From cdd4dc456e56bb4eb055e1cb7f2518d45fb3bfb9 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Sat, 20 Jan 2024 09:57:23 +0300
Subject: Fetch sample/case names from database

Fetch the sample/case names from the database rather than from a
static file in the repository.

Issue:
https://issues.genenetwork.org/issues/quality-control/read-samples-from-database-by-species
---
 qc_app/jobs.py | 19 +++++++++++++------
 1 file changed, 13 insertions(+), 6 deletions(-)

(limited to 'qc_app/jobs.py')

diff --git a/qc_app/jobs.py b/qc_app/jobs.py
index a8257a3..f5e5173 100644
--- a/qc_app/jobs.py
+++ b/qc_app/jobs.py
@@ -32,17 +32,24 @@ def initialise_job(# pylint: disable=[too-many-arguments]
     redis_conn.expire(name=the_job["job_id"], time=timedelta(seconds=ttl_seconds))
     return the_job
 
-def build_file_verification_job(
-        redis_conn: Redis, filepath: str, filetype: str, redisurl: str,
+def build_file_verification_job(#pylint: disable=[too-many-arguments]
+        redis_conn: Redis,
+        dburi: str,
+        redisuri: str,
+        speciesid: int,
+        filepath: str,
+        filetype: str,
         ttl_seconds: int):
     "Build a file verification job"
-    job_id = str(uuid4())
+    jobid = str(uuid4())
     command = [
-        sys.executable, "-m", "scripts.validate_file", filetype, filepath, redisurl,
-        job_id
+        sys.executable, "-m", "scripts.validate_file",
+        dburi, redisuri, jobid,
+        "--redisexpiry", str(ttl_seconds),
+        str(speciesid), filetype, filepath,
     ]
     return initialise_job(
-        redis_conn, job_id, command, "file-verification", ttl_seconds, {
+        redis_conn, jobid, command, "file-verification", ttl_seconds, {
             "filetype": filetype,
             "filename": os.path.basename(filepath), "percent": 0
         })
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