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Source code for galaxy.managers.collections
import logging
from sqlalchemy.orm import joinedload, Query
from galaxy import model
from galaxy.exceptions import (
ItemAccessibilityException,
MessageException,
RequestParameterInvalidException
)
from galaxy.managers.collections_util import validate_input_element_identifiers
from galaxy.model.dataset_collections import builder
from galaxy.model.dataset_collections.matching import MatchingCollections
from galaxy.model.dataset_collections.registry import DATASET_COLLECTION_TYPES_REGISTRY
from galaxy.model.dataset_collections.type_description import COLLECTION_TYPE_DESCRIPTION_FACTORY
from galaxy.model.mapping import GalaxyModelMapping
from galaxy.model.tags import GalaxyTagHandler
from galaxy.security.idencoding import IdEncodingHelper
from galaxy.util import (
validation
)
from .hdas import (
HDAManager,
HistoryDatasetAssociationNoHistoryException,
)
from .histories import HistoryManager
from .lddas import LDDAManager
log = logging.getLogger(__name__)
ERROR_INVALID_ELEMENTS_SPECIFICATION = "Create called with invalid parameters, must specify element identifiers."
ERROR_NO_COLLECTION_TYPE = "Create called without specifying a collection type."
[docs]class DatasetCollectionManager:
"""
Abstraction for interfacing with dataset collections instance - ideally abstracts
out model and plugin details.
"""
ELEMENTS_UNINITIALIZED = object()
[docs] def __init__(
self,
model: GalaxyModelMapping,
security: IdEncodingHelper,
hda_manager: HDAManager,
history_manager: HistoryManager,
tag_handler: GalaxyTagHandler,
ldda_manager: LDDAManager,
):
self.type_registry = DATASET_COLLECTION_TYPES_REGISTRY
self.collection_type_descriptions = COLLECTION_TYPE_DESCRIPTION_FACTORY
self.model = model
self.security = security
self.hda_manager = hda_manager
self.history_manager = history_manager
self.tag_handler = tag_handler
self.ldda_manager = ldda_manager
[docs] def precreate_dataset_collection_instance(self, trans, parent, name, structure, implicit_inputs=None, implicit_output_name=None, tags=None, completed_collection=None):
# TODO: prebuild all required HIDs and send them in so no need to flush in between.
dataset_collection = self.precreate_dataset_collection(structure, allow_unitialized_element=implicit_output_name is not None, completed_collection=completed_collection, implicit_output_name=implicit_output_name)
instance = self._create_instance_for_collection(
trans, parent, name, dataset_collection, implicit_inputs=implicit_inputs, implicit_output_name=implicit_output_name, flush=False, tags=tags
)
return instance
[docs] def precreate_dataset_collection(self, structure, allow_unitialized_element=True, completed_collection=None, implicit_output_name=None):
has_structure = not structure.is_leaf and structure.children_known
if not has_structure and allow_unitialized_element:
dataset_collection = model.DatasetCollectionElement.UNINITIALIZED_ELEMENT
elif not has_structure:
collection_type_description = structure.collection_type_description
dataset_collection = model.DatasetCollection(populated=False)
dataset_collection.collection_type = collection_type_description.collection_type
else:
collection_type_description = structure.collection_type_description
dataset_collection = model.DatasetCollection(populated=False)
dataset_collection.collection_type = collection_type_description.collection_type
elements = []
for index, (identifier, substructure) in enumerate(structure.children):
# TODO: Open question - populate these now or later?
element = None
if completed_collection and implicit_output_name:
job = completed_collection[index]
if job:
it = (jtiodca.dataset_collection for jtiodca in job.output_dataset_collections if jtiodca.name == implicit_output_name)
element = next(it, None)
if element is None:
if substructure.is_leaf:
element = model.DatasetCollectionElement.UNINITIALIZED_ELEMENT
else:
element = self.precreate_dataset_collection(substructure, allow_unitialized_element=allow_unitialized_element)
element = model.DatasetCollectionElement(
collection=dataset_collection,
element=element,
element_identifier=identifier,
element_index=index,
)
elements.append(element)
dataset_collection.element_count = len(elements)
return dataset_collection
[docs] def create(self, 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, history=None,
set_hid=True, flush=True, completed_job=None, output_name=None):
"""
PRECONDITION: security checks on ability to add to parent
occurred during load.
