diff options
Diffstat (limited to 'uploader/templates/populations')
8 files changed, 284 insertions, 54 deletions
diff --git a/uploader/templates/populations/create-population.html b/uploader/templates/populations/create-population.html index b05ce37..007b6bf 100644 --- a/uploader/templates/populations/create-population.html +++ b/uploader/templates/populations/create-population.html @@ -37,12 +37,15 @@ <div class="row"> <form method="POST" action="{{url_for('species.populations.create_population', - species_id=species.SpeciesId)}}"> + 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%} @@ -107,9 +110,12 @@ 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 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> @@ -148,24 +154,35 @@ {%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> + <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}}" - {%if error_values.population_family == family%} - selected="selected" - {%endif%}>{{family}}</option> + <option value="{{family}}">{{family}}</option> {%endfor%} - </select> + </datalist> <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> + 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> diff --git a/uploader/templates/populations/index.html b/uploader/templates/populations/index.html index 4354e02..d2bee77 100644 --- a/uploader/templates/populations/index.html +++ b/uploader/templates/populations/index.html @@ -22,3 +22,7 @@ {{select_species_form(url_for("species.populations.index"), species)}} </div> {%endblock%} + +{%block javascript%} +<script type="text/javascript" src="/static/js/species.js"></script> +{%endblock%} diff --git a/uploader/templates/populations/list-populations.html b/uploader/templates/populations/list-populations.html index 7c7145f..a092e34 100644 --- a/uploader/templates/populations/list-populations.html +++ b/uploader/templates/populations/list-populations.html @@ -51,10 +51,10 @@ <caption>Populations for {{species.FullName}}</caption> <thead> <tr> - <th>#</th> + <th></th> <th>Name</th> <th>Full Name</th> - <th>Description</th> + <th>Information</th> </tr> </thead> @@ -71,7 +71,10 @@ </a> </td> <td>{{population.FullName}}</td> - <td>{{population.Description}}</td> + <td><a href="https://info.genenetwork.org/species/source.php?SpeciesName={{species.Name}}&InbredSetName={{population.Name}}" + title="Link to detailed information on this population." + class="btn btn-info" + target="_blank">info</a></td> </tr> {%else%} <tr> diff --git a/uploader/templates/populations/macro-display-population-card.html b/uploader/templates/populations/macro-display-population-card.html index 79f7925..6b5f1e0 100644 --- a/uploader/templates/populations/macro-display-population-card.html +++ b/uploader/templates/populations/macro-display-population-card.html @@ -1,4 +1,4 @@ -{%from "species/macro-display-species-card.html" import display_species_card%} +{%from "species/macro-display-species-card.html" import display_species_card,display_sui_species_card%} {%macro display_population_card(species, population)%} {{display_species_card(species)}} @@ -33,14 +33,46 @@ <td>Family</td> <td>{{population.Family}}</td> </tr> - - <tr> - <td>Description</td> - <td>{{(population.Description or "")[0:500]}}…</td> - </tr> </tbody> </table> </div> </div> </div> {%endmacro%} + + +{%macro display_sui_population_card(species, population)%} +{{display_sui_species_card(species)}} + +<div class="row"> + <table class="table"> + <caption>Current population</caption> + <tbody> + <tr> + <th>Name</th> + <td>{{population.Name}}</td> + </tr> + + <tr> + <th>Full Name</th> + <td>{{population.FullName}}</td> + </tr> + + <tr> + <th>Code</th> + <td>{{population.InbredSetCode}}</td> + </tr> + + <tr> + <th>Genetic Type</th> + <td>{{population.GeneticType}}</td> + </tr> + + <tr> + <th>Family</th> + <td>{{population.Family}}</td> + </tr> + </tbody> + </table> +</div> +{%endmacro%} diff --git a/uploader/templates/populations/macro-select-population.html b/uploader/templates/populations/macro-select-population.html index af4fd3a..14b0510 100644 --- a/uploader/templates/populations/macro-select-population.html +++ b/uploader/templates/populations/macro-select-population.html @@ -1,30 +1,52 @@ -{%macro select_population_form(form_action, populations)%} -<form