('metadata_file', MetaData(bind=None), Column('id', Integer(), table=<metadata_file>, primary_key=True, nullable=False), Column('name', TEXT(), table=<metadata_file>), Column('hda_id', Integer(), ForeignKey('history_dataset_association.id'), table=<metadata_file>), Column('lda_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<metadata_file>), Column('create_time', DateTime(), table=<metadata_file>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<metadata_file>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('object_store_id', TrimmedString(length=255), table=<metadata_file>), Column('uuid', UUIDType(), table=<metadata_file>), Column('deleted', Boolean(), table=<metadata_file>, default=ColumnDefault(False)), Column('purged', Boolean(), table=<metadata_file>, default=ColumnDefault(False)), schema=None)¶
-
update_time
¶
-
uuid
¶
-
-
class
galaxy.model.
FormDefinition
(name=None, desc=None, fields=[], form_definition_current=None, form_type=None, layout=None)[source]¶ Bases:
galaxy.util.dictifiable.Dictifiable
,galaxy.model.RepresentById
-
supported_field_types
= [<class 'galaxy.util.form_builder.AddressField'>, <class 'galaxy.util.form_builder.CheckboxField'>, <class 'galaxy.util.form_builder.PasswordField'>, <class 'galaxy.util.form_builder.SelectField'>, <class 'galaxy.util.form_builder.TextArea'>, <class 'galaxy.util.form_builder.TextField'>, <class 'galaxy.util.form_builder.WorkflowField'>, <class 'galaxy.util.form_builder.WorkflowMappingField'>, <class 'galaxy.util.form_builder.HistoryField'>]¶
-
types
= <galaxy.util.bunch.Bunch object>¶
-
dict_collection_visible_keys
= ['id', 'name']¶
-
dict_element_visible_keys
= ['id', 'name', 'desc', 'form_definition_current_id', 'fields', 'layout']¶
-
__init__
(name=None, desc=None, fields=[], form_definition_current=None, form_type=None, layout=None)¶
-
name
¶
-
desc
¶
-
fields
¶
-
form_definition_current
¶
-
type
¶
-
layout
¶
-
create_time
¶
-
current
¶
-
form_definition_current_id
¶
-
id
¶
-
table
= Table('form_definition', MetaData(bind=None), Column('id', Integer(), table=<form_definition>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<form_definition>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<form_definition>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('name', TrimmedString(length=255), table=<form_definition>, nullable=False), Column('desc', TEXT(), table=<form_definition>), Column('form_definition_current_id', Integer(), ForeignKey('form_definition_current.id'), table=<form_definition>, nullable=False), Column('fields', JSONType(), table=<form_definition>), Column('type', TrimmedString(length=255), table=<form_definition>), Column('layout', JSONType(), table=<form_definition>), schema=None)¶
-
update_time
¶
-
-
class
galaxy.model.
FormDefinitionCurrent
(form_definition=None)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(form_definition=None)¶
-
latest_form
¶
-
create_time
¶
-
deleted
¶
-
forms
¶
-
id
¶
-
latest_form_id
¶
-
table
= Table('form_definition_current', MetaData(bind=None), Column('id', Integer(), table=<form_definition_current>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<form_definition_current>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<form_definition_current>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('latest_form_id', Integer(), ForeignKey('form_definition.id'), table=<form_definition_current>), Column('deleted', Boolean(), table=<form_definition_current>, default=ColumnDefault(False)), schema=None)¶
-
update_time
¶
-
-
class
galaxy.model.
FormValues
(form_def=None, content=None)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(form_def=None, content=None)¶
-
form_definition
¶
-
content
¶
-
create_time
¶
-
form_definition_id
¶
-
id
¶
-
table
= Table('form_values', MetaData(bind=None), Column('id', Integer(), table=<form_values>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<form_values>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<form_values>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('form_definition_id', Integer(), ForeignKey('form_definition.id'), table=<form_values>), Column('content', JSONType(), table=<form_values>), schema=None)¶
-
update_time
¶
-
-
class
galaxy.model.
UserAddress
(user=None, desc=None, name=None, institution=None, address=None, city=None, state=None, postal_code=None, country=None, phone=None)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(user=None, desc=None, name=None, institution=None, address=None, city=None, state=None, postal_code=None, country=None, phone=None)¶
-
user
¶
-
desc
¶
-
name
¶
-
institution
¶
-
address
¶
-
city
¶
-
state
¶
-
postal_code
¶
-
country
¶
-
phone
¶
-
create_time
¶
-
deleted
¶
-
id
¶
-
purged
¶
-
table
= Table('user_address', MetaData(bind=None), Column('id', Integer(), table=<user_address>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<user_address>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<user_address>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<user_address>), Column('desc', TrimmedString(length=255), table=<user_address>), Column('name', TrimmedString(length=255), table=<user_address>, nullable=False), Column('institution', TrimmedString(length=255), table=<user_address>), Column('address', TrimmedString(length=255), table=<user_address>, nullable=False), Column('city', TrimmedString(length=255), table=<user_address>, nullable=False), Column('state', TrimmedString(length=255), table=<user_address>, nullable=False), Column('postal_code', TrimmedString(length=255), table=<user_address>, nullable=False), Column('country', TrimmedString(length=255), table=<user_address>, nullable=False), Column('phone', TrimmedString(length=255), table=<user_address>), Column('deleted', Boolean(), table=<user_address>, default=ColumnDefault(False)), Column('purged', Boolean(), table=<user_address>, default=ColumnDefault(False)), schema=None)¶
-
update_time
¶
-
user_id
¶
-
-
class
galaxy.model.
PSAAssociation
(server_url=None, handle=None, secret=None, issued=None, lifetime=None, assoc_type=None)[source]¶ Bases:
social_core.storage.AssociationMixin
,galaxy.model.RepresentById
-
sa_session
= None¶
-
__init__
(server_url=None, handle=None, secret=None, issued=None, lifetime=None, assoc_type=None)¶
-
server_url
¶
-
handle
¶
-
secret
¶
-
issued
¶
-
lifetime
¶
-
assoc_type
¶
-
id
¶
-
table
= Table('psa_association', MetaData(bind=None), Column('id', Integer(), table=<psa_association>, primary_key=True, nullable=False), Column('server_url', VARCHAR(length=255), table=<psa_association>), Column('handle', VARCHAR(length=255), table=<psa_association>), Column('secret', VARCHAR(length=255), table=<psa_association>), Column('issued', Integer(), table=<psa_association>), Column('lifetime', Integer(), table=<psa_association>), Column('assoc_type', VARCHAR(length=64), table=<psa_association>), schema=None)¶
-
-
class
galaxy.model.
