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diff --git a/gn2/wqflask/templates/index_page.html b/gn2/wqflask/templates/index_page.html new file mode 100755 index 00000000..7b5a1d16 --- /dev/null +++ b/gn2/wqflask/templates/index_page.html @@ -0,0 +1,397 @@ +{% extends "base.html" %} +{% block title %}GeneNetwork{% endblock %} +{% block css %} +<!-- UIkit CSS --> +<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/uikit@3.7.4/dist/css/uikit.min.css" /> +<link rel="stylesheet" href="/static/new/css/index_page.css" /> +<link rel="stylesheet" href="/static/new/css/autocomplete.css"/> + +<!-- UIkit JS --> +<script src="https://cdn.jsdelivr.net/npm/uikit@3.7.4/dist/js/uikit.min.js"></script> +<script src="https://cdn.jsdelivr.net/npm/uikit@3.7.4/dist/js/uikit-icons.min.js"></script> +<script type="module" src="https://esm.sh/emfed"></script> +<link rel="stylesheet" type="text/css" + href="https://cdn.jsdelivr.net/gh/sampsyo/emfed@1/toots.css"> + +<style TYPE="text/css"> + p.interact { display: none; } + + + .media { + padding-bottom:10px; + border-bottom: 1px solid #c8ccc9; + } + + .media img { + + width: 95%; + height: 100%; + border-radius: 5px; + /*transform: scale(1.1); image small?*/ + border:1px solid #c8ccc9; + } + + .toots { + margin:0 auto; + max-width: 500px; + height: 160px; + position: relative; + border-radius:10px; + background-color: #F9F9F9; + + } + + h2 { + margin-bottom: 0px; + } + + ul { + margin-top: 0px; + } + + .toot { + padding-top:8px; + background:#f9f9f9; + color:#000; + + } +</style> +{% endblock %} +{% block content %} +<!-- Start of body --> + <div class="container-fluid" style="min-width: 1210px;"> + + {{ flash_me() }} + + {%if anon_collections | length > 0%} + <div class="panel panel-warning"> + <div class="panel-heading"> + <h3 class="panel-title">Import Anonymous Collections</h3> + </div> + <div class="panel-body"> + <p> + There {%if anon_collections | length > 1%}are{%else%}is{%endif%} + {{anon_collections | length}} anonymous + collection{%if anon_collections | length > 1%}s{%endif%} + associated with your current session. What do you wish to do? + </p> + <p class="text-danger" style="font-weight: bold;"> + <small> + If you choose to ignore this, the anonymous collections will be + eventually deleted and lost. + </small> + </p> + <form action="{{url_for('handle_anonymous_collections')}}" + method="POST"> + <div class="form-group"> + <input type="radio" id="rdo-import" value="import" + name="anon_choice" /> + <label for="rdo-import">Import</label> + <input type="radio" id="rdo-delete" value="delete" + name="anon_choice" /> + <label for="rdo-delete">Delete</label> + </div> + + <input type="submit" class="btn btn-warning" value="Submit" /> + </form> + </div> + </div> + {%endif%} + + <div class="row" style="width: 100%;"> + + <div class="col-xs-4" style="margin-right:50px; min-width: 530px; max-width: 550px;"> + <section id="search"> + <div class="page-header"> + <h2>Select and Search</h2> + </div> + <form method="get" action="/search" target="_blank" id="searchform" name="SEARCHFORM", + data-gn_server_url="{{gn_server_url}}"> + <fieldset> + <div style="padding-left: 20px; padding-right: 20px;" class="form-horizontal"> + + <div class="form-group"> + <label for="species" class="col-xs-1 control-label" style="width: 65px !important;">Species:</label> + <div class="col-xs-10 controls input-append" style="display: flex; padding-left: 20px;"> + <div class="col-9"> + <select name="species" id="species" class="form-control" style="width: 340px !important;"><option>Loading...