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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)

class galaxy.model.RepresentById[source]

Bases: object

exception galaxy.model.NoConverterException(value)[source]

Bases: exceptions.Exception

__init__(value)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

exception galaxy.model.ConverterDependencyException(value)[source]

Bases: exceptions.Exception

__init__(value)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

galaxy.model.set_datatypes_registry(d_registry)[source]

Set up datatypes_registry

class galaxy.model.HasTags[source]

Bases: object

dict_collection_visible_keys = ['tags']
dict_element_visible_keys = ['tags']
to_dict(*args, **kwargs)[source]
make_tag_string_list()[source]
copy_tags_from(target_user, source)[source]
auto_propagated_tags
class galaxy.model.SerializationOptions(for_edit, serialize_dataset_objects=None, serialize_files_handler=None, strip_metadata_files=None)[source]

Bases: object

__init__(for_edit, serialize_dataset_objects=None, serialize_files_handler=None, strip_metadata_files=None)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

attach_identifier(id_encoder, obj, ret_val)[source]
get_identifier(id_encoder, obj)[source]
get_identifier_for_id(id_encoder, obj_id)[source]
serialize_files(dataset, as_dict)[source]
class galaxy.model.HasName[source]

Bases: object

get_display_name()[source]

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[source]

Bases: object

seconds_since_updated
seconds_since_created
class galaxy.model.WorkerProcess(server_name, hostname)[source]

Bases: galaxy.model.UsesCreateAndUpdateTime

__init__(server_name, hostname)

x.__init__(…) initializes x; see help(type(x)) for signature

galaxy.model.cached_id(galaxy_model_object)[source]

Get model object id attribute without a firing a database query.

Useful to fetching the id of a typical Galaxy model object after a flush, where SA is going to mark the id attribute as unloaded but we know the id is immutable and so we can use the database identity to fetch.

With Galaxy’s default SA initialization - any flush marks all attributes as unloaded - even objects completely unrelated to the flushed changes and even attributes we know to be immutable like id. See test_galaxy_mapping.py for verification of this behavior. This method is a workaround that uses the fact that we know all Galaxy objects use the id attribute as identity and SA internals (_sa_instance_state) to infer the previously loaded ID value. I tried digging into the SA internals extensively and couldn’t find a way to get the previously loaded values after a flush to allow a generalization of this for other attributes.

class galaxy.model.JobLike[source]

Bases: object

MAX_NUMERIC = 9999999999999999999L
add_metric(plugin, metric_name, metric_value)[source]
metrics
set_streams(tool_stdout, tool_stderr, job_stdout=None, job_stderr=None, job_messages=None)[source]
log_str()[source]
get_stdout()[source]
set_stdout(stdout)[source]
get_stderr()[source]
set_stderr(stderr)[source]
stdout
stderr
class galaxy.model.User(email=None, password=None, username=None)[source]

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

use_pbkdf2 = True

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

dict_collection_visible_keys = ['id', 'email', 'username', 'deleted', 'active', 'last_password_change']
dict_element_visible_keys = ['id', 'email', 'username', 'total_disk_usage', 'nice_total_disk_usage', 'deleted', 'active', 'last_password_change']
__init__(email=None, password=None, username=None)

x.__init__(…) initializes x; see help(type(x)) for signature

extra_preferences
set_password_cleartext(cleartext)[source]

Set user password to the digest of cleartext.

set_random_password(length=16)[source]

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

check_password(cleartext)[source]

Check if cleartext matches user password when hashed.

system_user_pwent(real_system_username)[source]

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

all_roles()[source]

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

all_roles_exploiting_cache()[source]
get_disk_usage(nice_size=False)[source]

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

set_disk_usage(bytes)[source]

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)[source]
nice_total_disk_usage

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

calculate_disk_usage()[source]

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

calculate_and_set_disk_usage()[source]

Calculates and sets user disk usage.

static user_template_environment(user)[source]
>>> env = User.user_template_environment(None)
>>> env['__user_email__']
'Anonymous'
>>> env['__user_id__']
'Anonymous'
>>> user = User('foo@example.com')
>>> user.id = 6
>>> user.username = 'foo2'
>>> env = User.user_template_environment(user)
>>> env['__user_id__']
'6'
>>> env['__user_name__']
'foo2'
static expand_user_properties(user, in_string)[source]
is_active()[source]
is_authenticated()[source]
class galaxy.model.PasswordResetToken(user, token=None)[source]

Bases: object

__init__(user, token=None)

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.DynamicTool(tool_format=None, tool_id=None, tool_version=None, uuid=None, active=True, hidden=True, value=None)[source]

Bases: galaxy.util.dictifiable.Dictifiable

dict_collection_visible_keys = ('id', 'tool_id', 'tool_format', 'tool_version', 'uuid', 'active', 'hidden')
dict_element_visible_keys = ('id', 'tool_id', 'tool_format', 'tool_version', 'uuid', 'active', 'hidden')
__init__(tool_format=None, tool_id=None, tool_version=None, uuid=None, active=True, hidden=True, value=None)

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.BaseJobMetric(plugin, metric_name, metric_value)[source]

Bases: object

__init__(plugin, metric_name, metric_value)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.JobMetricText(plugin, metric_name, metric_value)[source]

Bases: galaxy.model.BaseJobMetric, galaxy.model.RepresentById

class galaxy.model.JobMetricNumeric(plugin, metric_name, metric_value)[source]

Bases: galaxy.model.BaseJobMetric, galaxy.model.RepresentById

class galaxy.model.TaskMetricText(plugin, metric_name, metric_value)[source]

Bases: galaxy.model.BaseJobMetric, galaxy.model.RepresentById

class galaxy.model.TaskMetricNumeric(plugin, metric_name, metric_value)[source]

Bases: galaxy.model.BaseJobMetric, galaxy.model.RepresentById

class galaxy.model.Job[source]

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

dict_collection_visible_keys = ['id', 'state', 'exit_code', 'update_time', 'create_time']
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__()

x.__init__(…) initializes x; see help(type(x)) for signature

finished
io_dicts()[source]
get_external_output_metadata()[source]

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

get_session_id()[source]
get_user_id()[source]
get_tool_id()[source]
get_tool_version()[source]
get_command_line()[source]
get_dependencies()[source]
get_param_filename()[source]
get_parameters()[source]
get_copied_from_job_id()[source]
get_input_datasets()[source]
get_output_datasets()[source]
get_input_library_datasets()[source]
get_output_library_datasets()[source]
get_state()[source]
get_info()[source]
get_job_runner_name()[source]
get_job_runner_external_id()[source]
get_post_job_actions()[source]
get_imported()[source]
get_handler()[source]
get_params()[source]
get_user()[source]
get_tasks()[source]
get_id_tag()[source]

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

set_session_id(session_id)[source]
set_user_id(user_id)[source]
set_tool_id(tool_id)[source]
set_tool_version(tool_version)[source]
set_command_line(command_line)[source]
set_dependencies(dependencies)[source]
set_param_filename(param_filename)[source]
set_parameters(parameters)[source]
set_copied_from_job_id(job_id)[source]
set_input_datasets(input_datasets)[source]
set_output_datasets(output_datasets)[source]
set_input_library_datasets(input_library_datasets)[source]
set_output_library_datasets(output_library_datasets)[source]
set_info(info)[source]
set_runner_name(job_runner_name)[source]
get_job()[source]
set_runner_external_id(job_runner_external_id)[source]
set_post_job_actions(post_job_actions)[source]
set_imported(imported)[source]
set_handler(handler)[source]
set_params(params)[source]
add_parameter(name, value)[source]
add_input_dataset(name, dataset=None, dataset_id=None)[source]
add_output_dataset(name, dataset)[source]
add_input_dataset_collection(name, dataset_collection)[source]
add_output_dataset_collection(name, dataset_collection_instance)[source]
add_implicit_output_dataset_collection(name, dataset_collection)[source]
add_input_library_dataset(name, dataset)[source]
add_output_library_dataset(name, dataset)[source]
add_post_job_action(pja)[source]
set_state(state)[source]

Save state history

get_param_values(app, ignore_errors=False)[source]

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

raw_param_dict()[source]
check_if_output_datasets_deleted()[source]

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

mark_deleted(track_jobs_in_database=False)[source]

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

mark_failed(info='Job execution failed', blurb=None, peek=None)[source]

Mark this job as failed, and mark any output datasets as errored.

