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-rw-r--r--uploader/templates/samples/select-population.html99
-rw-r--r--uploader/templates/samples/select-species.html30
-rw-r--r--uploader/templates/samples/upload-failure.html27
-rw-r--r--uploader/templates/samples/upload-progress.html22
-rw-r--r--uploader/templates/samples/upload-samples.html139
-rw-r--r--uploader/templates/samples/upload-success.html18
6 files changed, 335 insertions, 0 deletions
diff --git a/uploader/templates/samples/select-population.html b/uploader/templates/samples/select-population.html
new file mode 100644
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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
new file mode 100644
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--- /dev/null
+++ 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
new file mode 100644
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--- /dev/null
+++ 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
new file mode 100644
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--- /dev/null
+++ 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
index 0000000..e62de57
--- /dev/null
+++ b/uploader/templates/samples/upload-samples.html
@@ -0,0 +1,139 @@
+{%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
new file mode 100644
index 0000000..cb745c3
--- /dev/null
+++ 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%}