From 75add682a8d63a30e947b6bcd8d2e5dfee06c297 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Tue, 18 Feb 2025 16:24:14 -0600
Subject: Use new searchable list tables with off-ramps for data creation.

---
 uploader/genotypes/views.py                        | 21 +++++++++++++++----
 uploader/platforms/views.py                        |  8 +++++++-
 uploader/population/views.py                       | 10 ++++++++-
 uploader/samples/views.py                          | 24 ++++++++++++++++------
 uploader/templates/genotypes/index.html            |  4 ++++
 .../templates/genotypes/select-population.html     | 16 +++++----------
 uploader/templates/phenotypes/index.html           |  5 -----
 uploader/templates/platforms/index.html            |  4 ++++
 uploader/templates/populations/index.html          |  4 ++++
 .../populations/macro-select-population.html       |  4 ++++
 uploader/templates/samples/index.html              |  4 ++++
 uploader/templates/samples/select-population.html  | 23 +++++----------------
 12 files changed, 81 insertions(+), 46 deletions(-)

(limited to 'uploader')

diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py
index 0433420..5105730 100644
--- a/uploader/genotypes/views.py
+++ b/uploader/genotypes/views.py
@@ -35,8 +35,15 @@ def index():
     with database_connection(app.config["SQL_URI"]) as conn:
         if not bool(request.args.get("species_id")):
             return render_template("genotypes/index.html",
-                                   species=order_by_family(all_species(conn)),
+                                   species=all_species(conn),
                                    activelink="genotypes")
+
+        species_id = request.args.get("species_id")
+        if species_id == "CREATE-SPECIES":
+            return redirect(url_for(
+                "species.create_species",
+                return_to="species.populations.genotypes.select_population"))
+
         species = species_by_id(conn, request.args.get("species_id"))
         if not bool(species):
             flash(f"Could not find species with ID '{request.args.get('species_id')}'!",
@@ -56,11 +63,17 @@ def select_population(species: dict, species_id: int):
         if not bool(request.args.get("population_id")):
             return render_template("genotypes/select-population.html",
                                    species=species,
-                                   populations=order_by_family(
-                                       populations_by_species(conn, species_id),
-                                       order_key="FamilyOrder"),
+                                   populations=populations_by_species(
+                                       conn, species_id),
                                    activelink="genotypes")
 
+        population_id = request.args["population_id"]
+        if population_id == "CREATE-POPULATION":
+            return redirect(url_for(
+                "species.populations.create_population",
+                species_id=species["SpeciesId"],
+                return_to="species.populations.samples.list_genotypes"))
+
         population = population_by_species_and_id(
             conn, species_id, request.args.get("population_id"))
         if not bool(population):
diff --git a/uploader/platforms/views.py b/uploader/platforms/views.py
index c20ab44..114c1a9 100644
--- a/uploader/platforms/views.py
+++ b/uploader/platforms/views.py
@@ -29,9 +29,15 @@ def index():
         if not bool(request.args.get("species_id")):
             return render_template(
                 "platforms/index.html",
-                species=order_by_family(all_species(conn)),
+                species=all_species(conn),
                 activelink="platforms")
 
+        species_id = request.args.get("species_id")
+        if species_id == "CREATE-SPECIES":
+            return redirect(url_for(
+                "species.create_species",
+                return_to="species.platforms.list_platforms"))
+
         species = species_by_id(conn, request.args["species_id"])
         if not bool(species):
             flash("No species selected.", "alert-danger")
diff --git a/uploader/population/views.py b/uploader/population/views.py
index 1ece35f..f42e547 100644
--- a/uploader/population/views.py
+++ b/uploader/population/views.py
@@ -49,7 +49,15 @@ def index():
         if not bool(request.args.get("species_id")):
             return render_template(
                 "populations/index.html",
-                species=order_species_by_family(all_species(conn)))
+                species=all_species(conn),
+                activelink="populations")
+
+        species_id = request.args.get("species_id")
+        if species_id == "CREATE-SPECIES":
+            return redirect(url_for(
+                "species.create_species",
+                return_to="species.populations.list_species_populations"))
+
         species = species_by_id(conn, request.args.get("species_id"))
         if not bool(species):
             flash("Invalid species identifier provided!", "alert-danger")
diff --git a/uploader/samples/views.py b/uploader/samples/views.py
index ed79101..95a6f8c 100644
--- a/uploader/samples/views.py
+++ b/uploader/samples/views.py
@@ -40,8 +40,15 @@ def index():
         if not bool(request.args.get("species_id")):
             return render_template(
                 "samples/index.html",
-                species=order_species_by_family(all_species(conn)),
+                species=all_species(conn),
                 activelink="samples")
+
+        species_id = request.args.get("species_id")
+        if species_id == "CREATE-SPECIES":
+            return redirect(url_for(
+                "species.create_species",
+                return_to="species.populations.samples.select_population"))
+
         species = species_by_id(conn, request.args.get("species_id"))
         if not bool(species):
             flash("No such species!", "alert-danger")
@@ -63,13 +70,18 @@ def select_population(species_id: int):
         if not bool(request.args.get("population_id")):
             return render_template("samples/select-population.html",
                                    species=species,
-                                   populations=order_by_family(
-                                       populations_by_species(
-                                           conn,
-                                           species_id),
-                                       order_key="FamilyOrder"),
+                                   populations=populations_by_species(
+                                       conn,
+                                       species_id),
                                    activelink="samples")
 
