From 98293e5a4b68565bc0a26240d111f55c60907006 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 14 Mar 2016 15:49:13 +0000
Subject: Changed the way headers look across all pages

Changed the way details are displayed in show trait page

Changed search query so that it orders results by symbol
---
 wqflask/base/trait.py                              |  35 ------
 wqflask/wqflask/do_search.py                       |   4 +-
 .../wqflask/static/packages/bootstrap/css/docs.css |   4 +-
 wqflask/wqflask/templates/collections/view.html    |  12 +-
 wqflask/wqflask/templates/search_result_page.html  |  23 ++++
 wqflask/wqflask/templates/show_trait.html          |  37 ++++--
 wqflask/wqflask/templates/show_trait_details.html  | 133 +++++++++++----------
 7 files changed, 134 insertions(+), 114 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index eb9bc940..ff149ba3 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -221,32 +221,6 @@ class GeneralTrait(object):
         if samplelist == None:
             samplelist = []
 
-        #assert self.dataset
-
-        #if self.cellid:
-        #     #Probe Data
-        #    query = '''
-        #            SELECT
-        #                    Strain.Name, ProbeData.value, ProbeSE.error, ProbeData.Id
-        #            FROM
-        #                    (ProbeData, ProbeFreeze, ProbeSetFreeze, ProbeXRef,
-        #                    Strain, Probe, ProbeSet)
-        #            left join ProbeSE on
-        #                    (ProbeSE.DataId = ProbeData.Id AND ProbeSE.StrainId = ProbeData.StrainId)
-        #            WHERE
-        #                    Probe.Name = '%s' AND ProbeSet.Name = '%s' AND
-        #                    Probe.ProbeSetId = ProbeSet.Id AND
-        #                    ProbeXRef.ProbeId = Probe.Id AND
-        #                    ProbeXRef.ProbeFreezeId = ProbeFreeze.Id AND
-        #                    ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND
-        #                    ProbeSetFreeze.Name = '%s' AND
-        #                    ProbeXRef.DataId = ProbeData.Id AND
-        #                    ProbeData.StrainId = Strain.Id
-        #            Order BY
-        #                    Strain.Name
-        #            ''' % (self.cellid, self.name, self.dataset.name)
-        #
-        #else:
         results = self.dataset.retrieve_sample_data(self.name)
 
         # Todo: is this necessary? If not remove
@@ -260,15 +234,6 @@ class GeneralTrait(object):
                 if not samplelist or (samplelist and name in samplelist):
                     self.data[name] = webqtlCaseData(*item)   #name, value, variance, num_cases)
 
-    #def keys(self):
-    #    return self.__dict__.keys()
-    #
-    #def has_key(self, key):
-    #    return self.__dict__.has_key(key)
-    #
-    #def items(self):
-    #    return self.__dict__.items()
-
     def retrieve_info(self, get_qtl_info=False):
         assert self.dataset, "Dataset doesn't exist"
         if self.dataset.type == 'Publish':
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index a6f9c949..0e2dd27a 100755
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -171,6 +171,7 @@ class MrnaAssaySearch(DoSearch):
                 WHERE %s
                     and ProbeSet.Id = ProbeSetXRef.ProbeSetId
                     and ProbeSetXRef.ProbeSetFreezeId = %s
+                ORDER BY ProbeSet.symbol ASC
                             """ % (escape(from_clause),
                                     where_clause,
                                     escape(str(self.dataset.id))))
@@ -192,6 +193,7 @@ class MrnaAssaySearch(DoSearch):
                 WHERE %s
                     and ProbeSet.Id = ProbeSetXRef.ProbeSetId
                     and ProbeSetXRef.ProbeSetFreezeId = %s
+                ORDER BY ProbeSet.symbol ASC
                             """ % (escape(from_clause),
                                     where_clause,
                                     escape(str(self.dataset.id))))
@@ -205,7 +207,7 @@ class MrnaAssaySearch(DoSearch):
 
         print("Running ProbeSetSearch")
         where_clause = self.get_where_clause()
-        query = self.base_query + "WHERE " + where_clause
+        query = self.base_query + "WHERE " + where_clause + "ORDER BY ProbeSet.symbol ASC"
 
