From b40f14bb409d54fda957e2d8269f1bc86bd34e58 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 29 Dec 2025 11:42:58 -0600
Subject: Samples: Move feature to new UI templates.

---
 uploader/templates/samples/base.html               |  29 ++--
 uploader/templates/samples/list-samples.html       |  50 ++-----
 uploader/templates/samples/sui-base.html           |  25 ----
 uploader/templates/samples/sui-list-samples.html   |  98 -------------
 uploader/templates/samples/sui-upload-failure.html |  32 -----
 .../templates/samples/sui-upload-progress.html     |  26 ----
 uploader/templates/samples/sui-upload-samples.html | 153 ---------------------
 uploader/templates/samples/sui-upload-success.html |  31 -----
 uploader/templates/samples/upload-failure.html     |   5 -
 uploader/templates/samples/upload-progress.html    |   5 -
 uploader/templates/samples/upload-samples.html     |  81 +++++------
 uploader/templates/samples/upload-success.html     |   5 -
 12 files changed, 67 insertions(+), 473 deletions(-)
 delete mode 100644 uploader/templates/samples/sui-base.html
 delete mode 100644 uploader/templates/samples/sui-list-samples.html
 delete mode 100644 uploader/templates/samples/sui-upload-failure.html
 delete mode 100644 uploader/templates/samples/sui-upload-progress.html
 delete mode 100644 uploader/templates/samples/sui-upload-samples.html
 delete mode 100644 uploader/templates/samples/sui-upload-success.html

(limited to 'uploader/templates/samples')

diff --git a/uploader/templates/samples/base.html b/uploader/templates/samples/base.html
index 291782b..7fd5020 100644
--- a/uploader/templates/samples/base.html
+++ b/uploader/templates/samples/base.html
@@ -1,12 +1,25 @@
 {%extends "populations/base.html"%}
+{%from "populations/macro-display-population-card.html" import display_sui_population_card%}
 
-{%block lvl3_breadcrumbs%}
-<li {%if activelink=="samples"%}
-    class="breadcrumb-item active"
-    {%else%}
-    class="breadcrumb-item"
-    {%endif%}>
-  <a href="{{url_for('species.populations.samples.index')}}">Samples</a>
+{%block breadcrumbs%}
+{{super()}}
+<li class="breadcrumb-item">
+  <a href="{{url_for('species.populations.samples.list_samples',
+           species_id=species['SpeciesId'],
+           population_id=population.Id)}}">
+    Samples
+  </a>
 </li>
-{%block lvl4_breadcrumbs%}{%endblock%}
+{%endblock%}
+
+{%block contents%}
+<div class="row">
+  <h2 class="heading">{{population.FullName}} ({{population.Name}})</h2>
+</div>
+{%endblock%}
+
+
+
+{%block sidebarcontents%}
+{{display_sui_population_card(species, population)}}
 {%endblock%}
diff --git a/uploader/templates/samples/list-samples.html b/uploader/templates/samples/list-samples.html
index aed27c3..3aac984 100644
--- a/uploader/templates/samples/list-samples.html
+++ b/uploader/templates/samples/list-samples.html
@@ -1,53 +1,34 @@
 {%extends "samples/base.html"%}
 {%from "flash_messages.html" import flash_all_messages%}
 {%from "populations/macro-select-population.html" import select_population_form%}
-{%from "populations/macro-display-population-card.html" import display_population_card%}
 
 {%block title%}Samples &mdash; List Samples{%endblock%}
 
-{%block pagetitle%}Samples &mdash; List Samples{%endblock%}
-
-{%block lvl4_breadcrumbs%}
-<li {%if activelink=="list-samples"%}
-    class="breadcrumb-item active"
-    {%else%}
-    class="breadcrumb-item"
-    {%endif%}>
-  <a href="{{url_for('species.populations.samples.list_samples',
-           species_id=species.SpeciesId,
-           population_id=population.Id)}}">List</a>
-</li>
-{%endblock%}
-
 {%block contents%}
-{{flash_all_messages()}}
+{{super()}}
 
 <div class="row">
-  <p>
-    You selected the population "{{population.FullName}}" from the
-    "{{species.FullName}}" species.
-  </p>
+  <h3 class="subheading">manage samples</h3>
+  {{flash_all_messages()}}
 </div>
 