</option></select> + </div> + </div> + </div> + + <div class="form-group"> + <label for="group" class="col-xs-1 control-label" style="width: 65px !important;">Group:</label> + <div class="col-xs-10 controls input-append" style="display: flex; padding-left: 20px;"> + <div class="col-9"> + <select name="group" id="group" class="form-control" style="width: 340px !important;"><option>Loading...</option></select> + <i class="icon-question-sign"></i> + </div> + <div class="col-3" style="margin-left: 10px;"> + <button type="button" id="group_info" class="btn form-control info-button"><span class="glyphicon glyphicon-flag"></span> Info</button> + </div> + </div> + </div> + + <div class="form-group"> + <label for="tissue" class="col-xs-1 control-label" style="width: 65px !important;">Type:</label> + <div class="col-xs-10 controls input-append" style="display: flex; padding-left: 20px;"> + <div class="col-9"> + <select name="type" id="type" class="form-control" style="width: 340px !important;"><option>Loading...</option></select> + </div> + <div class="col-3" style="margin-left: 10px;"> + <button type="button" id="dataset_info" class="btn form-control info-button"><span class="glyphicon glyphicon-flag"></span> Info</button> + </div> + </div> + </div> + + <div class="form-group"> + <label for="dataset" class="col-xs-1 control-label" style="width: 65px !important;">Dataset:</label> + <div class="col-xs-10 controls" style="display: flex; padding-left: 20px;"> + <div class="col-9"> + <select name="dataset" id="dataset" class="form-control" style="max-width: 550px; width: 450px !important;"><option>Loading...</option></select> + <i class="icon-question-sign"></i> + </div> + </div> + </div> + <!-- GET ANY SEARCH --> + + <div class="form-group"> + <label for="or_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Get Any:</label> + <div class="col-xs-10 controls" style="padding-left: 20px;"> + <div class="col-8 autocomplete"> + <textarea id="myInput" onkeyup="pressed(event)" name="search_terms_or" rows="1" class="form-control search-query" style="resize: vertical; max-width: 550px; width: 450px !important;" id="or_search"></textarea> + </div> + </div> + </div> + + <!-- GET ANY HELP --> + <div class="form-group"> + <label for="btsearch" class="col-xs-1 control-label" style="width: 65px !important;"></label> + <div class="col-xs-10 controls" style="padding-left: 20px;"> + <div class="col-12 controls"> + Enter terms, genes, ID numbers in the <b>Search</b> field.<br> + Use <b>*</b> or <b>?</b> wildcards (Cyp*a?, synap*).<br> + Use <b>quotes</b> for terms such as <i>"tyrosine kinase"</i>. + + + <div><strong><a style="text-decoration: none;" href="https://issues.genenetwork.org/topics/xapian-search-queries" target=”_blank” >see more hints</a></strong></div> + </div> + </div> + </div> + + <div class="form-group"> + <label for="and_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Combined:</label> + <div class="col-xs-10 controls" style="padding-left: 20px;"> + <div class="col-8 autocomplete"> + <textarea id="myInput" onkeyup="pressed(event)" name="search_terms_and" rows="1" class="form-control search-query" style="resize: vertical; max-width: 550px; width: 450px !important;" id="and_search"></textarea> + </div> + </div> + </div> + + <div class="form-group"> + <label for="btsearch" class="col-xs-1 control-label" style="width: 65px !important;"></label> + <div class="col-xs-10 controls" style="display: flex; padding-left: 20px;"> + <div class="col-2 controls"> + <button id="btsearch" class="btn btn-primary form-control"><span class="glyphicon glyphicon-search"></span> Search</button> + </div> + <div class="col-2 align-self-end controls" style="padding-left: 20px;"> + <button type="button" id="make_default" class="btn form-control info-button"><span class="glyphicon glyphicon-pushpin"></span> Lock Menu</button> + </div> + </div> + </div> + + <!