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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)
- galaxy.model.now()¶
Return a new datetime representing UTC day and time.
- class galaxy.model.Base(**kwargs)[source]¶
Bases:
object
- metadata = MetaData()¶
- registry = <sqlalchemy.orm.decl_api.registry object>¶
- __init__(**kwargs)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- class galaxy.model.HasTags[source]¶
Bases:
object
- dict_collection_visible_keys = ['tags']¶
- dict_element_visible_keys = ['tags']¶
- tags: List[ItemTagAssociation]¶
- property auto_propagated_tags¶
- class galaxy.model.SerializeFilesHandler(*args, **kwds)[source]¶
Bases:
Protocol
- __init__(*args, **kwargs)¶
- class galaxy.model.SerializationOptions(for_edit: bool, serialize_dataset_objects: Optional[bool] = None, serialize_files_handler: Optional[SerializeFilesHandler] = None, strip_metadata_files: Optional[bool] = None)[source]¶
Bases:
object
- class galaxy.model.Serializable[source]¶
Bases:
RepresentById
- serialize(id_encoder: IdEncodingHelper, serialization_options: SerializationOptions, for_link: bool = False) Dict[str, Any] [source]¶
Serialize model for a re-population in (potentially) another Galaxy instance.
- class galaxy.model.UsesCreateAndUpdateTime[source]¶
Bases:
object
- update_time: DateTime¶
- property seconds_since_updated¶
- property seconds_since_created¶
- class galaxy.model.WorkerProcess(**kwargs)[source]¶
Bases:
Base
,UsesCreateAndUpdateTime
- id¶
- server_name¶
- hostname¶
- pid¶
- update_time: DateTime¶
- __init__(**kwargs)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('worker_process', MetaData(), 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)¶
- 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¶
- property metrics¶
- property stdout¶
- property stderr¶
- galaxy.model.calculate_user_disk_usage_statements(user_id, quota_source_map, for_sqlite=False)[source]¶
Standalone function so can be reused for postgres directly in pgcleanup.py.
- class galaxy.model.UserQuotaBasicUsage(*, quota_source_label: Optional[str] = None, total_disk_usage: float)[source]¶
Bases:
BaseModel
- class galaxy.model.UserQuotaUsage(*, quota_source_label: Optional[str] = None, total_disk_usage: float, quota_percent: Optional[float] = None, quota_bytes: Optional[int] = None, quota: Optional[str] = None)[source]¶
Bases:
UserQuotaBasicUsage
- class galaxy.model.User(email=None, password=None, username=None)[source]¶
Bases:
Base
,Dictifiable
,RepresentById
Data for a Galaxy user or admin and relations to their histories, credentials, and roles.
- use_pbkdf2 = True¶
- bootstrap_admin_user = False¶
- create_time¶
- update_time¶
- last_password_change¶
- form_values_id¶
- preferred_object_store_id¶
- disk_usage¶
- activation_token¶
- addresses¶
- cloudauthz¶
- custos_auth¶
- default_permissions¶
- groups¶
- histories¶
- active_histories¶
- galaxy_sessions¶
- quotas¶
- quota_source_usages¶
- social_auth¶
- values¶
- data_manager_histories¶
- roles¶
- stored_workflows¶
- all_notifications¶
- non_private_roles¶
- preferences: association_proxy = ColumnAssociationProxyInstance(AssociationProxy('_preferences', 'value'))¶
- 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', 'preferred_object_store_id']¶
- __init__(email=None, password=None, username=None)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- email¶
- password¶
- external¶
- deleted¶
- purged¶
- active¶
- username¶
- property 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, quota_source_label=None)[source]¶
Return byte count of disk space used by user or a human-readable string if nice_size is True.
- property total_disk_usage¶
Return byte count of disk space used by user or a human-readable string if nice_size is True.
- property nice_total_disk_usage¶
Return byte count of disk space used in a human-readable string.
- calculate_disk_usage_default_source(object_store)[source]¶
Return byte count total of disk space used by all non-purged, non-library HDAs in non-purged histories assigned to default quota source.
- 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'
- dictify_usage(object_store=None) List[UserQuotaBasicUsage] [source]¶
Include object_store to include empty/unused usage info.
- dictify_usage_for(quota_source_label: Optional[str]) UserQuotaBasicUsage [source]¶
- current_galaxy_session¶
- table = Table('galaxy_user', MetaData(), 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('preferred_object_store_id', String(length=255), 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)¶
- class galaxy.model.PasswordResetToken(user, token=None)[source]¶
Bases:
Base
- user_id¶
- __init__(user, token=None)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- token¶
- user¶
- expiration_time¶
- table = Table('password_reset_token', MetaData(), 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)¶
- class galaxy.model.DynamicTool(active=True, hidden=True, **kwd)[source]¶
Bases:
Base
,Dictifiable
,RepresentById
- create_time¶
- update_time¶
- tool_id¶
- tool_version¶
- tool_format¶
- tool_path¶
- tool_directory¶
- value¶
- 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__(active=True, hidden=True, **kwd)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- active¶
- uuid¶
- table = Table('dynamic_tool', MetaData(), 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', MutableJSONType(), table=<dynamic_tool>), schema=None)¶
- class galaxy.model.BaseJobMetric(plugin, metric_name, metric_value)[source]¶
Bases:
Base
- __init__(plugin, metric_name, metric_value)[source]¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- class galaxy.model.JobMetricText(plugin, metric_name, metric_value)[source]¶
Bases:
BaseJobMetric
,RepresentById
- job_id¶
- plugin¶
- metric_name¶
- metric_value¶
- __init__(plugin, metric_name, metric_value)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('job_metric_text', MetaData(), 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:
BaseJobMetric
,RepresentById
- job_id¶
- plugin¶
- metric_name¶
- metric_value¶
- __init__(plugin, metric_name, metric_value)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('job_metric_numeric', MetaData(), 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:
BaseJobMetric
,RepresentById
- task_id¶
- plugin¶
- metric_name¶
- metric_value¶
- __init__(plugin, metric_name, metric_value)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('task_metric_text', MetaData(), 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)¶
- class galaxy.model.TaskMetricNumeric(plugin, metric_name, metric_value)[source]¶
Bases:
BaseJobMetric
,RepresentById
- task_id¶
- plugin¶
- metric_name¶
- metric_value¶
- __init__(plugin, metric_name, metric_value)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('task_metric_numeric', MetaData(), 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)¶
- class galaxy.model.IoDicts(inp_data, out_data, out_collections)[source]¶
Bases:
tuple
- property inp_data¶
Alias for field number 0
- property out_data¶
Alias for field number 1
- property out_collections¶
Alias for field number 2
- class galaxy.model.Job[source]¶
Bases:
Base
,JobLike
,UsesCreateAndUpdateTime
,Dictifiable
,Serializable
A job represents a request to run a tool given input datasets, tool parameters, and output datasets.