resume(flush=True)[source]
serialize(id_encoder, serialization_options)[source]
to_dict(view='collection', system_details=False)[source]

Return item dictionary.

set_final_state(final_state)[source]
get_destination_configuration(dest_params, config, key, default=None)[source]

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

class galaxy.model.Task(job, working_directory, prepare_files_cmd)[source]

Bases: galaxy.model.JobLike, galaxy.model.RepresentById

A task represents a single component of a job.

states = <galaxy.util.bunch.Bunch object>
__init__(job, working_directory, prepare_files_cmd)

x.__init__(…) initializes x; see help(type(x)) for signature

get_param_values(app)[source]

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

get_id_tag()[source]

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

get_command_line()[source]
get_parameters()[source]
get_state()[source]
get_info()[source]
get_working_directory()[source]
get_task_runner_name()[source]
get_task_runner_external_id()[source]
get_job()[source]
get_prepare_input_files_cmd()[source]
get_external_output_metadata()[source]

The external_output_metadata is currently a backref to JobExternalOutputMetadata. It exists for a job but not a task, and when a task is cancelled its corresponding parent Job will be cancelled. So None is returned now, but that could be changed to self.get_job().get_external_output_metadata().

get_job_runner_name()[source]

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

get_job_runner_external_id()[source]

Runners will use the same methods to get information about the Task class as they will about the Job class, so this method just returns the task’s external id.

get_session_id()[source]
set_id(id)[source]
set_command_line(command_line)[source]
set_parameters(parameters)[source]
set_state(state)[source]
set_info(info)[source]
set_working_directory(working_directory)[source]
set_task_runner_name(task_runner_name)[source]
set_job_runner_external_id(task_runner_external_id)[source]
set_task_runner_external_id(task_runner_external_id)[source]
set_job(job)[source]
set_prepare_input_files_cmd(prepare_input_files_cmd)[source]
class galaxy.model.JobParameter(name, value)[source]

Bases: galaxy.model.RepresentById

__init__(name, value)

x.__init__(…) initializes x; see help(type(x)) for signature

copy()[source]
class galaxy.model.JobToInputDatasetAssociation(name, dataset)[source]

Bases: galaxy.model.RepresentById

__init__(name, dataset)

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.JobToOutputDatasetAssociation(name, dataset)[source]

Bases: galaxy.model.RepresentById

__init__(name, dataset)

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.JobToInputDatasetCollectionAssociation(name, dataset_collection)[source]

Bases: galaxy.model.RepresentById

__init__(name, dataset_collection)

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.JobToOutputDatasetCollectionAssociation(name, dataset_collection_instance)[source]

Bases: galaxy.model.RepresentById

__init__(name, dataset_collection_instance)

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.JobToImplicitOutputDatasetCollectionAssociation(name, dataset_collection)[source]

Bases: galaxy.model.RepresentById

__init__(name, dataset_collection)

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.JobToInputLibraryDatasetAssociation(name, dataset)[source]

Bases: galaxy.model.RepresentById

__init__(name, dataset)

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.JobToOutputLibraryDatasetAssociation(name, dataset)[source]

Bases: galaxy.model.RepresentById

__init__(name, dataset)

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.JobStateHistory(job)[source]

Bases: galaxy.model.RepresentById

__init__(job)

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.ImplicitlyCreatedDatasetCollectionInput(name, input_dataset_collection)[source]

Bases: galaxy.model.RepresentById

__init__(name, input_dataset_collection)

x.__init__(…) initializes x; see help(type(x)) for signature

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

Bases: galaxy.model.RepresentById

populated_states = <galaxy.util.bunch.Bunch object>
__init__(id=None, populated_state=None)

x.__init__(…) initializes x; see help(type(x)) for signature

job_list
serialize(id_encoder, serialization_options)[source]
class galaxy.model.ImplicitCollectionJobsJobAssociation[source]

Bases: galaxy.model.RepresentById

__init__()

x.__init__(…) initializes x; see help(type(x)) for signature

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

Bases: galaxy.model.RepresentById

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

x.__init__(…) initializes x; see help(type(x)) for signature

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

Bases: galaxy.model.RepresentById

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

x.__init__(…) initializes x; see help(type(x)) for signature

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

Bases: galaxy.model.RepresentById

__init__(job=None, dataset=None)

x.__init__(…) initializes x; see help(type(x)) for signature

dataset
class galaxy.model.JobExportHistoryArchive(job=None, history=None, dataset=None, compressed=False, history_attrs_filename=None)[source]

Bases: galaxy.model.RepresentById

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

x.__init__(…) initializes x; see help(type(x)) for signature

temp_directory
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)[source]

Bases: galaxy.model.RepresentById

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

x.__init__(…) initializes x; see help(type(x)) for signature

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

Bases: galaxy.model.RepresentById

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

x.__init__(…) initializes x; see help(type(x)) for signature

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

Bases: galaxy.model.RepresentById

states = <galaxy.util.bunch.Bunch object>
__init__(state=None, plugin=None, params=None)

x.__init__(…) initializes x; see help(type(x)) for signature

get_check_interval()[source]
set_check_interval(seconds)[source]
check_interval
get_last_check()[source]
set_last_check(seconds)[source]
last_check
is_check_time
class galaxy.model.Group(name=None)[source]

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

dict_collection_visible_keys = ['id', 'name']
dict_element_visible_keys = ['id', 'name']
__init__(name=None)

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.UserGroupAssociation(user, group)[source]

Bases: galaxy.model.RepresentById

__init__(user, group)

x.__init__(…) initializes x; see help(type(x)) for signature

galaxy.model.is_hda(d)[source]
class galaxy.model.History(id=None, name=None, user=None)[source]

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

dict_collection_visible_keys = ['id', 'name', 'published', 'deleted']
dict_element_visible_keys = ['id', 'name', 'genome_build', 'deleted', 'purged', 'update_time', 'published', 'importable', 'slug', 'empty']
default_name = 'Unnamed history'
__init__(id=None, name=None, user=None)

x.__init__(…) initializes x; see help(type(x)) for signature

empty
add_galaxy_session(galaxy_session, association=None)[source]
add_dataset(dataset, parent_id=None, genome_build=None, set_hid=True, quota=True)[source]
add_datasets(sa_session, datasets, parent_id=None, genome_build=None, set_hid=True, quota=True, flush=False)[source]

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

add_dataset_collection(history_dataset_collection, set_hid=True)[source]
copy(name=None, target_user=None, activatable=False, all_datasets=False)[source]

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

has_possible_members
activatable_datasets
serialize(id_encoder, serialization_options)[source]
to_dict(view='collection', value_mapper=None)[source]

Return item dictionary.

latest_export
unhide_datasets()[source]
resume_paused_jobs()[source]
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)[source]

Fetch filtered list of contents of history.

class galaxy.model.HistoryUserShareAssociation[source]

Bases: galaxy.model.RepresentById

__init__()

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.UserRoleAssociation(user, role)[source]

Bases: galaxy.model.RepresentById

__init__(user, role)

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.GroupRoleAssociation(group, role)[source]

Bases: galaxy.model.RepresentById

__init__(group, role)

x.__init__(…) initializes x; see help(type(x)) for signature

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

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

dict_collection_visible_keys = ['id', 'name']
dict_element_visible_keys = ['id', 'name', 'description', 'type']
private_id = None
types = <galaxy.util.bunch.Bunch object>
__init__(name='', description='', type='system', deleted=False)

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.UserQuotaAssociation(user, quota)[source]

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

dict_element_visible_keys = ['user']
__init__(user, quota)

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.GroupQuotaAssociation(group, quota)[source]

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

dict_element_visible_keys = ['group']
__init__(group, quota)

x.__init__(…) initializes x; see help(type(x)) for signature

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

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

dict_collection_visible_keys = ['id', 'name']
dict_element_visible_keys = ['id', 'name', 'description', 'bytes', 'operation', 'display_amount', 'default', 'users', 'groups']
valid_operations = ('+', '-', '=')
__init__(name='', description='', amount=0, operation='=')

x.__init__(…) initializes x; see help(type(x)) for signature

get_amount()[source]
set_amount(amount)[source]
amount
display_amount
class galaxy.model.DefaultQuotaAssociation(type, quota)[source]

