model Package

model Package

Galaxy data model classes

Naming: try to use class names that have a distinct plural form so that the relationship cardinalities are obvious (e.g. prefer Dataset to Data)

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

Bases: object

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

Bases: object

exception galaxy.model.ConverterDependencyException(value)

Bases: exceptions.Exception

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

Bases: object

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

Bases: object

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

Bases: object

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

engine = None

extra_files_path

file_name

file_path = '/tmp/'

full_delete()

Remove the file and extra files, marks deleted and purged

get_access_roles(trans)

get_extra_files_path()

get_file_name()

get_manage_permissions_roles(trans)

get_size(nice_size=False)

Returns the size of the data on disk

get_total_size()

has_data()

Detects whether there is any data

has_manage_permissions_roles(trans)

in_ready_state()

is_multi_byte()

mark_deleted(include_children=True)

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

object_store = None

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

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

set_extra_files_path(extra_files_path)

set_file_name(filename)

set_size()

Returns the size of the data on disk

set_total_size()

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

user_can_purge

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

Bases: object, galaxy.model.item_attrs.Dictifiable, galaxy.model.item_attrs.UsesAnnotations

copy(destination=None, element_destination=None)

dataset_elements

dataset_instances

dict_collection_visible_keys = ('id', 'collection_type')

dict_element_visible_keys = ('id', 'collection_type')

handle_population_failed(message)

mark_as_populated()

populated

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

set_from_dict(new_data)

state

validate()

waiting_for_elements

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

Bases: object, galaxy.model.item_attrs.Dictifiable

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

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

dataset

dataset_instance

dict_collection_visible_keys = ('id', 'element_type', 'element_index', 'element_identifier')

dict_element_visible_keys = ('id', 'element_type', 'element_index', 'element_identifier')

element_object

element_type

first_dataset_instance()

is_collection

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

Bases: object, galaxy.model.HasName

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.

state

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)

Bases: object

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

add_validation_error(validation_error)

as_display_type(type, **kwd)

can_convert_to(format)

change_datatype(new_ext)

clear_associated_files(metadata_safe=False, purge=False)

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

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.

creating_job

datatype

dbkey

display_info()

display_name()

display_peek()

ext

extend_validation_errors(validation_errors)

extra_files_path

file_name

find_conversion_destination(accepted_formats, **kwd)

Returns ( target_ext, existing converted dataset )

get_child_by_designation(designation)

get_converted_dataset(trans, target_ext)

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.

get_converted_dataset_deps(trans, target_ext)

Returns dict of { “dependency” => HDA }

get_converted_files_by_type(file_type)

get_converter_types()

get_dataset_state()

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>}).

get_dbkey()

get_display_applications(trans)

get_file_name()

get_metadata()

get_metadata_dataset(dataset_ext)

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

get_mime()

Returns the mime type of the data

get_raw_data()

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

get_size(nice_size=False)

Returns the size of the data on disk

get_total_size()

get_visualizations()

has_data()

Detects whether there is any data

init_meta(copy_from=None)

is_multi_byte()

Data consists of multi-byte characters

is_pending

Return true if the dataset is neither ready nor in error

mark_deleted(include_children=True)

mark_undeleted(include_children=True)

mark_unhidden(include_children=True)

metadata

missing_meta(**kwd)

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

set_dataset_state(state)

set_dbkey(value)

set_file_name(filename)

set_meta(**kwd)

set_metadata(bunch)

set_peek(is_multi_byte=False)

set_raw_data(data)

Saves the data on the disc

set_size()

Returns the size of the data on disk

set_total_size()

source_dataset_chain

source_library_dataset

state

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

undeletable()

write_from_stream(stream)

Writes data from a stream

class galaxy.model.DatasetPermissions(action, dataset, role)

Bases: object

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.DatasetToValidationErrorAssociation(dataset, validation_error)

Bases: object

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

Bases: object

class galaxy.model.DefaultQuotaAssociation(type, quota)

Bases: galaxy.model.Quota, galaxy.model.item_attrs.Dictifiable

dict_element_visible_keys = ('type',)

