Sequencing Platforms: Move feature to new UI templates.

7 files changed, 21 insertions, 253 deletions

diff --git a/uploader/platforms/views.py b/uploader/platforms/views.py
index 0092760..ba0f0ef 100644
--- a/uploader/platforms/views.py
+++ b/uploader/platforms/views.py
@@ -8,8 +8,6 @@ from flask import (
     Blueprint,
     current_app as app)
 
-from uploader.sui import sui_template
-
 from uploader.flask_extensions import url_for
 from uploader.ui import make_template_renderer
 from uploader.authorisation import require_login
@@ -62,7 +60,7 @@ def list_platforms(species_id: int):
         start_from = max(safe_int(request.args.get("start_from") or 0), 0)
         count = safe_int(request.args.get("count") or 20)
         return render_template(
-            sui_template("platforms/list-platforms.html"),
+            "platforms/list-platforms.html",
             species=species,
             platforms=enumerate_sequence(
                 platforms_by_species(conn,
@@ -89,7 +87,7 @@ def create_platform(species_id: int):
 
         if request.method == "GET":
             return render_template(
-                sui_template("platforms/create-platform.html"),
+                "platforms/create-platform.html",
                 species=species,
                 activelink="create-platform")
 
diff --git a/uploader/templates/platforms/base.html b/uploader/templates/platforms/base.html
index dac965f..d4f3686 100644
--- a/uploader/templates/platforms/base.html
+++ b/uploader/templates/platforms/base.html
@@ -1,13 +1,17 @@
 {%extends "species/base.html"%}
+{%from "species/macro-display-species-card.html" import display_sui_species_card%}
 
-{%block lvl3_breadcrumbs%}
-<li {%if activelink=="platforms"%}
-    class="breadcrumb-item active"
-    {%else%}
-    class="breadcrumb-item"
-    {%endif%}>
-  <a href="{{url_for('species.populations.platforms.index')}}">
-    Sequencing Platforms</a>
+{%block breadcrumbs%}
+{{super()}}
+<li class="breadcrumb-item">
+  <a href="{{url_for('species.platforms.list_platforms',
+           species_id=species['SpeciesId'])}}">
+    Platforms
+  </a>
 </li>
-{%block lvl4_breadcrumbs%}{%endblock%}
+{%endblock%}
+
+
+{%block sidebarcontents%}
+{{display_sui_species_card(species)}}
 {%endblock%}
diff --git a/uploader/templates/platforms/create-platform.html b/uploader/templates/platforms/create-platform.html
index 0866d5e..3a62472 100644
--- a/uploader/templates/platforms/create-platform.html
+++ b/uploader/templates/platforms/create-platform.html
@@ -1,19 +1,15 @@
 {%extends "platforms/base.html"%}
 {%from "flash_messages.html" import flash_all_messages%}
-{%from "species/macro-display-species-card.html" import display_species_card%}
 
 {%block title%}Platforms &mdash; Create Platforms{%endblock%}
 
-{%block pagetitle%}Platforms &mdash; Create Platforms{%endblock%}
-
-{%block lvl3_breadcrumbs%}
-<li {%if activelink=="create-platform"%}
-    class="breadcrumb-item active"
-    {%else%}
-    class="breadcrumb-item"
-    {%endif%}>
+{%block breadcrumbs%}
+{{super()}}
+<li class="breadcrumb-item">
   <a href="{{url_for('species.platforms.create_platform',
-           species_id=species.SpeciesId)}}">create platform</a>
+           species_id=species['SpeciesId'])}}">
+    Create
+  </a>
 </li>
 {%endblock%}
 
@@ -118,7 +114,3 @@
   </form>
 </div>
 {%endblock%}
-
-{%block sidebarcontents%}
-{{display_species_card(species)}}
-{%endblock%}
diff --git a/uploader/templates/platforms/list-platforms.html b/uploader/templates/platforms/list-platforms.html
index a6bcfdc..db14745 100644
--- a/uploader/templates/platforms/list-platforms.html
+++ b/uploader/templates/platforms/list-platforms.html
@@ -1,6 +1,5 @@
 {%extends "platforms/base.html"%}
 {%from "flash_messages.html" import flash_all_messages%}
-{%from "species/macro-display-species-card.html" import display_species_card%}
 
