Species: Move feature to new UI templates.

5 files changed, 111 insertions, 220 deletions

diff --git a/uploader/species/views.py b/uploader/species/views.py
index 9b14d01..4bfa7ae 100644
--- a/uploader/species/views.py
+++ b/uploader/species/views.py
@@ -8,8 +8,6 @@ from flask import (flash,
                    Blueprint,
                    current_app as app)
 
-from uploader.sui import sui_template
-
 from uploader.population import popbp
 from uploader.platforms import platformsbp
 from uploader.flask_extensions import url_for
@@ -56,7 +54,7 @@ def view_species(species_id: int):
                                         species_id=species_id,
                                         population_id=population["Id"]))
             return render_template(
-                sui_template("species/view-species.html"),
+                "species/view-species.html",
                 species=species,
                 activelink="view-species",
                 populations=populations_by_species(conn, species["SpeciesId"]))
diff --git a/uploader/templates/species/base.html b/uploader/templates/species/base.html
index f64f72b..a7c1a8f 100644
--- a/uploader/templates/species/base.html
+++ b/uploader/templates/species/base.html
@@ -1,17 +1,10 @@
 {%extends "base.html"%}
 
-{%block lvl1_breadcrumbs%}
-<li {%if activelink=="species"%}
-    class="breadcrumb-item active"
-    {%else%}
-    class="breadcrumb-item"
-    {%endif%}>
-  {%if species is mapping%}
-  <a href="{{url_for('species.view_species', species_id=species.SpeciesId)}}">
-    {{species.Name}}</a>
-  {%else%}
-  <a href="{{url_for('species.list_species')}}">Species</a>
-  {%endif%}
+{%block breadcrumbs%}
+{{super()}}
+<li class="breadcrumb-item">
+  <a href="{{url_for('species.view_species', species_id=species['SpeciesId'])}}">
+    {{species["Name"]|title}}
+  </a>
 </li>
-{%block lvl2_breadcrumbs%}{%endblock%}
 {%endblock%}
diff --git a/uploader/templates/species/sui-base.html b/uploader/templates/species/sui-base.html
deleted file mode 100644
index f7b4fef..0000000
--- a/uploader/templates/species/sui-base.html
+++ /dev/null
@@ -1,10 +0,0 @@
-{%extends "sui-base.html"%}
-
-{%block breadcrumbs%}
-{{super()}}
-<li class="breadcrumb-item">
-  <a href="{{url_for('species.view_species', species_id=species['SpeciesId'])}}">
-    {{species["Name"]|title}}
-  </a>
-</li>
-{%endblock%}
diff --git a/uploader/templates/species/sui-view-species.html b/uploader/templates/species/sui-view-species.html
deleted file mode 100644
index 4b6402e..0000000
--- a/uploader/templates/species/sui-view-species.html
+++ /dev/null
@@ -1,127 +0,0 @@
-{%extends "species/sui-base.html"%}
-{%from "flash_messages.html" import flash_all_messages%}
-{%from "macro-forms.html" import add_http_feature_flags%}
-{%from "macro-step-indicator.html" import step_indicator%}
-{%from "species/macro-display-species-card.html" import display_sui_species_card%}
-
-{%block title%}View Species{%endblock%}
-
-{%macro add_form_buttons()%}
-<div class="row form-buttons">
-  <div class="col">
-    <input type="submit"
-           value="use selected population"
-           class="btn btn-primary" />
-  </div>
-
-  <div class="col">
-    <a href="url_for('species.population.create_population',
-             species_id=species.SpeciesId,
-             return_to='species.view_species')"
-       title="Create a new population for species '{{species.Name}}'."
-       class="btn btn-outline-info">
-      Create a new population
-    </a>
-  </div>
-</div>
-{%endmacro%}
-
-
-{%block contents%}
-<div class="row">
-  <h2 class="heading">{{species.FullName}} ({{species.Name}})</h2>
-</div>
-
-<div class "row">
