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galaxy.managers package

Classes that manage resources (models, tools, etc.) by using the current Transaction.

Encapsulates the intersection of trans (or trans.sa_session), models, and Controllers.

Responsibilities:

• model operations that involve the trans/sa_session (CRUD)
• security: ownership, accessibility
• common aspect-oriented operations via new mixins: sharable, annotatable, tagable, ratable

Not responsible for:

• encoding/decoding ids
• any http gobblygook
• formatting of returned data (always python structures)
• formatting of raised errors

The goal is to have Controllers only handle:

• query-string/payload parsing and encoding/decoding ids
• http
• return formatting
• control, improve namespacing in Controllers
• DRY for Controller ops (define here - use in both UI/API Controllers)

In other words, ‘Business logic’ independent of web transactions/user context (trans) should be pushed into models - but logic that requires the context trans should be placed under this module.

Submodules

galaxy.managers.annotatable module

Mixins for Annotatable model managers and serializers.

class galaxy.managers.annotatable.AnnotatableManagerMixin

Bases: object

annotation_assoc = None

class of AnnotationAssociation (e.g. HistoryAnnotationAssociation)

annotation(item)

Return the annotation string made by the item’s owner or None if there is no annotation.

annotate(item, annotation, user=None, flush=True)

Create a new annotation on item or delete the existing if annotation is None.

class galaxy.managers.annotatable.AnnotatableSerializerMixin

Bases: object

add_serializers()

serialize_annotation(item, key, user=None, **context)

Get and serialize an item’s annotation.

class galaxy.managers.annotatable.AnnotatableDeserializerMixin

Bases: object

add_deserializers()

deserialize_annotation(item, key, val, user=None, **context)

Make sure val is a valid annotation and assign it, deleting any existing if val is None.

class galaxy.managers.annotatable.AnnotatableFilterMixin

Bases: object

filter_annotation_contains(item, val)

Test whether val is in the owner’s annotation.

galaxy.managers.api_keys module

class galaxy.managers.api_keys.ApiKeyManager(app)

Bases: object

__init__(app)

create_api_key(user)

get_or_create_api_key(user)

galaxy.managers.base module

Keeps the older BaseController security and fetching methods and also defines a base ModelManager, ModelSerializer, and ModelDeserializer.

ModelManagers are used for operations on models that occur outside the scope of a single model object, such as:

• object creation
• object lookup
• interactions between 2+ objects of different model classes

(Since these were to replace model Mixins from web/framework/base/controller.py the rule of thumb used there also generally has been applied here: if it uses the trans or sa_session, put it in a manager and not the model.)

ModelSerializers allow flexible conversion of model objects to dictionaries. They control what keys are sent, how values are simplified, can remap keys, and allow both predefined and user controlled key sets.

ModelDeserializers control how a model validates and process an incoming attribute change to a model object.

galaxy.managers.base.security_check(trans, item, check_ownership=False, check_accessible=False)

Security checks for an item: checks if (a) user owns item or (b) item is accessible to user. This is a generic method for dealing with objects uniformly from the older controller mixin code - however whenever possible the managers for a particular model should be used to perform security checks.

galaxy.managers.base.get_class(class_name)

Returns the class object that a string denotes. Without this method, we’d have to do eval(<class_name>).

galaxy.managers.base.decode_id(app, id)

galaxy.managers.base.get_object(trans, id, class_name, check_ownership=False, check_accessible=False, deleted=None)

Convenience method to get a model object with the specified checks. This is a generic method for dealing with objects uniformly from the older controller mixin code - however whenever possible the managers for a particular model should be used to load objects.

galaxy.managers.base.munge_lists(listA, listB)

Combine two lists into a single list.

(While allowing them to be None, non-lists, or lists.)

class galaxy.managers.base.ModelManager(app)

Bases: object

Base class for all model/resource managers.

Provides common queries and CRUD operations as a (hopefully) light layer over the ORM.

model_class

alias of __builtin__.object

foreign_key_name = None

__init__(app)

session()

query(eagerloads=True, **kwargs)

Return a basic query from model_class, filters, order_by, and limit and offset.

Set eagerloads to False to disable them for this query.

one(**kwargs)

Sends kwargs to build the query and returns one and only one model.

by_id(id, **kwargs)

Gets a model by primary id.

list(filters=None, order_by=None, limit=None, offset=None, **kwargs)

Returns all objects matching the given filters

by_ids(ids, filters=None, **kwargs)

Returns an in-order list of models with the matching ids in ids.

create(flush=True, *args, **kwargs)

Generically create a new model.

copy(item, **kwargs)

Clone or copy an item.

update(item, new_values, flush=True, **kwargs)

Given a dictionary of new values, update item and return it.

..note: NO validation or deserialization occurs here.

associate(associate_with, item, foreign_key_name=None)

Generically associate item with associate_with based on foreign_key_name.

query_associated(associated_model_class, item, foreign_key_name=None)

Generically query other items that have been associated with this item.

class galaxy.managers.base.HasAModelManager(app, manager=None, **kwargs)

Bases: object

Mixin used where serializers, deserializers, filter parsers, etc. need some functionality around the model they’re mainly concerned with and would perform that functionality with a manager.

model_manager_class = None

the class used to create this serializer’s generically accessible model_manager

__init__(app, manager=None, **kwargs)

manager

Return an appropriate manager if it exists, instantiate if not.

exception galaxy.managers.base.ModelSerializingError(err_msg=None, type='info', **extra_error_info)

Bases: galaxy.exceptions.InternalServerError

Thrown when request model values can’t be serialized

exception galaxy.managers.base.ModelDeserializingError(err_msg=None, type='info', **extra_error_info)

Bases: galaxy.exceptions.ObjectAttributeInvalidException

Thrown when an incoming value isn’t usable by the model (bad type, out of range, etc.)

exception galaxy.managers.base.SkipAttribute

Bases: exceptions.Exception

Raise this inside a serializer to prevent the returned dictionary from having a the associated key or value for this attribute.

class galaxy.managers.base.ModelSerializer(app, **kwargs)

Bases: galaxy.managers.base.HasAModelManager

Turns models into JSONable dicts.

Maintains a map of requestable keys and the Callable() serializer functions that should be called for those keys. E.g. { ‘x’ : lambda item, key: item.x, … }

Note: if a key to serialize is not listed in the Serializer.serializable_keyset or serializers, it will not be returned.

To serialize call:

my_serializer = MySerializer( app ) … keys_to_serialize = [ ‘id’, ‘name’, ‘attr1’, ‘attr2’, … ] item_dict = MySerializer.serialize( my_item, keys_to_serialize )

static url_for(*args, **kargs)

‘service’ to use for getting urls - use class var to allow overriding when testing

__init__(app, **kwargs)

Set up serializer map, any additional serializable keys, and views here.

add_serializers()

Register a map of attribute keys -> serializing functions that will serialize the attribute.

add_view(view_name, key_list, include_keys_from=None)

Add the list of serializable attributes key_list to the serializer’s view dictionary under the key view_name.

If include_keys_from is a proper view name, extend key_list by the list in that view.

serialize(item, keys, **context)

Serialize the model item to a dictionary.

Given model item and the list keys, create and return a dictionary built from each key in keys that also exists in serializers and values of calling the keyed/named serializers on item.

skip(msg='skipped')

To be called from inside a serializer to skip it.

Handy for config checks, information hiding, etc.

default_serializer(item, key, **context)

Serialize the item’s attribute named key.

serialize_date(item, key, **context)

Serialize a date attribute of item.

serialize_id(item, key, **context)

Serialize an id attribute of item.

serialize_type_id(item, key, **context)

Serialize an type-id for item.

serialize_to_view(item, view=None, keys=None, default_view=None, **context)

Use a predefined list of keys (the string view) and any additional keys listed in keys.

The combinations can be:

view only: return those keys listed in the named view keys only: return those keys listed no view or keys: use the default_view if any view and keys: combine both into one list of keys

class galaxy.managers.base.ModelDeserializer(app, validator=None, **kwargs)

Bases: galaxy.managers.base.HasAModelManager

An object that converts an incoming serialized dict into values that can be directly assigned to an item’s attributes and assigns them.

__init__(app, validator=None, **kwargs)

Set up deserializers and validator.

add_deserializers()

Register a map of attribute keys -> functions that will deserialize data into attributes to be assigned to the item.

deserialize(item, data, flush=True, **context)

Convert an incoming serialized dict into values that can be directly assigned to an item’s attributes and assign them

default_deserializer(item, key, val, **context)

If the incoming val is different than the item value change it and, in either case, return the value.

deserialize_basestring(item, key, val, convert_none_to_empty=False, **context)

deserialize_bool(item, key, val, **context)

deserialize_int(item, key, val, min=None, max=None, **context)

deserialize_genome_build(item, key, val, **context)

Make sure val is a valid dbkey and assign it.

class galaxy.managers.base.ModelValidator(app, *args, **kwargs)

Bases: galaxy.managers.base.HasAModelManager

An object that inspects a dictionary (generally meant to be a set of new/updated values for the model) and raises an error if a value is not acceptable.

