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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)

exception galaxy.model.NoConverterException(value)

Bases: exceptions.Exception

__init__(value)

exception galaxy.model.ConverterDependencyException(value)

Bases: exceptions.Exception

__init__(value)

galaxy.model.set_datatypes_registry(d_registry)

Set up datatypes_registry

class galaxy.model.HasTags

Bases: object

dict_collection_visible_keys = ['tags']

dict_element_visible_keys = ['tags']

to_dict(*args, **kwargs)

make_tag_string_list()

copy_tags_from(target_user, source)

auto_propagated_tags

class galaxy.model.HasName

Bases: object

get_display_name()

These objects have a name attribute can be either a string or a unicode object. If string, convert to unicode object assuming ‘utf-8’ format.

class galaxy.model.UsesCreateAndUpdateTime

Bases: object

seconds_since_updated

seconds_since_created

galaxy.model.cached_id(galaxy_model_object)

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

Bases: object

MAX_NUMERIC = 9999999999999999999L

add_metric(plugin, metric_name, metric_value)

metrics

set_streams(stdout, stderr)

log_str()

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

Bases: galaxy.util.dictifiable.Dictifiable

use_pbkdf2 = True

Data for a Galaxy user or admin and relations to their histories, credentials, and roles.

dict_collection_visible_keys = ['id', 'email', 'username', 'deleted', 'active', 'last_password_change']

dict_element_visible_keys = ['id', 'email', 'username', 'total_disk_usage', 'nice_total_disk_usage', 'deleted', 'active', 'last_password_change']

__init__(email=None, password=None, username=None)

extra_preferences

set_password_cleartext(cleartext)

Set user password to the digest of cleartext.

set_random_password(length=16)

Sets user password to a random string of the given length. :return: void

check_password(cleartext)

Check if cleartext matches user password when hashed.

system_user_pwent(real_system_username)

Gives the system user pwent entry based on e-mail or username depending on the value in real_system_username

all_roles()

Return a unique list of Roles associated with this user or any of their groups.

all_roles_exploiting_cache()

get_disk_usage(nice_size=False)

Return byte count of disk space used by user or a human-readable string if nice_size is True.

set_disk_usage(bytes)

Manually set the disk space used by a user to bytes.

total_disk_usage

Return byte count of disk space used by user or a human-readable string if nice_size is True.

adjust_total_disk_usage(amount)

nice_total_disk_usage

Return byte count of disk space used in a human-readable string.

calculate_disk_usage()

Return byte count total of disk space used by all non-purged, non-library HDAs in non-purged histories.

calculate_and_set_disk_usage()

Calculates and sets user disk usage.

static user_template_environment(user)

>>> 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'

static expand_user_properties(user, in_string)

is_active()

is_authenticated()

class galaxy.model.PasswordResetToken(user, token=None)

Bases: object

__init__(user, token=None)

class galaxy.model.BaseJobMetric(plugin, metric_name, metric_value)

Bases: object

__init__(plugin, metric_name, metric_value)

class galaxy.model.JobMetricText(plugin, metric_name, metric_value)

Bases: galaxy.model.BaseJobMetric

class galaxy.model.JobMetricNumeric(plugin, metric_name, metric_value)

Bases: galaxy.model.BaseJobMetric

class galaxy.model.TaskMetricText(plugin, metric_name, metric_value)

Bases: galaxy.model.BaseJobMetric

class galaxy.model.TaskMetricNumeric(plugin, metric_name, metric_value)

Bases: galaxy.model.BaseJobMetric

class galaxy.model.Job

Bases: galaxy.model.JobLike, galaxy.model.UsesCreateAndUpdateTime, galaxy.util.dictifiable.Dictifiable

dict_collection_visible_keys = ['id', 'state', 'exit_code', 'update_time', 'create_time']

dict_element_visible_keys = ['id', 'state', 'exit_code', 'update_time', 'create_time']

A job represents a request to run a tool given input datasets, tool parameters, and output datasets.

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

terminal_states = ['ok', 'error', 'deleted']

non_ready_states = ['new', 'resubmitted', 'upload', 'waiting', 'queued', 'running']

job states where the job hasn’t finished and the model may still change

__init__()

finished

get_external_output_metadata()

The external_output_metadata is currently a reference from Job to JobExternalOutputMetadata. It exists for a job but not a task.

get_session_id()

get_user_id()

get_tool_id()

get_tool_version()

get_command_line()

get_dependencies()

get_param_filename()

get_parameters()

get_copied_from_job_id()

get_input_datasets()

get_output_datasets()

get_input_library_datasets()

get_output_library_datasets()

get_state()

get_info()

get_job_runner_name()

get_job_runner_external_id()

get_post_job_actions()

get_imported()

get_handler()

get_params()

get_user()

get_id()

get_tasks()

get_id_tag()

Return a tag that can be useful in identifying a Job. This returns the Job’s get_id

set_session_id(session_id)

set_user_id(user_id)

set_tool_id(tool_id)

set_tool_version(tool_version)

set_command_line(command_line)

set_dependencies(dependencies)

set_param_filename(param_filename)

set_parameters(parameters)

set_copied_from_job_id(job_id)

set_input_datasets(input_datasets)

set_output_datasets(output_datasets)

set_input_library_datasets(input_library_datasets)

set_output_library_datasets(output_library_datasets)

set_info(info)

set_runner_name(job_runner_name)

get_job()

set_runner_external_id(job_runner_external_id)

set_post_job_actions(post_job_actions)

set_imported(imported)

set_handler(handler)

set_params(params)

add_parameter(name, value)

add_input_dataset(name, dataset=None, dataset_id=None)

add_output_dataset(name, dataset)

add_input_dataset_collection(name, dataset_collection)

add_output_dataset_collection(name, dataset_collection_instance)

add_implicit_output_dataset_collection(name, dataset_collection)

add_input_library_dataset(name, dataset)

add_output_library_dataset(name, dataset)

add_post_job_action(pja)

set_state(state)

Save state history

get_param_values(app, ignore_errors=False)

Read encoded parameter values from the database and turn back into a dict of tool parameter values.

raw_param_dict()

check_if_output_datasets_deleted()

Return true if all of the output datasets associated with this job are in the deleted state

mark_deleted(track_jobs_in_database=False)

Mark this job as deleted, and mark any output datasets as discarded.

resume(flush=True)

to_dict(view='collection', system_details=False)

set_final_state(final_state)

get_destination_configuration(dest_params, config, key, default=None)

Get a destination parameter that can be defaulted back in specified config if it needs to be applied globally.

class galaxy.model.Task(job, working_directory, prepare_files_cmd)

Bases: galaxy.model.JobLike

A task represents a single component of a job.

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

__init__(job, working_directory, prepare_files_cmd)

get_param_values(app)

Read encoded parameter values from the database and turn back into a dict of tool parameter values.

get_id()

get_id_tag()

Return an id tag suitable for identifying the task. This combines the task’s job id and the task’s own id.

get_command_line()

get_parameters()

get_state()

get_info()

get_working_directory()

get_task_runner_name()

get_task_runner_external_id()

get_job()

get_stdout()

get_stderr()

get_prepare_input_files_cmd()

get_external_output_metadata()

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()

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()

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.

get_session_id()

set_id(id)

set_command_line(command_line)

set_parameters(parameters)

set_state(state)

set_info(info)

set_working_directory(working_directory)

set_task_runner_name(task_runner_name)

set_job_runner_external_id(task_runner_external_id)

set_task_runner_external_id(task_runner_external_id)

set_job(job)

set_stdout(stdout)

set_stderr(stderr)

set_prepare_input_files_cmd(prepare_input_files_cmd)

class galaxy.model.JobParameter(name, value)

Bases: object

__init__(name, value)

copy()

class galaxy.model.JobToInputDatasetAssociation(name, dataset)

Bases: object

__init__(name, dataset)

class galaxy.model.JobToOutputDatasetAssociation(name, dataset)

Bases: object

__init__(name, dataset)

class galaxy.model.JobToInputDatasetCollectionAssociation(name, dataset_collection)

Bases: object

__init__(name, dataset_collection)

class galaxy.model.JobToOutputDatasetCollectionAssociation(name, dataset_collection_instance)

Bases: object

__init__(name, dataset_collection_instance)

class galaxy.model.JobToImplicitOutputDatasetCollectionAssociation(name, dataset_collection)

Bases: object

__init__(name, dataset_collection)

class galaxy.model.JobToInputLibraryDatasetAssociation(name, dataset)