 <div class="row">
-  <p>
+  <div class="col">
     <a href="{{url_for('species.populations.samples.upload_samples',
              species_id=species.SpeciesId,
              population_id=population.Id)}}"
        title="Add samples for population '{{population.FullName}}' from species
               '{{species.FullName}}'."
-       class="btn btn-primary">
-      add samples
-    </a>
-  </p>
+       class="btn btn-primary">add new samples</a>
+  </div>
 </div>
 
 {%if samples | length > 0%}
 <div class="row">
   <p>
-    This population already has <strong>{{total_samples}}</strong>
-    samples/individuals entered. You can explore the list of samples in this
-    population in the table below.
+    Population "{{population.FullName}} ({{population.Name}})" already has
+    <strong>{{total_samples}}</strong> samples/individuals entered. You can
+    explore the list of samples in the table below.
   </p>
 </div>
 
@@ -106,15 +87,6 @@
       {%endfor%}
     </tbody>
   </table>
-
-  <p>
-    <a href="#"
-       title="Delete samples from population '{{population.FullName}}' from species
-              '{{species.FullName}}'."
-       class="btn btn-danger not-implemented">
-      delete all samples
-    </a>
-  </p>
 </div>
 {%else%}
 <div class="row">
@@ -124,7 +96,3 @@
 {%endif%}
 