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

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

Bases: object

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

Bases: object

check_interval

get_check_interval()

get_last_check()

is_check_time

last_check

set_check_interval(seconds)

set_last_check(seconds)

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

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

Bases: object

class galaxy.model.ExtendedMetadata(data)

Bases: object

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

Bases: object

class galaxy.model.ExternalService(name=None, description=None, external_service_type_id=None, version=None, form_definition_id=None, form_values_id=None, deleted=None)

Bases: object

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

get_external_service_type(trans)

load_data_transfer_settings(trans)

populate_actions(trans, item, param_dict=None)

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

Bases: object, galaxy.model.item_attrs.Dictifiable

dict_collection_visible_keys = ('id', 'name')

dict_element_visible_keys = ('id', 'name', 'desc', 'form_definition_current_id', 'fields', 'layout')

field_as_html(field)

Generates disabled html for a field

get_widgets(user, contents={}, **kwd)

Return the list of widgets that comprise a form definition, including field contents if any.

grid_fields(grid_index)

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>

class galaxy.model.FormDefinitionCurrent(form_definition=None)

Bases: object

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

Bases: object

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

add_history(history, association=None)

get_disk_usage()

set_disk_usage(bytes)

total_disk_usage

class galaxy.model.GalaxySessionToHistoryAssociation(galaxy_session, history)

Bases: object

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

class galaxy.model.Group(name=None)

Bases: object, galaxy.model.item_attrs.Dictifiable

dict_collection_visible_keys = ('id', 'name')

dict_element_visible_keys = ('id', 'name')

class galaxy.model.GroupQuotaAssociation(group, quota)

Bases: object, galaxy.model.item_attrs.Dictifiable

dict_element_visible_keys = ('group',)

class galaxy.model.GroupRoleAssociation(group, role)

Bases: object

class galaxy.model.HasJobMetrics

add_metric(plugin, metric_name, metric_value)

metrics

class galaxy.model.HasName

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.History(id=None, name=None, user=None)

Bases: object, galaxy.model.item_attrs.Dictifiable, galaxy.model.item_attrs.UsesAnnotations, galaxy.model.HasName

activatable_datasets

active_contents

Return all active contents ordered by hid.

active_datasets_children_and_roles

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

add_dataset_collection(history_dataset_collection, set_hid=True)

add_galaxy_session(galaxy_session, association=None)

contents_iter(**kwds)

Fetch filtered list of contents of history.

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.

copy_tags_from(target_user, source_history)

default_name = 'Unnamed history'

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

dict_element_visible_keys = ('id', 'name', 'genome_build', 'deleted', 'purged', 'update_time', 'published', 'importable', 'slug', 'empty')

empty

get_disk_size(nice_size=False)

get_disk_size_bytes

latest_export

resume_paused_jobs()

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

unhide_datasets()

class galaxy.model.HistoryAnnotationAssociation

Bases: object

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.item_attrs.Dictifiable, galaxy.model.item_attrs.UsesAnnotations, galaxy.model.HasName

Resource class that creates a relation between a dataset and a user history.

clear_associated_files(metadata_safe=False, purge=False)

copy(copy_children=False, parent_id=None)

Create a copy of this HDA.

get_access_roles(trans)

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

history_content_type

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.

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

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

class galaxy.model.HistoryDatasetAssociationAnnotationAssociation

Bases: object

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

Bases: object

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

Bases: galaxy.model.ItemRatingAssociation

set_item(history_dataset_association)

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

Bases: object

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.HistoryDatasetCollectionAnnotationAssociation

Bases: object

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.item_attrs.Dictifiable

Associates a DatasetCollection with a History.

add_implicit_input_collection(name, history_dataset_collection)

copy(element_destination=None)

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

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

find_implicit_input_collection(name)

history_content_type

to_dict(view='collection')

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

Bases: galaxy.model.ItemRatingAssociation

set_item(dataset_collection)

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

Bases: galaxy.model.ItemRatingAssociation

set_item(history)

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.HistoryUserShareAssociation

Bases: object

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

Bases: object

clear(purge=False, delete_dataset=True)

class galaxy.model.ImplicitlyCreatedDatasetCollectionInput(name, input_dataset_collection)

Bases: object

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

Bases: object

set_item(item)

Set association’s item.

