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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.exceptions import RequestParameterInvalidException
from galaxy.managers import (
annotatable,
base,
deletable,
hdas,
secured,
taggable,
)
from galaxy.managers.collections_util import get_hda_and_element_identifiers
from galaxy.model.tags import GalaxyTagHandler
from galaxy.structured_app import (
MinimalManagerApp,
StructuredApp,
)
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,
)
write_dataset_collection(dataset_collection_instance, archive)
return archive
[docs]def write_dataset_collection(dataset_collection_instance, archive):
if not dataset_collection_instance.collection.populated_optimized:
raise RequestParameterInvalidException("Attempt to write dataset collection that has not been populated yet")
names, hdas = get_hda_and_element_identifiers(dataset_collection_instance)
for name, hda in zip(names, hdas):
if hda.state != hda.states.OK or hda.purged or hda.dataset.purged:
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,
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 __init__(self, app: MinimalManagerApp):
"""
Set up and initialize other managers needed by hdas.
"""
super().__init__(app)
self.tag_handler = app[GalaxyTagHandler]
[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: StructuredApp):
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: StructuredApp, 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.
"""
app: StructuredApp
[docs] def __init__(self, app: StructuredApp, 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: StructuredApp):
super().__init__(app)
self.hdca_manager = HDCAManager(app)
self.default_view = "summary"
self.add_view(
"summary",
[
"id",
"type_id",
"name",
"history_id",
"collection_id",
"hid",
"history_content_type",
"collection_type",
"populated_state",
"populated_state_message",
"element_count",
"job_source_id",
"job_source_type",
"job_state_summary",
"name",
"deleted",
"visible",
"type",
"url",
"create_time",
"update_time",
"tags",
"contents_url",
],
)
self.add_view(
"detailed",
[
"populated",
"elements",
"elements_datatypes",
],
include_keys_from="summary",
)
[docs] def add_serializers(self):
super().add_serializers()
taggable.TaggableSerializerMixin.add_serializers(self)
annotatable.AnnotatableSerializerMixin.add_serializers(self)
serializers: Dict[str, base.Serializer] = {
"model_class": lambda item, key, **context: self.hdca_manager.model_class.__class__.__name__,
# TODO: remove
"type": lambda item, key, **context: "collection",
# part of a history and container
"history_id": self.serialize_id,
"history_content_type": lambda item, key, **context: self.hdca_manager.model_class.content_type,
"type_id": self.serialize_type_id,
"job_source_id": self.serialize_id,
"url": lambda item, key, **context: self.url_for(
"history_content_typed",
history_id=self.app.security.encode_id(item.history_id),
id=self.app.security.encode_id(item.id),
type=self.hdca_manager.model_class.content_type,
context=context,
),
"contents_url": self.generate_contents_url,
"job_state_summary": self.serialize_job_state_summary,
"elements_datatypes": self.serialize_elements_datatypes,
"collection_id": self.serialize_id,
}
self.serializers.update(serializers)
[docs] def generate_contents_url(self, item, key, **context):
encode_id = self.app.security.encode_id
trans = context.get("trans")
url_for = trans.url_builder if trans and trans.url_builder else self.url_for
contents_url = url_for(
"contents_dataset_collection", hdca_id=encode_id(item.id), parent_id=encode_id(item.collection_id)
)
return contents_url
[docs] def serialize_job_state_summary(self, item, key, **context):
return item.job_state_summary_dict
[docs] def serialize_elements_datatypes(self, item, key, **context):
extensions_set = item.dataset_dbkeys_and_extensions_summary[1]
return list(extensions_set)