diff options
| -rw-r--r-- | gn3/jobs.py | 13 | ||||
| -rw-r--r-- | gn3/json_encoders_decoders.py | 31 | ||||
| -rw-r--r-- | scripts/search_phenotypes.py | 12 |
3 files changed, 47 insertions, 9 deletions
diff --git a/gn3/jobs.py b/gn3/jobs.py index 8854a61..1af63f7 100644 --- a/gn3/jobs.py +++ b/gn3/jobs.py @@ -5,9 +5,10 @@ from uuid import UUID, uuid4 from datetime import datetime from redis import Redis - from pymonad.either import Left, Right, Either +from gn3 import json_encoders_decoders as jed + JOBS_NAMESPACE = "GN3::JOBS" class InvalidCommand(Exception): @@ -22,8 +23,8 @@ def job(redisconn: Redis, job_id: UUID) -> Either: the_job = redisconn.hgetall(job_key(job_id)) if the_job: return Right({ - **the_job, - "search_results": json.loads(the_job["search_results"]) + key: json.loads(value, object_hook=jed.custom_json_decoder) + for key, value in the_job.items() }) return Left({ "error": "NotFound", @@ -48,8 +49,10 @@ def create_job(redisconn: Redis, job_details: dict[str, Any]) -> UUID: def __create__(_job_command): job_id = job_details.get("job_id", uuid4()) redisconn.hset(job_key(job_id), mapping={ - **job_details, "job_id": job_id, "created": datetime.now(), "stdout": "", - "stderr": "", "status": "queued" + key: json.dumps(value, cls=jed.CustomJSONEncoder) for key, value in { + **job_details, "job_id": job_id, "created": datetime.now(), + "status": "queued" + }.items() }) return job_id def __raise__(err): diff --git a/gn3/json_encoders_decoders.py b/gn3/json_encoders_decoders.py new file mode 100644 index 0000000..be15b34 --- /dev/null +++ b/gn3/json_encoders_decoders.py @@ -0,0 +1,31 @@ +"""Custom json encoders for various purposes.""" +import json +from uuid import UUID +from datetime import datetime + +__ENCODERS__ = { + UUID: lambda obj: {"__type": "UUID", "__value": str(obj)}, + datetime: lambda obj: {"__type": "DATETIME", "__value": obj.isoformat()} +} + +class CustomJSONEncoder(json.JSONEncoder): + """ + A custom JSON encoder to handle cases where the default encoder fails. + """ + def default(self, obj):# pylint: disable=[arguments-renamed] + """Return a serializable object for `obj`.""" + if type(obj) in __ENCODERS__: + return __ENCODERS__[type(obj)](obj) + return json.JSONEncoder.default(self, obj) + + +__DECODERS__ = { + "UUID": UUID, + "DATETIME": datetime.fromisoformat +} + +def custom_json_decoder(obj_dict): + """Decode custom types""" + if "__type" in obj_dict: + return __DECODERS__[obj_dict["__type"]](obj_dict["__value"]) + return obj_dict diff --git a/scripts/search_phenotypes.py b/scripts/search_phenotypes.py index 4533cce..7049834 100644 --- a/scripts/search_phenotypes.py +++ b/scripts/search_phenotypes.py @@ -44,6 +44,10 @@ def remove_linked(search_results, linked: tuple): """Remove any item that has been already linked to a user group.""" return (item for item in search_results if __filter_object__(item) not in linked) +def update_status(redisconn: redis.Redis, redisname, status: str): + """Update the status of the search.""" + redisconn.hset(redisname, "status", json.dumps(status)) + def update_search_results(redisconn: redis.Redis, redisname: str, results: tuple[dict[str, Any], ...]): """Save the results to redis db.""" @@ -83,7 +87,7 @@ def search(# pylint: disable=[too-many-arguments, too-many-locals] with (authdb.connection(auth_db_uri) as authconn, gn3db.database_connection(gn3_db_uri) as gn3conn, redis.Redis.from_url(redis_uri, decode_responses=True) as redisconn): - redisconn.hset(redisname, "status", "started") + update_status(redisconn, redisname, "started") update_search_results(redisconn, redisname, tuple()) # init search results try: search_query = f"species:{species}" + ( @@ -109,11 +113,11 @@ def search(# pylint: disable=[too-many-arguments, too-many-locals] except NoSearchResults as _nsr: pass except Exception as _exc: # pylint: disable=[broad-except] - redisconn.hset(redisname, "status", "failed") - redisconn.hset(redisname, "exception", traceback.format_exc()) + update_status(redisconn, redisname, "failed") + redisconn.hset(redisname, "exception", json.dumps(traceback.format_exc())) expire_redis_results(redisconn, redisname) return 1 - redisconn.hset(redisname, "status", "completed") + update_status(redisconn, redisname, "completed") expire_redis_results(redisconn, redisname) return 0 |