"""
# Trust embedded, newly created objects created by tool subsystem.
if trusted_identifiers is None:
trusted_identifiers = implicit_collection_info is not None
if element_identifiers and not trusted_identifiers:
validate_input_element_identifiers(element_identifiers)
if completed_job and output_name:
jtodca = next(a for a in completed_job.output_dataset_collection_instances if a.name == output_name)
dataset_collection = jtodca.dataset_collection_instance.collection
else:
dataset_collection = self.create_dataset_collection(
trans=trans,
collection_type=collection_type,
element_identifiers=element_identifiers,
elements=elements,
hide_source_items=hide_source_items,
copy_elements=copy_elements,
history=history,
)
implicit_inputs = []
if implicit_collection_info:
implicit_inputs = implicit_collection_info.get('implicit_inputs', [])
implicit_output_name = None
if implicit_collection_info:
implicit_output_name = implicit_collection_info["implicit_output_name"]
return self._create_instance_for_collection(
trans, parent, name, dataset_collection, implicit_inputs=implicit_inputs, implicit_output_name=implicit_output_name, tags=tags, set_hid=set_hid, flush=flush,
)
def _create_instance_for_collection(self, trans, parent, name, dataset_collection, implicit_output_name=None, implicit_inputs=None, tags=None, set_hid=True, flush=True):
if isinstance(parent, model.History):
dataset_collection_instance = model.HistoryDatasetCollectionAssociation(
collection=dataset_collection,
name=name,
)
if implicit_inputs:
for input_name, input_collection in implicit_inputs:
dataset_collection_instance.add_implicit_input_collection(input_name, input_collection)
if implicit_output_name:
dataset_collection_instance.implicit_output_name = implicit_output_name
log.debug("Created collection with %d elements" % (len(dataset_collection_instance.collection.elements)))
if set_hid:
parent.add_dataset_collection(dataset_collection_instance)
elif isinstance(parent, model.LibraryFolder):
dataset_collection_instance = model.LibraryDatasetCollectionAssociation(
collection=dataset_collection,
folder=parent,
name=name,
)
else:
message = "Internal logic error - create called with unknown parent type %s" % type(parent)
log.exception(message)
raise MessageException(message)
# Tags may be coming in as a dictionary of tag model objects if copying them from other
# existing Galaxy objects or as a list of strings if the tags are coming from user supplied
# values.
if isinstance(tags, list):
assert implicit_inputs is None, implicit_inputs
tags = self.tag_handler.add_tags_from_list(trans.user, dataset_collection_instance, tags)
else:
tags = self._append_tags(dataset_collection_instance, implicit_inputs, tags)
return self.__persist(dataset_collection_instance, flush=flush)
[docs] def create_dataset_collection(self, trans, collection_type, element_identifiers=None, elements=None,
hide_source_items=None, copy_elements=False, history=None):
# Make sure at least one of these is None.
assert element_identifiers is None or elements is None
if element_identifiers is None and elements is None:
raise RequestParameterInvalidException(ERROR_INVALID_ELEMENTS_SPECIFICATION)
if not collection_type:
raise RequestParameterInvalidException(ERROR_NO_COLLECTION_TYPE)
collection_type_description = self.collection_type_descriptions.for_collection_type(collection_type)
has_subcollections = collection_type_description.has_subcollections()
# If we have elements, this is an internal request, don't need to load
# objects from identifiers.
if elements is None:
elements = self._element_identifiers_to_elements(trans,
collection_type_description=collection_type_description,
element_identifiers=element_identifiers,
hide_source_items=hide_source_items,
copy_elements=copy_elements,
history=history)
else:
if has_subcollections:
