From bf1c2ec1b16b50f419a349a54031baf85fcd4abd Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 17 Jan 2024 05:38:29 +0300
Subject: UI: Initialise summary page.

---
 qc_app/db/datasets.py                    |  7 +++++++
 qc_app/db/species.py                     | 10 ++++------
 qc_app/templates/rqtl2/summary-info.html | 26 ++++++++++++++++++++++++++
 qc_app/upload/rqtl2.py                   | 20 ++++++++++++++------
 4 files changed, 51 insertions(+), 12 deletions(-)
 create mode 100644 qc_app/templates/rqtl2/summary-info.html

(limited to 'qc_app')

diff --git a/qc_app/db/datasets.py b/qc_app/db/datasets.py
index 3a27706..8122cfa 100644
--- a/qc_app/db/datasets.py
+++ b/qc_app/db/datasets.py
@@ -14,3 +14,10 @@ def geno_dataset_by_species_and_population(
             "WHERE iset.SpeciesId=%(sid)s AND iset.InbredSetId=%(pid)s",
             {"sid": speciesid, "pid": populationid})
         return tuple(dict(row) for row in cursor.fetchall())
+
+def geno_dataset_by_id(conn: mdb.Connection, dataset_id: int) -> dict:
+    """Retrieve genotype dataset by ID"""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute("SELECT * FROM GenoFreeze WHERE Id=%s",
+                       (dataset_id,))
+        return dict(cursor.fetchone())
diff --git a/qc_app/db/species.py b/qc_app/db/species.py
index 7006d15..653e59b 100644
--- a/qc_app/db/species.py
+++ b/qc_app/db/species.py
@@ -6,8 +6,8 @@ def species(conn: mdb.Connection) -> tuple:
     "Retrieve the species from the database."
     with conn.cursor(cursorclass=DictCursor) as cursor:
         cursor.execute(
-            "SELECT SpeciesId, SpeciesName, LOWER(Name) AS Name, MenuName "
-            "FROM Species")
+            "SELECT SpeciesId, SpeciesName, LOWER(Name) AS Name, MenuName, "
+            "FullName FROM Species")
         return tuple(cursor.fetchall())
 
     return tuple()
@@ -16,9 +16,7 @@ def species_by_id(conn: mdb.Connection, speciesid) -> dict:
     "Retrieve the species from the database by id."
     with conn.cursor(cursorclass=DictCursor) as cursor:
         cursor.execute(
-            (
-                "SELECT "
-                "SpeciesId, SpeciesName, LOWER(Name) AS Name, MenuName "
-                "FROM Species WHERE SpeciesId=%s"),
+            "SELECT SpeciesId, SpeciesName, LOWER(Name) AS Name, MenuName, "
+            "FullName FROM Species WHERE SpeciesId=%s",
             (speciesid,))
         return cursor.fetchone()
diff --git a/qc_app/templates/rqtl2/summary-info.html b/qc_app/templates/rqtl2/summary-info.html
new file mode 100644
index 0000000..c3a2ac0
--- /dev/null
+++ b/qc_app/templates/rqtl2/summary-info.html
@@ -0,0 +1,26 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+<h2 class="heading">Summary</h2>
+
+<div class="explainer">
+  <p>This is the information you have provided to accompany the R/qtl2 bundle
+    you have uploaded. Please verify the information is correct before
+    proceeding.</p>
+</div>
+
+<dl>
+  <dt>Species</dt>
+  <dd>{{species.SpeciesName}} ({{species.FullName}})</dd>
+
+  <dt>Population</dt>
+  <dd>{{population.InbredSetName}}</dd>
+
+  <dt>Genotype Dataset</dt>
+  <dd>{{geno_dataset.Name}} ({{geno_dataset.FullName}})</dd>
+</dl>
+
+{%endblock%}
diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index 7db005c..9bed4f1 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -23,8 +23,9 @@ from qc_app.db import (
     species_by_id,
     save_population,
     populations_by_species,
-    population_by_species_and_id,
-    geno_dataset_by_species_and_population)
+    population_by_species_and_id,)
+from qc_app.db.datasets import (
+    geno_dataset_by_id,  geno_dataset_by_species_and_population)
 
 rqtl2 = Blueprint("rqtl2", __name__)
 
@@ -214,20 +215,27 @@ def select_dataset_info(species_id: int, population_id: int):
         if bool(error_page):
             return error_page
 
+        species = species_by_id(conn, species_id)
+        population = population_by_species_and_id(
+            conn, species_id, population_id)
         thefile = fullpath(form["rqtl2_bundle_file"])
         with ZipFile(str(thefile), "r") as zfile:
             cdata = r_qtl2.control_data(zfile)
             if "geno" in cdata and not bool(form.get("geno-dataset-id")):
                 return render_template(
                     "rqtl2/select-geno-dataset.html",
-                    species=species_by_id(conn, species_id),
-                    population=population_by_species_and_id(
-                        conn, species_id, population_id),
+                    species=species,
+                    population=population,
                     rqtl2_bundle_file=thefile.name,
                     datasets=geno_dataset_by_species_and_population(
                         conn, species_id, population_id))
 
-    return "All data points collected. Should proceed to launching the job."
+            geno_dataset = geno_dataset_by_id(conn, form["geno-dataset-id"])
+
+    return render_template("rqtl2/summary-info.html",
+                           species=species,
+                           population=population,
+                           geno_dataset=geno_dataset)
 
 @rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
               "/rqtl2-bundle/select-geno-dataset"),
-- 
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