PSACode
(email, code)[source]¶ Bases:
social_core.storage.CodeMixin
,galaxy.model.RepresentById
-
sa_session
= None¶
-
__init__
(email, code)¶
-
email
¶
-
code
¶
-
id
¶
-
table
= Table('psa_code', MetaData(bind=None), Column('id', Integer(), table=<psa_code>, primary_key=True, nullable=False), Column('email', VARCHAR(length=200), table=<psa_code>), Column('code', VARCHAR(length=32), table=<psa_code>), schema=None)¶
-
-
class
galaxy.model.
PSANonce
(server_url, timestamp, salt)[source]¶ Bases:
social_core.storage.NonceMixin
,galaxy.model.RepresentById
-
sa_session
= None¶
-
__init__
(server_url, timestamp, salt)¶
-
server_url
¶
-
timestamp
¶
-
salt
¶
-
id
¶
-
table
= Table('psa_nonce', MetaData(bind=None), Column('id', Integer(), table=<psa_nonce>, primary_key=True, nullable=False), Column('server_url', VARCHAR(length=255), table=<psa_nonce>), Column('timestamp', Integer(), table=<psa_nonce>), Column('salt', VARCHAR(length=40), table=<psa_nonce>), schema=None)¶
-
-
class
galaxy.model.
PSAPartial
(token, data, next_step, backend)[source]¶ Bases:
social_core.storage.PartialMixin
,galaxy.model.RepresentById
-
sa_session
= None¶
-
__init__
(token, data, next_step, backend)¶
-
token
¶
-
data
¶
-
next_step
¶
-
backend
¶
-
id
¶
-
table
= Table('psa_partial', MetaData(bind=None), Column('id', Integer(), table=<psa_partial>, primary_key=True, nullable=False), Column('token', VARCHAR(length=32), table=<psa_partial>), Column('data', TEXT(), table=<psa_partial>), Column('next_step', Integer(), table=<psa_partial>), Column('backend', VARCHAR(length=32), table=<psa_partial>), schema=None)¶
-
-
class
galaxy.model.
UserAuthnzToken
(provider, uid, extra_data=None, lifetime=None, assoc_type=None, user=None)[source]¶ Bases:
social_core.storage.UserMixin
,galaxy.model.RepresentById
-
sa_session
= None¶
-
__init__
(provider, uid, extra_data=None, lifetime=None, assoc_type=None, user=None)¶
-
provider
¶
-
uid
¶
-
user_id
¶
-
extra_data
¶
-
lifetime
¶
-
assoc_type
¶
-
classmethod
create_user
(*args, **kwargs)[source]¶ This is used by PSA authnz, do not use directly. Prefer using the user manager.
-
cloudauthz
¶
-
id
¶
-
table
= Table('oidc_user_authnz_tokens', MetaData(bind=None), Column('id', Integer(), table=<oidc_user_authnz_tokens>, primary_key=True, nullable=False), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<oidc_user_authnz_tokens>), Column('uid', VARCHAR(length=255), table=<oidc_user_authnz_tokens>), Column('provider', VARCHAR(length=32), table=<oidc_user_authnz_tokens>), Column('extra_data', JSONType(), table=<oidc_user_authnz_tokens>), Column('lifetime', Integer(), table=<oidc_user_authnz_tokens>), Column('assoc_type', VARCHAR(length=64), table=<oidc_user_authnz_tokens>), schema=None)¶
-
user
¶
-
-
class
galaxy.model.
CustosAuthnzToken
(user, external_user_id, provider, access_token, id_token, refresh_token, expiration_time, refresh_expiration_time)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(user, external_user_id, provider, access_token, id_token, refresh_token, expiration_time, refresh_expiration_time)¶
-
id
¶
-
user
¶
-
external_user_id
¶
-
provider
¶
-
access_token
¶
-
id_token
¶
-
refresh_token
¶
-
expiration_time
¶
-
refresh_expiration_time
¶
-
table
= Table('custos_authnz_token', MetaData(bind=None), Column('id', Integer(), table=<custos_authnz_token>, primary_key=True, nullable=False), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<custos_authnz_token>), Column('external_user_id', String(length=64), table=<custos_authnz_token>), Column('provider', String(length=255), table=<custos_authnz_token>), Column('access_token', Text(), table=<custos_authnz_token>), Column('id_token', Text(), table=<custos_authnz_token>), Column('refresh_token', Text(), table=<custos_authnz_token>), Column('expiration_time', DateTime(), table=<custos_authnz_token>), Column('refresh_expiration_time', DateTime(), table=<custos_authnz_token>), schema=None)¶
-
user_id
¶
-
-
class
galaxy.model.
CloudAuthz
(user_id, provider, config, authn_id, description='')[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(user_id, provider, config, authn_id, description='')¶
-
id
¶
-
user_id
¶
-
provider
¶
-
config
¶
-
authn_id
¶
-
tokens
¶
-
last_update
¶
-
last_activity
¶
-
description
¶
-
authn
¶
-
create_time
¶
-
table
= Table('cloudauthz', MetaData(bind=None), Column('id', Integer(), table=<cloudauthz>, primary_key=True, nullable=False), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<cloudauthz>), Column('provider', String(length=255), table=<cloudauthz>), Column('config', JSONType(), table=<cloudauthz>), Column('authn_id', Integer(), ForeignKey('oidc_user_authnz_tokens.id'), table=<cloudauthz>), Column('tokens', JSONType(), table=<cloudauthz>), Column('last_update', DateTime(), table=<cloudauthz>), Column('last_activity', DateTime(), table=<cloudauthz>), Column('description', TEXT(), table=<cloudauthz>), Column('create_time', DateTime(), table=<cloudauthz>, default=ColumnDefault(<function datetime.utcnow>)), schema=None)¶
-
user
¶
-
-
class
galaxy.model.
Page
[source]¶ Bases:
galaxy.util.dictifiable.Dictifiable
,galaxy.model.RepresentById
-
dict_element_visible_keys
= ['id', 'title', 'latest_revision_id', 'slug', 'published', 'importable', 'deleted', 'username']¶
-
__init__
()¶
-
id
¶
-
user
¶
-
title
¶
-
slug
¶
-
latest_revision_id
¶
-
revisions
¶
-
importable
¶
-
published
¶
-
username
¶
-
annotations
¶
-
average_rating
¶
-
create_time
¶
-
deleted
¶
-
latest_revision
¶
-
ratings
¶
-
table
= Table('page', MetaData(bind=None), Column('id', Integer(), table=<page>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<page>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<page>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<page>, nullable=False), Column('latest_revision_id', Integer(), ForeignKey('page_revision.id'), table=<page>), Column('title', TEXT(), table=<page>), Column('deleted', Boolean(), table=<page>, default=ColumnDefault(False)), Column('importable', Boolean(), table=<page>, default=ColumnDefault(False)), Column('slug', TEXT(), table=<page>), Column('published', Boolean(), table=<page>, default=ColumnDefault(False)), schema=None)¶
-
update_time
¶
-
user_id
¶
-
-
class
galaxy.model.
