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Source code for galaxy.managers.hdcas
"""
Manager and Serializer for HDCAs.
HistoryDatasetCollectionAssociations (HDCAs) are datasets contained or created in a
history.
"""
import logging
from typing import Dict
from galaxy import model
from galaxy.managers import (
annotatable,
base,
deletable,
hdas,
secured,
taggable
)
from galaxy.managers.collections_util import get_hda_and_element_identifiers
from galaxy.structured_app import MinimalManagerApp
from galaxy.util.zipstream import ZipstreamWrapper
log = logging.getLogger(__name__)
[docs]def stream_dataset_collection(dataset_collection_instance, upstream_mod_zip=False, upstream_gzip=False):
archive_name = f"{dataset_collection_instance.hid}: {dataset_collection_instance.name}"
archive = ZipstreamWrapper(
archive_name=archive_name,
upstream_mod_zip=upstream_mod_zip,
upstream_gzip=upstream_gzip,
)
names, hdas = get_hda_and_element_identifiers(dataset_collection_instance)
for name, hda in zip(names, hdas):
if hda.state != hda.states.OK:
continue
for file_path, relpath in hda.datatype.to_archive(dataset=hda, name=name):
archive.write(file_path, relpath)
return archive
[docs]def set_collection_attributes(dataset_element, *payload):
for attribute, value in payload:
setattr(dataset_element, attribute[1], value[1])
# TODO: to DatasetCollectionInstanceManager
[docs]class HDCAManager(
base.ModelManager,
secured.AccessibleManagerMixin,
secured.OwnableManagerMixin,
deletable.PurgableManagerMixin,
taggable.TaggableManagerMixin,
annotatable.AnnotatableManagerMixin):
"""
Interface/service object for interacting with HDCAs.
"""
model_class = model.HistoryDatasetCollectionAssociation
foreign_key_name = 'history_dataset_collection_association'
tag_assoc = model.HistoryDatasetCollectionTagAssociation
annotation_assoc = model.HistoryDatasetCollectionAssociationAnnotationAssociation
[docs] def map_datasets(self, 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.
"""
returned = []
# lots of nesting going on within the nesting
collection = content.collection if hasattr(content, 'collection') else content
this_parents = (content, ) + parents
for element in collection.elements:
next_parents = (element, ) + this_parents
if element.is_collection:
processed_list = self.map_datasets(element.child_collection, fn, *next_parents)
returned.extend(processed_list)
else:
processed = fn(element.dataset_instance, *next_parents)
returned.append(processed)
return returned
[docs] def update_attributes(self, content, payload: Dict):
# pre-requisite checked that attributes are valid
self.map_datasets(content, fn=lambda item, *args: set_collection_attributes(item, payload.items()))
# serializers
# -----------------------------------------------------------------------------
[docs]class DCESerializer(base.ModelSerializer):
"""
Serializer for DatasetCollectionElements.
"""
[docs] def __init__(self, app: MinimalManagerApp):
super().__init__(app)
self.hda_serializer = hdas.HDASerializer(app)
self.dc_serializer = DCSerializer(app, dce_serializer=self)
self.default_view = 'summary'
self.add_view('summary', [
'id', 'model_class',
'element_index',
'element_identifier',
'element_type',
'object'
])
[docs] def add_serializers(self):
super().add_serializers()
self.serializers.update({
'model_class': lambda *a, **c: 'DatasetCollectionElement',
'object': self.serialize_object
})
[docs] def serialize_object(self, item, key, **context):
if item.hda:
return self.hda_serializer.serialize_to_view(item.hda, view='summary', **context)
if item.child_collection:
return self.dc_serializer.serialize_to_view(item.child_collection, view='detailed', **context)
return 'object'
[docs]class DCSerializer(base.ModelSerializer):
"""
Serializer for DatasetCollections.
"""
[docs] def __init__(self, app: MinimalManagerApp, dce_serializer=None):
super().__init__(app)
self.dce_serializer = dce_serializer or DCESerializer(app)
self.default_view = 'summary'
self.add_view('summary', [
'id',
'create_time',
'update_time',
'collection_type',
'populated_state',
'populated_state_message',
'element_count',
])
self.add_view('detailed', [
'populated',
'elements',
], include_keys_from='summary')
[docs] def add_serializers(self):
super().add_serializers()
self.serializers.update({
'model_class': lambda *a, **c: 'DatasetCollection',
'elements': self.serialize_elements,
})
[docs] def serialize_elements(self, item, key, **context):
returned = []
for element in item.elements:
serialized = self.dce_serializer.serialize_to_view(element, view='summary', **context)
returned.append(serialized)
return returned
[docs]class DCASerializer(base.ModelSerializer):
"""
Base (abstract) Serializer class for HDCAs and LDCAs.