__init__(app, *args, **kwargs)

type(key, val, types)

Check val against the type (or tuple of types) in types.

Raises:exceptions.RequestParameterInvalidException – if not an instance.

basestring(key, val)

bool(key, val)

int(key, val)

nullable_basestring(key, val)

Must be a basestring or None.

int_range(key, val, min=None, max=None)

Must be a int between min and max.

basestring_list(key, val)

Must be a list of basestrings.

genome_build(key, val)

Must be a valid base_string.

Note: no checking against installation’s ref list is done as many data sources consider this an open field.

class galaxy.managers.base.ModelFilterParser(app, **kwargs)

Bases: galaxy.managers.base.HasAModelManager

Converts string tuples (partially converted query string params) of attr, op, val into either:

• ORM based filters (filters that can be applied by the ORM at the SQL level) or
• functional filters (filters that use derived values or values not within the SQL tables)

These filters can then be applied to queries.

This abstraction allows ‘smarter’ application of limit and offset at either the SQL level or the generator/list level based on the presence of functional filters. In other words, if no functional filters are present, limit and offset may be applied at the SQL level. If functional filters are present, limit and offset need to applied at the list level.

These might be safely be replaced in the future by creating SQLAlchemy hybrid properties or more thoroughly mapping derived values.

model_class = None

model class

__init__(app, **kwargs)

Set up serializer map, any additional serializable keys, and views here.

date_string_re = None

regex for testing/dicing iso8601 date strings, with optional time and ms, but allowing only UTC timezone

fn_filter_parsers = None

dictionary containing parsing data for functional filters - applied after a query is made

parse_filters(filter_tuple_list)

Parse string 3-tuples (attr, op, val) into orm or functional filters.

parse_filter(attr, op, val)

Attempt to parse filter as a custom/fn filter, then an orm filter, and if neither work - raise an error.

Raises:exceptions.RequestParameterInvalidException – if no functional or orm filter can be parsed.

UNDERSCORED_OPS = ('lt', 'le', 'eq', 'ne', 'ge', 'gt')

these are the easier/shorter string equivalents to the python operator fn names that need ‘__’ around them

string_standard_ops(key)

parse_bool(bool_string)

Parse a boolean from a string.

parse_id_list(id_list_string, sep=', ')

Split id_list_string at sep.

parse_int_list(int_list_string, sep=', ')

Split int_list_string at sep and parse as ints.

parse_date(date_string)

Reformats a string containing either seconds from epoch or an iso8601 formated date string into a new date string usable within a filter query.

Seconds from epoch can be a floating point value as well (i.e containing ms).

galaxy.managers.citations module

class galaxy.managers.citations.CitationsManager(app)

Bases: object

__init__(app)

citations_for_tool(tool)

citations_for_tool_ids(tool_ids)

parse_citation(citation_elem, tool_directory)

class galaxy.managers.citations.DoiCache(config)

Bases: object

__init__(config)

get_bibtex(doi)

galaxy.managers.citations.parse_citation(elem, directory, citation_manager)

Parse an abstract citation entry from the specified XML element. The directory parameter should be used to find external files for this citation.

class galaxy.managers.citations.CitationCollection

Bases: object

__init__()

add(new_citation)

class galaxy.managers.citations.BaseCitation

Bases: object

to_dict(citation_format)

equals(other_citation)

has_doi()

class galaxy.managers.citations.BibtexCitation(elem, directory, citation_manager)

Bases: galaxy.managers.citations.BaseCitation

__init__(elem, directory, citation_manager)

to_bibtex()

class galaxy.managers.citations.DoiCitation(elem, directory, citation_manager)

Bases: galaxy.managers.citations.BaseCitation

BIBTEX_UNSET = <object object>

__init__(elem, directory, citation_manager)

has_doi()

doi()

to_bibtex()

galaxy.managers.cloud module

Manager and serializer for cloud-based storages.

class galaxy.managers.cloud.CloudManager(app, *args, **kwargs)

Bases: galaxy.managers.sharable.SharableModelManager

model_class

alias of galaxy.model.History

__init__(app, *args, **kwargs)

static configure_provider(provider, credentials)

Given a provider name and required credentials, it configures and returns a cloudbridge connection to the provider.

Parameters:provider (string) – the name of cloud-based resource provided. A list of supported providers is given in

SUPPORTED_PROVIDERS variable.

Parameters:credentials (dict) – a dictionary containing all the credentials required to authenticated to the

specified provider.

Return type:provider specific, e.g., cloudbridge.cloud.providers.aws.provider.AWSCloudProvider for AWS. Returns:a cloudbridge connection to the specified provider.

get(trans, history_id, bucket_name, objects, authz_id, input_args=None)

Implements the logic of getting a file from a cloud-based storage (e.g., Amazon S3) and persisting it as a Galaxy dataset.

This manager does NOT require use credentials, instead, it uses a more secure method, which leverages CloudAuthz (https://github.com/galaxyproject/cloudauthz) and automatically requests temporary credentials to access the defined resources.

Parameters:

• trans (galaxy.web.framework.webapp.GalaxyWebTransaction) – Galaxy web transaction
• history_id (string) – the (decoded) id of history to which the object should be received to.
• bucket_name (string) – the name of a bucket from which data should be fetched (e.g., a bucket name on AWS S3).
• objects (list of string) – the name of objects to be fetched.
• authz_id (int) – the ID of CloudAuthz to be used for authorizing access to the resource provider. You may get a list of the defined authorizations sending GET to /api/cloud/authz. Also, you can POST to /api/cloud/authz to define a new authorization.
• input_args (dict) – a [Optional] a dictionary of input parameters: dbkey, file_type, space_to_tab, to_posix_lines (see galaxy/webapps/galaxy/api/cloud.py)

Return type:

list of galaxy.model.Dataset

Returns:

a list of datasets created for the fetched files.

send(trans, history_id, bucket_name, authz_id, dataset_ids=None, overwrite_existing=False)

Implements the logic of sending dataset(s) from a given history to a given cloud-based storage (e.g., Amazon S3).

Parameters:

• trans (galaxy.web.framework.webapp.GalaxyWebTransaction) – Galaxy web transaction
• history_id (string) – the (encoded) id of history from which the object should be sent.
• bucket_name (string) – the name of a bucket to which data should be sent (e.g., a bucket name on AWS S3).
• authz_id (int) – the ID of CloudAuthz to be used for authorizing access to the resource provider. You may get a list of the defined authorizations via /api/cloud/authz. Also, you can use /api/cloud/authz/create to define a new authorization.
• dataset_ids (set) – [Optional] The list of (decoded) dataset ID(s) belonging to the given history which should be sent to the given provider. If not provided, Galaxy sends all the datasets belonging to the given history.
• overwrite_existing (boolean) – [Optional] If set to “True”, and an object with same name of the dataset to be sent already exist in the bucket, Galaxy replaces the existing object with the dataset to be sent. If set to “False”, Galaxy appends datetime to the dataset name to prevent overwriting the existing object.

Return type:

tuple

Returns:

A tuple of two lists of labels of the objects that were successfully and unsuccessfully sent to cloud.

galaxy.managers.collections module

class galaxy.managers.collections.DatasetCollectionManager(app)

Bases: object

Abstraction for interfacing with dataset collections instance - ideally abstracts out model and plugin details.

ELEMENTS_UNINITIALIZED = <object object>

__init__(app)

precreate_dataset_collection_instance(trans, parent, name, structure, implicit_inputs=None, implicit_output_name=None, tags=None)

precreate_dataset_collection(structure, allow_unitialized_element=True)

create(trans, parent, name, collection_type, element_identifiers=None, elements=None, implicit_collection_info=None, trusted_identifiers=None, hide_source_items=False, tags=None, copy_elements=False)

PRECONDITION: security checks on ability to add to parent occurred during load.

create_dataset_collection(trans, collection_type, element_identifiers=None, elements=None, hide_source_items=None, copy_elements=False)

set_collection_elements(dataset_collection, dataset_instances)

collection_builder_for(dataset_collection)

delete(trans, instance_type, id, recursive=False, purge=False)

update(trans, instance_type, id, payload)

copy(trans, parent, source, encoded_source_id, copy_elements=False)

PRECONDITION: security checks on ability to add to parent occurred during load.

history_dataset_collections(history, query)

match_collections(collections_to_match)

May seem odd to place it here, but planning to grow sophistication and get plugin types involved so it will likely make sense in the future.

get_dataset_collection_instance(trans, instance_type, id, **kwds)

get_dataset_collection(trans, encoded_id)

apply_rules(hdca, rule_set, handle_dataset)

galaxy.managers.collections_util module

galaxy.managers.collections_util.api_payload_to_create_params(payload)

Cleanup API payload to pass into dataset_collections.

galaxy.managers.collections_util.dictify_dataset_collection_instance(dataset_collection_instance, parent, security, view='element', fuzzy_count=None)

galaxy.managers.configuration module

Serializers for Galaxy config file data: ConfigSerializer for all users and a more expanded set of data for admin in AdminConfigSerializer.

