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-rw-r--r--uploader/templates/platforms/base.html13
-rw-r--r--uploader/templates/platforms/create-platform.html103
-rw-r--r--uploader/templates/platforms/index.html21
-rw-r--r--uploader/templates/platforms/list-platforms.html93
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
new file mode 100644
index 0000000..35b6464
--- /dev/null
+++ 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
index 0000000..718dd1d
--- /dev/null
+++ b/uploader/templates/platforms/list-platforms.html
@@ -0,0 +1,93 @@
+{%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%}