From 9cd33ddac3d6848c5443962d66494635feadef51 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 9 Sep 2024 14:06:31 -0500
Subject: Initialise samples uploads

* Move existing code to new module
* Rework the UI: create new templates
* Rework the routes: Select species and populations before attempting
  an upload.
---
 uploader/templates/base.html                       |   2 +-
 .../populations/macro-display-population-card.html |  32 +++++
 .../populations/macro-select-population.html       |  30 +++++
 .../templates/populations/view-population.html     |   6 +-
 uploader/templates/samples/base.html               |  12 ++
 uploader/templates/samples/index.html              |  21 ++++
 uploader/templates/samples/list-samples.html       | 114 +++++++++++++++++
 uploader/templates/samples/select-population.html  | 117 ++++-------------
 uploader/templates/samples/select-species.html     |  30 -----
 uploader/templates/samples/upload-failure.html     |  27 ----
 uploader/templates/samples/upload-progress.html    |  22 ----
 uploader/templates/samples/upload-samples.html     | 139 ---------------------
 uploader/templates/samples/upload-success.html     |  18 ---
 13 files changed, 241 insertions(+), 329 deletions(-)
 create mode 100644 uploader/templates/populations/macro-display-population-card.html
 create mode 100644 uploader/templates/populations/macro-select-population.html
 create mode 100644 uploader/templates/samples/base.html
 create mode 100644 uploader/templates/samples/index.html
 create mode 100644 uploader/templates/samples/list-samples.html
 delete mode 100644 uploader/templates/samples/select-species.html
 delete mode 100644 uploader/templates/samples/upload-failure.html
 delete mode 100644 uploader/templates/samples/upload-progress.html
 delete mode 100644 uploader/templates/samples/upload-samples.html
 delete mode 100644 uploader/templates/samples/upload-success.html

(limited to 'uploader/templates')

