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diff --git a/uploader/templates/index.html b/uploader/templates/index.html index aa1414e..6e9c777 100644 --- a/uploader/templates/index.html +++ b/uploader/templates/index.html @@ -1,107 +1,170 @@ {%extends "base.html"%} {%from "flash_messages.html" import flash_all_messages%} +{%from "macro-forms.html" import add_http_feature_flags%} {%block title%}Home{%endblock%} {%block pagetitle%}Home{%endblock%} -{%block contents%} - -<div class="row"> - {{flash_all_messages()}} - <div class="explainer"> - <p>Welcome to the <strong>GeneNetwork Data Upload and Quality Control - System</strong>.</p> - <p>This tool helps you prepare and upload research data to GeneNetwork for - analysis.</p> - - <h2 class="heading">Getting Started</h2> - <p>The sections below explain the features of the system. Review this guide - to learn how to use the system.</p> - - {%block extrapageinfo%}{%endblock%} - - <h3 class="subheading">Species</h3> - - <p>GeneNetwork supports genetic studies across multiple species (e.g. mice - [Mus musculus], human [homo sapiens], rats [Rattus norvegicus], etc.) . - Here you can:</p> - <ul> - <li>View all species that are currently supported</li> - <li>Add new species not yet in the system</li> - </ul> - - <h3 class="subheading">Populations</h3> - - <p>A "population" refers to a specific subgroup within a species that you’re - studying (e.g., BXD mice). Here you can:</p> - <ul> - <li>View the populations that exist for a selected species</li> - <li>Add new populations of study for a selected species</li> - </ul> - - <h3 class="subheading">Samples</h3> +{%block extra_breadcrumbs%}{%endblock%} - <p>Manage individual specimens or cases used in your experiments. These - include:</p> - - <ul> - <li>Experimental subjects</li> - <li>Data sources (e.g., tissue samples, clinical cases)</li> - <li>Strain means (instead of entering multiple BXD1 individuals, for - example, the mean would be entered for a single BXD1 strain)</li> - </ul> - - - <h3 class="subheading">Genotype Data</h3> - - <p>Upload and review genetic markers and allele encodings for your - population. Key details:</p> +{%block contents%} - <ul> - <li>Markers are species-level (e.g., mouse SNP databases).</li> - <li>Allele data is population-specific (tied to your experimental - samples).</li> - </ul> +{%macro add_form_buttons()%} +<div class="row form-buttons"> + <div class="col"> + <input type="submit" + class="btn btn-primary" + value="use selected species" /> + </div> + <div class="col"> + <a href="{{url_for('species.create_species', return_to='base.index')}}" + class="btn btn-outline-primary" + title="Add a new species to Genenetwork.">add a new Species</a> + </div> +</div> +{%endmacro%} - <p><strong>Requirement</strong>: Samples must already have been registered - in the system before uploading genotype data.</p> +<div class="row">{{flash_all_messages()}}</div> - <h3 class="subheading">Phenotype Data</h3> +{%if user_logged_in()%} - <p>Phenotypes are the visible traits or features of a living thing. For - example, phenotypes include:</p> +<div class="row"> + <ul class="nav nav-tabs" id="index-actions"> + <li class="nav-item presentation"> + <button class="nav-link active" + id="upload-data-tab" + data-bs-toggle="tab" + data-bs-target="#upload-data-content" + type="button" + role="tab" + aria-controls="upload-data-content" + aria-selected="false">Upload Data</button></li> + <li class="nav-item presentation"> + <button class="nav-link" + id="publications-tab" + data-bs-toggle="tab" + data-bs-target="#publications-content" + type="button" + role="tab" + aria-controls="publications-content" + aria-selected="true">Publications</button></li> + </ul> +</div> - <ul> - <li>Weight</li> - <li>Height</li> - <li>Color (such as the color of fur or eyes)</li> - </ul> +<div class="row"> + <div class="tab-content" id="upload-data-tabs-content"> + <div class="tab-pane fade show active" + id="upload-data-content" + role="tabpanel" + aria-labelledby="upload-data-content-tab"> + <h2 class="heading">Species</h2> + + <p>Select the species you want to work with.</p> + + <form method="GET" action="{{url_for('base.index')}}" class="form-horizontal"> + {{add_http_feature_flags()}} + + {{add_form_buttons()}} + + {%if species | length != 0%} + <div style="margin-top:1em;"> + <table id="tbl-select-species" class="table compact stripe" + data-species-list='{{species | tojson}}'> + <thead> + <tr> + <th></th> + <th>Species Name</th> + </tr> + </thead> + + <tbody></tbody> + </table> + </div> + + {%else%} + + <label class="control-label" for="rdo-cant-find-species"> + <input id="rdo-cant-find-species" type="radio" name="species_id" + value="CREATE-SPECIES" /> + There are no species to select from. Create the first one.</label> + + <div class="col-sm-offset-10 col-sm-2"> + <input type="submit" + class="btn btn-primary col-sm-offset-1" + value="continue" /> + </div> + + {%endif%} + + {{add_form_buttons()}} + + </form> + </div> + + <div class="tab-pane fade" + id="publications-content" + role="tabpanel" + aria-labelledby="publications-content-tab"> + <p>You can view, edit, and delete existing publications, as well as add + new ones, by clicking the button below.</p> + + <a href="{{url_for('publications.index')}}" + title="Manage publications." + class="btn btn-primary">manage publications</a> + </div> + </div> +</div> - <p>This part of the system will allow you to upload and manage the values - for different phenotypes from various samples in your studies.</p> +{%else%} - <!-- +<div class="row"> + <img src="/static/images/frontpage_banner.png" + alt="Banner image showing the process flow a user would follow." /> +</div> - <h3 class="subheading">Expression Data</h3> +<div class="row"> + <p>The GeneNetwork Uploader (gn-uploader) lets you easily add new data to the + GeneNetwork System. It automatically checks your data for quality and walks + you through fixing any issues before submission.</p> +</div> - <p class="text-danger"> - <span class="glyphicon glyphicon-exclamation-sign"></span> - <strong>TODO</strong>: Document this …</p> +<div class="row"> + <div class="col"> + <a href="{{authserver_authorise_uri()}}" + title="Sign in to the system" + class="btn btn-primary">Sign in</a> + </div> +</div> +{%endif%} - <h3 class="subheading">Individual Data</h3> +{%endblock%} - <p class="text-danger"> - <span class="glyphicon glyphicon-exclamation-sign"></span> - <strong>TODO</strong>: Document this …</p> - <h3 class="subheading">RNA-Seq Data</h3> - <p class="text-danger"> - <span class="glyphicon glyphicon-exclamation-sign"></span> - <strong>TODO</strong>: Document this …</p> - </div> - --> +{%block sidebarcontents%} +{%if view_under_construction%} +<div class="row"> + <p>The data in Genenetwork is related to one species or another. Use the form + provided to select from existing species, or click on the + "Create a New Species" button if you cannot find the species you want to + work with.</p> </div> +<div class="row"> + <form id="frm-quick-navigation"> + <legend>Quick Navigation</legend> + <div class="form-group"> + <label for="fqn-species-id">Species</label> + <select name="species_id"> + <option value="">Select species</option> + </select> + </div> + </form> +</div> +{%endif%} +{%endblock%} + +{%block javascript%} +<script type="text/javascript" src="/static/js/species.js"></script> {%endblock%} |