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{% extends "base.html" %}
{% block title %}Trait Submission{% endblock %}
{% block content %}
<!-- Start of body -->
<div class="container">
{% with messages = get_flashed_messages(category_filter=["warning"]) %}
{% if messages %}
{% for message in messages %}
<div class="alert alert-warning alert-dismissible" role="alert">
<button class="close" type="button" data-dismiss="alert" aria-label="Close">
<span aria-hidden="true">×</span>
</button>
{{ message }}
</div>
{% endfor %}
{% endif %}
{% endwith %}
{% with messages = get_flashed_messages(category_filter=["success"]) %}
{% if messages %}
{% for message in messages %}
<div class="alert alert-success alert-dismissible" role="alert">
<button class="close" type="button" data-dismiss="alert" aria-label="Close">
<span aria-hidden="true">×</span>
</button>
{{ message|safe }}
</div>
{% endfor %}
{% endif %}
{% endwith %}
<div class="page-header text-left">
<h1>Trait Metadata and Data Editing Form: {{ name }}</h1>
<small><a href="{{url_for('metadata_edit.show_history', dataset_id=dataset_id, name=name)}}" target="_blank">[View History]</a></small>
</div>
<form id="edit-form" class="form-horizontal" method="post" action="/datasets/traits/{{name}}?resource-id={{resource_id}}&dataset_id={{dataset_name}}" enctype='multipart/form-data'>
<div class="form-group">
<div class="controls left-block col-sm-8 col-lg-8" style="width: max-content;">
<input name="id" class="changed" type="hidden" value="{{ probeset.id_ }}"/>
<input name="old_id_" class="changed" type="hidden" value="{{ probeset.id_ }}"/>
<input name="probeset_name" class="changed" type="hidden" value="{{ probeset.name }}"/>
<input name="dataset_name" class="changed" type="hidden" value="{{ dataset_name }}"/>
<input name="edited" class="changed" type="hidden" value="false"/>
</div>
</div>
<div>
<h2>Edit Sample Data</h2>
<p>
Download a spreadsheet of sample values to edit in Excel (or a similar program) and then upload the edited file
</p>
<div>
<a href="/datasets/mrna/{{ probeset_id }}/dataset/{{ dataset_name }}/csv?resource-id={{ resource_id }}" class="btn btn-link">
Click to Download Sample Data
</a>
</div>
<div class="form-group">
<input type = "file" class="col-md-4 control-label text-left" name = "file" />
</div>
<input type="submit" style="width: 125px; margin-right: 25px;" class="btn btn-success form-control changed" value="Submit Change">
</div>
<hr>
<div>
<h2>Edit Metadata</h2>
<div class="form-group">
<label for="symbol" class="col-sm-3 col-lg-2 control-label text-left">Symbol</label>
<div class="col-sm-4">
<textarea name="symbol" class="form-control" rows="1">{{ probeset.symbol |default('', true) }}</textarea>
<input name="old_symbol" class="changed" type="hidden" value="{{ probeset.symbol |default('', true) }}"/>
</div>
</div>
<div class="form-group">
<label for="description" class="col-sm-3 col-lg-2 control-label text-left">Description</label>
<div class="col-sm-4">
<textarea name="description" class="form-control" rows="3">{{ probeset.description |default('', true) }}</textarea>
<input name="old_description" class="changed" type="hidden" value="{{ probeset.description |default('', true) }}"/>
</div>
</div>
<div class="form-group">
<label for="probe_target_description" class="col-sm-3 col-lg-2 control-label text-left">Probe Target Description</label>
<div class="col-sm-4">
<textarea name="probe_target_description" class="form-control" rows="4">{{ probeset.probe_target_description |default('', true) }}</textarea>
<input name="old_probe_target_description" class="changed" type="hidden" value="{{ probeset.probe_target_description |default('', true) }}"/>
</div>
</div>
<div class="form-group">
<label for="chr" class="col-sm-3 col-lg-2 control-label text-left">Chr</label>
<div class="col-sm-4">
<textarea name="chr" class="form-control" rows="1">{{ probeset.chr_ |default('', true) }}</textarea>
<input name="old_chr_" class="changed" type="hidden" value="{{ probeset.chr_ |default('', true) }}"/>
</div>
</div>
<div class="form-group">
<label for="mb" class="col-sm-3 col-lg-2 control-label text-left">Mb</label>
<div class="col-sm-4">
<textarea name="mb" class="form-control" rows="1">{{ probeset.mb |default('', true) }}</textarea>
<input name="old_mb" class="changed" type="hidden" value="{{ probeset.mb |default('', true) }}"/>