         #print("final query is:", pf(query))
 
diff --git a/wqflask/wqflask/static/packages/bootstrap/css/docs.css b/wqflask/wqflask/static/packages/bootstrap/css/docs.css
index 2d6a713c..31616821 100755
--- a/wqflask/wqflask/static/packages/bootstrap/css/docs.css
+++ b/wqflask/wqflask/static/packages/bootstrap/css/docs.css
@@ -94,7 +94,7 @@ hr.soften {
 .jumbotron {
   position: relative;
   padding: 0px 0;
-  color: #336699;
+  color: black;
   text-align: left;
   text-shadow: 0 1px 3px rgba(0,0,0,.4), 0 0 30px rgba(0,0,0,.075);
   background: #d5d5d5; /* Old browsers */
@@ -107,7 +107,7 @@ hr.soften {
   line-height: 1;
 }
 .jumbotron p {
-  font-size: 15px;
+  font-size: 20px;
   font-weight: 300;
   line-height: 20px;
   margin-bottom: 10px;
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index a53759c4..f92d9984 100755
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -8,13 +8,17 @@
 {% endblock %}
 {% block content %}
 <!-- Start of body -->
+
+    <div class="container">
     {% if uc %}
-        {{ header(uc.name,
-            'This collection has {}.'.format(numify(trait_obs|count, "record", "records"))) }}
+        <h2>{{ uc.name }}</h2>
+        <h3>{{ 'This collection has {}.'.format(numify(trait_obs|count, "record", "records")) }}</h3>
     {% else %}
-        {{ header('Your Collection',
-            'This collection has {}.'.format(numify(trait_obs|count, "record", "records"))) }}
+        <h2>Your Collection</h2>
+        <h3>{{ 'This collection has {}.'.format(numify(trait_obs|count, "record", "records")) }}</h3>
     {% endif %}
+    </div>
+
     <div class="container">
         <div>
             {% if uc %}
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index ff3e04bb..a4ef68b9 100755
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -2,6 +2,7 @@
 {% block title %}Search Results{% endblock %}
 {% block css %}
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+    <link rel="stylesheet" type="text/css" href="//cdn.datatables.net/scroller/1.4.1/css/scroller.dataTables.min.css">
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/dataTables.fixedHeader.css" >
     <link rel="stylesheet" type="text/css" href="//cdn.datatables.net/fixedcolumns/3.0.4/css/dataTables.fixedColumns.css">
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.bootstrap.css" />
@@ -161,6 +162,7 @@
     
     <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/1.10.8/js/jquery.dataTables.min.js"></script>
     <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js"></script>
+    <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/scroller/1.4.1/js/dataTables.scroller.min.js"></script>
     <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.html5.min.js"></script>
     <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.bootstrap.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
@@ -217,8 +219,29 @@
                 }
             });
 
+/*
+                serverSide: true,
+                ajax: function ( data, callback, settings ) {
+                    var out = [];
+ 
+                    for ( var i=data.start, ien=data.start+data.length ; i<ien ; i++ ) {
+                        out.push( [ i+'-1', i+'-2', i+'-3', i+'-4', i+'-5' ] );
+                    }
+ 
+                    setTimeout( function () {
+                        callback( {
+                            draw: data.draw,
+                            data: out,
+                            recordsTotal: 5000000,
+                            recordsFiltered: 5000000
+                        } );
+                    }, 50 );
+                },
+*/
+
             console.time("Creating table");
             {% if dataset.type == 'ProbeSet' %}
+            //ZS: Need to make sort by symbol, also need to make sure blank symbol fields at the bottom and symbols starting with numbers below letters
             $('#trait_table').DataTable( {
                 "columns": [
                     { "type": "natural" },
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 0d463d5b..4720f8ec 100755
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -16,13 +16,18 @@
 {% endblock %}
 {% block content %} <!-- Start of body -->
 
+<!--
     {% if this_trait.dataset.type != 'Geno' %}
 	{{ header("{}".format(this_trait.name_header_fmt),
 	    '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
     {% else %}
 	{{ header("{}".format(this_trait.name_header_fmt)) }}
     {% endif %}
-
+-->
+    <div class="container">
+        <h2>Trait Data and Analysis for <b>{{ this_trait.name }}</b></h2>
+        <h3>{{ this_trait.description_fmt }}</h3>
+    </div>
 
     <form method="post" target="_blank" action="/corr_compute" name="trait_page" id="trait_data_form"
     class="form-horizontal">
@@ -36,40 +41,50 @@
         <input type="hidden" name="temp_uuid" id="temp_uuid" value="{{ temp_uuid }}">
 
