From 445a28579e2139654132643cf9595acfd402c283 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Fri, 9 Feb 2024 17:31:06 +0300
Subject: Add scaffolding for running individual files' QC checks

---
 scripts/qc_on_rqtl2_bundle.py | 23 +++++++++++++++++++++--
 1 file changed, 21 insertions(+), 2 deletions(-)

(limited to 'scripts')

diff --git a/scripts/qc_on_rqtl2_bundle.py b/scripts/qc_on_rqtl2_bundle.py
index 63729b4..43f766a 100644
--- a/scripts/qc_on_rqtl2_bundle.py
+++ b/scripts/qc_on_rqtl2_bundle.py
@@ -43,7 +43,21 @@ def qc_missing_files(rconn: Redis, fqjobid: str,
 
     return missing
 
-def run_qc(rconn: Redis, args: Namespace, logger: Logger) -> int:
+def qc_geno_errors(_rconn, _fqjobid, _job) -> bool:
+    """Check for errors in `geno` file(s)."""
+    return False
+
+def qc_pheno_errors(_rconn, _fqjobid, _job) -> bool:
+    """Check for errors in `pheno` file(s)."""
+    return False
+
+def qc_phenocovar_errors(_rconn, _fqjobid, _job) -> bool:
+    """Check for errors in `phenocovar` file(s)."""
+    return False
+
+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)
@@ -53,7 +67,12 @@ def run_qc(rconn: Redis, args: Namespace, logger: Logger) -> int:
         logger.error("Missing files in the bundle!")
         return 1
 
-    return 0
+    return (
+        1 if any((
+            qc_geno_errors(rconn, fqjobid, thejob),
+            qc_pheno_errors(rconn, fqjobid, thejob),
+            qc_phenocovar_errors(rconn, fqjobid, thejob)))
+        else 0)
 
 if __name__ == "__main__":
     def main():
-- 
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