- create_time¶
- update_time: DateTime¶
- history_id¶
- library_folder_id¶
- tool_id¶
- tool_version¶
- galaxy_version¶
- dynamic_tool_id¶
- info¶
- copied_from_job_id¶
- command_line¶
- job_messages¶
- param_filename¶
- runner_name¶
- job_stdout¶
- job_stderr¶
- tool_stdout¶
- tool_stderr¶
- exit_code¶
- traceback¶
- session_id¶
- user_id¶
- job_runner_name¶
- job_runner_external_id¶
- destination_id¶
- destination_params¶
- object_store_id¶
- params¶
- handler¶
- preferred_object_store_id¶
- object_store_id_overrides¶
- user¶
- galaxy_session¶
- history¶
- library_folder¶
- parameters¶
- input_datasets¶
- input_dataset_collections¶
- input_dataset_collection_elements¶
- output_dataset_collection_instances¶
- output_dataset_collections¶
- post_job_actions¶
- input_library_datasets¶
- output_library_datasets¶
- external_output_metadata¶
- tasks¶
- output_datasets¶
- state_history¶
- text_metrics¶
- numeric_metrics¶
- interactivetool_entry_points¶
- implicit_collection_jobs_association¶
- container¶
- data_manager_association¶
- history_dataset_collection_associations¶
- workflow_invocation_step¶
- any_output_dataset_collection_instances_deleted: column_property¶
- any_output_dataset_deleted: column_property¶
- 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', 'copied_from_job_id']¶
- terminal_states = [<JobState.OK: 'ok'>, <JobState.ERROR: 'error'>, <JobState.DELETED: 'deleted'>]¶
- non_ready_states = [<JobState.NEW: 'new'>, <JobState.RESUBMITTED: 'resubmitted'>, <JobState.UPLOAD: 'upload'>, <JobState.WAITING: 'waiting'>, <JobState.QUEUED: 'queued'>, <JobState.RUNNING: 'running'>]¶
job states where the job hasn’t finished and the model may still change
- __init__()¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- dependencies¶
- state¶
- imported¶
- property running¶
- property 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
- property 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.
- property command_version¶
- table = Table('job', MetaData(), 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', MutableJSONType(), table=<job>), Column('job_messages', MutableJSONType(), 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', MutableJSONType(), 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>), Column('preferred_object_store_id', String(length=255), table=<job>), Column('object_store_id_overrides', JSONType(), table=<job>), schema=None)¶
- class galaxy.model.Task(job, working_directory, prepare_files_cmd)[source]¶
Bases:
Base
,JobLike
,RepresentById
A task represents a single component of a job.
- create_time¶
- execution_time¶
- update_time¶
- command_line¶
- param_filename¶
- runner_name¶
- job_stdout¶
- job_stderr¶
- tool_stdout¶
- tool_stderr¶
- exit_code¶
- job_messages¶
- info¶
- traceback¶
- job_id¶
- task_runner_name¶
- task_runner_external_id¶
- text_metrics¶
- numeric_metrics¶
- class states(value)[source]¶
-
An enumeration.
- NEW = 'new'¶
- WAITING = 'waiting'¶
- QUEUED = 'queued'¶
- RUNNING = 'running'¶
- OK = 'ok'¶
- ERROR = 'error'¶
- DELETED = 'deleted'¶
- __init__(job, working_directory, prepare_files_cmd)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- state¶
- working_directory¶
- job¶
- 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.
- table = Table('task', MetaData(), 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', MutableJSONType(), 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)¶
- class galaxy.model.JobParameter(name, value)[source]¶
Bases:
Base
,RepresentById
- job_id¶
- __init__(name, value)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- name¶
- value¶
- table = Table('job_parameter', MetaData(), 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:
Base
,RepresentById
- job_id¶
- dataset_id¶
- job¶
- __init__(name, dataset)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- name¶
- dataset¶
- dataset_version¶
- table = Table('job_to_input_dataset', MetaData(), 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:
Base
,RepresentById
- job_id¶
- dataset_id¶
- job¶
- __init__(name, dataset)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- name¶
- dataset¶
- property item¶
- table = Table('job_to_output_dataset', MetaData(), 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:
Base
,RepresentById
- job_id¶
- dataset_collection_id¶
- job¶
- __init__(name, dataset_collection)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- name¶
- dataset_collection¶
- table = Table('job_to_input_dataset_collection', MetaData(), 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', String(length=255), table=<job_to_input_dataset_collection>), schema=None)¶
- class galaxy.model.JobToInputDatasetCollectionElementAssociation(name, dataset_collection_element)[source]¶
Bases:
Base
,RepresentById
- job_id¶
- dataset_collection_element_id¶
- job¶
- __init__(name, dataset_collection_element)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- name¶
- dataset_collection_element¶
- table = Table('job_to_input_dataset_collection_element', MetaData(), Column('id', Integer(), table=<job_to_input_dataset_collection_element>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_to_input_dataset_collection_element>), Column('dataset_collection_element_id', Integer(), ForeignKey('dataset_collection_element.id'), table=<job_to_input_dataset_collection_element>), Column('name', Unicode(length=255), table=<job_to_input_dataset_collection_element>), schema=None)¶
- class galaxy.model.JobToOutputDatasetCollectionAssociation(name, dataset_collection_instance)[source]¶
Bases:
Base
,RepresentById
- job_id¶
- dataset_collection_id¶
- job¶
- __init__(name, dataset_collection_instance)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- name¶
- dataset_collection_instance¶
- property item¶
- table = Table('job_to_output_dataset_collection', MetaData(), 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:
Base
,RepresentById
- job_id¶
- dataset_collection_id¶
- job¶
- __init__(name, dataset_collection)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- name¶
- dataset_collection¶
- table = Table('job_to_implicit_output_dataset_collection', MetaData(), 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:
Base
,RepresentById
- job_id¶
- ldda_id¶
- job¶
- __init__(name, dataset)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- name¶
- dataset¶
- table = Table('job_to_input_library_dataset', MetaData(), 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', Unicode(length=255), table=<job_to_input_library_dataset>), schema=None)¶
- class galaxy.model.JobToOutputLibraryDatasetAssociation(name, dataset)[source]¶
Bases:
Base
,RepresentById
- job_id¶
- ldda_id¶
- job¶
