From 319d4bf99a67aa7183c5cf5ee4f60e56a558d624 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Fri, 13 Sep 2024 11:49:51 -0500
Subject: Leave notes on things that need to be handled in code and UI

---
 uploader/population/views.py                       |  3 ++
 uploader/samples/views.py                          |  5 ++++
 .../templates/populations/create-population.html   | 32 ++++++++++++++++++++--
 3 files changed, 38 insertions(+), 2 deletions(-)

(limited to 'uploader')

diff --git a/uploader/population/views.py b/uploader/population/views.py
index e870c85..f9041be 100644
--- a/uploader/population/views.py
+++ b/uploader/population/views.py
@@ -151,6 +151,9 @@ def create_population(species_id: int):
                                     species_id=species["SpeciesId"],
                                     error_values=values))
 
+        # TODO: Setup auth
+        # 1. Create new resource in gn-auth and add this population to it
+        # 2. Assign active user the "resource-creator" rights to the new resource
         new_population = save_population(conn, {
             "SpeciesId": species["SpeciesId"],
             "Name": population_name,
diff --git a/uploader/samples/views.py b/uploader/samples/views.py
index f444497..4332c21 100644
--- a/uploader/samples/views.py
+++ b/uploader/samples/views.py
@@ -200,6 +200,11 @@ def upload_samples(species_id: int, population_id: int):#pylint: disable=[too-ma
 
     redisuri = app.config["REDIS_URL"]
     with Redis.from_url(redisuri, decode_responses=True) as rconn:
+        #TODO: Add a QC step here — what do we check?
+        # 1. Does any sample in the uploaded file exist within the database?
+        #    If yes, what is/are its/their species and population?
+        # 2. If yes 1. above, provide error with notes on which species and
+        #    populations already own the samples.
         the_job = jobs.launch_job(
             jobs.initialise_job(
                 rconn,
diff --git a/uploader/templates/populations/create-population.html b/uploader/templates/populations/create-population.html
index b57afba..b05ce37 100644
--- a/uploader/templates/populations/create-population.html
+++ b/uploader/templates/populations/create-population.html
@@ -107,7 +107,10 @@
              value="{{error_values.population_code or ''}}"
              class="form-control" />
       <small class="form-text text-muted">
-        … document what this field is for …
+        <p class="text-danger">
+          <span class="glyphicon glyphicon-exclamation-sign"></span>
+          What is this field is for? Confirm with Arthur and the rest.
+        </p>
       </small>
     </div>
 
@@ -159,7 +162,10 @@
         {%endfor%}
       </select>
       <small class="form-text text-muted">
-        <p>… provide some documentation on what this field does …</p>
+        <p>
+          This is a rough grouping of the populations in GeneNetwork into lists
+          of common types of populations.
+        </p>
       </small>
     </div>
 
@@ -207,6 +213,28 @@
                 {%endif%}>{{gtype}}</option>
         {%endfor%}
       </select>
+      <small class="form-text text-muted text-danger">
+        <p>
+          <span class="glyphicon glyphicon-exclamation-sign"></span>
+          This might be a poorly named field.
+        </p>
+        <p>
+          It probably has more to do with the mating crosses/crossings used to
+          produce the individuals in the population. I am no biologist, however,
+          and I'm leaving this here to remind myself to confirm this.
+        </p>
+        <p>
+          I still don't know what riset is.<br />
+          … probably something to do with Recombinant Inbred Strains
+        </p>
+        <p>
+          Possible resources for this:
+          <ul>
+            <li>https://www.informatics.jax.org/silver/chapters/3-2.shtml</li>
+            <li>https://www.informatics.jax.org/silver/chapters/9-2.shtml</li>
+          </ul>
+        </p>
+      </small>
     </div>
 
     <div class="form-group">
-- 
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