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

dict_element_visible_keys = ['type']
types = <galaxy.util.bunch.Bunch object>
__init__(type, quota)

x.__init__(…) initializes x; see help(type(x)) for signature

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

Bases: galaxy.model.RepresentById

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

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.LibraryPermissions(action, library_item, role)[source]

Bases: galaxy.model.RepresentById

__init__(action, library_item, role)

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.LibraryFolderPermissions(action, library_item, role)[source]

Bases: galaxy.model.RepresentById

__init__(action, library_item, role)

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.LibraryDatasetPermissions(action, library_item, role)[source]

Bases: galaxy.model.RepresentById

__init__(action, library_item, role)

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.LibraryDatasetDatasetAssociationPermissions(action, library_item, role)[source]

Bases: galaxy.model.RepresentById

__init__(action, library_item, role)

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.DefaultUserPermissions(user, action, role)[source]

Bases: galaxy.model.RepresentById

__init__(user, action, role)

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.DefaultHistoryPermissions(history, action, role)[source]

Bases: galaxy.model.RepresentById

__init__(history, action, role)

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.StorableObject(id, uuid)[source]

Bases: object

__init__(id, uuid)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

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

Bases: galaxy.model.StorableObject, galaxy.model.RepresentById

states = <galaxy.util.bunch.Bunch object>
non_ready_states = ('new', 'upload', 'queued', 'running', 'setting_metadata')
ready_states = ('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)

x.__init__(…) initializes x; see help(type(x)) for signature

in_ready_state()[source]
get_file_name()[source]
set_file_name(filename)[source]
file_name
get_extra_files_path()[source]
create_extra_files_path()[source]
set_extra_files_path(extra_files_path)[source]
extra_files_path
extra_files_path_exists()[source]
get_size(nice_size=False)[source]

Returns the size of the data on disk

set_size(no_extra_files=False)[source]

Sets the size of the data on disk.

If the caller is sure there are no extra files, pass no_extra_files as True to optimize subsequent calls to get_total_size or set_total_size - potentially avoiding both a database flush and check against the file system.

get_total_size()[source]
set_total_size()[source]
has_data()[source]

Detects whether there is any data

mark_deleted()[source]
user_can_purge
full_delete()[source]

Remove the file and extra files, marks deleted and purged

get_access_roles(trans)[source]
get_manage_permissions_roles(trans)[source]
has_manage_permissions_roles(trans)[source]
serialize(id_encoder, serialization_options)[source]
class galaxy.model.DatasetSource[source]

Bases: galaxy.model.RepresentById

class galaxy.model.DatasetSourceHash[source]

Bases: galaxy.model.RepresentById

class galaxy.model.DatasetHash[source]

Bases: galaxy.model.RepresentById

serialize(id_encoder, serialization_options)[source]
galaxy.model.datatype_for_extension(extension, datatypes_registry=None)[source]
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)[source]

Bases: object

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

states = <galaxy.util.bunch.Bunch object>
conversion_messages = <galaxy.util.bunch.Bunch object>
permitted_actions = <galaxy.util.bunch.Bunch object>
__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)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

update()[source]
ext
get_dataset_state()[source]
raw_set_dataset_state(state)[source]
set_dataset_state(state)[source]
state
get_file_name()[source]
set_file_name(filename)[source]
file_name
extra_files_path
extra_files_path_exists()[source]
datatype
get_metadata()[source]
set_metadata_requires_flush
set_metadata(bunch)[source]
metadata
metadata_file_types
get_dbkey()[source]
set_dbkey(value)[source]
dbkey
change_datatype(new_ext)[source]
get_size(nice_size=False)[source]

Returns the size of the data on disk

set_size(**kwds)[source]

Sets and gets the size of the data on disk

get_total_size()[source]
set_total_size()[source]
has_data()[source]

Detects whether there is any data

get_created_from_basename()[source]
set_created_from_basename(created_from_basename)[source]
created_from_basename
get_raw_data()[source]

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

get_mime()[source]

Returns the mime type of the data

set_peek()[source]
init_meta(copy_from=None)[source]
set_meta(**kwd)[source]
missing_meta(**kwd)[source]
as_display_type(type, **kwd)[source]
display_peek()[source]
display_name()[source]
display_info()[source]
get_converted_files_by_type(file_type)[source]
get_converted_dataset_deps(trans, target_ext)[source]

Returns dict of { “dependency” => HDA }

get_converted_dataset(trans, target_ext, target_context=None, history=None)[source]

Return converted dataset(s) if they exist, along with a dict of dependencies. If not converted yet, do so and return None (the first time). If unconvertible, raise exception.

copy_attributes(new_dataset)[source]

Copies attributes to a new datasets, used for implicit conversions

get_metadata_dataset(dataset_ext)[source]

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

clear_associated_files(metadata_safe=False, purge=False)[source]
get_converter_types()[source]
can_convert_to(format)[source]
find_conversion_destination(accepted_formats, **kwd)[source]

Returns ( target_ext, existing converted dataset )

add_validation_error(validation_error)[source]
extend_validation_errors(validation_errors)[source]
mark_deleted()[source]
mark_undeleted()[source]
mark_unhidden()[source]
undeletable()[source]
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)[source]
get_visualizations()[source]
get_datasources(trans)[source]

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

convert_dataset(trans, target_type)[source]

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.

serialize(id_encoder, serialization_options, for_link=False)[source]
class galaxy.model.HistoryDatasetAssociation(hid=None, history=None, copied_from_history_dataset_association=None, copied_from_library_dataset_dataset_association=None, sa_session=None, **kwd)[source]

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

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

__init__(hid=None, history=None, copied_from_history_dataset_association=None, copied_from_library_dataset_dataset_association=None, sa_session=None, **kwd)

Create a a new HDA and associate it with the given history.

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

Create a copy of this HDA.

copy_tags_to(copy_tags=None)[source]
copy_attributes(new_dataset)[source]

Copies attributes to a new datasets, used for implicit conversions

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

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

clear_associated_files(metadata_safe=False, purge=False)[source]
get_access_roles(trans)[source]

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

quota_amount(user)[source]

Return the disk space used for this HDA relevant to user quotas.

If the user has multiple instances of this dataset, it will not affect their disk usage statistic.

serialize(id_encoder, serialization_options, for_link=False)[source]
to_dict(view='collection', expose_dataset_path=False)[source]

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

unpause_dependent_jobs(jobs=None)[source]
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)[source]

Bases: galaxy.model.RepresentById

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

x.__init__(…) initializes x; see help(type(x)) for signature

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

Bases: galaxy.model.RepresentById

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

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.HistoryDatasetAssociationSubset(hda, subset, location)[source]

Bases: galaxy.model.RepresentById

__init__(hda, subset, location)

x.__init__(…) initializes x; see help(type(x)) for signature

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

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

permitted_actions = <galaxy.util.bunch.Bunch object>
dict_collection_visible_keys = ['id', 'name']
dict_element_visible_keys = ['id', 'deleted', 'name', 'description', 'synopsis', 'root_folder_id', 'create_time']
__init__(name=None, description=None, synopsis=None, root_folder=None)

x.__init__(…) initializes x; see help(type(x)) for signature

serialize(id_encoder, serialization_options)[source]
to_dict(view='collection', value_mapper=None)[source]

We prepend an F to folders.

get_active_folders(folder, folders=None)[source]
get_access_roles(trans)[source]
class galaxy.model.LibraryFolder(name=None, description=None, item_count=0, order_id=None, genome_build=None)[source]

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

dict_element_visible_keys = ['id', 'parent_id', 'name', 'description', 'item_count', 'genome_build', 'update_time', 'deleted']
__init__(name=None, description=None, item_count=0, order_id=None, genome_build=None)

x.__init__(…) initializes x; see help(type(x)) for signature

add_library_dataset(library_dataset, genome_build=None)[source]
add_folder(folder)[source]
activatable_library_datasets
serialize(id_encoder, serialization_options)[source]
to_dict(view='collection', value_mapper=None)[source]

Return item dictionary.

library_path
parent_library
class galaxy.model.LibraryDataset(folder=None, order_id=None, name=None, info=None, library_dataset_dataset_association=None, **kwd)[source]