PageRevision
[source]¶ Bases:
galaxy.util.dictifiable.Dictifiable
,galaxy.model.RepresentById
-
DEFAULT_CONTENT_FORMAT
= 'html'¶
-
dict_element_visible_keys
= ['id', 'page_id', 'title', 'content', 'content_format']¶
-
__init__
()¶
-
title
¶
-
content
¶
-
content_format
¶
-
create_time
¶
-
id
¶
-
page
¶
-
page_id
¶
-
table
= Table('page_revision', MetaData(bind=None), Column('id', Integer(), table=<page_revision>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<page_revision>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<page_revision>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('page_id', Integer(), ForeignKey('page.id'), table=<page_revision>, nullable=False), Column('title', TEXT(), table=<page_revision>), Column('content', TEXT(), table=<page_revision>), Column('content_format', TrimmedString(length=32), table=<page_revision>), schema=None)¶
-
update_time
¶
-
Bases:
galaxy.model.RepresentById
-
class
galaxy.model.
Visualization
(id=None, user=None, type=None, title=None, dbkey=None, slug=None, latest_revision=None)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(id=None, user=None, type=None, title=None, dbkey=None, slug=None, latest_revision=None)¶
-
id
¶
-
user
¶
-
type
¶
-
title
¶
-
dbkey
¶
-
slug
¶
-
latest_revision
¶
-
revisions
¶
-
annotations
¶
-
average_rating
¶
-
create_time
¶
-
deleted
¶
-
importable
¶
-
latest_revision_id
¶
-
published
¶
-
ratings
¶
-
table
= Table('visualization', MetaData(bind=None), Column('id', Integer(), table=<visualization>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<visualization>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<visualization>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<visualization>, nullable=False), Column('latest_revision_id', Integer(), ForeignKey('visualization_revision.id'), table=<visualization>), Column('title', TEXT(), table=<visualization>), Column('type', TEXT(), table=<visualization>), Column('dbkey', TEXT(), table=<visualization>), Column('deleted', Boolean(), table=<visualization>, default=ColumnDefault(False)), Column('importable', Boolean(), table=<visualization>, default=ColumnDefault(False)), Column('slug', TEXT(), table=<visualization>), Column('published', Boolean(), table=<visualization>, default=ColumnDefault(False)), schema=None)¶
-
update_time
¶
-
user_id
¶
-
-
class
galaxy.model.
VisualizationRevision
(visualization=None, title=None, dbkey=None, config=None)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(visualization=None, title=None, dbkey=None, config=None)¶
-
id
¶
-
visualization
¶
-
title
¶
-
dbkey
¶
-
config
¶
-
create_time
¶
-
table
= Table('visualization_revision', MetaData(bind=None), Column('id', Integer(), table=<visualization_revision>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<visualization_revision>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<visualization_revision>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('visualization_id', Integer(), ForeignKey('visualization.id'), table=<visualization_revision>, nullable=False), Column('title', TEXT(), table=<visualization_revision>), Column('dbkey', TEXT(), table=<visualization_revision>), Column('config', JSONType(), table=<visualization_revision>), schema=None)¶
-
update_time
¶
-
visualization_id
¶
-
Bases:
galaxy.model.RepresentById
-
class
galaxy.model.
TransferJob
(state=None, path=None, info=None, pid=None, socket=None, params=None)[source]¶ Bases:
galaxy.model.RepresentById
-
states
= <galaxy.util.bunch.Bunch object>¶
-
terminal_states
= ['error', 'done']¶
-
__init__
(state=None, path=None, info=None, pid=None, socket=None, params=None)¶
-
state
¶
-
path
¶
-
info
¶
-
pid
¶
-
socket
¶
-
params
¶
-
create_time
¶
-
id
¶
-
table
= Table('transfer_job', MetaData(bind=None), Column('id', Integer(), table=<transfer_job>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<transfer_job>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<transfer_job>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('state', String(length=64), table=<transfer_job>), Column('path', String(length=1024), table=<transfer_job>), Column('info', TEXT(), table=<transfer_job>), Column('pid', Integer(), table=<transfer_job>), Column('socket', Integer(), table=<transfer_job>), Column('params', JSONType(), table=<transfer_job>), schema=None)¶
-
transfer_job
¶
-
update_time
¶
-
-
class
galaxy.model.
Tag
(id=None, type=None, parent_id=None, name=None)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(id=None, type=None, parent_id=None, name=None)¶
-
id
¶
-
type
¶
-
parent_id
¶
-
name
¶
-
children
¶
-
parent
¶
-
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)¶
-
tagged_datasets
¶
-
tagged_histories
¶
-
tagged_history_dataset_associations
¶
-
tagged_history_dataset_collections
¶
-
tagged_library_dataset_collections
¶
-
tagged_library_dataset_dataset_associations
¶
-
tagged_pages
¶
-
tagged_tools
¶
-
tagged_visualizations
¶
-
tagged_workflow_steps
¶
-
tagged_workflows
¶
-
-
class
galaxy.model.
ItemTagAssociation
(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)[source]¶ Bases:
galaxy.util.dictifiable.Dictifiable
-
dict_collection_visible_keys
= ['id', 'user_tname', 'user_value']¶
-
dict_element_visible_keys
= ['id', 'user_tname', 'user_value']¶
-
-
class
galaxy.model.
HistoryTagAssociation
(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)[source]¶ Bases:
galaxy.model.ItemTagAssociation
,galaxy.model.RepresentById
-
__init__
(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)¶
-
histories
¶
-
history_id
¶
-
id
¶
-
table
= Table('history_tag_association', MetaData(bind=None), Column('id', Integer(), table=<history_tag_association>, primary_key=True, nullable=False), Column('history_id', Integer(), ForeignKey('history.id'), table=<history_tag_association>), Column('tag_id', Integer(), ForeignKey('tag.id'), table=<history_tag_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history_tag_association>), Column('user_tname', TrimmedString(length=255), table=<history_tag_association>), Column('value', TrimmedString(length=255), table=<history_tag_association>), Column('user_value', TrimmedString(length=255), table=<history_tag_association>), schema=None)¶
-
tag
¶
-
tag_id
¶
-
user
¶
-
user_id
¶
-
user_tname
¶
-
user_value
¶
-
value
¶
-
-
class
galaxy.model.