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

Bases: object, galaxy.model.item_attrs.Dictifiable

copy()

dict_collection_visible_keys = ('id', 'user_tname', 'user_value')

dict_element_visible_keys = ('id', 'user_tname', 'user_value')

class galaxy.model.Job

Bases: object, galaxy.model.HasJobMetrics, galaxy.model.item_attrs.Dictifiable

add_implicit_output_dataset_collection(name, dataset_collection)

add_input_dataset(name, dataset)

add_input_dataset_collection(name, dataset)

add_input_library_dataset(name, dataset)

add_output_dataset(name, dataset)

add_output_dataset_collection(name, dataset_collection_instance)

add_output_library_dataset(name, dataset)

add_parameter(name, value)

add_post_job_action(pja)

check_if_output_datasets_deleted()

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

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.

finished

get_command_line()

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_handler()

get_id()

get_id_tag()

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

get_imported()

get_info()

get_input_datasets()

get_input_library_datasets()

get_job()

get_job_runner_external_id()

get_job_runner_name()

get_output_datasets()

get_output_library_datasets()

get_param_filename()

get_param_values(app, ignore_errors=False)

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

get_parameters()

get_params()

get_post_job_actions()

get_session_id()

get_state()

get_tasks()

get_tool_id()

get_tool_version()

get_user()

get_user_id()

mark_deleted(track_jobs_in_database=False)

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

raw_param_dict()

set_command_line(command_line)

set_final_state(final_state)

set_handler(handler)

set_imported(imported)

set_info(info)

set_input_datasets(input_datasets)

set_input_library_datasets(input_library_datasets)

set_output_datasets(output_datasets)

set_output_library_datasets(output_library_datasets)

set_param_filename(param_filename)

set_parameters(parameters)

set_params(params)

set_post_job_actions(post_job_actions)

set_runner_external_id(job_runner_external_id)

set_runner_name(job_runner_name)

set_session_id(session_id)

set_state(state)

Save state history

set_tool_id(tool_id)

set_tool_version(tool_version)

set_user_id(user_id)

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

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

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

export_name

preparing

ready

up_to_date

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

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

Bases: object

dataset

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

Bases: object

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

Bases: galaxy.model.BaseJobMetric

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

Bases: galaxy.model.BaseJobMetric

class galaxy.model.JobParameter(name, value)

Bases: object

class galaxy.model.JobStateHistory(job)

Bases: object

class galaxy.model.JobToImplicitOutputDatasetCollectionAssociation(name, dataset_collection)

Bases: object

class galaxy.model.JobToInputDatasetAssociation(name, dataset)

Bases: object

class galaxy.model.JobToInputDatasetCollectionAssociation(name, dataset)

Bases: object

class galaxy.model.JobToInputLibraryDatasetAssociation(name, dataset)

Bases: object

class galaxy.model.JobToOutputDatasetAssociation(name, dataset)

Bases: object

class galaxy.model.JobToOutputDatasetCollectionAssociation(name, dataset_collection_instance)

Bases: object

class galaxy.model.JobToOutputLibraryDatasetAssociation(name, dataset)

Bases: object

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

Bases: object, galaxy.model.item_attrs.Dictifiable, galaxy.model.HasName

dict_collection_visible_keys = ('id', 'name')

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

get_access_roles(trans)

get_active_folders(folder, folders=None)

get_info_association(restrict=False, inherited=False)

get_template_widgets(trans, get_contents=True)

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

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

We prepend an F to folders.

