diff options
Diffstat (limited to 'uploader/templates/populations')
5 files changed, 201 insertions, 130 deletions
diff --git a/uploader/templates/populations/base.html b/uploader/templates/populations/base.html index 9db8083..24cacc2 100644 --- a/uploader/templates/populations/base.html +++ b/uploader/templates/populations/base.html @@ -1,18 +1,20 @@ {%extends "species/base.html"%} +{%from "populations/macro-display-population-card.html" import display_sui_population_card%} -{%block lvl2_breadcrumbs%} -<li {%if activelink=="populations"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> - {%if population is mapping%} +{%block breadcrumbs%} +{{super()}} +{%if population%} +<li class="breadcrumb-item"> <a href="{{url_for('species.populations.view_population', - species_id=species.SpeciesId, - population_id=population.Id)}}">{{population.Name}}</a> - {%else%} - <a href="{{url_for('species.populations.index')}}">Populations</a> - {%endif%} + species_id=species['SpeciesId'], + population_id=population['Id'])}}"> + {{population["Name"]}} + </a> </li> -{%block lvl3_breadcrumbs%}{%endblock%} +{%endif%} +{%endblock%} + + +{%block sidebarcontents%} +{{display_sui_population_card(species, population)}} {%endblock%} diff --git a/uploader/templates/populations/create-population.html b/uploader/templates/populations/create-population.html index c0c4f45..d5359f5 100644 --- a/uploader/templates/populations/create-population.html +++ b/uploader/templates/populations/create-population.html @@ -1,20 +1,16 @@ {%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%}> +{%block breadcrumbs%} +{{super()}} +<li class="breadcrumb-item"> <a href="{{url_for('species.populations.create_population', - species_id=species.SpeciesId)}}">create population</a> + species_id=species['SpeciesId'])}}"> + create population</a> </li> {%endblock%} @@ -154,24 +150,35 @@ {%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> @@ -252,7 +259,3 @@ </form> </div> {%endblock%} - -{%block sidebarcontents%} -{{display_species_card(species)}} -{%endblock%} diff --git a/uploader/templates/populations/list-populations.html b/uploader/templates/populations/list-populations.html index f780e94..a092e34 100644 --- a/uploader/templates/populations/list-populations.html +++ b/uploader/templates/populations/list-populations.html @@ -54,7 +54,7 @@ <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 16b477f..f3040ea 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)}} @@ -39,3 +39,41 @@ </div> </div> {%endmacro%} + + +{%macro display_sui_population_card(species, population)%} +{{display_sui_species_card(species)}} +{%if population%} +<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> +{%endif%} +{%endmacro%} diff --git a/uploader/templates/populations/view-population.html b/uploader/templates/populations/view-population.html index b23caeb..ac89bc7 100644 --- a/uploader/templates/populations/view-population.html +++ b/uploader/templates/populations/view-population.html @@ -1,102 +1,127 @@ {%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%}Populations{%endblock%} - -{%block pagetitle%}Populations{%endblock%} - -{%block lvl3_breadcrumbs%} -<li {%if activelink=="view-population"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> - <a href="{{url_for('species.populations.view_population', - species_id=species.SpeciesId, - population_id=population.InbredSetId)}}">view</a> -</li> -{%endblock%} - +{%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>Population Details</h2> - - {{flash_all_messages()}} - - <dl> - <dt>Name</dt> - <dd>{{population.Name}}</dd> - - <dt>FullName</dt> - <dd>{{population.FullName}}</dd> - - <dt>Code</dt> - <dd>{{population.InbredSetCode}}</dd> - - <dt>Genetic Type</dt> - <dd>{{population.GeneticType}}</dd> - - <dt>Family</dt> - <dd>{{population.Family}}</dd> - - <dt>Description</dt> - <dd><pre>{{population.Description or "-"}}</pre></dd> - </dl> + <h2 class="heading">{{population.FullName}} ({{population.Name}})</h2> </div> <div class="row"> - … maybe provide a way to organise populations in the same family here … + <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"> - <h3>Actions</h3> - - <p> - Click any of the following links to use this population in performing the - subsequent operations. - </p> - - <nav class="nav"> - <ul> - <li> - <a href="{{url_for('species.populations.samples.list_samples', - species_id=species.SpeciesId, - population_id=population.Id)}}" - title="Manage samples: Add new or delete existing."> - manage samples</a> - </li> - <li> - <a href="{{url_for('species.populations.genotypes.list_genotypes', - species_id=species.SpeciesId, - population_id=population.Id)}}" - title="Manage genotypes for {{species.FullName}}">Manage Genotypes</a> - </li> - <li> - <a href="{{url_for('species.populations.phenotypes.list_datasets', - species_id=species.SpeciesId, - population_id=population.Id)}}" - title="Manage phenotype data.">manage phenotype data</a> - </li> - <li> - <a href="#" title="Manage expression data" - class="not-implemented">manage expression data</a> - </li> - <li> - <a href="#" title="Manage individual data" - class="not-implemented">manage individual data</a> - </li> - <li> - <a href="#" title="Manage RNA-Seq data" - class="not-implemented">manage RNA-Seq data</a> - </li> - </ul> - </nav> + <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). + </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> + <a href="{{url_for('species.populations.samples.list_samples', + species_id=species.SpeciesId, + population_id=population.Id)}}" + title="View and upload samples for population '{{population['Name']}}'" + class="btn btn-primary">Manage Samples</a> + </div> + + <div class="tab-pane fade show active" + id="phenotypes-content" + role="tabpanel" + aria-labelledby="phenotypes-content-tab"> + + <div class="row" style="margin-top: 1em;"> + <h3> Phenotypes in Population "{{population.FullName}} ({{population.Name}})"</h3> + + <p>To view existing phenotype traits, or upload new ones, click the button below:</p> + + <div class="row"> + <div class="col"> + <a href="{{url_for( + 'species.populations.phenotypes.list_datasets', + species_id=species.SpeciesId, + population_id=population.Id)}}" + title="View and upload phenotype traits" + class="btn btn-primary">Phenotypes</a> + </div> + </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%} -{{display_species_card(species)}} +<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> +{{super()}} +{%endblock%} + + + + +{%block javascript%} {%endblock%} |