Initialise "Platforms" section.

4 files changed, 230 insertions, 0 deletions

diff --git a/uploader/templates/platforms/base.html b/uploader/templates/platforms/base.html
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+++ b/uploader/templates/platforms/base.html
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+{%extends "species/base.html"%}
+
+{%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>
+</li>
+{%block lvl4_breadcrumbs%}{%endblock%}
+{%endblock%}
diff --git a/uploader/templates/platforms/create-platform.html b/uploader/templates/platforms/create-platform.html
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+++ b/uploader/templates/platforms/create-platform.html
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+{%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%}>
+  <a href="{{url_for('species.platforms.create_platform',
+           species_id=species.SpeciesId)}}">create platform</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">
+      <input type="submit"
+             value="create new platform"
+             class="btn btn-primary"  />
+    </div>
+  </form>
+</div>
+{%endblock%}
+
+{%block sidebarcontents%}
+{{display_species_card(species)}}
+{%endblock%}
diff --git a/uploader/templates/platforms/index.html b/uploader/templates/platforms/index.html
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+++ b/uploader/templates/platforms/index.html
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+{%extends "platforms/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+{%from "species/macro-select-species.html" import select_species_form%}
+
+{%block title%}Platforms{%endblock%}
+
+{%block pagetitle%}Platforms{%endblock%}
+
+
+{%block contents%}
+{{flash_all_messages()}}
+
+<div class="row">
+  <p>In this section, you will be able to view and manage the sequencing
+    platforms that are currently supported by GeneNetwork.</p>
+</div>
+
+<div class="row">
+  {{select_species_form(url_for("species.platforms.index"), species)}}
+</div>
+{%endblock%}
diff --git a/uploader/templates/platforms/list-platforms.html b/uploader/templates/platforms/list-platforms.html
new file mode 100644
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+++ b/uploader/templates/platforms/list-platforms.html
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+{%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%}
+
+{%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%}
+
+{%block sidebarcontents%}
+{{display_species_card(species)}}
+{%endblock%}