 {%endblock%}
-
-{%block sidebarcontents%}
-{{display_population_card(species, population)}}
-{%endblock%}
diff --git a/uploader/templates/samples/sui-base.html b/uploader/templates/samples/sui-base.html
deleted file mode 100644
index 8ec7505..0000000
--- a/uploader/templates/samples/sui-base.html
+++ /dev/null
@@ -1,25 +0,0 @@
-{%extends "populations/sui-base.html"%}
-{%from "populations/macro-display-population-card.html" import display_sui_population_card%}
-
-{%block breadcrumbs%}
-{{super()}}
-<li class="breadcrumb-item">
-  <a href="{{url_for('species.populations.samples.list_samples',
-           species_id=species['SpeciesId'],
-           population_id=population.Id)}}">
-    Samples
-  </a>
-</li>
-{%endblock%}
-
-{%block contents%}
-<div class="row">
-  <h2 class="heading">{{population.FullName}} ({{population.Name}})</h2>
-</div>
-{%endblock%}
-
-
-
-{%block sidebarcontents%}
-{{display_sui_population_card(species, population)}}
-{%endblock%}
diff --git a/uploader/templates/samples/sui-list-samples.html b/uploader/templates/samples/sui-list-samples.html
deleted file mode 100644
index e9ed71a..0000000
--- a/uploader/templates/samples/sui-list-samples.html
+++ /dev/null
@@ -1,98 +0,0 @@
-{%extends "samples/sui-base.html"%}
-{%from "flash_messages.html" import flash_all_messages%}
-{%from "populations/macro-select-population.html" import select_population_form%}
-
-{%block title%}Samples &mdash; List Samples{%endblock%}
-
-{%block contents%}
-{{super()}}
-
-<div class="row">
-  <h3 class="subheading">manage samples</h3>
-  {{flash_all_messages()}}
-</div>
-
-<div class="row">
-  <div class="col">
-    <a href="{{url_for('species.populations.samples.upload_samples',
-             species_id=species.SpeciesId,
-             population_id=population.Id)}}"
-       title="Add samples for population '{{population.FullName}}' from species
-              '{{species.FullName}}'."
-       class="btn btn-primary">add new samples</a>
-  </div>
-</div>
-
-{%if samples | length > 0%}
-<div class="row">
-  <p>
-    Population "{{population.FullName}} ({{population.Name}})" already has
-    <strong>{{total_samples}}</strong> samples/individuals entered. You can
-    explore the list of samples in the table below.
-  </p>
-</div>
-
-<div class="row">
-  <div class="col-md-2">
-    {%if offset > 0:%}
-    <a href="{{url_for('species.populations.samples.list_samples',
-             species_id=species.SpeciesId,
-             population_id=population.Id,
-             from=offset-count,
-             count=count)}}">
-      <span class="glyphicon glyphicon-backward"></span>
-      Previous
-    </a>
-    {%endif%}
-  </div>
-
-  <div class="col-md-8" style="text-align: center;">
-    Samples {{offset}} &mdash; {{offset+(count if offset + count < total_samples else total_samples - offset)}} / {{total_samples}}
-                                                                   </div>
-
-  <div class="col-md-2">
-    {%if offset + count < total_samples:%}
-    <a href="{{url_for('species.populations.samples.list_samples',
-             species_id=species.SpeciesId,
-             population_id=population.Id,
-             from=offset+count,
-             count=count)}}">
-      Next
-      <span class="glyphicon glyphicon-forward"></span>
-    </a>
-    {%endif%}
-  </div>
-</div>
-<div class="row">
-  <table class="table">
-    <thead>
-      <tr>
-        <th></th>
-        <th>Name</th>
-        <th>Auxilliary Name</th>
-        <th>Symbol</th>
-        <th>Alias</th>
-      </tr>
-    </thead>
-
-    <tbody>
-      {%for sample in samples%}
-      <tr>
-        <td>{{sample.sequence_number}}</td>
-        <td>{{sample.Name}}</td>
-        <td>{{sample.Name2}}</td>
-        <td>{{sample.Symbol or "-"}}</td>
-        <td>{{sample.Alias or "-"}}</td>
-      </tr>
-      {%endfor%}
-    </tbody>
-  </table>
-</div>
-{%else%}
-<div class="row">
-  <p>There are no samples entered for this population. Click the "Add Samples"
-    button above, to add some new samples.</p>
-</div>
-{%endif%}
-
-{%endblock%}
diff --git a/uploader/templates/samples/sui-upload-failure.html b/uploader/templates/samples/sui-upload-failure.html
deleted file mode 100644
index d950c50..0000000
--- a/uploader/templates/samples/sui-upload-failure.html
+++ /dev/null
@@ -1,32 +0,0 @@
-{%extends "sui-base.html"%}
-{%from "cli-output.html" import cli_output%}
-
-{%block title%}Samples Upload Failure{%endblock%}
-
-{%block contents%}
-<div class="row">
-<h2 class="heading">{{job.job_name[0:50]}}&hellip;</h2>
-
-<p>There was a failure attempting to upload the samples.</p>
-
-<p>Here is some information to help with debugging the issue. Provide this
-  information to the developer/maintainer.</p>
-
-<h3>Debugging Information</h3>
-<ul>
-  <li><strong>job id</strong>: {{job.jobid}}</li>
-  <li><strong>status</strong>: {{job.status}}</li>
-  <li><strong>job type</strong>: {{job["job-type"]}}</li>
-</ul>
-</div>
-
-<div class="row">
-<h4>stdout</h4>
-{{cli_output(job, "stdout")}}
-</div>
-
-<div class="row">
-<h4>stderr</h4>
-{{cli_output(job, "stderr")}}
-</div>
-{%endblock%}
diff --git a/uploader/templates/samples/sui-upload-progress.html b/uploader/templates/samples/sui-upload-progress.html
deleted file mode 100644
index 8412c46..0000000
--- a/uploader/templates/samples/sui-upload-progress.html
+++ /dev/null
@@ -1,26 +0,0 @@
-{%extends "samples/sui-base.html"%}
-{%from "cli-output.html" import cli_output%}
-
-{%block extrameta%}
-<meta http-equiv="refresh" content="5">
-{%endblock%}
-
-{%block title%}Job Status{%endblock%}
-
-{%block contents%}
-<div class="row" style="overflow-x: clip;">
-<h2 class="heading">{{job.job_name[0:50]}}&hellip;</h2>
-
-<p>
-<strong>status</strong>:
-<span>{{job["status"]}} ({{job.get("message", "-")}})</span><br />
-</p>
-
-<p>saving to database...</p>
-</div>
-
-<div class="row">
-  {{cli_output(job, "stdout")}}
-</div>
-
-{%endblock%}
diff --git a/uploader/templates/samples/sui-upload-samples.html b/uploader/templates/samples/sui-upload-samples.html
deleted file mode 100644
index 83c2061..0000000
--- a/uploader/templates/samples/sui-upload-samples.html
+++ /dev/null
@@ -1,153 +0,0 @@
-{%extends "samples/sui-base.html"%}
-{%from "flash_messages.html" import flash_all_messages%}
-