- __init__(name, dataset)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- name¶
- dataset¶
- table = Table('job_to_output_library_dataset', MetaData(), 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', Unicode(length=255), table=<job_to_output_library_dataset>), schema=None)¶
- class galaxy.model.JobStateHistory(job)[source]¶
Bases:
Base
,RepresentById
- create_time¶
- __init__(job)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- job_id¶
- state¶
- info¶
- table = Table('job_state_history', MetaData(), 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('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)¶
- class galaxy.model.ImplicitlyCreatedDatasetCollectionInput(name, input_dataset_collection)[source]¶
Bases:
Base
,RepresentById
- dataset_collection_id¶
- input_dataset_collection_id¶
- __init__(name, input_dataset_collection)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- name¶
- input_dataset_collection¶
- table = Table('implicitly_created_dataset_collection_inputs', MetaData(), 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(populated_state=None)[source]¶
Bases:
Base
,Serializable
- jobs¶
- __init__(populated_state=None)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- populated_state¶
- property job_list¶
- table = Table('implicit_collection_jobs', MetaData(), 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)¶
- class galaxy.model.ImplicitCollectionJobsJobAssociation(**kwargs)[source]¶
Bases:
Base
,RepresentById
- implicit_collection_jobs_id¶
- job_id¶
- order_index¶
- implicit_collection_jobs¶
- job¶
- __init__(**kwargs)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('implicit_collection_jobs_job_association', MetaData(), 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:
Base
,RepresentById
- workflow_step_id¶
- __init__(action_type, workflow_step=None, output_name=None, action_arguments=None)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- action_type¶
- output_name¶
- action_arguments¶
- workflow_step¶
- table = Table('post_job_action', MetaData(), 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', MutableJSONType(), table=<post_job_action>), schema=None)¶
- class galaxy.model.PostJobActionAssociation(pja, job=None, job_id=None)[source]¶
Bases:
Base
,RepresentById
- post_job_action_id¶
- __init__(pja, job=None, job_id=None)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- job¶
- job_id¶
- post_job_action¶
- table = Table('post_job_action_association', MetaData(), 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:
Base
,RepresentById
- job_id¶
- history_dataset_association_id¶
- library_dataset_dataset_association_id¶
- is_valid¶
- filename_in¶
- filename_out¶
- filename_results_code¶
- filename_kwds¶
- filename_override_metadata¶
- job_runner_external_pid¶
- __init__(job=None, dataset=None)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- job¶
- history_dataset_association¶
- library_dataset_dataset_association¶
- property dataset¶
- table = Table('job_external_output_metadata', MetaData(), 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.FakeDatasetAssociation(dataset=None)[source]¶
Bases:
object
- fake_dataset_association = True¶
- class galaxy.model.JobExportHistoryArchive(compressed=False, **kwd)[source]¶
Bases:
Base
,RepresentById
- job_id¶
- history_id¶
- dataset_id¶
- history_attrs_filename¶
- job¶
- dataset¶
- history¶
- ATTRS_FILENAME_HISTORY = 'history_attrs.txt'¶
- __init__(compressed=False, **kwd)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- compressed¶
- property fda¶
- property temp_directory¶
- property up_to_date¶
Return False, if a new export should be generated for corresponding history.
- property ready¶
- property preparing¶
- property export_name¶
- table = Table('job_export_history_archive', MetaData(), 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(**kwargs)[source]¶
Bases:
Base
,RepresentById
- job_id¶
- history_id¶
- archive_dir¶
- job¶
- history¶
- __init__(**kwargs)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('job_import_history_archive', MetaData(), 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.StoreExportAssociation(**kwargs)[source]¶
Bases:
Base
,RepresentById
- task_uuid¶
- create_time¶
- object_type¶
- object_id¶
- export_metadata¶
- __init__(**kwargs)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('store_export_association', MetaData(), Column('id', Integer(), table=<store_export_association>, primary_key=True, nullable=False), Column('task_uuid', UUIDType(), table=<store_export_association>), Column('create_time', DateTime(), table=<store_export_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('object_type', TrimmedString(length=32), table=<store_export_association>), Column('object_id', Integer(), table=<store_export_association>), Column('export_metadata', JSONType(), table=<store_export_association>), schema=None)¶
- class galaxy.model.JobContainerAssociation(**kwd)[source]¶
Bases:
Base
,RepresentById
- job_id¶
- container_type¶
- container_name¶
- created_time¶
- modified_time¶
- job¶
- __init__(**kwd)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- container_info¶
- table = Table('job_container_association', MetaData(), 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', MutableJSONType(), 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(requires_domain=True, configured=False, deleted=False, short_token=False, **kwd)[source]¶
Bases:
Base
,Dictifiable
,RepresentById
- job_id¶
- name¶
- tool_port¶
- host¶
- port¶
- protocol¶
- entry_url¶
- created_time¶
- modified_time¶
- job¶
- dict_collection_visible_keys = ['id', 'job_id', 'name', 'active', 'created_time', 'modified_time', 'output_datasets_ids']¶
- dict_element_visible_keys = ['id', 'job_id', 'name', 'active', 'created_time', 'modified_time', 'output_datasets_ids']¶
- __init__(requires_domain=True, configured=False, deleted=False, short_token=False, **kwd)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- requires_domain¶
- configured¶
- deleted¶
- token¶
- info¶
- property active¶
- property output_datasets_ids¶
- table = Table('interactivetool_entry_point', MetaData(), 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('requires_domain', Boolean(), table=<interactivetool_entry_point>, default=ColumnDefault(True)), Column('info', MutableJSONType(), 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(**kwargs)[source]¶
Bases:
Base
,RepresentById
- job_id¶
- dataset_id¶
- fasta_path¶
- created_time¶
- modified_time¶
- indexer¶
- user_id¶
- job¶
- dataset¶
- user¶
- __init__(**kwargs)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('genome_index_tool_data', MetaData(), 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('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)¶
