Rename module: qc_app --> uploader

6 files changed, 0 insertions, 335 deletions

diff --git a/qc_app/templates/samples/select-population.html b/qc_app/templates/samples/select-population.html
deleted file mode 100644
index da19ddc..0000000
--- a/qc_app/templates/samples/select-population.html
+++ /dev/null
@@ -1,99 +0,0 @@
-{%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/qc_app/templates/samples/select-species.html b/qc_app/templates/samples/select-species.html
deleted file mode 100644
index edadc61..0000000
--- a/qc_app/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('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/qc_app/templates/samples/upload-failure.html b/qc_app/templates/samples/upload-failure.html
deleted file mode 100644
index 09e2ecf..0000000
--- a/qc_app/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/qc_app/templates/samples/upload-progress.html b/qc_app/templates/samples/upload-progress.html
deleted file mode 100644
index 7bb02be..0000000
--- a/qc_app/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/qc_app/templates/samples/upload-samples.html b/qc_app/templates/samples/upload-samples.html
deleted file mode 100644
index e62de57..0000000
--- a/qc_app/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/qc_app/templates/samples/upload-success.html b/qc_app/templates/samples/upload-success.html
deleted file mode 100644
index cb745c3..0000000
--- a/qc_app/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%}