def test_from_baton_wrapper_file_replicas(self):
replicas = [
baton_models.DataObjectReplica(number=1, checksum="123abc"),
baton_models.DataObjectReplica(number=2, checksum="abc"),]
data_obj = baton_models.DataObject(path='/humgen/projects/helic/123.bam', replicas=replicas)
raw_meta = IrodsRawFileMetadata.from_baton_wrapper(data_obj)
self.assertEqual(len(raw_meta.file_replicas), 2)
def test_check_more_than_one_replicas_when_ok(self):
replicas = [
baton_models.DataObjectReplica(number=1, checksum="123abc"),
baton_models.DataObjectReplica(number=2, checksum="abc")]
raw_metadata = IrodsRawFileMetadata(fpath='/seq/123/123.cram', file_replicas=replicas)
result = raw_metadata.ReplicasChecks.check_more_than_one_replicas(raw_metadata.file_replicas)
self.assertEqual(result.result, RESULT.SUCCESS)
def test_from_raw_metadata_only_replicas(self):
replicas = [
baton_models.DataObjectReplica(number=1, checksum="123abc"),
baton_models.DataObjectReplica(number=2, checksum="abc"),]
raw_metadata = IrodsRawFileMetadata(fpath='/seq/123.bam', file_replicas=replicas)
seq_metadata = IrodsSeqFileMetadata.from_raw_metadata(raw_metadata)
expected = {'name': set(), 'accession_number': set(), 'internal_id': set()}
self.assertEqual(seq_metadata.samples, expected)
self.assertEqual(seq_metadata.libraries, expected)
self.assertEqual(seq_metadata.checksum_in_meta, set())
def test_from_baton_wrapper_full_obj(self):
user = "******"
acl = [baton_models.AccessControl(user, level=baton_models.AccessControl.Level.OWN)]
replicas = [
baton_models.DataObjectReplica(number=1, checksum="123abc", host='hgi-dev', resource_name='irods-s1', up_to_date=True),
baton_models.DataObjectReplica(number=2, checksum="abc", host='hgi-dev-wow', resource_name='irods-s2', up_to_date=True),]
metadata = baton_coll.IrodsMetadata({'study': set(['BLUEPRINT'])})
data_obj = baton_models.DataObject(path='/somepath/file.txt', access_controls=acl, metadata=metadata, replicas=replicas)
raw_meta = IrodsRawFileMetadata.from_baton_wrapper(data_obj)
self.assertEqual(raw_meta.fpath, '/somepath/file.txt')
self.assertEqual(len(raw_meta.file_replicas), 2)
self.assertEqual(len(raw_meta.acls), 1)
self.assertEqual(raw_meta.acls[0].zone, 'humgen')
self.assertEqual(raw_meta.acls[0].access_group, 'hgi')
def test_from_baton_wrapper_missing_bits(self):
replicas = [
baton_models.DataObjectReplica(number=1, checksum="123abc", host='hgi-dev', resource_name='irods-s1', up_to_date=True)]
metadata = baton_coll.IrodsMetadata({'study': set(['BLUEPRINT'])})
data_obj = baton_models.DataObject(path='/somepath/file.txt', metadata=metadata, replicas=replicas)
raw_meta = IrodsRawFileMetadata.from_baton_wrapper(data_obj)
self.assertEqual(len(raw_meta.file_replicas), 1)
self.assertEqual(len(raw_meta.acls), 0)
def test_from_baton_wrapper_all_ok(self):
user = "******"
acl = [baton_models.AccessControl(user, level=baton_models.AccessControl.Level.OWN)]
replicas = [
baton_models.DataObjectReplica(number=1, checksum="123abc", host='hgi-dev', resource_name='irods-s1', up_to_date=True)]
data_obj = baton_models.DataObject(path='/somepath/file.txt', access_controls=acl, replicas=replicas)
raw_meta = IrodsRawFileMetadata.from_baton_wrapper(data_obj)
self.assertEqual(raw_meta.fpath, '/somepath/file.txt')
self.assertEqual(len(raw_meta.file_replicas), 1)
self.assertEqual(len(raw_meta.acls), 1)
self.assertEqual(raw_meta.acls[0].zone, 'humgen')
self.assertEqual(raw_meta.acls[0].access_group, 'serapis')
def test_check_more_than_one_replicas_when_ok(self):
replicas = [
baton_models.DataObjectReplica(number=1, checksum="123abc"),
baton_models.DataObjectReplica(number=2, checksum="abc"),]
result = IrodsRawFileMetadata.ReplicasChecks.check_more_than_one_replicas(replicas)
self.assertEqual(result.result, RESULT.SUCCESS)