From a0d3ac85dab5bfba9107f63b3219902ebe32cdd9 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Fri, 9 Feb 2024 17:27:14 +0300
Subject: UI: Provide QC successful results page

---
 qc_app/templates/rqtl2/rqtl2-qc-job-results.html | 62 ++++++++++++++++++++++++
 qc_app/upload/rqtl2.py                           | 18 +++++--
 2 files changed, 75 insertions(+), 5 deletions(-)
 create mode 100644 qc_app/templates/rqtl2/rqtl2-qc-job-results.html

(limited to 'qc_app')

diff --git a/qc_app/templates/rqtl2/rqtl2-qc-job-results.html b/qc_app/templates/rqtl2/rqtl2-qc-job-results.html
new file mode 100644
index 0000000..46a168f
--- /dev/null
+++ b/qc_app/templates/rqtl2/rqtl2-qc-job-results.html
@@ -0,0 +1,62 @@
+{%extends "base.html"%}
+{%from "cli-output.html" import cli_output%}
+
+{%block title%}R/qtl2 bundle: QC job results{%endblock%}
+
+{%block contents%}
+<h1 class="heading">R/qtl2 bundle: QC job results</h1>
+
+<div class="explainer">
+  <p>The R/qtl2 bundle you uploaded has passed all automated quality-control
+    checks successfully.</p>
+  <p>You may now continue to load the data into GeneNetwork for the bundle, with
+    the following details:</p>
+</div>
+
+<form id="form-qc-job-results" action="#implement-this" method="POST">
+  <fieldset>
+    <legend>Species</legend>
+    <input type="hidden" name="speciesid" value="{{species.SpeciesId}}" />
+
+    <span class="form-col-1">Name</span>
+    <span class="form-col-2">{{species.Name | capitalize}}</span>
+
+    <span class="form-col-1">Scientific</span>
+    <span class="form-col-2">{{species.FullName | capitalize}}</span>
+  </fieldset>
+
+  <fieldset>
+    <legend>population</legend>
+    <input type="hidden" name="populationid" value="{{populationid}}" />
+
+    <span class="form-col-1">Name</span>
+    <span class="form-col-2">{{population.InbredSetName}}</span>
+
+    <span class="form-col-1">Full Name</span>
+    <span class="form-col-2">{{population.FullName}}</span>
+
+    <span class="form-col-1">Genetic Type</span>
+    <span class="form-col-2">{{population.GeneticType}}</span>
+
+    <span class="form-col-1">Description</span>
+    <span class="form-col-2">{{population.Description or "-"}}</span>
+  </fieldset>
+
+  <fieldset>
+    <legend>R/qtl2 Bundle File</legend>
+    <input type="hidden" name="rqtl2-bundle-file" value="{{rqtl2bundle}}" />
+    <input type="hidden" name="original-filename" value="{{rqtl2bundleorig}}" />
+
+    <span class="form-col-1">Original Name</span>
+    <span class="form-col-2">{{rqtl2bundleorig}}</span>
+
+    <span class="form-col-1">Internal Name</span>
+    <span class="form-col-2">{{rqtl2bundle.name[0:25]}}&hellip;</span>
+  </fieldset>
+
+  <fieldset>
+    <input type="submit" value="continue" class="btn btn-main form-col-2" />
+  </fieldset>
+</form>
+
+{%endblock%}
diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index c20bd8f..4b00891 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -183,7 +183,8 @@ def upload_rqtl2_bundle(species_id: int, population_id: int):
                     {"job-metadata": json.dumps({
                         "speciesid": species_id,
                         "populationid": population_id,
-                        "rqtl2-bundle-file": str(the_file.absolute())})}),
+                        "rqtl2-bundle-file": str(the_file.absolute()),
+                        "original-filename": request.files["rqtl2_bundle_file"].filename})}),
                 redisuri,
                 f"{app.config['UPLOAD_FOLDER']}/job_errors")
             return redirect(url_for(
@@ -193,7 +194,8 @@ def upload_rqtl2_bundle(species_id: int, population_id: int):
              methods=["GET", "POST"])
 def rqtl2_bundle_qc_status(jobid: UUID):
     """Check the status of the QC jobs."""
-    with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
+    with (Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn,
+          database_connection(app.config["SQL_URI"]) as dbconn):
         try:
             thejob = jobs.job(rconn, jobs.jobsnamespace(), jobid)
             messagelistname = thejob.get("log-messagelist")
@@ -207,9 +209,15 @@ def rqtl2_bundle_qc_status(jobid: UUID):
                                            thejob.get("errors-generic", "[]")),
                                        messages=logmessages)
             if jobstatus == "success":
-                return render_template("rqtl2/rqtl2-qc-job-results.html",
-                                       job=thejob,
-                                       messages=logmessages)
+                jobmeta = json.loads(thejob["job-metadata"])
+                species = species_by_id(dbconn, jobmeta["speciesid"])
+                return render_template(
+                    "rqtl2/rqtl2-qc-job-results.html",
+                    species=species,
+                    population=population_by_species_and_id(
+                        dbconn, species["SpeciesId"], jobmeta["populationid"]),
+                    rqtl2bundle=Path(jobmeta["rqtl2-bundle-file"]),
+                    rqtl2bundleorig=jobmeta["original-filename"])
 
             return render_template("rqtl2/rqtl2-qc-job-status.html",
                                    job=thejob,
-- 
cgit v1.2.3