Used by both the API and bootstrapped data.

class galaxy.managers.configuration.ConfigSerializer(app)

Bases: galaxy.managers.base.ModelSerializer

Configuration (galaxy.ini) settings viewable by all users

__init__(app)

default_serializer(config, key)

add_serializers()

class galaxy.managers.configuration.AdminConfigSerializer(app)

Bases: galaxy.managers.configuration.ConfigSerializer

Configuration attributes viewable only by admin users

add_serializers()

galaxy.managers.containers module

Manager mixins to unify the interface into things that can contain: Datasets and other (nested) containers.

(e.g. DatasetCollections, Histories, LibraryFolders)

class galaxy.managers.containers.ContainerManagerMixin

Bases: object

A class that tracks/contains two types of items:

1. some non-container object (such as datasets)
2. other sub-containers nested within this one

Levels of nesting are not considered here; In other words, each of the methods below only work on the first level of nesting.

contained_class = None

the classes that can be contained

subcontainer_class = None

default_order_by = None

how any contents lists produced are ordered - (string) attribute name to sort on or tuple of attribute names

contents(container)

Returns both types of contents: filtered and in some order.

contained(container, **kwargs)

Returns non-container objects.

subcontainers(container, **kwargs)

Returns only the containers within this one.

class galaxy.managers.containers.LibraryFolderAsContainerManagerMixin

Bases: galaxy.managers.containers.ContainerManagerMixin

contained_class

alias of galaxy.model.LibraryDataset

subcontainer_class

alias of galaxy.model.LibraryFolder

order_contents_on = <operator.attrgetter object>

class galaxy.managers.containers.DatasetCollectionAsContainerManagerMixin

Bases: galaxy.managers.containers.ContainerManagerMixin

contained_class

alias of galaxy.model.DatasetCollectionElement

subcontainer_class

alias of galaxy.model.DatasetCollection

order_contents_on = <operator.attrgetter object>

galaxy.managers.context module

Mixins for transaction-like objects.

class galaxy.managers.context.ProvidesAppContext

Bases: object

For transaction-like objects to provide Galaxy convience layer for database and event handling.

Mixed in class must provide app property.

log_action(user=None, action=None, context=None, params=None)

Application-level logging of user actions.

log_event(message, tool_id=None, **kwargs)

Application level logging. Still needs fleshing out (log levels and such) Logging events is a config setting - if False, do not log.

sa_session

Returns a SQLAlchemy session – currently just gets the current session from the threadlocal session context, but this is provided to allow migration toward a more SQLAlchemy 0.4 style of use.

expunge_all()

get_toolbox()

Returns the application toolbox

model

install_model

class galaxy.managers.context.ProvidesUserContext

Bases: object

For transaction-like objects to provide Galaxy convience layer for reasoning about users.

Mixed in class must provide user, api_inherit_admin, and app properties.

anonymous

get_current_user_roles()

user_is_admin

user_can_do_run_as

user_is_active

check_user_activation()

If user activation is enabled and the user is not activated throw an exception.

user_ftp_dir

class galaxy.managers.context.ProvidesHistoryContext

Bases: object

For transaction-like objects to provide Galaxy convience layer for reasoning about histories.

Mixed in class must provide user, history, and app properties.

db_dataset_for(dbkey)

Returns the db_file dataset associated/needed by dataset, or None.

db_builds

Returns the builds defined by galaxy and the builds defined by the user (chromInfo in history).

galaxy.managers.datasets module

Manager and Serializer for Datasets.

class galaxy.managers.datasets.DatasetManager(app)

Bases: galaxy.managers.base.ModelManager, galaxy.managers.secured.AccessibleManagerMixin, galaxy.managers.deletable.PurgableManagerMixin

Manipulate datasets: the components contained in DatasetAssociations/DatasetInstances/HDAs/LDDAs

model_class

alias of galaxy.model.Dataset

foreign_key_name = 'dataset'

__init__(app)

create(manage_roles=None, access_roles=None, flush=True, **kwargs)

Create and return a new Dataset object.

copy(dataset, **kwargs)

purge(dataset, flush=True)

Remove the object_store/file for this dataset from storage and mark as purged.

Raises:exceptions.ConfigDoesNotAllowException – if the instance doesn’t allow

error_unless_dataset_purge_allowed(msg=None)

is_accessible(dataset, user, **kwargs)

Is this dataset readable/viewable to user?

has_access_permission(dataset, user)

Return T/F if the user has role-based access to the dataset.

class galaxy.managers.datasets.DatasetRBACPermissions(app)

Bases: object

__init__(app)

available_roles(trans, dataset, controller='root')

get(dataset, flush=True)

set(dataset, manage_roles, access_roles, flush=True)

set_public_with_single_manager(dataset, user, flush=True)

set_private_to_one_user(dataset, user, flush=True)

class galaxy.managers.datasets.DatasetSerializer(app)

Bases: galaxy.managers.base.ModelSerializer, galaxy.managers.deletable.PurgableSerializerMixin

model_manager_class

alias of DatasetManager

__init__(app)

add_serializers()

serialize_file_name(dataset, key, user=None, **context)

If the config allows or the user is admin, return the file name of the file that contains this dataset’s data.

serialize_extra_files_path(dataset, key, user=None, **context)

If the config allows or the user is admin, return the file path.

serialize_permissions(dataset, key, user=None, **context)

class galaxy.managers.datasets.DatasetAssociationManager(app)

Bases: galaxy.managers.base.ModelManager, galaxy.managers.secured.AccessibleManagerMixin, galaxy.managers.deletable.PurgableManagerMixin

DatasetAssociation/DatasetInstances are intended to be working proxies to a Dataset, associated with either a library or a user/history (HistoryDatasetAssociation).

model_class

alias of galaxy.model.DatasetInstance

__init__(app)

is_accessible(dataset_assoc, user, **kwargs)

Is this DA accessible to user?

purge(dataset_assoc, flush=True)

Purge this DatasetInstance and the dataset underlying it.

by_user(user)

creating_job(dataset_assoc)

Return the Job that created this dataset or None if not found.

stop_creating_job(dataset_assoc)

Stops an dataset_assoc’s creating job if all the job’s other outputs are deleted.

is_composite(dataset_assoc)

Return True if this hda/ldda is a composite type dataset.

Note

see also (whereever we keep information on composite datatypes?)

extra_files(dataset_assoc)

Return a list of file paths for composite files, an empty list otherwise.

serialize_dataset_association_roles(trans, dataset_assoc)

update_permissions(trans, dataset_assoc, **kwd)

class galaxy.managers.datasets.DatasetAssociationSerializer(app)

Bases: galaxy.managers.datasets._UnflattenedMetadataDatasetAssociationSerializer

add_serializers()

serialize(dataset_assoc, keys, **context)

Override to add metadata as flattened keys on the serialized DatasetInstance.

class galaxy.managers.datasets.DatasetAssociationDeserializer(app, validator=None, **kwargs)

Bases: galaxy.managers.base.ModelDeserializer, galaxy.managers.deletable.PurgableDeserializerMixin

add_deserializers()

deserialize_metadata(dataset_assoc, metadata_key, metadata_dict, **context)

deserialize_metadatum(dataset_assoc, key, val, **context)

class galaxy.managers.datasets.DatasetAssociationFilterParser(app, **kwargs)

Bases: galaxy.managers.base.ModelFilterParser, galaxy.managers.deletable.PurgableFiltersMixin

eq_datatype(dataset_assoc, class_str)

Is the dataset_assoc datatype equal to the registered datatype class_str?

isinstance_datatype(dataset_assoc, class_strs)

Is the dataset_assoc datatype derived from any of the registered datatypes in the comma separated string class_strs?

galaxy.managers.deletable module

Many models in Galaxy are not meant to be removed from the database but only marked as deleted. These models have the boolean attribute ‘deleted’.

Other models are deletable and also may be purged. Most often these are models have some backing/supporting resources that can be removed as well (e.g. Datasets have data files on a drive). Purging these models removes the supporting resources as well. These models also have the boolean attribute ‘purged’.

class galaxy.managers.deletable.DeletableManagerMixin

Bases: object

A mixin/interface for a model that is deletable (i.e. has a ‘deleted’ attr).

Many resources in Galaxy can be marked as deleted - meaning (in most cases) that they are no longer needed, should not be displayed, or may be actually removed by an admin/script.

delete(item, flush=True, **kwargs)

Mark as deleted and return.

undelete(item, flush=True, **kwargs)

Mark as not deleted and return.

class galaxy.managers.deletable.DeletableSerializerMixin

Bases: object

add_serializers()

class galaxy.managers.deletable.DeletableDeserializerMixin

Bases: object

add_deserializers()

deserialize_deleted(item, key, val, **context)

Delete or undelete item based on val then return item.deleted.

class galaxy.managers.deletable.DeletableFiltersMixin

Bases: object

class galaxy.managers.deletable.PurgableManagerMixin

Bases: galaxy.managers.deletable.DeletableManagerMixin

A manager interface/mixin for a resource that allows deleting and purging where purging is often removal of some additional, non-db resource (e.g. a dataset’s file).

purge(item, flush=True, **kwargs)

Mark as purged and return.