Bases: object

__init__(name, dataset)

class galaxy.model.JobToOutputLibraryDatasetAssociation(name, dataset)

Bases: object

__init__(name, dataset)

class galaxy.model.JobStateHistory(job)

Bases: object

__init__(job)

class galaxy.model.ImplicitlyCreatedDatasetCollectionInput(name, input_dataset_collection)

Bases: object

__init__(name, input_dataset_collection)

class galaxy.model.ImplicitCollectionJobs(id=None, populated_state=None)

Bases: object

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

__init__(id=None, populated_state=None)

job_list

class galaxy.model.ImplicitCollectionJobsJobAssociation

Bases: object

__init__()

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

Bases: object

__init__(action_type, workflow_step, output_name=None, action_arguments=None)

class galaxy.model.PostJobActionAssociation(pja, job=None, job_id=None)

Bases: object

__init__(pja, job=None, job_id=None)

class galaxy.model.JobExternalOutputMetadata(job=None, dataset=None)

Bases: object

__init__(job=None, dataset=None)

dataset

class galaxy.model.JobExportHistoryArchive(job=None, history=None, dataset=None, compressed=False, history_attrs_filename=None, datasets_attrs_filename=None, jobs_attrs_filename=None)

Bases: object

__init__(job=None, history=None, dataset=None, compressed=False, history_attrs_filename=None, datasets_attrs_filename=None, jobs_attrs_filename=None)

up_to_date

Return False, if a new export should be generated for corresponding history.

ready

preparing

export_name

class galaxy.model.JobImportHistoryArchive(job=None, history=None, archive_dir=None)

Bases: object

__init__(job=None, history=None, archive_dir=None)

class galaxy.model.GenomeIndexToolData(job=None, params=None, dataset=None, deferred_job=None, transfer_job=None, fasta_path=None, created_time=None, modified_time=None, dbkey=None, user=None, indexer=None)

Bases: object

__init__(job=None, params=None, dataset=None, deferred_job=None, transfer_job=None, fasta_path=None, created_time=None, modified_time=None, dbkey=None, user=None, indexer=None)

class galaxy.model.DeferredJob(state=None, plugin=None, params=None)

Bases: object

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

__init__(state=None, plugin=None, params=None)

get_check_interval()

set_check_interval(seconds)

check_interval

get_last_check()

set_last_check(seconds)

last_check

is_check_time

class galaxy.model.Group(name=None)

Bases: galaxy.util.dictifiable.Dictifiable

dict_collection_visible_keys = ['id', 'name']

dict_element_visible_keys = ['id', 'name']

__init__(name=None)

class galaxy.model.UserGroupAssociation(user, group)

Bases: object

__init__(user, group)

galaxy.model.is_hda(d)

class galaxy.model.History(id=None, name=None, user=None)

Bases: galaxy.model.HasTags, galaxy.util.dictifiable.Dictifiable, galaxy.model.item_attrs.UsesAnnotations, galaxy.model.HasName

dict_collection_visible_keys = ['id', 'name', 'published', 'deleted']

dict_element_visible_keys = ['id', 'name', 'genome_build', 'deleted', 'purged', 'update_time', 'published', 'importable', 'slug', 'empty']

default_name = 'Unnamed history'

__init__(id=None, name=None, user=None)

empty

add_galaxy_session(galaxy_session, association=None)

add_dataset(dataset, parent_id=None, genome_build=None, set_hid=True, quota=True)

add_datasets(sa_session, datasets, parent_id=None, genome_build=None, set_hid=True, quota=True, flush=False)

Optimized version of add_dataset above that minimizes database interactions when adding many datasets to history at once.

add_dataset_collection(history_dataset_collection, set_hid=True)

copy(name=None, target_user=None, activatable=False, all_datasets=False)

Return a copy of this history using the given name and target_user. If activatable, copy only non-deleted datasets. If all_datasets, copy non-deleted, deleted, and purged datasets.

has_possible_members

activatable_datasets

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

latest_export

unhide_datasets()

resume_paused_jobs()

paused_jobs

disk_size

Return the size in bytes of this history by summing the ‘total_size’s of all non-purged, unique datasets within it.

disk_nice_size

Returns human readable size of history on disk.

active_datasets_and_roles

active_visible_datasets_and_roles

active_visible_dataset_collections

active_contents

Return all active contents ordered by hid.

contents_iter(**kwds)

Fetch filtered list of contents of history.

class galaxy.model.HistoryUserShareAssociation

Bases: object

__init__()

class galaxy.model.UserRoleAssociation(user, role)

Bases: object

__init__(user, role)

class galaxy.model.GroupRoleAssociation(group, role)

Bases: object

__init__(group, role)

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

Bases: galaxy.util.dictifiable.Dictifiable

dict_collection_visible_keys = ['id', 'name']

dict_element_visible_keys = ['id', 'name', 'description', 'type']

private_id = None

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

__init__(name='', description='', type='system', deleted=False)

class galaxy.model.UserQuotaAssociation(user, quota)

Bases: galaxy.util.dictifiable.Dictifiable

dict_element_visible_keys = ['user']

__init__(user, quota)

class galaxy.model.GroupQuotaAssociation(group, quota)

Bases: galaxy.util.dictifiable.Dictifiable

dict_element_visible_keys = ['group']

__init__(group, quota)

class galaxy.model.Quota(name='', description='', amount=0, operation='=')

Bases: galaxy.util.dictifiable.Dictifiable

dict_collection_visible_keys = ['id', 'name']

dict_element_visible_keys = ['id', 'name', 'description', 'bytes', 'operation', 'display_amount', 'default', 'users', 'groups']

valid_operations = ('+', '-', '=')

__init__(name='', description='', amount=0, operation='=')

get_amount()

set_amount(amount)

amount

display_amount

class galaxy.model.DefaultQuotaAssociation(type, quota)

Bases: galaxy.model.Quota, galaxy.util.dictifiable.Dictifiable

dict_element_visible_keys = ['type']

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

__init__(type, quota)

class galaxy.model.DatasetPermissions(action, dataset, role=None, role_id=None)

Bases: object

__init__(action, dataset, role=None, role_id=None)

class galaxy.model.LibraryPermissions(action, library_item, role)

Bases: object

__init__(action, library_item, role)

class galaxy.model.LibraryFolderPermissions(action, library_item, role)

Bases: object

__init__(action, library_item, role)

class galaxy.model.LibraryDatasetPermissions(action, library_item, role)

Bases: object

__init__(action, library_item, role)

class galaxy.model.LibraryDatasetDatasetAssociationPermissions(action, library_item, role)

Bases: object

__init__(action, library_item, role)

class galaxy.model.DefaultUserPermissions(user, action, role)

Bases: object

__init__(user, action, role)

class galaxy.model.DefaultHistoryPermissions(history, action, role)

Bases: object

__init__(history, action, role)

class galaxy.model.StorableObject(id, **kwargs)

Bases: object

__init__(id, **kwargs)

class galaxy.model.Dataset(id=None, state=None, external_filename=None, extra_files_path=None, file_size=None, purgable=True, uuid=None)

Bases: galaxy.model.StorableObject

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

non_ready_states = ('new', 'upload', 'queued', 'running', 'setting_metadata')

ready_states = ('discarded', 'ok', 'failed_metadata', 'paused', 'error', 'empty')

valid_input_states = ('ok', 'failed_metadata', 'upload', 'paused', 'running', 'setting_metadata', 'new', 'queued', 'empty')

terminal_states = ('ok', 'empty', 'error', 'discarded', 'failed_metadata')

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

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

file_path = '/tmp/'

object_store = None

engine = None

__init__(id=None, state=None, external_filename=None, extra_files_path=None, file_size=None, purgable=True, uuid=None)

in_ready_state()

get_file_name()

set_file_name(filename)

file_name

get_extra_files_path()

set_extra_files_path(extra_files_path)

extra_files_path

extra_files_path_exists()

get_size(nice_size=False)

Returns the size of the data on disk

set_size(no_extra_files=False)

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.

get_total_size()

set_total_size()

has_data()

Detects whether there is any data

mark_deleted()

user_can_purge

full_delete()

Remove the file and extra files, marks deleted and purged

get_access_roles(trans)

get_manage_permissions_roles(trans)

has_manage_permissions_roles(trans)

galaxy.model.datatype_for_extension(extension, datatypes_registry=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, validation_errors=None, visible=True, create_dataset=False, sa_session=None, extended_metadata=None, flush=True)