Bases: galaxy.model.RepresentById

upload_options = [('upload_file', 'Upload files'), ('upload_directory', 'Upload directory of files'), ('upload_paths', 'Upload files from filesystem paths'), ('import_from_history', 'Import datasets from your current history')]
__init__(folder=None, order_id=None, name=None, info=None, library_dataset_dataset_association=None, **kwd)

x.__init__(…) initializes x; see help(type(x)) for signature

set_library_dataset_dataset_association(ldda)[source]
get_info()[source]
set_info(info)[source]
info
get_name()[source]
set_name(name)[source]
name
display_name()[source]
serialize(id_encoder, serialization_options)[source]
to_dict(view='collection')[source]
class galaxy.model.LibraryDatasetDatasetAssociation(copied_from_history_dataset_association=None, copied_from_library_dataset_dataset_association=None, library_dataset=None, user=None, sa_session=None, **kwd)[source]

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

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

x.__init__(…) initializes x; see help(type(x)) for signature

to_history_dataset_association(target_history, parent_id=None, add_to_history=False)[source]
copy(parent_id=None, target_folder=None)[source]
clear_associated_files(metadata_safe=False, purge=False)[source]
get_access_roles(trans)[source]
get_manage_permissions_roles(trans)[source]
has_manage_permissions_roles(trans)[source]
serialize(id_encoder, serialization_options, for_link=False)[source]
to_dict(view='collection')[source]
class galaxy.model.ExtendedMetadata(data)[source]

Bases: galaxy.model.RepresentById

__init__(data)

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.ExtendedMetadataIndex(extended_metadata, path, value)[source]

Bases: galaxy.model.RepresentById

__init__(extended_metadata, path, value)

x.__init__(…) initializes x; see help(type(x)) for signature

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

Bases: galaxy.model.RepresentById

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

x.__init__(…) initializes x; see help(type(x)) for signature

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

Bases: galaxy.model.RepresentById

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

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.LibraryDatasetDatasetInfoAssociation(library_dataset_dataset_association, form_definition, info)[source]

Bases: galaxy.model.RepresentById

__init__(library_dataset_dataset_association, form_definition, info)

x.__init__(…) initializes x; see help(type(x)) for signature

inheritable
class galaxy.model.ValidationError(message=None, err_type=None, attributes=None)[source]

Bases: galaxy.model.RepresentById

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

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.DatasetToValidationErrorAssociation(dataset, validation_error)[source]

Bases: object

__init__(dataset, validation_error)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

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

Bases: galaxy.model.RepresentById

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

x.__init__(…) initializes x; see help(type(x)) for signature

clear(purge=False, delete_dataset=True)[source]
class galaxy.model.DatasetCollection(id=None, collection_type=None, populated=True, element_count=None)[source]

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

dict_collection_visible_keys = ['id', 'collection_type']
dict_element_visible_keys = ['id', 'collection_type']
populated_states = <galaxy.util.bunch.Bunch object>
__init__(id=None, collection_type=None, populated=True, element_count=None)

x.__init__(…) initializes x; see help(type(x)) for signature

dataset_states_and_extensions_summary
populated_optimized
populated
dataset_action_tuples
waiting_for_elements
mark_as_populated()[source]
handle_population_failed(message)[source]
finalize(collection_type_description)[source]
dataset_instances
dataset_elements
first_dataset_element
state
validate()[source]
copy(destination=None, element_destination=None)[source]
replace_failed_elements(replacements)[source]
set_from_dict(new_data)[source]
has_subcollections
serialize(id_encoder, serialization_options)[source]
class galaxy.model.DatasetCollectionInstance(collection=None, deleted=False)[source]

Bases: galaxy.model.HasName

__init__(collection=None, deleted=False)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

state
populated
dataset_instances
display_name()[source]
set_from_dict(new_data)[source]

Set object attributes to the values in dictionary new_data limiting to only those keys in dict_element_visible_keys.

Returns a dictionary of the keys, values that have been changed.

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

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

Associates a DatasetCollection with a History.

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

x.__init__(…) initializes x; see help(type(x)) for signature

history_content_type
content_type = u'dataset_collection'
type_id
job_source_type
job_source_id
to_hda_representative(multiple=False)[source]
serialize(id_encoder, serialization_options, for_link=False)[source]
to_dict(view='collection')[source]

Return item dictionary.

add_implicit_input_collection(name, history_dataset_collection)[source]
find_implicit_input_collection(name)[source]
copy(element_destination=None)[source]

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)[source]

Bases: galaxy.model.DatasetCollectionInstance, galaxy.model.RepresentById

Associates a DatasetCollection with a library folder.

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

x.__init__(…) initializes x; see help(type(x)) for signature

to_dict(view='collection')[source]
class galaxy.model.DatasetCollectionElement(id=None, collection=None, element=None, element_index=None, element_identifier=None)[source]

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

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

dict_collection_visible_keys = ['id', 'element_type', 'element_index', 'element_identifier']
dict_element_visible_keys = ['id', 'element_type', 'element_index', 'element_identifier']
UNINITIALIZED_ELEMENT = <object object>
__init__(id=None, collection=None, element=None, element_index=None, element_identifier=None)

x.__init__(…) initializes x; see help(type(x)) for signature

element_type
is_collection
element_object
dataset_instance
dataset
first_dataset_instance()[source]
dataset_instances
copy_to_collection(collection, destination=None, element_destination=None)[source]
serialize(id_encoder, serialization_options)[source]
class galaxy.model.Event(message=None, history=None, user=None, galaxy_session=None)[source]

Bases: galaxy.model.RepresentById

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

x.__init__(…) initializes x; see help(type(x)) for signature

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

Bases: galaxy.model.RepresentById

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

x.__init__(…) initializes x; see help(type(x)) for signature

add_history(history, association=None)[source]
get_disk_usage()[source]
set_disk_usage(bytes)[source]
total_disk_usage
class galaxy.model.GalaxySessionToHistoryAssociation(galaxy_session, history)[source]

Bases: galaxy.model.RepresentById

__init__(galaxy_session, history)

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.UCI[source]

Bases: object

__init__()[source]

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.StoredWorkflow[source]

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

dict_collection_visible_keys = ['id', 'name', 'published', 'deleted']
dict_element_visible_keys = ['id', 'name', 'published', 'deleted']
__init__()

x.__init__(…) initializes x; see help(type(x)) for signature

get_internal_version(version)[source]
show_in_tool_panel(user_id)[source]
copy_tags_from(target_user, source_workflow)[source]
to_dict(view='collection', value_mapper=None)[source]

Return item dictionary.

class galaxy.model.Workflow(uuid=None)[source]

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

dict_collection_visible_keys = ['name', 'has_cycles', 'has_errors']
dict_element_visible_keys = ['name', 'has_cycles', 'has_errors']
input_step_types = ['data_input', 'data_collection_input', 'parameter_input']
__init__(uuid=None)

x.__init__(…) initializes x; see help(type(x)) for signature

has_outputs_defined()[source]

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

to_dict(view='collection', value_mapper=None)[source]

Return item dictionary.

steps_by_id
step_by_index(order_index)[source]
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()[source]

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

log_str()[source]
class galaxy.model.WorkflowStep[source]

Bases: galaxy.model.RepresentById

__init__()

x.__init__(…) initializes x; see help(type(x)) for signature

tool_uuid
get_input(input_name)[source]
get_or_add_input(input_name)[source]
add_connection(input_name, output_name, output_step, input_subworkflow_step_index=None)[source]
input_connections
unique_workflow_outputs
content_id
input_connections_by_name
setup_input_connections_by_name()[source]
create_or_update_workflow_output(output_name, label, uuid)[source]
workflow_output_for(output_name)[source]
copy_to(copied_step, step_mapping)[source]
log_str()[source]
class galaxy.model.WorkflowStepInput(workflow_step)[source]

Bases: galaxy.model.RepresentById

default_merge_type = None
default_scatter_type = None
__init__(workflow_step)

x.__init__(…) initializes x; see help(type(x)) for signature

copy(copied_step)[source]
class galaxy.model.WorkflowStepConnection[source]

Bases: galaxy.model.RepresentById

NON_DATA_CONNECTION = '__NO_INPUT_OUTPUT_NAME__'
__init__()

x.__init__(…) initializes x; see help(type(x)) for signature

non_data_connection
input_name
input_step
input_step_id
copy()[source]
class galaxy.model.WorkflowOutput(workflow_step, output_name=None, label=None, uuid=None)[source]

Bases: galaxy.model.RepresentById

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

x.__init__(…) initializes x; see help(type(x)) for signature

copy(copied_step)[source]
class galaxy.model.StoredWorkflowUserShareAssociation[source]

