From 34eab8a50ce185aaf786fd7138a3bd0b7c5b0576 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Fri, 9 Feb 2024 05:29:08 +0300
Subject: Retrive and display generic bundle errors

Implement the first QC check for generic errors e.g. missing files in
bundle, etc. Display retrieved errors on UI.
---
 qc_app/static/css/styles.css                   |  8 ++++++++
 qc_app/templates/rqtl2/rqtl2-qc-job-error.html | 14 ++++++++++++--
 qc_app/upload/rqtl2.py                         | 13 +++++++++----
 3 files changed, 29 insertions(+), 6 deletions(-)

(limited to 'qc_app')

diff --git a/qc_app/static/css/styles.css b/qc_app/static/css/styles.css
index f6e829f..474c7f7 100644
--- a/qc_app/static/css/styles.css
+++ b/qc_app/static/css/styles.css
@@ -198,3 +198,11 @@ form fieldset legend {
     width: 90%;
     overflow: scroll;
 }
+
+.qc-error-display {
+    border-radius: 0.8em;
+    padding-top: 0.5em;
+    padding-bottom: 0.5em;
+    max-height: 250px;
+    overflow: scroll;
+}
diff --git a/qc_app/templates/rqtl2/rqtl2-qc-job-error.html b/qc_app/templates/rqtl2/rqtl2-qc-job-error.html
index 5d2ebee..f9a912c 100644
--- a/qc_app/templates/rqtl2/rqtl2-qc-job-error.html
+++ b/qc_app/templates/rqtl2/rqtl2-qc-job-error.html
@@ -12,9 +12,19 @@
     be uploaded onto GeneNetwork.</p>
 </div>
 
-<h2 class="heading">Errors</h2>
+{%if errorsgeneric | length > 0%}
+<h2 class="heading">Generic Errors ({{errorsgeneric | length}})</h3>
+<div class="explainer">
+  We found the following generic errors in your R/qtl2 bundle:
+</div>
+<ul class="alert-error qc-error-display">
+  {%for msg in errorsgeneric%}
+  <li>{{msg}}</li>
+  {%endfor%}
+</ul>
+{%endif%}
 
-<p><emph>list errors here by file type, I think &hellip;</emph></p>
+<p><emph>list other errors here by file type, I think &hellip;</emph></p>
 
 <h4>stdout</h4>
 {{cli_output(job, "stdout")}}
diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index b96d9f0..c20bd8f 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -175,12 +175,15 @@ def upload_rqtl2_bundle(species_id: int, population_id: int):
                     jobs.jobsnamespace(),
                     jobid,
                     [sys.executable, "-m", "scripts.qc_on_rqtl2_bundle",
-                    app.config["SQL_URI"], app.config["REDIS_URL"],
-                    jobs.jobsnamespace(), jobid, "--redisexpiry",
-                    str(redis_ttl_seconds)],
+                     app.config["SQL_URI"], app.config["REDIS_URL"],
+                     jobs.jobsnamespace(), jobid, "--redisexpiry",
+                     str(redis_ttl_seconds)],
                     "rqtl2-bundle-qc-job",
                     redis_ttl_seconds,
-                    {}),
+                    {"job-metadata": json.dumps({
+                        "speciesid": species_id,
+                        "populationid": population_id,
+                        "rqtl2-bundle-file": str(the_file.absolute())})}),
                 redisuri,
                 f"{app.config['UPLOAD_FOLDER']}/job_errors")
             return redirect(url_for(
@@ -200,6 +203,8 @@ def rqtl2_bundle_qc_status(jobid: UUID):
             if jobstatus == "error":
                 return render_template("rqtl2/rqtl2-qc-job-error.html",
                                        job=thejob,
+                                       errorsgeneric=json.loads(
+                                           thejob.get("errors-generic", "[]")),
                                        messages=logmessages)
             if jobstatus == "success":
                 return render_template("rqtl2/rqtl2-qc-job-results.html",
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