- class galaxy.model.Group(name=None)[source]¶
Bases:
Base
,Dictifiable
,RepresentById
- create_time¶
- update_time¶
- quotas¶
- roles¶
- users¶
- dict_collection_visible_keys = ['id', 'name']¶
- dict_element_visible_keys = ['id', 'name']¶
- __init__(name=None)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- name¶
- deleted¶
- table = Table('galaxy_group', MetaData(), 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)¶
- class galaxy.model.UserGroupAssociation(user, group)[source]¶
Bases:
Base
,RepresentById
- user_id¶
- group_id¶
- create_time¶
- update_time¶
- __init__(user, group)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- user¶
- group¶
- table = Table('user_group_association', MetaData(), 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)¶
- class galaxy.model.Notification(source, category, variant, content)[source]¶
Bases:
Base
,Dictifiable
,RepresentById
- create_time¶
- update_time¶
- publication_time¶
- expiration_time¶
- user_notification_associations¶
- __init__(source, category, variant, content)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- source¶
- category¶
- variant¶
- content¶
- table = Table('notification', MetaData(), Column('id', Integer(), table=<notification>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<notification>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<notification>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('publication_time', DateTime(), table=<notification>, default=ColumnDefault(<function datetime.utcnow>)), Column('expiration_time', DateTime(), table=<notification>, default=ColumnDefault(datetime.datetime(2025, 3, 26, 16, 7, 9, 457437))), Column('source', String(length=32), table=<notification>), Column('category', String(length=64), table=<notification>), Column('variant', String(length=16), table=<notification>), Column('content', DoubleEncodedJsonType(), table=<notification>), schema=None)¶
- class galaxy.model.UserNotificationAssociation(user, notification)[source]¶
Bases:
Base
,RepresentById
- user_id¶
- notification_id¶
- seen_time¶
- deleted¶
- update_time¶
- __init__(user, notification)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- user¶
- notification¶
- table = Table('user_notification_association', MetaData(), Column('id', Integer(), table=<user_notification_association>, primary_key=True, nullable=False), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<user_notification_association>), Column('notification_id', Integer(), ForeignKey('notification.id'), table=<user_notification_association>), Column('seen_time', DateTime(), table=<user_notification_association>), Column('deleted', Boolean(), table=<user_notification_association>, default=ColumnDefault(False)), Column('update_time', DateTime(), table=<user_notification_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)¶
- class galaxy.model.HistoryAudit(*args, **kwargs)[source]¶
Bases:
Base
,RepresentById
- history_id¶
- update_time¶
- __init__(*args, **kwargs)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('history_audit', MetaData(), Column('history_id', Integer(), ForeignKey('history.id'), table=<history_audit>, primary_key=True, nullable=False), Column('update_time', DateTime(), table=<history_audit>, primary_key=True, nullable=False, default=ColumnDefault(<function datetime.utcnow>)), schema=None)¶
- class galaxy.model.History(id=None, name=None, user=None)[source]¶
Bases:
Base
,HasTags
,Dictifiable
,UsesAnnotations
,HasName
,Serializable
- create_time¶
- user_id¶
- hid_counter¶
- genome_build¶
- importable¶
- slug¶
- preferred_object_store_id¶
- archived¶
- archive_export_id¶
- datasets¶
- exports¶
- active_datasets¶
- dataset_collections¶
- active_dataset_collections¶
- visible_datasets¶
- visible_dataset_collections¶
- tags: List[ItemTagAssociation]¶
- annotations¶
- ratings¶
- default_permissions¶
- galaxy_sessions¶
- workflow_invocations¶
- jobs¶
- update_time¶
- average_rating: column_property¶
- dict_collection_visible_keys = ['id', 'name', 'published', 'deleted']¶
- dict_element_visible_keys = ['id', 'name', 'genome_build', 'deleted', 'purged', 'archived', 'update_time', 'published', 'importable', 'slug', 'empty', 'preferred_object_store_id']¶
- default_name = 'Unnamed history'¶
- __init__(id=None, name=None, user=None)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- name¶
- deleted¶
- purged¶
- importing¶
- published¶
- user¶
- property empty¶
- property count¶
- 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 and collections 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.
- property has_possible_members¶
- property activatable_datasets¶
- property latest_export¶
- property 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.
- property disk_nice_size¶
Returns human readable size of history on disk.
- property active_dataset_and_roles_query¶
- property active_datasets_and_roles¶
- property active_visible_datasets_and_roles¶
- property active_visible_dataset_collections¶
- property active_contents¶
Return all active contents ordered by hid.
- table = Table('history', MetaData(), 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)), Column('preferred_object_store_id', String(length=255), table=<history>), Column('archived', Boolean(), table=<history>, default=ColumnDefault(False), server_default=DefaultClause(<sqlalchemy.sql.elements.False_ object>, for_update=False)), Column('archive_export_id', Integer(), ForeignKey('store_export_association.id'), table=<history>), schema=None)¶
Bases:
RepresentById
Bases:
Base
,UserShareAssociation
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- class galaxy.model.UserRoleAssociation(user, role)[source]¶
Bases:
Base
,RepresentById
- user_id¶
- role_id¶
- create_time¶
- update_time¶
- __init__(user, role)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- user¶
- role¶
- table = Table('user_role_association', MetaData(), 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)¶
- class galaxy.model.GroupRoleAssociation(group, role)[source]¶
Bases:
Base
,RepresentById
- group_id¶
- role_id¶
- create_time¶
- update_time¶
- __init__(group, role)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- group¶
- role¶
- table = Table('group_role_association', MetaData(), 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)¶
- class galaxy.model.Role(name=None, description=None, type=types.SYSTEM, deleted=False)[source]¶
Bases:
Base
,Dictifiable
,RepresentById
- create_time¶
- update_time¶
- dataset_actions¶
- groups¶
- users¶
- dict_collection_visible_keys = ['id', 'name']¶
- dict_element_visible_keys = ['id', 'name', 'description', 'type']¶
- private_id = None¶
- class types(value)[source]¶
-
An enumeration.