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

Bases: object

display_name()

get_info()

get_name()

info

name

set_info(info)

set_library_dataset_dataset_association(ldda)

set_name(name)

to_dict(view='collection')

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')]

class galaxy.model.LibraryDatasetCollectionAnnotationAssociation

Bases: object

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

Bases: galaxy.model.DatasetCollectionInstance, galaxy.model.item_attrs.Dictifiable

Associates a DatasetCollection with a library folder.

editable_keys = ('name', 'deleted')

to_dict(view='collection')

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

Bases: galaxy.model.ItemRatingAssociation

set_item(dataset_collection)

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.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

clear_associated_files(metadata_safe=False, purge=False)

copy(copy_children=False, parent_id=None, target_folder=None)

get_access_roles(trans)

get_info_association(restrict=False, inherited=False)

get_manage_permissions_roles(trans)

get_template_widgets(trans, get_contents=True)

has_manage_permissions_roles(trans)

templates_dict(use_name=False)

Returns a dict of template info

templates_json(use_name=False)

to_dict(view='collection')

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

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

Bases: object

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

Bases: object

inheritable

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

Bases: object

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

Bases: object, galaxy.model.item_attrs.Dictifiable, galaxy.model.HasName

activatable_library_datasets

add_folder(folder)

add_library_dataset(library_dataset, genome_build=None)

dict_element_visible_keys = ('id', 'parent_id', 'name', 'description', 'item_count', 'genome_build', 'update_time', 'deleted')

get_info_association(restrict=False, inherited=False)

get_template_widgets(trans, get_contents=True)

library_path

parent_library

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

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

Bases: object

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

Bases: object

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

Bases: object

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

Bases: object

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

Bases: object

file_name

exception galaxy.model.NoConverterException(value)

Bases: exceptions.Exception

class galaxy.model.Page

Bases: object, galaxy.model.item_attrs.Dictifiable

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

to_dict(view='element')

class galaxy.model.PageAnnotationAssociation

Bases: object

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

Bases: galaxy.model.ItemRatingAssociation

set_item(page)

class galaxy.model.PageRevision

Bases: object, galaxy.model.item_attrs.Dictifiable

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

to_dict(view='element')

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.PageUserShareAssociation

Bases: object

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

Bases: object

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

Bases: object

class galaxy.model.PostJobActionAssociation(pja, job)

Bases: object

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

Bases: object, galaxy.model.item_attrs.Dictifiable

amount

dict_collection_visible_keys = ('id', 'name')

dict_element_visible_keys = ('id', 'name', 'description', 'bytes', 'operation', 'display_amount', 'default', 'users', 'groups')

display_amount

get_amount()

set_amount(amount)

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

class galaxy.model.Request(name=None, desc=None, request_type=None, user=None, form_values=None, notification=None)

Bases: object, galaxy.model.item_attrs.Dictifiable

dict_collection_visible_keys = ('id', 'name', 'state')

get_sample(sample_name)

is_complete

is_new

is_rejected

is_submitted

is_unsubmitted

last_comment

latest_event

samples_have_common_state

Returns the state of this request’s samples when they are all in one common state. Otherwise returns False.

samples_with_bar_code

samples_without_library_destinations

send_email_notification(trans, common_state, final_state=False)

state

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

class galaxy.model.RequestEvent(request=None, request_state=None, comment='')

Bases: object

class galaxy.model.RequestType(name=None, desc=None, request_form=None, sample_form=None)

Bases: object, galaxy.model.item_attrs.Dictifiable

add_external_service_association(trans, external_service)

delete_external_service_associations(trans)

Deletes all external service associations.

dict_collection_visible_keys = ('id', 'name', 'desc')

dict_element_visible_keys = ('id', 'name', 'desc', 'request_form_id', 'sample_form_id')

external_services

final_sample_state

get_external_service(external_service_type_id)

get_external_services_for_manual_data_transfer(trans)

Returns all external services that use manual data transfer

get_template_widgets(trans, get_contents=True)

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

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

run_details

class galaxy.model.RequestTypeExternalServiceAssociation(request_type, external_service)

Bases: object

class galaxy.model.RequestTypePermissions(action, request_type, role)

Bases: object

class galaxy.model.RequestTypeRunAssociation(request_type, run)

Bases: object

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

Bases: object, galaxy.model.item_attrs.Dictifiable

dict_collection_visible_keys = ('id', 'name')

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

private_id = None

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

class galaxy.model.Run(form_definition, form_values, subindex=None)