Bases: galaxy.model.RepresentById

__init__()

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.StoredWorkflowMenuEntry[source]

Bases: galaxy.model.RepresentById

__init__()

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.WorkflowInvocation[source]

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

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__()

x.__init__(…) initializes x; see help(type(x)) for signature

create_subworkflow_invocation_for_step(step)[source]
attach_subworkflow_invocation_for_step(step, subworkflow_invocation)[source]
get_subworkflow_invocation_for_step(step)[source]
get_subworkflow_invocation_association_for_step(step)[source]
active

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

cancel()[source]
fail()[source]
step_states_by_step_id()[source]
step_invocations_by_step_id()[source]
step_invocation_for_step_id(step_id)[source]
static poll_unhandled_workflow_ids(sa_session)[source]
static poll_active_workflow_ids(sa_session, scheduler=None, handler=None)[source]
add_output(workflow_output, step, output_object)[source]
to_dict(view='collection', value_mapper=None, step_details=False, legacy_job_state=False)[source]

Return item dictionary.

update()
add_input(content, step_id)[source]
resource_parameters
has_input_for_step(step_id)[source]
set_handler(handler)[source]
log_str()[source]
class galaxy.model.WorkflowInvocationToSubworkflowInvocationAssociation[source]

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

dict_collection_visible_keys = ['id', 'workflow_step_id', 'workflow_invocation_id', 'subworkflow_invocation_id']
dict_element_visible_keys = ['id', 'workflow_step_id', 'workflow_invocation_id', 'subworkflow_invocation_id']
class galaxy.model.WorkflowInvocationStep[source]

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

dict_collection_visible_keys = ['id', 'update_time', 'job_id', 'workflow_step_id', 'state', 'action']
dict_element_visible_keys = ['id', 'update_time', 'job_id', 'workflow_step_id', 'state', 'action']
states = <galaxy.util.bunch.Bunch object>
update()[source]
is_new
add_output(output_name, output_object)[source]
jobs
to_dict(view='collection', value_mapper=None)[source]

Return item dictionary.

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

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

Workflow-related parameters not tied to steps or inputs.

dict_collection_visible_keys = ['id', 'name', 'value', 'type']
types = <galaxy.util.bunch.Bunch object>
__init__(name=None, value=None, type=None)

x.__init__(…) initializes x; see help(type(x)) for signature

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

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

Workflow step value parameters.

dict_collection_visible_keys = ['id', 'name', 'value', 'workflow_step_id']
__init__(workflow_step=None, name=None, value=None)

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.WorkflowRequestToInputDatasetAssociation[source]

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

Workflow step input dataset parameters.

dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_id', 'name']
class galaxy.model.WorkflowRequestToInputDatasetCollectionAssociation[source]

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

Workflow step input dataset collection parameters.

dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_collection_id', 'name']
class galaxy.model.WorkflowRequestInputStepParameter[source]

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

Workflow step parameter inputs.

dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'parameter_value']
class galaxy.model.WorkflowInvocationOutputDatasetAssociation[source]

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

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[source]

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

Represents links to output dataset collections for the workflow.

dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_collection_id', 'name']
class galaxy.model.WorkflowInvocationStepOutputDatasetAssociation[source]

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

Represents links to output datasets for the workflow.

dict_collection_visible_keys = ['id', 'workflow_invocation_step_id', 'dataset_id', 'output_name']
class galaxy.model.WorkflowInvocationStepOutputDatasetCollectionAssociation[source]

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

Represents links to output dataset collections for the workflow.

dict_collection_visible_keys = ['id', 'workflow_invocation_step_id', 'dataset_collection_id', 'output_name']
class galaxy.model.MetadataFile(dataset=None, name=None, uuid=None)[source]

Bases: galaxy.model.StorableObject, galaxy.model.RepresentById

__init__(dataset=None, name=None, uuid=None)

x.__init__(…) initializes x; see help(type(x)) for signature

file_name
serialize(id_encoder, serialization_options)[source]
class galaxy.model.FormDefinition(name=None, desc=None, fields=[], form_definition_current=None, form_type=None, layout=None)[source]

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

supported_field_types = [<class 'galaxy.util.form_builder.AddressField'>, <class 'galaxy.util.form_builder.CheckboxField'>, <class 'galaxy.util.form_builder.PasswordField'>, <class 'galaxy.util.form_builder.SelectField'>, <class 'galaxy.util.form_builder.TextArea'>, <class 'galaxy.util.form_builder.TextField'>, <class 'galaxy.util.form_builder.WorkflowField'>, <class 'galaxy.util.form_builder.WorkflowMappingField'>, <class 'galaxy.util.form_builder.HistoryField'>]
types = <galaxy.util.bunch.Bunch object>
dict_collection_visible_keys = ['id', 'name']
dict_element_visible_keys = ['id', 'name', 'desc', 'form_definition_current_id', 'fields', 'layout']
__init__(name=None, desc=None, fields=[], form_definition_current=None, form_type=None, layout=None)

x.__init__(…) initializes x; see help(type(x)) for signature

to_dict(user=None, values=None, security=None)[source]

Return item dictionary.

grid_fields(grid_index)[source]
class galaxy.model.FormDefinitionCurrent(form_definition=None)[source]

Bases: galaxy.model.RepresentById

__init__(form_definition=None)

x.__init__(…) initializes x; see help(type(x)) for signature

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

Bases: galaxy.model.RepresentById

__init__(form_def=None, content=None)

x.__init__(…) initializes x; see help(type(x)) for signature

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

Bases: galaxy.model.RepresentById

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

x.__init__(…) initializes x; see help(type(x)) for signature

to_dict(trans)[source]
class galaxy.model.PSAAssociation(server_url=None, handle=None, secret=None, issued=None, lifetime=None, assoc_type=None)[source]

Bases: social_core.storage.AssociationMixin, galaxy.model.RepresentById

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

x.__init__(…) initializes x; see help(type(x)) for signature

save()[source]
classmethod store(server_url, association)[source]

Create an Association instance

classmethod get(*args, **kwargs)[source]

Get an Association instance

classmethod remove(ids_to_delete)[source]

Remove an Association instance

class galaxy.model.PSACode(email, code)[source]

Bases: social_core.storage.CodeMixin, galaxy.model.RepresentById

sa_session = None
__init__(email, code)

x.__init__(…) initializes x; see help(type(x)) for signature

save()[source]
classmethod get_code(code)[source]
class galaxy.model.PSANonce(server_url, timestamp, salt)[source]

Bases: social_core.storage.NonceMixin, galaxy.model.RepresentById

sa_session = None
__init__(server_url, timestamp, salt)

x.__init__(…) initializes x; see help(type(x)) for signature

save()[source]
classmethod use(server_url, timestamp, salt)[source]

Create a Nonce instance

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

Bases: social_core.storage.PartialMixin, galaxy.model.RepresentById

sa_session = None
__init__(token, data, next_step, backend)

x.__init__(…) initializes x; see help(type(x)) for signature

save()[source]
classmethod load(token)[source]
classmethod destroy(token)[source]
class galaxy.model.UserAuthnzToken(provider, uid, extra_data=None, lifetime=None, assoc_type=None, user=None)[source]

Bases: social_core.storage.UserMixin, galaxy.model.RepresentById

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

x.__init__(…) initializes x; see help(type(x)) for signature

get_id_token(strategy)[source]
set_extra_data(extra_data=None)[source]
save()[source]
classmethod username_max_length()[source]

Return the max length for username

classmethod user_model()[source]

Return the user model

classmethod changed(user)[source]

The given user instance is ready to be saved

classmethod user_query()[source]
classmethod user_exists(*args, **kwargs)[source]

Return True/False if a User instance exists with the given arguments. Arguments are directly passed to filter() manager method.

classmethod get_username(user)[source]

Return the username for given user

classmethod create_user(*args, **kwargs)[source]

Create a user instance

classmethod get_user(pk)[source]

Return user instance for given id

classmethod get_users_by_email(email)[source]

Return users instances for given email address

classmethod get_social_auth(provider, uid)[source]

Return UserSocialAuth for given provider and uid

classmethod get_social_auth_for_user(user, provider=None, id=None)[source]

Return all the UserSocialAuth instances for given user

classmethod create_social_auth(user, uid, provider)[source]

Create a UserSocialAuth instance for given user

class galaxy.model.CustosAuthnzToken(user, external_user_id, provider, access_token, id_token, refresh_token, expiration_time, refresh_expiration_time)[source]

Bases: galaxy.model.RepresentById

__init__(user, external_user_id, provider, access_token, id_token, refresh_token, expiration_time, refresh_expiration_time)

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.CloudAuthz(user_id, provider, config, authn_id, description='')[source]

Bases: galaxy.model.RepresentById

__init__(user_id, provider, config, authn_id, description='')

x.__init__(…) initializes x; see help(type(x)) for signature

equals(user_id, provider, authn_id, config)[source]
class galaxy.model.Page[source]

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

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

x.__init__(…) initializes x; see help(type(x)) for signature

to_dict(view='element')[source]

Return item dictionary.

class galaxy.model.PageRevision[source]

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

dict_element_visible_keys = ['id', 'page_id', 'title', 'content']
__init__()

x.__init__(…) initializes x; see help(type(x)) for signature

to_dict(view='element')[source]

Return item dictionary.

class galaxy.model.PageUserShareAssociation[source]

Bases: galaxy.model.RepresentById

__init__()

x.__init__(…) initializes x; see help(type(x)) for signature

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

Bases: galaxy.model.RepresentById

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

x.__init__(…) initializes x; see help(type(x)) for signature

copy(user=None, title=None)[source]

Provide copy of visualization with only its latest revision.