         <div class="container">
-            
-            {% include 'show_trait_details.html' %}
             <div class="panel-group" id="accordion">
                 <div class="panel panel-default">
-                    <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseOne">
+                    <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseOne" aria-expanded="true">
+                        <h3 class="panel-title">
+                             <span class="glyphicon glyphicon-chevron-down"></span> Details and Links
+                        </h3>
+                    </div>
+                    <div id="collapseOne" class="panel-collapse collapse" aria-expanded="true">
+                        <div class="panel-body">
+                            {% include 'show_trait_details.html' %}
+                        </div>
+                    </div>
+                </div>    
+                <div class="panel panel-default">
+                    <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseTwo">
                         <h3 class="panel-title">
                              <span class="glyphicon glyphicon-chevron-down"></span> Statistics
                         </h3>
                     </div>
-                    <div id="collapseOne" class="panel-collapse collapse in">
+                    <div id="collapseTwo" class="panel-collapse collapse in">
                         <div class="panel-body">
                             {% include 'show_trait_statistics.html' %}
                         </div>
                     </div>
                 </div>                
                 <div class="panel panel-default">
-                    <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseTwo">
+                    <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseThree">
                         <h3 class="panel-title">
                              <span class="glyphicon glyphicon-chevron-down"></span> Calculate Correlations
                         </h3>
                     </div>
-                    <div id="collapseTwo" class="panel-collapse collapse in">
+                    <div id="collapseThree" class="panel-collapse collapse in">
                         <div class="panel-body">
                             {% include 'show_trait_calculate_correlations.html' %}
                         </div>
                     </div>
                 </div>                
                 <div class="panel panel-default">
-                    <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseThree">
+                    <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseFour">
                         <h3 class="panel-title">
                              <span class="glyphicon glyphicon-chevron-down"></span> Mapping Tools
                         </h3>
                     </div>
-                    <div id="collapseThree" class="panel-collapse collapse in">
+                    <div id="collapseFour" class="panel-collapse collapse in">
                         <div class="panel-body">
                             {% include 'show_trait_mapping_tools.html' %}
                         </div>
@@ -77,12 +92,12 @@
                     </div>
                 </div>                
                 <div class="panel panel-default">
-                    <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseFour" aria-expanded="true">
+                    <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseFive" aria-expanded="true">
                         <h3 class="panel-title">
                              <span class="glyphicon glyphicon-chevron-up"></span> Review and Edit Data
                         </h3>
                     </div>
-                    <div id="collapseFour" class="panel-collapse collapse" aria-expanded="true">
+                    <div id="collapseFive" class="panel-collapse collapse" aria-expanded="true">
                         <div class="panel-body">
                             {% include 'show_trait_edit_data.html' %}
                         </div>
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 16c5dc47..ccb3b51b 100755
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -1,71 +1,82 @@
-<dl class="dl-horizontal">
-    <dt>Species</dt>
-    <dd>{{ this_trait.dataset.group.species }}</dd>
-    <dt>Group</dt>
-    <dd>{{ this_trait.dataset.group.name }}</dd>
-    <dt>Tissue</dt>
-    <dd>{{ this_trait.dataset.tissue }}</dd>
+<table class="table">
+    <tr>
+        <td>Species</td>
+        <td>{{ this_trait.dataset.group.species }}</td>
+    </tr>
+    <tr>
+        <td>Group</td>
+        <td>{{ this_trait.dataset.group.name }}</td>
+    </tr>
+    <tr>
+        <td>Tissue</td>