+        population_id = request.args["population_id"]
+        if population_id == "CREATE-POPULATION":
+            return redirect(url_for(
+                "species.populations.create_population",
+                species_id=species["SpeciesId"],
+                return_to="species.populations.samples.list_samples"))
+
         population = population_by_id(conn, request.args.get("population_id"))
         if not bool(population):
             flash("Population not found!", "alert-danger")
diff --git a/uploader/templates/genotypes/index.html b/uploader/templates/genotypes/index.html
index e749f5a..b50ebc5 100644
--- a/uploader/templates/genotypes/index.html
+++ b/uploader/templates/genotypes/index.html
@@ -26,3 +26,7 @@
   species)}}
 </div>
 {%endblock%}
+
+{%block javascript%}
+<script type="text/javascript" src="/static/js/species.js"></script>
+{%endblock%}
diff --git a/uploader/templates/genotypes/select-population.html b/uploader/templates/genotypes/select-population.html
index 7c81943..acdd063 100644
--- a/uploader/templates/genotypes/select-population.html
+++ b/uploader/templates/genotypes/select-population.html
@@ -12,20 +12,14 @@
 {{flash_all_messages()}}
 
 <div class="row">
-  <p>
-    You have indicated that you intend to upload the genotypes for species
-    '{{species.FullName}}'. We now just require the population for your
-    experiment/study, and you should be good to go.
-  </p>
-</div>
-
-<div class="row">
-  {{select_population_form(url_for("species.populations.genotypes.select_population",
-  species_id=species.SpeciesId),
-  populations)}}
+  {{select_population_form(url_for("species.populations.genotypes.select_population", species_id=species.SpeciesId), species, populations)}}
 </div>
 {%endblock%}
 
 {%block sidebarcontents%}
 {{display_species_card(species)}}
 {%endblock%}
+
+{%block javascript%}
+<script type="text/javascript" src="/static/js/populations.js"></script>
+{%endblock%}
diff --git a/uploader/templates/phenotypes/index.html b/uploader/templates/phenotypes/index.html
index bffc278..689c28e 100644
--- a/uploader/templates/phenotypes/index.html
+++ b/uploader/templates/phenotypes/index.html
@@ -18,9 +18,4 @@
 
 {%block javascript%}
 <script type="text/javascript" src="/static/js/species.js"></script>
-<script type="text/javascript">
-  $(function() {
-      speciesDataTable(JSON.parse($("#tbl-select-species").attr("data-species-list")));
-  });
-  </script>
 {%endblock%}
diff --git a/uploader/templates/platforms/index.html b/uploader/templates/platforms/index.html
index 35b6464..555b444 100644
--- a/uploader/templates/platforms/index.html
+++ b/uploader/templates/platforms/index.html
@@ -19,3 +19,7 @@
   {{select_species_form(url_for("species.platforms.index"), species)}}
 </div>
 {%endblock%}
+
+{%block javascript%}
+<script type="text/javascript" src="/static/js/species.js"></script>
+{%endblock%}
diff --git a/uploader/templates/populations/index.html b/uploader/templates/populations/index.html
index 4354e02..d2bee77 100644
--- a/uploader/templates/populations/index.html
+++ b/uploader/templates/populations/index.html
@@ -22,3 +22,7 @@
   {{select_species_form(url_for("species.populations.index"), species)}}
 </div>
 {%endblock%}
+
+{%block javascript%}
+<script type="text/javascript" src="/static/js/species.js"></script>
+{%endblock%}
diff --git a/uploader/templates/populations/macro-select-population.html b/uploader/templates/populations/macro-select-population.html
index c223776..14b0510 100644
--- a/uploader/templates/populations/macro-select-population.html
+++ b/uploader/templates/populations/macro-select-population.html
@@ -42,6 +42,10 @@
     ({{species['SpeciesName']}}).<br />
     Click "Continue" to create the first!</p>
   <input type="hidden" name="population_id" value="CREATE-POPULATION" />
+
+  <div class="col-sm-offset-10 col-sm-2">
+    <input type="submit" value="continue" class="btn btn-primary" />
+  </div>
   {%endif%}
 
 </form>
diff --git a/uploader/templates/samples/index.html b/uploader/templates/samples/index.html
index ee4a63e..ee98734 100644
--- a/uploader/templates/samples/index.html
+++ b/uploader/templates/samples/index.html
@@ -17,3 +17,7 @@
   {{select_species_form(url_for("species.populations.samples.index"), species)}}
 </div>
 {%endblock%}
+
+{%block javascript%}
+<script type="text/javascript" src="/static/js/species.js"></script>
+{%endblock%}
diff --git a/uploader/templates/samples/select-population.html b/uploader/templates/samples/select-population.html
index f437780..1cc7573 100644
--- a/uploader/templates/samples/select-population.html
+++ b/uploader/templates/samples/select-population.html
@@ -11,29 +11,16 @@
 {%block contents%}
 {{flash_all_messages()}}
 
-<div class="row">
-  <p>You have selected "{{species.FullName}}" as the species that your data relates to.</p>
-  <p>Next, we need information regarding the population your data relates to. Do please select the population from the existing ones below</p>
-</div>
-
 <div class="row">
   {{select_population_form(
-  url_for("species.populations.samples.select_population", species_id=species.SpeciesId),
-  populations)}}
-</div>
-
-<div class="row">
-  <p>
-    If you cannot find the population your data relates to in the drop-down
-    above, you might want to
-    <a href="{{url_for('species.populations.create_population',
-             species_id=species.SpeciesId)}}"
-       title="Create a new population for species '{{species.FullName}},">
-      add a new population to GeneNetwork</a>
-    instead.
+  url_for("species.populations.samples.select_population", species_id=species.SpeciesId), species, populations)}}
 </div>
 {%endblock%}
 
 {%block sidebarcontents%}
 {{display_species_card(species)}}
 {%endblock%}
+
+{%block javascript%}
+<script type="text/javascript" src="/static/js/populations.js"></script>
+{%endblock%}
-- 
cgit v1.2.3