# Nested collection - recursively create collections as needed.
self.__recursively_create_collections_for_elements(trans, elements, hide_source_items, copy_elements=copy_elements, history=history)
# else if elements is set, it better be an ordered dict!
if elements is not self.ELEMENTS_UNINITIALIZED:
type_plugin = collection_type_description.rank_type_plugin()
dataset_collection = builder.build_collection(type_plugin, elements)
else:
dataset_collection = model.DatasetCollection(populated=False)
dataset_collection.collection_type = collection_type
return dataset_collection
def _element_identifiers_to_elements(self,
trans,
collection_type_description,
element_identifiers,
hide_source_items=False,
copy_elements=False,
history=None):
if collection_type_description.has_subcollections():
# Nested collection - recursively create collections and update identifiers.
self.__recursively_create_collections_for_identifiers(trans, element_identifiers, hide_source_items, copy_elements, history=history)
new_collection = False
for element_identifier in element_identifiers:
if element_identifier.get("src") == "new_collection" and element_identifier.get('collection_type') == '':
new_collection = True
elements = self.__load_elements(trans=trans,
element_identifiers=element_identifier['element_identifiers'],
hide_source_items=hide_source_items,
copy_elements=copy_elements,
history=history)
if not new_collection:
elements = self.__load_elements(trans=trans,
element_identifiers=element_identifiers,
hide_source_items=hide_source_items,
copy_elements=copy_elements,
history=history)
return elements
def _append_tags(self, dataset_collection_instance, implicit_inputs=None, tags=None):
tags = tags or {}
implicit_inputs = implicit_inputs or []
for _, v in implicit_inputs:
for tag in v.auto_propagated_tags:
tags[tag.value] = tag
for _, tag in tags.items():
dataset_collection_instance.tags.append(tag.copy(cls=model.HistoryDatasetCollectionTagAssociation))
[docs] def collection_builder_for(self, dataset_collection):
return builder.BoundCollectionBuilder(dataset_collection)
[docs] def delete(self, trans, instance_type, id, recursive=False, purge=False):
dataset_collection_instance = self.get_dataset_collection_instance(trans, instance_type, id, check_ownership=True)
dataset_collection_instance.deleted = True
trans.sa_session.add(dataset_collection_instance)
if recursive:
for dataset in dataset_collection_instance.collection.dataset_instances:
try:
self.hda_manager.error_unless_owner(dataset, user=trans.get_user(), current_history=trans.history)
except HistoryDatasetAssociationNoHistoryException:
log.info("Cannot delete HistoryDatasetAssociation {}, HistoryDatasetAssociation has no associated History, cannot verify owner".format(dataset.id))
continue
if not dataset.deleted:
dataset.deleted = True
if purge and not dataset.purged:
self.hda_manager.purge(dataset)
trans.sa_session.flush()
[docs] def update(self, trans, instance_type, id, payload):
dataset_collection_instance = self.get_dataset_collection_instance(trans, instance_type, id, check_ownership=True)
if trans.user is None:
anon_allowed_payload = {}
if 'deleted' in payload:
anon_allowed_payload['deleted'] = payload['deleted']
if 'visible' in payload:
anon_allowed_payload['visible'] = payload['visible']
payload = self._validate_and_parse_update_payload(anon_allowed_payload)
else:
payload = self._validate_and_parse_update_payload(payload)
changed = self._set_from_dict(trans, dataset_collection_instance, payload)
return changed
[docs] def copy(self, trans, parent, source, encoded_source_id, copy_elements=False, dataset_instance_attributes=None):
"""
PRECONDITION: security checks on ability to add to parent occurred
during load.
