diff options
| -rw-r--r-- | uploader/phenotypes/__init__.py | 2 | ||||
| -rw-r--r-- | uploader/phenotypes/views.py | 25 | ||||
| -rw-r--r-- | uploader/population/views.py | 2 | ||||
| -rw-r--r-- | uploader/templates/base.html | 3 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/base.html | 12 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/index.html | 26 |
6 files changed, 68 insertions, 2 deletions
diff --git a/uploader/phenotypes/__init__.py b/uploader/phenotypes/__init__.py new file mode 100644 index 0000000..c17d32c --- /dev/null +++ b/uploader/phenotypes/__init__.py @@ -0,0 +1,2 @@ +"""Package for handling ('classical') phenotype data""" +from .views import phenotypesbp diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py new file mode 100644 index 0000000..862a224 --- /dev/null +++ b/uploader/phenotypes/views.py @@ -0,0 +1,25 @@ +"""Views handling ('classical') phenotypes.""" +from flask import request, Blueprint, render_template, current_app as app + +from uploader.datautils import order_by_family +from uploader.authorisation import require_login +from uploader.db_utils import database_connection +from uploader.species.models import all_species, species_by_id + +phenotypesbp = Blueprint("phenotypes", __name__) + +@phenotypesbp.route("/phenotypes", methods=["GET"]) +@require_login +def index(): + """Direct entry-point for phenotypes data handling.""" + with database_connection(app.config["SQL_URI"]) as conn: + if not bool(request.args.get("species_id")): + return render_template("phenotypes/index.html", + species=order_by_family(all_species(conn)), + activelink="phenotypes") + + species = species_by_id(conn, request.args.get("species_id")) + if not bool(species): + flash("No such species!", "alert-danger") + return redirect(url_for("species.populations.phenotypes.index")) + return "Would lead you to go select population…" diff --git a/uploader/population/views.py b/uploader/population/views.py index 631f0be..23bf242 100644 --- a/uploader/population/views.py +++ b/uploader/population/views.py @@ -18,6 +18,7 @@ from uploader.oauth2.client import oauth2_post from uploader.ui import make_template_renderer from uploader.authorisation import require_login from uploader.genotypes.views import genotypesbp +from uploader.phenotypes.views import phenotypesbp from uploader.expression_data.views import exprdatabp from uploader.db_utils import database_connection from uploader.datautils import enumerate_sequence @@ -35,6 +36,7 @@ __active_link__ = "populations" popbp = Blueprint("populations", __name__) popbp.register_blueprint(samplesbp, url_prefix="/") popbp.register_blueprint(genotypesbp, url_prefix="/") +popbp.register_blueprint(phenotypesbp, url_prefix="/") popbp.register_blueprint(exprdatabp, url_prefix="/") render_template = make_template_renderer("populations") diff --git a/uploader/templates/base.html b/uploader/templates/base.html index b297669..019aa39 100644 --- a/uploader/templates/base.html +++ b/uploader/templates/base.html @@ -68,8 +68,7 @@ sections, etc. --> <li {%if activemenu=="phenotypes"%}class="activemenu"{%endif%}> - <a href="#" - class="not-implemented" + <a href="{{url_for('species.populations.phenotypes.index')}}" title="Upload phenotype data.">Phenotype Data</a></li> <li {%if activemenu=="expression-data"%}class="activemenu"{%endif%}> <a href="{{url_for('species.populations.expression-data.index')}}" diff --git a/uploader/templates/phenotypes/base.html b/uploader/templates/phenotypes/base.html new file mode 100644 index 0000000..3bc5dea --- /dev/null +++ b/uploader/templates/phenotypes/base.html @@ -0,0 +1,12 @@ +{%extends "populations/base.html"%} + +{%block lvl3_breadcrumbs%} +<li {%if activelink=="phenotypes"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.index')}}">Phenotypes</a> +</li> +{%block lvl4_breadcrumbs%}{%endblock%} +{%endblock%} diff --git a/uploader/templates/phenotypes/index.html b/uploader/templates/phenotypes/index.html new file mode 100644 index 0000000..0c691e6 --- /dev/null +++ b/uploader/templates/phenotypes/index.html @@ -0,0 +1,26 @@ +{%extends "phenotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-select-species.html" import select_species_form%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <p>This section deals with phenotypes that + <span class="text-warning"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + … what are the characteristics of these phenotypes? …</span></p> + <p>Select the species to begin the process of viewing/uploading data about + your phenotypes</p> +</div> + +<div class="row"> + {{select_species_form(url_for("species.populations.phenotypes.index"), + species)}} +</div> +{%endblock%} |