DatasetTagAssociation
(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)[source]¶ Bases:
galaxy.model.ItemTagAssociation
,galaxy.model.RepresentById
-
__init__
(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)¶
-
dataset_id
¶
-
datasets
¶
-
id
¶
-
table
= Table('dataset_tag_association', MetaData(bind=None), Column('id', Integer(), table=<dataset_tag_association>, primary_key=True, nullable=False), Column('dataset_id', Integer(), ForeignKey('dataset.id'), table=<dataset_tag_association>), Column('tag_id', Integer(), ForeignKey('tag.id'), table=<dataset_tag_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<dataset_tag_association>), Column('user_tname', TrimmedString(length=255), table=<dataset_tag_association>), Column('value', TrimmedString(length=255), table=<dataset_tag_association>), Column('user_value', TrimmedString(length=255), table=<dataset_tag_association>), schema=None)¶
-
tag
¶
-
tag_id
¶
-
user
¶
-
user_id
¶
-
user_tname
¶
-
user_value
¶
-
value
¶
-
-
class
galaxy.model.
HistoryDatasetAssociationTagAssociation
(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)[source]¶ Bases:
galaxy.model.ItemTagAssociation
,galaxy.model.RepresentById
-
__init__
(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)¶
-
history_dataset_association_id
¶
-
history_tag_associations
¶
-
id
¶
-
table
= Table('history_dataset_association_tag_association', MetaData(bind=None), Column('id', Integer(), table=<history_dataset_association_tag_association>, primary_key=True, nullable=False), Column('history_dataset_association_id', Integer(), ForeignKey('history_dataset_association.id'), table=<history_dataset_association_tag_association>), Column('tag_id', Integer(), ForeignKey('tag.id'), table=<history_dataset_association_tag_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history_dataset_association_tag_association>), Column('user_tname', TrimmedString(length=255), table=<history_dataset_association_tag_association>), Column('value', TrimmedString(length=255), table=<history_dataset_association_tag_association>), Column('user_value', TrimmedString(length=255), table=<history_dataset_association_tag_association>), schema=None)¶
-
tag
¶
-
tag_id
¶
-
user
¶
-
user_id
¶
-
user_tname
¶
-
user_value
¶
-
value
¶
-
-
class
galaxy.model.
LibraryDatasetDatasetAssociationTagAssociation
(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)[source]¶ Bases:
galaxy.model.ItemTagAssociation
,galaxy.model.RepresentById
-
__init__
(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)¶
-
history_tag_associations
¶
-
id
¶
-
library_dataset_dataset_association_id
¶
-
table
= Table('library_dataset_dataset_association_tag_association', MetaData(bind=None), Column('id', Integer(), table=<library_dataset_dataset_association_tag_association>, primary_key=True, nullable=False), Column('library_dataset_dataset_association_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<library_dataset_dataset_association_tag_association>), Column('tag_id', Integer(), ForeignKey('tag.id'), table=<library_dataset_dataset_association_tag_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<library_dataset_dataset_association_tag_association>), Column('user_tname', TrimmedString(length=255), table=<library_dataset_dataset_association_tag_association>), Column('value', TrimmedString(length=255), table=<library_dataset_dataset_association_tag_association>), Column('user_value', TrimmedString(length=255), table=<library_dataset_dataset_association_tag_association>), schema=None)¶
-
tag
¶
-
tag_id
¶
-
user
¶
-
user_id
¶
-
user_tname
¶
-
user_value
¶
-
value
¶
-
-
class
galaxy.model.
PageTagAssociation
(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)[source]¶ Bases:
galaxy.model.ItemTagAssociation
,galaxy.model.RepresentById
-
__init__
(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)¶
-
id
¶
-
page_id
¶
-
pages
¶
-
table
= Table('page_tag_association', MetaData(bind=None), Column('id', Integer(), table=<page_tag_association>, primary_key=True, nullable=False), Column('page_id', Integer(), ForeignKey('page.id'), table=<page_tag_association>), Column('tag_id', Integer(), ForeignKey('tag.id'), table=<page_tag_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<page_tag_association>), Column('user_tname', TrimmedString(length=255), table=<page_tag_association>), Column('value', TrimmedString(length=255), table=<page_tag_association>), Column('user_value', TrimmedString(length=255), table=<page_tag_association>), schema=None)¶
-
tag
¶
-
tag_id
¶
-
user
¶
-
user_id
¶
-
user_tname
¶
-
user_value
¶
-
value
¶
-
-
class
galaxy.model.
WorkflowStepTagAssociation
(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)[source]¶ Bases:
galaxy.model.ItemTagAssociation
,galaxy.model.RepresentById
-
__init__
(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)¶
-
id
¶
-
table
= Table('workflow_step_tag_association', MetaData(bind=None), Column('id', Integer(), table=<workflow_step_tag_association>, primary_key=True, nullable=False), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_step_tag_association>), Column('tag_id', Integer(), ForeignKey('tag.id'), table=<workflow_step_tag_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<workflow_step_tag_association>), Column('user_tname', Unicode(length=255), table=<workflow_step_tag_association>), Column('value', Unicode(length=255), table=<workflow_step_tag_association>), Column('user_value', Unicode(length=255), table=<workflow_step_tag_association>), schema=None)¶
-
tag
¶
-
tag_id
¶
-
user
¶
-
user_id
¶
-
user_tname
¶
-
user_value
¶
-
value
¶
-
workflow_step_id
¶
-
workflow_steps
¶
-
-
class
galaxy.model.
StoredWorkflowTagAssociation
(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)[source]¶ Bases:
galaxy.model.ItemTagAssociation
,galaxy.model.RepresentById
-
__init__
(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)¶
-
id
¶
-
stored_workflow_id
¶
-
stored_workflows
¶
-
table
= Table('stored_workflow_tag_association', MetaData(bind=None), Column('id', Integer(), table=<stored_workflow_tag_association>, primary_key=True, nullable=False), Column('stored_workflow_id', Integer(), ForeignKey('stored_workflow.id'), table=<stored_workflow_tag_association>), Column('tag_id', Integer(), ForeignKey('tag.id'), table=<stored_workflow_tag_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<stored_workflow_tag_association>), Column('user_tname', Unicode(length=255), table=<stored_workflow_tag_association>), Column('value', Unicode(length=255), table=<stored_workflow_tag_association>), Column('user_value', Unicode(length=255), table=<stored_workflow_tag_association>), schema=None)¶
-
tag
¶
-
tag_id
¶
-
user
¶
-
user_id
¶
-
user_tname
¶
-
user_value
¶
-
value
¶
-
-
class
galaxy.model.