 {%block title%}Platforms &mdash; List Platforms{%endblock%}
 
@@ -87,7 +86,3 @@
   {%endif%}
 </div>
 {%endblock%}
-
-{%block sidebarcontents%}
-{{display_species_card(species)}}
-{%endblock%}
diff --git a/uploader/templates/platforms/sui-base.html b/uploader/templates/platforms/sui-base.html
deleted file mode 100644
index 136b956..0000000
--- a/uploader/templates/platforms/sui-base.html
+++ /dev/null
@@ -1,17 +0,0 @@
-{%extends "species/sui-base.html"%}
-{%from "species/macro-display-species-card.html" import display_sui_species_card%}
-
-{%block breadcrumbs%}
-{{super()}}
-<li class="breadcrumb-item">
-  <a href="{{url_for('species.platforms.list_platforms',
-           species_id=species['SpeciesId'])}}">
-    Platforms
-  </a>
-</li>
-{%endblock%}
-
-
-{%block sidebarcontents%}
-{{display_sui_species_card(species)}}
-{%endblock%}
diff --git a/uploader/templates/platforms/sui-create-platform.html b/uploader/templates/platforms/sui-create-platform.html
deleted file mode 100644
index 25977a7..0000000
--- a/uploader/templates/platforms/sui-create-platform.html
+++ /dev/null
@@ -1,116 +0,0 @@
-{%extends "platforms/sui-base.html"%}
-{%from "flash_messages.html" import flash_all_messages%}
-
-{%block title%}Platforms &mdash; Create Platforms{%endblock%}
-
-{%block breadcrumbs%}
-{{super()}}
-<li class="breadcrumb-item">
-  <a href="{{url_for('species.platforms.create_platform',
-           species_id=species['SpeciesId'])}}">
-    Create
-  </a>
-</li>
-{%endblock%}
-
-{%block contents%}
-{{flash_all_messages()}}
-
-<div class="row">
-  <h2>Create New Platform</h2>
-
-  <p>You can create a new genetic sequencing platform below.</p>
-</div>
-
-<div class="row">
-  <form id="frm-create-platform"
-        method="POST"
-        action="{{url_for('species.platforms.create_platform',
-                species_id=species.SpeciesId)}}">
-
-    <div class="form-group">
-      <label for="txt-geo-platform" class="form-label">GEO Platform</label>
-      <input type="text"
-             id="txt-geo-platform"
-             name="geo-platform"
-             required="required"
-             class="form-control"  />
-      <small class="form-text text-muted">
-        <p>This is the platform's
-          <a href="https://www.ncbi.nlm.nih.gov/geo/browse/?view=platforms&tax={{species.TaxonomyId}}"
-             title="Platforms for '{{species.FullName}}' on NCBI">
-            accession value on NCBI</a>. If you do not know the value, click the
-          link and search on NCBI for species '{{species.FullName}}'.</p></small>
-    </div>
-
-    <div class="form-group">
-      <label for="txt-platform-name" class="form-label">Platform Name</label>
-      <input type="text"
-             id="txt-platform-name"
-             name="platform-name"
-             required="required"
-             class="form-control" />
-      <small class="form-text text-muted">
-        <p>This is name of the genetic sequencing platform.</p></small>
-    </div>
-
-    <div class="form-group">
-      <label for="txt-platform-shortname" class="form-label">
-        Platform Short Name</label>
-      <input type="text"
-             id="txt-platform-shortname"
-             name="platform-shortname"
-             required="required"
-             class="form-control" />
-      <small class="form-text text-muted">
-        <p>Use the following conventions for this field:
-          <ol>
-            <li>Start with a 4-letter vendor code, e.g. "Affy" for "Affymetrix", "Illu" for "Illumina", etc.</li>
-            <li>Append an underscore to the 4-letter vendor code</li>
-            <li>Use the name of the array given by the vendor, e.g.  U74AV2, MOE430A, etc.</li>
-          </ol>
-        </p>
-      </small>
-    </div>
-
-    <div class="form-group">
-      <label for="txt-platform-title" class="form-label">Platform Title</label>
-      <input type="text"
-             id="txt-platform-title"
-             name="platform-title"
-             required="required"
-             class="form-control"  />
-      <small class="form-text text-muted">
-        <p>The full platform title. Sometimes, this is the same as the Platform
-          Name above.</p></small>
-    </div>
-
-    <div class="form-group">
-      <label for="txt-go-tree-value" class="form-label">GO Tree Value</label>