Bases: object

class galaxy.model.Sample(name=None, desc=None, request=None, form_values=None, bar_code=None, library=None, folder=None, workflow=None, history=None)

Bases: object, galaxy.model.item_attrs.Dictifiable

adding_to_library_dataset_files

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

dict_collection_visible_keys = ('id', 'name')

get_template_widgets(trans, get_contents=True)

get_untransferred_dataset_size(filepath, scp_configs)

inprogress_dataset_files

latest_event

populate_external_services(param_dict=None, trans=None)

queued_dataset_files

run_details

state

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

transfer_error_dataset_files

transferred_dataset_files

transferring_dataset_files

untransferred_dataset_files

class galaxy.model.SampleDataset(sample=None, name=None, file_path=None, status=None, error_msg=None, size=None, external_service=None)

Bases: object

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

class galaxy.model.SampleEvent(sample=None, sample_state=None, comment='')

Bases: object

class galaxy.model.SampleRunAssociation(sample, run)

Bases: object

class galaxy.model.SampleState(name=None, desc=None, request_type=None)

Bases: object

class galaxy.model.StoredWorkflow

Bases: object, galaxy.model.item_attrs.Dictifiable

copy_tags_from(target_user, source_workflow)

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

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

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

class galaxy.model.StoredWorkflowAnnotationAssociation

Bases: object

class galaxy.model.StoredWorkflowMenuEntry

Bases: object

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

Bases: galaxy.model.ItemRatingAssociation

set_item(stored_workflow)

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.StoredWorkflowUserShareAssociation

Bases: object

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

Bases: object

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

Bases: object, galaxy.model.HasJobMetrics

A task represents a single component of a job.

get_command_line()

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_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_info()

get_job()

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_job_runner_name()

Since runners currently access Tasks the same way they access Jobs, this method just refers to this instance’s runner.

get_param_values(app)

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

get_parameters()

get_prepare_input_files_cmd()

get_session_id()

get_state()

get_stderr()

get_stdout()

get_task_runner_external_id()

get_task_runner_name()

get_working_directory()

set_command_line(command_line)

set_id(id)

set_info(info)

set_job(job)

set_job_runner_external_id(task_runner_external_id)

set_parameters(parameters)

set_prepare_input_files_cmd(prepare_input_files_cmd)

set_state(state)

set_stderr(stderr)

set_stdout(stdout)

set_task_runner_external_id(task_runner_external_id)

set_task_runner_name(task_runner_name)

set_working_directory(working_directory)

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

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

Bases: galaxy.model.ItemTagAssociation

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']

class galaxy.model.UCI

Bases: object

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

Bases: object, galaxy.model.item_attrs.Dictifiable

all_roles()

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

calculate_disk_usage()

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

check_password(cleartext)

Check if cleartext matches user password when hashed.

dict_collection_visible_keys = ('id', 'email', 'username')

dict_element_visible_keys = ('id', 'email', 'username', 'total_disk_usage', 'nice_total_disk_usage')

static expand_user_properties(user, in_string)

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.

nice_total_disk_usage

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

set_disk_usage(bytes)

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

set_password_cleartext(cleartext)

Set user password to the digest of cleartext.

total_disk_usage

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

use_pbkdf2 = True

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

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'

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

Bases: object

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

get_html()

class galaxy.model.UserGroupAssociation(user, group)

Bases: object

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

Bases: object

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

Bases: object

class galaxy.model.UserQuotaAssociation(user, quota)

Bases: object, galaxy.model.item_attrs.Dictifiable

dict_element_visible_keys = ('user',)

class galaxy.model.UserRoleAssociation(user, role)

Bases: object

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

Bases: object

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

Bases: object

copy(user=None, title=None)

Provide copy of visualization with only its latest revision.

class galaxy.model.VisualizationAnnotationAssociation

Bases: object

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

Bases: galaxy.model.ItemRatingAssociation

set_item(visualization)

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

Bases: object

copy(visualization=None)

Returns a copy of this object.