Bases: object

A base class for all ‘dataset instances’, HDAs, LDAs, etc

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

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

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

__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, validation_errors=None, visible=True, create_dataset=False, sa_session=None, extended_metadata=None, flush=True)

update()

ext

get_dataset_state()

raw_set_dataset_state(state)

set_dataset_state(state)

state

get_file_name()

set_file_name(filename)

file_name

link_to(path)

extra_files_path

extra_files_path_exists()

datatype

get_metadata()

set_metadata_requires_flush

set_metadata(bunch)

metadata

get_dbkey()

set_dbkey(value)

dbkey

change_datatype(new_ext)

get_size(nice_size=False)

Returns the size of the data on disk

set_size(**kwds)

Sets and gets the size of the data on disk

get_total_size()

set_total_size()

has_data()

Detects whether there is any data

get_raw_data()

Returns the full data. To stream it open the file_name and read/write as needed

get_mime()

Returns the mime type of the data

set_peek()

init_meta(copy_from=None)

set_meta(**kwd)

missing_meta(**kwd)

as_display_type(type, **kwd)

display_peek()

display_name()

display_info()

get_converted_files_by_type(file_type)

get_converted_dataset_deps(trans, target_ext)

Returns dict of { “dependency” => HDA }

get_converted_dataset(trans, target_ext, target_context=None, history=None)

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)

Copies attributes to a new datasets, used for implicit conversions

get_metadata_dataset(dataset_ext)

Returns an HDA that points to a metadata file which contains a converted data with the requested extension.

clear_associated_files(metadata_safe=False, purge=False)

get_converter_types()

can_convert_to(format)

find_conversion_destination(accepted_formats, **kwd)

Returns ( target_ext, existing converted dataset )

add_validation_error(validation_error)

extend_validation_errors(validation_errors)

mark_deleted()

mark_undeleted()

mark_unhidden()

undeletable()

is_ok

is_pending

Return true if the dataset is neither ready nor in error

source_library_dataset

source_dataset_chain

creating_job

get_display_applications(trans)

get_visualizations()

get_datasources(trans)

Returns datasources for dataset; if datasources are not available due to indexing, indexing is started. Return value is a dictionary with entries of type (<datasource_type> : {<datasource_name>, <indexing_message>}).

convert_dataset(trans, target_type)

Converts a dataset to the target_type and returns a message indicating status of the conversion. None is returned to indicate that dataset was converted successfully.

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)

Bases: galaxy.model.DatasetInstance, galaxy.model.HasTags, galaxy.util.dictifiable.Dictifiable, galaxy.model.item_attrs.UsesAnnotations, galaxy.model.HasName

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.

copy(parent_id=None, copy_tags=None, force_flush=True, copy_hid=True, new_name=None)

Create a copy of this HDA.

copy_tags_to(copy_tags=None)

copy_attributes(new_dataset)

to_library_dataset_dataset_association(trans, target_folder, replace_dataset=None, parent_id=None, user=None, roles=None, ldda_message='', element_identifier=None)

Copy this HDA to a library optionally replacing an existing LDDA.

clear_associated_files(metadata_safe=False, purge=False)

get_access_roles(trans)

Return The access roles associated with this HDA’s dataset.

quota_amount(user)

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)

Return attributes of this HDA that are exposed using the API.

history_content_type

content_type = u'dataset'

type_id

class galaxy.model.HistoryDatasetAssociationHistory(history_dataset_association_id, name, dbkey, update_time, version, extension, extended_metadata_id, metadata)

Bases: object

__init__(history_dataset_association_id, name, dbkey, update_time, version, extension, extended_metadata_id, metadata)

class galaxy.model.HistoryDatasetAssociationDisplayAtAuthorization(hda=None, user=None, site=None)

Bases: object

__init__(hda=None, user=None, site=None)

class galaxy.model.HistoryDatasetAssociationSubset(hda, subset, location)

Bases: object

__init__(hda, subset, location)

class galaxy.model.Library(name=None, description=None, synopsis=None, root_folder=None)

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.model.HasName

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)

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

We prepend an F to folders.

get_active_folders(folder, folders=None)

get_access_roles(trans)

class galaxy.model.LibraryFolder(name=None, description=None, item_count=0, order_id=None)

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.model.HasName

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)

add_library_dataset(library_dataset, genome_build=None)

add_folder(folder)

activatable_library_datasets

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

library_path

parent_library

class galaxy.model.LibraryDataset(folder=None, order_id=None, name=None, info=None, library_dataset_dataset_association=None, **kwd)

Bases: object

upload_options = [('upload_file', 'Upload files'), ('upload_directory', 'Upload directory of files'), ('upload_paths', 'Upload files from filesystem paths'), ('import_from_history', 'Import datasets from your current history')]

__init__(folder=None, order_id=None, name=None, info=None, library_dataset_dataset_association=None, **kwd)

set_library_dataset_dataset_association(ldda)

get_info()

set_info(info)

info

get_name()

set_name(name)

name

display_name()

to_dict(view='collection')

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)

Bases: galaxy.model.DatasetInstance, galaxy.model.HasName

__init__(copied_from_history_dataset_association=None, copied_from_library_dataset_dataset_association=None, library_dataset=None, user=None, sa_session=None, **kwd)

to_history_dataset_association(target_history, parent_id=None, add_to_history=False)

copy(parent_id=None, target_folder=None)

clear_associated_files(metadata_safe=False, purge=False)

get_access_roles(trans)

get_manage_permissions_roles(trans)

has_manage_permissions_roles(trans)

to_dict(view='collection')

class galaxy.model.ExtendedMetadata(data)

Bases: object

__init__(data)

class galaxy.model.ExtendedMetadataIndex(extended_metadata, path, value)

Bases: object

__init__(extended_metadata, path, value)

class galaxy.model.LibraryInfoAssociation(library, form_definition, info, inheritable=False)

Bases: object

__init__(library, form_definition, info, inheritable=False)

class galaxy.model.LibraryFolderInfoAssociation(folder, form_definition, info, inheritable=False)

Bases: object

__init__(folder, form_definition, info, inheritable=False)

class galaxy.model.LibraryDatasetDatasetInfoAssociation(library_dataset_dataset_association, form_definition, info)

Bases: object

__init__(library_dataset_dataset_association, form_definition, info)

inheritable

class galaxy.model.ValidationError(message=None, err_type=None, attributes=None)

Bases: object

__init__(message=None, err_type=None, attributes=None)

class galaxy.model.DatasetToValidationErrorAssociation(dataset, validation_error)

Bases: object

__init__(dataset, validation_error)

class galaxy.model.ImplicitlyConvertedDatasetAssociation(id=None, parent=None, dataset=None, file_type=None, deleted=False, purged=False, metadata_safe=True)

Bases: object

__init__(id=None, parent=None, dataset=None, file_type=None, deleted=False, purged=False, metadata_safe=True)

clear(purge=False, delete_dataset=True)

class galaxy.model.DatasetCollection(id=None, collection_type=None, populated=True, element_count=None)

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.model.item_attrs.UsesAnnotations

dict_collection_visible_keys = ['id', 'collection_type']

dict_element_visible_keys = ['id', 'collection_type']

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

__init__(id=None, collection_type=None, populated=True, element_count=None)

dataset_states_and_extensions_summary

populated_optimized

populated

dataset_action_tuples

waiting_for_elements

mark_as_populated()

handle_population_failed(message)

finalize()

dataset_instances

dataset_elements

first_dataset_element

state

validate()

copy(destination=None, element_destination=None)

replace_failed_elements(replacements)

set_from_dict(new_data)

has_subcollections

class galaxy.model.DatasetCollectionInstance(collection=None, deleted=False)

Bases: galaxy.model.HasName

__init__(collection=None, deleted=False)

state

populated

dataset_instances

display_name()

set_from_dict(new_data)

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.

class galaxy.model.HistoryDatasetCollectionAssociation(id=None, hid=None, collection=None, history=None, name=None, deleted=False, visible=True, copied_from_history_dataset_collection_association=None, implicit_output_name=None, implicit_input_collections=[])

Bases: galaxy.model.DatasetCollectionInstance, galaxy.model.HasTags, galaxy.util.dictifiable.Dictifiable, galaxy.model.item_attrs.UsesAnnotations

Associates a DatasetCollection with a History.

editable_keys = ('name', 'deleted', 'visible')

