From 58a214a4a9be5fb219a798b62cdbf43d72280c74 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Fri, 5 Jan 2024 13:08:38 +0300
Subject: Initialise R/qtl2 bundle upload path

Initialise the upload path for R/qtl2 bundles. This commit adds UI
that allows the user to select from existing species, before
proceeding to the next stage.
---
 qc_app/__init__.py                |  2 ++
 qc_app/templates/base.html        |  2 +-
 qc_app/templates/rqtl2/index.html | 34 ++++++++++++++++++++++++++++++++++
 qc_app/upload/__init__.py         |  7 +++++++
 qc_app/upload/rqtl2.py            | 31 +++++++++++++++++++++++++++++++
 5 files changed, 75 insertions(+), 1 deletion(-)
 create mode 100644 qc_app/templates/rqtl2/index.html
 create mode 100644 qc_app/upload/__init__.py
 create mode 100644 qc_app/upload/rqtl2.py

diff --git a/qc_app/__init__.py b/qc_app/__init__.py
index f2001ab..1215954 100644
--- a/qc_app/__init__.py
+++ b/qc_app/__init__.py
@@ -5,6 +5,7 @@ import os
 from flask import Flask
 
 from .entry import entrybp
+from .upload import upload
 from .parse import parsebp
 from .samples import samples
 from .dbinsert import dbinsertbp
@@ -30,6 +31,7 @@ def create_app(instance_dir):
     # setup blueprints
     app.register_blueprint(entrybp, url_prefix="/")
     app.register_blueprint(parsebp, url_prefix="/parse")
+    app.register_blueprint(upload, url_prefix="/upload")
     app.register_blueprint(dbinsertbp, url_prefix="/dbinsert")
     app.register_blueprint(samples, url_prefix="/samples")
 
diff --git a/qc_app/templates/base.html b/qc_app/templates/base.html
index 0cc970c..3b701bc 100644
--- a/qc_app/templates/base.html
+++ b/qc_app/templates/base.html
@@ -11,7 +11,7 @@
     <link rel="stylesheet" type="text/css" href="/static/css/styles.css" />
     {%block css%}{%endblock%}
 
-    <link rel="icon" type="image/png" sizes="64x64"
+    <link rel="shortcut icon" type="image/png" sizes="64x64"
 	  href="/static/images/CITGLogo.png" />
   </head>
 
diff --git a/qc_app/templates/rqtl2/index.html b/qc_app/templates/rqtl2/index.html
new file mode 100644
index 0000000..24f19fa
--- /dev/null
+++ b/qc_app/templates/rqtl2/index.html
@@ -0,0 +1,34 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Data Upload{%endblock%}
+
+{%block contents%}
+<h1 class="heading">R/qtl2 data upload</h1>
+
+<h2>R/qtl2 Upload</h2>
+
+<form method="POST" action="{{url_for('upload.rqtl2.select_species')}}"
+      id="frm-rqtl2-upload">
+  <legend class="heading">upload R/qtl2 bundle</legend>
+  {{flash_messages("error-rqtl2")}}
+  <fieldset>
+    <label for="select:species">Species</label>
+    <select id="select:species" name="species_id" required="required">
+      <option value="">Select species</option>
+      {%for spec in species%}
+      <option value="{{spec.SpeciesId}}">{{spec.MenuName}}</option>
+      {%endfor%}
+    </select>
+    <span class="form-input-help">
+      Data that you upload to the system should belong to a know species.
+      Here you can select the species that you wish to upload data for.
+    </span>
+  </fieldset>
+
+  <fieldset>
+    <input type="submit" value="submit" class="btn btn-main form-col-2" />
+  </fieldset>
+</form>
+
+{%endblock%}
diff --git a/qc_app/upload/__init__.py b/qc_app/upload/__init__.py
new file mode 100644
index 0000000..5f120d4
--- /dev/null
+++ b/qc_app/upload/__init__.py
@@ -0,0 +1,7 @@
+"""Package handling upload of files."""
+from flask import Blueprint
+
+from .rqtl2 import rqtl2
+
+upload = Blueprint("upload", __name__)
+upload.register_blueprint(rqtl2, url_prefix="/rqtl2")
diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
new file mode 100644
index 0000000..e54f141
--- /dev/null
+++ b/qc_app/upload/rqtl2.py
@@ -0,0 +1,31 @@
+"""Module to handle uploading of R/qtl2 bundles."""
+
+from flask import (
+    flash,
+    request,
+    url_for,
+    redirect,
+    Blueprint,
+    render_template)
+
+from qc_app.dbinsert import species as all_species
+from qc_app.dbinsert import species_by_id, groups_by_species
+from qc_app.db_utils import with_db_connection
+
+rqtl2 = Blueprint("rqtl2", __name__)
+
+@rqtl2.route("/", methods=["GET", "POST"])
+@rqtl2.route("/select-species", methods=["POST"])
+def select_species():
+    """Select the species."""
+    if request.method == "GET":
+        return render_template("rqtl2/index.html", species=all_species())
+
+    species_id = request.form.get("species_id")
+    species = with_db_connection(
+        lambda conn: species_by_id(conn, species_id))
+    if bool(species):
+        return redirect(url_for(
+            "upload.rqtl2.select_population", species_id=species_id))
+    flash("Invalid species or no species selected!", "alert-error error-rqtl2")
+    return redirect(url_for("upload.rqtl2.select_species"))
-- 
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