def test_build_hisat2_index_from_assembly_ok(self):
manager = Hisat2IndexManager(self.wsURL, self.callback_url,
self.scratch)
ws = Workspace(self.wsURL)
genome_obj_info = ws.get_objects2({
'objects': [{
'ref': self.genome_ref
}],
'no_data': 1
})
# get the list of genome refs from the returned info.
# if there are no refs (or something funky with the return), this will be an empty list.
# this WILL fail if data is an empty list. But it shouldn't be, and we know because
# we have a real genome reference, or get_objects2 would fail.
genome_obj_refs = genome_obj_info.get('data', [{}])[0].get('refs', [])
# see which of those are of an appropriate type (ContigSet or Assembly), if any.
assembly_ref = list()
ref_params = [{'ref': x} for x in genome_obj_refs]
ref_info = ws.get_object_info3({'objects': ref_params})
for idx, info in enumerate(ref_info.get('infos')):
if "KBaseGenomeAnnotations.Assembly" in info[
2] or "KBaseGenomes.ContigSet" in info[2]:
assembly_ref.append(";".join(ref_info.get('paths')[idx]))
assembly_ref = assembly_ref[0]
idx_prefix = manager.get_hisat2_index(assembly_ref)
self.assertIn("kb_hisat2_idx", idx_prefix)
def build_index(self, object_ref):
"""
Uses the Hisat2IndexManager to build/retrieve the HISAT2 index files
based on the object ref.
"""
idx_manager = Hisat2IndexManager(self.workspace_url, self.callback_url,
self.working_dir)
return idx_manager.get_hisat2_index(object_ref)
def test_build_hisat2_index_from_assembly_ok(self):
manager = Hisat2IndexManager(self.wsURL, self.callback_url,
self.scratch)
idx_prefix = manager.get_hisat2_index(self.assembly_ref)
self.assertIn("kb_hisat2_idx", idx_prefix)
def test_build_hisat2_index_no_object(self):
manager = Hisat2IndexManager(self.wsURL, self.callback_url,
self.scratch)
with self.assertRaises(ValueError) as err:
manager.get_hisat2_index(self.single_end_ref_wt_1)
self.assertIn("Missing reference object", err.exception)