__init__(id=None, hid=None, collection=None, history=None, name=None, deleted=False, visible=True, copied_from_history_dataset_collection_association=None, implicit_output_name=None, implicit_input_collections=[])

history_content_type

content_type = u'dataset_collection'

type_id

job_source_type

job_source_id

to_hda_representative(multiple=False)

to_dict(view='collection')

add_implicit_input_collection(name, history_dataset_collection)

find_implicit_input_collection(name)

copy(element_destination=None)

Create a copy of this history dataset collection association. Copy underlying collection.

class galaxy.model.LibraryDatasetCollectionAssociation(id=None, collection=None, name=None, deleted=False, folder=None)

Bases: galaxy.model.DatasetCollectionInstance

Associates a DatasetCollection with a library folder.

editable_keys = ('name', 'deleted')

__init__(id=None, collection=None, name=None, deleted=False, folder=None)

to_dict(view='collection')

class galaxy.model.DatasetCollectionElement(id=None, collection=None, element=None, element_index=None, element_identifier=None)

Bases: galaxy.util.dictifiable.Dictifiable

Associates a DatasetInstance (hda or ldda) with a DatasetCollection.

dict_collection_visible_keys = ['id', 'element_type', 'element_index', 'element_identifier']

dict_element_visible_keys = ['id', 'element_type', 'element_index', 'element_identifier']

UNINITIALIZED_ELEMENT = <object object>

__init__(id=None, collection=None, element=None, element_index=None, element_identifier=None)

element_type

is_collection

element_object

dataset_instance

dataset

first_dataset_instance()

dataset_instances

copy_to_collection(collection, destination=None, element_destination=None)

class galaxy.model.Event(message=None, history=None, user=None, galaxy_session=None)

Bases: object

__init__(message=None, history=None, user=None, galaxy_session=None)

class galaxy.model.GalaxySession(id=None, user=None, remote_host=None, remote_addr=None, referer=None, current_history=None, session_key=None, is_valid=False, prev_session_id=None, last_action=None)

Bases: object

__init__(id=None, user=None, remote_host=None, remote_addr=None, referer=None, current_history=None, session_key=None, is_valid=False, prev_session_id=None, last_action=None)

add_history(history, association=None)

get_disk_usage()

set_disk_usage(bytes)

total_disk_usage

class galaxy.model.GalaxySessionToHistoryAssociation(galaxy_session, history)

Bases: object

__init__(galaxy_session, history)

class galaxy.model.UCI

Bases: object

__init__()

class galaxy.model.StoredWorkflow

Bases: galaxy.model.HasTags, galaxy.util.dictifiable.Dictifiable

dict_collection_visible_keys = ['id', 'name', 'published', 'deleted']

dict_element_visible_keys = ['id', 'name', 'published', 'deleted']

__init__()

get_internal_version(version)

show_in_tool_panel(user_id)

copy_tags_from(target_user, source_workflow)

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

class galaxy.model.Workflow(uuid=None)

Bases: galaxy.util.dictifiable.Dictifiable

dict_collection_visible_keys = ['name', 'has_cycles', 'has_errors']

dict_element_visible_keys = ['name', 'has_cycles', 'has_errors']

input_step_types = ['data_input', 'data_collection_input', 'parameter_input']

__init__(uuid=None)

has_outputs_defined()

Returns true or false indicating whether or not a workflow has outputs defined.

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

steps_by_id

step_by_index(order_index)

input_steps

workflow_outputs

top_level_workflow

If this workflow is not attached to stored workflow directly, recursively grab its parents until it is the top level workflow which must have a stored workflow associated with it.

top_level_stored_workflow

If this workflow is not attached to stored workflow directly, recursively grab its parents until it is the top level workflow which must have a stored workflow associated with it and then grab that stored workflow.

copy()

Copy a workflow (without user information) for a new StoredWorkflow object.

log_str()

class galaxy.model.WorkflowStep

Bases: object

__init__()

unique_workflow_outputs

content_id

input_connections_by_name

setup_input_connections_by_name()

create_or_update_workflow_output(output_name, label, uuid)

workflow_output_for(output_name)

copy_to(copied_step, step_mapping)

log_str()

class galaxy.model.WorkflowStepConnection

Bases: object

NON_DATA_CONNECTION = '__NO_INPUT_OUTPUT_NAME__'

__init__()

set_non_data_connection()

non_data_connection

copy()

class galaxy.model.WorkflowOutput(workflow_step, output_name=None, label=None, uuid=None)

Bases: object

__init__(workflow_step, output_name=None, label=None, uuid=None)

copy(copied_step)

class galaxy.model.StoredWorkflowUserShareAssociation

Bases: object

__init__()

class galaxy.model.StoredWorkflowMenuEntry

Bases: object

__init__()

class galaxy.model.WorkflowInvocation

Bases: galaxy.model.UsesCreateAndUpdateTime, galaxy.util.dictifiable.Dictifiable

dict_collection_visible_keys = ['id', 'update_time', 'workflow_id', 'history_id', 'uuid', 'state']

dict_element_visible_keys = ['id', 'update_time', 'workflow_id', 'history_id', 'uuid', 'state']

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

__init__()

create_subworkflow_invocation_for_step(step)

attach_subworkflow_invocation_for_step(step, subworkflow_invocation)

get_subworkflow_invocation_for_step(step)

get_subworkflow_invocation_association_for_step(step)

active

Indicates the workflow invocation is somehow active - and in particular valid actions may be performed on its WorkflowInvocationSteps.

cancel()

fail()

step_states_by_step_id()

step_invocations_by_step_id()

step_invocation_for_step_id(step_id)

static poll_active_workflow_ids(sa_session, scheduler=None, handler=None)

add_output(workflow_output, step, output_object)

to_dict(view='collection', value_mapper=None, step_details=False, legacy_job_state=False)

update()

add_input(content, step_id)

resource_parameters

has_input_for_step(step_id)

class galaxy.model.WorkflowInvocationToSubworkflowInvocationAssociation

Bases: galaxy.util.dictifiable.Dictifiable

dict_collection_visible_keys = ['id', 'workflow_step_id', 'workflow_invocation_id', 'subworkflow_invocation_id']

dict_element_visible_keys = ['id', 'workflow_step_id', 'workflow_invocation_id', 'subworkflow_invocation_id']

class galaxy.model.WorkflowInvocationStep

Bases: galaxy.util.dictifiable.Dictifiable

dict_collection_visible_keys = ['id', 'update_time', 'job_id', 'workflow_step_id', 'state', 'action']

dict_element_visible_keys = ['id', 'update_time', 'job_id', 'workflow_step_id', 'state', 'action']

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

update()

is_new

add_output(output_name, output_object)

jobs

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

class galaxy.model.WorkflowInvocationStepJobAssociation

Bases: galaxy.util.dictifiable.Dictifiable

dict_collection_visible_keys = ('id', 'job_id', 'workflow_invocation_step_id')

dict_element_visible_keys = ('id', 'job_id', 'workflow_invocation_step_id')

class galaxy.model.WorkflowRequest

Bases: galaxy.util.dictifiable.Dictifiable

dict_collection_visible_keys = ['id', 'name', 'type', 'state', 'history_id', 'workflow_id']

dict_element_visible_keys = ['id', 'name', 'type', 'state', 'history_id', 'workflow_id']

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

class galaxy.model.WorkflowRequestInputParameter(name=None, value=None, type=None)

Bases: galaxy.util.dictifiable.Dictifiable

Workflow-related parameters not tied to steps or inputs.

dict_collection_visible_keys = ['id', 'name', 'value', 'type']

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

__init__(name=None, value=None, type=None)

class galaxy.model.WorkflowRequestStepState(workflow_step=None, name=None, value=None)

Bases: galaxy.util.dictifiable.Dictifiable

Workflow step value parameters.

dict_collection_visible_keys = ['id', 'name', 'value', 'workflow_step_id']

__init__(workflow_step=None, name=None, value=None)

class galaxy.model.WorkflowRequestToInputDatasetAssociation

Bases: galaxy.util.dictifiable.Dictifiable

Workflow step input dataset parameters.

dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_id', 'name']

class galaxy.model.WorkflowRequestToInputDatasetCollectionAssociation

Bases: galaxy.util.dictifiable.Dictifiable

Workflow step input dataset collection parameters.

dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_collection_id', 'name']

class galaxy.model.WorkflowRequestInputStepParmeter

Bases: galaxy.util.dictifiable.Dictifiable

Workflow step parameter inputs.

dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'parameter_value']

class galaxy.model.WorkflowInvocationOutputDatasetAssociation

Bases: galaxy.util.dictifiable.Dictifiable

Represents links to output datasets for the workflow.

dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_id', 'name']

class galaxy.model.WorkflowInvocationOutputDatasetCollectionAssociation

Bases: galaxy.util.dictifiable.Dictifiable

Represents links to output dataset collections for the workflow.

dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_collection_id', 'name']

class galaxy.model.WorkflowInvocationStepOutputDatasetAssociation

Bases: galaxy.util.dictifiable.Dictifiable

Represents links to output datasets for the workflow.

dict_collection_visible_keys = ['id', 'workflow_invocation_step_id', 'dataset_id', 'output_name']

class galaxy.model.WorkflowInvocationStepOutputDatasetCollectionAssociation

Bases: galaxy.util.dictifiable.Dictifiable

Represents links to output dataset collections for the workflow.

dict_collection_visible_keys = ['id', 'workflow_invocation_step_id', 'dataset_collection_id', 'output_name']

class galaxy.model.MetadataFile(dataset=None, name=None)

Bases: galaxy.model.StorableObject

__init__(dataset=None, name=None)

file_name

class galaxy.model.FormDefinition(name=None, desc=None, fields=[], form_definition_current=None, form_type=None, layout=None)

Bases: galaxy.util.dictifiable.Dictifiable

supported_field_types = [<class 'galaxy.web.form_builder.AddressField'>, <class 'galaxy.web.form_builder.CheckboxField'>, <class 'galaxy.web.form_builder.PasswordField'>, <class 'galaxy.web.form_builder.SelectField'>, <class 'galaxy.web.form_builder.TextArea'>, <class 'galaxy.web.form_builder.TextField'>, <class 'galaxy.web.form_builder.WorkflowField'>, <class 'galaxy.web.form_builder.WorkflowMappingField'>, <class 'galaxy.web.form_builder.HistoryField'>]

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

dict_collection_visible_keys = ['id', 'name']

dict_element_visible_keys = ['id', 'name', 'desc', 'form_definition_current_id', 'fields', 'layout']

__init__(name=None, desc=None, fields=[], form_definition_current=None, form_type=None, layout=None)

to_dict(user=None, values=None, security=None)

grid_fields(grid_index)

class galaxy.model.FormDefinitionCurrent(form_definition=None)

Bases: object

__init__(form_definition=None)

class galaxy.model.FormValues(form_def=None, content=None)

Bases: object

__init__(form_def=None, content=None)

class galaxy.model.UserAddress(user=None, desc=None, name=None, institution=None, address=None, city=None, state=None, postal_code=None, country=None, phone=None)

Bases: object

__init__(user=None, desc=None, name=None, institution=None, address=None, city=None, state=None, postal_code=None, country=None, phone=None)

to_dict(trans)

class galaxy.model.UserOpenID(user=None, session=None, openid=None)

Bases: object

__init__(user=None, session=None, openid=None)

class galaxy.model.PSAAssociation(server_url=None, handle=None, secret=None, issued=None, lifetime=None, assoc_type=None)

Bases: social_core.storage.AssociationMixin

trans = None

__init__(server_url=None, handle=None, secret=None, issued=None, lifetime=None, assoc_type=None)

save()

classmethod store(server_url, association)

classmethod get(*args, **kwargs)

classmethod remove(ids_to_delete)

class galaxy.model.PSACode(email, code)

Bases: social_core.storage.CodeMixin

trans = None

__init__(email, code)

save()

classmethod get_code(code)

class galaxy.model.PSANonce(server_url, timestamp, salt)

Bases: social_core.storage.NonceMixin

trans = None

__init__(server_url, timestamp, salt)

save()

classmethod use(server_url, timestamp, salt)

class galaxy.model.PSAPartial(token, data, next_step, backend)

Bases: social_core.storage.PartialMixin

trans = None

__init__(token, data, next_step, backend)

save()

classmethod load(token)

classmethod destroy(token)

class galaxy.model.UserAuthnzToken(provider, uid, extra_data=None, lifetime=None, assoc_type=None, user=None)

Bases: social_core.storage.UserMixin

trans = None

__init__(provider, uid, extra_data=None, lifetime=None, assoc_type=None, user=None)

get_id_token(strategy)

set_extra_data(extra_data=None)

save()

classmethod username_max_length()

classmethod user_model()

classmethod changed(user)

classmethod user_query()

classmethod user_exists(*args, **kwargs)

classmethod get_username(user)

classmethod create_user(*args, **kwargs)

classmethod get_user(pk)

classmethod get_users_by_email(email)

classmethod get_social_auth(provider, uid)

classmethod get_social_auth_for_user(user, provider=None, id=None)

classmethod create_social_auth(user, uid, provider)

class galaxy.model.Page

Bases: galaxy.util.dictifiable.Dictifiable

dict_element_visible_keys = ['id', 'title', 'latest_revision_id', 'slug', 'published', 'importable', 'deleted']

__init__()

to_dict(view='element')

class galaxy.model.PageRevision

Bases: galaxy.util.dictifiable.Dictifiable

dict_element_visible_keys = ['id', 'page_id', 'title', 'content']

__init__()

to_dict(view='element')

class galaxy.model.PageUserShareAssociation

Bases: object

__init__()

class galaxy.model.Visualization(id=None, user=None, type=None, title=None, dbkey=None, slug=None, latest_revision=None)

Bases: object

__init__(id=None, user=None, type=None, title=None, dbkey=None, slug=None, latest_revision=None)

copy(user=None, title=None)

Provide copy of visualization with only its latest revision.

class galaxy.model.VisualizationRevision(visualization=None, title=None, dbkey=None, config=None)

Bases: object

__init__(visualization=None, title=None, dbkey=None, config=None)

copy(visualization=None)

Returns a copy of this object.

class galaxy.model.VisualizationUserShareAssociation

Bases: object

__init__()

class galaxy.model.TransferJob(state=None, path=None, info=None, pid=None, socket=None, params=None)

Bases: object

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

terminal_states = ['error', 'done']

__init__(state=None, path=None, info=None, pid=None, socket=None, params=None)

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

Bases: object

__init__(id=None, type=None, parent_id=None, name=None)

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

Bases: galaxy.util.dictifiable.Dictifiable

dict_collection_visible_keys = ['id', 'user_tname', 'user_value']

dict_element_visible_keys = ['id', 'user_tname', 'user_value']

__init__(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)

copy(cls=None)

class galaxy.model.HistoryTagAssociation(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)

Bases: galaxy.model.ItemTagAssociation

class galaxy.model.DatasetTagAssociation(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)

Bases: galaxy.model.ItemTagAssociation

class galaxy.model.HistoryDatasetAssociationTagAssociation(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)

Bases: galaxy.model.ItemTagAssociation

class galaxy.model.LibraryDatasetDatasetAssociationTagAssociation(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)

Bases: galaxy.model.ItemTagAssociation

class galaxy.model.PageTagAssociation(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)

Bases: galaxy.model.ItemTagAssociation

class galaxy.model.WorkflowStepTagAssociation(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)

Bases: galaxy.model.ItemTagAssociation

class galaxy.model.StoredWorkflowTagAssociation(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)

Bases: galaxy.model.ItemTagAssociation

class galaxy.model.VisualizationTagAssociation(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)

Bases: galaxy.model.ItemTagAssociation

class galaxy.model.HistoryDatasetCollectionTagAssociation(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)

Bases: galaxy.model.ItemTagAssociation

class galaxy.model.LibraryDatasetCollectionTagAssociation(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)

Bases: galaxy.model.ItemTagAssociation

class galaxy.model.ToolTagAssociation(id=None, user=None, tool_id=None, tag_id=None, user_tname=None, value=None)

Bases: galaxy.model.ItemTagAssociation

__init__(id=None, user=None, tool_id=None, tag_id=None, user_tname=None, value=None)

class galaxy.model.WorkRequestTagAssociation(id=None, user=None, workflow_request_id=None, tag_id=None, user_tname=None, value=None)

Bases: galaxy.model.ItemTagAssociation

__init__(id=None, user=None, workflow_request_id=None, tag_id=None, user_tname=None, value=None)

class galaxy.model.HistoryAnnotationAssociation

Bases: object

class galaxy.model.HistoryDatasetAssociationAnnotationAssociation

Bases: object

class galaxy.model.StoredWorkflowAnnotationAssociation

Bases: object

class galaxy.model.WorkflowStepAnnotationAssociation

Bases: object

class galaxy.model.PageAnnotationAssociation

Bases: object

class galaxy.model.VisualizationAnnotationAssociation

Bases: object

class galaxy.model.HistoryDatasetCollectionAssociationAnnotationAssociation

Bases: object

class galaxy.model.LibraryDatasetCollectionAnnotationAssociation

Bases: object

class galaxy.model.ItemRatingAssociation(id=None, user=None, item=None, rating=0)

