Put populations under species: improve hierarchy.

Populations cannot exist without the species they are related to. This
commit updates the URI hierarchy to reflect that expectation.

10 files changed, 21 insertions, 21 deletions

diff --git a/uploader/__init__.py b/uploader/__init__.py
index 5028f79..347f170 100644
--- a/uploader/__init__.py
+++ b/uploader/__init__.py
@@ -10,7 +10,6 @@ from flask_session import Session
 from uploader.oauth2.client import user_logged_in, authserver_authorise_uri
 
 from .base_routes import base
-from .population import popbp
 from .species import speciesbp
 from .dbinsert import dbinsertbp
 from .oauth2.views import oauth2
@@ -84,7 +83,6 @@ def create_app():
     app.register_blueprint(base, url_prefix="/")
     app.register_blueprint(oauth2, url_prefix="/oauth2")
     app.register_blueprint(speciesbp, url_prefix="/species")
-    app.register_blueprint(popbp, url_prefix="/populations")
     app.register_blueprint(dbinsertbp, url_prefix="/dbinsert")
     app.register_blueprint(exprdatabp, url_prefix="/expression-data")
 
diff --git a/uploader/population/views.py b/uploader/population/views.py
index cd5e20b..3be46d4 100644
--- a/uploader/population/views.py
+++ b/uploader/population/views.py
@@ -21,7 +21,7 @@ popbp = Blueprint("populations", __name__)
 render_template = make_template_renderer("populations")
 
 
-@popbp.route("/", methods=["GET", "POST"])
+@popbp.route("/populations", methods=["GET", "POST"])
 @require_login
 def index():
     """Entry point for populations."""
@@ -33,11 +33,11 @@ def index():
         species = species_by_id(conn, request.args.get("species_id"))
         if not bool(species):
             flash("Invalid species identifier provided!", "alert-danger")
-            return redirect(url_for("populations.index"))
-        return redirect(url_for("populations.list_species_populations",
+            return redirect(url_for("species.populations.index"))
+        return redirect(url_for("species.populations.list_species_populations",
                                 species_id=species["SpeciesId"]))
 
-@popbp.route("/<int:species_id>", methods=["GET"])
+@popbp.route("/<int:species_id>/populations", methods=["GET"])
 @require_login
 def list_species_populations(species_id: int):
     """List a particular species' populations."""
@@ -45,7 +45,7 @@ def list_species_populations(species_id: int):
         species = species_by_id(conn, species_id)
         if not bool(species):
             flash("No species was found for given ID.", "alert-danger")
-            return redirect(url_for("populations.index"))
+            return redirect(url_for("species.populations.index"))
         return render_template(
             "populations/list-populations.html",
             species=species,
@@ -95,7 +95,7 @@ def create_population(species_id: int):
             error = True
 
         if error:
-            return redirect(url_for("populations.create_population",
+            return redirect(url_for("species.populations.create_population",
                                     **dict(request.args)))
 
         new_population = save_population(conn, {
@@ -107,7 +107,7 @@ def create_population(species_id: int):
             "Description": request.form.get("description") or None
         })
 
-        return redirect(url_for("populations.view_population",
+        return redirect(url_for("species.populations.view_population",
                                 species_id=species["SpeciesId"],
                                 population_id=new_population["InbredSetId"]))
 
diff --git a/uploader/species/views.py b/uploader/species/views.py
index 6f4d51f..77406a1 100644
--- a/uploader/species/views.py
+++ b/uploader/species/views.py
@@ -6,6 +6,7 @@ from flask import (flash,
                    Blueprint,
                    current_app as app)
 
+from uploader.population import popbp
 from uploader.ui import make_template_renderer
 from uploader.authorisation import require_login
 from uploader.db_utils import database_connection
@@ -14,6 +15,7 @@ from .models import all_species, save_species, species_by_id
 
 
 speciesbp = Blueprint("species", __name__)
+speciesbp.register_blueprint(popbp, url_prefix="/")
 render_template = make_template_renderer("species")
 