method="GET" action="{{form_action}}"> - <legend>Select Population</legend> - - <div class="form-group"> - <label for="select-population" class="form-label">Select Population</label> - <select id="select-population" - name="population_id" - class="form-control" - required="required"> - <option value="">Select Population</option> - {%for family in populations%} - <optgroup {%if family[0][1] is not none%} - label="{{family[0][1]}}" - {%else%} - label="Undefined" - {%endif%}> - {%for population in family[1]%} - <option value="{{population.Id}}">{{population.FullName}}</option> - {%endfor%} - </optgroup> - {%endfor%} - </select> +{%from "macro-step-indicator.html" import step_indicator%} + +{%macro select_population_form(form_action, species, populations)%} +<form method="GET" action="{{form_action}}" class="form-horizontal"> + + <h2>{{step_indicator("2")}} What population do you want to work with?</h2> + + {%if populations | length != 0%} + + <p class="form-text">Search for, and select the population from the table + below and click "Continue"</p> + + <div class="radio"> + <label class="control-label" for="rdo-cant-find-population"> + <input type="radio" id="rdo-cant-find-population" + name="population_id" value="CREATE-POPULATION" /> + I cannot find the population I want — create it! + </label> + </div> + + <div class="col-sm-offset-10 col-sm-2"> + <input type="submit" value="continue" class="btn btn-primary" /> + </div> + + <div style="margin-top:3em;"> + <table id="tbl-select-population" class="table compact stripe" + data-populations-list='{{populations | tojson}}'> + <thead> + <tr> + <th></th> + <th>Population</th> + </tr> + </thead> + + <tbody></tbody> + </table> </div> - <div class="form-group"> - <input type="submit" value="Select" class="btn btn-primary" /> + {%else%} + <p class="form-text"> + There are no populations currently defined for {{species['FullName']}} + ({{species['SpeciesName']}}).<br /> + Click "Continue" to create the first!</p> + <input type="hidden" name="population_id" value="CREATE-POPULATION" /> + + <div class="col-sm-offset-10 col-sm-2"> + <input type="submit" value="continue" class="btn btn-primary" /> </div> + {%endif%} + </form> {%endmacro%} diff --git a/uploader/templates/populations/sui-base.html b/uploader/templates/populations/sui-base.html new file mode 100644 index 0000000..cc01c9e --- /dev/null +++ b/uploader/templates/populations/sui-base.html @@ -0,0 +1,12 @@ +{%extends "species/sui-base.html"%} + +{%block breadcrumbs%} +{{super()}} +<li class="breadcrumb-item"> + <a href="{{url_for('species.populations.view_population', + species_id=species['SpeciesId'], + population_id=population['Id'])}}"> + {{population["FullName"]}} + </a> +</li> +{%endblock%} diff --git a/uploader/templates/populations/sui-view-population.html b/uploader/templates/populations/sui-view-population.html new file mode 100644 index 0000000..3bf8d0d --- /dev/null +++ b/uploader/templates/populations/sui-view-population.html @@ -0,0 +1,138 @@ +{%extends "populations/sui-base.html"%} +{%from "macro-step-indicator.html" import step_indicator%} +{%from "populations/macro-display-population-card.html" import display_sui_population_card%} + +{%block contents%} +<div class="row"> + <h2 class="heading">{{population.FullName}} ({{population.Name}})</h2> +</div> + +<div class="row"> + <ul class="nav nav-tabs" id="population-actions"> + <li class="nav-item presentation"> + <button class="nav-link" + id="samples-tab" + data-bs-toggle="tab" + data-bs-target="#samples-content" + type="button" + role="tab" + aria-controls="samples-content" + aria-selected="true">Samples</button></li> + <li class="nav-item presentation"> + <button class="nav-link active" + id="phenotypes-tab" + data-bs-toggle="tab" + data-bs-target="#phenotypes-content" + type="button" + role="tab" + aria-controls="phenotypes-content" + aria-selected="false">Phenotypes</button></li> + {%if view_under_construction%} + <li class="nav-item presentation"> + <button class="nav-link" + id="genotypes-tab" + data-bs-toggle="tab" + data-bs-target="#genotypes-content" + type="button" + role="tab" + aria-controls="genotypes-content" + aria-selected="false">Genotypes</button></li> + <li class="nav-item presentation"> + <button class="nav-link" + id="expression-data-tab" + data-bs-toggle="tab" + data-bs-target="#expression-data-content" + type="button" + role="tab" + aria-controls="expression-data-content" + aria-selected="false">Expression-Data</button></li> + {%endif%} + </ul> +</div> + +<div class="row"> + <div class="tab-content" id="populations-tabs-content"> + <div class="tab-pane fade" + id="samples-content" + role="tabpanel" + aria-labelledby="samples-content-tab"> + <p>Think of a <strong>"sample"</strong> as say a single case or individual + in the experiment. It could even be a single strain (where applicable) + under consideration.