6 files changed, 241 insertions, 58 deletions
diff --git a/uploader/templates/index2.html b/uploader/templates/index2.html
deleted file mode 100644
index 72fea2f..0000000
--- a/uploader/templates/index2.html
+++ /dev/null
@@ -1,48 +0,0 @@
-{%extends "base2.html"%}
-{%from "flash_messages.html" import flash_all_messages%}
-
-{%block title%}Home{%endblock%}
-
-{%block pagetitle%}Home{%endblock%}
-
-{%block extra_breadcrumbs%}{%endblock%}
-
-{%block contents%}
-
-<div class="row">{{flash_all_messages()}}</div>
-
-{%if user_logged_in()%}
-<div class="row">
-  <p>Select from:</p>
-  <ul>
-    <li>Species</li>
-    <li>Publications</li>
-  </ul>
-</div>
-{%else%}
-<div class="row">
-  <p>
-    <a href="{{authserver_authorise_uri()}}"
-       title="Sign in to the system"
-       class="btn btn-primary">Sign in</a>
-    to continue.</p>
-</div>
-{%endif%}
-
-{%endblock%}
-
-
-
-{%block sidebarcontents%}
-<div class="row">
-  <form id="frm-quick-navigation">
-    <legend>Quick Navigation</legend>
-    <div class="form-group">
-      <label for="fqn-species-id">Species</label>
-      <select name="species_id">
-        <option value="">Select species</option>
-      </select>
-    </div>
-  </form>
-</div>
-{%endblock%}
diff --git a/uploader/templates/species/macro-display-species-card.html b/uploader/templates/species/macro-display-species-card.html
index 166c7b9..d7c4082 100644
--- a/uploader/templates/species/macro-display-species-card.html
+++ b/uploader/templates/species/macro-display-species-card.html
@@ -20,3 +20,30 @@
   </div>
 </div>
 {%endmacro%}
+
+
+{%macro display_sui_species_card(species)%}
+<div class="row">
+  <table>
+    <caption>Selected Species</caption>
+    <tr>
+      <th>Name</th>
+      <td>{{species["Name"] | title}}</td>
+    </tr>
+    <tr>
+      <th>Scientific</th>
+      <td>{{species["FullName"]}}</td>
+    </tr>
+    {%if species["TaxonomyId"]%}
+    <tr>
+      <th>Taxonomy ID</th>
+      <td>
+        <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id={{species.TaxonomyId}}"
+           title="NCBI's Taxonomy Browser page for {{species.Name}}">
+          {{species.TaxonomyId}}</a>
+      </td>
+    </tr>
+    {%endif%}
+  </table>
+</div>
+{%endmacro%}
diff --git a/uploader/templates/species/sui-base.html b/uploader/templates/species/sui-base.html
new file mode 100644
index 0000000..5d2e6e3
--- /dev/null
+++ b/uploader/templates/species/sui-base.html
@@ -0,0 +1,10 @@
+{%extends "sui-base.html"%}
+
+{%block breadcrumbs%}
+{{super()}}
+<li class="breadcrumb-item">
+  <a href="{{url_for('species.view_species', species_id=species['SpeciesId'], streamlined_ui=streamlined_ui)}}">
+    {{species["Name"]|title}}
+  </a>
+</li>
+{%endblock%}
diff --git a/uploader/templates/species/sui-view-species.html b/uploader/templates/species/sui-view-species.html
new file mode 100644
index 0000000..5373766
--- /dev/null
+++ b/uploader/templates/species/sui-view-species.html
@@ -0,0 +1,91 @@
+{%extends "species/sui-base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+{%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 contents%}
+<div class="row">
+  <h2>{{step_indicator("2(a)")}} Select the Population</h2>
+
+  <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">
+    <input type="hidden" name="streamlined_ui" value="{{streamlined_ui}}" />
+    {%if populations | length != 0%}
+
+    <p class="form-text">Search for, and select the population from the table
+      below.</p>
+
+    <div style="margin-top: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%}
+
+    <div class="row form-buttons">
+      <div class="col">
+        <input type="submit"
+               value="use selected population"
+               class="btn btn-primary" />
+      </div>
+
+      <div class="col"><strong>OR</strong></div>
+
+      <div class="col">
+        <a href="url_for('species.population.create_population',
+                 species_id=species.SpeciesId,
+                 return_to='species.view_species',
+                 streamlined_ui=streamlined_ui)"
+           title="Create a new population for species '{{species.Name}}'."
+           class="btn btn-outline-info">
+          Create a new population
+        </a>
+      </div>
+    </div>
+
+  </form>
+</div>
+
+<div class="row">&nbsp;</div>
+
+<div class="row">
+  <h2>{{step_indicator("2(b)")}} Manage sequencing platforms</h2>
+  <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,
+             streamlined_ui=streamlined_ui)}}"
+       title="Manage sequencing platforms for {{species.Name}}">here</a>.