VisualizationTagAssociation
(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)[source]¶ Bases:
galaxy.model.ItemTagAssociation
,galaxy.model.RepresentById
-
__init__
(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)¶
-
id
¶
-
table
= Table('visualization_tag_association', MetaData(bind=None), Column('id', Integer(), table=<visualization_tag_association>, primary_key=True, nullable=False), Column('visualization_id', Integer(), ForeignKey('visualization.id'), table=<visualization_tag_association>), Column('tag_id', Integer(), ForeignKey('tag.id'), table=<visualization_tag_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<visualization_tag_association>), Column('user_tname', TrimmedString(length=255), table=<visualization_tag_association>), Column('value', TrimmedString(length=255), table=<visualization_tag_association>), Column('user_value', TrimmedString(length=255), table=<visualization_tag_association>), schema=None)¶
-
tag
¶
-
tag_id
¶
-
user
¶
-
user_id
¶
-
user_tname
¶
-
user_value
¶
-
value
¶
-
visualization_id
¶
-
visualizations
¶
-
-
class
galaxy.model.
HistoryDatasetCollectionTagAssociation
(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)[source]¶ Bases:
galaxy.model.ItemTagAssociation
,galaxy.model.RepresentById
-
__init__
(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)¶
-
dataset_collections
¶
-
history_dataset_collection_id
¶
-
id
¶
-
table
= Table('history_dataset_collection_tag_association', MetaData(bind=None), Column('id', Integer(), table=<history_dataset_collection_tag_association>, primary_key=True, nullable=False), Column('history_dataset_collection_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<history_dataset_collection_tag_association>), Column('tag_id', Integer(), ForeignKey('tag.id'), table=<history_dataset_collection_tag_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history_dataset_collection_tag_association>), Column('user_tname', TrimmedString(length=255), table=<history_dataset_collection_tag_association>), Column('value', TrimmedString(length=255), table=<history_dataset_collection_tag_association>), Column('user_value', TrimmedString(length=255), table=<history_dataset_collection_tag_association>), schema=None)¶
-
tag
¶
-
tag_id
¶
-
user
¶
-
user_id
¶
-
user_tname
¶
-
user_value
¶
-
value
¶
-
-
class
galaxy.model.
LibraryDatasetCollectionTagAssociation
(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)[source]¶ Bases:
galaxy.model.ItemTagAssociation
,galaxy.model.RepresentById
-
__init__
(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)¶
-
dataset_collections
¶
-
id
¶
-
library_dataset_collection_id
¶
-
table
= Table('library_dataset_collection_tag_association', MetaData(bind=None), Column('id', Integer(), table=<library_dataset_collection_tag_association>, primary_key=True, nullable=False), Column('library_dataset_collection_id', Integer(), ForeignKey('library_dataset_collection_association.id'), table=<library_dataset_collection_tag_association>), Column('tag_id', Integer(), ForeignKey('tag.id'), table=<library_dataset_collection_tag_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<library_dataset_collection_tag_association>), Column('user_tname', TrimmedString(length=255), table=<library_dataset_collection_tag_association>), Column('value', TrimmedString(length=255), table=<library_dataset_collection_tag_association>), Column('user_value', TrimmedString(length=255), table=<library_dataset_collection_tag_association>), schema=None)¶
-
tag
¶
-
tag_id
¶
-
user
¶
-
user_id
¶
-
user_tname
¶
-
user_value
¶
-
value
¶
-
-
class
galaxy.model.
ToolTagAssociation
(id=None, user=None, tool_id=None, tag_id=None, user_tname=None, value=None)[source]¶ Bases:
galaxy.model.ItemTagAssociation
,galaxy.model.RepresentById
-
__init__
(id=None, user=None, tool_id=None, tag_id=None, user_tname=None, value=None)¶
-
id
¶
-
user
¶
-
tool_id
¶
-
tag_id
¶
-
user_tname
¶
-
value
¶
-
user_value
¶
-
table
= Table('tool_tag_association', MetaData(bind=None), Column('id', Integer(), table=<tool_tag_association>, primary_key=True, nullable=False), Column('tool_id', TrimmedString(length=255), table=<tool_tag_association>), Column('tag_id', Integer(), ForeignKey('tag.id'), table=<tool_tag_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<tool_tag_association>), Column('user_tname', TrimmedString(length=255), table=<tool_tag_association>), Column('value', TrimmedString(length=255), table=<tool_tag_association>), Column('user_value', TrimmedString(length=255), table=<tool_tag_association>), schema=None)¶
-
tag
¶
-
user_id
¶
-
-
class
galaxy.model.
HistoryAnnotationAssociation
[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
()¶ Initialize self. See help(type(self)) for accurate signature.
-
annotation
¶
-
histories
¶
-
history
¶
-
history_id
¶
-
id
¶
-
table
= Table('history_annotation_association', MetaData(bind=None), Column('id', Integer(), table=<history_annotation_association>, primary_key=True, nullable=False), Column('history_id', Integer(), ForeignKey('history.id'), table=<history_annotation_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history_annotation_association>), Column('annotation', TEXT(), table=<history_annotation_association>), schema=None)¶
-
user
¶
-
user_id
¶
-
-
class
galaxy.model.
HistoryDatasetAssociationAnnotationAssociation
[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
()¶ Initialize self. See help(type(self)) for accurate signature.
-
annotation
¶
-
hda
¶
-
hdas
¶
-
history_dataset_association_id
¶
-
id
¶
-
table
= Table('history_dataset_association_annotation_association', MetaData(bind=None), Column('id', Integer(), table=<history_dataset_association_annotation_association>, primary_key=True, nullable=False), Column('history_dataset_association_id', Integer(), ForeignKey('history_dataset_association.id'), table=<history_dataset_association_annotation_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history_dataset_association_annotation_association>), Column('annotation', TEXT(), table=<history_dataset_association_annotation_association>), schema=None)¶
-
user
¶
-
user_id
¶
-
-
class
galaxy.model.
StoredWorkflowAnnotationAssociation
[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
()¶ Initialize self. See help(type(self)) for accurate signature.
-
annotation
¶
-
id
¶
-
stored_workflow
¶
-
stored_workflow_id
¶
-
stored_workflows
¶
-
table
= Table('stored_workflow_annotation_association', MetaData(bind=None), Column('id', Integer(), table=<stored_workflow_annotation_association>, primary_key=True, nullable=False), Column('stored_workflow_id', Integer(), ForeignKey('stored_workflow.id'), table=<stored_workflow_annotation_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<stored_workflow_annotation_association>), Column('annotation', TEXT(), table=<stored_workflow_annotation_association>), schema=None)¶
-
user
¶
-
user_id
¶
-
-
class
galaxy.model.
WorkflowStepAnnotationAssociation
[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
()¶ Initialize self. See help(type(self)) for accurate signature.
-
annotation
¶
-
id
¶
-
table
= Table('workflow_step_annotation_association', MetaData(bind=None), Column('id', Integer(), table=<workflow_step_annotation_association>, primary_key=True, nullable=False), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_step_annotation_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<workflow_step_annotation_association>), Column('annotation', TEXT(), table=<workflow_step_annotation_association>), schema=None)¶
-
user
¶
-
user_id
¶
-
workflow_step
¶
-
workflow_step_id
¶
-
workflow_steps
¶
-
-
class
galaxy.model.
