def _get_samples(self):
samples_map = {}
derived_from_graph = Graph()
project = self.manifest.get_project()
for biomaterial in self.manifest.get_biomaterials():
archive_entity = ArchiveEntity()
archive_entity.manifest_id = self.manifest.manifest_id
archive_type = "sample"
archive_entity.archive_entity_type = archive_type
archive_entity.id = self.generate_archive_entity_id(
archive_type, biomaterial.data)
archive_entity.data = {
'biomaterial': biomaterial.data,
'project': project
}
archive_entity.metadata_uuids = [
biomaterial.data['uuid']['uuid'], project['uuid']['uuid']
]
archive_entity.accessioned_metadata_uuids = [
biomaterial.data['uuid']['uuid']
]
if biomaterial.derived_by_process:
# TODO protocols will be needed for samples conversion
# archive_entity.data.update(biomaterial.derived_with_protocols)
sample_links = []
for derived_from in biomaterial.derived_from_biomaterials:
derived_from_alias = self.generate_archive_entity_id(
'sample', derived_from)
derived_from_graph.add_edge(derived_from_alias,
archive_entity.id)
sample_links.append({
'alias': derived_from_alias,
'relationshipNature': 'derived from'
})
links = {'sampleRelationships': sample_links}
archive_entity.links = links
samples_map[archive_entity.id] = archive_entity
sorted_samples = derived_from_graph.topological_sort()
priority_samples = [
samples_map.get(sample) for sample in sorted_samples
if samples_map.get(sample)
]
orphan_samples = [
samples_map.get(sample) for sample in samples_map.keys()
if sample not in priority_samples
]
return priority_samples + orphan_samples
def _get_sequencing_experiments(self):
process = self.manifest.get_assay_process()
if not process:
return []
input_biomaterial = self.manifest.get_input_biomaterial()
archive_entity = ArchiveEntity()
archive_entity.manifest_id = self.manifest.manifest_id
archive_type = "sequencingExperiment"
archive_entity.archive_entity_type = archive_type
archive_entity.id = self.generate_archive_entity_id(
archive_type, process)
lib_prep_protocol = self.manifest.get_library_preparation_protocol()
seq_protocol = self.manifest.get_sequencing_protocol()
archive_entity.data = {
'process': process,
'library_preparation_protocol': lib_prep_protocol,
'sequencing_protocol': seq_protocol,
'input_biomaterial': input_biomaterial
}
archive_entity.metadata_uuids = [
lib_prep_protocol['uuid']['uuid'],
seq_protocol['uuid']['uuid'],
input_biomaterial['uuid']['uuid'],
process['uuid']['uuid'],
]
archive_entity.accessioned_metadata_uuids = [process['uuid']['uuid']]
links = {}
links['studyRef'] = {
"alias":
self.generate_archive_entity_id('study',
self.manifest.get_project())
}
links['sampleUses'] = []
sample_ref = {
'sampleRef': {
"alias":
self.generate_archive_entity_id('sample', input_biomaterial)
}
}
links['sampleUses'].append(sample_ref)
archive_entity.links = links
return [archive_entity]
def _get_projects(self):
project = self.manifest.get_project()
if not project:
return []
archive_entity = ArchiveEntity()
archive_type = "project"
archive_entity.archive_entity_type = archive_type
archive_entity.id = self.generate_archive_entity_id(archive_type, project)
archive_entity.data = {"project": project}
archive_entity.metadata_uuids = [project['uuid']['uuid']]
archive_entity.accessioned_metadata_uuids = [project['uuid']['uuid']]
archive_entity.manifest_id = self.manifest.manifest_id
return [archive_entity]
def _get_studies(self):
project = self.manifest.get_project()
if not project:
return []
archive_entity = ArchiveEntity()
archive_entity.manifest_id = self.manifest.manifest_id
archive_type = "study"
archive_entity.archive_entity_type = archive_type
archive_entity.id = self.generate_archive_entity_id(archive_type, project)
archive_entity.data = {"project": project}
archive_entity.metadata_uuids = [project['uuid']['uuid']]
archive_entity.accessioned_metadata_uuids = [project['uuid']['uuid']]
archive_entity.links = {
"projectRef": {
"alias": self.generate_archive_entity_id('project', project)
}
}
return [archive_entity]
def _get_sequencing_runs(self):
process = self.manifest.get_assay_process()
lib_prep_protocol = self.manifest.get_library_preparation_protocol()
files = self.manifest.get_files()
lanes = {}
# Index files by lane index
for file in files:
lane_index = file.get('content').get('lane_index', 1)
if lane_index not in lanes:
lanes[lane_index] = []
lanes[lane_index].append(file)
archive_entities = []
for lane_index in lanes.keys():
lane_files = lanes.get(lane_index)
archive_entity = ArchiveEntity()
archive_entity.manifest_id = self.manifest.manifest_id
archive_type = "sequencingRun"
archive_entity.archive_entity_type = archive_type
archive_entity.id = self.generate_archive_entity_id(
archive_type, process)
archive_entity.data = {
'library_preparation_protocol': lib_prep_protocol,
'process': process,
'files': lane_files,
'manifest_id': archive_entity.manifest_id
}
metadata_uuids = [
lib_prep_protocol['uuid']['uuid'], process['uuid']['uuid']
]
file_uuids = [f['uuid']['uuid'] for f in lane_files]
metadata_uuids.extend(file_uuids)
archive_entity.metadata_uuids = metadata_uuids
archive_entity.accessioned_metadata_uuids = file_uuids
archive_entity.links = {
'assayRefs': [{
"alias":
self.generate_archive_entity_id('sequencingExperiment',
process)
}]
}
if len(lanes) > 1:
archive_entity.data['lane_index'] = lane_index
archive_entity.id = f'{archive_entity.id}_{lane_index}'
archive_entities.append(archive_entity)
return archive_entities