- PRIVATE = 'private'¶
- SYSTEM = 'system'¶
- USER = 'user'¶
- ADMIN = 'admin'¶
- SHARING = 'sharing'¶
- __init__(name=None, description=None, type=types.SYSTEM, deleted=False)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- name¶
- description¶
- type¶
- deleted¶
- table = Table('role', MetaData(), 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)¶
- class galaxy.model.UserQuotaSourceUsage(**kwargs)[source]¶
Bases:
Base
,Dictifiable
,RepresentById
- dict_element_visible_keys = ['disk_usage', 'quota_source_label']¶
- user_id¶
- quota_source_label¶
- disk_usage¶
- user¶
- __init__(**kwargs)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('user_quota_source_usage', MetaData(), Column('id', Integer(), table=<user_quota_source_usage>, primary_key=True, nullable=False), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<user_quota_source_usage>), Column('quota_source_label', String(length=32), table=<user_quota_source_usage>), Column('disk_usage', Numeric(precision=15, scale=0), table=<user_quota_source_usage>, nullable=False, default=ColumnDefault(0)), schema=None)¶
- class galaxy.model.UserQuotaAssociation(user, quota)[source]¶
Bases:
Base
,Dictifiable
,RepresentById
- user_id¶
- quota_id¶
- create_time¶
- update_time¶
- dict_element_visible_keys = ['user']¶
- __init__(user, quota)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- user¶
- quota¶
- table = Table('user_quota_association', MetaData(), 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)¶
- class galaxy.model.GroupQuotaAssociation(group, quota)[source]¶
Bases:
Base
,Dictifiable
,RepresentById
- group_id¶
- quota_id¶
- create_time¶
- update_time¶
- dict_element_visible_keys = ['group']¶
- __init__(group, quota)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- group¶
- quota¶
- table = Table('group_quota_association', MetaData(), 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)¶
- class galaxy.model.Quota(name=None, description=None, amount=0, operation='=', quota_source_label=None)[source]¶
Bases:
Base
,Dictifiable
,RepresentById
- create_time¶
- update_time¶
- deleted¶
- default¶
- groups¶
- users¶
- dict_collection_visible_keys = ['id', 'name', 'quota_source_label']¶
- dict_element_visible_keys = ['id', 'name', 'description', 'bytes', 'operation', 'display_amount', 'default', 'users', 'groups', 'quota_source_label']¶
- valid_operations = ('+', '-', '=')¶
- __init__(name=None, description=None, amount=0, operation='=', quota_source_label=None)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- name¶
- description¶
- bytes¶
- operation¶
- quota_source_label¶
- property amount¶
- property display_amount¶
- table = Table('quota', MetaData(), 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)), Column('quota_source_label', String(length=32), table=<quota>), schema=None)¶
- class galaxy.model.DefaultQuotaAssociation(type, quota)[source]¶
Bases:
Base
,Dictifiable
,RepresentById
- create_time¶
- update_time¶
- quota_id¶
- dict_element_visible_keys = ['type']¶
- class types(value)[source]¶
-
An enumeration.
- UNREGISTERED = 'unregistered'¶
- REGISTERED = 'registered'¶
- __init__(type, quota)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- type¶
- quota¶
- table = Table('default_quota_association', MetaData(), 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)¶
- class galaxy.model.DatasetPermissions(action, dataset, role=None, role_id=None)[source]¶
Bases:
Base
,RepresentById
- create_time¶
- update_time¶
- dataset_id¶
- __init__(action, dataset, role=None, role_id=None)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- action¶
- dataset¶
- role¶
- role_id¶
- table = Table('dataset_permissions', MetaData(), 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)¶
- class galaxy.model.LibraryPermissions(action, library_item, role)[source]¶
Bases:
Base
,RepresentById
- create_time¶
- update_time¶
- library_id¶
- role_id¶
- __init__(action, library_item, role)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- action¶
- library¶
- role¶
- table = Table('library_permissions', MetaData(), 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)¶
- class galaxy.model.LibraryFolderPermissions(action, library_item, role)[source]¶
Bases:
Base
,RepresentById
- create_time¶
- update_time¶
- library_folder_id¶
- role_id¶
- __init__(action, library_item, role)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- action¶
- folder¶
- role¶
- table = Table('library_folder_permissions', MetaData(), 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)¶
- class galaxy.model.LibraryDatasetPermissions(action, library_item, role)[source]¶
Bases:
Base
,RepresentById
- create_time¶
- update_time¶
- library_dataset_id¶
- role_id¶
- __init__(action, library_item, role)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- action¶
- library_dataset¶
- role¶
- table = Table('library_dataset_permissions', MetaData(), 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)¶
- class galaxy.model.LibraryDatasetDatasetAssociationPermissions(action, library_item, role)[source]¶
Bases:
Base
,RepresentById
- create_time¶
- update_time¶
- library_dataset_dataset_association_id¶
- role_id¶
- __init__(action, library_item, role)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- action¶
- library_dataset_dataset_association¶
- role¶
- table = Table('library_dataset_dataset_association_permissions', MetaData(), 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)¶
- class galaxy.model.DefaultUserPermissions(user, action, role)[source]¶
Bases:
Base
,RepresentById
- user_id¶
- role_id¶
- __init__(user, action, role)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- user¶
- action¶
- role¶
- table = Table('default_user_permissions', MetaData(), 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)¶
- class galaxy.model.DefaultHistoryPermissions(history, action, role)[source]¶
Bases:
Base
,RepresentById
- history_id¶
- role_id¶
- __init__(history, action, role)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- history¶
- action¶
- role¶
- table = Table('default_history_permissions', MetaData(), 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:
Base
,StorableObject
,Serializable
- job_id¶
- create_time¶
- update_time¶
- object_store_id¶
- created_from_basename¶
- total_size¶
- actions¶
- job¶
- active_history_associations¶
- purged_history_associations¶
- active_library_associations¶
- history_associations¶
- library_associations¶
- states¶
alias of
DatasetState
- non_ready_states = (<DatasetState.NEW: 'new'>, <DatasetState.UPLOAD: 'upload'>, <DatasetState.QUEUED: 'queued'>, <DatasetState.RUNNING: 'running'>, <DatasetState.SETTING_METADATA: 'setting_metadata'>)¶
- ready_states = (<DatasetState.OK: 'ok'>, <DatasetState.PAUSED: 'paused'>, <DatasetState.EMPTY: 'empty'>, <DatasetState.FAILED_METADATA: 'failed_metadata'>, <DatasetState.DISCARDED: 'discarded'>, <DatasetState.ERROR: 'error'>, <DatasetState.DEFERRED: 'deferred'>)¶
- valid_input_states = (<DatasetState.UPLOAD: 'upload'>, <DatasetState.OK: 'ok'>, <DatasetState.NEW: 'new'>, <DatasetState.PAUSED: 'paused'>, <DatasetState.RUNNING: 'running'>, <DatasetState.EMPTY: 'empty'>, <DatasetState.FAILED_METADATA: 'failed_metadata'>, <DatasetState.QUEUED: 'queued'>, <DatasetState.SETTING_METADATA: 'setting_metadata'>, <DatasetState.DEFERRED: 'deferred'>)¶
- no_data_states = (<DatasetState.PAUSED: 'paused'>, <DatasetState.DEFERRED: 'deferred'>, <DatasetState.DISCARDED: 'discarded'>, <DatasetState.NEW: 'new'>, <DatasetState.UPLOAD: 'upload'>, <DatasetState.QUEUED: 'queued'>, <DatasetState.RUNNING: 'running'>, <DatasetState.SETTING_METADATA: 'setting_metadata'>)¶
- terminal_states = (<DatasetState.OK: 'ok'>, <DatasetState.EMPTY: 'empty'>, <DatasetState.ERROR: 'error'>, <DatasetState.DEFERRED: 'deferred'>, <DatasetState.DISCARDED: 'discarded'>, <DatasetState.FAILED_METADATA: 'failed_metadata'>)¶
- class conversion_messages(value)[source]¶
-
An enumeration.