-- SEARCH, MAKE DEFAULT --> + <div class="form-group"> + </div> + + <input type="hidden" name="FormID" value="searchResult" class="form-control"> + </div> + </fieldset> + </form> + </section> + <section id="advanced"> + <div class="page-header"> + <h2>Advanced Commands</h2> + </div> + + <p>You can also use advanced commands. Copy these simple examples into the Get Any field for single term searches and Combined for searches with multiple terms:</p> + + <ul> + <li><b>POSITION=(chr1 25 30)</b> finds genes, markers, or transcripts on + chromosome 1 between 25 and 30 Mb.</li> + + <li><b>MEAN=(15 16)</b> in the <b>Combined</b> field finds + highly expressed genes (15 to 16 log2 units)</li> + + <li><b>RANGE=(1.5 2.5)</b> in the <b>Any</b> field finds traits with values with a specified fold-range (minimum = 1). + Useful for finding "housekeeping genes" <b>(1.0 1.2)</b> or highly variable molecular assays <b>(10 100)</b>.</li> + + <li><b>LRS=(15 1000)</b> or <b>LOD=(2 8)</b> finds all traits with peak LRS or LOD scores between lower and upper limits.</li> + + <li><b>LRS=(9 999 Chr4 122 155)</b> finds all traits on Chr 4 from 122 and 155 Mb with LRS scores between 9 and 999.</li> + + <li><b>cisLRS=(15 1000 5)</b> or <b>cisLOD=(2 8 5)</b> finds all cis eQTLs with peak LRS or LOD scores between lower and upper limits, + with an <b>inclusion</b> zone of 5 Mb around the parent gene.</li> + + <li><b>transLRS=(15 1000 5)</b> or <b>transLOD=(2 8 5)</b> finds all trans eQTLs with peak LRS or LOD scores between lower and upper limits, + with an <b>exclusion</b> zone of 5 Mb around the parent gene. You can also add a fourth term specifying which chromosome you want the transLRS to be on + (for example transLRS=(15 1000 5 7) would find all trans eQTLs with peak LRS on chromosome 7 that is also a trans eQTL with exclusionary zone of 5Mb).</li> + + <li><b>POSITION=(Chr4 122 130) cisLRS=(9 999 10)</b> + finds all traits on Chr 4 from 122 and 155 Mb with cisLRS scores + between 9 and 999 and an inclusion zone of 10 Mb.</li> + + <li><b>RIF=mitochondrial</b> searches RNA databases for <a href="https://en.wikipedia.org/wiki/GeneRIF"> + GeneRIF</a> links.</li> + + <li><b>WIKI=nicotine</b> searches <a href="http://gn1.genenetwork.org/webqtl/main.py?FormID=geneWiki"> + GeneWiki</a> for genes that you or other users have annotated + with the word <i>nicotine</i>.</li> + + <li><b>GO:0045202</b> searches for synapse-associated genes listed in the + <a href="http://amigo.geneontology.org/amigo/medial_search?q=GO%3A0045202"> + Gene Ontology</a>.</li> + + <li><b>RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)</b> + finds diabetes-associated transcripts with peak <a href="{{ url_for('glossary_blueprint.glossary') }}#E"> + trans eQTLs</a> on Chr 2 between 100 and 105 Mb with LRS + scores between 9 and 999.