</div>
</div>
<div class="form-group">
<label for="alias" class="col-sm-3 col-lg-2 control-label text-left">
Alias:
</label>
<div class="col-sm-4">
<textarea name="alias" class="form-control" rows="1">{{ probeset.alias |default('', true) }}</textarea>
<input name="old_alias" class="changed" type="hidden" value="{{ probeset.alias |default('', true) }}"/>
</div>
</div>
<div class="form-group">
<label for="geneid" class="col-sm-3 col-lg-2 control-label text-left">
Gene Id:
</label>
<div class="col-sm-4">
<textarea name="geneid" class="form-control" rows="1">{{ probeset.geneid |default('', true) }}</textarea>
<input name="old_geneid" class="changed" type="hidden" value="{{ probeset.geneid |default('', true) }}"/>
</div>
</div>
<div class="form-group">
<label for="homologeneid" class="col-sm-3 col-lg-2 control-label text-left">
Homologene Id:
</label>
<div class="col-sm-4">
<textarea name="homologeneid" class="form-control" rows="1">{{ probeset.homologeneid |default('', true) }}</textarea>
<input name="old_homologeneid" class="changed" type="hidden" value="{{ probeset.homologeneid |default('', true) }}"/>
</div>
</div>
<div class="form-group">
<label for="unigeneid" class="col-sm-3 col-lg-2 control-label text-left">
Unigene Id:
</label>
<div class="col-sm-4">
<textarea name="unigeneid" class="form-control" rows="1">{{ probeset.unigeneid |default('', true) }}</textarea>
<input name="old_unigeneid" class="changed" type="hidden" value="{{ probeset.unigeneid |default('', true) }}"/>
</div>
</div>
<div class="form-group">
<label for="omim" class="col-sm-3 col-lg-2 control-label text-left">OMIM</label>
<div class="col-sm-4">
<textarea name="omim" class="form-control" rows="1">{{ probeset.omim |default('', true) }}</textarea>
<input name="old_omim" class="changed" type="hidden" value="{{ probeset.omim |default('', true) }}"/>
</div>
</div>
<div class="form-group">
<label for="refseq_transcriptid" class="col-sm-3 col-lg-2 control-label text-left">
Refseq TranscriptId:
</label>
<div class="col-sm-4">
<textarea name="refseq_transcriptid" class="form-control" rows="1">{{ probeset.refseq_transcriptid |default('', true) }}</textarea>
<input name="old_refseq_transcriptid" class="changed" type="hidden" value="{{ probeset.refseq_transcriptid |default('', true) }}"/>
</div>
</div>
<div class="form-group">
<label for="blatseq" class="col-sm-3 col-lg-2 control-label text-left">BlatSeq</label>
<div class="col-sm-8">
<textarea name="blatseq" class="form-control" rows="6">{{ probeset.blatseq |default('', true) }}</textarea>
<input name="old_blatseq" class="changed" type="hidden" value="{{ probeset.blatseq |default('', true) }}"/>
</div>
</div>
<div class="form-group">
<label for="targetseq" class="col-sm-3 col-lg-2 control-label text-left">TargetSeq</label>
<div class="col-sm-8">
<textarea name="targetseq" class="form-control" rows="6">{{ probeset.targetseq |default('', true) }}</textarea>
<input name="old_targetseq" class="changed" type="hidden" value="{{ probeset.targetseq |default('', true) }}"/>
</div>
</div>
<div class="form-group">
<label for="strand_probe" class="col-sm-3 col-lg-2 control-label text-left">Strand Probe</label>
<div class="col-sm-2">
<textarea name="strand_probe" class="form-control" rows="1">{{ probeset.strand_probe |default('', true) }}</textarea>
<input name="old_strand_probe" class="changed" type="hidden" value="{{ probeset.strand_probe |default('', true) }}"/>
</div>
</div>
<div class="form-group">
<label for="probe_set_target_region" class="col-sm-3 col-lg-2 control-label text-left">Probe Set Target Region</label>
<div class="col-sm-8">
<textarea name="probe_set_target_region" class="form-control" rows="1">{{ probeset.probe_set_target_region |default('', true) }}</textarea>
<input name="old_probe_set_target_region" class="changed" type="hidden" value="{{ probeset.probe_set_target_region_ |default('', true) }}"/>
</div>
</div>
<div class="form-group">
<label for="probe_set_specificity" class="col-sm-3 col-lg-2 control-label text-left">Probeset Specificity</label>
<div class="col-sm-8">
<textarea name="probe_set_specificity" class="form-control" rows="1">{{ probeset.probe_set_specificity |default('', true) }}</textarea>
<input name="old_probe_set_specificity" class="changed" type="hidden" value="{{ probeset.probe_set_specificity |default('', true) }}"/>