PageAnnotationAssociation
[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
()¶ Initialize self. See help(type(self)) for accurate signature.
-
annotation
¶
-
id
¶
-
page
¶
-
page_id
¶
-
pages
¶
-
table
= Table('page_annotation_association', MetaData(bind=None), Column('id', Integer(), table=<page_annotation_association>, primary_key=True, nullable=False), Column('page_id', Integer(), ForeignKey('page.id'), table=<page_annotation_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<page_annotation_association>), Column('annotation', TEXT(), table=<page_annotation_association>), schema=None)¶
-
user
¶
-
user_id
¶
-
-
class
galaxy.model.
VisualizationAnnotationAssociation
[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
()¶ Initialize self. See help(type(self)) for accurate signature.
-
annotation
¶
-
id
¶
-
table
= Table('visualization_annotation_association', MetaData(bind=None), Column('id', Integer(), table=<visualization_annotation_association>, primary_key=True, nullable=False), Column('visualization_id', Integer(), ForeignKey('visualization.id'), table=<visualization_annotation_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<visualization_annotation_association>), Column('annotation', TEXT(), table=<visualization_annotation_association>), schema=None)¶
-
user
¶
-
user_id
¶
-
visualization
¶
-
visualization_id
¶
-
visualizations
¶
-
-
class
galaxy.model.
HistoryDatasetCollectionAssociationAnnotationAssociation
[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
()¶ Initialize self. See help(type(self)) for accurate signature.
-
annotation
¶
-
dataset_collections
¶
-
history_dataset_collection
¶
-
history_dataset_collection_id
¶
-
id
¶
-
table
= Table('history_dataset_collection_annotation_association', MetaData(bind=None), Column('id', Integer(), table=<history_dataset_collection_annotation_association>, primary_key=True, nullable=False), Column('history_dataset_collection_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<history_dataset_collection_annotation_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history_dataset_collection_annotation_association>), Column('annotation', TEXT(), table=<history_dataset_collection_annotation_association>), schema=None)¶
-
user
¶
-
user_id
¶
-
-
class
galaxy.model.
LibraryDatasetCollectionAnnotationAssociation
[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
()¶ Initialize self. See help(type(self)) for accurate signature.
-
annotation
¶
-
dataset_collections
¶
-
id
¶
-
library_dataset_collection
¶
-
library_dataset_collection_id
¶
-
table
= Table('library_dataset_collection_annotation_association', MetaData(bind=None), Column('id', Integer(), table=<library_dataset_collection_annotation_association>, primary_key=True, nullable=False), Column('library_dataset_collection_id', Integer(), ForeignKey('library_dataset_collection_association.id'), table=<library_dataset_collection_annotation_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<library_dataset_collection_annotation_association>), Column('annotation', TEXT(), table=<library_dataset_collection_annotation_association>), schema=None)¶
-
user
¶
-
user_id
¶
-
-
class
galaxy.model.
ItemRatingAssociation
(id=None, user=None, item=None, rating=0)[source]¶ Bases:
object
-
class
galaxy.model.
HistoryRatingAssociation
(id=None, user=None, item=None, rating=0)[source]¶ Bases:
galaxy.model.ItemRatingAssociation
,galaxy.model.RepresentById
-
__init__
(id=None, user=None, item=None, rating=0)¶
-
histories
¶
-
history
¶
-
history_id
¶
-
id
¶
-
rating
¶
-
table
= Table('history_rating_association', MetaData(bind=None), Column('id', Integer(), table=<history_rating_association>, primary_key=True, nullable=False), Column('history_id', Integer(), ForeignKey('history.id'), table=<history_rating_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history_rating_association>), Column('rating', Integer(), table=<history_rating_association>), schema=None)¶
-
user
¶
-
user_id
¶
-
-
class
galaxy.model.
HistoryDatasetAssociationRatingAssociation
(id=None, user=None, item=None, rating=0)[source]¶ Bases:
galaxy.model.ItemRatingAssociation
,galaxy.model.RepresentById
-
__init__
(id=None, user=None, item=None, rating=0)¶
-
hda
¶
-
hdas
¶
-
history_dataset_association_id
¶
-
id
¶
-
rating
¶
-
table
= Table('history_dataset_association_rating_association', MetaData(bind=None), Column('id', Integer(), table=<history_dataset_association_rating_association>, primary_key=True, nullable=False), Column('history_dataset_association_id', Integer(), ForeignKey('history_dataset_association.id'), table=<history_dataset_association_rating_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history_dataset_association_rating_association>), Column('rating', Integer(), table=<history_dataset_association_rating_association>), schema=None)¶
-
user
¶
-
user_id
¶
-
-
class
galaxy.model.
StoredWorkflowRatingAssociation
(id=None, user=None, item=None, rating=0)[source]¶ Bases:
galaxy.model.ItemRatingAssociation
,galaxy.model.RepresentById
-
__init__
(id=None, user=None, item=None, rating=0)¶
-
id
¶
-
rating
¶
-
stored_workflow
¶
-
stored_workflow_id
¶
-
stored_workflows
¶
-
table
= Table('stored_workflow_rating_association', MetaData(bind=None), Column('id', Integer(), table=<stored_workflow_rating_association>, primary_key=True, nullable=False), Column('stored_workflow_id', Integer(), ForeignKey('stored_workflow.id'), table=<stored_workflow_rating_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<stored_workflow_rating_association>), Column('rating', Integer(), table=<stored_workflow_rating_association>), schema=None)¶
-
user
¶
-
user_id
¶
-
-
class
galaxy.model.
PageRatingAssociation
(id=None, user=None, item=None, rating=0)[source]¶ Bases:
galaxy.model.ItemRatingAssociation
,galaxy.model.RepresentById
-
__init__
(id=None, user=None, item=None, rating=0)¶
-
id
¶
-
page
¶
-
page_id
¶
-
pages
¶
-
rating
¶
-
table
= Table('page_rating_association', MetaData(bind=None), Column('id', Integer(), table=<page_rating_association>, primary_key=True, nullable=False), Column('page_id', Integer(), ForeignKey('page.id'), table=<page_rating_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<page_rating_association>), Column('rating', Integer(), table=<page_rating_association>), schema=None)¶
-
user
¶
-
user_id
¶
-
-
class
galaxy.model.