diff --git a/uploader/templates/base.html b/uploader/templates/base.html
index 5c7f123..d68c6c0 100644
--- a/uploader/templates/base.html
+++ b/uploader/templates/base.html
@@ -50,7 +50,7 @@
                title="Upload Genotype data.">Genotype Data</a></li>
         <li><a href="{{url_for('species.populations.index')}}"
                title="View and manage species populations.">Populations</a></li>
-        <li><a href="#"
+        <li><a href="{{url_for('species.populations.samples.index')}}"
                title="Upload population samples.">Samples</a></li>
         <li><a href="{{url_for('expression-data.index.index')}}"
                title="Upload expression data.">Expression Data</a></li>
diff --git a/uploader/templates/populations/macro-display-population-card.html b/uploader/templates/populations/macro-display-population-card.html
new file mode 100644
index 0000000..e68f8e3
--- /dev/null
+++ b/uploader/templates/populations/macro-display-population-card.html
@@ -0,0 +1,32 @@
+{%from "species/macro-display-species-card.html" import display_species_card%}
+
+{%macro display_population_card(species, population)%}
+{{display_species_card(species)}}
+
+<div class="card">
+  <div class="card-body">
+    <h5 class="card-title">Population</h5>
+    <div class="card-text">
+      <dl>
+        <dt>Name</dt>
+        <dd>{{population.Name}}</dd>
+
+        <dt>Full Name</dt>
+        <dd>{{population.FullName}}</dd>
+
+        <dt>Code</dt>
+        <dd>{{population.InbredSetCode}}</dd>
+
+        <dt>Genetic Type</dt>
+        <dd>{{population.GeneticType}}</dd>
+
+        <dt>Family</dt>
+        <dd>{{population.Family}}</dd>
+
+        <dt>Description</dt>
+        <dd>{{population.Description or "-"}}</dd>
+      </dl>
+    </div>
+  </div>
+</div>
+{%endmacro%}
diff --git a/uploader/templates/populations/macro-select-population.html b/uploader/templates/populations/macro-select-population.html
new file mode 100644
index 0000000..af4fd3a
--- /dev/null
+++ b/uploader/templates/populations/macro-select-population.html
@@ -0,0 +1,30 @@
+{%macro select_population_form(form_action, populations)%}
+<form method="GET" action="{{form_action}}">
+  <legend>Select Population</legend>
+
+  <div class="form-group">
+    <label for="select-population" class="form-label">Select Population</label>
+    <select id="select-population"
+            name="population_id"
+            class="form-control"
+            required="required">
+      <option value="">Select Population</option>
+      {%for family in populations%}
+      <optgroup {%if family[0][1] is not none%}
+                label="{{family[0][1]}}"
+                {%else%}
+                label="Undefined"
+                {%endif%}>
+        {%for population in family[1]%}
+        <option value="{{population.Id}}">{{population.FullName}}</option>
+        {%endfor%}
+      </optgroup>
+      {%endfor%}
+    </select>
+  </div>
+
+  <div class="form-group">
+    <input type="submit" value="Select" class="btn btn-primary" />
+  </div>
+</form>
+{%endmacro%}
diff --git a/uploader/templates/populations/view-population.html b/uploader/templates/populations/view-population.html
index 52dadc4..31db54f 100644
--- a/uploader/templates/populations/view-population.html
+++ b/uploader/templates/populations/view-population.html
@@ -59,7 +59,11 @@
   <nav class="nav">
     <ul>
       <li>
-        <a href="#" title="Upload samples">upload samples</a>
+        <a href="{{url_for('species.populations.samples.list_samples',
+                 species_id=species.SpeciesId,
+                 population_id=population.Id)}}"
+           title="Manage samples: Add new or delete existing.">
+          manage samples</a>
       </li>
       <li>
         <a href="#" title="Upload expression data">upload expression data</a>
diff --git a/uploader/templates/samples/base.html b/uploader/templates/samples/base.html
new file mode 100644
index 0000000..291782b
--- /dev/null
+++ b/uploader/templates/samples/base.html
@@ -0,0 +1,12 @@
+{%extends "populations/base.html"%}
+
+{%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>
+</li>
+{%block lvl4_breadcrumbs%}{%endblock%}
+{%endblock%}
diff --git a/uploader/templates/samples/index.html b/uploader/templates/samples/index.html
new file mode 100644
index 0000000..7c88c01
--- /dev/null
+++ b/uploader/templates/samples/index.html
@@ -0,0 +1,21 @@
+{%extends "samples/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+{%from "species/macro-select-species.html" import select_species_form%}
+
+{%block title%}Populations{%endblock%}
+
+{%block pagetitle%}Populations{%endblock%}
+
+
+{%block contents%}
+{{flash_all_messages()}}
+
+<div class="row">
+  <p>Here, you can upload the samples/individuals that were used in your
+    experiments.</p>
+  <p>Since the samples are linked to specific species and populations, we will
+    need to first select them in the next few steps.</p>
+
+  {{select_species_form(url_for("species.populations.samples.index"), species)}}
+</div>
+{%endblock%}
diff --git a/uploader/templates/samples/list-samples.html b/uploader/templates/samples/list-samples.html
new file mode 100644
index 0000000..a29dc1c
--- /dev/null
+++ b/uploader/templates/samples/list-samples.html
@@ -0,0 +1,114 @@
+{%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()}}
+
+<div class="row">
+  <p>
+    Samples for population "{{population.FullName}}" from the
+    "{{species.FullName}}" species.
+  </p>
+
+  {%if samples | length > 0%}
+  <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>
+  <table class="table">
+    <thead>
+      <tr>
+        <th>Name</th>
+        <th>Auxilliary Name</th>
+        <th>Symbol</th>
+        <th>Alias</th>
+      </tr>
+    </thead>
+
+    <tbody>
+      {%for sample in samples%}
+      <tr>
+        <td>{{sample.Name}}</td>
+        <td>{{sample.Name2}}</td>
+        <td>{{sample.Symbol or "-"}}</td>
+        <td>{{sample.Alias or "-"}}</td>
+      </tr>
+      {%endfor%}
+    </tbody>
+  </table>
+
+  <p>
+    <a href="#"
+       title="Add samples for population '{{population.FullName}}' from species
+              '{{species.FullName}}'."
+       class="btn btn-danger">
+      delete all samples
+    </a>
+  </p>
+  {%else%}
+  <p class="text-danger">
+    <span class="glyphicon glyphicon-exclamation-sign"></span>
+    There are no samples for this population at this time.
+  </p>
+
+  <p>
+    <a href="#"
+       title="Add samples for population '{{population.FullName}}' from species
+              '{{species.FullName}}'."
+       class="btn btn-primary">
+      add samples
+    </a>
+  </p>
+  {%endif%}
+</div>
+{%endblock%}
+
+{%block sidebarcontents%}
+{{display_population_card(species, population)}}
+{%endblock%}
+
diff --git a/uploader/templates/samples/select-population.html b/uploader/templates/samples/select-population.html
index da19ddc..8e22ac1 100644
--- a/uploader/templates/samples/select-population.html
+++ b/uploader/templates/samples/select-population.html
@@ -1,99 +1,34 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
+{%extends "samples/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+{%from "populations/macro-select-population.html" import select_population_form%}
+{%from "species/macro-display-species-card.html" import display_species_card%}
 