-{%block title%}Samples &mdash; Upload Samples{%endblock%}
-
-{%block breadcrumbs%}
-{{super()}}
-<li class="breadcrumb-item">
-  <a href="{{url_for('species.populations.samples.upload_samples',
-           species_id=species['SpeciesId'],
-           population_id=population.Id)}}">
-    Upload
-  </a>
-</li>
-{%endblock%}
-
-{%block contents%}
-{{flash_all_messages()}}
-
-<div class="row">
-  <form id="form-samples"
-        method="POST"
-        action="{{url_for('species.populations.samples.upload_samples',
-                species_id=species.SpeciesId,
-                population_id=population.InbredSetId)}}"
-        enctype="multipart/form-data">
-    <legend class="heading">upload samples</legend>
-
-    <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
-    <input type="hidden" name="population_id" value="{{population.Id}}" />
-
-    <div class="form-group">
-      <label for="file-samples" class="form-label">select file</label>
-      <input type="file" name="samples_file" id="file-samples"
-	     accept="text/csv, text/tab-separated-values, text/plain"
-	     class="form-control" />
-      <small class="form-text text-muted">
-        See the <a href="#docs-samples-upload">documentation below</a> for
-        details on expected file format.</small>
-    </div>
-
-    <div class="form-group">
-      <label for="select-separator" class="form-label">field separator</label>
-      <select id="select-separator"
-	      name="separator"
-	      required="required"
-	      class="form-control">
-        <option value="">Select separator for your file: (default is comma)</option>
-        <option value="&#x0009;">TAB</option>
-        <option value="&#x0020;">Space</option>
-        <option value=",">Comma</option>
-        <option value=";">Semicolon</option>
-        <option value="other">Other</option>
-      </select>
-      <input id="txt-separator"
-	     type="text"
-	     name="other_separator"
-	     class="form-control" />
-      <small class="form-text text-muted">
-        If you select '<strong>Other</strong>' for the field separator value,
-        enter the character that separates the fields in your CSV file in the form
-        field below.
-      </small>
-    </div>
-
-    <div class="form-group form-check">
-      <input id="chk-heading"
-	     type="checkbox"
-	     name="first_line_heading"
-	     class="form-check-input" />
-      <label for="chk-heading" class="form-check-label">
-        first line is a heading?</label>
-      <small class="form-text text-muted">
-        Select this if the first line in your file contains headings for the
-        columns.
-      </small>
-    </div>
-
-    <div class="form-group">
-      <label for="txt-delimiter" class="form-label">field delimiter</label>
-      <input id="txt-delimiter"
-	     type="text"
-	     name="field_delimiter"
-	     maxlength="1"
-	     class="form-control" />
-      <small class="form-text text-muted">
-        If there is a character delimiting the string texts within particular
-        fields in your CSV, provide the character here. This can be left blank if
-        no such delimiters exist in your file.
-      </small>
-    </div>
-
-    <button type="submit"
-	    class="btn btn-primary">upload samples file</button>
-  </form>
-</div>
-
-<div class="row">
-  <h3>Preview File Content</h3>
-
-  <table id="tbl:samples-preview" class="table">
-    <caption class="heading">preview content</caption>
-
-    <thead>
-      <tr>
-        <th>Name</th>
-        <th>Name2</th>
-        <th>Symbol</th>
-        <th>Alias</th>
-      </tr>
-    </thead>
-
-    <tbody>
-      <tr id="default-row">
-        <td colspan="4">
-	  Please make some selections in the form above to preview the data.</td>
-      </tr>
-    </tbody>
-  </table>
-</div>
-
-
-
-<div class="row" id="docs-samples-upload">
-  <h3 class="subheading">File Format</h3>
-  <p>
-    Upload a <strong>character-separated value (CSV)</strong> file that contains
-    details about your samples. The CSV file should have the following fields:
-    <dl>
-      <dt>Name</dt>
-      <dd>The primary name/identifier for the sample/individual.</dd>
-
-      <dt>Name2</dt>
-      <dd>A secondary name for the sample. This can simply be the same as
-        <strong>Name</strong> above. This field <strong>MUST</strong> contain a
-        value.</dd>
-
-      <dt>Symbol</dt>
-      <dd>A symbol for the sample. This can be a strain name, e.g. 'BXD60' for
-        species that have strains. This field can be left empty for species like
-        Humans that do not have strains..</dd>
-
-      <dt>Alias</dt>
-      <dd>An alias for the sample. Can be an empty field, or take on the same
-        value as that of the Symbol.</dd>
-    </dl>
-  </p>
-</div>
-{%endblock%}
-
-{%block javascript%}
-<script src="/static/js/upload_samples.js" type="text/javascript"></script>
-{%endblock%}
diff --git a/uploader/templates/samples/sui-upload-success.html b/uploader/templates/samples/sui-upload-success.html
deleted file mode 100644
index 054bde8..0000000
--- a/uploader/templates/samples/sui-upload-success.html
+++ /dev/null
@@ -1,31 +0,0 @@
-{%extends "samples/sui-base.html"%}
-{%from "cli-output.html" import cli_output%}
-
-{%block title%}Job Status{%endblock%}
-
-{%block contents%}
-
-<div class="row" style="overflow-x: clip;">
-  <h2 class="heading">{{job.job_name[0:50]}}&hellip;</h2>
-
-  <p>
-    <strong>status</strong>:
-    <span>{{job["status"]}} ({{job.get("message", "-")}})</span><br />
-  </p>
-
-  <p>Successfully uploaded the samples.</p>
-  <p>
-    <a href="{{url_for('species.populations.samples.list_samples',
-             species_id=species.SpeciesId,
-             population_id=population.Id)}}"
-       title="View population samples">
-      View samples
-    </a>
-  </p>
-</div>
-
-<div class="row">
-  {{cli_output(job, "stdout")}}
-</div>
-
-{%endblock%}
diff --git a/uploader/templates/samples/upload-failure.html b/uploader/templates/samples/upload-failure.html
index 2cf8053..75192ec 100644
--- a/uploader/templates/samples/upload-failure.html
+++ b/uploader/templates/samples/upload-failure.html
@@ -1,6 +1,5 @@
 {%extends "base.html"%}
 {%from "cli-output.html" import cli_output%}
-{%from "populations/macro-display-population-card.html" import display_population_card%}
 