Override this in subclasses to do the additional resource removal.

class galaxy.managers.deletable.PurgableSerializerMixin

Bases: galaxy.managers.deletable.DeletableSerializerMixin

add_serializers()

class galaxy.managers.deletable.PurgableDeserializerMixin

Bases: galaxy.managers.deletable.DeletableDeserializerMixin

add_deserializers()

deserialize_purged(item, key, val, **context)

If val is True, purge item and return item.purged.

class galaxy.managers.deletable.PurgableFiltersMixin

Bases: galaxy.managers.deletable.DeletableFiltersMixin

galaxy.managers.folders module

Manager and Serializer for Library Folders.

class galaxy.managers.folders.FolderManager

Bases: object

Interface/service object for interacting with folders.

get(trans, decoded_folder_id, check_manageable=False, check_accessible=True)

Get the folder from the DB.

Parameters:

• decoded_folder_id (int) – decoded folder id
• check_manageable (bool) – flag whether the check that user can manage item
• check_accessible (bool) – flag whether to check that user can access item

Returns:

the requested folder

Return type:

LibraryFolder

Raises:

InconsistentDatabase, RequestParameterInvalidException, InternalServerError

secure(trans, folder, check_manageable=True, check_accessible=True)

Check if (a) user can manage folder or (b) folder is accessible to user.

Parameters:

• folder (LibraryFolder) – folder item
• check_manageable (bool) – flag whether to check that user can manage item
• check_accessible (bool) – flag whether to check that user can access item

Returns:

the original folder

Return type:

LibraryFolder

check_manageable(trans, folder)

Check whether the user can manage the folder.

Returns:the original folder Return type:LibraryFolder Raises:AuthenticationRequired, InsufficientPermissionsException

check_accessible(trans, folder)

Check whether the folder is accessible to current user. By default every folder is accessible (contents have their own permissions).

get_folder_dict(trans, folder)

Return folder data in the form of a dictionary.

Parameters:folder (LibraryFolder) – folder item Returns:dict with data about the folder Return type:dictionary

create(trans, parent_folder_id, new_folder_name, new_folder_description='')

Create a new folder under the given folder.

Parameters:

• parent_folder_id (int) – decoded id
• new_folder_name (str) – name of the new folder
• new_folder_description (str) – description of the folder (optional, defaults to empty string)

Returns:

the new folder

Return type:

LibraryFolder

Raises:

InsufficientPermissionsException

update(trans, folder, name=None, description=None)

Update the given folder’s name or description.

Parameters:

• folder (LibraryFolder) – the model object
• name (str) – new name for the library folder
• description (str) – new description for the library folder

Returns:

the folder

Return type:

LibraryFolder

Raises:

ItemAccessibilityException, InsufficientPermissionsException

delete(trans, folder, undelete=False)

Mark given folder deleted/undeleted based on the flag.

Parameters:

• folder (LibraryFolder) – the model object
• undelete (Bool) – flag whether to delete (when False) or undelete

Returns:

the folder

Return type:

LibraryFolder

Raises:

ItemAccessibilityException

get_current_roles(trans, folder)

Find all roles currently connected to relevant permissions on the folder.

Parameters:folder (LibraryFolder) – the model object Returns:dict of current roles for all available permission types Return type:dictionary

can_add_item(trans, folder)

Return true if the user has permissions to add item to the given folder.

cut_the_prefix(encoded_folder_id)

Remove the prefix from the encoded folder id.

Parameters:encoded_folder_id (string) – encoded id of the Folder object with ‘F’ prepended Returns:encoded Folder id without the ‘F’ prefix Return type:string Raises:MalformedId

decode_folder_id(trans, encoded_folder_id)

Decode the folder id given that it has already lost the prefixed ‘F’.

Parameters:encoded_folder_id (string) – encoded id of the Folder object Returns:decoded Folder id Return type:int Raises:MalformedId

cut_and_decode(trans, encoded_folder_id)

Cuts the folder prefix (the prepended ‘F’) and returns the decoded id.

Parameters:encoded_folder_id (string) – encoded id of the Folder object Returns:decoded Folder id Return type:int

galaxy.managers.hdas module

Manager and Serializer for HDAs.

HistoryDatasetAssociations (HDAs) are datasets contained or created in a history.

class galaxy.managers.hdas.HDAManager(app)

Bases: galaxy.managers.datasets.DatasetAssociationManager, galaxy.managers.secured.OwnableManagerMixin, galaxy.managers.taggable.TaggableManagerMixin, galaxy.managers.annotatable.AnnotatableManagerMixin

Interface/service object for interacting with HDAs.

model_class

alias of galaxy.model.HistoryDatasetAssociation

foreign_key_name = 'history_dataset_association'

tag_assoc

alias of galaxy.model.HistoryDatasetAssociationTagAssociation

annotation_assoc

alias of galaxy.model.HistoryDatasetAssociationAnnotationAssociation

__init__(app)

Set up and initialize other managers needed by hdas.

is_accessible(hda, user, **kwargs)

Override to allow owners (those that own the associated history).

is_owner(hda, user, current_history=None, **kwargs)

Use history to see if current user owns HDA.

create(history=None, dataset=None, flush=True, **kwargs)

Create a new hda optionally passing in it’s history and dataset.

..note: to explicitly set hid to None you must pass in hid=None, otherwise it will be automatically set.

copy(hda, history=None, hide_copy=False, **kwargs)

Copy hda, including annotation and tags, add to history and return the given HDA.

copy_ldda(history, ldda, **kwargs)

Copy this HDA as a LDDA and return.

purge(hda, flush=True)

Purge this HDA and the dataset underlying it.

error_if_uploading(hda)

Raise error if HDA is still uploading.

has_been_resubmitted(hda)

Return True if the hda’s job was resubmitted at any point.

data_conversion_status(hda)

Returns a message if an hda is not ready to be used in visualization.

text_data(hda, preview=True)

Get data from text file, truncating if necessary.

annotation(hda)

class galaxy.managers.hdas.HDASerializer(app)

Bases: galaxy.managers.datasets.DatasetAssociationSerializer, galaxy.managers.taggable.TaggableSerializerMixin, galaxy.managers.annotatable.AnnotatableSerializerMixin

model_manager_class

alias of HDAManager

__init__(app)

add_serializers()

serialize(hda, keys, user=None, **context)

Override to hide information to users not able to access.

serialize_display_apps(hda, key, trans=None, **context)

Return dictionary containing new-style display app urls.

serialize_old_display_applications(hda, key, trans=None, **context)

Return dictionary containing old-style display app urls.

serialize_visualization_links(hda, key, trans=None, **context)

Return a list of dictionaries with links to visualization pages for those visualizations that apply to this hda.

serialize_urls(hda, key, **context)

Return web controller urls useful for this HDA.

class galaxy.managers.hdas.HDADeserializer(app)

Bases: galaxy.managers.datasets.DatasetAssociationDeserializer, galaxy.managers.taggable.TaggableDeserializerMixin, galaxy.managers.annotatable.AnnotatableDeserializerMixin

Interface/service object for validating and deserializing dictionaries into histories.

model_manager_class

alias of HDAManager

__init__(app)

add_deserializers()

class galaxy.managers.hdas.HDAFilterParser(app, **kwargs)

Bases: galaxy.managers.datasets.DatasetAssociationFilterParser, galaxy.managers.taggable.TaggableFilterMixin, galaxy.managers.annotatable.AnnotatableFilterMixin

model_manager_class

alias of HDAManager

model_class

alias of galaxy.model.HistoryDatasetAssociation

galaxy.managers.hdcas module

Manager and Serializer for HDCAs.

HistoryDatasetCollectionAssociations (HDCAs) are datasets contained or created in a history.

class galaxy.managers.hdcas.HDCAManager(app)

Bases: galaxy.managers.base.ModelManager, galaxy.managers.secured.AccessibleManagerMixin, galaxy.managers.secured.OwnableManagerMixin, galaxy.managers.deletable.PurgableManagerMixin, galaxy.managers.taggable.TaggableManagerMixin, galaxy.managers.annotatable.AnnotatableManagerMixin

Interface/service object for interacting with HDCAs.

model_class

alias of galaxy.model.HistoryDatasetCollectionAssociation

foreign_key_name = 'history_dataset_collection_association'

tag_assoc

alias of galaxy.model.HistoryDatasetCollectionTagAssociation

annotation_assoc

alias of galaxy.model.HistoryDatasetCollectionAssociationAnnotationAssociation

__init__(app)

Set up and initialize other managers needed by hdcas.

map_datasets(content, fn, *parents)

Iterate over the datasets of a given collection, recursing into collections, and calling fn on each dataset.