-{%block title%}Select Grouping/Population{%endblock%}
+{%block title%}Samples &mdash; Select Population{%endblock%}
 
-{%block contents%}
-<h1 class="heading">Select grouping/population</h1>
-
-<div>
-  <p>We organise the samples/cases/strains in a hierarchichal form, starting
-    with <strong>species</strong> at the very top. Under species, we have a
-    grouping in terms of the relevant population
-    (e.g. Inbred populations, cell tissue, etc.)</p>
-</div>
-
-<form method="POST" action="{{url_for('samples.select_population',
-                            species_id=species.SpeciesId)}}">
-  <legend class="heading">select grouping/population</legend>
-  {{flash_messages("error-select-population")}}
-
-  <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
-
-  <div class="form-group">
-    <label for="select:inbredset" class="form-label">grouping/population</label>
-    <select id="select:inbredset"
-	    name="inbredset_id"
-	    required="required"
-	    class="form-control">
-      <option value="">Select a grouping/population</option>
-      {%for pop in populations%}
-      <option value="{{pop.InbredSetId}}">
-	{{pop.InbredSetName}} ({{pop.FullName}})</option>
-      {%endfor%}
-    </select>
-  </div>
-
-  <button type="submit" class="btn btn-primary">select population</button>
-</form>
-
-<p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
-
-<form method="POST" action="{{url_for('samples.create_population',
-                            species_id=species.SpeciesId)}}">
-  <legend class="heading">create new grouping/population</legend>
-  {{flash_messages("error-create-population")}}
+{%block pagetitle%}Samples &mdash; Select Population{%endblock%}
 
-  <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
-  <div class="form-group">
-    <legend>mandatory</legend>
 
-    <label for="txt:inbredset-name" class="form-label">name</label>
-    <input id="txt:inbredset-name"
-	   name="inbredset_name"
-	   type="text"
-	   required="required"
-	   placeholder="Enter grouping/population name"
-	   class="form-control" />
-
-    <label for="txt:" class="form-label">full name</label>
-    <input id="txt:inbredset-fullname"
-	   name="inbredset_fullname"
-	   type="text"
-	   required = "required"
-	   placeholder="Enter the grouping/population's full name"
-	   class="form-control" />
-  </div>
-  <div class="form-group">
-    <legend>Optional</legend>
-
-    <label for="num:public" class="form-label">public?</label>
-    <input id="num:public"
-	   name="public"
-	   type="number"
-	   min="0" max="2" value="2"
-	   class="form-control" />
-
-    <label for="txt:inbredset-family" class="form-label">family</label>
-    <input id="txt:inbredset-family"
-	   name="inbredset_family"
-	   type="text"
-	   placeholder="I am not sure what this is about."
-	   class="form-control" />
-
-    <label for="txtarea:" class="form-label">Description</label>
-    <textarea id="txtarea:description"
-	      name="description"
-	      rows="5"
-	      placeholder="Enter a description of this grouping/population"
-	      class="form-control"></textarea>
-  </div>
-
-  <button type="submit" class="btn btn-primary">create grouping/population</button>
-</form>
+{%block contents%}
+{{flash_all_messages()}}
 
+<div class="row">
+  <p>Select the population to use with your samples:</p>
+  {{select_population_form(
+  url_for("species.populations.samples.select_population", species_id=species.SpeciesId),
+  populations)}}
+</div>
+<div class="row">
+  <p><strong>Cannot find your population in the list?</strong></p>
+
+  <p>If you cannot find the population you want in the drop-down above, you can
+    instead,
+    <a href="{{url_for('species.populations.create_population',
+             species_id=species.SpeciesId)}}"
+       title="Create a new population for species '{{species.FullName}},">
+      create a new population</a>.
+</div>
 {%endblock%}
 