 
diff --git a/uploader/templates/base.html b/uploader/templates/base.html
index fd6010b..d9696d0 100644
--- a/uploader/templates/base.html
+++ b/uploader/templates/base.html
@@ -45,7 +45,7 @@
       <ul class="nav flex-column">
         <li><a href="/" >Home</a></li>
         <li><a href="{{url_for('species.list_species')}}" >Species</a></li>
-        <li><a href="{{url_for('populations.index')}}">Populations</a></li>
+        <li><a href="{{url_for('species.populations.index')}}">Populations</a></li>
         <li><a href="{{url_for('expression-data.index.index')}}" >Expression Data</a></li>
       </ul>
     </aside>
@@ -63,7 +63,7 @@
                 {%endif%}>
               <a href="{{url_for('base.index')}}">Home</a>
             </li>
-            {%block breadcrumbs%}{%endblock%}
+            {%block lvl1_breadcrumbs%}{%endblock%}
           </ol>
         </nav>
       </div>
diff --git a/uploader/templates/populations/base.html b/uploader/templates/populations/base.html
index 1033927..d763fc1 100644
--- a/uploader/templates/populations/base.html
+++ b/uploader/templates/populations/base.html
@@ -1,12 +1,12 @@
-{%extends "base.html"%}
+{%extends "species/base.html"%}
 
-{%block breadcrumbs%}
+{%block lvl2_breadcrumbs%}
 <li {%if activelink=="populations"%}
     class="breadcrumb-item active"
     {%else%}
     class="breadcrumb-item"
     {%endif%}>
-  <a href="{{url_for('populations.index')}}">Populations</a>
+  <a href="{{url_for('species.populations.index')}}">Populations</a>
 </li>
 {%block lvl3_breadcrumbs%}{%endblock%}
 {%endblock%}
diff --git a/uploader/templates/populations/index.html b/uploader/templates/populations/index.html
index 14cf547..061ca1d 100644
--- a/uploader/templates/populations/index.html
+++ b/uploader/templates/populations/index.html
@@ -11,6 +11,6 @@
 <div class="row">
   To continue, you need to select the species:
 
-  {{select_species_form(url_for("populations.index"), species)}}
+  {{select_species_form(url_for("species.populations.index"), species)}}
 </div>
 {%endblock%}
diff --git a/uploader/templates/populations/list-populations.html b/uploader/templates/populations/list-populations.html
index bf6cf98..c14a28c 100644
--- a/uploader/templates/populations/list-populations.html
+++ b/uploader/templates/populations/list-populations.html
@@ -12,7 +12,7 @@
     {%else%}
     class="breadcrumb-item"
     {%endif%}>
-  <a href="{{url_for('populations.list_species_populations',
+  <a href="{{url_for('species.populations.list_species_populations',
            species_id=species.SpeciesId)}}">List</a>
 </li>
 {%endblock%}
@@ -35,7 +35,7 @@
     exist, click on the "Create Population" button below to create a new one.
   </p>
   <p>
-    <a href="{{url_for('populations.create_population',
+    <a href="{{url_for('species.populations.create_population',
              species_id=species.SpeciesId)}}"
        title="Create a new population for species '{{species.FullName}}'."
        class="btn btn-danger">
diff --git a/uploader/templates/species/base.html b/uploader/templates/species/base.html
index 8fb697d..04391db 100644
--- a/uploader/templates/species/base.html
+++ b/uploader/templates/species/base.html
@@ -1,6 +1,6 @@
 {%extends "base.html"%}
 
-{%block breadcrumbs%}
+{%block lvl1_breadcrumbs%}
 <li {%if activelink=="species"%}
     class="breadcrumb-item active"
     {%else%}
@@ -8,5 +8,5 @@
     {%endif%}>
   <a href="{{url_for('species.list_species')}}">Species</a>
 </li>
-{%block lvl3_breadcrumbs%}{%endblock%}
+{%block lvl2_breadcrumbs%}{%endblock%}
 {%endblock%}
diff --git a/uploader/templates/species/create-species.html b/uploader/templates/species/create-species.html
index 678b010..1bc3b61 100644
--- a/uploader/templates/species/create-species.html
+++ b/uploader/templates/species/create-species.html
@@ -5,7 +5,7 @@
 
 {%block pagetitle%}Create Species{%endblock%}
 
-{%block lvl3_breadcrumbs%}
+{%block lvl2_breadcrumbs%}
 <li {%if activelink=="create-species"%}
     class="breadcrumb-item active"
     {%else%}
diff --git a/uploader/templates/species/view-species.html b/uploader/templates/species/view-species.html
index 0a3b0dd..0364c97 100644
--- a/uploader/templates/species/view-species.html
+++ b/uploader/templates/species/view-species.html
@@ -22,7 +22,7 @@
 </style>
 {%endblock%}
 
-{%block lvl3_breadcrumbs%}
+{%block lvl2_breadcrumbs%}
 <li {%if activelink=="view-species"%}
     class="breadcrumb-item active"
     {%else%}