From 27eec3300eddbc17214b3ff3ffbd8bea867db401 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Fri, 20 Sep 2024 16:10:50 -0500
Subject: Initialise UI for managing genotype datasets.

---
 uploader/genotypes/models.py                     | 21 +++++---
 uploader/genotypes/views.py                      | 29 ++++++++++-
 uploader/templates/genotypes/list-genotypes.html | 10 ++++
 uploader/templates/genotypes/view-dataset.html   | 61 ++++++++++++++++++++++++
 4 files changed, 112 insertions(+), 9 deletions(-)
 create mode 100644 uploader/templates/genotypes/view-dataset.html

(limited to 'uploader')

diff --git a/uploader/genotypes/models.py b/uploader/genotypes/models.py
index 29acd0b..1fe5929 100644
--- a/uploader/genotypes/models.py
+++ b/uploader/genotypes/models.py
@@ -44,19 +44,26 @@ def genotype_markers(
 def genotype_dataset(
         conn: mdb.Connection,
         species_id: int,
-        population_id: int
+        population_id: int,
+        dataset_id: Optional[int] = None
 ) -> Optional[dict]:
     """Retrieve genotype datasets from the database.
 
     Apparently, you should only ever have one genotype dataset for a population.
     """
+    _query = (
+        "SELECT gf.* FROM Species AS s INNER JOIN InbredSet AS iset "
+        "ON s.Id=iset.SpeciesId INNER JOIN GenoFreeze AS gf "
+        "ON iset.Id=gf.InbredSetId "
+        "WHERE s.Id=%s AND iset.Id=%s")
+    _params = (species_id, population_id)
+    if bool(dataset_id):
+        _query = _query + " AND gf.Id=%s"
+        _params = _params + (dataset_id,)
+
     with conn.cursor(cursorclass=DictCursor) as cursor:
-        cursor.execute(
-            "SELECT gf.* FROM Species AS s INNER JOIN InbredSet AS iset "
-            "ON s.Id=iset.SpeciesId INNER JOIN GenoFreeze AS gf "
-            "ON iset.Id=gf.InbredSetId "
-            "WHERE s.Id=%s AND iset.Id=%s",
-            (species_id, population_id))
+        cursor.execute(_query, _params)
+        debug_query(cursor)
         result = cursor.fetchone()
         if bool(result):
             return dict(result)
diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py
index 8752b02..4158491 100644
--- a/uploader/genotypes/views.py
+++ b/uploader/genotypes/views.py
@@ -136,5 +136,30 @@ def list_markers(species_id: int):
 @require_login
 def view_dataset(species_id: int, population_id: int, dataset_id: int):
     """View details regarding a specific dataset."""
-    return (f"Genotype dataset '{dataset_id}, from population '{population_id}' "
-            f"of species '{species_id}'.")
+    with database_connection(app.config["SQL_URI"]) as conn:
+        species = species_by_id(conn, species_id)
+        if not bool(species):
+            flash("Invalid species provided!", "alert-danger")
+            return redirect(url_for("species.populations.genotypes.index"))
+
+        population = population_by_species_and_id(
+            conn, species_id, population_id)
+        if not bool(population):
+            flash("Invalid population selected!", "alert-danger")
+            return redirect(url_for(
+                "species.populations.genotypes.select_population",
+                species_id=species_id))
+
+        dataset = genotype_dataset(conn, species_id, population_id, dataset_id)
+        if not bool(dataset):
+            flash("Could not find such a dataset!", "alert-danger")
+            return redirect(url_for(
+                "species.populations.genotypes.list_genotypes",
+                species_id=species_id,
+                population_id=population_id))
+
+        return render_template("genotypes/view-dataset.html",
+                               species=species,
+                               population=population,
+                               dataset=dataset,
+                               activelink="view-dataset")
diff --git a/uploader/templates/genotypes/list-genotypes.html b/uploader/templates/genotypes/list-genotypes.html
index 3780f85..864e1ec 100644
--- a/uploader/templates/genotypes/list-genotypes.html
+++ b/uploader/templates/genotypes/list-genotypes.html
@@ -129,6 +129,16 @@
       create new genotype dataset</a></p>
   {%endif%}
 </div>
+<div class="row text-warning">
+  <p>
+    <span class="glyphicon glyphicon-exclamation-sign"></span>
+    <strong>NOTE</strong>: Currently the GN2 (and related) system(s) expect a
+    single genotype dataset. If there is more than one, the system apparently
+    fails in unpredictable ways.
+  </p>
+  <p>Fix this to allow multiple datasets, each with a different assembly from
+    all the rest.</p>
+</div>
 {%endblock%}
 
 {%block sidebarcontents%}
diff --git a/uploader/templates/genotypes/view-dataset.html b/uploader/templates/genotypes/view-dataset.html
new file mode 100644
index 0000000..e7ceb36
--- /dev/null
+++ b/uploader/templates/genotypes/view-dataset.html
@@ -0,0 +1,61 @@
+{%extends "genotypes/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+{%from "populations/macro-display-population-card.html" import display_population_card%}
+
+{%block title%}Genotypes: View Dataset{%endblock%}
+
+{%block pagetitle%}Genotypes: View Dataset{%endblock%}
+
+{%block lvl4_breadcrumbs%}
+<li {%if activelink=="view-dataset"%}
+    class="breadcrumb-item active"
+    {%else%}
+    class="breadcrumb-item"
+    {%endif%}>
+  <a href="{{url_for('species.populations.genotypes.view_dataset',
+           species_id=species.SpeciesId,
+           population_id=population.Id,
+           dataset_id=dataset.Id)}}">view dataset</a>
+</li>
+{%endblock%}
+
+{%block contents%}
+{{flash_all_messages()}}
+
+<div class="row">
+  <h2>Genotype Dataset Details</h2>
+  <table class="table">
+    <thead>
+      <tr>
+        <th>Name</th>
+        <th>Full Name</th>
+      </tr>
+    </thead>
+
+    <tbody>
+      <tr>
+        <td>{{dataset.Name}}</td>
+        <td>{{dataset.FullName}}</td>
+      </tr>
+    </tbody>
+  </table>
+</div>
+
+<div class="row text-warning">
+  <h2>Assembly Details</h2>
+
+  <p>Maybe include the assembly details here if found to be necessary.</p>
+</div>
+
+<div class="row">
+  <h2>Genotype Data</h2>
+
+  <p class="text-danger">
+    Provide link to enable uploading of genotype data here.</p>
+</div>
+
+{%endblock%}
+
+{%block sidebarcontents%}
+{{display_population_card(species, population)}}
+{%endblock%}
-- 
cgit v1.2.3