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

Bases: galaxy.model.RepresentById

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

x.__init__(…) initializes x; see help(type(x)) for signature

copy(visualization=None)[source]

Returns a copy of this object.

class galaxy.model.VisualizationUserShareAssociation[source]

Bases: galaxy.model.RepresentById

__init__()

x.__init__(…) initializes x; see help(type(x)) for signature

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

Bases: galaxy.model.RepresentById

states = <galaxy.util.bunch.Bunch object>
terminal_states = ['error', 'done']
__init__(state=None, path=None, info=None, pid=None, socket=None, params=None)

x.__init__(…) initializes x; see help(type(x)) for signature

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

Bases: galaxy.model.RepresentById

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

x.__init__(…) initializes x; see help(type(x)) for signature

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

Bases: galaxy.util.dictifiable.Dictifiable

dict_collection_visible_keys = ['id', 'user_tname', 'user_value']
dict_element_visible_keys = ['id', 'user_tname', 'user_value']
__init__(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

copy(cls=None)[source]
class galaxy.model.HistoryTagAssociation(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)[source]

Bases: galaxy.model.ItemTagAssociation, galaxy.model.RepresentById

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

Bases: galaxy.model.ItemTagAssociation, galaxy.model.RepresentById

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

Bases: galaxy.model.ItemTagAssociation, galaxy.model.RepresentById

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

Bases: galaxy.model.ItemTagAssociation, galaxy.model.RepresentById

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

Bases: galaxy.model.ItemTagAssociation, galaxy.model.RepresentById

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

Bases: galaxy.model.ItemTagAssociation, galaxy.model.RepresentById

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

Bases: galaxy.model.ItemTagAssociation, galaxy.model.RepresentById

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

Bases: galaxy.model.ItemTagAssociation, galaxy.model.RepresentById

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

Bases: galaxy.model.ItemTagAssociation, galaxy.model.RepresentById

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

Bases: galaxy.model.ItemTagAssociation, galaxy.model.RepresentById

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

Bases: galaxy.model.ItemTagAssociation, galaxy.model.RepresentById

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

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.HistoryAnnotationAssociation[source]

Bases: galaxy.model.RepresentById

class galaxy.model.HistoryDatasetAssociationAnnotationAssociation[source]

Bases: galaxy.model.RepresentById

class galaxy.model.StoredWorkflowAnnotationAssociation[source]

Bases: galaxy.model.RepresentById

class galaxy.model.WorkflowStepAnnotationAssociation[source]

Bases: galaxy.model.RepresentById

class galaxy.model.PageAnnotationAssociation[source]

Bases: galaxy.model.RepresentById

class galaxy.model.VisualizationAnnotationAssociation[source]

Bases: galaxy.model.RepresentById

class galaxy.model.HistoryDatasetCollectionAssociationAnnotationAssociation[source]

Bases: galaxy.model.RepresentById

class galaxy.model.LibraryDatasetCollectionAnnotationAssociation[source]

Bases: galaxy.model.RepresentById

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

Bases: object

__init__(id=None, user=None, item=None, rating=0)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

set_item(item)[source]

Set association’s item.

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

Bases: galaxy.model.ItemRatingAssociation, galaxy.model.RepresentById

set_item(history)[source]

Set association’s item.

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

Bases: galaxy.model.ItemRatingAssociation, galaxy.model.RepresentById

set_item(history_dataset_association)[source]

Set association’s item.

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

Bases: galaxy.model.ItemRatingAssociation, galaxy.model.RepresentById

set_item(stored_workflow)[source]

Set association’s item.

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

Bases: galaxy.model.ItemRatingAssociation, galaxy.model.RepresentById

set_item(page)[source]

Set association’s item.

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

Bases: galaxy.model.ItemRatingAssociation, galaxy.model.RepresentById

set_item(visualization)[source]

Set association’s item.

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

Bases: galaxy.model.ItemRatingAssociation, galaxy.model.RepresentById

set_item(dataset_collection)[source]

Set association’s item.

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

Bases: galaxy.model.ItemRatingAssociation, galaxy.model.RepresentById

set_item(dataset_collection)[source]

Set association’s item.

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

Bases: galaxy.model.RepresentById

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

x.__init__(…) initializes x; see help(type(x)) for signature

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

Bases: galaxy.model.RepresentById

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

x.__init__(…) initializes x; see help(type(x)) for signature

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

Bases: galaxy.model.RepresentById

__init__(name=None, value=None)

x.__init__(…) initializes x; see help(type(x)) for signature

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

Bases: galaxy.model.RepresentById

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

x.__init__(…) initializes x; see help(type(x)) for signature

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

Bases: galaxy.model.RepresentById

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

x.__init__(…) initializes x; see help(type(x)) for signature

galaxy.model.copy_list(lst, *args, **kwds)[source]

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)[source]

Bases: galaxy.util.bunch.Bunch

__init__(model_modules, engine)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

Session

For backward compat., deprecated.

galaxy.model.base.versioned_objects(iter)[source]
galaxy.model.base.versioned_session(session)[source]

galaxy.model.custom_types module

class galaxy.model.custom_types.SafeJsonEncoder(skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, encoding='utf-8', default=None)[source]

Bases: json.encoder.JSONEncoder

default(obj)[source]

Implement this method in a subclass such that it returns a serializable object for o, or calls the base implementation (to raise a TypeError).

For example, to support arbitrary iterators, you could implement default like this:

def default(self, o):
    try:
        iterable = iter(o)
    except TypeError:
        pass
    else:
        return list(iterable)
    # Let the base class default method raise the TypeError
    return JSONEncoder.default(self, o)
class galaxy.model.custom_types.GalaxyLargeBinary(length=None)[source]

Bases: sqlalchemy.sql.sqltypes.LargeBinary

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

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)[source]

Receive a bound parameter value to be converted.

Subclasses override this method to return the value that should be passed along to the underlying TypeEngine object, and from there to the DBAPI execute() method.

The operation could be anything desired to perform custom behavior, such as transforming or serializing data. This could also be used as a hook for validating logic.

This operation should be designed with the reverse operation in mind, which would be the process_result_value method of this class.

Parameters:
  • value – Data to operate upon, of any type expected by this method in the subclass. Can be None.
  • dialect – the Dialect in use.
process_result_value(value, dialect)[source]

Receive a result-row column value to be converted.

Subclasses should implement this method to operate on data fetched from the database.

Subclasses override this method to return the value that should be passed back to the application, given a value that is already processed by the underlying TypeEngine object, originally from the DBAPI cursor method fetchone() or similar.

The operation could be anything desired to perform custom behavior, such as transforming or serializing data. This could also be used as a hook for validating logic.

Parameters:
  • value – Data to operate upon, of any type expected by this method in the subclass. Can be None.
  • dialect – the Dialect in use.

This operation should be designed to be reversible by the “process_bind_param” method of this class.

load_dialect_impl(dialect)[source]

Return a TypeEngine object corresponding to a dialect.

This is an end-user override hook that can be used to provide differing types depending on the given dialect. It is used by the TypeDecorator implementation of type_engine() to help determine what type should ultimately be returned for a given TypeDecorator.

