def test_get_db_credentials_exceptions(env_prefix, skipos, user, password,
defaults, expected):
if not skipos:
os.environ[env_prefix + 'USER'] = user
os.environ[env_prefix + 'PASSWORD'] = password
try:
with pytest.raises(qu.CredentialsException):
qu.get_db_credentials(env_prefix=env_prefix, **defaults)
finally:
if not skipos:
os.environ.pop(env_prefix + 'USER')
os.environ.pop(env_prefix + 'PASSWORD')
def set_segmentation_run_id(self, data, **kwargs):
"""if segmentation_run_id not provided, query the database
using the other provided args
"""
# If we already have a prod manifest no need to query DB
if "prod_segmentation_run_manifest" in data:
return data
if "segmentation_run_id" not in data:
if not all(
i in data for i in
["ophys_experiment_id", "ophys_segmentation_commit_hash"]):
raise TransformPipelineException(
"if omitting arg segmentation_run_id, must "
"include args ophys_experiment_id and "
"ophys_segmentation_commit_hash")
db_credentials = query_utils.get_db_credentials(
env_prefix="LABELING_", **query_utils.label_defaults)
db_connection = query_utils.DbConnection(**db_credentials)
query_string = (
"SELECT id FROM segmentation_runs WHERE "
f"ophys_experiment_id={data['ophys_experiment_id']} AND "
"ophys_segmentation_commit_hash="
f"'{data['ophys_segmentation_commit_hash']}'")
entries = db_connection.query(query_string)
if len(entries) != 1:
raise TransformPipelineException(
f"{query_string} did not return exactly 1 result")
data['segmentation_run_id'] = entries[0]['id']
return data
def test_get_db_credentials(env_prefix, user, password, defaults, expected):
os.environ[env_prefix + 'USER'] = user
os.environ[env_prefix + 'PASSWORD'] = password
try:
creds = qu.get_db_credentials(env_prefix=env_prefix, **defaults)
assert creds == expected
finally:
os.environ.pop(env_prefix + 'USER')
os.environ.pop(env_prefix + 'PASSWORD')
# LIMS is a little weird for not storing the actual movie path
# check to be sure.
raise SegmentationManifestException(
f"for experiment {result['id']} LIMS has "
f"nframes = {result['nframes']} "
f"but the found video file {video_path} "
f"has nframes = {nframes_h5}")
manifest['manifest'].append({
'experiment_id': result['id'],
'nbinned': int(result['nframes'] / self.args['bin_size']),
'input_video': str(video_path)
})
self.output(manifest, indent=2)
self.logger.info(f"wrote {self.args['output_json']}")
if __name__ == "__main__": # pragma: no cover
lims_credentials = qu.get_db_credentials(
env_prefix="LIMS_",
**qu.lims_defaults)
lims_connection = qu.DbConnection(**lims_credentials)
label_credentials = qu.get_db_credentials(
env_prefix="LABELING_",
**qu.label_defaults)
label_connection = qu.DbConnection(**label_credentials)
sm = SegmentationManifest()
sm.run(lims_connection, label_connection)
manifest['full-video-source-ref'] = str(full_video_path)
manifest['video-source-ref'] = str(sub_video_path)
manifest['max-source-ref'] = str(max_proj_path)
manifest['avg-source-ref'] = str(avg_proj_path)
manifest['trace-source-ref'] = str(trace_path)
manifest['full-outline-source-ref'] = str(full_outline_path)
if 'output_manifest' in self.args:
manifests.append(manifest)
else:
insert_str = insert_str_template.format(
json.dumps(manifest), os.environ['TRANSFORM_HASH'],
roi.roi_id)
insert_statements.append(insert_str)
if 'output_manifest' in self.args:
with open(self.args['output_manifest'], "w") as fp:
jsonlines.Writer(fp).write_all(manifests)
else:
db_conn.bulk_insert(insert_statements)
if __name__ == "__main__": # pragma: no cover
db_credentials = query_utils.get_db_credentials(
env_prefix="LABELING_", **query_utils.label_defaults)
db_connection = query_utils.DbConnection(**db_credentials)
pipeline = TransformPipeline()
pipeline.run(db_connection)