+        <td>{{ this_trait.dataset.tissue }}</td>
+    </tr>
     {% if this_trait.dataset.type == 'ProbeSet' %}
-    <dt>Aliases</dt>
-    <dd>{{ this_trait.alias_fmt }}</dd>
+    <tr>
+        <td>Aliases</td>
+        <td>{{ this_trait.alias_fmt|replace(",",";") }}</td>
+    </tr>
     {% endif %}
-
     {% if this_trait.dataset.type != 'Publish' %}
-    <dt>Location</dt>
-    <dd>{{ this_trait.location_fmt }}</dd>
+    <tr>
+        <td>Location</td>
+        <td>{{ this_trait.location_fmt }}</td>
+    </tr>
     {% endif %}
-
-    <dt>Database</dt>
-    <dd>
-        <a href="{{ url_for('static', filename='dbdoc/' + dataset.fullname + '.html') }}" target="_blank">
-            {{ dataset.name }}
-        </a>
-    </dd>
-
+    <tr>
+        <td>Database</td>
+        <td>
+            <a href="{{ url_for('static', filename='dbdoc/' + dataset.fullname + '.html') }}" target="_blank">
+                {{ dataset.fullname }}
+            </a>
+        </td>
+    </tr>
     {% if this_trait.probe_set_specificity %}
-    <dt>
-        <a href="/blatInfo.html" target="_blank"
-           title="Values higher than 2 for the specificity are good">
-            BLAT Specificity
-        </a>
-    </dt>
-    <dd>{{ "%0.3f" | format(this_trait.probe_set_specificity|float) }}</dd>
+    <tr>
+        <td>Target Score</td>
+        <td>
+            <a href="/blatInfo.html" target="_blank"
+               title="Values higher than 2 for the specificity are good">
+                BLAT Specificity
+            </a>: 
+            {{ "%0.3f" | format(this_trait.probe_set_specificity|float) }}
+            &nbsp;&nbsp;
+            {% if this_trait.probe_set_blat_score %}
+            Score: {{ "%0.3f" | format(this_trait.probe_set_blat_score|float) }}
+            {% endif %}
+        </td>
+    </tr>
     {% endif %}
-    {% if this_trait.probe_set_blat_score %}
-    <dt>BLAT Score</dt>
-    <dd>{{ "%0.3f" | format(this_trait.probe_set_blat_score|float) }}</dd>
-    {% endif %}
-    <dt>Resource Links</dt>
-    {% if this_trait.dataset.type == 'ProbeSet' %}
-    <dd>
-        {% if this_trait.geneid != None %}
-        <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids={{ this_trait.geneid }}" target="_blank" title="Info from NCBI Entrez Gene">
-            Gene
-        </a>
-        &nbsp;&nbsp;
+    <tr>
+        <td>Resource Links</td>
+        <td>
+            {% if this_trait.geneid != None %}
+            <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids={{ this_trait.geneid }}" target="_blank" title="Info from NCBI Entrez Gene">
+                Gene
+            </a>
+            &nbsp;&nbsp;
+            {% endif %}
+            {% if this_trait.omim != None %}
+            <a href="http://www.ncbi.nlm.nih.gov/omim/{{ this_trait.omim }}" target="_blank" title="Summary from On Mendelion Inheritance in Man">
+                OMIM
+            </a>
+            &nbsp;&nbsp;
+            {% endif %}
+            {% if this_trait.genbankid != None %}
+            <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=search&doptcmdl=DocSum&term={{ this_trait.genbankid }}" target="_blank" title="Find the original GenBank sequence used to design the probes">
+                GenBank
+            </a>
+            &nbsp;&nbsp;
+            {% endif %}
+            {% if this_trait.symbol != None %}
+            <a href="http://www.genotation.org/Getd2g.pl?gene_list={{ this_trait.symbol }}" target="_blank" title="Related descriptive, genomic, clinical, functional and drug-therapy information">
+                Genotation
+            </a>
+            &nbsp;&nbsp;
         {% endif %}
-        {% if this_trait.omim != None %}
-        <a href="http://www.ncbi.nlm.nih.gov/omim/{{ this_trait.omim }}" target="_blank" title="Summary from On Mendelion Inheritance in Man">
-            OMIM
-        </a>
-        &nbsp;&nbsp;
-        {% endif %}
-        {% if this_trait.genbankid != None %}
-        <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=search&doptcmdl=DocSum&term={{ this_trait.genbankid }}" target="_blank" title="Find the original GenBank sequence used to design the probes">
-            GenBank
-        </a>
-        &nbsp;&nbsp;
-        {% endif %}
-        {% if this_trait.symbol != None %}
-        <a href="http://www.genotation.org/Getd2g.pl?gene_list={{ this_trait.symbol }}" target="_blank" title="Related descriptive, genomic, clinical, functional and drug-therapy information">
-            Genotation
-        </a>
-        &nbsp;&nbsp;
-        {% endif %}
-    </dd>
-    {% endif %}
-</dl>
-
+        </td>
+    </tr>
+</table>
 
 <div style="margin-bottom:15px;" class="btn-toolbar">
     <div class="btn-group">
-- 
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