By default returns self.impl.

copy_value(value)[source]
compare_values(x, y)[source]

Given two values, compare them for equality.

By default this calls upon TypeEngine.compare_values() of the underlying “impl”, which in turn usually uses the Python equals operator ==.

This function is used by the ORM to compare an original-loaded value with an intercepted “changed” value, to determine if a net change has occurred.

class galaxy.model.custom_types.MutationObj[source]

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)[source]

Given a value, coerce it into the target type.

Can be overridden by custom subclasses to coerce incoming data into a particular type.

By default, raises ValueError.

This method is called in different scenarios depending on if the parent class is of type Mutable or of type MutableComposite. In the case of the former, it is called for both attribute-set operations as well as during ORM loading operations. For the latter, it is only called during attribute-set operations; the mechanics of the composite() construct handle coercion during load operations.

Parameters:
  • key – string name of the ORM-mapped attribute being set.
  • value – the incoming value.
Returns:

the method should return the coerced value, or raise ValueError if the coercion cannot be completed.

class galaxy.model.custom_types.MutationDict[source]

Bases: galaxy.model.custom_types.MutationObj, dict

classmethod coerce(key, value)[source]

Convert plain dictionary to MutationDict

class galaxy.model.custom_types.MutationList[source]

Bases: galaxy.model.custom_types.MutationObj, list

classmethod coerce(key, value)[source]

Convert plain list to MutationList

append(value)[source]

L.append(object) – append object to end

insert(idx, value)[source]

L.insert(index, object) – insert object before index

extend(values)[source]

L.extend(iterable) – extend list by appending elements from the iterable

pop([index]) → item -- remove and return item at index (default last).[source]

Raises IndexError if list is empty or index is out of range.

remove(value)[source]

L.remove(value) – remove first occurrence of value. Raises ValueError if the value is not present.

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

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)[source]

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)[source]

Receive a bound parameter value to be converted.

Subclasses override this method to return the value that should be passed along to the underlying TypeEngine object, and from there to the DBAPI execute() method.

The operation could be anything desired to perform custom behavior, such as transforming or serializing data. This could also be used as a hook for validating logic.

This operation should be designed with the reverse operation in mind, which would be the process_result_value method of this class.

Parameters:
  • value – Data to operate upon, of any type expected by this method in the subclass. Can be None.
  • dialect – the Dialect in use.
process_result_value(value, dialect)[source]

Receive a result-row column value to be converted.

Subclasses should implement this method to operate on data fetched from the database.

Subclasses override this method to return the value that should be passed back to the application, given a value that is already processed by the underlying TypeEngine object, originally from the DBAPI cursor method fetchone() or similar.

The operation could be anything desired to perform custom behavior, such as transforming or serializing data. This could also be used as a hook for validating logic.

Parameters:
  • value – Data to operate upon, of any type expected by this method in the subclass. Can be None.
  • dialect – the Dialect in use.

This operation should be designed to be reversible by the “process_bind_param” method of this class.

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

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)[source]

Return a TypeEngine object corresponding to a dialect.

This is an end-user override hook that can be used to provide differing types depending on the given dialect. It is used by the TypeDecorator implementation of type_engine() to help determine what type should ultimately be returned for a given TypeDecorator.

By default returns self.impl.

process_bind_param(value, dialect)[source]

Receive a bound parameter value to be converted.

Subclasses override this method to return the value that should be passed along to the underlying TypeEngine object, and from there to the DBAPI execute() method.

The operation could be anything desired to perform custom behavior, such as transforming or serializing data. This could also be used as a hook for validating logic.

This operation should be designed with the reverse operation in mind, which would be the process_result_value method of this class.

Parameters:
  • value – Data to operate upon, of any type expected by this method in the subclass. Can be None.
  • dialect – the Dialect in use.
process_result_value(value, dialect)[source]

Receive a result-row column value to be converted.

Subclasses should implement this method to operate on data fetched from the database.

Subclasses override this method to return the value that should be passed back to the application, given a value that is already processed by the underlying TypeEngine object, originally from the DBAPI cursor method fetchone() or similar.

The operation could be anything desired to perform custom behavior, such as transforming or serializing data. This could also be used as a hook for validating logic.

Parameters:
  • value – Data to operate upon, of any type expected by this method in the subclass. Can be None.
  • dialect – the Dialect in use.

This operation should be designed to be reversible by the “process_bind_param” method of this class.

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

Bases: sqlalchemy.sql.type_api.TypeDecorator

impl

alias of sqlalchemy.sql.sqltypes.String

process_bind_param(value, dialect)[source]

Automatically truncate string values

galaxy.model.item_attrs module

class galaxy.model.item_attrs.UsesItemRatings[source]

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)[source]

Returns the average rating for an item.

rate_item(db_session, user, item, rating, webapp_model=None)[source]

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

get_user_item_rating(db_session, user, item, webapp_model=None)[source]

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

class galaxy.model.item_attrs.UsesAnnotations[source]

Bases: object

Mixin for getting and setting item annotations.

get_item_annotation_str(db_session, user, item)[source]
get_item_annotation_obj(db_session, user, item)[source]
add_item_annotation(db_session, user, item, annotation)[source]
delete_item_annotation(db_session, user, item)[source]
copy_item_annotation(db_session, source_user, source_item, target_user, target_item)[source]

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

galaxy.model.item_attrs.get_foreign_key(source_class, target_class)[source]

Returns foreign key in source class that references target class.

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)[source]
galaxy.model.mapping.tag_mapping(tag_association_class, backref_name)[source]
galaxy.model.mapping.annotation_mapping(annotation_class, **kwds)[source]
galaxy.model.mapping.rating_mapping(rating_class, **kwds)[source]
galaxy.model.mapping.db_next_hid(self)[source]

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)[source]

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)[source]

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)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

classmethod process(element)[source]
class galaxy.model.metadata.MetadataCollection(parent)[source]

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)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

get_parent()[source]
set_parent(parent)[source]
parent
spec
get(key, default=None)[source]
items()[source]
remove_key(name)[source]
element_is_set(name)[source]
get_metadata_parameter(name, **kwd)[source]
make_dict_copy(to_copy)[source]

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)[source]
to_JSON_dict(filename=None)[source]
class galaxy.model.metadata.MetadataSpecCollection(dict=None)[source]

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)[source]
append(item)[source]
iter()[source]
class galaxy.model.metadata.MetadataParameter(spec)[source]

Bases: object

__init__(spec)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

get_field(value=None, context=None, other_values=None, **kwd)[source]
to_string(value)[source]
to_safe_string(value)[source]
make_copy(value, target_context=None, source_context=None)[source]
classmethod marshal(value)[source]

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

validate(value)[source]

Throw an exception if the value is invalid.

unwrap(form_value)[source]

Turns a value into its storable form.

wrap(value, session)[source]

Turns a value into its usable form.

from_external_value(value, parent)[source]

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

to_external_value(value)[source]

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)[source]

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)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

get(name, default=None)[source]
wrap(value, session)[source]

Turns a stored value into its usable form.

unwrap(value)[source]

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)[source]

Bases: galaxy.model.metadata.MetadataParameter

__init__(spec)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

to_string(value)[source]
get_field(value=None, context=None, other_values=None, values=None, **kwd)[source]
wrap(value, session)[source]

Turns a value into its usable form.

classmethod marshal(value)[source]

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

class galaxy.model.metadata.DBKeyParameter(spec)[source]

Bases: galaxy.model.metadata.SelectParameter

get_field(value=None, context=None, other_values=None, values=None, **kwd)[source]
class galaxy.model.metadata.RangeParameter(spec)[source]

Bases: galaxy.model.metadata.SelectParameter

__init__(spec)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

get_field(value=None, context=None, other_values=None, values=None, **kwd)[source]
classmethod marshal(value)[source]

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

class galaxy.model.metadata.ColumnParameter(spec)[source]

Bases: galaxy.model.metadata.RangeParameter

get_field(value=None, context=None, other_values=None, values=None, **kwd)[source]
class galaxy.model.metadata.ColumnTypesParameter(spec)[source]

Bases: galaxy.model.metadata.MetadataParameter

to_string(value)[source]
class galaxy.model.metadata.ListParameter(spec)[source]

Bases: galaxy.model.metadata.MetadataParameter

to_string(value)[source]
class galaxy.model.metadata.DictParameter(spec)[source]