VisualizationRatingAssociation
(id=None, user=None, item=None, rating=0)[source]¶ Bases:
galaxy.model.ItemRatingAssociation
,galaxy.model.RepresentById
-
__init__
(id=None, user=None, item=None, rating=0)¶
-
id
¶
-
rating
¶
-
table
= Table('visualization_rating_association', MetaData(bind=None), Column('id', Integer(), table=<visualization_rating_association>, primary_key=True, nullable=False), Column('visualization_id', Integer(), ForeignKey('visualization.id'), table=<visualization_rating_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<visualization_rating_association>), Column('rating', Integer(), table=<visualization_rating_association>), schema=None)¶
-
user
¶
-
user_id
¶
-
visualizaiton
¶
-
visualization_id
¶
-
visualizations
¶
-
-
class
galaxy.model.
HistoryDatasetCollectionRatingAssociation
(id=None, user=None, item=None, rating=0)[source]¶ Bases:
galaxy.model.ItemRatingAssociation
,galaxy.model.RepresentById
-
__init__
(id=None, user=None, item=None, rating=0)¶
-
dataset_collections
¶
-
history_dataset_collection
¶
-
history_dataset_collection_id
¶
-
id
¶
-
rating
¶
-
table
= Table('history_dataset_collection_rating_association', MetaData(bind=None), Column('id', Integer(), table=<history_dataset_collection_rating_association>, primary_key=True, nullable=False), Column('history_dataset_collection_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<history_dataset_collection_rating_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history_dataset_collection_rating_association>), Column('rating', Integer(), table=<history_dataset_collection_rating_association>), schema=None)¶
-
user
¶
-
user_id
¶
-
-
class
galaxy.model.
LibraryDatasetCollectionRatingAssociation
(id=None, user=None, item=None, rating=0)[source]¶ Bases:
galaxy.model.ItemRatingAssociation
,galaxy.model.RepresentById
-
__init__
(id=None, user=None, item=None, rating=0)¶
-
dataset_collections
¶
-
id
¶
-
libary_dataset_collection
¶
-
library_dataset_collection_id
¶
-
rating
¶
-
table
= Table('library_dataset_collection_rating_association', MetaData(bind=None), Column('id', Integer(), table=<library_dataset_collection_rating_association>, primary_key=True, nullable=False), Column('library_dataset_collection_id', Integer(), ForeignKey('library_dataset_collection_association.id'), table=<library_dataset_collection_rating_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<library_dataset_collection_rating_association>), Column('rating', Integer(), table=<library_dataset_collection_rating_association>), schema=None)¶
-
user
¶
-
user_id
¶
-
-
class
galaxy.model.
DataManagerHistoryAssociation
(id=None, history=None, user=None)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(id=None, history=None, user=None)¶
-
id
¶
-
history
¶
-
user
¶
-
create_time
¶
-
history_id
¶
-
table
= Table('data_manager_history_association', MetaData(bind=None), Column('id', Integer(), table=<data_manager_history_association>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<data_manager_history_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<data_manager_history_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('history_id', Integer(), ForeignKey('history.id'), table=<data_manager_history_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<data_manager_history_association>), schema=None)¶
-
update_time
¶
-
user_id
¶
-
-
class
galaxy.model.
DataManagerJobAssociation
(id=None, job=None, data_manager_id=None)[source]¶ Bases:
galaxy.model.RepresentById
-
__init__
(id=None, job=None, data_manager_id=None)¶
-
id
¶
-
create_time
¶
-
job
¶
-
job_id
¶
-
table
= Table('data_manager_job_association', MetaData(bind=None), Column('id', Integer(), table=<data_manager_job_association>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<data_manager_job_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<data_manager_job_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('job_id', Integer(), ForeignKey('job.id'), table=<data_manager_job_association>), Column('data_manager_id', TEXT(), table=<data_manager_job_association>), schema=None)¶
-
update_time
¶
-
data_manager_id
¶
-
-
class
galaxy.model.
UserPreference
(name=None, value=None)[source]¶ Bases:
galaxy.model.RepresentById
-
id
¶
-
table
= Table('user_preference', MetaData(bind=None), Column('id', Integer(), table=<user_preference>, primary_key=True, nullable=False), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<user_preference>), Column('name', Unicode(length=255), table=<user_preference>), Column('value', Text(), table=<user_preference>), schema=None)¶
-
user
¶
-
user_id
¶
-
__init__
(name=None, value=None)¶
-
name
¶
-
value
¶
-
-
class
galaxy.model.
UserAction
(id=None, create_time=None, user_id=None, session_id=None, action=None, params=None, context=None)[source]¶ Bases:
galaxy.model.RepresentById
-
table
= Table('user_action', MetaData(bind=None), Column('id', Integer(), table=<user_action>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<user_action>, default=ColumnDefault(<function datetime.utcnow>)), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<user_action>), Column('session_id', Integer(), ForeignKey('galaxy_session.id'), table=<user_action>), Column('action', Unicode(length=255), table=<user_action>), Column('context', Unicode(length=512), table=<user_action>), Column('params', Unicode(length=1024), table=<user_action>), schema=None)¶
-
user
¶
-
__init__
(id=None, create_time=None, user_id=None, session_id=None, action=None, params=None, context=None)¶
-
id
¶
-
create_time
¶
-
user_id
¶
-
session_id
¶
-
action
¶
-
params
¶
-
context
¶
-
-
class
galaxy.model.
