diff options
Diffstat (limited to 'uploader')
| -rw-r--r-- | uploader/species/views.py | 25 | ||||
| -rw-r--r-- | uploader/static/js/populations.js | 2 | ||||
| -rw-r--r-- | uploader/templates/species/macro-display-species-card.html | 27 | ||||
| -rw-r--r-- | uploader/templates/species/sui-base.html | 10 | ||||
| -rw-r--r-- | uploader/templates/species/sui-view-species.html | 91 |
5 files changed, 150 insertions, 5 deletions
diff --git a/uploader/species/views.py b/uploader/species/views.py index cea2f68..a490b0f 100644 --- a/uploader/species/views.py +++ b/uploader/species/views.py @@ -15,6 +15,8 @@ from uploader.ui import make_template_renderer from uploader.oauth2.client import oauth2_get, oauth2_post from uploader.authorisation import require_login, require_token from uploader.datautils import order_by_family, enumerate_sequence +from uploader.population.models import (populations_by_species, + population_by_species_and_id) from .models import (all_species, save_species, @@ -41,15 +43,30 @@ def list_species(): @require_login def view_species(species_id: int): """View details of a particular species and menus to act upon it.""" + streamlined_ui = request.args.get("streamlined_ui") with database_connection(app.config["SQL_URI"]) as conn: species = species_by_id(conn, species_id) if bool(species): - return render_template("species/view-species.html", - species=species, - activelink="view-species") + population = population_by_species_and_id( + conn, species_id, request.args.get("population_id")) + if bool(population): + return redirect(url_for("species.populations.view_population", + species_id=species_id, + population_id=population["Id"], + streamlined_ui=streamlined_ui)) + return render_template( + ("species/sui-view-species.html" + if bool(streamlined_ui) + else "species/view-species.html"), + species=species, + activelink="view-species", + streamlined_ui=streamlined_ui, + populations=populations_by_species(conn, species["SpeciesId"])) flash("Could not find a species with the given identifier.", "alert-danger") - return redirect(url_for("species.view_species")) + return redirect(url_for( + ("base.index" if streamlined_ui else "species.view_species"), + streamlined_ui=streamlined_ui)) @speciesbp.route("/create", methods=["GET", "POST"]) @require_login diff --git a/uploader/static/js/populations.js b/uploader/static/js/populations.js index 89ededa..111ebb7 100644 --- a/uploader/static/js/populations.js +++ b/uploader/static/js/populations.js @@ -22,7 +22,7 @@ $(() => { { select: "single", paging: true, - scrollY: 700, + scrollY: 500, deferRender: true, scroller: true, scrollCollapse: true, diff --git a/uploader/templates/species/macro-display-species-card.html b/uploader/templates/species/macro-display-species-card.html index 166c7b9..d7c4082 100644 --- a/uploader/templates/species/macro-display-species-card.html +++ b/uploader/templates/species/macro-display-species-card.html @@ -20,3 +20,30 @@ </div> </div> {%endmacro%} + + +{%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> + {%endif%} + </table> +</div> +{%endmacro%} diff --git a/uploader/templates/species/sui-base.html b/uploader/templates/species/sui-base.html new file mode 100644 index 0000000..5d2e6e3 --- /dev/null +++ b/uploader/templates/species/sui-base.html @@ -0,0 +1,10 @@ +{%extends "sui-base.html"%} + +{%block breadcrumbs%} +{{super()}} +<li class="breadcrumb-item"> + <a href="{{url_for('species.view_species', species_id=species['SpeciesId'], streamlined_ui=streamlined_ui)}}"> + {{species["Name"]|title}} + </a> +</li> +{%endblock%} diff --git a/uploader/templates/species/sui-view-species.html b/uploader/templates/species/sui-view-species.html new file mode 100644 index 0000000..5373766 --- /dev/null +++ b/uploader/templates/species/sui-view-species.html @@ -0,0 +1,91 @@ +{%extends "species/sui-base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "macro-step-indicator.html" import step_indicator%} +{%from "species/macro-display-species-card.html" import display_sui_species_card%} + +{%block title%}View Species{%endblock%} + + +{%block contents%} +<div class="row"> + <h2>{{step_indicator("2(a)")}} Select the Population</h2> + + <p>Data belonging to a particular species is further divided into one or more + populations for easier handling. Please select the population you want to work + with.</p> + + <form method="GET" + action="{{url_for('species.view_species', species_id=species.SpeciesId)}}" + class="form-horizontal"> + <input type="hidden" name="streamlined_ui" value="{{streamlined_ui}}" /> + {%if populations | length != 0%} + + <p class="form-text">Search for, and select the population from the table + below.</p> + + <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> + + {%else%} + <p class="form-text"> + There are no populations currently defined for {{species['FullName']}} + ({{species['SpeciesName']}}).</p> + {%endif%} + + <div class="row form-buttons"> + <div class="col"> + <input type="submit" + value="use selected population" + class="btn btn-primary" /> + </div> + + <div class="col"><strong>OR</strong></div> + + <div class="col"> + <a href="url_for('species.population.create_population', + species_id=species.SpeciesId, + return_to='species.view_species', + streamlined_ui=streamlined_ui)" + title="Create a new population for species '{{species.Name}}'." + class="btn btn-outline-info"> + Create a new population + </a> + </div> + </div> + + </form> +</div> + +<div class="row"> </div> + +<div class="row"> + <h2>{{step_indicator("2(b)")}} Manage sequencing platforms</h2> + <p>Upload and manage the sequencing platforms for species + '{{species.Name | title}} ({{species.FullName}})' + <a href="{{url_for('species.platforms.list_platforms', + species_id=species.SpeciesId, + streamlined_ui=streamlined_ui)}}" + title="Manage sequencing platforms for {{species.Name}}">here</a>. + </p> +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_sui_species_card(species)}} +{%endblock%} + + +{%block javascript%} +<script type="text/javascript" src="/static/js/populations.js"></script> +{%endblock%} |