- PENDING = 'pending'¶
- NO_DATA = 'no data'¶
- NO_CHROMOSOME = 'no chromosome'¶
- NO_CONVERTER = 'no converter'¶
- NO_TOOL = 'no tool'¶
- DATA = 'data'¶
- ERROR = 'error'¶
- OK = 'ok'¶
- permitted_actions = <galaxy.util.bunch.Bunch object>¶
- file_path = '/tmp/'¶
- object_store: Optional[ObjectStore] = None¶
- engine = None¶
- __init__(id=None, state=None, external_filename=None, extra_files_path=None, file_size=None, purgable=True, uuid=None)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- uuid¶
- state¶
- deleted¶
- purged¶
- purgable¶
- external_filename¶
- file_size¶
- sources¶
- hashes¶
- property is_new¶
Return True if placed into an objectstore not labeled as
private
.
- property quota_source_label¶
- property quota_source_info¶
- property file_name¶
- property extra_files_path¶
- property store_by¶
- property extra_files_path_name¶
- get_size(nice_size: typing_extensions.Literal[False], calculate_size: bool = True) int [source]¶
- get_size(nice_size: typing_extensions.Literal[True], calculate_size: bool = True) str
Returns the size of the data on disk
- 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.
- property user_can_purge¶
- table = Table('dataset', MetaData(), Column('id', Integer(), table=<dataset>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<dataset>), 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)¶
- class galaxy.model.DatasetSource(**kwargs)[source]¶
Bases:
Base
,Dictifiable
,Serializable
- dataset_id¶
- source_uri¶
- extra_files_path¶
- transform¶
- dataset¶
- hashes¶
- dict_collection_visible_keys = ['id', 'source_uri', 'extra_files_path', 'transform']¶
- dict_element_visible_keys = ['id', 'source_uri', 'extra_files_path', 'transform']¶
- copy() DatasetSource [source]¶
- __init__(**kwargs)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('dataset_source', MetaData(), 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', MutableJSONType(), table=<dataset_source>), schema=None)¶
- class galaxy.model.DatasetSourceHash(**kwargs)[source]¶
Bases:
Base
,Serializable
- dataset_source_id¶
- hash_function¶
- hash_value¶
- source¶
- copy() DatasetSourceHash [source]¶
- __init__(**kwargs)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('dataset_source_hash', MetaData(), 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(**kwargs)[source]¶
Bases:
Base
,Dictifiable
,Serializable
- dataset_id¶
- hash_function¶
- hash_value¶
- extra_files_path¶
- dataset¶
- dict_collection_visible_keys = ['id', 'hash_function', 'hash_value', 'extra_files_path']¶
- dict_element_visible_keys = ['id', 'hash_function', 'hash_value', 'extra_files_path']¶
- copy() DatasetHash [source]¶
- __init__(**kwargs)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('dataset_hash', MetaData(), 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=DatasetValidatedState.UNKNOWN, validated_state_message=None, visible=True, create_dataset=False, sa_session=None, extended_metadata=None, flush=True, metadata_deferred=False, creating_job_id=None)[source]¶
Bases:
UsesCreateAndUpdateTime
,object
A base class for all ‘dataset instances’, HDAs, LDAs, etc
- states¶
alias of
DatasetState
- class conversion_messages(value)¶
-
An enumeration.
- PENDING = 'pending'¶
- NO_DATA = 'no data'¶
- NO_CHROMOSOME = 'no chromosome'¶
- NO_CONVERTER = 'no converter'¶
- NO_TOOL = 'no tool'¶
- DATA = 'data'¶
- ERROR = 'error'¶
- OK = 'ok'¶
- permitted_actions = <galaxy.util.bunch.Bunch object>¶
- creating_job_associations: List[Union[JobToOutputDatasetCollectionAssociation, JobToOutputDatasetAssociation]]¶
- validated_states¶
alias of
DatasetValidatedState
- __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=DatasetValidatedState.UNKNOWN, validated_state_message=None, visible=True, create_dataset=False, sa_session=None, extended_metadata=None, flush=True, metadata_deferred=False, creating_job_id=None)[source]¶
- property peek¶
- property ext¶
- property has_deferred_data¶
- property state¶
- property extra_files_path¶
- property set_metadata_requires_flush¶
- property metadata¶
- property has_metadata_files¶
- property metadata_file_types¶
- property dbkey¶
- property created_from_basename¶
- property sources¶
- property hashes¶
- 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: List[str], **kwd) Tuple[bool, Optional[str], Optional[DatasetInstance]] [source]¶
Returns ( target_ext, existing converted dataset )
- property is_ok¶
- property is_pending¶
Return true if the dataset is neither ready nor in error
- property source_library_dataset¶
- property source_dataset_chain¶
- property creating_job¶
- 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:
DatasetInstance
,HasTags
,Dictifiable
,UsesAnnotations
,HasName
,Serializable
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¶
- property user¶
- copy(parent_id=None, copy_tags=None, flush=True, copy_hid=True, new_name=None)[source]¶
Create a copy of this HDA.
