Rename module: qc_app --> uploader

6 files changed, 335 insertions, 0 deletions

diff --git a/uploader/templates/samples/select-population.html b/uploader/templates/samples/select-population.html
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+++ b/uploader/templates/samples/select-population.html
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+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Select Grouping/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")}}
+
+  <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>
+
+{%endblock%}
+
+
+{%block javascript%}
+{%endblock%}
diff --git a/uploader/templates/samples/select-species.html b/uploader/templates/samples/select-species.html
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+++ b/uploader/templates/samples/select-species.html
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+{%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('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
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+++ b/uploader/templates/samples/upload-failure.html
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+{%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
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+++ b/uploader/templates/samples/upload-progress.html
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+{%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
new file mode 100644
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+++ b/uploader/templates/samples/upload-samples.html
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+{%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
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+++ b/uploader/templates/samples/upload-success.html
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+{%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%}