+  </p>
+</div>
+{%endblock%}
+
+{%block sidebarcontents%}
+{{display_sui_species_card(species)}}
+{%endblock%}
+
+
+{%block javascript%}
+<script type="text/javascript" src="/static/js/populations.js"></script>
+{%endblock%}
diff --git a/uploader/templates/base2.html b/uploader/templates/sui-base.html
index 4c5d613..b247c3c 100644
--- a/uploader/templates/base2.html
+++ b/uploader/templates/sui-base.html
@@ -50,17 +50,9 @@
     <main id="main" class="main">
       <nav id="breadcrumbs" aria-label="breadcrumb">
         <ol class="breadcrumb">
+          {%block breadcrumbs%}
           <li class="breadcrumb-item">
-            <a href="{{url_for('base.index')}}">Home</a></li>
-          {%block extra_breadcrumbs%}
-          <li class="breadcrumb-item">
-            <a href="{{url_for('base.index')}}">Page01</a></li>
-          <li class="breadcrumb-item">
-            <a href="{{url_for('base.index')}}">Page02</a></li>
-          <li class="breadcrumb-item">
-            <a href="{{url_for('base.index')}}">Page03</a></li>
-          <li class="breadcrumb-item">
-            <a href="{{url_for('base.index')}}">Page04</a></li>
+            <a href="{{url_for('base.index', streamlined_ui='true')}}">Home</a></li>
           {%endblock%}
         </ol>
       </nav>
diff --git a/uploader/templates/sui-index.html b/uploader/templates/sui-index.html
new file mode 100644
index 0000000..e6873e2
--- /dev/null
+++ b/uploader/templates/sui-index.html
@@ -0,0 +1,111 @@
+{%extends "sui-base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+{%from "macro-step-indicator.html" import step_indicator%}
+
+{%block title%}Home{%endblock%}
+
+{%block pagetitle%}Home{%endblock%}
+
+{%block extra_breadcrumbs%}{%endblock%}
+
+{%block contents%}
+
+<div class="row">{{flash_all_messages()}}</div>
+
+{%if user_logged_in()%}
+
+<div class="row">
+  <div class="row">
+    <h2>{{step_indicator("1")}} Select the Species</h2>
+
+    <p>The data in Genenetwork is related to one species or another. To get
+      started, please select the species you want to work with.</p>
+  </div>
+</div>
+
+<div class="row">
+  <form method="GET" action="{{url_for('base.index')}}" class="form-horizontal">
+    <input type="hidden" name="streamlined_ui", value="{{streamlined_ui}}" />
+
+    {%if species | length != 0%}
+    <div style="margin-top:3em;">
+      <table id="tbl-select-species" class="table compact stripe"
+             data-species-list='{{species | tojson}}'>
+        <thead>
+          <tr>
+            <th></th>
+            <th>Species Name</th>
+          </tr>
+        </thead>
+
+        <tbody></tbody>
+      </table>
+    </div>
+
+    {%else%}
+
+    <label class="control-label" for="rdo-cant-find-species">
+      <input id="rdo-cant-find-species" type="radio" name="species_id"
+             value="CREATE-SPECIES" />
+      There are no species to select from. Create the first one.</label>
+
+    <div class="col-sm-offset-10 col-sm-2">
+      <input type="submit"
+             class="btn btn-primary col-sm-offset-1"
+             value="continue" />
+    </div>
+
+    {%endif%}
+
+    <div class="row form-buttons">
+      <div class="col">
+        <input type="submit"
+               class="btn btn-primary"
+               value="continue with selected" />
+      </div>
+      <div class="col"><strong>OR</strong></div>
+      <div class="col">
+        <a href="{{url_for('species.create_species', return_to='base.index')}}"
+           title="Create a new species.">Create a new Species</a>
+      </div>
+    </div>
+
+  </form>
+</div>
+
+{%else%}
+
+<div class="row">
+  <p>The Genenetwork Uploader (<em>gn-uploader</em>) enables upload of new data
+    into the Genenetwork System. It provides Quality Control over data, and
+    guidance in case you data does not meet the standards for acceptance.</p>
+  <p>
+    <a href="{{authserver_authorise_uri()}}"
+       title="Sign in to the system"
+       class="btn btn-primary">Sign in</a>
+    to get started.</p>
+</div>
+{%endif%}
+
+{%endblock%}
+
+
+
+{%block sidebarcontents%}
+<div class="row">
+  <form id="frm-quick-navigation">
+    <legend>Quick Navigation</legend>
+    <div class="form-group">
+      <label for="fqn-species-id">Species</label>
+      <select name="species_id">
+        <option value="">Select species</option>
+      </select>
+    </div>
+  </form>
+</div>
+{%endblock%}
+
+
+{%block javascript%}
+<script type="text/javascript" src="/static/js/species.js"></script>
+{%endblock%}