From abb55d7e03bf207ebf00b4c71f1bbdd8f58a0ad3 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 12 Feb 2024 10:44:35 +0300
Subject: Check for errors in the 'phenose' file.

---
 scripts/qc_on_rqtl2_bundle.py | 59 ++++++++++++++++++++++++++++++-------------
 1 file changed, 42 insertions(+), 17 deletions(-)

(limited to 'scripts')

diff --git a/scripts/qc_on_rqtl2_bundle.py b/scripts/qc_on_rqtl2_bundle.py
index aea1baa..c3e8b66 100644
--- a/scripts/qc_on_rqtl2_bundle.py
+++ b/scripts/qc_on_rqtl2_bundle.py
@@ -14,6 +14,7 @@ from qc_app import jobs
 from qc_app.db_utils import database_connection
 from qc_app.check_connections import check_db, check_redis
 
+from r_qtl import r_qtl2 as rqtl2
 from r_qtl import r_qtl2_qc as rqc
 from r_qtl import fileerrors as rqfe
 
@@ -59,31 +60,54 @@ def qc_missing_files(rconn: Redis,
 def qc_geno_errors(rconn, fqjobid, zfile, logger) -> bool:
     """Check for errors in `geno` file(s)."""
     logger.info("Checking for errors in the 'geno' file…")
-    gerrs = tuple(rqc.geno_errors(zfile))
-    add_to_errors(rconn, fqjobid, "errors-generic", tuple(
-        err for err in gerrs if isinstance(err, rqfe.MissingFile)))
-    add_to_errors(rconn, fqjobid, "errors-geno", tuple(
-        err for err in gerrs if not isinstance(err, rqfe.MissingFile)))
-    if len(gerrs) > 0:
-        logger.error("The 'geno' file has errors.")
-        return True
+    cdata = rqtl2.control_data(zfile)
+    if "geno" in cdata:
+        gerrs = tuple(rqc.geno_errors(zfile))
+        add_to_errors(rconn, fqjobid, "errors-generic", tuple(
+            err for err in gerrs if isinstance(err, rqfe.MissingFile)))
+        add_to_errors(rconn, fqjobid, "errors-geno", tuple(
+            err for err in gerrs if not isinstance(err, rqfe.MissingFile)))
+        if len(gerrs) > 0:
+            logger.error("The 'geno' file has errors.")
+            return True
+
     logger.info("No errors found in the 'geno' file.")
     return False
 
 def qc_pheno_errors(rconn, fqjobid, zfile, logger) -> bool:
     """Check for errors in `pheno` file(s)."""
-    logger.info("Checking for errors in the 'pheno' file …")
-    perrs = tuple(rqc.pheno_errors(zfile))
-    add_to_errors(rconn, fqjobid, "errors-generic", tuple(
-        err for err in perrs if isinstance(err, rqfe.MissingFile)))
-    add_to_errors(rconn, fqjobid, "errors-pheno", tuple(
-        err for err in perrs if not isinstance(err, rqfe.MissingFile)))
-    if len(perrs) > 0:
-        logger.error("The 'pheno' file has errors.")
-        return True
+    logger.info("Checking for errors in the 'pheno' file…")
+    cdata = rqtl2.control_data(zfile)
+    if "pheno" in cdata:
+        perrs = tuple(rqc.pheno_errors(zfile))
+        add_to_errors(rconn, fqjobid, "errors-generic", tuple(
+            err for err in perrs if isinstance(err, rqfe.MissingFile)))
+        add_to_errors(rconn, fqjobid, "errors-pheno", tuple(
+            err for err in perrs if not isinstance(err, rqfe.MissingFile)))
+        if len(perrs) > 0:
+            logger.error("The 'pheno' file has errors.")
+            return True
+
     logger.info("No errors found in the 'pheno' file.")
     return False
 
+def qc_phenose_errors(rconn, fqjobid, zfile, logger) -> bool:
+    """Check for errors in `phenose` file(s)."""
+    logger.info("Checking for errors in the 'phenose' file…")
+    cdata = rqtl2.control_data(zfile)
+    if "phenose" in cdata:
+        perrs = tuple(rqc.phenose_errors(zfile))
+        add_to_errors(rconn, fqjobid, "errors-generic", tuple(
+            err for err in perrs if isinstance(err, rqfe.MissingFile)))
+        add_to_errors(rconn, fqjobid, "errors-phenose", tuple(
+            err for err in perrs if not isinstance(err, rqfe.MissingFile)))
+        if len(perrs) > 0:
+            logger.error("The 'phenose' file has errors.")
+            return True
+
+    logger.info("No errors found in the 'phenose' file.")
+    return False
+
 def qc_phenocovar_errors(_rconn, _fqjobid, _zfile, _logger) -> bool:
     """Check for errors in `phenocovar` file(s)."""
     return False
@@ -104,6 +128,7 @@ def run_qc(rconn: Redis,
             1 if any((
                 qc_geno_errors(rconn, fqjobid, zfile, logger),
                 qc_pheno_errors(rconn, fqjobid, zfile, logger),
+                qc_phenose_errors(rconn, fqjobid, zfile, logger),
                 qc_phenocovar_errors(rconn, fqjobid, zfile, logger)))
             else 0)
 
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