- copy_attributes(new_dataset)[source]¶
Copies attributes to a new datasets, used for implicit conversions
- to_library_dataset_dataset_association(trans, target_folder, replace_dataset=None, parent_id=None, roles=None, ldda_message='', element_identifier=None)[source]¶
Copy this HDA to a library optionally replacing an existing LDDA.
- get_access_roles(security_agent)[source]¶
Return The access roles associated with this HDA’s dataset.
- purge_usage_from_quota(user, quota_source_info)[source]¶
Remove this HDA’s quota_amount from user’s quota.
- 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.
- property 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: List[Union[JobToOutputDatasetCollectionAssociation, JobToOutputDatasetAssociation]]¶
- dataset¶
- dataset_id¶
- deleted¶
- dependent_jobs¶
- designation¶
- extended_metadata¶
- extended_metadata_id¶
- extension¶
- history_id¶
- implicitly_converted_datasets¶
- implicitly_converted_parent_datasets¶
- info¶
- metadata_deferred¶
- name¶
- parent_id¶
- ratings¶
- table = Table('history_dataset_association', MetaData(), 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('metadata_deferred', Boolean(), table=<history_dataset_association>), 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)¶
- tags: List[ItemTagAssociation]¶
- tool_version¶
- update_time: DateTime¶
- 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:
Base
,Serializable
- __init__(history_dataset_association_id, name, dbkey, update_time, version, extension, extended_metadata_id, metadata)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- history_dataset_association_id¶
- name¶
- update_time¶
- version¶
- extension¶
- extended_metadata_id¶
- table = Table('history_dataset_association_history', MetaData(), 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>), 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:
Base
,RepresentById
- create_time¶
- update_time¶
- history_dataset_association_id¶
- user_id¶
- __init__(hda=None, user=None, site=None)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- history_dataset_association¶
- user¶
- site¶
- table = Table('history_dataset_association_display_at_authorization', MetaData(), 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)¶
- class galaxy.model.HistoryDatasetAssociationSubset(hda, subset, location)[source]¶
Bases:
Base
,RepresentById
- history_dataset_association_id¶
- history_dataset_association_subset_id¶
- __init__(hda, subset, location)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- hda¶
- subset¶
- location¶
- table = Table('history_dataset_association_subset', MetaData(), 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:
Base
,Dictifiable
,HasName
,Serializable
- root_folder_id¶
- create_time¶
- update_time¶
- deleted¶
- purged¶
- actions¶
- 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)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- name¶
- description¶
- synopsis¶
- root_folder¶
- table = Table('library', MetaData(), 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)¶
- class galaxy.model.LibraryFolder(name=None, description=None, item_count=0, order_id=None, genome_build=None)[source]¶
Bases:
Base
,Dictifiable
,HasName
,Serializable
- parent_id¶
- create_time¶
- update_time¶
- deleted¶
- purged¶
- folders¶
- parent¶
- active_folders¶
- datasets¶
- active_datasets¶
- library_root¶
- actions¶
- 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)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- name¶
- description¶
- item_count¶
- order_id¶
- genome_build¶
- property activatable_library_datasets¶
- property library_path¶
- property parent_library¶
- table = Table('library_folder', MetaData(), 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)¶
- class galaxy.model.LibraryDataset(**kwargs)[source]¶
Bases:
Base
,Serializable
- library_dataset_dataset_association_id¶
- folder_id¶
- order_id¶
- create_time¶
- update_time¶
- deleted¶
- purged¶
- folder¶
- library_dataset_dataset_association¶
- expired_datasets¶
- actions¶
- 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')]¶
- property info¶
- property name¶
- __init__(**kwargs)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('library_dataset', MetaData(), 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>), Column('info', TrimmedString(length=255), table=<library_dataset>), Column('deleted', Boolean(), table=<library_dataset>, default=ColumnDefault(False)), Column('purged', Boolean(), table=<library_dataset>, default=ColumnDefault(False)), schema=None)¶
- 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:
DatasetInstance
,HasName
,Serializable
- __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: List[Union[JobToOutputDatasetCollectionAssociation, JobToOutputDatasetAssociation]]¶
- dataset¶
- dataset_id¶
- deleted¶
- dependent_jobs¶
- designation¶
- extended_metadata¶
- extended_metadata_id¶
- extension¶
- implicitly_converted_datasets¶
- implicitly_converted_parent_datasets¶
- info¶
- library_dataset_id¶
- message¶
- metadata_deferred¶
- name¶
- parent_id¶
- table = Table('library_dataset_dataset_association', MetaData(), 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('metadata_deferred', Boolean(), table=<library_dataset_dataset_association>), 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)¶
- tags¶
- tool_version¶
- update_time: DateTime¶
- user_id¶
- validated_state¶
- validated_state_message¶
- visible¶
- class galaxy.model.ExtendedMetadata(data)[source]¶
Bases:
Base
,RepresentById
- children¶
- __init__(data)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- data¶
- table = Table('extended_metadata', MetaData(), Column('id', Integer(), table=<extended_metadata>, primary_key=True, nullable=False), Column('data', MutableJSONType(), table=<extended_metadata>), schema=None)¶
- class galaxy.model.ExtendedMetadataIndex(extended_metadata, path, value)[source]¶
Bases:
Base
,RepresentById
- extended_metadata_id¶
- __init__(extended_metadata, path, value)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- extended_metadata¶
- path¶
- value¶
- table = Table('extended_metadata_index', MetaData(), 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:
Base
,RepresentById
- library_id¶
- form_definition_id¶
- form_values_id¶
- deleted¶
- __init__(library, form_definition, info, inheritable=False)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- library¶
- template¶
- info¶
- inheritable¶
- table = Table('library_info_association', MetaData(), 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:
Base
,RepresentById
- library_folder_id¶
- form_definition_id¶
- form_values_id¶
- deleted¶
- __init__(folder, form_definition, info, inheritable=False)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- folder¶