-
-{%block javascript%}
+{%block sidebarcontents%}
+{{display_species_card(species)}}
 {%endblock%}
diff --git a/uploader/templates/samples/select-species.html b/uploader/templates/samples/select-species.html
deleted file mode 100644
index aa64ecf..0000000
--- a/uploader/templates/samples/select-species.html
+++ /dev/null
@@ -1,30 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_all_messages%}
-
-{%block title%}Select Grouping/Population{%endblock%}
-
-{%block contents%}
-<h2 class="heading">upload samples/cases</h2>
-
-<p>We need to know what species your data belongs to.</p>
-
-{{flash_all_messages()}}
-
-<form method="POST" action="{{url_for('expression-data.samples.select_species')}}">
-  <legend class="heading">upload samples</legend>
-  <div class="form-group">
-    <label for="select_species02" class="form-label">Species</label>
-    <select id="select_species02"
-            name="species_id"
-            required="required"
-            class="form-control">
-      <option value="">Select species</option>
-      {%for spec in species%}
-      <option value="{{spec.SpeciesId}}">{{spec.MenuName}}</option>
-      {%endfor%}
-    </select>
-  </div>
-
-  <button type="submit" class="btn btn-primary">submit</button>
-</form>
-{%endblock%}
diff --git a/uploader/templates/samples/upload-failure.html b/uploader/templates/samples/upload-failure.html
deleted file mode 100644
index 09e2ecf..0000000
--- a/uploader/templates/samples/upload-failure.html
+++ /dev/null
@@ -1,27 +0,0 @@
-{%extends "base.html"%}
-{%from "cli-output.html" import cli_output%}
-
-{%block title%}Samples Upload Failure{%endblock%}
-
-{%block contents%}
-<h1 class="heading">{{job.job_name}}</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.job_id}}</li>
-  <li><strong>status</strong>: {{job.status}}</li>
-  <li><strong>job type</strong>: {{job["job-type"]}}</li>
-</ul>
-
-<h4>stdout</h4>
-{{cli_output(job, "stdout")}}
-
-<h4>stderr</h4>
-{{cli_output(job, "stderr")}}
-
-{%endblock%}
diff --git a/uploader/templates/samples/upload-progress.html b/uploader/templates/samples/upload-progress.html
deleted file mode 100644
index 7bb02be..0000000
--- a/uploader/templates/samples/upload-progress.html
+++ /dev/null
@@ -1,22 +0,0 @@
-{%extends "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%}
-<h1 class="heading">{{job.job_name}}</h2>
-
-<p>
-<strong>status</strong>:
-<span>{{job["status"]}} ({{job.get("message", "-")}})</span><br />
-</p>
-
-<p>saving to database...</p>
-
-{{cli_output(job, "stdout")}}
-
-{%endblock%}
diff --git a/uploader/templates/samples/upload-samples.html b/uploader/templates/samples/upload-samples.html
deleted file mode 100644
index e62de57..0000000
--- a/uploader/templates/samples/upload-samples.html
+++ /dev/null
@@ -1,139 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Upload Samples{%endblock%}
-
-{%block css%}{%endblock%}
-
-{%block contents%}
-<h1 class="heading">upload samples</h1>
-
-{{flash_messages("alert-success")}}
-
-<p>You can now upload a character-separated value (CSV) file that contains
-  details about your samples. The CSV file should have the following fields:
-  <dl>
-    <dt>Name</dt>
-    <dd>The primary name for the sample</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. Can be an empty field.</dd>
-
-    <dt>Alias</dt>
-    <dd>An alias for the sample. Can be an empty field.</dd>
-  </dl>
-</p>
-
-<form id="form-samples"
-      method="POST"
-      action="{{url_for('samples.upload_samples',
-              species_id=species.SpeciesId,
-              population_id=population.InbredSetId)}}"
-      enctype="multipart/form-data">
-  <legend class="heading">upload samples</legend>
-
-  <div class="form-group">
-    <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
-    <label class="form-label">species:</label>
-    <span class="form-text">{{species.SpeciesName}} [{{species.MenuName}}]</span>
-  </div>
-
-  <div class="form-group">
-    <input type="hidden" name="inbredset_id" value="{{population.InbredSetId}}" />
-    <label class="form-label">grouping/population:</label>
-    <span class="form-text">{{population.Name}} [{{population.FullName}}]</span>
-  </div>
-
-  <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"
-	   class="form-control" />
-  </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>
-
-<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 to preview the data.</td>
-    </tr>
-  </tbody>
-</table>
-
-{%endblock%}
-
-
-{%block javascript%}
-<script src="/static/js/upload_samples.js" type="text/javascript"></script>
-{%endblock%}
diff --git a/uploader/templates/samples/upload-success.html b/uploader/templates/samples/upload-success.html
deleted file mode 100644
index cb745c3..0000000
--- a/uploader/templates/samples/upload-success.html
+++ /dev/null
@@ -1,18 +0,0 @@
-{%extends "base.html"%}
-{%from "cli-output.html" import cli_output%}
-
-{%block title%}Job Status{%endblock%}
-
-{%block contents%}
-<h1 class="heading">{{job.job_name}}</h2>
-
-<p>
-<strong>status</strong>:
-<span>{{job["status"]}} ({{job.get("message", "-")}})</span><br />
-</p>
-
-<p>Successfully uploaded the samples.</p>
-
-{{cli_output(job, "stdout")}}
-
-{%endblock%}
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