</li> + </ul> + </section> + </div> + + <div class="col-xs-4" style="width: 600px !important;"> + <section id="tutorials"> + <div class="page-header"> + <h2>Tutorials</h2> + </div> + <div class="uk-grid-match uk-child-width-1-3@m" uk-grid> + <div> + <strong><a class="uk-link-text" href="/tutorials">Webinars & Courses</a></strong><br> + In-person courses, live webinars and webinar recordings<br> + <a href="/tutorials" class="uk-icon-link" uk-icon="laptop" ratio="2"></a> + </div> + <div> + <strong><a class="uk-link-text" href="/tutorials">Tutorials</a></strong><br> + Tutorials: Training materials in HTML, PDF and video formats<br> + <a href="/tutorials" class="uk-icon-link" uk-icon="file-text" ratio="2"></a> + </div> + <div> + <strong><a class="uk-link-text" href="/tutorials">Documentation</a></strong><br> + Online manuals, handbooks, fact sheets and FAQs<br> + <a href="/tutorials" class="uk-icon-link" uk-icon="album" ratio="2"></a> + </div> + </div> + </section> + <section id="news-section"> + <div class="page-header"> + <h2>News</h2> + </div> + <div id="mastadon" style="height: 405px; overflow: scroll; overflow-x: hidden;"> + <a class="mastodon-feed" target="_blank" + href="https://genomic.social/@genenetwork" + data-toot-limit="5" + >Genenetwork mastadon</a> + + </div> + <div align="right"> + + <a href="https://genomic.social/@genenetwork">more news items...</a> + </div> + </section> + <section id="websites"> + <div class="page-header"> + <h2>Links</h2> + </div> + <ul> + <li>Github</li> + <ul> + <li><a href="https://github.com/genenetwork/genenetwork2">GN2 Source Code</a></li> + <li><a href="https://github.com/genenetwork/genenetwork3">GN3 Source Code</a></li> + <li><a href="https://github.com/genenetwork/genenetwork">GN1 Source Code</a></li> + <li><a href="https://github.com/genenetwork/sysmaintenance">System Maintenance Code</a></li> + </ul> + </ul> + <ul> + <li>GeneNetwork v2</li> + <ul> + <li><a href="https://genenetwork.org/">Main website</a> at UTHSC</li> + </ul> + </ul> + <ul> + <li>GeneNetwork v1</li> + <ul> + <li><a href="http://gn1.genenetwork.org/">Main website</a> at UTHSC</li> + </ul> + </ul> + <ul> + <li>Affiliates</li> + <ul> + <li><b><a href="http://gn1.genenetwork.org">GeneNetwork 1</a> at UTHSC</b></li> + <li><a href="https://systems-genetics.org/">Systems Genetics</a> at EPFL</li> + <li><a href="http://bnw.genenetwork.org/">Bayesian Network Web Server</a> at UTHSC</li> + <li><a href="https://www.geneweaver.org/">GeneWeaver</a></li> + <li><a href="https://phenogen.org/">PhenoGen</a> at University of Colorado</li> + <li><a href="http://www.webgestalt.org/">WebGestalt</a> at Baylor</li> + </ul> + </ul> + <ul> + <li>GeneNetwork hosted portals</li> + <ul> + <li><a href="https://www.opar.io/">Omics Portal For Addiction Research</a></li> + <li><a href="https://msk.genenetwork.org/">GN4MSK musculoskeletal</a></li> + <li><a href="https://genecup.org/">GeneCup: Mining PubMed for Gene Relationships using Custom Ontologies</a></li> + </ul> + </ul> + </section> + </div> + </div> + </div> + +{%endblock%} + +{% block js %} + + <script src="/static/new/javascript/dataset_select_menu_orig.js"></script> + + + <script type="text/javascript"> + +$(document).on('submit', '#searchform', function(event){ + + event.preventDefault() + let user_searches = []; + $(".search-query").each(function() { + this_search = $(this).val().trim(); + if (this_search != ""){ + user_searches.push(this_search); + } + }); + + for (i=0; i<user_searches.length; ++i){ + saveBeforeSubmit(user_searches[i]) + } + $( "#searchform" )[0].submit(); + +}); + </script> + + <script> + function pressed(e) { + // Has the enter key been pressed? + if ( (window.event ? event.keyCode : e.which) == 13) { + e.preventDefault(); + // If enter key has been pressed and the search fields are non-empty + // manually submit the <form> + + if( event.target.value.trim() != "" ) { + saveBeforeSubmit(event.target.value.trim()) + $("#searchform")[0].submit(); + + } + + } + } + + </script> +{% endblock %} |