- template¶
- info¶
- inheritable¶
- table = Table('library_folder_info_association', MetaData(), 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:
Base
,RepresentById
- library_dataset_dataset_association_id¶
- form_definition_id¶
- form_values_id¶
- deleted¶
- __init__(library_dataset_dataset_association, form_definition, info)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- library_dataset_dataset_association¶
- template¶
- info¶
- property inheritable¶
- table = Table('library_dataset_dataset_info_association', MetaData(), 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.ImplicitlyConvertedDatasetAssociation(id=None, parent=None, dataset=None, file_type=None, deleted=False, purged=False, metadata_safe=True)[source]¶
Bases:
Base
,RepresentById
- create_time¶
- update_time¶
- hda_id¶
- ldda_id¶
- hda_parent_id¶
- ldda_parent_id¶
- __init__(id=None, parent=None, dataset=None, file_type=None, deleted=False, purged=False, metadata_safe=True)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- dataset¶
- dataset_ldda¶
- parent_hda¶
- parent_ldda¶
- type¶
- deleted¶
- metadata_safe¶
- table = Table('implicitly_converted_dataset_association', MetaData(), 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)¶
- class galaxy.model.InnerCollectionFilter(column, operator_function, expected_value)[source]¶
Bases:
tuple
- property column¶
Alias for field number 0
- property operator_function¶
Alias for field number 1
- property expected_value¶
Alias for field number 2
- class galaxy.model.DatasetCollection(id=None, collection_type=None, populated=True, element_count=None)[source]¶
Bases:
Base
,Dictifiable
,UsesAnnotations
,Serializable
- populated_state_message¶
- create_time¶
- update_time¶
- elements¶
- dict_collection_visible_keys = ['id', 'collection_type']¶
- dict_element_visible_keys = ['id', 'collection_type']¶
- populated_states¶
alias of
DatasetCollectionPopulatedState
- __init__(id=None, collection_type=None, populated=True, element_count=None)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- collection_type¶
- populated_state¶
- element_count¶
- property dataset_states_and_extensions_summary¶
- property has_deferred_data¶
- property populated_optimized¶
- property populated¶
- property dataset_action_tuples¶
- property element_identifiers_extensions_and_paths¶
- property waiting_for_elements¶
- property dataset_instances¶
- property dataset_elements¶
- property first_dataset_element¶
- property state¶
- copy(destination=None, element_destination=None, dataset_instance_attributes=None, flush=True, minimize_copies=False)[source]¶
- property has_subcollections¶
- table = Table('dataset_collection', MetaData(), 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)¶
- class galaxy.model.DatasetCollectionInstance[source]¶
Bases:
HasName
,UsesCreateAndUpdateTime
- property state¶
- property populated¶
- property dataset_instances¶
- set_from_dict(new_data)[source]¶
Set object attributes to the values in dictionary new_data limiting to only those keys in dict_element_visible_keys.
Returns a dictionary of the keys, values that have been changed.
- property has_deferred_data¶
- update_time: DateTime¶
- class galaxy.model.HistoryDatasetCollectionAssociation(deleted=False, visible=True, **kwd)[source]¶
Bases:
Base
,DatasetCollectionInstance
,HasTags
,Dictifiable
,UsesAnnotations
,Serializable
Associates a DatasetCollection with a History.
- collection_id¶
- history_id¶
- name¶
- hid¶
- copied_from_history_dataset_collection_association_id¶
- implicit_output_name¶
- job_id¶
- implicit_collection_jobs_id¶
- create_time¶
- update_time: DateTime¶
- collection¶
- history¶
- copied_from_history_dataset_collection_association¶
- copied_to_history_dataset_collection_association¶
- implicit_collection_jobs¶
- job¶
- tags: List[ItemTagAssociation]¶
- annotations¶
- ratings¶
- creating_job_associations¶
- dict_dbkeysandextensions_visible_keys = ['dbkeys', 'extensions']¶
- editable_keys = ('name', 'deleted', 'visible')¶
- __init__(deleted=False, visible=True, **kwd)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- deleted¶
- visible¶
- implicit_input_collections¶
- property history_content_type¶
- content_type = 'dataset_collection'¶
- type_id¶
- property job_source_type¶
- property job_state_summary¶
Aggregate counts of jobs by state, stored in a JobStateSummary object.
- property job_state_summary_dict¶
- property dataset_dbkeys_and_extensions_summary¶
- property job_source_id¶
- copy(element_destination=None, dataset_instance_attributes=None, flush=True, set_hid=True, minimize_copies=False)[source]¶
Create a copy of this history dataset collection association. Copy underlying collection.
- property waiting_for_elements¶
- contains_collection(collection_id)[source]¶
Checks to see that the indicated collection is a member of the hdca by using a recursive CTE sql query to find the collection’s parents and checking to see if any of the parents are associated with this hdca
- table = Table('history_dataset_collection_association', MetaData(), 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>), Column('create_time', DateTime(), table=<history_dataset_collection_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<history_dataset_collection_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)¶
- class galaxy.model.LibraryDatasetCollectionAssociation(deleted=False, **kwd)[source]¶
Bases:
Base
,DatasetCollectionInstance
,RepresentById
Associates a DatasetCollection with a library folder.
- collection_id¶
- folder_id¶
- name¶
- collection¶
- folder¶
- tags¶
- annotations¶
- ratings¶
- editable_keys = ('name', 'deleted')¶
- __init__(deleted=False, **kwd)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- deleted¶
- table = Table('library_dataset_collection_association', MetaData(), 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:
Base
,Dictifiable
,Serializable
Associates a DatasetInstance (hda or ldda) with a DatasetCollection.
- dataset_collection_id¶
- hda_id¶
- ldda_id¶
- child_collection_id¶
- 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)¶
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- hda¶
- ldda¶
- child_collection¶
- collection¶
- element_index¶
- element_identifier¶
- property element_type¶
- property is_collection¶
- property element_object¶
- property dataset_instance¶
- property dataset¶
- property dataset_instances¶
- property has_deferred_data¶
- copy_to_collection(collection, destination=None, element_destination=None, dataset_instance_attributes=None, flush=True, minimize_copies=False)[source]¶
- table = Table('dataset_collection_element', MetaData(), 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)¶