Bases: object

__init__(id=None, user=None, item=None, rating=0)

set_item(item)

Set association’s item.

class galaxy.model.HistoryRatingAssociation(id=None, user=None, item=None, rating=0)

Bases: galaxy.model.ItemRatingAssociation

set_item(history)

class galaxy.model.HistoryDatasetAssociationRatingAssociation(id=None, user=None, item=None, rating=0)

Bases: galaxy.model.ItemRatingAssociation

set_item(history_dataset_association)

class galaxy.model.StoredWorkflowRatingAssociation(id=None, user=None, item=None, rating=0)

Bases: galaxy.model.ItemRatingAssociation

set_item(stored_workflow)

class galaxy.model.PageRatingAssociation(id=None, user=None, item=None, rating=0)

Bases: galaxy.model.ItemRatingAssociation

set_item(page)

class galaxy.model.VisualizationRatingAssociation(id=None, user=None, item=None, rating=0)

Bases: galaxy.model.ItemRatingAssociation

set_item(visualization)

class galaxy.model.HistoryDatasetCollectionRatingAssociation(id=None, user=None, item=None, rating=0)

Bases: galaxy.model.ItemRatingAssociation

set_item(dataset_collection)

class galaxy.model.LibraryDatasetCollectionRatingAssociation(id=None, user=None, item=None, rating=0)

Bases: galaxy.model.ItemRatingAssociation

set_item(dataset_collection)

class galaxy.model.DataManagerHistoryAssociation(id=None, history=None, user=None)

Bases: object

__init__(id=None, history=None, user=None)

class galaxy.model.DataManagerJobAssociation(id=None, job=None, data_manager_id=None)

Bases: object

__init__(id=None, job=None, data_manager_id=None)

class galaxy.model.UserPreference(name=None, value=None)

Bases: object

__init__(name=None, value=None)

class galaxy.model.UserAction(id=None, create_time=None, user_id=None, session_id=None, action=None, params=None, context=None)

Bases: object

__init__(id=None, create_time=None, user_id=None, session_id=None, action=None, params=None, context=None)

class galaxy.model.APIKeys(id=None, user_id=None, key=None)

Bases: object

__init__(id=None, user_id=None, key=None)

galaxy.model.copy_list(lst, *args, **kwds)

Subpackages

• galaxy.model.migrate package
  • Submodules
  • galaxy.model.migrate.check module
• galaxy.model.orm package
  • Submodules
  • galaxy.model.orm.engine_factory module
  • galaxy.model.orm.logging_connection_proxy module
  • galaxy.model.orm.now module
  • galaxy.model.orm.scripts module
• galaxy.model.tool_shed_install package
  • Subpackages
    • galaxy.model.tool_shed_install.migrate package
      • Submodules
      • galaxy.model.tool_shed_install.migrate.check module
  • Submodules
  • galaxy.model.tool_shed_install.mapping module

Submodules

galaxy.model.base module

Shared model and mapping code between Galaxy and Tool Shed, trying to generalize to generic database connections.

class galaxy.model.base.ModelMapping(model_modules, engine)

Bases: galaxy.util.bunch.Bunch

__init__(model_modules, engine)

Session

For backward compat., deprecated.

galaxy.model.base.versioned_objects(iter)

galaxy.model.base.versioned_session(session)

galaxy.model.custom_types module

class galaxy.model.custom_types.GalaxyLargeBinary(length=None)

Bases: sqlalchemy.sql.sqltypes.LargeBinary

class galaxy.model.custom_types.JSONType(*args, **kwargs)

Bases: sqlalchemy.sql.type_api.TypeDecorator

Represents an immutable structure as a json-encoded string.

If default is, for example, a dict, then a NULL value in the database will be exposed as an empty dict.

impl

alias of GalaxyLargeBinary

process_bind_param(value, dialect)

process_result_value(value, dialect)

load_dialect_impl(dialect)

copy_value(value)

compare_values(x, y)

class galaxy.model.custom_types.MutationObj

Bases: sqlalchemy.ext.mutable.Mutable

Mutable JSONType for SQLAlchemy from original gist: https://gist.github.com/dbarnett/1730610

Using minor changes from this fork of the gist: https://gist.github.com/miracle2k/52a031cced285ba9b8cd

And other minor changes to make it work for us.

classmethod coerce(key, value)

class galaxy.model.custom_types.MutationDict

Bases: galaxy.model.custom_types.MutationObj, dict

classmethod coerce(key, value)

Convert plain dictionary to MutationDict

class galaxy.model.custom_types.MutationList

Bases: galaxy.model.custom_types.MutationObj, list

classmethod coerce(key, value)

Convert plain list to MutationList

append(value)

insert(idx, value)

extend(values)

pop(*args, **kw)

remove(value)

galaxy.model.custom_types.total_size(o, handlers={}, verbose=False)

Returns the approximate memory footprint an object and all of its contents.

Automatically finds the contents of the following builtin containers and their subclasses: tuple, list, deque, dict, set and frozenset. To search other containers, add handlers to iterate over their contents:

handlers = {SomeContainerClass: iter,

OtherContainerClass: OtherContainerClass.get_elements}

Recipe from: https://code.activestate.com/recipes/577504-compute-memory-footprint-of-an-object-and-its-cont/

class galaxy.model.custom_types.MetadataType(*args, **kwargs)

Bases: galaxy.model.custom_types.JSONType

Backward compatible metadata type. Can read pickles or JSON, but always writes in JSON.

process_bind_param(value, dialect)

process_result_value(value, dialect)

class galaxy.model.custom_types.UUIDType(*args, **kwargs)

Bases: sqlalchemy.sql.type_api.TypeDecorator

Platform-independent UUID type.

Based on http://docs.sqlalchemy.org/en/rel_0_8/core/types.html#backend-agnostic-guid-type Changed to remove sqlalchemy 0.8 specific code

CHAR(32), storing as stringified hex values.

impl

alias of sqlalchemy.sql.sqltypes.CHAR

load_dialect_impl(dialect)

process_bind_param(value, dialect)

process_result_value(value, dialect)

class galaxy.model.custom_types.TrimmedString(*args, **kwargs)

Bases: sqlalchemy.sql.type_api.TypeDecorator

impl

alias of sqlalchemy.sql.sqltypes.String

process_bind_param(value, dialect)

Automatically truncate string values

galaxy.model.item_attrs module

exception galaxy.model.item_attrs.RuntimeException

Bases: exceptions.Exception

class galaxy.model.item_attrs.UsesItemRatings

Bases: object

Mixin for getting and setting item ratings.

Class makes two assumptions: (1) item-rating association table is named <item_class>RatingAssocation (2) item-rating association table has a column with a foreign key referencing item table that contains the item’s id.

get_ave_item_rating_data(db_session, item, webapp_model=None)

Returns the average rating for an item.

rate_item(db_session, user, item, rating, webapp_model=None)

Rate an item. Return type is <item_class>RatingAssociation.

get_user_item_rating(db_session, user, item, webapp_model=None)

Returns user’s rating for an item. Return type is <item_class>RatingAssociation.

class galaxy.model.item_attrs.UsesAnnotations

Bases: object

Mixin for getting and setting item annotations.

get_item_annotation_str(db_session, user, item)

Returns a user’s annotation string for an item.

get_item_annotation_obj(db_session, user, item)

Returns a user’s annotation object for an item.

add_item_annotation(db_session, user, item, annotation)

Add or update an item’s annotation; a user can only have a single annotation for an item.

delete_item_annotation(db_session, user, item)

copy_item_annotation(db_session, source_user, source_item, target_user, target_item)

Copy an annotation from a user/item source to a user/item target.

galaxy.model.mapping module

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

galaxy.model.mapping.simple_mapping(model, **kwds)

galaxy.model.mapping.tag_mapping(tag_association_class, backref_name)

galaxy.model.mapping.annotation_mapping(annotation_class, **kwds)

galaxy.model.mapping.rating_mapping(rating_class, **kwds)

galaxy.model.mapping.db_next_hid(self)

Override __next_hid to generate from the database in a concurrency safe way. Loads the next history ID from the DB and returns it. It also saves the future next_id into the DB.