"""
assert source == "hdca" # for now
source_hdca = self.__get_history_collection_instance(trans, encoded_source_id)
copy_kwds = {}
if copy_elements:
copy_kwds["element_destination"] = parent # e.g. a history
if dataset_instance_attributes is not None:
copy_kwds["dataset_instance_attributes"] = dataset_instance_attributes
new_hdca = source_hdca.copy(**copy_kwds)
new_hdca.copy_tags_from(target_user=trans.get_user(), source=source_hdca)
if not copy_elements:
parent.add_dataset_collection(new_hdca)
trans.sa_session.flush()
return new_hdca
def _set_from_dict(self, trans, dataset_collection_instance, new_data):
# send what we can down into the model
changed = dataset_collection_instance.set_from_dict(new_data)
# the rest (often involving the trans) - do here
if 'annotation' in new_data.keys() and trans.get_user():
dataset_collection_instance.add_item_annotation(trans.sa_session, trans.get_user(), dataset_collection_instance, new_data['annotation'])
changed['annotation'] = new_data['annotation']
if 'tags' in new_data.keys() and trans.get_user():
# set_tags_from_list will flush on its own, no need to add to 'changed' here and incur a second flush.
self.tag_handler.set_tags_from_list(trans.get_user(), dataset_collection_instance, new_data['tags'])
if changed.keys():
trans.sa_session.flush()
return changed
def _validate_and_parse_update_payload(self, payload):
validated_payload = {}
for key, val in payload.items():
if val is None:
continue
if key in ('name'):
val = validation.validate_and_sanitize_basestring(key, val)
validated_payload[key] = val
if key in ('deleted', 'visible'):
validated_payload[key] = validation.validate_boolean(key, val)
elif key == 'tags':
validated_payload[key] = validation.validate_and_sanitize_basestring_list(key, val)
return validated_payload
[docs] def history_dataset_collections(self, history, query):
collections = history.active_dataset_collections
collections = list(filter(query.direct_match, collections))
return collections
def __persist(self, dataset_collection_instance, flush=True):
context = self.model.context
context.add(dataset_collection_instance)
if flush:
context.flush()
return dataset_collection_instance
def __recursively_create_collections_for_identifiers(self, trans, element_identifiers, hide_source_items, copy_elements, history=None):
for element_identifier in element_identifiers:
try:
if element_identifier.get("src") != "new_collection":
# not a new collection, keep moving...
continue
except KeyError:
# Not a dictionary, just an id of an HDA - move along.
continue
# element identifier is a dict with src new_collection...
collection_type = element_identifier.get("collection_type")
collection = self.create_dataset_collection(
trans=trans,
collection_type=collection_type,
element_identifiers=element_identifier["element_identifiers"],
hide_source_items=hide_source_items,
copy_elements=copy_elements,
history=history,
)
element_identifier["__object__"] = collection
return element_identifiers
def __recursively_create_collections_for_elements(self, trans, elements, hide_source_items, copy_elements, history=None):
if elements is self.ELEMENTS_UNINITIALIZED:
return
new_elements = {}
for key, element in elements.items():
if isinstance(element, model.DatasetCollection):
continue
if element.get("src") != "new_collection":
continue
# element is a dict with src new_collection and
# and dict of named elements
collection_type = element.get("collection_type")
sub_elements = element["elements"]
collection = self.create_dataset_collection(
trans=trans,
collection_type=collection_type,
elements=sub_elements,
hide_source_items=hide_source_items,
copy_elements=copy_elements,
history=history,
)
new_elements[key] = collection
elements.update(new_elements)
def __load_elements(self, trans, element_identifiers, hide_source_items=False, copy_elements=False, history=None):
elements = {}
for element_identifier in element_identifiers:
elements[element_identifier["name"]] = self.__load_element(trans,
element_identifier=element_identifier,
hide_source_items=hide_source_items,
copy_elements=copy_elements,
history=history)
return elements
def __load_element(self, trans, element_identifier, hide_source_items, copy_elements, history=None):