-  <ul class="nav nav-tabs" id="species-actions">
-    <li class="nav-item presentation">
-      <button class="nav-link active"
-              id="populations-tab"
-              data-bs-toggle="tab"
-              data-bs-target="#populations-content"
-              type="button"
-              role="tab"
-              aria-controls="populations-content"
-              aria-selected="true">Populations</button>
-    </li>
-    <li class="nav-item presentation">
-      <button class="nav-link"
-              id="sequencing-platforms-tab"
-              data-bs-toggle="tab"
-              data-bs-target="#sequencing-platforms-content"
-              type="button"
-              role="tab"
-              aria-controls="sequencing-platforms-content"
-              aria-selected="true">Sequencing Platforms</button>
-    </li>
-  </ul>
-</div>
-
-<div class="row">
-  <div class="tab-content" id="species-tabs-content">
-    <div class="tab-pane fade show active"
-         id="populations-content"
-         role="tabpanel"
-         aria-labelledby="populations-content-tab">
-      <p>Data belonging to a particular species is further divided into one or more
-        populations for easier handling. Please select the population you want to work
-        with.</p>
-
-      <form method="GET"
-            action="{{url_for('species.view_species', species_id=species.SpeciesId)}}"
-            class="form-horizontal">
-        {{add_http_feature_flags()}}
-        {{add_form_buttons()}}
-
-        {%if populations | length != 0%}
-        <div style="margin-top:0.3em;">
-          <table id="tbl-select-population" class="table compact stripe"
-                 data-populations-list='{{populations | tojson}}'>
-            <thead>
-              <tr>
-                <th></th>
-                <th>Population</th>
-              </tr>
-            </thead>
-
-            <tbody></tbody>
-          </table>
-        </div>
-
-        {%else%}
-        <p class="form-text">
-          There are no populations currently defined for {{species['FullName']}}
-          ({{species['SpeciesName']}}).</p>
-        {%endif%}
-
-        {{add_form_buttons()}}
-
-      </form>
-    </div>
-    <div class="tab-pane fade"
-         id="sequencing-platforms-content"
-         role="tabpanel"
-         aria-labelledby="sequencing-platforms-content-tab">
-      <p>Upload and manage the sequencing platforms for species
-        '{{species.Name | title}} ({{species.FullName}})'
-        <a href="{{url_for('species.platforms.list_platforms',
-                 species_id=species.SpeciesId)}}"
-           title="Manage sequencing platforms for {{species.Name}}">here</a>.
-      </p>
-    </div>
-  </div>
-</div>
-{%endblock%}
-
-{%block sidebarcontents%}
-<div class="row">
-  <p>You can manage species' populations and sequencing platforms here. Select
-    the tab for the feature you wish to continue working on.</p>
-</div>
-{{display_sui_species_card(species)}}
-{%endblock%}
-
-
-{%block javascript%}
-<script type="text/javascript" src="/static/js/populations.js"></script>
-{%endblock%}
diff --git a/uploader/templates/species/view-species.html b/uploader/templates/species/view-species.html
index 2d02f7e..48fd6cc 100644
--- a/uploader/templates/species/view-species.html
+++ b/uploader/templates/species/view-species.html
@@ -1,90 +1,127 @@
 {%extends "species/base.html"%}
 {%from "flash_messages.html" import flash_all_messages%}
+{%from "macro-forms.html" import add_http_feature_flags%}
+{%from "macro-step-indicator.html" import step_indicator%}
+{%from "species/macro-display-species-card.html" import display_sui_species_card%}
 