Return type:int Returns:the next history id

galaxy.model.mapping.init(file_path, url, engine_options=None, create_tables=False, map_install_models=False, database_query_profiling_proxy=False, object_store=None, trace_logger=None, use_pbkdf2=True, slow_query_log_threshold=0, thread_local_log=None)

Connect mappings to the database

galaxy.model.mapping.now()

Return a new datetime representing UTC day and time.

galaxy.model.metadata module

Galaxy Metadata

class galaxy.model.metadata.Statement(target)

Bases: object

This class inserts its target into a list in the surrounding class. the data.Data class has a metaclass which executes these statements. This is how we shove the metadata element spec into the class.

__init__(target)

classmethod process(element)

class galaxy.model.metadata.MetadataCollection(parent)

Bases: object

MetadataCollection is not a collection at all, but rather a proxy to the real metadata which is stored as a Dictionary. This class handles processing the metadata elements when they are set and retrieved, returning default values in cases when metadata is not set.

__init__(parent)

get_parent()

set_parent(parent)

parent

spec

get(key, default=None)

items()

remove_key(name)

element_is_set(name)

get_metadata_parameter(name, **kwd)

make_dict_copy(to_copy)

Makes a deep copy of input iterable to_copy according to self.spec

requires_dataset_id

from_JSON_dict(filename=None, path_rewriter=None, json_dict=None)

to_JSON_dict(filename=None)

class galaxy.model.metadata.MetadataSpecCollection(dict=None)

Bases: galaxy.util.odict.odict

A simple extension of dict which allows cleaner access to items and allows the values to be iterated over directly as if it were a list. append() is also implemented for simplicity and does not “append”.

__init__(dict=None)

append(item)

iter()

class galaxy.model.metadata.MetadataParameter(spec)

Bases: object

__init__(spec)

get_field(value=None, context=None, other_values=None, **kwd)

to_string(value)

to_safe_string(value)

make_copy(value, target_context=None, source_context=None)

classmethod marshal(value)

This method should/can be overridden to convert the incoming value to whatever type it is supposed to be.

validate(value)

Throw an exception if the value is invalid.

unwrap(form_value)

Turns a value into its storable form.

wrap(value, session)

Turns a value into its usable form.

from_external_value(value, parent)

Turns a value read from an external dict into its value to be pushed directly into the metadata dict.

to_external_value(value)

Turns a value read from a metadata into its value to be pushed directly into the external dict.

class galaxy.model.metadata.MetadataElementSpec(datatype, name=None, desc=None, param=<class 'galaxy.model.metadata.MetadataParameter'>, default=None, no_value=None, visible=True, set_in_upload=False, **kwargs)

Bases: object

Defines a metadata element and adds it to the metadata_spec (which is a MetadataSpecCollection) of datatype.

__init__(datatype, name=None, desc=None, param=<class 'galaxy.model.metadata.MetadataParameter'>, default=None, no_value=None, visible=True, set_in_upload=False, **kwargs)

get(name, default=None)

wrap(value, session)

Turns a stored value into its usable form.

unwrap(value)

Turns an incoming value into its storable form.

galaxy.model.metadata.MetadataElement = <galaxy.model.metadata.Statement object>

MetadataParameter sub-classes.

class galaxy.model.metadata.SelectParameter(spec)

Bases: galaxy.model.metadata.MetadataParameter

__init__(spec)

to_string(value)

get_field(value=None, context=None, other_values=None, values=None, **kwd)

wrap(value, session)

classmethod marshal(value)

class galaxy.model.metadata.DBKeyParameter(spec)

Bases: galaxy.model.metadata.SelectParameter

get_field(value=None, context=None, other_values=None, values=None, **kwd)

class galaxy.model.metadata.RangeParameter(spec)

Bases: galaxy.model.metadata.SelectParameter

__init__(spec)

get_field(value=None, context=None, other_values=None, values=None, **kwd)

classmethod marshal(value)

class galaxy.model.metadata.ColumnParameter(spec)

Bases: galaxy.model.metadata.RangeParameter

get_field(value=None, context=None, other_values=None, values=None, **kwd)

class galaxy.model.metadata.ColumnTypesParameter(spec)

Bases: galaxy.model.metadata.MetadataParameter

to_string(value)

class galaxy.model.metadata.ListParameter(spec)

Bases: galaxy.model.metadata.MetadataParameter

to_string(value)

class galaxy.model.metadata.DictParameter(spec)

Bases: galaxy.model.metadata.MetadataParameter

to_string(value)

to_safe_string(value)

class galaxy.model.metadata.PythonObjectParameter(spec)

Bases: galaxy.model.metadata.MetadataParameter

to_string(value)

get_field(value=None, context=None, other_values=None, **kwd)

classmethod marshal(value)

class galaxy.model.metadata.FileParameter(spec)

Bases: galaxy.model.metadata.MetadataParameter

to_string(value)

to_safe_string(value)

get_field(value=None, context=None, other_values=None, **kwd)

wrap(value, session)

make_copy(value, target_context, source_context)

classmethod marshal(value)

from_external_value(value, parent, path_rewriter=None)

Turns a value read from a external dict into its value to be pushed directly into the metadata dict.

to_external_value(value)

Turns a value read from a metadata into its value to be pushed directly into the external dict.

new_file(dataset=None, **kwds)

class galaxy.model.metadata.MetadataTempFile(**kwds)

Bases: object

tmp_dir = 'database/tmp'

__init__(**kwds)

file_name

to_JSON()

classmethod from_JSON(json_dict)

classmethod is_JSONified_value(value)

classmethod cleanup_from_JSON_dict_filename(filename)

class galaxy.model.metadata.JobExternalOutputMetadataWrapper(job)

Bases: object

Class with methods allowing set_meta() to be called externally to the Galaxy head. This class allows access to external metadata filenames for all outputs associated with a job. We will use JSON as the medium of exchange of information, except for the DatasetInstance object which will use pickle (in the future this could be JSONified as well)

__init__(job)

get_output_filenames_by_dataset(dataset, sa_session)

get_dataset_metadata_key(dataset)

invalidate_external_metadata(datasets, sa_session)

setup_external_metadata(datasets, sa_session, exec_dir=None, tmp_dir=None, dataset_files_path=None, output_fnames=None, config_root=None, config_file=None, datatypes_config=None, job_metadata=None, compute_tmp_dir=None, include_command=True, max_metadata_value_size=0, kwds=None)

external_metadata_set_successfully(dataset, sa_session)

cleanup_external_metadata(sa_session)

set_job_runner_external_pid(pid, sa_session)

galaxy.model.search module

The GQL (Galaxy Query Language) search engine parsers a simple ‘SQL-Like’ query syntax to obtain items from the Galaxy installations. Rather then allow/force the user to do queries on the Galaxy schema, it uses a small set of ‘Views’ which are simple table representations of complex galaxy ideas. So while a history and its tags may exist in seperate tables in the real schema, in GQL they exist in the same view

Example Queries:

select name, id, file_size from hda

select name from hda

select name, model_class from ldda

select * from history

select * from workflow

select id, name from history where name=’Unnamed history’

select * from history where name=’Unnamed history’

class galaxy.model.search.ViewField(name, sqlalchemy_field=None, handler=None, post_filter=None, id_decode=False)

Bases: object

A ViewField defines a field in a view that filter operations can be applied to These filter operations are either handled with standard sqlalchemy filter calls, or passed to specialized handlers (such as when a table join would be needed to do the filtering)

Parameters:

sqlalchemy_field - Simple filtering using existing table columns, the argument is an sqlalchemy column

that the right hand value will be compared against

handler - Requires more specialized code to do filtering, usually requires a table join in order to

process the conditional

post_filter - Unable to do simple sqlalchemy based table filtering, filter is applied to loaded object

Thus methods avalible to the object can be used for filtering. example: a library folder must climb its chain of parents to find out which library it belongs to

__init__(name, sqlalchemy_field=None, handler=None, post_filter=None, id_decode=False)

class galaxy.model.search.ViewQueryBaseClass

Bases: object

FIELDS = {}

VIEW_NAME = 'undefined'

__init__()

decode_query_ids(trans, conditional)

filter(left, operator, right)

search(trans)

get_results(force_query=False)

galaxy.model.search.library_extended_metadata_filter(view, left, operator, right)

galaxy.model.search.ldda_parent_library_filter(item, left, operator, right)

class galaxy.model.search.LibraryDatasetDatasetView

Bases: galaxy.model.search.ViewQueryBaseClass

VIEW_NAME = 'library_dataset_dataset'

