diff options
| -rw-r--r-- | uploader/base_routes.py | 5 | ||||
| -rw-r--r-- | uploader/templates/base.html | 4 | ||||
| -rw-r--r-- | uploader/templates/index.html | 80 | ||||
| -rw-r--r-- | uploader/templates/login.html | 2 |
4 files changed, 86 insertions, 5 deletions
diff --git a/uploader/base_routes.py b/uploader/base_routes.py index 88247b2..a20b7ff 100644 --- a/uploader/base_routes.py +++ b/uploader/base_routes.py @@ -1,5 +1,6 @@ """Basic routes required for all pages""" import os +from urllib.parse import urljoin from flask import ( Blueprint, @@ -23,7 +24,9 @@ def favicon(): @base.route("/", methods=["GET"]) def index(): """Load the landing page""" - return render_template("index.html" if user_logged_in() else "login.html") + return render_template("index.html" if user_logged_in() else "login.html", + gn2server_intro=urljoin(app.config["GN2_SERVER_URL"], + "/intro")) def appenv(): """Get app's guix environment path.""" diff --git a/uploader/templates/base.html b/uploader/templates/base.html index 3af14ef..886f503 100644 --- a/uploader/templates/base.html +++ b/uploader/templates/base.html @@ -48,10 +48,10 @@ title="View and manage species information.">Species</a></li> <li><a href="{{url_for('species.populations.index')}}" title="View and manage species populations.">Populations</a></li> - <li><a href="{{url_for('species.populations.genotypes.index')}}" - title="Upload Genotype data.">Genotype Data</a></li> <li><a href="{{url_for('species.populations.samples.index')}}" title="Upload population samples.">Samples</a></li> + <li><a href="{{url_for('species.populations.genotypes.index')}}" + title="Upload Genotype data.">Genotype Data</a></li> <li><a href="{{url_for('expression-data.index.index')}}" title="Upload expression data.">Expression Data</a></li> <li><a href="#" diff --git a/uploader/templates/index.html b/uploader/templates/index.html index e3f5af4..0fa4a1b 100644 --- a/uploader/templates/index.html +++ b/uploader/templates/index.html @@ -18,9 +18,87 @@ <div class="explainer"> <p>Welcome to the <strong>GeneNetwork Data Quality Control and Upload System</strong>. This system is provided to help in uploading your data onto GeneNetwork where you can do analysis on it.</p> - <p>Click on the menu items on the left to select the kind of data you want to upload.</p> + <p>The sections below provide an overview of what features the menu items on + the left provide to you. Please peruse the information to get a good + big-picture understanding of what the system provides you and how to get + the most out of it.</p> {%block extrapageinfo%}{%endblock%} + + <h2>Species</h2> + + <p>The GeneNetwork service provides datasets and tools for doing genetic + studies — from + <a href="{{gn2server_intro}}" + target="_blank" + title="GeneNetwork introduction — opens in a new tab."> + its introduction</a>: + + <blockquote class="blockquote"> + <p>GeneNetwork is a group of linked data sets and tools used to study + complex networks of genes, molecules, and higher order gene function + and phenotypes. …</p> + </blockquote> + </p> + + <p>With this in mind, it follows that the data in the system is centered + aroud a variety of species. The <strong>species section</strong> will + list the currently available species in the system, and give you the + ability to add new ones, if the one you want to work on does not currently + exist on GeneNetwork</p> + + <h2>Populations</h2> + + <p>Your studies will probably focus on a particular subset of the entire + species you are interested in &ndash your population.</p> + <p>Populations are a way to organise the species data so as to link data to + specific know populations for a particular species, e.g. The BXD + population of mice (Mus musculus)</p> + <p>In older GeneNetwork documentation, you might run into the term + <em>InbredSet</em>. Should you run into it, it is a term that we've + deprecated that essentially just means the population.</p> + + <h2>Samples</h2> + + <p>These are the samples or individuals (sometimes cases) that were involved + in the experiment, and from whom the data was derived.</p> + + <h2>Genotype Data</h2> + + <p>This section will allow you to view and upload the genetic markers for + your species, and the genotype encodings used for your particular + population.</p> + <p>While, technically, genetic markers relate to the species in general, and + not to a particular population, the data (allele information) itself + relates to the particular population it was generated from – + specifically, to the actual individuals used in the experiment.</p> + <p>This is the reason why the genotype data information comes under the + population, and will check for the prior existence of the related + samples/individuals before attempting an upload of your data.</p> + + <h2>Expression Data</h2> + + <p class="text-danger"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + <strong>TODO</strong>: Document this …</p> + + <h2>Phenotype Data</h2> + + <p class="text-danger"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + <strong>TODO</strong>: Document this …</p> + + <h2>Individual Data</h2> + + <p class="text-danger"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + <strong>TODO</strong>: Document this …</p> + + <h2>RNA-Seq Data</h2> + + <p class="text-danger"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + <strong>TODO</strong>: Document this …</p> </div> </div> diff --git a/uploader/templates/login.html b/uploader/templates/login.html index bbca42f..1f71416 100644 --- a/uploader/templates/login.html +++ b/uploader/templates/login.html @@ -5,7 +5,7 @@ {%block pagetitle%}log in{%endblock%} {%block extrapageinfo%} -<p> +<p class="text-dark text-primary"> You <strong>do need to be logged in</strong> to upload data onto this system. Please do that by clicking the "Log In" button at the top of the page.</p> {%endblock%} |