From 5e96d27f3d96c84fc5a15d7040843b379b701d20 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 12 Jun 2024 12:48:56 -0500
Subject: Make URI and UI correspond to each other.

Formerly, the URI and UI were not corresponding to each other,
e.g. the URI /upload/samples/select_species would display the UI for
selecting/creating the population. This was very confusing. This
commit fixes that.

The commit also adds in user input validation to catch input errors.
---
 qc_app/templates/index.html                     | 19 +++-------------
 qc_app/templates/samples/select-population.html |  6 +++--
 qc_app/templates/samples/select-species.html    | 29 +++++++++++++++++++++++++
 qc_app/templates/samples/upload-samples.html    |  6 +++--
 4 files changed, 40 insertions(+), 20 deletions(-)
 create mode 100644 qc_app/templates/samples/select-species.html

(limited to 'qc_app/templates')

diff --git a/qc_app/templates/index.html b/qc_app/templates/index.html
index 588133a..6e98849 100644
--- a/qc_app/templates/index.html
+++ b/qc_app/templates/index.html
@@ -114,22 +114,9 @@
   <p>This section gives you the opportunity to upload any missing samples</p>
 </div>
 
-<form method="POST" action="{{url_for('samples.select_species')}}">
-  <legend class="heading">upload samples</legend>
-  <fieldset>
-    <label for="select_species02">Species</label>
-    <select id="select_species02" name="species_id" required="required">
-      <option value="">Select species</option>
-      {%for spec in species%}
-      <option value="{{spec.SpeciesId}}">{{spec.MenuName}}</option>
-      {%endfor%}
-    </select>
-  </fieldset>
-
-  <fieldset>
-    <input type="submit" value="submit" class="btn btn-main form-col-2" />
-  </fieldset>
-</form>
+<a href={{url_for("samples.select_species")}}
+   title="Upload samples/cases/individuals for your data">
+  upload Samples/Cases</a>
 
 {%endblock%}
 
diff --git a/qc_app/templates/samples/select-population.html b/qc_app/templates/samples/select-population.html
index 24decb4..4bb4cc1 100644
--- a/qc_app/templates/samples/select-population.html
+++ b/qc_app/templates/samples/select-population.html
@@ -15,7 +15,8 @@
 
 <hr />
 
-<form method="POST" action="{{url_for('samples.select_population')}}">
+<form method="POST" action="{{url_for('samples.select_population',
+                            species_id=species.SpeciesId)}}">
   <legend class="heading">select grouping/population</legend>
   {{flash_messages("error-select-population")}}
 
@@ -43,7 +44,8 @@
 
 <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
 
-<form method="POST" action="{{url_for('samples.create_population')}}">
+<form method="POST" action="{{url_for('samples.create_population',
+                            species_id=species.SpeciesId)}}">
   <legend class="heading">create new grouping/population</legend>
   {{flash_messages("error-create-population")}}
 
diff --git a/qc_app/templates/samples/select-species.html b/qc_app/templates/samples/select-species.html
new file mode 100644
index 0000000..6aa4781
--- /dev/null
+++ b/qc_app/templates/samples/select-species.html
@@ -0,0 +1,29 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+
+{%block title%}Select Grouping/Population{%endblock%}
+
+{%block contents%}
+<h2 class="heading">upload samples/cases</h2>
+
+<p>We need to know what species your data belongs to.</p>
+
+{{flash_all_messages()}}
+
+<form method="POST" action="{{url_for('samples.select_species')}}">
+  <legend class="heading">upload samples</legend>
+  <fieldset>
+    <label for="select_species02">Species</label>
+    <select id="select_species02" name="species_id" required="required">
+      <option value="">Select species</option>
+      {%for spec in species%}
+      <option value="{{spec.SpeciesId}}">{{spec.MenuName}}</option>
+      {%endfor%}
+    </select>
+  </fieldset>
+
+  <fieldset>
+    <input type="submit" value="submit" class="btn btn-main form-col-2" />
+  </fieldset>
+</form>
+{%endblock%}
diff --git a/qc_app/templates/samples/upload-samples.html b/qc_app/templates/samples/upload-samples.html
index 5d1ec4c..d04df61 100644
--- a/qc_app/templates/samples/upload-samples.html
+++ b/qc_app/templates/samples/upload-samples.html
@@ -40,7 +40,9 @@
 
 <form id="form-samples"
       method="POST"
-      action="{{url_for('samples.upload_samples')}}"
+      action="{{url_for('samples.upload_samples',
+              species_id=species.SpeciesId,
+              population_id=population.InbredSetId)}}"
       enctype="multipart/form-data">
   <legend class="heading">upload samples</legend>
   <fieldset>
@@ -69,7 +71,7 @@
 	    name="separator"
 	    required="required"
 	    class="form-col-2">
-      <option value="">Select separator for your file</option>
+      <option value="">Select separator for your file: (default is comma)</option>
       <option value="&#x0009;">TAB</option>
       <option value="&#x0020;">Space</option>
       <option value=",">Comma</option>
-- 
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