FIELDS = {'data_type': <galaxy.model.search.ViewField object at 0x7fbb2cadf3d0>, 'deleted': <galaxy.model.search.ViewField object at 0x7fbb2cadf710>, 'extended_metadata': <galaxy.model.search.ViewField object at 0x7fbb2cadffd0>, 'id': <galaxy.model.search.ViewField object at 0x7fbb2cadf310>, 'name': <galaxy.model.search.ViewField object at 0x7fbb2cadf650>, 'parent_library_id': <galaxy.model.search.ViewField object at 0x7fbb2cadfc50>}

search(trans)

class galaxy.model.search.LibraryView

Bases: galaxy.model.search.ViewQueryBaseClass

VIEW_NAME = 'library'

FIELDS = {'deleted': <galaxy.model.search.ViewField object at 0x7fbb2cadf190>, 'id': <galaxy.model.search.ViewField object at 0x7fbb2cadfd50>, 'name': <galaxy.model.search.ViewField object at 0x7fbb2cadf8d0>}

search(trans)

galaxy.model.search.library_folder_parent_library_id_filter(item, left, operator, right)

galaxy.model.search.library_path_filter(item, left, operator, right)

class galaxy.model.search.LibraryFolderView

Bases: galaxy.model.search.ViewQueryBaseClass

VIEW_NAME = 'library_folder'

FIELDS = {'id': <galaxy.model.search.ViewField object at 0x7fbb2d73ff10>, 'library_path': <galaxy.model.search.ViewField object at 0x7fbb2d73f6d0>, 'name': <galaxy.model.search.ViewField object at 0x7fbb2d73f610>, 'parent_id': <galaxy.model.search.ViewField object at 0x7fbb2d73f590>, 'parent_library_id': <galaxy.model.search.ViewField object at 0x7fbb2d73f5d0>}

search(trans)

galaxy.model.search.library_dataset_name_filter(item, left, operator, right)

class galaxy.model.search.LibraryDatasetView

Bases: galaxy.model.search.ViewQueryBaseClass

VIEW_NAME = 'library_dataset'

FIELDS = {'folder_id': <galaxy.model.search.ViewField object at 0x7fbb2d73f450>, 'id': <galaxy.model.search.ViewField object at 0x7fbb2d73f710>, 'name': <galaxy.model.search.ViewField object at 0x7fbb2d73f690>}

search(trans)

class galaxy.model.search.ToolView

Bases: galaxy.model.search.ViewQueryBaseClass

VIEW_NAME = 'tool'

FIELDS = {'id': <galaxy.model.search.ViewField object at 0x7fbb2d73fc90>, 'tool_id': <galaxy.model.search.ViewField object at 0x7fbb2d73fc50>}

search(trans)

galaxy.model.search.history_dataset_handle_tag(view, left, operator, right)

galaxy.model.search.history_dataset_extended_metadata_filter(view, left, operator, right)

class galaxy.model.search.HistoryDatasetView

Bases: galaxy.model.search.ViewQueryBaseClass

DOMAIN = 'history_dataset'

FIELDS = {'copied_from_hda_id': <galaxy.model.search.ViewField object at 0x7fbb2d73f890>, 'copied_from_ldda_id': <galaxy.model.search.ViewField object at 0x7fbb2d73fa50>, 'deleted': <galaxy.model.search.ViewField object at 0x7fbb2d73f9d0>, 'extended_metadata': <galaxy.model.search.ViewField object at 0x7fbb2d73fb90>, 'history_id': <galaxy.model.search.ViewField object at 0x7fbb2d73fcd0>, 'id': <galaxy.model.search.ViewField object at 0x7fbb2d73f090>, 'name': <galaxy.model.search.ViewField object at 0x7fbb2d73f3d0>, 'tag': <galaxy.model.search.ViewField object at 0x7fbb2d73ffd0>}

search(trans)

galaxy.model.search.history_handle_tag(view, left, operator, right)

galaxy.model.search.history_handle_annotation(view, left, operator, right)

class galaxy.model.search.HistoryView

Bases: galaxy.model.search.ViewQueryBaseClass

DOMAIN = 'history'

FIELDS = {'annotation': <galaxy.model.search.ViewField object at 0x7fbb2d73fb50>, 'deleted': <galaxy.model.search.ViewField object at 0x7fbb2d73fd50>, 'id': <galaxy.model.search.ViewField object at 0x7fbb2d73fb10>, 'name': <galaxy.model.search.ViewField object at 0x7fbb2d73f790>, 'tag': <galaxy.model.search.ViewField object at 0x7fbb2d73ff90>}

search(trans)

galaxy.model.search.workflow_tag_handler(view, left, operator, right)

class galaxy.model.search.WorkflowView

Bases: galaxy.model.search.ViewQueryBaseClass

DOMAIN = 'workflow'

FIELDS = {'deleted': <galaxy.model.search.ViewField object at 0x7fbb2d73fd90>, 'id': <galaxy.model.search.ViewField object at 0x7fbb2d73f350>, 'name': <galaxy.model.search.ViewField object at 0x7fbb2d73f310>, 'tag': <galaxy.model.search.ViewField object at 0x7fbb2d73fe90>}

search(trans)

galaxy.model.search.job_param_filter(view, left, operator, right)

galaxy.model.search.job_input_hda_filter(view, left, operator, right)

galaxy.model.search.job_input_ldda_filter(view, left, operator, right)

galaxy.model.search.job_output_hda_filter(view, left, operator, right)

class galaxy.model.search.JobView

Bases: galaxy.model.search.ViewQueryBaseClass

DOMAIN = 'job'

FIELDS = {'input_hda': <galaxy.model.search.ViewField object at 0x7fbb2d73f910>, 'input_ldda': <galaxy.model.search.ViewField object at 0x7fbb2d73fc10>, 'output_hda': <galaxy.model.search.ViewField object at 0x7fbb2d73fa10>, 'param': <galaxy.model.search.ViewField object at 0x7fbb2d73f850>, 'state': <galaxy.model.search.ViewField object at 0x7fbb2d73fe10>, 'tool_name': <galaxy.model.search.ViewField object at 0x7fbb2d73f750>}

search(trans)

class galaxy.model.search.PageView

Bases: galaxy.model.search.ViewQueryBaseClass

DOMAIN = 'page'

FIELDS = {'deleted': <galaxy.model.search.ViewField object at 0x7fbb2d73fa90>, 'id': <galaxy.model.search.ViewField object at 0x7fbb2d73fbd0>, 'slug': <galaxy.model.search.ViewField object at 0x7fbb2d73f950>, 'title': <galaxy.model.search.ViewField object at 0x7fbb2d73f990>}

search(trans)

class galaxy.model.search.PageRevisionView

Bases: galaxy.model.search.ViewQueryBaseClass

DOMAIN = 'page_revision'

FIELDS = {'id': <galaxy.model.search.ViewField object at 0x7fbb2d73f390>, 'page_id': <galaxy.model.search.ViewField object at 0x7fbb2d73fed0>, 'title': <galaxy.model.search.ViewField object at 0x7fbb2d73f2d0>}

search(trans)

class galaxy.model.search.GalaxyQuery(field_list, table_name, conditional)

Bases: object

This class represents a data structure of a compiled GQL query

__init__(field_list, table_name, conditional)

class galaxy.model.search.GalaxyQueryComparison(left, operator, right)

Bases: object

This class represents the data structure of the comparison arguments of a compiled GQL query (ie where name=’Untitled History’)

__init__(left, operator, right)

class galaxy.model.search.GalaxyQueryAnd(left, right)

Bases: object

This class represents the data structure of the comparison arguments of a compiled GQL query (ie where name=’Untitled History’)

__init__(left, right)

exception galaxy.model.search.GalaxyParseError

Bases: exceptions.Exception

class galaxy.model.search.SearchQuery(view, query)

Bases: object

__init__(view, query)

decode_query_ids(trans)

process(trans)

item_to_api_value(item)

class galaxy.model.search.GalaxySearchEngine

Bases: object

Primary class for searching. Parses GQL (Galaxy Query Language) queries and returns a ‘SearchQuery’ class

__init__()

query(query_text)

galaxy.model.util module

Utility helpers related to the model

galaxy.model.util.pgcalc(sa_session, id, dryrun=False)

Utility method for quickly recalculating user disk usage in postgres.

TODO: Check against the recently updated versions of sqlalchemy if this ‘special’ postgresql version is even necessary.