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{%extends "populations/base.html"%}
{%from "flash_messages.html" import flash_all_messages%}
{%from "species/macro-select-species.html" import select_species_form%}
{%from "species/macro-display-species-card.html" import display_species_card%}
{%block title%}Create Population{%endblock%}
{%block pagetitle%}Create Population{%endblock%}
{%block lvl3_breadcrumbs%}
<li {%if activelink=="create-population"%}
class="breadcrumb-item active"
{%else%}
class="breadcrumb-item"
{%endif%}>
<a href="{{url_for('species.populations.create_population',
species_id=species.SpeciesId)}}">create population</a>
</li>
{%endblock%}
{%block contents%}
<div class="row">
<p>The population is the next hierarchical node under Species. Data is grouped under a specific population, under a particular species.</p>
<p>
This page enables you to create a new population, in the case that you
cannot find the population you want in the
<a
href="{{url_for('species.populations.list_species_populations',
species_id=species.SpeciesId)}}"
title="Population for species '{{species.FullName}}'.">
list of species populations
</a>
</p>
</div>
<div class="row">
<form method="POST"
action="{{url_for('species.populations.create_population',
species_id=species.SpeciesId)}}">
<legend>Create Population</legend>
{{flash_all_messages()}}
<div {%if errors.population_fullname%}
class="form-group has-error"
{%else%}
class="form-group"
{%endif%}>
<label for="txt-population-fullname" class="form-label">Full Name</label>
{%if errors.population_fullname%}
<small class="form-text text-danger">{{errors.population_fullname}}</small>
{%endif%}
<input type="text"
id="txt-population-fullname"
name="population_fullname"
required="required"
minLength="3"
maxLength="100"
value="{{error_values.population_fullname or ''}}"
class="form-control" />
<small class="form-text text-muted">
<p>
This is a descriptive name for your population — useful for
humans.
</p>
</small>
</div>
<div {%if errors.population_name%}
class="form-group has-error"
{%else%}
class="form-group"
{%endif%}>
<label for="txt-population-name" class="form-label">Name</label>
{%if errors.population_name%}
<small class="form-text text-danger">{{errors.population_name}}</small>
{%endif%}
<input type="text"
id="txt-population-name"
name="population_name"
required="required"
minLength="3"
maxLength="30"
value="{{error_values.population_name or ''}}"
class="form-control" />
<small class="form-text text-muted">
<p>
This is a short representative, but constrained name for your
population.
<br />
The field will only accept letters ('A-Za-z'), numbers (0-9), hyphens
and underscores. Any other character will cause the name to be
rejected.
</p>
</small>
</div>
<div class="form-group">
<label for="txt-population-code" class="form-label">Population Code</label>
<input type="text"
id="txt-population-code"
name="population_code"
maxLength="5"
minLength="3"
value="{{error_values.population_code or ''}}"
class="form-control" />
<small class="form-text text-muted">
<p class="text-danger">
<span class="glyphicon glyphicon-exclamation-sign"></span>
What is this field is for? Confirm with Arthur and the rest.
</p>
</small>
</div>
<div {%if errors.population_description%}
class="form-group has-error"
{%else%}
class="form-group"
{%endif%}>
<label for="txt-population-description" class="form-label">
Description
</label>
{%if errors.population_description%}
<small class="form-text text-danger">{{errors.population_description}}</small>
{%endif%}
<textarea
id="txt-population-description"
name="population_description"
required="required"
class="form-control"
rows="5">{{error_values.population_description or ''}}</textarea>
<small class="form-text text-muted">
<p>
This is a more detailed description for your population. This is
useful to communicate with other researchers some details regarding
your population, and what its about.
<br />
Put, here, anything that describes your population but does not go
cleanly under metadata.
</p>
</small>
</div>
<div {%if errors.population_family%}
class="form-group has-error"
{%else%}
class="form-group"
{%endif%}>
<label for="select-population-family" class="form-label">Family</label>
<select id="select-population-family"
name="population_family"
class="form-control"
required="required">
<option value="">Please select a family</option>
{%for family in families%}
<option value="{{family}}"
{%if error_values.population_family == family%}
selected="selected"
{%endif%}>{{family}}</option>
{%endfor%}
</select>
<small class="form-text text-muted">
<p>
This is a rough grouping of the populations in GeneNetwork into lists
of common types of populations.
</p>
</small>
</div>
<div {%if errors.population_mapping_method_id%}
class="form-group has-error"
{%else%}
class="form-group"
{%endif%}>
<label for="select-population-mapping-methods"
class="form-label">Mapping Methods</label>
<select id="select-population-mapping-methods"
name="population_mapping_method_id"
class="form-control"
required="required">
<option value="">Select appropriate mapping methods</option>
{%for mmethod in mapping_methods%}
<option value="{{mmethod.id}}"
{%if error_values.population_mapping_method_id == mmethod.id%}
selected="selected"
{%endif%}>{{mmethod.value}}</option>
{%endfor%}
</select>
<small class="form-text text-muted">
<p>Select the mapping methods that your population will support.</p>
</small>
</div>
<div {%if errors.population_genetic_type%}
class="form-group has-error"
{%else%}
class="form-group"
{%endif%}>
<label for="select-population-genetic-type"
class="form-label">Genetic Type</label>
<select id="select-population-genetic-type"
name="population_genetic_type"
class="form-control">
<option value="">Select proper genetic type</option>
{%for gtype in genetic_types%}
<option value="{{gtype}}"
{%if error_values.population_genetic_type == gtype%}
selected="selected"
{%endif%}>{{gtype}}</option>
{%endfor%}
</select>
<small class="form-text text-muted text-danger">
<p>
<span class="glyphicon glyphicon-exclamation-sign"></span>
This might be a poorly named field.
</p>
<p>
It probably has more to do with the mating crosses/crossings used to
produce the individuals in the population. I am no biologist, however,
and I'm leaving this here to remind myself to confirm this.
</p>
<p>
I still don't know what riset is.<br />
… probably something to do with Recombinant Inbred Strains
</p>
<p>
Possible resources for this:
<ul>
<li>https://www.informatics.jax.org/silver/chapters/3-2.shtml</li>
<li>https://www.informatics.jax.org/silver/chapters/9-2.shtml</li>
</ul>
</p>
</small>
</div>
<div class="form-group">
<input type="submit"
value="create population"
class="btn btn-primary" />
</div>
</form>
</div>
{%endblock%}
{%block sidebarcontents%}
{{display_species_card(species)}}
{%endblock%}
|
