diff options
| -rw-r--r-- | uploader/population/views.py | 21 | ||||
| -rw-r--r-- | uploader/templates/populations/macro-display-population-card.html | 39 | ||||
| -rw-r--r-- | uploader/templates/populations/sui-base.html | 13 | ||||
| -rw-r--r-- | uploader/templates/populations/sui-view-population.html | 122 | ||||
| -rw-r--r-- | uploader/templates/species/macro-display-species-card.html | 40 |
5 files changed, 212 insertions, 23 deletions
diff --git a/uploader/population/views.py b/uploader/population/views.py index 87a33d9..cfc3b70 100644 --- a/uploader/population/views.py +++ b/uploader/population/views.py @@ -19,6 +19,7 @@ from uploader.authorisation import require_login from uploader.genotypes.views import genotypesbp from uploader.datautils import enumerate_sequence from uploader.phenotypes.views import phenotypesbp +from uploader.phenotypes.models import datasets_by_population from uploader.expression_data.views import exprdatabp from uploader.species.models import all_species, species_by_id from uploader.monadic_requests import make_either_error_handler @@ -193,10 +194,15 @@ def create_population(species_id: int): @require_login def view_population(species_id: int, population_id: int): """View the details of a population.""" + streamlined_ui = request.args.get("streamlined_ui") with database_connection(app.config["SQL_URI"]) as conn: species = species_by_id(conn, species_id) population = population_by_species_and_id(conn, species_id, population_id) + datasets = datasets_by_population(conn, species_id, population_id) error = False + if len(datasets) > 1: + error = True + flash("Got more than one dataset for the population.", "alert alert-danger") if not bool(species): flash("You must select a species.", "alert-danger") @@ -207,9 +213,18 @@ def view_population(species_id: int, population_id: int): error = True if error: - return redirect(url_for("species.populations.index")) + return redirect(url_for(("species.view_species" + if bool(streamlined_ui) + else "species.populations.index"), + species_id=species["SpeciesId"], + streamlined_ui=streamlined_ui)) - return render_template("populations/view-population.html", + return render_template(("populations/sui-view-population.html" + if bool(streamlined_ui) + else "populations/view-population.html"), species=species, population=population, - activelink="view-population") + **({"dataset": datasets[0]} if len(datasets) == 1 else {}), + activelink="view-population", + streamlined_ui=streamlined_ui, + view_under_construction=request.args.get("view_under_construction", False)) diff --git a/uploader/templates/populations/macro-display-population-card.html b/uploader/templates/populations/macro-display-population-card.html index 16b477f..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)}} @@ -39,3 +39,40 @@ </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/sui-base.html b/uploader/templates/populations/sui-base.html new file mode 100644 index 0000000..88d3f54 --- /dev/null +++ b/uploader/templates/populations/sui-base.html @@ -0,0 +1,13 @@ +{%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'], + streamlined_ui=streamlined_ui)}}"> + {{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..a9f506a --- /dev/null +++ b/uploader/templates/populations/sui-view-population.html @@ -0,0 +1,122 @@ +{%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>{{step_indicator("3")}} Choose population action</h2> + + <p>The tabs below present the actions/features available under a population. + Do have a look at each to decide your next option.</p> +</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="myTabContent"> + <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, + streamlined_ui=streamlined_ui)}}" + 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>This will allow you to upload new phenotypes intended for publication + (or already published) to the system.</p> + <p>The new phenotypes will be grouped under the + "<em>{{population.FullName}} ({{population.Name}})</em>" population of + the "<em>{{species.FullName}} ({{species.Name}})</em>" species, as + selected in previous steps.</p> + <p>Please click the button below to proceed.</p> + <a href="{{url_for('species.populations.phenotypes.view_dataset', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + streamlined_ui=streamlined_ui)}}" + title="Upload phenotype data for population '{{population['Name']}}'" + class="btn btn-primary">Upload Phenotypes</a> + </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, + streamlined_ui=streamlined_ui)}}" + 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_sui_population_card(species, population)}} +{%endblock%} + + diff --git a/uploader/templates/species/macro-display-species-card.html b/uploader/templates/species/macro-display-species-card.html index d7c4082..30c564f 100644 --- a/uploader/templates/species/macro-display-species-card.html +++ b/uploader/templates/species/macro-display-species-card.html @@ -24,25 +24,27 @@ {%macro display_sui_species_card(species)%} <div class="row"> - <table> - <caption>Selected Species</caption> - <tr> - <th>Name</th> - <td>{{species["Name"] | title}}</td> - </tr> - <tr> - <th>Scientific</th> - <td>{{species["FullName"]}}</td> - </tr> - {%if species["TaxonomyId"]%} - <tr> - <th>Taxonomy ID</th> - <td> - <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id={{species.TaxonomyId}}" - title="NCBI's Taxonomy Browser page for {{species.Name}}"> - {{species.TaxonomyId}}</a> - </td> - </tr> + <table class="table"> + <caption>Current Species</caption> + <tbody> + <tr> + <th>Name</th> + <td>{{species["Name"] | title}}</td> + </tr> + <tr> + <th>Scientific</th> + <td>{{species["FullName"]}}</td> + </tr> + {%if species["TaxonomyId"]%} + <tr> + <th>Taxonomy ID</th> + <td> + <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id={{species.TaxonomyId}}" + title="NCBI's Taxonomy Browser page for {{species.Name}}"> + {{species.TaxonomyId}}</a> + </td> + </tr> + </tbody> {%endif%} </table> </div> |