Uses the same kwargs as contents above.

class galaxy.managers.hdcas.DCESerializer(app)

Bases: galaxy.managers.base.ModelSerializer

Serializer for DatasetCollectionElements.

__init__(app)

add_serializers()

serialize_object(item, key, **context)

class galaxy.managers.hdcas.DCSerializer(app, dce_serializer=None)

Bases: galaxy.managers.base.ModelSerializer

Serializer for DatasetCollections.

__init__(app, dce_serializer=None)

add_serializers()

serialize_elements(item, key, **context)

class galaxy.managers.hdcas.DCASerializer(app, dce_serializer=None)

Bases: galaxy.managers.base.ModelSerializer

Base (abstract) Serializer class for HDCAs and LDCAs.

__init__(app, dce_serializer=None)

add_serializers()

class galaxy.managers.hdcas.HDCASerializer(app)

Bases: galaxy.managers.hdcas.DCASerializer, galaxy.managers.taggable.TaggableSerializerMixin, galaxy.managers.annotatable.AnnotatableSerializerMixin

Serializer for HistoryDatasetCollectionAssociations.

__init__(app)

add_serializers()

galaxy.managers.histories module

Manager and Serializer for histories.

Histories are containers for datasets or dataset collections created (or copied) by users over the course of an analysis.

class galaxy.managers.histories.HistoryManager(app, *args, **kwargs)

Bases: galaxy.managers.sharable.SharableModelManager, galaxy.managers.deletable.PurgableManagerMixin

model_class

alias of galaxy.model.History

foreign_key_name = 'history'

user_share_model

alias of galaxy.model.HistoryUserShareAssociation

tag_assoc

alias of galaxy.model.HistoryTagAssociation

annotation_assoc

alias of galaxy.model.HistoryAnnotationAssociation

rating_assoc

alias of galaxy.model.HistoryRatingAssociation

__init__(app, *args, **kwargs)

copy(history, user, **kwargs)

Copy and return the given history.

by_user(user, current_history=None, **kwargs)

Get all the histories for a given user (allowing anon users’ theirs) ordered by update time.

is_owner(history, user, current_history=None, **kwargs)

True if the current user is the owner of the given history.

most_recent(user, filters=None, current_history=None, **kwargs)

Return the most recently update history for the user.

If user is anonymous, return the current history. If the user is anonymous and the current history is deleted, return None.

purge(history, flush=True, **kwargs)

Purge this history and all HDAs, Collections, and Datasets inside this history.

get_current(trans)

Return the current history.

set_current(trans, history)

Set the current history.

set_current_by_id(trans, history_id)

Set the current history by an id.

parse_order_by(order_by_string, default=None)

Return an ORM compatible order_by using the given string

non_ready_jobs(history)

Return the currently running job objects associated with this history.

Where running is defined as new, waiting, queued, running, resubmitted, and upload.

class galaxy.managers.histories.HistorySerializer(app, **kwargs)

Bases: galaxy.managers.sharable.SharableModelSerializer, galaxy.managers.deletable.PurgableSerializerMixin

Interface/service object for serializing histories into dictionaries.

model_manager_class

alias of HistoryManager

SINGLE_CHAR_ABBR = 'h'

__init__(app, **kwargs)

add_serializers()

serialize_state_ids(history, key, **context)

Return a dictionary keyed to possible dataset states and valued with lists containing the ids of each HDA in that state.

serialize_state_counts(history, key, exclude_deleted=True, exclude_hidden=False, **context)

Return a dictionary keyed to possible dataset states and valued with the number of datasets in this history that have those states.

serialize_history_state(history, key, **context)

Returns the history state based on the states of the HDAs it contains.

serialize_contents(history, key, trans=None, user=None, **context)

serialize_contents_states(history, key, trans=None, **context)

Return a dictionary containing the counts of all contents in each state keyed by the distinct states.

Note: does not include deleted/hidden contents.

serialize_contents_active(history, key, **context)

Return a dictionary keyed with ‘deleted’, ‘hidden’, and ‘active’ with values for each representing the count of contents in each state.

Note: counts for deleted and hidden overlap; In other words, a dataset that’s both deleted and hidden will be added to both totals.

class galaxy.managers.histories.HistoryDeserializer(app)

Bases: galaxy.managers.sharable.SharableModelDeserializer, galaxy.managers.deletable.PurgableDeserializerMixin

Interface/service object for validating and deserializing dictionaries into histories.

model_manager_class

alias of HistoryManager

__init__(app)

add_deserializers()

class galaxy.managers.histories.HistoryFilters(app, **kwargs)

Bases: galaxy.managers.sharable.SharableModelFilters, galaxy.managers.deletable.PurgableFiltersMixin

model_class

alias of galaxy.model.History

model_manager_class

alias of HistoryManager

galaxy.managers.history_contents module

Heterogenous lists/contents are difficult to query properly since unions are not easily made.

class galaxy.managers.history_contents.HistoryContentsManager(app)

Bases: galaxy.managers.containers.ContainerManagerMixin

root_container_class

alias of galaxy.model.History

contained_class

alias of galaxy.model.HistoryDatasetAssociation

contained_class_manager_class

alias of galaxy.managers.hdas.HDAManager

contained_class_type_name = 'dataset'

subcontainer_class

alias of galaxy.model.HistoryDatasetCollectionAssociation

subcontainer_class_manager_class

alias of galaxy.managers.hdcas.HDCAManager

subcontainer_class_type_name = 'dataset_collection'

common_columns = ('history_id', 'history_content_type', 'id', 'type_id', 'hid', 'dataset_id', 'collection_id', 'name', 'state', 'deleted', 'purged', 'visible', 'create_time', 'update_time')

the columns which are common to both subcontainers and non-subcontainers.

default_order_by = 'hid'

__init__(app)

contained(container, filters=None, limit=None, offset=None, order_by=None, **kwargs)

Returns non-subcontainer objects within container.

subcontainers(container, filters=None, limit=None, offset=None, order_by=None, **kwargs)

Returns only the containers within container.

contents(container, filters=None, limit=None, offset=None, order_by=None, **kwargs)

Returns a list of both/all types of contents, filtered and in some order.

contents_count(container, filters=None, limit=None, offset=None, order_by=None, **kwargs)

Returns a count of both/all types of contents, based on the given filters.

contents_query(container, filters=None, limit=None, offset=None, order_by=None, **kwargs)

Returns the contents union query for subqueries, etc.

parse_order_by(order_by_string, default=None)

Return an ORM compatible order_by using the given string

state_counts(history)

Return a dictionary containing the counts of all contents in each state keyed by the distinct states.

Note: does not include deleted/hidden contents.

active_counts(history)

Return a dictionary keyed with ‘deleted’, ‘hidden’, and ‘active’ with values for each representing the count of contents in each state.

Note: counts for deleted and hidden overlap; In other words, a dataset that’s both deleted and hidden will be added to both totals.

map_datasets(history, fn, **kwargs)

Iterate over the datasets of a given history, recursing into collections, and calling fn on each dataset.

Uses the same kwargs as contents above.

class galaxy.managers.history_contents.HistoryContentsSerializer(app, **kwargs)

Bases: galaxy.managers.base.ModelSerializer, galaxy.managers.deletable.PurgableSerializerMixin

Interface/service object for serializing histories into dictionaries.

model_manager_class

alias of HistoryContentsManager

__init__(app, **kwargs)

add_serializers()

serialize_id_or_skip(content, key, **context)

Serialize id or skip if attribute with key is not present.

class galaxy.managers.history_contents.HistoryContentsFilters(app, **kwargs)

Bases: galaxy.managers.base.ModelFilterParser, galaxy.managers.deletable.PurgableFiltersMixin

model_class

alias of galaxy.model.HistoryDatasetAssociation

decode_type_id(type_id)

parse_type_id_list(type_id_list_string, sep=', ')

Split type_id_list_string at sep.

galaxy.managers.jobs module

galaxy.managers.jobs.get_path_key(path_tuple)

class galaxy.managers.jobs.JobSearch(app)

Bases: object

Search for jobs using tool inputs or other jobs

__init__(app)

by_tool_input(trans, tool_id, tool_version, param=None, param_dump=None, job_state='ok')

Search for jobs producing same results using the ‘inputs’ part of a tool POST.

galaxy.managers.jobs.fetch_job_states(app, sa_session, job_source_ids, job_source_types)

galaxy.managers.jobs.summarize_jobs_to_dict(sa_session, jobs_source)

Proudce a summary of jobs for job summary endpoints.

Parameters:jobs_source (a Job or ImplicitCollectionJobs or None) – the object to summarize Return type:dict Returns:dictionary containing job summary information

galaxy.managers.lddas module

class galaxy.managers.lddas.LDDAManager(app)

Bases: galaxy.managers.datasets.DatasetAssociationManager

A fairly sparse manager for LDDAs.

model_class

alias of galaxy.model.LibraryDatasetDatasetAssociation

__init__(app)

Set up and initialize other managers needed by lddas.

get(trans, id, check_accessible=True)

galaxy.managers.libraries module

Manager and Serializer for libraries.

class galaxy.managers.libraries.LibraryManager(*args, **kwargs)

Bases: object

Interface/service object for interacting with libraries.

