From 4729abd0ab7a8fbeb700a278ac8bdfcf62ab79ac Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Sat, 10 Feb 2024 06:57:23 +0300
Subject: Collect and display errors on 'geno' files in the bundle.

---
 qc_app/static/css/styles.css                   |  6 +---
 qc_app/templates/rqtl2/rqtl2-qc-job-error.html | 49 +++++++++++++++++++++++++-
 qc_app/upload/rqtl2.py                         |  6 ++++
 3 files changed, 55 insertions(+), 6 deletions(-)

(limited to 'qc_app')

diff --git a/qc_app/static/css/styles.css b/qc_app/static/css/styles.css
index 474c7f7..79dab0e 100644
--- a/qc_app/static/css/styles.css
+++ b/qc_app/static/css/styles.css
@@ -134,11 +134,7 @@ form fieldset:nth-child(odd) {
 }
 
 @media(min-width: 1250px) {
-    form {
-	width: 65ch;
-    }
-
-    .explainer {
+    form, .explainer, .error-table {
 	width: 65ch;
     }
 }
diff --git a/qc_app/templates/rqtl2/rqtl2-qc-job-error.html b/qc_app/templates/rqtl2/rqtl2-qc-job-error.html
index f9a912c..49df061 100644
--- a/qc_app/templates/rqtl2/rqtl2-qc-job-error.html
+++ b/qc_app/templates/rqtl2/rqtl2-qc-job-error.html
@@ -3,6 +3,31 @@
 
 {%block title%}R/qtl2 bundle: QC Job Error{%endblock%}
 
+{%macro errors_table(tableid, errors)%}
+<table id="{{tableid}}"
+       class="error-table"
+       style="display: block; overflow: scroll; max-height: 250px;">
+  <thead style="position: sticky; top: 0;">
+    <tr>
+      <th>Line</th>
+      <th>Column</th>
+      <th>Value</th>
+      <th>Message</th>
+    </tr>
+  </thead>
+  <tbody>
+    {%for error in errors%}
+    <tr>
+      <td>{{error.line}}</td>
+      <td>{{error.column}}</td>
+      <td>{{error.value}}</td>
+      <td>{{error.message}}</td>
+    </tr>
+    {%endfor%}
+  </tbody>
+</table>
+{%endmacro%}
+
 {%block contents%}
 <h1 class="heading">R/qtl2 bundle: QC job Error</h1>
 
@@ -24,7 +49,29 @@
 </ul>
 {%endif%}
 
-<p><emph>list other errors here by file type, I think &hellip;</emph></p>
+{%if errorsgeno | length > 0%}
+<h2 class="heading">Geno Errors ({{errorsgeno | length}})</h3>
+<div class="explainer">
+  We found the following errors in the 'geno' file in your R/qtl2 bundle:
+</div>
+{{errors_table("tbl-errors-geno", errorsgeno[0:50])}}
+{%endif%}
+
+{%if errorspheno | length > 0%}
+<h2 class="heading">Pheno Errors ({{errorspheno | length}})</h3>
+<div class="explainer">
+  We found the following errors in the 'pheno' file in your R/qtl2 bundle:
+</div>
+{{errorspheno}}
+{%endif%}
+
+{%if errorsphenocovar | length > 0%}
+<h2 class="heading">Phenocovar Errors ({{errorsphenocovar | length}})</h3>
+<div class="explainer">
+  We found the following errors in the 'phenocovar' file in your R/qtl2 bundle:
+</div>
+{{errorsphenocovar}}
+{%endif%}
 
 <h4>stdout</h4>
 {{cli_output(job, "stdout")}}
diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index 4b00891..c45952c 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -207,6 +207,12 @@ def rqtl2_bundle_qc_status(jobid: UUID):
                                        job=thejob,
                                        errorsgeneric=json.loads(
                                            thejob.get("errors-generic", "[]")),
+                                       errorsgeno=json.loads(
+                                           thejob.get("errors-geno", "[]")),
+                                       errorspheno=json.loads(
+                                           thejob.get("errors-pheno", "[]")),
+                                       errorsphenocovar=json.loads(
+                                           thejob.get("errors-phenocovar", "[]")),
                                        messages=logmessages)
             if jobstatus == "success":
                 jobmeta = json.loads(thejob["job-metadata"])
-- 
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