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{%extends "species/base.html"%}
{%from "flash_messages.html" import flash_all_messages%}
{%block title%}Create Species{%endblock%}
{%block pagetitle%}Create Species{%endblock%}
{%block lvl2_breadcrumbs%}
<li {%if activelink=="create-species"%}
class="breadcrumb-item active"
{%else%}
class="breadcrumb-item"
{%endif%}>
<a href="{{url_for('species.create_species')}}">Create</a>
</li>
{%endblock%}
{%block contents%}
<div class="row">
<form id="frm-create-species"
method="POST"
action="{{url_for('species.create_species')}}">
<legend>Create Species</legend>
{{flash_all_messages()}}
<div class="form-group">
<label for="txt-taxonomy-id" class="form-label">
Taxonomy ID</label>
<div class="input-group">
<input id="txt-taxonomy-id"
name="species_taxonomy_id"
type="text"
class="form-control" />
<span class="input-group-btn">
<button id="btn-search-taxonid" class="btn btn-info">Search</button>
</span>
</div>
<small class="form-text text-small text-muted">Provide the taxonomy ID for
your species that can be used to link to external sites like NCBI. Enter
the taxonomy ID and click "Search" to auto-fill the form with data.
<br />
While it is recommended to provide a value for this field, doing so is
optional.
</small>
</div>
<div class="form-group">
<label for="txt-species-name" class="form-label">Common Name</label>
<input id="txt-species-name"
name="common_name"
type="text"
class="form-control"
required="required" />
<small class="form-text text-muted">Provide the common, possibly
non-scientific name for the species here, e.g. Human, Mouse, etc.</small>
</div>
<div class="form-group">
<label for="txt-species-scientific" class="form-label">
Scientific Name</label>
<input id="txt-species-scientific"
name="scientific_name"
type="text"
class="form-control"
required="required" />
<small class="form-text text-muted">Provide the scientific name for the
species you are creating, e.g. Homo sapiens, Mus musculus, etc.</small>
</div>
<div class="form-group">
<label for="select-species-family" class="form-label">Family</label>
<select id="select-species-family"
name="species_family"
required="required"
class="form-control">
<option value="">Please select a grouping</option>
{%for family in families%}
<option value="{{family}}">{{family}}</option>
{%endfor%}
</select>
<small class="form-text text-muted">
This is a generic grouping for the species that determines under which
grouping the species appears in the GeneNetwork menus</small>
</div>
<div class="form-group">
<input type="submit"
value="create new species"
class="btn btn-primary" />
</div>
</form>
</div>
{%endblock%}
{%block javascript%}
<script>
var lastTaxonId = null;
var fetch_taxonomy = (taxonId) => {
var uri = (
"https://rest.uniprot.org/taxonomy/" + encodeURIComponent(taxonId));
$.get(
uri,
{},
(data, textStatus, jqXHR) => {
if(textStatus == "success") {
lastTaxonId = taxonId;
$("#txt-species-scientific").val(data.scientificName);
$("#txt-species-name").val(data.commonName);
return false;
}
msg = (
"Request to '${uri}' failed with message '${textStatus}'. "
+ "Please try again later, or fill the details manually.");
alert(msg);
console.error(msg, data, textStatus);
return false;
},
"json");
};
$("#btn-search-taxonid").on("click", (event) => {
event.preventDefault();
taxonId = $("#txt-taxonomy-id").val();
if((taxonId !== "") && (taxonId !== lastTaxonId)) {
fetch_taxonomy(taxonId);
}
});
</script>
{%endblock%}
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