# if not isinstance( element_identifier, dict ):
# # Is allowing this to just be the id of an hda too clever? Somewhat
# # consistent with other API methods though.
# element_identifier = dict( src='hda', id=str( element_identifier ) )
# Previously created collection already found in request, just pass
# through as is.
if "__object__" in element_identifier:
the_object = element_identifier["__object__"]
if the_object is not None and the_object.id:
context = self.model.context
if the_object not in context:
the_object = context.query(type(the_object)).get(the_object.id)
return the_object
# dataset_identifier is dict {src=hda|ldda|hdca|new_collection, id=<encoded_id>}
try:
src_type = element_identifier.get('src', 'hda')
except AttributeError:
raise MessageException("Dataset collection element definition (%s) not dictionary-like." % element_identifier)
encoded_id = element_identifier.get('id')
if not src_type or not encoded_id:
message_template = "Problem decoding element identifier %s - must contain a 'src' and a 'id'."
message = message_template % element_identifier
raise RequestParameterInvalidException(message)
tags = element_identifier.pop('tags', None)
tag_str = ''
if tags:
tag_str = ",".join(str(_) for _ in tags)
if src_type == 'hda':
decoded_id = int(trans.app.security.decode_id(encoded_id))
hda = self.hda_manager.get_accessible(decoded_id, trans.user)
if copy_elements:
element = self.hda_manager.copy(hda, history=history or trans.history, hide_copy=True)
else:
element = hda
if hide_source_items and self.hda_manager.get_owned(hda.id, user=trans.user, current_history=history or trans.history):
hda.visible = False
self.tag_handler.apply_item_tags(user=trans.user, item=element, tags_str=tag_str)
elif src_type == 'ldda':
element = self.ldda_manager.get(trans, encoded_id, check_accessible=True)
element = element.to_history_dataset_association(history or trans.history, add_to_history=True, visible=not hide_source_items)
self.tag_handler.apply_item_tags(user=trans.user, item=element, tags_str=tag_str)
elif src_type == 'hdca':
# TODO: Option to copy? Force copy? Copy or allow if not owned?
element = self.__get_history_collection_instance(trans, encoded_id).collection
# TODO: ldca.
else:
raise RequestParameterInvalidException("Unknown src_type parameter supplied '%s'." % src_type)
return element
[docs] def match_collections(self, 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.
"""
return MatchingCollections.for_collections(collections_to_match, self.collection_type_descriptions)
[docs] def get_dataset_collection_instance(self, trans, instance_type, id, **kwds):
"""
"""
if instance_type == "history":
return self.__get_history_collection_instance(trans, id, **kwds)
elif instance_type == "library":
return self.__get_library_collection_instance(trans, id, **kwds)
[docs] def get_dataset_collection(self, trans, encoded_id):
collection_id = int(trans.app.security.decode_id(encoded_id))
collection = trans.sa_session.query(trans.app.model.DatasetCollection).get(collection_id)
return collection
[docs] def apply_rules(self, hdca, rule_set, handle_dataset):
hdca_collection = hdca.collection
collection_type = hdca_collection.collection_type
elements = hdca_collection.elements
collection_type_description = self.collection_type_descriptions.for_collection_type(collection_type)
initial_data, initial_sources = self.__init_rule_data(elements, collection_type_description)
data, sources = rule_set.apply(initial_data, initial_sources)
collection_type = rule_set.collection_type
collection_type_description = self.collection_type_descriptions.for_collection_type(collection_type)
elements = self._build_elements_from_rule_data(collection_type_description, rule_set, data, sources, handle_dataset)
return elements
def _build_elements_from_rule_data(self, collection_type_description, rule_set, data, sources, handle_dataset):
identifier_columns = rule_set.identifier_columns
mapping_as_dict = rule_set.mapping_as_dict
elements = {}
for data_index, row_data in enumerate(data):
# For each row, find place in depth for this element.
collection_type_at_depth = collection_type_description
elements_at_depth = elements
for i, identifier_column in enumerate(identifier_columns):
identifier = row_data[identifier_column]
if i + 1 == len(identifier_columns):
# At correct final position in nested structure for this dataset.
if collection_type_at_depth.collection_type == "paired":
if identifier.lower() in ["f", "1", "r1", "forward"]:
identifier = "forward"
elif identifier.lower() in ["r", "2", "r2", "reverse"]:
identifier = "reverse"
else:
raise Exception("Unknown indicator of paired status encountered - only values of F, R, 1, 2, R1, R2, forward, or reverse are allowed.")