</div>
</div>
<div class="form-group">
<label for="probe_set_blat_score" class="col-sm-3 col-lg-2 control-label text-left">Probeset Blat Score</label>
<div class="col-sm-8">
<textarea name="probe_set_blat_score" class="form-control" rows="1">{{ probeset.probe_set_blat_score |default('', true) }}</textarea>
<input name="old_probe_set_blat_score" class="changed" type="hidden" value="{{ probeset.probe_set_blat_score |default('', true) }}"/>
</div>
</div>
<div class="form-group">
<label for="probe_set_blat_mb_start" class="col-sm-3 col-lg-2 control-label text-left">
Probeset Blat Mb Start</label>
<div class="col-sm-8">
<textarea name="probe_set_blat_mb_start" class="form-control" rows="1">{{ probeset.probe_set_blat_mb_start |default('', true) }}</textarea>
<input name="old_probe_set_blat_mb_start" class="changed" type="hidden" value="{{ probeset.probe_set_blat_mb_start |default('', true) }}"/>
</div>
</div>
<div class="form-group">
<label for="probe_set_blat_mb_end" class="col-sm-3 col-lg-2 control-label text-left">Probeset Blat Mb End</label>
<div class="col-sm-8">
<textarea name="probe_set_blat_mb_end" class="form-control" rows="1">{{ probeset.probe_set_blat_mb_end |default('', true) }}</textarea>
<input name="old_probe_set_blat_mb_end" class="changed" type="hidden" value="{{ probeset.probe_set_blat_mb_end |default('', true) }}"/>
</div>
</div>
<div class="form-group">
<label for="probe_set_strand" class="col-sm-3 col-lg-2 control-label text-left">Probeset Strand</label>
<div class="col-sm-8">
<textarea name="probe_set_strand" class="form-control" rows="6">{{ probeset.probe_set_strand |default('', true) }}</textarea>
<input name="old_probe_set_strand" class="changed" type="hidden" value="{{ probeset.probe_set_strand |default('', true) }}"/>
</div>
</div>
<div class="form-group">
<label for="probe_set_note_by_rw" class="col-sm-3 col-lg-2 control-label text-left">Probeset Strand</label>
<div class="col-sm-8">
<textarea name="probe_set_note_by_rw" class="form-control" rows="6">{{ probeset.probe_set_note_by_rw |default('', true) }}</textarea>
<input name="old_probe_set_note_by_rw" class="changed" type="hidden" value="{{ probeset.probe_set_note_by_rw |default('', true) }}"/>
</div>
</div>
<input type="submit" style="width: 125px; margin-right: 25px;" class="btn btn-success form-control col-xs-2 changed" value="Submit Change">
</div>
<div style="padding-top: 20px;">
<p class="text-info" style="padding-left: 5em;">
<strong>Type "x" to delete a value.</strong>
</p>
<table style="width: 500px;" class="table table-hover table-striped table-bordered left-float">
<thead>
<th></th>
<th>ID</th>
<th>Sample</th>
<th>Value</th>
<th></th>
<th>SE</th>
<th>N</th>
</thead>
<tbody>
{% for sample in sample_list %}
<tr>
<td><input type="checkbox"></td>
<td>{{ loop.index }}</td>
<td>{{ sample }}</td>
<td><input type="text" name="value:{{ sample }}" class="table_input" value="{% if sample_data.get(sample) %}{{ '%0.3f' | format(sample_data.get(sample).value | float) }}{% else %}x{% endif %}" size=4 maxlength=6></input></td>
<td>±</td>
<td><input type="text" name="error:{{ sample }}" class="table_input" value="{% if sample_data.get(sample).error %}{{ '%0.3f' | format(sample_data.get(sample).error | float) }}{% else %}x{% endif %}" size=4 maxlength=5></input></td>
<td><input type="text" name="n_cases:{{ sample }}" class="table_input" value="{% if sample_data.get(sample).n_cases %}{{ sample_data.get(sample).n_cases }}{% else %}x{% endif %}" size=3 maxlength=3></input></td>
</tr>
{% endfor %}
</tbody>
</table>
</div>
</form>
</div>
{%endblock%}
{% block js %}
<script>
gn_server_url = "{{ gn_server_url }}";
spans = document.querySelectorAll("[data-message-id]")
spans.forEach((span) => {
span.innerHTML = $("[for='" + span.getAttribute("data-message-id") + "']").text();
});
$("[data-message-id]").lead
function MarkAsChanged(){
$(this).addClass("changed");
}
$(":input").blur(MarkAsChanged).change(MarkAsChanged);
$("input[type=submit]").click(function(){
$(":input:not(.changed)").attr("disabled", "disabled");
});
// This is an awkward way to detect changes to table data, so it doesn't process it otherwise
$(".table_input").change(function(){
$("input[name=edited]").val("true");
});
</script>
{% endblock %}
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