__init__(*args, **kwargs)

get(trans, decoded_library_id, check_accessible=True)

Get the library from the DB.

Parameters:

• decoded_library_id (int) – decoded library id
• check_accessible (bool) – flag whether to check that user can access item

Returns:

the requested library

Return type:

galaxy.model.Library

create(trans, name, description='', synopsis='')

Create a new library.

update(trans, library, name=None, description=None, synopsis=None)

Update the given library

delete(trans, library, undelete=False)

Mark given library deleted/undeleted based on the flag.

list(trans, deleted=False)

Return a list of libraries from the DB.

Parameters:deleted (boolean (optional)) – if True, show only deleted libraries, if False show only non-deleted Returns:query that will emit all accessible libraries Return type:sqlalchemy query Returns:dict of 3 sets with available actions for user’s accessible libraries and a set of ids of all public libraries. These are used for limiting the number of queries when dictifying the libraries later on. Return type:dict

secure(trans, library, check_accessible=True)

Check if library is accessible to user.

Parameters:

• library (galaxy.model.Library) – library
• check_accessible (bool) – flag whether to check that user can access library

Returns:

the original library

Return type:

Library

check_accessible(trans, library)

Check whether the library is accessible to current user.

get_library_dict(trans, library, prefetched_ids=None)

Return library data in the form of a dictionary.

Parameters:

• library (galaxy.model.Library) – library
• prefetched_ids (dict) – dict of 3 sets with available actions for user’s accessible libraries and a set of ids of all public libraries. These are used for limiting the number of queries when dictifying a set of libraries.

Returns:

dict with data about the library

Return type:

dictionary

get_current_roles(trans, library)

Load all permissions currently related to the given library.

Parameters:library (galaxy.model.Library) – the model object Return type:dictionary Returns:dict of current roles for all available permission types

get_access_roles(trans, library)

Load access roles for all library permissions

get_modify_roles(trans, library)

Load modify roles for all library permissions

get_manage_roles(trans, library)

Load manage roles for all library permissions

get_add_roles(trans, library)

Load add roles for all library permissions

set_permission_roles(trans, library, access_roles, modify_roles, manage_roles, add_roles)

Set permissions on the given library.

make_public(trans, library)

Makes the given library public (removes all access roles)

is_public(trans, library)

Return true if lib is public.

galaxy.managers.library_datasets module

Manager and Serializer for library datasets.

class galaxy.managers.library_datasets.LibraryDatasetsManager(app)

Bases: galaxy.managers.datasets.DatasetAssociationManager

Interface/service object for interacting with library datasets.

__init__(app)

get(trans, decoded_library_dataset_id, check_accessible=True)

Get the library dataset from the DB.

Parameters:

• decoded_library_dataset_id (int) – decoded library dataset id
• check_accessible (bool) – flag whether to check that user can access item

Returns:

the requested library dataset

Return type:

galaxy.model.LibraryDataset

update(trans, ld, payload)

Update the given library dataset - the latest linked ldda. Updating older lddas (versions) is not allowed.

Parameters:

• ld (LibraryDataset) – library dataset to change
• payload (dict) – dictionary structure containing:: :param name: new ld’s name, must be longer than 0 :type name: str :param misc_info: new ld’s misc info :type misc_info: str :param file_ext: new ld’s extension, must exist in the Galaxy registry :type file_ext: str :param genome_build: new ld’s genome build :type genome_build: str

Returns:

the changed library dataset

Return type:

galaxy.model.LibraryDataset

secure(trans, ld, check_accessible=True, check_ownership=False)

Check if library dataset is accessible to current user or the user is an admin.

Parameters:

• ld (galaxy.model.LibraryDataset) – library dataset
• check_accessible (bool) – flag whether to check that user can access library dataset

Returns:

the original library dataset

Return type:

galaxy.model.LibraryDataset

check_accessible(trans, ld)

Check whether the current user has permissions to access library dataset.

Parameters:ld (galaxy.model.LibraryDataset) – library dataset Returns:the original library dataset Return type:galaxy.model.LibraryDataset Raises:ObjectNotFound

check_modifiable(trans, ld)

Check whether the current user has permissions to modify library dataset.

Parameters:ld (galaxy.model.LibraryDataset) – library dataset Returns:the original library dataset Return type:galaxy.model.LibraryDataset Raises:ObjectNotFound

serialize(trans, ld)

Serialize the library dataset into a dictionary.

galaxy.managers.pages module

Manager and Serializers for Pages.

Pages are markup created and saved by users that can contain Galaxy objects (such as datasets) and are often used to describe or present an analysis from within Galaxy.

class galaxy.managers.pages.PageManager(app, *args, **kwargs)

Bases: galaxy.managers.sharable.SharableModelManager

model_class

alias of galaxy.model.Page

foreign_key_name = 'page'

user_share_model

alias of galaxy.model.PageUserShareAssociation

tag_assoc

alias of galaxy.model.PageTagAssociation

annotation_assoc

alias of galaxy.model.PageAnnotationAssociation

rating_assoc

alias of galaxy.model.PageRatingAssociation

__init__(app, *args, **kwargs)

copy(trans, page, user, **kwargs)

class galaxy.managers.pages.PageSerializer(app)

Bases: galaxy.managers.sharable.SharableModelSerializer

Interface/service object for serializing pages into dictionaries.

model_manager_class

alias of PageManager

SINGLE_CHAR_ABBR = 'p'

__init__(app)

add_serializers()

class galaxy.managers.pages.PageDeserializer(app)

Bases: galaxy.managers.sharable.SharableModelDeserializer

Interface/service object for validating and deserializing dictionaries into pages.

model_manager_class

alias of PageManager

__init__(app)

add_deserializers()

galaxy.managers.ratable module

Mixins for Ratable model managers and serializers.

class galaxy.managers.ratable.RatableManagerMixin

Bases: object

rating_assoc = None

class of RatingAssociation (e.g. HistoryRatingAssociation)

rating(item, user, as_int=True)

Returns the integer rating given to this item by the user.

Returns the full rating model if as_int is False.

ratings(item)

Returns a list of all rating values given to this item.

ratings_avg(item)

Returns the average of all ratings given to this item.

ratings_count(item)

Returns the number of ratings given to this item.

rate(item, user, value, flush=True)

Updates or creates a rating for this item and user. Returns the rating

class galaxy.managers.ratable.RatableSerializerMixin

Bases: object

add_serializers()

serialize_user_rating(item, key, user=None, **context)

Returns the integer rating given to this item by the user.

serialize_community_rating(item, key, **context)

Returns a dictionary containing:

average the (float) average of all ratings of this object count the number of ratings

class galaxy.managers.ratable.RatableDeserializerMixin

Bases: object

add_deserializers()

deserialize_rating(item, key, val, user=None, **context)

class galaxy.managers.ratable.RatableFilterMixin

Bases: object

galaxy.managers.rbac_secured module

exception galaxy.managers.rbac_secured.RBACPermissionFailedException(err_msg=None, type='info', **extra_error_info)

Bases: galaxy.exceptions.InsufficientPermissionsException

class galaxy.managers.rbac_secured.RBACPermission(app)

Bases: object

Base class for wrangling/controlling the permissions ORM models (*Permissions, Roles) that control which users can perform certain actions on their associated models (Libraries, Datasets).

permissions_class = None

permission_failed_error_class

alias of RBACPermissionFailedException

__init__(app)

session()

is_permitted(item, user, trans=None)

error_unless_permitted(item, user, trans=None)

grant(item, user, flush=True)

revoke(item, user, flush=True)

class galaxy.managers.rbac_secured.DatasetRBACPermission(app)

Bases: galaxy.managers.rbac_secured.RBACPermission

Base class for the manage and access RBAC permissions used by dataset security.

The DatasetPermissions used by the RBAC agent are associations between a Dataset and a single Role.

DatasetPermissions are typed (but not polymorphic themselves) by a string ‘action’. There are two types:

• manage permissions : can a role manage the permissions on a dataset
• access : can a role read/look at/copy a dataset

permissions_class

alias of galaxy.model.DatasetPermissions

action_name = None

by_dataset(dataset)

by_roles(dataset, roles)

by_role(dataset, role)

set(dataset, roles, flush=True)

clear(dataset, flush=True)

galaxy.managers.rbac_secured.iterable_has_all(iterable, has_these)

exception galaxy.managers.rbac_secured.DatasetManagePermissionFailedException(err_msg=None, type='info', **extra_error_info)

Bases: galaxy.managers.rbac_secured.RBACPermissionFailedException

class galaxy.managers.rbac_secured.ManageDatasetRBACPermission(app)

Bases: galaxy.managers.rbac_secured.DatasetRBACPermission

A class that controls the dataset permissions that control who can manage that dataset’s permissions.