 {%block title%}Samples Upload Failure{%endblock%}
 
@@ -31,7 +30,3 @@
 {{cli_output(job, "stderr")}}
 </div>
 {%endblock%}
-
-{%block sidebarcontents%}
-{{display_population_card(species, population)}}
-{%endblock%}
diff --git a/uploader/templates/samples/upload-progress.html b/uploader/templates/samples/upload-progress.html
index 677d457..38f931b 100644
--- a/uploader/templates/samples/upload-progress.html
+++ b/uploader/templates/samples/upload-progress.html
@@ -1,6 +1,5 @@
 {%extends "samples/base.html"%}
 {%from "cli-output.html" import cli_output%}
-{%from "populations/macro-display-population-card.html" import display_population_card%}
 
 {%block extrameta%}
 <meta http-equiv="refresh" content="5">
@@ -25,7 +24,3 @@
 </div>
 
 {%endblock%}
-
-{%block sidebarcontents%}
-{{display_population_card(species, population)}}
-{%endblock%}
diff --git a/uploader/templates/samples/upload-samples.html b/uploader/templates/samples/upload-samples.html
index 4aa2f7f..1f665a3 100644
--- a/uploader/templates/samples/upload-samples.html
+++ b/uploader/templates/samples/upload-samples.html
@@ -1,56 +1,22 @@
 {%extends "samples/base.html"%}
 {%from "flash_messages.html" import flash_all_messages%}
-{%from "populations/macro-select-population.html" import select_population_form%}
-{%from "populations/macro-display-population-card.html" import display_population_card%}
 