"""
[docs] def __init__(self, app: MinimalManagerApp, dce_serializer=None):
super().__init__(app)
self.dce_serializer = dce_serializer or DCESerializer(app)
self.default_view = 'summary'
self.add_view('summary', [
'id',
'create_time', 'update_time',
'collection_type',
'populated_state',
'populated_state_message',
'element_count',
])
self.add_view('detailed', [
'populated',
'elements',
], include_keys_from='summary')
[docs] def add_serializers(self):
super().add_serializers()
# most attributes are (kinda) proxied from DCs - we need a serializer to proxy to
self.dc_serializer = DCSerializer(self.app)
# then set the serializers to point to it for those attrs
collection_keys = [
'create_time',
'update_time',
'collection_type',
'populated',
'populated_state',
'populated_state_message',
'elements',
'element_count',
]
for key in collection_keys:
self.serializers[key] = self._proxy_to_dataset_collection(key=key)
def _proxy_to_dataset_collection(self, serializer=None, key=None):
# dataset_collection associations are (rough) proxies to datasets - access their serializer using this remapping fn
# remapping done by either kwarg key: IOW dataset attr key (e.g. populated_state)
# or by kwarg serializer: a function that's passed in (e.g. elements)
if key:
return lambda i, k, **c: self.dc_serializer.serialize(i.collection, [k], **c)[k]
if serializer:
return lambda i, k, **c: serializer(i.collection, key or k, **c)
raise TypeError('kwarg serializer or key needed')
[docs]class HDCASerializer(
DCASerializer,
taggable.TaggableSerializerMixin,
annotatable.AnnotatableSerializerMixin):
"""
Serializer for HistoryDatasetCollectionAssociations.
"""
[docs] def __init__(self, app: MinimalManagerApp):
super().__init__(app)
self.hdca_manager = HDCAManager(app)
self.default_view = 'summary'
self.add_view('summary', [
'id',
'type_id',
'name',
'history_id', 'hid',
'history_content_type',
'collection_type',
'populated_state',
'populated_state_message',
'element_count',
'job_source_id',
'job_source_type',
'name',
'type_id',
'deleted',
# 'purged',
'visible',
'type', 'url',
'create_time', 'update_time',
'tags', # TODO: detail view only (maybe),
'contents_url'
])
self.add_view('detailed', [
'populated',
'elements'
], include_keys_from='summary')
# fields for new beta web client, there is no summary/detailed split any more
self.add_view('betawebclient', [
# common to hda
'create_time',
'deleted',
'hid',
'history_content_type',
'history_id',
'id',
'name',
'tags',
'type',
'type_id',
'update_time',
'url',
'visible',
# hdca only
'collection_id',
'collection_type',
'contents_url',
'element_count',
'job_source_id',
'job_source_type',
'job_state_summary',
'populated',
'populated_state',
'populated_state_message',
])
[docs] def add_serializers(self):
super().add_serializers()
taggable.TaggableSerializerMixin.add_serializers(self)
annotatable.AnnotatableSerializerMixin.add_serializers(self)
self.serializers.update({
'model_class': lambda *a, **c: self.hdca_manager.model_class.__class__.__name__,
# TODO: remove
'type': lambda *a, **c: 'collection',
# part of a history and container
'history_id': self.serialize_id,
'history_content_type': lambda *a, **c: self.hdca_manager.model_class.content_type,
'type_id': self.serialize_type_id,
'job_source_id': self.serialize_id,
'url': lambda i, k, **c: self.url_for('history_content_typed',
history_id=self.app.security.encode_id(i.history_id),
id=self.app.security.encode_id(i.id),
type=self.hdca_manager.model_class.content_type),
'contents_url': self.generate_contents_url,
'job_state_summary': self.serialize_job_state_summary
})
[docs] def generate_contents_url(self, hdca, key, **context):
encode_id = self.app.security.encode_id
contents_url = self.url_for('contents_dataset_collection',
hdca_id=encode_id(hdca.id),
parent_id=encode_id(hdca.collection_id))
return contents_url
[docs] def serialize_job_state_summary(self, hdca, key, **context):
states = hdca.job_state_summary.__dict__.copy()
del states['_sa_instance_state']
del states['hdca_id']
return states