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.VisualizationUserShareAssociation

Bases: object

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

Bases: galaxy.model.ItemTagAssociation

class galaxy.model.Workflow(uuid=None)

Bases: object, galaxy.model.item_attrs.Dictifiable

dict_collection_visible_keys = ('name', 'has_cycles', 'has_errors')

dict_element_visible_keys = ('name', 'has_cycles', 'has_errors')

has_outputs_defined()

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

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

class galaxy.model.WorkflowInvocation

Bases: object, galaxy.model.item_attrs.Dictifiable

active

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

add_input(content, step_id)

cancel()

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')

fail()

has_input_for_step(step_id)

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

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

step_invocations_by_step_id()

step_invocations_for_step_id(step_id)

step_states_by_step_id()

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

update()

class galaxy.model.WorkflowInvocationStep

Bases: object, galaxy.model.item_attrs.Dictifiable

dict_collection_visible_keys = ('id', 'update_time', 'job_id', 'workflow_step_id', 'action')

dict_element_visible_keys = ('id', 'update_time', 'job_id', 'workflow_step_id', 'action')

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

update()

class galaxy.model.WorkflowOutput(workflow_step, output_name)

Bases: object

class galaxy.model.WorkflowRequest

Bases: object, galaxy.model.item_attrs.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: object, galaxy.model.item_attrs.Dictifiable

Workflow-related parameters not tied to steps or inputs.

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

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

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

Bases: object, galaxy.model.item_attrs.Dictifiable

Workflow step value parameters.

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

class galaxy.model.WorkflowRequestToInputDatasetAssociation

Bases: object, galaxy.model.item_attrs.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: object, galaxy.model.item_attrs.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.WorkflowStep

Bases: object

class galaxy.model.WorkflowStepAnnotationAssociation

Bases: object

class galaxy.model.WorkflowStepConnection

Bases: object

NON_DATA_CONNECTION = '__NO_INPUT_OUTPUT_NAME__'

non_data_connection

set_non_data_connection()

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

Bases: galaxy.model.ItemTagAssociation

galaxy.model.set_datatypes_registry(d_registry)

Set up datatypes_registry

custom_types Module

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.

compare_values(x, y)

copy_value(value)

impl

alias of LargeBinary

load_dialect_impl(dialect)

process_bind_param(value, dialect)

process_result_value(value, dialect)

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_result_value(value, dialect)

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

append(value)

classmethod coerce(key, value)

Convert plain list to MutationList

extend(values)

insert(idx, value)

pop(*args, **kw)

remove(value)

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.TrimmedString(*args, **kwargs)

Bases: sqlalchemy.sql.type_api.TypeDecorator

impl

alias of String

process_bind_param(value, dialect)

Automatically truncate string values

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 CHAR

load_dialect_impl(dialect)

process_bind_param(value, dialect)

process_result_value(value, dialect)

item_attrs Module

class galaxy.model.item_attrs.Dictifiable

Mixin that enables objects to be converted to dictionaries. This is useful when for sharing objects across boundaries, such as the API, tool scripts, and JavaScript code.

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

Return item dictionary.

exception galaxy.model.item_attrs.RuntimeException

Bases: exceptions.Exception

class galaxy.model.item_attrs.UsesAnnotations

Mixin for getting and setting item annotations.

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.

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.

delete_item_annotation(db_session, user, item)

get_item_annotation_obj(db_session, user, item)

Returns a user’s annotation object for an item.

get_item_annotation_str(db_session, user, item)

Returns a user’s annotation string for an item.

class galaxy.model.item_attrs.UsesItemRatings

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.

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

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

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

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

mapping Module

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

galaxy.model.mapping.annotation_mapping(annotation_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={}, create_tables=False, map_install_models=False, database_query_profiling_proxy=False, object_store=None, trace_logger=None, use_pbkdf2=True)

Connect mappings to the database

galaxy.model.mapping.now()

Return a new datetime representing UTC day and time.

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

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

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

mapping_tests Module

Subpackages

• migrate Package
  • check Module
• orm Package
  • orm Package
  • logging_connection_proxy Module
  • Subpackages
    • ext Package
      • ext Package
      • assignmapper Module