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.

---
 qc_app/templates/rqtl2/rqtl2-qc-job-error.html | 8 ++++++++
 qc_app/upload/rqtl2.py                         | 2 ++
 2 files changed, 10 insertions(+)

(limited to 'qc_app')

diff --git a/qc_app/templates/rqtl2/rqtl2-qc-job-error.html b/qc_app/templates/rqtl2/rqtl2-qc-job-error.html
index 1650a79..524282b 100644
--- a/qc_app/templates/rqtl2/rqtl2-qc-job-error.html
+++ b/qc_app/templates/rqtl2/rqtl2-qc-job-error.html
@@ -90,6 +90,14 @@
 {{errors_table("tbl-errors-pheno", errorspheno[0:50])}}
 {%endif%}
 
+{%if errorsphenose | length > 0%}
+<h2 class="heading">Phenose Errors ({{errorsphenose | length}})</h3>
+<div class="explainer">
+  We found the following errors in the 'phenose' file in your R/qtl2 bundle:
+</div>
+{{errors_table("tbl-errors-phenose", errorsphenose[0:50])}}
+{%endif%}
+
 {%if errorsphenocovar | length > 0%}
 <h2 class="heading">Phenocovar Errors ({{errorsphenocovar | length}})</h3>
 <div class="explainer">
diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index c45952c..66b219d 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -211,6 +211,8 @@ def rqtl2_bundle_qc_status(jobid: UUID):
                                            thejob.get("errors-geno", "[]")),
                                        errorspheno=json.loads(
                                            thejob.get("errors-pheno", "[]")),
+                                       errorsphenose=json.loads(
+                                           thejob.get("errors-phenose", "[]")),
                                        errorsphenocovar=json.loads(
                                            thejob.get("errors-phenocovar", "[]")),
                                        messages=logmessages)
-- 
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