 {%block title%}View Species{%endblock%}
 
-{%block pagetitle%}View Species{%endblock%}
+{%macro add_form_buttons()%}
+<div class="row form-buttons">
+  <div class="col">
+    <input type="submit"
+           value="use selected population"
+           class="btn btn-primary" />
+  </div>
+
+  <div class="col">
+    <a href="url_for('species.population.create_population',
+             species_id=species.SpeciesId,
+             return_to='species.view_species')"
+       title="Create a new population for species '{{species.Name}}'."
+       class="btn btn-outline-info">
+      Create a new population
+    </a>
+  </div>
+</div>
+{%endmacro%}
 
-{%block lvl2_breadcrumbs%}
-<li {%if activelink=="view-species"%}
-    class="breadcrumb-item active"
-    {%else%}
-    class="breadcrumb-item"
-    {%endif%}>
-  <a href="{{url_for('species.view_species', species_id=species.SpeciesId)}}">View</a>
-</li>
-{%endblock%}
 
 {%block contents%}
-{{flash_all_messages()}}
 <div class="row">
-  <h2>Details on species {{species.FullName}}</h2>
+  <h2 class="heading">{{species.FullName}} ({{species.Name}})</h2>
+</div>
 
-  <dl>
-    <dt>Common Name</dt>
-    <dd>{{species.SpeciesName}}</dd>
+<div class "row">
+  <ul class="nav nav-tabs" id="species-actions">
+    <li class="nav-item presentation">
+      <button class="nav-link active"
+              id="populations-tab"
+              data-bs-toggle="tab"
+              data-bs-target="#populations-content"
+              type="button"
+              role="tab"
+              aria-controls="populations-content"
+              aria-selected="true">Populations</button>
+    </li>
+    <li class="nav-item presentation">
+      <button class="nav-link"
+              id="sequencing-platforms-tab"
+              data-bs-toggle="tab"
+              data-bs-target="#sequencing-platforms-content"
+              type="button"
+              role="tab"
+              aria-controls="sequencing-platforms-content"
+              aria-selected="true">Sequencing Platforms</button>
+    </li>
+  </ul>
+</div>
 
-    <dt>Scientific Name</dt>
-    <dd>{{species.FullName}}</dd>
+<div class="row">
+  <div class="tab-content" id="species-tabs-content">
+    <div class="tab-pane fade show active"
+         id="populations-content"
+         role="tabpanel"
+         aria-labelledby="populations-content-tab">
+      <p>Data belonging to a particular species is further divided into one or more
+        populations for easier handling. Please select the population you want to work
+        with.</p>
 
-    <dt>Taxonomy ID</dt>
-    <dd>{{species.TaxonomyId}}</dd>
-  </dl>
+      <form method="GET"
+            action="{{url_for('species.view_species', species_id=species.SpeciesId)}}"
+            class="form-horizontal">
+        {{add_http_feature_flags()}}
+        {{add_form_buttons()}}
 
-  <h3>Actions</h3>
+        {%if populations | length != 0%}
+        <div style="margin-top:0.3em;">
+          <table id="tbl-select-population" class="table compact stripe"
+                 data-populations-list='{{populations | tojson}}'>
+            <thead>
+              <tr>
+                <th></th>
+                <th>Population</th>
+              </tr>
+            </thead>
 
-  <p>
-    You can proceed to perform any of the following actions for species
-    {{species.FullName}}
-  </p>
+            <tbody></tbody>
+          </table>
+        </div>
 
-  <ol>
-    <li>
-      <a href="{{url_for('species.populations.list_species_populations',
-               species_id=species.SpeciesId)}}"
-         title="Create/Edit populations for {{species.FullName}}">
-        Manage populations</a>
-    </li>
-    <li>
-      <a href="{{url_for('species.platforms.list_platforms',
-               species_id=species.SpeciesId)}}"
-         title="Create/Edit sequencing platforms for {{species.FullName}}">
-        Manage sequencing platforms</a>
-    </li>
-  </ol>
+        {%else%}
+        <p class="form-text">
+          There are no populations currently defined for {{species['FullName']}}
+          ({{species['SpeciesName']}}).</p>
+        {%endif%}
 
-  
+        {{add_form_buttons()}}
+
+      </form>
+    </div>
+    <div class="tab-pane fade"
+         id="sequencing-platforms-content"
+         role="tabpanel"
+         aria-labelledby="sequencing-platforms-content-tab">
+      <p>Upload and manage the sequencing platforms for species
+        '{{species.Name | title}} ({{species.FullName}})'
+        <a href="{{url_for('species.platforms.list_platforms',
+                 species_id=species.SpeciesId)}}"
+           title="Manage sequencing platforms for {{species.Name}}">here</a>.
+      </p>
+    </div>
+  </div>
 </div>
 {%endblock%}
 
 {%block sidebarcontents%}
-<div class="card">
-  <div class="card-body">
-    <h5 class="card-title">Species Extras</h5>
-    <div class="card-text">
-      <p>Some extra internal-use details (mostly for UI concerns on GeneNetwork)</p>
-      <p>
-        <small>
-          If you do not understand what the following are about, simply ignore them
-          &mdash;
-          They have no bearing whatsoever on your data, or its analysis.
-        </small>
-      </p>
-      <dl>
-        <dt>Family</dt>
-        <dd>{{species.Family}}</dd>
+<div class="row">
+  <p>You can manage species' populations and sequencing platforms here. Select
+    the tab for the feature you wish to continue working on.</p>
+</div>
+{{display_sui_species_card(species)}}
+{%endblock%}
 
-        <dt>FamilyOrderId</dt>
-        <dd>{{species.FamilyOrderId}}</dd>
 
-        <dt>OrderId</dt>
-        <dd>{{species.OrderId}}</dd>
-      </dl>
-    </div>
-    <a href="{{url_for('species.edit_species_extra',
-             species_id=species.SpeciesId)}}"
-       class="card-link"
-       title="Edit the species' internal-use details.">Edit</a>
-  </div>
-</div>
+{%block javascript%}
+<script type="text/javascript" src="/static/js/populations.js"></script>
 {%endblock%}