APIKeys
(id=None, user_id=None, key=None)[source]¶ Bases:
galaxy.model.RepresentById
-
create_time
¶
-
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 datetime.utcnow>)), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<api_keys>), Column('key', TrimmedString(length=32), table=<api_keys>), schema=None)¶
-
user
¶
-
__init__
(id=None, user_id=None, key=None)¶
-
id
¶
-
user_id
¶
-
key
¶
-
Subpackages¶
- galaxy.model.dataset_collections package
- Subpackages
- Submodules
- galaxy.model.dataset_collections.builder module
- galaxy.model.dataset_collections.matching module
- galaxy.model.dataset_collections.registry module
- galaxy.model.dataset_collections.structure module
- galaxy.model.dataset_collections.subcollections module
- galaxy.model.dataset_collections.type_description module
- galaxy.model.migrate package
- Subpackages
- galaxy.model.migrate.versions package
- Submodules
- galaxy.model.migrate.versions.0001_initial_tables module
- galaxy.model.migrate.versions.0002_metadata_file_table module
- galaxy.model.migrate.versions.0003_security_and_libraries module
- galaxy.model.migrate.versions.0004_indexes_and_defaults module
- galaxy.model.migrate.versions.0005_cleanup_datasets_fix module
- galaxy.model.migrate.versions.0006_change_qual_datatype module
- galaxy.model.migrate.versions.0007_sharing_histories module
- galaxy.model.migrate.versions.0008_galaxy_forms module
- galaxy.model.migrate.versions.0009_request_table module
- galaxy.model.migrate.versions.0010_hda_display_at_authz_table module
- galaxy.model.migrate.versions.0011_v0010_mysql_index_fix module
- galaxy.model.migrate.versions.0012_user_address module
- galaxy.model.migrate.versions.0013_change_lib_item_templates_to_forms module
- galaxy.model.migrate.versions.0014_pages module
- galaxy.model.migrate.versions.0015_tagging module
- galaxy.model.migrate.versions.0016_v0015_mysql_index_fix module
- galaxy.model.migrate.versions.0017_library_item_indexes module
- galaxy.model.migrate.versions.0018_ordered_tags_and_page_tags module
- galaxy.model.migrate.versions.0019_request_library_folder module
- galaxy.model.migrate.versions.0020_library_upload_job module
- galaxy.model.migrate.versions.0021_user_prefs module
- galaxy.model.migrate.versions.0022_visualization_tables module
- galaxy.model.migrate.versions.0023_page_published_and_deleted_columns module
- galaxy.model.migrate.versions.0024_page_slug_unique_constraint module
- galaxy.model.migrate.versions.0025_user_info module
- galaxy.model.migrate.versions.0026_cloud_tables module
- galaxy.model.migrate.versions.0027_request_events module
- galaxy.model.migrate.versions.0028_external_metadata_file_override module
- galaxy.model.migrate.versions.0029_user_actions module
- galaxy.model.migrate.versions.0030_history_slug_column module
- galaxy.model.migrate.versions.0031_community_and_workflow_tags module
- galaxy.model.migrate.versions.0032_stored_workflow_slug_column module
- galaxy.model.migrate.versions.0033_published_cols_for_histories_and_workflows module
- galaxy.model.migrate.versions.0034_page_user_share_association module
- galaxy.model.migrate.versions.0035_item_annotations_and_workflow_step_tags module
- galaxy.model.migrate.versions.0036_add_deleted_column_to_library_template_assoc_tables module
- galaxy.model.migrate.versions.0037_samples_library module
- galaxy.model.migrate.versions.0038_add_inheritable_column_to_library_template_assoc_tables module
- galaxy.model.migrate.versions.0039_add_synopsis_column_to_library_table module
- galaxy.model.migrate.versions.0040_page_annotations module
- galaxy.model.migrate.versions.0041_workflow_invocation module
- galaxy.model.migrate.versions.0042_workflow_invocation_fix module
- galaxy.model.migrate.versions.0043_visualization_sharing_tagging_annotating module
- galaxy.model.migrate.versions.0044_add_notify_column_to_request_table module
- galaxy.model.migrate.versions.0045_request_type_permissions_table module
- galaxy.model.migrate.versions.0046_post_job_actions module
- galaxy.model.migrate.versions.0047_job_table_user_id_column module
- galaxy.model.migrate.versions.0048_dataset_instance_state_column module
- galaxy.model.migrate.versions.0049_api_keys_table module
- galaxy.model.migrate.versions.0050_drop_cloud_tables module
- galaxy.model.migrate.versions.0051_imported_col_for_jobs_table module
- galaxy.model.migrate.versions.0052_sample_dataset_table module
- galaxy.model.migrate.versions.0053_item_ratings module
- galaxy.model.migrate.versions.0054_visualization_dbkey module
- galaxy.model.migrate.versions.0055_add_pja_assoc_for_jobs module
- galaxy.model.migrate.versions.0056_workflow_outputs module
- galaxy.model.migrate.versions.0057_request_notify module
- galaxy.model.migrate.versions.0058_history_import_export module
- galaxy.model.migrate.versions.0059_sample_dataset_file_path module
- galaxy.model.migrate.versions.0060_history_archive_import module
- galaxy.model.migrate.versions.0061_tasks module
- galaxy.model.migrate.versions.0062_user_openid_table module
- galaxy.model.migrate.versions.0063_sequencer_table module
- galaxy.model.migrate.versions.0064_add_run_and_sample_run_association_tables module
- galaxy.model.migrate.versions.0065_add_name_to_form_fields_and_values module
- galaxy.model.migrate.versions.0066_deferred_job_and_transfer_job_tables module
- galaxy.model.migrate.versions.0067_populate_sequencer_table module
- galaxy.model.migrate.versions.0068_rename_sequencer_to_external_services module
- galaxy.model.migrate.versions.0069_rename_sequencer_form_type module
- galaxy.model.migrate.versions.0070_add_info_column_to_deferred_job_table module
- galaxy.model.migrate.versions.0071_add_history_and_workflow_to_sample module
- galaxy.model.migrate.versions.0072_add_pid_and_socket_columns_to_transfer_job_table module
- galaxy.model.migrate.versions.0073_add_ldda_to_implicit_conversion_table module
- galaxy.model.migrate.versions.0074_add_purged_column_to_library_dataset_table module
- galaxy.model.migrate.versions.0075_add_subindex_column_to_run_table module
- galaxy.model.migrate.versions.0076_fix_form_values_data_corruption module
- galaxy.model.migrate.versions.0077_create_tool_tag_association_table module
- galaxy.model.migrate.versions.0078_add_columns_for_disk_usage_accounting module
- galaxy.model.migrate.versions.0079_input_library_to_job_table module
- galaxy.model.migrate.versions.0080_quota_tables module
- galaxy.model.migrate.versions.0081_add_tool_version_to_hda_ldda module
- galaxy.model.migrate.versions.0082_add_tool_shed_repository_table module
- galaxy.model.migrate.versions.0083_add_prepare_files_to_task module
- galaxy.model.migrate.versions.0084_add_ldda_id_to_implicit_conversion_table module
- galaxy.model.migrate.versions.0085_add_task_info module
- galaxy.model.migrate.versions.0086_add_tool_shed_repository_table_columns module
- galaxy.model.migrate.versions.0087_tool_id_guid_map_table module
- galaxy.model.migrate.versions.0088_add_installed_changeset_revison_column module
- galaxy.model.migrate.versions.0089_add_object_store_id_columns module
- galaxy.model.migrate.versions.0090_add_tool_shed_repository_table_columns module
- galaxy.model.migrate.versions.0091_add_tool_version_tables module
- galaxy.model.migrate.versions.0092_add_migrate_tools_table module
- galaxy.model.migrate.versions.0093_add_job_params_col module
- galaxy.model.migrate.versions.0094_add_job_handler_col module
- galaxy.model.migrate.versions.0095_hda_subsets module
- galaxy.model.migrate.versions.0096_openid_provider module
- galaxy.model.migrate.versions.0097_add_ctx_rev_column module
- galaxy.model.migrate.versions.0098_genome_index_tool_data_table module
- galaxy.model.migrate.versions.0099_add_tool_dependency_table module
- galaxy.model.migrate.versions.0100_alter_tool_dependency_table_version_column module
- galaxy.model.migrate.versions package
- Subpackages