-      <input type="text"
-             id="txt-go-tree-value"
-             name="go-tree-value"
-             class="form-control"  />
-      <small class="form-text text-muted">
-        <p>This is a Chip identification value useful for analysis with the
-          <strong>
-            <a href="https://www.geneweaver.org/"
-               title="Go to the GeneWeaver site."
-               target="_blank">GeneWeaver</a></strong>
-          and
-          <strong>
-            <a href="https://www.webgestalt.org/"
-               title="Go to the WEB-based GEne SeT AnaLysis Toolkit site."
-               target="_blank">WebGestalt</a></strong>
-          tools.<br />
-        This can be left blank for custom platforms.</p></small>
-    </div>
-
-    <div class="form-group">
-      <input type="submit"
-             value="create new platform"
-             class="btn btn-primary"  />
-    </div>
-  </form>
-</div>
-{%endblock%}
diff --git a/uploader/templates/platforms/sui-list-platforms.html b/uploader/templates/platforms/sui-list-platforms.html
deleted file mode 100644
index f4c17e8..0000000
--- a/uploader/templates/platforms/sui-list-platforms.html
+++ /dev/null
@@ -1,88 +0,0 @@
-{%extends "platforms/sui-base.html"%}
-{%from "flash_messages.html" import flash_all_messages%}
-
-{%block title%}Platforms &mdash; List Platforms{%endblock%}
-
-{%block pagetitle%}Platforms &mdash; List Platforms{%endblock%}
-
-
-{%block contents%}
-{{flash_all_messages()}}
-
-<div class="row">
-  <p>View the list of the genetic sequencing platforms that are currently
-    supported by GeneNetwork.</p>
-  <p>If you cannot find the platform you wish to use, you can add it by clicking
-    the "New Platform" button below.</p>
-  <p><a href="{{url_for('species.platforms.create_platform',
-              species_id=species.SpeciesId)}}"
-        title="Create a new genetic sequencing platform for species {{species.FullName}}"
-        class="btn btn-primary">Create Platform</a></p>
-</div>
-
-<div class="row">
-  <h2>Supported Platforms</h2>
-  {%if platforms is defined and platforms | length > 0%}
-  <p>There are {{total_platforms}} platforms supported by GeneNetwork</p>
-
-  <div class="row">
-    <div class="col-md-2" style="text-align: start;">
-      {%if start_from > 0%}
-      <a href="{{url_for('species.platforms.list_platforms',
-               species_id=species.SpeciesId,
-               start_from=start_from-count,
-               count=count)}}">
-        <span class="glyphicon glyphicon-backward"></span>
-        Previous
-      </a>
-      {%endif%}
-    </div>
-    <div class="col-md-8" style="text-align: center;">
-      Displaying platforms {{start_from+1}} to {{start_from+count if start_from+count < total_platforms else total_platforms}} of
-      {{total_platforms}}
-    </div>
-    <div class="col-md-2" style="text-align: end;">
-      {%if start_from + count < total_platforms%}
-      <a href="{{url_for('species.platforms.list_platforms',
-               species_id=species.SpeciesId,
-               start_from=start_from+count,
-               count=count)}}">
-        Next
-        <span class="glyphicon glyphicon-forward"></span>
-      </a>
-      {%endif%}
-    </div>
-  </div>
-
-  <table class="table">
-    <thead>
-      <tr>
-        <th></th>
-        <th>Platform Name</th>
-        <th><a href="https://www.ncbi.nlm.nih.gov/geo/browse/?view=platforms&tax={{species.TaxonomyId}}"
-               title="Gene Expression Omnibus: Platforms section"
-               target="_blank">GEO Platform</a></th>
-        <th>Title</th>
-      </tr>
-    </thead>
-
-    <tbody>
-      {%for platform in platforms%}
-      <tr>
-        <td>{{platform.sequence_number}}</td>
-        <td>{{platform.GeneChipName}}</td>
-        <td><a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={{platform.GeoPlatform}}"
-               title="View platform on the Gene Expression Omnibus"
-               target="_blank">{{platform.GeoPlatform}}</a></td>
-        <td>{{platform.Title}}</td>
-      </tr>
-      {%endfor%}
-    </tbody>
-  </table>
-  {%else%}
-  <p class="text-warning">
-    <span class="glyphicon glyphicon-exclamation-sign"></span>
-    There are no platforms supported at this time!</p>
-  {%endif%}
-</div>
-{%endblock%}