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Diffstat (limited to 'uploader/templates/populations/create-population.html')
| -rw-r--r-- | uploader/templates/populations/create-population.html | 269 |
1 files changed, 269 insertions, 0 deletions
diff --git a/uploader/templates/populations/create-population.html b/uploader/templates/populations/create-population.html new file mode 100644 index 0000000..007b6bf --- /dev/null +++ b/uploader/templates/populations/create-population.html @@ -0,0 +1,269 @@ +{%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, + return_to=return_to)}}"> + + <legend>Create Population</legend> + + {{flash_all_messages()}} + + <input type="hidden" name="return_to" value="{{return_to}}"> + + <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="form-text text-muted"> + This is a 3-character code for your population, that is prepended to + the phenotype identifiers. e.g. For the "BXD Family" population, the + code is "BXD" and therefore, the phenotype identifiers for the + population look like the following examples: <em>BXD_10148</em>, + <em>BXD_10180</em>, <em>BXD_10197</em>, etc. + </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="txt-population-family" class="form-label">Family</label> + <input type="text" + id="txt-population-family" + name="population_family" + class="form-control" + list="families-list" /> + <datalist id="families-list"> + {%for family in families%} + <option value="{{family}}">{{family}}</option> + {%endfor%} + </datalist> + <small class="form-text text-muted"> + <p> + This is <strong>optional</strong> metadata. It is used to group + populations into "families" for presentation in the menus. + {%if families | length > 0%} + Examples of currently existing families are: + <ul> + {%for family in families[0:7]%} + <li>{{family}}</li> + {%endfor%} + <li>etc.</li> + </ul> + {%endif%} + + You can + {%if families|length>0%} select from existing families, or {%endif%} + create a new family by typing in the input box above. You can also + leave the family blank.</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%} |