From 16e5241b2225ee84e31625a2b1b806a60472252f Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Fri, 24 Jan 2025 11:36:57 -0600
Subject: Provide UI for editing a specific phenotype.

---
 uploader/templates/phenotypes/edit-phenotype.html | 195 ++++++++++++++++++++++
 1 file changed, 195 insertions(+)
 create mode 100644 uploader/templates/phenotypes/edit-phenotype.html

(limited to 'uploader/templates')

diff --git a/uploader/templates/phenotypes/edit-phenotype.html b/uploader/templates/phenotypes/edit-phenotype.html
new file mode 100644
index 0000000..8b1642c
--- /dev/null
+++ b/uploader/templates/phenotypes/edit-phenotype.html
@@ -0,0 +1,195 @@
+{%extends "phenotypes/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+{%from "populations/macro-display-population-card.html" import display_population_card%}
+
+{%block title%}Phenotypes{%endblock%}
+
+{%block pagetitle%}Phenotypes{%endblock%}
+
+{%block lvl4_breadcrumbs%}
+<li {%if activelink=="edit-phenotype"%}
+    class="breadcrumb-item active"
+    {%else%}
+    class="breadcrumb-item"
+    {%endif%}>
+  <a href="{{url_for('species.populations.phenotypes.edit_phenotype_data',
+           species_id=species.SpeciesId,
+           population_id=population.Id,
+           dataset_id=dataset.Id,
+           xref_id=xref_id)}}">View Datasets</a>
+</li>
+{%endblock%}
+
+{%block contents%}
+{{flash_all_messages()}}
+
+<div class="row">
+  <h2 class="heading">edit phenotype data</h2>
+  <p>The two (2) forms provided in this page help you update the data for the
+    phenotypes, and the publication information for the phenotype,
+    respectively.</p>
+</div>
+
+<div class="row">
+  <h3 class="subheading">phenotype data</h3>
+  <form id="frm-edit-phenotype-data">
+    <div style="max-height: 23.37em;overflow-y: scroll;">
+    <table class="table table-striped table-responsive table-form-table">
+      <thead style="position: sticky; top: 0;">
+        <tr>
+          <th>#</th>
+          <th>Sample</th>
+          <th>Value</th>
+          {%if population.Family in families_with_se_and_n%}
+          <th>Standard-Error</th>
+          <th>Number of Samples</th>
+          {%endif%}
+        </tr>
+      </thead>
+
+      <tbody>
+        {%for item in phenotype.data%}
+        <tr>
+          <td>{{loop.index}}</td>
+          <td>{{item.StrainName}}</td>
+          <td>
+            <input type="text"
+                   name="value::{{item.DataId}}::{{item.StrainId}}"
+                   value="{{item.value}}"
+                   data-original-value="{{item.value}}"
+                   class="form-control" /></td>
+          {%if population.Family in families_with_se_and_n%}
+          <td>
+            <input type="text"
+                   name="se::{{item.DataId}}::{{item.StrainId}}"
+                   value="{{item.error or ''}}"
+                   data-original-value="{{item.error or ''}}"
+                   class="form-control" /></td>
+          <td><input type="text"
+                     name="n::{{item.DataId}}::{{item.StrainId}}"
+                     value="{{item.count or ''}}"
+                     data-original-value="{{item.count or "-"}}"
+                     class="form-control" /></td>
+          {%endif%}
+        </tr>
+        {%endfor%}
+      </tbody>
+    </table>
+    </div>
+    <div class="form-group">
+      <input type="submit"
+             name="submit"
+             class="btn btn-primary not-implemented"
+             value="update data" />
+    </div>
+  </form>
+</div>
+
+<div class="row">
+  <h3 class="subheading">publication information</h3>
+  <p>Use the form below to update the publication information for this
+    phenotype.</p>
+  <form id="frm-edit-phenotype-pub-data"
+        method="POST"
+        action="#">
+    <div class="form-group">
+      <label for="txt-pubmed-id" class="form-label">Pubmed ID</label>
+      <input id="txt-pubmed-id" name="pubmed-id" type="text"
+             class="form-control" />
+      <span class="form-text text-muted">
+        Enter your publication's PubMed ID.
+      </span>
+    </div>
+
+    <div class="form-group">
+      <label for="txt-publication-authors" class="form-label">Authors</label>
+      <input id="txt-publication-authors" name="publication-authors"
+             type="text" class="form-control" />
+      <span class="form-text text-muted">
+        Enter the authors.</span>
+    </div>
+
+    <div class="form-group">
+      <label for="txt-publication-title" class="form-label">
+        Publication Title</label>
+      <input id="txt-publication-title" name="publication-title" type="text"
+             class="form-control" />
+      <span class="form-text text-muted">
+        Enter your publication's title.</span>
+    </div>
+
+    <div class="form-group">
+      <label for="txt-publication-abstract" class="form-label">
+        Publication Abstract</label>
+      <textarea id="txt-publication-abstract" name="publication-abstract"
+                class="form-control" rows="10"></textarea>
+      <span class="form-text text-muted">
+        Enter the abstract for your publication.</span>
+    </div>
+
+    <div class="form-group">
+      <label for="txt-publication-journal" class="form-label">Journal</label>
+      <input id="txt-publication-journal" name="journal" type="text"
+             class="form-control" />
+      <span class="form-text text-muted">
+        Enter the name of the journal where your work was published.</span>
+    </div>
+
+    <div class="form-group">
+      <label for="txt-publication-volume" class="form-label">Volume</label>
+      <input id="txt-publication-volume" name="publication-volume" type="text"
+             class="form-control" />
+      <span class="form-text text-muted">
+        Enter the volume in the following format &hellip;</span>
+    </div>
+
+    <div class="form-group">
+      <label for="txt-publication-pages" class="form-label">Pages</label>
+      <input id="txt-publication-pages" name="publication-pages" type="text"
+             class="form-control" />
+      <span class="form-text text-muted">
+        Enter the journal volume where your work was published.</span>
+    </div>
+
+    <div class="form-group">
+      <label for="select-publication-month" class="form-label">
+        Publication Month</label>
+      <select id="select-publication-month" name="publication-month"
+              class="form-control">
+        {%for month in monthnames%}
+        <option value="{{month | lower}}"
+                {%if current_month | lower == month | lower%}
+                selected="selected"
+                {%endif%}>{{month | capitalize}}</option>
+        {%endfor%}
+      </select>
+      <span class="form-text text-muted">
+        Select the month when the work was published.
+        <span class="text-danger">
+          This cannot be before, say 1600 and cannot be in the future!</span></span>
+    </div>
+
+    <div class="form-group">
+      <label for="txt-publication-year" class="form-label">Publication Year</label>
+      <input id="txt-publication-year" name="publication-year" type="text"
+             class="form-control" value="{{current_year}}" />
+      <span class="form-text text-muted">
+        Enter the year your work was published.
+        <span class="text-danger">
+          This cannot be before, say 1600 and cannot be in the future!</span>
+      </span>
+    </div>
+    <div class="form-group">
+      <input type="submit"
+             name="submit"
+             class="btn btn-primary not-implemented"
+             value="update publication" />
+    </div>
+  </form>
+</div>
+
+{%endblock%}
+
+{%block sidebarcontents%}
+{{display_population_card(species, population)}}
+{%endblock%}
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