def get_dbmapping(syn: Synapse, projectid: str) -> dict:
"""Gets database mapping information
Args:
syn: Synapse connection
projectid: Project id where new data lives
Returns:
{'synid': database mapping syn id,
'df': database mapping pd.DataFrame}
"""
project_ent = syn.get(projectid)
dbmapping_synid = project_ent.annotations.get("dbMapping", "")[0]
database_mapping = syn.tableQuery(f"select * from {dbmapping_synid}")
database_mappingdf = database_mapping.asDataFrame()
return {"synid": dbmapping_synid, "df": database_mappingdf}
def get_center_invalid_errors(syn: Synapse, error_tracker_synid: str) -> dict:
"""Get all invalid errors per center
Args:
syn: Synapse connection
error_tracker_synid: Synapse id of invalid error database table
Returns:
dict: center - file error string
"""
error_tracker = syn.tableQuery(f"SELECT * FROM {error_tracker_synid}")
error_trackerdf = error_tracker.asDataFrame()
center_errorsdf = error_trackerdf.groupby("center")
center_error_map = {}
for center, df in center_errorsdf:
center_error_map[center] = _combine_center_file_errors(syn, df)
return center_error_map
def stop_submission_over_quota(syn: Synapse,
submission_view: Union[str,
SubmissionViewSchema],
quota: int = sys.maxsize):
"""Stops any submission that has exceeded the run time quota by using
submission views. A submission view must first exist.
Rerunning submissions will require setting TimeRemaining annotation
to a positive integer.
Args:
syn: Synapse connection
submission_view: Submission View or its Synapse Id.
quota: Quota in milliseconds. Default is sys.maxsize.
One hour is 3600000.
"""
if not isinstance(quota, int):
raise ValueError("quota must be an integer")
if quota <= 0:
raise ValueError("quota must be larger than 0")
try:
view_query = syn.tableQuery(
f"select {WORKFLOW_LAST_UPDATED_KEY}, {WORKFLOW_START_KEY}, id, "
f"status from {id_of(submission_view)} where "
"status = 'EVALUATION_IN_PROGRESS'")
except SynapseHTTPError as http_error:
raise ValueError(
"Submission view must have columns: "
f"{WORKFLOW_LAST_UPDATED_KEY}, {WORKFLOW_START_KEY}, id"
) from http_error
view_querydf = view_query.asDataFrame()
runtime = (view_querydf[WORKFLOW_LAST_UPDATED_KEY] -
view_querydf[WORKFLOW_START_KEY])
submissions_over_quota_idx = runtime > quota
over_quotadf = view_querydf[submissions_over_quota_idx]
for index, row in over_quotadf.iterrows():
add_annotations = {TIME_REMAINING_KEY: 0}
annotations.annotate_submission(syn,
row['id'],
add_annotations,
is_private=False,
force=True)