From b7eb549bb02eaba22ba06b0ddf5d04c9b4fe0f66 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Fri, 9 Feb 2024 16:12:45 +0300
Subject: Extract missing files check to external function

---
 scripts/qc_on_rqtl2_bundle.py | 24 ++++++++++++++++--------
 1 file changed, 16 insertions(+), 8 deletions(-)

(limited to 'scripts/qc_on_rqtl2_bundle.py')

diff --git a/scripts/qc_on_rqtl2_bundle.py b/scripts/qc_on_rqtl2_bundle.py
index 8dd6b7e..63729b4 100644
--- a/scripts/qc_on_rqtl2_bundle.py
+++ b/scripts/qc_on_rqtl2_bundle.py
@@ -1,9 +1,10 @@
 """Run Quality Control checks on R/qtl2 bundle."""
 import sys
 import json
-from typing import Sequence
+from pathlib import Path
 from zipfile import ZipFile
 from argparse import Namespace
+from typing import Union, Sequence
 from logging import Logger, getLogger, StreamHandler
 
 from redis import Redis
@@ -26,12 +27,11 @@ def add_to_errors(rconn: Redis, fqjobid: str, key: str, errors: Sequence[rqfe.Mi
         [error.message for error in errors]))
     rconn.hset(fqjobid, key, json.dumps(errs))
 
-def run_qc(rconn: Redis, args: Namespace, logger: Logger) -> int:
-    """Run the QC programs."""
-    fqjobid = jobs.job_key(args.redisprefix, args.jobid)
-    thejob = parse_job(rconn, args.redisprefix, args.jobid)
-    meta = thejob["job-metadata"]
-    with ZipFile(meta["rqtl2-bundle-file"], "r") as zfile:
+def qc_missing_files(rconn: Redis, fqjobid: str,
+                     bundlefilepath: Union[str, Path]) -> tuple[
+                         tuple[str, str], ...]:
+    """Run QC for files listed in control file that don't exist in bundle."""
+    with ZipFile(str(bundlefilepath), "r") as zfile:
         missing = rqc.missing_files(zfile)
         add_to_errors(rconn, fqjobid, "errors-generic", tuple(
             rqfe.MissingFile(
@@ -41,7 +41,15 @@ def run_qc(rconn: Redis, args: Namespace, logger: Logger) -> int:
                     "the bundle."))
             for mfile in missing))
 
-    if len(missing) > 0:
+    return missing
+
+def run_qc(rconn: Redis, args: Namespace, logger: Logger) -> int:
+    """Run the QC programs."""
+    fqjobid = jobs.job_key(args.redisprefix, args.jobid)
+    thejob = parse_job(rconn, args.redisprefix, args.jobid)
+    jobmeta = thejob["job-metadata"]
+
+    if len(qc_missing_files(rconn, fqjobid, jobmeta["rqtl2-bundle-file"])) > 0:
         logger.error("Missing files in the bundle!")
         return 1
 
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