 {%block title%}Samples &mdash; Upload Samples{%endblock%}
 
-{%block pagetitle%}Samples &mdash; Upload Samples{%endblock%}
-
-{%block lvl4_breadcrumbs%}
-<li {%if activelink=="uploade-samples"%}
-    class="breadcrumb-item active"
-    {%else%}
-    class="breadcrumb-item"
-    {%endif%}>
+{%block breadcrumbs%}
+{{super()}}
+<li class="breadcrumb-item">
   <a href="{{url_for('species.populations.samples.upload_samples',
-           species_id=species.SpeciesId,
-           population_id=population.Id)}}">List</a>
+           species_id=species['SpeciesId'],
+           population_id=population.Id)}}">
+    Upload
+  </a>
 </li>
 {%endblock%}
 
 {%block contents%}
 {{flash_all_messages()}}
 
-<div class="row">
-  <p>
-    You can now upload the samples for the "{{population.FullName}}" population
-    from the "{{species.FullName}}" species here.
-  </p>
-  <p>
-    Upload a <strong>character-separated value (CSV)</strong> file that contains
-    details about your samples. The CSV file should have the following fields:
-    <dl>
-      <dt>Name</dt>
-      <dd>The primary name/identifier for the sample/individual.</dd>
-
-      <dt>Name2</dt>
-      <dd>A secondary name for the sample. This can simply be the same as
-        <strong>Name</strong> above. This field <strong>MUST</strong> contain a
-        value.</dd>
-
-      <dt>Symbol</dt>
-      <dd>A symbol for the sample. This can be a strain name, e.g. 'BXD60' for
-        species that have strains. This field can be left empty for species like
-        Humans that do not have strains..</dd>
-
-      <dt>Alias</dt>
-      <dd>An alias for the sample. Can be an empty field, or take on the same
-        value as that of the Symbol.</dd>
-    </dl>
-  </p>
-</div>
-
 <div class="row">
   <form id="form-samples"
         method="POST"
@@ -68,6 +34,9 @@
       <input type="file" name="samples_file" id="file-samples"
 	     accept="text/csv, text/tab-separated-values, text/plain"
 	     class="form-control" />
+      <small class="form-text text-muted">
+        See the <a href="#docs-samples-upload">documentation below</a> for
+        details on expected file format.</small>
     </div>
 
     <div class="form-group">
@@ -149,10 +118,34 @@
     </tbody>
   </table>
 </div>
-{%endblock%}
 
-{%block sidebarcontents%}
-{{display_population_card(species, population)}}
+
+
+<div class="row" id="docs-samples-upload">
+  <h3 class="subheading">File Format</h3>
+  <p>
+    Upload a <strong>character-separated value (CSV)</strong> file that contains
+    details about your samples. The CSV file should have the following fields:
+    <dl>
+      <dt>Name</dt>
+      <dd>The primary name/identifier for the sample/individual.</dd>
+
+      <dt>Name2</dt>
+      <dd>A secondary name for the sample. This can simply be the same as
+        <strong>Name</strong> above. This field <strong>MUST</strong> contain a
+        value.</dd>
+
+      <dt>Symbol</dt>
+      <dd>A symbol for the sample. This can be a strain name, e.g. 'BXD60' for
+        species that have strains. This field can be left empty for species like
+        Humans that do not have strains..</dd>
+
+      <dt>Alias</dt>
+      <dd>An alias for the sample. Can be an empty field, or take on the same
+        value as that of the Symbol.</dd>
+    </dl>
+  </p>
+</div>
 {%endblock%}
 
 {%block javascript%}
diff --git a/uploader/templates/samples/upload-success.html b/uploader/templates/samples/upload-success.html
index 881d466..d6318e9 100644
--- a/uploader/templates/samples/upload-success.html
+++ b/uploader/templates/samples/upload-success.html
@@ -1,6 +1,5 @@
 {%extends "samples/base.html"%}
 {%from "cli-output.html" import cli_output%}
-{%from "populations/macro-display-population-card.html" import display_population_card%}
 
 {%block title%}Job Status{%endblock%}
 
@@ -30,7 +29,3 @@
 </div>
 
 {%endblock%}
-
-{%block sidebarcontents%}
-{{display_population_card(species, population)}}
-{%endblock%}
-- 
cgit 1.4.1