def prepare(self, data_set):
data = super(DataSetIndex, self).prepare(data_set)
investigation = data_set.get_investigation()
nodes = []
# TODO: optimize this query
if investigation is not None:
studies = investigation.study_set.all()
for study in studies:
assays = study.assay_set.all()
for assay in assays:
node_types = get_node_types(study.uuid, assay.uuid, files_only=True, filter_set=Node.FILES)
for node_type in node_types:
nodes = nodes + list( AnnotatedNode.objects.filter( node_type=node_type, study=study, assay=assay ).values() )
#for node in nodes:
# print node["node_name"] + " " + node["attribute_type"] + " " + node["attribute_value"]
# perform the template processing to render the
# text field with *all* of our node data visible for indexing
t = loader.select_template(('search/indexes/core/dataset_text.txt', ))
data['text'] = t.render(Context({'object': data_set,
'nodes': nodes}))
return data
def annotate_nodes(investigation_uuid):
"""
Adds all nodes in this investigation to the annotated nodes table for faster lookup.
"""
investigation = Investigation.objects.get(uuid=investigation_uuid)
studies = investigation.study_set.all()
for study in studies:
assays = study.assay_set.all()
for assay in assays:
node_types = get_node_types(study.uuid,
assay.uuid,
files_only=True,
filter_set=Node.FILES)
for node_type in node_types:
update_annotated_nodes(node_type,
study.uuid,
assay.uuid,
update=True)
index_annotated_nodes(node_type, study.uuid, assay.uuid)
# initialize attribute order for this assay
attribute_count = initialize_attribute_order(study, assay)
logger.info(
"Initialized attribute order with %d attributes for study = %s and assay = %s"
% (attribute_count, study, assay))
def annotate_nodes(investigation_uuid):
"""
Adds all nodes in this investigation to the annotated nodes table for faster lookup.
"""
investigation = Investigation.objects.get(uuid=investigation_uuid)
studies = investigation.study_set.all()
for study in studies:
assays = study.assay_set.all()
for assay in assays:
node_types = get_node_types(study.uuid, assay.uuid, files_only=True, filter_set=Node.FILES)
for node_type in node_types:
update_annotated_nodes( node_type, study.uuid, assay.uuid, update=True )
index_annotated_nodes( node_type, study.uuid, assay.uuid )
# initialize attribute order for this assay
attribute_count = initialize_attribute_order( study, assay )
logger.info( "Initialized attribute order with %d attributes for study = %s and assay = %s" % ( attribute_count, study, assay ) )
def prepare(self, data_set):
data = super(DataSetIndex, self).prepare(data_set)
investigation = data_set.get_investigation()
nodes = []
# TODO: optimize this query
if investigation is not None:
studies = investigation.study_set.all()
for study in studies:
assays = study.assay_set.all()
for assay in assays:
node_types = get_node_types(study.uuid,
assay.uuid,
files_only=True,
filter_set=Node.FILES)
for node_type in node_types:
nodes = nodes + list(
AnnotatedNode.objects.filter(node_type=node_type,
study=study,
assay=assay).values())
#for node in nodes:
# print node["node_name"] + " " + node["attribute_type"] + " " + node["attribute_value"]
# perform the template processing to render the
# text field with *all* of our node data visible for indexing
t = loader.select_template(
('search/indexes/core/dataset_text.txt', ))
data['text'] = t.render(
Context({
'object': data_set,
'nodes': nodes
}))
return data
