From 523bd6634539a2e646a7cd4215ad3ee7dbbeeb66 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 12 Feb 2024 10:14:27 +0300
Subject: Check for errors in the 'pheno' file.

---
 qc_app/templates/rqtl2/rqtl2-qc-job-error.html |  2 +-
 scripts/qc_on_rqtl2_bundle.py                  | 15 +++++++++++++--
 2 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/qc_app/templates/rqtl2/rqtl2-qc-job-error.html b/qc_app/templates/rqtl2/rqtl2-qc-job-error.html
index e809e7c..1650a79 100644
--- a/qc_app/templates/rqtl2/rqtl2-qc-job-error.html
+++ b/qc_app/templates/rqtl2/rqtl2-qc-job-error.html
@@ -87,7 +87,7 @@
 <div class="explainer">
   We found the following errors in the 'pheno' file in your R/qtl2 bundle:
 </div>
-{{errorspheno}}
+{{errors_table("tbl-errors-pheno", errorspheno[0:50])}}
 {%endif%}
 
 {%if errorsphenocovar | length > 0%}
diff --git a/scripts/qc_on_rqtl2_bundle.py b/scripts/qc_on_rqtl2_bundle.py
index 02c8c3a..aea1baa 100644
--- a/scripts/qc_on_rqtl2_bundle.py
+++ b/scripts/qc_on_rqtl2_bundle.py
@@ -58,7 +58,7 @@ 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 geno errors…")
+    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)))
@@ -67,10 +67,21 @@ def qc_geno_errors(rconn, fqjobid, zfile, logger) -> bool:
     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:
+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("No errors found in the 'pheno' file.")
     return False
 
 def qc_phenocovar_errors(_rconn, _fqjobid, _zfile, _logger) -> bool:
-- 
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