From 8b6785be9a61d7ba17a2320a79184bee0914a2f1 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 18 Jan 2024 15:03:36 +0300
Subject: UI: Display summary information.

---
 qc_app/db/datasets.py                    | 15 ++++++++++++++-
 qc_app/templates/rqtl2/summary-info.html | 28 ++++++++++++++++++++++++++++
 qc_app/upload/rqtl2.py                   | 25 ++++++++++++++++++++++++-
 3 files changed, 66 insertions(+), 2 deletions(-)

diff --git a/qc_app/db/datasets.py b/qc_app/db/datasets.py
index 5816146..448db18 100644
--- a/qc_app/db/datasets.py
+++ b/qc_app/db/datasets.py
@@ -1,5 +1,6 @@
 """Functions for accessing the database relating to datasets."""
 from datetime import date
+from typing import Optional
 
 import MySQLdb as mdb
 from MySQLdb.cursors import DictCursor
@@ -109,7 +110,7 @@ def probeset_create_dataset(conn: mdb.Connection,#pylint: disable=[too-many-argu
         }
         cursor.execute(
             """
-            insert into ProbeSetFreeze(
+            INSERT INTO ProbeSetFreeze(
               ProbeFreezeId, AvgId, Name, Name2, FullName, ShortName,
               CreateTime, public, DataScale)
             VALUES(
@@ -118,3 +119,15 @@ def probeset_create_dataset(conn: mdb.Connection,#pylint: disable=[too-many-argu
             """,
             dataset)
         return {**dataset, "datasetid": cursor.lastrowid}
+
+def probeset_dataset_by_id(
+        conn: mdb.Connection, datasetid: int) -> Optional[dict]:
+    """Fetch a ProbeSet dataset by its ID"""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute("SELECT * FROM ProbeSetFreeze WHERE Id=%s",
+                       (datasetid,))
+        result = cursor.fetchone()
+        if bool(result):
+            return dict(result)
+
+    return None
diff --git a/qc_app/templates/rqtl2/summary-info.html b/qc_app/templates/rqtl2/summary-info.html
index c3a2ac0..3882c9c 100644
--- a/qc_app/templates/rqtl2/summary-info.html
+++ b/qc_app/templates/rqtl2/summary-info.html
@@ -21,6 +21,34 @@
 
   <dt>Genotype Dataset</dt>
   <dd>{{geno_dataset.Name}} ({{geno_dataset.FullName}})</dd>
+
+  <dt>ProbeSet Study</dt>
+  <dd>{{probe_study.Name}} ({{probe_study.FullName}})</dd>
+
+  <dt>ProbeSet Dataset</dt>
+  <dd>{{probe_dataset.Name2}} ({{probe_dataset.FullName}})</dd>
 </dl>
 
+<form id="frm:confirm-rqtl2bundle-details"
+      action="{{url_for('upload.rqtl2.confirm_bundle_details',
+	      species_id=species.SpeciesId,
+	      population_id=population.InbredSetId)}}"
+      method="POST"
+      enctype="multipart/form-data">
+  <legend class="heading">Create ProbeSet dataset</legend>
+
+  <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+  <input type="hidden" name="population_id"
+	 value="{{population.InbredSetId}}" />
+  <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" />
+  <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
+  <input type="hidden" name="probe-study-id" value="{{probe_study.Id}}" />
+  <input type="hidden" name="probe-dataset-id" value="{{probe_dataset.Id}}" />
+
+  <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 0b446ac..7609fa9 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -34,6 +34,7 @@ from qc_app.db.datasets import (
 
     probeset_study_by_id,
     probeset_create_study,
+    probeset_dataset_by_id,
     probeset_create_dataset,
     probeset_datasets_by_study,
     probeset_studies_by_species_and_population)
@@ -512,8 +513,30 @@ def select_dataset_info(species_id: int, population_id: int):
                     datasets=probeset_datasets_by_study(
                         conn, int(form["probe-study-id"])),
                     avgmethods=averaging_methods(conn))
+            probeset_study = probeset_study_by_id(
+                conn, int(form["probe-study-id"]))
+            probeset_dataset = probeset_dataset_by_id(
+                conn, int(form["probe-dataset-id"]))
 
     return render_template("rqtl2/summary-info.html",
                            species=species,
                            population=population,
-                           geno_dataset=geno_dataset)
+                           geno_dataset=geno_dataset,
+                           probe_study=probeset_study,
+                           probe_dataset=probeset_dataset)
+
+
+
+@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
+              "/rqtl2-bundle/confirm-bundle-details"),
+             methods=["POST"])
+def confirm_bundle_details(species_id: int, population_id: int):
+    """Confirm the details and trigger R/qtl2 bundle processing..."""
+    with database_connection(app.config["SQL_URI"]) as conn:
+        error = check_errors(
+            conn, "species", "population", "rqtl2_bundle_file", "geno-dataset",
+            "probe-study-id", "probe-dataset-id")
+        if bool(error):
+            return error
+
+        raise NotImplementedError
-- 
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