Bases: galaxy.model.metadata.MetadataParameter

to_string(value)[source]
to_safe_string(value)[source]
class galaxy.model.metadata.PythonObjectParameter(spec)[source]

Bases: galaxy.model.metadata.MetadataParameter

to_string(value)[source]
get_field(value=None, context=None, other_values=None, **kwd)[source]
classmethod marshal(value)[source]

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

class galaxy.model.metadata.FileParameter(spec)[source]

Bases: galaxy.model.metadata.MetadataParameter

to_string(value)[source]
to_safe_string(value)[source]
get_field(value=None, context=None, other_values=None, **kwd)[source]
wrap(value, session)[source]

Turns a value into its usable form.

make_copy(value, target_context, source_context)[source]
classmethod marshal(value)[source]

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

from_external_value(value, parent, path_rewriter=None)[source]

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

to_external_value(value)[source]

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

new_file(dataset=None, **kwds)[source]
class galaxy.model.metadata.MetadataTempFile(**kwds)[source]

Bases: object

tmp_dir = 'database/tmp'
__init__(**kwds)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

file_name
to_JSON()[source]
classmethod from_JSON(json_dict)[source]
classmethod is_JSONified_value(value)[source]
classmethod cleanup_from_JSON_dict_filename(filename)[source]

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)[source]

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)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.search.ViewQueryBaseClass[source]

Bases: object

FIELDS = {}
VIEW_NAME = 'undefined'
__init__()[source]

x.__init__(…) initializes x; see help(type(x)) for signature

decode_query_ids(trans, conditional)[source]
filter(left, operator, right)[source]
search(trans)[source]
get_results(force_query=False)[source]
galaxy.model.search.library_extended_metadata_filter(view, left, operator, right)[source]
galaxy.model.search.ldda_parent_library_filter(item, left, operator, right)[source]
class galaxy.model.search.LibraryDatasetDatasetView[source]

Bases: galaxy.model.search.ViewQueryBaseClass

VIEW_NAME = 'library_dataset_dataset'
FIELDS = {'data_type': <galaxy.model.search.ViewField object>, 'deleted': <galaxy.model.search.ViewField object>, 'extended_metadata': <galaxy.model.search.ViewField object>, 'id': <galaxy.model.search.ViewField object>, 'name': <galaxy.model.search.ViewField object>, 'parent_library_id': <galaxy.model.search.ViewField object>}
search(trans)[source]
class galaxy.model.search.LibraryView[source]

Bases: galaxy.model.search.ViewQueryBaseClass

VIEW_NAME = 'library'
FIELDS = {'deleted': <galaxy.model.search.ViewField object>, 'id': <galaxy.model.search.ViewField object>, 'name': <galaxy.model.search.ViewField object>}
search(trans)[source]
galaxy.model.search.library_folder_parent_library_id_filter(item, left, operator, right)[source]
galaxy.model.search.library_path_filter(item, left, operator, right)[source]
class galaxy.model.search.LibraryFolderView[source]

Bases: galaxy.model.search.ViewQueryBaseClass

VIEW_NAME = 'library_folder'
FIELDS = {'id': <galaxy.model.search.ViewField object>, 'library_path': <galaxy.model.search.ViewField object>, 'name': <galaxy.model.search.ViewField object>, 'parent_id': <galaxy.model.search.ViewField object>, 'parent_library_id': <galaxy.model.search.ViewField object>}
search(trans)[source]
galaxy.model.search.library_dataset_name_filter(item, left, operator, right)[source]
class galaxy.model.search.LibraryDatasetView[source]

Bases: galaxy.model.search.ViewQueryBaseClass

VIEW_NAME = 'library_dataset'
FIELDS = {'folder_id': <galaxy.model.search.ViewField object>, 'id': <galaxy.model.search.ViewField object>, 'name': <galaxy.model.search.ViewField object>}
search(trans)[source]
class galaxy.model.search.ToolView[source]

Bases: galaxy.model.search.ViewQueryBaseClass

VIEW_NAME = 'tool'
FIELDS = {'id': <galaxy.model.search.ViewField object>, 'tool_id': <galaxy.model.search.ViewField object>}
search(trans)[source]
galaxy.model.search.history_dataset_handle_tag(view, left, operator, right)[source]
galaxy.model.search.history_dataset_extended_metadata_filter(view, left, operator, right)[source]
class galaxy.model.search.HistoryDatasetView[source]

Bases: galaxy.model.search.ViewQueryBaseClass

DOMAIN = 'history_dataset'
FIELDS = {'copied_from_hda_id': <galaxy.model.search.ViewField object>, 'copied_from_ldda_id': <galaxy.model.search.ViewField object>, 'deleted': <galaxy.model.search.ViewField object>, 'extended_metadata': <galaxy.model.search.ViewField object>, 'history_id': <galaxy.model.search.ViewField object>, 'id': <galaxy.model.search.ViewField object>, 'name': <galaxy.model.search.ViewField object>, 'tag': <galaxy.model.search.ViewField object>}
search(trans)[source]
galaxy.model.search.history_handle_tag(view, left, operator, right)[source]
galaxy.model.search.history_handle_annotation(view, left, operator, right)[source]
class galaxy.model.search.HistoryView[source]

Bases: galaxy.model.search.ViewQueryBaseClass

DOMAIN = 'history'
FIELDS = {'annotation': <galaxy.model.search.ViewField object>, 'deleted': <galaxy.model.search.ViewField object>, 'id': <galaxy.model.search.ViewField object>, 'name': <galaxy.model.search.ViewField object>, 'tag': <galaxy.model.search.ViewField object>}
search(trans)[source]
galaxy.model.search.workflow_tag_handler(view, left, operator, right)[source]
class galaxy.model.search.WorkflowView[source]

Bases: galaxy.model.search.ViewQueryBaseClass

DOMAIN = 'workflow'
FIELDS = {'deleted': <galaxy.model.search.ViewField object>, 'id': <galaxy.model.search.ViewField object>, 'name': <galaxy.model.search.ViewField object>, 'tag': <galaxy.model.search.ViewField object>}
search(trans)[source]
galaxy.model.search.job_param_filter(view, left, operator, right)[source]
galaxy.model.search.job_input_hda_filter(view, left, operator, right)[source]
galaxy.model.search.job_input_ldda_filter(view, left, operator, right)[source]
galaxy.model.search.job_output_hda_filter(view, left, operator, right)[source]
class galaxy.model.search.JobView[source]

Bases: galaxy.model.search.ViewQueryBaseClass

DOMAIN = 'job'
FIELDS = {'input_hda': <galaxy.model.search.ViewField object>, 'input_ldda': <galaxy.model.search.ViewField object>, 'output_hda': <galaxy.model.search.ViewField object>, 'param': <galaxy.model.search.ViewField object>, 'state': <galaxy.model.search.ViewField object>, 'tool_name': <galaxy.model.search.ViewField object>}
search(trans)[source]
class galaxy.model.search.PageView[source]

Bases: galaxy.model.search.ViewQueryBaseClass

DOMAIN = 'page'
FIELDS = {'deleted': <galaxy.model.search.ViewField object>, 'id': <galaxy.model.search.ViewField object>, 'slug': <galaxy.model.search.ViewField object>, 'title': <galaxy.model.search.ViewField object>}
search(trans)[source]
class galaxy.model.search.PageRevisionView[source]

Bases: galaxy.model.search.ViewQueryBaseClass

DOMAIN = 'page_revision'
FIELDS = {'id': <galaxy.model.search.ViewField object>, 'page_id': <galaxy.model.search.ViewField object>, 'title': <galaxy.model.search.ViewField object>}
search(trans)[source]
class galaxy.model.search.GalaxyQuery(field_list, table_name, conditional)[source]

Bases: object

This class represents a data structure of a compiled GQL query

__init__(field_list, table_name, conditional)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

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

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)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.search.GalaxyQueryAnd(left, right)[source]

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)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

exception galaxy.model.search.GalaxyParseError[source]

Bases: exceptions.Exception

class galaxy.model.search.SearchQuery(view, query)[source]

Bases: object

__init__(view, query)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

decode_query_ids(trans)[source]
process(trans)[source]
item_to_api_value(item)[source]
class galaxy.model.search.GalaxySearchEngine[source]

Bases: object

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

__init__()[source]

x.__init__(…) initializes x; see help(type(x)) for signature

query(query_text)[source]

galaxy.model.util module

Utility helpers related to the model

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

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.