When checking permissions for a user, if any of the user’s roles have permission on the dataset

action_name = 'manage permissions'

permission_failed_error_class

alias of DatasetManagePermissionFailedException

is_permitted(dataset, user, trans=None)

grant(dataset, user, flush=True)

revoke(dataset, user, flush=True)

exception galaxy.managers.rbac_secured.DatasetAccessPermissionFailedException(err_msg=None, type='info', **extra_error_info)

Bases: galaxy.managers.rbac_secured.RBACPermissionFailedException

class galaxy.managers.rbac_secured.AccessDatasetRBACPermission(app)

Bases: galaxy.managers.rbac_secured.DatasetRBACPermission

A class to manage access permissions on a dataset.

An user must have all the Roles of all the access permissions associated with a dataset in order to access it.

action_name = 'access'

permission_failed_error_class

alias of DatasetAccessPermissionFailedException

is_permitted(dataset, user, trans=None)

grant(item, user)

revoke(item, user)

is_public(dataset)

set_private(dataset, user, flush=True)

galaxy.managers.roles module

Manager and Serializer for Roles.

class galaxy.managers.roles.RoleManager(app)

Bases: galaxy.managers.base.ModelManager

Business logic for roles.

model_class

alias of galaxy.model.Role

foreign_key_name = 'role'

user_assoc

alias of galaxy.model.UserRoleAssociation

group_assoc

alias of galaxy.model.GroupRoleAssociation

__init__(app)

get(trans, decoded_role_id)

Method loads the role from the DB based on the given role id.

Parameters:decoded_role_id (int) – id of the role to load from the DB Returns:the loaded Role object Return type:galaxy.model.Role Raises:InconsistentDatabase, RequestParameterInvalidException, InternalServerError

galaxy.managers.secured module

Accessible models can be read and copied but not modified or deleted.

Owned models can be modified and deleted.

class galaxy.managers.secured.AccessibleManagerMixin

Bases: object

A security interface to check if a User can read/view an item’s.

This can also be thought of as ‘read but not modify’ privileges.

is_accessible(item, user, **kwargs)

Return True if the item accessible to user.

get_accessible(id, user, **kwargs)

Return the item with the given id if it’s accessible to user, otherwise raise an error.

Raises:exceptions.ItemAccessibilityException –

error_unless_accessible(item, user, **kwargs)

Raise an error if the item is NOT accessible to user, otherwise return the item.

Raises:exceptions.ItemAccessibilityException –

list_accessible(user, **kwargs)

Return a list of items accessible to the user, raising an error if ANY are inaccessible.

Raises:exceptions.ItemAccessibilityException –

filter_accessible(user, **kwargs)

Return a list of items accessible to the user.

class galaxy.managers.secured.OwnableManagerMixin

Bases: object

A security interface to check if a User is an item’s owner.

Some resources are associated with the User that created or imported them and these Users can be considered the models’ owner.

This can also be thought of as write/edit privileges.

is_owner(item, user, **kwargs)

Return True if user owns the item.

get_owned(id, user, **kwargs)

Return the item with the given id if owned by the user, otherwise raise an error.

Raises:exceptions.ItemOwnershipException –

error_unless_owner(item, user, **kwargs)

Raise an error if the item is NOT owned by user, otherwise return the item.

Raises:exceptions.ItemAccessibilityException –

list_owned(user, **kwargs)

Return a list of items owned by the user, raising an error if ANY are not.

Raises:exceptions.ItemAccessibilityException –

filter_owned(user, **kwargs)

Return a list of items owned by the user.

galaxy.managers.sharable module

Superclass Manager and Serializers for Sharable objects.

A sharable Galaxy object:

has an owner/creator User is sharable with other, specific Users is importable (copyable) by users that have access has a slug which can be used as a link to view the resource can be published effectively making it available to all other Users can be rated

class galaxy.managers.sharable.SharableModelManager(app)

Bases: galaxy.managers.base.ModelManager, galaxy.managers.secured.OwnableManagerMixin, galaxy.managers.secured.AccessibleManagerMixin, galaxy.managers.taggable.TaggableManagerMixin, galaxy.managers.annotatable.AnnotatableManagerMixin, galaxy.managers.ratable.RatableManagerMixin

user_share_model = None

the model used for UserShareAssociations with this model

SINGLE_CHAR_ABBR = None

the single character abbreviation used in username_and_slug: e.g. ‘h’ for histories: u/user/h/slug

__init__(app)

by_user(user, filters=None, **kwargs)

Return list for all items (of model_class type) associated with the given user.

is_owner(item, user, **kwargs)

Return true if this sharable belongs to user (or user is an admin).

is_accessible(item, user, **kwargs)

If the item is importable, is owned by user, or (the valid) user is in ‘users shared with’ list for the item: return True.

make_importable(item, flush=True)

Makes item accessible–viewable and importable–and sets item’s slug. Does not flush/commit changes, however. Item must have name, user, importable, and slug attributes.

make_non_importable(item, flush=True)

Makes item accessible–viewable and importable–and sets item’s slug. Does not flush/commit changes, however. Item must have name, user, importable, and slug attributes.

publish(item, flush=True)

Set both the importable and published flags on item to True.

unpublish(item, flush=True)

Set the published flag on item to False.

list_published(filters=None, **kwargs)

Return a list of all published items.

get_share_assocs(item, user=None)

Get the UserShareAssociations for the item.

Optionally send in user to test for a single match.

share_with(item, user, flush=True)

Get or create a share for the given user (or users if user is a list).

unshare_with(item, user, flush=True)

Delete a user share (or list of shares) from the database.

list_shared_with(user, filters=None, order_by=None, limit=None, offset=None, **kwargs)

Return a list of those models shared with a particular user.

set_slug(item, new_slug, user, flush=True)

Validate and set the new slug for item.

is_valid_slug(slug)

Returns true if slug is valid.

get_unique_slug(item)

Returns a slug that is unique among user’s importable items for item’s class.

create_unique_slug(item, flush=True)

Set a new, unique slug on the item.

class galaxy.managers.sharable.SharableModelSerializer(app, **kwargs)

Bases: galaxy.managers.base.ModelSerializer, galaxy.managers.taggable.TaggableSerializerMixin, galaxy.managers.annotatable.AnnotatableSerializerMixin, galaxy.managers.ratable.RatableSerializerMixin

SINGLE_CHAR_ABBR = None

__init__(app, **kwargs)

add_serializers()

serialize_title(item, key, **context)

serialize_username_and_slug(item, key, **context)

serialize_users_shared_with(item, key, user=None, **context)

Returns a list of encoded ids for users the item has been shared.

Skipped if the requesting user is not the owner.

class galaxy.managers.sharable.SharableModelDeserializer(app, validator=None, **kwargs)

Bases: galaxy.managers.base.ModelDeserializer, galaxy.managers.taggable.TaggableDeserializerMixin, galaxy.managers.annotatable.AnnotatableDeserializerMixin, galaxy.managers.ratable.RatableDeserializerMixin

add_deserializers()

deserialize_published(item, key, val, **context)

deserialize_importable(item, key, val, **context)

deserialize_users_shared_with(item, key, val, **context)

Accept a list of encoded user_ids, validate them as users, and then add or remove user shares in order to update the users_shared_with to match the given list finally returning the new list of shares.

class galaxy.managers.sharable.SharableModelFilters(app, **kwargs)

Bases: galaxy.managers.base.ModelFilterParser, galaxy.managers.taggable.TaggableFilterMixin, galaxy.managers.annotatable.AnnotatableFilterMixin, galaxy.managers.ratable.RatableFilterMixin

galaxy.managers.taggable module

Mixins for Taggable model managers and serializers.

class galaxy.managers.taggable.TaggableManagerMixin

Bases: object

tag_assoc = None

class of TagAssociation (e.g. HistoryTagAssociation)

get_tags(item)

Return a list of tag strings.

set_tags(item, new_tags, user=None)

Set an item’s tags from a list of strings.

class galaxy.managers.taggable.TaggableSerializerMixin

Bases: object

add_serializers()

serialize_tags(item, key, **context)

Return tags as a list of strings.

class galaxy.managers.taggable.TaggableDeserializerMixin

Bases: object

add_deserializers()

deserialize_tags(item, key, val, user=None, **context)

Make sure val is a valid list of tag strings and assign them.

Note: this will erase any previous tags.

class galaxy.managers.taggable.TaggableFilterMixin

Bases: object

filter_has_partial_tag(item, val)

Return True if any tag partially contains val.

filter_has_tag(item, val)

Return True if any tag exactly equals val.

galaxy.managers.tags module

class galaxy.managers.tags.ItemTagAssocInfo(item_class, tag_assoc_class, item_id_col)

Bases: object

__init__(item_class, tag_assoc_class, item_id_col)

class galaxy.managers.tags.TagManager(sa_session)

Bases: object

Manages CRUD operations related to tagging objects.