tags = []
if "group_tags" in mapping_as_dict:
columns = mapping_as_dict["group_tags"]["columns"]
for tag_column in columns:
tag = row_data[tag_column]
tags.append("group:%s" % tag)
if "tags" in mapping_as_dict:
columns = mapping_as_dict["tags"]["columns"]
for tag_column in columns:
tag = row_data[tag_column]
tags.append(tag)
effective_dataset = handle_dataset(sources[data_index]["dataset"], tags)
elements_at_depth[identifier] = effective_dataset
# log.info("Handling dataset [%s] with sources [%s], need to add tags [%s]" % (effective_dataset, sources, tags))
else:
collection_type_at_depth = collection_type_at_depth.child_collection_type_description()
found = False
if identifier in elements_at_depth:
elements_at_depth = elements_at_depth[identifier]["elements"]
found = True
if not found:
sub_collection = {}
sub_collection["src"] = "new_collection"
sub_collection["collection_type"] = collection_type_at_depth.collection_type
sub_collection["elements"] = {}
elements_at_depth[identifier] = sub_collection
elements_at_depth = sub_collection["elements"]
return elements
def __init_rule_data(self, elements, collection_type_description, parent_identifiers=None):
parent_identifiers = parent_identifiers or []
data, sources = [], []
for element in elements:
element_object = element.element_object
identifiers = parent_identifiers + [element.element_identifier]
if not element.is_collection:
data.append([])
source = {"identifiers": identifiers, "dataset": element_object, "tags": element_object.make_tag_string_list()}
sources.append(source)
else:
child_collection_type_description = collection_type_description.child_collection_type_description()
element_data, element_sources = self.__init_rule_data(
element_object.elements, child_collection_type_description, identifiers
)
data.extend(element_data)
sources.extend(element_sources)
return data, sources
def __get_history_collection_instance(self, trans, id, check_ownership=False, check_accessible=True):
instance_id = int(trans.app.security.decode_id(id))
collection_instance = trans.sa_session.query(trans.app.model.HistoryDatasetCollectionAssociation).get(instance_id)
if not collection_instance:
raise RequestParameterInvalidException(f"History dataset collection association {id} not found")
history = getattr(trans, 'history', collection_instance.history)
if check_ownership:
self.history_manager.error_unless_owner(collection_instance.history, trans.user, current_history=history)
if check_accessible:
self.history_manager.error_unless_accessible(collection_instance.history, trans.user, current_history=history)
return collection_instance
def __get_library_collection_instance(self, trans, id, check_ownership=False, check_accessible=True):
if check_ownership:
raise NotImplementedError("Functionality (getting library dataset collection with ownership check) unimplemented.")
instance_id = int(trans.security.decode_id(id))
collection_instance = trans.sa_session.query(trans.app.model.LibraryDatasetCollectionAssociation).get(instance_id)
if not collection_instance:
raise RequestParameterInvalidException(f"Library dataset collection association {id} not found")
if check_accessible:
if not trans.app.security_agent.can_access_library_item(trans.get_current_user_roles(), collection_instance, trans.user):
raise ItemAccessibilityException("LibraryDatasetCollectionAssociation is not accessible to the current user", type='error')
return collection_instance
[docs] def get_collection_contents_qry(self, parent_id, limit=None, offset=None):
"""Find first level of collection contents by containing collection parent_id"""
DCE = model.DatasetCollectionElement
qry = Query(DCE).filter(DCE.dataset_collection_id == parent_id)
qry = qry.order_by(DCE.element_index)
qry = qry.options(joinedload('child_collection'), joinedload('hda'))
if limit is not None:
qry = qry.limit(int(limit))
if offset is not None:
qry = qry.offset(int(offset))
return qry