</p> + <p>This is a convenience feature for when you want to upload phenotypes to + the system, but do not have the genotypes data ready yet.</p> + <p>Please click the button below to provide the samples that will be used + in your data.</p> + <a href="{{url_for('species.populations.samples.list_samples', + species_id=species.SpeciesId, + population_id=population.Id)}}" + title="Upload samples for population '{{population['Name']}}'" + class="btn btn-primary">Upload Samples</a> + </div> + + <div class="tab-pane fade show active" + id="phenotypes-content" + role="tabpanel" + aria-labelledby="phenotypes-content-tab"> + <p>Upload and manage phenotypes and publications for population + "<em>{{population.FullName}} ({{population.Name}})</em>" of species + "<em>{{species.FullName}} ({{species.Name}})</em>".</p> + + <p class="text-danger">Tabs will not work nicely here. Maybe present + options e.g.: + </p> + <div class="row"> + <div class="col"> + <a href="{{url_for('species.populations.phenotypes.view_dataset', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}" + title="Upload phenotype data for population '{{population['Name']}}'" + class="btn btn-primary">Upload new Phenotypes</a> + <!-- Go straight to upload form(s). --> + </div> + <div class="col"> + <a href="#" + title="List all existing phenotypes for this population." + class="btn btn-info not-implemented">list existing phenotypes</a> + <!-- Means and QTLReaper will be computed in this page. --> + </div> + <div class="col"> + <a href="#" + title="List all existing publications for this population." + class="btn btn-info not-implemented">list existing publications</a> + <!-- Maybe, actually filter publications by population? --> + <!-- Provide other features for publications on loaded page. --> + </div> + </div> + </div> + <div class="tab-pane fade" + id="genotypes-content" + role="tabpanel" + aria-labelledby="genotypes-content-tab"> + <p>This allows you to upload the data that concerns your genotypes.</p> + <p>Any samples/individuals/cases/strains that do not already exist in the + system will be added. This does not delete any existing data.</p> + <a href="{{url_for('species.populations.genotypes.list_genotypes', + species_id=species.SpeciesId, + population_id=population.Id)}}" + title="Upload genotype information for the '{{population.FullName}}' population of the '{{species.FullName}}' species." + class="btn btn-primary">upload genotypes</a> + </div> + <div class="tab-pane fade" id="expression-data-content" role="tabpanel" aria-labelledby="expression-data-content-tab"> + <p>Upload expression data (mRNA data) for this population.</p> + <a href="#" title="" class="btn btn-primary">upload genotypes</a> + </div> + </div> +</div> +{%endblock%} + +{%block sidebarcontents%} +<div class="row"> + <p>Each tab presents a feature that's available at the population level. + Select the tab that allows you to continue with your task.</p> +</div> +{{display_sui_population_card(species, population)}} +{%endblock%} + + diff --git a/uploader/templates/populations/view-population.html b/uploader/templates/populations/view-population.html index b23caeb..3b9661b 100644 --- a/uploader/templates/populations/view-population.html +++ b/uploader/templates/populations/view-population.html @@ -42,8 +42,10 @@ <dt>Family</dt> <dd>{{population.Family}}</dd> - <dt>Description</dt> - <dd><pre>{{population.Description or "-"}}</pre></dd> + <dt>Information</dt> + <dd><a href="https://info.genenetwork.org/species/source.php?SpeciesName={{species.Name}}&InbredSetName={{population.Name}}" + title="Link to detailed information on this population." + target="_blank">Population Information</a></dd> </dl> </div> |