__init__(sa_session)

add_tags_from_list(user, item, new_tags_list)

remove_tags_from_list(user, item, tag_to_remove_list)

set_tags_from_list(user, item, new_tags_list)

get_tag_assoc_class(item_class)

Returns tag association class for item class.

get_id_col_in_item_tag_assoc_table(item_class)

Returns item id column in class’ item-tag association table.

get_community_tags(item=None, limit=None)

Returns community tags for an item.

get_tool_tags()

remove_item_tag(user, item, tag_name)

Remove a tag from an item.

delete_item_tags(user, item)

Delete tags from an item.

item_has_tag(user, item, tag)

Returns true if item is has a given tag.

apply_item_tag(user, item, name, value=None)

apply_item_tags(user, item, tags_str)

Apply tags to an item.

get_tags_str(tags)

Build a string from an item’s tags.

get_tag_by_id(tag_id)

Get a Tag object from a tag id.

get_tag_by_name(tag_name)

Get a Tag object from a tag name (string).

parse_tags(tag_str)

Returns a list of raw (tag-name, value) pairs derived from a string; method scrubs tag names and values as well. Return value is a list of (tag_name, tag_value) tuples.

class galaxy.managers.tags.GalaxyTagManager(sa_session)

Bases: galaxy.managers.tags.TagManager

__init__(sa_session)

class galaxy.managers.tags.CommunityTagManager(sa_session)

Bases: galaxy.managers.tags.TagManager

__init__(sa_session)

galaxy.managers.users module

Manager and Serializer for Users.

class galaxy.managers.users.UserManager(app)

Bases: galaxy.managers.base.ModelManager, galaxy.managers.deletable.PurgableManagerMixin

model_class

alias of galaxy.model.User

foreign_key_name = 'user'

create(webapp_name=None, **kwargs)

Create a new user.

delete(user)

by_email(email, filters=None, **kwargs)

Find a user by their email.

by_email_like(email_with_wildcards, filters=None, order_by=None, **kwargs)

Find a user searching with SQL wildcards.

is_admin(user, trans=None)

Return True if this user is an admin (or session is authenticated as admin).

Do not pass trans to simply check if an existing user object is an admin user, pass trans when checking permissions.

admins(filters=None, **kwargs)

Return a list of admin Users.

error_unless_admin(user, msg='Administrators only', **kwargs)

Raise an error if user is not an admin.

Raises:exceptions.AdminRequiredException – if user is not an admin.

is_anonymous(user)

Return True if user is anonymous.

error_if_anonymous(user, msg='Log-in required', **kwargs)

Raise an error if user is anonymous.

current_user(trans)

create_api_key(user)

Create and return an API key for user.

valid_api_key(user)

Return this most recent APIKey for this user or None if none have been created.

get_or_create_valid_api_key(user)

Return this most recent APIKey for this user or create one if none have been created.

preferences(user)

private_role(user)

sharing_roles(user)

default_permissions(user)

quota(user, total=False)

tags_used(user, tag_models=None)

Return a list of distinct ‘user_tname:user_value’ strings that the given user has used.

class galaxy.managers.users.UserSerializer(app)

Bases: galaxy.managers.base.ModelSerializer, galaxy.managers.deletable.PurgableSerializerMixin

model_manager_class

alias of UserManager

__init__(app)

Convert a User and associated data to a dictionary representation.

add_serializers()

class galaxy.managers.users.UserDeserializer(app, validator=None, **kwargs)

Bases: galaxy.managers.base.ModelDeserializer

Service object for validating and deserializing dictionaries that update/alter users.

model_manager_class

alias of UserManager

add_deserializers()

deserialize_username(item, key, username, trans=None, **context)

class galaxy.managers.users.CurrentUserSerializer(app)

Bases: galaxy.managers.users.UserSerializer

model_manager_class

alias of UserManager

serialize(user, keys, **kwargs)

Override to return at least some usage info if user is anonymous.

serialize_current_anonymous_user(user, keys, trans=None, **kwargs)

class galaxy.managers.users.AdminUserFilterParser(app, **kwargs)

Bases: galaxy.managers.base.ModelFilterParser, galaxy.managers.deletable.PurgableFiltersMixin

model_manager_class

alias of UserManager

model_class

alias of galaxy.model.User

galaxy.managers.visualizations module

Manager and Serializers for Visualizations.

Visualizations are saved configurations/variables used to reproduce a specific view in a Galaxy visualization.

class galaxy.managers.visualizations.VisualizationManager(app, *args, **kwargs)

Bases: galaxy.managers.sharable.SharableModelManager

Handle operations outside and between visualizations and other models.

model_class

alias of galaxy.model.Visualization

foreign_key_name = 'visualization'

user_share_model

alias of galaxy.model.VisualizationUserShareAssociation

tag_assoc

alias of galaxy.model.VisualizationTagAssociation

annotation_assoc

alias of galaxy.model.VisualizationAnnotationAssociation

rating_assoc

alias of galaxy.model.VisualizationRatingAssociation

__init__(app, *args, **kwargs)

class galaxy.managers.visualizations.VisualizationSerializer(app)

Bases: galaxy.managers.sharable.SharableModelSerializer

Interface/service object for serializing visualizations into dictionaries.

model_manager_class

alias of VisualizationManager

SINGLE_CHAR_ABBR = 'v'

__init__(app)

add_serializers()

class galaxy.managers.visualizations.VisualizationDeserializer(app)

Bases: galaxy.managers.sharable.SharableModelDeserializer

Interface/service object for validating and deserializing dictionaries into visualizations.

model_manager_class

alias of VisualizationManager

__init__(app)

add_deserializers()

galaxy.managers.workflows module

class galaxy.managers.workflows.WorkflowsManager(app)

Bases: object

Handle CRUD type operations related to workflows. More interesting stuff regarding workflow execution, step sorting, etc… can be found in the galaxy.workflow module.

__init__(app)

get_stored_workflow(trans, workflow_id)

Use a supplied ID (UUID or encoded stored workflow ID) to find a workflow.

get_stored_accessible_workflow(trans, workflow_id)

Get a stored workflow from a encoded stored workflow id and make sure it accessible to the user.

get_owned_workflow(trans, encoded_workflow_id)

Get a workflow (non-stored) from a encoded workflow id and make sure it accessible to the user.

check_security(trans, has_workflow, check_ownership=True, check_accessible=True)

check accessibility or ownership of workflows, storedworkflows, and workflowinvocations. Throw an exception or returns True if user has needed level of access.

get_invocation(trans, decoded_invocation_id)

cancel_invocation(trans, decoded_invocation_id)

get_invocation_step(trans, decoded_workflow_invocation_step_id)

update_invocation_step(trans, decoded_workflow_invocation_step_id, action)

build_invocations_query(trans, stored_workflow_id=None, history_id=None, user_id=None)

Get invocations owned by the current user.

serialize_workflow_invocation(invocation, **kwd)

serialize_workflow_invocations(invocations, **kwd)

class galaxy.managers.workflows.CreatedWorkflow(stored_workflow, workflow, missing_tools)

Bases: tuple

missing_tools

Alias for field number 2

stored_workflow

Alias for field number 0

workflow

Alias for field number 1

class galaxy.managers.workflows.WorkflowContentsManager(app)

Bases: galaxy.model.item_attrs.UsesAnnotations

__init__(app)

ensure_raw_description(dict_or_raw_description)

normalize_workflow_format(trans, as_dict)

Process incoming workflow descriptions for consumption by other methods.

Currently this mostly means converting format 2 workflows into standard Galaxy workflow JSON for consumption for the rest of this module. In the future we will want to be a lot more percise about this - preserve the original description along side the data model and apply updates in a way that largely preserves YAML structure so workflows can be extracted.

build_workflow_from_raw_description(trans, raw_workflow_description, source=None, add_to_menu=False, publish=False, create_stored_workflow=True, exact_tools=True, fill_defaults=False)

update_workflow_from_raw_description(trans, stored_workflow, raw_workflow_description, **kwds)

workflow_to_dict(trans, stored, style='export', version=None)

Export the workflow contents to a dictionary ready for JSON-ification and to be sent out via API for instance. There are three styles of export allowed ‘export’, ‘instance’, and ‘editor’. The Galaxy team will do its best to preserve the backward compatibility of the ‘export’ style - this is the export method meant to be portable across Galaxy instances and over time. The ‘editor’ style is subject to rapid and unannounced changes. The ‘instance’ export option describes the workflow in a context more tied to the current Galaxy instance and includes fields like ‘url’ and ‘url’ and actual unencoded step ids instead of ‘order_index’.

exception galaxy.managers.workflows.MissingToolsException(workflow, errors)

Bases: galaxy.exceptions.MessageException

__init__(workflow, errors)

class galaxy.managers.workflows.RawWorkflowDescription(as_dict, workflow_path=None)

Bases: object

__init__(as_dict, workflow_path=None)

class galaxy.managers.workflows.Format2ConverterGalaxyInterface

Bases: gxformat2.interface.ImporterGalaxyInterface

import_workflow(workflow, **kwds)