Hook up code to use external search script for phenotypes

1 files changed, 58 insertions, 0 deletions

diff --git a/gn3/jobs.py b/gn3/jobs.py
new file mode 100644
index 0000000..8854a61
--- /dev/null
+++ b/gn3/jobs.py
@@ -0,0 +1,58 @@
+"""Handle external processes in a consistent manner."""
+import json
+from typing import Any
+from uuid import UUID, uuid4
+from datetime import datetime
+
+from redis import Redis
+
+from pymonad.either import Left, Right, Either
+
+JOBS_NAMESPACE = "GN3::JOBS"
+
+class InvalidCommand(Exception):
+    """Raise if the command to run is invalid."""
+
+def job_key(job_id: UUID, namespace_prefix: str = JOBS_NAMESPACE):
+    """Build the namespace key for a specific job."""
+    return f"{namespace_prefix}::{job_id}"
+
+def job(redisconn: Redis, job_id: UUID) -> Either:
+    """Retrive the job details of a job identified by `job_id`."""
+    the_job = redisconn.hgetall(job_key(job_id))
+    if the_job:
+        return Right({
+            **the_job,
+            "search_results": json.loads(the_job["search_results"])
+        })
+    return Left({
+        "error": "NotFound",
+        "error_description": f"Job '{job_id}' was not found."
+    })
+
+def __command_valid__(job_command: Any) -> Either:
+    if not isinstance(job_command, list):
+        return Left({
+            "error": "InvalidJobCommand",
+            "error_description": "The job command MUST be a list."
+        })
+    if not all((isinstance(val, str) for val in job_command)):
+        return Left({
+            "error": "InvalidJobCommand",
+            "error_description": "All parts of the command MUST be strings."
+        })
+    return Right(job_command)
+
+def create_job(redisconn: Redis, job_details: dict[str, Any]) -> UUID:
+    """Create a new job and put it on Redis."""
+    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"
+        })
+        return job_id
+    def __raise__(err):
+        raise InvalidCommand(err["error_description"])
+    return __command_valid__(job_details.get("command")).either(
+        __raise__, __create__)